Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020906.1 Corchorus olitorius cultivar O-4 contig20939, 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: 99874
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1090 original size:40 final size:40
Alignment explanation
Indices: 1032--1111 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1022 GGGTGATTCA
1032 AGGTACTATGAAAAGCAAAAGGAATTGTAAATAAAAGATG
1 AGGTACTATGAAAAGCAAAAGGAATTGTAAATAAAAGATG
* *
1072 AGGTACTATGCAAGGCAAAAGGAATTGTAAATAAAAGATG
1 AGGTACTATGAAAAGCAAAAGGAATTGTAAATAAAAGATG
1112 GGCCAATACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.20
Consensus pattern (40 bp):
AGGTACTATGAAAAGCAAAAGGAATTGTAAATAAAAGATG
Found at i:4277 original size:29 final size:29
Alignment explanation
Indices: 4233--4334 Score: 141
Period size: 29 Copynumber: 3.5 Consensus size: 29
4223 ACCTAGAGTA
* * * **
4233 TGCAAAAACGATCAAAATGTCCCAAAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
*
4262 TGCAAAAATGAGCAAAATGCCCCTGAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
*
4291 TGCAAAAATGACCAAAAGGCCCCTGAATG
1 TGCAAAAATGACCAAAATGCCCCTGAATG
4320 TGCAAAAATGACCAA
1 TGCAAAAATGACCAA
4335 TTAAGAAGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.16
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGAATG
Found at i:5473 original size:21 final size:21
Alignment explanation
Indices: 5449--5561 Score: 167
Period size: 21 Copynumber: 5.4 Consensus size: 21
5439 CTTAGGCAGT
*
5449 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5470 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5491 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
5512 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
* *
5533 TCCATTGAGCTTTGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
5554 TCCAATGA
1 TCCAATGA
5562 ACTCCTAGCA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 84 0.97
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:5766 original size:58 final size:58
Alignment explanation
Indices: 5667--5862 Score: 365
Period size: 58 Copynumber: 3.4 Consensus size: 58
5657 TTGGCGCATC
*
5667 AGACCTCGACCAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
1 AGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
5726 AGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
1 AGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
*
5784 AGACCTCGAGCAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
1 AGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
5842 AGACCTCGAACAGGATTTTAA
1 AGACCTCGAACAGGATTTTAA
5863 TCTCTAACAA
Statistics
Matches: 134, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
58 116 0.87
59 18 0.13
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (58 bp):
AGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAACAG
Found at i:5870 original size:31 final size:31
Alignment explanation
Indices: 5832--5893 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
5822 AATTGAAAAC
* *
5832 TCTCTAACAGAGACCTCGAACAGGATTTTAA
1 TCTCTAACAAAGACCTCGAACAAGATTTTAA
5863 TCTCTAACAAAGACCTCGAACAAGATTTTAA
1 TCTCTAACAAAGACCTCGAACAAGATTTTAA
5894 AACAAGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (31 bp):
TCTCTAACAAAGACCTCGAACAAGATTTTAA
Found at i:5925 original size:89 final size:89
Alignment explanation
Indices: 5774--5951 Score: 329
Period size: 89 Copynumber: 2.0 Consensus size: 89
5764 AATTGAAAAC
* * *
5774 TCTCTAACAGAGACCTCGAGCAGGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
1 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
5839 CAGAGACCTCGAACAGGATTTTAA
66 CAGAGACCTCGAACAGGATTTTAA
5863 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
1 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
5928 CAGAGACCTCGAACAGGATTTTAA
66 CAGAGACCTCGAACAGGATTTTAA
5952 AACAAGATAA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (89 bp):
TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGAATTGAAAACTCTCTAA
CAGAGACCTCGAACAGGATTTTAA
Found at i:5953 original size:58 final size:57
Alignment explanation
Indices: 5863--5978 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 57
5853 AGGATTTTAA
5863 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGAATTGAAAAC
1 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTG-ATTGAAAAC
* * *
5921 TCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAGATAAGATTTTGATTTAAAAC
1 TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGATTGAAAAC
5978 T
1 T
5979 AAAACTCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 9 0.16
58 46 0.84
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.28
Consensus pattern (57 bp):
TCTCTAACAAAGACCTCGAACAAGATTTTAAAACAAGATAAGATTTTGATTGAAAAC
Found at i:6904 original size:1 final size:1
Alignment explanation
Indices: 6898--6925 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6888 TTAGGTCCAG
6898 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
6926 AGCTCCGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6910 original size:38 final size:38
Alignment explanation
Indices: 6791--6910 Score: 163
Period size: 38 Copynumber: 3.2 Consensus size: 38
6781 TTATTTATTA
* * *
6791 TTTTTTTCTGACCTCTTTCT-GTTTAGG-CTAGGTTTTT
1 TTTTTTTC-GACCTCTTTCTATTTTAGGTCCAGTTTTTT
*
6828 TCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
1 TTTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
* *
6866 CTTTTTTCGACCTCTCTCTATTTTAGGTCCAGTTTTTT
1 TTTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
6904 TTTTTTT
1 TTTTTTT
6911 TTTTTTTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
36 11 0.15
37 13 0.18
38 49 0.67
ACGTcount: A:0.09, C:0.19, G:0.12, T:0.60
Consensus pattern (38 bp):
TTTTTTTCGACCTCTTTCTATTTTAGGTCCAGTTTTTT
Found at i:15854 original size:12 final size:12
Alignment explanation
Indices: 15837--15884 Score: 96
Period size: 12 Copynumber: 4.0 Consensus size: 12
15827 GGCTGGGACA
15837 TCGGCATCCAAT
1 TCGGCATCCAAT
15849 TCGGCATCCAAT
1 TCGGCATCCAAT
15861 TCGGCATCCAAT
1 TCGGCATCCAAT
15873 TCGGCATCCAAT
1 TCGGCATCCAAT
15885 CCACCATCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (12 bp):
TCGGCATCCAAT
Found at i:15892 original size:24 final size:24
Alignment explanation
Indices: 15841--15893 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
15831 GGGACATCGG
* **
15841 CATCCAATTCGGCATCCAATTCGG
1 CATCCAATTCGGCATCCAATCCAC
15865 CATCCAATTCGGCATCCAATCCAC
1 CATCCAATTCGGCATCCAATCCAC
15889 CATCC
1 CATCC
15894 GATGCCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.23
Consensus pattern (24 bp):
CATCCAATTCGGCATCCAATCCAC
Found at i:25750 original size:13 final size:13
Alignment explanation
Indices: 25732--25756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25722 AACATACTTA
25732 AAAACACTTTTGG
1 AAAACACTTTTGG
25745 AAAACACTTTTG
1 AAAACACTTTTG
25757 ATTTTTTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AAAACACTTTTGG
Found at i:30014 original size:29 final size:29
Alignment explanation
Indices: 29981--30084 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
29971 GAACCTAGAG
* *
29981 TATGCAAAAACGACCAAAATGCCCCAAAA
1 TATGCAAAAATGACCAAAATGCCCCAGAA
*
30010 TATGCAAAAATGACCAAAATGCCCCTGAA
1 TATGCAAAAATGACCAAAATGCCCCAGAA
*
30039 TGTGCAAAAATGACCAAAATGCCCCAGAA
1 TATGCAAAAATGACCAAAATGCCCCAGAA
*
30068 TGTGCAAAAATGACCAA
1 TATGCAAAAATGACCAA
30085 TTAAGAAGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.14
Consensus pattern (29 bp):
TATGCAAAAATGACCAAAATGCCCCAGAA
Found at i:39064 original size:943 final size:936
Alignment explanation
Indices: 37228--38944 Score: 2674
Period size: 943 Copynumber: 1.8 Consensus size: 936
37218 AATTGGCTAA
* * *
37228 GAGGGAATATTCTAGACCAACAGGAAGCTTCCAAATCTTCTCAAACGGCTGGTTTTTCCGTCCAA
1 GAGGGAATATTCTAGACCAACAGGAAGCTTCCAAATCATCTCAAACAGCTGGTTATTCCGTCCAA
* * * *
37293 TTAGTGTTCAAGTCGGCAAAGAACTCCAATTGTAACTAGGAATGTAGTCCATTCTGTCCAGATTA
66 TTACTGTCCAAGTCGGCAAAGAACTCCAATTGTAACTAGGAATGCAGTCCATTCTATCCAGATTA
* * * * *
37358 CCTCAAGGGCATTTTCGACATTCTTCCCAGCAGAATTAGGTTTCGAGGTCTATAGATAAGTTGTA
131 CCTCAAGGGCATTTTCGACATTCTTCACAGCAAAATTAAGCTTCGAGGTCTAAAGATAAGTTGTA
* *
37423 GAGCATGGAAGTAACTTTCCAATGGTACCTCATTTGCATTCTTCTGAGCTCTGGATCAAAAAATT
196 GAGCATGGAAGTAACTTTCCAACGGTACCTCATTTGCATTCTTCTGAGCTCTGGATCAAAAAATA
* * *
37488 TGAATTTTGTTCTAAACTGCTGCATATCCAATCCTAGTCAACATAGGACTTTGAATTATGAGATC
261 TGAATTTTCTTCTAAACTGCTACATATCAAATCCTAGTCAACATAGGACTTTGAATTATGAGATC
*
37553 TTCAGAATTATTGGAAATTACTGCATCATAATTATTAATTGGGCTTCGAATAAATCATTGGGCTT
326 TTCAGAATTATTGGAAATTACTGCATCATAATTATTAATTGGGCTTAGAATAAATCATTGGGCTT
* * *
37618 CAATTATGTAGATCCGGGCCTAGAGAAGTCAAGACTGGATCTCCACAGATTCAGAATTATCTTCA
391 CAATTATGTAGATCCGGGCCTAGAGAAATAAAGACTGGATCTCCACAAATTCAGAATTATCTTCA
*
37683 GGCTTCATGGGCTCTCAATGGGCTAAATAGGACCAAAATCAGTAGTTTCTCCAAAATGATCCAAA
456 GGCTTCATGGGCTCTCAATGAGCTAAATAGGACCAAAATCAGTAGTTTCTCCAAAATGATCCAAA
* * *
37748 ATTGCTCCAAATCTTCATATTTGTAAATAATGGCTCCAATTGGTCGTAAAAATAGCAAAAATGAG
521 ACTGCTCCAAATCTTCATATTTGTAAATAATGGCTCCAATTGGTCCTAAAAATAACAAAAATGAG
* * * *
37813 AAATATGGGGTTAAATATGCATTTACAATTACCAAAACAGGTAAAATTGCATAGAAAAGATAGAA
586 AAATATGGGGTTAAATAAGCACTTACAACTACCAAAAAAGGTAAAATTGCATAGAAAAGATAGAA
* * *
37878 CAAATTAGGTCCTTATTAAAGCTCACCACCACCTGAACTCAAACAGATACATATAACACCACTAT
651 CAAATTAGGTCCTTATCAAAGCTCACCACCACCTGAACTCAAACAGATACAGAAAACACCACTAT
* * *
37943 TTGAGGATCAAAATGGATACATATACTTCTATTATTCCAAGGTCAAAACAGATACTGAAATCATC
716 TTGAGGATCAAAATGGATACAGATACTTCTATTATTCCAAGATCAAAACAGATACAGAAATCATC
*
38008 TAGACAAGGTTACAAGCTCATGAACATAAGTTCTAAATTTCAAAATACAAGTCCAAGGAACAAAC
781 TAGACAAGG-TACAAGCTCATG-A-ATAAG-CCTAAA--TCAAAATACAAGTCCAAGGAACAAAC
* ** * * ** *
38073 TAGCTTCCTAAAGCTTATATATGAGCTATTAGGAGCTAAAACAAGCTTAACTAAGTTAATTAAAC
840 TAACTTCAAAAAAC-TATATATGAGCAAGAACGAGCTAAAACAAGCTTAACTAAGTTAATTAAAC
38138 GTACTTAGTTAATTATTCTAGAAAAGACAAGTT
904 GTACTTAGTTAATTATTCTAGAAAAGACAAGTT
* *
38171 GAGGGAATATTCTATG-CCAATC-GGAAGCTTCTAAATCATCTCAAACAGCTGGTTATTCCGTCT
1 GAGGGAATATTCTA-GACCAA-CAGGAAGCTTCCAAATCATCTCAAACAGCTGGTTATTCCGTCC
38234 AATTACTGTCCAAGTCGGCAAAGAACTCCAATTGTAACTAGGAATGCAGTCCATTCTATCCAGAT
64 AATTACTGTCCAAGTCGGCAAAGAACTCCAATTGTAACTAGGAATGCAGTCCATTCTATCCAGAT
* * *
38299 TA-TTCAAGGGCATTTTCTACGTTCTTCACAGCAAAATTAAGCTTCGAGGTCTAAAGATAAGTTG
129 TACCTCAAGGGCATTTTCGACATTCTTCACAGCAAAATTAAGCTTCGAGGTCTAAAGATAAGTTG
* * * *
38363 TAGAGCTTGGAAGTAGCTTTCCAGCGGTACCTCATTTGCATT-TTCTGAGCTCTGGTATCAAAAG
194 TAGAGCATGGAAGTAACTTTCCAACGGTACCTCATTTGCATTCTTCTGAGCTCTGG-ATCAAAAA
38427 ATATGAATTTTCTTCTAAACTGCTACATATCAAATCCTAGTCAACATAGGGACTTTGAATTATGA
258 ATATGAATTTTCTTCTAAACTGCTACATATCAAATCCTAGTCAACATA-GGACTTTGAATTATGA
*
38492 GATCTTCAGAATTATTGGAAATTACTTCATCATAATTATTAATTGGGCTTAGAATAAATCATTGG
322 GATCTTCAGAATTATTGGAAATTACTGCATCATAATTATTAATTGGGCTTAGAATAAATCATTGG
* * *
38557 GCTTCAATTATCG-AGATTCGGGCCTAGAGAAATAAAGATTGGATCTCCACAAATTCGGAATTAT
387 GCTTCAATTAT-GTAGATCCGGGCCTAGAGAAATAAAGACTGGATCTCCACAAATTCAGAATTAT
* *
38621 CTTCATGCTTCATGGGCTCTCAATGAGCTAAATATGACCAAAATCAGTAGTTTCTCCAAAATGAT
451 CTTCAGGCTTCATGGGCTCTCAATGAGCTAAATAGGACCAAAATCAGTAGTTTCTCCAAAATGAT
*
38686 CCAAAACTGCTCCAAATCTTCATATTTGTAAATAATGGCTCCAATTGGTCCT-AAAATAACAAAT
516 CCAAAACTGCTCCAAATCTTCATATTTGTAAATAATGGCTCCAATTGGTCCTAAAAATAACAAAA
*
38750 ATGAGAAATATGGGGTTAAATAAGCACTTACAACTACCAAAATAAGGTAAAATTGCATAGAAAAT
581 ATGAGAAATATGGGGTTAAATAAGCACTTACAACTACCAAAA-AAGGTAAAATTGCATAGAAAAG
38815 ATAGAACAAATTAGGT-CTTATCAAAGCTCACCACCACCTGAACTCAAACAGATACAGAAAACAC
645 ATAGAACAAATTAGGTCCTTATCAAAGCTCACCACCACCTGAACTCAAACAGATACAGAAAACAC
* * * * *
38879 CACTATTTGAGTATCAAAATGGATAGAGATACTTCTATTATTCTAAGATCAAAAGAGGTACAGAA
710 CACTATTTGAGGATCAAAATGGATACAGATACTTCTATTATTCCAAGATCAAAACAGATACAGAA
38944 A
775 A
38945 ATCAGCACTC
Statistics
Matches: 711, Mismatches: 57, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
941 13 0.02
942 295 0.41
943 400 0.56
944 3 0.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (936 bp):
GAGGGAATATTCTAGACCAACAGGAAGCTTCCAAATCATCTCAAACAGCTGGTTATTCCGTCCAA
TTACTGTCCAAGTCGGCAAAGAACTCCAATTGTAACTAGGAATGCAGTCCATTCTATCCAGATTA
CCTCAAGGGCATTTTCGACATTCTTCACAGCAAAATTAAGCTTCGAGGTCTAAAGATAAGTTGTA
GAGCATGGAAGTAACTTTCCAACGGTACCTCATTTGCATTCTTCTGAGCTCTGGATCAAAAAATA
TGAATTTTCTTCTAAACTGCTACATATCAAATCCTAGTCAACATAGGACTTTGAATTATGAGATC
TTCAGAATTATTGGAAATTACTGCATCATAATTATTAATTGGGCTTAGAATAAATCATTGGGCTT
CAATTATGTAGATCCGGGCCTAGAGAAATAAAGACTGGATCTCCACAAATTCAGAATTATCTTCA
GGCTTCATGGGCTCTCAATGAGCTAAATAGGACCAAAATCAGTAGTTTCTCCAAAATGATCCAAA
ACTGCTCCAAATCTTCATATTTGTAAATAATGGCTCCAATTGGTCCTAAAAATAACAAAAATGAG
AAATATGGGGTTAAATAAGCACTTACAACTACCAAAAAAGGTAAAATTGCATAGAAAAGATAGAA
CAAATTAGGTCCTTATCAAAGCTCACCACCACCTGAACTCAAACAGATACAGAAAACACCACTAT
TTGAGGATCAAAATGGATACAGATACTTCTATTATTCCAAGATCAAAACAGATACAGAAATCATC
TAGACAAGGTACAAGCTCATGAATAAGCCTAAATCAAAATACAAGTCCAAGGAACAAACTAACTT
CAAAAAACTATATATGAGCAAGAACGAGCTAAAACAAGCTTAACTAAGTTAATTAAACGTACTTA
GTTAATTATTCTAGAAAAGACAAGTT
Found at i:40831 original size:17 final size:17
Alignment explanation
Indices: 40809--40857 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
40799 TCTCCTTGAT
40809 CTTCATGCTTCTCCATG
1 CTTCATGCTTCTCCATG
*
40826 CTTCATTGC-ACTCCATG
1 CTTCA-TGCTTCTCCATG
*
40843 C-TCATCCTT-TCCATG
1 CTTCATGCTTCTCCATG
40858 ATCTCCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 13 0.48
18 3 0.11
ACGTcount: A:0.14, C:0.37, G:0.10, T:0.39
Consensus pattern (17 bp):
CTTCATGCTTCTCCATG
Found at i:42481 original size:21 final size:22
Alignment explanation
Indices: 42448--42496 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
42438 CTCCTCCTGG
*
42448 GCACCCACATGG-TTGCCTTGA
1 GCACCCACATGGTTTGCCTTAA
**
42469 GCACCCATGTGGTTTGCCTTAA
1 GCACCCACATGGTTTGCCTTAA
42491 G-ACCCA
1 GCACCCA
42497 GCTGGGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.24
Consensus pattern (22 bp):
GCACCCACATGGTTTGCCTTAA
Found at i:42585 original size:76 final size:76
Alignment explanation
Indices: 42434--42578 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
42424 GACAAGGGCT
* * * *
42434 CCGACTCCTCCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCCAGC
1 CCGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAGC
*
42499 TGGGCAGTGTC
66 TAGGCAGTGTC
** * * *
42510 CCGACTCCACCTGGGTGCCCACATGGTTTG-TTTGAGGACCCATGTGATTTGCCTGATCACCCAG
1 CCGACTCCACCTGGGCACCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
*
42574 GTAGG
65 CTAGG
42579 ATGTGTCATG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 54 0.95
77 3 0.05
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.25
Consensus pattern (76 bp):
CCGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAGC
TAGGCAGTGTC
Found at i:48773 original size:12 final size:13
Alignment explanation
Indices: 48750--48778 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
48740 TTTAGCACTT
48750 AAATGAAAAATAA
1 AAATGAAAAATAA
48763 AAATG-AAAATAA
1 AAATGAAAAATAA
48775 AAAT
1 AAAT
48779 AAAGTAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AAATGAAAAATAA
Found at i:49273 original size:76 final size:76
Alignment explanation
Indices: 49134--49274 Score: 176
Period size: 76 Copynumber: 1.9 Consensus size: 76
49124 TGACAAGGGC
* * * *
49134 CCCGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTTAAGACCCAG
1 CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
49199 CTGGGTAGTGT
66 CTGGGTAGTGT
* * * * * *
49210 CCCGACTCCACCTGGGTGGCCACATGGTTTGTC-TGAGGACCCATGTTATTTGCCTGATCACCCA
1 CCCGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCA
49274 G
65 G
49275 GTAGGTTGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
76 50 0.93
77 4 0.07
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (76 bp):
CCCGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGATTTGCCTGAACACCCAG
CTGGGTAGTGT
Found at i:49484 original size:16 final size:15
Alignment explanation
Indices: 49446--49487 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
49436 ACAGAGGTTG
*
49446 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
49461 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
49476 ACTAGAAAACAA
1 AC-AGAAAACAA
49488 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:59252 original size:22 final size:22
Alignment explanation
Indices: 59224--59267 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59214 AGTTATGAGG
59224 CTACCCGGCCCCAGGCACCCCC
1 CTACCCGGCCCCAGGCACCCCC
* *
59246 CTACCCGGCCCCGGGTACCCCC
1 CTACCCGGCCCCAGGCACCCCC
59268 AGAAACTTTA
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:0.11, C:0.61, G:0.20, T:0.07
Consensus pattern (22 bp):
CTACCCGGCCCCAGGCACCCCC
Found at i:63819 original size:27 final size:27
Alignment explanation
Indices: 63789--63850 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
63779 AGGGGTCACC
*
63789 CAGGGGCATTTTAGTCATTCGCATGTT
1 CAGGGGCATTTTAGTCATTCGCATATT
* *
63816 CAGGGGCATTTTGGTCATTTGCATATT
1 CAGGGGCATTTTAGTCATTCGCATATT
63843 CAGGGGCA
1 CAGGGGCA
63851 CGTTGGTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (27 bp):
CAGGGGCATTTTAGTCATTCGCATATT
Found at i:63856 original size:27 final size:27
Alignment explanation
Indices: 63802--63859 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
63792 GGGCATTTTA
* **
63802 GTCATTCGCATGTTCAGGGGCATTTTG
1 GTCATTCGCATATTCAGGGGCACGTTG
*
63829 GTCATTTGCATATTCAGGGGCACGTTG
1 GTCATTCGCATATTCAGGGGCACGTTG
63856 GTCA
1 GTCA
63860 CTTTAAGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.34
Consensus pattern (27 bp):
GTCATTCGCATATTCAGGGGCACGTTG
Found at i:66554 original size:41 final size:41
Alignment explanation
Indices: 66497--66630 Score: 205
Period size: 41 Copynumber: 3.3 Consensus size: 41
66487 TTCTCGTGTT
* *
66497 CAATTTAGTCCCTGATTCAGGATTCTAGTTACTATTTGATA
1 CAATTTAGTCCCTGATTTAGGATTATAGTTACTATTTGATA
* *
66538 CAATTTAGTCCCTGATTTAGAATTATATTTACTATTTGATA
1 CAATTTAGTCCCTGATTTAGGATTATAGTTACTATTTGATA
* *
66579 CAATTTAGTCCCTGATTTAGGATTTTAGTTACTATTTGATT
1 CAATTTAGTCCCTGATTTAGGATTATAGTTACTATTTGATA
*
66620 CAATTTGGTCC
1 CAATTTAGTCC
66631 TTATTTTTCT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (41 bp):
CAATTTAGTCCCTGATTTAGGATTATAGTTACTATTTGATA
Found at i:67501 original size:21 final size:22
Alignment explanation
Indices: 67477--67523 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
67467 AAAATGGAGG
* *
67477 TTTTCAAAGCA-AAGTAAAAGA
1 TTTTAAAAGCAGAAATAAAAGA
*
67498 TTTTAAAAGCAGAAATAAAAGG
1 TTTTAAAAGCAGAAATAAAAGA
67520 TTTT
1 TTTT
67524 GACACAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (22 bp):
TTTTAAAAGCAGAAATAAAAGA
Found at i:67523 original size:22 final size:21
Alignment explanation
Indices: 67474--67523 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
67464 ACTAAAATGG
* *
67474 AGGTTTTCAAAGCAAAGTAAA
1 AGGTTTTAAAAGCAAAATAAA
*
67495 AGATTTTAAAAGCAGAAATAAA
1 AGGTTTTAAAAGCA-AAATAAA
67517 AGGTTTT
1 AGGTTTT
67524 GACACAGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (21 bp):
AGGTTTTAAAAGCAAAATAAA
Found at i:70231 original size:14 final size:15
Alignment explanation
Indices: 70198--70233 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
70188 AAAGACATGT
*
70198 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATGG
70213 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATGG
70227 TTTTCAA
1 TTTTCAA
70234 AAGGTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATGG
Found at i:73108 original size:67 final size:66
Alignment explanation
Indices: 73018--73216 Score: 263
Period size: 67 Copynumber: 3.0 Consensus size: 66
73008 TAGAGAATTT
*
73018 AAGGAATACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCA
1 AAGG-ATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCA
73083 TTA
65 -TA
* * * *
73086 AAGGATACATCGGATGACGGTTTGCTAGAAAGAATTTGCAGAAGATGATTGGAAGACAATCTCAT
1 AAGGATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
*
73151 C
66 A
* * * * *
73152 AAGAAGTACATTGGAAGACGGTTTGTTAGAAATAATTTTCAAAATATTGATTGGAAGACAATCTC
1 AAGGA-TACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAA-GTTGATTGGAAGACAATCTC
73217 TCATCAAGAA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
66 5 0.04
67 87 0.76
68 22 0.19
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (66 bp):
AAGGATACATCGGAAGACGGTTTGCTAGAAAGAATTTTCAAAAGTTGATTGGAAGACAATCTCAT
A
Found at i:73470 original size:65 final size:64
Alignment explanation
Indices: 73235--73570 Score: 399
Period size: 64 Copynumber: 5.2 Consensus size: 64
73225 AAGTACATCA
* * * *
73235 GAAGACGATCTTGTCAAGAAGTACAACAGAAGATGGTTTCTCAAGAACTTTCAAAAGTTGAACG
1 GAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAATTTTCAGAAGTTGATCG
* * *
73299 GAAGACGATCTCGTCAAAAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCG
1 GAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAATTTTCAGAAGTTGATCG
* *
73363 GAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAGTTTTCAGAAGTTGGTCG
1 GAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAATTTTCAGAAGTTGATCG
* * * * * *
73427 GAAAACGTTCTTGTCAAAGAAGTACACCAGAAGATGGTTTCTCAACAACTTTCAGAAGATGATAG
1 GAAGACGATCTTGTC-AAGAAGTACACCAGAAGATGGTTTCTCAAGAATTTTCAGAAGTTGATCG
* * * * **
73492 G-AGCACGATCTCGTCCAGAAGTACACCCGAAGATAGTTTTCTCGAA-AAAGTTCA-AAGGTTGA
1 GAAG-ACGATCTTGTCAAGAAGTACACCAGAAGAT-GGTTTCTC-AAGAATTTTCAGAA-GTTGA
**
73554 TTA
62 TCG
73557 GAAGACGATCTTGT
1 GAAGACGATCTTGT
73571 TGAGAGATGC
Statistics
Matches: 234, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
64 149 0.64
65 81 0.35
66 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (64 bp):
GAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAGAATTTTCAGAAGTTGATCG
Found at i:73832 original size:50 final size:50
Alignment explanation
Indices: 73775--74304 Score: 784
Period size: 50 Copynumber: 10.6 Consensus size: 50
73765 GATGATTTTC
*
73775 TTAAGATT-AGATTGGAAGACAATTCAAAGGATTAGCGGAAGACGGTCCTT
1 TTAAGATTGA-ATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
* *
73825 TTAAGATTGATTTGGAAGACAATTCAAAGGATTAGCGGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
73875 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
**
73925 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACAATCCTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
73975 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
74025 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGT-CTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
* *
74074 TTGAAGATTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTT
1 TT-AAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
* * * *
74125 TTAAGATTGATTTGGAAGACAGTTCAATGGATAAGCGGAAGACGATCCTT
1 TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
* * * *
74175 TTACGATT-AGATTGGAAGACAGTTCAAGGGATAAGCGAAAGACGGTCCCTT
1 TTAAGATTGA-ATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGT-CCTT
* *
74226 TTGAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-G-ACTCT
1 TT-AAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCT-T
* *
74276 TTAATATT-AGATTGAAAGACAATTCAAAG
1 TTAAGATTGA-ATTGGAAGACAATTCAAAG
74305 AAGTTGATCC
Statistics
Matches: 446, Mismatches: 25, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
48 1 0.00
49 30 0.07
50 365 0.82
51 13 0.03
52 36 0.08
53 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (50 bp):
TTAAGATTGAATTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTT
Found at i:73891 original size:27 final size:27
Alignment explanation
Indices: 73861--73944 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
73851 AAGGATTAGC
73861 GGAAGACGGTCCTTTTAAGATTGAATT
1 GGAAGACGGTCCTTTTAAGATTGAATT
** ** **
73888 GGAAGAC---AATTCAAAGGA-T-AAGC
1 GGAAGACGGTCCTTTTAA-GATTGAATT
73911 GGAAGACGGTCCTTTTAAGATTGAATT
1 GGAAGACGGTCCTTTTAAGATTGAATT
73938 GGAAGAC
1 GGAAGAC
73945 AATTCAAAGG
Statistics
Matches: 39, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
23 9 0.23
24 5 0.13
25 4 0.10
26 5 0.13
27 16 0.41
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (27 bp):
GGAAGACGGTCCTTTTAAGATTGAATT
Found at i:73968 original size:23 final size:23
Alignment explanation
Indices: 73938--74017 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
73928 AGATTGAATT
73938 GGAAGACAATTCAAAGGATAAGC
1 GGAAGACAATTCAAAGGATAAGC
** **
73961 GGAAGACAATCCTTTTAA-GATTGAATT
1 GGAAGACAA---TTCAAAGGA-T-AAGC
73988 GGAAGACAATTCAAAGGATAAGC
1 GGAAGACAATTCAAAGGATAAGC
74011 GGAAGAC
1 GGAAGAC
74018 GGTCCTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
23 18 0.42
24 5 0.12
25 4 0.09
26 5 0.12
27 11 0.26
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (23 bp):
GGAAGACAATTCAAAGGATAAGC
Found at i:74682 original size:26 final size:26
Alignment explanation
Indices: 74601--74682 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 26
74591 GGTCACCCAG
* *
74601 GGGCATTTTGGTCATTCACATGTTCA
1 GGGCATTTTGGTCATTTACATATTCA
*
74627 GGGGCATTTTGGTCATTTTTACA-A-TAA
1 -GGGCATTTTGGTCA--TTTACATATTCA
*
74654 GGGCATTTTGGTCATTTGCATATTCA
1 GGGCATTTTGGTCATTTACATATTCA
74680 GGG
1 GGG
74683 ACACGTTGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.11
25 1 0.02
26 19 0.41
27 16 0.35
29 5 0.11
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.39
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTACATATTCA
Found at i:88340 original size:135 final size:135
Alignment explanation
Indices: 88098--88369 Score: 535
Period size: 135 Copynumber: 2.0 Consensus size: 135
88088 TTAAATACTT
88098 ATATTTATTTTCTAATTAGTAGTTTTATTTAAAATGGGTAGCTTTTATTTTATTATTTTGAATTT
1 ATATTTATTTTCTAATTAGTAGTTTTATTTAAAATGGGTAGCTTTTATTTTATTATTTTGAATTT
88163 TTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGAACTTACCTTTATAATTAG
66 TTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGAACTTACCTTTATAATTAG
88228 TATAG
131 TATAG
88233 ATATTTATTTTCTAATTAGTAGTTTTATTTAAAATGGGTAGCTTTTATTTTATTATTTTGAATTT
1 ATATTTATTTTCTAATTAGTAGTTTTATTTAAAATGGGTAGCTTTTATTTTATTATTTTGAATTT
*
88298 TTAAAAATTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGAACTTACCTTTATAATTAG
66 TTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGAACTTACCTTTATAATTAG
88363 TATAG
131 TATAG
88368 AT
1 AT
88370 TATCATTATA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (135 bp):
ATATTTATTTTCTAATTAGTAGTTTTATTTAAAATGGGTAGCTTTTATTTTATTATTTTGAATTT
TTAAAAACTGAGTTTGTATCCGAGTCAACTCGTGACACAAACTCAGAACTTACCTTTATAATTAG
TATAG
Found at i:88772 original size:25 final size:27
Alignment explanation
Indices: 88744--88798 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
88734 TCGTGTTATA
88744 TGAATATCACG-T-TTTAGGCCGGATT
1 TGAATATCACGATATTTAGGCCGGATT
**
88769 TG-A-ATCGTGATATTTAGGCCGGATT
1 TGAATATCACGATATTTAGGCCGGATT
88794 TGAAT
1 TGAAT
88799 CGTGATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.17
24 2 0.08
25 17 0.71
26 1 0.04
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (27 bp):
TGAATATCACGATATTTAGGCCGGATT
Found at i:88799 original size:25 final size:25
Alignment explanation
Indices: 88756--88806 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
88746 AATATCACGT
88756 TTTAGGCCGGATTTGAATCGTGATA
1 TTTAGGCCGGATTTGAATCGTGATA
88781 TTTAGGCCGGATTTGAATCGTGATA
1 TTTAGGCCGGATTTGAATCGTGATA
88806 T
1 T
88807 ATGATTACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (25 bp):
TTTAGGCCGGATTTGAATCGTGATA
Found at i:89264 original size:15 final size:15
Alignment explanation
Indices: 89244--89274 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
89234 CTCTCCAAAC
*
89244 TTTTTTGTTTGTATT
1 TTTTTTGTTTATATT
89259 TTTTTTGTTTATATT
1 TTTTTTGTTTATATT
89274 T
1 T
89275 CTCAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (15 bp):
TTTTTTGTTTATATT
Found at i:94906 original size:3 final size:3
Alignment explanation
Indices: 94900--94926 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
94890 TACTACTATA
94900 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
94927 ATTTATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:94932 original size:9 final size:9
Alignment explanation
Indices: 94896--94973 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 9
94886 TTACTACTAC
94896 TATATATTAT
1 TATAT-TTAT
94906 TAT-TATTAT
1 TATAT-TTAT
94915 TAT-TATTAT
1 TATAT-TTAT
94924 TATATTTAT
1 TATATTTAT
*
94933 TAGATTTAT
1 TATATTTAT
*
94942 T-TATTTTT
1 TATATTTAT
*
94950 TATTTTTTAT
1 TA-TATTTAT
*
94960 TATACTATAT
1 TATA-TTTAT
94970 TATA
1 TATA
94974 AAAAACAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 6 0.11
9 32 0.56
10 19 0.33
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
TATATTTAT
Found at i:96955 original size:35 final size:33
Alignment explanation
Indices: 96902--97073 Score: 146
Period size: 35 Copynumber: 4.8 Consensus size: 33
96892 ACTGGAACCG
* *
96902 AACTGACGGGAACTTTCCCTAAATTGAAAACTAA
1 AACTGATGGGAACTTTCCC-AATTTGAAAACTAA
* *
96936 AACCTGATGGGAACTTTCCCAATTTGAAAATTTGA
1 AA-CTGATGGGAACTTTCCCAATTTGAAAA-CTAA
*
96971 AACAGAATGGGAACTTTCCCAATTTGAAAACTTCAA
1 AACTG-ATGGGAACTTTCCCAATTTGAAAAC-T-AA
* * **
97007 AATTTGGTGGGAACTTTCCCCAATTTTGACAATTTTGAA
1 AA-CTGATGGGAACTTT-CCCAA-TTTGA-AA-ACT-AA
97046 AACTGGATGGGAACTTTCCCAATTTGAA
1 AACT-GATGGGAACTTTCCCAATTTGAA
97074 GACTTGCTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
34 13 0.12
35 45 0.40
36 14 0.12
37 11 0.10
38 11 0.10
39 18 0.16
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (33 bp):
AACTGATGGGAACTTTCCCAATTTGAAAACTAA
Found at i:97064 original size:75 final size:70
Alignment explanation
Indices: 96909--97078 Score: 207
Period size: 75 Copynumber: 2.4 Consensus size: 70
96899 CCGAACTGAC
*
96909 GGGAACTTTCCCTAAATTGAAAAC-TAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAA
1 GGGAACTTTCCC-AATTTGAAAACTTAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAA
96973 CAGAAT
65 CAGAAT
** * *
96979 GGGAACTTTCCCAATTTGAAAACTTCAAAATTTGGTGGGAACTTTCCCCAATTTTGACAATTTTG
1 GGGAACTTTCCCAATTTGAAAACTT-AAAACCTGATGGGAACTTT-CCCAA-TTTGA-AAATTTG
* *
97044 AAAACTGGAT
62 -AAACAGAAT
*
97054 GGGAACTTTCCCAATTTGAAGACTT
1 GGGAACTTTCCCAATTTGAAAACTT
97079 GCTAAATTGA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
69 10 0.12
70 13 0.15
71 16 0.19
72 5 0.06
73 5 0.06
74 6 0.07
75 31 0.36
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (70 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAACCTGATGGGAACTTTCCCAATTTGAAAATTTGAAAC
AGAAT
Found at i:98919 original size:2 final size:2
Alignment explanation
Indices: 98912--98937 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98902 ATGAGAAGAA
98912 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
98938 GCATGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.