Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016917.1 Corchorus olitorius cultivar O-4 contig16950, 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: 54577
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:6171 original size:22 final size:21
Alignment explanation
Indices: 6143--6196 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
6133 GGAGTTCGTG
6143 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
6165 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
6184 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
6197 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:11049 original size:10 final size:10
Alignment explanation
Indices: 11031--11064 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
11021 CCAAATGTCC
*
11031 GATTAACAAA
1 GATTCACAAA
11041 GATTCACAAA
1 GATTCACAAA
*
11051 GATTCGCAAA
1 GATTCACAAA
11061 GATT
1 GATT
11065 ATTTCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (10 bp):
GATTCACAAA
Found at i:13452 original size:51 final size:51
Alignment explanation
Indices: 13392--13499 Score: 216
Period size: 51 Copynumber: 2.1 Consensus size: 51
13382 TTCAGGTGGC
13392 AAATTCCAACTAAGAAAAGTTGTTAGCCTCCAAAAGATTTCACCCTAGAGA
1 AAATTCCAACTAAGAAAAGTTGTTAGCCTCCAAAAGATTTCACCCTAGAGA
13443 AAATTCCAACTAAGAAAAGTTGTTAGCCTCCAAAAGATTTCACCCTAGAGA
1 AAATTCCAACTAAGAAAAGTTGTTAGCCTCCAAAAGATTTCACCCTAGAGA
13494 AAATTC
1 AAATTC
13500 TCCAAGAGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (51 bp):
AAATTCCAACTAAGAAAAGTTGTTAGCCTCCAAAAGATTTCACCCTAGAGA
Found at i:13539 original size:12 final size:12
Alignment explanation
Indices: 13522--13557 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
13512 ACGAGAATCT
13522 TCCAAGTTCTCC
1 TCCAAGTTCTCC
13534 TCCAAGTTCTCC
1 TCCAAGTTCTCC
13546 TCCAAGTTCTCC
1 TCCAAGTTCTCC
13558 AAGGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.42, G:0.08, T:0.33
Consensus pattern (12 bp):
TCCAAGTTCTCC
Found at i:15518 original size:150 final size:150
Alignment explanation
Indices: 15247--15555 Score: 539
Period size: 150 Copynumber: 2.1 Consensus size: 150
15237 TGTTGAACGT
*
15247 AATTTCCGATTCCGTTGTACCCTTGACTTCCTTAGAATGATTATTCATGCGGTGGATATGGATCT
1 AATTTCCGATTCCGCTGTACCCTTGACTTCCTTAGAATGATTATTCATGCGGTGGATATGGATCT
*
15312 TGCGAAAAATGTCTAGGTTTAGCAAAGAAGAGGGAAATAATTCATATGGAATTGGGGGGAGAGAG
66 TGCGAAAAATGTCTAGGTTTAGCAAAGAAGAGGGAAAGAATTCATATGGAATTGGGGGGAGAGAG
15377 GAGAGTCTGTTGAACTCATC
131 GAGAGTCTGTTGAACTCATC
*
15397 AATTTCCGATTCCGCTGTACCCTTGACTTCCTTAGAATGATTTTTCATGCGGTGGATATGGATGC
1 AATTTCCGATTCCGCTGTACCCTTGACTTCCTTAGAATGATTATTCATGCGGTGGATATGGAT-C
* * * *
15462 -TGTGAAAAATGTCTAGGTTTTGCAAAGCAGGGGGAAAGAATTCATATGGAATTGGGGGGAGAGA
65 TTGCGAAAAATGTCTAGGTTTAGCAAAGAAGAGGGAAAGAATTCATATGGAATTGGGGGGAGAGA
15526 GGAGAGTCTGTTGAACTCATC
130 GGAGAGTCTGTTGAACTCATC
15547 AATTTCCGA
1 AATTTCCGA
15556 GTCTTGTAAC
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
150 150 0.99
151 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (150 bp):
AATTTCCGATTCCGCTGTACCCTTGACTTCCTTAGAATGATTATTCATGCGGTGGATATGGATCT
TGCGAAAAATGTCTAGGTTTAGCAAAGAAGAGGGAAAGAATTCATATGGAATTGGGGGGAGAGAG
GAGAGTCTGTTGAACTCATC
Found at i:16998 original size:16 final size:16
Alignment explanation
Indices: 16979--17062 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
16969 AACGCGAATC
16979 AACCTGACCCAAATTT
1 AACCTGACCCAAATTT
* * **
16995 AACCCGAATCTGAA-TT
1 AACCTG-ACCCAAATTT
17011 AACCTGACCCAAATTT
1 AACCTGACCCAAATTT
* * * *
17027 AACCCGAATCCGAA-TC
1 AACCTG-ACCCAAATTT
*
17043 AATCTGACCCAAATTT
1 AACCTGACCCAAATTT
17059 AACC
1 AACC
17063 CAACTTGACT
Statistics
Matches: 46, Mismatches: 18, Indels: 8
0.64 0.25 0.11
Matches are distributed among these distances:
15 9 0.20
16 28 0.61
17 9 0.20
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (16 bp):
AACCTGACCCAAATTT
Found at i:17015 original size:32 final size:32
Alignment explanation
Indices: 16963--17063 Score: 159
Period size: 32 Copynumber: 3.2 Consensus size: 32
16953 ACTCAACCCG
16963 AACCCGAA-CGCGAATCAACCTGACCCAAATTT
1 AACCCGAATC-CGAATCAACCTGACCCAAATTT
* *
16995 AACCCGAATCTGAATTAACCTGACCCAAATTT
1 AACCCGAATCCGAATCAACCTGACCCAAATTT
*
17027 AACCCGAATCCGAATCAATCTGACCCAAATTT
1 AACCCGAATCCGAATCAACCTGACCCAAATTT
17059 AACCC
1 AACCC
17064 AACTTGACTC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 62 0.98
33 1 0.02
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.20
Consensus pattern (32 bp):
AACCCGAATCCGAATCAACCTGACCCAAATTT
Found at i:18292 original size:5 final size:5
Alignment explanation
Indices: 18282--18306 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18272 ATTTTTCCCC
18282 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
18307 GGGACAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:18835 original size:16 final size:17
Alignment explanation
Indices: 18811--18843 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18801 ACGGTGTACG
18811 TATAAATTATAT-TTAA
1 TATAAATTATATATTAA
*
18827 TATATATTATATATTAA
1 TATAAATTATATATTAA
18844 CAAATAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATTATATATTAA
Found at i:18889 original size:5 final size:5
Alignment explanation
Indices: 18879--18903 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18869 TTTCCTTAAT
18879 CGGGC CGGGC CGGGC CGGGC CGGGC
1 CGGGC CGGGC CGGGC CGGGC CGGGC
18904 TTGAGCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:22442 original size:17 final size:17
Alignment explanation
Indices: 22420--22462 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
22410 CTGACTTAAT
22420 AATAATTATTATTATAA
1 AATAATTATTATTATAA
* **
22437 AATAATAATTATTATTC
1 AATAATTATTATTATAA
22454 AATAATTAT
1 AATAATTAT
22463 CTCCTCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAATTATTATTATAA
Found at i:25017 original size:2 final size:2
Alignment explanation
Indices: 25010--25039 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25000 CTCAGCTTTA
25010 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25040 AATTTAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25170 original size:21 final size:21
Alignment explanation
Indices: 25146--25191 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25136 AATTGATTAT
25146 TTAATT-AGAATCTATTAATAA
1 TTAATTAAGAAT-TATTAATAA
* *
25167 TTAATTAAGTATTATTAATTA
1 TTAATTAAGAATTATTAATAA
25188 TTAA
1 TTAA
25192 ATATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAATTAAGAATTATTAATAA
Found at i:25179 original size:18 final size:17
Alignment explanation
Indices: 25158--25191 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25148 AATTAGAATC
25158 TATTAATAATTAATTAAG
1 TATTAATAATT-ATTAAG
*
25176 TATTATTAATTATTAA
1 TATTAATAATTATTAA
25192 ATATAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTAATAATTATTAAG
Found at i:26798 original size:75 final size:75
Alignment explanation
Indices: 26655--26806 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 75
26645 AAATAAAAAA
* *
26655 CACATGGCAAGGAAAGTTTAGGAAAGAAAGTGTGTGCAACTCGATAAATTATTAGATGCAACAGT
1 CACATGGCAAGGAAAGATTAGGAAAGAAAGTGTGTGCAACTCGATAAATTATTAGATGCAACAAT
26720 CTCACCTCGT
66 CTCACCTCGT
* * *
26730 CACATGGCAATGAAAGATTAGGAAAGAAAGTGTGTGCAACTCGATAAATTATTGGATG-AGATAA
1 CACATGGCAAGGAAAGATTAGGAAAGAAAGTGTGTGCAACTCGATAAATTATTAGATGCA-ACAA
*
26794 TCTCACCTTGT
65 TCTCACCTCGT
26805 CA
1 CA
26807 TCCATGGGAC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 1 0.01
75 69 0.99
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (75 bp):
CACATGGCAAGGAAAGATTAGGAAAGAAAGTGTGTGCAACTCGATAAATTATTAGATGCAACAAT
CTCACCTCGT
Found at i:29831 original size:19 final size:19
Alignment explanation
Indices: 29807--29846 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29797 AAAGTGATTC
*
29807 CATTACACCAAATAATGAT
1 CATTACACCAAACAATGAT
*
29826 CATTACATCAAACAATGAT
1 CATTACACCAAACAATGAT
29845 CA
1 CA
29847 CTTTTTCATA
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:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (19 bp):
CATTACACCAAACAATGAT
Found at i:36897 original size:23 final size:22
Alignment explanation
Indices: 36871--36923 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
36861 AAGAAAAGAG
36871 AAGATTAAACGAAATAAAAATAA
1 AAGATTAAAC-AAATAAAAATAA
* *
36894 AAGA-TAGAACAAATTAAAATAG
1 AAGATTA-AACAAATAAAAATAA
36916 AA-ATTAAA
1 AAGATTAAA
36924 GTGTTCCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (22 bp):
AAGATTAAACAAATAAAAATAA
Found at i:39075 original size:26 final size:27
Alignment explanation
Indices: 39014--39072 Score: 102
Period size: 26 Copynumber: 2.2 Consensus size: 27
39004 TCCATGCTTT
39014 ATTTCAATTTCTCTCTCCACATGCCCA
1 ATTTCAATTTCTCTCTCCACATGCCCA
*
39041 A-TTCAATTTCTTTCTCCACATGCCCA
1 ATTTCAATTTCTCTCTCCACATGCCCA
39067 ATTTCA
1 ATTTCA
39073 TTTAAAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.24, C:0.34, G:0.03, T:0.39
Consensus pattern (27 bp):
ATTTCAATTTCTCTCTCCACATGCCCA
Found at i:39330 original size:17 final size:17
Alignment explanation
Indices: 39285--39336 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
39275 TTATTTTCGT
*
39285 TCAAATTTCAAAATTT-
1 TCAATTTTCAAAATTTC
*
39301 TCAATTCTCTCAAATTTTC
1 TCAATT-T-TCAAAATTTC
*
39320 TCAATTTTCAAACTTTC
1 TCAATTTTCAAAATTTC
39337 AAACCTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.17
17 10 0.33
18 9 0.30
19 6 0.20
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTTCAAAATTTC
Found at i:40050 original size:12 final size:12
Alignment explanation
Indices: 40033--40057 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40023 CTACGTCAGC
40033 CAAAAAATTCTA
1 CAAAAAATTCTA
40045 CAAAAAATTCTA
1 CAAAAAATTCTA
40057 C
1 C
40058 GTAAGCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (12 bp):
CAAAAAATTCTA
Found at i:41085 original size:12 final size:12
Alignment explanation
Indices: 41068--41092 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41058 CTTTAGAGGA
41068 GGAAACAAAATT
1 GGAAACAAAATT
41080 GGAAACAAAATT
1 GGAAACAAAATT
41092 G
1 G
41093 AAGCTATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (12 bp):
GGAAACAAAATT
Found at i:44460 original size:13 final size:13
Alignment explanation
Indices: 44444--44475 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
44434 ATCATATACC
44444 ATCTTATCTTACT
1 ATCTTATCTTACT
44457 ATCTTATCTTACT
1 ATCTTATCTTACT
44470 ATCTTA
1 ATCTTA
44476 CTACTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (13 bp):
ATCTTATCTTACT
Found at i:47221 original size:22 final size:22
Alignment explanation
Indices: 47191--47318 Score: 100
Period size: 22 Copynumber: 5.8 Consensus size: 22
47181 CATAGGAAAC
* *
47191 TTATTAAAATTTCATACTGTAA
1 TTATCAAAATTTCATACTGTAG
* * *
47213 TTACCAAAACTTCATA-TGGACG
1 TTATCAAAATTTCATACTGTA-G
*
47235 TTATCAAAATTTCATAATGTAG
1 TTATCAAAATTTCATACTGTAG
*
47257 TTATCAAAATTTCATACAG-AGG
1 TTATCAAAATTTCATACTGTA-G
* * **
47279 TAACCAAAAATTTCATA-AATATG
1 TTATC-AAAATTTCATACTGTA-G
47302 TTATCAAAATTTCATAC
1 TTATCAAAATTTCATAC
47319 GAAGGTTATT
Statistics
Matches: 84, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.05
22 61 0.73
23 19 0.23
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATACTGTAG
Found at i:47287 original size:44 final size:45
Alignment explanation
Indices: 47196--47318 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 45
47186 GAAACTTATT
* * * * ** * *
47196 AAAATTTCATACTGTAATTACCAAAACTTCATATGGACGTTATC-
1 AAAATTTCATAATGTAGTTATCAAAATTTCATACAGACGTAACCA
*
47240 AAAATTTCATAATGTAGTTATCAAAATTTCATACAGAGGTAACCA
1 AAAATTTCATAATGTAGTTATCAAAATTTCATACAGACGTAACCA
*
47285 AAAATTTCATAA-ATATGTTATCAAAATTTCATAC
1 AAAATTTCATAATGTA-GTTATCAAAATTTCATAC
47319 GAAGGTTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 37 0.55
45 30 0.45
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (45 bp):
AAAATTTCATAATGTAGTTATCAAAATTTCATACAGACGTAACCA
Found at i:47400 original size:47 final size:47
Alignment explanation
Indices: 47346--47436 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
47336 TATAGTGTGA
47346 TTATCAAAATTAAT-TA-GAACATTAACAAAATTTCACAGGGAGGGAGG
1 TTATCAAAA--AATCTAGGAACATTAACAAAATTTCACAGGGAGGGAGG
** *
47393 TTATCAAAAAATCCTAGGAAGGTTAACAAAATTTCATAGGGAGG
1 TTATCAAAAAAT-CTAGGAACATTAACAAAATTTCACAGGGAGG
47437 TTATGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
45 3 0.08
47 11 0.29
48 24 0.63
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (47 bp):
TTATCAAAAAATCTAGGAACATTAACAAAATTTCACAGGGAGGGAGG
Found at i:47432 original size:22 final size:22
Alignment explanation
Indices: 47173--47474 Score: 95
Period size: 22 Copynumber: 13.5 Consensus size: 22
47163 ACAATAAAAC
* **
47173 CAAAATTACATAGGAAACTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
47195 TAAAATTTCATACTGTAA--TTAC
1 CAAAATTTCATA--GGAAGGTTAT
* *
47217 CAAAACTTCATATGG-ACGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
47239 CAAAATTTCATAATGTA-GTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
* * *
47261 CAAAATTTCATA-CAGAGGTAAC
1 CAAAATTTCATAGGA-AGGTTAT
* *
47283 CAAAAATTTCATA-AATATGTTAT
1 C-AAAATTTCATAGGA-AGGTTAT
*
47306 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
** * * *
47328 TGAAATTTTATAGTG-TGATTAT
1 CAAAATTTCATAG-GAAGGTTAT
* ** *
47350 CAAAA-TTAATTA-GAACATTAA
1 CAAAATTTCA-TAGGAAGGTTAT
*
47371 CAAAATTTCACAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
** * *
47397 CAAAAAATCCTAGGAAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
*
47419 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
47441 GAAAATGTT-AT-GGAGAGGTTAT
1 CAAAAT-TTCATAGGA-AGGTTAT
*
47463 CAAAATTACATA
1 CAAAATTTCATA
47475 TAGAGGACAT
Statistics
Matches: 205, Mismatches: 52, Indels: 45
0.68 0.17 0.15
Matches are distributed among these distances:
20 2 0.01
21 20 0.10
22 140 0.68
23 25 0.12
24 3 0.01
25 3 0.01
26 12 0.06
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:47540 original size:22 final size:22
Alignment explanation
Indices: 47515--47739 Score: 118
Period size: 22 Copynumber: 10.3 Consensus size: 22
47505 GAAGTTAGCG
*
47515 AAATTTCATGGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* **
47537 AAATTTTATGAG-AAGGTTATCA
1 AAATTTCAT-AGTGTGGTTATCA
* *
47559 AAATTTTCAGAGTG-CGTTA-C-
1 AAA-TTTCATAGTGTGGTTATCA
* ** * *
47579 CAATTTTTTAATGTGATTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
47601 AAATTTCACACTGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
47623 AAACTTCATTGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* *
47645 GAATTTCACAGTGTGGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* * *
47667 AATTTTCATAAG-GAGGTTATCG
1 AAATTTCAT-AGTGTGGTTATCA
* * **
47689 AAATTTCACAATGAAGTTATCA
1 AAATTTCATAGTGTGGTTATCA
* ** *
47711 AATTTTCGCAGTGTGATTATCA
1 AAATTTCATAGTGTGGTTATCA
*
47733 ATATTTC
1 AAATTTC
47740 TACGTTGGAG
Statistics
Matches: 146, Mismatches: 49, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
19 6 0.04
20 5 0.03
21 3 0.02
22 125 0.86
23 7 0.05
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
AAATTTCATAGTGTGGTTATCA
Found at i:47675 original size:44 final size:45
Alignment explanation
Indices: 47590--47717 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 45
47580 AATTTTTTAA
* * * ** *
47590 TGTGATTATCAAAATTTCACACTGAGGTTATCAAAACTTCAT-TG
1 TGTGGTTATCAGAATTTCACAATGAGGTTATCAAATTTTCATAAG
* *
47634 TGTGGTTATCAGAATTTCACAGTGTGGTTATCAAATTTTCATAAG
1 TGTGGTTATCAGAATTTCACAATGAGGTTATCAAATTTTCATAAG
* *
47679 -GAGGTTATC-GAAATTTCACAATGAAGTTATCAAATTTTC
1 TGTGGTTATCAG-AATTTCACAATGAGGTTATCAAATTTTC
47718 GCAGTGTGAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 69 0.97
45 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (45 bp):
TGTGGTTATCAGAATTTCACAATGAGGTTATCAAATTTTCATAAG
Found at i:47731 original size:44 final size:43
Alignment explanation
Indices: 47590--47739 Score: 131
Period size: 44 Copynumber: 3.4 Consensus size: 43
47580 AATTTTTTAA
* ** **
47590 TGTGATTATCAAAATTTCACACTGAGGTTATCAAAACTTCATTG
1 TGTGATTATC-AAATTTCACAATGAGGTTATCAAATTTTCAAAG
* * *
47634 TGTGGTTATCAGAATTTCACAGTGTGGTTATCAAATTTTCATAAG
1 TGTGATTATCA-AATTTCACAATGAGGTTATCAAATTTTCA-AAG
* * * **
47679 -GAGGTTATCGAAATTTCACAATGAAGTTATCAAATTTTCGCAG
1 TGTGATTATC-AAATTTCACAATGAGGTTATCAAATTTTCAAAG
47722 TGTGATTATCAATATTTC
1 TGTGATTATCAA-ATTTC
47740 TACGTTGGAG
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
43 5 0.06
44 79 0.92
45 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (43 bp):
TGTGATTATCAAATTTCACAATGAGGTTATCAAATTTTCAAAG
Found at i:53769 original size:21 final size:22
Alignment explanation
Indices: 53721--53769 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
53711 TAACTAACAC
* *
53721 CTAACCATAGGTTAGTTGTATA
1 CTAACCATAGATTAGTTATATA
53743 CTTAACCATAGATTAGTTATA-A
1 C-TAACCATAGATTAGTTATATA
53765 CTAAC
1 CTAAC
53770 TAACAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 17 0.71
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
CTAACCATAGATTAGTTATATA
Done.