Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 19 of 120
Found at i:5076434 original size:29 final size:29
Alignment explanation
Indices: 5076265--5076448 Score: 185
Period size: 30 Copynumber: 6.2 Consensus size: 29
5076255 GCTAAACTTG
* * *
5076265 AATTTTTAGGAAGTTTGGGGGTTAAATCT
1 AATTTTTAGAAAGTTTGAGGGTCAAATCT
*
5076294 AAATTTTTGGAAAGTTTGAGGGTCAAATCT
1 -AATTTTTAGAAAGTTTGAGGGTCAAATCT
* *
5076324 AAGTTTTTGGGAAGTTTGAGGGTCAAATCT
1 AA-TTTTTAGAAAGTTTGAGGGTCAAATCT
* * *
5076354 AAATGTTAGAAAGTTTGAGGGTCAAAACT
1 AATTTTTAGAAAGTTTGAGGGTCAAATCT
5076383 CAATTTTTCA-AAAGTTT-AGGGGTCAAATCT
1 -AATTTTT-AGAAAGTTTGA-GGGTCAAATCT
* *
5076413 AGATTTTTAGAAAATTTG-GGGTCAAAACAT
1 A-ATTTTTAGAAAGTTTGAGGGTCAAATC-T
5076443 AATTTT
1 AATTTT
5076449 GGATAGTTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
29 41 0.31
30 89 0.68
31 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (29 bp):
AATTTTTAGAAAGTTTGAGGGTCAAATCT
Found at i:5078995 original size:19 final size:20
Alignment explanation
Indices: 5078973--5079010 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5078963 AGATAAAATT
*
5078973 TTTCAAATGTAAA-TAATAA
1 TTTCAAATATAAATTAATAA
5078992 TTTCAAATATAAATTAATA
1 TTTCAAATATAAATTAATA
5079011 CATGATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
TTTCAAATATAAATTAATAA
Found at i:5079408 original size:31 final size:31
Alignment explanation
Indices: 5079339--5079398 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
5079329 ATGATCACCA
*
5079339 AACTATTTCAAAGTTTTTATTTAAGTCACAT
1 AACTATTTCAAAGTTTTTATTTAAATCACAT
*
5079370 AACTATTTGAAAGTTTTTATTTAAATCAC
1 AACTATTTCAAAGTTTTTATTTAAATCAC
5079399 TTGGTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (31 bp):
AACTATTTCAAAGTTTTTATTTAAATCACAT
Found at i:5083572 original size:23 final size:23
Alignment explanation
Indices: 5083537--5083591 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
5083527 GTTGTCCATG
*
5083537 GGCCGGGTCCTAACAAAATTCTA
1 GGCCGGATCCTAACAAAATTCTA
* *
5083560 GGCCGGATTCTAATAAAATTCTA
1 GGCCGGATCCTAACAAAATTCTA
*
5083583 GGCCCGATC
1 GGCCGGATC
5083592 TGCCCATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (23 bp):
GGCCGGATCCTAACAAAATTCTA
Found at i:5084348 original size:17 final size:17
Alignment explanation
Indices: 5084328--5084361 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5084318 TTATAGTTTT
*
5084328 TAAAAAATATTTTTAAA
1 TAAAAAATAATTTTAAA
*
5084345 TAAAAGATAATTTTAAA
1 TAAAAAATAATTTTAAA
5084362 AAATCAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAAATAATTTTAAA
Found at i:5091892 original size:18 final size:19
Alignment explanation
Indices: 5091869--5091904 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5091859 ATGATTTTTT
*
5091869 TCTT-AAATGATAAAAAAA
1 TCTTAAAATAATAAAAAAA
5091887 TCTTAAAATAATAAAAAA
1 TCTTAAAATAATAAAAAA
5091905 TGAATTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (19 bp):
TCTTAAAATAATAAAAAAA
Found at i:5094446 original size:16 final size:17
Alignment explanation
Indices: 5094425--5094459 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5094415 TTTTTATATA
*
5094425 TATACATATATG-TTGT
1 TATACATACATGATTGT
5094441 TATACATACATGATTGT
1 TATACATACATGATTGT
5094458 TA
1 TA
5094460 CAAAATTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
TATACATACATGATTGT
Found at i:5095807 original size:63 final size:62
Alignment explanation
Indices: 5095712--5095842 Score: 169
Period size: 67 Copynumber: 2.1 Consensus size: 62
5095702 TTGGTTTGTT
* *
5095712 ATTTATTTATTTATTTATAATAATAAATAAAT-AATAA-AACA-AAATTAATATTATTTTAC
1 ATTTATTTATTTATTTATAATAATAAATAAATAAATAATAAAAGAAATTAATATTATTGTAC
5095771 ATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATGAAATTAATATTATTGT
1 ATTTATTTATTTAT-TT-AT--AATAATAAATAAATAAATAATAAAA-GAAATTAATATTATTGT
*
5095836 AT
61 AC
5095838 ATTTA
1 ATTTA
5095843 ATAAATAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
59 14 0.23
60 2 0.03
61 2 0.03
63 14 0.23
64 5 0.08
65 3 0.05
67 21 0.34
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (62 bp):
ATTTATTTATTTATTTATAATAATAAATAAATAAATAATAAAAGAAATTAATATTATTGTAC
Found at i:5100644 original size:51 final size:51
Alignment explanation
Indices: 5100582--5100678 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
5100572 TTTCTCAAAC
* *
5100582 AAAATAATAAAA-ATA-AAAAATTTATCATAAAATATAAAATATTAAATATTT
1 AAAAAAATAAAATATATAAAAACTTAT-A-AAAATATAAAATATTAAATATTT
* *
5100633 AAAAAAATAAAATTTATATAAACTTATAAAAATATAAAATATTAAA
1 AAAAAAATAAAATATATAAAAACTTATAAAAATATAAAATATTAAA
5100679 GACTTTAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
51 29 0.73
52 3 0.08
53 8 0.20
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (51 bp):
AAAAAAATAAAATATATAAAAACTTATAAAAATATAAAATATTAAATATTT
Found at i:5100678 original size:43 final size:42
Alignment explanation
Indices: 5100582--5100678 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 42
5100572 TTTCTCAAAC
*
5100582 AAAATAATAAAAATAAAAAATTTATCATAAAATATAAAATAT
1 AAAATATTAAAAATAAAAAATTTATCATAAAATATAAAATAT
* *
5100624 TAAATATTTAAAAA-AATAAAATTTAT-ATAAACTTATAAAAATAT
1 AAAATA-TTAAAAATAA-AAAATTTATCATAAA-ATAT-AAAATAT
5100668 AAAATATTAAA
1 AAAATATTAAA
5100679 GACTTTAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
42 12 0.26
43 23 0.49
44 12 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (42 bp):
AAAATATTAAAAATAAAAAATTTATCATAAAATATAAAATAT
Found at i:5102764 original size:29 final size:30
Alignment explanation
Indices: 5102725--5102802 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
5102715 ACATAAGTAC
* *
5102725 GGTTTGCACATATAGGGTTCACATAAATA-
1 GGTTCGCACATATAGGGTTCACACAAATAG
* * *
5102754 GGTTCGTACATATAGGGTTAACACATATAG
1 GGTTCGCACATATAGGGTTCACACAAATAG
5102784 GGTTCGCACATAT-GGGTTC
1 GGTTCGCACATATAGGGTTC
5102803 GCCTATAAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 29 0.71
30 12 0.29
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (30 bp):
GGTTCGCACATATAGGGTTCACACAAATAG
Found at i:5102772 original size:15 final size:15
Alignment explanation
Indices: 5102725--5102819 Score: 90
Period size: 15 Copynumber: 6.5 Consensus size: 15
5102715 ACATAAGTAC
*
5102725 GGTTTGCACATATAG
1 GGTTCGCACATATAG
* * *
5102740 GGTTCACATAAATA-
1 GGTTCGCACATATAG
*
5102754 GGTTCGTACATATAG
1 GGTTCGCACATATAG
**
5102769 GGTTAACACATATAG
1 GGTTCGCACATATAG
5102784 GGTTCGCACATAT-G
1 GGTTCGCACATATAG
5102798 GGTTCGC-C-TATAAG
1 GGTTCGCACATAT-AG
5102812 GGTTCGCA
1 GGTTCGCA
5102820 TACAAGGGCT
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
12 3 0.05
13 1 0.02
14 26 0.41
15 33 0.52
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (15 bp):
GGTTCGCACATATAG
Found at i:5102819 original size:28 final size:28
Alignment explanation
Indices: 5102782--5102875 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 28
5102772 TAACACATAT
* *
5102782 AGGGTTCGCACATATGGG-TTCGCCTATA
1 AGGGTTCGCACACAAGGGCTT-GCCTATA
*
5102810 AGGGTTCGCATACAAGGGCTTGCCTATA
1 AGGGTTCGCACACAAGGGCTTGCCTATA
* * * *
5102838 AGGTTTCGTATACAGGGGCTTGCCTATA
1 AGGGTTCGCACACAAGGGCTTGCCTATA
*
5102866 GGGGTTCGCA
1 AGGGTTCGCA
5102876 TGTTACTACA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 54 0.96
29 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (28 bp):
AGGGTTCGCACACAAGGGCTTGCCTATA
Found at i:5102826 original size:14 final size:14
Alignment explanation
Indices: 5102777--5102876 Score: 62
Period size: 14 Copynumber: 7.2 Consensus size: 14
5102767 AGGGTTAACA
5102777 CATAT-AGGGTTCG
1 CATATAAGGGTTCG
* *
5102790 CACATATGGGTTCG
1 CATATAAGGGTTCG
*
5102804 CCTATAAGGGTTCG
1 CATATAAGGGTTCG
*
5102818 CATACAAGGGCTT-G
1 CATATAAGGG-TTCG
* *
5102832 CCTATAAGGTTTCG
1 CATATAAGGGTTCG
* * *
5102846 TATACAGGGGCTT-G
1 CATATAAGGG-TTCG
* *
5102860 CCTATAGGGGTTCG
1 CATATAAGGGTTCG
5102874 CAT
1 CAT
5102877 GTTACTACAT
Statistics
Matches: 63, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
13 8 0.13
14 51 0.81
15 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (14 bp):
CATATAAGGGTTCG
Found at i:5102911 original size:22 final size:23
Alignment explanation
Indices: 5102867--5102911 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5102857 TTGCCTATAG
**
5102867 GGGTTCGCATGTTACTACATGTA
1 GGGTTCGCATAATACTACATGTA
5102890 GGGTTCGCATAATAC-ACATGTA
1 GGGTTCGCATAATACTACATGTA
5102912 AGTTTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (23 bp):
GGGTTCGCATAATACTACATGTA
Found at i:5113279 original size:21 final size:21
Alignment explanation
Indices: 5113250--5113294 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5113240 GATGAAGCCA
* *
5113250 TTTCTTCTCTTCTTCTTTTTT
1 TTTCCTCTCTTCTTCTTTTCT
*
5113271 TTTCCTCTCTTTTTCTTTTCT
1 TTTCCTCTCTTCTTCTTTTCT
5113292 TTT
1 TTT
5113295 GTGTTGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCCTCTCTTCTTCTTTTCT
Found at i:5117736 original size:18 final size:18
Alignment explanation
Indices: 5117713--5117749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5117703 ACAATTCATA
5117713 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
5117731 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
5117749 T
1 T
5117750 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:5122600 original size:44 final size:44
Alignment explanation
Indices: 5122537--5122625 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
5122527 TTCATGCACA
*
5122537 AGCTGATACAATACGAACTCAAGCTTGCTAATATAGTTTAATAC
1 AGCTGATACAATACAAACTCAAGCTTGCTAATATAGTTTAATAC
*
5122581 AGCTGATATAATACAAACTCAAGCTTGCTAATATAGTTTAATAC
1 AGCTGATACAATACAAACTCAAGCTTGCTAATATAGTTTAATAC
5122625 A
1 A
5122626 AACTCAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (44 bp):
AGCTGATACAATACAAACTCAAGCTTGCTAATATAGTTTAATAC
Found at i:5122672 original size:2 final size:2
Alignment explanation
Indices: 5122665--5122697 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5122655 TCAGGTTGTG
5122665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5122698 ACTTGAGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5136042 original size:34 final size:34
Alignment explanation
Indices: 5136004--5136079 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
5135994 AGTAAACAAC
*
5136004 ATTTGGGTAAGGTAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
5136038 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
5136072 ATTTGGGT
1 ATTTGGGT
5136080 TTAGTTTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
Found at i:5139440 original size:21 final size:21
Alignment explanation
Indices: 5139390--5139442 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
5139380 AAAACTATAT
5139390 AAAATTCATA-AAACTTATTAA
1 AAAATT-ATATAAACTTATTAA
*
5139411 AAACCTTATATAAA-TTATTCAA
1 AAA-ATTATATAAACTTATT-AA
5139433 AAAATTATAT
1 AAAATTATAT
5139443 TTATATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTATATAAACTTATTAA
Found at i:5139483 original size:15 final size:15
Alignment explanation
Indices: 5139463--5139526 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 15
5139453 GTTATTTCCA
5139463 AGTTTTGCAATCTTT
1 AGTTTTGCAATCTTT
5139478 AGTTTTG-ATATTCTTT
1 AGTTTTGCA-A-TCTTT
5139494 AGTTTTGCAATCTTT
1 AGTTTTGCAATCTTT
*
5139509 AGTTTTGATAATCTTT
1 AGTTTTG-CAATCTTT
5139525 AG
1 AG
5139527 AATTTGGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 1 0.02
15 20 0.45
16 22 0.50
17 1 0.02
ACGTcount: A:0.22, C:0.09, G:0.14, T:0.55
Consensus pattern (15 bp):
AGTTTTGCAATCTTT
Found at i:5139501 original size:31 final size:31
Alignment explanation
Indices: 5139463--5139526 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
5139453 GTTATTTCCA
*
5139463 AGTTTTGCAATCTTTAGTTTTGATATTCTTT
1 AGTTTTGCAATCTTTAGTTTTGATAATCTTT
5139494 AGTTTTGCAATCTTTAGTTTTGATAATCTTT
1 AGTTTTGCAATCTTTAGTTTTGATAATCTTT
5139525 AG
1 AG
5139527 AATTTGGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.14, T:0.55
Consensus pattern (31 bp):
AGTTTTGCAATCTTTAGTTTTGATAATCTTT
Found at i:5140240 original size:11 final size:11
Alignment explanation
Indices: 5140161--5140242 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
5140151 ATAATCTAGT
5140161 TTTTTTAATAAA
1 TTTTTTAAT-AA
*
5140173 TTCTTTAATAA
1 TTTTTTAATAA
5140184 -TTTTT-AT-A
1 TTTTTTAATAA
* *
5140192 GTTATTAATACA
1 TTTTTTAATA-A
5140204 -TTTTTATATAA
1 TTTTTTA-ATAA
**
5140215 TTTTTTTGTAA
1 TTTTTTAATAA
*
5140226 TTTTTTAATAG
1 TTTTTTAATAA
5140237 TTTTTT
1 TTTTTT
5140243 TTTATAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.02
9 6 0.11
10 6 0.11
11 25 0.45
12 17 0.31
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (11 bp):
TTTTTTAATAA
Found at i:5140307 original size:30 final size:32
Alignment explanation
Indices: 5140257--5140336 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 32
5140247 TAAATTTTCT
*
5140257 ATAATTTCTAAAATTCAATTAAA-CATT-AGTAAA
1 ATAATTT-AAAAATTCAATTAAATC-TTCA-TAAA
5140290 ATAA-TTAAAAATT-AATTAAATCTTCATAAA
1 ATAATTTAAAAATTCAATTAAATCTTCATAAA
*
5140320 ATAATTTAAAAAATCAA
1 ATAATTTAAAAATTCAA
5140337 ATCAAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
30 17 0.41
31 16 0.39
32 4 0.10
33 4 0.10
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (32 bp):
ATAATTTAAAAATTCAATTAAATCTTCATAAA
Found at i:5149589 original size:2 final size:2
Alignment explanation
Indices: 5149584--5149626 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5149574 TCACTGTGTG
5149584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5149626 T
1 T
5149627 TAGCACATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5152536 original size:30 final size:32
Alignment explanation
Indices: 5152502--5152563 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
5152492 TAACTGATCG
5152502 AATCGAATTAATTCAGTT-A-ATCGGTTAATT
1 AATCGAATTAATTCAGTTAAGATCGGTTAATT
* *
5152532 AATCGATTTAATTCGGTTGAAGATCGGTTAAT
1 AATCGAATTAATTCAGTT-AAGATCGGTTAAT
5152564 GGTTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 16 0.59
32 1 0.04
33 10 0.37
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (32 bp):
AATCGAATTAATTCAGTTAAGATCGGTTAATT
Found at i:5152683 original size:19 final size:18
Alignment explanation
Indices: 5152659--5152708 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
5152649 TATATATTAC
*
5152659 TAATTCGGTTAATTTTGAT
1 TAATTCGGTTAA-TTTAAT
*
5152678 TAATTCCAGTTAATTTAAT
1 TAATT-CGGTTAATTTAAT
*
5152697 TAATTTGGTTAA
1 TAATTCGGTTAA
5152709 CCAAAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.19
19 15 0.58
20 6 0.23
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (18 bp):
TAATTCGGTTAATTTAAT
Found at i:5155936 original size:21 final size:21
Alignment explanation
Indices: 5155894--5155943 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5155884 AACTTAAACA
*
5155894 CTAAACCTCATATCCTTGAACC
1 CTAAA-CTCATATCCATGAACC
5155916 CTAAACTCATATCCCAT-AACC
1 CTAAACTCATAT-CCATGAACC
*
5155937 TTAAACT
1 CTAAACT
5155944 TAAATCTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.36, C:0.34, G:0.02, T:0.28
Consensus pattern (21 bp):
CTAAACTCATATCCATGAACC
Found at i:5155958 original size:20 final size:20
Alignment explanation
Indices: 5155933--5155981 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5155923 CATATCCCAT
* *
5155933 AACCTTAAACTTAAATCTTG
1 AACCTTAAACCTAAATCTCG
5155953 AACCTTAAACCTAAATCTCG
1 AACCTTAAACCTAAATCTCG
5155973 AACCTTAAA
1 AACCTTAAA
5155982 TCTCGAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (20 bp):
AACCTTAAACCTAAATCTCG
Found at i:5155983 original size:14 final size:13
Alignment explanation
Indices: 5155960--5155989 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5155950 TTGAACCTTA
5155960 AACCTAAATCTCG
1 AACCTAAATCTCG
5155973 AACCTTAAATCTCG
1 AACC-TAAATCTCG
5155987 AAC
1 AAC
5155990 TCAAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (13 bp):
AACCTAAATCTCG
Found at i:5167332 original size:16 final size:16
Alignment explanation
Indices: 5167313--5167343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5167303 CGTTTGGTTC
5167313 ACTGGAATGGAATAGG
1 ACTGGAATGGAATAGG
*
5167329 ACTGTAATGGAATAG
1 ACTGGAATGGAATAG
5167344 AGTTGCAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (16 bp):
ACTGGAATGGAATAGG
Found at i:5167372 original size:32 final size:32
Alignment explanation
Indices: 5167318--5167380 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
5167308 GGTTCACTGG
** *
5167318 AATGGAATAGGACTGTAATGGAATAGAGTTGC
1 AATGGAATAAAACTATAATGGAATAGAGTTGC
* *
5167350 AATGGAATAAAACTATATTGGAATAGCGTTG
1 AATGGAATAAAACTATAATGGAATAGAGTTG
5167381 TAATCAGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (32 bp):
AATGGAATAAAACTATAATGGAATAGAGTTGC
Found at i:5177378 original size:21 final size:21
Alignment explanation
Indices: 5177364--5177403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5177354 AGATTTTGAG
*
5177364 TTTAAAATTTAAGATCTCAAC
1 TTTAAAATTTAAGATTTCAAC
*
5177385 TTTAAAATTTAGGATTTCA
1 TTTAAAATTTAAGATTTCA
5177404 GTATTTATTT
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:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTAAAATTTAAGATTTCAAC
Found at i:5184006 original size:115 final size:116
Alignment explanation
Indices: 5183803--5184034 Score: 376
Period size: 115 Copynumber: 2.0 Consensus size: 116
5183793 ACAAATTGAA
* *
5183803 ATCCAAACTAAGAACACCCATTAGAAAAAAAATCTAGACTTAGAACACCTATCAATCCATTAGAA
1 ATCCAAACTAAGAACACCCATTAGAAAAAAAATCTAGACTTAGAACACCCATCAATCCATTAAAA
* *
5183868 AGCCAGAAACTTAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
66 AACCAAAAACTTAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
* * * *
5183919 ATCCAAACTTAGAACACCCATTAG-AAAAAAGTTTATACTTAGAACACCCATCAATCCATTAAAA
1 ATCCAAACTAAGAACACCCATTAGAAAAAAAATCTAGACTTAGAACACCCATCAATCCATTAAAA
*
5183983 AACCAAAAACTTAACATCACAAATAAAACCCTAAAAATTAACATGTCAAAC
66 AACCAAAAACTTAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
5184034 A
1 A
5184035 AAACCCATCA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
115 84 0.79
116 23 0.21
ACGTcount: A:0.52, C:0.23, G:0.05, T:0.20
Consensus pattern (116 bp):
ATCCAAACTAAGAACACCCATTAGAAAAAAAATCTAGACTTAGAACACCCATCAATCCATTAAAA
AACCAAAAACTTAACATCACAAATAAAACCCTAAAAATTAACATATCAAAC
Found at i:5184018 original size:27 final size:27
Alignment explanation
Indices: 5183987--5184040 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5183977 TTAAAAAACC
*
5183987 AAAAACTTAACATCACAAATAAAACCCT
1 AAAAA-TTAACATCACAAACAAAACCCT
**
5184015 AAAAATTAACATGTCAAACAAAACCC
1 AAAAATTAACATCACAAACAAAACCC
5184041 ATCAATCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.57, C:0.24, G:0.02, T:0.17
Consensus pattern (27 bp):
AAAAATTAACATCACAAACAAAACCCT
Found at i:5187471 original size:13 final size:13
Alignment explanation
Indices: 5187439--5187470 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5187429 TTAAATAGTG
5187439 AATAAAATAAATA
1 AATAAAATAAATA
5187452 AATAAAATAAAT-
1 AATAAAATAAATA
5187464 AATAAAA
1 AATAAAA
5187471 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:5195704 original size:22 final size:21
Alignment explanation
Indices: 5195679--5195735 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
5195669 GGAGAGAAAA
*
5195679 GAAAAAAAATAAATGGAAATGG
1 GAAAAAAAATAAAAGGAAA-GG
*
5195701 G-AAAAAAATAAAAGGGAAGG
1 GAAAAAAAATAAAAGGAAAGG
* *
5195721 GAAAAACAAGAAAAG
1 GAAAAAAAATAAAAG
5195736 AAAATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.87
22 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.25, T:0.07
Consensus pattern (21 bp):
GAAAAAAAATAAAAGGAAAGG
Found at i:5195707 original size:21 final size:20
Alignment explanation
Indices: 5195681--5195726 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
5195671 AGAGAAAAGA
*
5195681 AAAAAAATAAATGGAAATGGG
1 AAAAAAATAAAAGGAAA-GGG
*
5195702 AAAAAAATAAAAGGGAAGGG
1 AAAAAAATAAAAGGAAAGGG
5195722 AAAAA
1 AAAAA
5195727 CAAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (20 bp):
AAAAAAATAAAAGGAAAGGG
Found at i:5196672 original size:3 final size:3
Alignment explanation
Indices: 5196664--5196693 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5196654 TACATCCCAA
5196664 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5196694 GAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5197772 original size:20 final size:20
Alignment explanation
Indices: 5197747--5197812 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
5197737 AAAGTCAACG
5197747 GTCAACGGTCAACGGTCAAA
1 GTCAACGGTCAACGGTCAAA
*
5197767 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAA-A
*
5197788 GTCAA-AGTCAACGGTCAAA
1 GTCAACGGTCAACGGTCAAA
5197807 GGTCAA
1 -GTCAA
5197813 TCAACACCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
20 36 0.88
21 5 0.12
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCAAA
Found at i:5197775 original size:27 final size:27
Alignment explanation
Indices: 5197737--5197812 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
5197727 GTTTTTTAAA
5197737 AAAGTCAACGGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
5197764 AAAGTCAACGGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAACGGTCAACGGTC
*
5197791 AAAGTCAACGGTCAAAGGTCAA
1 AAAGTCAACGGTCAACGGTCAA
5197813 TCAACACCGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.37, C:0.24, G:0.25, T:0.14
Consensus pattern (27 bp):
AAAGTCAACGGTCAACGGTCAACGGTC
Found at i:5197831 original size:7 final size:7
Alignment explanation
Indices: 5197740--5197812 Score: 105
Period size: 7 Copynumber: 10.7 Consensus size: 7
5197730 TTTTAAAAAA
5197740 GTCAACG
1 GTCAACG
5197747 GTCAACG
1 GTCAACG
5197754 GTCAACG
1 GTCAACG
*
5197761 GTCAA-A
1 GTCAACG
5197767 GTCAACG
1 GTCAACG
5197774 GTCAACG
1 GTCAACG
5197781 GTCAACG
1 GTCAACG
*
5197788 GTCAA-A
1 GTCAACG
5197794 GTCAACG
1 GTCAACG
*
5197801 GTCAAAG
1 GTCAACG
5197808 GTCAA
1 GTCAA
5197813 TCAACACCGG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
6 10 0.17
7 49 0.83
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:5197943 original size:21 final size:22
Alignment explanation
Indices: 5197917--5197966 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
5197907 TTGGTTCAAA
5197917 TGGGTTTGGTTTAAA-AGAATT
1 TGGGTTTGGTTTAAATAGAATT
*
5197938 TGGGTTTGGTTTAAATAGGATT
1 TGGGTTTGGTTTAAATAGAATT
5197960 TGGGTTT
1 TGGGTTT
5197967 AATGGGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (22 bp):
TGGGTTTGGTTTAAATAGAATT
Found at i:5198367 original size:11 final size:11
Alignment explanation
Indices: 5198334--5198408 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
5198324 AAGTGTGATT
*
5198334 AAAAGAGGAAG
1 AAAAGAGAAAG
*
5198345 AAAATAGAAAAG
1 AAAAGAG-AAAG
5198357 AAAAGAGAAAG
1 AAAAGAGAAAG
5198368 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
5198380 AATGAGAAAAAG
1 AA-AAGAGAAAG
5198392 AAAAGAGAAAG
1 AAAAGAGAAAG
*
5198403 GAAAGA
1 AAAAGA
5198409 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:5198376 original size:23 final size:23
Alignment explanation
Indices: 5198334--5198406 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
5198324 AAGTGTGATT
*
5198334 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
5198357 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
5198380 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
5198404 AAA
1 AAA
5198407 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:5202586 original size:46 final size:45
Alignment explanation
Indices: 5202536--5202625 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
5202526 AGAATGAATA
*
5202536 GAAATAAAGAAATGAAAAACATTCAGAAAT-TATTATGGTTTTCTCC
1 GAAATAAAGAAAT-AAAAACATTCAGAAATAAATT-TGGTTTTCTCC
** * **
5202582 GAAATGGAGAAATAAAATCATTTGGAAATAAATTTGGTTTTCTC
1 GAAATAAAGAAATAAAAACATTCAGAAATAAATTTGGTTTTCTC
5202626 AAAATGGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
45 23 0.62
46 14 0.38
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (45 bp):
GAAATAAAGAAATAAAAACATTCAGAAATAAATTTGGTTTTCTCC
Found at i:5203488 original size:40 final size:40
Alignment explanation
Indices: 5203433--5203508 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
5203423 GAAATCTCTT
*
5203433 ATTTTACTATAACGACAATAGAACGAATAGTACAAAGATA
1 ATTTTACTATAACGACAATAGAACGAATAATACAAAGATA
*
5203473 ATTTTACTATAACGACAATAGAATGAATAATACAAA
1 ATTTTACTATAACGACAATAGAACGAATAATACAAA
5203509 AGATGGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (40 bp):
ATTTTACTATAACGACAATAGAACGAATAATACAAAGATA
Found at i:5203693 original size:24 final size:24
Alignment explanation
Indices: 5203660--5203711 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5203650 TTTGTAGGTC
*
5203660 AAATAAATTATGCTAATAAATACA
1 AAATAAATTATACTAATAAATACA
* *
5203684 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
5203708 AAAT
1 AAAT
5203712 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:5205652 original size:23 final size:23
Alignment explanation
Indices: 5205626--5205670 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5205616 ATTCGTTGGT
*
5205626 CAAATAAATTATGCTAATAAATG
1 CAAATAAATTATACTAATAAATG
*
5205649 CAAATATATTATACTAATAAAT
1 CAAATAAATTATACTAATAAAT
5205671 ACTAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (23 bp):
CAAATAAATTATACTAATAAATG
Found at i:5206207 original size:28 final size:27
Alignment explanation
Indices: 5206176--5206241 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 27
5206166 AACACTAAAA
5206176 TTTATAATTTTA-AATATTTTTAATAATT
1 TTTATAATTTTACAATATTTTT-AT-ATT
5206204 TTTATAATTTTACAATATTTTTATATT
1 TTTATAATTTTACAATATTTTTATATT
5206231 TTT-TAATTTTA
1 TTTATAATTTTA
5206242 TTTTTTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
26 8 0.22
27 6 0.16
28 14 0.38
29 9 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTATAATTTTACAATATTTTTATATT
Found at i:5206213 original size:19 final size:18
Alignment explanation
Indices: 5206176--5206240 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
5206166 AACACTAAAA
*
5206176 TTTATAATTTTAAATATT
1 TTTATAATTTTTAATATT
*
5206194 TTTAATAATTTTT-ATAAT
1 TTT-ATAATTTTTAATATT
* *
5206212 TTTACAATATTTTTATATT
1 TTTATAAT-TTTTAATATT
5206231 TTT-TAATTTT
1 TTTATAATTTT
5206241 ATTTTTTAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 7 0.18
18 17 0.44
19 15 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATAATTTTTAATATT
Found at i:5208604 original size:27 final size:26
Alignment explanation
Indices: 5208555--5208614 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
5208545 TTTTAAGTTG
5208555 TTTTTTATCAACAAAATTGAAAAATTAA
1 TTTTTTATCAACAAAATTG-AAAA-TAA
** *
5208583 TTTTTTAT-AACAATTTTTAAAATAA
1 TTTTTTATCAACAAAATTGAAAATAA
5208608 TTTTTTA
1 TTTTTTA
5208615 ACCACAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 10 0.34
26 4 0.14
27 7 0.24
28 8 0.28
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTTTATCAACAAAATTGAAAATAA
Found at i:5217729 original size:17 final size:17
Alignment explanation
Indices: 5217709--5217745 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5217699 AGTTTTTCTA
*
5217709 AAATTTAAACTTAATAT
1 AAATTTAAACTTAAAAT
*
5217726 AAATTTAAATTTAAAAT
1 AAATTTAAACTTAAAAT
5217743 AAA
1 AAA
5217746 AATTAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:5218515 original size:21 final size:21
Alignment explanation
Indices: 5218476--5218515 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5218466 GTGTTAACGT
* *
5218476 TTTTTAGTAATTATTAATAGA
1 TTTTTAGTAATAATAAATAGA
*
5218497 TTTTTATTAATAATAAATA
1 TTTTTAGTAATAATAAATA
5218516 ATGATGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTTAGTAATAATAAATAGA
Found at i:5219735 original size:30 final size:30
Alignment explanation
Indices: 5219700--5219967 Score: 119
Period size: 29 Copynumber: 9.1 Consensus size: 30
5219690 TAAACTTTCC
* *
5219700 AAAATTTCATTTTTGACCTCGATTTCACCA
1 AAAATTCCATTTTTGACCCCGATTTCACCA
5219730 AAAATTACCA-TTTT-ACCCCCGAACTTT--CC-
1 AAAATT-CCATTTTTGA-CCCCG-A-TTTCACCA
*
5219759 AAAATCCCATTTTTGACCCCGATTTCACCA
1 AAAATTCCATTTTTGACCCCGATTTCACCA
*
5219789 AAAATTACCA-TTTT-ACCCTCAAACTTT--CC-
1 AAAATT-CCATTTTTGACCC-C-GA-TTTCACCA
* * *
5219818 AAAATCCCA-TTTTAACCCTGATTTCACCA
1 AAAATTCCATTTTTGACCCCGATTTCACCA
5219847 AAAATTACCA-TTTT-ACCCTCGAACTTT--CC-
1 AAAATT-CCATTTTTGACCC-CG-A-TTTCACCA
* *
5219876 AAAATCCCATTTTTGACCCCGAATTT-ATCA
1 AAAATTCCATTTTTGACCCCG-ATTTCACCA
* *
5219906 AAAATTACCA-TTTT-ACCCCTTAATTT-TCC-
1 AAAATT-CCATTTTTGACCCC--GATTTCACCA
* * *
5219935 AAAATTCCATTTTTAACCTCGATTTTACCA
1 AAAATTCCATTTTTGACCCCGATTTCACCA
5219965 AAA
1 AAA
5219968 GTTACTATTT
Statistics
Matches: 187, Mismatches: 19, Indels: 64
0.69 0.07 0.24
Matches are distributed among these distances:
26 3 0.02
27 4 0.02
28 26 0.14
29 70 0.37
30 64 0.34
31 11 0.06
32 9 0.05
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCCGATTTCACCA
Found at i:5219784 original size:59 final size:59
Alignment explanation
Indices: 5219692--5219985 Score: 394
Period size: 59 Copynumber: 5.0 Consensus size: 59
5219682 TAGGTCTCTA
** *
5219692 AACTTTCCAAAATTTCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCCCG
1 AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
* *
5219751 AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCTCA
1 AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
* * *
5219810 AACTTTCCAAAATCCCA-TTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCTCG
1 AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
* **
5219868 AACTTTCCAAAATCCCATTTTTGACCCCGAATTT-ATCAAAAATTACCATTTTACCCCTT
1 AACTTTCCAAAATCCCATTTTTGACCCCG-ATTTCACCAAAAATTACCATTTTACCCCCG
* * * * * * * *
5219927 AATTTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAGTTACTATTTTGCCCCCG
1 AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
5219986 GGAATCCAAA
Statistics
Matches: 208, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
58 59 0.28
59 145 0.70
60 4 0.02
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (59 bp):
AACTTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCCCG
Found at i:5219908 original size:117 final size:118
Alignment explanation
Indices: 5219689--5219985 Score: 440
Period size: 117 Copynumber: 2.5 Consensus size: 118
5219679 CCGTAGGTCT
* *
5219689 CTAAACTTTCCAAAATTTCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAAC
1 CTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAAC
5219754 TTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTA-CC
66 TTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCC
* *
5219806 CTCAAACTTTCCAAAATCCCA-TTTTAACC-CTGATTTCACCAAAAATTACCATTTTACCCTCGA
1 CT-AAACTTTCCAAAATTCCATTTTTAACCTC-GATTTCACCAAAAATTACCATTTTACCCCCGA
*
5219869 ACTTTCCAAAATCCCATTTTTGACCCCGAATTT-ATCAAAAATTACCATTTTACCC
64 ACTTTCCAAAATCCCATTTTTGACCCCG-ATTTCACCAAAAATTACCATTTTACCC
* * * * * *
5219924 CTTAATTTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAGTTACTATTTTGCCCCCG
1 CTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCG
5219986 GGAATCCAAA
Statistics
Matches: 161, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
116 1 0.01
117 101 0.63
118 58 0.36
119 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (118 bp):
CTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAAC
TTTCCAAAATCCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCC
Found at i:5230950 original size:11 final size:11
Alignment explanation
Indices: 5230934--5230960 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5230924 GTCTCTATTC
5230934 AAAAAAAAGAA
1 AAAAAAAAGAA
5230945 AAAAAAAAGAA
1 AAAAAAAAGAA
5230956 AAAAA
1 AAAAA
5230961 GGGTTCACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:5232153 original size:200 final size:200
Alignment explanation
Indices: 5231801--5232907 Score: 1741
Period size: 200 Copynumber: 5.5 Consensus size: 200
5231791 AACAAACAGT
* *
5231801 GAGGTGGTAATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
*
5231866 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAACAATAAAATGGTTAGCTTCC
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
* *
5231931 TGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGTGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
5231996 CAAGC
196 CAAGC
5232001 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
*
5232066 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAACAATAAAATGGTTAGCTTCC
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
* * *
5232131 TGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
*
5232196 CAAGT
196 CAAGC
*
5232201 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAACCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
*
5232266 TTTCGAACCCAGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
** *
5232331 TGATGAGATACAGAGAAGTGGACCAAATTAATCTTCCTGAAGAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
5232396 CAAGC
196 CAAGC
* ** *
5232401 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAATGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
*
5232466 TTTCGAACTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
* * * *
5232531 TGATGAGATACAGAGAAGTGGACTAGATTCGTCTTCTTGAGGAGATACAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
5232596 CAAGC
196 CAAGC
* * * ** *
5232601 GAGGCGGTTATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAATGCTCAATGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* *
5232666 TTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
* * *
5232731 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTAAGGAGATCTAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
*
5232796 CAATC
196 CAAGC
* * * * * * * * * * *
5232801 AAAGCGGTCATCTTTCTGATGATACACTGAGAAGAAGACCAAATCAA-ACT-AACGCGAGCGAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* * * *
5232864 CTTCGATCCCAGCTTCCTGATGAGACATTGAGAAGCAGATCGAA
66 TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAA
5232908 GTCAACGAAA
Statistics
Matches: 846, Mismatches: 61, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
198 50 0.06
199 2 0.00
200 794 0.94
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
TTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
CAAGC
Found at i:5234097 original size:21 final size:21
Alignment explanation
Indices: 5234058--5234097 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5234048 GTGTTAACGT
* *
5234058 TTTTTAGTAATTATTAATAGA
1 TTTTTAGTAATAATAAATAGA
*
5234079 TTTTTATTAATAATAAATA
1 TTTTTAGTAATAATAAATA
5234098 ATAATGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTTAGTAATAATAAATAGA
Found at i:5234651 original size:26 final size:26
Alignment explanation
Indices: 5234621--5234679 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
5234611 GGCACCCGTG
5234621 GGCGACGACCGGTACAGCGCGTGGCC
1 GGCGACGACCGGTACAGCGCGTGGCC
5234647 GGCGACGACCGGTACAGCGCGTGGCC
1 GGCGACGACCGGTACAGCGCGTGGCC
5234673 GGCGACG
1 GGCGACG
5234680 CGCGTCGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.15, C:0.34, G:0.44, T:0.07
Consensus pattern (26 bp):
GGCGACGACCGGTACAGCGCGTGGCC
Found at i:5235327 original size:29 final size:28
Alignment explanation
Indices: 5235289--5235388 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
5235279 TAGGTCCCTA
*
5235289 AATTTTCCAAAATTCCATTTTTGACCTCG
1 AATTTACCAAAATTCCATTTTT-ACCTCG
* * *
5235318 AATTCACCAAAAATTACCA-TTTTACCCCTT
1 AATTTACC-AAAATT-CCATTTTTACCTC-G
* *
5235348 AATTTTCCAAAATTCCATTTTTAACCTTG
1 AATTTACCAAAATTCCATTTTT-ACCTCG
*
5235377 ATTTTACCAAAA
1 AATTTACCAAAA
5235389 GTTACTATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
28 3 0.05
29 30 0.55
30 19 0.35
31 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (28 bp):
AATTTACCAAAATTCCATTTTTACCTCG
Found at i:5235386 original size:59 final size:59
Alignment explanation
Indices: 5235284--5235399 Score: 169
Period size: 59 Copynumber: 2.0 Consensus size: 59
5235274 CTCCATAGGT
*
5235284 CCCTAAATTTTCCAAAATTCCATTTTTGACCTCGAATTCACCAAAAATTACCATTTTAC
1 CCCTAAATTTTCCAAAATTCCATTTTTAACCTCGAATTCACCAAAAATTACCATTTTAC
* * * * * *
5235343 CCCTTAATTTTCCAAAATTCCATTTTTAACCTTGATTTTACCAAAAGTTACTATTTT
1 CCCTAAATTTTCCAAAATTCCATTTTTAACCTCGAATTCACCAAAAATTACCATTTT
5235400 GCCTCCGGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (59 bp):
CCCTAAATTTTCCAAAATTCCATTTTTAACCTCGAATTCACCAAAAATTACCATTTTAC
Found at i:5244439 original size:18 final size:18
Alignment explanation
Indices: 5244418--5244461 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5244408 ACTACAAATC
5244418 ATAAAAAAAATCAGAAAA
1 ATAAAAAAAATCAGAAAA
* * * *
5244436 ATAAGAAAATTTATAAAA
1 ATAAAAAAAATCAGAAAA
5244454 ATAAAAAA
1 ATAAAAAA
5244462 GTTATAATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAAAAAAATCAGAAAA
Found at i:5244488 original size:18 final size:19
Alignment explanation
Indices: 5244433--5244479 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5244423 AAAAATCAGA
*
5244433 AAAATAAGAAAATTTAT-A-
1 AAAATAA-AAAAGTTATAAT
5244451 AAAATAAAAAAGTTATAAT
1 AAAATAAAAAAGTTATAAT
5244470 AAAATAAAAA
1 AAAATAAAAA
5244480 TATTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 10 0.38
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAATAAAAAAGTTATAAT
Found at i:5244518 original size:9 final size:9
Alignment explanation
Indices: 5244501--5244606 Score: 69
Period size: 9 Copynumber: 11.8 Consensus size: 9
5244491 AAATCTGATA
*
5244501 TAAACTTAT
1 TAAAATTAT
5244510 TAAAATTAT
1 TAAAATTAT
*
5244519 AAAAACTTA-
1 TAAAA-TTAT
5244528 TAAATATTA-
1 TAAA-ATTAT
*
5244537 TAAAACTAT
1 TAAAATTAT
* *
5244546 AAAAATTAA
1 TAAAATTAT
5244555 T-AAATTAT
1 TAAAATTAT
*
5244563 AAAAATTA-
1 TAAAATTAT
*
5244571 TAAAATTAA
1 TAAAATTAT
5244580 TAAAATTTATT
1 TAAAA-TTA-T
5244591 TAAAA-TATT
1 TAAAATTA-T
5244600 TAAAATT
1 TAAAATT
5244607 GAAAAGAACA
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
8 16 0.21
9 48 0.62
10 8 0.10
11 5 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (9 bp):
TAAAATTAT
Found at i:5244521 original size:17 final size:17
Alignment explanation
Indices: 5244499--5244586 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
5244489 TTAAATCTGA
5244499 TATAAACTTATTAAAAT
1 TATAAACTTATTAAAAT
5244516 TATAAAAACTTA-TAAATAT
1 TAT--AAACTTATTAAA-AT
*
5244535 TATAAAAC-TATAAAAAT
1 TAT-AAACTTATTAAAAT
*
5244552 TAATAAA-TTATAAAAAT
1 T-ATAAACTTATTAAAAT
* *
5244569 TATAAAATTAATAAAAT
1 TATAAACTTATTAAAAT
5244586 T
1 T
5244587 TATTTAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.08
17 30 0.49
18 14 0.23
19 12 0.20
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAACTTATTAAAAT
Found at i:5244526 original size:19 final size:19
Alignment explanation
Indices: 5244502--5244575 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 19
5244492 AATCTGATAT
*
5244502 AAACTTATTAAAATTATAA
1 AAACTTATAAAAATTATAA
*
5244521 AAACTTATAAATATTAT-A
1 AAACTTATAAAAATTATAA
*
5244539 AAAC-TATAAAAATTA-AT
1 AAACTTATAAAAATTATAA
5244556 AAA-TTATAAAAATTATAA
1 AAACTTATAAAAATTATAA
5244574 AA
1 AA
5244576 TTAATAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
17 24 0.51
18 8 0.17
19 15 0.32
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AAACTTATAAAAATTATAA
Found at i:5244529 original size:27 final size:25
Alignment explanation
Indices: 5244499--5244583 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 25
5244489 TTAAATCTGA
5244499 TATAAACTTATTAAAATTATAAAAACT
1 TATAAA-TTATTAAAATTATAAAAA-T
*
5244526 TATAAA-TATTATAAAACTATAAAAAT
1 TATAAATTA-T-TAAAATTATAAAAAT
*
5244552 TAATAAATTATAAAAATTAT-AAAAT
1 T-ATAAATTATTAAAATTATAAAAAT
5244577 TAATAAA
1 T-ATAAA
5244584 ATTTATTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 14 0.27
26 10 0.20
27 25 0.49
28 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TATAAATTATTAAAATTATAAAAAT
Found at i:5244585 original size:34 final size:36
Alignment explanation
Indices: 5244499--5244586 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 36
5244489 TTAAATCTGA
* * *
5244499 TATAAACTTATTAAAATTATAAAAACTTATAAATAT
1 TATAAAATTAATAAAATTATAAAAACTTATAAAAAT
* *
5244535 TATAAAACT-ATAAAAATTA-ATAAA-TTATAAAAAT
1 TATAAAATTAAT-AAAATTATAAAAACTTATAAAAAT
5244569 TATAAAATTAATAAAATT
1 TATAAAATTAATAAAATT
5244587 TATTTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 23 0.52
35 7 0.16
36 14 0.32
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (36 bp):
TATAAAATTAATAAAATTATAAAAACTTATAAAAAT
Found at i:5245070 original size:9 final size:9
Alignment explanation
Indices: 5245056--5245209 Score: 85
Period size: 10 Copynumber: 15.7 Consensus size: 9
5245046 CCCATTCAAG
5245056 TTTTTATAA
1 TTTTTATAA
5245065 TTTTTATAA
1 TTTTTATAA
*
5245074 GTTTATATCAA
1 -TTTTTAT-AA
*
5245085 TTTTAAT-A
1 TTTTTATAA
5245093 TTTTTATAA
1 TTTTTATAA
5245102 TTTTTATAAAA
1 TTTTTAT--AA
* *
5245113 TTTTGATACG
1 TTTTTATA-A
*
5245123 TTTTTTTAA
1 TTTTTATAA
*
5245132 TGTTTTAAATA
1 T-TTTTATA-A
5245143 TGTTTTATTAA
1 T-TTTTA-TAA
*
5245154 TTTTATTAGAA
1 -TTT-TTATAA
5245165 TTTTTATAA
1 TTTTTATAA
5245174 TTTTTTATAAA
1 -TTTTTAT-AA
*
5245185 TTTATATCAA
1 TTTTTAT-AA
* *
5245195 TTTTCATAT
1 TTTTTATAA
5245204 TTTTTA
1 TTTTTA
5245210 AAAAATTATC
Statistics
Matches: 112, Mismatches: 20, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
8 7 0.06
9 30 0.27
10 45 0.40
11 25 0.22
12 5 0.04
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5246619 original size:15 final size:15
Alignment explanation
Indices: 5246583--5246638 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
5246573 CAAACGGTTA
5246583 ATTAATCG-ATTAAT
1 ATTAATCGAATTAAT
*
5246597 -TAAATCGAATTAAT
1 ATTAATCGAATTAAT
*
5246611 ATTAATCGAACTAAT
1 ATTAATCGAATTAAT
5246626 ATTAATCGAATTA
1 ATTAATCGAATTA
5246639 GATTAAGTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 6 0.17
14 6 0.17
15 24 0.67
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (15 bp):
ATTAATCGAATTAAT
Found at i:5246649 original size:15 final size:14
Alignment explanation
Indices: 5246583--5246649 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 14
5246573 CAAACGGTTA
5246583 ATTAATCG-ATTA-
1 ATTAATCGAATTAT
5246595 ATTAAATCGAATTAAT
1 ATT-AATCGAATT-AT
*
5246611 ATTAATCGAACTAAT
1 ATTAATCGAA-TTAT
*
5246626 ATTAATCGAATTAG
1 ATTAATCGAATTAT
5246640 ATTAAGTCGA
1 ATTAA-TCGA
5246650 TCGGTTAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 3 0.07
13 5 0.11
14 10 0.22
15 24 0.52
16 4 0.09
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (14 bp):
ATTAATCGAATTAT
Found at i:5258438 original size:18 final size:17
Alignment explanation
Indices: 5258387--5258438 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
5258377 GTCCAACCCA
* *
5258387 TTTTAAATT-TGTAATA
1 TTTTATATTATGTAATT
* *
5258403 TTTTATATTATATTATT
1 TTTTATATTATGTAATT
5258420 TTTATATATTATGTAATT
1 TTT-TATATTATGTAATT
5258438 T
1 T
5258439 AGAACATATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTTATATTATGTAATT
Found at i:5261044 original size:17 final size:20
Alignment explanation
Indices: 5261013--5261056 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
5261003 AATTTGAGAA
*
5261013 ATAAGTTTTATTAAT-TTTT
1 ATAATTTTTATTAATATTTT
5261032 -TAATTTTTA-TAATATTTT
1 ATAATTTTTATTAATATTTT
5261050 ATAATTT
1 ATAATTT
5261057 ATTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATAATTTTTATTAATATTTT
Found at i:5261049 original size:10 final size:9
Alignment explanation
Indices: 5261013--5261056 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
5261003 AATTTGAGAA
*
5261013 ATAAGTTTT
1 ATAATTTTT
5261022 ATTAATTTTT
1 A-TAATTTTT
5261032 -TAATTTTT
1 ATAATTTTT
5261040 ATAATATTTT
1 ATAAT-TTTT
5261050 ATAATTT
1 ATAATTT
5261057 ATTCAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 8 0.26
9 7 0.23
10 16 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5262595 original size:42 final size:42
Alignment explanation
Indices: 5262548--5262631 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
5262538 AAAATGAGTT
*
5262548 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGAGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTA
* *
5262590 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTA
5262632 AAAATATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTA
Found at i:5266014 original size:11 final size:11
Alignment explanation
Indices: 5265998--5266023 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5265988 TGTGTGTATA
5265998 TATTTATTTAT
1 TATTTATTTAT
5266009 TATTTATTTAT
1 TATTTATTTAT
5266020 TATT
1 TATT
5266024 CATTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTTATTTAT
Found at i:5266368 original size:31 final size:29
Alignment explanation
Indices: 5266304--5266387 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 29
5266294 CATTTAAACT
*
5266304 ATTTAAA-ATTTATAAAAAT-AAAATTATA
1 ATTTAAATTTTTA-AAAAATAAAAATTATA
*
5266332 TTTTAAATTTTCTTAAAATAATAAAAATT-TA
1 ATTTAAA-TTT-TTAAAA-AATAAAAATTATA
5266363 ATTTAAATTTTTAAAAAATAAAAAT
1 ATTTAAATTTTTAAAAAATAAAAAT
5266388 ATAGGTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
28 15 0.31
29 6 0.12
30 7 0.15
31 14 0.29
32 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTAAATTTTTAAAAAATAAAAATTATA
Found at i:5267517 original size:37 final size:37
Alignment explanation
Indices: 5267467--5267543 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
5267457 ACTCGTTTTT
5267467 GAAGAAAAATCACATTTCAATTTAATTTAATTGAGAG
1 GAAGAAAAATCACATTTCAATTTAATTTAATTGAGAG
5267504 GAAGAAAAATCACATTTCAATTTAATTTAATTGAGAG
1 GAAGAAAAATCACATTTCAATTTAATTTAATTGAGAG
5267541 GAA
1 GAA
5267544 ATCAAAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (37 bp):
GAAGAAAAATCACATTTCAATTTAATTTAATTGAGAG
Found at i:5268490 original size:4 final size:4
Alignment explanation
Indices: 5268481--5268551 Score: 88
Period size: 4 Copynumber: 17.2 Consensus size: 4
5268471 AAATATTTTG
* * * *
5268481 TTTA TTTA TTTA GTTA TTTA TTTTA TTTA TTTA GTTA ATTA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5268530 TTTTA TTTA TTTA TTTA TTTA T
1 -TTTA TTTA TTTA TTTA TTTA T
5268552 ATCGTAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 50 0.86
5 8 0.14
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:5268502 original size:25 final size:24
Alignment explanation
Indices: 5268474--5268551 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 24
5268464 ATTTTAAAAA
*
5268474 TATTTTGTTTATTTATTTAGTTATT
1 TATTTT-TTTATTTATTTAATTATT
* *
5268499 TATTTTATTTATTTAGTTAATTATA
1 TATTTT-TTTATTTATTTAATTATT
*
5268524 TATTTATTTTATTTATTTATTTATT
1 TATTT-TTTTATTTATTTAATTATT
5268549 TAT
1 TAT
5268552 ATCGTAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 44 0.98
26 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.71
Consensus pattern (24 bp):
TATTTTTTTATTTATTTAATTATT
Found at i:5268527 original size:29 final size:29
Alignment explanation
Indices: 5268495--5268553 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
5268485 TTTATTTAGT
5268495 TATTTATTTTATTTATTTAGTTAATTATA
1 TATTTATTTTATTTATTTAGTTAATTATA
* *
5268524 TATTTATTTTATTTATTTATTTATTTATA
1 TATTTATTTTATTTATTTAGTTAATTATA
5268553 T
1 T
5268554 CGTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (29 bp):
TATTTATTTTATTTATTTAGTTAATTATA
Found at i:5268550 original size:21 final size:20
Alignment explanation
Indices: 5268481--5268551 Score: 97
Period size: 21 Copynumber: 3.5 Consensus size: 20
5268471 AAATATTTTG
5268481 TTTATTTATTTAGTTATTTA
1 TTTATTTATTTAGTTATTTA
*
5268501 TTTTATTTATTTAGTTAATTA
1 -TTTATTTATTTAGTTATTTA
* *
5268522 TATATTTATTTTATTTATTTA
1 TTTATTTA-TTTAGTTATTTA
5268543 TTTATTTAT
1 TTTATTTAT
5268552 ATCGTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 8 0.18
21 36 0.82
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTAGTTATTTA
Found at i:5270003 original size:18 final size:19
Alignment explanation
Indices: 5269966--5270012 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5269956 AATGAAAATT
* *
5269966 ATTTAAAATAAAATATTAA
1 ATTTAAATTAAAATAATAA
5269985 ATTTAAATTAAAA-AATAA
1 ATTTAAATTAAAATAATAA
5270003 ATTTATAATT
1 ATTTA-AATT
5270013 TTAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTAAATTAAAATAATAA
Found at i:5270242 original size:20 final size:20
Alignment explanation
Indices: 5270196--5270242 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5270186 TTAAAAATAA
5270196 TATTTAAAAATTGAAAAGTG
1 TATTTAAAAATTGAAAAGTG
* *
5270216 T-TATAAAAATTTTAAAAGT-
1 TATTTAAAAA-TTGAAAAGTG
5270235 TATTTAAA
1 TATTTAAA
5270243 TTTCAAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
TATTTAAAAATTGAAAAGTG
Found at i:5270382 original size:11 final size:11
Alignment explanation
Indices: 5270351--5270387 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5270341 AAAACTTTTT
*
5270351 AATTTTTTTAT
1 AATTTTTTTAC
5270362 AA-TTTTTTAC
1 AATTTTTTTAC
5270372 AATTTTTTTAC
1 AATTTTTTTAC
5270383 -ATTTT
1 AATTTT
5270388 CTTAGCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTTTTTTAC
Found at i:5270386 original size:10 final size:10
Alignment explanation
Indices: 5270346--5270387 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
5270336 TTTTTAAAAC
5270346 TTTTTA-ATT
1 TTTTTACATT
* *
5270355 TTTTTATAAT
1 TTTTTACATT
5270365 TTTTTACAATT
1 TTTTTAC-ATT
5270376 TTTTTACATT
1 TTTTTACATT
5270386 TT
1 TT
5270388 CTTAGCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 6 0.21
10 13 0.46
11 9 0.32
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTACATT
Found at i:5275660 original size:18 final size:17
Alignment explanation
Indices: 5275637--5275670 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5275627 TTCAGATTAA
5275637 TGTAAAAAAATATTATTC
1 TGTAAAAAAAT-TTATTC
*
5275655 TGTAAATAAATTTATT
1 TGTAAAAAAATTTATT
5275671 TATAAGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TGTAAAAAAATTTATTC
Found at i:5276223 original size:12 final size:13
Alignment explanation
Indices: 5276177--5276223 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
5276167 TTAAAATTTT
5276177 ATATATAAAATTAC
1 ATATATAAAATT-C
*
5276191 ATAAAATCAAAATTC
1 AT-ATAT-AAAATTC
5276206 ATATATAAAATT-
1 ATATATAAAATTC
5276218 ATATAT
1 ATATAT
5276224 TAGACTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 6 0.21
13 6 0.21
14 5 0.17
15 6 0.21
16 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATATAAAATTC
Found at i:5278775 original size:12 final size:12
Alignment explanation
Indices: 5278758--5278782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5278748 ACTGTTGCTT
5278758 CTTCTTCTTCTC
1 CTTCTTCTTCTC
5278770 CTTCTTCTTCTC
1 CTTCTTCTTCTC
5278782 C
1 C
5278783 CTTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCTTCTTCTC
Found at i:5278793 original size:2 final size:2
Alignment explanation
Indices: 5278786--5278811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5278776 CTTCTCCCTT
5278786 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5278812 GAAATAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5280169 original size:2 final size:2
Alignment explanation
Indices: 5280162--5280188 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5280152 CTGTGCCCAG
5280162 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5280189 GCTCAGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5282960 original size:11 final size:11
Alignment explanation
Indices: 5282944--5282968 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5282934 GTTCTCTCTT
5282944 TTTTTTAAATA
1 TTTTTTAAATA
5282955 TTTTTTAAATA
1 TTTTTTAAATA
5282966 TTT
1 TTT
5282969 AACTATACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:5287367 original size:21 final size:21
Alignment explanation
Indices: 5287343--5287396 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5287333 CCGTTGACCA
5287343 TTGACCGTTGACAGTTGATCG
1 TTGACCGTTGACAGTTGATCG
* *
5287364 TTGACCATTAACAGTTGATCG
1 TTGACCGTTGACAGTTGATCG
*
5287385 TTGACTGTTGAC
1 TTGACCGTTGAC
5287397 TTTTTGGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
TTGACCGTTGACAGTTGATCG
Found at i:5287409 original size:20 final size:20
Alignment explanation
Indices: 5287384--5287421 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5287374 ACAGTTGATC
*
5287384 GTTGACTGTTGACTTTTTGG
1 GTTGACCGTTGACTTTTTGG
*
5287404 GTTGACCGTTGAGTTTTT
1 GTTGACCGTTGACTTTTT
5287422 TTTGAAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.50
Consensus pattern (20 bp):
GTTGACCGTTGACTTTTTGG
Found at i:5287415 original size:7 final size:7
Alignment explanation
Indices: 5287331--5287396 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
5287321 GACCGAACTC
5287331 GACCGTT
1 GACCGTT
*
5287338 GACCATT
1 GACCGTT
5287345 GACCGTT
1 GACCGTT
*
5287352 GACAGTT
1 GACCGTT
*
5287359 GATCGTT
1 GACCGTT
*
5287366 GACCATT
1 GACCGTT
* *
5287373 AACAGTT
1 GACCGTT
*
5287380 GATCGTT
1 GACCGTT
*
5287387 GACTGTT
1 GACCGTT
5287394 GAC
1 GAC
5287397 TTTTTGGGTT
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (7 bp):
GACCGTT
Found at i:5288814 original size:7 final size:7
Alignment explanation
Indices: 5288804--5288828 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5288794 TAAAAATTAT
5288804 TTTTGAA
1 TTTTGAA
5288811 TTTTGAA
1 TTTTGAA
5288818 TTTTGAA
1 TTTTGAA
5288825 TTTT
1 TTTT
5288829 AAAGAGTTTT
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:5293216 original size:297 final size:297
Alignment explanation
Indices: 5292682--5293272 Score: 1182
Period size: 297 Copynumber: 2.0 Consensus size: 297
5292672 TACGCATCAA
5292682 ACCAATAAGTTTTAAATACTCCCCATTACAATTGATTTTTGGTCAAAAGCTAAATATTTCTCATC
1 ACCAATAAGTTTTAAATACTCCCCATTACAATTGATTTTTGGTCAAAAGCTAAATATTTCTCATC
5292747 TTTGAATTTTTGTATGTGCGTATATGTTCCAATTGCTTCAGCACAACGCATAAAGATGAGTGAAT
66 TTTGAATTTTTGTATGTGCGTATATGTTCCAATTGCTTCAGCACAACGCATAAAGATGAGTGAAT
5292812 CCTCAAAGAAAGTTGGGAATATATATTAATTATGGGTCTCCTTTTATTATTATACATTAAATGTA
131 CCTCAAAGAAAGTTGGGAATATATATTAATTATGGGTCTCCTTTTATTATTATACATTAAATGTA
5292877 TTAGAGATTCAATTATGACATGATTTATGATTACTATTTTGATTCGATAGTTTTCTCGACATAAG
196 TTAGAGATTCAATTATGACATGATTTATGATTACTATTTTGATTCGATAGTTTTCTCGACATAAG
5292942 GGGGAGAGAAATAATTACTTGTAATGAGTTAGGGTTT
261 GGGGAGAGAAATAATTACTTGTAATGAGTTAGGGTTT
5292979 ACCAATAAGTTTTAAATACTCCCCATTACAATTGATTTTTGGTCAAAAGCTAAATATTTCTCATC
1 ACCAATAAGTTTTAAATACTCCCCATTACAATTGATTTTTGGTCAAAAGCTAAATATTTCTCATC
5293044 TTTGAATTTTTGTATGTGCGTATATGTTCCAATTGCTTCAGCACAACGCATAAAGATGAGTGAAT
66 TTTGAATTTTTGTATGTGCGTATATGTTCCAATTGCTTCAGCACAACGCATAAAGATGAGTGAAT
5293109 CCTCAAAGAAAGTTGGGAATATATATTAATTATGGGTCTCCTTTTATTATTATACATTAAATGTA
131 CCTCAAAGAAAGTTGGGAATATATATTAATTATGGGTCTCCTTTTATTATTATACATTAAATGTA
5293174 TTAGAGATTCAATTATGACATGATTTATGATTACTATTTTGATTCGATAGTTTTCTCGACATAAG
196 TTAGAGATTCAATTATGACATGATTTATGATTACTATTTTGATTCGATAGTTTTCTCGACATAAG
5293239 GGGGAGAGAAATAATTACTTGTAATGAGTTAGGG
261 GGGGAGAGAAATAATTACTTGTAATGAGTTAGGG
5293273 AAAGAGTAAT
Statistics
Matches: 294, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 294 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (297 bp):
ACCAATAAGTTTTAAATACTCCCCATTACAATTGATTTTTGGTCAAAAGCTAAATATTTCTCATC
TTTGAATTTTTGTATGTGCGTATATGTTCCAATTGCTTCAGCACAACGCATAAAGATGAGTGAAT
CCTCAAAGAAAGTTGGGAATATATATTAATTATGGGTCTCCTTTTATTATTATACATTAAATGTA
TTAGAGATTCAATTATGACATGATTTATGATTACTATTTTGATTCGATAGTTTTCTCGACATAAG
GGGGAGAGAAATAATTACTTGTAATGAGTTAGGGTTT
Found at i:5295090 original size:30 final size:30
Alignment explanation
Indices: 5295010--5295090 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
5295000 TTCAAATTTT
*
5295010 TGTTCATGTTCGTTTATCTAAAATTATGTG
1 TGTTCATGTTCGTTTATTTAAAATTATGTG
5295040 TGTTCATGTTCGTTTATTTAAAATTATGTG
1 TGTTCATGTTCGTTTATTTAAAATTATGTG
* * *
5295070 TGTTCATATTCATTTGTTTAA
1 TGTTCATGTTCGTTTATTTAA
5295091 TGTTCAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.53
Consensus pattern (30 bp):
TGTTCATGTTCGTTTATTTAAAATTATGTG
Found at i:5295436 original size:22 final size:22
Alignment explanation
Indices: 5295411--5295462 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5295401 AACTTAGTAA
*
5295411 ACGAA-GATTATATGAATGGTTC
1 ACGAACGATT-TACGAATGGTTC
*
5295433 ACGAACGGTTTACGAATGGTTC
1 ACGAACGATTTACGAATGGTTC
5295455 ATCGAACG
1 A-CGAACG
5295463 TTCTGTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (22 bp):
ACGAACGATTTACGAATGGTTC
Found at i:5296461 original size:59 final size:57
Alignment explanation
Indices: 5296303--5296499 Score: 189
Period size: 59 Copynumber: 3.3 Consensus size: 57
5296293 TTGATTTTTA
* * * *
5296303 GGGGTAAAATGGTAATTTTTGTGAAATCGGGGTTAAAAATGGAA-TTTGGTAAGTTTGG
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGG-TAAAAATGGAATTTTGGAAAG-TTCG
** * * *
5296361 GGGGAATAAAATGGTAAATTTTGGCAAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTCG
1 GGGG--TAAAATGGT-AATTTTGGTGAAATCGAGGT-AAAAATGGAATTTTGGAAAGTTCG
* * * * *
5296422 GAGGTAAAACGGTAAGTTTTGGTGAAATCGAGGATAAAAATGGGATTTAGGAAAGTTTG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGG-TAAAAATGGAATTTTGGAAAGTTCG
5296481 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
5296500 TAAAGGTTTT
Statistics
Matches: 111, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
58 10 0.09
59 54 0.49
60 11 0.10
61 28 0.25
62 8 0.07
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.29
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTAAAAATGGAATTTTGGAAAGTTCG
Found at i:5296513 original size:30 final size:29
Alignment explanation
Indices: 5296473--5296777 Score: 335
Period size: 30 Copynumber: 10.3 Consensus size: 29
5296463 GGGATTTAGG
* *
5296473 AAAGTTTGGGGGT-AAAATGGTAATTTTTA
1 AAAGTTTTGGGGTCAAAAT-ATAATTTTTA
*
5296502 AAGGTTTTGGGGTCAAAATAT-ATTTTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTT--A
5296532 AAAGTTTTGGGGTCAAAATATAATTTTTA
1 AAAGTTTTGGGGTCAAAATATAATTTTTA
* *
5296561 GAAAGTTTTGGGGTCAAAATATTATTTTGGA
1 -AAAGTTTTGGGGTCAAAATATAATTTT-TA
* * **
5296592 AAAGTTTAGGGGTCAAAATGTAATTTTGG
1 AAAGTTTTGGGGTCAAAATATAATTTTTA
*
5296621 AAAGTTTCGGGGTCAAAATATAATTTTTA
1 AAAGTTTTGGGGTCAAAATATAATTTTTA
* * *
5296650 GAAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 -AAAGTTTTGGGGTCAAAATATAATTTT-TA
* **
5296681 AAAGTTTTAGGGTCAAAATATAATTTGGA
1 AAAGTTTTGGGGTCAAAATATAATTTTTA
* *
5296710 AAAGTTTAGGGGTCAAAATGTAATTTTTA
1 AAAGTTTTGGGGTCAAAATATAATTTTTA
* *
5296739 GAAAGTTTCGGGGTCAAAATATAATTTTCAA
1 -AAAGTTTTGGGGTCAAAATATAATTTT-TA
5296770 AAAGTTTT
1 AAAGTTTT
5296778 AAGGTTGAAA
Statistics
Matches: 237, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.03
29 65 0.27
30 157 0.66
31 9 0.04
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAGTTTTGGGGTCAAAATATAATTTTTA
Found at i:5296536 original size:59 final size:59
Alignment explanation
Indices: 5296473--5296776 Score: 375
Period size: 59 Copynumber: 5.1 Consensus size: 59
5296463 GGGATTTAGG
* *
5296473 AAAGTTTGGGGGT-AAAATGGTAATTTTTAAAGGTTTTGGGGTCAAAATATATTTTTGGA
1 AAAGTTTAGGGGTCAAAAT-GTAATTTTTAAAAGTTTTGGGGTCAAAATATATTTTTGGA
* *
5296532 AAAGTTTTGGGGTCAAAATATAATTTTTAGAAAGTTTTGGGGTCAAAATAT-TATTTTGGA
1 AAAGTTTAGGGGTCAAAATGTAATTTTTA-AAAGTTTTGGGGTCAAAATATAT-TTTTGGA
** * *
5296592 AAAGTTTAGGGGTCAAAATGTAATTTTGGAAAGTTTCGGGGTCAAAATATAATTTTTAG-
1 AAAGTTTAGGGGTCAAAATGTAATTTTTAAAAGTTTTGGGGTCAAAATAT-ATTTTTGGA
* * *
5296651 AAAGTTTTA-GGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATA-ATTTGGA
1 AAAG-TTTAGGGGTCAAAATGTAATTTT-TAAAAGTTTTGGGGTCAAAATATATTTTTGGA
* * **
5296710 AAAGTTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTCGGGGTCAAAATATAATTTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTTTA-AAAGTTTTGGGGTCAAAATATATTTTTGGA
5296770 AAAGTTT
1 AAAGTTT
5296777 TAAGGTTGAA
Statistics
Matches: 214, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
58 9 0.04
59 107 0.50
60 97 0.45
61 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTTAAAAGTTTTGGGGTCAAAATATATTTTTGGA
Found at i:5296574 original size:89 final size:89
Alignment explanation
Indices: 5296467--5296777 Score: 412
Period size: 89 Copynumber: 3.5 Consensus size: 89
5296457 AAAAATGGGA
* * * *
5296467 TTTAGGAAAGTTTGGGGGT-AAAATGGTAATTTT-TAAAGGTTTTGGGGTCAAAATATATTTTTG
1 TTTA-GAAAGTTTTGGGGTCAAAAT-ATAATTTTGGAAAAGTTTTGGGGTCAAAATATA-TTTTG
*
5296530 GAAAAGTTTTGGGGTCAAAATATAATT
63 GAAAAGTTTAGGGGTCAAAATATAATT
* * *
5296557 TTTAGAAAGTTTTGGGGTCAAAATATTATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGG-
1 TTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATAT-ATTTTGGA
*
5296621 AAAGTTTCGGGGTCAAAATATAATT
65 AAAGTTTAGGGGTCAAAATATAATT
* * * *
5296646 TTTAGAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTGGAA
1 TTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATATTTTGGAA
*
5296711 AAGTTTAGGGGTCAAAATGTAATT
66 AAGTTTAGGGGTCAAAATATAATT
* **
5296735 TTTAGAAAGTTTCGGGGTCAAAATATAATTTTCAAAAAGTTTT
1 TTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTT
5296778 AAGGTTGAAA
Statistics
Matches: 195, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
88 6 0.03
89 154 0.79
90 34 0.17
91 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (89 bp):
TTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATATTTTGGAA
AAGTTTAGGGGTCAAAATATAATT
Found at i:5297559 original size:14 final size:14
Alignment explanation
Indices: 5297540--5297567 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5297530 TAAAACCTTC
5297540 CCAGATCTGGAAAT
1 CCAGATCTGGAAAT
5297554 CCAGATCTGGAAAT
1 CCAGATCTGGAAAT
5297568 TCCTTAGCAC
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:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
CCAGATCTGGAAAT
Found at i:5298526 original size:6 final size:6
Alignment explanation
Indices: 5298517--5298565 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
5298507 GACATTGGAC
*
5298517 TTTTAA TTTTAAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTT
1 TTTTAA TTTT-AA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
5298566 AAAGTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 25 0.66
7 4 0.11
8 7 0.18
9 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:5298566 original size:6 final size:6
Alignment explanation
Indices: 5298538--5298617 Score: 76
Period size: 6 Copynumber: 13.3 Consensus size: 6
5298528 AATGTTTAGT
* * * *
5298538 ATTTTA ATTTTA ATTTTA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
5298587 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA AT
5298618 AAAATCAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 50 0.77
7 1 0.02
8 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:5298566 original size:11 final size:11
Alignment explanation
Indices: 5298540--5298617 Score: 61
Period size: 11 Copynumber: 7.1 Consensus size: 11
5298530 TGTTTAGTAT
*
5298540 TTTAATTTTAAT
1 TTTAA-TTTAAA
5298552 TTTAATTTAAA
1 TTTAATTTAAA
**
5298563 TTTAAAGTAAA
1 TTTAATTTAAA
*
5298574 TTTAA-AT-AA
1 TTTAATTTAAA
*
5298583 TTAAATTTAAA
1 TTTAATTTAAA
**
5298594 TTTAAGATAAA
1 TTTAATTTAAA
5298605 TTTAAATTTAAA
1 TTT-AATTTAAA
5298617 T
1 T
5298618 AAAATCAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.12
10 2 0.04
11 32 0.62
12 12 0.23
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5298566 original size:17 final size:16
Alignment explanation
Indices: 5298540--5298620 Score: 76
Period size: 17 Copynumber: 5.0 Consensus size: 16
5298530 TGTTTAGTAT
* *
5298540 TTTAATTTTAATTTTAA
1 TTTAAATTTAA-TTAAA
*
5298557 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AATTAAA
5298574 TTTAAA--TAATTAAA
1 TTTAAATTTAATTAAA
*
5298588 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
*
5298605 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
5298621 ATCAATTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.22
15 1 0.02
16 8 0.15
17 32 0.58
18 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:5298622 original size:17 final size:16
Alignment explanation
Indices: 5298555--5298620 Score: 91
Period size: 17 Copynumber: 4.1 Consensus size: 16
5298545 TTTTAATTTT
5298555 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TA
*
5298572 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
5298586 AATTTAAATTTAAGATA
1 AATTTAAATTTAA-ATA
5298603 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
5298619 AA
1 AA
5298621 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.23
15 3 0.07
16 8 0.18
17 23 0.52
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:5299137 original size:68 final size:71
Alignment explanation
Indices: 5298991--5299150 Score: 188
Period size: 68 Copynumber: 2.3 Consensus size: 71
5298981 ATGCTTCGTC
*
5298991 TTGCTCTTACTTCAATTTCAGAAGGACGAAGGCTCATTATCCAGCTTTACTTCAATTTCAAAGGG
1 TTGCTCTTACTTCAATTTCAGAAGGACAAAGGCTCATTATCCAGCTTTACTTCAATTTCAAAGGG
*
5299056 ATGACG
66 ATGACA
* * *
5299062 TTCCTCTTACTTCAATTTCAG-A-GATAAAGGCGT-GTTATCCA-CTCTT-CTTCAATTTC-AAG
1 TTGCTCTTACTTCAATTTCAGAAGGACAAAGGC-TCATTATCCAGCT-TTACTTCAATTTCAAAG
*
5299121 AGGATGGCA
64 -GGATGACA
*
5299130 TTGCTCTTACTTCAAATTCAG
1 TTGCTCTTACTTCAATTTCAG
5299151 CGGATGACGT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
67 3 0.04
68 37 0.47
69 16 0.21
70 2 0.03
71 20 0.26
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (71 bp):
TTGCTCTTACTTCAATTTCAGAAGGACAAAGGCTCATTATCCAGCTTTACTTCAATTTCAAAGGG
ATGACA
Found at i:5299156 original size:30 final size:30
Alignment explanation
Indices: 5299103--5299862 Score: 147
Period size: 31 Copynumber: 22.7 Consensus size: 30
5299093 GTGTTATCCA
*
5299103 CTCTT-CTTCAATTTCAAGAGGATGGCATTG
1 CTCTTACTTCAATTTC-AGAGGATGACATTG
* * *
5299133 CTCTTACTTCAAATTCAGCGGATGACGTTG
1 CTCTTACTTCAATTTCAGAGGATGACATTG
* *
5299163 CTCTTACTTCAATTTCAGA-GATAAAGACGTGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GAC---AT-TG
* * *
5299199 CACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
*
5299231 CTCTTACTTCAATTTCAGA-GATGAAGACTTG
1 CTCTTACTTCAATTTCAGAGGATG-ACA-TTG
* * * *
5299262 TTATCCACTCAACTTCAATTTCAAGCGGATGACGTTG
1 -----CTCT-TACTTCAATTTC-AGAGGATGACATTG
* *
5299299 CTCTTACTTCAATTTTAGA-GATAAAGACATGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GACA---T-TG
* * *
5299335 CACTCTACTTCAATTTCAAGCGGATGACGTTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
* *
5299367 CTCTTACTTCAATTTCAGA-GATAAAGACGTGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GAC---AT-TG
* * * *
5299403 CACTCTACTTCAATTTCAAGGGGATAACGTTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
*
5299435 CTCTTACTTCAATTTCAGA-GATGAAGACTTG
1 CTCTTACTTCAATTTCAGAGGATG-ACA-TTG
* * * * *
5299466 TTATCCACTCAATTTCAATTTCAAGCGGATGACGTTG
1 -----CTCT-TACTTCAATTTC-AGAGGATGACATTG
* * *
5299503 CTCTTACTTCAATTTTAGA-TATAAAGACGTGTTG
1 CTCTTACTTCAATTTCAGAGGAT---GAC--ATTG
* * * *
5299537 TCCACTCTACTCCAATTTCAAGGGGATGACGTTG
1 --CTCT-TACTTCAATTTC-AGAGGATGACATTG
*
5299571 CTCTTACTTCAATTTCAGA-GATAAAGACATGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GACA---T-TG
* *
5299607 CACTCTACTTCAATTTCAAGGGGAT-AGCATTG
1 CTCT-TACTTCAATTTC-AGAGGATGA-CATTG
*
5299639 CTCTTACTTCAATTTCAGA-GATAAAGACATGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GACA---T-TG
* *
5299675 CACTCTACTTCAATTTCAAGCGGATGACATTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
* *
5299707 CTCTTACTTCAATTTCAGA-GATAAAGACGTGTTATC
1 CTCTTACTTCAATTTCAGAGGAT---GAC---AT-TG
* * *
5299743 CACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
* *
5299775 CTCTTACTTCAATTTCAGAGATGAAGACATGTTATC
1 CTCTTACTTCAATTTCAGAG--GATGACA---T-TG
* *
5299811 CACTCTACTTCAATTTCAAGGGGATGACATTG
1 CTCT-TACTTCAATTTC-AGAGGATGACATTG
5299843 CTCTTACTTCAATTTCAGAG
1 CTCTTACTTCAATTTCAGAG
5299863 ATGCAGACGT
Statistics
Matches: 533, Mismatches: 96, Indels: 202
0.64 0.12 0.24
Matches are distributed among these distances:
29 27 0.05
30 57 0.11
31 129 0.24
32 62 0.12
33 8 0.02
34 8 0.02
35 8 0.02
36 63 0.12
37 120 0.23
38 23 0.04
39 28 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (30 bp):
CTCTTACTTCAATTTCAGAGGATGACATTG
Found at i:5299245 original size:68 final size:68
Alignment explanation
Indices: 5299137--5299903 Score: 1241
Period size: 68 Copynumber: 11.3 Consensus size: 68
5299127 GCATTGCTCT
*
5299137 TACTTCAAATTC-AGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299201 CTC
66 CTC
* * *
5299204 TACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299269 CTC
66 CTC
* * *
5299272 AACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTTAGAGATAAAGACATGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299337 CTC
66 CTC
5299340 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299405 CTC
66 CTC
* * * *
5299408 TACTTCAATTTCAAGGGGATAACGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299473 CTC
66 CTC
* * * * *
5299476 AATTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTTAGATATAAAGACGTGTTGTCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299541 CTC
66 CTC
* * *
5299544 TACTCCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299609 CTC
66 CTC
* * *
5299612 TACTTCAATTTCAAGGGGAT-AGCATTGCTCTTACTTCAATTTCAGAGATAAAGACATGTTATCC
1 TACTTCAATTTCAAGCGGATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC
5299676 ACTC
65 ACTC
*
5299680 TACTTCAATTTCAAGCGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299745 CTC
66 CTC
* * *
5299748 TACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299813 CTC
66 CTC
* * **
5299816 TACTTCAATTTCAAGGGGATGACATTGCTCTTACTTCAATTTCAGAGATGCAGACGTGTTATCCA
1 TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
5299881 CTC
66 CTC
5299884 TACTTCAATTTCAAGCGGAT
1 TACTTCAATTTCAAGCGGAT
5299904 TGGAAATGAT
Statistics
Matches: 652, Mismatches: 45, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
67 12 0.02
68 639 0.98
69 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (68 bp):
TACTTCAATTTCAAGCGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA
CTC
Found at i:5311483 original size:59 final size:57
Alignment explanation
Indices: 5311400--5311601 Score: 183
Period size: 59 Copynumber: 3.4 Consensus size: 57
5311390 AATTTGGGTT
*
5311400 TTTAGGGGTAAAATGGTAATTTTTGTGAAATCAGGGTTAAAAATGGAATTTGGTAAG
1 TTTAGGGGTAAAATGGTAATTTTTGTGAAATCAGGGTTAAAAATGGAATTTGGAAAG
* * * * **
5311457 TTTAGGGGAATAAAATGGTAAATTTTG-GCAAAAACAAGGTCAAAAATAAAATTTTGGAAAG
1 TTTAGGGG--TAAAATGGTAATTTTTGTG--AAATCAGGGTTAAAAATGGAA-TTTGGAAAG
* * * * * * *
5311518 -TTCGGAGGTAAAACGGTAAGTTTTGGTGAAATCGGGGATAAAAATGGGATTTAGGGAAG
1 TTTAGG-GGTAAAATGGTAA-TTTTTGTGAAATCAGGGTTAAAAATGGAATTT-GGAAAG
*
5311577 TTTGGGGGTAAAATGGTAATTTTTG
1 TTTAGGGGTAAAATGGTAATTTTTG
5311602 AAGGTTTTGG
Statistics
Matches: 112, Mismatches: 23, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
57 8 0.07
58 9 0.08
59 56 0.50
60 28 0.25
61 11 0.10
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (57 bp):
TTTAGGGGTAAAATGGTAATTTTTGTGAAATCAGGGTTAAAAATGGAATTTGGAAAG
Found at i:5311613 original size:30 final size:30
Alignment explanation
Indices: 5311577--5311699 Score: 149
Period size: 30 Copynumber: 4.1 Consensus size: 30
5311567 TTTAGGGAAG
* * *
5311577 TTTGGGGGTAAAATGGTAATTTTTG-AAGGT
1 TTTGGGGTTAAAAT-ATAATTTTTGAAAAGT
*
5311607 TTTGGGGTTAAAATATAATTTTGGAAAAGT
1 TTTGGGGTTAAAATATAATTTTTGAAAAGT
* *
5311637 TTAGGGGTTAAAATGTAATTTTTGAAAAGT
1 TTTGGGGTTAAAATATAATTTTTGAAAAGT
* **
5311667 TTCGGGGTTAAAATATAATTTTCAAAAAGT
1 TTTGGGGTTAAAATATAATTTTTGAAAAGT
5311697 TTT
1 TTT
5311700 AAGGTCGAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 8 0.10
30 72 0.90
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.41
Consensus pattern (30 bp):
TTTGGGGTTAAAATATAATTTTTGAAAAGT
Found at i:5311681 original size:60 final size:59
Alignment explanation
Indices: 5311574--5311720 Score: 181
Period size: 60 Copynumber: 2.5 Consensus size: 59
5311564 GGATTTAGGG
* * * **
5311574 AAGTTT-GGGGGTAAAATGGTAATTTTTGAAGGTTTTGGGGTTAAAATATAATTTTGGAA
1 AAGTTTAGGGGTTAAAAT-GTAATTTTTGAAAGTTTCGGGGTTAAAATATAATTTTCAAA
5311633 AAGTTTAGGGGTTAAAATGTAATTTTTGAAAAGTTTCGGGGTTAAAATATAATTTTCAAA
1 AAGTTTAGGGGTTAAAATGTAATTTTTG-AAAGTTTCGGGGTTAAAATATAATTTTCAAA
* **
5311693 AAGTTTTA-AGGTCGAAATGTAATTTTTG
1 AAG-TTTAGGGGTTAAAATGTAATTTTTG
5311721 GACAATTTAG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
59 16 0.21
60 57 0.74
61 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (59 bp):
AAGTTTAGGGGTTAAAATGTAATTTTTGAAAGTTTCGGGGTTAAAATATAATTTTCAAA
Found at i:5313470 original size:6 final size:6
Alignment explanation
Indices: 5313454--5313521 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
5313444 AATGTTTAGT
* *
5313454 ATTTTA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
5313503 GA--TAA ATTTAA ATTTAA AT
1 -ATTTAA ATTTAA ATTTAA AT
5313522 AAAATCAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 38 0.72
7 1 0.02
8 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:5313526 original size:11 final size:10
Alignment explanation
Indices: 5313463--5313515 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 10
5313453 TATTTTAATT
5313463 TAAATTTAAA
1 TAAATTTAAA
5313473 GTAAATTTAAA
1 -TAAATTTAAA
5313484 T-AA-TTAAA
1 TAAATTTAAA
5313492 TTTAAATTTAAGA
1 --TAAATTTAA-A
5313505 TAAATTTAAA
1 TAAATTTAAA
5313515 T
1 T
5313516 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 5 0.14
9 2 0.05
10 4 0.11
11 21 0.57
12 4 0.11
13 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (10 bp):
TAAATTTAAA
Done.