Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001844.1 Hibiscus syriacus cultivar Beakdansim tig00003738_pilon, whole genome shotgun sequence
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: 147535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4592 original size:27 final size:28
Alignment explanation
Indices: 4554--4608 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4544 AACTTCTACG
* *
4554 TTAACACTGTG-ACCGTCACGTTAACAC
1 TTAACACCGTGAACCGTCACGGTAACAC
*
4581 TTAACACCGTGAACTGTCACGGTAACAC
1 TTAACACCGTGAACCGTCACGGTAACAC
4609 GATAACGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (28 bp):
TTAACACCGTGAACCGTCACGGTAACAC
Found at i:8097 original size:13 final size:13
Alignment explanation
Indices: 8072--8116 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
8062 CACTAGGCAT
8072 CCGAGGCCATCCGA
1 CCGAGG-CATCCGA
8086 CCGAGGCATCCGA
1 CCGAGGCATCCGA
8099 CCGA-GCTATCCGA
1 CCGAGGC-ATCCGA
*
8112 GCGAG
1 CCGAG
8117 CTATGCGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 20 0.71
14 6 0.21
ACGTcount: A:0.22, C:0.38, G:0.31, T:0.09
Consensus pattern (13 bp):
CCGAGGCATCCGA
Found at i:8117 original size:13 final size:13
Alignment explanation
Indices: 8080--8120 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
8070 ATCCGAGGCC
8080 ATCCGACCGAGGC-
1 ATCCGACCGA-GCT
8093 ATCCGACCGAGCT
1 ATCCGACCGAGCT
*
8106 ATCCGAGCGAGCT
1 ATCCGACCGAGCT
8119 AT
1 AT
8121 GCGAGGGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 2 0.08
13 24 0.92
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.15
Consensus pattern (13 bp):
ATCCGACCGAGCT
Found at i:14881 original size:2 final size:2
Alignment explanation
Indices: 14874--14930 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
14864 ATTAATCTTT
14874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14916 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
14931 GTGTGTGTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20449 original size:57 final size:57
Alignment explanation
Indices: 20355--20479 Score: 169
Period size: 57 Copynumber: 2.2 Consensus size: 57
20345 ACACCCGGAC
* *
20355 CGTTGTACATCCCAGGCCTAAAGGCATGACACGCCTAAGACATCGGCAAAATTCTAA
1 CGTTGTACATCCCAGGCCTAAAGGCATGACACACCTAAGACATCGGCAAAATTCGAA
* * * * * * *
20412 TGTTGTACATCCCAGGCTTAGATGCATGGCACACCTAAGACATCGGCACAATTCGAC
1 CGTTGTACATCCCAGGCCTAAAGGCATGACACACCTAAGACATCGGCAAAATTCGAA
20469 CGTTGTACATC
1 CGTTGTACATC
20480 TTGTCAAGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (57 bp):
CGTTGTACATCCCAGGCCTAAAGGCATGACACACCTAAGACATCGGCAAAATTCGAA
Found at i:27636 original size:24 final size:24
Alignment explanation
Indices: 27591--27637 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
27581 CAATTATGAT
*
27591 TAAATTTTTAAAATCTATAATTTA
1 TAAATTTTTAAAATCTACAATTTA
*
27615 TAAA-TTTTAAGATCTAACAATTT
1 TAAATTTTTAAAATCT-ACAATTT
27638 CAATTATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (24 bp):
TAAATTTTTAAAATCTACAATTTA
Found at i:27712 original size:6 final size:6
Alignment explanation
Indices: 27701--27746 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
27691 TTTTGTTTAA
** *
27701 TAATTT TAATTT TAATTT TAATTT TAAAAT GAATTT ATAATTT TAA
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT -TAATTT TAA
27747 AATAAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TAATTT
Found at i:27743 original size:19 final size:19
Alignment explanation
Indices: 27700--27754 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
27690 CTTTTGTTTA
** *
27700 ATAATTTTAATTTTAATTT
1 ATAATTTTAAAATAAATTT
*
27719 -TAATTTTAAAATGAATTT
1 ATAATTTTAAAATAAATTT
27737 ATAATTTTAAAATAAATT
1 ATAATTTTAAAATAAATT
27755 ATGAAATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATAATTTTAAAATAAATTT
Found at i:28431 original size:15 final size:15
Alignment explanation
Indices: 28393--28431 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28383 TAATGCAAAA
*
28393 CCACCCCGCCCCGCC
1 CCACCCCGTCCCGCC
*
28408 CCACTCCGTCCCGCC
1 CCACCCCGTCCCGCC
*
28423 CCGCCCCGT
1 CCACCCCGT
28432 TGCCACCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.72, G:0.15, T:0.08
Consensus pattern (15 bp):
CCACCCCGTCCCGCC
Found at i:28495 original size:8 final size:8
Alignment explanation
Indices: 28482--28513 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28472 TTTAATATTT
28482 ATTTTAAA
1 ATTTTAAA
28490 ATTTTAAA
1 ATTTTAAA
28498 ATTTTAAA
1 ATTTTAAA
*
28506 ATATTAAA
1 ATTTTAAA
28514 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTTTAAA
Found at i:29374 original size:2 final size:2
Alignment explanation
Indices: 29367--29395 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29357 ACCATATAAG
29367 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29396 TCTTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30687 original size:20 final size:20
Alignment explanation
Indices: 30640--30693 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
30630 TCATGGTTAG
30640 GATTTTAGAAATTTGAGGTT
1 GATTTTAGAAATTTGAGGTT
* * *
30660 -ATAGTTAGAGATTTGTGGTT
1 GAT-TTTAGAAATTTGAGGTT
*
30680 GATTTTAGGAATTT
1 GATTTTAGAAATTT
30694 TTTTATGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (20 bp):
GATTTTAGAAATTTGAGGTT
Found at i:35033 original size:20 final size:20
Alignment explanation
Indices: 35008--35047 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34998 CCGTTAGACA
*
35008 GGGGGAATCGGTACTCCCTG
1 GGGGGAATCGGTACCCCCTG
*
35028 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
35048 AACAATCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:35404 original size:16 final size:16
Alignment explanation
Indices: 35385--35417 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35375 AACACTTCTC
35385 CCCTTTAACACCTTAA
1 CCCTTTAACACCTTAA
35401 CCCTTTAACACCTTAA
1 CCCTTTAACACCTTAA
35417 C
1 C
35418 ACTTCTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.30
Consensus pattern (16 bp):
CCCTTTAACACCTTAA
Found at i:36509 original size:19 final size:20
Alignment explanation
Indices: 36466--36513 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
36456 TCTAAATCCT
*
36466 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
36486 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
36505 TTTTCAAAA
1 TTTTCAAAA
36514 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:50606 original size:19 final size:19
Alignment explanation
Indices: 50582--50642 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
50572 TTTTGGTGCA
*
50582 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
50601 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
50622 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
50643 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:52646 original size:9 final size:8
Alignment explanation
Indices: 52624--52674 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
52614 TGTTTCAACA
52624 TTTTGGAT
1 TTTTGGAT
52632 ATTTTGGAT
1 -TTTTGGAT
52641 TGTTT-GAT
1 T-TTTGGAT
52649 TTTGTGGAT
1 TTT-TGGAT
*
52658 TGTTGGA-
1 TTTTGGAT
52665 TTTTGGAT
1 TTTTGGAT
52673 TT
1 TT
52675 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:52658 original size:17 final size:17
Alignment explanation
Indices: 52626--52669 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
52616 TTTCAACATT
52626 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
52643 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
52660 TTGGATTTTG
1 TTGGATTTTG
52670 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:53423 original size:75 final size:75
Alignment explanation
Indices: 53274--53479 Score: 288
Period size: 75 Copynumber: 2.7 Consensus size: 75
53264 CAAAGCCAAA
* * * **
53274 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
53339 TTGGCTCCGAG
65 TTGGCTCCGAG
*
53350 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
53415 TTGCTCCGAG
66 TGGCTCCGAG
* * * *
53425 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCC
53480 TTGTACAACG
Statistics
Matches: 117, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
75 85 0.73
76 32 0.27
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:54360 original size:15 final size:15
Alignment explanation
Indices: 54340--54370 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54330 CAACAAATAG
54340 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
54355 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
54370 A
1 A
54371 TTTAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:55563 original size:20 final size:20
Alignment explanation
Indices: 55535--55573 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55525 AATTTTAGAA
*
55535 AATAGTTAAT-AAATAATAAT
1 AATAATTAATGAAA-AATAAT
55555 AATAATTAATGAAAAATAA
1 AATAATTAATGAAAAATAA
55574 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAATTAATGAAAAATAAT
Found at i:64574 original size:238 final size:239
Alignment explanation
Indices: 64156--64636 Score: 865
Period size: 238 Copynumber: 2.0 Consensus size: 239
64146 CTCTTGCCAT
*
64156 CAACCTTGATTGGCCCTTGACTCAGTTAGATGTTAAAAATGATTTCCTCAATGGTGAGTTAAACA
1 CAACCTTGATTGGCCCTTGACTCAATTAGATGTTAAAAATGATTTCCTCAATGGTGAGTTAAACA
*
64221 ATGAGGTATATATGGAATTTCCATCGGGATATGAATAAGAAAAGGGTCAAGTGTGCAAGCTAGAA
66 ATGAGGTATATATGGAATTTCCATCGGGATATGAATAAGAAAAGGGTCAAGTGTGCAAGCTAAAA
*
64286 AAATCTTTATACAGGCTGAAATAGTCCCAAAGAGCATGGTTCAGTTGTTTTGCTAAGGCCATGAC
131 AAATCTTTATACAGGCTGAAATAGTCCCAAAGAGCATGGCTCAGTTGTTTTGCTAAGGCCATGAC
* *
64351 CAGCAGGGAGTATACTC-GGGCAGACATACCACACTTTGTTCTA
196 CAGCAGGGAGTATACTCAGGGCAGACAGACCACAATTTGTTCTA
64394 CAACCTTGATTGGCCCTTGACTCAATTAGATGTTAAAAATGATTTCCTCAATGGTGAGTTAAACA
1 CAACCTTGATTGGCCCTTGACTCAATTAGATGTTAAAAATGATTTCCTCAATGGTGAGTTAAACA
*
64459 ATGAGGTATATATGGAATTTCCATCGGGATATGAATAAGAAAAGGGTCGAGTGTGCAAGCTAAAA
66 ATGAGGTATATATGGAATTTCCATCGGGATATGAATAAGAAAAGGGTCAAGTGTGCAAGCTAAAA
* *
64524 AAATCTTTATACAGGCTGAAATAGTTCCTAAGAGCATGGCTCAGTTGTTTTGCTAAGGCCATGAC
131 AAATCTTTATACAGGCTGAAATAGTCCCAAAGAGCATGGCTCAGTTGTTTTGCTAAGGCCATGAC
*
64589 CAGCAGGGAGTATACTCAGGGGCAGGCAGACCACAATTTGTTCTA
196 CAGCAGGGAGTATACTCA-GGGCAGACAGACCACAATTTGTTCTA
64634 CAA
1 CAA
64637 ACACTCGGAA
Statistics
Matches: 232, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
238 206 0.89
240 26 0.11
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (239 bp):
CAACCTTGATTGGCCCTTGACTCAATTAGATGTTAAAAATGATTTCCTCAATGGTGAGTTAAACA
ATGAGGTATATATGGAATTTCCATCGGGATATGAATAAGAAAAGGGTCAAGTGTGCAAGCTAAAA
AAATCTTTATACAGGCTGAAATAGTCCCAAAGAGCATGGCTCAGTTGTTTTGCTAAGGCCATGAC
CAGCAGGGAGTATACTCAGGGCAGACAGACCACAATTTGTTCTA
Found at i:70800 original size:59 final size:59
Alignment explanation
Indices: 70727--70852 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
70717 AAATTTAAGT
*
70727 AAATGGACTAACAAAATATTCTATTGACTGAAATATCATGAT-GAAAATTTTAAAATACA
1 AAATGAACTAACAAAATATTCTATTGACTGAAATATCATGATAG-AAATTTTAAAATACA
* * * * * *
70786 AAATGAACTAACAAATTATTCTATTGATTGAAGTATCGTGATAGAATTTTTAAAATATA
1 AAATGAACTAACAAAATATTCTATTGACTGAAATATCATGATAGAAATTTTAAAATACA
70845 AAATGAAC
1 AAATGAAC
70853 ATAAAAATGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 58 0.98
60 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (59 bp):
AAATGAACTAACAAAATATTCTATTGACTGAAATATCATGATAGAAATTTTAAAATACA
Found at i:74546 original size:21 final size:21
Alignment explanation
Indices: 74497--74546 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
74487 GTTTCCAGAT
*
74497 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
74518 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
74539 TCGTAATG
1 TCGCAATG
74547 AATTCAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:75982 original size:6 final size:6
Alignment explanation
Indices: 75941--75981 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
75931 CAATTGGTAT
*
75941 ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC CCGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
75982 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:79491 original size:6 final size:6
Alignment explanation
Indices: 79480--79509 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
79470 ATTTGACAGA
79480 TTCATG TTCATG TTCATG TTCATG -TCATG T
1 TTCATG TTCATG TTCATG TTCATG TTCATG T
79510 GTTTGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TTCATG
Found at i:83156 original size:15 final size:15
Alignment explanation
Indices: 83133--83188 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
83123 CCCCGCATCT
* * *
83133 GCCCTGCATCCGCTC
1 GCCCCGCATCCACCC
83148 GCCCCGCATCCACCC
1 GCCCCGCATCCACCC
*
83163 GCCCCGCATCCACCT
1 GCCCCGCATCCACCC
*
83178 GCCCCACATCC
1 GCCCCGCATCC
83189 GCCCACCCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.12, C:0.61, G:0.14, T:0.12
Consensus pattern (15 bp):
GCCCCGCATCCACCC
Found at i:89801 original size:19 final size:22
Alignment explanation
Indices: 89756--89806 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
89746 TTCTATTCTG
*
89756 GAAATTAGATTTTTAGAATATT
1 GAAATTAGATTTTTAAAATATT
89778 G-AATTA-A-TTTTAAAATA-T
1 GAAATTAGATTTTTAAAATATT
89796 GAAATTAGATT
1 GAAATTAGATT
89807 ACTTTGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 2 0.08
21 6 0.24
22 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (22 bp):
GAAATTAGATTTTTAAAATATT
Found at i:90346 original size:19 final size:19
Alignment explanation
Indices: 90322--90359 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
90312 ATTGGAATCG
90322 AATATTAAAATATTGATTT
1 AATATTAAAATATTGATTT
* *
90341 AATATTGAAATGTTGATTT
1 AATATTAAAATATTGATTT
90360 TGAACTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
AATATTAAAATATTGATTT
Found at i:91957 original size:16 final size:16
Alignment explanation
Indices: 91936--91974 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
91926 TTATTTTTAT
91936 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
91952 TATGTTTCTTAATGGA
1 TATGTTTCTTAATGGA
*
91968 AATGTTT
1 TATGTTT
91975 TTTTATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (16 bp):
TATGTTTCTTAATGGA
Found at i:96219 original size:21 final size:21
Alignment explanation
Indices: 96185--96239 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
96175 TATTAACCAT
*
96185 TATAGATTGTCACATCAGTAC
1 TATAGATCGTCACATCAGTAC
*
96206 TATGGATCGTCACATCAGTAC
1 TATAGATCGTCACATCAGTAC
96227 TATAGATCGTCAC
1 TATAGATCGTCAC
96240 TTTAGCACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (21 bp):
TATAGATCGTCACATCAGTAC
Found at i:96376 original size:14 final size:16
Alignment explanation
Indices: 96357--96396 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
96347 TGAAATGAAA
*
96357 TAAAATGAAAAT-T-T
1 TAAAATGAAAATGTAC
96371 TAAAATGAAAATGTAC
1 TAAAATGAAAATGTAC
96387 TAAAATGAAA
1 TAAAATGAAA
96397 CTAAAACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.52
15 1 0.04
16 10 0.43
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (16 bp):
TAAAATGAAAATGTAC
Found at i:96611 original size:31 final size:31
Alignment explanation
Indices: 96573--96642 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
96563 TGTGGTCCTG
* *
96573 TATTACATCATCCACGCAT-TCTCATTAACAA
1 TATTACATCATACAAGCATCT-TCATTAACAA
96604 TATTACATCATACAAGCATCTTCATTAACAA
1 TATTACATCATACAAGCATCTTCATTAACAA
*
96635 TTTTACAT
1 TATTACAT
96643 TTCTGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (31 bp):
TATTACATCATACAAGCATCTTCATTAACAA
Found at i:101162 original size:18 final size:19
Alignment explanation
Indices: 101128--101164 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
101118 AAAAAAATAA
101128 TTTTTATTTAATGTTAATT
1 TTTTTATTTAATGTTAATT
101147 TTTTTATTTAAT-TTAATT
1 TTTTTATTTAATGTTAATT
101165 AATAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTATTTAATGTTAATT
Found at i:101504 original size:14 final size:14
Alignment explanation
Indices: 101485--101534 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
101475 TGAACATTCA
101485 GTTATGTTCGTTCG
1 GTTATGTTCGTTCG
101499 GTTATGTTCG-T--
1 GTTATGTTCGTTCG
*
101510 -TTATGTTTGTTCG
1 GTTATGTTCGTTCG
101523 GTTATGTTCGTT
1 GTTATGTTCGTT
101535 TTTTTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
13 1 0.03
14 20 0.67
ACGTcount: A:0.08, C:0.10, G:0.26, T:0.56
Consensus pattern (14 bp):
GTTATGTTCGTTCG
Found at i:101513 original size:24 final size:24
Alignment explanation
Indices: 101486--101535 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
101476 GAACATTCAG
101486 TTATGTTCGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
*
101510 TTATGTTTGTTCGGTTATGTTCGT
1 TTATGTTCGTTCGGTTATGTTCGT
101534 TT
1 TT
101536 TTTTTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.10, G:0.24, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTCGGTTATGTTCGT
Found at i:102511 original size:16 final size:16
Alignment explanation
Indices: 102462--102516 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
102452 GGGTCTCCAA
102462 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
102478 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
102494 CGTTTATGTTCGTATT
1 CGTTTATGTTCGTGTT
*
102510 CGGTTAT
1 CGTTTAT
102517 TTATTAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.55
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:104781 original size:26 final size:25
Alignment explanation
Indices: 104733--104781 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
104723 TAATAACAAT
** *
104733 TGAAAAAATTCAACGGTAGAGTTAC
1 TGAAAAAATTCAACCATAAAGTTAC
104758 TGAAAAAATTCAATCCATAAAGTT
1 TGAAAAAATTCAA-CCATAAAGTT
104782 CAGTGAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (25 bp):
TGAAAAAATTCAACCATAAAGTTAC
Found at i:105563 original size:24 final size:25
Alignment explanation
Indices: 105519--105565 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
105509 TATTAAAATT
*
105519 ATTTTATATTTATATTGATTTTTGA
1 ATTTTATATTTATAATGATTTTTGA
105544 ATTTT-TATTTATAAAT-ATTTTT
1 ATTTTATATTTAT-AATGATTTTT
105566 AACATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
ATTTTATATTTATAATGATTTTTGA
Found at i:105930 original size:20 final size:19
Alignment explanation
Indices: 105890--105927 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
105880 TTTTATTCGA
105890 AATTATGTTTTATTTAATT
1 AATTATGTTTTATTTAATT
105909 AATTAATGTTTT-TTTAATT
1 AATT-ATGTTTTATTTAATT
105928 TAACTATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
AATTATGTTTTATTTAATT
Found at i:107488 original size:2 final size:2
Alignment explanation
Indices: 107481--107535 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
107471 GAATTAAGCT
*
107481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
107523 TA TA TT TA TA TA T
1 TA TA TA TA TA TA T
107536 GCATATGTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:111296 original size:16 final size:16
Alignment explanation
Indices: 111272--111304 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
111262 TATCGCCAAC
*
111272 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
111288 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
111304 C
1 C
111305 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:111772 original size:37 final size:36
Alignment explanation
Indices: 111713--111832 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
111703 ATCCCATTAT
* *
111713 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
111749 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
111785 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
111820 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
111833 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:111788 original size:21 final size:21
Alignment explanation
Indices: 111764--111824 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
111754 TTCAAAGAAA
111764 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
111785 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
111799 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
111820 CATTT
1 CATTT
111825 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:111841 original size:35 final size:36
Alignment explanation
Indices: 111715--111859 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
111705 CCCATTATCA
*
111715 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
111750 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
111787 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*** *
111823 TTTTTCAAAG-TTGGTTACCAAAC-TTAAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
111857 TTT
1 TTT
111860 AATACTTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.13
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:129241 original size:21 final size:20
Alignment explanation
Indices: 129214--129312 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
129204 AATCAGTTTC
129214 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
129235 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
129256 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
129276 CCAAAATCGAAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
129297 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
129313 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:129322 original size:20 final size:20
Alignment explanation
Indices: 129299--129508 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
129289 GCGAATATGA
* *
129299 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
129319 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
129339 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
129359 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
129379 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
129399 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
129419 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
129439 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
129459 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
129479 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
129499 AAATCACAAC
1 AAATCGCAAC
129509 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 159 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:130230 original size:24 final size:24
Alignment explanation
Indices: 130191--130237 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
130181 AAATTTGGTC
130191 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
130215 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
130238 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:130429 original size:12 final size:12
Alignment explanation
Indices: 130412--130436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
130402 ATATAATCCT
130412 GAAGAAGAAAAA
1 GAAGAAGAAAAA
130424 GAAGAAGAAAAA
1 GAAGAAGAAAAA
130436 G
1 G
130437 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:132771 original size:33 final size:34
Alignment explanation
Indices: 132720--132950 Score: 237
Period size: 33 Copynumber: 6.7 Consensus size: 34
132710 CGGAAATTAC
*
132720 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
132753 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
132787 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
132820 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
132853 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
*
132891 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
132924 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--CG--ATGAAAATCGCAA
132951 CGAGAGAATC
Statistics
Matches: 171, Mismatches: 9, Indels: 31
0.81 0.04 0.15
Matches are distributed among these distances:
32 1 0.01
33 95 0.56
34 31 0.18
35 7 0.04
36 4 0.02
37 3 0.02
38 30 0.18
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:132825 original size:19 final size:19
Alignment explanation
Indices: 132734--132950 Score: 249
Period size: 19 Copynumber: 12.4 Consensus size: 19
132724 GCAACGAGAG
132734 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
132753 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
132767 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
132787 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
132801 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
132820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
132839 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
132853 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
132872 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
132891 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
132905 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
132924 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
132943 AATCGCAA
1 AATCGCAA
132951 CGAGAGAATC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 7 0.04
17 6 0.04
18 4 0.02
19 94 0.56
20 13 0.08
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:132961 original size:33 final size:33
Alignment explanation
Indices: 132820--132972 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
132810 GCGAAATGAA
132820 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
132853 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
132885 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
132924 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
132957 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
132973 TATAAACGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 56 0.57
34 1 0.01
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:132988 original size:52 final size:52
Alignment explanation
Indices: 132762--132972 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
132752 AAATCCCAAC
132762 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
132815 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
132867 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
132919 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
132971 AT
1 AT
132973 TATAAACGCA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 142 0.90
53 16 0.10
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:133091 original size:52 final size:53
Alignment explanation
Indices: 132979--133094 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
132969 AAATTATAAA
132979 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
133032 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
133084 CGCATTGCGAT
1 CGCATTGCGAT
133095 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:133102 original size:19 final size:19
Alignment explanation
Indices: 132997--133094 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
132987 GATTCTCTCG
132997 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
133017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
133036 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
133050 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
133069 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
133088 TTGCGAT
1 TTGCGAT
133095 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:133220 original size:14 final size:14
Alignment explanation
Indices: 133201--133237 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
133191 CATCAATTAC
133201 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
133215 ACAAATCATCTTTT
1 ACAAATCAACTTTT
133229 ACAAATCAA
1 ACAAATCAA
133238 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:135205 original size:19 final size:19
Alignment explanation
Indices: 135165--135285 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
135155 TAGTTTACTT
* *
135165 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
135185 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
135204 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
135223 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
135237 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
135256 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
135275 TCGCAATGCGA
1 TCGCAACGCGA
135286 TTTTGGTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
14 8 0.09
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:135368 original size:20 final size:19
Alignment explanation
Indices: 135281--135376 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
135271 AAAATCGCAA
135281 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
135300 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
135314 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
135333 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* * *
135352 TGAGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
135372 TGCGA
1 TGCGA
135377 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 38 0.58
20 12 0.18
ACGTcount: A:0.09, C:0.15, G:0.30, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:135540 original size:93 final size:93
Alignment explanation
Indices: 135424--135706 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
135414 ATGGATTGCA
135424 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
135488 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
135516 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
135581 TAGCAGAATTGACAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
135609 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
135674 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
135702 TTACT
1 TTACT
135707 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
92 4 0.02
93 181 0.98
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:137431 original size:14 final size:14
Alignment explanation
Indices: 137412--137501 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
137402 TTGAAATGAA
137412 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
137426 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
137445 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
137459 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
137478 AATCGCAACGAGAG
1 AATCGCAACGAGAG
137492 AATCGCAACG
1 AATCGCAACG
137502 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:137449 original size:33 final size:33
Alignment explanation
Indices: 137404--137518 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
137394 TCTTTTGGTT
137404 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
137437 GAAATGACAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
137470 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
137503 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
137519 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:137450 original size:19 final size:18
Alignment explanation
Indices: 137404--137523 Score: 84
Period size: 19 Copynumber: 7.1 Consensus size: 18
137394 TCTTTTGGTT
137404 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
137421 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
*
137437 GAAATGACAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
137454 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
137470 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
137487 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
137503 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
137522 GA
1 GA
137524 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
14 30 0.37
15 3 0.04
16 6 0.07
17 5 0.06
18 3 0.04
19 34 0.42
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGC
Found at i:137554 original size:14 final size:14
Alignment explanation
Indices: 137535--137591 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
137525 TTTGGTTTCG
137535 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
137549 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
137568 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
137582 CGTTGCGATT
1 CGTTGCGATT
137592 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:137567 original size:33 final size:33
Alignment explanation
Indices: 137519--137599 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
137509 AAAATCGCAA
**
137519 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
137552 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
137585 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
137600 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:137602 original size:21 final size:21
Alignment explanation
Indices: 137576--137651 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
137566 CGCGTTGCGA
137576 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
137597 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
137617 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
137638 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
137652 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:137632 original size:41 final size:41
Alignment explanation
Indices: 137575--137652 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
137565 TCGCGTTGCG
*
137575 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
137616 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
137653 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:137777 original size:19 final size:19
Alignment explanation
Indices: 137753--137796 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
137743 CGAGAGAATA
137753 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
137772 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
137791 GCAACG
1 GCAACG
137797 ACAGAATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:138054 original size:22 final size:22
Alignment explanation
Indices: 138002--138056 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
137992 TGGTTGTGAG
**
138002 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
138024 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
138046 GGATTTCTTCG
1 GGATTTCTTCG
138057 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:138228 original size:20 final size:20
Alignment explanation
Indices: 138203--138396 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
138193 CTTTAAATAT
138203 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
138223 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
138245 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
138264 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
138284 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
138304 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
138324 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
138344 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
138364 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
138384 CGCGTTGCGATTT
1 CGCGTTGCGATTT
138397 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:138390 original size:60 final size:60
Alignment explanation
Indices: 138203--138396 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
138193 CTTTAAATAT
**
138203 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
138264 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
138324 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
138384 CGCGTTGCGATTT
1 CGCGTTGCGATTT
138397 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:138413 original size:21 final size:21
Alignment explanation
Indices: 138383--138465 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
138373 ATTTTCATAT
*
138383 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
138404 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
138425 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
138446 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
138466 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:138456 original size:42 final size:43
Alignment explanation
Indices: 138363--138461 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
138353 ATTTATGTGT
* *
138363 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
138404 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
138446 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
138462 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:144743 original size:24 final size:24
Alignment explanation
Indices: 144716--144770 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
144706 TATTATAAAT
144716 AATATTTTAA-ATTTAAATTTTTAA
1 AATATTTTAATA-TTAAATTTTTAA
* * *
144740 AATAGTTTAATATTGATTTTTTAA
1 AATATTTTAATATTAAATTTTTAA
144764 AATATTT
1 AATATTT
144771 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AATATTTTAATATTAAATTTTTAA
Found at i:144769 original size:16 final size:16
Alignment explanation
Indices: 144748--144778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
144738 AAAATAGTTT
144748 AATATTGATTTTTTAA
1 AATATTGATTTTTTAA
*
144764 AATATTTATTTTTTA
1 AATATTGATTTTTTA
144779 TTCCAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
AATATTGATTTTTTAA
Found at i:144831 original size:20 final size:20
Alignment explanation
Indices: 144791--144836 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
144781 CCAAAAAAAG
*
144791 TTAAATAATTTAATTTTTAA
1 TTAAATAATTTAATTTATAA
**
144811 TTAAATAATTTGGTTTATAA
1 TTAAATAATTTAATTTATAA
*
144831 TAAAAT
1 TTAAAT
144837 GTCTTATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTAAATAATTTAATTTATAA
Found at i:145577 original size:2 final size:2
Alignment explanation
Indices: 145570--145594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
145560 CCCTAAATTA
145570 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
145595 AGAAGGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:145860 original size:2 final size:2
Alignment explanation
Indices: 145853--145894 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
145843 TACTTATGAA
145853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145895 GTGTGTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.