Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008557.1 Corchorus capsularis cultivar CVL-1 contig08578, 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: 60123
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3971 original size:2 final size:2
Alignment explanation
Indices: 3964--3989 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3954 TTATAAACTG
3964 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
3990 CATGTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4790 original size:17 final size:17
Alignment explanation
Indices: 4764--4822 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
4754 TTATTTTTGA
*
4764 TTTAAGATAAATAAATG
1 TTTAACATAAATAAATG
4781 TTTAACAT-AA-AAAT-
1 TTTAACATAAATAAATG
* *
4795 ATTAA-ATATAGTAAATG
1 TTTAACATA-AATAAATG
4812 TTTAACATAAA
1 TTTAACATAAA
4823 AATAAGTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
13 2 0.06
14 4 0.12
15 5 0.16
16 6 0.19
17 12 0.38
18 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (17 bp):
TTTAACATAAATAAATG
Found at i:7687 original size:61 final size:61
Alignment explanation
Indices: 7592--7718 Score: 218
Period size: 61 Copynumber: 2.1 Consensus size: 61
7582 ATTGTTGGGG
*
7592 AAAGTGTTTGTTGGCTCATAGATTAGCGTTTCGGTAATGTAGGTAATCATGTAGCAGTTTA
1 AAAGTGTTTGTTGGCTCATAGATTAGCGTTTCGGTAATCTAGGTAATCATGTAGCAGTTTA
* *
7653 AAAGTGTTTGTTGGCTCATAGATTAGCGTTTCGGTTATCTTGGTAATCATGTAGCAGTTTA
1 AAAGTGTTTGTTGGCTCATAGATTAGCGTTTCGGTAATCTAGGTAATCATGTAGCAGTTTA
*
7714 CAAGT
1 AAAGT
7719 CTTCCAGTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (61 bp):
AAAGTGTTTGTTGGCTCATAGATTAGCGTTTCGGTAATCTAGGTAATCATGTAGCAGTTTA
Found at i:11628 original size:20 final size:20
Alignment explanation
Indices: 11603--11654 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
11593 ACGGACAAAT
11603 TCCGTAGCAAAAGGCGAAAA
1 TCCGTAGCAAAAGGCGAAAA
11623 TCCGTAGCAAAAGGCGAAAA
1 TCCGTAGCAAAAGGCGAAAA
11643 TCCGTAGCAAAA
1 TCCGTAGCAAAA
11655 ACAAATCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
TCCGTAGCAAAAGGCGAAAA
Found at i:12238 original size:34 final size:34
Alignment explanation
Indices: 12200--12267 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
12190 TAACAATTAA
12200 ACAAAACTCCAAGTACATTCACCACATCTAACTT
1 ACAAAACTCCAAGTACATTCACCACATCTAACTT
* *
12234 ACAAAATTCCAAGTACATTCATCACATCTAACTT
1 ACAAAACTCCAAGTACATTCACCACATCTAACTT
12268 TCCATAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.26
Consensus pattern (34 bp):
ACAAAACTCCAAGTACATTCACCACATCTAACTT
Found at i:13750 original size:24 final size:24
Alignment explanation
Indices: 13718--13766 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13708 TACTCATGTA
13718 CTCAACAATCATAACTGGCATTAT
1 CTCAACAATCATAACTGGCATTAT
13742 CTCAACAATCATAACTGGCATTAT
1 CTCAACAATCATAACTGGCATTAT
13766 C
1 C
13767 AAAATCACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.29
Consensus pattern (24 bp):
CTCAACAATCATAACTGGCATTAT
Found at i:13778 original size:21 final size:23
Alignment explanation
Indices: 13716--13779 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 23
13706 GATACTCATG
13716 TACTCAACAATCATAACTGGCAT
1 TACTCAACAATCATAACTGGCAT
13739 TATCTCAACAATCATAACTGGCAT
1 TA-CTCAACAATCATAACTGGCAT
*
13763 TA-TCAA-AATCACAACTG
1 TACTCAACAATCATAACTG
13780 AGGTTTAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 10 0.26
22 4 0.10
23 2 0.05
24 23 0.59
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (23 bp):
TACTCAACAATCATAACTGGCAT
Found at i:14211 original size:2 final size:2
Alignment explanation
Indices: 14204--14228 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14194 TTAGACAAAA
14204 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14229 GAGAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15110 original size:15 final size:15
Alignment explanation
Indices: 15075--15103 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15065 TAATTTTCTA
15075 ATATTT-TATTTATT
1 ATATTTGTATTTATT
15089 ATATTTGTATTTATT
1 ATATTTGTATTTATT
15104 TAGTTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATATTTGTATTTATT
Found at i:15781 original size:24 final size:25
Alignment explanation
Indices: 15754--15806 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
15744 TGTATATAAT
*
15754 AATATAATT-ATAATAA-TATTTATC
1 AATATAATTCA-AAAAAGTATTTATC
*
15778 AATATACTTCAAAAAAGTATTTATC
1 AATATAATTCAAAAAAGTATTTATC
15803 AATA
1 AATA
15807 AATATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (25 bp):
AATATAATTCAAAAAAGTATTTATC
Found at i:19369 original size:24 final size:25
Alignment explanation
Indices: 19323--19370 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
19313 ATTGGAGTAT
*
19323 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
19348 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
19371 TATTGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:24975 original size:33 final size:33
Alignment explanation
Indices: 24928--24999 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
24918 AGGAGTCGAT
*
24928 TTCCCGTGATCGACATGAGC-AATAACAGA-CATA
1 TTCCTGTGATCGACATGA-CAAATAACA-ATCATA
*
24961 TTCCTGTGATCGACATGACAAATAATAATCATA
1 TTCCTGTGATCGACATGACAAATAACAATCATA
24994 TTCCTG
1 TTCCTG
25000 ATATTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (33 bp):
TTCCTGTGATCGACATGACAAATAACAATCATA
Found at i:29185 original size:7 final size:7
Alignment explanation
Indices: 29173--29206 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
29163 TGAAAATTGG
29173 ATATGTC
1 ATATGTC
29180 ATATGTC
1 ATATGTC
29187 ATATGTC
1 ATATGTC
29194 ATATGTC
1 ATATGTC
29201 ATATGT
1 ATATGT
29207 AAGGAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (7 bp):
ATATGTC
Found at i:32216 original size:23 final size:24
Alignment explanation
Indices: 32187--32243 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
32177 ATTTTTTTTC
*
32187 TATGTAAGTGATTATTTCTTTGTAA
1 TATGTAAGTG-TAATTTCTTTGTAA
*
32212 -A-GTAAAATGTAATTTCTTTGTAA
1 TATGT-AAGTGTAATTTCTTTGTAA
32235 TATGTAAGT
1 TATGTAAGT
32244 TCTTTTCTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
23 15 0.58
24 9 0.35
25 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
TATGTAAGTGTAATTTCTTTGTAA
Found at i:32239 original size:18 final size:18
Alignment explanation
Indices: 32213--32248 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32203 TCTTTGTAAA
*
32213 GTAAAATGTAATTTCTTT
1 GTAAAATGTAAGTTCTTT
*
32231 GTAATATGTAAGTTCTTT
1 GTAAAATGTAAGTTCTTT
32249 TCTACGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
GTAAAATGTAAGTTCTTT
Found at i:32813 original size:48 final size:48
Alignment explanation
Indices: 32731--32828 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
32721 GAAAAGAATG
* *
32731 AAGCAACAAGCAACGTGGATTTATAGAAACCAAAAACTGAAATCAACA
1 AAGCAACAAGCAACGTAGATTTAGAGAAACCAAAAACTGAAATCAACA
* * ** *
32779 AAGCAAGAGGCAACGTAGATTTAGAGAAGTCAAAAATTGAAATCAACA
1 AAGCAACAAGCAACGTAGATTTAGAGAAACCAAAAACTGAAATCAACA
32827 AA
1 AA
32829 AACACCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.15
Consensus pattern (48 bp):
AAGCAACAAGCAACGTAGATTTAGAGAAACCAAAAACTGAAATCAACA
Found at i:34759 original size:98 final size:98
Alignment explanation
Indices: 34604--34788 Score: 284
Period size: 98 Copynumber: 1.9 Consensus size: 98
34594 ATTATATCCC
* * **
34604 TTTTTTTCAAATATTTTTTCTAAATTGCCATTATTAAAATATTTTAATTATGTCATTATTAAAAT
1 TTTTTTTCAAATATATTTTCTAAATTGCCATTATTAAAATATTTTAACTATACCATTATTAAAAT
34669 ATAATTTTATGTA-TTTTTTTCCGATTGTACTA
66 ATAATTTTATGTACTTTTTTTCCGATTGTACTA
*
34701 TTTTTTTCAAATATATTTT-TAAATTGTCATTATTAAAATATACTTTAACTATACCATTATTAAA
1 TTTTTTTCAAATATATTTTCTAAATTGCCATTATTAAAATAT--TTTAACTATACCATTATTAAA
*
34765 ATATAATTTTGTGTACTTTTTTTC
64 ATATAATTTTATGTACTTTTTTTC
34789 AAATATATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
96 21 0.27
97 18 0.23
98 32 0.41
99 8 0.10
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (98 bp):
TTTTTTTCAAATATATTTTCTAAATTGCCATTATTAAAATATTTTAACTATACCATTATTAAAAT
ATAATTTTATGTACTTTTTTTCCGATTGTACTA
Found at i:35985 original size:332 final size:331
Alignment explanation
Indices: 34830--36006 Score: 1322
Period size: 332 Copynumber: 3.6 Consensus size: 331
34820 AATATAATTT
* *
34830 TTTAATTAGAAATTAATTCAGAAAAAGGTAGGAAAAGC-GATATTAGAAGC--GAAAGAAGCCCT
1 TTTAATTAGAAATTAATTCGGAAAAA-ATAGGAAAA-CAGATATTAGAAGCGTGAAA-AA-CCCT
* * * * * * *
34892 TCATTCTTTTTGACGTCGAGTTATATATTTTTTATTAGTATTGTGGCCCAAAATTGAGGAGAAAT
62 TCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAAT
* * *** * *
34957 T-TCTCGGGTCAA-TTTTGCAAAATTTTATTTGAAATCGTGCACTAACCATCACGGTTTTTGATT
127 TCTTTCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACT
* * * * *
35020 AAAAACGCGTTCTGGAGCCCCGGCTCAGTTTTGCACGATTTTTAGCG-CAAGTGTCATTGAAATA
192 AAAAACGCTTTCAGG-GTCCCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATA
* *
35084 TCTATATCCATCTAACCAAATCTTACCCACATTGGATTTAAGGATTTGTTTTTACAAGCATATGA
256 TCTATATCCATCTAA-CAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATATGA
35149 ATCATGTTTCAA
320 ATCATGTTTCAA
* * * * * *
35161 TTCAATTAGGAATTAATTTGGAAAAAATAGGAAAA-ACGATATTAGAAGCGTGAATAGCCTTTCA
1 TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAACA-GATATTAGAAGCGTGAAAAACCCTTCA
* *
35225 ATCTTTTTTGTGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAATTCT
65 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCT
*
35289 TTCGGGTCAATTTTT-ACAAAATTTTAGCCGAAATCGTGTA-T-----T-ACGGTTTTTGGCTAA
130 TTCGGGTCAATTTTTGA-AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAA
* * * *
35346 AAACG-TGTTCCGAGGTCCCGGCTCAGTTTTACATGATTTTTAGCGCCAAGACTCATTAAAATAT
194 AAACGCT-TTCAG-GGTCCCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATAT
** ** * *
35410 CTATATTTATCTAACGAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTCAA
257 CTATATCCATCTAAC-AAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATATGAA
* *
35475 TTC-GGTTTCGA
321 -TCATGTTTCAA
* * * *
35486 TTTAATTAG-AATTAATTCGTG-AAAAATAGAAAAAAAAACA-ATATTAGAAGCATGAGAAGCCC
1 TTTAATTAGAAATTAATTCG-GAAAAAATAG----GAAAACAGATATTAGAAGCGTGAAAAACCC
* * * **
35548 TTCAATCTTTTTGGCGTTGAATTATATATTATTTATGAATATGGTGGCCGGAAATTGAGGAGAAA
61 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAA
* * * **
35613 -TGTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAATTTTTGAC
126 TTCTTTCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGAC
* * *
35677 TAAAAACGCCTTTCAGGGTCCCTGCTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAAT
191 TAAAAACG-CTTTCAGGGTCCCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAAT
* * *
35742 ATCTTATATCCATCTAATCAAATCTCAACCACATTGGATTTAAAGATTT-TTTTTACGAGCATTT
255 ATC-TATATCCATCTAA-CAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATAT
35806 GAATCATGTTTCAA
318 GAATCATGTTTCAA
* *
35820 TTTAATTAGAAATTAATTTGGAAAAAATAGGAAAACAGATATTAGAAGCGTGAAAAACCTTTCAA
1 TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAACAGATATTAGAAGCGTGAAAAACCCTTCAA
* * * * * *
35885 TATTTTTGGCGTTTAATTATATATTGTTTATGGGTATCGTGGCAAAAAATTTAGGA-AAATTCTT
66 TCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTT
* * * *
35949 TCGGGTAAATTTTTGAAAAATTTTAACCGGAATCGTGTATTAACCATCACGGTTTTTG
131 TCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
36007 GTAACAAAAG
Statistics
Matches: 706, Mismatches: 104, Indels: 71
0.80 0.12 0.08
Matches are distributed among these distances:
324 68 0.10
325 88 0.12
326 2 0.00
327 111 0.16
328 8 0.01
329 6 0.01
330 85 0.12
331 55 0.08
332 125 0.18
333 3 0.00
334 94 0.13
335 59 0.08
336 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAACAGATATTAGAAGCGTGAAAAACCCTTCAA
TCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAGAAATTCTT
TCGGGTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAA
ACGCTTTCAGGGTCCCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGTCTCATTGAAATATCTAT
ATCCATCTAACAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATATGAATCATG
TTTCAA
Found at i:36240 original size:132 final size:134
Alignment explanation
Indices: 36000--36265 Score: 464
Period size: 132 Copynumber: 2.0 Consensus size: 134
35990 AACCATCACG
* *
36000 GTTTTTGGTAACAAAAGGACAATGATAAAATGAAACATATAAAAAAAATGTTGTATAGAAAGGAG
1 GTTTTTGGTAACAAAAGGACAATGACAAAATGAAACATATAAAAAAAATGTTGTATAGAAAGAAG
*
36065 TTATACTTTCGTAGCCTGTTGCGTTTCAATAATGAGATGCGTTAATTTATAATTAATTTCATATA
66 TTATACTTTCGTAGCCTGTTGCATTTCAATAATGAGATGCGTTAATTTATAATTAATTTCATATA
36130 TATT
131 TATT
36134 GTTTTTGGTAAC-AAAGGACAATGACAAAATGAAACATAT-AAAAAAATGTTGTATAGAAAGAAG
1 GTTTTTGGTAACAAAAGGACAATGACAAAATGAAACATATAAAAAAAATGTTGTATAGAAAGAAG
* * *
36197 TTATACTTTCGTAGCCTGTTGCATTTCAATAATGAGTTTCGTTAATTTATAATTAGTTTCATATA
66 TTATACTTTCGTAGCCTGTTGCATTTCAATAATGAGATGCGTTAATTTATAATTAATTTCATATA
36262 TATT
131 TATT
36266 TAATACTTAA
Statistics
Matches: 126, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
132 88 0.70
133 26 0.21
134 12 0.10
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (134 bp):
GTTTTTGGTAACAAAAGGACAATGACAAAATGAAACATATAAAAAAAATGTTGTATAGAAAGAAG
TTATACTTTCGTAGCCTGTTGCATTTCAATAATGAGATGCGTTAATTTATAATTAATTTCATATA
TATT
Found at i:36784 original size:24 final size:24
Alignment explanation
Indices: 36757--36805 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
36747 AACACACGTG
*
36757 AAAACTAACACTATGTAGGGAACT
1 AAAACTAAAACTATGTAGGGAACT
36781 AAAACTAAAACTATGTAGGGAACT
1 AAAACTAAAACTATGTAGGGAACT
36805 A
1 A
36806 TGGCGGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.20
Consensus pattern (24 bp):
AAAACTAAAACTATGTAGGGAACT
Found at i:41754 original size:22 final size:21
Alignment explanation
Indices: 41698--42371 Score: 195
Period size: 22 Copynumber: 29.9 Consensus size: 21
41688 GTCTCTATGT
**
41698 GGTTATCAAAATTTCATAAAA
1 GGTTATCAAAATTTCATAGGA
* * *
41719 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
41742 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
41764 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
41786 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
41808 GGTTACCAAAATTTTATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
41832 GGTTATTAAAATTTCTTAGGTT
1 GGTTATCAAAATTTCATAGG-A
**
41854 GGTTATTGAAATTTCATAGG-
1 GGTTATCAAAATTTCATAGGA
* * *
41874 GTGATTAATTTTCACAATTTTATAGAAA
1 G-G-TT-A---TCAAAATTTCATAG-GA
41902 GGTTATCAAAGAGATTATCATAGTGA
1 GGTTATC-AA-A-ATT-TCATAG-GA
*
41928 GGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAA-AATTTCATAG-GA
* *
41950 GGTTAACAAAATTACATTAGGA
1 GGTTATCAAAATTTCA-TAGGA
* *
41972 GGTTA-CTAATATTTCATGGGGA
1 GGTTATC-AAAATTTCAT-AGGA
* *
41994 GGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
42016 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GGA
**
42038 GGCTATAAAAGTCTCAATTTCATA--A
1 GG-T-T---A-TCAAAATTTCATAGGA
* * * *
42063 GGAGTACCAAAATTTAATAGAA
1 GG-TTATCAAAATTTCATAGGA
* *
42085 GGTTAT-TAAATCTCATA-GA
1 GGTTATCAAAATTTCATAGGA
*
42104 GTGATTATCGAAATTTCATAGAGATTA
1 G-G-TTATCAAAATTTCATAG-G---A
*
42131 GATTATCAAAATTT-ATAGGAA
1 GGTTATCAAAATTTCATAGG-A
* *
42152 GATTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
42174 GATTATCAAAATTTCA-GGGT
1 GGTTATCAAAATTTCATAGGA
42194 GTGATTA-CTAACAATTGATCATATGGA
1 G-G-TTATC-AA-AATT--TCATA-GGA
* * * *
42221 GGTTTTTAAATTTTCATAACGTA
1 GGTTATCAAAATTTCAT-A-GGA
* *
42244 -GTTATCAATATATCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* * *
42265 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATTTCATAG-G-A
* *
42288 GGTTATCAAAAGTTCATTGGGA
1 GGTTATCAAAATTTCA-TAGGA
* *
42310 AGTTATCAAAATTTCATATTGA
1 GGTTATCAAAATTTCATA-GGA
* *
42332 GGTCT-TCAAAATTACTTAGGGA
1 GGT-TATCAAAATTTCATA-GGA
42354 GGTTAAT-AAAATTTCATA
1 GGTT-ATCAAAATTTCATA
42372 AGAATGTTAA
Statistics
Matches: 484, Mismatches: 106, Indels: 124
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.00
20 22 0.05
21 38 0.08
22 279 0.58
23 41 0.08
24 33 0.07
25 25 0.05
26 25 0.05
27 7 0.01
28 12 0.02
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:44274 original size:15 final size:15
Alignment explanation
Indices: 44254--44283 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44244 ATCAGGCTGC
*
44254 CACGATACACGATAT
1 CACGATACACAATAT
44269 CACGATACACAATAT
1 CACGATACACAATAT
44284 TTCAACCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:45647 original size:2 final size:2
Alignment explanation
Indices: 45640--45678 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45630 AAGGAAAGTG
45640 TA TA TA TA TA 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 TA TA TA TA TA T
45679 GACTAACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51118 original size:2 final size:2
Alignment explanation
Indices: 51111--51145 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51101 AAGGAAAGTG
51111 TA TA TA 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 TA TA TA T
51146 GACTAACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.