Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020783.1 Corchorus olitorius cultivar O-4 contig20816, 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: 78837
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:680 original size:28 final size:27
Alignment explanation
Indices: 612--680 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
602 TTCTACAAAC
* *
612 TTAAGTGACCAAATCCTTATTTTTTTA
1 TTAAGTGACAAAATCCTTATTTTTTAA
* * * *
639 TTTACTCAAAAAAATCCTTATTTTTATAA
1 TTAAGT-GACAAAATCCTTATTTTT-TAA
668 TTAAGTGACAAAA
1 TTAAGTGACAAAA
681 ATAGAAAATC
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
27 4 0.13
28 20 0.67
29 6 0.20
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (27 bp):
TTAAGTGACAAAATCCTTATTTTTTAA
Found at i:1125 original size:21 final size:21
Alignment explanation
Indices: 1101--1182 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 21
1091 AATTTTGGAA
* *
1101 GTTATCAAAATTCATTGTGTG
1 GTTATCAAAATTTATAGTGTG
1122 GTTA-CTAAAATTTATAGTGTG
1 GTTATC-AAAATTTATAGTGTG
*
1143 GTTCTCAAAATTTTATAGTGTG
1 GTTATCAAAA-TTTATAGTGTG
*
1165 GTTACCAAAATTTCATAG
1 GTTATCAAAATTT-ATAG
1183 GTAGGATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.02
21 27 0.52
22 24 0.46
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (21 bp):
GTTATCAAAATTTATAGTGTG
Found at i:1160 original size:22 final size:23
Alignment explanation
Indices: 1101--1182 Score: 95
Period size: 22 Copynumber: 3.8 Consensus size: 23
1091 AATTTTGGAA
* *
1101 GTTA-TCAAAA-TTCATTGTGTG
1 GTTACTCAAAATTTTATAGTGTG
1122 GTTACT-AAAA-TTTATAGTGTG
1 GTTACTCAAAATTTTATAGTGTG
1143 GTT-CTCAAAATTTTATAGTGTG
1 GTTACTCAAAATTTTATAGTGTG
*
1165 GTTAC-CAAAATTTCATAG
1 GTTACTCAAAATTTTATAG
1183 GTAGGATGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
20 2 0.04
21 24 0.44
22 27 0.50
23 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (23 bp):
GTTACTCAAAATTTTATAGTGTG
Found at i:1291 original size:22 final size:22
Alignment explanation
Indices: 1230--1493 Score: 189
Period size: 22 Copynumber: 11.8 Consensus size: 22
1220 TCCATGGGTT
*
1230 GTTATCAAATTTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
1252 GTTATTAAAATAAAATTTCATAAGGAT
1 GTTA-T----CAAAATTTCATAAGGAG
*
1279 GTTATCAAAATTTTCATATGGAG
1 GTTATCAAAA-TTTCATAAGGAG
1302 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
1324 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAAGG-AG
* *
1345 GTTGTCAAAATTTCACAAGGAG
1 GTTATCAAAATTTCATAAGGAG
****
1367 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAAGGAG
* *
1389 GTTATCAAAATTTCATAGGGCG
1 GTTATCAAAATTTCATAAGGAG
* * *
1411 ATTATCGAAATCTT-ATATGGAG
1 GTTATCAAAAT-TTCATAAGGAG
*
1433 GTTATTAAAATTTCAT-AGGAAG
1 GTTATCAAAATTTCATAAGG-AG
* *
1455 ATTATCAAAATTTCAT-AGTGTG
1 GTTATCAAAATTTCATAAG-GAG
* *
1477 CTTATAAAAATTTCATA
1 GTTATCAAAATTTCATA
1494 GTGTGCTTAT
Statistics
Matches: 190, Mismatches: 36, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.01
21 20 0.11
22 122 0.64
23 27 0.14
26 1 0.01
27 18 0.09
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:1353 original size:43 final size:44
Alignment explanation
Indices: 1263--2275 Score: 219
Period size: 44 Copynumber: 22.8 Consensus size: 44
1253 TTATTAAAAT
* *
1263 AAAATTTCATAAGGATGTTATCAAAATTTTCATATGGAGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAA-TTTCATAGGGAGGTTATC
* *
1308 AAAATTTCATAAGGAGGTTATCGAAA-TTCAT-GGGAAGGTTGTC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGG-AGGTTATC
* ****
1351 AAAATTTCACAAGGAGGTTA-CTAAAATTTCATACTCTGGTTATC
1 AAAATTTCATAAGGAGGTTATC-AAAATTTCATAGGGAGGTTATC
* * * * * *
1395 AAAATTTCATAGGGCGATTATCGAAATCTT-ATATGGAGGTTATT
1 AAAATTTCATAAGGAGGTTATCAAAAT-TTCATAGGGAGGTTATC
* * * * *
1439 AAAATTTCAT-AGGAAGATTATCAAAATTTCATAGTGTGCTTATA
1 AAAATTTCATAAGG-AGGTTATCAAAATTTCATAGGGAGGTTATC
* * * *
1483 AAAATTTCAT-AGTGTGCTTATAAAAATTACATAGTGAGATAGAGTGAGCTTAAT-
1 AAAATTTCATAAG-GAGGTTATCAAAATTTCATA--G-G---GA--G-G-TT-ATC
* * * * * ** *
1537 AAAATTTC--AAGTGTTGTTCTCTTCACAATTTCA-AGTGTTGTTACC
1 AAAATTTCATAAG-G-AGGT-T-ATCAAAATTTCATAGGGAGGTTATC
* * * * * *
1582 AAAATTTCATATGTA-ATAATCACAATTTCATA--GAGGTTAAC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
** * * * *
1623 AAAATTTCATGGGGAGATTATCAAAATTTTAGAGGG-GATAATATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGT--TATC
* * * **
1668 AAAATTTCAT-AGTGTGGTTATCAAAATTTTATA---ATGTGGT-
1 AAAATTTCATAAG-GAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * * *
1708 ---ATTTCA-AAGGGAGAGGTTATTAAATTTTGATTGTGTGG-TAGTT
1 AAAATTTCATAA--G-GAGGTTATCAAAATTTCATAGGGAGGTTA-TC
* * * * *
1751 AAAATTTCATAATGAGTTTATCAAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
** * * * * * *
1794 AAAATTTGGTAATGTGGTTCTCAAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* ** * **
1838 AAAATTTCAT-AGGTAAGTTATCGTAATTTTAT-GGTGTAATTAATTATC
1 AAAATTTCATAAGG-AGGTTATCAAAATTTCATAGG-G--A--GGTTATC
* * * * ***
1886 AAAATTTCAT-TGGGGGTTATCAAAATTTAATAGTGTTCTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
** ** * * * * * *
1929 AAAATTTTGT-AGTTGGTTAACGAAATTTTATAAGGAGATTATAA
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTAT-C
* * *
1973 AAAATTT-ATAGGGATGTTATCAAAATTTCATA-AGATGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGA-GGTTATC
* * * *
2016 AAAATTTCATAAGGTGGTTTTCAAAATTTCAAATGGAGGTTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGG-TTATC
* * * * *
2061 AGAATTTTAT-AGGAAAGTTTATAAAAATTTCATAGTGAGG-TATC
1 AAAATTTCATAAGG--AGGTTATCAAAATTTCATAGGGAGGTTATC
* * * ** * *
2105 ACAATTT--TATGGTATGGTTATCAGAATTTCATAATGTGATTATC
1 AAAATTTCATAAGG-A-GGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * * *
2149 AATATTTTAT-TGGAAGGTTATCAAAATATCATAAGGTGCGCTTAAC
1 AAAATTTCATAAGG-AGGTTATCAAAATTTCAT-AGG-GAGGTTATC
* ** * *
2195 AACATTTCATTGGGAGGCTATCAAAATTTCATA-GGTGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * *
2238 AAAATTTCATTAGGTGGTTATTAAAATTTTTATAGGGA
1 AAAATTTCATAAGGAGGTTATCAAAA-TTTCATAGGGA
2276 TCTGAATTGT
Statistics
Matches: 704, Mismatches: 190, Indels: 148
0.68 0.18 0.14
Matches are distributed among these distances:
37 7 0.01
39 16 0.02
41 19 0.03
42 31 0.04
43 167 0.24
44 244 0.35
45 91 0.13
46 58 0.08
47 20 0.03
48 18 0.03
49 1 0.00
50 1 0.00
52 1 0.00
53 5 0.01
54 13 0.02
55 4 0.01
56 8 0.01
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (44 bp):
AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
Found at i:1494 original size:22 final size:22
Alignment explanation
Indices: 1434--1518 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
1424 TATATGGAGG
* * *
1434 TTATTAAAATTTCATAG-GAAGA
1 TTATAAAAATTTCATAGTG-TGC
*
1456 TTATCAAAATTTCATAGTGTGC
1 TTATAAAAATTTCATAGTGTGC
1478 TTATAAAAATTTCATAGTGTGC
1 TTATAAAAATTTCATAGTGTGC
*
1500 TTATAAAAATTACATAGTG
1 TTATAAAAATTTCATAGTG
1519 AGATAGAGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 56 0.98
23 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (22 bp):
TTATAAAAATTTCATAGTGTGC
Found at i:1587 original size:21 final size:23
Alignment explanation
Indices: 1537--1590 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1527 TGAGCTTAAT
*
1537 AAAATTTCAAGTGTTGTTCTCTTC
1 AAAATTTCAAGTGTTGTTCAC-TC
*
1561 ACAATTTCAAGTGTTGTT-AC-C
1 AAAATTTCAAGTGTTGTTCACTC
1582 AAAATTTCA
1 AAAATTTCA
1591 TATGTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.33
23 1 0.04
24 17 0.63
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (23 bp):
AAAATTTCAAGTGTTGTTCACTC
Found at i:1650 original size:22 final size:22
Alignment explanation
Indices: 1622--1696 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1612 TAGAGGTTAA
1622 CAAAATTTCATGGGGAGATTAT
1 CAAAATTTCATGGGGAGATTAT
* * * *
1644 CAAAATTTTAGAGGGGATAATAT
1 CAAAATTTCA-TGGGGAGATTAT
* * * *
1667 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATGGGGAGATTAT
1689 CAAAATTT
1 CAAAATTT
1697 TATAATGTGG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 22 0.55
23 18 0.45
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATGGGGAGATTAT
Found at i:1705 original size:22 final size:22
Alignment explanation
Indices: 1664--1707 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1654 GAGGGGATAA
*
1664 TATCAAAATTTCATAGTGTGGT
1 TATCAAAATTTCATAATGTGGT
*
1686 TATCAAAATTTTATAATGTGGT
1 TATCAAAATTTCATAATGTGGT
1708 ATTTCAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (22 bp):
TATCAAAATTTCATAATGTGGT
Found at i:1850 original size:22 final size:22
Alignment explanation
Indices: 1751--1849 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
1741 TGTGGTAGTT
* * *
1751 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAGTGAGATTAAC
1773 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
** * * * **
1794 AAAATTTGGTAATGTGGTTCTC
1 AAAATTTCATAGTGAGATTAAC
* *
1816 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
1838 AAAATTTCATAG
1 AAAATTTCATAG
1850 GTAAGTTATC
Statistics
Matches: 58, Mismatches: 18, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 18 0.31
22 40 0.69
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAAC
Found at i:2111 original size:111 final size:110
Alignment explanation
Indices: 1967--2266 Score: 277
Period size: 111 Copynumber: 2.7 Consensus size: 110
1957 TATAAGGAGA
*
1967 TTATAAAAAATTT-ATAGGGATGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAAGGT
1 TTAT-AAAAATTTCATAGGGA-GGTATCAAAATTTCAT-AGATGGTTATCAAAATTTCATAAGGT
* * * *
2031 GGTTTTCAAAATTTCAAATGG-AGGTTTATCAGAATTTTAT-AGGAAAGT
63 GGTTTTCAAAATTT-AAATGGAAGG-TTATCAAAATATCATAAGGAAAGC
* * * * * * *
2079 TTATAAAAATTTCATAGTGAGGTATCACAATTTTATGGTATGGTTATCAGAATTTCATAATGTGA
1 TTATAAAAATTTCATAGGGAGGTATCAAAATTTCATAG-ATGGTTATCAAAATTTCATAAGGTGG
* * * * ***
2144 TTATCAATATTTTATTGGAAGGTTATCAAAATATCATAAGGTGCGC
65 TTTTCAAAATTTAAATGGAAGGTTATCAAAATATCATAAGGAAAGC
* * * *
2190 TTA-ACAACATTTCATTGGGAGGCTATCAAAATTTCATAGGTGGTTATCAAAATTTCATTAGGTG
1 TTATA-AAAATTTCATAGGGAGG-TATCAAAATTTCATAGATGGTTATCAAAATTTCATAAGGTG
2254 GTTATT-AAAATTT
64 GTT-TTCAAAATTT
2267 TTATAGGGAT
Statistics
Matches: 149, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
110 18 0.12
111 107 0.72
112 24 0.16
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (110 bp):
TTATAAAAATTTCATAGGGAGGTATCAAAATTTCATAGATGGTTATCAAAATTTCATAAGGTGGT
TTTCAAAATTTAAATGGAAGGTTATCAAAATATCATAAGGAAAGC
Found at i:2273 original size:22 final size:21
Alignment explanation
Indices: 1881--2266 Score: 195
Period size: 22 Copynumber: 17.6 Consensus size: 21
1871 GTGTAATTAA
* *
1881 TTATCAAAATTTCATTGGGGG
1 TTATCAAAATTTCATAGGTGG
* **
1902 TTATCAAAATTTAATAGTGTTC
1 TTATCAAAATTTCATAG-GTGG
** *
1924 TTATCAAAATTTTGTAGTTGG
1 TTATCAAAATTTCATAGGTGG
* * * * *
1945 TTAACGAAATTTTATAAGGAGA
1 TTATCAAAATTTCAT-AGGTGG
*
1967 TTATAAAAAATTT-ATAGG-GATG
1 TTAT-CAAAATTTCATAGGTG--G
*
1989 TTATCAAAATTTCATAAGATGG
1 TTATCAAAATTTCAT-AGGTGG
2011 TTATCAAAATTTCATAAGGTGG
1 TTATCAAAATTTCAT-AGGTGG
* * *
2033 TTTTCAAAATTTCAAATGGAGG
1 TTATCAAAATTTCATA-GGTGG
* * * *
2055 TTTATCAGAATTTTATAGGAAAGT
1 -TTATCAAAATTTCATAGG--TGG
*
2079 TTATAAAAATTTCATA-GTGAG
1 TTATCAAAATTTCATAGGTG-G
* * *
2100 GTATCACAATTTTAT-GGTATGG
1 TTATCAAAATTTCATAGG--TGG
* * *
2122 TTATCAGAATTTCATAATGTGA
1 TTATCAAAATTTCAT-AGGTGG
* * * *
2144 TTATCAATATTTTATTGGAAGG
1 TTATCAAAATTTCATAGG-TGG
*
2166 TTATCAAAATATCATAAGGTGCG
1 TTATCAAAATTTCAT-AGGTG-G
* * * *
2189 CTTAACAACATTTCATTGGGAGG
1 -TTATCAAAATTTCA-TAGGTGG
*
2212 CTATCAAAATTTCATAGGTGG
1 TTATCAAAATTTCATAGGTGG
2233 TTATCAAAATTTCATTAGGTGG
1 TTATCAAAATTTCA-TAGGTGG
*
2255 TTATTAAAATTT
1 TTATCAAAATTT
2267 TTATAGGGAT
Statistics
Matches: 272, Mismatches: 69, Indels: 47
0.70 0.18 0.12
Matches are distributed among these distances:
20 2 0.01
21 70 0.26
22 142 0.52
23 39 0.14
24 18 0.07
25 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:2384 original size:22 final size:22
Alignment explanation
Indices: 2288--2420 Score: 64
Period size: 22 Copynumber: 6.2 Consensus size: 22
2278 TGAATTGTAA
* *
2288 CAAAATTTTATAG-GAAAGTTAA
1 CAAAATTTTATAGTGGAA-TTAT
* *
2310 CAAAATTTCATA-TGGACATTCT
1 CAAAATTTTATAGTGGA-ATTAT
* * *
2332 CGAAATTCTATAGT--ATATCAT
1 CAAAATTTTATAGTGGA-ATTAT
* * *
2353 AAAAACTTTATAGTGTAATTAT
1 CAAAATTTTATAGTGGAATTAT
* *
2375 CAAAATTTTATA-TGGAGGTTAG
1 CAAAATTTTATAGTGGA-ATTAT
*
2397 CAGAATTTTATAGT-G-ATTAT
1 CAAAATTTTATAGTGGAATTAT
2417 CAAA
1 CAAA
2421 TTTCATAAAA
Statistics
Matches: 80, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
20 6 0.08
21 17 0.21
22 53 0.66
23 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
CAAAATTTTATAGTGGAATTAT
Found at i:12237 original size:2 final size:2
Alignment explanation
Indices: 12232--12260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12222 ACGGCTTTTA
12232 AT 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 AT A
12261 AGGATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16025 original size:31 final size:29
Alignment explanation
Indices: 15973--16070 Score: 178
Period size: 29 Copynumber: 3.3 Consensus size: 29
15963 ATTTTTAAAT
15973 AAAGCACAATTTACTTTTTTTTTGGCACA
1 AAAGCACAATTTACTTTTTTTTTGGCACA
16002 AAAGCACAATTTACTTTTTTTTTTTGGCACA
1 AAAGCACAATTTAC--TTTTTTTTTGGCACA
16033 AAAGCACAATTTACTTTTTTTTTGGCACA
1 AAAGCACAATTTACTTTTTTTTTGGCACA
16062 AAAGCACAA
1 AAAGCACAA
16071 GTAAATCCTT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
29 38 0.57
31 29 0.43
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (29 bp):
AAAGCACAATTTACTTTTTTTTTGGCACA
Found at i:32868 original size:206 final size:206
Alignment explanation
Indices: 32511--32909 Score: 690
Period size: 206 Copynumber: 1.9 Consensus size: 206
32501 TATGATTGAA
*
32511 GGCAAATTATACAATACACCGGCGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGA
1 GGCAAATTATACAATACACCGACGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGA
*
32576 CATATGTCCTTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTG
66 CATATGTCATTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTG
* **
32641 TCAACTCCACAACCTGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCAT
131 TCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTACCCAT
32706 GATTGAATTAT
196 GATTGAATTAT
* * * *
32717 GGCAAATTATACAATATACCGATGGTGGAGTTTAGCAGACTACACAAGCGGGTTCTGAAGGGTGA
1 GGCAAATTATACAATACACCGACGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGA
* * *
32782 CATGTGTTATTTAGGGATTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTG
66 CATATGTCATTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTG
32847 TCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTACCC
131 TCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTACCC
32910 TTGAATTATA
Statistics
Matches: 181, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
206 181 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (206 bp):
GGCAAATTATACAATACACCGACGGTGGAGTTTAGCAAACTACACAAGCGGGTCCTGAAGGGTGA
CATATGTCATTTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTG
TCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTACCCAT
GATTGAATTAT
Found at i:51310 original size:112 final size:112
Alignment explanation
Indices: 51182--51406 Score: 423
Period size: 112 Copynumber: 2.0 Consensus size: 112
51172 CCTACTCCCC
51182 AATCCCAAACCAAAACAGAAAAAAGAAATGCATACAATGACATAACAAAGCACATATGGTAGGCA
1 AATCCCAAACCAAAACAGAAAAAAGAAATGCATACAATGACATAACAAAGCACATATGGTAGGCA
51247 CCTAAGAACGCTATTACAAAGTACACATTCCTCTATTGAATATTCAT
66 CCTAAGAACGCTATTACAAAGTACACATTCCTCTATTGAATATTCAT
* *
51294 AATCCCAAACCAAAACAGAAAAAAGAATTGCATACAATGACATAACAAAGCACATATGTTAGGCA
1 AATCCCAAACCAAAACAGAAAAAAGAAATGCATACAATGACATAACAAAGCACATATGGTAGGCA
*
51359 CCTAAGAATGCTATTACAAAGTACACATTCCTCTATTGAATATTCAT
66 CCTAAGAACGCTATTACAAAGTACACATTCCTCTATTGAATATTCAT
51406 A
1 A
51407 TCAATAACAG
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (112 bp):
AATCCCAAACCAAAACAGAAAAAAGAAATGCATACAATGACATAACAAAGCACATATGGTAGGCA
CCTAAGAACGCTATTACAAAGTACACATTCCTCTATTGAATATTCAT
Found at i:53397 original size:21 final size:20
Alignment explanation
Indices: 53364--53403 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53354 ATTAAAGCTT
* *
53364 TTTTCTTTTCTTTTTTGTTA
1 TTTTCTTTACTTTCTTGTTA
53384 TTTTCTTTAACTTTCTTGTT
1 TTTTCTTT-ACTTTCTTGTT
53404 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTCTTTACTTTCTTGTTA
Found at i:56546 original size:26 final size:24
Alignment explanation
Indices: 56512--56559 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
56502 ATGTCAATGG
56512 CAAACAAG-TCATTGCATTGCTTAAC
1 CAAACAAGTTCATT-CATT-CTTAAC
56537 CAAACCAAGTTCATTCATTCTTA
1 CAAA-CAAGTTCATTCATTCTTA
56560 CACTAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 8 0.38
26 8 0.38
27 5 0.24
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (24 bp):
CAAACAAGTTCATTCATTCTTAAC
Found at i:70741 original size:18 final size:19
Alignment explanation
Indices: 70718--70753 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
70708 AACTCAAAGC
*
70718 ATGATAA-AATCCTTCTTA
1 ATGATAAGAATCCATCTTA
70736 ATGATAAGAATCCATCTT
1 ATGATAAGAATCCATCTT
70754 TAAGATCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
ATGATAAGAATCCATCTTA
Found at i:72025 original size:15 final size:15
Alignment explanation
Indices: 72005--72047 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
71995 AAAACTATAT
72005 AAAATTAAATTTTAA
1 AAAATTAAATTTTAA
72020 AAAATTAAATTTTAA
1 AAAATTAAATTTTAA
*
72035 AAAATTATATTTT
1 AAAATTAAATTTT
72048 TGATTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTAAATTTTAA
Done.