Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold159
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: 985711
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 53909 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:803587 original size:83 final size:83
Alignment explanation
Indices: 803377--803620 Score: 318
Period size: 83 Copynumber: 3.0 Consensus size: 83
803367 TTGTATAAAA
* * *
803377 CACCGGCAT-AAAGCCTGCTAGGCACAAAGCCTG--ATACATTCCACCGGCA-CAAAGCCTGCTA
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATA-ATT-CACCGGCATC-AAGCCTGCTA
* * * *
803438 GACATAAGGTCTGATACATTT
63 GACGTAAAGTCTGAAACAATT
* * *
803459 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGGCATCAATCCTGCTAGAC
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
*
803523 GTAAAGTCTGAAATAATT
66 GTAAAGTCTGAAACAATT
*
803541 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
803606 GTAAAGTCTGAAACA
66 GTAAAGTCTGAAACA
803621 TCTTATTTTC
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
82 69 0.49
83 70 0.50
84 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (83 bp):
CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATTCACCGGCATCAAGCCTGCTAGAC
GTAAAGTCTGAAACAATT
Found at i:803618 original size:41 final size:42
Alignment explanation
Indices: 803377--803618 Score: 300
Period size: 41 Copynumber: 5.9 Consensus size: 42
803367 TTGTATAAAA
* * *
803377 CACCGGCAT-AAAGCCTGCTAGGCACAAAGCCTG--ATACATT
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATA-ATT
* * * *
803417 CCACCGGCA-CAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATT
* *
803459 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATT
* *
803500 CACCGGCATC-AATCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
803541 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATT
*
803583 CACCGGCATC-AAGCCTGCTAGACGTAAAGTCTGAAA
1 CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAA
803619 CATCTTATTT
Statistics
Matches: 180, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
41 135 0.75
42 43 0.24
43 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (42 bp):
CACCGGCATCAAAGCCTGCTAGACATAAAGTCTGAAATAATT
Found at i:808712 original size:40 final size:40
Alignment explanation
Indices: 808659--808737 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
808649 GCGTTTGGAT
808659 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
1 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
* * * * *
808699 AAAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTT
1 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTT
808738 TGGAAAGCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
Found at i:808983 original size:41 final size:41
Alignment explanation
Indices: 808827--808984 Score: 149
Period size: 41 Copynumber: 3.9 Consensus size: 41
808817 CTTTGAGTTT
* * * * **
808827 TCGGGGCTTTAGTGTCGTTTTT-GAAAAAGCGTCACTAACGC
1 TCGGGGCTTTAGCGGCGTTTTTAG-AAAAGCGCCGCTAATAC
* *
808868 AT-GGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
1 -TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
* * *
808909 TTGGGGCTTTAGCGGCGCTTCTAGAAAAGCGCCGCTAATAC
1 TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
* * * *
808950 TCGGGGCTTTAGCTGCATTTTTTGAAAAACGCCGC
1 TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGC
808985 AAAAATATTT
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 95 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
Found at i:809387 original size:14 final size:14
Alignment explanation
Indices: 809377--809410 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
809367 GGTTTAAGGT
809377 TTAGGGGTTAAATG
1 TTAGGGGTTAAATG
809391 TTAGGGGTT-AATAG
1 TTAGGGGTTAAAT-G
809405 TTAGGG
1 TTAGGG
809411 CTTTAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (14 bp):
TTAGGGGTTAAATG
Found at i:811281 original size:16 final size:16
Alignment explanation
Indices: 811260--811299 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
811250 CGTTTGGTTC
811260 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
811276 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
811292 ACTGTAAT
1 GCTGTAAT
811300 AATAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:811345 original size:45 final size:44
Alignment explanation
Indices: 811281--811373 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
811271 ATAGAGCTGT
811281 AATGGAATAGAACTGTAATAATAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAT-ATTC-ATGTGTTTGGTTGAATGG
* *
811326 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
811370 AATG
1 AATG
811374 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:817373 original size:150 final size:151
Alignment explanation
Indices: 817186--817457 Score: 528
Period size: 150 Copynumber: 1.8 Consensus size: 151
817176 GCCGAAGTGC
817186 AATTCTCTGCCCCTTTCACATAATCAAGTCTTTTTTTTTTTTTTAAATTTCATTAATTGTTATAT
1 AATTCTCTGCCCCTTTCACATAATCAAGTCTTTTTTTTTTTTTTAAATTTCATTAATTGTTATAT
*
817251 CTTTTTAAAATTTACTAGTATTATTTGTTGTTTTACGATGAGCTTTTAATTTTATAATTAATCTA
66 CTTTTTAAAATTTACTAGTATTATTTGGTGTTTTACGATGAGCTTTTAATTTTATAATTAATCTA
817316 TTTAATTAATAGTAGAAATTA
131 TTTAATTAATAGTAGAAATTA
817337 AATTCTCTG-CCCTTTCACATAATCAAGTCTTTTTTTTTTTTTTAAATTTCATTAATTGTTATAT
1 AATTCTCTGCCCCTTTCACATAATCAAGTCTTTTTTTTTTTTTTAAATTTCATTAATTGTTATAT
817401 CTTTTTAAAATTTACTAGTATTATTTGGTGTTTTACGATGAGCTTTTAATTTTATAA
66 CTTTTTAAAATTTACTAGTATTATTTGGTGTTTTACGATGAGCTTTTAATTTTATAA
817458 AANNNNNNNN
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
150 111 0.93
151 9 0.08
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (151 bp):
AATTCTCTGCCCCTTTCACATAATCAAGTCTTTTTTTTTTTTTTAAATTTCATTAATTGTTATAT
CTTTTTAAAATTTACTAGTATTATTTGGTGTTTTACGATGAGCTTTTAATTTTATAATTAATCTA
TTTAATTAATAGTAGAAATTA
Found at i:821078 original size:17 final size:17
Alignment explanation
Indices: 821052--821121 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 17
821042 AATTTACAAG
*
821052 TATTTTATTTTAAGATT
1 TATTTAATTTTAAGATT
*
821069 TATTTAATTTCATAATTGATGAA
1 TATTTAATTT--TAA--GAT--T
*
821092 TATTTTATATTTAAGATT
1 TATTTAAT-TTTAAGATT
821110 TATTTAATTTTA
1 TATTTAATTTTA
821122 TTATTTGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
17 13 0.32
18 7 0.17
19 3 0.07
20 3 0.07
21 3 0.07
22 3 0.07
23 7 0.17
24 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTAATTTTAAGATT
Found at i:821135 original size:41 final size:40
Alignment explanation
Indices: 821052--821138 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 40
821042 AATTTACAAG
*
821052 TATTTTATTTTAAGATTTATTTAATTTCATAATTGATGAA
1 TATTTTATTTTAAGATTTATTTAATTTCATAATTGATAAA
* *
821092 TATTTTATATTTAAGATTTATTTAATTTTATTATTTG-TAAA
1 TATTTTAT-TTTAAGATTTATTTAATTTCA-TAATTGATAAA
821133 TATTTT
1 TATTTT
821139 TTATATACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 8 0.19
41 29 0.69
42 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (40 bp):
TATTTTATTTTAAGATTTATTTAATTTCATAATTGATAAA
Found at i:822707 original size:15 final size:16
Alignment explanation
Indices: 822682--822711 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
822672 TTTGTGCAGT
822682 TTTTCTATTTTTATTG
1 TTTTCTATTTTTATTG
822698 TTTT-TATTTTTATT
1 TTTTCTATTTTTATT
822712 TAAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTCTATTTTTATTG
Found at i:823529 original size:27 final size:27
Alignment explanation
Indices: 823499--823555 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
823489 CAGAGCCGAT
* * *
823499 ACCAGTCAAGCCTTTCCCATAGGCGGC
1 ACCAATCAAGCCATCCCCATAGGCGGC
*
823526 ACCAATCAAGCCATCCCCATAGGTGGC
1 ACCAATCAAGCCATCCCCATAGGCGGC
823553 ACC
1 ACC
823556 CACTCCCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.39, G:0.19, T:0.16
Consensus pattern (27 bp):
ACCAATCAAGCCATCCCCATAGGCGGC
Found at i:823576 original size:6 final size:6
Alignment explanation
Indices: 823554--823590 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
823544 ATAGGTGGCA
823554 CCCACTC CCCA-C CCCATC CCCATC CCCATC CCCATC C
1 CCCA-TC CCCATC CCCATC CCCATC CCCATC CCCATC C
823591 GACTCTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.69
7 4 0.14
ACGTcount: A:0.16, C:0.70, G:0.00, T:0.14
Consensus pattern (6 bp):
CCCATC
Found at i:827532 original size:62 final size:64
Alignment explanation
Indices: 827456--827620 Score: 194
Period size: 62 Copynumber: 2.6 Consensus size: 64
827446 CAATGTAGCT
* *
827456 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAAT-TTAT-A-TAA-CA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTATAATTAATC-
827517 A
64 A
* * * * *
827518 AATTTATATTACAAAGTTTGTTACAAGTTTTAGTGTTTTAATGTTGTAATGTTTTAATTAATCT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTATAATTAATCA
**
827582 AATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTG
1 AATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTG
827621 CAATTAATCT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
61 5 0.06
62 43 0.50
63 1 0.01
64 10 0.12
65 27 0.31
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (64 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTATAATTAATCA
Found at i:827610 original size:65 final size:69
Alignment explanation
Indices: 827483--827619 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 69
827473 TTGTTCCAAT
**
827483 TTTTAATGTTGTAATGTATTTAATTTATATAACAAAATTTATATTACAAAGTTTGTTACAAGTTT
1 TTTTAATGTTGTAATGTATTTAATTTATAT-ACAAAATTTATACCACAAAGTTTGTTACAAGTTT
*
827548 TAGTG
65 TAATG
* *
827553 TTTTAATGTTGTAATGT-TTTAA-TTA-AT-C-TAATTTATGACCACAAAGTTTGTTCCAAGTTT
1 TTTTAATGTTGTAATGTATTTAATTTATATACAAAATTTAT-ACCACAAAGTTTGTTACAAGTTT
827613 TAATG
65 TAATG
827618 TT
1 TT
827620 GCAATTAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
64 7 0.11
65 27 0.44
67 2 0.03
68 3 0.05
69 5 0.08
70 17 0.28
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (69 bp):
TTTTAATGTTGTAATGTATTTAATTTATATACAAAATTTATACCACAAAGTTTGTTACAAGTTTT
AATG
Found at i:830036 original size:26 final size:26
Alignment explanation
Indices: 829993--830045 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
829983 ATTTTATATT
*
829993 AAAATACTAAAAATAACATGCCAATAA
1 AAAATACTAAAAATAACATACC-ATAA
830020 AAAATA-TAACAAA-AACATACCATAA
1 AAAATACTAA-AAATAACATACCATAA
830045 A
1 A
830046 CGATACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAATACTAAAAATAACATACCATAA
Found at i:830728 original size:14 final size:14
Alignment explanation
Indices: 830711--830737 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
830701 ACCTTTTCTT
830711 TTCTATTTTTTTCA
1 TTCTATTTTTTTCA
830725 TTCTATTTTTTTC
1 TTCTATTTTTTTC
830738 TTTTTTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTATTTTTTTCA
Found at i:832890 original size:21 final size:21
Alignment explanation
Indices: 832864--832904 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
832854 CAATAATGTT
*
832864 AGAAAAATTCTGGTGTAAGAA
1 AGAAAAATTCTGGTGCAAGAA
* *
832885 AGAAAATTTGTGGTGCAAGA
1 AGAAAAATTCTGGTGCAAGA
832905 TAACGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (21 bp):
AGAAAAATTCTGGTGCAAGAA
Found at i:833806 original size:20 final size:20
Alignment explanation
Indices: 833763--833811 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
833753 AGGAGCCAAT
* *
833763 AAATCAATTTGATTAAAATT
1 AAATCAAATTGATTAAAATA
*
833783 AAATCAAATTGATTAGAATA
1 AAATCAAATTGATTAAAATA
*
833803 AAATAAAAT
1 AAATCAAAT
833812 AAGATAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:837433 original size:27 final size:27
Alignment explanation
Indices: 837403--837485 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 27
837393 AACTCTGAGA
837403 GAATGATATGTGTGACGAACTCTAAAG
1 GAATGATATGTGTGACGAACTCTAAAG
* ** *
837430 GAATAATATGTACGACAAACTCTAAAG
1 GAATGATATGTGTGACGAACTCTAAAG
* * ** *
837457 GAACGGTATGTGTGGTGAACTCTGAAG
1 GAATGATATGTGTGACGAACTCTAAAG
837484 GA
1 GA
837486 TTAGTACGTA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (27 bp):
GAATGATATGTGTGACGAACTCTAAAG
Found at i:842510 original size:50 final size:50
Alignment explanation
Indices: 842399--842689 Score: 316
Period size: 50 Copynumber: 5.7 Consensus size: 50
842389 ATTTGGGTAA
* * *
842399 AGAGATCCCATGTACGACCATGTCTGGGACATGGC-ATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGA-TGGCA-C--CGAG---ATG
842455 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * *
842505 AGAGGTCCCATGTAAGACTATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * **
842555 AGAGGCCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * *
842605 AGAGGTCCCGTGTAAGACCATGTCTGGGACATGGC-ATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGAT-GGCACCGAGATG
** ** * * *
842655 AGAACTCTTATGTAAGACCATATGTGGGATATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
842690 ATTGGCAGTA
Statistics
Matches: 208, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.00
50 164 0.79
53 3 0.01
55 1 0.00
56 38 0.18
57 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
Found at i:842683 original size:150 final size:154
Alignment explanation
Indices: 842405--842696 Score: 387
Period size: 150 Copynumber: 1.9 Consensus size: 154
842395 GTAAAGAGAT
* *
842405 CCCATGTACGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-T-AGATGATGAGAGGTCCCATGTAA
** * * *
842470 GACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAGGTCCCATGTAAGACTATGTTTGGGAC
64 GACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGAC
*
842535 ATGGCGTTGGCACCGAGATGAGAGGC
129 ATGGCATTGGCACCGAGATGAGAGGC
* *
842561 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CA-A-A-GATGAGAGGTCCCGTGTAAGA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATGATGAGAGGTCCCATGTAAGA
* * ** *
842622 CCATGTCTGGGACATGGC-ATGGGCACCTATATGAGAACTCTTATGTAAGACCATATGTGGGATA
66 CCATGTCTGGGACATGGCGAT-GGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGACA
842686 TGGCATTGGCA
130 TGGCATTGGCA
842697 GTACAAGAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
149 2 0.02
150 80 0.67
151 1 0.01
152 1 0.01
155 2 0.02
156 34 0.28
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (154 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATGATGAGAGGTCCCATGTAAGA
CCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGACAT
GGCATTGGCACCGAGATGAGAGGC
Found at i:848521 original size:50 final size:50
Alignment explanation
Indices: 848410--848697 Score: 373
Period size: 50 Copynumber: 5.7 Consensus size: 50
848400 ATTTGGGTAA
* ** *
848410 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCA-C--CGAG---ATG
*
848466 AGAGGTCCCATGTAAGACCATGTCTGGGACACGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
* * *
848516 AGAGGTCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGTACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
848565 AGAGGTCCCATGTAAGA-CATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
* * *
848614 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
** * *
848664 AGAGGTCCCCCGTAAGACCATGTTTGGGGCATGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
848698 CATGGGCAGC
Statistics
Matches: 212, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
48 11 0.05
49 67 0.32
50 92 0.43
53 3 0.01
55 1 0.00
56 38 0.18
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
Found at i:848632 original size:148 final size:152
Alignment explanation
Indices: 848409--848691 Score: 412
Period size: 148 Copynumber: 1.9 Consensus size: 152
848399 CATTTGGGTA
*
848409 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATGAGAGGTCC
* *
848474 CATGTAAGACCATGTCTGGGACACGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGT
63 CATGTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGT
848539 CTGGGAATGGCGTTGGTACCGAGAT
128 CTGGGAATGGCGTTGGTACCGAGAT
* **
848564 AAGAGGTCCCATGTAAGA-CATGTCTGGGACATGGTGTTGGCA-C-CGAG-ATGAGAGGTCCCAT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCAT
* * * * *
848625 GTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATTAGAGGTCCCCCGTAAGACCATGTTTG
66 GTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGTCTG
848690 GG
131 GG
848692 GCATGGCATG
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
148 74 0.63
151 3 0.03
153 1 0.01
154 22 0.19
155 17 0.15
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (152 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCAT
GTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGTCTG
GGAATGGCGTTGGTACCGAGAT
Found at i:848734 original size:100 final size:98
Alignment explanation
Indices: 848415--848755 Score: 313
Period size: 98 Copynumber: 3.4 Consensus size: 98
848405 GGTAAAGAGA
* * *
848415 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCA---AGA-TA--AGAGGTCCCACGTA
* ** * **
848480 AGACCATGTCTGGGACACGGTGTTGGCACCGAGATGAGAGG
59 AGA-CATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
848521 TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGTACCGAGATAAGAGGTCCCATGTAAGACATG
1 TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGACATG
** * **
848586 TCTGGGACATGGTGTTGGCACCGAGATGAGAGG
66 TCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
848619 TCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATTAGAGGTCCCCCGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGA-CA
* * * * *
848684 TGTTTGGGGCATGGCATGGGCAGCTATATGAGAAC
64 TGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
** * *
848719 TTTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCA
848756 GTACAAGAAG
Statistics
Matches: 204, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
98 59 0.29
99 48 0.24
100 57 0.28
101 2 0.01
102 3 0.01
105 11 0.05
106 24 0.12
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (98 bp):
TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGACATG
TCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:851445 original size:22 final size:22
Alignment explanation
Indices: 851420--851463 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
851410 CACTAATCAC
851420 AATAAGCTTATATTTGACTAGA
1 AATAAGCTTATATTTGACTAGA
* *
851442 AATAAGTTTATATTTTACTAGA
1 AATAAGCTTATATTTGACTAGA
851464 TTATGACATG
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:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
AATAAGCTTATATTTGACTAGA
Found at i:861591 original size:10 final size:11
Alignment explanation
Indices: 861567--861600 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
861557 GAAAAGTTGC
861567 AGAAAAACCTA
1 AGAAAAACCTA
861578 AGAAAAACCT-
1 AGAAAAACCTA
*
861588 AGAAAAAACTA
1 AGAAAAACCTA
861599 AG
1 AG
861601 GTTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.65, C:0.15, G:0.12, T:0.09
Consensus pattern (11 bp):
AGAAAAACCTA
Found at i:864198 original size:46 final size:44
Alignment explanation
Indices: 864133--864218 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 44
864123 ATAGTGTGGT
* * *
864133 GTTCATCATACCAAGGTTCCTATCATCCTTGATAGTGGGTTGAG
1 GTTCATCATACCAAGGTTCCTACCATACTTGATAGAGGGTTGAG
*
864177 GTTCATCTTATACCAAGGTTCCTACCATAGTTGATAGAGGGT
1 GTTCATC--ATACCAAGGTTCCTACCATACTTGATAGAGGGT
864219 CAAGGTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 7 0.19
46 29 0.81
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (44 bp):
GTTCATCATACCAAGGTTCCTACCATACTTGATAGAGGGTTGAG
Found at i:867129 original size:17 final size:18
Alignment explanation
Indices: 867109--867147 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
867099 CTACTTCTTC
867109 TTTAGGTTAATT-AGAGT
1 TTTAGGTTAATTGAGAGT
* *
867126 TTTAGTTTACTTGAGAGT
1 TTTAGGTTAATTGAGAGT
867144 TTTA
1 TTTA
867148 TTTGGATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (18 bp):
TTTAGGTTAATTGAGAGT
Found at i:869010 original size:2 final size:2
Alignment explanation
Indices: 869003--869554 Score: 1095
Period size: 2 Copynumber: 276.0 Consensus size: 2
868993 CACGCGCATT
869003 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869045 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869087 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869129 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869171 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869213 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869255 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869297 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869339 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869381 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869423 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869465 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
869507 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
869549 CA CA CA
1 CA CA CA
869555 TTATTGCTTT
Statistics
Matches: 548, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 548 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:870475 original size:29 final size:31
Alignment explanation
Indices: 870410--870479 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
870400 CCTACAAAAA
* **
870410 TAGTCACTTTTGTTTGACTTAGATTACATTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
*
870441 TAGTCACTTATGTTTGAAAT-G-TTACGTTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
870470 TAGTCACTTA
1 TAGTCACTTA
870480 CATTATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.49
30 1 0.03
31 17 0.49
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (31 bp):
TAGTCACTTATGTTTGAAATAGATTACATTT
Found at i:870950 original size:55 final size:55
Alignment explanation
Indices: 870866--870973 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
870856 ATTGACAGTT
870866 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
1 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
870921 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAG
1 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAG
870974 CCTTTTGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (55 bp):
TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
Found at i:879534 original size:25 final size:23
Alignment explanation
Indices: 879506--879557 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
879496 TTTTTTATAT
879506 TTTTTTATAAGAATATGTTTTTGAA
1 TTTTTTAT-A-AATATGTTTTTGAA
*
879531 TTTTTTATAATTATGTTTTTGAA
1 TTTTTTATAAATATGTTTTTGAA
879554 TTTT
1 TTTT
879558 AGAATTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 17 0.65
24 1 0.04
25 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTTTATAAATATGTTTTTGAA
Found at i:879563 original size:21 final size:22
Alignment explanation
Indices: 879515--879563 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
879505 TTTTTTTATA
879515 AGAA-TATGTTTTTGAATTTTTT
1 AGAATTATGTTTTTGAA-TTTTT
*
879537 ATAATTATGTTTTTGAA-TTTT
1 AGAATTATGTTTTTGAATTTTT
879558 AGAATT
1 AGAATT
879564 GAGACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (22 bp):
AGAATTATGTTTTTGAATTTTT
Found at i:882111 original size:25 final size:25
Alignment explanation
Indices: 882064--882111 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
882054 ATTGTTAATC
** *
882064 GTTTTTTTTTTTATTTTTTGTTGTT
1 GTTTTTTTTTTTAAATTTGGTTGTT
882089 GTTTTTTTTTTTAAATTTGGTTG
1 GTTTTTTTTTTTAAATTTGGTTG
882112 CTATTTATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (25 bp):
GTTTTTTTTTTTAAATTTGGTTGTT
Found at i:885570 original size:23 final size:23
Alignment explanation
Indices: 885514--885600 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
885504 TCTCTGTGAC
* * *
885514 GCCTTTGTAGAGTATTTTGTAAA
1 GCCTTTGTGGTGTATTCTGTAAA
885537 GCCTTTGTGGTGTATTCTGTAAA
1 GCCTTTGTGGTGTATTCTGTAAA
* * * *
885560 GCCTTTTTGGTGTATTCAGTGAT
1 GCCTTTGTGGTGTATTCTGTAAA
* *
885583 GCCTGTGTGGTATATTCT
1 GCCTTTGTGGTGTATTCT
885601 ATGACATTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (23 bp):
GCCTTTGTGGTGTATTCTGTAAA
Found at i:905414 original size:45 final size:45
Alignment explanation
Indices: 905345--905435 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
905335 ATTTAAAGAC
* * *
905345 AAAATGGGCCAGTATGCGAGATAGGAAATAAGTGGTGCCAAAAAT
1 AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
*
905390 AAAATGGGCCAGCATGTGAAATAGGAAAGAAGTGGTGCCAAAAAT
1 AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
905435 A
1 A
905436 CAAAGTGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (45 bp):
AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
Found at i:909583 original size:26 final size:26
Alignment explanation
Indices: 909547--909608 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
909537 CCTGTAAGTG
*
909547 TTCTAAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* **
909573 TTCTGAAACTGATATATTTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
909599 TTCTGAAACT
1 TTCTGAAACT
909609 ACTGTAGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:919890 original size:15 final size:15
Alignment explanation
Indices: 919870--919901 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
919860 CCCAATTTCG
919870 GCACAAGTAGATGCT
1 GCACAAGTAGATGCT
919885 GCACAAGTAGATGCT
1 GCACAAGTAGATGCT
919900 GC
1 GC
919902 CCAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (15 bp):
GCACAAGTAGATGCT
Found at i:921337 original size:7 final size:7
Alignment explanation
Indices: 921325--921364 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
921315 ACATTACTAA
921325 TTTATTC
1 TTTATTC
921332 TTTATTC
1 TTTATTC
*
921339 TTTATTT
1 TTTATTC
921346 TTTATT-
1 TTTATTC
921352 TTTATTC
1 TTTATTC
921359 TTTATT
1 TTTATT
921365 TGTGATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTATTC
Found at i:921357 original size:20 final size:21
Alignment explanation
Indices: 921325--921365 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
921315 ACATTACTAA
921325 TTTATTCTTTATTCTTTATTT
1 TTTATTCTTTATTCTTTATTT
921346 TTTATT-TTTATTCTTTATTT
1 TTTATTCTTTATTCTTTATTT
921366 GTGATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTCTTTATTCTTTATTT
Found at i:921372 original size:20 final size:20
Alignment explanation
Indices: 921332--921372 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
921322 TAATTTATTC
* *
921332 TTTATTCTTTATTTTTTATT
1 TTTATTCTTTATTTGTGATT
921352 TTTATTCTTTATTTGTGATT
1 TTTATTCTTTATTTGTGATT
921372 T
1 T
921373 ATTTATCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTATTCTTTATTTGTGATT
Found at i:921372 original size:27 final size:28
Alignment explanation
Indices: 921325--921378 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
921315 ACATTACTAA
*
921325 TTTATTCTTTATTCTTTATTT-TTTATT
1 TTTATTCTTTATTCTTGATTTATTTATT
921352 TTTATTCTTTATT-TGTGATTTATTTAT
1 TTTATTCTTTATTCT-TGATTTATTTAT
921379 CAGGTGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 18 0.75
28 5 0.21
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTATTCTTTATTCTTGATTTATTTATT
Found at i:923027 original size:25 final size:25
Alignment explanation
Indices: 922976--923027 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
922966 ACTAGTAAAA
*
922976 TTATCTCCTCAAAAAACTTGTAGAT
1 TTATCTCCTCAAAAAACTTGTACAT
* *
923001 TTATCTCCTCAAAAAAGTTGTCCAT
1 TTATCTCCTCAAAAAACTTGTACAT
923026 TT
1 TT
923028 CAACCTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (25 bp):
TTATCTCCTCAAAAAACTTGTACAT
Found at i:923884 original size:46 final size:46
Alignment explanation
Indices: 923814--924000 Score: 367
Period size: 46 Copynumber: 4.1 Consensus size: 46
923804 TATTAAATTT
923814 TTGA-AAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
1 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
923859 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
1 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
923905 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
1 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
923951 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
1 TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
923997 TTGA
1 TTGA
924001 TTATTTTATT
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
45 4 0.03
46 137 0.97
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (46 bp):
TTGAGAAAATAGCCATAAAACATGTCGAAAAACACGATACTATGAA
Found at i:928128 original size:5 final size:5
Alignment explanation
Indices: 928114--928144 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
928104 GCATTGGAAC
928114 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
928145 CTTGGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:928996 original size:15 final size:16
Alignment explanation
Indices: 928978--929008 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
928968 ATAAAATGGT
928978 TACC-AAAAAAAGGTG
1 TACCAAAAAAAAGGTG
928993 TACCAAAAAAAAGGTG
1 TACCAAAAAAAAGGTG
929009 GAATCACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (16 bp):
TACCAAAAAAAAGGTG
Found at i:931176 original size:26 final size:26
Alignment explanation
Indices: 931096--931176 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
931086 TTCGATCACG
931096 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
931122 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
931147 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
931173 TGTG
1 TGTG
931177 AACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:931269 original size:46 final size:43
Alignment explanation
Indices: 931178--931262 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
931168 TACTATGTGA
*
931178 ACCGGTATCATTAATTATAAGGTGGTTGTTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGTTATGTGCTGATCCC
* *
931221 ACCGGATATCATTGATTACAAAGGGTGGTTGTTGTGTGCTGA
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGTTATGTGCTGA
931263 ATCCACCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 2 0.06
46 18 0.50
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGTTATGTGCTGATCCC
Found at i:931421 original size:16 final size:16
Alignment explanation
Indices: 931400--931431 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
931390 TGATTGAAAG
*
931400 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
931416 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
931432 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:934820 original size:19 final size:18
Alignment explanation
Indices: 934773--934819 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
934763 ATTTTAAAAT
934773 TTTTATTTTTAACT-TTAA
1 TTTTATTTTTAA-TGTTAA
934791 TTTCTATTTTTAATGTTAA
1 TTT-TATTTTTAATGTTAA
934810 TTTTATTTTT
1 TTTTATTTTT
934820 TTATGTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATTTTTAATGTTAA
Found at i:934829 original size:20 final size:20
Alignment explanation
Indices: 934770--934830 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
934760 TTAATTTTAA
* *
934770 AATTTTTATTTTTAA-CTTT
1 AATTTCTATTTTTAATGTTT
934789 AATTTCTATTTTTAATG-TT
1 AATTTCTATTTTTAATGTTT
*
934808 AATTT-TATTTTTTTATGTTT
1 AATTTCTA-TTTTTAATGTTT
934828 AAT
1 AAT
934831 AAGGGGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.06
19 29 0.81
20 5 0.14
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
AATTTCTATTTTTAATGTTT
Found at i:937614 original size:22 final size:23
Alignment explanation
Indices: 937574--937624 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
937564 AAAAGAAGAA
**
937574 TCAAAGAACAAAGCTAAGTTT-C
1 TCAAAGAACAAAGAAAAGTTTGC
937596 TTCAAAG-ACAAAGAAAAGTTTGC
1 -TCAAAGAACAAAGAAAAGTTTGC
937619 TCAAAG
1 TCAAAG
937625 TCTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (23 bp):
TCAAAGAACAAAGAAAAGTTTGC
Found at i:941393 original size:5 final size:5
Alignment explanation
Indices: 941385--941413 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
941375 GATGGTATGG
941385 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
941414 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:945158 original size:19 final size:19
Alignment explanation
Indices: 945123--945167 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
945113 CCCAATCTCC
*
945123 AAAATAATTAAACAGCCTA
1 AAAATAATTAAACAGCCCA
*
945142 AAAATGAATTACA-AGCCCA
1 AAAAT-AATTAAACAGCCCA
945161 AAAATAA
1 AAAATAA
945168 GAAAAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 15 0.65
20 6 0.26
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.18
Consensus pattern (19 bp):
AAAATAATTAAACAGCCCA
Found at i:946743 original size:38 final size:39
Alignment explanation
Indices: 946681--946757 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
946671 CACACCTATT
946681 TTAATTCATACACACATGTACATATGCATTATTTATTTTG
1 TTAATTCATA-ACACATGTACATATGCATTATTTATTTTG
946721 TTAATTCAT-ACACATGTACATATGCATTATTTATTTT
1 TTAATTCATAACACATGTACATATGCATTATTTATTTT
946758 TAAATTGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 28 0.76
40 9 0.24
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.47
Consensus pattern (39 bp):
TTAATTCATAACACATGTACATATGCATTATTTATTTTG
Found at i:963724 original size:9 final size:10
Alignment explanation
Indices: 963706--963734 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
963696 CTAGATAACA
963706 AATCATATAT
1 AATCATATAT
963716 AAT-ATATAT
1 AATCATATAT
963725 AATCATATAT
1 AATCATATAT
963735 TATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCATATAT
Found at i:963837 original size:27 final size:28
Alignment explanation
Indices: 963780--963838 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
963770 AAATTCAAAA
* *
963780 TTTTAAATATTTATCGGGTTAGGTCGTT
1 TTTTAAATATTTATCGGATTAGGTCGAT
* *
963808 TTTTAAATATTTGT-GGATTAGGTTGAT
1 TTTTAAATATTTATCGGATTAGGTCGAT
963835 TTTT
1 TTTT
963839 GAAAATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.22, C:0.03, G:0.20, T:0.54
Consensus pattern (28 bp):
TTTTAAATATTTATCGGATTAGGTCGAT
Found at i:969826 original size:50 final size:50
Alignment explanation
Indices: 969759--969904 Score: 175
Period size: 50 Copynumber: 2.9 Consensus size: 50
969749 TTTTCTGTAC
* * **
969759 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATAACAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACAA
* ** ** **
969809 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACAA
* *
969859 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATA
969905 GTCTCAATGA
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACAA
Found at i:976185 original size:50 final size:50
Alignment explanation
Indices: 976092--976289 Score: 162
Period size: 50 Copynumber: 3.8 Consensus size: 50
976082 TTTTCTGTAT
* * * ** * ** *
976092 TGCCAATGTCATATCCCAGATATGGAATTACATGGGAGTTCTCATAACAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
* * * * *
976142 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
* * *
976192 TGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATA---TC-A-G
* * *
976247 ATGCCAATGCCATGTTCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
976290 TTACCCAAAT
Statistics
Matches: 116, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
50 75 0.65
53 2 0.02
55 1 0.01
56 38 0.33
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCAG
Found at i:979452 original size:18 final size:19
Alignment explanation
Indices: 979426--979462 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
979416 AATTTTGGAA
979426 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
979444 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
979463 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Done.