Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020110.1 Corchorus olitorius cultivar O-4 contig20143, 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: 66593
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:15930 original size:40 final size:41
Alignment explanation
Indices: 15847--15955 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
15837 CTTGGTTTGC
** * *
15847 TATTTATATTTATCTCACCTAGGGTTTAGCTTAGTTTTGGGG
1 TATTTAT-TTTATCTTTCTTAGGGTTTAACTTAGTTTTGGGG
15889 TATTTATTTTATCTTTCTTAGGGTTTAACTTAGTTTT-GGG
1 TATTTATTTTATCTTTCTTAGGGTTTAACTTAGTTTTGGGG
* *
15929 TATTTATCTTCT-TTTACTTAGGGTTTA
1 TATTTATTTTATCTTT-CTTAGGGTTTA
15956 GTATGAATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
39 3 0.05
40 24 0.40
41 26 0.43
42 7 0.12
ACGTcount: A:0.18, C:0.10, G:0.17, T:0.54
Consensus pattern (41 bp):
TATTTATTTTATCTTTCTTAGGGTTTAACTTAGTTTTGGGG
Found at i:28816 original size:31 final size:31
Alignment explanation
Indices: 28781--28845 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
28771 CACAGTGACA
28781 AACTAATGGATAGTTTTATGTTAGTAAAAAC
1 AACTAATGGATAGTTTTATGTTAGTAAAAAC
28812 AACTAATGGATAGTTTTATGTTAGTAAAAAC
1 AACTAATGGATAGTTTTATGTTAGTAAAAAC
28843 AAC
1 AAC
28846 AAATACTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (31 bp):
AACTAATGGATAGTTTTATGTTAGTAAAAAC
Found at i:29736 original size:15 final size:15
Alignment explanation
Indices: 29716--29748 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
29706 AAGATCATAT
29716 AAGACTAATTTTATC
1 AAGACTAATTTTATC
29731 AAGACTAATTTTATC
1 AAGACTAATTTTATC
29746 AAG
1 AAG
29749 TTCAGGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (15 bp):
AAGACTAATTTTATC
Found at i:30861 original size:19 final size:18
Alignment explanation
Indices: 30837--30896 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
30827 TCATAGGCAC
30837 GTACATCACCATAAACTTA
1 GTACATCA-CATAAACTTA
**
30856 GTACAT-AGGTAAA--TA
1 GTACATCACATAAACTTA
30871 GGTACATCATCATAAACTTA
1 -GTACATCA-CATAAACTTA
30891 GTACAT
1 GTACAT
30897 AGGTAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 5 0.16
18 5 0.16
19 12 0.38
20 2 0.06
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (18 bp):
GTACATCACATAAACTTA
Found at i:30877 original size:35 final size:35
Alignment explanation
Indices: 30837--30904 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
30827 TCATAGGCAC
30837 GTACATCACCATAAACTTAGTACATAGGTAAATAG
1 GTACATCACCATAAACTTAGTACATAGGTAAATAG
*
30872 GTACATCATCATAAACTTAGTACATAGGTAAAT
1 GTACATCACCATAAACTTAGTACATAGGTAAAT
30905 GTGAGTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (35 bp):
GTACATCACCATAAACTTAGTACATAGGTAAATAG
Found at i:33536 original size:23 final size:23
Alignment explanation
Indices: 33502--33545 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
33492 TATAACAACT
*
33502 TTACAAATTAAATTTGAATGAGA
1 TTACAAAGTAAATTTGAATGAGA
33525 TTACAAAGTAAATTTGAATGA
1 TTACAAAGTAAATTTGAATGA
33546 AGATACGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (23 bp):
TTACAAAGTAAATTTGAATGAGA
Found at i:34569 original size:20 final size:22
Alignment explanation
Indices: 34527--34582 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
34517 TAATTTTCTG
34527 ATTTTTCCAC--TT-TT-TTTC
1 ATTTTTCCACTTTTCTTCTTTC
34545 ATTTTT-C-CTTTTCTTCTTTC
1 ATTTTTCCACTTTTCTTCTTTC
*
34565 TTTTTTCCACTTTTCTTC
1 ATTTTTCCACTTTTCTTC
34583 AAATTTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.03
17 1 0.03
18 8 0.26
19 2 0.06
20 9 0.29
21 1 0.03
22 9 0.29
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTTCCACTTTTCTTCTTTC
Found at i:36655 original size:47 final size:47
Alignment explanation
Indices: 36602--36692 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
36592 TTACCTGAAT
36602 TGGGTATGAGTCGAATTTAGGGTTAGTATAAATACTAACCCCTTAAC
1 TGGGTATGAGTCGAATTTAGGGTTAGTATAAATACTAACCCCTTAAC
36649 TGGGTATGAGTCGAATTTAGGGTTAGTATAAATACTAACCCCTT
1 TGGGTATGAGTCGAATTTAGGGTTAGTATAAATACTAACCCCTT
36693 TTTCTTCCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (47 bp):
TGGGTATGAGTCGAATTTAGGGTTAGTATAAATACTAACCCCTTAAC
Found at i:41701 original size:2 final size:2
Alignment explanation
Indices: 41694--41722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41684 AAAAAGCCAT
41694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41723 TGATTGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47073 original size:5 final size:5
Alignment explanation
Indices: 47060--47089 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
47050 ACTTTCCTCC
*
47060 CCTTC CCTTT CCTTT CCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
47090 AAAAACTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:49077 original size:199 final size:199
Alignment explanation
Indices: 48736--50273 Score: 2152
Period size: 199 Copynumber: 7.7 Consensus size: 199
48726 CACTTTTATT
* * *
48736 ATTTTTCTTATAGGATTATTATACAATACATTTTTCAGTGTAAATTTT-ACACTCCATAAGCGGG
1 ATTTTTCTTATAGGATTATTATACAATACA-CTGTCAATGTAAATTTTGA-ACTCCATAAGCGGG
* * * * * *
48800 TTAAGAAGTTGACACATAACACATTTCATAATCAATTAAATATTTAATATTAATACTTATTCCTT
64 TTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCT
* *
48865 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAATTCGACTGACGGTGTAT
129 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
48930 AGTATA
194 AGTATA
48936 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * * * *
49001 AAGAAATTGACATATATCTCATTTCATCATTAATTAAATATATAA-ATTTAATACATATTCCCTA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATA-TTAATACATATTCCCTA
* * * *
49065 AGGTGACACATGTCAACTCTTAAAACCTGCACATGCAGTCTGCTAAACTCCACTGACGGTGTATA
130 AGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATA
*
49130 GTAAAA
195 GT-ATA
* * * * *
49136 ATTTTTCTTATAGGATTATTATACAATACAATGTCAGTGTAAATTTTGGATTCCATAAGCGGTTT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * * *
49201 AATAATTTGACATATACCCCATTTCATATTTAATAAAATATTTAATATTAATACATATTCCCTAA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
* * *
49266 GGGGACATATGTCAACCCTTAAAGCCAGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTA
131 GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-TA
49331 -TATA
195 GTATA
* * * *
49335 ATTGTTCTTATAGGATTATCATACAATACATTGTCAATGTAAATTTTGCACTCCATAAGCGGGTT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * *
49400 AAGAAGTTGACATATACCGCATTTCATAATTAATTAAATAATTAATATTAATAAATATTCCCTAA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
* * *
49465 GGGAACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAAATCCACTGACGGTGTATAG
131 GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAG
49530 TATA
196 TATA
49534 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * * * * *
49599 AAGAAATTGACATATATCTCATTTCATCATTAATTAAATATATAATATTAATACATACTCCCTAA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
* *
49664 GGTGACACATGTCAACCCTTAAACCCTGCACATGCAGTCTGCTAAACTCCACTGACGGTGTATAG
131 GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAG
49729 TATA
196 TATA
* * * * *
49733 AATTTTCTTATAGGATTATTATACAATACAATGTCAGTGTAAGA-TTTGGACTCCAAAAGCGGGT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAA-ATTTTGAACTCCATAAGCGGGT
* * *
49797 TAAGAAGTTGACATATATCCCATTTCATAATTAATTAAATATTTAATATTAAAACATCTTCCCTA
65 TAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* * * * *
49862 AGGGGACACATGTCAACCTTTAAACCCCGCACGTGCAGTTTGCTAAAATCCATTGACGGTGTATT
130 AGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-T
49927 A-TATA
194 AGTATA
* * * * * * * *
49932 ATTTTTCTTATAGAATTATTATATAACACGCTGTCAATGTAAAATTTGCACTCTATAAGCGGATT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * * * *
49997 AAGAAGTTGAAACATACCCCATTTCATCATTAATTAAATATATAACATTAATACATATTCCCTAA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
* * * * *
50062 GGGGACACATGTCAA-CCTTAAACCATGCACGTGCAGTCTGTTAAACTCCATTGACGGTGCATTG
131 GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAG
50126 TATA
196 TATA
* *
50130 ATTGTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTT
1 ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
* * *** *
50195 AAGAAGTTGGCACATACTTAATTTCATAATTAACTAAATATTTAATATTAATACATATTCCCTAA
66 AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
*
50260 GGGAACACATGTCA
131 GGGGACACATGTCA
50274 CAATTTTTTT
Statistics
Matches: 1188, Mismatches: 140, Indels: 22
0.88 0.10 0.02
Matches are distributed among these distances:
197 1 0.00
198 172 0.14
199 804 0.68
200 208 0.18
201 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (199 bp):
ATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGTT
AAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAG
TATA
Found at i:51215 original size:26 final size:26
Alignment explanation
Indices: 51186--51236 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
51176 TAACCTCACA
* *
51186 TTCTTAGAACTTTTAATAACCTTTCC
1 TTCTTACAAATTTTAATAACCTTTCC
*
51212 TTCTTACAAATTTTAGTAACCTTTC
1 TTCTTACAAATTTTAATAACCTTTC
51237 ATCAGTATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (26 bp):
TTCTTACAAATTTTAATAACCTTTCC
Found at i:51933 original size:2 final size:2
Alignment explanation
Indices: 51926--51955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51916 AACACAATAG
51926 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
51956 TGGAATTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54183 original size:3 final size:3
Alignment explanation
Indices: 54175--54315 Score: 246
Period size: 3 Copynumber: 46.3 Consensus size: 3
54165 GTTACGAAAA
*
54175 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54223 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
*
54271 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT ATAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT T
54316 TGCTTAAATT
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
3 126 0.95
4 7 0.05
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:59891 original size:20 final size:21
Alignment explanation
Indices: 59861--59904 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
59851 GGTTATAAAA
59861 AAAACTTCATAATGTT-ACTAT
1 AAAACTTCATAA-GTTAACTAT
59882 AAAA-TTCATAAGTTAACTAT
1 AAAACTTCATAAGTTAACTAT
59902 AAA
1 AAA
59905 TCTTACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAACTTCATAAGTTAACTAT
Found at i:60070 original size:85 final size:86
Alignment explanation
Indices: 59967--60144 Score: 304
Period size: 85 Copynumber: 2.1 Consensus size: 86
59957 TAAGATCACT
*
59967 AAAAATCTTAAACGAGGTGATTGAACAAATTTAAGAAAACTATTTAAAAAGC-TTTAAATTTAAT
1 AAAAATCTTAAACAAGGTGATTGAACAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
*
60031 GAAAATTTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
* *
60052 AAAAATCTTAAACAAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAAGCTTTTAAGTTTAAT
1 AAAAATCTTAAACAAGGTGATTGAACAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
60117 GAAAAATTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
60138 AGAAAAT
1 A-AAAAT
60145 TTACAAGGTT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 50 0.57
86 32 0.37
87 5 0.06
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.31
Consensus pattern (86 bp):
AAAAATCTTAAACAAGGTGATTGAACAAATTTAAGAAAACTATTTAAAAAGCTTTTAAATTTAAT
GAAAAATTTATAAGCTTACCA
Found at i:60197 original size:21 final size:20
Alignment explanation
Indices: 60173--60211 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60163 GTTTTACCGG
*
60173 TTACAATAAAAGTTAAATAGT
1 TTACAA-AAAAGCTAAATAGT
*
60194 TTACTAAAAAGCTAAATA
1 TTACAAAAAAGCTAAATA
60212 AGATTACCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (20 bp):
TTACAAAAAAGCTAAATAGT
Found at i:60340 original size:25 final size:25
Alignment explanation
Indices: 60298--60348 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
60288 TATTATTATT
60298 AAAAATAGGTTACTTAAATTAGTTA
1 AAAAATAGGTTACTTAAATTAGTTA
*
60323 AAAAATAAGGTTAC-TAAATTGGTTA
1 AAAAAT-AGGTTACTTAAATTAGTTA
60348 A
1 A
60349 TTACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (25 bp):
AAAAATAGGTTACTTAAATTAGTTA
Found at i:60556 original size:21 final size:22
Alignment explanation
Indices: 60532--60605 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
60522 TAAAATCCAC
* *
60532 AATAAGATTACTAAAAA-TCTT
1 AATAAGGTTACTAAAAACACTT
*
60553 AATAAGGTTAGGTAAAAACACTT
1 AATAAGGTTA-CTAAAAACACTT
* *
60576 AATAAGGTGACTAAAAAAACTT
1 AATAAGGTTACTAAAAACACTT
*
60598 TATAAGGT
1 AATAAGGT
60606 CAAAAAAGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.20
22 23 0.52
23 12 0.27
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (22 bp):
AATAAGGTTACTAAAAACACTT
Found at i:60626 original size:27 final size:27
Alignment explanation
Indices: 60588--60639 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
60578 TAAGGTGACT
*
60588 AAAAAAACTTTATAAGGTCAAAAAAGG
1 AAAAAAACTTTAAAAGGTCAAAAAAGG
* *
60615 AAAAAAAGTTTAAAAGGTTAAAAAA
1 AAAAAAACTTTAAAAGGTCAAAAAA
60640 AGCTCAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.19
Consensus pattern (27 bp):
AAAAAAACTTTAAAAGGTCAAAAAAGG
Found at i:60709 original size:20 final size:20
Alignment explanation
Indices: 60684--60758 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
60674 TAATACTTGC
60684 TTATTAAAAAGGTTT-TAAGG
1 TTATTAAAAA-GTTTATAAGG
60704 TTATTAAAAAGTTTATAAGG
1 TTATTAAAAAGTTTATAAGG
*** * *
60724 TGGCTAATAAA-TTTAAAATG
1 TTATTAA-AAAGTTTATAAGG
60744 TTATTAAAAAGTTTA
1 TTATTAAAAAGTTTA
60759 ACATTAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.16
20 34 0.77
21 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.15, T:0.40
Consensus pattern (20 bp):
TTATTAAAAAGTTTATAAGG
Found at i:61099 original size:16 final size:16
Alignment explanation
Indices: 61074--61104 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61064 TCTACAAATT
*
61074 ATAAAGATTTAGTAAA
1 ATAAAAATTTAGTAAA
61090 ATAAAAATTTAGTAA
1 ATAAAAATTTAGTAA
61105 TATTTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
ATAAAAATTTAGTAAA
Done.