Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016332.1 Corchorus capsularis cultivar CVL-1 contig16353, 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: 33724
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Found at i:84 original size:22 final size:21
Alignment explanation
Indices: 15--307 Score: 136
Period size: 22 Copynumber: 13.6 Consensus size: 21
5 TTATGGAAGA
** *
15 TATCAAAATTTCAGGGA-GGA
1 TATCAAAATTTCATAGAGGGT
* ***
35 TATCAAAATTTTATAGTTTAGT
1 TATCAAAATTTCATAG-AGGGT
*
57 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGAGGGT
*
79 TATCAAAATTTCATAGTA-TGT
1 TATCAAAATTTCATAG-AGGGT
*
100 AGATCAAAATTTCATAG-GGAGAT
1 -TATCAAAATTTCATAGAGG-G-T
*
123 TAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGA-G-GGT
** * *
145 TATCAAAAAATCCTAGGGAGGT
1 TATCAAAATTTCATAGAG-GGT
*
167 TATCAAAATTT-GT--A--GT
1 TATCAAAATTTCATAGAGGGT
* *
183 TATCAAGATTTCATAAGAGAGT
1 TATCAAAATTTCAT-AGAGGGT
* *
205 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATA--GAGGGT
* * **
228 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATA-G-AGGGT
*
251 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGAG-GGT
* *
273 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGAG-GGT
295 TATCAAAATTTCA
1 TATCAAAATTTCA
308 GAGTATGATT
Statistics
Matches: 209, Mismatches: 42, Indels: 42
0.71 0.14 0.14
Matches are distributed among these distances:
16 12 0.06
17 1 0.00
20 14 0.07
21 7 0.03
22 134 0.64
23 40 0.19
24 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATAGAGGGT
Found at i:150 original size:44 final size:44
Alignment explanation
Indices: 15--551 Score: 278
Period size: 44 Copynumber: 12.3 Consensus size: 44
5 TTATGGAAGA
* *
15 TATCAAAATTTC--AGGGAGGA-TATCAAAATTTTATAGTTTA-GT
1 TATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAG-TGAGGT
* *
57 TTTCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAGTGAGGT
* * *
100 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
** * *
145 TATCAAAAAATCCTAGGGAGGTTATCAAAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * *
183 TATCAAGATTTCATA-AGAGAGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGG-T
* * * *
228 TATTAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * * *
273 TATCAAAATTTCATAGTGTGATTATCAAAATTTCAGAGT-ATGAT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGA-GGT
* * * * * * *
317 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAATGTGGT
1 TATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * *
361 TATCAATATATCATATGGAGGTTATCAACATCTT-ATAGTGTTA-GT
1 TATCAAAATTTCATAGGGAGATTATCAAAAT-TTCATAGTG--AGGT
* *
406 TATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATACTGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * * * *
450 CT-TCAAAA-TTCCTCAGGGAGGTTAACAAAATTTCATAAG-AAGCT
1 -TATCAAAATTTCAT-AGGGAGATTATCAAAATTTCAT-AGTGAGGT
** * *** * *
494 TAAAAAAAATT-ATAAAAAGGTTCTCAAAATTTCATAG-GAAGGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGGT
537 TATCAAAATTTCATA
1 TATCAAAATTTCATA
552 ATGGGATTAT
Statistics
Matches: 373, Mismatches: 83, Indels: 76
0.70 0.16 0.14
Matches are distributed among these distances:
37 3 0.01
38 22 0.06
39 3 0.01
40 1 0.00
41 2 0.01
42 17 0.05
43 46 0.12
44 179 0.48
45 75 0.20
46 25 0.07
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
Found at i:235 original size:23 final size:23
Alignment explanation
Indices: 182--551 Score: 134
Period size: 22 Copynumber: 16.7 Consensus size: 23
172 AAATTTGTAG
* *
182 TTATCAAGATTTCATA-AGAGAG-
1 TTATCAAAATTTCATAGGGAG-GT
*
204 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * * *
227 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
250 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * *
272 TTATCAAAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* * * *
294 TTATCAAAATTTCAGA-GTATGA
1 TTATCAAAATTTCATAGGGAGGT
*
316 TTA-CTAACAA-TTCATATGGAGGT
1 TTATC-AA-AATTTCATAGGGAGGT
* * ** *
339 TT-TTAAATTTTCATAATGTGG-
1 TTATCAAAATTTCATAGGGAGGT
* * *
360 TTATCAATATATCATATGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* *
382 TTATCAACATCTT-ATAGTGTTA-G-
1 TTATCAAAAT-TTCATAG-G-GAGGT
* *
405 TTATCAAAATTTCATTGGGAAG-
1 TTATCAAAATTTCATAGGGAGGT
**
427 TTATCAAAATTTCATACTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* *
450 CT-TCAAAA-TTCCTCAGGGAGG-
1 TTATCAAAATTTCAT-AGGGAGGT
* * * *
471 TTAACAAAATTTCATA-AGAAGC
1 TTATCAAAATTTCATAGGGAGGT
** * ***
493 TTAAAAAAAATT-ATAAAAAGG-
1 TTATCAAAATTTCATAGGGAGGT
* *
514 TTCTCAAAATTTCATAGGAAGG-
1 TTATCAAAATTTCATAGGGAGGT
536 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
552 ATGGGATTAT
Statistics
Matches: 263, Mismatches: 63, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
21 25 0.10
22 170 0.65
23 67 0.25
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:281 original size:126 final size:125
Alignment explanation
Indices: 53--280 Score: 303
Period size: 126 Copynumber: 1.8 Consensus size: 125
43 TTTTATAGTT
* * * *
53 TAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGG
1 TAGTTATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGG
* *
118 GAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCCTAGGGAGGTTATCAAAATTTG
66 AAGATTAACAAAATTTCATAACGAGGTTATC-AAAAATCCTAGGGAGGTTATCAAAATTTG
* * ** * *
179 TAGTTATCAAGATTTCATAAGAGAGTTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAG
1 TAGTTATCAAAATTTCATAAGAGAGTTATCAAAATTTCATA-GGAGGTAGATCAAAATTTCATAG
* *
244 GAAGATTTATCAAAATTTCATAGCGAGGTTATCAAAA
65 GAAGA-TTAACAAAATTTCATAACGAGGTTATCAAAA
281 TTTCATAGTG
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
126 37 0.43
127 25 0.29
128 24 0.28
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (125 bp):
TAGTTATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGG
AAGATTAACAAAATTTCATAACGAGGTTATCAAAAATCCTAGGGAGGTTATCAAAATTTG
Found at i:1310 original size:22 final size:22
Alignment explanation
Indices: 1276--1414 Score: 102
Period size: 22 Copynumber: 6.2 Consensus size: 22
1266 GTCTCTATGC
*
1276 GGTTATCAAAATTTCATAAGAT
1 GGTTATTAAAATTTCATAAGAT
*
1298 GGTTATTATAATTTCATGAAGA-
1 GGTTATTAAAATTTCAT-AAGAT
* * *
1320 GGTTATCAAAATTCCAT-AGTGT
1 GGTTATTAAAATTTCATAAG-AT
* *
1342 GGTTATCAAAATTTCATAGGAT
1 GGTTATTAAAATTTCATAAGAT
* * * *
1364 CAGGTTATTAAAATCTCTTAGGTT
1 --GGTTATTAAAATTTCATAAGAT
* * *
1388 GGTTATTGAAATTTCATAGGGT
1 GGTTATTAAAATTTCATAAGAT
1410 GGTTA
1 GGTTA
1415 ATTATCACAA
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.02
22 69 0.73
23 5 0.05
24 18 0.19
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAAGAT
Found at i:1495 original size:22 final size:22
Alignment explanation
Indices: 1450--1525 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
1440 ATCAAAGAGA
* * *
1450 TTATCAAAATGTCATAACGAGG
1 TTATAAAAATTTCATAATGAGG
* *
1472 TTATAAAAATTTCATAGTGTGG
1 TTATAAAAATTTCATAATGAGG
*
1494 TTA-ACAAAATTTTATAATGAGG
1 TTATA-AAAATTTCATAATGAGG
1516 TTATCAAAAA
1 TTAT-AAAAA
1526 AATCATAGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.02
22 37 0.86
23 4 0.09
24 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATAAAAATTTCATAATGAGG
Found at i:1619 original size:19 final size:19
Alignment explanation
Indices: 1589--1636 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1579 TTATGGAGTA
1589 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
*
1609 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
1628 ATCAAAATT
1 ATCAAAATT
1637 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:1655 original size:22 final size:21
Alignment explanation
Indices: 1589--2032 Score: 153
Period size: 22 Copynumber: 20.7 Consensus size: 21
1579 TTATGGAGTA
* *
1589 ATCAAAATTTCA-AGGAGGAT
1 ATCAAAATTTCATATGAGGTT
** *
1609 ATCAAAA-TTCA-GGGAGGAT
1 ATCAAAATTTCATATGAGGTT
1628 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATG-AGGTT
*
1650 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA--TGAGGTT
* * *
1672 TTCAAAATTTCACAAGAGTGTT
1 ATCAAAATTTCATATGAG-GTT
* *
1694 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATG-AGGT-T
* * *
1716 ATCAAATTTTCATAGGTAGATT
1 ATCAAAATTTCATATG-AGGTT
*
1738 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
** *
1760 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
*
1782 ATCAAAA-TT--TGT-A-GTT
1 ATCAAAATTTCATATGAGGTT
* * *
1798 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATG-AGGTT
* * *
1820 ATTAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-TGAGG-TT
* * *
1843 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATG-AG-GTT
1866 ATCAAAATTTCATA-GA--TT
1 ATCAAAATTTCATATGAGGTT
* * *
1884 ATCACAATTTCATAGTGCGATT
1 ATCAAAATTTCATA-TGAGGTT
* * *
1906 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATA-TGAGGTT
1928 A-CTAACAA-TTCATATGGAGGTTT
1 ATC-AA-AATTTCATAT-GAGG-TT
* * * ** **
1951 TTTAAATTTTCATAACATAATT
1 ATCAAAATTTCATATGA-GGTT
* *
1973 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAT-GAGGTT
* * *
1995 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TG-AGGTT
2018 ATCAAAATTTCATAT
1 ATCAAAATTTCATAT
2033 TGAGATCTTC
Statistics
Matches: 320, Mismatches: 68, Indels: 70
0.70 0.15 0.15
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 15 0.05
19 20 0.06
20 13 0.04
21 10 0.03
22 179 0.56
23 70 0.22
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATATGAGGTT
Found at i:1682 original size:44 final size:43
Alignment explanation
Indices: 1627--1917 Score: 190
Period size: 44 Copynumber: 6.8 Consensus size: 43
1617 TCAGGGAGGA
*
1627 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-TTAGT
* * *
1671 TTTCAAAATTTCACAAG-AGTGTTATCAAAATTTCATAG-TATGT
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTA-GT
* * * * * * *
1714 AGATCAAATTTTCATAGGTAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-GT
** *
1759 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGT
* * * * * **
1797 TATCAAGATTTCATAAGAAAGTTATTAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTA-G-T
* *
1842 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG--A-T
1 TATCAAAATTTCATAGGAAG-GTTATCAAAATTTCATAGTTAGT
* * *
1883 TATCACAATTTCATAGTG-CGATTATCAAAATTTCA
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCA
1918 GAGTGTGATT
Statistics
Matches: 192, Mismatches: 41, Indels: 32
0.72 0.15 0.12
Matches are distributed among these distances:
38 25 0.13
39 3 0.02
40 14 0.07
41 18 0.09
42 4 0.02
43 7 0.04
44 84 0.44
45 22 0.11
46 15 0.08
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTAGT
Found at i:1704 original size:66 final size:65
Alignment explanation
Indices: 1622--1791 Score: 173
Period size: 66 Copynumber: 2.6 Consensus size: 65
1612 AAAATTCAGG
* * **
1622 GAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCACA
1 GAGGTTATCAAAATTTCATA-GAAGGTTATCAAAATTTCATAG-GTAGATTAACAAAATTTCACA
1686 A-
64 AT
* * * * *
1687 GAGTGTTATCAAAATTTCATAGTATGTAGATCAAATTTTCATAGGTAGATTAACAAAATTTCATA
1 GAG-GTTATCAAAATTTCATAGAAGGT-TATCAAAATTTCATAGGTAGATTAACAAAATTTCACA
1752 AT
64 AT
** *
1754 GAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTT
1 GAGGTTATCAAAATTTCATA-GAAGGTTATCAAAATTT
1792 GTAGTTATCA
Statistics
Matches: 85, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
65 10 0.12
66 68 0.80
67 7 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (65 bp):
GAGGTTATCAAAATTTCATAGAAGGTTATCAAAATTTCATAGGTAGATTAACAAAATTTCACAAT
Found at i:1844 original size:23 final size:23
Alignment explanation
Indices: 1796--1880 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1786 AAATTTGTAG
* * * *
1796 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* * *
1818 TTATTAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
1841 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
1864 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
1881 ATTATCACAA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 15 0.29
23 36 0.71
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:3485 original size:4 final size:5
Alignment explanation
Indices: 3460--3491 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3450 TCGGGCGTCT
3460 TTTTA TTTTA TTTTA TTTTA -TTTA TTTT- TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3492 CTCTGCGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:3485 original size:9 final size:10
Alignment explanation
Indices: 3460--3491 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
3450 TCGGGCGTCT
3460 TTTTATTTTA
1 TTTTATTTTA
3470 TTTTATTTTA
1 TTTTATTTTA
3480 -TTTATTTT-
1 TTTTATTTTA
3488 TTTT
1 TTTT
3492 CTCTGCGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.52
10 10 0.48
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:4163 original size:22 final size:22
Alignment explanation
Indices: 4137--4182 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
4127 ATTTATTCAT
4137 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
4159 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
4181 TA
1 TA
4183 ATATATAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:4179 original size:11 final size:11
Alignment explanation
Indices: 4137--4179 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
4127 ATTTATTCAT
*
4137 TATTAATTAAC
1 TATTAATTAGC
*
4148 TATTAATTAGA
1 TATTAATTAGC
4159 TATTAATTAGC
1 TATTAATTAGC
4170 TATTAATTAG
1 TATTAATTAG
4180 ATAATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:5898 original size:15 final size:17
Alignment explanation
Indices: 5880--5911 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5870 ATTCGGAATT
5880 ATTAAGG-TTTG-GGTC
1 ATTAAGGATTTGAGGTC
5895 ATTAAGGATTTGAGGTC
1 ATTAAGGATTTGAGGTC
5912 GGGTCATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (17 bp):
ATTAAGGATTTGAGGTC
Found at i:7829 original size:7 final size:7
Alignment explanation
Indices: 7820--7849 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
7810 AGGCATCTTT
*
7820 AAGTTTT
1 AAGTTTC
7827 AAGTTTC
1 AAGTTTC
7834 AAGTTTC
1 AAGTTTC
7841 AAGTTTC
1 AAGTTTC
7848 AA
1 AA
7850 CTTTTTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (7 bp):
AAGTTTC
Found at i:7839 original size:14 final size:14
Alignment explanation
Indices: 7820--7854 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7810 AGGCATCTTT
7820 AAGTTTTAAGTTTC
1 AAGTTTTAAGTTTC
*
7834 AAGTTTCAAGTTTC
1 AAGTTTTAAGTTTC
*
7848 AACTTTT
1 AAGTTTT
7855 TTGTCAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (14 bp):
AAGTTTTAAGTTTC
Found at i:13635 original size:14 final size:14
Alignment explanation
Indices: 13616--13646 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
13606 ATTGTTTTTA
13616 AGTACCAAAGAATC
1 AGTACCAAAGAATC
13630 AGTACCAAAGAATC
1 AGTACCAAAGAATC
13644 AGT
1 AGT
13647 TGAGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.16
Consensus pattern (14 bp):
AGTACCAAAGAATC
Found at i:13942 original size:185 final size:185
Alignment explanation
Indices: 13630--13996 Score: 599
Period size: 185 Copynumber: 2.0 Consensus size: 185
13620 CCAAAGAATC
* * *
13630 AGTACCAAAGAATCAGTTGAGAAAACTCACCACATTCACCCAAGAACAAATTATCAGAGGTATTT
1 AGTACCAAAAAACCAGTTGAGAAAACTCACCACATACACCCAAGAACAAATTATCAGAGGTATTT
* * *
13695 CGGTACTTTTGTGCTTGGTTTTTTTATTATTTCGGTTGATGGTTGAGGGCGTTTTGGGAAGTTTG
66 CGGTACTTTTGTACTTGGCTTTTTTATTATTTCGGTTGATGGTTGAGGCCGTTTTGGGAAGTTTG
**
13760 AAACAAAGTTACTATTACTGGCCCTGCTTATAATAAACAAATCATTTTTTTGCTG
131 AAACAAAGTTACTATTACTGGCCCCACTTATAATAAACAAATCATTTTTTTGCTG
* * *
13815 AGTACCAAAAAACCAGTTGAGAAATCTCACCACATACACCCAAGAACAAATTGTCAGGGGTATTT
1 AGTACCAAAAAACCAGTTGAGAAAACTCACCACATACACCCAAGAACAAATTATCAGAGGTATTT
* *
13880 TGGTACTTTTGTACTTGGCTTTTTTGTTATTTCGGTTGATGGTTGAGGCCGTTTTGGGAAGTTTG
66 CGGTACTTTTGTACTTGGCTTTTTTATTATTTCGGTTGATGGTTGAGGCCGTTTTGGGAAGTTTG
**
13945 AAACAAAGTTACTATTACTGGCCCCACTTATAATAAACAAATTTTTTTTTTG
131 AAACAAAGTTACTATTACTGGCCCCACTTATAATAAACAAATCATTTTTTTG
13997 GTTTATTTAT
Statistics
Matches: 167, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
185 167 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (185 bp):
AGTACCAAAAAACCAGTTGAGAAAACTCACCACATACACCCAAGAACAAATTATCAGAGGTATTT
CGGTACTTTTGTACTTGGCTTTTTTATTATTTCGGTTGATGGTTGAGGCCGTTTTGGGAAGTTTG
AAACAAAGTTACTATTACTGGCCCCACTTATAATAAACAAATCATTTTTTTGCTG
Found at i:14807 original size:439 final size:435
Alignment explanation
Indices: 13977--14937 Score: 1291
Period size: 439 Copynumber: 2.2 Consensus size: 435
13967 CCCACTTATA
*
13977 ATAAACAAAT-TTTTTTTTTGGTTTATTTATCAAATGATCCCTATACTTTTATACA-TTATGCTA
1 ATAAACAAATATTTTTTTTTGGATTATTTATCAAATGATCCC-ATACTTTTATA-ATTTATGCTA
** * * * * *
14040 TTTAGCCCCTCACAATTTTTGGGTTGGACGATTGAACATTTCGGCTTTAATTCTTTTATTTCTTG
64 TTTAATCCTTTACAA-TTATGGGTTGGACAATTGAACATTTCGACTTTAATTCTTTTATTTCTTG
* * * * * * *
14105 TTTTGTTTGTCCGATGAAGGTGATTTAAGTGTCTATTAAAAGGTGATTTCATGATCTACAACTTC
128 TTTTATTTGACCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTCCATGATCTACAAATTC
* * * *
14170 CATGAAGGACTTAAAAGTCAATTTTAATGTTTTGATTCAAAAAATTGCTTTTGAAATTTTGTAGT
193 CATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTCAAAAAATTGCTTCTAAAATTTTGTAGT
* * *
14235 CTCAATTGTCGGTATATTTGATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAA
258 CTCAATTGTCGGTATATCTAATATCGTATAAATTTCGCTCCACTTGTCCGATTGAGGTTGTTCAA
* * * * *
14300 GTGTCGGTTAAAAGATTATTGTGTGATCTATGACTTTCGTTAAGGGTCTGAAAGCTGAATTTGAT
323 GTGTCGATTAAAAGATTATTGTGTGATCTACGACTTTCGCTAAGGGCCTGAAAGCTGAATTCGAT
** *
14365 TAATGAGTTTTGTGGAGAATTCAAGAGGGAATTTTTATGTTTGGTCTCC
388 TAATGAGTTCCGTGGAG-ATTCAAGAGGGAATTTTTATGTTTGGCCTCC
* *
14414 ATAAACAAATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGTT
1 ATAAACAAAT-ATTTTTTT-TTGGATTATTTATCAAATGATCC-CATACTTTTATAATTTATGCT
** *
14479 ATTTAATCCTTTACAATTATGGGTTGGACAATTGAATGTTTCGACTTTAATTCTTTTATTT-TTT
63 ATTTAATCCTTTACAATTATGGGTTGGACAATTGAACATTTCGACTTTAATTCTTTTATTTCTTG
* * * *
14543 TTTCTATTTGACCGATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTTTACAAATT
128 TTT-TATTTGACCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTCCATGATCTACAAATT
* * *
14608 TCATGAAGGACTCAAAAGCCAATTTTGATGTTTTGATTCTAAAAAA-TGCTTCTAAAATTTTGTG
192 CCATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTC-AAAAAATTGCTTCTAAAATTTTGTA
* * * * *
14672 GTCTCGATTGTCGGTTTATCTAATATTGTATAATTTTCGCTTCACTTGTCCGATTGAGGTTGTTC
256 GTCTCAATTGTCGGTATATCTAATATCGTATAAATTTCGCTCCACTTGTCCGATTGAGGTTGTTC
* * *
14737 AAGTGTCGATTGAAAGGTTATTGTGTTATCTACGACTTTCGCTAAGGGCCTGAAAGCTGAATTCG
321 AAGTGTCGATTAAAAGATTATTGTGTGATCTACGACTTTCGCTAAGGGCCTGAAAGCTGAATTCG
* *
14802 ATTAATGAGTTCCGTGGAGGTTCAAGAGGGAATTTTTATGTTTGGCCTTC
386 ATTAATGAGTTCCGTGGAGATTCAAGAGGGAATTTTTATGTTTGGCCTCC
* * *
14852 ATAAACAAATATTTTTTTCCTTGGATTATTTATCAAATGACCCCCATACTTTTATGATCTATGCT
1 ATAAACAAATATTTTTTT--TTGGATTATTTATCAAATGA-TCCCATACTTTTATAATTTATGCT
14917 ATTTAATCCTTTACAATTATG
63 ATTTAATCCTTTACAATTATG
14938 ATTTATGCTA
Statistics
Matches: 457, Mismatches: 58, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
437 18 0.04
438 101 0.22
439 281 0.61
440 56 0.12
441 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (435 bp):
ATAAACAAATATTTTTTTTTGGATTATTTATCAAATGATCCCATACTTTTATAATTTATGCTATT
TAATCCTTTACAATTATGGGTTGGACAATTGAACATTTCGACTTTAATTCTTTTATTTCTTGTTT
TATTTGACCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTCCATGATCTACAAATTCCAT
GAAGGACTCAAAAGCCAATTTTAATGTTTTGATTCAAAAAATTGCTTCTAAAATTTTGTAGTCTC
AATTGTCGGTATATCTAATATCGTATAAATTTCGCTCCACTTGTCCGATTGAGGTTGTTCAAGTG
TCGATTAAAAGATTATTGTGTGATCTACGACTTTCGCTAAGGGCCTGAAAGCTGAATTCGATTAA
TGAGTTCCGTGGAGATTCAAGAGGGAATTTTTATGTTTGGCCTCC
Found at i:14939 original size:30 final size:30
Alignment explanation
Indices: 14903--14967 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
14893 CCCCATACTT
14903 TTATGATCTATGCTATTTAATCCTTTACAA
1 TTATGATCTATGCTATTTAATCCTTTACAA
* *
14933 TTATGATTTATGCTATTTAATTCTTTACAA
1 TTATGATCTATGCTATTTAATCCTTTACAA
14963 TTATG
1 TTATG
14968 GGTTGGACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (30 bp):
TTATGATCTATGCTATTTAATCCTTTACAA
Found at i:18888 original size:4 final size:4
Alignment explanation
Indices: 18879--18905 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18869 TAGAGATAAG
18879 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
18906 TTGTTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:26310 original size:18 final size:18
Alignment explanation
Indices: 26266--26302 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
26256 CTCATGGAAA
*
26266 TCAACAAAAAGGAACTTG
1 TCAAGAAAAAGGAACTTG
26284 TCAAGAAAAAGGAACTTG
1 TCAAGAAAAAGGAACTTG
26302 T
1 T
26303 AGGAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (18 bp):
TCAAGAAAAAGGAACTTG
Found at i:32093 original size:28 final size:28
Alignment explanation
Indices: 32052--32105 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
32042 TTTTTATGAT
32052 ACTAAACCTAATTT-GAGTGTTGTTTGCC
1 ACTAAACCTAATTTAG-GTGTTGTTTGCC
* *
32080 ACTAAATCTGATTTAGGTGTTGTTTG
1 ACTAAACCTAATTTAGGTGTTGTTTG
32106 TGATAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (28 bp):
ACTAAACCTAATTTAGGTGTTGTTTGCC
Found at i:32249 original size:30 final size:29
Alignment explanation
Indices: 32142--32253 Score: 93
Period size: 33 Copynumber: 3.7 Consensus size: 29
32132 CTAATTGTGA
* *
32142 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAAATCTGTTTTGGTTG---AT-GCAT
* * *
32175 TAAAAATAATTTTGTTTTGGTTGAT-CAT
1 TGAAAATAAATCTGTTTTGGTTGATGCAT
*
32203 ATGCAAAT-AATCCTGTTTTGGTTGATGGCAT
1 -TGAAAATAAAT-CTGTTTTGGTTGAT-GCAT
32234 TGAAAATAAATCTGTTTTGG
1 TGAAAATAAATCTGTTTTGG
32254 GTGACGAGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
28 5 0.08
29 18 0.27
30 17 0.26
31 6 0.09
33 20 0.30
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (29 bp):
TGAAAATAAATCTGTTTTGGTTGATGCAT
Done.