Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010168.1 Corchorus capsularis cultivar CVL-1 contig10189, 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: 79496
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8023 original size:23 final size:22
Alignment explanation
Indices: 7989--8032 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
7979 CATTTTTAGA
7989 ATAATTAAAAAAAATCAAAACT
1 ATAATTAAAAAAAATCAAAACT
8011 ATAATTTAAAAAAAATCAAAAC
1 ATAA-TTAAAAAAAATCAAAAC
8033 AATGACTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAATTAAAAAAAATCAAAACT
Found at i:8150 original size:159 final size:157
Alignment explanation
Indices: 7931--8246 Score: 578
Period size: 159 Copynumber: 2.0 Consensus size: 157
7921 TAAATCGTCG
*
7931 GACGTGGCATTGACACCATCAACTCTGCTGATGTGTCATCAGCCAGGTCATTTTTAGAATAATTA
1 GACGTGGCAGTGACACCATCAACTCTGCTGATGTGTCATCAGCCAGGTCATTTTTAGAATAATTA
*
7996 AAAAAAATCAAAACTATAATTTAAAAAAAATCAAAACAATGACTCGGTGACTTTTTTTTTTTGGT
66 AAAAAAATCAAAACTATAA-TTAAAAAAAACCAAAACAATGACTCGGTGACTTTTTTTTTTT-GT
*
8061 TAAAACCGATTCAATGCCCAATTTTTTTC
129 TAAAACCGATTCAATGCCCAATATTTTTC
*
8090 GACGTGGCAGTGACACCATCAACTCTGCTGATGTGTCATCTGCCAGGTCATTTTTAGAATAATTA
1 GACGTGGCAGTGACACCATCAACTCTGCTGATGTGTCATCAGCCAGGTCATTTTTAGAATAATTA
8155 AAAAAAATCAAAACTATAATTAAAAAAAACCAAAACAATGACTCGGTGACTTTTTTTTTTTGTTA
66 AAAAAAATCAAAACTATAATTAAAAAAAACCAAAACAATGACTCGGTGACTTTTTTTTTTTGTTA
8220 AAACCGATTCAATGCCCAATATTTTTC
131 AAACCGATTCAATGCCCAATATTTTTC
8247 CTTCTTTTTT
Statistics
Matches: 153, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
157 30 0.20
158 41 0.27
159 82 0.54
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (157 bp):
GACGTGGCAGTGACACCATCAACTCTGCTGATGTGTCATCAGCCAGGTCATTTTTAGAATAATTA
AAAAAAATCAAAACTATAATTAAAAAAAACCAAAACAATGACTCGGTGACTTTTTTTTTTTGTTA
AAACCGATTCAATGCCCAATATTTTTC
Found at i:8176 original size:22 final size:22
Alignment explanation
Indices: 8148--8190 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8138 CATTTTTAGA
*
8148 ATAATTAAAAAAAATCAAAACT
1 ATAATTAAAAAAAACCAAAACT
8170 ATAATTAAAAAAAACCAAAAC
1 ATAATTAAAAAAAACCAAAAC
8191 AATGACTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (22 bp):
ATAATTAAAAAAAACCAAAACT
Found at i:16103 original size:21 final size:21
Alignment explanation
Indices: 16077--16126 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
16067 TCGCTGATTA
16077 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGTATC
* * *
16098 TAATCTGATCTGTACAGTGTT
1 TAATCTCATCTGTACAGTATC
16119 TAATCTCA
1 TAATCTCA
16127 CAACTCCAGT
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:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTATC
Found at i:16307 original size:16 final size:16
Alignment explanation
Indices: 16274--16307 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16264 GGTGAGAGAG
*
16274 AAAAAAGAAAAGGAAA
1 AAAAAAGAAAAAGAAA
16290 AAAAAAGAAAAAGTAAA
1 AAAAAAGAAAAAG-AAA
16307 A
1 A
16308 GAAATTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:16576 original size:16 final size:17
Alignment explanation
Indices: 16548--16580 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
16538 TTGAAGTATG
16548 GAAAAGACAAGAGAATA
1 GAAAAGACAAGAGAATA
16565 GAAAAG-CAAGAGAATA
1 GAAAAGACAAGAGAATA
16581 TAGAGAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.64, C:0.06, G:0.24, T:0.06
Consensus pattern (17 bp):
GAAAAGACAAGAGAATA
Found at i:16597 original size:17 final size:17
Alignment explanation
Indices: 16554--16621 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
16544 TATGGAAAAG
*
16554 ACAAGAG-A-ATAGAAA
1 ACAAGAGAATATAGAGA
16569 AGCAAGAGAATATAGAGA
1 A-CAAGAGAATATAGAGA
*
16587 ACAAGATAATATAGAGA
1 ACAAGAGAATATAGAGA
* *
16604 AGAAGAGAATATGGAGA
1 ACAAGAGAATATAGAGA
16621 A
1 A
16622 TGAGAGAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 6 0.13
17 31 0.69
18 7 0.16
ACGTcount: A:0.59, C:0.04, G:0.25, T:0.12
Consensus pattern (17 bp):
ACAAGAGAATATAGAGA
Found at i:16627 original size:17 final size:16
Alignment explanation
Indices: 16573--16628 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
16563 TAGAAAAGCA
*
16573 AGAGAATATAGAGAACA
1 AGAGAATATAGAGAA-G
*
16590 AGATAATATAGAGAAG
1 AGAGAATATAGAGAAG
*
16606 AAGAGAATATGGAGAATG
1 -AGAGAATATAGAGAA-G
16624 AGAGA
1 AGAGA
16629 GATTGTTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 32 0.97
18 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (16 bp):
AGAGAATATAGAGAAG
Found at i:17619 original size:26 final size:26
Alignment explanation
Indices: 17590--17657 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
17580 TTCCTTCATT
17590 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
17616 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
17642 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
17658 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:17620 original size:15 final size:15
Alignment explanation
Indices: 17590--17657 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
17580 TTCCTTCATT
17590 TTAATCATAAACTAA
1 TTAATCATAAACTAA
17605 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
17616 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
17631 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
17642 TTAAACATAAACTAA
1 TTAATCATAAACTAA
17657 T
1 T
17658 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:17726 original size:11 final size:11
Alignment explanation
Indices: 17710--17750 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
17700 CTAATTAATA
17710 TTAAAAAAAAT
1 TTAAAAAAAAT
17721 TTAAAAAAAAAT
1 TT-AAAAAAAAT
17733 TT-AAAAAAAT
1 TTAAAAAAAAT
*
17743 ATAAAAAA
1 TTAAAAAA
17751 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TTAAAAAAAAT
Found at i:17729 original size:12 final size:12
Alignment explanation
Indices: 17712--17741 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17702 AATTAATATT
17712 AAAAAAAATTTA
1 AAAAAAAATTTA
17724 AAAAAAAATTTA
1 AAAAAAAATTTA
17736 AAAAAA
1 AAAAAA
17742 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAAAATTTA
Found at i:17756 original size:22 final size:22
Alignment explanation
Indices: 17706--17756 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17696 TAAACTAATT
* *
17706 AATATTAAAAAAAATTTAAAAA
1 AATATTTAAAAAAATATAAAAA
*
17728 AAAATTTAAAAAAATATAAAAA
1 AATATTTAAAAAAATATAAAAA
*
17750 ATTATTT
1 AATATTT
17757 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATATTTAAAAAAATATAAAAA
Found at i:17931 original size:22 final size:22
Alignment explanation
Indices: 17906--17952 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
17896 GTGTCAAAAA
17906 TTATAAAAAGGGGGGGCGGTGT
1 TTATAAAAAGGGGGGGCGGTGT
17928 TTATAAAAAGGGGGGGCGGTGT
1 TTATAAAAAGGGGGGGCGGTGT
17950 TTA
1 TTA
17953 GCAAACCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.43, T:0.26
Consensus pattern (22 bp):
TTATAAAAAGGGGGGGCGGTGT
Found at i:18382 original size:31 final size:31
Alignment explanation
Indices: 18344--18420 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
18334 GAACAAAGTT
18344 TCACTTCAGGGACCAAAATGAACATTTCAGC
1 TCACTTCAGGGACCAAAATGAACATTTCAGC
*
18375 TCACTTCAGGGACCAAAATGAATATTTCAGC
1 TCACTTCAGGGACCAAAATGAACATTTCAGC
18406 TCACTTCAGGGACCA
1 TCACTTCAGGGACCA
18421 TTTGTGTACT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (31 bp):
TCACTTCAGGGACCAAAATGAACATTTCAGC
Found at i:21156 original size:19 final size:18
Alignment explanation
Indices: 21132--21167 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21122 ACCCAGCCCG
*
21132 TTTTACATGATAATATATA
1 TTTTACATAAT-ATATATA
21151 TTTTACATAATATATAT
1 TTTTACATAATATATAT
21168 CTTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTACATAATATATATA
Found at i:21162 original size:16 final size:17
Alignment explanation
Indices: 21141--21172 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21131 GTTTTACATG
21141 ATAATATATAT-TTTAC
1 ATAATATATATCTTTAC
21157 ATAATATATATCTTTA
1 ATAATATATATCTTTA
21173 TTATTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATATATATCTTTAC
Found at i:21481 original size:59 final size:59
Alignment explanation
Indices: 21365--21484 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
21355 GGGCAAGCAA
* *
21365 GATGTCTATTATTATTACCTAGTCAAAGCCCGGTCTGAACCCGACCCGACCCGGTCCAT
1 GATGTCTATTATTATTACCTAGTCAAAACCCGGTCTGAACCCGACCCGACCCAGTCCAT
* * * ** *
21424 GATGTCTATTATTATTACCTAGTTAAAACGCGGTCTGAACCTGGTCCGGCCCAGTCCAT
1 GATGTCTATTATTATTACCTAGTCAAAACCCGGTCTGAACCCGACCCGACCCAGTCCAT
21483 GA
1 GA
21485 GCAGGTCTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (59 bp):
GATGTCTATTATTATTACCTAGTCAAAACCCGGTCTGAACCCGACCCGACCCAGTCCAT
Found at i:24361 original size:33 final size:33
Alignment explanation
Indices: 24316--24480 Score: 258
Period size: 33 Copynumber: 5.0 Consensus size: 33
24306 TCTTCAAGTG
*
24316 TCAATTGTAAAATCATGACAACTTTCGGTGTCA
1 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
*
24349 TCAATTGCAAAATCATGACAACTTTCAGTGTCA
1 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
24382 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
1 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
*
24415 TCAATTGCAAAATCATGACAACTTTCAGTGTCA
1 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
* * * * *
24448 TCAATTGTAAGACCATGACACCTTCCGGTGTCA
1 TCAATTGCAAAATCATGACAACTTTCGGTGTCA
24481 ATTGTAAGAC
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 122 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (33 bp):
TCAATTGCAAAATCATGACAACTTTCGGTGTCA
Found at i:24400 original size:66 final size:66
Alignment explanation
Indices: 24316--24480 Score: 285
Period size: 66 Copynumber: 2.5 Consensus size: 66
24306 TCTTCAAGTG
24316 TCAATTGTAAAATCATGACAACTTTCGGTGTCATCAATTGCAAAATCATGACAACTTTCAGTGTC
1 TCAATTGTAAAATCATGACAACTTTCGGTGTCATCAATTGCAAAATCATGACAACTTTCAGTGTC
24381 A
66 A
*
24382 TCAATTGCAAAATCATGACAACTTTCGGTGTCATCAATTGCAAAATCATGACAACTTTCAGTGTC
1 TCAATTGTAAAATCATGACAACTTTCGGTGTCATCAATTGCAAAATCATGACAACTTTCAGTGTC
24447 A
66 A
* * * *
24448 TCAATTGTAAGACCATGACACCTTCCGGTGTCA
1 TCAATTGTAAAATCATGACAACTTTCGGTGTCA
24481 ATTGTAAGAC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 93 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (66 bp):
TCAATTGTAAAATCATGACAACTTTCGGTGTCATCAATTGCAAAATCATGACAACTTTCAGTGTC
A
Found at i:28439 original size:154 final size:153
Alignment explanation
Indices: 28160--28460 Score: 460
Period size: 154 Copynumber: 2.0 Consensus size: 153
28150 AAGACTTGGT
* * *
28160 GACTCAAAATGTTTGACTTCTCACTCCGTGTTGCCAAAGGTTTTTCCAATTTTTAAATCGGCGAT
1 GACTCAAAATGATTGACTTCTCACTCCATGTTGCCAAAGGTTTTTCCAATTTTTAAATCGGCGAG
** * *
28225 CCCTGTTATTGCTTTTAAGATTTTCGTTACTTTGGTGACTGTCCTACTTCAACCGCACCAAAACA
66 CCCTGACATTGCTTTTAAGATTTTCGTTACTTTGATGACTGTCCCACTTCAACCGCACCAAAACA
28290 TCTCTTTTTGACACGCCTAGTAG
131 TCTCTTTTTGACACGCCTAGTAG
*
28313 GACTCAAAATGATTGACTTCTCACTCCATGTTGCCAAAGGTTTTTTCAATTTCTTAAATCGGCGA
1 GACTCAAAATGATTGACTTCTCACTCCATGTTGCCAAAGGTTTTTCCAATTT-TTAAATCGGCGA
* * * *
28378 GCGCC-GACGTTGTTTTTAAGATTTTCGTTACTTTGATGACTGTCCCACTTCGACTGCACCAAAA
65 GC-CCTGACATTGCTTTTAAGATTTTCGTTACTTTGATGACTGTCCCACTTCAACCGCACCAAAA
*
28442 CATCTCTTTTTGCCACGCC
129 CATCTCTTTTTGACACGCC
28461 CAATGGGACC
Statistics
Matches: 133, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
153 49 0.37
154 82 0.62
155 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (153 bp):
GACTCAAAATGATTGACTTCTCACTCCATGTTGCCAAAGGTTTTTCCAATTTTTAAATCGGCGAG
CCCTGACATTGCTTTTAAGATTTTCGTTACTTTGATGACTGTCCCACTTCAACCGCACCAAAACA
TCTCTTTTTGACACGCCTAGTAG
Found at i:36217 original size:27 final size:24
Alignment explanation
Indices: 36160--36215 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
36150 AAAAGTAACT
36160 TTCTTCTTTATTGGCAAATCCACA
1 TTCTTCTTTATTGGCAAATCCACA
36184 TTCTTCTTTATTGGCAAATCCACA
1 TTCTTCTTTATTGGCAAATCCACA
*
36208 TCCTTCTT
1 TTCTTCTT
36216 CTCAATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.21, C:0.27, G:0.07, T:0.45
Consensus pattern (24 bp):
TTCTTCTTTATTGGCAAATCCACA
Found at i:40070 original size:18 final size:19
Alignment explanation
Indices: 40047--40083 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40037 AGCGAAGGTA
*
40047 AAAATAAT-TTTTTCCCAC
1 AAAATAATAATTTTCCCAC
40065 AAAATAATAATTTTCCCAC
1 AAAATAATAATTTTCCCAC
40084 TCATTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATAATTTTCCCAC
Found at i:45421 original size:2 final size:2
Alignment explanation
Indices: 45414--45470 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
45404 AACATACTAA
45414 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
45456 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
45471 CTATATATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:45761 original size:40 final size:40
Alignment explanation
Indices: 45712--45791 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
45702 GTTTGATTTG
* *
45712 ATTTGATTCAAGAGTC-GAATGACTTAATCTTGAATTGATA
1 ATTTAATTCAAGAGTCTG-ACGACTTAATCTTGAATTGATA
* *
45752 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGAGTC-TGACGACTTAATCTTGAATTGAT
45792 GACTTGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 14 0.41
41 19 0.56
42 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGAGTCTGACGACTTAATCTTGAATTGATA
Found at i:45814 original size:94 final size:95
Alignment explanation
Indices: 45707--45885 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 95
45697 TGAGAGTTTG
45707 ATTTGATTTGATTCAAGAGTC-GAATGACTT-A-ATC-TTGAATTGATAATTTAATTCAAGGGTC
1 ATTTGATTTGATTCAAGAGTCTG-ATGACTTGATATCGTTG-A-TGATAATTTAATTCAAGGGTC
45768 TTGACGACTTGATCTTGAATTGATGACTTGGGA
63 TTGACGACTTGATCTTGAATTGATGACTTGGGA
* * *
45801 ATTTGATTTGATTCGAGGGTCTTTGATGACTTGATATCGAGTTGATGATAATTTGATTCAAGGGT
1 ATTTGATTTGATTCAAGAGTC--TGATGACTTGATATC--GTTGATGATAATTTAATTCAAGGGT
45866 CTTGACGACTTGATCTTGAA
62 CTTGACGACTTGATCTTGAA
45886 CAAACAAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
94 19 0.26
96 7 0.09
97 2 0.03
98 3 0.04
99 39 0.53
100 1 0.01
101 3 0.04
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (95 bp):
ATTTGATTTGATTCAAGAGTCTGATGACTTGATATCGTTGATGATAATTTAATTCAAGGGTCTTG
ACGACTTGATCTTGAATTGATGACTTGGGA
Found at i:47011 original size:65 final size:64
Alignment explanation
Indices: 46935--47068 Score: 205
Period size: 65 Copynumber: 2.1 Consensus size: 64
46925 CGTAGTTCAA
* * * * *
46935 TTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGTAGGATTTTCAACTTAGTGAGCCTTTTT
1 TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGAG-CTTTTT
*
47000 TTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGAGCTTTTT
1 TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGAGCTTTTT
47064 TTTTT
1 TTTTT
47069 GGGTTGACTG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 11 0.17
65 52 0.83
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (64 bp):
TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGAGCTTTTT
Found at i:50183 original size:13 final size:13
Alignment explanation
Indices: 50146--50204 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
50136 TTGAGGGACT
*
50146 TGTTTTTATT-AC
1 TGTTTTTATTAAA
* *
50158 TATTTTTAATAAA
1 TGTTTTTATTAAA
50171 GTGTTTTT-TTAAA
1 -TGTTTTTATTAAA
50184 TGATTTTTATTAAAA
1 TG-TTTTTATT-AAA
50199 TGTTTT
1 TGTTTT
50205 GGGTGCATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 10 0.27
13 10 0.27
14 12 0.32
15 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (13 bp):
TGTTTTTATTAAA
Found at i:52455 original size:2 final size:2
Alignment explanation
Indices: 52448--52474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52438 GATGACAATA
52448 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 A
52475 AAATAGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54064 original size:2 final size:2
Alignment explanation
Indices: 54047--54081 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
54037 TTCAGCAACC
* *
54047 AT AT AT AC AT AC 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 AT A
54082 ATGATTGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:54457 original size:58 final size:59
Alignment explanation
Indices: 54367--54482 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 59
54357 GAGGTCTTGG
*
54367 GTTCTAGTCTCACAGAATGTGAGTTTATTTGTAATTTATTTATTTGTGTAT-TTGGTAA
1 GTTCTAGTCTCACAGAATGTGAGTTTATTTGTAATTTATTTATTTATGTATCTTGGTAA
* *
54425 GTTCTAGTCTCACGGAATGTGAGTTTATTTGTAGTTTATTTATTTATGTATCTTGGTA
1 GTTCTAGTCTCACAGAATGTGAGTTTATTTGTAATTTATTTATTTATGTATCTTGGTA
54483 TGTTTGGTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 48 0.89
59 6 0.11
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.50
Consensus pattern (59 bp):
GTTCTAGTCTCACAGAATGTGAGTTTATTTGTAATTTATTTATTTATGTATCTTGGTAA
Found at i:54633 original size:20 final size:20
Alignment explanation
Indices: 54596--54634 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54586 GTAATCTCTA
*
54596 ATTATTGATTAATGAAAATG
1 ATTATTGATTAATAAAAATG
54616 ATTATTTGATTAA-AAAAAT
1 ATTA-TTGATTAATAAAAAT
54635 AATTTTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTATTGATTAATAAAAATG
Found at i:55131 original size:20 final size:19
Alignment explanation
Indices: 55096--55145 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
55086 ATATTCGAAA
*
55096 TAAAATTATATATTAA-ACTT
1 TAAAATTAAAT-TTAATA-TT
55116 TAAAAGTTAAATTTAATATT
1 TAAAA-TTAAATTTAATATT
55136 TAAAATTAAA
1 TAAAATTAAA
55146 AAGGGCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 16 0.59
21 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAATTAAATTTAATATT
Found at i:57881 original size:18 final size:18
Alignment explanation
Indices: 57858--57899 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
57848 AATGATCCCC
57858 ATATTTTTCTCCTTTATG
1 ATATTTTTCTCCTTTATG
57876 ATATTTTTCTCCTTTATG
1 ATATTTTTCTCCTTTATG
*
57894 CTATTT
1 ATATTT
57900 AATCCTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTTTCTCCTTTATG
Found at i:65421 original size:13 final size:13
Alignment explanation
Indices: 65403--65429 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65393 CTCTATAACC
65403 TCATAAATCATAT
1 TCATAAATCATAT
65416 TCATAAATCATAT
1 TCATAAATCATAT
65429 T
1 T
65430 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:68098 original size:19 final size:19
Alignment explanation
Indices: 68084--68120 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
68074 ACTATTATTT
68084 TTTTAATTTAATATTTTAC
1 TTTTAATTTAATATTTTAC
68103 TTTTAATTTCAAT-TTTTA
1 TTTTAATTT-AATATTTTA
68121 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTAATATTTTAC
Found at i:68314 original size:22 final size:22
Alignment explanation
Indices: 68286--68450 Score: 118
Period size: 22 Copynumber: 7.3 Consensus size: 22
68276 TGTCTCTATG
*
68286 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* **
68308 TGGTTATTACGATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
68331 -GGTTATCAAAATTCCATAGTGTA
1 TGGTTATCAAAATTTCATAG-G-A
*
68354 CTGGTTACCAAAATTTCATAGTG-
1 -TGGTTATCAAAATTTCATAG-GA
* *
68377 TGGTTACCAAAATTTTATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
68399 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
68423 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
68445 TGGTTA
1 TGGTTA
68451 ATTATCACAA
Statistics
Matches: 114, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
21 3 0.03
22 72 0.63
23 4 0.04
24 16 0.14
25 19 0.17
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:68365 original size:25 final size:22
Alignment explanation
Indices: 68331--68390 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
68321 TTCATGAGGA
*
68331 GGTTATCAAAATTCCATAGTGTACT
1 GGTTACCAAAATTCCATAGTG---T
*
68356 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTCCATAGTGT
68378 GGTTACCAAAATT
1 GGTTACCAAAATT
68391 TTATAGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 14 0.42
25 19 0.58
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTCCATAGTGT
Found at i:68726 original size:22 final size:22
Alignment explanation
Indices: 68633--68873 Score: 121
Period size: 22 Copynumber: 10.9 Consensus size: 22
68623 TGATCAAAGG
* **
68633 TTATC-AAATCTCATAAAGTGA
1 TTATCAAAATTTCATAGTGTGA
* *
68654 TTTATCTAAATTTCATAGAGATCGAA
1 -TTATCAAAATTTCATAGTG-T-G-A
***
68680 TTATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATAGTGTGA
68701 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGTG-TGA
* * *
68723 TTATCAAAATTTCAAAGCGAGA
1 TTATCAAAATTTCATAGTGTGA
* *
68745 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGTGA
* * * *
68767 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGTGA
* * * ** * *
68789 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGTGA
** * *
68811 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGTGA
* * *
68833 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGA
68855 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
68874 GTATTTCTGG
Statistics
Matches: 172, Mismatches: 39, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.09
22 126 0.73
23 12 0.07
24 6 0.03
25 12 0.07
26 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:68797 original size:66 final size:66
Alignment explanation
Indices: 68699--68846 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
68689 TTTATAGAAA
* ** * * *
68699 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGATTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGATTATCAAAATTACATAAT
68763 GT
65 GT
* * * * *
68765 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGATTATCAAAATTACATAATG
*
68830 A
66 T
* *
68831 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
68847 AAATGTGATT
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGATTATCAAAATTACATAATG
T
Found at i:69106 original size:22 final size:22
Alignment explanation
Indices: 68982--69304 Score: 188
Period size: 22 Copynumber: 14.9 Consensus size: 22
68972 TTAAAAATTC
68982 AGGGAGGA-TATCAAAATTTCAT
1 AGGGA-GATTATCAAAATTTCAT
* * *
69004 A-TGAAACTTATTAAAATTTCAT
1 AGGGAGA-TTATCAAAATTTCAT
** * *
69026 AGTTTAG-TTTTCAAAATTTCACA
1 AG-GGAGATTATCAAAATTTCA-T
69049 AGAGG-G-TTATCAAAATTTCAT
1 AG-GGAGATTATCAAAATTTCAT
* *
69070 A-GTATG-TAGATCAAAATTTCAT
1 AGGGA-GAT-TATCAAAATTTCAT
*
69092 AGGGAGATTAACAAAATTTCAT
1 AGGGAGATTATCAAAATTTCAT
*
69114 AGGGAGATTAACAAAATTTCAT
1 AGGGAGATTATCAAAATTTCAT
** * **
69136 AATGAGGTTATCAAAAAATCAT
1 AGGGAGATTATCAAAATTTCAT
*
69158 AGGGAGGTTATCAAAATTT-AT
1 AGGGAGATTATCAAAATTTCAT
*
69179 ----AG-TTATCAAGATTTCAT
1 AGGGAGATTATCAAAATTTCAT
* * *
69196 A-AGAAAGTTATCAAAATTTTAT
1 AGGGAGA-TTATCAAAATTTCAT
* *
69218 AGGGAGGTTTATCAAAATTTTAT
1 AGGGA-GATTATCAAAATTTCAT
*
69241 AGGAAGATTTATCAAAATTTCAT
1 AGGGAGA-TTATCAAAATTTCAT
** * *
69264 AGCAAGGTTATCACAATTTCAT
1 AGGGAGATTATCAAAATTTCAT
* *
69286 AGTGTGATTATCAAAATTT
1 AGGGAGATTATCAAAATTT
69305 TAGAGTGTGA
Statistics
Matches: 236, Mismatches: 46, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
16 11 0.05
17 4 0.02
19 1 0.00
20 2 0.01
21 7 0.03
22 164 0.69
23 45 0.19
24 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
AGGGAGATTATCAAAATTTCAT
Found at i:69129 original size:44 final size:44
Alignment explanation
Indices: 68982--69304 Score: 211
Period size: 44 Copynumber: 7.4 Consensus size: 44
68972 TTAAAAATTC
* * ** *
68982 AGGGAGGA-TATCAAAATTTCATATGAAACTTATTAAAATTTCAT
1 AGGGA-GATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
** * * *
69026 AGTTTAG-TTTTCAAAATTTCACA-AGAGGGTTATCAAAATTTCAT
1 AG-GGAGATTATCAAAATTTCATAGGGA-GGTTATCAAAATTTCAT
* * * *
69070 A-GTATG-TAGATCAAAATTTCATAGGGAGATTAACAAAATTTCAT
1 AGGGA-GAT-TATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
* ** **
69114 AGGGAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCAT
1 AGGGAGATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
* *
69158 AGGGAGGTTATCAAAATTT-AT----A-GTTATCAAGATTTCAT
1 AGGGAGATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
* * * *
69196 A-AGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTAT
1 AGGGAGA-TTATCAAAATTTCATAGGGAGG-TTATCAAAATTTCAT
* ** *
69241 AGGAAGATTTATCAAAATTTCATAGCAAGGTTATCACAATTTCAT
1 AGGGAGA-TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
* *
69286 AGTGTGATTATCAAAATTT
1 AGGGAGATTATCAAAATTT
69305 TAGAGTGTGA
Statistics
Matches: 215, Mismatches: 47, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
37 2 0.01
38 26 0.12
39 3 0.01
42 2 0.01
43 6 0.03
44 118 0.55
45 37 0.17
46 21 0.10
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (44 bp):
AGGGAGATTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT
Found at i:69222 original size:60 final size:61
Alignment explanation
Indices: 69079--69308 Score: 173
Period size: 60 Copynumber: 3.6 Consensus size: 61
69069 TAGTATGTAG
* * *
69079 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTT-AT----AGATTAACAAAATTTCATAATGAAGT
69144 T
61 T
** * *
69145 ATCAAAAAATCATAGGGAGGTTATCAAAATTTATAG-TTATCAAGATTTCATAA-GAAAGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTATAGATTAACAAAATTTCATAATG-AAGTT
* *
69205 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCAT-A-GCA
1 ATCAAAATTTCATAGGGAGG-TTATCAAAA-TTTAT----AGA-TTAACAAAATTTCATAATG-A
69268 AGGTT
58 A-GTT
* * * *
69273 ATCACAATTTCATAGTGTGATTATCAAAATTT-TAGA
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTATAGA
69309 GTGTGATTAC
Statistics
Matches: 137, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
59 1 0.01
60 36 0.26
61 14 0.10
62 5 0.04
65 3 0.02
66 33 0.24
67 13 0.09
68 32 0.23
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (61 bp):
ATCAAAATTTCATAGGGAGGTTATCAAAATTTATAGATTAACAAAATTTCATAATGAAGTT
Found at i:69231 original size:23 final size:23
Alignment explanation
Indices: 69181--69287 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
69171 AAATTTATAG
* * * *
69181 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAGGAAGGT
*
69203 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
*
69226 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGGT
* *
69249 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTTATAGGAAGGT
* *
69271 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
69288 TGTGATTATC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 33 0.45
23 40 0.55
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:69311 original size:22 final size:22
Alignment explanation
Indices: 69271--69317 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
69261 CATAGCAAGG
* *
69271 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
69293 TTATCAAAATTTTAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
69315 TTA
1 TTA
69318 CTAACAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:69508 original size:22 final size:22
Alignment explanation
Indices: 69473--69529 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
69463 AAAAAGGTTC
* *
69473 TCAAAA-TTCAATAGTATCGTTA
1 TCAAAATTTC-ATAGGAACGTTA
* *
69495 TTAAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAGGAACGTTA
69517 TCAAAATTTCATA
1 TCAAAATTTCATA
69530 ATGGGATCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGGAACGTTA
Found at i:69681 original size:14 final size:14
Alignment explanation
Indices: 69662--69688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69652 TTATAAAATA
69662 TATATAAAATAATT
1 TATATAAAATAATT
69676 TATATAAAATAAT
1 TATATAAAATAAT
69689 GATCTCACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATATAAAATAATT
Found at i:69982 original size:18 final size:18
Alignment explanation
Indices: 69959--69995 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
69949 TCTACTCACC
69959 TTCTTTATCCCAAATTTG
1 TTCTTTATCCCAAATTTG
69977 TTCTTTATCCCAAATTTG
1 TTCTTTATCCCAAATTTG
69995 T
1 T
69996 AGAGGTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (18 bp):
TTCTTTATCCCAAATTTG
Found at i:71138 original size:48 final size:47
Alignment explanation
Indices: 71067--71168 Score: 188
Period size: 48 Copynumber: 2.2 Consensus size: 47
71057 TGACGTCGTT
71067 TTATATATAGAGTTTAGTTTTGATTTTTATTTTTAACTTTAATTAGTA
1 TTATATATAGAGTTTAGTTTTGATTTTTATTTTTAACTTTAATTA-TA
71115 TTATATATAGAGTTTAGTTTTGATTTTTATTTTTAACTTTAATTATA
1 TTATATATAGAGTTTAGTTTTGATTTTTATTTTTAACTTTAATTATA
71162 -TATATAT
1 TTATATAT
71169 TATAACTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 7 0.13
47 2 0.04
48 45 0.83
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (47 bp):
TTATATATAGAGTTTAGTTTTGATTTTTATTTTTAACTTTAATTATA
Found at i:72337 original size:139 final size:139
Alignment explanation
Indices: 72087--72369 Score: 566
Period size: 139 Copynumber: 2.0 Consensus size: 139
72077 TGCAAGTCTC
72087 GTACCATGCTTAGACAAGCCATGTGTATCCTTACGAAAAGCTATGACAAGCTACAAAAATAGTAT
1 GTACCATGCTTAGACAAGCCATGTGTATCCTTACGAAAAGCTATGACAAGCTACAAAAATAGTAT
72152 GCATGGATCAAAAACAACTCTCCTTTGCATCCTCATGCGTGACACTAGCAACATAAGTAAATTAG
66 GCATGGATCAAAAACAACTCTCCTTTGCATCCTCATGCGTGACACTAGCAACATAAGTAAATTAG
72217 AGAGTGCTT
131 AGAGTGCTT
72226 GTACCATGCTTAGACAAGCCATGTGTATCCTTACGAAAAGCTATGACAAGCTACAAAAATAGTAT
1 GTACCATGCTTAGACAAGCCATGTGTATCCTTACGAAAAGCTATGACAAGCTACAAAAATAGTAT
72291 GCATGGATCAAAAACAACTCTCCTTTGCATCCTCATGCGTGACACTAGCAACATAAGTAAATTAG
66 GCATGGATCAAAAACAACTCTCCTTTGCATCCTCATGCGTGACACTAGCAACATAAGTAAATTAG
72356 AGAGTGCTT
131 AGAGTGCTT
72365 GTACC
1 GTACC
72370 TCATAACTCA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 144 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (139 bp):
GTACCATGCTTAGACAAGCCATGTGTATCCTTACGAAAAGCTATGACAAGCTACAAAAATAGTAT
GCATGGATCAAAAACAACTCTCCTTTGCATCCTCATGCGTGACACTAGCAACATAAGTAAATTAG
AGAGTGCTT
Found at i:73242 original size:19 final size:21
Alignment explanation
Indices: 73204--73242 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
73194 GTTAAAAGTG
*
73204 AAAATATAGATATATTTGATA
1 AAAATATAGATATATATGATA
73225 AAAATATA-A-ATATATGAT
1 AAAATATAGATATATATGAT
73243 GGGTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAATATAGATATATATGATA
Found at i:73935 original size:24 final size:24
Alignment explanation
Indices: 73883--73935 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
73873 ATCACCGCCT
* *
73883 CCTCCACCATCACCACCCCCACCT
1 CCTCCACCATCACCACCACCACCA
* * *
73907 TCTCCACCATCCCCACCACCATCA
1 CCTCCACCATCACCACCACCACCA
73931 CCTCC
1 CCTCC
73936 TCCTCCTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.64, G:0.00, T:0.15
Consensus pattern (24 bp):
CCTCCACCATCACCACCACCACCA
Found at i:75134 original size:215 final size:215
Alignment explanation
Indices: 74892--75308 Score: 694
Period size: 216 Copynumber: 1.9 Consensus size: 215
74882 TTGTTGGGGA
74892 TTTTTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTCGAAAGTATTGGAAGGTAAA
1 TTTTTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTCGAAAGTATTGGAAGGTAAA
* *
74957 ATTCTATATTTTCTACAGATTT-AAATTT-TATTATATTAAATATAATATCTGTAGTACTTAGCT
66 AGTCTATATTTTCTACAGATTTGAAATTTATATTATATT-AATATAATATATGTAGTACTTAGCT
*
75020 AAATTCTTAACTATAAACTTTTAGAAGTAAATGGAGTATGAATTTTCTAATATGACCTTCTAATT
130 AAATTCTTAACTATAAACTTTTAGAAGTAAATGGAGTATGAATTTTCTAACATGACCTTCTAATT
75085 GGGCAACATTCTTGTTGGTTT
195 GGGCAACATTCTTGTTGGTTT
* * *
75106 TTTTTTTCTTTTGGCTTGATTTTAGCTAAGGTTTTTGGAAATCTGTGGAAAGTATTGGAAGGTAA
1 TTTTTTT-TTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTCGAAAGTATTGGAAGGTAA
* *
75171 AAGTCTATATTTTTTACAGATTTGAAGTTTATATTATATTAATATAATATATGTAGTACTTAGCT
65 AAGTCTATATTTTCTACAGATTTGAAATTTATATTATATTAATATAATATATGTAGTACTTAGCT
* * * *
75236 AAATTGTTAACTGTAAACTTTTAGAAGTAAATGGAGTATGAATTTTCTAACATGGCCTTCTTATT
130 AAATTCTTAACTATAAACTTTTAGAAGTAAATGGAGTATGAATTTTCTAACATGACCTTCTAATT
75301 GGGCAACA
195 GGGCAACA
75309 GGAATGTAAG
Statistics
Matches: 188, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
214 7 0.04
215 75 0.40
216 97 0.52
217 9 0.05
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (215 bp):
TTTTTTTTTTTGGCTTGATTCTAGCTAAGGTTTTTGAAAATCTGTCGAAAGTATTGGAAGGTAAA
AGTCTATATTTTCTACAGATTTGAAATTTATATTATATTAATATAATATATGTAGTACTTAGCTA
AATTCTTAACTATAAACTTTTAGAAGTAAATGGAGTATGAATTTTCTAACATGACCTTCTAATTG
GGCAACATTCTTGTTGGTTT
Found at i:78698 original size:31 final size:31
Alignment explanation
Indices: 78660--78723 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
78650 ATATATATAT
78660 ATATTAATCATTAAAACCATAAATACTTTAG
1 ATATTAATCATTAAAACCATAAATACTTTAG
78691 ATATTAATCATTAAAACCATAAATACTTTAG
1 ATATTAATCATTAAAACCATAAATACTTTAG
78722 AT
1 AT
78724 CTAGCCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (31 bp):
ATATTAATCATTAAAACCATAAATACTTTAG
Done.