Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 268 of 292
Found at i:77112106 original size:2 final size:2
Alignment explanation
Indices: 77112099--77112124 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77112089 TTTTCATTAA
77112099 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
77112125 GAGATTTTAA
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):
AT
Found at i:77112653 original size:31 final size:31
Alignment explanation
Indices: 77112610--77112668 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
77112600 GTGTAATTTA
* *
77112610 TATTCGAGTTAAATAAAAAAATTTAATTTTT
1 TATTCGAATTAAATAAAAAAACTTAATTTTT
* *
77112641 TATTCGAATTAAATCAAATAACTTAATT
1 TATTCGAATTAAATAAAAAAACTTAATT
77112669 AACTCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
TATTCGAATTAAATAAAAAAACTTAATTTTT
Found at i:77112668 original size:18 final size:18
Alignment explanation
Indices: 77112647--77112684 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
77112637 TTTTTATTCG
77112647 AATTAAATCAAATAACTT
1 AATTAAATCAAATAACTT
*
77112665 AATTAACTCAAATAACTT
1 AATTAAATCAAATAACTT
77112683 AA
1 AA
77112685 ACTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAAATCAAATAACTT
Found at i:77113169 original size:21 final size:22
Alignment explanation
Indices: 77113143--77113187 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
77113133 TAGAAAGATA
77113143 AAAAAT-AATTTTAAATT-AAAT
1 AAAAATAAATTTT-AATTCAAAT
77113164 AAAAATAAATTTTAATTCAAAT
1 AAAAATAAATTTTAATTCAAAT
77113186 AA
1 AA
77113188 TCGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATAAATTTTAATTCAAAT
Found at i:77113684 original size:16 final size:17
Alignment explanation
Indices: 77113665--77113705 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
77113655 ATATAAATCC
*
77113665 ATTCAAATTC-AAATTA
1 ATTCAAATTCGAAATAA
77113681 ATTCAAATTCGAAATAA
1 ATTCAAATTCGAAATAA
77113698 ATT-AAATT
1 ATTCAAATT
77113706 GTGGTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTCAAATTCGAAATAA
Found at i:77114641 original size:26 final size:27
Alignment explanation
Indices: 77114619--77114670 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
77114609 TAGTTTATGT
77114619 AATTT-GTTTTTAATTAAATTTTATTG
1 AATTTAGTTTTTAATTAAATTTTATTG
* * *
77114645 AATTTATTTTTTAATTCAATTCTATT
1 AATTTAGTTTTTAATTAAATTTTATT
77114671 TTGTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (27 bp):
AATTTAGTTTTTAATTAAATTTTATTG
Found at i:77116617 original size:22 final size:20
Alignment explanation
Indices: 77116576--77116618 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
77116566 GACGACATTT
*
77116576 TTATAAAAAAAAGCAATATA
1 TTATAAAAAAAAGAAATATA
*
77116596 TTATATAAAAAAGTAAACTATA
1 TTATAAAAAAAAG-AAA-TATA
77116618 T
1 T
77116619 AGATAGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 2 0.11
22 5 0.26
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
TTATAAAAAAAAGAAATATA
Found at i:77117622 original size:2 final size:2
Alignment explanation
Indices: 77117615--77117659 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
77117605 CCAGATTTGT
77117615 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
77117657 TC T
1 TC T
77117660 TTCCAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:77120507 original size:17 final size:18
Alignment explanation
Indices: 77120473--77120508 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77120463 AATAAAACTT
77120473 TTTAAATTTCACTTATTA
1 TTTAAATTTCACTTATTA
*
77120491 TTTAAATTTTA-TTATTA
1 TTTAAATTTCACTTATTA
77120508 T
1 T
77120509 ACAAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATTTCACTTATTA
Found at i:77126810 original size:15 final size:15
Alignment explanation
Indices: 77126767--77126814 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
77126757 AACCGCGAGC
77126767 AATTAAAATGATAAA
1 AATTAAAATGATAAA
* * *
77126782 AAATACAACT-ATAAT
1 AATTA-AAATGATAAA
77126797 AATTAAAATGATAAA
1 AATTAAAATGATAAA
77126812 AAT
1 AAT
77126815 ATATAATAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (15 bp):
AATTAAAATGATAAA
Found at i:77126909 original size:3 final size:3
Alignment explanation
Indices: 77126901--77126941 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
77126891 ATAGTTTACG
77126901 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
77126942 TGTGGATGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:77127318 original size:31 final size:29
Alignment explanation
Indices: 77127283--77127345 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
77127273 TTTAATTAAT
77127283 TTTTTAAAATTTAAAAAATATATAAAAATTA
1 TTTTTAAAATTT-AAAAAT-TATAAAAATTA
*
77127314 TTTTTAAAATTTAAAAATTATTAAAATTA
1 TTTTTAAAATTTAAAAATTATAAAAATTA
77127343 TTT
1 TTT
77127346 AAAACTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.42
30 6 0.19
31 12 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTTAAAATTTAAAAATTATAAAAATTA
Found at i:77127345 original size:20 final size:19
Alignment explanation
Indices: 77127322--77127359 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
77127312 TATTTTTAAA
77127322 ATTTAAAAATTATTAAAATT
1 ATTTAAAAATTA-TAAAATT
*
77127342 ATTTAAAACTTATAAAAT
1 ATTTAAAAATTATAAAAT
77127360 AATATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAAAATTATAAAATT
Found at i:77127349 original size:51 final size:53
Alignment explanation
Indices: 77127291--77127391 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 53
77127281 ATTTTTTAAA
*
77127291 ATTTAAAAAATATATAAAA-ATTATTTTTAA-A-ATTTAAAAATT-ATTAAAATT
1 ATTT-AAAAAT-TATAAAATAATATTTTTAATATATTTAAAAATTAATTAAAATT
* *
77127342 ATTTAAAACTTATAAAATAATATTTTTAATATTTTTAAAAATTAATTAAA
1 ATTTAAAAATTATAAAATAATATTTTTAATATATTTAAAAATTAATTAAA
77127392 TGTTATCGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
49 7 0.16
50 15 0.35
51 5 0.12
52 10 0.23
53 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (53 bp):
ATTTAAAAATTATAAAATAATATTTTTAATATATTTAAAAATTAATTAAAATT
Found at i:77127357 original size:29 final size:29
Alignment explanation
Indices: 77127280--77127358 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
77127270 GCATTTAATT
*
77127280 AATTTTTTAAAATT-TAAAAAATATATAAA
1 AATTATTTAAAATTAT-AAAAATATATAAA
*
77127309 AATTATTTTTAAAATT-TAAAAAT-TATTAA
1 AATTA--TTTAAAATTATAAAAATATATAAA
77127338 AATTATTTAAAACTTATAAAA
1 AATTATTTAAAA-TTATAAAA
77127359 TAATATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 7 0.16
28 2 0.05
29 19 0.43
30 6 0.14
31 10 0.23
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
AATTATTTAAAATTATAAAAATATATAAA
Found at i:77128847 original size:20 final size:18
Alignment explanation
Indices: 77128794--77128849 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 18
77128784 AAACCTGTAA
*
77128794 ATTTTTTTGTTGTTTTTT
1 ATTTTCTTGTTGTTTTTT
* *
77128812 ACTTTCTT-TCTTTTTTTGCT
1 ATTTTCTTGT-TGTTTTT--T
77128832 ATTTTCTTGTTGTTTTTT
1 ATTTTCTTGTTGTTTTTT
77128850 CATGATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
20 14 0.48
21 1 0.03
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (18 bp):
ATTTTCTTGTTGTTTTTT
Found at i:77130086 original size:16 final size:16
Alignment explanation
Indices: 77130065--77130119 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
77130055 GTTTGGTTCA
*
77130065 TTGTAATGGAATAGGG
1 TTGTAATGGAATAGAG
*
77130081 TTGTAATTGAATAGAG
1 TTGTAATGGAATAGAG
*
77130097 CTGTAATGGAATAGAG
1 TTGTAATGGAATAGAG
*
77130113 CTGTAAT
1 TTGTAAT
77130120 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (16 bp):
TTGTAATGGAATAGAG
Found at i:77130187 original size:44 final size:46
Alignment explanation
Indices: 77130101--77130194 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
77130091 ATAGAGCTGT
77130101 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
* ***
77130147 AATGGAGTAGAGCTGTAAT-AG-AATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
77130191 AATG
1 AATG
77130195 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.55
45 2 0.05
46 18 0.41
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGG
Found at i:77130309 original size:25 final size:25
Alignment explanation
Indices: 77130265--77130315 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
77130255 GTTGATAGAT
77130265 GATTATTGTTATTAAA-TTTTAATAA
1 GATTATTGTTA-TAAATTTTTAATAA
77130290 GATTATTGTTA-AATATTTTTTAATAA
1 GATTATTGTTATAA-A-TTTTTAATAA
77130316 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 1 0.04
25 11 0.48
26 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
GATTATTGTTATAAATTTTTAATAA
Found at i:77130344 original size:58 final size:57
Alignment explanation
Indices: 77130291--77130409 Score: 148
Period size: 58 Copynumber: 2.1 Consensus size: 57
77130281 TTTTAATAAG
* **
77130291 ATTATTGTTAAATATTTTTTAATAAAAAAAATAAATAATTTAATCATATTTTAACATA
1 ATTATTATTAAATATAATTTAAT-AAAAAAATAAATAATTTAATCATATTTTAACATA
* * * * *
77130349 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTATTAATATA
1 ATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAATCATATT-TTAACATA
77130407 ATT
1 ATT
77130410 TTTAATAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 22 0.42
58 30 0.58
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (57 bp):
ATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAATCATATTTTAACATA
Found at i:77132919 original size:40 final size:40
Alignment explanation
Indices: 77132875--77132955 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
77132865 TTAGTTATAC
*
77132875 TGCAGATACTTAAGCAAATAAGTTATTTTGCCAATTTAGA
1 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
*
77132915 TGCAGATACTCAAGCAAATAAGTTATTTTTCCAATTTAGA
1 TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
77132955 T
1 T
77132956 AGAGTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (40 bp):
TGCAGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGA
Found at i:77135134 original size:6 final size:6
Alignment explanation
Indices: 77135123--77135151 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
77135113 ACTCCCTTCC
77135123 CACCAT CACCAT CACCAT CACCAT CACCA
1 CACCAT CACCAT CACCAT CACCAT CACCA
77135152 CCCCTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (6 bp):
CACCAT
Found at i:77142599 original size:26 final size:24
Alignment explanation
Indices: 77142569--77142617 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
77142559 AAATAAAAAT
*
77142569 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
77142595 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
77142618 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:77142637 original size:21 final size:21
Alignment explanation
Indices: 77142588--77142646 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
77142578 ATAATAAATC
*
77142588 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
77142608 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
77142630 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
77142647 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:77146317 original size:2 final size:2
Alignment explanation
Indices: 77146310--77146349 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
77146300 GTAATTCATA
77146310 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
77146350 ATTGTTTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:77147747 original size:2 final size:2
Alignment explanation
Indices: 77147740--77147777 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
77147730 ATAATAGTAT
*
77147740 TA TA TA TA TA TC 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
77147778 ATACAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77148656 original size:2 final size:2
Alignment explanation
Indices: 77148643--77148673 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
77148633 AAGAATTCGA
*
77148643 AT AT AC 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 A
77148674 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:77149832 original size:38 final size:38
Alignment explanation
Indices: 77149765--77149926 Score: 171
Period size: 38 Copynumber: 4.3 Consensus size: 38
77149755 CATGTAAAAT
* ** * * *
77149765 AGTAGACATGTTTAACATGTATTCAGTTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTTGGTTCAACAGCAAC
* *
77149803 ATTAGACATGCTTAACATGTATTTGGTTCAACAGCAAT
1 AGTAGACATGCTTAACATGTATTTGGTTCAACAGCAAC
* * *
77149841 AGTAGACATGCTTAACATTTATTTGGTTCAACAACAAT
1 AGTAGACATGCTTAACATGTATTTGGTTCAACAGCAAC
* * * * *
77149879 AGTGGACATGCTTAACATGTATTTAGTTTAACAGTATC
1 AGTAGACATGCTTAACATGTATTTGGTTCAACAGCAAC
*
77149917 AGTAGGCATG
1 AGTAGACATG
77149927 TTGAATGTGC
Statistics
Matches: 103, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 103 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTTGGTTCAACAGCAAC
Found at i:77155015 original size:27 final size:29
Alignment explanation
Indices: 77154962--77155015 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
77154952 GAGAAGTTTC
* **
77154962 ATTATTATTATAAATATTAAATTAATAAA
1 ATTATTATTATAAAAATTAAAAAAATAAA
77154991 ATTATT-TTA-AAAAATTAAAAAAATA
1 ATTATTATTATAAAAATTAAAAAAATA
77155016 TACATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 13 0.59
28 3 0.14
29 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATTATTATTATAAAAATTAAAAAAATAAA
Found at i:77158038 original size:5 final size:5
Alignment explanation
Indices: 77158017--77158069 Score: 70
Period size: 5 Copynumber: 10.0 Consensus size: 5
77158007 TGTTAAAATA
*
77158017 TATAT TAAAT TATTAT TATAT TATAT TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
77158065 TATAT
1 TATAT
77158070 AAATAAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 33 0.77
6 6 0.14
7 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:77158060 original size:12 final size:12
Alignment explanation
Indices: 77158015--77158070 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
77158005 TGTGTTAAAA
*
77158015 TATATATTAAAT
1 TATATATTATAT
77158027 TAT-TATTATATT
1 TATATATTATA-T
77158039 ATATTATATTATAT
1 -TA-TATATTATAT
77158053 TATATATTATAT
1 TATATATTATAT
77158065 TATATA
1 TATATA
77158071 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATATTATAT
Found at i:77159406 original size:18 final size:19
Alignment explanation
Indices: 77159385--77159423 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
77159375 ATATATAGAT
77159385 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
77159403 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
77159422 AT
1 AT
77159424 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:77159773 original size:39 final size:39
Alignment explanation
Indices: 77159663--77159797 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
77159653 GACCTCGAGT
* * * *
77159663 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
77159704 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
77159742 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
77159781 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
77159798 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:77159941 original size:18 final size:19
Alignment explanation
Indices: 77159920--77159960 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
77159910 AATGAAATGA
77159920 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
77159938 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
77159957 GAAA
1 GAAA
77159961 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:77161302 original size:2 final size:2
Alignment explanation
Indices: 77161295--77161344 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
77161285 AATATTGAAA
*
77161295 AT AT AT AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
77161336 TT AT AT AT A
1 AT AT AT AT A
77161345 ACATAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77161391 original size:20 final size:22
Alignment explanation
Indices: 77161347--77161397 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
77161337 TATATATAAC
* *
77161347 ATAATATTAAAAACACATATAT
1 ATAATATGAAAAACAAATATAT
77161369 ATAATATGAAAAA-AAATTATAT
1 ATAATATGAAAAACAAA-TATAT
77161391 ATAATAT
1 ATAATAT
77161398 AATACATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAATATGAAAAACAAATATAT
Found at i:77162094 original size:12 final size:12
Alignment explanation
Indices: 77162069--77162101 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
77162059 ACGTATGAGT
77162069 AGAA-AAAAAAA
1 AGAAGAAAAAAA
*
77162080 AGAAGAAAAAGA
1 AGAAGAAAAAAA
77162092 AGAAGAAAAA
1 AGAAGAAAAA
77162102 TAACAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAAA
Found at i:77180144 original size:28 final size:31
Alignment explanation
Indices: 77180084--77180146 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 31
77180074 ATAAACTATT
* *
77180084 AAAATGATAAAATTATATTTTTATTATCGTA
1 AAAATGATAAAATTATATTTTAATTATCCTA
*
77180115 AAAATTAT-AAATTA-ATTTTAATT-TCCTA
1 AAAATGATAAAATTATATTTTAATTATCCTA
77180143 AAAA
1 AAAA
77180147 AAATCTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 8 0.28
30 6 0.21
31 7 0.24
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAATGATAAAATTATATTTTAATTATCCTA
Found at i:77180772 original size:70 final size:70
Alignment explanation
Indices: 77180695--77180831 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 70
77180685 TGGACTCAGA
*
77180695 TTCATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGGAC-AAAAATCTAAATTCAGGT
1 TTCATGGTTCAAATAAGTCACTTACC-TTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGT
77180759 GTTAGG
65 GTTAGG
* * *
77180765 TTCATGGTTTAAATAAGTCATTTACCTTTAAGTACTAATTTGGACAAAAAATCTAAATTCAAGTG
1 TTCATGGTTCAAATAAGTCACTTACCTTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGTG
77180830 TT
66 TT
77180832 GATTTAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 18 0.29
70 44 0.71
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (70 bp):
TTCATGGTTCAAATAAGTCACTTACCTTTAAGTACTAAATTGGACAAAAAATCTAAATTCAAGTG
TTAGG
Found at i:77184137 original size:23 final size:23
Alignment explanation
Indices: 77184111--77184156 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
77184101 AGACATGGAT
77184111 AGTGCCAGTGCTCTTCCCCCGCC
1 AGTGCCAGTGCTCTTCCCCCGCC
77184134 AGTGCCAGTGCTCTTCCCCCGCC
1 AGTGCCAGTGCTCTTCCCCCGCC
77184157 CCCCTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.48, G:0.22, T:0.22
Consensus pattern (23 bp):
AGTGCCAGTGCTCTTCCCCCGCC
Found at i:77184535 original size:21 final size:21
Alignment explanation
Indices: 77184509--77184551 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
77184499 TCCTTAAGTA
77184509 ACTATCTTTGAACTGAATAGC
1 ACTATCTTTGAACTGAATAGC
77184530 ACTATCTTTGAACTGAATAGC
1 ACTATCTTTGAACTGAATAGC
77184551 A
1 A
77184552 TAGCTGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
ACTATCTTTGAACTGAATAGC
Found at i:77185899 original size:15 final size:17
Alignment explanation
Indices: 77185872--77185906 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
77185862 AATTTCAGTA
77185872 ATTATTGTTATTTC-TC
1 ATTATTGTTATTTCTTC
77185888 ATTATT-TTATTTCTTC
1 ATTATTGTTATTTCTTC
77185904 ATT
1 ATT
77185907 TATCTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTGTTATTTCTTC
Found at i:77200600 original size:26 final size:24
Alignment explanation
Indices: 77200566--77200627 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 24
77200556 AATTTTTGAA
77200566 ATTTTAAAATTGAAAAATTAAGAATT
1 ATTTTAAAATT-AAAAATT-AGAATT
*
77200592 ATTTTAAAAATTAAAAATTATAATT
1 ATTTT-AAAATTAAAAATTAGAATT
*
77200617 TTTTTAAAATT
1 ATTTTAAAATT
77200628 TAAGTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 6 0.18
25 9 0.27
26 12 0.36
27 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
ATTTTAAAATTAAAAATTAGAATT
Found at i:77200607 original size:25 final size:25
Alignment explanation
Indices: 77200566--77200630 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
77200556 AATTTTTGAA
77200566 ATTTT-AAAATTGAAAAATTAAGAATT
1 ATTTTAAAAATT-AAAAATT-AGAATT
*
77200592 ATTTTAAAAATTAAAAATTATAATT
1 ATTTTAAAAATTAAAAATTAGAATT
* *
77200617 TTTTTAAAATTTAA
1 ATTTTAAAAATTAA
77200631 GTAATTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.49
26 12 0.34
27 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTTTAAAAATTAAAAATTAGAATT
Found at i:77207069 original size:6 final size:6
Alignment explanation
Indices: 77207022--77207065 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
77207012 ACGACGAAAT
* *
77207022 AAAAGG -AAAGG TAAAGG AAAAGG AAAAGG AAAAGG AAATGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAA
77207066 TGGAGAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.05
Consensus pattern (6 bp):
AAAAGG
Found at i:77213726 original size:13 final size:13
Alignment explanation
Indices: 77213708--77213734 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
77213698 CTAAACAGGG
77213708 TGAATTACACTCA
1 TGAATTACACTCA
77213721 TGAATTACACTCA
1 TGAATTACACTCA
77213734 T
1 T
77213735 CTTAATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
TGAATTACACTCA
Found at i:77215332 original size:43 final size:45
Alignment explanation
Indices: 77215280--77215381 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 45
77215270 TGTCTTTGAC
* * *
77215280 ATGGACTTACATGAATTATTCCT-TCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
77215323 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
77215369 ATGGACTTACATG
1 ATGGACTTACATG
77215382 GCTCATTTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 19 0.38
44 13 0.26
46 18 0.36
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:77215378 original size:46 final size:43
Alignment explanation
Indices: 77215280--77215386 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 43
77215270 TGTCTTTGAC
** * * *
77215280 ATGGACTTACATGAATTATTCCTTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTTCTCCAAAGCCATATATAAT
*
77215323 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCT-TCTCCAAAGCCATA--TATAAT
77215369 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
77215387 TTTCGTTCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 19 0.35
44 13 0.24
46 23 0.42
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (43 bp):
ATGGACTTACATGGCTCAATCCTTCTCCAAAGCCATATATAAT
Found at i:77222306 original size:46 final size:44
Alignment explanation
Indices: 77222202--77222309 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
77222192 TGTCTTTGAC
** * * *
77222202 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
77222246 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
77222292 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
77222310 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:77243998 original size:5 final size:6
Alignment explanation
Indices: 77243983--77244007 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77243973 TACTTTTTCA
77243983 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
77244008 TGTAGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:77246216 original size:30 final size:30
Alignment explanation
Indices: 77246182--77246238 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
77246172 TTATTTAAAA
77246182 ATTTTTAACTTAGAAGTTTTAAA-AAAATTT
1 ATTTTTAACTTA-AAGTTTTAAATAAAATTT
* *
77246212 ATTTTTACCTTAAATTTTTAAATAAAA
1 ATTTTTAACTTAAAGTTTTAAATAAAA
77246239 AATTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (30 bp):
ATTTTTAACTTAAAGTTTTAAATAAAATTT
Found at i:77250529 original size:18 final size:19
Alignment explanation
Indices: 77250506--77250543 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
77250496 ATTTTAAAAA
77250506 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
77250524 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
77250543 T
1 T
77250544 GTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:77250553 original size:19 final size:19
Alignment explanation
Indices: 77250509--77250554 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
77250499 TTAAAAATAT
77250509 AAATTTTAGAATTTTTATA
1 AAATTTTAGAATTTTTATA
*
77250528 AATATTTT-GAATTTTTGTTA
1 AA-ATTTTAGAATTTTT-ATA
77250548 AAATTTT
1 AAATTTT
77250555 TGTTGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
AAATTTTAGAATTTTTATA
Found at i:77256705 original size:16 final size:17
Alignment explanation
Indices: 77256675--77256707 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
77256665 ATATAATTAA
*
77256675 AATATATTAATTTATTT
1 AATATATTAAATTATTT
77256692 AATA-ATTAAATTATTT
1 AATATATTAAATTATTT
77256708 GTACAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATATTAAATTATTT
Found at i:77257074 original size:22 final size:22
Alignment explanation
Indices: 77257046--77257089 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
77257036 TTAACTTAAA
* *
77257046 TTTAATACTTAATTTCTTAATT
1 TTTAATACCTAATTACTTAATT
77257068 TTTAATACCTAATTACTTAATT
1 TTTAATACCTAATTACTTAATT
77257090 ATTGTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATACCTAATTACTTAATT
Found at i:77258407 original size:3 final size:3
Alignment explanation
Indices: 77258399--77258437 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
77258389 TTAAATATTT
77258399 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
77258438 TCTTTTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:77264824 original size:31 final size:29
Alignment explanation
Indices: 77264789--77264868 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
77264779 AATCCCAAAA
*
77264789 CTATACATGAATTATAATTTAATGTGAAATT
1 CTATACATGAATTATAATTTAACGT--AATT
* * * *
77264820 CTATACATTAATTTTGATTTTACGTAATT
1 CTATACATGAATTATAATTTAACGTAATT
*
77264849 TTATACATGGAATTATAATT
1 CTATACAT-GAATTATAATT
77264869 CTATACATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 11 0.28
30 8 0.21
31 20 0.51
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (29 bp):
CTATACATGAATTATAATTTAACGTAATT
Found at i:77264990 original size:30 final size:31
Alignment explanation
Indices: 77264954--77265018 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
77264944 CCAAACCAAA
77264954 AAACCCC-TACCCAGGCCTGATCAATTTTCT
1 AAACCCCTTACCCAGGCCTGATCAATTTTCT
*
77264984 AAACCCCTTACCTAGGCCTGATCAATTTTCT
1 AAACCCCTTACCCAGGCCTGATCAATTTTCT
77265015 AAAC
1 AAAC
77265019 AAGTATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.28
Consensus pattern (31 bp):
AAACCCCTTACCCAGGCCTGATCAATTTTCT
Found at i:77265334 original size:4 final size:4
Alignment explanation
Indices: 77265320--77265348 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
77265310 TTCAAGCAAT
77265320 ATTA A-TA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
77265349 AATAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:77265394 original size:23 final size:24
Alignment explanation
Indices: 77265360--77265405 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
77265350 ATAGATAAAA
*
77265360 ATTTTATAAATA-ATATTTTATTT
1 ATTTTATAAATAGAAATTTTATTT
77265383 ATTTT-TAGAATAGAAATTTTATT
1 ATTTTATA-AATAGAAATTTTATT
77265406 CTTTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 9 0.45
24 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTTATAAATAGAAATTTTATTT
Found at i:77276166 original size:22 final size:22
Alignment explanation
Indices: 77276141--77276183 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
77276131 TGTCCCTATT
77276141 TTGCTACCATTTTATTATTATA
1 TTGCTACCATTTTATTATTATA
** *
77276163 TTGCTATTATTTTATTGTTAT
1 TTGCTACCATTTTATTATTAT
77276184 TGTTTAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (22 bp):
TTGCTACCATTTTATTATTATA
Found at i:77281416 original size:2 final size:2
Alignment explanation
Indices: 77281411--77281439 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77281401 ATATTCAGTT
77281411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
77281440 TGATGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77281945 original size:12 final size:12
Alignment explanation
Indices: 77281921--77281965 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
77281911 ATAATAAGAG
77281921 AAGAAGAAAAAAA
1 AAGAAG-AAAAAA
77281934 AAGAAGAAAAAA
1 AAGAAGAAAAAA
77281946 AAGAAGAAAAAA
1 AAGAAGAAAAAA
*
77281958 AAGGAGAA
1 AAGAAGAA
77281966 GAGAAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 25 0.81
13 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAA
Found at i:77281979 original size:16 final size:15
Alignment explanation
Indices: 77281922--77281980 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 15
77281912 TAATAAGAGA
77281922 AGAAGAAAAAAAA--
1 AGAAGAAAAAAAAGG
77281935 AGAAG-AAAAAAA--
1 AGAAGAAAAAAAAGG
77281947 AGAAGAAAAAAAAGG
1 AGAAGAAAAAAAAGG
*
77281962 AGAAGAGAAAAAACGG
1 AGAAGA-AAAAAAAGG
77281978 AGA
1 AGA
77281981 TTGTAACAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
12 12 0.29
13 12 0.29
15 6 0.15
16 11 0.27
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAAAAGG
Found at i:77284190 original size:39 final size:39
Alignment explanation
Indices: 77284144--77284283 Score: 199
Period size: 39 Copynumber: 3.6 Consensus size: 39
77284134 GCTCTGGTGA
*
77284144 GCTTCAGTTAGCCTTTGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
77284183 GCTTCAGTCAGCCTTCGGGCTTCTGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* * *
77284222 GCTTCAGTTAGCCTCCGAGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* **
77284261 GCTTCAGCTAAACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
77284284 AGATCACGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:77285542 original size:49 final size:49
Alignment explanation
Indices: 77285470--77285565 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
77285460 GTTAGACTTT
* *
77285470 AATTTTCCCTTTCATAAATCTTTGGGTTTTTATGGAGGAAATCAATTTC
1 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTC
77285519 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
1 AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATT
77285566 GGGATACCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (49 bp):
AATTTCCCCTTTCATAAATCTTTGGGTTTTCATGGAGGAAATCAATTTC
Found at i:77287021 original size:9 final size:9
Alignment explanation
Indices: 77287009--77287033 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
77286999 TATTATATTT
77287009 ATTATTATC
1 ATTATTATC
77287018 ATTATTATC
1 ATTATTATC
77287027 ATTATTA
1 ATTATTA
77287034 ACTATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTATC
Found at i:77287046 original size:2 final size:2
Alignment explanation
Indices: 77287039--77287066 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77287029 TATTAACTAT
77287039 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
77287067 AGATATAAAA
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):
TA
Found at i:77287107 original size:14 final size:13
Alignment explanation
Indices: 77287074--77287115 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
77287064 ATAAGATATA
77287074 AAAGAAATGAAAG-
1 AAAGAAA-GAAAGC
77287087 AAAGAAAGAAAGC
1 AAAGAAAGAAAGC
77287100 ACAAGAAAGAATAGC
1 A-AAGAAAGAA-AGC
77287115 A
1 A
77287116 GAAACCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.19
13 8 0.31
14 9 0.35
15 4 0.15
ACGTcount: A:0.67, C:0.07, G:0.21, T:0.05
Consensus pattern (13 bp):
AAAGAAAGAAAGC
Found at i:77287649 original size:15 final size:14
Alignment explanation
Indices: 77287613--77287652 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
77287603 ATTTGATTGG
77287613 AAAATGAATT-AAA
1 AAAATGAATTAAAA
*
77287626 AATATGAATTAAACA
1 AAAATGAATTAAA-A
77287641 AAAATGAATTAA
1 AAAATGAATTAA
77287653 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (14 bp):
AAAATGAATTAAAA
Found at i:77288024 original size:23 final size:23
Alignment explanation
Indices: 77287994--77288104 Score: 115
Period size: 23 Copynumber: 5.0 Consensus size: 23
77287984 GGCTTTGCCG
*
77287994 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
*
77288017 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* **
77288040 TTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACCTTATGTGTCGTAT
**
77288061 ATCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
77288083 -TCAGGCA-CTTATGTATCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
77288104 A
1 A
77288105 CTGATCAGGT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
20 9 0.12
21 28 0.36
22 1 0.01
23 39 0.51
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:77288065 original size:21 final size:21
Alignment explanation
Indices: 77288007--77288090 Score: 96
Period size: 21 Copynumber: 3.8 Consensus size: 21
77287997 AGGCACTTTA
* **
77288007 TGTGTCGTATATCAGGCACTTTA
1 TGTGTCG--TATCAGGCACCTCG
77288030 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
77288053 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
*
77288074 TGTGTCGTTTCAGGCAC
1 TGTGTCGTATCAGGCAC
77288091 TTATGTATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
21 30 0.55
23 25 0.45
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:77288079 original size:44 final size:43
Alignment explanation
Indices: 77288007--77288090 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
77287997 AGGCACTTTA
* *
77288007 TGTGTCGTATATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCG
1 TGTGTCG-ATATCAGGCACCTCATGTGTCG--TTTCAGGCACCTCG
*
77288053 TGTGTCG-TATCAGGCACCTCGTGTGTCGTTTCAGGCAC
1 TGTGTCGATATCAGGCACCTCATGTGTCGTTTCAGGCAC
77288091 TTATGTATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 10 0.29
44 18 0.51
46 7 0.20
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (43 bp):
TGTGTCGATATCAGGCACCTCATGTGTCGTTTCAGGCACCTCG
Found at i:77289341 original size:21 final size:21
Alignment explanation
Indices: 77289317--77289357 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
77289307 CAACGTGGCA
77289317 AGTTAA-TTGGCCACATCAGCT
1 AGTTAACTT-GCCACATCAGCT
77289338 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
77289358 AGTCCTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:77293189 original size:11 final size:11
Alignment explanation
Indices: 77293173--77293198 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
77293163 ATGACTTTTG
77293173 AGAACCGAAGA
1 AGAACCGAAGA
77293184 AGAACCGAAGA
1 AGAACCGAAGA
77293195 AGAA
1 AGAA
77293199 TGGTGGTTGC
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:0.58, C:0.15, G:0.27, T:0.00
Consensus pattern (11 bp):
AGAACCGAAGA
Found at i:77293293 original size:40 final size:40
Alignment explanation
Indices: 77293238--77293319 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
77293228 TATTACAATT
77293238 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
1 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
* *
77293278 GTGGATTGCTTGGCCAAGTTGGGTTTTACATGGAATTTAA
1 GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
77293318 GT
1 GT
77293320 CTTCAAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (40 bp):
GTGGATTGCTTGGCCAAGTTGGGTTTTAAATGGAATTCAA
Found at i:77294509 original size:12 final size:12
Alignment explanation
Indices: 77294492--77294516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77294482 TAAGCTAAAT
77294492 AATAATTAAAAA
1 AATAATTAAAAA
77294504 AATAATTAAAAA
1 AATAATTAAAAA
77294516 A
1 A
77294517 GAATCTGGTA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATTAAAAA
Found at i:77294813 original size:15 final size:16
Alignment explanation
Indices: 77294783--77294816 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
77294773 TTTTATATGA
*
77294783 AATTTTAATTTAATTT
1 AATTTTAATATAATTT
77294799 AATTTT-ATATAATTT
1 AATTTTAATATAATTT
77294814 AAT
1 AAT
77294817 ATATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTAATATAATTT
Found at i:77299650 original size:24 final size:24
Alignment explanation
Indices: 77299623--77299703 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
77299613 TAATCTACAT
77299623 TATTTAAATTACTTGTGATCTTTA
1 TATTTAAATTACTTGTGATCTTTA
* * *
77299647 TATTTAAGTTAGGTCTCTCTACATCTTTA
1 TATTTAAATTA---CT-TGT-GATCTTTA
77299676 TATTTAAATTACTTGTGATCTTTA
1 TATTTAAATTACTTGTGATCTTTA
77299700 TATT
1 TATT
77299704 ATTCCACCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 21 0.46
25 2 0.04
26 2 0.04
27 2 0.04
28 2 0.04
29 17 0.37
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
TATTTAAATTACTTGTGATCTTTA
Found at i:77302838 original size:18 final size:18
Alignment explanation
Indices: 77302815--77302850 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
77302805 CTTTTAAATG
*
77302815 ATATTTTATTAAGTAATA
1 ATATTTTAATAAGTAATA
*
77302833 ATATTTTAATAATTAATA
1 ATATTTTAATAAGTAATA
77302851 TTATAATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTTTAATAAGTAATA
Found at i:77304826 original size:18 final size:18
Alignment explanation
Indices: 77304803--77304844 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
77304793 TATTAATAAT
77304803 ATTTATATTCATGC-TTTA
1 ATTTATATTCAT-CATTTA
* *
77304821 ATTTATTTTTATCATTTA
1 ATTTATATTCATCATTTA
77304839 ATTTAT
1 ATTTAT
77304845 GATCAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTATATTCATCATTTA
Found at i:77305739 original size:61 final size:60
Alignment explanation
Indices: 77305562--77305745 Score: 153
Period size: 61 Copynumber: 3.0 Consensus size: 60
77305552 TTTATTGGTC
* * * *
77305562 AAAT-AATAAATTTAGCCCTCAA-ATGTTTATACATTCTATCAATTTGA-TTCTAAATATAAAA
1 AAATCAATAAATTTAGCCCTCAATAT-TTTAAAAATT-T-TCAATTT-ATTTCTAATTCTAAAA
* * * * * * *
77305623 AATTCAACAAATTCAGCCCTCAAT-GTTTACGAAAATTTTTATTTTAGTTT-GAATTCTAAAA
1 AAATCAATAAATTTAGCCCTCAATATTTTA--AAAATTTTCAATTTA-TTTCTAATTCTAAAA
*
77305684 AAATCATTAAATTTAGCCCTCAATATTTTAAAAATTTGTCAATTTATTTCTAATTCTAAAA
1 AAATCAATAAATTTAGCCCTCAATATTTTAAAAATTT-TCAATTTATTTCTAATTCTAAAA
77305745 A
1 A
77305746 TTTTAAAAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
60 11 0.12
61 57 0.60
62 23 0.24
63 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (60 bp):
AAATCAATAAATTTAGCCCTCAATATTTTAAAAATTTTCAATTTATTTCTAATTCTAAAA
Found at i:77308003 original size:18 final size:18
Alignment explanation
Indices: 77307980--77308017 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
77307970 GAAGAAATAT
*
77307980 GATAAT-AATTAAAGGTAA
1 GATAATGAACTAAA-GTAA
77307998 GATAATGAACTAAAGTAA
1 GATAATGAACTAAAGTAA
77308016 GA
1 GA
77308018 ATGATTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (18 bp):
GATAATGAACTAAAGTAA
Found at i:77317488 original size:2 final size:2
Alignment explanation
Indices: 77317481--77317519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
77317471 TCATATAATT
77317481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
77317520 CCAAATGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77319079 original size:50 final size:50
Alignment explanation
Indices: 77319006--77319109 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
77318996 TTCCTCCAAT
77319006 TTTATGATATTGGTTAGATCACCAATTCTCACTTCAATCAATCGGACTAA
1 TTTATGATATTGGTTAGATCACCAATTCTCACTTCAATCAATCGGACTAA
77319056 TTTATGATATTGGTTAGATCACCAATTCTCACTTCAATCAATCGGACTAA
1 TTTATGATATTGGTTAGATCACCAATTCTCACTTCAATCAATCGGACTAA
77319106 TTTA
1 TTTA
77319110 ATTTAATTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (50 bp):
TTTATGATATTGGTTAGATCACCAATTCTCACTTCAATCAATCGGACTAA
Found at i:77320763 original size:3 final size:3
Alignment explanation
Indices: 77320755--77320799 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
77320745 ATTTATATAC
77320755 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77320800 AAGATGTATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:77321744 original size:14 final size:15
Alignment explanation
Indices: 77321713--77321747 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
77321703 TGATGACATT
*
77321713 AATAATAGATATTAA
1 AATAATAGATACTAA
77321728 AATAATA-ATACTAA
1 AATAATAGATACTAA
77321742 AATAAT
1 AATAAT
77321748 TAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATAATAGATACTAA
Found at i:77324422 original size:23 final size:23
Alignment explanation
Indices: 77324396--77324439 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
77324386 GTTCTACTAT
*
77324396 GAAAT-GTTGGATTTTTTGTCATG
1 GAAATAGTT-GATTTATTGTCATG
77324419 GAAATAGTTGATTTATTGTCA
1 GAAATAGTTGATTTATTGTCA
77324440 CAAAATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (23 bp):
GAAATAGTTGATTTATTGTCATG
Found at i:77326850 original size:40 final size:40
Alignment explanation
Indices: 77326803--77326879 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
77326793 ACACACCATG
*
77326803 TGGGGATAGAATCGA-CCCACCCAACCTTACACACCAAGTA
1 TGGGGATAGAATC-ACCCCACCCAACCCTACACACCAAGTA
* * *
77326843 TGGGGATATAATCACCCCATCCAACCCTACACCCCAA
1 TGGGGATAGAATCACCCCACCCAACCCTACACACCAA
77326880 AAGGTACCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (40 bp):
TGGGGATAGAATCACCCCACCCAACCCTACACACCAAGTA
Found at i:77329592 original size:75 final size:75
Alignment explanation
Indices: 77329464--77329615 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
77329454 TATGAGATTA
*
77329464 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAGCCA
1 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
77329529 CAACATGATC
66 CAACATGATC
* * *
77329539 AAGAGACCCCATCATTTCATCAACGGAGAGAACTGGAAGGTCTTTGGATTCTTCTATAACAACCA
1 AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
77329604 CAACATGATC
66 CAACATGATC
77329614 AA
1 AA
77329616 ATTTTATCGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (75 bp):
AAGAAACCCCATCAGTTCATCAACGGAGAGAACTGAAAGGTCTTTGGATTCTTCTATAACAACCA
CAACATGATC
Found at i:77330646 original size:380 final size:380
Alignment explanation
Indices: 77329941--77330701 Score: 1333
Period size: 380 Copynumber: 2.0 Consensus size: 380
77329931 TTGGTTTCTT
*
77329941 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTTGACCAAGTCC
1 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAGTCC
*
77330006 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTTCACCACTCATATTTCTCACCATT
66 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
* *
77330071 AAAAATGGGTATGAGTGGTTGAAAGGAAGAAAAACCAGCTGATGCTATTCCAAGAACACACACTC
131 AAAAATAGGTATGAGTGGTTGAAAGGAAAAAAAACCAGCTGATGCTATTCCAAGAACACACACTC
** * * *
77330136 TCTTTTCTCGTGTTTCCTAAAGACCTAAAAAGGTGTTTCTCTCAAATACCTAATGGACCCAAACC
196 TCTCCTCTCGTATTTCCTAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
*
77330201 TAACTTTCACTCAATTGCCTAAGAGATCGAACCTTGCTCTGATACCAAATTTATTGAAAAAGGAA
261 TAACTTTCACTCAATTGCCTAAAAGATCGAACCTTGCTCTGATACCAAATTTATTGAAAAAGGAA
* *
77330266 ACTTAAAAGAGACAATTATAATATGCATCAAAGTTATTCTATTATTGATAAACAC
326 ACGTAAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
* * *
77330321 TCAATCTTTTTTCTTCTTCTTCATCAGGTTCAAGTATGTCAGCGAACCCGTACTCGACCAAGTCT
1 TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAGTCC
77330386 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
66 CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
* *
77330451 GAAAATAGGTATGAGTGGTTGAGAGGAAAAAAAACCAGCTGATGCTATTCCAAGAACACACACTC
131 AAAAATAGGTATGAGTGGTTGAAAGGAAAAAAAACCAGCTGATGCTATTCCAAGAACACACACTC
*
77330516 TCTCCTCTCGTATTTTCTAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
196 TCTCCTCTCGTATTTCCTAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
*
77330581 TAACTTTCACTCAATTGCCTAAAAGATCGAACCTTGCTCTGATACCAAATTTATTGAAGAAGGAA
261 TAACTTTCACTCAATTGCCTAAAAGATCGAACCTTGCTCTGATACCAAATTTATTGAAAAAGGAA
* *
77330646 ACGTGAAAGAGATAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
326 ACGTAAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
77330701 T
1 T
77330702 GAATTGCTAA
Statistics
Matches: 360, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
380 360 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (380 bp):
TCAATCTTTTTTCTTCTTCTTCATCAAGTTCAAGTATGTCAGCGAACCAGTACTCGACCAAGTCC
CATAGCTCTTGTAATTTGAGCAATGTCTTCACCTTGATGCTCCACCACTCATATTTCTCACCATT
AAAAATAGGTATGAGTGGTTGAAAGGAAAAAAAACCAGCTGATGCTATTCCAAGAACACACACTC
TCTCCTCTCGTATTTCCTAAAGACCCAAAAAGGTGTTTCTCTCAAATACCCAATGGACCCAAACC
TAACTTTCACTCAATTGCCTAAAAGATCGAACCTTGCTCTGATACCAAATTTATTGAAAAAGGAA
ACGTAAAAGAGACAATTACAATATGCATCAAAGTTATTCTATTATTGATAAACAC
Found at i:77334777 original size:3 final size:3
Alignment explanation
Indices: 77334769--77334793 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
77334759 ACATATTTTT
77334769 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
77334794 CAAATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:77342523 original size:101 final size:101
Alignment explanation
Indices: 77342348--77342552 Score: 392
Period size: 101 Copynumber: 2.0 Consensus size: 101
77342338 ATAATTCAAT
77342348 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
1 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
77342413 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
66 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
77342449 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
1 AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
* *
77342514 CAATTTTTAAAATGGAAGTATTTGTAAGCAATACTC
66 CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
77342550 AAA
1 AAA
77342553 CTTCTATTTG
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (101 bp):
AAATTTAACCCTTCACATTTACAAATTCTATCAATTTGATTATCAAACTTCCTAATCAAAGCTTT
CAACTTTTAAAACGGAAGTATTTGTAAGCAATACTC
Found at i:77343802 original size:30 final size:30
Alignment explanation
Indices: 77343768--77343826 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
77343758 AATCTTAGCC
*
77343768 TTTTTCACCACCAACTCCACTAGCCACACA
1 TTTTTCACCACCAAATCCACTAGCCACACA
77343798 TTTTTCACCACCAAATCCACTAGCCACAC
1 TTTTTCACCACCAAATCCACTAGCCACAC
77343827 TTGCTCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.42, G:0.03, T:0.24
Consensus pattern (30 bp):
TTTTTCACCACCAAATCCACTAGCCACACA
Found at i:77344172 original size:21 final size:21
Alignment explanation
Indices: 77344146--77344206 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
77344136 AGTTCTTTGT
77344146 TTACTTATTGTTTTCTTTTCA
1 TTACTTATTGTTTTCTTTTCA
*
77344167 TTACTTATTGTTTTCCTTTCA
1 TTACTTATTGTTTTCTTTTCA
* *
77344188 AT-CTTATTTTGTTTCTTTT
1 TTACTTATTGT-TTTCTTTT
77344207 ATACGAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (21 bp):
TTACTTATTGTTTTCTTTTCA
Found at i:77344413 original size:23 final size:23
Alignment explanation
Indices: 77344376--77344505 Score: 65
Period size: 22 Copynumber: 5.5 Consensus size: 23
77344366 TTTTTTTTGT
77344376 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
77344399 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
77344421 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* * *
77344444 TATTACGTATATATATATTTTACTATTT
1 TA-T---TATATATAT-TCTTAATATTA
77344472 TATT-TATATA-TCTTTAATATTA
1 TATTATATATATTC-TTAATATTA
*
77344494 TATTATTTATAT
1 TATTATATATAT
77344506 ATATAAATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
21 4 0.05
22 26 0.33
23 26 0.33
24 6 0.08
27 8 0.10
28 4 0.05
29 4 0.05
30 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:77344479 original size:25 final size:26
Alignment explanation
Indices: 77344441--77344510 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 26
77344431 ATTTTAAATT
** *
77344441 CTATATTACGTATATATATATT-TTA
1 CTATATTATTTATATATATATTAATA
* *
77344466 CTATTTTATTTATATATCT-TTAATA
1 CTATATTATTTATATATATATTAATA
*
77344491 TTATATTATTTATATATATA
1 CTATATTATTTATATATATA
77344511 AATTTTTTTC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (26 bp):
CTATATTATTTATATATATATTAATA
Found at i:77344561 original size:22 final size:24
Alignment explanation
Indices: 77344533--77344591 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
77344523 ACATGTTATC
77344533 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
77344555 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
77344580 TTATGTACATAT
1 TTATGTATATAT
77344592 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:77344581 original size:25 final size:25
Alignment explanation
Indices: 77344549--77344597 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
77344539 ATATATCTTA
**
77344549 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
77344574 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
77344598 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:77344775 original size:16 final size:15
Alignment explanation
Indices: 77344751--77344798 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
77344741 TAATTATTAT
*
77344751 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
77344767 TATTTTAATATTTTA
1 TATTTTAATATTTTA
77344782 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
77344798 T
1 T
77344799 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:77344786 original size:7 final size:8
Alignment explanation
Indices: 77344751--77344802 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
77344741 TAATTATTAT
*
77344751 TATTCTAA
1 TATTTTAA
*
77344759 TATTTTGA
1 TATTTTAA
77344767 TATTTTAA
1 TATTTTAA
77344775 TATTTT-A
1 TATTTTAA
77344782 TATTTTATA
1 TATTTTA-A
*
77344791 TATTTTAT
1 TATTTTAA
77344799 TATT
1 TATT
77344803 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:77347580 original size:30 final size:30
Alignment explanation
Indices: 77347536--77347594 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
77347526 AACTTTTTAT
77347536 TTTCCCCCAAAATTTTTAC-TCCCTCCCAC
1 TTTCCCCCAAAATTTTTACTTCCCTCCCAC
*
77347565 TTTCCCCCTAAAATTTTTACTTCCTTCCCA
1 TTTCCCCC-AAAATTTTTACTTCCCTCCCA
77347595 TCCCACATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.30
30 11 0.41
31 8 0.30
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTCCCCCAAAATTTTTACTTCCCTCCCAC
Found at i:77348267 original size:10 final size:10
Alignment explanation
Indices: 77348252--77348277 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
77348242 AATATATTTG
77348252 ATTCGATTCA
1 ATTCGATTCA
77348262 ATTCGATTCA
1 ATTCGATTCA
77348272 ATTCGA
1 ATTCGA
77348278 ATTCCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (10 bp):
ATTCGATTCA
Found at i:77350525 original size:7 final size:7
Alignment explanation
Indices: 77350513--77350543 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
77350503 CTAAAATCAT
77350513 AACCCTA
1 AACCCTA
*
77350520 ACCCCTA
1 AACCCTA
77350527 AACCCTA
1 AACCCTA
77350534 AACCCTA
1 AACCCTA
77350541 AAC
1 AAC
77350544 TCGTGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCTA
Found at i:77351172 original size:30 final size:30
Alignment explanation
Indices: 77351136--77351234 Score: 180
Period size: 30 Copynumber: 3.3 Consensus size: 30
77351126 CTAGCCTTTG
77351136 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
77351166 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
77351196 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
77351226 CCACCACCA
1 CCACCACCA
77351235 CTTGTACCTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:77351823 original size:25 final size:25
Alignment explanation
Indices: 77351716--77351925 Score: 78
Period size: 23 Copynumber: 8.5 Consensus size: 25
77351706 TTTTTTTGTA
* *
77351716 ATTAT-TATAT-TTTTTAATATTAT
1 ATTATGTATATATATTTAATACTAT
* ** *
77351739 ATTATATATATATATATCTTTTAATAT
1 ATTATGTATATATAT-T-TAATACTAT
* * * *
77351766 ATTAGGTATAT-T-CTAAATTCTAT
1 ATTATGTATATATATTTAATACTAT
*
77351789 ATTACGTATATATA-TT-ATACTAT
1 ATTATGTATATATATTTAATACTAT
* *
77351812 TTTATGTATATATCTTTAATACTAT
1 ATTATGTATATATATTTAATACTAT
* * * **
77351837 ATTATTTATATTTTTTTTTCTAC-AT
1 ATTATGTATA-TATATTTAATACTAT
* *
77351862 GTTATCTTATATATATATTTAAT--TAT
1 ATTA---TGTATATATATTTAATACTAT
* * * *
77351888 ATTATGTATGTATTTTTTACACTAT
1 ATTATGTATATATATTTAATACTAT
*
77351913 ATTATGTACATAT
1 ATTATGTATATAT
77351926 TTTTTTTATA
Statistics
Matches: 134, Mismatches: 38, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
23 47 0.35
24 10 0.07
25 36 0.27
26 15 0.11
27 21 0.16
28 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTATGTATATATATTTAATACTAT
Found at i:77351847 original size:48 final size:48
Alignment explanation
Indices: 77351721--77351847 Score: 114
Period size: 48 Copynumber: 2.6 Consensus size: 48
77351711 TTGTAATTAT
* * *
77351721 TATATTTTTTAATATTATATTATATATATATATATCTTTTAATATATTAGG
1 TATATTCTTTAATACTATATTAT-T-TATATATA-CTTATAATATATTAGG
* * ** * * *
77351772 TATATTC-TAAATTCTATATTACGTATATATA-TTATACTATTTTATG
1 TATATTCTTTAATACTATATTATTTATATATACTTATAATATATTAGG
77351818 TATATATCTTTAATACTATATTATTTATAT
1 TATAT-TCTTTAATACTATATTATTTATAT
77351848 TTTTTTTTCT
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
46 16 0.27
47 2 0.03
48 25 0.42
50 11 0.18
51 6 0.10
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (48 bp):
TATATTCTTTAATACTATATTATTTATATATACTTATAATATATTAGG
Found at i:77351892 original size:21 final size:21
Alignment explanation
Indices: 77351863--77351902 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
77351853 TTTCTACATG
*
77351863 TTATCTTATATATATATTTAA
1 TTATATTATATATATATTTAA
* *
77351884 TTATATTATGTATGTATTT
1 TTATATTATATATATATTT
77351903 TTTACACTAT
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:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATATTATATATATATTTAA
Found at i:77352020 original size:25 final size:24
Alignment explanation
Indices: 77351992--77352047 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
77351982 GTTATATTTT
*
77351992 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
77352017 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
77352040 CACTATTA
1 CACTATTA
77352048 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:77370029 original size:8 final size:8
Alignment explanation
Indices: 77369990--77370032 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
77369980 TAAAATAATG
*
77369990 ATATGTAC
1 ATATATAC
* *
77369998 AAATATAT
1 ATATATAC
*
77370006 ATATATAT
1 ATATATAC
77370014 ATATATAC
1 ATATATAC
77370022 ATATATAC
1 ATATATAC
77370030 ATA
1 ATA
77370033 AAATATACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATATAC
Found at i:77370215 original size:39 final size:37
Alignment explanation
Indices: 77370118--77370215 Score: 99
Period size: 39 Copynumber: 2.6 Consensus size: 37
77370108 TATGGTATTG
* * * *
77370118 AAAATATATATAT-ATATGTATATATAATAGTATTTA
1 AAAATATATACATAATATATATATATAATAGCATTAA
* * * *
77370154 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATAT-A-TAATAGCATTAA
77370193 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
77370216 AAATACCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 11 0.23
37 7 0.15
38 1 0.02
39 29 0.60
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (37 bp):
AAAATATATACATAATATATATATATAATAGCATTAA
Found at i:77370736 original size:25 final size:25
Alignment explanation
Indices: 77370700--77370748 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
77370690 GTTTCTTGTT
*
77370700 TTTTTTTTGGGGGGTTAGGTTTTTC
1 TTTTTTTGGGGGGGTTAGGTTTTTC
*
77370725 TTTTTTTGGGGGGGTTTGGTTTTT
1 TTTTTTTGGGGGGGTTAGGTTTTT
77370749 TTGGGGGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.02, C:0.02, G:0.35, T:0.61
Consensus pattern (25 bp):
TTTTTTTGGGGGGGTTAGGTTTTTC
Found at i:77375224 original size:3 final size:3
Alignment explanation
Indices: 77375216--77375251 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
77375206 GGCCCCCTCT
*
77375216 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA ACA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
77375252 ACCCCAGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.33, G:0.31, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:77378519 original size:31 final size:31
Alignment explanation
Indices: 77378481--77378545 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
77378471 AATTGTACCA
* *
77378481 AATCAAAGTTTACCTTTAAAATTACACATTG
1 AATCAAAGTTTACATATAAAATTACACATTG
*
77378512 AATCAAAGTTTATATATAAAATTACACATTG
1 AATCAAAGTTTACATATAAAATTACACATTG
77378543 AAT
1 AAT
77378546 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.35
Consensus pattern (31 bp):
AATCAAAGTTTACATATAAAATTACACATTG
Found at i:77379033 original size:19 final size:20
Alignment explanation
Indices: 77378999--77379042 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
77378989 TTTTTTTAAA
*
77378999 GTTATAAATTTTTATAAGTT
1 GTTATAAATATTTATAAGTT
77379019 GTTAT-AATATTTATAAGTT
1 GTTATAAATATTTATAAGTT
*
77379038 TTTAT
1 GTTAT
77379043 GAATGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
GTTATAAATATTTATAAGTT
Found at i:77379051 original size:19 final size:19
Alignment explanation
Indices: 77379010--77379051 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
77379000 TTATAAATTT
*
77379010 TTATAAGTTGTTATAATAT
1 TTATAAGTTGTTATAATAG
*
77379029 TTATAAGTTTTTATGAAT-G
1 TTATAAGTTGTTAT-AATAG
77379048 TTAT
1 TTAT
77379052 TTTTAGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TTATAAGTTGTTATAATAG
Found at i:77379144 original size:46 final size:47
Alignment explanation
Indices: 77379000--77379144 Score: 109
Period size: 51 Copynumber: 3.0 Consensus size: 47
77378990 TTTTTTAAAG
* * * *
77379000 TTATAAATTTTTATAAGTTGTTATAATATTTATAAGTTTTTATGAATGTT
1 TTATAAGTTTCTACAAGTT-TTATAATATTTATAAGTTTATAT-AAT-TT
* * * ** *
77379050 ATTTTTAGTTTCTACAAGTTTATATAATTTTTAT-TTTTTA-ATACTTT
1 -TTATAAGTTTCTACAAGTTT-TATAATATTTATAAGTTTATATAATTT
*
77379097 TTATAAGTGTT-TACAA-TTTTATAATCTTTATAAGTTTATATAATTT
1 TTATAAGT-TTCTACAAGTTTTATAATATTTATAAGTTTATATAATTT
77379143 TT
1 TT
77379145 TTAAAATAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
44 11 0.15
45 7 0.09
46 19 0.26
47 4 0.05
48 2 0.03
49 2 0.03
50 4 0.05
51 25 0.34
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (47 bp):
TTATAAGTTTCTACAAGTTTTATAATATTTATAAGTTTATATAATTT
Found at i:77380684 original size:29 final size:30
Alignment explanation
Indices: 77380637--77380695 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
77380627 TAATTGGATC
* *
77380637 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCAAGTATAAAATTGCACA
*
77380667 AAATC-AAAGTTCAAGTATACAATTGCACA
1 AAATCAAAAGTTCAAGTATAAAATTGCACA
77380696 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATCAAAAGTTCAAGTATAAAATTGCACA
Found at i:77391566 original size:28 final size:28
Alignment explanation
Indices: 77391512--77391568 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
77391502 CATTATCAAT
*
77391512 CCCATAAGTTATAAAACTCTTCTTATAC
1 CCCATAAGTTATAAAACTCTTCCTATAC
* * *
77391540 CCCATAAGTTATGAGACTTTTCCTATAC
1 CCCATAAGTTATAAAACTCTTCCTATAC
77391568 C
1 C
77391569 TCATTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (28 bp):
CCCATAAGTTATAAAACTCTTCCTATAC
Found at i:77396970 original size:28 final size:28
Alignment explanation
Indices: 77396930--77396992 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
77396920 GTCATTATCA
77396930 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * * *
77396958 ACCCCATAAGTTATGAGACTTTTCTTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
77396986 ACCCCAT
1 ACCCCAT
77396993 TAATATAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Done.