Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013537.1 Corchorus capsularis cultivar CVL-1 contig13558, 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: 115346
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2586 original size:22 final size:22
Alignment explanation
Indices: 2549--2622 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
2539 TTTGAGGTTA
*
2549 TCAAAA-TTCATTGTGTTGTTAC
1 TCAAAATTTTATTGTGTTGTT-C
*
2571 T-AAAATTTTATTGTGTGGTTC
1 TCAAAATTTTATTGTGTTGTTC
* *
2592 TCAAAATTTT-TT-AG-TGTTA
1 TCAAAATTTTATTGTGTTGTTC
2611 TCAAAATTTTAT
1 TCAAAATTTTAT
2623 AATGAGGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 13 0.30
20 2 0.05
21 8 0.18
22 21 0.48
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (22 bp):
TCAAAATTTTATTGTGTTGTTC
Found at i:2747 original size:27 final size:27
Alignment explanation
Indices: 2700--2753 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2690 GGATATTATC
*
2700 AAAATCTCATAAGGAGGTTATTAAAAT
1 AAAATCTCATAAGGAGGTTATCAAAAT
* **
2727 AAAATTTCATAAGGATTTTATCAAAAT
1 AAAATCTCATAAGGAGGTTATCAAAAT
2754 TTCATATGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAATCTCATAAGGAGGTTATCAAAAT
Found at i:2755 original size:22 final size:22
Alignment explanation
Indices: 2674--2786 Score: 77
Period size: 23 Copynumber: 4.9 Consensus size: 22
2664 TATAGAGTAG
* * *
2674 TTATCACAATTTCAT-GGGATA
1 TTATCAAAATTTCATAAGGATT
*
2695 TTATCAAAATCTCATAAGGAGGTT
1 TTATCAAAATTTCATAAGGA--TT
2719 ATTAAAAT-AAAATTTCATAAGGATT
1 -TT---ATCAAAATTTCATAAGGATT
* **
2744 TTATCAAAATTTCATATGGGAGG
1 TTATCAAAATTTCATA-AGGATT
*
2767 TTATCAAATTTTCATAAGGA
1 TTATCAAAATTTCATAAGGA
2787 GGTGTTAATG
Statistics
Matches: 73, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
21 15 0.21
22 17 0.23
23 18 0.25
24 3 0.04
25 4 0.05
27 14 0.19
28 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGATT
Found at i:2787 original size:22 final size:22
Alignment explanation
Indices: 2607--2789 Score: 81
Period size: 22 Copynumber: 8.1 Consensus size: 22
2597 ATTTTTTAGT
*
2607 GTTATCAAAATTTT-ATAATGAG
1 GTTATC-AAATTTTCATAAGGAG
* *
2629 GTTACCAAAATTTCAT-AGGTAG
1 GTTATCAAATTTTCATAAGG-AG
* * *
2651 GATATTAAAATTTT-ATAGAGTA-
1 GTTA-TCAAATTTTCATA-AGGAG
* *
2673 GTTATCACAA-TTTCAT-GGGAT
1 GTTATCA-AATTTTCATAAGGAG
* * *
2694 ATTATCAAAATCTCATAAGGAG
1 GTTATCAAATTTTCATAAGGAG
* *
2716 GTTATTAAAATAAAATTTCATAAGGAT
1 GTTA-TCAAAT----TTTCATAAGGAG
* * *
2743 TTTATCAAAATTTCATATGGGAG
1 GTTATCAAATTTTCATA-AGGAG
2766 GTTATCAAATTTTCATAAGGAG
1 GTTATCAAATTTTCATAAGGAG
2788 GT
1 GT
2790 GTTAATGGTC
Statistics
Matches: 116, Mismatches: 29, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
20 4 0.03
21 24 0.21
22 40 0.34
23 29 0.25
24 2 0.02
26 4 0.03
27 13 0.11
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATCAAATTTTCATAAGGAG
Found at i:7176 original size:31 final size:31
Alignment explanation
Indices: 7089--7164 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
7079 GTATCCGACT
* *
7089 TGGCATGCCACGTGGATCAAAAAGTAACACA
1 TGGCACGCCACGTGGATCAAAAAGTGACACA
* **
7120 TGGCAGGCCACGTGGATCAAAAAGTGACATG
1 TGGCACGCCACGTGGATCAAAAAGTGACACA
7151 TGGCACGCCACGTG
1 TGGCACGCCACGTG
7165 TGCCAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.29, T:0.16
Consensus pattern (31 bp):
TGGCACGCCACGTGGATCAAAAAGTGACACA
Found at i:7177 original size:24 final size:24
Alignment explanation
Indices: 7150--7200 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
7140 AAAGTGACAT
* *
7150 GTGGCACGCCACGTGTGCCAAAAA
1 GTGGCACGCCACATGTACCAAAAA
*
7174 GTGGCACGTCACATGTACCAAAAA
1 GTGGCACGCCACATGTACCAAAAA
7198 GTG
1 GTG
7201 ATACGTGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.16
Consensus pattern (24 bp):
GTGGCACGCCACATGTACCAAAAA
Found at i:7910 original size:12 final size:12
Alignment explanation
Indices: 7893--7918 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7883 GGGAAGAGAC
7893 TATTTTAATTTA
1 TATTTTAATTTA
7905 TATTTTAATTTA
1 TATTTTAATTTA
7917 TA
1 TA
7919 AGTTGGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTTAATTTA
Found at i:11267 original size:140 final size:139
Alignment explanation
Indices: 11119--11431 Score: 484
Period size: 140 Copynumber: 2.2 Consensus size: 139
11109 AAGTTAGTGA
* * *
11119 TCGTTAGTTAATTTTGTCAATCAAAGTCGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAACTTTACCATAAAAT
*
11183 CGCTACCAAAAAAACTAACATAAAGAAATAAATTAATTAGTAATTATGTTACCAAAAATATAAAT
66 CGCCACCAAAAAAACTAACATAAA-AAATAAATTAATTAGTAATTATGTTACCAAAAA-ATAAAT
11248 TATTGAACATG
129 TATTGAACATG
* *
11259 TCGTTAGTTAATTTTGTTAATCAAAGTTGTAATTGATTGATGATTATATAACTTTACCATAAAAT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAACTTTACCATAAAAT
* * * *
11324 CGCCACCAAAAAAATTACCATAAAAAATAAATTAATTAGTAATTGTGTTACCAAAAAATAAATTT
66 CGCCACCAAAAAAACTAACATAAAAAATAAATTAATTAGTAATTATGTTACCAAAAAATAAATTA
*
11389 TTGAATATG
131 TTGAACATG
* *
11398 TCATTAGTTAATTTTGCCAATCAAAGTTGTAATT
1 TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATT
11432 AGATAATCCA
Statistics
Matches: 158, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
139 46 0.29
140 87 0.55
141 25 0.16
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (139 bp):
TCGTTAGTTAATTTTGTCAATCAAAGTTGTAATTGATTGATAATTATATAACTTTACCATAAAAT
CGCCACCAAAAAAACTAACATAAAAAATAAATTAATTAGTAATTATGTTACCAAAAAATAAATTA
TTGAACATG
Found at i:18962 original size:54 final size:54
Alignment explanation
Indices: 18898--19008 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
18888 TCCCTAGTAA
*
18898 AAATCCCAATTAAAACCAGGTTCAACCCCAAATCAACAACAAATAATTATATAT
1 AAATCCCAATTAAAACCAGATTCAACCCCAAATCAACAACAAATAATTATATAT
*
18952 AAATCCCAATTAAAACCAGATTTAACCCCAAATCAACAACAAATAATTATATAT
1 AAATCCCAATTAAAACCAGATTCAACCCCAAATCAACAACAAATAATTATATAT
19006 AAA
1 AAA
19009 GATTATTCCT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.23
Consensus pattern (54 bp):
AAATCCCAATTAAAACCAGATTCAACCCCAAATCAACAACAAATAATTATATAT
Found at i:19119 original size:68 final size:68
Alignment explanation
Indices: 19039--19174 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
19029 ACATTCCCCA
*
19039 TAGGGTTTTAGAATGAAAATATAAAATTTAAATTTAACTAGGCAAATAAGGAATAACATTAAAAA
1 TAGGGTTTTAGAATGAAAATATAAAATTTAAATTTAACTAGGCAAATAAGAAATAACATTAAAAA
19104 CTG
66 CTG
19107 TAGGGTTTTAGAATGAAAATATAAAATTTAAATTTAACTAGGCAAATAAGAAATAACATTAAAAA
1 TAGGGTTTTAGAATGAAAATATAAAATTTAAATTTAACTAGGCAAATAAGAAATAACATTAAAAA
19172 CTG
66 CTG
19175 AAAAAGGACA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (68 bp):
TAGGGTTTTAGAATGAAAATATAAAATTTAAATTTAACTAGGCAAATAAGAAATAACATTAAAAA
CTG
Found at i:23986 original size:14 final size:14
Alignment explanation
Indices: 23964--23993 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23954 GTCCTCATTA
23964 TTATATTGCTCTGC
1 TTATATTGCTCTGC
*
23978 TTATGTTGCTCTGC
1 TTATATTGCTCTGC
23992 TT
1 TT
23994 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.53
Consensus pattern (14 bp):
TTATATTGCTCTGC
Found at i:36387 original size:24 final size:24
Alignment explanation
Indices: 36360--36414 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
36350 AATATAATTA
*
36360 TTGGGAGAGACCAAGTAGCGATTT
1 TTGGGAGAGACCAAGTACCGATTT
* *
36384 TTGGGTGATAGACCAATTACCGATTT
1 TT-GG-GAGAGACCAAGTACCGATTT
36410 TTGGG
1 TTGGG
36415 TGATGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 4 0.15
26 19 0.73
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (24 bp):
TTGGGAGAGACCAAGTACCGATTT
Found at i:36397 original size:26 final size:26
Alignment explanation
Indices: 36367--36418 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
36357 TTATTGGGAG
*
36367 AGACCAAGTAGCGATTTTTGGGTGAT
1 AGACCAAGTACCGATTTTTGGGTGAT
*
36393 AGACCAATTACCGATTTTTGGGTGAT
1 AGACCAAGTACCGATTTTTGGGTGAT
36419 GGAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (26 bp):
AGACCAAGTACCGATTTTTGGGTGAT
Found at i:36933 original size:34 final size:34
Alignment explanation
Indices: 36890--36958 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
36880 CCAAGCCAAG
36890 GGAAATCCTCCAGCCATAAGGATGGATGTTCGAT
1 GGAAATCCTCCAGCCATAAGGATGGATGTTCGAT
36924 GGAAATCCTCCAGCCATAAGGATGGATGTTCGAT
1 GGAAATCCTCCAGCCATAAGGATGGATGTTCGAT
36958 G
1 G
36959 CCCAGTAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (34 bp):
GGAAATCCTCCAGCCATAAGGATGGATGTTCGAT
Found at i:37912 original size:19 final size:19
Alignment explanation
Indices: 37888--37927 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
37878 TTGCCCCTCT
37888 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAG
* *
37907 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCCCCCACTAAG
37926 TC
1 TC
37928 AAGATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAG
Found at i:38377 original size:31 final size:31
Alignment explanation
Indices: 38337--38479 Score: 153
Period size: 31 Copynumber: 4.6 Consensus size: 31
38327 ACGTGACATG
* *
38337 CCACATGTACCAAAAGGTGACATGTGACACA
1 CCACGTGTACCAAAAAGTGACATGTGACACA
* * *
38368 CCATGTGTACCAAAAAGTGATATGTGGCACA
1 CCACGTGTACCAAAAAGTGACATGTGACACA
* *
38399 CTACGTGTACCAAAAAGTGACATGTGGCA-A
1 CCACGTGTACCAAAAAGTGACATGTGACACA
* ** *
38429 CGCTACGTGTATCAAAAAGTGACACATGTCACA
1 C-C-ACGTGTACCAAAAAGTGACATGTGACACA
*
38462 CCACGTGTACGAAAAAGT
1 CCACGTGTACCAAAAAGT
38480 AACACGTGGC
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
30 2 0.02
31 66 0.70
32 24 0.26
33 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (31 bp):
CCACGTGTACCAAAAAGTGACATGTGACACA
Found at i:38450 original size:63 final size:62
Alignment explanation
Indices: 38337--38490 Score: 166
Period size: 63 Copynumber: 2.5 Consensus size: 62
38327 ACGTGACATG
* * * * * **
38337 CCACATGTACCAAAAGGTGACATGTGACACACCATGTGTACCAAAAAGTGATATGTGGCACA
1 CCACGTGTACCAAAAAGTGACATGTGGCACACCACGTGTACCAAAAAGTGACACATGGCACA
* * *
38399 CTACGTGTACCAAAAAGTGACATGTGGCA-ACGCTACGTGTATCAAAAAGTGACACATGTCACA
1 CCACGTGTACCAAAAAGTGACATGTGGCACAC-C-ACGTGTACCAAAAAGTGACACATGGCACA
* * *
38462 CCACGTGTACGAAAAAGTAACACGTGGCA
1 CCACGTGTACCAAAAAGTGACATGTGGCA
38491 TGCCACATGT
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
61 2 0.03
62 26 0.34
63 48 0.63
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (62 bp):
CCACGTGTACCAAAAAGTGACATGTGGCACACCACGTGTACCAAAAAGTGACACATGGCACA
Found at i:38509 original size:63 final size:62
Alignment explanation
Indices: 38395--38515 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
38385 TGATATGTGG
* * * * *
38395 CACACTACGTGTACCAAAAAGTGACATGTGGCAACGCTACGTGTATCAAAAAGTGACACATGT
1 CACACCACGTGTACCAAAAAGTAACACGTGGCAACGCCACATGTATCAAAAA-TGACACATGT
* * *
38458 CACACCACGTGTACGAAAAAGTAACACGTGGC-ATGCCACATGTTTCAAAAAATGACAC
1 CACACCACGTGTACCAAAAAGTAACACGTGGCAACGCCACATGTATC-AAAAATGACAC
38516 GTGGCATGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 16 0.33
63 33 0.67
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (62 bp):
CACACCACGTGTACCAAAAAGTAACACGTGGCAACGCCACATGTATCAAAAATGACACATGT
Found at i:38546 original size:28 final size:29
Alignment explanation
Indices: 38481--38546 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
38471 CGAAAAAGTA
*
38481 ACACGTGGCATGCCACATGTTTCAAAAAATG
1 ACACGTGGCATGCCACATG--TCAAAAAAGG
*
38512 ACACGTGGCATGCCACATG-CACAAAAGG
1 ACACGTGGCATGCCACATGTCAAAAAAGG
*
38540 ATACGTG
1 ACACGTG
38547 CCACGTGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.41
31 19 0.59
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (29 bp):
ACACGTGGCATGCCACATGTCAAAAAAGG
Found at i:39011 original size:10 final size:10
Alignment explanation
Indices: 38989--39027 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
38979 AAATCTCGAT
*
38989 ATATCCGTAA
1 ATATCCATAA
38999 ATATCCATAA
1 ATATCCATAA
*
39009 ATATCCGTAA
1 ATATCCATAA
39019 ATATCCATA
1 ATATCCATA
39028 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:39012 original size:20 final size:20
Alignment explanation
Indices: 38989--39027 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
38979 AAATCTCGAT
38989 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
39009 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
39028 TTAAATTAAA
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:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:40060 original size:12 final size:12
Alignment explanation
Indices: 40043--40097 Score: 101
Period size: 12 Copynumber: 4.5 Consensus size: 12
40033 CATCGATACC
40043 TCGATATATCCG
1 TCGATATATCCG
40055 TCGATATATCCG
1 TCGATATATCCG
40067 TCGATATATCCG
1 TCGATATATCCG
40079 TTCGATATATCCG
1 -TCGATATATCCG
40092 TCGATA
1 TCGATA
40098 CCTGTATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:40089 original size:25 final size:24
Alignment explanation
Indices: 40043--40097 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
40033 CATCGATACC
40043 TCGATATATCCGTCGATATATCCG
1 TCGATATATCCGTCGATATATCCG
40067 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCG-TCGATATATCCG
40092 TCGATA
1 TCGATA
40098 CCTGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (24 bp):
TCGATATATCCGTCGATATATCCG
Found at i:55424 original size:17 final size:17
Alignment explanation
Indices: 55381--55424 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
55371 AAATGATATT
*
55381 TTTATAATTAAAAGGAA
1 TTTATAATTTAAAGGAA
**
55398 -TTATTTTTTAAAGGAA
1 TTTATAATTTAAAGGAA
55414 TTTATAATTTA
1 TTTATAATTTA
55425 TTAAAAGGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
TTTATAATTTAAAGGAA
Found at i:56339 original size:22 final size:22
Alignment explanation
Indices: 56289--56364 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
56279 TGATAACTAC
*
56289 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
** *
56311 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCACTATG
* * *
56333 AAATTTTGTTAATCTTC-CTATA
1 AAATTTTGATAA-CCTCACTATG
56355 AAATTTTGAT
1 AAATTTTGAT
56365 CTACATATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 39 0.93
23 3 0.07
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:61344 original size:25 final size:25
Alignment explanation
Indices: 61315--61369 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
61305 TTTTGTACAT
61315 GTGGCGTGTGGACAAAAAATGACAC
1 GTGGCGTGTGGACAAAAAATGACAC
61340 GTGGCGTGTGGACAAAAAATGACAC
1 GTGGCGTGTGGACAAAAAATGACAC
61365 GTGGC
1 GTGGC
61370 ATGTATCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (25 bp):
GTGGCGTGTGGACAAAAAATGACAC
Found at i:81415 original size:20 final size:21
Alignment explanation
Indices: 81390--81449 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 21
81380 TCATAGCTGG
81390 TATATAT-ATGAGATTACTAC
1 TATATATAATGAGATTACTAC
*
81410 TATATATAATGAGACAATACTAC
1 TATATATAATGAG--ATTACTAC
81433 TATATATAATGAGATTA
1 TATATATAATGAGATTA
81450 ATCTTTATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.20
21 8 0.23
23 20 0.57
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (21 bp):
TATATATAATGAGATTACTAC
Found at i:88527 original size:31 final size:31
Alignment explanation
Indices: 88463--88598 Score: 166
Period size: 31 Copynumber: 4.4 Consensus size: 31
88453 TTTGTGCACA
* * ** *
88463 TGGCATGCCACGTGCCA-TTTTTGAAACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
*
88493 TGGCATGCCACGTGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
* * * *
88524 TGGCGTGACATGTGTCACTTTTTTGTACATG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
*
88555 TGGCGTGCCACATGTCACTTTTTGGTACACG
1 TGGCGTGCCACGTGTCACTTTTTGGTACACG
88586 TGGCGTGCCACGT
1 TGGCGTGCCACGT
88599 CAGACACCGT
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 16 0.18
31 74 0.82
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (31 bp):
TGGCGTGCCACGTGTCACTTTTTGGTACACG
Found at i:93659 original size:14 final size:14
Alignment explanation
Indices: 93640--93670 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
93630 TTTTTTTTGG
93640 GGGGGGGGGGGGAT
1 GGGGGGGGGGGGAT
*
93654 GGGGGGGGGGGGTT
1 GGGGGGGGGGGGAT
93668 GGG
1 GGG
93671 TGAGGTGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.87, T:0.10
Consensus pattern (14 bp):
GGGGGGGGGGGGAT
Found at i:110138 original size:2 final size:2
Alignment explanation
Indices: 110131--110157 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110121 ACATTAAGAC
110131 AT 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 AT A
110158 CCCTAAACAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.