Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012175.1 Kokia drynarioides strain JFW-HI SEQ_127176, 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: 284896
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:612 original size:41 final size:40
Alignment explanation
Indices: 552--723 Score: 159
Period size: 41 Copynumber: 4.2 Consensus size: 40
542 GTTTATATAA
* *
552 GCTAATGCTCTGGCCTTTAGCAGCGCTTTCCCATAAGCGTC
1 GCTAATGCTCCGACCTTTAGC-GCGCTTTCCCATAAGCGTC
* * * *
593 GCTAATGCTCCGTCTTTTAGCGGCGCTTTTCCC-TAAGTGTT
1 GCTAATGCTCCGACCTTTAGC-GCGC-TTTCCCATAAGCGTC
* *
634 GCTAATGTTCCGACCTTTAGCGACGCTTTCTCATAAGCGTC
1 GCTAATGCTCCGACCTTTAGCG-CGCTTTCCCATAAGCGTC
** * * * *
675 GCTAATGCT-TTACCTTTTGCGACGTTTTCCCATAAGTGTT
1 GCTAATGCTCCGACCTTTAGCG-CGCTTTCCCATAAGCGTC
715 GCTAATGCT
1 GCTAATGCT
724 TTACCTTTTG
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
40 39 0.36
41 63 0.58
42 6 0.06
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (40 bp):
GCTAATGCTCCGACCTTTAGCGCGCTTTCCCATAAGCGTC
Found at i:692 original size:82 final size:81
Alignment explanation
Indices: 565--721 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 81
555 AATGCTCTGG
** *
565 CCTTTAGCAGCGCTTTCCCATAAGCGTCGCTAATGCTCCGTCTTTTAGCGGCGCTTTTCCC-TAA
1 CCTTTAGCAGCGCTTTCCCATAAGCGTCGCTAATGCTCCACCTTTT-GCGACG-TTTTCCCATAA
629 GTGTTGCTAATGTTCCGA
64 GTGTTGCTAATGTTCCGA
* **
647 CCTTTAGC-GACGCTTTCTCATAAGCGTCGCTAATGCTTTACCTTTTGCGACGTTTTCCCATAAG
1 CCTTTAGCAG-CGCTTTCCCATAAGCGTCGCTAATGCTCCACCTTTTGCGACGTTTTCCCATAAG
711 TGTTGCTAATG
65 TGTTGCTAATG
722 CTTTACCTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 7 0.10
81 21 0.31
82 39 0.58
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (81 bp):
CCTTTAGCAGCGCTTTCCCATAAGCGTCGCTAATGCTCCACCTTTTGCGACGTTTTCCCATAAGT
GTTGCTAATGTTCCGA
Found at i:743 original size:40 final size:40
Alignment explanation
Indices: 578--734 Score: 147
Period size: 40 Copynumber: 3.9 Consensus size: 40
568 TTAGCAGCGC
**** *
578 TTTCCCATAAGCGTCGCTAATGCTCCGTCTTTTAGCGGCGCT
1 TTTCCCATAAGCGTCGCTAATGCTTTACCTTTT-GCGACG-T
* * * * *
620 TTTCCC-TAAGTGTTGCTAATG-TTCCGACCTTTAGCGACGC
1 TTTCCCATAAGCGTCGCTAATGCTT--TACCTTTTGCGACGT
*
660 TTTCTCATAAGCGTCGCTAATGCTTTACCTTTTGCGACGT
1 TTTCCCATAAGCGTCGCTAATGCTTTACCTTTTGCGACGT
* *
700 TTTCCCATAAGTGTTGCTAATGCTTTACCTTTTGC
1 TTTCCCATAAGCGTCGCTAATGCTTTACCTTTTGC
735 TGTGTTTTCT
Statistics
Matches: 93, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
40 50 0.54
41 31 0.33
42 12 0.13
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (40 bp):
TTTCCCATAAGCGTCGCTAATGCTTTACCTTTTGCGACGT
Found at i:5726 original size:29 final size:29
Alignment explanation
Indices: 5663--5728 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
5653 AATTAATAAC
* *
5663 ACAATAAAAATATAATTATAGTATTAAAT
1 ACAATAAAAATATAATCATAGTAATAAAT
* *
5692 AAAATAATAATATAATCATAGTAAT-AAT
1 ACAATAAAAATATAATCATAGTAATAAAT
5720 GACAATAAA
1 -ACAATAAA
5729 TATTAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (29 bp):
ACAATAAAAATATAATCATAGTAATAAAT
Found at i:5920 original size:17 final size:16
Alignment explanation
Indices: 5900--5955 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
5890 AAATGAAGGC
5900 AAAAATACAAATAACAT
1 AAAAATACAAATAA-AT
*
5917 AAAAAATAACAAACAAAT
1 -AAAAAT-ACAAATAAAT
5935 -AAAATACGTAAATAAAT
1 AAAAATAC--AAATAAAT
5952 AAAA
1 AAAA
5956 TTAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.06
16 5 0.16
17 7 0.22
18 11 0.34
19 7 0.22
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAATACAAATAAAT
Found at i:5921 original size:18 final size:18
Alignment explanation
Indices: 5900--5938 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5890 AAATGAAGGC
*
5900 AAAAAT-ACAAATAACATA
1 AAAAATAACAAACAA-ATA
5918 AAAAATAACAAACAAATA
1 AAAAATAACAAACAAATA
5936 AAA
1 AAA
5939 TACGTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAATAACAAACAAATA
Found at i:6139 original size:20 final size:20
Alignment explanation
Indices: 6108--6164 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
6098 TTAATGATAA
6108 ATAAATAGATAATAAATTAAAT
1 ATAAATA-ATAATAAA-TAAAT
* *
6130 GTCAA-AATAAATAAATAAAT
1 ATAAATAAT-AATAAATAAAT
6150 ATAAATAATAATAAA
1 ATAAATAATAATAAA
6165 AAAGAATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 16 0.55
21 10 0.34
22 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAATAATAATAAATAAAT
Found at i:6453 original size:24 final size:24
Alignment explanation
Indices: 6426--6484 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
6416 ATCTTATTCC
* *
6426 AAAAAAAATTC-TCTCTTAACAAA
1 AAAAAAAATCCTTCTCTAAACAAA
6449 AAAAAAAATCCTTCTCTAAACAAA
1 AAAAAAAATCCTTCTCTAAACAAA
6473 AAAAAAAATCCT
1 AAAAAAAATCCT
6485 CCCCCTTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAAAAATCCTTCTCTAAACAAA
Found at i:7093 original size:52 final size:54
Alignment explanation
Indices: 7037--7153 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 54
7027 TTTTTTTTAG
* * *
7037 GTGTAAGATTTGTCGTTGC-GACTTTAATCTGTTCCCAC-TTTTT-TTTCAAAAA
1 GTGTAAGATTTGTCATTGCAG-CTTCAATATGTTCCCACTTTTTTCTTTCAAAAA
* * *
7089 GTGTAAAATTTGTCATTGCAGCTTCAATATGTTCCCTCTTTTTTTCTTTCAAAAG
1 GTGTAAGATTTGTCATTGCAGCTTCAATATGTTCCCAC-TTTTTTCTTTCAAAAA
7144 GTGTAAGATT
1 GTGTAAGATT
7154 CTCTGTTGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
52 31 0.57
53 1 0.02
54 5 0.09
55 17 0.31
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (54 bp):
GTGTAAGATTTGTCATTGCAGCTTCAATATGTTCCCACTTTTTTCTTTCAAAAA
Found at i:7294 original size:98 final size:99
Alignment explanation
Indices: 7187--7393 Score: 233
Period size: 98 Copynumber: 2.1 Consensus size: 99
7177 CCCTATTTGG
* * * *
7187 TTTTAAGGTGTTAA-ATCTGCCGTCATGGCTTCAATC-TATCCCTCTAT-GGTTTTAGGGTTTTA
1 TTTTAAGGTGTTAAGATCTACCGTCATGACTTCAATCAT-TCCCTCT-TCGATTTTAGGGTGTTA
*
7249 GATCCACAATCACGGCTTCAACCTATCCCTCTTCAA
64 GATCCACAATCACAGCTTCAACCTATCCCTCTTCAA
* ** *
7285 TTTTAAGGTG-TAAGATCTATCGTTGTGACTTCAATCATTCCCTCTTCGATTTTAGGGTGTTAGG
1 TTTTAAGGTGTTAAGATCTACCGTCATGACTTCAATCATTCCCTCTTCGATTTTAGGGTGTTAGA
* ** * * *
7349 TTCACCGTTACAGCTTCGACCTATCCCTCTTCAG
66 TCCACAATCACAGCTTCAACCTATCCCTCTTCAA
7383 TTTTAAGGTGT
1 TTTTAAGGTGT
7394 AAGGTTCGCC
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
97 4 0.04
98 85 0.94
99 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (99 bp):
TTTTAAGGTGTTAAGATCTACCGTCATGACTTCAATCATTCCCTCTTCGATTTTAGGGTGTTAGA
TCCACAATCACAGCTTCAACCTATCCCTCTTCAA
Found at i:7807 original size:49 final size:49
Alignment explanation
Indices: 7213--7813 Score: 330
Period size: 49 Copynumber: 12.3 Consensus size: 49
7203 CTGCCGTCAT
* * * * * * *
7213 GGCTTCAATCTATCCCTCTATGGTTTTAGGGTTTTAGATCCACAATCAC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
** * * * * * * **
7262 GGCTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCTATCGTTGT
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * * * *
7311 GACTTCAATC-ATTCCCTCTTCGATTTTAGGGTGTTAGGTTCACCGTTAC
1 GGCTTCAACCTA-TCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * * * * * *
7360 AGCTTCGACCTATCCCTC-TTCAGTTTTAAGGTGTAAGGTTCGCCATTAC
1 GGCTTCAACCTATCCCTCTTTGA-TTTTAGGGTGTTAGGTCCACCATTAC
* * * * * ** *
7409 AGCTTCAACCTTTCCCTCTTTGGTTTTAAGGTGTTAGATCCGTCATTGC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* ** * * *
7458 GGCTTTAATATATCCCTCTTTAATTTTAGGGTTTTAGGTCCATCATTAC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * * * * * * *
7507 GACTTCAACCTATCCCTCTTCGATTTTAAGGTGTAAGATCCATCGTTGC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * * * * * *** *
7556 GACTTTAATCT-TCCCT-TCTTCATTTTTTGGGTGTTAAGTCTGTCGTTAC
1 GGCTTCAACCTATCCCTCT-TTGA-TTTTAGGGTGTTAGGTCCACCATTAC
** * * * **
7605 GGCTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGATCCACCGCTAC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * * * * * * *
7654 GGCTTCAATCTTTTCCTCTTCGATTTTAGGGTATTAGATCCACCATAAT
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
* * **** *
7703 GGCTTCAATCTATCCCT-TTTCGATCTTAGGGTGTTAGGTTTTTCATTGC
1 GGCTTCAACCTATCCCTCTTT-GATTTTAGGGTGTTAGGTCCACCATTAC
* * * * *
7752 GACTTCAACCTATCCCTCTTTGATTTTAGGATGTTAGGTTCGCCGTTAC
1 GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
7801 GGCTTCAACCTAT
1 GGCTTCAACCTAT
7814 TCCTTTTTAA
Statistics
Matches: 413, Mismatches: 129, Indels: 20
0.73 0.23 0.04
Matches are distributed among these distances:
47 1 0.00
48 12 0.03
49 386 0.93
50 13 0.03
51 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (49 bp):
GGCTTCAACCTATCCCTCTTTGATTTTAGGGTGTTAGGTCCACCATTAC
Found at i:8790 original size:6 final size:6
Alignment explanation
Indices: 8779--8860 Score: 94
Period size: 6 Copynumber: 13.3 Consensus size: 6
8769 TCTCAGCCCC
*
8779 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTC TTCATTT TTCTTT TTCTTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT TTCTTT TTCTT-T
* * *
8829 TTTTTT TTCTTT TAT-TCT CTCTTT TTCTTT TT
1 TTCTTT TTCTTT T-TCTTT TTCTTT TTCTTT TT
8861 GCTAGTTTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
5 1 0.02
6 52 0.81
7 11 0.17
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:8820 original size:37 final size:37
Alignment explanation
Indices: 8781--8860 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
8771 TCAGCCCCTT
*
8781 CTTTTTCTT-TTTCTTTTTCTTTTTCTTCT-TCATTTTT
1 CTTTTTCTTCTTTCTTTTTC-TTTTATTCTCTC-TTTTT
*
8818 CTTTTTCTTCTTTTTTTTTCTTTTATTCTCTCTTTTT
1 CTTTTTCTTCTTTCTTTTTCTTTTATTCTCTCTTTTT
8855 CTTTTT
1 CTTTTT
8861 GCTAGTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 28 0.72
38 11 0.28
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.79
Consensus pattern (37 bp):
CTTTTTCTTCTTTCTTTTTCTTTTATTCTCTCTTTTT
Found at i:8856 original size:10 final size:9
Alignment explanation
Indices: 8778--8857 Score: 65
Period size: 10 Copynumber: 8.3 Consensus size: 9
8768 ATCTCAGCCC
8778 CTTCTTTTT
1 CTTCTTTTT
8787 CTT-TTTCTT
1 CTTCTTT-TT
*
8796 TTTCTTTTT
1 CTTCTTTTT
8805 CTTCTTCATTT
1 CTTCTT--TTT
8816 -TTCTTTTT
1 CTTCTTTTT
8824 CTTCTTTTTT
1 CTTC-TTTTT
*
8834 TTTCTTTTATT
1 CTTC-TTT-TT
8845 CTCTCTTTTT
1 CT-TCTTTTT
8855 CTT
1 CTT
8858 TTTGCTAGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
8 6 0.10
9 18 0.31
10 24 0.41
11 9 0.15
12 2 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTCTTTTT
Found at i:16527 original size:21 final size:21
Alignment explanation
Indices: 16503--16560 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
16493 AATAAATATC
**
16503 AATCAATTAAAAATATTCTCA
1 AATCAATTAAAAATATAATCA
*
16524 AATC-ATGAAAAATAATAATCA
1 AATCAATTAAAAAT-ATAATCA
*
16545 AATTAATGTAAAAATA
1 AATCAAT-TAAAAATA
16561 GAAAATAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.28
21 12 0.41
22 3 0.10
23 6 0.21
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (21 bp):
AATCAATTAAAAATATAATCA
Found at i:23056 original size:21 final size:21
Alignment explanation
Indices: 23032--23071 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23022 ACTGTATTTC
*
23032 TATACAATTTGAAATTTAGTA
1 TATACAATTTAAAATTTAGTA
* *
23053 TATATATTTTAAAATTTAG
1 TATACAATTTAAAATTTAG
23072 AAATTATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
TATACAATTTAAAATTTAGTA
Found at i:24793 original size:29 final size:29
Alignment explanation
Indices: 24713--24792 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
24703 ATATCAAAAT
* *
24713 TATACATGAATTATAGTTTAATGTGCAATTG
1 TATACATGAATTTTAATTT--TGTGCAATTG
* *
24744 TATGCATGAATTTTAATTTTGTGCAATTT
1 TATACATGAATTTTAATTTTGTGCAATTG
*
24773 TATACATGAAATTTTGATTT
1 TATACATG-AATTTTAATTT
24793 GATCAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.38
30 10 0.24
31 16 0.38
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (29 bp):
TATACATGAATTTTAATTTTGTGCAATTG
Found at i:24894 original size:29 final size:29
Alignment explanation
Indices: 24841--24896 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
24831 TAACATCATT
* *
24841 TTATATTTATATATTACAAACATAAATAA
1 TTATATTTATATAATACAAAAATAAATAA
* *
24870 TTATATTTATTTAATATAAAAATAAAT
1 TTATATTTATATAATACAAAAATAAAT
24897 TGATGTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TTATATTTATATAATACAAAAATAAATAA
Found at i:25008 original size:29 final size:31
Alignment explanation
Indices: 24936--25023 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
24926 ATTAAATCAA
* * * *
24936 AATTAAAGTTTTAAGTATA-TATATGAACCAC
1 AATTAAAGTTTCACGTATACAAT-TGTACCAC
* * *
24967 AATTAGAGTTTCACGTGTATAATTGTACCA-
1 AATTAAAGTTTCACGTATACAATTGTACCAC
24997 AATTAAAG-TTCACGTATACAATTGTAC
1 AATTAAAGTTTCACGTATACAATTGTAC
25024 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 17 0.36
30 7 0.15
31 21 0.45
32 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
AATTAAAGTTTCACGTATACAATTGTACCAC
Found at i:28580 original size:15 final size:15
Alignment explanation
Indices: 28556--28585 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28546 ATTTGGGACT
*
28556 TCTACTGATACTATG
1 TCTACCGATACTATG
28571 TCTACCGATACTATG
1 TCTACCGATACTATG
28586 GTCATATCTA
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:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TCTACCGATACTATG
Found at i:30081 original size:88 final size:90
Alignment explanation
Indices: 29890--30094 Score: 238
Period size: 88 Copynumber: 2.3 Consensus size: 90
29880 TTAATGATGT
* ** ** *
29890 AAAAAGCCCTCAAACTTTTTCAAAAAAGACAATTAAGCCCTAACTTTTTTTTTTACTAAATTGGG
1 AAAAAGCCCTCAAACTTTTTAAAAAAAGACAATTAAGCCCTAACTAATTTTTGCACTAAATTGAG
29955 TACTTAAACTATCAAAAATGAATAA
66 TACTTAAACTATCAAAAATGAATAA
* * * *
29980 AAAAA-CCCACAAACTTTTTAAAAAGAAG-CAATTAAGCCCTTA-TAATTTTTGCATTCAATTGA
1 AAAAAGCCCTCAAACTTTTTAAAAA-AAGACAATTAAGCCCTAACTAATTTTTGCACTAAATTGA
* ** *
30042 GTACTTGAACT-TTTAAAATGCATAA
65 GTACTTAAACTATCAAAAATGAATAA
30067 AAAAAGCCCTCAAACTTTTTCAAAAAAA
1 AAAAAGCCCTCAAACTTTTT-AAAAAAA
30095 TAAATAAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
87 16 0.16
88 38 0.39
89 35 0.36
90 8 0.08
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (90 bp):
AAAAAGCCCTCAAACTTTTTAAAAAAAGACAATTAAGCCCTAACTAATTTTTGCACTAAATTGAG
TACTTAAACTATCAAAAATGAATAA
Found at i:30255 original size:30 final size:31
Alignment explanation
Indices: 30219--30296 Score: 117
Period size: 30 Copynumber: 2.6 Consensus size: 31
30209 AATGATAAAA
*
30219 AATAAAAAACAATAAAAATTA-TTAAATTTT
1 AATAAAAAACTATAAAAATTATTTAAATTTT
30249 AATAAAAAACTATAAAAA-TATTTAAATTTT
1 AATAAAAAACTATAAAAATTATTTAAATTTT
*
30279 -ATAAAAAATTATAAAAAT
1 AATAAAAAACTATAAAAAT
30297 CTTAAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 18 0.41
30 26 0.59
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
AATAAAAAACTATAAAAATTATTTAAATTTT
Found at i:30408 original size:20 final size:21
Alignment explanation
Indices: 30338--30411 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 21
30328 AAAAAGTTAT
* * * *
30338 AAAATTTTATAAAGTCGTAAG
1 AAAATTATAGAAAATCGTAAA
*
30359 AAAATTTTAGAAAAT-GTAAA
1 AAAATTATAGAAAATCGTAAA
* *
30379 GAAA-TATA-AAATTCGTAAA
1 AAAATTATAGAAAATCGTAAA
30398 AAAATTATA-AAAAT
1 AAAATTATAGAAAAT
30412 TATAGTACTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 4 0.09
19 11 0.26
20 15 0.35
21 13 0.30
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAATTATAGAAAATCGTAAA
Found at i:30412 original size:21 final size:21
Alignment explanation
Indices: 30338--30412 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
30328 AAAAAGTTAT
* * * *
30338 AAAATTTTATAAAGTCGTAAG
1 AAAATTATAAAAATTCGTAAA
*
30359 AAAATTTTAGAAAA-T-GTAAA
1 AAAATTATA-AAAATTCGTAAA
*
30379 GAAA-TAT-AAAATTCGTAAA
1 AAAATTATAAAAATTCGTAAA
30398 AAAATTATAAAAATT
1 AAAATTATAAAAATT
30413 ATAGTACTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 10 0.23
20 10 0.23
21 16 0.36
22 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAAATTCGTAAA
Found at i:30687 original size:19 final size:20
Alignment explanation
Indices: 30645--30708 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 20
30635 TGTTTATGAT
*
30645 TTTATAATTTTTTATCT-AAC
1 TTTATAATTTTTTAT-TAAAA
30665 TTTAT-ATTTTTTATTAAAA
1 TTTATAATTTTTTATTAAAA
*
30684 TTTAATAATTTTTTA-TAAAT
1 TTT-ATAATTTTTTATTAAAA
30704 TTTAT
1 TTTAT
30709 TTATTATAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.03
19 16 0.41
20 14 0.36
21 8 0.21
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATAATTTTTTATTAAAA
Found at i:31065 original size:82 final size:85
Alignment explanation
Indices: 30901--31090 Score: 201
Period size: 81 Copynumber: 2.2 Consensus size: 85
30891 TTTTGAACCA
* * * *
30901 TTAAAATACATAAAAAAGACCCTCAAACTTTTCAAAAAAAGTAATTAAGCCCCTACTTTTATTTT
1 TTAAAATACATAAAAAA-AACCTCAAAC--TTCAAAAAAAATAATTAAGCCCCCACATTTATTTT
*
30966 ACAATCAATTGGATACTTGAAATT
63 ACAATCAATTGGATACTTG-AACT
* *
30990 TTAAAATACATAAAAAAAACCTCAAAC-T-AAAAAAAATAATTAATCCCCCA-ATTT-TTTTGCA
1 TTAAAATACATAAAAAAAACCTCAAACTTCAAAAAAAATAATTAAGCCCCCACATTTATTTTACA
*
31051 TTCAATT-GAGTACTTGAACT
66 ATCAATTGGA-TACTTGAACT
* * *
31071 GTCAAATACATCAAAAAAAC
1 TTAAAATACATAAAAAAAAC
31091 TTTTTGACAC
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
81 22 0.25
82 18 0.20
83 3 0.03
84 19 0.21
85 1 0.01
88 9 0.10
89 17 0.19
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (85 bp):
TTAAAATACATAAAAAAAACCTCAAACTTCAAAAAAAATAATTAAGCCCCCACATTTATTTTACA
ATCAATTGGATACTTGAACT
Found at i:31250 original size:24 final size:23
Alignment explanation
Indices: 31223--31274 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
31213 TAAAAATTAT
31223 TAAATTTTAATAAAATATTAAAAA
1 TAAATTTTAATAAAA-ATTAAAAA
* *
31247 TAAAATTTATTAAAAATTAAAAA
1 TAAATTTTAATAAAAATTAAAAA
*
31270 AAAAT
1 TAAAT
31275 ATAAAAAACC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATTTTAATAAAAATTAAAAA
Found at i:31269 original size:23 final size:24
Alignment explanation
Indices: 31223--31291 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 24
31213 TAAAAATTAT
*
31223 TAAATTTTAATAAAATATTAAAAA
1 TAAAATTTAATAAAATATTAAAAA
*
31247 TAAAATTTATTAAAA-ATTAAAAA
1 TAAAATTTAATAAAATATTAAAAA
* **
31270 -AAAATATAA-AAAACCTTAAAAA
1 TAAAATTTAATAAAATATTAAAAA
31292 AGCCTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 4 0.10
22 14 0.36
23 8 0.21
24 13 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAATTTAATAAAATATTAAAAA
Found at i:31554 original size:91 final size:92
Alignment explanation
Indices: 31418--31607 Score: 229
Period size: 91 Copynumber: 2.1 Consensus size: 92
31408 AGCTTAATTG
** * ** * *
31418 TTTTTTTGAAAAAGTTTGAAGGTTTTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTG
1 TTTTTTTGAAAAAGTTTGAAGGTCCTCTTTGATGCATTTCAAAAGTTCAAGTATCCAAATAAGTG
* *
31483 TAAAATAAAAGCAGGGGCTTAACTGCT
66 TAAAATAAAAACAAGGGCTTAACTGCT
* * **
31510 TTTTTTTGATAAAGTTT-CAGGTCCTCTTTGATGCATTTCAAAAGTTCAAGTATTTAAATAAGTG
1 TTTTTTTGAAAAAGTTTGAAGGTCCTCTTTGATGCATTTCAAAAGTTCAAGTATCCAAATAAGTG
* * *
31574 TAAAATAAAAATAAGGGCTTAATTGTT
66 TAAAATAAAAACAAGGGCTTAACTGCT
31601 TTTTTTT
1 TTTTTTT
31608 TTTAAATTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
91 66 0.80
92 16 0.20
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (92 bp):
TTTTTTTGAAAAAGTTTGAAGGTCCTCTTTGATGCATTTCAAAAGTTCAAGTATCCAAATAAGTG
TAAAATAAAAACAAGGGCTTAACTGCT
Found at i:39034 original size:24 final size:24
Alignment explanation
Indices: 39006--39080 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
38996 AGAAATAATC
* *
39006 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
39030 TTTCAATTAAACT-TGGTTTAGTTG
1 TTTCAATTAAACTCT-GTTTAGTTG
*
39054 TTTCAATTAAACTCAGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
39078 TTT
1 TTT
39081 AAGTCAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:42899 original size:24 final size:24
Alignment explanation
Indices: 42871--42945 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
42861 AGAAATAATC
*
42871 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
42895 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
42919 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
42943 TTT
1 TTT
42946 GAGTCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:47559 original size:3 final size:3
Alignment explanation
Indices: 47551--47588 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
47541 CCTCGACAGG
* *
47551 TTC TTC TTC TTC TTC TTG TTC TTG TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
47589 TCTCTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:47594 original size:12 final size:13
Alignment explanation
Indices: 47551--47607 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
47541 CCTCGACAGG
47551 TTCTTCTTCTTC-
1 TTCTTCTTCTTCT
* *
47563 TTCTTGTTCTT-G
1 TTCTTCTTCTTCT
47575 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
*
47588 TTC-TCTTTTTCT
1 TTCTTCTTCTTCT
47600 TTC-TCTTC
1 TTCTTCTTC
47608 CTCATCTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 35 0.92
13 3 0.08
ACGTcount: A:0.00, C:0.28, G:0.04, T:0.68
Consensus pattern (13 bp):
TTCTTCTTCTTCT
Found at i:53943 original size:15 final size:15
Alignment explanation
Indices: 53923--53963 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
53913 ATTGGCATTG
*
53923 TAACCTCTTTGTTTA
1 TAACCTCCTTGTTTA
53938 TAACCTCCTTGTTTA
1 TAACCTCCTTGTTTA
53953 TAACCTCCTTG
1 TAACCTCCTTG
53964 ATTTGAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (15 bp):
TAACCTCCTTGTTTA
Found at i:68008 original size:19 final size:19
Alignment explanation
Indices: 67968--68008 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
67958 GAATGTCAAT
* * *
67968 TTGGTATCAATACTTGACC
1 TTGGTATCAATACCTAAAC
67987 TTGGTATCAATACCTAAAC
1 TTGGTATCAATACCTAAAC
68006 TTG
1 TTG
68009 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGGTATCAATACCTAAAC
Found at i:71087 original size:7 final size:7
Alignment explanation
Indices: 71075--71113 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
71065 TTGATCAAGT
71075 GTTTAAG
1 GTTTAAG
71082 GTTTAAG
1 GTTTAAG
* *
71089 GTTTTAT
1 GTTTAAG
71096 GTTTAAG
1 GTTTAAG
*
71103 GTTTAGG
1 GTTTAAG
71110 GTTT
1 GTTT
71114 CAAGTGTAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (7 bp):
GTTTAAG
Found at i:71100 original size:21 final size:21
Alignment explanation
Indices: 71074--71113 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
71064 TTTGATCAAG
71074 TGTTTAAGGTTTAAGGTTTTA
1 TGTTTAAGGTTTAAGGTTTTA
*
71095 TGTTTAAGGTTTAGGGTTT
1 TGTTTAAGGTTTAAGGTTT
71114 CAAGTGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (21 bp):
TGTTTAAGGTTTAAGGTTTTA
Found at i:71210 original size:21 final size:20
Alignment explanation
Indices: 71175--71214 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
71165 TTAAGGTTCA
71175 AGATTTAAGTTTAGGGTTTG
1 AGATTTAAGTTTAGGGTTTG
*
71195 AGATTTAGGATTTAGGGTTT
1 AGATTTAAG-TTTAGGGTTT
71215 AATATTCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (20 bp):
AGATTTAAGTTTAGGGTTTG
Found at i:72389 original size:9 final size:10
Alignment explanation
Indices: 72368--72392 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
72358 TTATTAATTT
72368 AAAATTTTAA
1 AAAATTTTAA
72378 AAAATTTTAA
1 AAAATTTTAA
72388 AAAAT
1 AAAAT
72393 CTAAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:75642 original size:93 final size:93
Alignment explanation
Indices: 75483--75668 Score: 338
Period size: 93 Copynumber: 2.0 Consensus size: 93
75473 AGCATGTTGG
75483 TTGAATTTTTATGAATGGTGAATTACTCAATTTTTATTAATAGAACTGAAATATGTTTATGGTTC
1 TTGAATTTTTATGAATGGTGAATTACTCAATTTTTATTAATAGAACTGAAATATGTTTATGGTTC
*
75548 CATAATTAATTTGGAAATTTGGAAATTT
66 CATAATTAATCTGGAAATTTGGAAATTT
*
75576 TTGAATTTTTATGAATGGT-AGATTACTCTATTTTTATTAATAGAACTGAAATATGTTTATGGTT
1 TTGAATTTTTATGAATGGTGA-ATTACTCAATTTTTATTAATAGAACTGAAATATGTTTATGGTT
75640 CCATAATTAATCTGGAAATTTGGAAATTT
65 CCATAATTAATCTGGAAATTTGGAAATTT
75669 ATGCTTAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
92 1 0.01
93 89 0.99
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (93 bp):
TTGAATTTTTATGAATGGTGAATTACTCAATTTTTATTAATAGAACTGAAATATGTTTATGGTTC
CATAATTAATCTGGAAATTTGGAAATTT
Found at i:80300 original size:24 final size:24
Alignment explanation
Indices: 80239--80301 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
80229 TAGTGTAATA
* *
80239 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
80263 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
80287 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
80302 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:82263 original size:24 final size:24
Alignment explanation
Indices: 82236--82286 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
82226 CATTTAACTC
*
82236 AAACAAATAAACATAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
82260 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
82284 AAA
1 AAA
82287 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:85346 original size:30 final size:30
Alignment explanation
Indices: 85270--85329 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
85260 ACTCTTTTTA
85270 AATAATAATTGATATTAAATTATTTAAAAT
1 AATAATAATTGATATTAAATTATTTAAAAT
85300 AATAATAATTGATATTAAATTATTTAAAAT
1 AATAATAATTGATATTAAATTATTTAAAAT
85330 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
AATAATAATTGATATTAAATTATTTAAAAT
Found at i:85383 original size:38 final size:39
Alignment explanation
Indices: 85336--85460 Score: 141
Period size: 38 Copynumber: 3.2 Consensus size: 39
85326 AAATTATTAT
85336 TATT-ATTATTATTTATCTAAAACTCTTTTAAATAATAA
1 TATTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
*
85374 TA-TAATTATTATTTATCTAAAACTCTTTTAATTAA-AA
1 TATTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
* *
85411 TTCTATTTAATTATCT-TTTATTTAAAACTCTTTTAAGTAATAA
1 ---TA-TTAATTAT-TATTTATCTAAAACTCTTTTAAATAATAA
85454 TAATTAA
1 T-ATTAA
85461 ATTCTATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
37 3 0.04
38 32 0.43
40 7 0.09
41 1 0.01
42 29 0.39
43 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (39 bp):
TATTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
Found at i:85421 original size:16 final size:15
Alignment explanation
Indices: 85391--85446 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
85381 ATTATTTATC
85391 TAAAACTCTTTTAAT
1 TAAAACTCTTTTAAT
*
85406 TAAAATTCTATTTAAT
1 TAAAACTCT-TTTAAT
*
85422 T---A-TCTTTTATT
1 TAAAACTCTTTTAAT
85433 TAAAACTCTTTTAA
1 TAAAACTCTTTTAA
85447 GTAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 1 0.03
14 1 0.03
15 15 0.45
16 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAAACTCTTTTAAT
Found at i:85458 original size:52 final size:52
Alignment explanation
Indices: 85402--85506 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 52
85392 AAAACTCTTT
* *
85402 TAATTAAAATTCTA-TTTAATTATCT-TTTATTTAAAACTCTTTTAAGTAATAA
1 TAATT-AAATTCTATTTTAATTAT-TATTTATCTAAAACTCTTTTAAATAATAA
85454 TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
1 TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
85506 T
1 T
85507 TAGATTCTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
51 9 0.18
52 40 0.82
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (52 bp):
TAATTAAATTCTATTTTAATTATTATTTATCTAAAACTCTTTTAAATAATAA
Found at i:85496 original size:26 final size:25
Alignment explanation
Indices: 85404--85498 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
85394 AACTCTTTTA
*
85404 ATTAAAATTCTATTTAATTATCT-TTT
1 ATTAAAACTCT-TTTAATTAT-TATTT
* * * *
85430 ATTTAAAACTCTTTTAAGTAATAATA
1 A-TTAAAACTCTTTTAATTATTATTT
* *
85456 ATTAAATTCTATTTTAATTATTATTT
1 ATTAAA-ACTCTTTTAATTATTATTT
85482 ATCTAAAACTCTTTTAA
1 AT-TAAAACTCTTTTAA
85499 ATAATAATTA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
25 6 0.12
26 33 0.63
27 13 0.25
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTAAAACTCTTTTAATTATTATTT
Found at i:94968 original size:145 final size:148
Alignment explanation
Indices: 94798--95092 Score: 488
Period size: 147 Copynumber: 2.0 Consensus size: 148
94788 AATCAATGTA
* *
94798 ACTGTTTTGTTCGGCAAACCAAAGTTGAGTAATTATTAATGTAATTTACCCT-AAAAAAAACTAA
1 ACTGTTTTGTTCAGCAAACCAAAGTTGAGTAATTATAAATGTAATTTACCCTAAAAAAAAACTAA
*
94862 ATCTTTAACCTATGCATTGTATAATAAAAAACTAATAGTAAAATTTTACTT-AAAA-TTTGAAAC
66 ATCTTTAACCTATGCATTGTATAATAAAAAACAAATAGTAAAATTTTACTTAAAAATTTTGAAAC
94925 ATTATAAATTACTTTGAC
131 ATTATAAATTACTTTGAC
* * *
94943 ACTGTTTTGTTCAGCAGATCAAAGTTGAGTAATTGTAAATGTAATTTACCCTAAAAAAAAAACTA
1 ACTGTTTTGTTCAGCAAACCAAAGTTGAGTAATTATAAATGTAATTTACCCT-AAAAAAAAACTA
*
95008 AATCTTTAACCTATGCATTGTATAATAAGAAACAAATAGTAAAATTTTACTTAAAAAATTTTGAA
65 AATCTTTAACCTATGCATTGTATAATAAAAAACAAATAGTAAAATTTTACTT-AAAAATTTTGAA
95073 ACATTATAAATTACTTTGAC
129 ACATTATAAATTACTTTGAC
95093 GGTTGCATAT
Statistics
Matches: 138, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
145 47 0.34
147 61 0.44
149 4 0.03
150 26 0.19
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.35
Consensus pattern (148 bp):
ACTGTTTTGTTCAGCAAACCAAAGTTGAGTAATTATAAATGTAATTTACCCTAAAAAAAAACTAA
ATCTTTAACCTATGCATTGTATAATAAAAAACAAATAGTAAAATTTTACTTAAAAATTTTGAAAC
ATTATAAATTACTTTGAC
Found at i:100433 original size:65 final size:65
Alignment explanation
Indices: 100329--100458 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
100319 ATTTGAACAG
100329 CACAAAATTAGCTTTTGGAAGAATTATTCGGAGGTCCTTACACTTGCATAACAATTAAAATCAGC
1 CACAAAATTAGCTTTTGGAAGAATTATTCGGAGGTCCTTACACTTGCATAACAATTAAAATCAGC
100394 CACAAAATTAGCTTTTGGAAGAATTATTCGGAGGTCCTTACACTTGCATAACAATTAAAATCAGC
1 CACAAAATTAGCTTTTGGAAGAATTATTCGGAGGTCCTTACACTTGCATAACAATTAAAATCAGC
100459 TCCTAACAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (65 bp):
CACAAAATTAGCTTTTGGAAGAATTATTCGGAGGTCCTTACACTTGCATAACAATTAAAATCAGC
Found at i:101521 original size:198 final size:198
Alignment explanation
Indices: 101174--101568 Score: 709
Period size: 198 Copynumber: 2.0 Consensus size: 198
101164 ATGGACGCAG
101174 TAATTGAAAGGTGCAAGCTTGATTTAGATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTCA
1 TAATTGAAAGGTGCAAGCTTGATTTAGATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTCA
* * * *
101239 AGAGAGCTATATTACCTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACCTAACCCG
66 AAAGAGCTATATTAACTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACATAACACG
* *
101304 TCCCTGTTATTTTACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCATGT
131 TCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCATGT
101369 TTA
196 TTA
*
101372 TAATTGAAAGGTGCAAGCTTGATTTATATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTCA
1 TAATTGAAAGGTGCAAGCTTGATTTAGATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTCA
* *
101437 AAAGAGCTATATTAACTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACATAGCATG
66 AAAGAGCTATATTAACTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACATAACACG
101502 TCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCATGT
131 TCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCATGT
101567 TT
196 TT
101569 TTCTAAGTAA
Statistics
Matches: 188, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
198 188 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (198 bp):
TAATTGAAAGGTGCAAGCTTGATTTAGATCTTAGCCCGATTAAATTAAAGGTTTTTAATAACTCA
AAAGAGCTATATTAACTTGCATAACTTTTAAATTTGTGTGATTAAACTATTTCAAACATAACACG
TCCCTGTTACTTCACATAAACTCTATGAAACCCTTAGTTAAATATGATCATGGTAGTATGCATGT
TTA
Found at i:102729 original size:22 final size:22
Alignment explanation
Indices: 102704--102746 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
102694 ATACTACCTG
*
102704 AGATATCACGATATCATCTTTT
1 AGATATCACGATATCACCTTTT
**
102726 AGATATCGTGATATCACCTTT
1 AGATATCACGATATCACCTTT
102747 GTCAAGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (22 bp):
AGATATCACGATATCACCTTTT
Found at i:105701 original size:41 final size:41
Alignment explanation
Indices: 105634--105725 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
105624 TAATTCTCCT
* *
105634 TAAAGGCGTCTTAATTAGCTTTACC-AATTGAGTCTCACCTC
1 TAAAGGCGTCTTAATTAGCTTCACCAAATTAAG-CTCACCTC
* * *
105675 TAAAGGCGTCTTATTTTGCTTCACCAAATTAAGCTCACCTT
1 TAAAGGCGTCTTAATTAGCTTCACCAAATTAAGCTCACCTC
*
105716 TATAGGCGTC
1 TAAAGGCGTC
105726 GTGTTTTCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 38 0.86
42 6 0.14
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (41 bp):
TAAAGGCGTCTTAATTAGCTTCACCAAATTAAGCTCACCTC
Found at i:108837 original size:41 final size:41
Alignment explanation
Indices: 108792--108872 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
108782 TTTTAAGTTA
**
108792 ATTTTTTCTTCCAAATTCATAACGAATGAACCATCAGCATG
1 ATTTTTTCTTCCAAATTCATAACGAACAAACCATCAGCATG
*
108833 ATTTTTTCTTCCAAATTCATAACGAACAAACCATTAGCAT
1 ATTTTTTCTTCCAAATTCATAACGAACAAACCATCAGCAT
108873 CCAGTTCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (41 bp):
ATTTTTTCTTCCAAATTCATAACGAACAAACCATCAGCATG
Found at i:119938 original size:21 final size:21
Alignment explanation
Indices: 119912--119961 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
119902 CTCTTTCCAA
*
119912 AAGTTCCTAAAGCTGTAACTT
1 AAGTTCCTAAAGCTGCAACTT
* *
119933 AAGTTCTTGAAGCTGCAACTT
1 AAGTTCCTAAAGCTGCAACTT
119954 AAGTTCCT
1 AAGTTCCT
119962 TCAGCTCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (21 bp):
AAGTTCCTAAAGCTGCAACTT
Found at i:119967 original size:21 final size:21
Alignment explanation
Indices: 119912--119967 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
119902 CTCTTTCCAA
* *
119912 AAGTTCCTAAAGCTGTAACTT
1 AAGTTCCTTAAGCTGCAACTT
119933 AAGTT-CTTGAAGCTGCAACTT
1 AAGTTCCTT-AAGCTGCAACTT
*
119954 AAGTTCCTTCAGCT
1 AAGTTCCTTAAGCT
119968 CCTTCAGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (21 bp):
AAGTTCCTTAAGCTGCAACTT
Found at i:125919 original size:6 final size:6
Alignment explanation
Indices: 125898--125929 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
125888 TACAACTCAA
125898 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
125930 TTATGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:128061 original size:2 final size:2
Alignment explanation
Indices: 128054--128087 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
128044 CATTAAACAG
128054 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
128088 TAATAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137216 original size:18 final size:18
Alignment explanation
Indices: 137172--137218 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
137162 TTATTTTTCT
137172 AATAAAAAAATCATAAAA
1 AATAAAAAAATCATAAAA
* **
137190 ATTGTAAAAATCATAAAA
1 AATAAAAAAATCATAAAA
137208 AATAAAAAAAT
1 AATAAAAAAAT
137219 GTTAAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
AATAAAAAAATCATAAAA
Found at i:137235 original size:19 final size:20
Alignment explanation
Indices: 137213--137252 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
137203 TAAAAAATAA
*
137213 AAAAATGTT-AAAATTTTAT
1 AAAAATATTAAAAATTTTAT
137232 AAAAATATTAAAAATTTTAT
1 AAAAATATTAAAAATTTTAT
137252 A
1 A
137253 TAAACTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAAATATTAAAAATTTTAT
Found at i:137245 original size:36 final size:36
Alignment explanation
Indices: 137172--137246 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
137162 TTATTTTTCT
*
137172 AATAAAAAAATCATAAAAATTGTAAAAATCATAAAA
1 AATAAAAAAATCATAAAAATTATAAAAATCATAAAA
** * *
137208 AATAAAAAAATGTTAAAATTTTATAAAAAT-ATTAAA
1 AATAAAAAAATCATAAAA-ATTATAAAAATCATAAAA
137244 AAT
1 AAT
137247 TTTATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (36 bp):
AATAAAAAAATCATAAAAATTATAAAAATCATAAAA
Found at i:137265 original size:29 final size:29
Alignment explanation
Indices: 137176--137313 Score: 106
Period size: 29 Copynumber: 4.8 Consensus size: 29
137166 TTTTCTAATA
* *
137176 AAAAAATCATAAAA-ATTGTAAAAA-TCAT
1 AAAAAATCA-AAAATATTATAAAAACTTAT
* **
137204 AAAAAAT-AAAAAAATGT-TAAAATTTTAT
1 AAAAAATCAAAAATAT-TATAAAAACTTAT
* * *
137232 AAAAATATTAAAAATTTTATATAAACTTAT
1 AAAAA-ATCAAAAATATTATAAAAACTTAT
*
137262 AAAAAATCATAAATATTATAAAAACTTAT
1 AAAAAATCAAAAATATTATAAAAACTTAT
* *
137291 AAAACATCCTAAAA-ATTATAAAA
1 AAAAAAT-CAAAAATATTATAAAA
137314 TAAAATAAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.04
27 8 0.09
28 16 0.18
29 38 0.43
30 23 0.26
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAAAATCAAAAATATTATAAAAACTTAT
Found at i:137266 original size:22 final size:20
Alignment explanation
Indices: 137222--137268 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
137212 AAAAAATGTT
*
137222 AAAATTTTATAAAAATATTA
1 AAAATTTTATAAAAATATAA
*
137242 AAAATTTTATATAAACTTATAA
1 AAAATTTTATA-AAA-ATATAA
137264 AAAAT
1 AAAAT
137269 CATAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
22 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTTATAAAAATATAA
Found at i:137312 original size:9 final size:9
Alignment explanation
Indices: 137177--137313 Score: 80
Period size: 9 Copynumber: 14.4 Consensus size: 9
137167 TTTCTAATAA
*
137177 AAAAATCAT
1 AAAAATTAT
*
137186 AAAAATTGT
1 AAAAATTAT
*
137195 AAAAATCAT
1 AAAAATTAT
* *
137204 AAAAAATAA
1 AAAAATTAT
137213 AAAAATGT-T
1 AAAAAT-TAT
*
137222 AAAATTTTAT
1 AAAA-ATTAT
137232 AAAAA-TATT
1 AAAAATTA-T
137241 AAAAATTTTAT
1 AAAAA--TTAT
*
137252 ATAAACTTAT
1 A-AAAATTAT
*
137262 AAAAAATCAT
1 -AAAAATTAT
*
137272 AAATATTAT
1 AAAAATTAT
137281 AAAAACTTAT
1 AAAAA-TTAT
**
137291 AAAACATCCT
1 AAAA-ATTAT
137301 AAAAATTAT
1 AAAAATTAT
137310 AAAA
1 AAAA
137314 TAAAATAAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
8 2 0.02
9 54 0.56
10 31 0.32
11 4 0.04
12 5 0.05
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:137716 original size:27 final size:26
Alignment explanation
Indices: 137652--137742 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 26
137642 TTATAAAAAA
* *
137652 TATATTTTATTAAAATTTATAGAGGTTTT
1 TATATTTTA-TAATATTTATA-A-GTCTT
137681 TATACTTTTATAATATTTATAAGTCTT
1 TATA-TTTTATAATATTTATAAGTCTT
*
137708 TATGATTTTATATATCTTTTATAAG--TT
1 TAT-ATTTTATA-AT-ATTTATAAGTCTT
137735 TATATTTT
1 TATATTTT
137743 TTTAAATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
26 5 0.09
27 19 0.35
28 4 0.07
29 22 0.40
30 5 0.09
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (26 bp):
TATATTTTATAATATTTATAAGTCTT
Found at i:137728 original size:19 final size:19
Alignment explanation
Indices: 137677--137739 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
137667 TTTATAGAGG
137677 TTTT-TATA-CTTTTATAA
1 TTTTATATATCTTTTATAA
*
137694 TATTTATA-AGTC-TTTATGA
1 T-TTTATATA-TCTTTTATAA
137713 TTTTATATATCTTTTATAA
1 TTTTATATATCTTTTATAA
*
137732 GTTTATAT
1 TTTTATAT
137740 TTTTTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 23 0.62
20 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATATATCTTTTATAA
Found at i:137743 original size:27 final size:25
Alignment explanation
Indices: 137679--137753 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 25
137669 TATAGAGGTT
*
137679 TTTATACTTTTATAATATTTATAAG
1 TTTATATTTTTATAATATTTATAAG
*
137704 TCTT-TATGATTTTATATATCTTTTATAAG
1 T-TTATAT--TTTTATA-AT-ATTTATAAG
*
137733 TTTATATTTTTTTAAATATTT
1 TTTATATTTTTAT-AATATTT
137754 TTAATGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
25 3 0.08
26 5 0.13
27 14 0.36
28 5 0.13
29 12 0.31
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTATATTTTTATAATATTTATAAG
Found at i:137745 original size:29 final size:28
Alignment explanation
Indices: 137696--137756 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
137686 TTTTATAATA
*
137696 TTTATAAGTCTTTATGATTTTATATATCT
1 TTTATAAGTCTTTATGATTTTAAATAT-T
**
137725 TTTATAAGT-TTATATTTTTTTAAATATT
1 TTTATAAGTCTT-TATGATTTTAAATATT
137753 TTTA
1 TTTA
137757 ATGTGTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (28 bp):
TTTATAAGTCTTTATGATTTTAAATATT
Found at i:137803 original size:28 final size:27
Alignment explanation
Indices: 137771--137843 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 27
137761 GTTTTACTAT
*
137771 TTTTATAATTTATTAGAATTTATTATAAG
1 TTTTATAATTT-TTAGAATTT-TTATAAA
*
137800 TTTATATAATTTTTATAATTTTTATAAA
1 TTT-TATAATTTTTAGAATTTTTATAAA
137828 TTTATATAAGTTTTTA
1 TTT-TATAA-TTTTTA
137844 ATATCAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 15 0.38
29 17 0.43
30 8 0.20
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTATAATTTTTAGAATTTTTATAAA
Found at i:137807 original size:10 final size:9
Alignment explanation
Indices: 137769--137836 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 9
137759 GTGTTTTACT
*
137769 ATTTTTATA
1 ATTTATATA
*
137778 ATTTATTAGA
1 ATTTA-TATA
137788 ATTTATTATA
1 ATTTA-TATA
137798 AGTTTATATA
1 A-TTTATATA
*
137808 ATTTTTATA
1 ATTTATATA
*
137817 ATTTTTATAA
1 ATTTATAT-A
137827 ATTTATATA
1 ATTTATATA
137836 A
1 A
137837 GTTTTTAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
9 21 0.41
10 26 0.51
11 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTTATATA
Found at i:144676 original size:13 final size:13
Alignment explanation
Indices: 144658--144682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
144648 TTGTGTGTTG
144658 CAAGGTGTGTGTA
1 CAAGGTGTGTGTA
144671 CAAGGTGTGTGT
1 CAAGGTGTGTGT
144683 TTCTTGTCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.40, T:0.32
Consensus pattern (13 bp):
CAAGGTGTGTGTA
Found at i:151637 original size:17 final size:17
Alignment explanation
Indices: 151592--151637 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
151582 AATGAATTGC
*
151592 AATTTAATTTTAAGATTA
1 AATTTAATTTT-AGATCA
*
151610 AA-TTAAATTTAGATCA
1 AATTTAATTTTAGATCA
151626 AATTTAATTTTA
1 AATTTAATTTTA
151638 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.29
17 15 0.62
18 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
AATTTAATTTTAGATCA
Found at i:154082 original size:16 final size:17
Alignment explanation
Indices: 154046--154082 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
154036 AATTTTATTT
*
154046 TAATAATAAATTTTAAA
1 TAATAATAAATATTAAA
154063 -AATAA-AAATATTAAA
1 TAATAATAAATATTAAA
154078 TAATA
1 TAATA
154083 TTCTTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAAATATTAAA
Found at i:154136 original size:15 final size:14
Alignment explanation
Indices: 154102--154167 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 14
154092 TATTATTGAA
154102 AAATATTTAAT-AT
1 AAATATTTAATAAT
*
154115 TAATATTGTAATAAT
1 AAATATT-TAATAAT
154130 AAATATTTATTACAATAAT
1 AAATA--T-TT--AATAAT
154149 AAATATATTAATAAT
1 AAATAT-TTAATAAT
154164 AAAT
1 AAAT
154168 GCTTTGTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.14
14 4 0.09
15 16 0.36
17 6 0.14
18 1 0.02
19 11 0.25
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
AAATATTTAATAAT
Found at i:154466 original size:23 final size:25
Alignment explanation
Indices: 154407--154461 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
154397 TGAATTGAAC
154407 AAAATATGACATATTTTAACCTAGTATA
1 AAAATATGA-ATATTTTAA-CTA-TATA
*
154435 AAAATATGAATATTTTAATTATATA
1 AAAATATGAATATTTTAACTATATA
154460 AA
1 AA
154462 TATGAGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 2 0.08
27 9 0.35
28 9 0.35
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (25 bp):
AAAATATGAATATTTTAACTATATA
Found at i:156088 original size:18 final size:19
Alignment explanation
Indices: 156046--156088 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
156036 ATAACATCCA
*
156046 AACAACAGAAACAACAATC
1 AACAACAGAAACAAAAATC
*
156065 AA-AACAGAAGCAAAAAT-
1 AACAACAGAAACAAAAATC
156082 AACAACA
1 AACAACA
156089 AAATAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.81
19 2 0.10
ACGTcount: A:0.67, C:0.21, G:0.07, T:0.05
Consensus pattern (19 bp):
AACAACAGAAACAAAAATC
Found at i:156090 original size:12 final size:12
Alignment explanation
Indices: 156075--156147 Score: 64
Period size: 12 Copynumber: 6.4 Consensus size: 12
156065 AAAACAGAAG
156075 CAAAAATAACAA
1 CAAAAATAACAA
*
156087 C-AAAATAATAA
1 CAAAAATAACAA
156098 C--AAA-AACAA
1 CAAAAATAACAA
** *
156107 CAAAAATAGTAG
1 CAAAAATAACAA
*
156119 CAAAAACAACAA
1 CAAAAATAACAA
*
156131 TAAAAATAACAA
1 CAAAAATAACAA
156143 CAAAA
1 CAAAA
156148 GCAGCATCAA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
9 5 0.11
10 3 0.07
11 13 0.28
12 25 0.54
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.10
Consensus pattern (12 bp):
CAAAAATAACAA
Found at i:156106 original size:44 final size:45
Alignment explanation
Indices: 156046--156147 Score: 116
Period size: 44 Copynumber: 2.2 Consensus size: 45
156036 ATAACATCCA
* * *
156046 AACAACAGAAACAACAATCAAAACAGAAGCAAAAATAACAA-CAAAAT
1 AACAACAAAAACAAC-A--AAAACAGAAGCAAAAACAACAATAAAAAT
* * *
156093 AATAACAAAAACAACAAAAATAGTAGCAAAAACAACAATAAAAAT
1 AACAACAAAAACAACAAAAACAGAAGCAAAAACAACAATAAAAAT
156138 AACAACAAAA
1 AACAACAAAA
156148 GCAGCATCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 19 0.40
45 14 0.30
46 1 0.02
47 13 0.28
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.08
Consensus pattern (45 bp):
AACAACAAAAACAACAAAAACAGAAGCAAAAACAACAATAAAAAT
Found at i:156114 original size:21 final size:21
Alignment explanation
Indices: 156082--156142 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
156072 AAGCAAAAAT
156082 AACAAC-AAAATAATAACAAA
1 AACAACAAAAATAATAACAAA
* *
156102 AACAACAAAAATAGTAGCAAA
1 AACAACAAAAATAATAACAAA
156123 AACAACAATAAA-AATAACAA
1 AACAACAA-AAATAATAACAA
156143 CAAAAGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.17
21 26 0.74
22 3 0.09
ACGTcount: A:0.72, C:0.15, G:0.03, T:0.10
Consensus pattern (21 bp):
AACAACAAAAATAATAACAAA
Found at i:156135 original size:24 final size:23
Alignment explanation
Indices: 156054--156138 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 23
156044 CAAACAACAG
* * *
156054 AAACAACAATCAAAACAGAAGCAA
1 AAACAACAA-AAAAATAGTAGCAA
* * * *
156078 AAATAACAACAAAATAATAACAA
1 AAACAACAAAAAAATAGTAGCAA
156101 AAACAAC--AAAAATAGTAGCAA
1 AAACAACAAAAAAATAGTAGCAA
156122 AAACAACAATAAAAATA
1 AAACAACAA-AAAAATA
156139 ACAACAAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 18 0.37
23 16 0.33
24 15 0.31
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.09
Consensus pattern (23 bp):
AAACAACAAAAAAATAGTAGCAA
Found at i:156159 original size:23 final size:23
Alignment explanation
Indices: 156133--156176 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
156123 AACAACAATA
156133 AAAATAACAA-CAAAAGCAGCATC
1 AAAATAACAATCAAAA-CAGCATC
*
156156 AAAATAGCAATCAAAACAGCA
1 AAAATAACAATCAAAACAGCA
156177 AAAAGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAATAACAATCAAAACAGCATC
Found at i:156261 original size:20 final size:20
Alignment explanation
Indices: 156203--156266 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
156193 TAATAAAAAA
**
156203 AAAAACAACACCAAAACAAC
1 AAAAACAACACCAAAACAGT
* *
156223 AAAAATATAGCATCAAAACAGT
1 AAAAACA-A-CACCAAAACAGT
156245 AAAAACAACACCAAAACAGT
1 AAAAACAACACCAAAACAGT
156265 AA
1 AA
156267 TATAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 19 0.53
21 2 0.06
22 15 0.42
ACGTcount: A:0.66, C:0.22, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAAACAACACCAAAACAGT
Found at i:159208 original size:18 final size:17
Alignment explanation
Indices: 159175--159215 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
159165 GTTTAAAGAT
159175 ATAATAGAATAATTTAAA
1 ATAA-AGAATAATTTAAA
*
159193 TTAAAGAATCAATTTAAA
1 ATAAAGAAT-AATTTAAA
159211 ATAAA
1 ATAAA
159216 CATAACAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAAAGAATAATTTAAA
Found at i:160059 original size:16 final size:16
Alignment explanation
Indices: 160038--160075 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
160028 AAGTAGTAAC
* *
160038 TTAAAAATAATAAAAT
1 TTAAAAAAAAAAAAAT
160054 TTAAAAAAAAAAAAAT
1 TTAAAAAAAAAAAAAT
160070 TTAAAA
1 TTAAAA
160076 CACGAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TTAAAAAAAAAAAAAT
Found at i:161532 original size:17 final size:17
Alignment explanation
Indices: 161477--161538 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 17
161467 ATATTAATAA
161477 TTTAATAATAAATATTT
1 TTTAATAATAAATATTT
* *
161494 ATTACAATTATAAATA--T
1 -TT-TAATAATAAATATTT
*
161511 ATTAATAATAAATATTT
1 TTTAATAATAAATATTT
161528 TTTAAT-ATAAA
1 TTTAATAATAAA
161539 GGTTAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 7 0.20
18 2 0.06
19 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATAATAAATATTT
Found at i:165008 original size:16 final size:16
Alignment explanation
Indices: 164987--165018 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
164977 ATAAATATTT
164987 TATAAATATATTTTTA
1 TATAAATATATTTTTA
*
165003 TATAAATTTATTTTTA
1 TATAAATATATTTTTA
165019 ACCCACATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAAATATATTTTTA
Found at i:172938 original size:22 final size:24
Alignment explanation
Indices: 172912--172966 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
172902 CAACAAATTA
172912 TTTCTTTTTTCATT-CTTTTCT-C
1 TTTCTTTTTTCATTACTTTTCTCC
* * *
172934 TTTCTCTTTTCTTTATTTTTCTCC
1 TTTCTTTTTTCATTACTTTTCTCC
172958 TTT-TTTTTT
1 TTTCTTTTTT
172967 ATAGGTGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 12 0.44
23 11 0.41
24 4 0.15
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCTTTTTTCATTACTTTTCTCC
Found at i:186030 original size:20 final size:20
Alignment explanation
Indices: 186001--186040 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
185991 ATTCCACTAT
186001 TAAACAAATTAACAATCGAA
1 TAAACAAATTAACAATCGAA
*
186021 TAAACCAATTAACAATCGAA
1 TAAACAAATTAACAATCGAA
186041 ATTATATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAACAAATTAACAATCGAA
Found at i:186203 original size:15 final size:14
Alignment explanation
Indices: 186170--186226 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
186160 AATCTATATT
186170 TCTA-TATTATTTA
1 TCTATTATTATTTA
186183 T-T-TTATTATTCTA
1 TCTATTATTATT-TA
186196 TCTATTATTATATTA
1 TCTATTATTAT-TTA
*
186211 TCTACTATTATATTA
1 TCTATTATTAT-TTA
186226 T
1 T
186227 TCTTATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 8 0.21
13 4 0.11
14 1 0.03
15 24 0.63
16 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTATTATTATTTA
Found at i:186203 original size:20 final size:18
Alignment explanation
Indices: 186180--186227 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
186170 TCTATATTAT
186180 TTATTTTATTATTCTATCTA
1 TTATTTTATTA-TCTA-CTA
*
186200 TTATTATATTATCTACTA
1 TTATTTTATTATCTACTA
*
186218 TTATATTATT
1 TTATTTTATT
186228 CTTATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 4 0.16
20 10 0.40
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTATTATCTACTA
Found at i:187204 original size:21 final size:21
Alignment explanation
Indices: 187178--187227 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
187168 CGTGCAGAAA
187178 TTCTACTGGTACTTGAATGGG
1 TTCTACTGGTACTTGAATGGG
187199 TTCTACTGGTACTTGAATGGG
1 TTCTACTGGTACTTGAATGGG
187220 TTCTACTG
1 TTCTACTG
187228 ATATAACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (21 bp):
TTCTACTGGTACTTGAATGGG
Found at i:187443 original size:21 final size:21
Alignment explanation
Indices: 187418--187473 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
187408 TCCCTTATAC
187418 TTCTACCGAAACCTTGTGGAG
1 TTCTACCGAAACCTTGTGGAG
* *
187439 TTCTATCGGAACCTTGTGGAG
1 TTCTACCGAAACCTTGTGGAG
*
187460 TTCTACTGAAACCT
1 TTCTACCGAAACCT
187474 CAAAATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TTCTACCGAAACCTTGTGGAG
Found at i:195084 original size:11 final size:11
Alignment explanation
Indices: 195068--195110 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
195058 TATAGTAATA
195068 TTTT-TTTTTC
1 TTTTCTTTTTC
195078 TTTT-TTTCTT-
1 TTTTCTTT-TTC
195088 TTTTCTTTTTC
1 TTTTCTTTTTC
195099 TTTTCTTTTTC
1 TTTTCTTTTTC
195110 T
1 T
195111 CATTCAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:195091 original size:18 final size:18
Alignment explanation
Indices: 195068--195108 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
195058 TATAGTAATA
*
195068 TTTTTT-TTTCTTTTTTTC
1 TTTTTTCTTT-TTCTTTTC
195086 TTTTTTCTTTTTCTTTTC
1 TTTTTTCTTTTTCTTTTC
195104 TTTTT
1 TTTTT
195109 CTCATTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTCTTTTTCTTTTC
Found at i:219190 original size:22 final size:23
Alignment explanation
Indices: 219162--219225 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 23
219152 TTGTGCCCTT
*
219162 TGTTCAGCACTTTGTGTG-CTTC
1 TGTTCAGCACTTTGTGTGCCTAC
219184 TGTTCAGCACTTTGTGTGCCTAC
1 TGTTCAGCACTTTGTGTGCCTAC
219207 TGTTGCCAGCACTTATGTG
1 TGTT--CAGCACTT-TGTG
219226 CCCTCCGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 18 0.49
23 7 0.19
25 8 0.22
26 4 0.11
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (23 bp):
TGTTCAGCACTTTGTGTGCCTAC
Found at i:222781 original size:17 final size:15
Alignment explanation
Indices: 222755--222795 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
222745 AAAAAGTGAG
222755 AAAAAGAAAGAAAAGA
1 AAAAAGAAAG-AAAGA
*
222771 AAAAGAGAAAGAATGA
1 AAAA-AGAAAGAAAGA
222787 AAAAAGAAA
1 AAAAAGAAA
222796 TAATTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:228263 original size:18 final size:17
Alignment explanation
Indices: 228240--228293 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
228230 CGAGGTAACA
228240 TCTTCTTTCTCTTCCTTC
1 TCTTCTTTCTCTT-CTTC
*
228258 TCTTCTTTTTCTTCTTC
1 TCTTCTTTCTCTTCTTC
*
228275 TTTTCTTTCTTCTTCTTC
1 TCTTCTTTC-TCTTCTTC
228293 T
1 T
228294 GCCTCAATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTCTTTCTCTTCTTC
Found at i:228264 original size:3 final size:3
Alignment explanation
Indices: 228240--228293 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
228230 CGAGGTAACA
*
228240 TCT TCT T-T CTCT TCCT TC- TCT TCT TTT TCT TCT TCT T-T TCTT TCT
1 TCT TCT TCT -TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
228285 TCT TCT TCT
1 TCT TCT TCT
228294 GCCTCAATAC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 5 0.12
3 31 0.72
4 7 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:233562 original size:15 final size:15
Alignment explanation
Indices: 233544--233578 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
233534 TCTGCTTTCC
233544 TCTTTTTCTTTGCTT
1 TCTTTTTCTTTGCTT
*
233559 TCTTTTTCTTTTCTT
1 TCTTTTTCTTTGCTT
233574 T-TTTT
1 TCTTTT
233579 AAACGTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (15 bp):
TCTTTTTCTTTGCTT
Found at i:234179 original size:17 final size:17
Alignment explanation
Indices: 234159--234193 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
234149 AAATGAATTA
*
234159 ACAAGAAAAATGCAATG
1 ACAACAAAAATGCAATG
*
234176 ACAACTAAAATGCAATG
1 ACAACAAAAATGCAATG
234193 A
1 A
234194 TAATTAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (17 bp):
ACAACAAAAATGCAATG
Found at i:238882 original size:26 final size:27
Alignment explanation
Indices: 238830--238893 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
238820 TGAGGAGTAA
*
238830 TCTGATTCTGGCTCGAAAAAGCGTTAT
1 TCTGATTCTGGCTCGAAAAAGCATTAT
238857 TCTGATTCTGGCTCG-AAAAGCATTAT
1 TCTGATTCTGGCTCGAAAAAGCATTAT
*
238883 TCCGATTCTGG
1 TCTGATTCTGG
238894 GCTCATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTGATTCTGGCTCGAAAAAGCATTAT
Found at i:238920 original size:24 final size:24
Alignment explanation
Indices: 238887--238980 Score: 125
Period size: 24 Copynumber: 3.9 Consensus size: 24
238877 CATTATTCCG
238887 ATTCTGGGCTCATAAGAGCTAACC
1 ATTCTGGGCTCATAAGAGCTAACC
* *
238911 ATTCTAGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCATAAGAGCTAACC
* * *
238935 ATTTTGGGCTCGTAAGAACTAACC
1 ATTCTGGGCTCATAAGAGCTAACC
**
238959 ATTCTGGGCTCATGTGAGCTAA
1 ATTCTGGGCTCATAAGAGCTAA
238981 GTTGTTAGTG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
ATTCTGGGCTCATAAGAGCTAACC
Found at i:254863 original size:25 final size:23
Alignment explanation
Indices: 254834--254879 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
254824 GTTGGATCCA
254834 AATTAAACTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
254859 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
254880 CTCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:259069 original size:14 final size:14
Alignment explanation
Indices: 259050--259083 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
259040 TTGAAACAAG
259050 ATTTATTTTACTTT
1 ATTTATTTTACTTT
*
259064 ATTTATTTTATTTT
1 ATTTATTTTACTTT
259078 AGTTTA
1 A-TTTA
259084 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (14 bp):
ATTTATTTTACTTT
Found at i:259091 original size:19 final size:19
Alignment explanation
Indices: 259051--259090 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
259041 TGAAACAAGA
*
259051 TTTATTTTACTTTATTTAT
1 TTTATTTTACTTTATATAT
*
259070 TTTATTTTAGTTTA-ATAT
1 TTTATTTTACTTTATATAT
259088 TTT
1 TTT
259091 TTCTCTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTTTACTTTATATAT
Found at i:276528 original size:13 final size:14
Alignment explanation
Indices: 276506--276534 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
276496 TTTTGAGCAA
276506 TTTAT-TTTTTTCT
1 TTTATGTTTTTTCT
276519 TTTATGTTTTTTCT
1 TTTATGTTTTTTCT
276533 TT
1 TT
276535 ATTTTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTATGTTTTTTCT
Found at i:276535 original size:13 final size:13
Alignment explanation
Indices: 276506--276540 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
276496 TTTTGAGCAA
276506 TTTATTTTTTTCT
1 TTTATTTTTTTCT
276519 TTTATGTTTTTTC-
1 TTTAT-TTTTTTCT
276532 TTTATTTTT
1 TTTATTTTT
276541 CATTCTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 10 0.48
14 7 0.33
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTATTTTTTTCT
Found at i:279040 original size:24 final size:23
Alignment explanation
Indices: 279013--279137 Score: 81
Period size: 24 Copynumber: 5.2 Consensus size: 23
279003 CAGACAATAT
279013 TTAGCCCATACGAACCCAGAATGG
1 TTAGCCC-TACGAACCCAGAATGG
*
279037 TTAGCTCCTAC-AAGCCCAGAACGG
1 TTAGC-CCTACGAA-CCCAGAATGG
* * *
279061 TTAGCCTTTACGAGCCTAGAATGG
1 TTAGCC-CTACGAACCCAGAATGG
*** * * *
279085 TTAGTTTTCACGAGCCTAAAATGG
1 TTAGCCCT-ACGAACCCAGAATGG
* *
279109 TTAGCCCTCACGAGCCAAGAATGG
1 TTAGCCCT-ACGAACCCAGAATGG
279133 TTAGC
1 TTAGC
279138 TCTTTTGAGC
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.06
24 75 0.90
25 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (23 bp):
TTAGCCCTACGAACCCAGAATGG
Found at i:279084 original size:48 final size:49
Alignment explanation
Indices: 279013--279139 Score: 132
Period size: 48 Copynumber: 2.6 Consensus size: 49
279003 CAGACAATAT
* * * *
279013 TTAGCCCATACGAACCCAGAATGGTTAGCTCCT-ACAAGCCCAGAACGG
1 TTAGCCCTTACGAGCCAAGAATGGTTAGCTCCTCACAAGCCCAAAACGG
* * ** * * *
279061 TTAGCCTTTACGAGCCTAGAATGGTTAG-TTTTCACGAGCCTAAAATGG
1 TTAGCCCTTACGAGCCAAGAATGGTTAGCTCCTCACAAGCCCAAAACGG
*
279109 TTAGCCCTCACGAGCCAAGAATGGTTAGCTC
1 TTAGCCCTTACGAGCCAAGAATGGTTAGCTC
279140 TTTTGAGCCA
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
47 2 0.03
48 60 0.95
49 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (49 bp):
TTAGCCCTTACGAGCCAAGAATGGTTAGCTCCTCACAAGCCCAAAACGG
Found at i:279211 original size:27 final size:27
Alignment explanation
Indices: 279136--279211 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
279126 AGAATGGTTA
*
279136 GCTCTTTTGAGCCAGAATCAAAATAAC
1 GCTCTTTTGAGCCAGAATCAGAATAAC
* * * *
279163 ACTCTTTTAAGCCAAAAACAGAATAAC
1 GCTCTTTTGAGCCAGAATCAGAATAAC
* *
279190 GCTCTTTCGAGTCAGAATCAGA
1 GCTCTTTTGAGCCAGAATCAGA
279212 TTACTCCTCA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (27 bp):
GCTCTTTTGAGCCAGAATCAGAATAAC
Found at i:282755 original size:21 final size:21
Alignment explanation
Indices: 282729--282768 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
282719 TACCCTGTAC
282729 TTCTACCGAAACATACATGAG
1 TTCTACCGAAACATACATGAG
*
282750 TTCTACTGAAACATACATG
1 TTCTACCGAAACATACATG
282769 CAAGATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACATACATGAG
Found at i:283364 original size:24 final size:24
Alignment explanation
Indices: 283262--283356 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
283252 TTTAGCCCAT
* *
283262 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTC
*
283286 ACGAGCCCAGAACGGTTAGCTCTC
1 ACGAGCCCAGAATGGTTAGCTCTC
283310 ACGAGCCCAGAATGGTTAGCTCTC
1 ACGAGCCCAGAATGGTTAGCTCTC
*
283334 ATGAGCCCAGAATGGTTAGCTCT
1 ACGAGCCCAGAATGGTTAGCTCT
283357 TTTGAGCCAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTC
Found at i:283384 original size:27 final size:27
Alignment explanation
Indices: 283352--283425 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
283342 AGAATGGTTA
*
283352 GCTCTTTTGAGCCAGAATCAGACTAAC
1 GCTCTTTTGAGCCAGAATCAGAATAAC
283379 GCTCTTTTGAGCCAGAATCAGAATAAC
1 GCTCTTTTGAGCCAGAATCAGAATAAC
*
283406 GCTCTTTCGAGCCAGAATCA
1 GCTCTTTTGAGCCAGAATCA
283426 AATTACTCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (27 bp):
GCTCTTTTGAGCCAGAATCAGAATAAC
Found at i:284250 original size:23 final size:23
Alignment explanation
Indices: 284176--284318 Score: 97
Period size: 23 Copynumber: 6.5 Consensus size: 23
284166 TAAACGGAAC
* *
284176 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
284198 AAATAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
284220 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
284246 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
284266 --AC--TGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
284285 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
284308 AATCAGAGAGC
1 AAACAGAGAGC
284319 GCGCTAGTGT
Statistics
Matches: 95, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
16 9 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 17 0.18
23 43 0.45
25 12 0.13
26 7 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Done.