Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006931.1 Corchorus capsularis cultivar CVL-1 contig06952, 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: 54441
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:579 original size:2 final size:2
Alignment explanation
Indices: 572--601 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
562 TAACATTTAG
572 TA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
602 TATTTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6499 original size:2 final size:2
Alignment explanation
Indices: 6492--6528 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
6482 GAAGTTACGG
6492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
6529 ATAACTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7882 original size:15 final size:16
Alignment explanation
Indices: 7862--7892 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
7852 GTTAAACTTC
7862 ATTATATGAA-AAATA
1 ATTATATGAATAAATA
7877 ATTATATGAATAAATA
1 ATTATATGAATAAATA
7893 CTAAATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTATATGAATAAATA
Found at i:8782 original size:2 final size:2
Alignment explanation
Indices: 8771--8801 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8761 TATAATTAGA
8771 AT AT AT -T 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
8802 GATAGGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9470 original size:31 final size:31
Alignment explanation
Indices: 9415--9509 Score: 90
Period size: 33 Copynumber: 3.1 Consensus size: 31
9405 GAATTTAATA
*
9415 TATATAACTTTAAGAA-TTAA-ATATAACGT
1 TATATAACATTAAGAATTTAATATATAACGT
9444 TATATAACATTAAGAATTTAATATATATAACGT
1 TATATAACATTAAGAATTT-A-ATATATAACGT
* * *
9477 TAAAAATAA-A-TAAAAATTAAATATATAACGT
1 T--ATATAACATTAAGAATTTAATATATAACGT
9508 TA
1 TA
9510 AAATATAACG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
29 16 0.29
30 2 0.04
31 13 0.23
32 2 0.04
33 17 0.30
34 1 0.02
35 5 0.09
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (31 bp):
TATATAACATTAAGAATTTAATATATAACGT
Found at i:9479 original size:23 final size:23
Alignment explanation
Indices: 9395--9488 Score: 82
Period size: 23 Copynumber: 3.9 Consensus size: 23
9385 AACCCTAAAC
*
9395 ATAACGTTAAGAATTTAATATAT
1 ATAACGTTAAGAATTAAATATAT
*
9418 ATAACTTTAAGAATTAAATATAACGTTAT
1 ATAACGTTAAGAATT-AA-AT-A---TAT
* *
9447 ATAACATTAAGAATTTAATATAT
1 ATAACGTTAAGAATTAAATATAT
*
9470 ATAACGTTAA-AAATAAATA
1 ATAACGTTAAGAATTAAATA
9489 AAAATTAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
22 7 0.12
23 26 0.45
24 1 0.02
25 2 0.03
26 2 0.03
27 2 0.03
28 1 0.02
29 17 0.29
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.36
Consensus pattern (23 bp):
ATAACGTTAAGAATTAAATATAT
Found at i:9501 original size:52 final size:54
Alignment explanation
Indices: 9390--9501 Score: 142
Period size: 52 Copynumber: 2.1 Consensus size: 54
9380 GACATAACCC
* * * * **
9390 TAAACATAACGTTAAGAATTTAATATATATAACTTTAAGAATTAAATATAACGT
1 TAAATATAACATTAAGAATTTAATATATATAACGTTAAGAAATAAATATAAAAT
9444 T--ATATAACATTAAGAATTTAATATATATAACGTTAA-AAATAAATA-AAAAT
1 TAAATATAACATTAAGAATTTAATATATATAACGTTAAGAAATAAATATAAAAT
9494 TAAATATA
1 TAAATATA
9502 TAACGTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
50 4 0.08
51 8 0.16
52 37 0.74
54 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (54 bp):
TAAATATAACATTAAGAATTTAATATATATAACGTTAAGAAATAAATATAAAAT
Found at i:9513 original size:15 final size:15
Alignment explanation
Indices: 9461--9516 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
9451 CATTAAGAAT
*
9461 TTAATATATATAACG
1 TTAAAATATATAACG
* **
9476 TTAAAAATAAATAAAAA
1 TT-AAAATATAT-AACG
9493 TT-AAATATATAACG
1 TTAAAATATATAACG
9507 TTAAAATATA
1 TTAAAATATA
9517 ACGTTAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 4 0.13
15 16 0.52
16 7 0.23
17 4 0.13
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (15 bp):
TTAAAATATATAACG
Found at i:9517 original size:13 final size:14
Alignment explanation
Indices: 9461--9522 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 14
9451 CATTAAGAAT
9461 TTAATATATATAACG
1 TTAA-ATATATAACG
* **
9476 TTAAAAATAAATAAAAA
1 TT--AAATATAT-AACG
9493 TTAAATATATAACG
1 TTAAATATATAACG
9507 TTAAA-ATATAACG
1 TTAAATATATAACG
9520 TTA
1 TTA
9523 GAATTTAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
13 11 0.29
14 7 0.18
15 9 0.24
16 5 0.13
17 6 0.16
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (14 bp):
TTAAATATATAACG
Found at i:10927 original size:79 final size:79
Alignment explanation
Indices: 10796--10954 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
10786 ATACTTTTTA
10796 ACATAGTATATATATACTTTTTAATATAGTATAGATAAAAAAACAAGCGAAAGATCATCATGTTA
1 ACATAGTATATATATACTTTTTAATATAGTATAGATAAAAAAACAAGCGAAAGATCATCATGTTA
10861 TTTATTTATATGTT
66 TTTATTTATATGTT
10875 ACATAGTATATATATACTTTTTAATATAGTATAGATAAAAAAACAAGCGAAAGATCATCATGTTA
1 ACATAGTATATATATACTTTTTAATATAGTATAGATAAAAAAACAAGCGAAAGATCATCATGTTA
10940 TTTATTTATATGTT
66 TTTATTTATATGTT
10954 A
1 A
10955 AAGGAAAAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (79 bp):
ACATAGTATATATATACTTTTTAATATAGTATAGATAAAAAAACAAGCGAAAGATCATCATGTTA
TTTATTTATATGTT
Found at i:18937 original size:9 final size:9
Alignment explanation
Indices: 18923--18957 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
18913 CTCAGTCTGA
18923 CTCCTTTCT
1 CTCCTTTCT
18932 CTCCTTTCT
1 CTCCTTTCT
18941 CTCCTTTCT
1 CTCCTTTCT
18950 CTCCTTTC
1 CTCCTTTC
18958 ATTCCCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (9 bp):
CTCCTTTCT
Found at i:21164 original size:17 final size:19
Alignment explanation
Indices: 21127--21169 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
21117 TCAAGGCGCG
21127 GAGGTTGTCACTGGAGAGA
1 GAGGTTGTCACTGGAGAGA
21146 GAGGTTGTCACTGGAGAGA
1 GAGGTTGTCACTGGAGAGA
*
21165 AAGGT
1 GAGGT
21170 GGGAGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.42, T:0.21
Consensus pattern (19 bp):
GAGGTTGTCACTGGAGAGA
Found at i:24041 original size:14 final size:15
Alignment explanation
Indices: 24017--24048 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
24007 TGCACATCAC
24017 TTTAGCAAATAAATA
1 TTTAGCAAATAAATA
24032 TTTA-CAAATAAATA
1 TTTAGCAAATAAATA
24046 TTT
1 TTT
24049 TCATTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTAGCAAATAAATA
Found at i:25430 original size:41 final size:38
Alignment explanation
Indices: 25343--25432 Score: 92
Period size: 41 Copynumber: 2.3 Consensus size: 38
25333 CCGAACCGTT
* *
25343 TAATAATATATATTATTTTTATATAAATATATAATATA
1 TAATAATTTATATTATTTTAATATAAATATATAATATA
* * *
25381 TCAGAATTTATATTAAATTATTAATATAAA-ATATATATTTA
1 TAATAATTTATATT--ATT-TTAATATAAATATATA-ATATA
25422 TAATAATTTAT
1 TAATAATTTAT
25433 TATTTATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
38 11 0.27
40 8 0.20
41 22 0.54
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (38 bp):
TAATAATTTATATTATTTTAATATAAATATATAATATA
Found at i:26300 original size:2 final size:2
Alignment explanation
Indices: 26232--26281 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
26222 TTTTACACAT
*
26232 TA TA TA TA TA TA TA TA -A TGA TGA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA
26275 TA TA TA T
1 TA TA TA T
26282 GTACGTACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.86
3 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:30433 original size:46 final size:46
Alignment explanation
Indices: 30366--30894 Score: 445
Period size: 46 Copynumber: 12.0 Consensus size: 46
30356 GACCGGTTCA
* *
30366 CTTATTCCAGTTTGCCCTTCCCCAACGGAAGGTGTTGTCTAATTGT
1 CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * *
30412 CTTATTCCAGTTTGCCCTT-CCC-CCGGAAGGTATTGCTTAAGTTGC
1 CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA-TTGT
* *
30457 CTTATTCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAATTGT
1 CTTATT-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * * *
30504 CTTATTCCAGTTTGCCCATCCTCATCGGAAGGTGTTGTTTAAAT-T
1 CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * *
30549 C-----CCAATTTGCCCTTCCCCACCGGAAGGTGTTCTTTAGTTG-
1 CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * *
30589 CTTATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAT-T
1 CTTATT-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* *
30635 C-----CCCGTTTGCCCTTCCCCACCGGAAGGTGTTG-TTAGTTG-
1 CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * * *
30674 CTTATTCCCAGTTTGCCCTTACTCATCGGAAGGTGTTGTTTAGTTG-
1 CTTATT-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
* * * * * *
30720 CTTATCCCCAGTTTTCCCTTCCTCATCAGAATGTGTTGTTT-A----
1 CTTAT-TCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
30762 CTT-TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA----
1 CTTATT-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
30804 ---ATTCCAAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTTGT
1 CTTATTCC-AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA--TTGT
* ****
30850 CTTATTCCTGTTTTGCCCTTCCTGGTCGGAAGGTGTTGTTTAATT
1 CTTATTCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATT
30895 TTATCTTGAT
Statistics
Matches: 393, Mismatches: 55, Indels: 69
0.76 0.11 0.13
Matches are distributed among these distances:
39 7 0.02
40 96 0.24
41 30 0.08
42 4 0.01
44 14 0.04
45 41 0.10
46 138 0.35
47 14 0.04
48 16 0.04
49 33 0.08
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (46 bp):
CTTATTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTGT
Found at i:30573 original size:40 final size:40
Alignment explanation
Indices: 30510--30843 Score: 290
Period size: 40 Copynumber: 7.9 Consensus size: 40
30500 TTGTCTTATT
* * *
30510 CCAGTTTGCCCATCCTCATCGGAAGGTGTTGTTTAAATTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTC
* * *
30550 CCAATTTGCCCTTCCCCACCGGAAGGTGTTCTTTAGTTGCTTATTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA------AATTC
* *
30596 CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTC
* **
30636 CCCGTTTGCCCTTCCCCACCGGAAGGTGTTGTTAGTTGCTTATTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTG-T--TT--AAATTC
* * * * *
30681 CCAGTTTGCCCTTACTCATCGGAAGGTGTTGTTTAGTTGCTTATCC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA------AATTC
* * * * * **
30727 CCAGTTTTCCCTTCCTCATCAGAATGTGTTGTTTACTTTTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA-AATTC
30768 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTC
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTC
*
30808 CAAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA
1 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA
30844 TTTTGTCTTA
Statistics
Matches: 240, Mismatches: 37, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
40 100 0.42
41 34 0.14
42 2 0.01
43 2 0.01
44 1 0.00
45 31 0.13
46 70 0.29
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (40 bp):
CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTC
Found at i:30600 original size:86 final size:86
Alignment explanation
Indices: 30460--30892 Score: 497
Period size: 86 Copynumber: 5.0 Consensus size: 86
30450 AAGTTGCCTT
* * * *
30460 ATTCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAATTGTCTTATT-CCAGTTTGCCCATC
1 ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTG-CTTATTCCCAGTTTGCCCTTC
30524 CTCATCGGAAGGTGTTGTTTAA
65 CTCATCGGAAGGTGTTGTTTAA
*
30546 ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTCTTTAGTTGCTTATTCCCAGTTTGCCCTTCC
1 ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCC
30611 TCATCGGAAGGTGTTGTTTAA
66 TCATCGGAAGGTGTTGTTTAA
** *
30632 ATTCCCCGTTTGCCCTTCCCCACCGGAAGGTGTTG-TTAGTTGCTTATTCCCAGTTTGCCCTTAC
1 ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCC
*
30696 TCATCGGAAGGTGTTGTTTAGTTGCTT
66 TCATCGGAAGGTGTTGTTTA------A
* * * * * * *
30723 ATCCCCAGTTTTCCCTTCCTCATCAGAATGTGTTGTTTA----CTT-TTCCCAGTTTGCCCTTCC
1 ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCC
* *
30783 CCACCGGAAGGTGTTGTTTAA
66 TCATCGGAAGGTGTTGTTTAA
* *
30804 ATT-CCAAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTTGTCTTATT-CCTGTTTTGCC
1 ATTCCCAA-TTTGCCCTTCCCCACCGGAAGGTGTTGTTT-A-GTTG-CTTATTCCCAG-TTTGCC
**
30867 CTTCCTGGTCGGAAGGTGTTGTTTAA
61 CTTCCTCATCGGAAGGTGTTGTTTAA
30893 TTTTATCTTG
Statistics
Matches: 296, Mismatches: 33, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
80 3 0.01
81 27 0.09
82 1 0.00
85 54 0.18
86 106 0.36
87 35 0.12
88 9 0.03
89 30 0.10
91 28 0.09
92 3 0.01
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (86 bp):
ATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTGCTTATTCCCAGTTTGCCCTTCC
TCATCGGAAGGTGTTGTTTAA
Found at i:39191 original size:21 final size:21
Alignment explanation
Indices: 39165--39206 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39155 ATCCCTGCAC
*
39165 GAGATCAATCTTCTCGTTTGT
1 GAGATCAACCTTCTCGTTTGT
39186 GAGATCAACCTTCTCGTTTGT
1 GAGATCAACCTTCTCGTTTGT
39207 TGCAATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (21 bp):
GAGATCAACCTTCTCGTTTGT
Found at i:42397 original size:32 final size:33
Alignment explanation
Indices: 42361--42425 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
42351 TTTAAAAAAA
* *
42361 AAGAATATAATTAATA-GGATCAAAGTAAACCT
1 AAGAATACAACTAATATGGATCAAAGTAAACCT
* *
42393 AAGAATACCACTCATATGGATCAAAGTAAACCT
1 AAGAATACAACTAATATGGATCAAAGTAAACCT
42426 CACCTTTGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.23
Consensus pattern (33 bp):
AAGAATACAACTAATATGGATCAAAGTAAACCT
Found at i:47087 original size:320 final size:321
Alignment explanation
Indices: 46504--47148 Score: 1283
Period size: 320 Copynumber: 2.0 Consensus size: 321
46494 GAAGACAATC
46504 GAAAGAAAATCTAAGATATACCACCGTCTACATCAAGCAATACTCTGCCACAAATGACTAAACTG
1 GAAAGAAAATCTAAGATATACCACCGTCTACATCAAGCAATACTCTGCCACAAATGACTAAACTG
46569 GATATTATGTAAACTGGCCAGAAAAAAAAAAACTGTATATATGTAATCCAAAACAACACTATATT
66 GATATTATGTAAACTGGCCAGAAAAAAAAAAACTGTATATATGTAATCCAAAACAACACTATATT
46634 GCGGAAATTCATAGGGAAATAGTTTCAACAAAACCAAGTTGGCAAAAAGAAGAATAACAAGAATT
131 GCGGAAATTCATAGGGAAATAGTTTCAACAAAACCAAGTTGGCAAAAAGAAGAATAACAAGAATT
46699 AAAGAAATCGCATAATGCTTAGGGTGTTGTAGTAACAACTCTCATAGAAAACAATGATTATTATG
196 AAAGAAATCGCATAATGCTTAGGGTGTTGTAGTAACAACTCTCATAGAAAACAATGATTATTATG
46764 AACTTGTTTGTCCAATGTCTTCAACAACGTAGATATTAGGCCTGGCTTTGAAGGAAGAATG
261 AACTTGTTTGTCCAATGTCTTCAACAACGTAGATATTAGGCCTGGCTTTGAAGGAAGAATG
46825 GAAAGAAAATCTAAGATATACCACCGTCTACATCAAGCAATACTCTGCCACAAATGACTAAACTG
1 GAAAGAAAATCTAAGATATACCACCGTCTACATCAAGCAATACTCTGCCACAAATGACTAAACTG
46890 GATATTATGTAAACTGGCCAG-AAAAAAAAAACTGTATATATGTAATCCAAAACAACACTATATT
66 GATATTATGTAAACTGGCCAGAAAAAAAAAAACTGTATATATGTAATCCAAAACAACACTATATT
46954 GCGGAAATTCATAGGGAAATAGTTTCAACAAAACCAAGTTGGCAAAAAGAAGAATAACAAGAATT
131 GCGGAAATTCATAGGGAAATAGTTTCAACAAAACCAAGTTGGCAAAAAGAAGAATAACAAGAATT
47019 AAAGAAATCGCATAATGCTTAGGGTGTTGTAGTAACAACTCTCATAGAAAACAATGATTATTATG
196 AAAGAAATCGCATAATGCTTAGGGTGTTGTAGTAACAACTCTCATAGAAAACAATGATTATTATG
47084 AACTTGTTTGTCCAATGTCTTCAACAACGTAGATATTAGGCCTGGCTTTGAAGGAAGAATG
261 AACTTGTTTGTCCAATGTCTTCAACAACGTAGATATTAGGCCTGGCTTTGAAGGAAGAATG
47145 GAAA
1 GAAA
47149 ATTTTTGGAT
Statistics
Matches: 324, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
320 238 0.73
321 86 0.27
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (321 bp):
GAAAGAAAATCTAAGATATACCACCGTCTACATCAAGCAATACTCTGCCACAAATGACTAAACTG
GATATTATGTAAACTGGCCAGAAAAAAAAAAACTGTATATATGTAATCCAAAACAACACTATATT
GCGGAAATTCATAGGGAAATAGTTTCAACAAAACCAAGTTGGCAAAAAGAAGAATAACAAGAATT
AAAGAAATCGCATAATGCTTAGGGTGTTGTAGTAACAACTCTCATAGAAAACAATGATTATTATG
AACTTGTTTGTCCAATGTCTTCAACAACGTAGATATTAGGCCTGGCTTTGAAGGAAGAATG
Found at i:54017 original size:15 final size:15
Alignment explanation
Indices: 53959--54028 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 15
53949 GACCGATTGA
53959 ATTTATATAAATTAAT
1 ATTTATAT-AATTAAT
53975 ATTATATATATAATATATGAT
1 A-T-T-TATATAAT-TA--AT
* *
53996 ATATATATAATTTAT
1 ATTTATATAATTAAT
*
54011 ATTTATATTATTAAT
1 ATTTATATAATTAAT
54026 ATT
1 ATT
54029 AATAATATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
15 17 0.40
16 1 0.02
17 2 0.05
18 12 0.28
19 7 0.16
20 1 0.02
21 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATTTATATAATTAAT
Done.