Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015640.1 Corchorus olitorius cultivar O-4 contig15673, 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: 49251
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:20875 original size:19 final size:18
Alignment explanation
Indices: 20838--20884 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
20828 TGAAATTTAT
20838 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
*
20856 TAATTATTT-TT-AAGAA
1 TAATTATTTATTAAATAA
20872 TAATTA-TTATTAA
1 TAATTATTTATTAA
20885 TATTTCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 3 0.12
18 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:23466 original size:86 final size:87
Alignment explanation
Indices: 23321--23488 Score: 266
Period size: 86 Copynumber: 1.9 Consensus size: 87
23311 ATATTTGAAC
* *
23321 ATTTCTTAAGATAAGAAACTGATCCAGAACCATCAATTGAGTTGGGAATATTAATGCATGGCCAA
1 ATTTCTTAAGATAAGAAACTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
*
23386 ATTGGAG-GAAGATTTGAAAAT
66 ATTGGAGAAAAGATTTGAAAAT
** * *
23407 ATTTCTTAAGATGGGAAGCTGATCCGGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
1 ATTTCTTAAGATAAGAAACTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
23472 ATTGGAGAAAAGATTTG
66 ATTGGAGAAAAGATTTG
23489 GGGCATCAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 66 0.89
87 8 0.11
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (87 bp):
ATTTCTTAAGATAAGAAACTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
ATTGGAGAAAAGATTTGAAAAT
Found at i:24289 original size:37 final size:37
Alignment explanation
Indices: 24225--24733 Score: 325
Period size: 37 Copynumber: 13.8 Consensus size: 37
24215 CAAAACCTCA
* * * * * *
24225 AAATCCTTGTTCAAGATCCATGATTAGGTTACTTATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* *
24262 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* * * * *
24299 AAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTTATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTC-TTATC
* **
24337 AAATCCTTATTTAAGGTCCCTGTTTAGGTATCCCATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* * * * * *
24374 AAAACCTTGTTGAAGATTCTTGTTTAGGTTTTCTTATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGG-TTTCTTATC
* * *
24412 AAATCCTTATTTAAGG-CCCTATTTAGGTGTCTCATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* * * * * * *
24448 AAAACCTTGTTCAAGATTCCTGTTTAGATTTCTTAAC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
*
24485 AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCT-TC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCT-TATC
** * * * *
24522 AAAAACTTGTTCAAGATTCCC-GTTTAGATTTCTTATC
1 AAATCCTTATTTAAG-GTCCCTGTTTAGGTTTCTTATC
* * *
24559 AAATCCTTATTTAAGGT-CCTATTTAGGTGTCTCATC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* ** * * *
24595 GAAAT-CTTGTCCAAGCT-CCTATTTAGGTTTCTT-GC
1 -AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* * * * * * * * *
24630 AAATTCTTGTTTAAGATACTTGTTTATGTGTCTCACC
1 AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
* * * *
24667 GAAAT-TTTGTTCAAAGATCCCTGTTTAGGTTTCTT-TAC
1 -AAATCCTTATT-TAAGGTCCCTGTTTAGGTTTCTTAT-C
*
24705 AAATCCTTATTTAAGGTCCCTATTTAGGT
1 AAATCCTTATTTAAGGTCCCTGTTTAGGT
24734 GTTTGAAATT
Statistics
Matches: 353, Mismatches: 104, Indels: 30
0.72 0.21 0.06
Matches are distributed among these distances:
34 4 0.01
35 12 0.03
36 66 0.19
37 192 0.54
38 79 0.22
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (37 bp):
AAATCCTTATTTAAGGTCCCTGTTTAGGTTTCTTATC
Found at i:24472 original size:74 final size:74
Alignment explanation
Indices: 24222--24735 Score: 644
Period size: 74 Copynumber: 6.9 Consensus size: 74
24212 ATTCAAAACC
* *
24222 TCAAAATCCTTGTTCAAGA-TCCATGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCCTGTT
1 TCAAAA-CCTTGTTCAAGATTCC-TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTT
24286 TAGGTGTCTCA
64 TAGGTGTCTCA
24297 TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTTATCAAATCCTTATTTAAGGTCCCTGTTT
1 TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTC-TTATCAAATCCTTATTTAAGGTCCCTGTTT
* *
24362 AGGTATCCCA
65 AGGTGTCTCA
* * *
24372 TCAAAACCTTGTTGAAGATTCTTGTTTAGGTTTTCTTATCAAATCCTTATTTAAGG-CCCTATTT
1 TCAAAACCTTGTTCAAGATTCCTGTTTAGG-TTTCTTATCAAATCCTTATTTAAGGTCCCTGTTT
24436 AGGTGTCTCA
65 AGGTGTCTCA
* *
24446 TCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCTTAACAAATCCTTATTTAAGGTCCCTGTTTA
1 TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTA
*
24511 GGTGTCTCT
66 GGTGTCTCA
* * * *
24520 TCAAAAACTTGTTCAAGATTCCCGTTTAGATTTCTTATCAAATCCTTATTTAAGGT-CCTATTTA
1 TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTA
24584 GGTGTCTCA
66 GGTGTCTCA
* * * * * * * * * * *
24593 TCGAAATCTTGTCCAAG-CTCCTATTTAGGTTTCTT-GCAAATTCTTGTTTAAGATACTTGTTTA
1 TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTA
*
24656 TGTGTCTCA
66 GGTGTCTCA
* * ** * *
24665 CCGAAATTTTGTTCAAAGATCCCTGTTTAGGTTTCTT-TACAAATCCTTATTTAAGGTCCCTATT
1 TCAAAACCTTGTTC-AAGATTCCTGTTTAGGTTTCTTAT-CAAATCCTTATTTAAGGTCCCTGTT
24729 TAGGTGT
64 TAGGTGT
24736 TTGAAATTCA
Statistics
Matches: 383, Mismatches: 48, Indels: 16
0.86 0.11 0.04
Matches are distributed among these distances:
71 15 0.04
72 39 0.10
73 56 0.15
74 148 0.39
75 121 0.32
76 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (74 bp):
TCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTA
GGTGTCTCA
Found at i:24860 original size:7 final size:7
Alignment explanation
Indices: 24850--24921 Score: 81
Period size: 7 Copynumber: 10.3 Consensus size: 7
24840 TTTTTCATTC
24850 TTCAAAA
1 TTCAAAA
24857 TTCAAAA
1 TTCAAAA
24864 TTCAAAA
1 TTCAAAA
*
24871 TTCAATA
1 TTCAAAA
*
24878 TTCAAGA
1 TTCAAAA
*
24885 TTCAAGA
1 TTCAAAA
**
24892 TTCATGA
1 TTCAAAA
*
24899 TTCAAGA
1 TTCAAAA
24906 TTCAAAA
1 TTCAAAA
*
24913 TTTAAAA
1 TTCAAAA
24920 TT
1 TT
24922 AATGGTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (7 bp):
TTCAAAA
Found at i:25023 original size:27 final size:28
Alignment explanation
Indices: 24989--25046 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
24979 GTCAATAGTT
*
24989 AAAATTTAAAATTTCCATTTCAT-TTCA
1 AAAATTTAAAATTTCCATGTCATGTTCA
*
25016 AAAATTTAAAATTTGCATGTCATGTTCA
1 AAAATTTAAAATTTCCATGTCATGTTCA
25044 AAA
1 AAA
25047 GTCAAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (28 bp):
AAAATTTAAAATTTCCATGTCATGTTCA
Found at i:25053 original size:27 final size:27
Alignment explanation
Indices: 24996--25054 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
24986 GTTAAAATTT
* * *
24996 AAAATTTCCATTTCATTTCAAAAATTT
1 AAAATTTCCATGTCATTTCAAAAAGTC
*
25023 AAAATTTGCATGTCATGTTC-AAAAGTC
1 AAAATTTCCATGTCAT-TTCAAAAAGTC
25050 AAAAT
1 AAAAT
25055 CCAAAATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (27 bp):
AAAATTTCCATGTCATTTCAAAAAGTC
Found at i:25322 original size:54 final size:54
Alignment explanation
Indices: 25162--25307 Score: 247
Period size: 54 Copynumber: 2.7 Consensus size: 54
25152 GTTTTCTGGT
* * *
25162 TTAAGATGACCTAGTGTGGTCTTTCACAGAAGTTTTCAGAGATCTAAGTTGATC
1 TTAAGATGACCCAGTATGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATC
25216 TTAAGATGACCCAGTATGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATC
1 TTAAGATGACCCAGTATGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATC
* *
25270 TTAAGATGACCCAATTTGGTCTTTCATAGAAGTTTTCA
1 TTAAGATGACCCAGTATGGTCTTTCATAGAAGTTTTCA
25308 ATGATCAGAG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (54 bp):
TTAAGATGACCCAGTATGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATC
Found at i:25358 original size:108 final size:108
Alignment explanation
Indices: 25162--25378 Score: 239
Period size: 108 Copynumber: 2.0 Consensus size: 108
25152 GTTTTCTGGT
* * **
25162 TTAAGATGACCTAGTGTGGTCTTTCACAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
1 TTAAGATGACCCAATGTGGTCTTTCACAGAAGTTTTCAGAGATCTAAGTTGATCCCAAGATGACC
* *
25227 CAGTATGGTCTTTCATAGAAG-TTTTCAGAGATCTA-AGTTGATC
66 CAGTACGGTCTTCCATAGAAGTTTTTCAG-GATC-AGAGTTGATC
* *
25270 TTAAGATGACCCAATTTGGTCTTTCATAGAAGTTTTCA-ATGATC-AGAGTTGATTCCCAA-ATG
1 TTAAGATGACCCAATGTGGTCTTTCACAGAAGTTTTCAGA-GATCTA-AGTTGA-TCCCAAGATG
* * *
25332 ATCCAGTGCGGTCATTCCA-AGGAGTTTTTCAGGATCAGAGTTGATC
63 ACCCAGTACGGTC-TTCCATAGAAGTTTTTCAGGATCAGAGTTGATC
25378 T
1 T
25379 AGTGCGGTCG
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
107 3 0.03
108 74 0.80
109 15 0.16
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (108 bp):
TTAAGATGACCCAATGTGGTCTTTCACAGAAGTTTTCAGAGATCTAAGTTGATCCCAAGATGACC
CAGTACGGTCTTCCATAGAAGTTTTTCAGGATCAGAGTTGATC
Found at i:32154 original size:19 final size:19
Alignment explanation
Indices: 32126--32163 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32116 AAAAGGGGAT
* *
32126 GGCGATGAAGAGGGAGAGA
1 GGCGAAGAAGAGGCAGAGA
32145 GGCGAAGAAGAGGCAGAGA
1 GGCGAAGAAGAGGCAGAGA
32164 TTTGGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.50, T:0.03
Consensus pattern (19 bp):
GGCGAAGAAGAGGCAGAGA
Found at i:35746 original size:23 final size:25
Alignment explanation
Indices: 35694--35746 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
35684 CATGATAATA
* *
35694 ATAAAAAATAATAATGCAAGCTTTT
1 ATAAAATATAATAATGCAAGATTTT
35719 -T-AAATATAATAATG-AA-ATTTT
1 ATAAAATATAATAATGCAAGATTTT
35740 ATAAAAT
1 ATAAAAT
35747 CTTAGTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 16 0.67
24 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (25 bp):
ATAAAATATAATAATGCAAGATTTT
Found at i:44787 original size:31 final size:31
Alignment explanation
Indices: 44749--44823 Score: 125
Period size: 31 Copynumber: 2.4 Consensus size: 31
44739 AAAAAAAGGA
*
44749 TCAATTTAGTCCCTTTACTTGTA-AGATTGGG
1 TCAATTTAGTCCCTCTACTTG-ACAGATTGGG
44780 TCAATTTAGTCCCTCTACTTGACAGATTGGG
1 TCAATTTAGTCCCTCTACTTGACAGATTGGG
44811 TCAATTTAGTCCC
1 TCAATTTAGTCCC
44824 ATGATAACAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 1 0.02
31 41 0.98
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (31 bp):
TCAATTTAGTCCCTCTACTTGACAGATTGGG
Found at i:44940 original size:21 final size:21
Alignment explanation
Indices: 44910--44966 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
44900 GTAATTTTAT
44910 TTTTTAAAAATAAGAAAAA-AAA
1 TTTTT-AAAA-AAGAAAAAGAAA
44932 TTTTT-AAAAAGAAAAATGAAA
1 TTTTTAAAAAAGAAAAA-GAAA
44953 -TTTTAAAAAA-AAAA
1 TTTTTAAAAAAGAAAA
44967 TATCCTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 8 0.25
20 11 0.34
21 8 0.25
22 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
TTTTTAAAAAAGAAAAAGAAA
Found at i:44956 original size:20 final size:20
Alignment explanation
Indices: 44921--44968 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
44911 TTTTAAAAAT
44921 AAGAAAAA-AAATTTTTAAA
1 AAGAAAAATAAATTTTTAAA
44940 AAGAAAAATGAAA-TTTTAAA
1 AAGAAAAAT-AAATTTTTAAA
44960 AA-AAAAATA
1 AAGAAAAATA
44969 TCCTTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 9 0.33
21 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAGAAAAATAAATTTTTAAA
Found at i:44962 original size:22 final size:20
Alignment explanation
Indices: 44911--44963 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
44901 TAATTTTATT
44911 TTTTAAAAATAAGAAAAAAAA
1 TTTTAAAAA-AAGAAAAAAAA
*
44932 TTTT-TAAAAAGAAAAATGAAA
1 TTTTAAAAAAAGAAAAA--AAA
44953 TTTTAAAAAAA
1 TTTTAAAAAAA
44964 AAATATCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.30
20 3 0.11
21 11 0.41
22 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (20 bp):
TTTTAAAAAAAGAAAAAAAA
Found at i:45793 original size:67 final size:67
Alignment explanation
Indices: 45418--46184 Score: 743
Period size: 67 Copynumber: 11.5 Consensus size: 67
45408 AAGCTTGTCG
* * * ** *
45418 TTCGACCGAAAGGGCATTTTTGGAAA-GTAGAA---TAAACTGAAATGCGGAAATGACGAAACTG
1 TTCGACCGAAAGGGTATTTTTGGAAATG-AAAATGCTAAACTCAAATGCAAAAAT-ACGAAAATG
*
45479 ACCTT
64 ACC-C
* * * * *
45484 TTC-ACCGAAAGGGTATTTTAGGAAATCAAAA-G-TGAACTCAAATGCAAGAATGAC-AGAATTG
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAAT-ACGA-AAATG
45545 ACCC
64 ACCC
* * * ** *
45549 TTTGACCGAAAGGGTATTCTTTGGAAA-G-AAA-GACTAGACTTAAATGCATCAACCTGATGAAA
1 TTCGACCGAAAGGGTATT-TTTGGAAATGAAAATG-CTAAACTCAAATGCA--AAAAT-ACGAAA
*
45611 CTGACCC
61 ATGACCC
* * ** * *
45618 TTCGACCGAAAGGGTATTTTTGGAAA-GTAGAA---TAAACTGAAATGTGAAAATGATGAAACTG
1 TTCGACCGAAAGGGTATTTTTGGAAATG-AAAATGCTAAACTCAAATGCAAAAAT-ACGAAAATG
45679 ACCC
64 ACCC
45683 TTTC-ACCGAAAGGGTATTTTTGGAAATTTGAAAATGCTAAACTCAAATGCAAAAATACGAAAAT
1 -TTCGACCGAAAGGGTATTTTTGGAAA--TGAAAATGCTAAACTCAAATGCAAAAATACGAAAAT
45747 GACCC
63 GACCC
*
45752 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGC-AAAAGACGAAAATGAC
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAATACGAAAATGAC
45816 CC
66 CC
* * *
45818 TTCGACCGAAAGGTTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAAGACGAAAGTGAC
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAATACGAAAATGAC
45883 CC
66 CC
* * *** * *
45885 TTCGACCGAAAGGGTATTTTTGGAAA-G-AAA-GACTAGACTGAAATGTGGAAATGATGAAACTG
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATG-CTAAACTCAAATGCAAAAAT-ACGAAAATG
45947 ACCC
64 ACCC
* *
45951 TTTC-ACCGAAAGGGTATTTTTGGAAATTTGAAAATGCTAAACTCAAATGGAAAAATGCGAAAAT
1 -TTCGACCGAAAGGGTATTTTTGGAAA--TGAAAATGCTAAACTCAAATGCAAAAATACGAAAAT
46015 GACCC
63 GACCC
* * * *
46020 TTCGACCGAGAGGATATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAAGATGAAAATGAC
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAATACGAAAATGAC
46085 CC
66 CC
* * * * * *
46087 TCCGACCGAAAGGGTATTTTTGGAAATGAAAAT--AAAACTTAAAAGCAAAAAGATGAAAATGAC
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAATACGAAAATGAC
*
46150 CT
66 CC
*
46152 TTCTACCGAAAGGGTATTTTTGGAAATGAAAAT
1 TTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
46185 AAAACTTTAA
Statistics
Matches: 600, Mismatches: 71, Indels: 61
0.82 0.10 0.08
Matches are distributed among these distances:
64 1 0.00
65 145 0.24
66 142 0.24
67 165 0.28
68 16 0.03
69 93 0.16
70 37 0.06
71 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (67 bp):
TTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTCAAATGCAAAAATACGAAAATGAC
CC
Found at i:45947 original size:268 final size:268
Alignment explanation
Indices: 45450--46182 Score: 1000
Period size: 268 Copynumber: 2.7 Consensus size: 268
45440 GAAAGTAGAA
* ** * * * *
45450 TAAACTGAAATGCGGAAATGACGAAACTGACCTTTTC-ACCGAAAGGGTATTTTAGGAAATCAAA
1 TAAACTCAAATGCAAAAAT-ACGAAAATGACC-CTTCGACCGAAAGGGTATTTTTGGAAATGAAA
* * *
45514 A-G-TGAACTCAAATGCAAGAATGAC-AGAATTGACCCTTTGACCGAAAGGGTATTCTTTGGAAA
64 ATGCTAAACTCAAATGCAA-AA-GACGA-AAATGACCCTTCGACCGAAAGGGTATT-TTTGGAAA
* ** *
45576 -G-AAA-GACTAGACTTAAATGCATCAACCTGATGAAACTGACCCTTCGACCGAAAGGGTATTTT
125 TGAAAATG-CTAAACTTAAATGCA--AA-AAGATGAAAATGACCCTTCGACCGAAAGGGTATTTT
*
45638 TGGAAAG-TAGAATAAACTGAAATGTGAAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTT
186 TGGAAAGAAAGAATAAACTGAAATGTGAAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTT
45702 TTGGAAATTTGAAAATGC
251 TTGGAAATTTGAAAATGC
45720 TAAACTCAAATGCAAAAATACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
1 TAAACTCAAATGCAAAAATACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
*
45785 GCTAAACTCAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGTTATTTTTGGAAATGAAAA
66 GCTAAACTCAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
* * *
45850 TGCTAAACTCAAATGCAAAAAGACGAAAGTGACCCTTCGACCGAAAGGGTATTTTTGGAAAGAAA
131 TGCTAAACTTAAATGCAAAAAGATGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAGAAA
* * *
45915 GACTAGACTGAAATGTGGAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATTT
196 GAATAAACTGAAATGTGAAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATTT
45980 GAAAATGC
261 GAAAATGC
* * * *
45988 TAAACTCAAATGGAAAAATGCGAAAATGACCCTTCGACCGAGAGGATATTTTTGGAAATGAAAAT
1 TAAACTCAAATGCAAAAATACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
* *
46053 GCTAAACTCAAATGCAAAAAGATGAAAATGACCCTCCGACCGAAAGGGTATTTTTGGAAATGAAA
66 GCTAAACTCAAATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAA
* * * *
46118 AT--AAAACTTAAAAGCAAAAAGATGAAAATGACCTTTCTACCGAAAGGGTATTTTTGGAAATGA
130 ATGCTAAACTTAAATGCAAAAAGATGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAA-GA
46181 AA
194 AA
46183 ATAAAACTTT
Statistics
Matches: 418, Mismatches: 35, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
267 90 0.22
268 164 0.39
269 113 0.27
270 36 0.09
271 15 0.04
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (268 bp):
TAAACTCAAATGCAAAAATACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAAT
GCTAAACTCAAATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAA
TGCTAAACTTAAATGCAAAAAGATGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAGAAA
GAATAAACTGAAATGTGAAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATTT
GAAAATGC
Found at i:47637 original size:2 final size:2
Alignment explanation
Indices: 47630--47675 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
47620 TCTGTGTTTT
* *
47630 TA TA TA TA TA TA TA TA TA TA TA TA T- TC TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47671 TA TA T
1 TA TA T
47676 GTTGCTGCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47662 original size:21 final size:21
Alignment explanation
Indices: 47636--47675 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47626 TTTTTATATA
*
47636 TATATATATATATATATATTC
1 TATATATATACATATATATTC
47657 TATATATATACATATATAT
1 TATATATATACATATATAT
47676 GTTGCTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATACATATATATTC
Done.