Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold312
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: 931450
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 39452 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:703766 original size:35 final size:33
Alignment explanation
Indices: 703660--703784 Score: 126
Period size: 35 Copynumber: 3.6 Consensus size: 33
703650 AAATCAGGGG
*
703660 TTAGAGTTTTTT-TAAAAATTAATTAAATTAGGTT
1 TTAG-GTTTTTTAAAAAAATTAATTAAATTAGG-T
** *
703694 TTAGGGGTTTAAAATAAAATTAATTAAATTAGGGT
1 TTAGGTTTTTTAAA-AAAATTAATTAAATTA-GGT
*
703729 TTAGAGTTTTTTAAAAAAAGTAATTAAATTATGGT
1 TTAG-GTTTTTTAAAAAAATTAATTAAATTA-GGT
*
703764 TTAGTTTTTTTAAAAATAATT
1 TTAGGTTTTTTAAAAA-AATT
703785 TTGTGTTTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
33 4 0.05
34 16 0.21
35 46 0.61
36 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (33 bp):
TTAGGTTTTTTAAAAAAATTAATTAAATTAGGT
Found at i:704079 original size:126 final size:125
Alignment explanation
Indices: 703846--704229 Score: 540
Period size: 126 Copynumber: 3.1 Consensus size: 125
703836 TTGTTTTTAC
* * * *
703846 AGTTCC-TGAAAAATAATTTTGAGAATACGGTTCTGAAAAGATAATGTCAAAAACGTTTCAAGCA
1 AGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTGAAAA-ATAGTGTCAAAAACGCTTCAAGCA
* * *
703910 GGATACACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTACAAT
65 GGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGT
703971 AGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTGAATAAATAGTGTCAAAAACGCTTCAAGCA
1 AGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGTCAAAAACGCTTCAAGCA
* * * *
704036 AGATGCACTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGGATGCTCTTTTTCTACTGT
65 GGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGT
* *
704097 AGTT-CTTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACTCTTCAAGC
1 AGTTCCTT-AAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGTCAAAAACGCTTCAAGC
* * * * *
704161 AGGATGCATTATCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGAACGCTTTTTTTCTGCAGT
64 AGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGT
704223 AGTTCCT
1 AGTTCCT
704230 GTTTGGCCTT
Statistics
Matches: 231, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
125 9 0.04
126 217 0.94
127 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (125 bp):
AGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTGAAAAATAGTGTCAAAAACGCTTCAAGCAG
GATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGT
Found at i:706403 original size:6 final size:6
Alignment explanation
Indices: 706396--706437 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
706386 AAATTTGCTA
706396 TTATTAT TTATTT TTATTT TTATTT TTATTT TTA-TT TTATTT
1 TTATT-T TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
706438 ATTCGCTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:708383 original size:126 final size:126
Alignment explanation
Indices: 708233--708474 Score: 333
Period size: 126 Copynumber: 1.9 Consensus size: 126
708223 AAGCGCTCAA
* * * * *
708233 GTGGGAGCTTTTTTCAGTATTTTTGCTGACAATACATCTTGCTTGGAGCCTTTTTGACACTAT-T
1 GTGGGAGCTTTTTTCAATAATTTTGCTGACAATACATCCTACTTGAAGCCTTTTTGACACTATCT
* *
708297 TGTTTAAAACCGTCTTCTCAAAATTATTTTTTCAGGAACTACTGTAGAAAAAGAGTGTCCAC
66 T-TTCAAAACCGTCTTCTCAAAATTATTTTTTCAGGAACCACTGTAGAAAAAGAGTGTCCAC
* * * * * *
708359 GTGGGAGCTTTTTTTAATAATTTTGCTGACAGTGCATCCTACTTGAAGCGTTTTTTACATTATCT
1 GTGGGAGCTTTTTTCAATAATTTTGCTGACAATACATCCTACTTGAAGCCTTTTTGACACTATCT
* *
708424 TTTCAAAATCGTCTTCTCAAAATTATTTTTTCAGGAACCATTGTAGAAAAA
66 TTTCAAAACCGTCTTCTCAAAATTATTTTTTCAGGAACCACTGTAGAAAAA
708475 AAAACAAAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
126 98 0.98
127 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (126 bp):
GTGGGAGCTTTTTTCAATAATTTTGCTGACAATACATCCTACTTGAAGCCTTTTTGACACTATCT
TTTCAAAACCGTCTTCTCAAAATTATTTTTTCAGGAACCACTGTAGAAAAAGAGTGTCCAC
Found at i:708598 original size:34 final size:33
Alignment explanation
Indices: 708549--708647 Score: 119
Period size: 35 Copynumber: 2.9 Consensus size: 33
708539 TTTTTTAAAA
* *
708549 CTAAACCATAATTTAATTAATTTTCTTAAAAACT
1 CTAAACCCTAATTTAATTAATTTT-TTAAAAACC
* *
708583 CTAAACCCTAGTTTAATTAATTTTATTTAAAACCC
1 CTAAACCCTAATTTAATTAA-TTT-TTTAAAAACC
*
708618 CTAAAACCTAATTTAATT-ATTTTTTAAAAA
1 CTAAACCCTAATTTAATTAATTTTTTAAAAA
708648 AAACTCTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 7 0.12
33 3 0.05
34 19 0.34
35 26 0.46
36 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.41
Consensus pattern (33 bp):
CTAAACCCTAATTTAATTAATTTTTTAAAAACC
Found at i:708622 original size:35 final size:34
Alignment explanation
Indices: 708549--708647 Score: 121
Period size: 34 Copynumber: 2.9 Consensus size: 34
708539 TTTTTTAAAA
* *
708549 CTAAACCATAATTTAATTAATTTTCTTAAAAACT
1 CTAAACCCTAATTTAATTAATTTTCTTAAAAACC
* * *
708583 CTAAACCCTAGTTTAATTAATTTTATTTAAAACCC
1 CTAAACCCTAATTTAATTAATTTT-CTTAAAAACC
*
708618 CTAAAACCTAATTTAATT-ATTTT-TTAAAAA
1 CTAAACCCTAATTTAATTAATTTTCTTAAAAA
708648 AAACTCTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.11
34 27 0.48
35 23 0.41
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.41
Consensus pattern (34 bp):
CTAAACCCTAATTTAATTAATTTTCTTAAAAACC
Found at i:710797 original size:226 final size:228
Alignment explanation
Indices: 710356--710810 Score: 761
Period size: 226 Copynumber: 2.0 Consensus size: 228
710346 GACCCCGTCG
710356 TCGTTCTCATCGGTTTCGTGGCTACCAGAGGAGGCTAGGGATAGTCTTGGCCTGAGAACAGCGCG
1 TCGTTCTCATCGGTTTCGTGGCTACCAGAGGAGGCTAGGGATAGTCTTGGCCTGAGAACAGCGCG
* *
710421 AAGGGAGAGAGGAAGCATAAAGTTTTTTTTCTTTTTTTTTTTTTTGTTTCTTTAGAAGCCGATTA
66 AAGGGAGAGAGGAAGCATAAAG-TTTTTTTCTTTCTTTTTTTTCTGTTTCTTTAGAAGCCGATTA
* * * * ** *
710486 ACCTAGTTAGGTTTTTATAGTTGATTCTTGCAGGGGTTCAACGGTACCGTTTGGGGCTTGAATCA
130 ACCTAATTAGGTTTTTATAGTCGATTCTTGCAGGGGCTAAACGGTACCGTTTGGGGCCCGAACCA
710551 GTGGCTCCCAAAACGGTGTCGTATTACCCAACAA
195 GTGGCTCCCAAAACGGTGTCGTATTACCCAACAA
* * *
710585 TCGTTCTCATCGGTTTCGTGGCTACCGGAGGAGGTTAGGGATAGTCTTGGCCTGAGAACGGCGCG
1 TCGTTCTCATCGGTTTCGTGGCTACCAGAGGAGGCTAGGGATAGTCTTGGCCTGAGAACAGCGCG
*
710650 AAGGGAGAGAGGAAGCATAAAG-TTTTTTC-TTCTTTTTTTTCTGTTTCTTTAGAAGTCGATTAA
66 AAGGGAGAGAGGAAGCATAAAGTTTTTTTCTTTCTTTTTTTTCTGTTTCTTTAGAAGCCGATTAA
*
710713 CCTAATTAGGTTTTTTTAGTCGATTCTTGCAGGGGCTAAACGGTACCGTTTGGGGCCCGAACCAG
131 CCTAATTAGGTTTTTATAGTCGATTCTTGCAGGGGCTAAACGGTACCGTTTGGGGCCCGAACCAG
710778 TGGCTCCCAAAACGGTGTCGTATTACCCAACAA
196 TGGCTCCCAAAACGGTGTCGTATTACCCAACAA
710811 CCCACGCGTG
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
226 121 0.57
227 7 0.03
229 84 0.40
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (228 bp):
TCGTTCTCATCGGTTTCGTGGCTACCAGAGGAGGCTAGGGATAGTCTTGGCCTGAGAACAGCGCG
AAGGGAGAGAGGAAGCATAAAGTTTTTTTCTTTCTTTTTTTTCTGTTTCTTTAGAAGCCGATTAA
CCTAATTAGGTTTTTATAGTCGATTCTTGCAGGGGCTAAACGGTACCGTTTGGGGCCCGAACCAG
TGGCTCCCAAAACGGTGTCGTATTACCCAACAA
Found at i:711370 original size:3 final size:3
Alignment explanation
Indices: 711362--711399 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
711352 CATTACATTT
711362 TTA TTA TTA TTTA TGTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
711400 AAATCTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:715844 original size:74 final size:74
Alignment explanation
Indices: 715766--715922 Score: 210
Period size: 74 Copynumber: 2.1 Consensus size: 74
715756 TTTCTGTTAA
* * * * * *
715766 ATTGTAAAT-ATTGATATATTATTGATGTAAAATATAATAGAATA-AATATAAATATTTTTTTAT
1 ATTGTAAATAAGT-ATATATTATTGATATAAAATACAATAGAATACAACAAAAATATTTTTTAAT
715829 TTTTCTCGTAG
65 TTTT-TCGTAG
*
715840 ATTGTAAATAAGTATATATTATTGATATGAAATACAATAGAATACAACAAAAATATTTTTTAATT
1 ATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAACAAAAATATTTTTTAATT
*
715905 TTTTCTTAG
66 TTTTCGTAG
715914 ATTGTAAAT
1 ATTGTAAAT
715923 GAGTGTAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
74 51 0.70
75 22 0.30
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (74 bp):
ATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAACAAAAATATTTTTTAATT
TTTTCGTAG
Found at i:717249 original size:50 final size:50
Alignment explanation
Indices: 717191--717384 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 50
717181 TATTGAGGTT
* *
717191 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * * *
717241 ATGAGAGGTCCCCCGTAAGACCATGTTTGAGG-CATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTG-GGACATGGCATTGGCACCGAC
** * * * * * *
717291 ATGAGAACTCTCATGTAAGACCATATTTGGGATATGGCATTAGTA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** *
717340 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
717385 TGTTATTATC
Statistics
Matches: 113, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.33
50 73 0.65
51 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:717611 original size:20 final size:20
Alignment explanation
Indices: 717586--717624 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
717576 TGAGTTATTT
717586 AAATAAGCA-AGTAAGTAAAC
1 AAATAAG-AGAGTAAGTAAAC
717606 AAATAAGAGAGTAAGTAAA
1 AAATAAGAGAGTAAGTAAA
717625 GAAGAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (20 bp):
AAATAAGAGAGTAAGTAAAC
Found at i:719735 original size:26 final size:26
Alignment explanation
Indices: 719706--719758 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
719696 AGATAAAAGA
719706 GTTTGTTGTTCTAGTTGAAAGAGCCT
1 GTTTGTTGTTCTAGTTGAAAGAGCCT
719732 GTTTGTTGTTCTAGTTGAAAGAGCCT
1 GTTTGTTGTTCTAGTTGAAAGAGCCT
719758 G
1 G
719759 AAAGGCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (26 bp):
GTTTGTTGTTCTAGTTGAAAGAGCCT
Found at i:724992 original size:50 final size:50
Alignment explanation
Indices: 724937--725130 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
724927 TATTGAGGTT
* *
724937 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * * *
724987 ATGAGAGGTCCCCCGTAAGACCATGTTTGAGG-CATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTG-GGACATGGCATTGGCACCGAC
** * * * * *
725037 ATGAGAACTCCCATGTAAGACCATATTTGGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * *
725086 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
725131 TGTTATTATC
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.33
50 76 0.64
51 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:728490 original size:24 final size:24
Alignment explanation
Indices: 728440--728491 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
728430 TTTCTAGAAG
* *
728440 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
728464 ATTTAGCATTTATTAGCATTATTT
1 ATTTAGCATTTATTAGCATAATAT
728488 ATTT
1 ATTT
728492 GACCTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:730407 original size:24 final size:24
Alignment explanation
Indices: 730380--730425 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
730370 TTTCTAGAAG
*
730380 ATTTAGTATTCATTAGTATAATAT
1 ATTTAGTATTCATTAGCATAATAT
*
730404 ATTTAGTATTTATTAGCATAAT
1 ATTTAGTATTCATTAGCATAAT
730426 TTAGTTGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTAGTATTCATTAGCATAATAT
Found at i:733375 original size:18 final size:18
Alignment explanation
Indices: 733348--733398 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
733338 GTTTATAGAT
*
733348 ATCCTTGGACTTACAACA
1 ATCCTAGGACTTACAACA
* * * *
733366 ATCCTCGGACTTGCAGCG
1 ATCCTAGGACTTACAACA
733384 ATCCTAGGACTTACA
1 ATCCTAGGACTTACA
733399 TCACTCATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (18 bp):
ATCCTAGGACTTACAACA
Found at i:734223 original size:6 final size:6
Alignment explanation
Indices: 734212--734241 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
734202 TCAATGATGG
734212 CTGATT CTGATT CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT
734242 GTGAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:737208 original size:14 final size:14
Alignment explanation
Indices: 737188--737228 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
737178 TTTGATTGTC
737188 AGTAAAATATTTTT
1 AGTAAAATATTTTT
*
737202 CGTAAAATTATTTTT
1 AGTAAAA-TATTTTT
737217 AG-AAAATATTTT
1 AGTAAAATATTTT
737229 ACTTTTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (14 bp):
AGTAAAATATTTTT
Found at i:737241 original size:34 final size:34
Alignment explanation
Indices: 737198--737263 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
737188 AGTAAAATAT
* *
737198 TTTTCGTAAAATTATTT-TTAGAAAATATTTTAC
1 TTTTCGTAAAATAATTTACTAGAAAATATTTTAC
*
737231 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATAATTTACTAGAAAATATTTT
737264 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (34 bp):
TTTTCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:738548 original size:14 final size:14
Alignment explanation
Indices: 738529--738558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
738519 AGGTGAACTA
738529 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
738543 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
738557 GC
1 GC
738559 TGCAATCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:738638 original size:24 final size:24
Alignment explanation
Indices: 738581--738630 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
738571 GGTAAAGAGA
738581 GTGAAGAGAGGAGCTGTGGAAATG
1 GTGAAGAGAGGAGCTGTGGAAATG
738605 GTGAAGAGAGGAGCTGTGGAAATG
1 GTGAAGAGAGGAGCTGTGGAAATG
738629 GT
1 GT
738631 TTCAAGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.04, G:0.46, T:0.18
Consensus pattern (24 bp):
GTGAAGAGAGGAGCTGTGGAAATG
Found at i:740785 original size:34 final size:34
Alignment explanation
Indices: 740747--740834 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 34
740737 TAAATGAATC
* *
740747 TTTAATTAATGTCTTGCATTAT-TGATCTACATCT
1 TTTAA-TAATGACATGCATTATGTGATCTACATCT
* *
740781 TTTAATCATGACATGCATTATGTGTTCTACA---
1 TTTAATAATGACATGCATTATGTGATCTACATCT
* *
740812 TTTAATAAAGTCATGCATTATGT
1 TTTAATAATGACATGCATTATGT
740835 TACTCTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 20 0.43
33 13 0.28
34 13 0.28
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (34 bp):
TTTAATAATGACATGCATTATGTGATCTACATCT
Found at i:743270 original size:26 final size:26
Alignment explanation
Indices: 743228--743284 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
743218 TCTCATCTTT
* *
743228 ATTTTACCTCTAGTAAAATTTTAACG
1 ATTTTACCTCGAGTAAAATTTTAACA
*
743254 ATTTTACCTCCGA-TAAAATTTTGACA
1 ATTTTACCT-CGAGTAAAATTTTAACA
743280 ATTTT
1 ATTTT
743285 GCCCTTGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (26 bp):
ATTTTACCTCGAGTAAAATTTTAACA
Found at i:747787 original size:25 final size:25
Alignment explanation
Indices: 747754--747819 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
747744 GATTGTAAAT
* *
747754 AAGTGTACATTTTGGATGTAAAACA
1 AAGTATACATTTTGGATCTAAAACA
* *
747779 AAGTATACATTTAGAATCTAAAACA
1 AAGTATACATTTTGGATCTAAAACA
* *
747804 AAGTATAAAATTTGGA
1 AAGTATACATTTTGGA
747820 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (25 bp):
AAGTATACATTTTGGATCTAAAACA
Found at i:761603 original size:18 final size:18
Alignment explanation
Indices: 761582--761772 Score: 229
Period size: 18 Copynumber: 10.6 Consensus size: 18
761572 GTCCACACTA
* * *
761582 TGCTCTAAGTTAGCATTG
1 TGCTCCAAGTTTGCAATG
*
761600 TGCTCCAAGTTAGCAATG
1 TGCTCCAAGTTTGCAATG
* *
761618 TGCTCTAAGTTTGCATTG
1 TGCTCCAAGTTTGCAATG
*
761636 TGCTCCAAGTTTGCAATC
1 TGCTCCAAGTTTGCAATG
** *
761654 TGCTGTAAGTTTGCAATA
1 TGCTCCAAGTTTGCAATG
*
761672 TGCTCCAAGTTTGCATTG
1 TGCTCCAAGTTTGCAATG
*
761690 TGCTCCAAGTTTGCCATG
1 TGCTCCAAGTTTGCAATG
761708 TGCTCCAAGTTTGCAATG
1 TGCTCCAAGTTTGCAATG
* * *
761726 TGCTCCAAGTTCGCATTT
1 TGCTCCAAGTTTGCAATG
* *
761744 TGTTCCAAGTTTGCACTG
1 TGCTCCAAGTTTGCAATG
761762 TGCTCCAAGTT
1 TGCTCCAAGTT
761773 CAAATCATGC
Statistics
Matches: 147, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 147 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (18 bp):
TGCTCCAAGTTTGCAATG
Found at i:767932 original size:129 final size:129
Alignment explanation
Indices: 767607--767908 Score: 559
Period size: 129 Copynumber: 2.3 Consensus size: 129
767597 TTCAATAAAT
* *
767607 ATGTGAGCAATTATAAAAAGACTGCATGAAAGGATAAGAAGAAAAAAATAGGGAAATGATTTTTT
1 ATGTGAGCAATTAT-AACATA-TGCATGAAAGGATAAGAAGAAAAAAATAGGGAAATGATTTTTT
767672 TAATTTATTTTAATAAAGTGAGAGAAAAATTCTCAATTATTAATTATTGATCAACTATTTAAGGA
64 TAATTTATTTTAATAAAGTGAGAGAAAAATTCTCAATTATTAATTATTGATCAACTATTTAAGGA
767737 A
129 A
767738 ATGTGAGCAATTATAACATATGCATGAAAGGATAAGAAGAAAAAAATAGGGAAATGATTTTTTTA
1 ATGTGAGCAATTATAACATATGCATGAAAGGATAAGAAGAAAAAAATAGGGAAATGATTTTTTTA
767803 ATTTATTTTAATAAAGTGAGAGAAAAATTCTCAATTATTAATTATTGATCAACTATTTAAGGAA
66 ATTTATTTTAATAAAGTGAGAGAAAAATTCTCAATTATTAATTATTGATCAACTATTTAAGGAA
*
767867 ATGTGAGCAATTATAACATATGCATGAAAGGATGAGAAGAAA
1 ATGTGAGCAATTATAACATATGCATGAAAGGATAAGAAGAAA
767909 CAATGTTTTT
Statistics
Matches: 168, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
129 150 0.89
130 4 0.02
131 14 0.08
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (129 bp):
ATGTGAGCAATTATAACATATGCATGAAAGGATAAGAAGAAAAAAATAGGGAAATGATTTTTTTA
ATTTATTTTAATAAAGTGAGAGAAAAATTCTCAATTATTAATTATTGATCAACTATTTAAGGAA
Found at i:780010 original size:18 final size:18
Alignment explanation
Indices: 779983--780049 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 18
779973 TTTATTTTTT
779983 ATTTTT-AAACACGAAAA
1 ATTTTTAAAACACGAAAA
* *
780000 ATTTTTAAAACA-GGAGA
1 ATTTTTAAAACACGAAAA
*
780017 A-TTTTAGAGACACG-AAA
1 ATTTTTA-AAACACGAAAA
*
780034 ATTCTTAAAAACACGA
1 ATT-TTTAAAACACGA
780050 CAATTTTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.13
17 17 0.45
18 13 0.34
19 3 0.08
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (18 bp):
ATTTTTAAAACACGAAAA
Found at i:780021 original size:16 final size:16
Alignment explanation
Indices: 779983--780072 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 16
779973 TTTATTTTTT
* *
779983 ATTTTTAAACACGAAAA
1 ATTTTAAAACACG-AGA
*
780000 ATTTTTAAAACAGGAGA
1 A-TTTTAAAACACGAGA
* *
780017 ATTTTAGAGACACGAAA
1 ATTTTA-AAACACGAGA
*
780034 ATTCTTAAAAACACGACA
1 ATT-TT-AAAACACGAGA
* *
780052 ATTTTGAAACACGCGA
1 ATTTTAAAACACGAGA
780068 ATTTT
1 ATTTT
780073 TTTTTGAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
16 18 0.31
17 16 0.28
18 23 0.40
19 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (16 bp):
ATTTTAAAACACGAGA
Found at i:780064 original size:34 final size:34
Alignment explanation
Indices: 779983--780064 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
779973 TTTATTTTTT
* * * *
779983 ATTTTTAAACACGAAAAATTTTTAAAACAGGAGA
1 ATTTTGAAACACGAAAAATTTTAAAAACACGACA
*
780017 ATTTTAGAGACACG-AAAATTCTTAAAAACACGACA
1 ATTTT-GAAACACGAAAAATT-TTAAAAACACGACA
780052 ATTTTGAAACACG
1 ATTTTGAAACACG
780065 CGAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 18 0.45
35 22 0.55
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (34 bp):
ATTTTGAAACACGAAAAATTTTAAAAACACGACA
Found at i:780135 original size:17 final size:18
Alignment explanation
Indices: 780090--780137 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
780080 AAACCCTAAA
* *
780090 ATTTTTGAAACACCGGAG
1 ATTTTTGAAACACAGAAG
780108 -TTTTTGAAA-ACAAGAAG
1 ATTTTTGAAACAC-AGAAG
780125 ATTTTTGAAACAC
1 ATTTTTGAAACAC
780138 GAATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 9 0.36
19 2 0.08
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTTGAAACACAGAAG
Found at i:780475 original size:13 final size:14
Alignment explanation
Indices: 780457--780487 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
780447 AAAATTGGAT
780457 TAAATA-AAAAATA
1 TAAATACAAAAATA
780470 TAAATACAAAAATA
1 TAAATACAAAAATA
780484 TAAA
1 TAAA
780488 AATGCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAATACAAAAATA
Found at i:780760 original size:50 final size:52
Alignment explanation
Indices: 780651--780798 Score: 198
Period size: 50 Copynumber: 2.9 Consensus size: 52
780641 GCCTGCTTCG
*
780651 GATTGGGCCTGGGCCTGCTGGACA-GCCTGCTTT-TT-CTGCTGGGCCGCCTGCT
1 GATTGGGCCT--G-CTGCTGGACAGGCCTGCTTTGTTGCTGCTGGGCTGCCTGCT
780703 GATTGGGCCTGCTGCTGGACAGGCCTGCTTTGTTGCTGCTGGGCTGCCTGC-
1 GATTGGGCCTGCTGCTGGACAGGCCTGCTTTGTTGCTGCTGGGCTGCCTGCT
* **
780754 G-TTGGGCCTGCTACTGGACAGGCCTGCTTTGAAGCTGCTGGGCTG
1 GATTGGGCCTGCTGCTGGACAGGCCTGCTTTGTTGCTGCTGGGCTG
780799 TTTTTTTTCT
Statistics
Matches: 89, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 10 0.11
50 51 0.57
51 3 0.03
52 25 0.28
ACGTcount: A:0.07, C:0.28, G:0.36, T:0.28
Consensus pattern (52 bp):
GATTGGGCCTGCTGCTGGACAGGCCTGCTTTGTTGCTGCTGGGCTGCCTGCT
Found at i:780978 original size:11 final size:11
Alignment explanation
Indices: 780943--780989 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
780933 TTATTATTTT
780943 TTTCTTCTTTC
1 TTTCTTCTTTC
**
780954 -TTCTTC-CCC
1 TTTCTTCTTTC
780963 TTTTCTTCTTTC
1 -TTTCTTCTTTC
780975 TTTCTTCTTTC
1 TTTCTTCTTTC
780986 TTTC
1 TTTC
780990 CCGATCAGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 1 0.03
10 6 0.21
11 21 0.72
12 1 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:781157 original size:21 final size:21
Alignment explanation
Indices: 781112--781161 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
781102 CCCTTTTTTG
*
781112 TTTGCTGTTTTTTTTCTTTGTC
1 TTTGCT-TTTTTTTTCTTTGGC
781134 TTTGCTTTTTTTTT-TATTGGC
1 TTTGCTTTTTTTTTCT-TTGGC
781155 TTT-CTTT
1 TTTGCTTT
781162 GTCTTTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 15 0.58
22 6 0.23
ACGTcount: A:0.02, C:0.12, G:0.12, T:0.74
Consensus pattern (21 bp):
TTTGCTTTTTTTTTCTTTGGC
Found at i:781169 original size:16 final size:16
Alignment explanation
Indices: 781124--781169 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
781114 TGCTGTTTTT
781124 TTTCTTTGTCTTT-GC
1 TTTCTTTGTCTTTGGC
* *
781139 TTT-TTTTTTTATTGGC
1 TTTCTTTGTCT-TTGGC
781155 TTTCTTTGTCTTTGG
1 TTTCTTTGTCTTTGG
781170 TGGATGGGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 9 0.38
17 5 0.21
ACGTcount: A:0.02, C:0.13, G:0.15, T:0.70
Consensus pattern (16 bp):
TTTCTTTGTCTTTGGC
Found at i:781552 original size:29 final size:30
Alignment explanation
Indices: 781483--781553 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
781473 TAGAAGGCGT
*
781483 AAAATTTTTGGGACAAAAGTGTAATTTTAA
1 AAAATTTTAGGGACAAAAGTGTAATTTTAA
* * *
781513 AAAAATATAGGG-CTAAAA-TGTAATTTTTA
1 AAAATTTTAGGGAC-AAAAGTGTAATTTTAA
*
781542 GAAATTTTAGGG
1 AAAATTTTAGGG
781554 GCCCGAATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (30 bp):
AAAATTTTAGGGACAAAAGTGTAATTTTAA
Found at i:784481 original size:16 final size:17
Alignment explanation
Indices: 784444--784485 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
784434 ACAATATCCG
*
784444 AATTTAATTTTCAATTT
1 AATTTAATTTCCAATTT
784461 AATTTAATTTCCAA-TT
1 AATTTAATTTCCAATTT
*
784477 GATTTAATT
1 AATTTAATT
784486 ATTTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTAATTTCCAATTT
Found at i:788213 original size:40 final size:40
Alignment explanation
Indices: 788138--788218 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
788128 TTGGGGATTT
* *
788138 GGGGAAATGAAATTGGGGAAATTAGGGGAAAAGGAATTGG
1 GGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAAATGG
* * * *
788178 GGGGAAATGAAATCGGGGAAGTTGGGGGGATAGGAAATGG
1 GGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAAATGG
788218 G
1 G
788219 AAATTAGGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.01, G:0.47, T:0.16
Consensus pattern (40 bp):
GGGGAAATGAAATCGGGGAAATTAGGGGAAAAGGAAATGG
Found at i:788596 original size:115 final size:112
Alignment explanation
Indices: 788360--788750 Score: 401
Period size: 115 Copynumber: 3.4 Consensus size: 112
788350 AAAAAATCCC
* *
788360 AGATAGAAAACGACAATGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATAATAAAAACGC
1 AGATA-AAAACGACAACGTTTAGCAAACACTTATAACATAATTGCGGC-TTT-TAATAAAAACGC
* ** * * *
788425 CACTAAACTATATCCTTTACCGGCATTTTAGTACAAACGCCACTAAAAACGT
63 CACTACAC-ATATCCTTTTGCGGCGTTTTTGTAAAAACGCCACT-AAAACGT
* *
788477 AGATAAAAACGACAACGTTTAGCGAACACTTATAACATAATTGCGGCATTTTTATAAAAACGCCA
1 AGATAAAAACGACAACGTTTAGCAAACACTTATAACATAATTGCGGC-TTTTAATAAAAACGCCA
* *
788542 CTATCACATAACCTTTTGCGGCGTTTTTGTAAAAACGCCACTAATAATGT
65 CTA-CACATATCCTTTTGCGGCGTTTTTGTAAAAACGCCACTAA-AACGT
* * * * * *
788592 AGATAAAAACGACAACGTTTA-CAAAAGACTAATAACATAATTGCGAC-GTTACCTGAAAACGCC
1 AGATAAAAACGACAACGTTTAGC-AAACACTTATAACATAATTGCGGCTTTTA-ATAAAAACGCC
* * * *
788655 ACTAACACATATCATTTTGCGGCG-TTTTGCAAAAAATGCCACTGAAAACAT
64 ACT-ACACATATCCTTTTGCGGCGTTTTTG-TAAAAACGCCACT-AAAACGT
* * ** *
788706 AGATAAAAACGACAACGTTTAACAAAGACAAAAAACATAATTGCG
1 AGATAAAAACGACAACGTTTAGCAAACACTTATAACATAATTGCG
788751 TCGTTTTTCG
Statistics
Matches: 237, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
113 7 0.03
114 87 0.37
115 94 0.40
116 44 0.19
117 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (112 bp):
AGATAAAAACGACAACGTTTAGCAAACACTTATAACATAATTGCGGCTTTTAATAAAAACGCCAC
TACACATATCCTTTTGCGGCGTTTTTGTAAAAACGCCACTAAAACGT
Found at i:788709 original size:114 final size:113
Alignment explanation
Indices: 788360--788817 Score: 356
Period size: 115 Copynumber: 4.0 Consensus size: 113
788350 AAAAAATCCC
* * * *
788360 AGATAGAAAACGACAATGTTTAGC-AAACACTTAA-AACATAATTGCGGCGTTTATAATAAAAAC
1 AGATA-AAAACGACAACGTTTA-CAAAAGAC-TAATAACATAATTGCGACG-TTA-CATAAAAAC
* * ** * * * *
788423 GCCACTAA-ACTATATCCTTTACCGGCATTTTAGTACAAACGCCACTAAAAACGT
61 GCCACTAACAC-ATAACATTTTGCGGCGTTTTTGAAAAAACGCCACT-AAAACGT
* * * * * **
788477 AGATAAAAACGACAACGTTTAGC-GAACACTTATAACATAATTGCGGCATTTTTATAAAAACGCC
1 AGATAAAAACGACAACGTTTA-CAAAAGACTAATAACATAATTGCGAC-GTTACATAAAAACGCC
* * * *
788541 ACTATCACATAACCTTTTGCGGCGTTTTTGTAAAAACGCCACTAATAATGT
64 ACTAACACATAACATTTTGCGGCGTTTTTGAAAAAACGCCACTAA-AACGT
* *
788592 AGATAAAAACGACAACGTTTACAAAAGACTAATAACATAATTGCGACGTTACCTGAAAACGCCAC
1 AGATAAAAACGACAACGTTTACAAAAGACTAATAACATAATTGCGACGTTACATAAAAACGCCAC
* * *
788657 TAACACATATCATTTTGCGGCG-TTTTGCAAAAAATGCCACTGAAAACAT
66 TAACACATAACATTTTGCGGCGTTTTTG-AAAAAACGCCACT-AAAACGT
* * * * * *
788706 AGATAAAAACGACAACGTTTA-ACAAAGACAAAAAACATAATTGCGTCGTTTTTCGTAGAAACGC
1 AGATAAAAACGACAACGTTTACA-AAAGACTAATAACATAATTGCGACG--TTACATAAAAACGC
* * ** *
788770 CACT-A-ATATAACTCATTTTGCGGCATTTAAGAAAAATCGCCACTAAAA
63 CACTAACACATAA--CATTTTGCGGCGTTTTTGAAAAAACGCCACTAAAA
788818 AATTAGACAA
Statistics
Matches: 284, Mismatches: 44, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
113 6 0.02
114 96 0.34
115 98 0.35
116 76 0.27
117 8 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (113 bp):
AGATAAAAACGACAACGTTTACAAAAGACTAATAACATAATTGCGACGTTACATAAAAACGCCAC
TAACACATAACATTTTGCGGCGTTTTTGAAAAAACGCCACTAAAACGT
Found at i:789208 original size:7 final size:7
Alignment explanation
Indices: 789192--789260 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
789182 ACCCTAAGCT
789192 ATAAACC
1 ATAAACC
*
789199 ATAAATC
1 ATAAACC
**
789206 ATAAATT
1 ATAAACC
789213 ATAAACC
1 ATAAACC
* *
789220 CTAAAATC
1 AT-AAACC
*
789228 ATAAATC
1 ATAAACC
*
789235 TTAAACC
1 ATAAACC
789242 ATAAACC
1 ATAAACC
789249 ATAAACC
1 ATAAACC
*
789256 CTAAA
1 ATAAA
789261 TCTTATGAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
7 45 0.90
8 5 0.10
ACGTcount: A:0.55, C:0.22, G:0.00, T:0.23
Consensus pattern (7 bp):
ATAAACC
Found at i:789229 original size:22 final size:23
Alignment explanation
Indices: 789190--789246 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
789180 GCACCCTAAG
789190 CTATAAACCAT-AAATCATAAAT
1 CTATAAACCATAAAATCATAAAT
*
789212 -TATAAACCCTAAAATCATAAAT
1 CTATAAACCATAAAATCATAAAT
789234 CT-TAAACCATAAA
1 CTATAAACCATAAA
789247 CCATAAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 9 0.29
22 21 0.68
23 1 0.03
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.26
Consensus pattern (23 bp):
CTATAAACCATAAAATCATAAAT
Found at i:789234 original size:29 final size:29
Alignment explanation
Indices: 789198--789253 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
789188 AGCTATAAAC
** *
789198 CATAAATCATAAATTATAAACCCTAAAAT
1 CATAAATCATAAACCATAAACCATAAAAT
*
789227 CATAAATCTTAAACCATAAACCATAAA
1 CATAAATCATAAACCATAAACCATAAA
789254 CCCTAAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (29 bp):
CATAAATCATAAACCATAAACCATAAAAT
Found at i:799554 original size:23 final size:22
Alignment explanation
Indices: 799524--799594 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
799514 TTTTTTTCAT
799524 TTTTAAAAAGTTTTAAATTTTTA
1 TTTTAAAAAGTTTTAAA-TTTTA
*
799547 TTTTAAAAAGTTTTAAAATGTTA
1 TTTTAAAAAGTTTT-AAATTTTA
*
799570 TTTTAAAAAGTTAT-AATTTTA
1 TTTTAAAAAGTTTTAAATTTTA
799591 TTTT
1 TTTT
799595 TATTCTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 10 0.23
23 31 0.70
24 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTAAAAAGTTTTAAATTTTA
Found at i:799575 original size:13 final size:13
Alignment explanation
Indices: 799544--799583 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
799534 TTTTAAATTT
799544 TTATTTTAAAAAG
1 TTATTTTAAAAAG
*
799557 ---TTTTAAAATG
1 TTATTTTAAAAAG
799567 TTATTTTAAAAAG
1 TTATTTTAAAAAG
799580 TTAT
1 TTAT
799584 AATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 9 0.41
13 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTATTTTAAAAAG
Found at i:802069 original size:109 final size:109
Alignment explanation
Indices: 801878--802257 Score: 622
Period size: 109 Copynumber: 3.5 Consensus size: 109
801868 NNNNNNNNNN
801878 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
1 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
801943 TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
66 TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
801987 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
1 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
802052 TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
66 TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
* *
802096 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATTGCTAAATATCCTTTCAAAAAT
1 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
* * * * *
802161 TTCAAAATAAGGCAATGCTTTGCGTTTGGAAATTCGAG-GAACG
66 TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
* * * * * *
802204 TGCCATTAGGTGCTGGGTTTCGA--TTTCTCGTTTAACCAAATTGCCAAATATCCT
1 TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
802258 CTTGAATTTT
Statistics
Matches: 259, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
106 29 0.11
108 23 0.09
109 207 0.80
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (109 bp):
TGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAT
TTTACAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACA
Found at i:820851 original size:176 final size:176
Alignment explanation
Indices: 820552--820902 Score: 596
Period size: 176 Copynumber: 2.0 Consensus size: 176
820542 CAAAACGAGG
* *
820552 TCACCGTTAAAGAGTTATAGGACAAATTTGAGACAAGATACATCACCGAAGATGTTACAAGTAAG
1 TCACCGTTAAAGAGTTATAGGACAAATTAGAGACAAGATACATCACCAAAGATGTTACAAGTAAG
* * *
820617 AAATTTCTTGTCAGTCATTTCAATAATTATCAAATAGTTGCTGGTTGTTCTATTATGGAACAA-T
66 AAATTTCTTCTCAGCCATTTCAATAATTATCAAATAGTTGCTGGTCGTTCTATTATGGAACAATT
820681 TCTGTGATATTGAAAAGATGTTGAATCAATTCAAGCAATATGATATT
131 TC-GTGATATTGAAAAGATGTTGAATCAATTCAAGCAATATGATATT
* * *
820728 TCACCGTTAAAGAGTTATGGGACAAATTAGAGATAAGATACATGACCAAAGATGTTACAAGTAAG
1 TCACCGTTAAAGAGTTATAGGACAAATTAGAGACAAGATACATCACCAAAGATGTTACAAGTAAG
* *
820793 AAATTTCTTCTCAGCCATTTCAATAATTATCAAATGGTTGCTGGTCGTTCTGTTATGGAACAATT
66 AAATTTCTTCTCAGCCATTTCAATAATTATCAAATAGTTGCTGGTCGTTCTATTATGGAACAATT
820858 TCGTGATATTGAAAAGATGTTGAATCAATTCAAGCAATATGATAT
131 TCGTGATATTGAAAAGATGTTGAATCAATTCAAGCAATATGATAT
820903 GAAAATGGAT
Statistics
Matches: 164, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
176 161 0.98
177 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (176 bp):
TCACCGTTAAAGAGTTATAGGACAAATTAGAGACAAGATACATCACCAAAGATGTTACAAGTAAG
AAATTTCTTCTCAGCCATTTCAATAATTATCAAATAGTTGCTGGTCGTTCTATTATGGAACAATT
TCGTGATATTGAAAAGATGTTGAATCAATTCAAGCAATATGATATT
Found at i:824993 original size:20 final size:20
Alignment explanation
Indices: 824959--825000 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
824949 AACTATTTAA
** *
824959 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
824979 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
824999 AT
1 AT
825001 GTGTTTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:825738 original size:42 final size:42
Alignment explanation
Indices: 825650--825743 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
825640 TTGGTTTAGT
*
825650 CGATGATGCACTTACGTGCGAGTATAATTAGTTCGGTACATT
1 CGATGATGCACTTACGTGCGAGTATAATTAGTTCGGTACATC
* * * * **
825692 CGATGATGCACTTACGTTCTAGTATGATT-GTTTCTGTTTATC
1 CGATGATGCACTTACGTGCGAGTATAATTAG-TTCGGTACATC
825734 CGATGATGCA
1 CGATGATGCA
825744 TTATGCGTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (42 bp):
CGATGATGCACTTACGTGCGAGTATAATTAGTTCGGTACATC
Found at i:825827 original size:43 final size:43
Alignment explanation
Indices: 825780--825870 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
825770 GCTTGTTCAG
** *
825780 TGATGCACTATGTGTACCAGTATACATTCTTCAATTTATTCGA
1 TGATGCACTATGCATACCAGTACACATTCTTCAATTTATTCGA
* * * **
825823 TGATGCACTATGCATGCTAGTACACTTTCTTCGGTTTATTCGA
1 TGATGCACTATGCATACCAGTACACATTCTTCAATTTATTCGA
825866 TGATG
1 TGATG
825871 TACTGTGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (43 bp):
TGATGCACTATGCATACCAGTACACATTCTTCAATTTATTCGA
Found at i:829689 original size:25 final size:24
Alignment explanation
Indices: 829661--829714 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
829651 ATTATTTAAA
829661 AATTTTGTAAAAAAATAAAAAATAT
1 AATTTTGTAAAAAAATAAAAAAT-T
* * *
829686 AATTTTTTTTAAAAATTAAAAAATT
1 AA-TTTTGTAAAAAAATAAAAAATT
829711 AATT
1 AATT
829715 ATAGATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.08
25 5 0.20
26 18 0.72
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTTTGTAAAAAAATAAAAAATT
Found at i:840976 original size:2 final size:2
Alignment explanation
Indices: 840969--841007 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
840959 AATTCCAAAC
840969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
841008 ACACCAGGTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:842626 original size:5 final size:5
Alignment explanation
Indices: 842616--842645 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
842606 AGGTGTTTAT
842616 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
842646 TCCTCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:844509 original size:33 final size:32
Alignment explanation
Indices: 844467--844540 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 32
844457 ATTATTATGG
*
844467 GATATTATCTTTTAGCAATTTGATTCATAATAA
1 GATATTATCTCTTAGCAATTTGATTCATAAT-A
*
844500 GATATTATCTCTTAGCAATTTGATTCCTAATA
1 GATATTATCTCTTAGCAATTTGATTCATAATA
844532 GAATATTAT
1 G-ATATTAT
844541 ATGATATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (32 bp):
GATATTATCTCTTAGCAATTTGATTCATAATA
Found at i:846831 original size:27 final size:29
Alignment explanation
Indices: 846781--846848 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 29
846771 AGAAGTATTT
846781 TTTATAA-TTTTTATACTTTTAAAATA-AA
1 TTTATAACTTTTTATACTTTTAAAA-ACAA
846809 TTTA-ATACTTTTTA-A-TTTTAAAAACAA
1 TTTATA-ACTTTTTATACTTTTAAAAACAA
846836 TTTATAACTTTTT
1 TTTATAACTTTTT
846849 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
26 1 0.03
27 22 0.61
28 7 0.19
29 6 0.17
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTATAACTTTTTATACTTTTAAAAACAA
Found at i:846849 original size:29 final size:29
Alignment explanation
Indices: 846781--846856 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 29
846771 AGAAGTATTT
* *
846781 TTTATAA-TTTTTATACTTTTAAAATAAA
1 TTTATAACTTTTTTTAATTTTAAAATAAA
846809 TTTA-ATAC--TTTTTAATTTTAAAA-ACAA
1 TTTATA-ACTTTTTTTAATTTTAAAATA-AA
846836 TTTATAACTTTTTTTAATTTT
1 TTTATAACTTTTTTTAATTTT
846857 TTAATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
26 1 0.03
27 22 0.55
28 6 0.15
29 11 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTATAACTTTTTTTAATTTTAAAATAAA
Found at i:847555 original size:30 final size:31
Alignment explanation
Indices: 847516--847575 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
847506 NNNNNTGAAA
*
847516 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
847547 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
847576 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:848501 original size:20 final size:19
Alignment explanation
Indices: 848476--848515 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
848466 ACACTGTCCA
*
848476 TGCACACGGGCGTGTGAGGT
1 TGCACACAGGCGTGT-AGGT
*
848496 TGCACACAGGTGTGTAGGT
1 TGCACACAGGCGTGTAGGT
848515 T
1 T
848516 AACCACACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.25
Consensus pattern (19 bp):
TGCACACAGGCGTGTAGGT
Found at i:853460 original size:22 final size:22
Alignment explanation
Indices: 853425--853492 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
853415 CTCTATTTTC
* *
853425 TAGCACGTCAGTGCTCTCCGTT
1 TAGCACCTAAGTGCTCTCCGTT
* * *
853447 TAGCATGCT-TGTGCTCTCCGTA
1 TAGCA-CCTAAGTGCTCTCCGTT
853469 TAGCACCTAAGTGCTCTCCGTT
1 TAGCACCTAAGTGCTCTCCGTT
853491 TA
1 TA
853493 TTTGTGCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.05
22 34 0.92
23 1 0.03
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (22 bp):
TAGCACCTAAGTGCTCTCCGTT
Found at i:856885 original size:44 final size:44
Alignment explanation
Indices: 856837--856969 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 44
856827 GATTCGTGGT
*
856837 TTTAATCTACTCCACTGCAACATCAGGGAGATAAGACTTGTTA-C
1 TTTAATCTGCTCCACTGCAAC-TCAGGGAGATAAGACTTGTTATC
* * *** ** *
856881 TTTAACCTGTTCCACTGTGGCTTCAGGGAGATAAGGTTTGATATC
1 TTTAATCTGCTCCACTGCAAC-TCAGGGAGATAAGACTTGTTATC
* * *
856926 TTTAGTTTGCTCCACTGCAACTCTAGGGAAATAAGACTTGTTAT
1 TTTAATCTGCTCCACTGCAACTC-AGGGAGATAAGACTTGTTAT
856970 AGTGTGATCC
Statistics
Matches: 66, Mismatches: 21, Indels: 3
0.73 0.23 0.03
Matches are distributed among these distances:
44 35 0.53
45 31 0.47
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTCAGGGAGATAAGACTTGTTATC
Found at i:857247 original size:147 final size:147
Alignment explanation
Indices: 856975--857299 Score: 632
Period size: 147 Copynumber: 2.2 Consensus size: 147
856965 GTTATAGTGT
* *
856975 GATCCGCTCTGCTGCAACTTCAGAGAGATAAAATCTGTGGCTCTTCGAGGAAACATTTGCTATCT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTGGCTCTTCGAGGAAACATTTGCTATCT
857040 CCAGTCTGCTACACGGCAACCTCAGTGAGATAAGACTTGTAGCTTCAACTTGTTTTACTGCATCT
66 CCAGTCTGCTACACGGCAACCTCAGTGAGATAAGACTTGTAGCTTCAACTTGTTTTACTGCATCT
857105 TTAATAAAATCTGATGC
131 TTAATAAAATCTGATGC
857122 GATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTGGCTCTTCGAGGAAACATTTGCTATCT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTGGCTCTTCGAGGAAACATTTGCTATCT
857187 CCAGTCTGCTACACGGCAACCTCAGTGAGATAAGACTTGTAGCTTCAACTTGTTTTACTGCATCT
66 CCAGTCTGCTACACGGCAACCTCAGTGAGATAAGACTTGTAGCTTCAACTTGTTTTACTGCATCT
857252 TTAATAAAATCTGATGC
131 TTAATAAAATCTGATGC
857269 GATCTGCTCTACTGCAACTTCAGAGAGATAA
1 GATCTGCTCTACTGCAACTTCAGAGAGATAA
857300 GATTCATCAT
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 176 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (147 bp):
GATCTGCTCTACTGCAACTTCAGAGAGATAAAATCTGTGGCTCTTCGAGGAAACATTTGCTATCT
CCAGTCTGCTACACGGCAACCTCAGTGAGATAAGACTTGTAGCTTCAACTTGTTTTACTGCATCT
TTAATAAAATCTGATGC
Found at i:857461 original size:44 final size:43
Alignment explanation
Indices: 857270--857592 Score: 209
Period size: 44 Copynumber: 7.5 Consensus size: 43
857260 ATCTGATGCG
* * *
857270 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCATCATTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TCGTGATTTTA
* * * *
857314 ACCCGCTTCACTGCAACTTCA-AGAAGATAGGAT--TGACTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCGTGA-TT-TT-A
* *
857358 ATTTGCTCCACTGCAACTTCAG-GAAGATAAGATTG-GA--TTA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCGTGATTTTA
*
857398 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTA
1 -ATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-CGTGATTTTA
* * * * * * *
857443 ATCCGTTCCACTGCAACTTCAGGGAGATAGGATTG-GTTTCTTCT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCGTGATT-TT-A
* * ** * * ***
857487 GTCTGCTCCACTACTGCTT-AGGGAGATAAGA-CTTGA-TGCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCGTGATTTTA
*
857527 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-CGTGATTTTA
* *
857571 ATCCGTTCCACTGCAACTTCAG
1 ATCTGCTCCACTGCAACTTCAG
857593 GTAGATAGGA
Statistics
Matches: 211, Mismatches: 48, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
40 15 0.07
41 44 0.21
42 8 0.04
43 26 0.12
44 113 0.54
45 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCGTGATTTTA
Found at i:857563 original size:128 final size:128
Alignment explanation
Indices: 857263--857688 Score: 631
Period size: 128 Copynumber: 3.3 Consensus size: 128
857253 TAATAAAATC
* * * *
857263 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCATCATTTTAACCCGCTT-CACTG
1 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCG-TTCCACTG
* * ** * * ** *
857327 CAACTTCAAGAAGATAGGATTGACTTCTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGA-T
65 CAACTTCAGGAAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTT-AGGGAGATAAGACT
**
857391 TGGATTAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCGTTCCACTG
1 T-GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCGTTCCACTG
* *
857456 CAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
65 CAACTTCAGGAAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
857520 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCGTTCCACTGC
1 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCGTTCCACTGC
* *
857585 AACTTCAGGTAGATAGGATTGATTTCTTCTGTCTGCTCCGCTACTGCTTAGGGAGATAAGACT
66 AACTTCAGGAAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
*
857648 TGATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATC
1 TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATC
857689 TGTGGCTCTT
Statistics
Matches: 272, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
128 176 0.65
129 96 0.35
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (128 bp):
TGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCGTGATTTTAATCCGTTCCACTGC
AACTTCAGGAAGATAGGATTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACT
Found at i:858852 original size:13 final size:13
Alignment explanation
Indices: 858836--858860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
858826 ACCTTAATTA
858836 TACCCAATAATAG
1 TACCCAATAATAG
858849 TACCCAATAATA
1 TACCCAATAATA
858861 ATAATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (13 bp):
TACCCAATAATAG
Found at i:858860 original size:3 final size:3
Alignment explanation
Indices: 858854--858889 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
858844 AATAGTACCC
858854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
858890 GTGTATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:859580 original size:21 final size:21
Alignment explanation
Indices: 859542--859581 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
859532 ATTTTAAAAT
**
859542 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
859563 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
859582 GGTATTTTAT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:859588 original size:22 final size:20
Alignment explanation
Indices: 859541--859589 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
859531 AATTTTAAAA
* *
859541 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
859561 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
859584 TATTTT
1 TATTTT
859590 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 11 0.46
22 11 0.46
23 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:865685 original size:26 final size:26
Alignment explanation
Indices: 865650--865700 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
865640 TAAGATTCGG
*
865650 TAATAAAGAAGTAATTTCAATACCAA
1 TAATAAAGAAATAATTTCAATACCAA
* *
865676 TAATATAGAAATAATTTTAATACCA
1 TAATAAAGAAATAATTTCAATACCA
865701 CTTAATTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (26 bp):
TAATAAAGAAATAATTTCAATACCAA
Found at i:869866 original size:79 final size:79
Alignment explanation
Indices: 869772--869929 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
869762 ACCAGAATGC
869772 AAAAAAAAAAAAAAAAAAGGAAAAAATCCCATAAAAATAAGTTAAAACCCATCATATGGCCATGA
1 AAAAAAAAAAAAAAAAAAGGAAAAAATCCCATAAAAATAAGTTAAAACCCATCATATGGCCATGA
869837 CATCAAAAGAATTA
66 CATCAAAAGAATTA
*
869851 AAAAAAAAAAAAAAAAAAGGATAAAATCCCATAAAAATAAGTTAAAACCCATCATATGGCCATGA
1 AAAAAAAAAAAAAAAAAAGGAAAAAATCCCATAAAAATAAGTTAAAACCCATCATATGGCCATGA
869916 CATCAAAAGAATTA
66 CATCAAAAGAATTA
869930 CAAATCGGAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.61, C:0.14, G:0.09, T:0.16
Consensus pattern (79 bp):
AAAAAAAAAAAAAAAAAAGGAAAAAATCCCATAAAAATAAGTTAAAACCCATCATATGGCCATGA
CATCAAAAGAATTA
Found at i:870516 original size:2 final size:2
Alignment explanation
Indices: 870509--870538 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
870499 TGGTGTCAAA
870509 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
870539 GCTTCTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:871942 original size:17 final size:17
Alignment explanation
Indices: 871920--871952 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
871910 TAGAATGTGG
871920 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
*
871937 TTGAGAAATTAATTTA
1 TTGAGAAAATAATTTA
871953 GTTGGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:871978 original size:22 final size:21
Alignment explanation
Indices: 871950--871991 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
871940 AGAAATTAAT
* *
871950 TTAGTTGGTTTAATTAAATAAA
1 TTAGTT-GATTAAATAAATAAA
871972 TTAGTTGATTAAATAAATAA
1 TTAGTTGATTAAATAAATAA
871992 TATTTGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (21 bp):
TTAGTTGATTAAATAAATAAA
Found at i:881951 original size:21 final size:20
Alignment explanation
Indices: 881913--881950 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
881903 AGGTATTATA
881913 TTTTATTCTAATACTTTTCG
1 TTTTATTCTAATACTTTTCG
*
881933 TTTTTTTCATAATA-TTTT
1 TTTTATTC-TAATACTTTT
881951 TTATTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTATTCTAATACTTTTCG
Found at i:885129 original size:15 final size:16
Alignment explanation
Indices: 885109--885155 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
885099 AAGTCTACGC
885109 ATATTTTTTAATTTA-
1 ATATTTTTTAATTTAT
* *
885124 ATATTTAATAAATTTAT
1 ATATTT-TTTAATTTAT
885141 ATATTTTTT-ATTTAT
1 ATATTTTTTAATTTAT
885156 CATAGTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.46
16 8 0.31
17 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTTTTTAATTTAT
Found at i:891302 original size:21 final size:21
Alignment explanation
Indices: 891273--891315 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
891263 AAGTTAAAGT
891273 TAAGTCCTCCAAATTTTTCTGA
1 TAAGTCCTCCAAATTTTT-TGA
*
891295 TAAG-CCTCTAAATTTTTTGA
1 TAAGTCCTCCAAATTTTTTGA
891315 T
1 T
891316 TTAAAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (21 bp):
TAAGTCCTCCAAATTTTTTGA
Found at i:921884 original size:17 final size:17
Alignment explanation
Indices: 921862--921894 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
921852 AATCAAATTG
*
921862 AATATTATTTTTTATTT
1 AATATTAATTTTTATTT
921879 AATATTAATTTTTATT
1 AATATTAATTTTTATT
921895 AGGTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATATTAATTTTTATTT
Found at i:927565 original size:27 final size:28
Alignment explanation
Indices: 927533--927587 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
927523 TGTAAAAGGT
*
927533 TTTTAGTTGAG-CACCAAAGCTAGAGGG
1 TTTTAGTTGAGCCACAAAAGCTAGAGGG
*
927560 TTTTAGTTGAGCCATAAAAGCTAGAGGG
1 TTTTAGTTGAGCCACAAAAGCTAGAGGG
927588 AAGGTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (28 bp):
TTTTAGTTGAGCCACAAAAGCTAGAGGG
Found at i:928320 original size:16 final size:16
Alignment explanation
Indices: 928299--928368 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
928289 TTTGGTTCGC
928299 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
928315 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAGG
*
928331 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
* *
928347 CGTAATGGAATATAGG
1 TGTAATGGAATAGAGG
*
928363 CGTAAT
1 TGTAAT
928369 AGGTAATTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.39, C:0.03, G:0.31, T:0.27
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:928429 original size:44 final size:46
Alignment explanation
Indices: 928350--928442 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
928340 ATAGATGCGT
* * * *
928350 AATGGAATATAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
928396 AATGGAATAGAGACATAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
928440 AAT
1 AAT
928443 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.56
45 3 0.07
46 16 0.37
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:929824 original size:14 final size:14
Alignment explanation
Indices: 929805--929844 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
929795 GATTGGCAGT
*
929805 AAAATGTTTTCCGG
1 AAAATGTTTTACGG
* *
929819 AAAATGATTTATGG
1 AAAATGTTTTACGG
929833 AAAATGTTTTAC
1 AAAATGTTTTAC
929845 TTTTCTGTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (14 bp):
AAAATGTTTTACGG
Found at i:930251 original size:43 final size:43
Alignment explanation
Indices: 930190--930289 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
930180 AATAATATTA
*
930190 TCCAAATACATAATTAGTAGTACACCACATAGTGACAACATTG
1 TCCAAATACATAATTAGTAGTACACCACATAGTAACAACATTG
930233 TCCAAATACATAATTAGTAGTACACCACATAGTAACAACATTG
1 TCCAAATACATAATTAGTAGTACACCACATAGTAACAACATTG
* *
930276 TCCAAGTGCATAAT
1 TCCAAATACATAAT
930290 ATTACACCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (43 bp):
TCCAAATACATAATTAGTAGTACACCACATAGTAACAACATTG
Found at i:931298 original size:35 final size:36
Alignment explanation
Indices: 931254--931322 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
931244 ATTCAACCAT
*
931254 TTCATTATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
931289 TTCAATATCCAACAAGGTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
931323 TCTAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:931320 original size:27 final size:28
Alignment explanation
Indices: 931290--931358 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
931280 AATAATAAAT
*
931290 TCAATATCCAACAAGGTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
931317 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
931345 TCAAAATCCAACAA
1 TCAATATCCAACAA
931359 TCTAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.57
28 13 0.37
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Done.