Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013953.1 Corchorus olitorius cultivar O-4 contig13986, 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: 74578
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:713 original size:71 final size:73
Alignment explanation
Indices: 596--730 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 73
586 CCTCCCTGCG
* *
596 GGATATCCAATGATCTTATAGCACTGATCTTTTGTGTGCCCCATC-TTTTGACAATGTCCACACC
1 GGATATCCAATGATCTCATAGCACTGATCTTTCGTGTGCCCCATCTTTTTGACAATGTCCACACC
660 TTGCAGCA
66 TTGCAGCA
* *
668 GGATATCCAATGA-CTCATAGCATTGATCTTTCGTGTGCCCCATCTTTTTGACAATGTTCACAC
1 GGATATCCAATGATCTCATAGCACTGATCTTTCGTGTGCCCCATCTTTTTGACAATGTCCACAC
731 ATTGGCTTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 28 0.48
72 30 0.52
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (73 bp):
GGATATCCAATGATCTCATAGCACTGATCTTTCGTGTGCCCCATCTTTTTGACAATGTCCACACC
TTGCAGCA
Found at i:4341 original size:29 final size:31
Alignment explanation
Indices: 4309--4373 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
4299 TATGGGATTT
4309 ATTTGTCCCAAAA-A-AAAGTTAAGGGGCCA
1 ATTTGTCCCAAAATAGAAAGTTAAGGGGCCA
* * * *
4338 ATTTGTTCCAAAATAGATAGTTGAGGGGCTA
1 ATTTGTCCCAAAATAGAAAGTTAAGGGGCCA
4369 ATTTG
1 ATTTG
4374 GATATGAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.40
30 1 0.03
31 17 0.57
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (31 bp):
ATTTGTCCCAAAATAGAAAGTTAAGGGGCCA
Found at i:10965 original size:31 final size:29
Alignment explanation
Indices: 10943--11067 Score: 141
Period size: 29 Copynumber: 4.3 Consensus size: 29
10933 TAAGGTTTGT
10943 CGAAAAACGCAATTTGGAATATAACGTTA
1 CGAAAAACGCAATTTGGAATATAACGTTA
* *
10972 C-AAAACAAGCAA-TTGAAGATATAACGTTA
1 CGAAAA-ACGCAATTTGGA-ATATAACGTTA
11001 CGAAAAACGCAATTTGGAATATAACGTTA
1 CGAAAAACGCAATTTGGAATATAACGTTA
* **
11030 C-AAAACAAGCAA-TTAAAGATATAACGTTA
1 CGAAAA-ACGCAATTTGGA-ATATAACGTTA
11059 CGAAAAACG
1 CGAAAAACG
11068 ATCAATTAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
28 15 0.19
29 54 0.67
30 12 0.15
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (29 bp):
CGAAAAACGCAATTTGGAATATAACGTTA
Found at i:10993 original size:29 final size:30
Alignment explanation
Indices: 10961--11064 Score: 144
Period size: 29 Copynumber: 3.6 Consensus size: 30
10951 GCAATTTGGA
10961 ATATAACGTTAC-AAAACAAGCAATTGAAG
1 ATATAACGTTACGAAAACAAGCAATTGAAG
* *
10990 ATATAACGTTACGAAAA-ACGCAATTTGGA-
1 ATATAACGTTACGAAAACAAGCAA-TTGAAG
*
11019 ATATAACGTTAC-AAAACAAGCAATTAAAG
1 ATATAACGTTACGAAAACAAGCAATTGAAG
11048 ATATAACGTTACGAAAA
1 ATATAACGTTACGAAAA
11065 ACGATCAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
28 7 0.11
29 46 0.71
30 12 0.18
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (30 bp):
ATATAACGTTACGAAAACAAGCAATTGAAG
Found at i:11012 original size:58 final size:58
Alignment explanation
Indices: 10943--11067 Score: 241
Period size: 58 Copynumber: 2.2 Consensus size: 58
10933 TAAGGTTTGT
*
10943 CGAAAAACGCAATTTGGAATATAACGTTACAAAACAAGCAATTGAAGATATAACGTTA
1 CGAAAAACGCAATTTGGAATATAACGTTACAAAACAAGCAATTAAAGATATAACGTTA
11001 CGAAAAACGCAATTTGGAATATAACGTTACAAAACAAGCAATTAAAGATATAACGTTA
1 CGAAAAACGCAATTTGGAATATAACGTTACAAAACAAGCAATTAAAGATATAACGTTA
11059 CGAAAAACG
1 CGAAAAACG
11068 ATCAATTAAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (58 bp):
CGAAAAACGCAATTTGGAATATAACGTTACAAAACAAGCAATTAAAGATATAACGTTA
Found at i:11074 original size:31 final size:29
Alignment explanation
Indices: 10961--11083 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 29
10951 GCAATTTGGA
*
10961 ATATAACGTTACAAAACAAGCAATTGAAG
1 ATATAACGTTACAAAACAAGCAATTAAAG
* **
10990 ATATAACGTTACGAAAA-ACGCAATT-TGG
1 ATATAACGTTAC-AAAACAAGCAATTAAAG
11018 AATATAACGTTACAAAACAAGCAATTAAAG
1 -ATATAACGTTACAAAACAAGCAATTAAAG
* * *
11048 ATATAACGTTACGAAAAACGATCAATTAAGG
1 ATATAACGTTAC--AAAACAAGCAATTAAAG
11079 ATATA
1 ATATA
11084 GTCAGCTAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
28 5 0.06
29 50 0.63
30 5 0.06
31 19 0.24
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (29 bp):
ATATAACGTTACAAAACAAGCAATTAAAG
Found at i:11238 original size:31 final size:31
Alignment explanation
Indices: 11203--11282 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
11193 CCTATCTGAT
*
11203 TATATCCTTAATTGTTTGAAATAAAAAACAA
1 TATATCCTTAATTGCTTGAAATAAAAAACAA
* ***
11234 TATATCTTTAATTGCTTGAAATAAAAAATGT
1 TATATCCTTAATTGCTTGAAATAAAAAACAA
11265 TATATCCTTAATTGCTTG
1 TATATCCTTAATTGCTTG
11283 GGGGCAGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (31 bp):
TATATCCTTAATTGCTTGAAATAAAAAACAA
Found at i:11379 original size:19 final size:19
Alignment explanation
Indices: 11349--11405 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
11339 AGAAAAGAAA
11349 ATAATTTGAATA-TTATTT
1 ATAATTTGAATATTTATTT
11367 ATAATTATGAATATTTATTT
1 ATAATT-TGAATATTTATTT
* * *
11387 -TGATTTGAAAATATATTT
1 ATAATTTGAATATTTATTT
11405 A
1 A
11406 ATTATTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 17 0.52
19 10 0.30
20 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (19 bp):
ATAATTTGAATATTTATTT
Found at i:12147 original size:31 final size:31
Alignment explanation
Indices: 12107--12186 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
12097 TTTGCTGCCG
* *
12107 CAAGCAATTAAGGATATAACATTTTCGATTT
1 CAAGAAATTAAGGATATAACATTTTCAATTT
* *
12138 TAAGAAATTAAGGATATAACGTTTTCAATTT
1 CAAGAAATTAAGGATATAACATTTTCAATTT
*
12169 CAAGCAATTAAGGATATA
1 CAAGAAATTAAGGATATA
12187 GTCAGTTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (31 bp):
CAAGAAATTAAGGATATAACATTTTCAATTT
Found at i:12357 original size:29 final size:31
Alignment explanation
Indices: 12295--12361 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
12285 TCTAACTGAC
*
12295 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGATCGCTTTTCGTAACGT
* * *
12326 TATATCCTTGATTGATTG-TTTT-GTAATGT
1 TATATCCTTAATTGATCGCTTTTCGTAACGT
12355 TATATCC
1 TATATCC
12362 CAATTTGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGATCGCTTTTCGTAACGT
Found at i:12652 original size:22 final size:22
Alignment explanation
Indices: 12620--12685 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
12610 CCTTGTGGGT
*
12620 GTGTCTTAGTGCCAGGAAGTCGG
1 GTGT-TTAGTGGCAGGAAGTCGG
**
12643 GTGTTTAGTGGCAGGAAGTTAG
1 GTGTTTAGTGGCAGGAAGTCGG
*
12665 ATGTTTAGTGGCAGGAAGTCG
1 GTGTTTAGTGGCAGGAAGTCG
12686 AGGGTAAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (22 bp):
GTGTTTAGTGGCAGGAAGTCGG
Found at i:14140 original size:17 final size:17
Alignment explanation
Indices: 14105--14157 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
14095 AACCCATGTA
* *
14105 ATCTTTGATCAC-CGTG
1 ATCTTAGATCACTAGTG
*
14121 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
14138 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTAGTG
14155 ATC
1 ATC
14158 CCGGGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 1 0.03
16 10 0.31
17 20 0.62
18 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:24231 original size:26 final size:28
Alignment explanation
Indices: 24178--24232 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
24168 ATGAACGGAC
24178 GATAATGAATGAATGTATTTAACCAAAAAA
1 GATAATGAATGAATGTA-TTAA-CAAAAAA
*
24208 GATAATGGATGAATGTA-TAA-AAAAA
1 GATAATGAATGAATGTATTAACAAAAA
24233 TAACACAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (28 bp):
GATAATGAATGAATGTATTAACAAAAAA
Found at i:31735 original size:76 final size:76
Alignment explanation
Indices: 31508--31738 Score: 354
Period size: 76 Copynumber: 3.0 Consensus size: 76
31498 AATTTTGAAG
*
31508 AAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCACGGTG
1 AAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTCGGTG
* *
31573 TCCCTGTATAG
66 TCCCCGTATAA
* ** *
31584 AAATAAACAAAACGATCGTCTCCTTTGAGACTTTCGTCGCGAACGGCCGAACACCAACCTTGGTG
1 AAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTCGGTG
31649 TCCCCGTATAA
66 TCCCCGTATAA
* * * * *
31660 AAATAAACGAAACAATCGTCTCCTTTGAGACTCTCGTTACGGACGGTCGAAAACCAACCTCGGTG
1 AAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTCGGTG
31725 TCCCCGTATAA
66 TCCCCGTATAA
31736 AAA
1 AAA
31739 ACAAATAAAA
Statistics
Matches: 139, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 139 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (76 bp):
AAATAAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTCGGTG
TCCCCGTATAA
Found at i:38022 original size:19 final size:19
Alignment explanation
Indices: 37972--38022 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
37962 TGTGGGATTT
37972 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
37990 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
38009 TTAATAATTAATTA
1 TTAATAATTAATTA
38023 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:39964 original size:22 final size:22
Alignment explanation
Indices: 39915--39965 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
39905 AAATATTACC
* **
39915 ATAATTATTTTTGGCAACCATA
1 ATAATTATTTTTGCCAAAAATA
39937 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCCAA-AAATA
39960 A-AATTA
1 ATAATTA
39966 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAAAAATA
Found at i:43402 original size:22 final size:22
Alignment explanation
Indices: 43370--43419 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
43360 GTCGGAGCCA
* *
43370 TGGCCTTGTGTGTGCTGCGTGC
1 TGGCCTGGTGTGTGCTGCGCGC
43392 TGGCCTGGTGTGTGCTGCGCGC
1 TGGCCTGGTGTGTGCTGCGCGC
43414 TGGCCT
1 TGGCCT
43420 TGCTTGTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.42, T:0.32
Consensus pattern (22 bp):
TGGCCTGGTGTGTGCTGCGCGC
Found at i:52256 original size:19 final size:18
Alignment explanation
Indices: 52223--52258 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52213 TTGAAGTAAC
52223 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
52241 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
52259 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:52266 original size:11 final size:10
Alignment explanation
Indices: 52223--52269 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
52213 TTGAAGTAAC
52223 TCTTCAATGA
1 TCTTCAATGA
52233 TCTTCAA--A
1 TCTTCAATGA
*
52241 TCTTCAAATTA
1 TCTTC-AATGA
52252 TCTTCAATGA
1 TCTTCAATGA
52262 GTCTTCAA
1 -TCTTCAA
52270 ACACGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:57875 original size:193 final size:193
Alignment explanation
Indices: 57536--57923 Score: 742
Period size: 193 Copynumber: 2.0 Consensus size: 193
57526 GAATAAGATT
57536 TTATTATCTAAAAAAGACGTAAATATATAGTGTAAAAGGAGTTAACCCCGTAATAAATCCCCACA
1 TTATTATCTAAAAAAGACGTAAATATATAGTGTAAAAGGAGTTAACCCCGTAATAAATCCCCACA
57601 CAAATAATTCGAAACATTATTGATACTACCTACGTATGGTTAATCAAAGTTTGTTAGTTAGGACT
66 CAAATAATTCGAAACATTATTGATACTACCTACGTATGGTTAATCAAAGTTTGTTAGTTAGGACT
57666 CTGTTTGAAGATGGAGCGATTTAAGTAAAACTTAAAGTCTTGGTCATTCAATGGATTCCATGAG
131 CTGTTTGAAGATGGAGCGATTTAAGTAAAACTTAAAGTCTTGGTCATTCAATGGATT-CATGAG
57730 TTATTATCT-AAAAAGACGTAAATATATAGTGTAAAAGGAGTTAACCCCGTAATAAATCCCCACA
1 TTATTATCTAAAAAAGACGTAAATATATAGTGTAAAAGGAGTTAACCCCGTAATAAATCCCCACA
* *
57794 CAAATAATTCTAAGCATTATTGATACTACCTACGTATGGTTAATCAAAGTTTGTTAGTTAGGACT
66 CAAATAATTCGAAACATTATTGATACTACCTACGTATGGTTAATCAAAGTTTGTTAGTTAGGACT
57859 CTGTTTGAAGATGGAGCGATTTAAGTAAAACTTAAAGTCTTGGTCATTCAATGGATTCATGAG
131 CTGTTTGAAGATGGAGCGATTTAAGTAAAACTTAAAGTCTTGGTCATTCAATGGATTCATGAG
57922 TT
1 TT
57924 TGTATGCATA
Statistics
Matches: 192, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
192 8 0.04
193 175 0.91
194 9 0.05
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (193 bp):
TTATTATCTAAAAAAGACGTAAATATATAGTGTAAAAGGAGTTAACCCCGTAATAAATCCCCACA
CAAATAATTCGAAACATTATTGATACTACCTACGTATGGTTAATCAAAGTTTGTTAGTTAGGACT
CTGTTTGAAGATGGAGCGATTTAAGTAAAACTTAAAGTCTTGGTCATTCAATGGATTCATGAG
Found at i:58962 original size:17 final size:17
Alignment explanation
Indices: 58906--58962 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
58896 TCATTGTGCC
*
58906 AACTTGCGTTATTTTATT
1 AACTT-CGTTATATTATT
* *
58924 AATTTTGTTATATTAGTT
1 AACTTCGTTATATTA-TT
*
58942 -ACTTCGTTATCTTATT
1 AACTTCGTTATATTATT
58958 AACTT
1 AACTT
58963 ATCTAAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 2 0.06
17 23 0.74
18 6 0.19
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.56
Consensus pattern (17 bp):
AACTTCGTTATATTATT
Found at i:60408 original size:580 final size:575
Alignment explanation
Indices: 59308--60468 Score: 1721
Period size: 580 Copynumber: 2.0 Consensus size: 575
59298 AAAGAATTAA
* * * *
59308 AGAATTTTTGAATAACTTGATGAGACGCCTTAGTCCTTACAGTTAGCATAAACCCAATCGCAATT
1 AGAATTTTCGAATAACTGGATGAGACGCCTTAGTCCCTACAGTTAGCAAAAACCCAATCGCAATT
* ** * * **
59373 ACCCCTACTATGTTTTGGACGGGCTTGTCGCTTATAAATAAGCATACAATAATTGTTGCGACAAG
66 ACCCCTACTATGTTTTCGACGAACTTGTCGCTCACAAATAAGCATACAATAAACGTTGCGACAAG
*
59438 CATAAAGGCAGAGAAAGACACTCTCAGAATAAAGCTCAATTCTTTGATGGCATGCCATAGGTTCT
131 CATAAAGGCAGAGAAAGACACTCTCAGAATAAAGCTCAATTCTTTGATGGCATGCCATAGGTTAT
* * * * *
59503 CCACTGGCCGTATGAATTCAAAGAGCAGGAATGGGATGCTGGAGTAAAGTACTCTATAAGATCAT
196 ACACTAGCCGTATGAATTCAAAGAGCAGGAATGAGATGCTGGACTAAAGTACTCGATAAGATCAT
* * * *
59568 TTATGGTGAAGACAATAGGGTTGCTGTAGAGTTAAGAAAAATCGGTTTGCTACAATATTTTTTAT
261 TTATAGTGAAGACAAGAGGGTTGCTATAGAGTTAAGAAAAATCGGTTCGCTACAATATTTTTTAT
*
59633 AATTTTTTTTCAGCCCTAGGTGATTGTTTTTCTAGGAGCATAAGGCTGATGCTCATTTTGGTTTT
326 AATTTTTTTTCAGCCCTAGGTGATTGTTTTTCTAGGAGCATAAGGCTGATGCTCATTTGGGTTTT
* *
59698 CAAGAAGGCTACCTCAAAAATCCCAGAAAATCGTGTTGGACAAAGAGAGCGGTTAATTCTTTTTT
391 CAAGAAGGCTACCTCAAAAATCCCAGAAAATCGGGTTGGACAAAAAGAGCGGTTAATTCTTTTTT
*
59763 TTTCTTTGCCATTAACCACATTTAAGAATTTCCTATTGTATTATATATGCGTATGTGTCTGTGTA
456 TTTCTTTACCATTAACCACATTTAAGAATTTCCTATTG--TTATATA---GTATGTGTCTGTGTA
59828 TTATATTTTTATAAGAGAGTACTTAATGAAAAAAAAAGTGAAAAATTAAGCGCAACATGC
516 TTATATTTTTATAAGAGAGTACTTAATGAAAAAAAAAGTGAAAAATTAAGCGCAACATGC
*
59888 AGAATTTTCGAATAACTGGATGAGACGCCTTA-TGCCCTACAGTTAGCAAAAACCCGATC-CAAA
1 AGAATTTTCGAATAACTGGATGAGACGCCTTAGT-CCCTACAGTTAGCAAAAACCCAATCGC-AA
* *
59951 TTCCCCCTACTATGTTTTCGACGAACTTGTCGCTCACATATAAGCATACAATAAACGTTGCGACA
64 TTACCCCTACTATGTTTTCGACGAACTTGTCGCTCACAAATAAGCATACAATAAACGTTGCGACA
* *
60016 AGCA-AAACGGCAGA-AAAGCACACTCTCACG-ATAAAGCTTAATTTTTTGATGGCATGCC-TCA
129 AGCATAAA-GGCAGAGAAAG-ACACTCTCA-GAATAAAGCTCAATTCTTTGATGGCATGCCAT-A
*
60077 GGTTATACACTAGCCGTATGAATTCAAAGAGCAGGAATGAGATGTTGGACTAAAGTACTCGATAA
190 GGTTATACACTAGCCGTATGAATTCAAAGAGCAGGAATGAGATGCTGGACTAAAGTACTCGATAA
* *
60142 GATCATTTATAGTGAAGACAAGAGGTTTGCTATAGAGTT-GGAAAAAATCGGTTCGCTACAATAT
255 GATCATTTATAGTGAAGACAAGAGGGTTGCTATAGAGTTAAG-AAAAATCGGTTCGCTACAATAT
* *
60206 TTTTTATAATTTTTTTGTTTCAGCCCTAGGTGATTGTTTTTTTAGGAGCATGAGGCTGATGCTCA
319 TTTTTATAA--TTTTT-TTTCAGCCCTAGGTGATTGTTTTTCTAGGAGCATAAGGCTGATGCTCA
* * *
60271 TTTGGGTTTTCAAGAAGGCTGCCTCAAAAATCCTAGAAAATCGGGTTGGACAAAAAGAGGGGTTA
381 TTTGGGTTTTCAAGAAGGCTACCTCAAAAATCCCAGAAAATCGGGTTGGACAAAAAGAGCGGTTA
*
60336 GTTCTTTTTTTTCTTTTTCTTTACCATTAACCACATTTAAGAATTTCCTATTG-TAT-TA-TATG
446 ATTC----TTTT-TTTTTCTTTACCATTAACCACATTTAAGAATTTCCTATTGTTATATAGTATG
60398 TGTCTGTGTATTATATTTTTATAAGAGAGTACTTAATGAAAAAAAAAGTGAAAAATTAAGCGCAA
506 TGTCTGTGTATTATATTTTTATAAGAGAGTACTTAATGAAAAAAAAAGTGAAAAATTAAGCGCAA
60463 CATGC
571 CATGC
60468 A
1 A
60469 AGTAAATTTG
Statistics
Matches: 527, Mismatches: 39, Indels: 30
0.88 0.07 0.05
Matches are distributed among these distances:
579 11 0.02
580 354 0.67
581 1 0.00
582 5 0.01
583 108 0.20
584 2 0.00
585 3 0.01
587 4 0.01
588 39 0.07
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (575 bp):
AGAATTTTCGAATAACTGGATGAGACGCCTTAGTCCCTACAGTTAGCAAAAACCCAATCGCAATT
ACCCCTACTATGTTTTCGACGAACTTGTCGCTCACAAATAAGCATACAATAAACGTTGCGACAAG
CATAAAGGCAGAGAAAGACACTCTCAGAATAAAGCTCAATTCTTTGATGGCATGCCATAGGTTAT
ACACTAGCCGTATGAATTCAAAGAGCAGGAATGAGATGCTGGACTAAAGTACTCGATAAGATCAT
TTATAGTGAAGACAAGAGGGTTGCTATAGAGTTAAGAAAAATCGGTTCGCTACAATATTTTTTAT
AATTTTTTTTCAGCCCTAGGTGATTGTTTTTCTAGGAGCATAAGGCTGATGCTCATTTGGGTTTT
CAAGAAGGCTACCTCAAAAATCCCAGAAAATCGGGTTGGACAAAAAGAGCGGTTAATTCTTTTTT
TTTCTTTACCATTAACCACATTTAAGAATTTCCTATTGTTATATAGTATGTGTCTGTGTATTATA
TTTTTATAAGAGAGTACTTAATGAAAAAAAAAGTGAAAAATTAAGCGCAACATGC
Found at i:62167 original size:28 final size:28
Alignment explanation
Indices: 62136--62196 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
62126 TGCGAAAAAC
62136 AAAAAGACAG-AAAAACACACCCTCGAG
1 AAAAAGACAGAAAAAACACACCCTCGAG
*
62163 AAAAAGGCAGAAAAAACACACCCTCGAG
1 AAAAAGACAGAAAAAACACACCCTCGAG
62191 AAAAAG
1 AAAAAG
62197 CTTAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.57, C:0.23, G:0.16, T:0.03
Consensus pattern (28 bp):
AAAAAGACAGAAAAAACACACCCTCGAG
Found at i:62757 original size:22 final size:24
Alignment explanation
Indices: 62732--62782 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
62722 AAGATTTTTT
62732 TTATTTG-TATA-TAGATAAGTTG
1 TTATTTGTTATATTAGATAAGTTG
* *
62754 TTATTTTGTTATATTAGTTAATTTG
1 TTA-TTTGTTATATTAGATAAGTTG
62779 TTAT
1 TTAT
62783 CTTATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 4 0.17
24 5 0.21
25 12 0.50
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (24 bp):
TTATTTGTTATATTAGATAAGTTG
Found at i:63849 original size:17 final size:17
Alignment explanation
Indices: 63809--63842 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63799 TAGATAAGTT
* *
63809 GTTATTTTGTTATGTTA
1 GTTACTTTGTTATCTTA
63826 GTTACTTTGTTATCTTA
1 GTTACTTTGTTATCTTA
63843 TTAACTTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (17 bp):
GTTACTTTGTTATCTTA
Found at i:67521 original size:2 final size:2
Alignment explanation
Indices: 67508--67543 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
67498 GAATACATAG
* *
67508 AT AT AT AG AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67544 TCGTGGAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:67525 original size:12 final size:12
Alignment explanation
Indices: 67508--67543 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
67498 GAATACATAG
67508 ATATATAGATAT
1 ATATATAGATAT
67520 ATATATAGATAT
1 ATATATAGATAT
*
67532 ATATATATATAT
1 ATATATAGATAT
67544 TCGTGGAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (12 bp):
ATATATAGATAT
Found at i:70392 original size:2 final size:2
Alignment explanation
Indices: 70385--70409 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70375 GTTGTGCACA
70385 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
70410 ATCCTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70700 original size:46 final size:46
Alignment explanation
Indices: 70633--70729 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
70623 CCATTATTTT
* * *
70633 ATGTCTCCATTTTAAGTATAAATTGTTAAGTTCTTAAACTTTAGCA
1 ATGTCTCCATTTGAAGTATAAATTCTCAAGTTCTTAAACTTTAGCA
*
70679 ATGTCTCCATTTGAAGTATAAATTCTCAAGTTCTTCAACTTTAGCA
1 ATGTCTCCATTTGAAGTATAAATTCTCAAGTTCTTAAACTTTAGCA
70725 ATGTC
1 ATGTC
70730 GATTCTACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (46 bp):
ATGTCTCCATTTGAAGTATAAATTCTCAAGTTCTTAAACTTTAGCA
Done.