Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010259.1 Corchorus capsularis cultivar CVL-1 contig10280, 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: 77368
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5158 original size:3 final size:3
Alignment explanation
Indices: 5150--5216 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
5140 TGTAAGCTTA
5150 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5198 TAT CAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
5217 CAATAATGGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14779 original size:18 final size:17
Alignment explanation
Indices: 14756--14792 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
14746 ATTAATGTAA
*
14756 TTTGTATTTGTAAATGTT
1 TTTGTATTCGTAAAT-TT
14774 TTTGTATTCGTAAATTT
1 TTTGTATTCGTAAATTT
14791 TT
1 TT
14793 AACCATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (17 bp):
TTTGTATTCGTAAATTT
Found at i:15098 original size:120 final size:120
Alignment explanation
Indices: 14958--15197 Score: 462
Period size: 120 Copynumber: 2.0 Consensus size: 120
14948 CTAATTAGAA
14958 GTATTAATAATAATAACATAAGAACAAACAAAAGAAAAGCTTCATAATTTACATATTAGGTTGTT
1 GTATTAATAATAATAACATAAGAACAAACAAAAGAAAAGCTTCATAATTTACATATTAGGTTGTT
15023 ATGTTTAATATTATAGCTACACCATACATGTAGCTCAAAATATATAGAGTTATAC
66 ATGTTTAATATTATAGCTACACCATACATGTAGCTCAAAATATATAGAGTTATAC
15078 GTATTAATAATAATAACATAAGAACAAACAAAAGAAAAGCTTCATAATTTACATATTAGGTTGTT
1 GTATTAATAATAATAACATAAGAACAAACAAAAGAAAAGCTTCATAATTTACATATTAGGTTGTT
* *
15143 GTGTTTAATATTATAGCTACACCATACATTTAGCTCAAAATATATAGAGTTATAC
66 ATGTTTAATATTATAGCTACACCATACATGTAGCTCAAAATATATAGAGTTATAC
15198 ACACAAAAAT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (120 bp):
GTATTAATAATAATAACATAAGAACAAACAAAAGAAAAGCTTCATAATTTACATATTAGGTTGTT
ATGTTTAATATTATAGCTACACCATACATGTAGCTCAAAATATATAGAGTTATAC
Found at i:16629 original size:2 final size:2
Alignment explanation
Indices: 16624--16650 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16614 TATATATATA
16624 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
16651 ATAGATTCCA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17514 original size:43 final size:43
Alignment explanation
Indices: 17430--17514 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
17420 ACTATCAAAA
* *
17430 ACTGTACAAAGGAAAAGAGTTCACTTAAAAATGTATATCAATT
1 ACTGTACAAAGGAAAAGAGATCACTTAAAAATGTAAATCAATT
17473 ACTGTACAAAGGAAAAGAGATCACTTAAAAATG-AAACTCAAT
1 ACTGTACAAAGGAAAAGAGATCACTTAAAAATGTAAA-TCAAT
17515 CCTAAGGCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 2 0.05
43 37 0.95
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (43 bp):
ACTGTACAAAGGAAAAGAGATCACTTAAAAATGTAAATCAATT
Found at i:25125 original size:20 final size:20
Alignment explanation
Indices: 25100--25138 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
25090 GGCCAAACAA
25100 ATACAACAAAAGAATATCAG
1 ATACAACAAAAGAATATCAG
25120 ATACAACAAAAGAATATCA
1 ATACAACAAAAGAATATCA
25139 TGTTTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (20 bp):
ATACAACAAAAGAATATCAG
Found at i:29081 original size:16 final size:15
Alignment explanation
Indices: 29060--29104 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
29050 ATTATCATAA
29060 ATTATTCATATAATT
1 ATTATTCATATAATT
29075 GATTATTCATATAATT
1 -ATTATTCATATAATT
*
29091 ATCATTCATATAAT
1 ATTATTCATATAAT
29105 GAAATTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTATTCATATAATT
Found at i:29099 original size:15 final size:16
Alignment explanation
Indices: 29063--29104 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
29053 ATCATAAATT
*
29063 ATTCATATAATTGATT
1 ATTCATATAATTGATC
29079 ATTCATATAATT-ATC
1 ATTCATATAATTGATC
29094 ATTCATATAAT
1 ATTCATATAAT
29105 GAAATTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTCATATAATTGATC
Found at i:30488 original size:14 final size:15
Alignment explanation
Indices: 30469--30501 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30459 ACAGTTCTTT
*
30469 AAAAAAATGTAAAA-
1 AAAAAAATCTAAAAC
30483 AAAAAAATCTAAAAC
1 AAAAAAATCTAAAAC
30498 AAAA
1 AAAA
30502 TCAACTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAAAAATCTAAAAC
Found at i:30743 original size:33 final size:33
Alignment explanation
Indices: 30706--30771 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
30696 AATTGTTTCT
30706 TCTAAATTAAAACAAGCTTGCAAAACCCAAAGA
1 TCTAAATTAAAACAAGCTTGCAAAACCCAAAGA
*
30739 TCTAAATTGAAACAAGCTTGCAAAACCCAAAGA
1 TCTAAATTAAAACAAGCTTGCAAAACCCAAAGA
30772 AAAAAAGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (33 bp):
TCTAAATTAAAACAAGCTTGCAAAACCCAAAGA
Found at i:36241 original size:22 final size:22
Alignment explanation
Indices: 36211--36294 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
36201 ATTAAATATT
*
36211 CTTATGAAATTGTGATAATCCTC
1 CTTATGAAATT-TGATAATACTC
36234 C-TATGAAATTTGGATAA-ACTC
1 CTTATGAAATTT-GATAATACTC
*
36255 CTTATGAAATTTTGATAATA-TT
1 CTTATGAAA-TTTGATAATACTC
*
36277 CTTATAAAATTTTGATAA
1 CTTATGAAA-TTTGATAA
36295 CGACATTATG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.09
22 44 0.81
23 5 0.09
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (22 bp):
CTTATGAAATTTGATAATACTC
Found at i:36287 original size:44 final size:44
Alignment explanation
Indices: 36211--36294 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
36201 ATTAAATATT
* *
36211 CTTATGAAATTGTGATAATCCTCCTATGAAATTTGGATAAACTC
1 CTTATGAAATTGTGATAATACTCCTATAAAATTTGGATAAACTC
* * * *
36255 CTTATGAAATTTTGATAATATTCTTATAAAATTTTGATAA
1 CTTATGAAATTGTGATAATACTCCTATAAAATTTGGATAA
36295 CGACATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (44 bp):
CTTATGAAATTGTGATAATACTCCTATAAAATTTGGATAAACTC
Found at i:36304 original size:44 final size:44
Alignment explanation
Indices: 36212--36310 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
36202 TTAAATATTC
* * * * *
36212 TTATGAAATTGTGATAATCCTCCTATGAAATTTGGATAAACTCC
1 TTATGAAATTTTGATAATACTCCTATAAAATTTGGATAAACACA
* * *
36256 TTATGAAATTTTGATAATATTCTTATAAAATTTTGAT-AACGACA
1 TTATGAAATTTTGATAATACTCCTATAAAATTTGGATAAAC-ACA
*
36300 TTATGTAATTT
1 TTATGAAATTT
36311 CGAAAACCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.07
44 42 0.93
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (44 bp):
TTATGAAATTTTGATAATACTCCTATAAAATTTGGATAAACACA
Found at i:36363 original size:22 final size:22
Alignment explanation
Indices: 36338--36380 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36328 GATTTCAAGA
* *
36338 ACCTCCCTAAGGAATTTTGATT
1 ACCTCACTAAGAAATTTTGATT
*
36360 ACCTCACTATGAAATTTTGAT
1 ACCTCACTAAGAAATTTTGAT
36381 AATTTCCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
ACCTCACTAAGAAATTTTGATT
Found at i:36583 original size:23 final size:23
Alignment explanation
Indices: 36531--36588 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
36521 TCGTACTATG
*
36531 AAATTTTGATAAACATTCCTGTA
1 AAATTTTGATAAACACTCCTGTA
*
36554 AATTTTTGATAAAC-CTCCT-TA
1 AAATTTTGATAAACACTCCTGTA
36575 TAGAATTTTGATAA
1 -A-AATTTTGATAA
36589 TTTTCGTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 5 0.17
23 23 0.77
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACACTCCTGTA
Found at i:36620 original size:22 final size:22
Alignment explanation
Indices: 36526--37133 Score: 246
Period size: 22 Copynumber: 27.8 Consensus size: 22
36516 AATAATCGTA
* *
36526 CTATGAAATTTTGATAAACATTC
1 CTATGAAATTTTGAT-AACCTCC
*
36549 CTGT-AAATTTTTGATAAACCTCC
1 CTATGAAA-TTTTGAT-AACCTCC
* ** *
36572 TTAT-AGAATTTTGATAATTTTC
1 CTATGA-AATTTTGATAACCTCC
* *
36594 GTATGAAATTTTGATAAGCTCC
1 CTATGAAATTTTGATAACCTCC
** * **
36616 CTATGATTTTTTTATAACCTAA
1 CTATGAAATTTTGATAACCTCC
* *
36638 TTATGAAATTTTGTTAACCTCAC
1 CTATGAAATTTTGATAACCTC-C
* * * *
36661 C-ATGAACTTTTGATAGCCACA
1 CTATGAAATTTTGATAACCTCC
*
36682 CTATGAAATTTTGATAA-C-AC
1 CTATGAAATTTTGATAACCTCC
* **
36702 CTATGAAATTTTGA-AAACTAAA
1 CTATGAAATTTTGATAACCT-CC
36724 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* *
36746 CTATGAAATTTTAAATAACCTTC
1 CTATGAAATTTT-GATAACCTCC
* * * *
36769 ATATAAAATTTTGGTAA-CTACA
1 CTATGAAATTTTGATAACCT-CC
36791 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* *
36813 CTATG-AA-----AT-ACCACA
1 CTATGAAATTTTGATAACCTCC
** * * *** *
36828 CTATACAGTTTTTATAATGACA
1 CTATGAAATTTTGATAACCTCC
* * *
36850 CTATGAAATTTCGATGACCTCT
1 CTATGAAATTTTGATAACCTCC
* * * *
36872 TTATAAAAAATTCGATAACCTCC
1 CTAT-GAAATTTTGATAACCTCC
* *
36895 ATATGAAATTTT-ATTAACCTCT
1 CTATGAAATTTTGA-TAACCTCC
* * *
36917 CTATAAAATTTTGATAATCATACT
1 CTATGAAATTTTGATAA-CCT-CC
* * *
36941 ATATGAAA-TTTG-TAACTTTC
1 CTATGAAATTTTGATAACCTCC
* * *
36961 GTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCTCC
* *
36983 CTGTGAAAATTTTTGATAACCTCA
1 CTATG-AAA-TTTTGATAACCTCC
* *
37007 CTA-GAATTATTTGATAACCTCG
1 CTATGAAAT-TTTGATAACCTCC
* * * *
37029 CTTTAAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAACCTCC
* * *
37051 TTATGAAATTTTGATAGCCAT-G
1 CTATGAAATTTTGATAACC-TCC
* * ** *
37073 CTTTAAAATTTTGATAATATCT
1 CTATGAAATTTTGATAACCTCC
* * *
37095 CTATGAAATTTTGGTAACCACG
1 CTATGAAATTTTGATAACCTCC
37117 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
37134 AAATCATGAT
Statistics
Matches: 429, Mismatches: 124, Indels: 65
0.69 0.20 0.11
Matches are distributed among these distances:
15 8 0.02
16 3 0.01
19 2 0.00
20 22 0.05
21 17 0.04
22 269 0.63
23 83 0.19
24 25 0.06
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:38002 original size:16 final size:16
Alignment explanation
Indices: 37981--38012 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
37971 ATATCATCAT
37981 ATATAAATAAAAATAA
1 ATATAAATAAAAATAA
*
37997 ATATAAATAATAATAA
1 ATATAAATAAAAATAA
38013 TAATACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATAAATAAAAATAA
Found at i:39069 original size:32 final size:33
Alignment explanation
Indices: 39033--39138 Score: 162
Period size: 33 Copynumber: 3.2 Consensus size: 33
39023 AAAATGGCCG
39033 AGCCGCCCAAGC-TGGGCGGCCTTG-CCATGGCT
1 AGCCGCCC-AGCGTGGGCGGCCTTGCCCATGGCT
*
39065 AGCCGCCCAGCGTGGGCGGCCTTGCCCTTGGCT
1 AGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCT
* *
39098 AGCCGCCCAGCTTGGGCGGCCTTGCCCATGGCG
1 AGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCT
39131 AGCCGCCC
1 AGCCGCCC
39139 TGGGTGACAA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 3 0.04
32 20 0.29
33 45 0.66
ACGTcount: A:0.09, C:0.41, G:0.35, T:0.15
Consensus pattern (33 bp):
AGCCGCCCAGCGTGGGCGGCCTTGCCCATGGCT
Found at i:39384 original size:9 final size:9
Alignment explanation
Indices: 39372--39416 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
39362 CTTTTTTCTT
39372 TTTTTTTAA
1 TTTTTTTAA
39381 -TTTTTTAA
1 TTTTTTTAA
39389 TTTTTTTAA
1 TTTTTTTAA
39398 TTTTTTTAA
1 TTTTTTTAA
39407 TTTTTTTAA
1 TTTTTTTAA
39416 T
1 T
39417 ATTAATTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:39384 original size:17 final size:16
Alignment explanation
Indices: 39364--39416 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
39354 ACCATTTTCT
39364 TTTTTCTTTTTTTTTAA
1 TTTTT-TTTTTTTTTAA
*
39381 TTTTTTAATTTTTTTAA
1 TTTTTT-TTTTTTTTAA
39398 TTTTTTTAATTTTTTTAA
1 TTTTTTT--TTTTTTTAA
39416 T
1 T
39417 ATTAATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 1 0.03
17 20 0.65
18 10 0.32
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTTTTTTAA
Found at i:39386 original size:18 final size:17
Alignment explanation
Indices: 39372--39416 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
39362 CTTTTTTCTT
*
39372 TTTTTTTAATTTTTTAA
1 TTTTTTTAATTTTTTTA
39389 TTTTTTTAATTTTTTTAA
1 TTTTTTTAATTTTTTT-A
39407 TTTTTTTAAT
1 TTTTTTTAAT
39417 ATTAATTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTAATTTTTTTA
Found at i:39498 original size:26 final size:26
Alignment explanation
Indices: 39468--39535 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
39458 TACTTAGTTT
39468 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
39494 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
* *
39520 ATTAATTTATGATTAA
1 ATTAGTTTATGTTTAA
39536 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:39579 original size:24 final size:24
Alignment explanation
Indices: 39545--39602 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
39535 AAATGAAGGA
*
39545 AAATGAATTTGAAG-ATTTGTTAG
1 AAATGAATTTGAAGAAGTTGTTAG
39568 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAA-TTTGAAGAAGTTGTTAG
39593 AAATGAATTT
1 AAATGAATTT
39603 TAGGGTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 7 0.22
24 10 0.31
25 15 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.36
Consensus pattern (24 bp):
AAATGAATTTGAAGAAGTTGTTAG
Found at i:48863 original size:31 final size:31
Alignment explanation
Indices: 48825--48886 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
48815 AAAATAAAAT
*
48825 GGGAAAAAGAAATGTAAGATTGGAATGTGAA
1 GGGAAAAAAAAATGTAAGATTGGAATGTGAA
48856 GGGAAAAAAAAATGTAAGATTGGAATGTGAA
1 GGGAAAAAAAAATGTAAGATTGGAATGTGAA
48887 TTACAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (31 bp):
GGGAAAAAAAAATGTAAGATTGGAATGTGAA
Found at i:57728 original size:29 final size:28
Alignment explanation
Indices: 57659--57739 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
57649 GCTTAATACC
**
57659 CAAATTGGCCCCTTAACTATCCATTTTGGGA
1 CAAATTGGCCCCTTAA-T-T-TTTTTTGGGA
57690 CAAATTGGCCCCTTAATTTTTTTTGGGGA
1 CAAATTGGCCCCTTAATTTTTTTT-GGGA
*
57719 CAAATTGGCCCCTTAACTTTT
1 CAAATTGGCCCCTTAATTTTT
57740 AAAAACGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 4 0.09
29 25 0.54
30 1 0.02
31 16 0.35
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (28 bp):
CAAATTGGCCCCTTAATTTTTTTTGGGA
Found at i:58499 original size:31 final size:29
Alignment explanation
Indices: 58433--58509 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
58423 ATTTTTAAAG
*
58433 GTTAAGGGGTCAATTTGTCCACAAAAAAA
1 GTTAAGGGGCCAATTTGTCCACAAAAAAA
*
58462 GTTAAGGGGCCAATTTGTCC-CAAAATGGATA
1 GTTAAGGGGCCAATTTGTCCACAAAA---AAA
*
58493 GTTAAGGGGCTAATTTG
1 GTTAAGGGGCCAATTTG
58510 GGTATTAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 5 0.12
29 19 0.45
31 18 0.43
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (29 bp):
GTTAAGGGGCCAATTTGTCCACAAAAAAA
Found at i:61572 original size:2 final size:2
Alignment explanation
Indices: 61561--61595 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
61551 ATAAGTTAGC
61561 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61596 CATAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:62886 original size:183 final size:176
Alignment explanation
Indices: 62533--62893 Score: 605
Period size: 183 Copynumber: 2.0 Consensus size: 176
62523 TCCATAAACA
*
62533 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
* * *
62598 CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTCTATTTGACCG
66 CATTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTATTTTTTTTTCTATTTGACCG
*
62663 ATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTAC
131 ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
62709 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
1 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
*
62774 TCAATTACAATTATAGGTTGTACGATTGAATGTTTCGGCTTTAATTCTTTTATTTTTTTTTCTAT
65 TC-ATTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAA-----TTATTTTTTTTTCTAT
62839 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
124 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
62892 AA
1 AA
62894 CTTTCATGAA
Statistics
Matches: 172, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
176 5 0.03
177 60 0.35
178 38 0.22
183 69 0.40
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (176 bp):
AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
CATTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTATTTTTTTTTCTATTTGACCG
ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Found at i:67219 original size:18 final size:18
Alignment explanation
Indices: 67196--67230 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
67186 CAACCTTTAA
*
67196 ATATATACACATGTATGC
1 ATATATACACACGTATGC
*
67214 ATATATATACACGTATG
1 ATATATACACACGTATG
67231 ACGTATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
ATATATACACACGTATGC
Found at i:68762 original size:18 final size:19
Alignment explanation
Indices: 68734--68776 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
68724 ACTCATATTC
*
68734 AAACT-AACTG-ATTCAAA
1 AAACTGAACTGAACTCAAA
68751 AAACTGAACTGAACTCAAA
1 AAACTGAACTGAACTCAAA
68770 AAACTGA
1 AAACTGA
68777 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 13 0.57
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (19 bp):
AAACTGAACTGAACTCAAA
Found at i:68873 original size:64 final size:65
Alignment explanation
Indices: 68804--68929 Score: 227
Period size: 64 Copynumber: 2.0 Consensus size: 65
68794 ATAGATCTGA
*
68804 GGACTTTATTCTAAAATAAAAGTAAAAAAGGATCAGGCTCCTCCT-CCCCTTGACAAAAGAGTGG
1 GGACTTTATTCTAAAATAAAAGTAAAAAAGGATCAGACTCCTCCTCCCCCTTGACAAAAGAGTGG
*
68868 GGACTTTATTTTAAAATAAAAGTAAAAAAGGATCAGACTCCTCCTCCCCCTTGACAAAAGAG
1 GGACTTTATTCTAAAATAAAAGTAAAAAAGGATCAGACTCCTCCTCCCCCTTGACAAAAGAG
68930 CCCTTGACAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 43 0.73
65 16 0.27
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (65 bp):
GGACTTTATTCTAAAATAAAAGTAAAAAAGGATCAGACTCCTCCTCCCCCTTGACAAAAGAGTGG
Found at i:68935 original size:15 final size:15
Alignment explanation
Indices: 68915--68944 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68905 CTCCTCCTCC
68915 CCCTTGACAAAAGAG
1 CCCTTGACAAAAGAG
68930 CCCTTGACAAAAGAG
1 CCCTTGACAAAAGAG
68945 TCAGAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (15 bp):
CCCTTGACAAAAGAG
Found at i:77314 original size:2 final size:2
Alignment explanation
Indices: 77304--77339 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
77294 TCACTCTCTC
*
77304 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77340 GAGTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Done.