Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016220.1 Corchorus olitorius cultivar O-4 contig16253, 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: 75096
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:255 original size:17 final size:18
Alignment explanation
Indices: 230--263 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
220 TGGTTCCCTT
*
230 TCTTTCATGT-TTCTTTG
1 TCTTGCATGTCTTCTTTG
247 TCTTGCATGTCTTCTTT
1 TCTTGCATGTCTTCTTT
264 TATTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.21, G:0.12, T:0.62
Consensus pattern (18 bp):
TCTTGCATGTCTTCTTTG
Found at i:2169 original size:1 final size:1
Alignment explanation
Indices: 2165--2194 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2155 TTAGGCCCAG
*
2165 TTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2195 AACGTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:9637 original size:35 final size:35
Alignment explanation
Indices: 9584--9651 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
9574 TATCATAAAA
*
9584 CCATTGTTCCGAGGATAAAAGTTAAGGATTACAGG
1 CCATTGTTCCGAGAATAAAAGTTAAGGATTACAGG
* *
9619 CCATTGTTCTGAGAATAAAATTTAAGGATTACA
1 CCATTGTTCCGAGAATAAAAGTTAAGGATTACA
9652 AACCATCGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (35 bp):
CCATTGTTCCGAGAATAAAAGTTAAGGATTACAGG
Found at i:13239 original size:47 final size:48
Alignment explanation
Indices: 13173--14055 Score: 1307
Period size: 47 Copynumber: 19.1 Consensus size: 48
13163 TTGACTACTC
*
13173 TTTACTACTTAGTTCAATTACCT-GAACTTAAACTAAT-TTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAA-TTAAACTAATCTTCTTCTTCT
13220 TTTACTACTTAGTTTAATTACC-----TTAAACTAA---T-TTCTTC-
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13258 --T--T-CTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
* *
13300 TTTACTACTTAG-TTAATTA-CTAGAATTAAGCTAAT-TTCTCCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13345 TTTAATACTTAGTTTAATTACCTAGAATTAAACTAATCTT-TTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
* *
13392 TTTACTACTTAGTTTAATTACCTAGAACTAAACTAAT-TTATTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
13439 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13486 TTTACTACTTAGTTTAATTACCTAGAACTAAACTAAT-TTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
* *
13533 TTTACTACTTTGTTTAATTACCTAGAATTAAACTAAT-TTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
13580 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13627 TTTACTACTTAGTTTAATTACCTAAAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13674 TTTACTACTTAGTTTAATTACCTAGAATTAAATTAATCTT-TCTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCT-TCTTCT
* *
13722 TTTACTACTTAGTTTAATTACTTAGAATTAAACTTATCTT-TTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
13769 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTT-TCTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCT-TCTTCT
*
13817 TTTACTACTTAGTTTAATTACTTAGAATTAAACTAATCTT-TTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
13864 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
* * *
13911 TTTACTACTTAGTTTAATTAGCTAGAATTAAATTAAT-TTCCTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
13958 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAAT-TTCTTTTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
*
14005 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTC-TATTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
14052 TTTA
1 TTTA
14056 GTTTAAAATT
Statistics
Matches: 774, Mismatches: 35, Indels: 54
0.90 0.04 0.06
Matches are distributed among these distances:
33 15 0.02
34 1 0.00
36 1 0.00
38 9 0.01
39 6 0.01
40 2 0.00
41 5 0.01
42 9 0.01
44 1 0.00
45 34 0.04
46 23 0.03
47 568 0.73
48 100 0.13
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (48 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATCTTCTTCTTCT
Found at i:16680 original size:17 final size:18
Alignment explanation
Indices: 16655--16688 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16645 TGGTTCCCTT
*
16655 TCTTTCATGT-TTCTTTG
1 TCTTGCATGTCTTCTTTG
16672 TCTTGCATGTCTTCTTT
1 TCTTGCATGTCTTCTTT
16689 TATTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.21, G:0.12, T:0.62
Consensus pattern (18 bp):
TCTTGCATGTCTTCTTTG
Found at i:17631 original size:6 final size:6
Alignment explanation
Indices: 17620--17648 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
17610 TGACATGCAA
17620 TATAAT TATAAT TATAA- TATAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATAAT
17649 GAAATAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TATAAT
Found at i:19114 original size:27 final size:27
Alignment explanation
Indices: 19084--19136 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
19074 GTAATTTTTG
*
19084 TAAGAGCG-TAAATTCCCGTTTTACCCT
1 TAAGAG-GATAAATTCCCATTTTACCCT
* *
19111 TAAGTGGATAAATTTCCATTTTACCC
1 TAAGAGGATAAATTCCCATTTTACCC
19137 CTAAATTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (27 bp):
TAAGAGGATAAATTCCCATTTTACCCT
Found at i:20798 original size:23 final size:23
Alignment explanation
Indices: 20771--20846 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
20761 TATCCTTGAA
20771 AAATAAACAAAACCCAGATCTGC
1 AAATAAACAAAACCCAGATCTGC
* *
20794 AAATAAATC-AAA--C-TATCCTTGAA
1 AAATAAA-CAAAACCCAGAT-C-TG-C
*
20817 AAATAAACAAAGCCCAGATCTGC
1 AAATAAACAAAACCCAGATCTGC
20840 AAATAAA
1 AAATAAA
20847 TCAACATAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 3 0.08
23 26 0.65
24 3 0.08
25 2 0.05
26 2 0.05
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.17
Consensus pattern (23 bp):
AAATAAACAAAACCCAGATCTGC
Found at i:20809 original size:46 final size:46
Alignment explanation
Indices: 20759--20850 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
20749 AAAACCCATC
20759 ACTATCCTTGAAAAATAAACAAAACCCAGATCTGCAAATAAATCAA
1 ACTATCCTTGAAAAATAAACAAAACCCAGATCTGCAAATAAATCAA
*
20805 ACTATCCTTGAAAAATAAACAAAGCCCAGATCTGCAAATAAATCAA
1 ACTATCCTTGAAAAATAAACAAAACCCAGATCTGCAAATAAATCAA
20851 CATAGCCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.20
Consensus pattern (46 bp):
ACTATCCTTGAAAAATAAACAAAACCCAGATCTGCAAATAAATCAA
Found at i:20871 original size:46 final size:46
Alignment explanation
Indices: 20769--20871 Score: 120
Period size: 46 Copynumber: 2.2 Consensus size: 46
20759 ACTATCCTTG
* * **
20769 AAAAATAAACAAAACCCAGATCTGCAAATAAATCAAACTATCCTTG
1 AAAAAAAAACAAAACCCAGATCTGCAAATAAATCAAACTAGCCTAA
* *
20815 AAAAATAAACAAAGCCCAGATCTGCAAATAAATC-AACATAGCC-AA
1 AAAAAAAAACAAAACCCAGATCTGCAAATAAATCAAAC-TAGCCTAA
20860 AAAGAAAAAACA
1 AAA-AAAAAACA
20872 TTTACAATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
45 6 0.12
46 44 0.88
ACGTcount: A:0.57, C:0.20, G:0.08, T:0.15
Consensus pattern (46 bp):
AAAAAAAAACAAAACCCAGATCTGCAAATAAATCAAACTAGCCTAA
Found at i:21311 original size:11 final size:11
Alignment explanation
Indices: 21249--21305 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
21239 ATTTAGGTTA
*
21249 ATATTTAATAT
1 ATATATAATAT
* *
21260 ATATATAACAA
1 ATATATAATAT
21271 ATTATATAAT-T
1 A-TATATAATAT
*
21282 AT-TATTATAT
1 ATATATAATAT
21292 ATATATAATAT
1 ATATATAATAT
21303 ATA
1 ATA
21306 CTTAATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 20 0.56
12 7 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATAATAT
Found at i:23796 original size:25 final size:26
Alignment explanation
Indices: 23768--23816 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
23758 AAAAAAATTC
*
23768 TAAAGAAAAGCAATTAAA-CTAAAAA
1 TAAAGAAAAGAAATTAAATCTAAAAA
* *
23793 TAAAGCAAATAAATTAAATCTAAA
1 TAAAGAAAAGAAATTAAATCTAAA
23817 CTATAGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.20
Consensus pattern (26 bp):
TAAAGAAAAGAAATTAAATCTAAAAA
Found at i:27352 original size:18 final size:18
Alignment explanation
Indices: 27317--27350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27307 TCTTGGATGT
27317 TTGAGTCAGTTTAGTTTG
1 TTGAGTCAGTTTAGTTTG
*
27335 TTGATTCAGTTT-GTTT
1 TTGAGTCAGTTTAGTTT
27351 TGAATTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.06, G:0.24, T:0.56
Consensus pattern (18 bp):
TTGAGTCAGTTTAGTTTG
Found at i:29678 original size:55 final size:55
Alignment explanation
Indices: 29602--29709 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
29592 CGTCAGCAAT
*
29602 TAATGGCCACATCAGTGATTAAGGTTGGATTTAACGGAACCGTTAGTCACGTGCC
1 TAATGGCCACATCAGTGATTAAGGTTAGATTTAACGGAACCGTTAGTCACGTGCC
29657 TAATGGCCACATCAGTGATTAAGGTTAGATTTAACGGAACCGTTAGTCACGTG
1 TAATGGCCACATCAGTGATTAAGGTTAGATTTAACGGAACCGTTAGTCACGTG
29710 ATGACACGTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (55 bp):
TAATGGCCACATCAGTGATTAAGGTTAGATTTAACGGAACCGTTAGTCACGTGCC
Found at i:31317 original size:18 final size:18
Alignment explanation
Indices: 31294--31328 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31284 ACCATTTCTG
31294 ATTC-GGTTCGGTCGGTTT
1 ATTCGGGTT-GGTCGGTTT
31312 ATTCGGGTTGGTCGGTT
1 ATTCGGGTTGGTCGGTT
31329 CTTGCACAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.06, C:0.14, G:0.37, T:0.43
Consensus pattern (18 bp):
ATTCGGGTTGGTCGGTTT
Found at i:35113 original size:18 final size:19
Alignment explanation
Indices: 35087--35122 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35077 CCAAACAGCC
35087 AAAAAAAAAGGA-AAAAAG
1 AAAAAAAAAGGAGAAAAAG
*
35105 AAAAGAAAAGGAGAAAAA
1 AAAAAAAAAGGAGAAAAA
35123 AAATATAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGGAGAAAAAG
Found at i:35295 original size:6 final size:6
Alignment explanation
Indices: 35281--35330 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
35271 ATTTTGGAAT
* *
35281 AAAG-A AAAGGA AAAGAA AAGGAA AAAGAA TAAA-AA AAAGGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAA-GAA AAAGAA
35329 AA
1 AA
35331 TAAAAGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
5 7 0.18
6 23 0.61
7 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:35297 original size:11 final size:11
Alignment explanation
Indices: 35281--35339 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
35271 ATTTTGGAAT
35281 AAAGAAAAGGA
1 AAAGAAAAGGA
35292 AAAGAAAAGGA
1 AAAGAAAAGGA
* *
35303 AAA-AGAA-TA
1 AAAGAAAAGGA
35312 AAA-AAAAGGAA
1 AAAGAAAAGG-A
*
35323 AAAGAAAA-TA
1 AAAGAAAAGGA
35333 AAAGAAA
1 AAAGAAA
35340 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 7 0.17
10 11 0.28
11 18 0.45
12 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGGA
Found at i:35320 original size:19 final size:20
Alignment explanation
Indices: 35291--35339 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 20
35281 AAAGAAAAGG
35291 AAAAGAAAAGGAAAAAGAAT
1 AAAAGAAAAGGAAAAAGAAT
35311 AAAA-AAAAGGAAAAAGAAAAT
1 AAAAGAAAAGGAAAAAG--AAT
35332 AAAAGAAA
1 AAAAGAAA
35340 TAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.46
20 4 0.15
21 7 0.27
22 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAGGAAAAAGAAT
Found at i:35348 original size:25 final size:24
Alignment explanation
Indices: 35281--35350 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
35271 ATTTTGGAAT
*
35281 AAAGAAAAGGAAAAGAAAAGGAAAAA
1 AAAGAAAA--AAAAGAAAAAGAAAAA
* *
35307 GAATAAAAAAAAGGAAAAAGAAAATA
1 AAAGAAAAAAAA-GAAAAAGAAAA-A
*
35333 AAAGAAATAAAAGAAAAA
1 AAAGAAAAAAAAGAAAAA
35351 TTTTAGAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 4 0.11
25 16 0.44
26 16 0.44
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAGAAAAAAAAGAAAAAGAAAAA
Found at i:38936 original size:15 final size:16
Alignment explanation
Indices: 38916--38947 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38906 ACCAAACCTA
38916 AAACTAG-AGAAAAAT
1 AAACTAGAAGAAAAAT
38931 AAACTAGAAGAAAAAT
1 AAACTAGAAGAAAAAT
38947 A
1 A
38948 GATGAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.12
Consensus pattern (16 bp):
AAACTAGAAGAAAAAT
Found at i:40333 original size:20 final size:19
Alignment explanation
Indices: 40302--40339 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40292 TTGTGTTTTT
40302 TTTTTCATTTCCTATTTCA
1 TTTTTCATTTCCTATTTCA
*
40321 TTTTTCATATTCCTTTTTC
1 TTTTTCAT-TTCCTATTTC
40340 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTCATTTCCTATTTCA
Found at i:41363 original size:13 final size:13
Alignment explanation
Indices: 41345--41370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41335 CTGGAAAATC
41345 AACTTGTGTTCAT
1 AACTTGTGTTCAT
41358 AACTTGTGTTCAT
1 AACTTGTGTTCAT
41371 GATTTTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
AACTTGTGTTCAT
Found at i:42632 original size:42 final size:42
Alignment explanation
Indices: 42568--42657 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
42558 AGGAAGAGAG
* *
42568 AGAAGAGCAGGAAGAATGAGAAGATAATTCTGAGGAGACTAA
1 AGAAGAGCAGGAAGAATGAGAAGAGAAATCTGAGGAGACTAA
* * *
42610 AGAAGAGGAGGAGGAA-GAAGAAGAGAAATCTGAGGGGACTAA
1 AGAAGAGCAGGAAGAATG-AGAAGAGAAATCTGAGGAGACTAA
42652 AGAAGA
1 AGAAGA
42658 AGAGAAAGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.49, C:0.06, G:0.36, T:0.10
Consensus pattern (42 bp):
AGAAGAGCAGGAAGAATGAGAAGAGAAATCTGAGGAGACTAA
Found at i:54663 original size:32 final size:33
Alignment explanation
Indices: 54616--54679 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
54606 GGAGATAAAA
*
54616 AAAATTTACTGCTATACATTGGCTTTGTGATTT
1 AAAATTTACTACTATACATTGGCTTTGTGATTT
54649 AAAA-TTACTACTATACATTGGCTTTGTGATT
1 AAAATTTACTACTATACATTGGCTTTGTGATT
54680 CATGTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (33 bp):
AAAATTTACTACTATACATTGGCTTTGTGATTT
Found at i:55176 original size:22 final size:20
Alignment explanation
Indices: 55134--55178 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
55124 ACAACCGCAT
*
55134 AAATCGGACGGTTGAATCAG
1 AAATCGGACGGTTGAACCAG
*
55154 AAATCGGACCGAGTTGAGCCAG
1 AAATCGGA-CG-GTTGAACCAG
55176 AAA
1 AAA
55179 AACCGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 2 0.10
22 11 0.52
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.16
Consensus pattern (20 bp):
AAATCGGACGGTTGAACCAG
Found at i:56437 original size:18 final size:17
Alignment explanation
Indices: 56414--56457 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
56404 AATCGTACAC
*
56414 TATATCTATAACGATAT
1 TATATCTATAACAATAT
56431 ATATATCTATAACAATAT
1 -TATATCTATAACAATAT
56449 TATTATCTA
1 TA-TATCTA
56458 ATATAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (17 bp):
TATATCTATAACAATAT
Found at i:56955 original size:42 final size:44
Alignment explanation
Indices: 56905--56998 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
56895 AATGCATTAT
*
56905 CTAA-ATTCTACT-T-CATCTCTAGGTAATAT-ATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAAT-TCATCAAAATAAAG
*
56946 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
56991 CTAATATT
1 CTAATATT
56999 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 2 0.04
45 32 0.70
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:60590 original size:38 final size:38
Alignment explanation
Indices: 60491--60638 Score: 217
Period size: 38 Copynumber: 3.9 Consensus size: 38
60481 GGCTGTGCAT
*
60491 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGT-AAG
* *
60530 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
* *
60568 AGTGGACCCGTGCCTCAAGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
**
60606 AGTGGACCCGTGTCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
60639 CTAGACTCGA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 9 0.09
38 59 0.59
39 32 0.32
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG
Found at i:60679 original size:6 final size:6
Alignment explanation
Indices: 60668--60711 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
60658 CGTTAACGGA
60668 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TG
60712 GTGCAGCCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:63257 original size:476 final size:479
Alignment explanation
Indices: 62351--63320 Score: 1793
Period size: 476 Copynumber: 2.0 Consensus size: 479
62341 TTTGCTTCAA
62351 TCTGACTTGTCCTGCTTTAATTGCTTCTCGAATCTGACCTCTCAGAAAATCTTCAGGAAACTTCC
1 TCTGACTTGTCCTGCTTTAATTGCTTCTCGAATCTGACCTCTCAGAAAATCTTCAGGAAACTTCC
62416 AAGATGACTTTCAACTTTGATCAACCTTAAATGACCACCCTAAAATGACCACCCAAGGCGACCAT
66 AAGATGACTTTCAACTTTGATCAACC----AT-------CTAAAATGACCACCCAAGGCGACCAT
62481 ATCTTCCCAAAAAATGACTTGGACGAAATCTGCCTCCAATCTGATACAATCCAGTCTGATTCAGG
120 ATCTTCCCAAAAAATGACTTGGACGAAATCTGCCTCCAATCTGATACAATCCAGTCTGATTCAGG
62546 TTTTGATTGTGCTGCACTGTATATTGATTGCTGTCAAAAATAACCAAAATGACCTCATATTCGAC
185 TTTTGATTGTGCTGCACTGTATATTGATTGCTGTCAAAAATAACCAAAATGACCTCATATTCGAC
*
62611 CAGAACCTCCTAGGCCACGAAATTGATCATAAATTGATCATTCTTGGCCATTAATTTGGTCAGAA
250 CAGAACCGCCTAGGCCACGAAATTGATCATAAATTGATCATTCTTGGCCATTAATTTGGTCAGAA
62676 CAGAAATCAGATTCAATTTTGACTAAAGCGGGGTCAAAAGCTCTCGTCCTTAACTGAAAAATATG
315 CAGAAATCAGATTCAATTTTGACTAAAGCGGGGTCAAAAGCTCTCGTCCTTAACTGAAAAATATG
62741 GAAAAAGTTGCAAACGAAGTCAGATTGAGTCCAAATTTCACCAGTATGGTTCGGCTATCATATTA
380 GAAAAAGTTGCAAACGAAGTCAGATTGAGTCCAAATTTCACCAGTATGGTTCGGCTATCATATTA
*
62806 AGACCATAGGAAAAATCTTGGTCGAAAATGAGCTC
445 AGACCATAGAAAAAATCTTGGTCGAAAATGAGCTC
62841 TCTGACTTGTCCTGCTTTAATTGCTTCTCGAATCTGACCTCTCAGAAAATCTTCAGGAAACTTCC
1 TCTGACTTGTCCTGCTTTAATTGCTTCTCGAATCTGACCTCTCAGAAAATCTTCAGGAAACTTCC
62906 AAGATGACTTTCAACTTTGATCAACC-T-T-AAATGACCACCCAAGGCGACCATATCTTCCCAAA
66 AAGATGACTTTCAACTTTGATCAACCATCTAAAATGACCACCCAAGGCGACCATATCTTCCCAAA
62968 AAATGACTTGGACGAAATCTGCCTCCAATCTGATACAATCCAGTCTGATTCAGGTTTTGATTGTG
131 AAATGACTTGGACGAAATCTGCCTCCAATCTGATACAATCCAGTCTGATTCAGGTTTTGATTGTG
63033 CTGCACTGTATATTGATTGCTGTCAAAAATAACCAAAATGACCTCATATTCGACCAGAACCGCCT
196 CTGCACTGTATATTGATTGCTGTCAAAAATAACCAAAATGACCTCATATTCGACCAGAACCGCCT
*
63098 AGGCCTCGAAATTGATCATAAATTGATCATTCTTGGCCATTAATTTGGTCAGAACAGAAATCAGA
261 AGGCCACGAAATTGATCATAAATTGATCATTCTTGGCCATTAATTTGGTCAGAACAGAAATCAGA
63163 TTCAATTTTGACTAAAGCGGGGTCAAAAGCTCTCGTCCTTAACTGAAAAATATGGAAAAAGTTGC
326 TTCAATTTTGACTAAAGCGGGGTCAAAAGCTCTCGTCCTTAACTGAAAAATATGGAAAAAGTTGC
63228 AAACGAAGTCAGATTGAGTCCAAATTTCACCAGTATGGTTCGGCTATCATATTAAGACCATAGAA
391 AAACGAAGTCAGATTGAGTCCAAATTTCACCAGTATGGTTCGGCTATCATATTAAGACCATAGAA
63293 AAAATCTTGGTCGAAAATGAGCTC
456 AAAATCTTGGTCGAAAATGAGCTC
63317 TCTG
1 TCTG
63321 TCATGGTGAA
Statistics
Matches: 477, Mismatches: 3, Indels: 14
0.97 0.01 0.03
Matches are distributed among these distances:
476 384 0.81
477 1 0.00
485 1 0.00
490 91 0.19
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (479 bp):
TCTGACTTGTCCTGCTTTAATTGCTTCTCGAATCTGACCTCTCAGAAAATCTTCAGGAAACTTCC
AAGATGACTTTCAACTTTGATCAACCATCTAAAATGACCACCCAAGGCGACCATATCTTCCCAAA
AAATGACTTGGACGAAATCTGCCTCCAATCTGATACAATCCAGTCTGATTCAGGTTTTGATTGTG
CTGCACTGTATATTGATTGCTGTCAAAAATAACCAAAATGACCTCATATTCGACCAGAACCGCCT
AGGCCACGAAATTGATCATAAATTGATCATTCTTGGCCATTAATTTGGTCAGAACAGAAATCAGA
TTCAATTTTGACTAAAGCGGGGTCAAAAGCTCTCGTCCTTAACTGAAAAATATGGAAAAAGTTGC
AAACGAAGTCAGATTGAGTCCAAATTTCACCAGTATGGTTCGGCTATCATATTAAGACCATAGAA
AAAATCTTGGTCGAAAATGAGCTC
Found at i:73845 original size:10 final size:10
Alignment explanation
Indices: 73830--73857 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
73820 TCCCCCTAAT
73830 AAAAAAAAGA
1 AAAAAAAAGA
73840 AAAAAAAAGA
1 AAAAAAAAGA
73850 AAAAAAAA
1 AAAAAAAA
73858 AGAAGGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:73846 original size:11 final size:11
Alignment explanation
Indices: 73830--73861 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
73820 TCCCCCTAAT
73830 AAAAAAAAG-A
1 AAAAAAAAGAA
73840 AAAAAAAAGAA
1 AAAAAAAAGAA
73851 AAAAAAAAGAA
1 AAAAAAAAGAA
73862 GGCAGGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Done.