Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007993.1 Corchorus capsularis cultivar CVL-1 contig08014, 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: 50078
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2300 original size:16 final size:16
Alignment explanation
Indices: 2279--2309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2269 TTGCATTGTT
2279 TTGCTTCGATTGATTA
1 TTGCTTCGATTGATTA
*
2295 TTGCTTTGATTGATT
1 TTGCTTCGATTGATT
2310 GCCTATTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.19, T:0.55
Consensus pattern (16 bp):
TTGCTTCGATTGATTA
Found at i:3901 original size:30 final size:30
Alignment explanation
Indices: 3866--3925 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3856 AAGTTCGTGT
* *
3866 TTGAAGACTTATTG-AAGATAATTTCAAGAA
1 TTGAAGAC-CATTGAAAAATAATTTCAAGAA
*
3896 TTGAAGACCATTGAAAAATTATTTCAAGAA
1 TTGAAGACCATTGAAAAATAATTTCAAGAA
3926 GCAAAAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
TTGAAGACCATTGAAAAATAATTTCAAGAA
Found at i:6181 original size:49 final size:50
Alignment explanation
Indices: 6021--6273 Score: 339
Period size: 50 Copynumber: 5.1 Consensus size: 50
6011 AGATGTGAAG
* * * *
6021 AGAAAAC-TGGACCTTCCGACCGGGAAGGGACATTTTGGGAAACAAATTAG
1 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAA-CAA
* * *
6071 AGAAAACATGGACCTTCCAACCAGGAAGGGGCATTTTGGGAAACAAACAA
1 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * *
6121 AGGAAATAAGGACCTTCCGACCAGGAAGGGGCATTTT-GGAAACAAACAA
1 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* *
6170 AGAAAACAAGGACCTTCAGACCGGGTAGGGGCATTTTGGGAAACAAACAA
1 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
* * * *
6220 AGGAAACAAGGACCTTCTGACCGGGAAGGGGCATTTTTGGAAACAAAGAA
1 AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
6270 AGAA
1 AGAA
6274 GGGGCATTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 44 0.24
50 101 0.56
51 36 0.20
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (50 bp):
AGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGAAACAAACAA
Found at i:6207 original size:99 final size:99
Alignment explanation
Indices: 6029--6273 Score: 357
Period size: 99 Copynumber: 2.4 Consensus size: 99
6019 AGAGAAAACT
* * * *
6029 GGACCTTCCGACCGGGAAGGGACATTTTGGGAAACAAATTAGAGAAAACATGGACCTTCCAACCA
1 GGACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAA-CAAAGAAAACAAGGACCTTCCAACCA
*
6094 GGAAGGGGCATTTTGGGAAACAAACAAAGGAAATAA
64 GGAAGGGGCATTTTGGGAAACAAACAAAGGAAACAA
* *
6130 GGACCTTCCGACCAGGAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTT-CAGACCGG
1 GGACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTTCCA-ACCAG
*
6194 GTAGGGGCATTTTGGGAAACAAACAAAGGAAACAA
65 GAAGGGGCATTTTGGGAAACAAACAAAGGAAACAA
* *
6229 GGACCTTCTGACCGGGAAGGGGCATTTTTGGAAACAAAGAAAGAA
1 GGACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAACAAAGAA
6274 GGGGCATTTT
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
98 2 0.02
99 75 0.57
100 28 0.21
101 26 0.20
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (99 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTTCCAACCAGG
AAGGGGCATTTTGGGAAACAAACAAAGGAAACAA
Found at i:6282 original size:27 final size:27
Alignment explanation
Indices: 6244--6300 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
6234 TTCTGACCGG
6244 GAAGGGGCATTTTTGGAAACAAAGAAA
1 GAAGGGGCATTTTTGGAAACAAAGAAA
6271 GAAGGGGCATTTTTGGAAACAAAGAAA
1 GAAGGGGCATTTTTGGAAACAAAGAAA
6298 GAA
1 GAA
6301 AGAGGGACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.30, T:0.18
Consensus pattern (27 bp):
GAAGGGGCATTTTTGGAAACAAAGAAA
Found at i:6326 original size:126 final size:126
Alignment explanation
Indices: 6145--6387 Score: 371
Period size: 126 Copynumber: 1.9 Consensus size: 126
6135 TTCCGACCAG
*
6145 GAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTTCAGACCGGGTAGGGGCATTTTGGG
1 GAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTTCAGACCGGGAAGGGGCATTTTGGG
* *
6210 AAACAAACAAAGGAAACAAGGACCTTCTGACCGGGAAGGGGCATTTTTGGAAACAAAGAAA
66 AAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAGAAA
* * * * *
6271 GAAGGGGCATTTTTGGAAACAAAGAAAG-AAAGAGGGACCTTCCGACTGGGAAGGGGCATTTTGG
1 GAAGGGGCA-TTTTGGAAACAAACAAAGAAAACAAGGACCTTCAGACCGGGAAGGGGCATTTTGG
* * *
6335 GAAACAAATAGAGAAAACATGGACCTTCCGACCGGGAAGGGGCATTTTTGGAA
65 GAAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTTGGAA
6388 TAAGTGAAGT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
126 88 0.84
127 17 0.16
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.16
Consensus pattern (126 bp):
GAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTTCAGACCGGGAAGGGGCATTTTGGG
AAACAAACAAAGAAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAAGAAA
Found at i:6329 original size:76 final size:77
Alignment explanation
Indices: 6196--6342 Score: 224
Period size: 76 Copynumber: 1.9 Consensus size: 77
6186 CAGACCGGGT
* *
6196 AGGGGCATTTTGGGAAACAAACAAAGGAAACAAGGACCTTCTGACCGGGAAGGGGCATTTTTGGA
1 AGGGGCATTTTGGGAAACAAACAAAGGAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGA
6261 AACAAAGAAAGA
66 AACAAAGAAAGA
* * * * *
6273 AGGGGCATTTTTGGAAACAAAGAAA-GAAAGAGGGACCTTCCGACTGGGAAGGGGCATTTTGGGA
1 AGGGGCATTTTGGGAAACAAACAAAGGAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGA
6337 AACAAA
66 AACAAA
6343 TAGAGAAAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
76 40 0.63
77 23 0.37
ACGTcount: A:0.39, C:0.14, G:0.31, T:0.16
Consensus pattern (77 bp):
AGGGGCATTTTGGGAAACAAACAAAGGAAACAAGGACCTTCCGACCGGGAAGGGGCATTTTGGGA
AACAAAGAAAGA
Found at i:6350 original size:49 final size:50
Alignment explanation
Indices: 6271--6387 Score: 173
Period size: 50 Copynumber: 2.4 Consensus size: 50
6261 AACAAAGAAA
* *
6271 GAAGGGGCATTTTTGGAAACAAAGAAAG-AAAGAGGGACCTTCCGACTGG
1 GAAGGGGCATTTTTGGAAACAAAGAAAGAAAACAGGGACCTTCCGACCGG
* * * *
6320 GAAGGGGCATTTTGGGAAACAAATAGAGAAAACATGGACCTTCCGACCGG
1 GAAGGGGCATTTTTGGAAACAAAGAAAGAAAACAGGGACCTTCCGACCGG
6370 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
6388 TAAGTGAAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
49 25 0.42
50 35 0.58
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (50 bp):
GAAGGGGCATTTTTGGAAACAAAGAAAGAAAACAGGGACCTTCCGACCGG
Found at i:6492 original size:41 final size:39
Alignment explanation
Indices: 6397--6515 Score: 159
Period size: 41 Copynumber: 3.0 Consensus size: 39
6387 ATAAGTGAAG
* * *
6397 TAAACAACACCTTCCGATAGGGTATGGCAGACT-AGAAAC
1 TAAACAACACCTTCCGAT-GGGGAAGGTAGACTGAGAAAC
6436 TAAACAACACCTTCCGATGGGGAAGAGTAGACTGAGAAAC
1 TAAACAACACCTTCCGATGGGGAAG-GTAGACTGAGAAAC
*
6476 TTAAACAACACCTTCCGATGGGGAAGGGTAGACTGGGAAA
1 -TAAACAACACCTTCCGATGGGGAA-GGTAGACTGAGAAA
6516 TGAGAAATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
38 5 0.07
39 24 0.33
40 6 0.08
41 36 0.50
42 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (39 bp):
TAAACAACACCTTCCGATGGGGAAGGTAGACTGAGAAAC
Found at i:7858 original size:51 final size:51
Alignment explanation
Indices: 7802--8070 Score: 190
Period size: 51 Copynumber: 5.3 Consensus size: 51
7792 TTTGGTTCAA
* *
7802 AAATTAATCACAACTTCAATCATTTAATTTAAAGATTTCATTTTTATTTAC
1 AAATTAATCAAAACTTCAATCATTTAATTCAAAGATTTCATTTTTATTTAC
* * * ** *
7853 AAATTAATCAAAAGTTTAATTA-TTAACTT-AAAGATTTCACCTTTA-TCACC
1 AAATTAATCAAAACTTCAATCATTTAA-TTCAAAGATTTCATTTTTATTTA-C
** * *
7903 AAATTAATCCAAAGTTTC-ATCTTTTAGTTCAAAGATTTCATTTTTATTTAC
1 AAATTAAT-CAAAACTTCAATCATTTAATTCAAAGATTTCATTTTTATTTAC
* * * * *
7954 AAATCAATCAAAAATTTCTAAT-TTTTAGTTCAAAGATCTCA-TTTTATTTAC
1 AAATTAATC-AAAACTTC-AATCATTTAATTCAAAGATTTCATTTTTATTTAC
* * * * *** * * *
8005 AAGTTAATAAAAACTTTACTCATTTAACAAAAAAAAATCTCATTCTTATTTAC
1 AAATTAATCAAAACTTCAATCATTT-A-ATTCAAAGATTTCATTTTTATTTAC
8058 AAATTAATCAAAA
1 AAATTAATCAAAA
8071 GTTTAATTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
49 4 0.02
50 41 0.24
51 75 0.44
52 29 0.17
53 22 0.13
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (51 bp):
AAATTAATCAAAACTTCAATCATTTAATTCAAAGATTTCATTTTTATTTAC
Found at i:7884 original size:50 final size:51
Alignment explanation
Indices: 7832--8128 Score: 208
Period size: 51 Copynumber: 5.8 Consensus size: 51
7822 CATTTAATTT
7832 AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAATTATTAACTT-
1 AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAATTATTAACTTC
** * * * * *
7882 AAAGATTTCACCTTTA-TCACCAAATTAATCCAAAGTTTCATCT-TTTAGTTC
1 AAAGATTTCATTTTTATTTA-CAAATTAATCAAAAGTTTAAT-TATTAACTTC
* * * *
7933 AAAGATTTCATTTTTATTTACAAATCAATCAAAAATTTCTAATT-TTTAGTTC
1 AAAGATTTCATTTTTATTTACAAATTAATC-AAAAGTT-TAATTATTAACTTC
* * * * * * ***
7985 AAAGATCTCA-TTTTATTTACAAGTTAATAAAAACTTTACTCATTTAACAAAA
1 AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAATTA-TTAAC-TTC
* * * * ** *
8037 AAAAATCTCATTCTTATTTACAAATTAATCAAAAGTTTAATTTTTAGTTTA
1 AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAATTATTAACTTC
** * * * *
8088 AAAGACATAATTTTCATTTACAAATTTACCAAAAGTTTAAT
1 AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAAT
8129 CTTTTACTTA
Statistics
Matches: 191, Mismatches: 46, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
49 5 0.03
50 44 0.23
51 77 0.40
52 37 0.19
53 28 0.15
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (51 bp):
AAAGATTTCATTTTTATTTACAAATTAATCAAAAGTTTAATTATTAACTTC
Found at i:12931 original size:2 final size:2
Alignment explanation
Indices: 12924--13045 Score: 84
Period size: 2 Copynumber: 65.0 Consensus size: 2
12914 TAAAGCAATA
* *
12924 AT AT AT AT AA AT AT AT -T AT AT AT AT AT A- AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
12964 AT AT -T AT -T GCT TT GT -T AT AT AT AT AT -T AT AT AT -T AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
13002 A- AT AT AT TT AT AT AT AT -T AT -T GCT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
13042 AT AT
1 AT AT
13046 TACCAAAGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
1 10 0.10
2 86 0.88
3 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:12945 original size:15 final size:14
Alignment explanation
Indices: 12921--13021 Score: 53
Period size: 15 Copynumber: 6.9 Consensus size: 14
12911 AAATAAAGCA
*
12921 ATAATATATATAAAT
1 ATAATATAT-TATAT
*
12936 ATATTATA-TATAT
1 ATAATATATTATAT
12949 ATAATATATTTATAT
1 ATAATATA-TTATAT
* * *
12964 ATATTAT-TGCTTTGTT
1 ATAATATAT--TAT-AT
12980 ATATATATATTATAT
1 ATA-ATATATTATAT
* *
12995 ATTATATAATATAT
1 ATAATATATTATAT
*
13009 TTATATATATTAT
1 ATA-ATATATTAT
13022 TGCTTTATAT
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
13 12 0.19
14 11 0.17
15 31 0.48
16 6 0.09
17 3 0.05
18 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (14 bp):
ATAATATATTATAT
Found at i:12962 original size:13 final size:13
Alignment explanation
Indices: 12934--13015 Score: 60
Period size: 13 Copynumber: 6.4 Consensus size: 13
12924 ATATATATAA
* *
12934 ATATATTATATAT
1 ATATAATATATTT
12947 ATATAATATATTT
1 ATATAATATATTT
*
12960 ATAT-ATATTATTG
1 ATATAATA-TATTT
* * ** *
12973 CTTTGTTATATAT
1 ATATAATATATTT
*
12986 ATATTATATA-TT
1 ATATAATATATTT
12998 ATATAATATATTT
1 ATATAATATATTT
13011 ATATA
1 ATATA
13016 TATTATTGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
12 13 0.25
13 37 0.71
14 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (13 bp):
ATATAATATATTT
Found at i:13014 original size:51 final size:50
Alignment explanation
Indices: 12927--13047 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 50
12917 AGCAATAATA
*
12927 TATATAAATATATTATATA-TATATAATATATTTATATATATTATTGCTT
1 TATATATATATATTATATATTATATAATATATTTATATATATTATTGCTT
*
12976 TGTTATATATATATTATATATTATATAATATATTTATATATATTATTGCTT
1 T-ATATATATATATTATATATTATATAATATATTTATATATATTATTGCTT
13027 TATATATATATA-TATATATTA
1 TATATATATATATTATATATTA
13048 CCAAAGAAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
49 10 0.15
50 26 0.39
51 31 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (50 bp):
TATATATATATATTATATATTATATAATATATTTATATATATTATTGCTT
Found at i:25469 original size:16 final size:17
Alignment explanation
Indices: 25432--25469 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
25422 ATACTCTATT
*
25432 ATGAGCATCAGATTCATG
1 ATGAGCAACAGATT-ATG
25450 ATGAGCAACAGATT-TG
1 ATGAGCAACAGATTATG
25466 ATGA
1 ATGA
25470 AGGAAGAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (17 bp):
ATGAGCAACAGATTATG
Found at i:25861 original size:235 final size:235
Alignment explanation
Indices: 25450--25888 Score: 815
Period size: 235 Copynumber: 1.9 Consensus size: 235
25440 CAGATTCATG
25450 ATGAGCAACAGATTTGATGAAGGAAGAGGTCTAGGAATGGACTTGCAAGGGGTTACATAGGCTGT
1 ATGAGCAACAGATTTGATGAAGGAAGAGGTCTAGGAATGGACTTGCAAGGGGTTACATAGGCTGT
* * *
25515 TGAATTCCTTGTACATGAGGGCCCTTTCGAATTTGGATTTAAGCTGACGACTAAGAACTGGGCAG
66 TGAATTACTTGTACATGAGGGCCCTTTCGAATTGGGATTTAAGCCGACGACTAAGAACTGGGCAG
25580 AAGCTGAAGTAAGGATGAAACTAAAGAGATTGGCAAGTATGGGACACATACTAGAAGAGGAAAAG
131 AAGCTGAAGTAAGGATGAAACTAAAGAGATTGGCAAGTATGGGACACATACTAGAAGAGGAAAAG
25645 ATGGAATTCTTTTCCTAAGAGCATGATGGAATACTCTATT
196 ATGGAATTCTTTTCCTAAGAGCATGATGGAATACTCTATT
25685 ATGAGCAACAGATTTGATGAAGGAAGAGGTCTAGGAATGGACTTGCAAGGGGTTACATAGGCTGT
1 ATGAGCAACAGATTTGATGAAGGAAGAGGTCTAGGAATGGACTTGCAAGGGGTTACATAGGCTGT
*
25750 TGAATTACTTGTACATGAGGGCCCTTTCGAATTGGGATTTAAGCCGACGGCTAAGAACTGGGCAG
66 TGAATTACTTGTACATGAGGGCCCTTTCGAATTGGGATTTAAGCCGACGACTAAGAACTGGGCAG
* * *
25815 AAGTTGAAGTAAGGATGAAACTAAGGAGATTGGCAAGTATGGGACACATACTAGAAGAGGAAACG
131 AAGCTGAAGTAAGGATGAAACTAAAGAGATTGGCAAGTATGGGACACATACTAGAAGAGGAAAAG
25880 ATGGAATTC
196 ATGGAATTC
25889 CCGCCTTTGT
Statistics
Matches: 197, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
235 197 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (235 bp):
ATGAGCAACAGATTTGATGAAGGAAGAGGTCTAGGAATGGACTTGCAAGGGGTTACATAGGCTGT
TGAATTACTTGTACATGAGGGCCCTTTCGAATTGGGATTTAAGCCGACGACTAAGAACTGGGCAG
AAGCTGAAGTAAGGATGAAACTAAAGAGATTGGCAAGTATGGGACACATACTAGAAGAGGAAAAG
ATGGAATTCTTTTCCTAAGAGCATGATGGAATACTCTATT
Found at i:26341 original size:2 final size:2
Alignment explanation
Indices: 26334--26364 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
26324 TCTTCTTTCT
*
26334 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26365 TATTGATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38401 original size:30 final size:30
Alignment explanation
Indices: 38365--38422 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
38355 CATCTTAACG
38365 GCATCTCCATGAGACTTAACGATTCCATTA
1 GCATCTCCATGAGACTTAACGATTCCATTA
**
38395 GCATCTCCATGAGACTTTGCGATTCCAT
1 GCATCTCCATGAGACTTAACGATTCCAT
38423 CCTCTCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (30 bp):
GCATCTCCATGAGACTTAACGATTCCATTA
Found at i:40190 original size:50 final size:50
Alignment explanation
Indices: 40112--40278 Score: 189
Period size: 50 Copynumber: 3.3 Consensus size: 50
40102 AAATTCTTTA
* * *
40112 ACTTCTTAACTTAATCACTCTGATTTAAGCCAATTACTTATTACTATTTT
1 ACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTTATTACTATTTT
* * * *
40162 ACTTTTTAACTTAATTACTAC-GAATTAAGCCCATTACTAATTACCATTTC
1 ACTTTTTAACTTAATTACT-CTGAATTAAGCCAATTACTTATTACTATTTT
*
40212 ACTTTTTAACCT-ATTACTCTGAATTAAGCCAATTA-TTGATTA-TCATTTT
1 ACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTT-ATTACT-ATTTT
*
40261 ACTTTTTAAATTTAATTA
1 ACTTTTT-AACTTAATTA
40279 TTGATTACCA
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
48 2 0.02
49 35 0.36
50 55 0.57
51 5 0.05
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (50 bp):
ACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTTATTACTATTTT
Found at i:40341 original size:82 final size:82
Alignment explanation
Indices: 40194--40368 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
40184 AATTAAGCCC
* * * *
40194 ATTACTAATTACCATTTCACTTTTTAACCTATTACTCTGAATTAAGCCAATTATTGATTATCATT
1 ATTACTGATTACCATTTCACTTTTTAACCTATTACTCTGAATTAAGCCAATTACTAATTACCATT
*
40259 TTAC-TTTTTAAATTTA
66 TTACTTTTTTAAACTTA
* * * * *
40275 ATTATTGATTACCATTTTACTTTTTGACTTAATTACTCTGAATTAAGTCAATTACTAATTACCAT
1 ATTACTGATTACCATTTCACTTTTTAACCT-ATTACTCTGAATTAAGCCAATTACTAATTACCAT
*
40340 TTTACTTTTTTAAACTTG
65 TTTACTTTTTTAAACTTA
40358 ATTACTGATTA
1 ATTACTGATTA
40369 TTACTCTGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
81 25 0.31
82 35 0.44
83 20 0.25
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (82 bp):
ATTACTGATTACCATTTCACTTTTTAACCTATTACTCTGAATTAAGCCAATTACTAATTACCATT
TTACTTTTTTAAACTTA
Found at i:40374 original size:144 final size:143
Alignment explanation
Indices: 40223--40564 Score: 580
Period size: 144 Copynumber: 2.4 Consensus size: 143
40213 CTTTTTAACC
* * *
40223 TATTACTCTGAATTAAGCCAATTATTGATTATCATTTTACTTTTTAAATTTAATTATTGATTACC
1 TATTACTCTGAATTAAGCCAATTAATGATTACCATTTTACTTTTTAAACTTAATTATTGATTACC
40288 ATTTTACTTTTTGACTTAATTACTCTGAATTAAG-TCAATTACTAATTACCATTTTACTTTTTTA
66 ATTTTACTTTTTGACTTAATTACTCTGAATTAAGAT-AATTACTAATTACCATTTTAC-TTTTTA
40352 AACTTGATTACTGAT
129 AACTTGATTACTGAT
*
40367 TATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTATTGATTACC
1 TATTACTCTGAATTAAGCCAATTAATGATTACCATTTTACTTTTTAAACTTAATTATTGATTACC
40432 ATTTTACTTTTTGACTTAATTACTCTGAATTAAGATAATTACTAATTACCATTTTACTTTTTAAA
66 ATTTTACTTTTTGACTTAATTACTCTGAATTAAGATAATTACTAATTACCATTTTACTTTTTAAA
*
40497 CTTGTTTACTGAT
131 CTTGATTACTGAT
* * *
40510 TATTATTCTGAATTAAGCCAATTAATAATTACCATTTTACTTTTT-AACTTGATTA
1 TATTACTCTGAATTAAGCCAATTAATGATTACCATTTTACTTTTTAAACTTAATTA
40565 CTCTGAATTA
Statistics
Matches: 189, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
142 9 0.05
143 62 0.33
144 117 0.62
145 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (143 bp):
TATTACTCTGAATTAAGCCAATTAATGATTACCATTTTACTTTTTAAACTTAATTATTGATTACC
ATTTTACTTTTTGACTTAATTACTCTGAATTAAGATAATTACTAATTACCATTTTACTTTTTAAA
CTTGATTACTGAT
Found at i:40376 original size:62 final size:61
Alignment explanation
Indices: 40306--40429 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 61
40296 TTTTGACTTA
* *
40306 ATTACTCTGAATTAAGTCAATTACTAATTACCATTTTACTTTTTTAAACTTGATTACTGATT
1 ATTACTCTGAATTAAGCCAATTACTAATTACCATTTTAC-TTTTTAAACTTAATTACTGATT
* *
40368 ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTATTGATT
1 ATTACTCTGAATTAAGCCAATTACTAATTACCATTTTACTTTTTAAACTTAATTACTGATT
40429 A
1 A
40430 CCATTTTACT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 21 0.36
62 37 0.64
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (61 bp):
ATTACTCTGAATTAAGCCAATTACTAATTACCATTTTACTTTTTAAACTTAATTACTGATT
Found at i:40452 original size:31 final size:32
Alignment explanation
Indices: 40386--40455 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
40376 GAATTAAGCC
40386 AATTACTGATTACCATTTTACTTTTTAAACTT
1 AATTACTGATTACCATTTTACTTTTTAAACTT
* *
40418 AATTATTGATTACCATTTTACTTTTT-GACTT
1 AATTACTGATTACCATTTTACTTTTTAAACTT
40449 AATTACT
1 AATTACT
40456 CTGAATTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.51
Consensus pattern (32 bp):
AATTACTGATTACCATTTTACTTTTTAAACTT
Found at i:40472 original size:50 final size:50
Alignment explanation
Indices: 40426--40617 Score: 213
Period size: 50 Copynumber: 3.6 Consensus size: 50
40416 TTAATTATTG
* **
40426 ATTACCATTTTACTTTTTGACTTAATTACTCTGAATTAAGATAATTACTA
1 ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTA
* *
40476 ATTACCATTTTACTTTTTAAACTTGTTTACTGATTATTATTCTGAATTAAGCCAATTAATA
1 ATTACCATTTTACTTTTT-AAC-----T--T-A--ATTACTCTGAATTAAGCCAATTACTA
* *
40537 ATTACCATTTTACTTTTTAACTTGATTACTCTGAATTAAGCCAATTACTG
1 ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTA
40587 ATTACCATTTTACTTTTTAAACTTAATTACT
1 ATTACCATTTTACTTTTT-AACTTAATTACT
40618 GATTACCATT
Statistics
Matches: 120, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
50 59 0.49
51 13 0.11
53 1 0.01
55 1 0.01
56 1 0.01
58 1 0.01
59 1 0.01
60 3 0.03
61 40 0.33
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (50 bp):
ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTA
Found at i:40526 original size:61 final size:60
Alignment explanation
Indices: 40450--40566 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 60
40440 TTTTGACTTA
* * *
40450 ATTACTCTGAATTAAGATAATTACTAATTACCATTTTACTTTTTAAACTTGTTTACTGATT
1 ATTACTCTGAATTAAGACAATTAATAATTACCATTTTACTTTTT-AACTTGATTACTGATT
* *
40511 ATTATTCTGAATTAAGCCAATTAATAATTACCATTTTACTTTTTAACTTGATTACT
1 ATTACTCTGAATTAAGACAATTAATAATTACCATTTTACTTTTTAACTTGATTACT
40567 CTGAATTAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 11 0.22
61 40 0.78
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (60 bp):
ATTACTCTGAATTAAGACAATTAATAATTACCATTTTACTTTTTAACTTGATTACTGATT
Found at i:40567 original size:193 final size:193
Alignment explanation
Indices: 40368--40718 Score: 612
Period size: 193 Copynumber: 1.8 Consensus size: 193
40358 ATTACTGATT
*
40368 ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTATTGATTACCA
1 ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTACTGATTACCA
* *
40433 TTTTACTTTTTGACTTAATTACTCTGAATTAAGATAATTACTAATTACCATTTTACTTTTTAAAC
66 TTTTACTTTTTAACTTAATTACTCTGAATTAAGACAATTACTAATTACCATTTTACTTTTTAAAC
* * ** *
40498 TTGTTTACTGATTATTATTCTGAATTAAGCCAATTAATAATTACCATTTTACTTTTTAACTTG
131 TTGATTACTAAACATTACTCTGAATTAAGCCAATTAATAATTACCATTTTACTTTTTAACTTG
40561 ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTACTGATTACCA
1 ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTACTGATTACCA
* *
40626 TTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTAATTATCATTTTACTTTTTAAAC
66 TTTTACTTTTTAACTTAATTACTCTGAATTAAGACAATTACTAATTACCATTTTACTTTTTAAAC
40691 TTGATTACTAAACATTACTCTGAATTAA
131 TTGATTACTAAACATTACTCTGAATTAA
40719 ACAAATTTTT
Statistics
Matches: 148, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 148 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (193 bp):
ATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTTTTTAAACTTAATTACTGATTACCA
TTTTACTTTTTAACTTAATTACTCTGAATTAAGACAATTACTAATTACCATTTTACTTTTTAAAC
TTGATTACTAAACATTACTCTGAATTAAGCCAATTAATAATTACCATTTTACTTTTTAACTTG
Found at i:40623 original size:82 final size:82
Alignment explanation
Indices: 40537--40699 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
40527 CCAATTAATA
* *
40537 ATTACCATTTTACTTTTTAACTTGATTACTCTGAATTAAGCCAATTACTGATTACCATTTTACTT
1 ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTAATTACCATTTTACTT
40602 TTTAAACTTAATTACTG
66 TTTAAACTTAATTACTG
*
40619 ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTAATTATCATTTTACTT
1 ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTAATTACCATTTTACTT
*
40684 TTTAAACTTGATTACT
66 TTTAAACTTAATTACT
40700 AAACATTACT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (82 bp):
ATTACCATTTTACTTTTTAACTTAATTACTCTGAATTAAGCCAATTACTAATTACCATTTTACTT
TTTAAACTTAATTACTG
Found at i:40644 original size:31 final size:32
Alignment explanation
Indices: 40579--40648 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
40569 GAATTAAGCC
40579 AATTACTGATTACCATTTTACTTTTTAAACTT
1 AATTACTGATTACCATTTTACTTTTTAAACTT
40611 AATTACTGATTACCATTTTACTTTTT-AACTT
1 AATTACTGATTACCATTTTACTTTTTAAACTT
40642 AATTACT
1 AATTACT
40649 CTGAATTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (32 bp):
AATTACTGATTACCATTTTACTTTTTAAACTT
Found at i:40783 original size:7 final size:7
Alignment explanation
Indices: 40771--40827 Score: 71
Period size: 7 Copynumber: 8.0 Consensus size: 7
40761 CCCGTTTTCA
40771 TTCTTTT
1 TTCTTTT
40778 TTCTTTT
1 TTCTTTT
40785 TTCTTTT
1 TTCTTTT
*
40792 TTGTTTT
1 TTCTTTT
*
40799 TTGTTTT
1 TTCTTTT
40806 TTCTTTT
1 TTCTTTT
40813 TT-TTGATT
1 TTCTT--TT
40821 TTCTTTT
1 TTCTTTT
40828 ATGATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
6 2 0.04
7 37 0.82
8 4 0.09
9 2 0.04
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (7 bp):
TTCTTTT
Done.