Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 10 of 135
Found at i:4522477 original size:31 final size:29
Alignment explanation
Indices: 4522412--4522481 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
4522402 AAATCAAAAT
**
4522412 TTCATGTATACAATTGCACAAAATTAAAG
1 TTCATGTATACAATTGCACAAAACCAAAG
*
4522441 TTCATGTATACAATTGCACATTAAACCATAG
1 TTCATGTATACAATTGCACA--AAACCAAAG
4522472 TTCATGTATA
1 TTCATGTATA
4522482 GTTTTGGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 20 0.56
31 16 0.44
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (29 bp):
TTCATGTATACAATTGCACAAAACCAAAG
Found at i:4535847 original size:3 final size:3
Alignment explanation
Indices: 4535839--4535869 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
4535829 CTTCTGGATG
4535839 ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
4535870 CGCAGAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4537767 original size:29 final size:29
Alignment explanation
Indices: 4537733--4537788 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
4537723 TATTGGAGAG
4537733 AAAAACTAGTAAGGAATGAAGTAAATACT
1 AAAAACTAGTAAGGAATGAAGTAAATACT
4537762 AAAAACTAGTAAGGAATGAAGTAAATA
1 AAAAACTAGTAAGGAATGAAGTAAATA
4537789 ATAACCTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (29 bp):
AAAAACTAGTAAGGAATGAAGTAAATACT
Found at i:4538873 original size:159 final size:160
Alignment explanation
Indices: 4538582--4538886 Score: 542
Period size: 159 Copynumber: 1.9 Consensus size: 160
4538572 CATGATCCTG
4538582 ATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTTCTTTTTTAACT
1 ATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTTCTTTTTTAACT
* * *
4538647 AAGATATAACATAAGAAATCAAAAGATCAGAGGAAGAAATCCAAACTAACCTGCGCCCAACTTGA
66 AAGATATAACATAAGAAATCAAAAGATCAGAGAAAGAAATCCAAACTAACCTGCGACCAACTGGA
4538712 TCTGGAGCGTTCATCTCGTTGGTGATCTTC
131 TCTGGAGCGTTCATCTCGTTGGTGATCTTC
*
4538742 ATCCCCTGACACCGCCTGCGAACATTATCAAACTCAATCAGCAA-TTTTTTTTTCTTTTTTAACT
1 ATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTTCTTTTTTAACT
*
4538806 AAGATATAACATAAGAAATCAAAAGATCAG-GAAAAGAAATCCAAACTAACCTGCGACGAACTGG
66 AAGATATAACATAAGAAATCAAAAGATCAGAG-AAAGAAATCCAAACTAACCTGCGACCAACTGG
4538870 ATCTGGAGCGTTCATCT
130 ATCTGGAGCGTTCATCT
4538887 TGAGACTCAT
Statistics
Matches: 139, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
158 1 0.01
159 95 0.68
160 43 0.31
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (160 bp):
ATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTTCTTTTTTAACT
AAGATATAACATAAGAAATCAAAAGATCAGAGAAAGAAATCCAAACTAACCTGCGACCAACTGGA
TCTGGAGCGTTCATCTCGTTGGTGATCTTC
Found at i:4544463 original size:18 final size:19
Alignment explanation
Indices: 4544440--4544479 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
4544430 TAATAAATTA
4544440 TTTATTT-GCCAGTTGTTT
1 TTTATTTAGCCAGTTGTTT
4544458 TTTATTTCAAGCCAGTTGTTT
1 TTTATTT--AGCCAGTTGTTT
4544479 T
1 T
4544480 CCATTTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
21 12 0.63
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (19 bp):
TTTATTTAGCCAGTTGTTT
Found at i:4545000 original size:14 final size:14
Alignment explanation
Indices: 4544971--4545013 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
4544961 TTTATATAGA
*
4544971 TAAAAAGTTATTAAT
1 TAAAAAG-TATAAAT
4544986 TAAAAAGTATAAAT
1 TAAAAAGTATAAAT
4545000 TAAAATA-TATAAAT
1 TAAAA-AGTATAAAT
4545014 ATTTCATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (14 bp):
TAAAAAGTATAAAT
Found at i:4545033 original size:24 final size:24
Alignment explanation
Indices: 4544998--4545052 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
4544988 AAAAGTATAA
* *
4544998 ATTAAAAT-ATATAAATATTTCAT
1 ATTAAATTCATATAAATAGTTCAT
* * *
4545021 ATTTAATTCATATAGATCGTTCAT
1 ATTAAATTCATATAAATAGTTCAT
4545045 ATTAAATT
1 ATTAAATT
4545053 TAACATAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTAAATTCATATAAATAGTTCAT
Found at i:4548313 original size:7 final size:7
Alignment explanation
Indices: 4548301--4548350 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
4548291 TATTTTTCTC
4548301 AAATTTA
1 AAATTTA
4548308 AAATTTA
1 AAATTTA
4548315 AAATTTA
1 AAATTTA
4548322 AAATTTA
1 AAATTTA
4548329 AAATTTA
1 AAATTTA
4548336 AAATTTA
1 AAATTTA
4548343 AAATTTA
1 AAATTTA
4548350 A
1 A
4548351 TTTCTATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:4555053 original size:13 final size:13
Alignment explanation
Indices: 4555035--4555062 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4555025 AACAACCACC
4555035 ATTAAATTAGTTT
1 ATTAAATTAGTTT
4555048 ATTAAATTAGTTT
1 ATTAAATTAGTTT
4555061 AT
1 AT
4555063 AGTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTAAATTAGTTT
Found at i:4557129 original size:6 final size:6
Alignment explanation
Indices: 4557118--4557162 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
4557108 AAGAGCAGAG
4557118 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATG
4557163 AAAAAGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
ATGGAA
Found at i:4561037 original size:15 final size:16
Alignment explanation
Indices: 4561017--4561046 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4561007 AAAAACAATC
4561017 CAATAT-TTTAAAAAT
1 CAATATATTTAAAAAT
4561032 CAATATATTTAAAAA
1 CAATATATTTAAAAA
4561047 AAAATGTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
CAATATATTTAAAAAT
Found at i:4563500 original size:23 final size:23
Alignment explanation
Indices: 4563468--4563515 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4563458 TAAAAGTAAA
4563468 TTTTCATTTGTACTGCCTTACTT
1 TTTTCATTTGTACTGCCTTACTT
* *
4563491 TTTTCTTTTGTACTGCCTTTCTT
1 TTTTCATTTGTACTGCCTTACTT
4563514 TT
1 TT
4563516 CCCATGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.08, C:0.21, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTTCATTTGTACTGCCTTACTT
Found at i:4567012 original size:7 final size:7
Alignment explanation
Indices: 4567000--4567025 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4566990 CCATCACATG
4567000 ATGCACC
1 ATGCACC
4567007 ATGCACC
1 ATGCACC
4567014 ATGCACC
1 ATGCACC
4567021 ATGCA
1 ATGCA
4567026 TCATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCACC
Found at i:4577453 original size:14 final size:14
Alignment explanation
Indices: 4577434--4577463 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4577424 AGGGTTTAAA
4577434 AATTTTAATTAATT
1 AATTTTAATTAATT
*
4577448 AATTTTATTTAATT
1 AATTTTAATTAATT
4577462 AA
1 AA
4577464 AAATTTATTC
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTTAATTAATT
Found at i:4583954 original size:49 final size:49
Alignment explanation
Indices: 4583895--4584044 Score: 248
Period size: 49 Copynumber: 3.1 Consensus size: 49
4583885 AAGAAAAAAG
* *
4583895 CATGTAGAAGTCTAATATCCTTGAAAGGCAACCTACAAAGAATCACTAT
1 CATGTAGAAGTCTAATATCCTTCAACGGCAACCTACAAAGAATCACTAT
* *
4583944 CATGTAGAAGTCCAATATCCTTCAACGGGAACCTACAAAGAATCACTAT
1 CATGTAGAAGTCTAATATCCTTCAACGGCAACCTACAAAGAATCACTAT
4583993 CATGTAGAAGTCTAATATCCTTCAACGGCAACCTACAAAGAAAT-ACTAT
1 CATGTAGAAGTCTAATATCCTTCAACGGCAACCTACAAAG-AATCACTAT
4584042 CAT
1 CAT
4584045 AAAATATTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 91 0.97
50 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.24
Consensus pattern (49 bp):
CATGTAGAAGTCTAATATCCTTCAACGGCAACCTACAAAGAATCACTAT
Found at i:4593227 original size:25 final size:25
Alignment explanation
Indices: 4593199--4593249 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
4593189 TCATTTTATG
4593199 TTTATATAT-TATATATAAAAATAAT
1 TTTATATATCTA-ATATAAAAATAAT
*
4593224 TTTATTTATCTAATATAAAAATAAT
1 TTTATATATCTAATATAAAAATAAT
4593249 T
1 T
4593250 GATGTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTATATATCTAATATAAAAATAAT
Found at i:4593898 original size:28 final size:29
Alignment explanation
Indices: 4593849--4593903 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
4593839 TTTGATTCTT
*
4593849 TTTAATAGTATAAAAATAAA-TTGATCCA
1 TTTAATAGTAGAAAAATAAATTTGATCCA
** *
4593877 TTTAATAGTAGATGAATTAATTTGATC
1 TTTAATAGTAGAAAAATAAATTTGATC
4593904 AAATATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.73
29 6 0.27
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (29 bp):
TTTAATAGTAGAAAAATAAATTTGATCCA
Found at i:4613820 original size:33 final size:33
Alignment explanation
Indices: 4613781--4613856 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
4613771 GCCAAATAAT
* *
4613781 AAAAAATATTTTACACATATTCATCCAAATACC
1 AAAAAATATTTTACACATATTCATCCAAACACA
* *
4613814 AGAAAATATTTTACACATATTCATTCAAACACA
1 AAAAAATATTTTACACATATTCATCCAAACACA
4613847 AAAAAATATT
1 AAAAAATATT
4613857 AACTTTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (33 bp):
AAAAAATATTTTACACATATTCATCCAAACACA
Found at i:4620085 original size:22 final size:21
Alignment explanation
Indices: 4620046--4620089 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
4620036 AGCCTTTATT
4620046 TTGAAAAGCAGTTGTTAATGAC
1 TTGAAAAGCAGTTGTTAA-GAC
*
4620068 TTGAAATGACAGTT-TTAAGAC
1 TTGAAAAG-CAGTTGTTAAGAC
4620089 T
1 T
4620090 ACAAGTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (21 bp):
TTGAAAAGCAGTTGTTAAGAC
Found at i:4639524 original size:29 final size:28
Alignment explanation
Indices: 4639480--4639584 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
4639470 TTAATATAAT
* *
4639480 ATTTGGTACTTGAACTTGACATTTTTTTA
1 ATTTGGTACCTAAACTTG-CATTTTTTTA
4639509 ATTTGGTACCTAAACTT---TTTTTTGACTCA
1 ATTTGGTACCTAAACTTGCATTTTTT---T-A
* * *
4639538 ATTTGGTACTTGAACTTGGCATTTTTCCTA
1 ATTTGGTACCTAAACTT-GCATTTTT-TTA
4639568 ATTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
4639585 TTTTTGAACC
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
25 6 0.10
28 1 0.02
29 31 0.52
30 16 0.27
31 1 0.02
33 5 0.08
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (28 bp):
ATTTGGTACCTAAACTTGCATTTTTTTA
Found at i:4639599 original size:59 final size:58
Alignment explanation
Indices: 4639480--4639669 Score: 220
Period size: 62 Copynumber: 3.2 Consensus size: 58
4639470 TTAATATAAT
* * *
4639480 ATTTGGTACTTGAACTTGACATTTTT-TTAATTTGGTACCTAAACTTTTTTTTGACTCA
1 ATTTGGTACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGACCCA
4639538 ATTTGGTACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTGAACCCA
1 ATTTGGTACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTG-ACCCA
* * * * * **
4639597 ATTTGATACCTGAACTTGGTATTTTTTTTCCTAATTTGGTACTTAAGCTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGGCA---TTTTTCCTAATTTGGTACCTAAACTTTTTTT-GACCCA
*
4639659 ATTTGTTACTT
1 ATTTGGTACTT
4639670 AAATTTATTA
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
58 33 0.29
59 39 0.34
62 41 0.36
63 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (58 bp):
ATTTGGTACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTGACCCA
Found at i:4639661 original size:62 final size:58
Alignment explanation
Indices: 4639480--4639663 Score: 208
Period size: 59 Copynumber: 3.1 Consensus size: 58
4639470 TTAATATAAT
* * * *
4639480 ATTTGGTACTTGAACTTGACATTTTT-TTAATTTGGTACCTAAACTTTTTTTTGACTCA
1 ATTTGATACCTGAACTTGGCATTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGACTCA
* * *
4639538 ATTTGGTACTTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTGAACCCA
1 ATTTGATACCTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTG-ACTCA
* * * *
4639597 ATTTGATACCTGAACTTGGTATTTTTTTTCCTAATTTGGTACTTAAGCTTTTTTTAGATTCA
1 ATTTGATACCTGAACTTGGCA---TTTTTCCTAATTTGGTACCTAAACTTTTTTT-GACTCA
4639659 ATTTG
1 ATTTG
4639664 TTACTTAAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
58 33 0.30
59 39 0.35
62 37 0.34
63 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (58 bp):
ATTTGATACCTGAACTTGGCATTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCA
Found at i:4639883 original size:67 final size:67
Alignment explanation
Indices: 4639810--4639947 Score: 276
Period size: 67 Copynumber: 2.1 Consensus size: 67
4639800 CGAAATAATA
4639810 TTAAAAAAATTAAGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCAAAAA
1 TTAAAAAAATTAAGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCAAAAA
4639875 GT
66 GT
4639877 TTAAAAAAATTAAGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCAAAAA
1 TTAAAAAAATTAAGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCAAAAA
4639942 GT
66 GT
4639944 TTAA
1 TTAA
4639948 GTACCAACTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (67 bp):
TTAAAAAAATTAAGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCAAAAA
GT
Found at i:4639976 original size:30 final size:31
Alignment explanation
Indices: 4639819--4640077 Score: 162
Period size: 31 Copynumber: 8.5 Consensus size: 31
4639809 ATTAAAAAAA
* *
4639819 TTAAGTATCAAATTAGAAAAAAGAGTCAAGT
1 TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
* * * * **
4639850 TTAGGTACCAAATTGGACCCAAAAAGTTTAAAAAAA
1 TTAAGTACCAAATTAGA---AAAAAGTGT--CAAGT
* *
4639886 TTAAGTATCAAATTAGAAAAAAGAGTCAAGT
1 TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
* * **
4639917 TTAGGTACCAAATTGGACCCAAA-----AAGT
1 TTAAGTACCAAATTAGA-AAAAAGTGTCAAGT
*
4639944 TTAAGTACCAACTTA-AAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
* *
4639974 TTAGGTACCAAATTAGGAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
* *
4640005 TTGAGTACCAAATTGGATCAAAAA-----AAGT
1 TTAAGTACCAAATTAGA--AAAAAGTGTCAAGT
* * *
4640033 TTAGGTATCAAATTAAAAAAAAGTGTCAAGT
1 TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
*
4640064 TCAAGTACCAAATT
1 TTAAGTACCAAATT
4640078 TCATATTAAG
Statistics
Matches: 168, Mismatches: 41, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
25 3 0.02
26 6 0.04
27 16 0.10
28 16 0.10
30 17 0.10
31 72 0.43
32 3 0.02
33 12 0.07
34 7 0.04
36 16 0.10
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (31 bp):
TTAAGTACCAAATTAGAAAAAAGTGTCAAGT
Found at i:4639986 original size:88 final size:90
Alignment explanation
Indices: 4639888--4640077 Score: 260
Period size: 88 Copynumber: 2.1 Consensus size: 90
4639878 TAAAAAAATT
* **
4639888 AAGTATCAAATTAGAAAAAAGAGTCAAGTTT-AGGTACCAAATTGGA-CCCAAAAAGTTTAAGTA
1 AAGTACCAAATTAGAAAAAAGAGTCAAGTTTGA-GTACCAAATTGGATCAAAAAAAGTTTAAGTA
* *
4639951 CCAACTT-AAAAAAAGTGTCAAGTTT
65 CCAAATTAAAAAAAAGTGTCAAGTTC
* * * * *
4639976 AGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAGTTTAGGTAT
1 AAGTACCAAATTAGAAAAAAGAGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAGTTTAAGTAC
4640041 CAAATTAAAAAAAAGTGTCAAGTTC
66 CAAATTAAAAAAAAGTGTCAAGTTC
4640066 AAGTACCAAATT
1 AAGTACCAAATT
4640078 TCATATTAAG
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 40 0.45
89 20 0.23
90 28 0.32
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (90 bp):
AAGTACCAAATTAGAAAAAAGAGTCAAGTTTGAGTACCAAATTGGATCAAAAAAAGTTTAAGTAC
CAAATTAAAAAAAAGTGTCAAGTTC
Found at i:4641383 original size:12 final size:12
Alignment explanation
Indices: 4641366--4641390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4641356 TGAGTTTTTT
4641366 TTTTAAAGGTAA
1 TTTTAAAGGTAA
4641378 TTTTAAAGGTAA
1 TTTTAAAGGTAA
4641390 T
1 T
4641391 CATTATTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTTTAAAGGTAA
Found at i:4649677 original size:18 final size:17
Alignment explanation
Indices: 4649638--4649688 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
4649628 ATGTTACGTC
4649638 AATAAATAATTT-AAAAT
1 AATAAA-AATTTCAAAAT
*
4649655 TATAAAAATATTCAAAAT
1 AATAAAAAT-TTCAAAAT
*
4649673 AATAATAATTTTCAAA
1 AATAA-AAATTTCAAA
4649689 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.11
17 7 0.25
18 15 0.54
19 3 0.11
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAAAATTTCAAAAT
Found at i:4650483 original size:23 final size:26
Alignment explanation
Indices: 4650457--4650503 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4650447 CCAATATTTT
4650457 AAAT-ATAT-ATAT-ATTTATTAACA
1 AAATAATATCATATGATTTATTAACA
4650480 AAATAATATCATATGATTTATTAA
1 AAATAATATCATATGATTTATTAA
4650504 TAATACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 4 0.19
26 9 0.43
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
AAATAATATCATATGATTTATTAACA
Found at i:4657836 original size:4 final size:4
Alignment explanation
Indices: 4657827--4657894 Score: 100
Period size: 4 Copynumber: 17.0 Consensus size: 4
4657817 CTCTCAATCT
* * *
4657827 TGTA TGTA TGTA TGTA CGTA TGTA TGTA GGCA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
4657875 TGTA TGTA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA
4657895 AAGCTCAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.44
Consensus pattern (4 bp):
TGTA
Found at i:4673274 original size:27 final size:28
Alignment explanation
Indices: 4673222--4673277 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
4673212 AATTTGATCA
*
4673222 AATCAAAATTTTATATATAAAATTACAC
1 AATCAAAATTTCATATATAAAATTACAC
* *
4673250 AATCAAAA-TTCATGTATATAATTACAC
1 AATCAAAATTTCATATATAAAATTACAC
4673277 A
1 A
4673278 TTAAACCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (28 bp):
AATCAAAATTTCATATATAAAATTACAC
Found at i:4679267 original size:22 final size:23
Alignment explanation
Indices: 4679242--4679284 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4679232 ACTTGAATCT
4679242 TTAAATT-TAAAAAACAAAAAAA
1 TTAAATTCTAAAAAACAAAAAAA
* *
4679264 TTAAATTCTTAAAAATAAAAA
1 TTAAATTCTAAAAAACAAAAA
4679285 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAAATTCTAAAAAACAAAAAAA
Found at i:4679279 original size:15 final size:14
Alignment explanation
Indices: 4679259--4679304 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
4679249 TAAAAAACAA
4679259 AAAAATTAAATTCTT
1 AAAAATTAAATT-TT
* * *
4679274 AAAAATAAAAATTA
1 AAAAATTAAATTTT
4679288 AAAAATTAAATTTT
1 AAAAATTAAATTTT
4679302 AAA
1 AAA
4679305 TGCACAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTAAATTTT
Found at i:4680179 original size:18 final size:18
Alignment explanation
Indices: 4680156--4680194 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
4680146 CCAGGAGTTA
4680156 AAAGCTAAAAGAAAGAGT
1 AAAGCTAAAAGAAAGAGT
4680174 AAAGCTAAAAGAAAGAGT
1 AAAGCTAAAAGAAAGAGT
4680192 AAA
1 AAA
4680195 AGGACTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAGCTAAAAGAAAGAGT
Found at i:4681635 original size:24 final size:24
Alignment explanation
Indices: 4681608--4681664 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
4681598 ATATTTAAAA
*
4681608 GAATTATATTAAATATATAT-AATT
1 GAATT-TATTAAAAATATATAAATT
*
4681632 GAA-TTATTAAAAATATTTAAATT
1 GAATTTATTAAAAATATATAAATT
4681655 GAATTT-TTAA
1 GAATTTATTAA
4681665 CATTTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 12 0.41
23 12 0.41
24 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
GAATTTATTAAAAATATATAAATT
Found at i:4681639 original size:22 final size:23
Alignment explanation
Indices: 4681614--4681664 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
4681604 AAAAGAATTA
*
4681614 TATTAAATATATAT-AATTGAAT
1 TATTAAAAATATATAAATTGAAT
*
4681636 TATTAAAAATATTTAAATTGAAT
1 TATTAAAAATATATAAATTGAAT
*
4681659 TTTTAA
1 TATTAA
4681665 CATTTTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TATTAAAAATATATAAATTGAAT
Found at i:4682212 original size:19 final size:19
Alignment explanation
Indices: 4682182--4682238 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
4682172 TCAACAAAAA
4682182 TTATAAAAAATTCAAAATAAT
1 TTAT-AAAAATTCAAAAT-AT
*
4682203 TT-TTAAAATTCAAAATAT
1 TTATAAAAATTCAAAATAT
4682221 TTATAAAAATTTCAAAAT
1 TTATAAAAA-TTCAAAAT
4682239 GTATATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.12
19 17 0.53
20 9 0.28
21 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TTATAAAAATTCAAAATAT
Found at i:4682245 original size:20 final size:19
Alignment explanation
Indices: 4682178--4682245 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
4682168 TCTCTCAACA
4682178 AAAAT-TATA-AAAAATTC
1 AAAATATATATAAAAATTC
* *
4682195 AAAATA-ATTTTTAAAATTC
1 AAAATATA-TATAAAAATTC
*
4682214 AAAATATTTATAAAAATTTC
1 AAAATATATATAAAAA-TTC
*
4682234 AAAATGTATATA
1 AAAATATATATA
4682246 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 19 0.49
20 13 0.33
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAATATATATAAAAATTC
Found at i:4684053 original size:25 final size:24
Alignment explanation
Indices: 4684007--4684053 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4683997 TTTATTTTAA
*
4684007 CAAAATTTATCAACATAATATATT
1 CAAAATTTATAAACATAATATATT
* *
4684031 CAAAATATTATAAATATATTATA
1 CAAAAT-TTATAAACATAATATA
4684054 ATCCATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (24 bp):
CAAAATTTATAAACATAATATATT
Found at i:4687285 original size:22 final size:20
Alignment explanation
Indices: 4687229--4687292 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 20
4687219 TATAACTTGA
4687229 TAATAATG-TTTTGTTTTTT
1 TAATAATGTTTTTGTTTTTT
*
4687248 T-ATAATTTATTCTTGTTCTTTT
1 TAATAATGT-TT-TTGTT-TTTT
*
4687270 TAAATAATGTTTTTGTTATTT
1 T-AATAATGTTTTTGTTTTTT
4687291 TA
1 TA
4687293 TACTTTGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 3 0.08
21 9 0.25
22 10 0.28
23 2 0.06
24 6 0.17
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (20 bp):
TAATAATGTTTTTGTTTTTT
Found at i:4696263 original size:15 final size:17
Alignment explanation
Indices: 4696238--4696269 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4696228 AGAGATAGGA
4696238 AAATGGAA-TTTGGTAT
1 AAATGGAATTTTGGTAT
4696254 AAAT-GAATTTTGGTAT
1 AAATGGAATTTTGGTAT
4696270 TCCCCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (17 bp):
AAATGGAATTTTGGTAT
Found at i:4697717 original size:51 final size:52
Alignment explanation
Indices: 4697645--4697770 Score: 148
Period size: 52 Copynumber: 2.4 Consensus size: 52
4697635 TTTCATTTAA
* * *
4697645 TACTCACGAT-AACACTGAGTCATAGGACATTT-AATCCATCATGGATTCATT
1 TACTCACGATGAA-ACTTAGTCATAGGACATTTAAATCCATAAAGGATTCATT
* * * *
4697696 TACTCACGATGAAACTTAGTCATCGGACCTTTAAATTCGTAAAGGATTCATT
1 TACTCACGATGAAACTTAGTCATAGGACATTTAAATCCATAAAGGATTCATT
* *
4697748 TACTCACGATGACACTTTGTCAT
1 TACTCACGATGAAACTTAGTCAT
4697771 CGAATCCTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 26 0.41
52 38 0.59
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (52 bp):
TACTCACGATGAAACTTAGTCATAGGACATTTAAATCCATAAAGGATTCATT
Found at i:4701206 original size:2 final size:2
Alignment explanation
Indices: 4701194--4701241 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4701184 CTATTCTTTT
*
4701194 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4701236 TA TA TA
1 TA TA TA
4701242 ATTTTACGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4701323 original size:33 final size:32
Alignment explanation
Indices: 4701250--4701324 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
4701240 TAATTTTACG
*
4701250 TAATAATATTTTATGTTATATTTACCAAATATA
1 TAAT-ATATATTATGTTATATTTACCAAATATA
* *
4701283 TATATATATATTATGTTATAGTATTTCTAAATAT-
1 TA-ATATATATTATGTTATA-T-TTACCAAATATA
4701317 TAATATAT
1 TAATATAT
4701325 TTCCAATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 22 0.61
34 5 0.14
35 9 0.25
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (32 bp):
TAATATATATTATGTTATATTTACCAAATATA
Found at i:4703428 original size:19 final size:20
Alignment explanation
Indices: 4703406--4703444 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4703396 TCTTTTATAA
*
4703406 AATATAGATT-TTTTTATTT
1 AATATAGATTACTTTTATTT
*
4703425 AATATTGATTACTTTTATTT
1 AATATAGATTACTTTTATTT
4703445 TTTGAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
AATATAGATTACTTTTATTT
Found at i:4703914 original size:23 final size:23
Alignment explanation
Indices: 4703888--4703979 Score: 65
Period size: 23 Copynumber: 4.3 Consensus size: 23
4703878 TTTATATTGT
4703888 TGTTTTGGTGTTGTTTTTTTTAC
1 TGTTTTGGTGTTGTTTTTTTTAC
* * *
4703911 TGTTTT-G-GTTGCTATTTTTGC
1 TGTTTTGGTGTTGTTTTTTTTAC
4703932 TG-TTT--TG--GTTTTTTTTAC
1 TGTTTTGGTGTTGTTTTTTTTAC
* * *
4703950 TATTTTGGTTGCT-TTTTTTTTAT
1 TGTTTTGG-TGTTGTTTTTTTTAC
4703973 TGTTTTG
1 TGTTTTG
4703980 ATGCTATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
18 9 0.17
19 3 0.06
20 4 0.08
21 13 0.25
22 3 0.06
23 21 0.40
ACGTcount: A:0.05, C:0.05, G:0.20, T:0.70
Consensus pattern (23 bp):
TGTTTTGGTGTTGTTTTTTTTAC
Found at i:4703928 original size:21 final size:20
Alignment explanation
Indices: 4703903--4703967 Score: 89
Period size: 21 Copynumber: 3.3 Consensus size: 20
4703893 TGGTGTTGTT
4703903 TTTTTTACTGTTTTGGTTGC
1 TTTTTTACTGTTTTGGTTGC
*
4703923 TATTTTTGCTGTTTTGGTT--
1 T-TTTTTACTGTTTTGGTTGC
*
4703942 TTTTTTACTATTTTGGTTGC
1 TTTTTTACTGTTTTGGTTGC
4703962 TTTTTT
1 TTTTTT
4703968 TTTATTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 7 0.18
21 16 0.41
ACGTcount: A:0.06, C:0.08, G:0.17, T:0.69
Consensus pattern (20 bp):
TTTTTTACTGTTTTGGTTGC
Found at i:4703955 original size:18 final size:18
Alignment explanation
Indices: 4703900--4703959 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
4703890 TTTTGGTGTT
4703900 GTTTTTTTTACTGTTTTG
1 GTTTTTTTTACTGTTTTG
*
4703918 GTTGCTATTTTTGCTGTTTTG
1 GTT--T-TTTTTACTGTTTTG
*
4703939 GTTTTTTTTACTATTTTG
1 GTTTTTTTTACTGTTTTG
4703957 GTT
1 GTT
4703960 GCTTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 18 0.50
19 1 0.03
20 1 0.03
21 16 0.44
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (18 bp):
GTTTTTTTTACTGTTTTG
Found at i:4703968 original size:21 final size:21
Alignment explanation
Indices: 4703888--4703968 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
4703878 TTTATATTGT
*
4703888 TGTTTTGGTGTTGTTTTTTTTAC
1 TGTTTT-G-GTTGCTTTTTTTAC
* *
4703911 TGTTTTGGTTGCTATTTTTGC
1 TGTTTTGGTTGCTTTTTTTAC
4703932 TGTTTTGG-T--TTTTTTTAC
1 TGTTTTGGTTGCTTTTTTTAC
*
4703950 TATTTTGGTTGCTTTTTTT
1 TGTTTTGGTTGCTTTTTTT
4703969 TTATTGTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
18 14 0.29
19 1 0.02
20 1 0.02
21 26 0.53
22 1 0.02
23 6 0.12
ACGTcount: A:0.05, C:0.06, G:0.20, T:0.69
Consensus pattern (21 bp):
TGTTTTGGTTGCTTTTTTTAC
Found at i:4703984 original size:22 final size:24
Alignment explanation
Indices: 4703940--4704017 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 24
4703930 GCTGTTTTGG
* * *
4703940 TTTTTTTTACTATTTTGGTTGCT-
1 TTTTTTTTATTGTTTTGGATGCTA
4703963 TTTTTTTTATTGTTTT-GATGCTA
1 TTTTTTTTATTGTTTTGGATGCTA
* * *
4703986 TTATTTTTGTTGTTGTTTTTGTTGCTA
1 -T-TTTTT-TTATTGTTTTGGATGCTA
4704013 TTTTT
1 TTTTT
4704018 GTTGTTTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 5 0.11
23 14 0.31
24 1 0.02
25 9 0.20
26 10 0.22
27 6 0.13
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.72
Consensus pattern (24 bp):
TTTTTTTTATTGTTTTGGATGCTA
Found at i:4704004 original size:61 final size:61
Alignment explanation
Indices: 4703897--4704052 Score: 153
Period size: 61 Copynumber: 2.6 Consensus size: 61
4703887 TTGTTTTGGT
* * *
4703897 GTTG-TTTTTTTTACTGTTTTGGTTGCTATTTTTGCTGTTTTGGTTTTTTTTACTATTTTG
1 GTTGTTTTTTTTTATTGTTTTGGATGCTATTTTTGCTGTTTTGGTTTTTGTTACTATTTTG
* * *
4703957 GTTGCTTTTTTTTTATTGTTTT-GATGCTATTATTT-TTGTTGTT-GTTTTTGTTGCTATTTTT
1 GTTG-TTTTTTTTTATTGTTTTGGATGCTATT-TTTGCTGTT-TTGGTTTTTGTTACTATTTTG
* * * *
4704018 GTTG-TTTTTGTTATTATTTT-GCTGTTATTTTTGCT
1 GTTGTTTTTTTTTATTGTTTTGGATGCTATTTTTGCT
4704053 ACTATTTTGG
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
58 3 0.04
59 22 0.28
60 4 0.05
61 31 0.39
62 20 0.25
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (61 bp):
GTTGTTTTTTTTTATTGTTTTGGATGCTATTTTTGCTGTTTTGGTTTTTGTTACTATTTTG
Found at i:4704005 original size:27 final size:27
Alignment explanation
Indices: 4703975--4704029 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4703965 TTTTTTATTG
4703975 TTTTGATGCTATTATTT-TTGTTGTTGT
1 TTTTGATGCTATT-TTTGTTGTTGTTGT
* *
4704002 TTTTGTTGCTATTTTTGTTGTTTTTGT
1 TTTTGATGCTATTTTTGTTGTTGTTGT
4704029 T
1 T
4704030 ATTATTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.71
Consensus pattern (27 bp):
TTTTGATGCTATTTTTGTTGTTGTTGT
Found at i:4704021 original size:21 final size:21
Alignment explanation
Indices: 4703995--4704067 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
4703985 ATTATTTTTG
*
4703995 TTGTTGTTTTTGTTGCTATTT
1 TTGTTGTTTTTGTTACTATTT
*
4704016 TTGTTGTTTTTGTTATTATTT
1 TTGTTGTTTTTGTTACTATTT
* *
4704037 TGCTGTTATTTTTGCTACTATTT
1 T--TGTTGTTTTTGTTACTATTT
*
4704060 TGGTTGTT
1 TTGTTGTT
4704068 ATTTTGATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 25 0.58
23 18 0.42
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.68
Consensus pattern (21 bp):
TTGTTGTTTTTGTTACTATTT
Found at i:4704049 original size:44 final size:46
Alignment explanation
Indices: 4703966--4704067 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 46
4703956 GGTTGCTTTT
* * * * *
4703966 TTTTTATTGTTTTGATGCTATTATTTTTGTTGTTGTTTTTGTTGCTA
1 TTTTTGTTGTTTT-ATGCTATTATTTTTGCTGTTATTTTTGCTACTA
*
4704013 TTTTTGTTGTTTT-TGTTATTA-TTTTGCTGTTATTTTTGCTACTA
1 TTTTTGTTGTTTTATGCTATTATTTTTGCTGTTATTTTTGCTACTA
*
4704057 TTTTGGTTGTT
1 TTTTTGTTGTT
4704068 ATTTTGATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 29 0.60
45 7 0.15
47 12 0.25
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.69
Consensus pattern (46 bp):
TTTTTGTTGTTTTATGCTATTATTTTTGCTGTTATTTTTGCTACTA
Found at i:4704067 original size:24 final size:23
Alignment explanation
Indices: 4703981--4704072 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
4703971 ATTGTTTTGA
* *
4703981 TGCTATTATTTTTGTTGTTGTTTT
1 TGCTACTA-TTTTGTTGTTATTTT
* * *
4704005 TGTTGCTA-TTT-TTGTTGTTTT
1 TGCTACTATTTTGTTGTTATTTT
* * *
4704026 TGTTATTATTTTGCTGTTATTTT
1 TGCTACTATTTTGTTGTTATTTT
4704049 TGCTACTATTTTGGTTGTTATTTT
1 TGCTACTATTTT-GTTGTTATTTT
4704073 GATTGTTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
21 16 0.29
22 6 0.11
23 18 0.33
24 15 0.27
ACGTcount: A:0.10, C:0.05, G:0.16, T:0.68
Consensus pattern (23 bp):
TGCTACTATTTTGTTGTTATTTT
Found at i:4704073 original size:12 final size:12
Alignment explanation
Indices: 4703986--4704072 Score: 74
Period size: 12 Copynumber: 7.6 Consensus size: 12
4703976 TTTGATGCTA
4703986 TTATTTTTGTTG
1 TTATTTTTGTTG
*
4703998 TTGTTTTTGTTG
1 TTATTTTTGTTG
*
4704010 CTATTTTTGTTG
1 TTATTTTTGTTG
*
4704022 ---TTTTTGTTA
1 TTATTTTTGTTG
*
4704031 TTA-TTTTGCTG
1 TTATTTTTGTTG
* *
4704042 TTATTTTTGCTA
1 TTATTTTTGTTG
* *
4704054 CTATTTTGGTTG
1 TTATTTTTGTTG
4704066 TTATTTT
1 TTATTTT
4704073 GATTGTTTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 8 0.14
11 9 0.15
12 42 0.71
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.70
Consensus pattern (12 bp):
TTATTTTTGTTG
Found at i:4704143 original size:23 final size:23
Alignment explanation
Indices: 4704099--4704143 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4704089 TTTTTATGCG
* * *
4704099 TTTTTATTATTGTTTCATTATTT
1 TTTTTAATATTATTTCAATATTT
*
4704122 TTTTTAATATTATTTGAATATT
1 TTTTTAATATTATTTCAATATT
4704144 CTAGAACTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTAATATTATTTCAATATTT
Found at i:4704233 original size:21 final size:22
Alignment explanation
Indices: 4704209--4704254 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
4704199 ATATAAAGAA
4704209 TTTTTAATGTAT-TTTAAATTT
1 TTTTTAATGTATGTTTAAATTT
* *
4704230 TTTTTAATGTTTGTTTTAATTT
1 TTTTTAATGTATGTTTAAATTT
4704252 TTT
1 TTT
4704255 AAGTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTAATGTATGTTTAAATTT
Found at i:4706670 original size:389 final size:387
Alignment explanation
Indices: 4705874--4706841 Score: 1271
Period size: 389 Copynumber: 2.5 Consensus size: 387
4705864 GGACGTTATT
* * * ** * *
4705874 ATATACAAAAGTCTTATTCTTCAAAACTTA-AACA-ATTGTTCAAAATTTAAAAGCAATTCATTT
1 ATATACAAAAGTCTTGTTCATCAAAGCTTAGAA-AGATT-TTCAAAATTTAAAATTAACTCATAT
* * * * * * * *
4705937 CATTCTTGAAACATTCGGTGCATTTATTTAAAACACAAAAAAATGCAATAAAAATGATATCTGCG
64 CTTTCTTGAAACGTTCCGTGCTTTTATTTAAAACACGAAAAAATACAATAAAAATGATATTTGTG
* * * *
4706002 TATATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTTAGATTTATTTAAATTTTCAGT
129 TGTATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTTCAAT
* * * *
4706067 GAACGTTAATATATACATGAAAACTTAAGATGTTCAAAATTTAAAATTAACTCATATCTTTTTTT
194 GAACGTTAACATATACATAAAAACTTAAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTG
* * *
4706132 AAACATCATGTGTTTTCATTTAAAACACGACAAAATATAATCAAAAATAATATATGTGTGTATTT
259 AAACATCA-GTGCTTTCATTTAAAACACGACAAAATACAATCAAAAATAATATATGTGTCTATTT
* ** *
4706197 AATAGTTATAAATAAAAAGAATAATCTATTTGTTGCAGTTTTTTTTAATTTTCTGTGAACGTTAA
323 AATAGTTATAAATAAAAAGAATAATCTATTTGTTACAGGGTTTTTT-ATTTTCAGTGAACGTTAA
4706262 C
387 C
* * *
4706263 ACATGCAAAAGCCTTGTTCATCAAAGCTTAGAAAGATTTTCAAAATTTAAAATTAACTCATATCT
1 ATATACAAAAGTCTTGTTCATCAAAGCTTAGAAAGATTTTCAAAATTTAAAATTAACTCATATCT
* * *
4706328 TTCTTGAAACGTTCCATGCTTTTATTTAAAACACGACAAAATACAATAAAAATTATATTTGTGTG
66 TTCTTGAAACGTTCCGTGCTTTTATTTAAAACACGAAAAAATACAATAAAAATGATATTTGTGTG
* *
4706393 TATTTAATTGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAAATTTATTTAAATTTTCAATGA
131 TATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTTCAATGA
*
4706458 ACGTTAACATATACATAAAAACTTAGGAAGATGTTCAAACTTTAAAATTAACTCATATCTTTCTT
196 ACGTTAACATATACATAAAAACTT---AAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTT
* ** * *
4706523 GAAACGTTC-GATGCTTTCATTTAAAACACGGTAAAATACAAT-AAAAATGATATTTGTGTCTAT
258 GAAAC-ATCAG-TGCTTTCATTTAAAACACGACAAAATACAATCAAAAATAATATATGTGTCTAT
* * * **
4706586 TTAATAGTTATAAATAAAAAGAATAATTTGTTTGTTATAGGGTTTTTT-TTTTCAGTGAATTTTA
321 TTAATAGTTATAAATAAAAAGAATAATCTATTTGTTACAGGGTTTTTTATTTTCAGTGAACGTTA
*
4706650 AG
386 AC
*
4706652 ATATACAAAAGTCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATCT
1 ATATACAAAAGTCTTGTTCATCAAAGCTTAGAAAGATTTTCAAAATTTAAAATTAACTCATATCT
* * ** * *
4706717 TCCTTGAAAGGTTTTGTGCTTTCATTTAAAACACGATAAAATACAATAAAAATGATATTTGTGTG
66 TTCTTGAAACGTTCCGTGCTTTTATTTAAAACACGAAAAAATACAATAAAAATGATATTTGTGTG
* * *
4706782 TATTCAATAGTTATAAACAATAAGAAGAATTTGTTTGTTGTCAAAATTTATTTAAATTTT
131 TATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTC-AAATTTATTTAAATTTT
4706842 GGCTTAATAT
Statistics
Matches: 504, Mismatches: 67, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
389 352 0.70
390 22 0.04
391 61 0.12
392 67 0.13
393 2 0.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (387 bp):
ATATACAAAAGTCTTGTTCATCAAAGCTTAGAAAGATTTTCAAAATTTAAAATTAACTCATATCT
TTCTTGAAACGTTCCGTGCTTTTATTTAAAACACGAAAAAATACAATAAAAATGATATTTGTGTG
TATTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTTCAATGA
ACGTTAACATATACATAAAAACTTAAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAA
ACATCAGTGCTTTCATTTAAAACACGACAAAATACAATCAAAAATAATATATGTGTCTATTTAAT
AGTTATAAATAAAAAGAATAATCTATTTGTTACAGGGTTTTTTATTTTCAGTGAACGTTAAC
Found at i:4707999 original size:189 final size:189
Alignment explanation
Indices: 4707674--4708431 Score: 828
Period size: 190 Copynumber: 3.9 Consensus size: 189
4707664 AAAGCTTAGA
* * **
4707674 AAGATGTTCAAATTTTAAAATTAACTCATATTTTTCTTG-AACGTTCCGTGTTTTCATTTAAAAC
1 AAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTATGTGTTTTCATTTAAAAC
* * * *
4707738 AAAACAAAATACAATAAAAATGATATCTGTGTGTATTTAATAGTTATAAATAAAAAGAAGAATTT
66 ACAACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAATAATCT
* * *
4707803 TTTTGTTGTCAAATTTATTTAAATTTCCAATGAACGTTAATATATACATGAAAACTTAAG
131 ATTTGTTG-CAAATTTATTTAAATTTTCAATGAACGTTAACATATACATGAAAACTTAAG
* * * *
4707863 AAGATGTTCAAAATTTAAAATTAACTCATATCTTTTTTTAAACATTATGTGTTTTCATATAAAAC
1 AAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTATGTGTTTTCATTTAAAAC
* *
4707928 ACGA-AAAATACAATAAAAATGATATATGTGTGTATTTAATAGTTATAAATAAAAAGAATAATCT
66 ACAACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAATAATCT
** * * **
4707992 ATTTGTTGCAGTTTTTTTTTAATTTTCTGTGAACGTTAACATATACAAAAGCCTTGTTCATCAAA
131 ATTTGTTGCAAATTTATTTAAATTTTCAATGAACGTTAACATATAC---A----TG---A--AAA
4708057 GCTT-AG
184 -CTTAAG
*
4708063 AAAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTCCATG-CTTTT-ATTTAA
1 -AAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTT--ATGTGTTTTCATTTAA
* * *
4708126 AACACAACAAAATACAATAAAAATTATTTTTGTGTGTATTTAATTGTTATAAATAAAAAGAATAA
63 AACACAACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAATAA
* * * * * * * *
4708191 TTTGTTTGTTGTCAAATTTATTTAAATTTTTAGTGAGCATTAACATATACATAAAAACTTAGG
128 TCTATTTGTTG-CAAATTTATTTAAATTTTCAATGAACGTTAACATATACATGAAAACTTAAG
* * *** **
4708254 AAGATAG-TCAAAATTTAAAATTAACTCGTATATTTCTTGAAACGTCCGGTACTTTCATTTAAAA
1 AAGAT-GTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTATGTGTTTTCATTTAAAA
* * *
4708318 TACAACAAAATACAATAAAAATAATATTTGAGTGTATTTAATAGTTATAAATAAAAAGAATGAA-
65 CACAACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAAT-AAT
* * * * *
4708382 CTACTTGTTGCAAAATTTATTGAAATTTTTAATCAACGTTAATATATACA
129 CTATTTGTTGC-AAATTTATTTAAATTTTCAATGAACGTTAACATATACA
4708432 AAAACCTTGT
Statistics
Matches: 479, Mismatches: 65, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
188 31 0.06
189 103 0.22
190 170 0.35
191 8 0.02
193 1 0.00
195 2 0.00
196 1 0.00
198 1 0.00
200 6 0.01
201 57 0.12
202 66 0.14
203 33 0.07
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (189 bp):
AAGATGTTCAAAATTTAAAATTAACTCATATCTTTCTTGAAACGTTATGTGTTTTCATTTAAAAC
ACAACAAAATACAATAAAAATGATATTTGTGTGTATTTAATAGTTATAAATAAAAAGAATAATCT
ATTTGTTGCAAATTTATTTAAATTTTCAATGAACGTTAACATATACATGAAAACTTAAG
Found at i:4708494 original size:391 final size:390
Alignment explanation
Indices: 4707580--4708633 Score: 1286
Period size: 391 Copynumber: 2.7 Consensus size: 390
4707570 TTTTTTTGAA
* *
4707580 TATAAATAAAAAGAATAATTTATTTGTTGCTAAATTTATTTAAATTTTTAGTGAATGTTAACATA
1 TATAAATAAAAAGAATAATCTATTTGTTGC-AAATTTATTTAAATTTTTAGTGAACGTTAACATA
* * * *
4707645 TACAAAAGTCTTGTTCATTAAAGCTTAGAAAGATGTTCAAATTTTAAAATTAACTCATATTTTTC
65 TACAAAAGCCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCA-ATCTTTC
4707710 TTG-AACGTTCCGTG-TTTTCATTTAAAACAAAACAAAATACAATAAAAATGATATCTGTGTGTA
129 TTGAAACGTTCCGTGCTTTT-ATTTAAAACAAAACAAAATACAATAAAAATGATATCTGTGTGTA
*
4707773 TTTAATAGTTATAAATAAAAAGAAGAATTTTTTTGTTGTCAAATTTATTTAAATTTCCAATGAAC
193 TTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTCCAATGAAC
* * * * * *
4707838 GTTAATATATACATGAAAACTTAAGAAGATGTTCAAAATTTAAAATTAACTCATATCTTTTTTTA
258 ATTAACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGA
* * ** * * *
4707903 AACATTATGTGTTTTCATATAAAACACGAAAAATACAATAAAAATGATATATGTGTGTATTTAAT
323 AACATCAGGTACTTTCATATAAAACACAAAAAATACAATAAAAATAATATATGAGTGTATTTAAT
4707968 AGT
388 AGT
** * *
4707971 TATAAATAAAAAGAATAATCTATTTGTTGCAGTTTTTTTTTAATTTTCT-GTGAACGTTAACATA
1 TATAAATAAAAAGAATAATCTATTTGTTGCAAATTTATTTAAATTTT-TAGTGAACGTTAACATA
4708035 TACAAAAGCCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCATATCTTTC
65 TACAAAAGCCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCA-ATCTTTC
* * * * *
4708100 TTGAAACGTTCCATGCTTTTATTTAAAACACAACAAAATACAATAAAAATTATTTTTGTGTGTAT
129 TTGAAACGTTCCGTGCTTTTATTTAAAACAAAACAAAATACAATAAAAATGATATCTGTGTGTAT
* * ** * *
4708165 TTAATTGTTATAAATAAAAAGAATAATTTGTTTGTTGTCAAATTTATTTAAATTTTTAGTGAGCA
194 TTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTCCAATGAACA
* *
4708230 TTAACATATACATAAAAACTTAGGAAGATAG-TCAAAATTTAAAATTAACTCGTATATTTCTTGA
259 TTAACATATACATAAAAACTTAAGAAGAT-GTTCAAAATTTAAAATTAACTCATATATTTCTTGA
* * * * *
4708294 AACGTCCGGTACTTTCATTTAAAATACAACAAAATACAATAAAAATAATATTTGAGTGTATTTAA
323 AACATCAGGTACTTTCATATAAAACACAA-AAAATACAATAAAAATAATATATGAGTGTATTTAA
4708359 TAGT
387 TAGT
* * * * *
4708363 TATAAATAAAAAGAATGAA-CTACTTGTTGCAAAATTTATTGAAATTTTTAATCAACGTTAATAT
1 TATAAATAAAAAGAAT-AATCTATTTGTTGC-AAATTTATTTAAATTTTTAGTGAACGTTAACAT
* * * * * *
4708427 ATACAAAAACCTTGTTCATCAAAACTTAAAAAGATATTCAAAATTTAGAATTAACTC-ATCGTTC
64 ATACAAAAGCCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCAATCTTTC
* ** * * *** * *
4708491 TTGAAACATTTTGTGCTTTCAATTAAAACATGGCAAAATACAATAAAAATGATATAC-GAGTAT-
129 TTGAAACGTTCCGTGCTTTTATTTAAAACAAAACAAAATACAATAAAAATGATAT-CTGTGTGTA
* * * * * *
4708554 TTTAATAGTTAT-AA-GAAAAGTAGAATTTCTTTGTTGCCAAATTTATTCAAAATTT-CGATGAA
193 TTTAATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATT-TAAATTTCCAATGAA
**
4708616 TGTTAACATATACA-AAAA
257 CATTAACATATACATAAAA
4708634 CCTTGTTTAT
Statistics
Matches: 569, Mismatches: 84, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
387 4 0.01
388 43 0.08
389 8 0.01
390 102 0.18
391 267 0.47
392 68 0.12
393 77 0.14
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (390 bp):
TATAAATAAAAAGAATAATCTATTTGTTGCAAATTTATTTAAATTTTTAGTGAACGTTAACATAT
ACAAAAGCCTTGTTCATCAAAGCTTAGAAAGATGTTCAAAATTTAAAATTAACTCAATCTTTCTT
GAAACGTTCCGTGCTTTTATTTAAAACAAAACAAAATACAATAAAAATGATATCTGTGTGTATTT
AATAGTTATAAATAAAAAGAAGAATTTGTTTGTTGTCAAATTTATTTAAATTTCCAATGAACATT
AACATATACATAAAAACTTAAGAAGATGTTCAAAATTTAAAATTAACTCATATATTTCTTGAAAC
ATCAGGTACTTTCATATAAAACACAAAAAATACAATAAAAATAATATATGAGTGTATTTAATAGT
Found at i:4708633 original size:198 final size:202
Alignment explanation
Indices: 4708244--4708720 Score: 500
Period size: 198 Copynumber: 2.4 Consensus size: 202
4708234 CATATACATA
** * * * * * * *
4708244 AAAACTTAGGAAGATAGTCAAAATTTAAAATTAACTCGTATATTTCTTGAAAC-GTCCGGTACTT
1 AAAACTTAAAAAGATATTCAAAATTTCAAATTAACTCG-ATAGTTCTTAAAACATTTC-GTGCTT
* * *** ** *
4708308 TCATTTAAAATACAACAAAATACAATAAAAATAATATTTGAGTGTATTTAATAGTTATAAATAAA
64 TCAATTAAAACATGGCAAAATACAATAAAAATAATATACGAGTATATTTAATAGTTATAAATAAA
* * * *
4708373 AAGAATGAACTACTTGTTGCAAAATTTATTGAAATTTTTAATCAACGTTAATATATACAAAAACC
129 AAGAATGAACTACTTGTTGCAAAATTTATTCAAAATTTCAATCAACGTTAACATATACAAAAACC
4708438 TTGTTCATC
194 TTGTTCATC
* * *
4708447 AAAACTTAAAAAGATATTCAAAATTT-AGAATTAACTC-ATCGTTCTTGAAACATTTTGTGCTTT
1 AAAACTTAAAAAGATATTCAAAATTTCA-AATTAACTCGATAGTTCTTAAAACATTTCGTGCTTT
* *
4708510 CAATTAAAACATGGCAAAATACAATAAAAATGATATACGAGTAT-TTTAATAGTTAT-AA-GAAA
65 CAATTAAAACATGGCAAAATACAATAAAAATAATATACGAGTATATTTAATAGTTATAAATAAAA
* * * * * * *
4708572 AGTA-GAATTTCTTTGTTGCCAAATTTATTCAAAATTTCGATGAATGTTAACATATACAAAAACC
130 AGAATGAACTAC-TTGTTGCAAAATTTATTCAAAATTTCAATCAACGTTAACATATACAAAAACC
* *
4708636 TTGTTTATT
194 TTGTTCATC
* * *
4708645 AAATCTTAGAAAGATATTCAAAATTTCAAATTAACTCGTATATTTCTTAAAACATTTCGTGCTTT
1 AAAACTTAAAAAGATATTCAAAATTTCAAATTAACTCG-ATAGTTCTTAAAACATTTCGTGCTTT
* *
4708710 TATTTAAAACA
65 CAATTAAAACA
4708721 CAACAAACAA
Statistics
Matches: 228, Mismatches: 40, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
197 5 0.02
198 90 0.39
199 3 0.01
200 43 0.19
201 53 0.23
202 2 0.01
203 32 0.14
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (202 bp):
AAAACTTAAAAAGATATTCAAAATTTCAAATTAACTCGATAGTTCTTAAAACATTTCGTGCTTTC
AATTAAAACATGGCAAAATACAATAAAAATAATATACGAGTATATTTAATAGTTATAAATAAAAA
GAATGAACTACTTGTTGCAAAATTTATTCAAAATTTCAATCAACGTTAACATATACAAAAACCTT
GTTCATC
Found at i:4715082 original size:4 final size:4
Alignment explanation
Indices: 4715073--4715100 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4715063 TCCCTTCCTC
4715073 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
4715101 TATTGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:4727043 original size:63 final size:62
Alignment explanation
Indices: 4726975--4727098 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 62
4726965 TTCATATTGG
* *
4726975 GTTTATGTTAATTGTTTTCGTATCATCGTAAATTTAATTTAATTTATATTTTGTATAGTGTGA
1 GTTTATGTTAATTGTTTTCGTACCATCATAAATTTAA-TTAATTTATATTTTGTATAGTGTGA
*
4727038 GTTTATGTTAATTGTTTTCGTACCATCATAAATTTAATTATTTTATATTTTGTATAGTGTG
1 GTTTATGTTAATTGTTTTCGTACCATCATAAATTTAATTAATTTATATTTTGTATAGTGTG
4727099 TCATTGAGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 23 0.40
63 35 0.60
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.54
Consensus pattern (62 bp):
GTTTATGTTAATTGTTTTCGTACCATCATAAATTTAATTAATTTATATTTTGTATAGTGTGA
Found at i:4745875 original size:78 final size:78
Alignment explanation
Indices: 4745746--4745890 Score: 274
Period size: 78 Copynumber: 1.9 Consensus size: 78
4745736 CAAAATTTAG
4745746 GATTATCCTTAATCTATAATAGATAAGATTAGATACCAAATCCTTTCTCGGATTTCAATTTGCTT
1 GATTATCCTTAATCTATAATAGATAAGATTAGATACCAAATCCTTTCTCGGATTTCAATTTGCTT
4745811 GAACAGATTAATC
66 GAACAGATTAATC
4745824 GATTA-CCATTAATCTATAATAGATAAGATTAGATACCAAATCCTTTCTCGGATTTCAATTTGCT
1 GATTATCC-TTAATCTATAATAGATAAGATTAGATACCAAATCCTTTCTCGGATTTCAATTTGCT
4745888 TGA
65 TGA
4745891 CTGGTATTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
77 2 0.03
78 64 0.97
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (78 bp):
GATTATCCTTAATCTATAATAGATAAGATTAGATACCAAATCCTTTCTCGGATTTCAATTTGCTT
GAACAGATTAATC
Found at i:4755002 original size:18 final size:18
Alignment explanation
Indices: 4754967--4755004 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4754957 CGATTAGAGT
*
4754967 AACTTAATGATCACGAAA
1 AACTTAATCATCACGAAA
4754985 AACTTGAATCATCA-GAAA
1 AACTT-AATCATCACGAAA
4755003 AA
1 AA
4755005 GTGACACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (18 bp):
AACTTAATCATCACGAAA
Found at i:4755956 original size:16 final size:16
Alignment explanation
Indices: 4755937--4755968 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4755927 AAATCTGAAA
4755937 AAAAATATTAAAATTT
1 AAAAATATTAAAATTT
4755953 AAAAATATTAAAATTT
1 AAAAATATTAAAATTT
4755969 CTGAAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATTAAAATTT
Found at i:4756133 original size:19 final size:18
Alignment explanation
Indices: 4756104--4756149 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
4756094 GATGGTCACC
*
4756104 TTAAAAAATTAT-TCATT
1 TTAAAAAATTATATAATT
4756121 TGTAAAAATATTATATAATT
1 T-TAAAAA-ATTATATAATT
4756141 TTAAAAAAT
1 TTAAAAAAT
4756150 ATCTTGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 11 0.44
20 5 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAAAAAATTATATAATT
Found at i:4757783 original size:18 final size:16
Alignment explanation
Indices: 4757760--4757795 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
4757750 GTTTAAAATT
4757760 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
4757778 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
4757794 TT
1 TT
4757796 CTCATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:4761668 original size:43 final size:43
Alignment explanation
Indices: 4761620--4761703 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
4761610 AAAAGAATTG
*
4761620 TTTATGAGTGTTATTT-AAGAATAAAATTATATTTGGGTTTAGT
1 TTTATGAGTGTT-TTTGAAAAATAAAATTATATTTGGGTTTAGT
*
4761663 TTTATGAGTGTTTTTGAAAAATGAAATTATATTTGGGTTTA
1 TTTATGAGTGTTTTTGAAAAATAAAATTATATTTGGGTTTA
4761704 AAAATATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 3 0.08
43 35 0.92
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (43 bp):
TTTATGAGTGTTTTTGAAAAATAAAATTATATTTGGGTTTAGT
Found at i:4765404 original size:21 final size:21
Alignment explanation
Indices: 4765380--4765446 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
4765370 CACTACAGGG
*
4765380 AAAATTACACAAAATACACGA
1 AAAATTATACAAAATACACGA
** ***
4765401 AAAAAAATACTTGA-ACACTGA
1 AAAATTATACAAAATACAC-GA
4765422 AAAATTATACAAAATACACGA
1 AAAATTATACAAAATACACGA
4765443 AAAA
1 AAAA
4765447 AATAACGAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.63, C:0.15, G:0.06, T:0.16
Consensus pattern (21 bp):
AAAATTATACAAAATACACGA
Found at i:4765731 original size:30 final size:32
Alignment explanation
Indices: 4765669--4765733 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
4765659 GAAAGTTATA
*
4765669 TTTTGTTTAGTATTTATTGTTTTAAGTTATTTG
1 TTTTGTTTAG-ATTTAATGTTTTAAGTTATTTG
4765702 TTTTGTTTA-ATTTAAT-TTTTAA-TTGATTTG
1 TTTTGTTTAGATTTAATGTTTTAAGTT-ATTTG
4765732 TT
1 TT
4765734 ATTTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (32 bp):
TTTTGTTTAGATTTAATGTTTTAAGTTATTTG
Found at i:4765764 original size:11 final size:11
Alignment explanation
Indices: 4765716--4765764 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
4765706 GTTTAATTTA
4765716 ATTTTTAATTG
1 ATTTTTAATTG
* *
4765727 ATTTGTTATTTA
1 ATTT-TTAATTG
4765739 ATTTTTAAGTT-
1 ATTTTTAA-TTG
4765750 ATTTTTAATTG
1 ATTTTTAATTG
4765761 ATTT
1 ATTT
4765765 GTTATTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 2 0.06
11 19 0.59
12 11 0.34
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTTTAATTG
Found at i:4765786 original size:20 final size:20
Alignment explanation
Indices: 4765761--4765891 Score: 93
Period size: 20 Copynumber: 6.0 Consensus size: 20
4765751 TTTTTAATTG
*
4765761 ATTTGTTATTTAGTGTTTTT
1 ATTTGTTATTTAATGTTTTT
*
4765781 ATTTGTTATTTAATTTTTAATT
1 ATTTGTTATTTAATGTTT--TT
4765803 GATTTGTTATTTAATGTTTTT
1 -ATTTGTTATTTAATGTTTTT
*
4765824 ATTTAGTTGAGTAAATTTAATCTTTAATT
1 ATTT-G-T---T--ATTTAATGTTT--TT
*
4765853 GATTTGTTATTTAATATTTTT
1 -ATTTGTTATTTAATGTTTTT
*
4765874 ATTTTTTATTTAAT-TTTT
1 ATTTGTTATTTAATGTTTT
4765892 AAGTTATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 27
0.74 0.05 0.22
Matches are distributed among these distances:
19 4 0.04
20 33 0.36
21 5 0.05
22 3 0.03
23 27 0.29
25 2 0.02
27 10 0.11
28 1 0.01
29 3 0.03
30 4 0.04
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (20 bp):
ATTTGTTATTTAATGTTTTT
Found at i:4765801 original size:77 final size:79
Alignment explanation
Indices: 4765711--4765921 Score: 250
Period size: 77 Copynumber: 2.8 Consensus size: 79
4765701 GTTTTGTTTA
* *
4765711 ATTTAATTTTTAATTGATTTGTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAGTG
1 ATTTAATTTTTAATTGATTTGTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAATC
4765776 TTT-TT-ATTTGTT
66 TTTATTGATTTGTT
* * *
4765788 ATTTAATTTTTAATTGATTTGTTATTTAATGTTT---TTA--TTTAGTTGA---GTAAATTTAAT
1 ATTTAATTTTTAATTGATTTGTTATTTAATTTTTAAGTTATTTTTAATTGATTTGT-TATTTAAT
4765845 CTTTAATTGATTTGTT
65 CTTT-ATTGATTTGTT
* *
4765861 ATTTAATATTT--TT-ATTTTTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAAT
1 ATTTAATTTTTAATTGATTTGTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAAT
4765922 TTTTCGTGTA
Statistics
Matches: 112, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
69 2 0.02
70 25 0.22
71 2 0.02
72 10 0.09
73 20 0.18
74 3 0.03
75 8 0.07
77 40 0.36
78 2 0.02
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64
Consensus pattern (79 bp):
ATTTAATTTTTAATTGATTTGTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAATC
TTTATTGATTTGTT
Found at i:4765803 original size:43 final size:43
Alignment explanation
Indices: 4765750--4765893 Score: 189
Period size: 43 Copynumber: 3.2 Consensus size: 43
4765740 TTTTTAAGTT
*
4765750 ATTTTTAATTGATTTGTTATTTAGTGTTTTTATTTGTTATTTA
1 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
4765793 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTAGTTGAGTAAATTTA
1 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTT-G-T---T--ATTTA
* * *
4765843 ATCTTTAATTGATTTGTTATTTAATATTTTTATTTTTTATTTA
1 ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
4765886 ATTTTTAA
1 ATTTTTAA
4765894 GTTATTTTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
43 46 0.52
44 1 0.01
45 2 0.02
48 2 0.02
50 38 0.43
ACGTcount: A:0.26, C:0.01, G:0.09, T:0.65
Consensus pattern (43 bp):
ATTTTTAATTGATTTGTTATTTAATGTTTTTATTTGTTATTTA
Found at i:4765893 original size:50 final size:49
Alignment explanation
Indices: 4765776--4765925 Score: 153
Period size: 50 Copynumber: 2.9 Consensus size: 49
4765766 TTATTTAGTG
*
4765776 TTTTTATTT-GTTATTTAATTTTTAATTGATTTGTTATTTAATGTTTTTAT
1 TTTTTATTTAATT-TTTAATTTTTAATTGATTTGTTATTTAAT-TTTTTAT
* * * *
4765826 TTAGTTGA-GTAA-ATTTAATCTTTAATTGATTTGTTATTTAATATTTTTAT
1 TT--TTTATTTAATTTTTAATTTTTAATTGATTTGTTATTTAAT-TTTTTAT
4765876 TTTTTATTTAATTTTTAAGTTATTTTTAATTGATTTGTTATTTAATTTTT
1 TTTTTATTTAATTTTT-A---ATTTTTAATTGATTTGTTATTTAATTTTT
4765926 CGTGTATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 15
0.76 0.09 0.14
Matches are distributed among these distances:
48 3 0.04
49 3 0.04
50 42 0.52
51 2 0.02
52 3 0.04
53 4 0.05
54 24 0.30
ACGTcount: A:0.25, C:0.01, G:0.08, T:0.66
Consensus pattern (49 bp):
TTTTTATTTAATTTTTAATTTTTAATTGATTTGTTATTTAATTTTTTAT
Found at i:4765944 original size:21 final size:21
Alignment explanation
Indices: 4765918--4765988 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
4765908 ATTTGTTATT
4765918 TAATTTTTCGTGTATTTTGTA
1 TAATTTTTCGTGTATTTTGTA
* ***
4765939 TAATTTTTCAATGT-TCAGGTA
1 TAATTTTTC-GTGTATTTTGTA
* *
4765960 T-TTTTTTGGTGTATTTTGTA
1 TAATTTTTCGTGTATTTTGTA
4765980 TAATTTTTC
1 TAATTTTTC
4765989 CCTGTAGTGT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 19 0.54
22 3 0.09
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.61
Consensus pattern (21 bp):
TAATTTTTCGTGTATTTTGTA
Found at i:4766056 original size:50 final size:52
Alignment explanation
Indices: 4765983--4766089 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 52
4765973 TTTTGTATAA
* * *
4765983 TTTTTCCCTGTAGTGTCACCATTTGATAATTCTC-CACTAATATAATATT-T
1 TTTTTCCCTGTAGTGCCACCATTTGATAACTCCCTCACTAATATAATATTAT
* **
4766033 TTTTTCCCTGTGGTGCCTGCATTTGATAACTCCCTCACTAATATAATATTAT
1 TTTTTCCCTGTAGTGCCACCATTTGATAACTCCCTCACTAATATAATATTAT
4766085 TTTTT
1 TTTTT
4766090 ATTTTTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
50 28 0.57
51 15 0.31
52 6 0.12
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (52 bp):
TTTTTCCCTGTAGTGCCACCATTTGATAACTCCCTCACTAATATAATATTAT
Found at i:4766142 original size:59 final size:58
Alignment explanation
Indices: 4766028--4766216 Score: 213
Period size: 58 Copynumber: 3.2 Consensus size: 58
4766018 ACTAATATAA
* *
4766028 TATTTTTTTTCCCTGTGGTGCCTGCATTTGATAACTCC-CTCACTAATATAATATTATTTTT
1 TATTTTTTTT-CCTGTAGTG-CTCCATTTGATAAC-CCTC-CACTAATATAATATTATTTTT
*
4766089 TATTTTTTTTCCTGTAGTGCTACCATTTGATAACCCTCCATTAATATAATATTA-TTTT
1 TATTTTTTTTCCTGTAGTGCT-CCATTTGATAACCCTCCACTAATATAATATTATTTTT
* * * *
4766147 T-TTATTTTTCTCTGTAGTGCCGCCATTTGATAACACTCCACTAATATAATATCATTTTT
1 TATTTTTTTTC-CTGTAGTG-CTCCATTTGATAACCCTCCACTAATATAATATTATTTTT
*
4766206 TTTATTTTTTT
1 TAT-TTTTTTT
4766217 AATATATAAA
Statistics
Matches: 112, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
57 8 0.07
58 42 0.38
59 25 0.22
60 21 0.19
61 16 0.14
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.51
Consensus pattern (58 bp):
TATTTTTTTTCCTGTAGTGCTCCATTTGATAACCCTCCACTAATATAATATTATTTTT
Found at i:4766162 original size:58 final size:59
Alignment explanation
Indices: 4766033--4766214 Score: 219
Period size: 59 Copynumber: 3.1 Consensus size: 59
4766023 TATAATATTT
* **
4766033 TTTTTC-CCTGTGGTGCCTGCATTTGATAACTCC-CTCACTAATATAATATTA-TTTTTTA
1 TTTTTCTCCTGTAGTGCCACCATTTGATAAC-CCTC-CACTAATATAATATTATTTTTTTA
* * *
4766091 TTTTTTTTCCTGTAGTGCTACCATTTGATAACCCTCCATTAATATAATATTATTTTTTTA
1 -TTTTTCTCCTGTAGTGCCACCATTTGATAACCCTCCACTAATATAATATTATTTTTTTA
* * *
4766151 TTTTTCT-CTGTAGTGCCGCCATTTGATAACACTCCACTAATATAATATCATTTTTTTTA
1 TTTTTCTCCTGTAGTGCCACCATTTGATAACCCTCCACTAATATAATATTA-TTTTTTTA
4766210 TTTTT
1 TTTTT
4766215 TTAATATATA
Statistics
Matches: 107, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
58 38 0.36
59 41 0.38
60 28 0.26
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (59 bp):
TTTTTCTCCTGTAGTGCCACCATTTGATAACCCTCCACTAATATAATATTATTTTTTTA
Found at i:4775286 original size:2 final size:2
Alignment explanation
Indices: 4775281--4775309 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4775271 TGTGTGTGTG
4775281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4775310 GACTTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4778473 original size:20 final size:19
Alignment explanation
Indices: 4778448--4778492 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4778438 TTTTCCAAAA
*
4778448 TTAAAAATCATTAAAATTAT
1 TTAAAAAT-ATAAAAATTAT
4778468 TTAAAAAATATAAAAATTAT
1 TT-AAAAATATAAAAATTAT
4778488 TTAAA
1 TTAAA
4778493 TGTTGACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAATATAAAAATTAT
Found at i:4780491 original size:27 final size:27
Alignment explanation
Indices: 4780453--4780542 Score: 144
Period size: 27 Copynumber: 3.3 Consensus size: 27
4780443 GTATAAGTGG
4780453 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
* *
4780480 GTGGTGCGTACCTGACAGGCGGCACTA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
4780507 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
4780534 ATGGTGCCT
1 GTGGTGCCT
4780543 TTCTGTCAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.17, C:0.30, G:0.34, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:4780557 original size:27 final size:27
Alignment explanation
Indices: 4780454--4780561 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 27
4780444 TATAAGTGGG
* * *
4780454 TGGTGCCTACCTGACAGGCGGCACCAG
1 TGGTGCCTACCTGTCAAGCGGCACCAA
* * * * *
4780481 TGGTGCGTACCTGACAGGCGGCACTAG
1 TGGTGCCTACCTGTCAAGCGGCACCAA
*
4780508 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTGTCAAGCGGCACCAA
** *
4780535 TGGTGCCTTTCTGTCAAGTGGCACCAA
1 TGGTGCCTACCTGTCAAGCGGCACCAA
4780562 CTCGTATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.20
Consensus pattern (27 bp):
TGGTGCCTACCTGTCAAGCGGCACCAA
Found at i:4780629 original size:14 final size:14
Alignment explanation
Indices: 4780578--4780630 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
4780568 TTTTTATTAC
*
4780578 AAAACTAATACAAAA
1 AAAATTAATAC-AAA
**
4780593 AAAATT-ATACACC
1 AAAATTAATACAAA
4780606 AAAATATAATACAAA
1 AAAAT-TAATACAAA
4780621 AAAATTAATA
1 AAAATTAATA
4780631 ACTTAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 6 0.19
14 10 0.32
15 15 0.48
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATTAATACAAA
Found at i:4780851 original size:58 final size:56
Alignment explanation
Indices: 4780751--4780883 Score: 157
Period size: 58 Copynumber: 2.4 Consensus size: 56
4780741 AAAAATTAAA
* *
4780751 TTAAATATTAAATAAGAATAACTCAATATTTTTAAATAAATAATATAA-AAAAATAT
1 TTAAATATAAAATAATAATAACTCAATATTTTTAAATAAATAATATAAGAAAAA-AT
**
4780807 TTATTTATCAAAATAATAATAATCTCCAA-ATTTTTACAAT-AATAATATAAGAAAAAAT
1 TTAAATAT-AAAATAATAATAA-CT-CAATATTTTTA-AATAAATAATATAAGAAAAAAT
4780865 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
4780884 CACTTTTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
56 13 0.20
57 15 0.23
58 27 0.41
59 11 0.17
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (56 bp):
TTAAATATAAAATAATAATAACTCAATATTTTTAAATAAATAATATAAGAAAAAAT
Found at i:4780919 original size:15 final size:15
Alignment explanation
Indices: 4780899--4780933 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4780889 TTATATATTT
4780899 TTAAATTAAAAAAAA
1 TTAAATTAAAAAAAA
*
4780914 TTAAATTAAATAAAA
1 TTAAATTAAAAAAAA
4780929 TTAAA
1 TTAAA
4780934 ATTTGACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAATTAAAAAAAA
Found at i:4781048 original size:25 final size:25
Alignment explanation
Indices: 4781013--4781062 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4781003 CAGATCTGTT
4781013 TAACAGCAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
*
4781038 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
4781063 AGGAAGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGCAAATTTTTGAAGAAGGAA
Found at i:4783954 original size:26 final size:26
Alignment explanation
Indices: 4783905--4783954 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4783895 TCTATTTAAA
**
4783905 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
4783931 TTTGAATTTATTTAATTAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
4783955 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:4784031 original size:6 final size:6
Alignment explanation
Indices: 4784020--4784060 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
4784010 ATATTTGCAT
*
4784020 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
4784061 TTTAATGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:4784272 original size:27 final size:27
Alignment explanation
Indices: 4784229--4784284 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4784219 TTCTGTTGCG
* * *
4784229 GTAATGGGCGAGGAGGAGTAGAGTACT
1 GTAATGGGCGAGAAGGAATAGAGAACT
4784256 GTAATGGGCTGA-AAGGAATAGAGAACT
1 GTAATGGGC-GAGAAGGAATAGAGAACT
4784283 GT
1 GT
4784285 GGTGGTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.34, C:0.07, G:0.39, T:0.20
Consensus pattern (27 bp):
GTAATGGGCGAGAAGGAATAGAGAACT
Found at i:4784497 original size:6 final size:6
Alignment explanation
Indices: 4784486--4784516 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4784476 ATAGTGCTGC
4784486 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
4784517 CCGGCTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:4786485 original size:13 final size:13
Alignment explanation
Indices: 4786469--4786495 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4786459 TAATTTTTCA
4786469 TTTAAAAAATATT
1 TTTAAAAAATATT
4786482 TTTAAAAAATATT
1 TTTAAAAAATATT
4786495 T
1 T
4786496 AATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:4786516 original size:17 final size:17
Alignment explanation
Indices: 4786487--4786534 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4786477 ATATTTTTAA
4786487 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
4786503 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
4786520 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
4786535 AAATAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:4789453 original size:16 final size:17
Alignment explanation
Indices: 4789416--4789455 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4789406 CTTTTTTTTG
4789416 AATTATTTATATTTATAT
1 AATT-TTTATATTTATAT
4789434 --TTTTTAT-TTTATAT
1 AATTTTTATATTTATAT
4789448 AATTTTTA
1 AATTTTTA
4789456 AACTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 7 0.35
15 5 0.25
16 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTATATTTATAT
Found at i:4798099 original size:35 final size:35
Alignment explanation
Indices: 4798053--4798127 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4798043 TAAATGTTGT
*
4798053 TTTAGTTGGAATGGTAGAGTTTGATTATTGTATGC
1 TTTAGTTGGAATGGTAGAGTTAGATTATTGTATGC
**
4798088 TTTAGTTGGAATGGTATTGTTAGATTATTGTATGC
1 TTTAGTTGGAATGGTAGAGTTAGATTATTGTATGC
4798123 TTTAG
1 TTTAG
4798128 GTTCAAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.48
Consensus pattern (35 bp):
TTTAGTTGGAATGGTAGAGTTAGATTATTGTATGC
Found at i:4799696 original size:15 final size:17
Alignment explanation
Indices: 4799673--4799707 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4799663 AATATAATAT
4799673 AATATAATAT-TAAAAA
1 AATATAATATATAAAAA
4799689 AATA-AATATATAAAAA
1 AATATAATATATAAAAA
4799705 AAT
1 AAT
4799708 GAGACAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATAATATATAAAAA
Found at i:4801507 original size:19 final size:19
Alignment explanation
Indices: 4801483--4801519 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4801473 AAAATTCTTT
*
4801483 AAATTTGTGTAATTTATTC
1 AAATTTGTATAATTTATTC
*
4801502 AAATTTTTATAATTTATT
1 AAATTTGTATAATTTATT
4801520 TTTTAAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
AAATTTGTATAATTTATTC
Found at i:4803342 original size:12 final size:12
Alignment explanation
Indices: 4803321--4803366 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
4803311 ACAATGCCAT
4803321 TAAAAAATTATA
1 TAAAAAATTATA
*
4803333 TAATAAATTATA
1 TAAAAAATTATA
4803345 -AAAAAATTGATA
1 TAAAAAATT-ATA
4803357 TAAAAAATTA
1 TAAAAAATTA
4803367 AATGTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 7 0.23
12 15 0.50
13 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TAAAAAATTATA
Found at i:4803368 original size:22 final size:23
Alignment explanation
Indices: 4803322--4803368 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4803312 CAATGCCATT
*
4803322 AAAAAATTATATAATAAATTATA
1 AAAAAATTATATAATAAAATATA
4803345 AAAAAATTGATATAA-AAAAT-TA
1 AAAAAATT-ATATAATAAAATATA
4803367 AA
1 AA
4803369 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAATTATATAATAAAATATA
Found at i:4816293 original size:17 final size:17
Alignment explanation
Indices: 4816273--4816306 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4816263 TTAGGGAAAA
4816273 TAATCTTAA-AAGATTTG
1 TAATC-TAATAAGATTTG
4816290 TAATCTAATAAGATTTG
1 TAATCTAATAAGATTTG
4816307 GTTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TAATCTAATAAGATTTG
Found at i:4817271 original size:29 final size:28
Alignment explanation
Indices: 4817215--4817271 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
4817205 TTTCTATTAG
*
4817215 ATAAATATAATCATTTGTATATATAATAT
1 ATAAATATAA-CATTTATATATATAATAT
4817244 ATAAATATAA-ATTTATGATATATCAATA
1 ATAAATATAACATTTAT-ATATAT-AATA
4817272 ATGATAACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 6 0.24
29 14 0.56
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (28 bp):
ATAAATATAACATTTATATATATAATAT
Found at i:4820884 original size:16 final size:18
Alignment explanation
Indices: 4820863--4820895 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4820853 ATATCTTCCA
4820863 TTAATT-GTAT-ATAATT
1 TTAATTGGTATAATAATT
4820879 TTAATTGGTATAATAAT
1 TTAATTGGTATAATAAT
4820896 AAATTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (18 bp):
TTAATTGGTATAATAATT
Found at i:4822644 original size:25 final size:24
Alignment explanation
Indices: 4822609--4822676 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
4822599 TATACCCTTT
*
4822609 TTTTTCAATATTTATTTATATTTTAC
1 TTTTT-AATA-TTATTTATATTATAC
* * *
4822635 TTTTTAATATCATTAATATTATAT
1 TTTTTAATATTATTTATATTATAC
4822659 TTTTATAATATTATTTAT
1 TTTT-TAATATTATTTAT
4822677 TAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 15 0.43
25 15 0.43
26 5 0.14
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTAATATTATTTATATTATAC
Found at i:4824293 original size:15 final size:15
Alignment explanation
Indices: 4824269--4824298 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4824259 TGTATGTATG
4824269 TATTTATTTATTATT
1 TATTTATTTATTATT
*
4824284 TATTTGTTTATTATT
1 TATTTATTTATTATT
4824299 CATTAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:4824342 original size:23 final size:23
Alignment explanation
Indices: 4824315--4824394 Score: 160
Period size: 23 Copynumber: 3.5 Consensus size: 23
4824305 TATTGTTCGT
4824315 GAACATGTTCGATTAAGTTAAAC
1 GAACATGTTCGATTAAGTTAAAC
4824338 GAACATGTTCGATTAAGTTAAAC
1 GAACATGTTCGATTAAGTTAAAC
4824361 GAACATGTTCGATTAAGTTAAAC
1 GAACATGTTCGATTAAGTTAAAC
4824384 GAACATGTTCG
1 GAACATGTTCG
4824395 TGAACATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (23 bp):
GAACATGTTCGATTAAGTTAAAC
Found at i:4829940 original size:31 final size:31
Alignment explanation
Indices: 4829905--4829969 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
4829895 CACTTCCGTT
* *
4829905 CTTAATATTATCAGACATTTTTAATTTAATC
1 CTTAATATTATCAAACATTTTCAATTTAATC
*
4829936 CTTAATATTATCAAACGTTTTCAATTTAATC
1 CTTAATATTATCAAACATTTTCAATTTAATC
4829967 CTT
1 CTT
4829970 TAGATGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (31 bp):
CTTAATATTATCAAACATTTTCAATTTAATC
Found at i:4831370 original size:6 final size:6
Alignment explanation
Indices: 4831345--4831383 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4831335 ACAATTCATA
* * *
4831345 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
4831384 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:4836747 original size:18 final size:18
Alignment explanation
Indices: 4836724--4836760 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4836714 ACAATTCATA
4836724 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
4836742 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
4836760 T
1 T
4836761 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:4864066 original size:18 final size:17
Alignment explanation
Indices: 4864028--4864069 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
4864018 CAAAACTAAG
4864028 ATTTTTTTAAAATATTT
1 ATTTTTTTAAAATATTT
*
4864045 ATTTTATTTTAAAT-TTT
1 ATTTT-TTTAAAATATTT
4864062 CATTTTTT
1 -ATTTTTT
4864070 ATAATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTTAAAATATTT
Found at i:4874217 original size:2 final size:2
Alignment explanation
Indices: 4874210--4874239 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4874200 TTCCTCTTTA
*
4874210 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4874240 GTATTCCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4878522 original size:2 final size:2
Alignment explanation
Indices: 4878515--4878550 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4878505 TCCAAATCCA
4878515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4878551 AACTAAGCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4879277 original size:5 final size:5
Alignment explanation
Indices: 4879267--4879292 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4879257 GGGGGTAATC
4879267 TTATG TTATG TTATG TTATG TTATG T
1 TTATG TTATG TTATG TTATG TTATG T
4879293 ATGGAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTATG
Found at i:4883646 original size:18 final size:19
Alignment explanation
Indices: 4883619--4883657 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4883609 CTGGACTTGG
*
4883619 ATTTGCTGAACTTTCA-GC
1 ATTTGCTGAAATTTCATGC
*
4883637 ATTTGTTGAAATTTCATGC
1 ATTTGCTGAAATTTCATGC
4883656 AT
1 AT
4883658 GGAATTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (19 bp):
ATTTGCTGAAATTTCATGC
Found at i:4888094 original size:21 final size:19
Alignment explanation
Indices: 4888052--4888094 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
4888042 AAAATGATTT
* *
4888052 AAAAGTAAAAATATTTATA
1 AAAAGTAAAAATATTCAAA
4888071 AAAAGTCAAATAATATTCAAA
1 AAAAGT-AAA-AATATTCAAA
4888092 AAA
1 AAA
4888095 TTATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAGTAAAAATATTCAAA
Found at i:4888360 original size:69 final size:69
Alignment explanation
Indices: 4888287--4888424 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
4888277 AAACGTTATT
* * *
4888287 CTTCTATTCAATCAATTTTTTTTCTAAGTAGTAAAAGCATAGATCTTTGGGGCATAATAAATAAC
1 CTTCTATTCAATCAATTTTTTTTCCAAGCAGTAAAAGCATAGATCTTCGGGGCATAATAAATAAC
4888352 AATA
66 AATA
*
4888356 CTTCTATTCAATCAATTTTTTTTCCAAGCAGTAAAAGCATAGATCTTCGGGGCATAATAAATAAT
1 CTTCTATTCAATCAATTTTTTTTCCAAGCAGTAAAAGCATAGATCTTCGGGGCATAATAAATAAC
4888421 AATA
66 AATA
4888425 ATTGTTATAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (69 bp):
CTTCTATTCAATCAATTTTTTTTCCAAGCAGTAAAAGCATAGATCTTCGGGGCATAATAAATAAC
AATA
Found at i:4899483 original size:23 final size:24
Alignment explanation
Indices: 4899431--4899483 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
4899421 AACTATTTTT
*
4899431 AAAAAATTAAAGGTCAAAATTAAC
1 AAAAAATAAAAGGTCAAAATTAAC
* *
4899455 -ATAAATAAAAGGTCAGAA-TAAC
1 AAAAAATAAAAGGTCAAAATTAAC
4899477 AAAAAAT
1 AAAAAAT
4899484 GTAAACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.64, C:0.08, G:0.09, T:0.19
Consensus pattern (24 bp):
AAAAAATAAAAGGTCAAAATTAAC
Found at i:4907408 original size:2 final size:2
Alignment explanation
Indices: 4907401--4907431 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4907391 CTACCAGAAA
4907401 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4907432 TAAATCAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4913674 original size:115 final size:115
Alignment explanation
Indices: 4913472--4913707 Score: 454
Period size: 115 Copynumber: 2.1 Consensus size: 115
4913462 TGAGAGCTAC
4913472 TTTGGAGCAGTTTTTATCATTGTTGTAAAGCAAGAGATCTAGAAAATGGTGCTTGTTGTAGACAG
1 TTTGGAGCAGTTTTTATCATTGTTGTAAAGCAAGAGATCTAGAAAATGGTGCTTGTTGTAGACAG
*
4913537 TAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTTTTTACACTATAG
66 TAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTTACACTATAG
*
4913587 TTTGGAGTAGTTTTTATCATTGTTGTAAAGCAAGAGATCTAGAAAATGGTGCTTGTTGTAGACAG
1 TTTGGAGCAGTTTTTATCATTGTTGTAAAGCAAGAGATCTAGAAAATGGTGCTTGTTGTAGACAG
4913652 TAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTTACACTATAG
66 TAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTTACACTATAG
4913702 TTTGGA
1 TTTGGA
4913708 AAATGCTCAT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 119 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (115 bp):
TTTGGAGCAGTTTTTATCATTGTTGTAAAGCAAGAGATCTAGAAAATGGTGCTTGTTGTAGACAG
TAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTTACACTATAG
Found at i:4913750 original size:47 final size:47
Alignment explanation
Indices: 4913651--4913787 Score: 157
Period size: 47 Copynumber: 2.9 Consensus size: 47
4913641 GTTGTAGACA
* * *
4913651 GTAGTTTGGAAAATATTCATCTGAAATCTTTTAGTTCTGTTTACACT
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTTACACT
* * * * **
4913698 ATAGTTTGGAAAATGCTCATCTGAAATCTTATGGTACTTTTTATGCT
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTTACACT
* * * *
4913745 GTAGTTCGGGAAATGTTCATCTCAAATCTTATAGTATTGTTTA
1 GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTTA
4913788 GATCTGATTC
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (47 bp):
GTAGTTTGGAAAATGTTCATCTGAAATCTTATAGTACTGTTTACACT
Done.