Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015309.1 Kokia drynarioides strain JFW-HI SEQ_130354, 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: 296964
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 394 characters in sequence are not A, C, G, or T
Found at i:2679 original size:20 final size:20
Alignment explanation
Indices: 2654--2692 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2644 GGTAAGAAGG
*
2654 AACATCTAATCCTTTCAACC
1 AACATCTAATCCTTCCAACC
*
2674 AACATCTTATCCTTCCAAC
1 AACATCTAATCCTTCCAAC
2693 GACTACAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (20 bp):
AACATCTAATCCTTCCAACC
Found at i:5873 original size:2 final size:2
Alignment explanation
Indices: 5838--5863 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5828 TGGATAGCCT
5838 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5864 CTAAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7325 original size:30 final size:28
Alignment explanation
Indices: 7273--7355 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 28
7263 TAAAAAAATT
* *
7273 TTAAATTTTTTTTTTAA-ATTTAAAAGA
1 TTAAATTTTTTTTTCAACTTTTAAAAGA
*
7300 TCTAAACTTTTTTTTTCAACTTTTAAAAGG
1 T-TAAA-TTTTTTTTTCAACTTTTAAAAGA
*
7330 TTCAAAATTTCTTTTATCAACTTTTA
1 TT--AAATTT-TTTTTTCAACTTTTA
7356 CTGAGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 4 0.09
29 12 0.26
30 12 0.26
31 17 0.37
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.53
Consensus pattern (28 bp):
TTAAATTTTTTTTTCAACTTTTAAAAGA
Found at i:8132 original size:3 final size:3
Alignment explanation
Indices: 8094--8118 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8084 TTCAAAACAA
8094 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
8119 TACTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21762 original size:4 final size:4
Alignment explanation
Indices: 21755--21781 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21745 ATATATATAT
21755 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
21782 TGGCCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:25751 original size:15 final size:17
Alignment explanation
Indices: 25717--25753 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
25707 ATAAATATTC
25717 ATATTTATATAATAAAA
1 ATATTTATATAATAAAA
*
25734 ATATTTAT-T-ATTAAA
1 ATATTTATATAATAAAA
25749 ATATT
1 ATATT
25754 GATGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 1 0.05
17 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTTATATAATAAAA
Found at i:25859 original size:17 final size:16
Alignment explanation
Indices: 25839--25872 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25829 TAAATTAAAA
25839 TTATAATATTAAATAAT
1 TTATAATATT-AATAAT
*
25856 TTATTATATTAATAAT
1 TTATAATATTAATAAT
25872 T
1 T
25873 AAATATGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAATATTAATAAT
Found at i:27193 original size:6 final size:6
Alignment explanation
Indices: 27182--27218 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
27172 TGGGTAGCAT
*
27182 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGA GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG G
27219 CGCTTAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:27844 original size:16 final size:17
Alignment explanation
Indices: 27801--27844 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
27791 ATTATATTTT
*
27801 TTTAAAAAAAAACTTAT
1 TTTAAAAAAAAACTTAA
**
27818 TTTAAGTAAAAA-TTAA
1 TTTAAAAAAAAACTTAA
27834 TTTAAAAAAAA
1 TTTAAAAAAAA
27845 CTTTTTAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
TTTAAAAAAAAACTTAA
Found at i:40482 original size:21 final size:21
Alignment explanation
Indices: 40452--40492 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40442 GTATCCATAT
**
40452 CCAGGATAACTTGGCATGTAG
1 CCAGGATAACCAGGCATGTAG
*
40473 CCAGGGTAACCAGGCATGTA
1 CCAGGATAACCAGGCATGTA
40493 TCCATATCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
CCAGGATAACCAGGCATGTAG
Found at i:48682 original size:10 final size:9
Alignment explanation
Indices: 48665--48690 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
48655 TTATGTGTTC
48665 TATTTTTTT
1 TATTTTTTT
48674 TATTTTTTT
1 TATTTTTTT
48683 TATTTTTT
1 TATTTTTT
48691 AAATTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:59311 original size:6 final size:6
Alignment explanation
Indices: 59300--59339 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
59290 CTTAATTTGC
59300 TATACA TATACA TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATA
59340 AAGAGTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:61175 original size:24 final size:24
Alignment explanation
Indices: 61143--61197 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
61133 CAAATCAACT
*
61143 TCACACCAACATGATTATATAATA
1 TCACTCCAACATGATTATATAATA
61167 TCACTCCAACATGATTATATAATA
1 TCACTCCAACATGATTATATAATA
61191 TCACTCC
1 TCACTCC
61198 TTTCATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (24 bp):
TCACTCCAACATGATTATATAATA
Found at i:72557 original size:17 final size:17
Alignment explanation
Indices: 72537--72569 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
72527 TTAAAAATAA
72537 TAAA-AGTATAAATTATT
1 TAAATAGTA-AAATTATT
72554 TAAATAGTAAAATTAT
1 TAAATAGTAAAATTAT
72570 GTCTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
TAAATAGTAAAATTATT
Found at i:75972 original size:19 final size:19
Alignment explanation
Indices: 75948--75984 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
75938 TAGTAGAATG
*
75948 ATTTTATCATATTTAATTC
1 ATTTTATCACATTTAATTC
*
75967 ATTTTATCGCATTTAATT
1 ATTTTATCACATTTAATT
75985 TTGTGCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTATCACATTTAATTC
Found at i:76558 original size:31 final size:31
Alignment explanation
Indices: 76523--76593 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
76513 CTTTAAATGT
76523 GTACAATTGAATCAAAATCAAAATTTCATAC
1 GTACAATTGAATCAAAATCAAAATTTCATAC
* ** *
76554 GTAC-ATATAAATCATGATCAAAATTTCATAT
1 GTACAAT-TGAATCAAAATCAAAATTTCATAC
*
76585 GTATAATTG
1 GTACAATTG
76594 CATGAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
30 2 0.06
31 28 0.88
32 2 0.06
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (31 bp):
GTACAATTGAATCAAAATCAAAATTTCATAC
Found at i:81293 original size:22 final size:23
Alignment explanation
Indices: 81263--81317 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
81253 ACGTTAACAC
81263 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
*
81286 GCTT-CTGTTCAGCGCTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
*
81308 GCCTACTGTT
1 GCTTACTGTT
81318 TCTCAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.09, C:0.24, G:0.27, T:0.40
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:81341 original size:24 final size:25
Alignment explanation
Indices: 81313--81366 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
81303 TGTGTGCCTA
*
81313 CTGTTT-CTCAGCACTTATGCGCTT
1 CTGTTTCCCCAGCACTTATGCGCTT
81337 CTGTTTCCCCAGCACTTATGCGCTT
1 CTGTTTCCCCAGCACTTATGCGCTT
81362 CTGTT
1 CTGTT
81367 AAGTACTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.11, C:0.31, G:0.17, T:0.41
Consensus pattern (25 bp):
CTGTTTCCCCAGCACTTATGCGCTT
Found at i:86326 original size:5 final size:5
Alignment explanation
Indices: 86316--86341 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
86306 AGTACCACCT
86316 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
86342 ACATATCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:105846 original size:22 final size:22
Alignment explanation
Indices: 105808--105849 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
105798 TACTTTCAAC
*
105808 TATTTTCAAATTAATTAATTTT
1 TATTTTCAAAGTAATTAATTTT
105830 TATTTT-AAAGTAGATTAATT
1 TATTTTCAAAGTA-ATTAATT
105850 CCCATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTTCAAAGTAATTAATTTT
Found at i:108636 original size:3 final size:3
Alignment explanation
Indices: 108628--108653 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
108618 TAGACGAGTT
108628 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
108654 TGCTTGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:115644 original size:2 final size:2
Alignment explanation
Indices: 115637--115669 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
115627 TTAATTGATA
115637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115670 GTGGTGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:124733 original size:25 final size:25
Alignment explanation
Indices: 124699--124786 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
124689 TAAATGCGTA
*
124699 ATCATTAAAATCGTTATTATTATCG
1 ATCACTAAAATCGTTATTATTATCG
* * *
124724 ATCACTAAAAATAATGATATT-TTAACG
1 ATCACT-AAAAT--CGTTATTATTATCG
** * *
124751 ATCGTTAAAATCATTATTATTATTG
1 ATCACTAAAATCGTTATTATTATCG
*
124776 ACCACTAAAAT
1 ATCACTAAAAT
124787 TGATATATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
24 4 0.09
25 17 0.38
26 10 0.22
27 9 0.20
28 5 0.11
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (25 bp):
ATCACTAAAATCGTTATTATTATCG
Found at i:128178 original size:31 final size:29
Alignment explanation
Indices: 128142--128200 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
128132 TGTAATGTGT
*
128142 ATAATTGAATAAAAATTAAAATTTGATGTAC
1 ATAATTGAA-AAAAATCAAAATTT-ATGTAC
* *
128173 ATAATTGCACAAAATCAAAATTTATGTA
1 ATAATTGAAAAAAATCAAAATTTATGTA
128201 TTGAATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
30 12 0.48
31 8 0.32
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (29 bp):
ATAATTGAAAAAAATCAAAATTTATGTAC
Found at i:129049 original size:20 final size:21
Alignment explanation
Indices: 129026--129068 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
129016 AACTTTAATC
129026 TTAAACTCTAAA-TTTGAGGT
1 TTAAACTCTAAAGTTTGAGGT
* *
129046 TTAAAGTTTAAAGTTTGAGGT
1 TTAAACTCTAAAGTTTGAGGT
129067 TT
1 TT
129069 GAAGTTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (21 bp):
TTAAACTCTAAAGTTTGAGGT
Found at i:129064 original size:21 final size:20
Alignment explanation
Indices: 129034--129074 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
129024 TCTTAAACTC
129034 TAAATTTGAGGTTTAAAGTT
1 TAAATTTGAGGTTTAAAGTT
*
129054 TAAAGTTTGAGGTTTGAAGTT
1 TAAA-TTTGAGGTTTAAAGTT
129075 CGAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (20 bp):
TAAATTTGAGGTTTAAAGTT
Found at i:129080 original size:21 final size:21
Alignment explanation
Indices: 129038--129082 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
129028 AAACTCTAAA
*
129038 TTTGAGGTTTAAAGTTTAAAG
1 TTTGAGGTTTAAAGTTCAAAG
* *
129059 TTTGAGGTTTGAAGTTCGAAG
1 TTTGAGGTTTAAAGTTCAAAG
129080 TTT
1 TTT
129083 AATATCAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (21 bp):
TTTGAGGTTTAAAGTTCAAAG
Found at i:136795 original size:17 final size:17
Alignment explanation
Indices: 136768--136843 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 17
136758 CGTGACACGT
136768 AAAAAAT-TAAAAATTA
1 AAAAAATATAAAAATTA
136784 AAAAAATATAAAAATATTA
1 AAAAAATAT-AAAA-ATTA
* *
136803 AAAATATGATCAAAA-TA
1 AAAAAAT-ATAAAAATTA
* *
136820 AAAAAAAATCAAAATTA
1 AAAAAATATAAAAATTA
136837 TAAAAAA
1 -AAAAAA
136844 AACTATGGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 14 0.28
17 10 0.20
18 11 0.22
19 13 0.26
20 2 0.04
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (17 bp):
AAAAAATATAAAAATTA
Found at i:136830 original size:16 final size:18
Alignment explanation
Indices: 136811--136845 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
136801 TAAAAATATG
136811 ATCAAAA-TA-AAAAAAA
1 ATCAAAATTATAAAAAAA
136827 ATCAAAATTATAAAAAAA
1 ATCAAAATTATAAAAAAA
136845 A
1 A
136846 CTATGGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
ATCAAAATTATAAAAAAA
Found at i:137216 original size:20 final size:21
Alignment explanation
Indices: 137188--137228 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
137178 GTGACAAGGA
137188 AAGGCAAAGGAGAAA-GGGGG
1 AAGGCAAAGGAGAAATGGGGG
* *
137208 AAGGGAAAGGGGAAATGGGGG
1 AAGGCAAAGGAGAAATGGGGG
137229 TGAGGCTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.54, T:0.02
Consensus pattern (21 bp):
AAGGCAAAGGAGAAATGGGGG
Found at i:139533 original size:237 final size:238
Alignment explanation
Indices: 139091--139609 Score: 887
Period size: 237 Copynumber: 2.2 Consensus size: 238
139081 TGGCTTTTAA
* * * * * *
139091 AAAAAAAATTAAAGTATCGTTGAATAATTTAAATTATTTTAATTACAGAAGGATGTCTTTGTCTT
1 AAAAAAGATTAAAATATCATCGAATAATATAATTTATTTTAATTACAGAAGGA-----TTGTCTT
* * * *
139156 TGTAATTTCCTTAAGTGAGTTGCTGTTAATTGGTTCCAGTTTGACTTGTGACAACAACTCAATCA
61 TGTAATTTCCCTAAGTAAGTTGCTGCTAATTGGTTCCAGATTGACTTGTGACAACAACTCAATCA
139221 GATGCTTAAATAATAGTATATATATTATAGATACTAGAAACTCTATCACACGCGTATGCGTGTGG
126 GATGCTTAAATAATAGTATATATATTATAGATACTAGAAACTCTATCACACGCGTATGCGTGTGG
139286 ACATCTCCTATTTAGAATATAGAGGGTACAATTGTTTATTTTTTCAAT
191 ACATCTCCTATTTAGAATATAGAGGGTACAATTGTTTATTTTTTCAAT
139334 AAAAAAGATTAAAATATCATCGAATAATATAATTTATTTTAATTACAGAAGGA-TGTCTTTGTAA
1 AAAAAAGATTAAAATATCATCGAATAATATAATTTATTTTAATTACAGAAGGATTGTCTTTGTAA
*
139398 TTTCCCTAAGTAAGTTGCTGCTAATTGGTTCCAGATTGACTTGTGACAACAACTCAGTCAGATGC
66 TTTCCCTAAGTAAGTTGCTGCTAATTGGTTCCAGATTGACTTGTGACAACAACTCAATCAGATGC
139463 TTAAATAATAGTATATATATTATAGATACTAGAAACTCTATCACACGCGTATGCGTGTGGACATC
131 TTAAATAATAGTATATATATTATAGATACTAGAAACTCTATCACACGCGTATGCGTGTGGACATC
139528 TCCTATTTAGAATATAGAGGGTACAATTGTTTATTTTTTCAAT
196 TCCTATTTAGAATATAGAGGGTACAATTGTTTATTTTTTCAAT
139571 AAAAAAGATTAAAATATCATCGAATAATATAATTTATTT
1 AAAAAAGATTAAAATATCATCGAATAATATAATTTATTT
139610 CAAATACGAA
Statistics
Matches: 265, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
237 218 0.82
243 47 0.18
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (238 bp):
AAAAAAGATTAAAATATCATCGAATAATATAATTTATTTTAATTACAGAAGGATTGTCTTTGTAA
TTTCCCTAAGTAAGTTGCTGCTAATTGGTTCCAGATTGACTTGTGACAACAACTCAATCAGATGC
TTAAATAATAGTATATATATTATAGATACTAGAAACTCTATCACACGCGTATGCGTGTGGACATC
TCCTATTTAGAATATAGAGGGTACAATTGTTTATTTTTTCAAT
Found at i:140614 original size:3 final size:3
Alignment explanation
Indices: 140608--140653 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
140598 TTTTTGGGTA
140608 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
140654 GTTTATTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:152616 original size:5 final size:5
Alignment explanation
Indices: 152572--152615 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
152562 AGTGACAGAT
* * *
152572 ATATG ATATA ATATA ATATA ATATA ATATA ATATT ATATT ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
152616 TGCAACTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (5 bp):
ATATA
Found at i:158299 original size:12 final size:12
Alignment explanation
Indices: 158278--158310 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
158268 TCAAAATTTC
158278 CACA-ATTACCA
1 CACATATTACCA
158289 CACATATTACCA
1 CACATATTACCA
158301 CACATATTAC
1 CACATATTAC
158311 ATGCAATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (12 bp):
CACATATTACCA
Found at i:177307 original size:3 final size:3
Alignment explanation
Indices: 177299--177330 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
177289 TCCTCTACCA
177299 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
177331 AAAAAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:186935 original size:76 final size:77
Alignment explanation
Indices: 186788--186936 Score: 212
Period size: 76 Copynumber: 1.9 Consensus size: 77
186778 ATTTAAAAGT
* * * *
186788 TAATCCCTACATTTTAATTTTGCTGTTTTTTTGGGTTAATATGCCAAAGGTTTATGTATCATTTG
1 TAATCCATACATTTTAATTTCGCTGTTTTTTTGGATTAATATGCCAAAGGTTTATATATCATTTG
186853 AAATTTAAATAC
66 AAATTTAAATAC
* *
186865 TAATCCATATATTTTAATTTCGCTG-TTTTTTGGATTTATATGCCAAAGGTTCT-TATATCATTT
1 TAATCCATACATTTTAATTTCGCTGTTTTTTTGGATTAATATGCCAAAGGTT-TATATATCATTT
*
186928 GATATTTAA
65 GAAATTTAA
186937 TCCCTATATT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
76 41 0.64
77 23 0.36
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (77 bp):
TAATCCATACATTTTAATTTCGCTGTTTTTTTGGATTAATATGCCAAAGGTTTATATATCATTTG
AAATTTAAATAC
Found at i:187415 original size:29 final size:28
Alignment explanation
Indices: 187379--187468 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
187369 GTTTTGTTGC
187379 TGTTTTTTTACTATTTTGGTTGCTGTTTTT
1 TGTTTTTTTACTATTTTGGTTG-T-TTTTT
* * *
187409 T-TTTTTTTGCTTTTTTTGTTGTTTTTT
1 TGTTTTTTTACTATTTTGGTTGTTTTTT
* *
187436 TGTTGTTTTTACTGTTTTGATTGTTATTTT
1 TGTT-TTTTTACTATTTTGGTTGTT-TTTT
187466 TGT
1 TGT
187469 GTTGTTTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 6 0.12
28 3 0.06
29 33 0.66
30 8 0.16
ACGTcount: A:0.06, C:0.04, G:0.16, T:0.74
Consensus pattern (28 bp):
TGTTTTTTTACTATTTTGGTTGTTTTTT
Found at i:187424 original size:11 final size:11
Alignment explanation
Indices: 187402--187532 Score: 63
Period size: 12 Copynumber: 11.7 Consensus size: 11
187392 TTTTGGTTGC
*
187402 TGTTTTTTTTT
1 TGTTGTTTTTT
*
187413 TTTTGCTTTTTT
1 TGTTG-TTTTTT
187425 TGTTGTTTTTT
1 TGTTGTTTTTT
*
187436 TGTTGTTTTTAC
1 TGTTGTTTTT-T
**
187448 TG-T-TTTGAT
1 TGTTGTTTTTT
* *
187457 TGTTATTTTTG
1 TGTTGTTTTTT
187468 TGTTG--TTTT
1 TGTTGTTTTTT
*
187477 TGCTGTTATTTT
1 TGTTGTT-TTTT
* *
187489 TGTTACTGTTTT
1 TGTT-GTTTTTT
*
187501 TGTTGCTATTTT
1 TGTTG-TTTTTT
* *
187513 TATTGTTTTTAA
1 TGTTGTTTTT-T
187525 TGTTGTTT
1 TGTTGTTT
187533 GCTATTATTT
Statistics
Matches: 88, Mismatches: 22, Indels: 19
0.68 0.17 0.15
Matches are distributed among these distances:
9 9 0.10
10 4 0.05
11 31 0.35
12 43 0.49
13 1 0.01
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.73
Consensus pattern (11 bp):
TGTTGTTTTTT
Found at i:187428 original size:23 final size:22
Alignment explanation
Indices: 187402--187532 Score: 63
Period size: 23 Copynumber: 5.9 Consensus size: 22
187392 TTTTGGTTGC
* *
187402 TGTTTTTTTTTTTTTGCTTTTTT
1 TGTTGTTTTTTTGTTG-TTTTTT
*
187425 TGTTGTTTTTTTGTTGTTTTTAC
1 TGTTGTTTTTTTGTTGTTTTT-T
** * *
187448 TG-T-TTTGATTGTTATTTTTG
1 TGTTGTTTTTTTGTTGTTTTTT
*
187468 TGTTG--TTTTTGCTGTTATTTT
1 TGTTGTTTTTTTGTTGTT-TTTT
* * *
187489 TGTTACTGTTTTTGTTGCTATTTT
1 TGTT-GTTTTTTTGTTG-TTTTTT
* *
187513 TATTGTTTTTAATGTTGTTT
1 TGTTGTTTTT-TTGTTGTTT
187533 GCTATTATTT
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
20 9 0.11
21 21 0.27
22 6 0.08
23 22 0.28
24 20 0.25
25 1 0.01
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.73
Consensus pattern (22 bp):
TGTTGTTTTTTTGTTGTTTTTT
Found at i:187483 original size:12 final size:11
Alignment explanation
Indices: 187457--187491 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
187447 CTGTTTTGAT
187457 TGTTATTTTTG
1 TGTTATTTTTG
*
187468 TGTTGTTTTTG
1 TGTTATTTTTG
187479 CTGTTATTTTTG
1 -TGTTATTTTTG
187491 T
1 T
187492 TACTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.06, C:0.03, G:0.20, T:0.71
Consensus pattern (11 bp):
TGTTATTTTTG
Found at i:187492 original size:32 final size:31
Alignment explanation
Indices: 187419--187493 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
187409 TTTTTTTTGC
* *
187419 TTTTTTTGTTGTTTTTTTGTTGTTTTTACTG
1 TTTTTTTGTTATTTTTGTGTTGTTTTTACTG
* *
187450 TTTTGATTGTTATTTTTGTGTTGTTTTTGCTG
1 TTTT-TTTGTTATTTTTGTGTTGTTTTTACTG
187482 TTATTTTTGTTA
1 TT-TTTTTGTTA
187494 CTGTTTTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 4 0.11
32 31 0.84
33 2 0.05
ACGTcount: A:0.07, C:0.03, G:0.17, T:0.73
Consensus pattern (31 bp):
TTTTTTTGTTATTTTTGTGTTGTTTTTACTG
Found at i:187512 original size:12 final size:12
Alignment explanation
Indices: 187421--187595 Score: 76
Period size: 12 Copynumber: 13.9 Consensus size: 12
187411 TTTTTTGCTT
187421 TTTTTGTTGTT-
1 TTTTTGTTGTTA
187432 TTTTTGTTGTTTTTA
1 TTTTTGTTG---TTA
187447 CTGTTTTGATTGTTA
1 -T-TTTTG-TTGTTA
*
187462 TTTTTG-TGTTG
1 TTTTTGTTGTTA
*
187473 TTTTTGCTGTTA
1 TTTTTGTTGTTA
** *
187485 TTTTTGTTACTG
1 TTTTTGTTGTTA
*
187497 TTTTTGTTGCTA
1 TTTTTGTTGTTA
* *
187509 TTTTTATTGTTT
1 TTTTTGTTGTTA
*
187521 TTAATGTTGTTTGCTA
1 TT--T-TTG-TTGTTA
187537 TTATTT-TTGTTA
1 TT-TTTGTTGTTA
187549 CTGTTTTGGTTGTTA
1 -T-TTTT-GTTGTTA
187564 --TTT-TTGTTA
1 TTTTTGTTGTTA
*
187573 -TTTTGATGTTA
1 TTTTTGTTGTTA
187584 TTTTTGTGTGTT
1 TTTTTGT-TGTT
187596 TTTACTATTG
Statistics
Matches: 127, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
9 6 0.05
10 3 0.02
11 27 0.21
12 43 0.34
13 13 0.10
14 7 0.06
15 13 0.10
16 7 0.06
17 5 0.04
18 3 0.02
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:187568 original size:24 final size:24
Alignment explanation
Indices: 187444--187572 Score: 102
Period size: 24 Copynumber: 5.1 Consensus size: 24
187434 TTTGTTGTTT
187444 TTACTG-TTTTGATTGTTATTTTTG
1 TTACTGTTTTTG-TTGTTATTTTTG
*
187468 TGT--TGTTTTTGCTGTTATTTTTG
1 T-TACTGTTTTTGTTGTTATTTTTG
*
187491 TTACTGTTTTTGTTGCTATTTTTATTG
1 TTACTGTTTTTGTTG-T-TATTT-TTG
* * *
187518 TTTTTAATGTTGTTTGCTATTATTTTTG
1 ---TTACTGTT-TTTGTTGTTATTTTTG
*
187546 TTACTGTTTTGGTTGTTATTTTTG
1 TTACTGTTTTTGTTGTTATTTTTG
187570 TTA
1 TTA
187573 TTTTGATGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.01
23 14 0.17
24 32 0.39
25 9 0.11
26 4 0.05
27 3 0.04
28 3 0.04
29 4 0.05
30 8 0.10
31 5 0.06
ACGTcount: A:0.11, C:0.05, G:0.17, T:0.67
Consensus pattern (24 bp):
TTACTGTTTTTGTTGTTATTTTTG
Found at i:204633 original size:16 final size:16
Alignment explanation
Indices: 204608--204641 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
204598 AGAAATCTTA
204608 TTTTATTTTTAATAATT
1 TTTTATTTTTAA-AATT
204625 TTTTA-TTTTAAAATT
1 TTTTATTTTTAAAATT
204640 TT
1 TT
204642 ACTTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTTAAAATT
Found at i:205128 original size:39 final size:39
Alignment explanation
Indices: 205071--205149 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
205061 ATAAGACTAC
205071 TAAATTAATGTTACATATATTAGATTGAACAAAAAAAAG
1 TAAATTAATGTTACATATATTAGATTGAACAAAAAAAAG
*
205110 TAAATTAATGTTATATATATTAGATTGAACAAAAAAAAG
1 TAAATTAATGTTACATATATTAGATTGAACAAAAAAAAG
205149 T
1 T
205150 TATATAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (39 bp):
TAAATTAATGTTACATATATTAGATTGAACAAAAAAAAG
Found at i:213956 original size:35 final size:37
Alignment explanation
Indices: 213912--213987 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 37
213902 TAAAAGTAAA
* *
213912 ATATAATCATTAAAGA-CATAATATTAAAAT-ATATGT
1 ATATAATCA-TAAAGATCAAAATATTAAAATCATACGT
* *
213948 ATAT-ATCATAAATATTAAAATATTAAAATCATACGT
1 ATATAATCATAAAGATCAAAATATTAAAATCATACGT
213984 ATAT
1 ATAT
213988 TAAACAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 5 0.15
35 16 0.47
36 13 0.38
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.37
Consensus pattern (37 bp):
ATATAATCATAAAGATCAAAATATTAAAATCATACGT
Found at i:214587 original size:17 final size:17
Alignment explanation
Indices: 214565--214597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
214555 TACCTTTATT
*
214565 AATTTAAAATTTTAAAA
1 AATTTAAAAGTTTAAAA
214582 AATTTAAAAGTTTAAA
1 AATTTAAAAGTTTAAA
214598 TAGAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATTTAAAAGTTTAAAA
Found at i:224584 original size:270 final size:269
Alignment explanation
Indices: 224152--224888 Score: 842
Period size: 270 Copynumber: 2.7 Consensus size: 269
224142 CTACACAATG
*
224152 TAAATTCCTATGCTTTTCAATGAA--TGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGATTTA
1 TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
* * * * * * *
224215 CTGCTTCCATTGTG-TTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTAGTCATAGG
66 TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATAGG
* * * ** *
224279 CTT-CCCGATGTGAAGTTCTAACCTTTTAAATAATTTGTGACTGCACAACGGCAGATTCTCGGAA
131 -TTACCCAATGTGAA-TTCTAA-GTTTTCAATAATTTGTGAAAGCACAACAGCAGATTCTC-GAA
* * * * * *
224343 GTGGGATTTAATAGTTCGATTGTGCTTTACACCTTTGCCATAGATGGAGTTTTGATAGGGAGGAA
192 GTGGGATTTAACAGGTCCATTGTGCTTTACACATTTGCCATAGATGGAGATTTGATAGGGAAGAA
* **
224408 CTGTGGTAAACTA
257 CCGTAATAAACTA
* * * *
224421 TAAATTCCTATACTTTTCAA-GAATTTGTGAGTGCGCTATGGCAGATTTTCTGAAGTAGAATTTA
1 TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
* * *
224485 TTGGTTCCACTATGCTTTTTGCTCTT-CTCTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATAG
66 TTGGTTCCATTGTGCTTTATGCTCTTAC-CTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATAG
* *
224549 GTTACCCTATGTGAATTCATAAGTTTTCAATAATTTGTGAAAGCACAATAGCAGATTCTCGAGAG
130 GTTACCCAATGTGAATTC-TAAGTTTTCAATAATTTGTGAAAGCACAACAGCAGATTCTCGA-AG
* ** * * * * *
224614 TAGGATTTTCCGGGTCCATTGTGCTTTACACATTTTCCTTAGGTGGGGATTTGATAGGGAAGAAC
193 TGGGATTTAACAGGTCCATTGTGCTTTACACATTTGCCATAGATGGAGATTTGATAGGGAAGAAC
*
224679 CGTAATAGACTA
258 CGTAATAAACTA
* * *
224691 TAAATTCCTATGGTTTTCAATG-ATTTGTGAATGCACTGTGACAGATTTTCTGAAGTAGGATTTA
1 TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
* * *
224755 TTGGTTCCGTTGTGCTTTATGCTCTTACCTTAGATGGGAATTTGCTAGGGAAGAGTTGTAATTGG
66 TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATAGG
* * ** * *
224820 CTACCCAAAGTGAATGTCTAAG-CGTCATTATAATTTGTGAAGGCACAACAGCTGATTCTCAGAA
131 TTACCCAATGTGAAT-TCTAAGTTTTCA--ATAATTTGTGAAAGCACAACAGCAGATTCTC-GAA
224884 GTGGG
192 GTGGG
224889 TTTGAGTCTG
Statistics
Matches: 393, Mismatches: 62, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
268 3 0.01
269 24 0.06
270 272 0.69
271 92 0.23
272 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (269 bp):
TAAATTCCTATGCTTTTCAATGAATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATAGG
TTACCCAATGTGAATTCTAAGTTTTCAATAATTTGTGAAAGCACAACAGCAGATTCTCGAAGTGG
GATTTAACAGGTCCATTGTGCTTTACACATTTGCCATAGATGGAGATTTGATAGGGAAGAACCGT
AATAAACTA
Found at i:224816 original size:132 final size:133
Alignment explanation
Indices: 224151--224816 Score: 476
Period size: 132 Copynumber: 5.0 Consensus size: 133
224141 GCTACACAAT
* * *
224151 GTAAATTCCTATGCTTTTCAATGA-ATGTGAATGCACTATGGCAGGTTTTCTGAAGTAGGATTTA
1 GTAAATTCCTATACTTTTCAATGATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
* * * * * * *
224215 CTGCTTCCATTGTG-TTTATGCCCTTACCTTTGATGGGGATTTGATAGGGAAGAGTAGTCATAGG
66 TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGATAGGGAAGAGTTGTAATAGA
224279 CTTCCCGA
131 C-T----A
* * * * * * * * *
224287 TGTGAAGTT-CTA-ACCTTTTAAATAATTTGTGACTGCACAACGGCAGATTCTCGGAAGTGGGAT
1 -GT-AAATTCCTATA-CTTTTCAATGATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGAT
* * * ** * * * * * ** **
224350 TTAATAGTTCGATTGTGCTTTACAC-CTTTGCCATAGATGGAGTTTTGATAGGGAGGAACTGTGG
63 TTATTGGTTCCATTGTGCTTTATGCTC-TTACCTTAGATGGGGATTTGATAGGGAAGAGTTGTAA
*
224414 TAAACTA
127 TAGACTA
* * *
224421 -TAAATTCCTATACTTTTCAA-GAATTTGTGAGTGCGCTATGGCAGATTTTCTGAAGTAGAATTT
1 GTAAATTCCTATACTTTTCAATG-ATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTT
* * * *
224484 ATTGGTTCCACTATGCTTTTTGCTCTT-CTCTTAGATGGGGATTTGCTAGGGAAGAGTTGTAATA
65 ATTGGTTCCATTGTGCTTTATGCTCTTAC-CTTAGATGGGGATTTGATAGGGAAGAGTTGTAATA
224548 GGTTACCCTA
129 -G--A--CTA
* * * * * * * *
224558 TGTGAATTCATA-AGTTTTCAATAATTTGTGAAAGCACAATAGCAGATTCTC-GAGAGTAGGATT
1 -GTAAATTCCTATACTTTTCAATGATTTGTGAATGCACTATGGCAGATTTTCTGA-AGTAGGATT
* * ** * * ***
224621 T-TCCGGGTCCATTGTGCTTTACACAT-TTTCCTTAGGTGGGGATTTGATAGGGAAGAACCGTAA
64 TAT-TGGTTCCATTGTGCTTTATGC-TCTTACCTTAGATGGGGATTTGATAGGGAAGAGTTGTAA
224684 TAGACTA
127 TAGACTA
** * *
224691 -TAAATTCCTATGGTTTTCAATGATTTGTGAATGCACTGTGACAGATTTTCTGAAGTAGGATTTA
1 GTAAATTCCTATACTTTTCAATGATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
* * *
224755 TTGGTTCCGTTGTGCTTTATGCTCTTACCTTAGATGGGAATTTGCTAGGGAAGAGTTGTAAT
66 TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGATAGGGAAGAGTTGTAAT
224817 TGGCTACCCA
Statistics
Matches: 398, Mismatches: 105, Indels: 57
0.71 0.19 0.10
Matches are distributed among these distances:
131 14 0.04
132 175 0.44
133 8 0.02
134 1 0.00
135 2 0.01
137 21 0.05
138 133 0.33
139 44 0.11
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (133 bp):
GTAAATTCCTATACTTTTCAATGATTTGTGAATGCACTATGGCAGATTTTCTGAAGTAGGATTTA
TTGGTTCCATTGTGCTTTATGCTCTTACCTTAGATGGGGATTTGATAGGGAAGAGTTGTAATAGA
CTA
Found at i:228480 original size:30 final size:31
Alignment explanation
Indices: 228414--228485 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
228404 TTACATTAAC
** *
228414 GACTAAATTGTGATTTTAGTGAAACTTAAGG
1 GACTAAATTGAAATGTTAGTGAAACTTAAGG
**
228445 G-CTAAATTGAAATGTTAGTGAAA-TTTGGG
1 GACTAAATTGAAATGTTAGTGAAACTTAAGG
228474 GACTAAATTGAA
1 GACTAAATTGAA
228486 CTCTGATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 5 0.14
30 29 0.83
31 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (31 bp):
GACTAAATTGAAATGTTAGTGAAACTTAAGG
Found at i:231517 original size:29 final size:29
Alignment explanation
Indices: 231484--231565 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 29
231474 CGCTAGGTGT
231484 CGGTGTTTACAGTTCTAGGTACTATGCAC
1 CGGTGTTTACAGTTCTAGGTACTATGCAC
* * * * **
231513 CGGTGTTT-CATTTCCAGGCACTCTGTGC
1 CGGTGTTTACAGTTCTAGGTACTATGCAC
*
231541 CGGTGATTAC-GATTCTAGGTACTAT
1 CGGTGTTTACAG-TTCTAGGTACTAT
231566 ACCGGTAGTG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 21 0.52
29 19 0.47
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (29 bp):
CGGTGTTTACAGTTCTAGGTACTATGCAC
Found at i:233573 original size:21 final size:21
Alignment explanation
Indices: 233534--233574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
233524 ATTTTCACTA
233534 TTTTAAATATAAAATATTAAT
1 TTTTAAATATAAAATATTAAT
*
233555 TTTTATATCATAAAA-ATTAA
1 TTTTAAAT-ATAAAATATTAA
233575 AATTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAATATAAAATATTAAT
Found at i:234580 original size:285 final size:285
Alignment explanation
Indices: 234070--234644 Score: 1125
Period size: 285 Copynumber: 2.0 Consensus size: 285
234060 TTTTAATCGA
234070 GATTAATTTACTCAATTTCGAAATTAAAAAAGATCAAAAAGTTCTTTTTATCTACAACTTTTTAA
1 GATTAATTTACTCAATTTCGAAATTAAAAAAGATCAAAAAGTTCTTTTTATCTACAACTTTTTAA
* *
234135 CTTAAAGTTAAACCTGCTTATGGATTGGGTCACTTGTCTTAGCCTGAAAGCCCACCTGAAAAATA
66 CTTAAAGTTAAACCTGCTTATGGATTGGATCACCTGTCTTAGCCTGAAAGCCCACCTGAAAAATA
234200 AAAAGGTTTGAACAAAATATGAGGCTCGAAAAATGGGCTTGAGTAAAATTTAAAACTCGTTTTCT
131 AAAAGGTTTGAACAAAATATGAGGCTCGAAAAATGGGCTTGAGTAAAATTTAAAACTCGTTTTCT
234265 ATATGGATTAGGCCTTAGGCAAGATTTTTTTGCTCGAACTCTGTCTGACTCGAATATTATGTTAT
196 ATATGGATTAGGCCTTAGGCAAGATTTTTTTGCTCGAACTCTGTCTGACTCGAATATTATGTTAT
234330 AAAACAATATTATATTAATTAATAT
261 AAAACAATATTATATTAATTAATAT
234355 GATTAATTTACTCAATTTCGAAATTAAAAAAGATCAAAAAGTTCTTTTTATCTACAACTTTTTAA
1 GATTAATTTACTCAATTTCGAAATTAAAAAAGATCAAAAAGTTCTTTTTATCTACAACTTTTTAA
234420 CTTAAAGTTAAACCTGCTTATGGATTGGATCACCTGTCTTAGCCTGAAAGCCCACCTGAAAAATA
66 CTTAAAGTTAAACCTGCTTATGGATTGGATCACCTGTCTTAGCCTGAAAGCCCACCTGAAAAATA
234485 AAAAGGTTTGAACAAAATATGAGGCTCGAAAAATGGGCTTGAGTAAAATTTAAAACTCGTTTTCT
131 AAAAGGTTTGAACAAAATATGAGGCTCGAAAAATGGGCTTGAGTAAAATTTAAAACTCGTTTTCT
234550 ATATGGATTAGGCCTTAGGCAAGATTTTTTTGCTCGAACTCTGTCTGACTCGAATATTATGTTAT
196 ATATGGATTAGGCCTTAGGCAAGATTTTTTTGCTCGAACTCTGTCTGACTCGAATATTATGTTAT
234615 AAAACAATATTATATTAATTAATAT
261 AAAACAATATTATATTAATTAATAT
234640 G-TTAA
1 GATTAA
234645 ATAATAATTA
Statistics
Matches: 288, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
284 4 0.01
285 284 0.99
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (285 bp):
GATTAATTTACTCAATTTCGAAATTAAAAAAGATCAAAAAGTTCTTTTTATCTACAACTTTTTAA
CTTAAAGTTAAACCTGCTTATGGATTGGATCACCTGTCTTAGCCTGAAAGCCCACCTGAAAAATA
AAAAGGTTTGAACAAAATATGAGGCTCGAAAAATGGGCTTGAGTAAAATTTAAAACTCGTTTTCT
ATATGGATTAGGCCTTAGGCAAGATTTTTTTGCTCGAACTCTGTCTGACTCGAATATTATGTTAT
AAAACAATATTATATTAATTAATAT
Found at i:234800 original size:38 final size:38
Alignment explanation
Indices: 234758--234838 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
234748 AAAATATTAA
**
234758 ATATTAAAATTTA-TATTTAATACAATAAAATGTTTATT
1 ATATT-AAATTTATTATTTAATACAATAAAACATTTATT
* * * *
234796 ATATTTATTTTATTTTTTAATATAATAAAACATTTATT
1 ATATTAAATTTATTATTTAATACAATAAAACATTTATT
234834 ATATT
1 ATATT
234839 TATGATAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (38 bp):
ATATTAAATTTATTATTTAATACAATAAAACATTTATT
Found at i:234885 original size:16 final size:18
Alignment explanation
Indices: 234866--234908 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
234856 ATATAAATAC
234866 TTTTTAATGTT-ACAT-T
1 TTTTTAATGTTAACATGT
*
234882 TTTTT-ATTTTAACATGT
1 TTTTTAATGTTAACATGT
234899 TTTTTAATGT
1 TTTTTAATGT
234909 ATTTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 6 0.27
18 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTTAATGTTAACATGT
Found at i:252795 original size:24 final size:21
Alignment explanation
Indices: 252762--252814 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
252752 TTTGTAAATA
* *
252762 ATTAATATTAATTATTTAGATAT
1 ATTAAAATTAA-TATTT-CATAT
252785 ATTTAAAATTAATATTTCATAT
1 A-TTAAAATTAATATTTCATAT
252807 ATTAAAAT
1 ATTAAAAT
252815 ATTAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 5 0.19
23 6 0.22
24 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAAAATTAATATTTCATAT
Found at i:253029 original size:14 final size:13
Alignment explanation
Indices: 252995--253026 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
252985 ATTAAATCAA
252995 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
253008 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
253021 ACTTTT
1 ACTTTT
253027 TCACCACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:256243 original size:4 final size:4
Alignment explanation
Indices: 256234--256269 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
256224 TATACAAACT
*
256234 TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTTT TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
256270 AAACCGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTA
Found at i:256765 original size:22 final size:22
Alignment explanation
Indices: 256737--256796 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
256727 ATATTCAAAC
256737 AACAATAACAAAATAATAGCAA
1 AACAATAACAAAATAATAGCAA
* * * *
256759 TATAATAACGAAATGATAGCAA
1 AACAATAACAAAATAATAGCAA
*
256781 AACAACAACAAAATAA
1 AACAATAACAAAATAA
256797 CATAAAAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.65, C:0.13, G:0.07, T:0.15
Consensus pattern (22 bp):
AACAATAACAAAATAATAGCAA
Found at i:263054 original size:43 final size:42
Alignment explanation
Indices: 263002--263083 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
262992 TCCTTGTATC
**
263002 TAGTGAAAAGCACGTCCAACTAGG-TGAGCTTTCTTACCATAA
1 TAGTGAAAAGCACACCCAACT-GGATGAGCTTTCTTACCATAA
*
263044 TAGTAGAAAAGCTCACCCAACTGGATGAGCTTTCTTACCA
1 TAGT-GAAAAGCACACCCAACTGGATGAGCTTTCTTACCA
263084 CCACTACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 6 0.17
43 29 0.83
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (42 bp):
TAGTGAAAAGCACACCCAACTGGATGAGCTTTCTTACCATAA
Found at i:267053 original size:20 final size:19
Alignment explanation
Indices: 267028--267081 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
267018 TAAAATTATT
267028 TTTAAAAAAATATAAAATAA
1 TTTAAAAAAATATAAAAT-A
** * *
267048 TTTAAATTAATTTAAAATT
1 TTTAAAAAAATATAAAATA
*
267067 TTTAAAAATATATAA
1 TTTAAAAAAATATAA
267082 TTATTAAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAAAATATAAAATA
Found at i:267133 original size:6 final size:6
Alignment explanation
Indices: 267126--267156 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
267116 AATCCCCCCC
*
267126 TTCCCC TTCCCT TTCCCT TTCCCT TTCCCT T
1 TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT T
267157 CTTATTTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TTCCCT
Found at i:267143 original size:11 final size:11
Alignment explanation
Indices: 267123--267157 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
267113 TTGAATCCCC
*
267123 CCCTTCCCCTT
1 CCCTTTCCCTT
267134 CCCTTTCCCTTT
1 CCCTTTCCC-TT
267146 CCCTTTCCCTT
1 CCCTTTCCCTT
267157 C
1 C
267158 TTATTTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (11 bp):
CCCTTTCCCTT
Found at i:289594 original size:20 final size:19
Alignment explanation
Indices: 289544--289599 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
289534 TAGTCAAAAT
*
289544 TTGTTATTTTCTTATTTTTG
1 TTGTTATTTTCTT-TTTTAG
* *
289564 TTTTTATTTTTATTTTTTAAG
1 TTGTTA-TTTTCTTTTTT-AG
289585 TTGTTATTTTCTTTT
1 TTGTTATTTTCTTTT
289600 GACTAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.12, C:0.04, G:0.07, T:0.77
Consensus pattern (19 bp):
TTGTTATTTTCTTTTTTAG
Done.