Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011636.1 Corchorus capsularis cultivar CVL-1 contig11657, 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: 50443
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:729 original size:12 final size:12
Alignment explanation
Indices: 712--736 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
702 ATTTGCTATC
712 TGATAATGAAAT
1 TGATAATGAAAT
724 TGATAATGAAAT
1 TGATAATGAAAT
736 T
1 T
737 TCAAAATCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TGATAATGAAAT
Found at i:2696 original size:168 final size:168
Alignment explanation
Indices: 2414--2747 Score: 641
Period size: 168 Copynumber: 2.0 Consensus size: 168
2404 AATTTTACAT
2414 GCATAAATTCAAAAGTAACGGCTACAAGAAACAAGCTCCTGAATCATAAACATTATACAATCAAT
1 GCATAAATTCAAAAGTAACGGCTACAAGAAACAAGCTCCTGAATCATAAACATTATACAATCAAT
*
2479 CACAATTTTTATGCATCATCTGTCTCTCTAGTAAGATTGGTGTAGATTGACAAAATCAAAATTGA
66 CACAATTTTTATGCATCATCTGTCTCTCTAGTAAGATTGGTGAAGATTGACAAAATCAAAATTGA
*
2544 ACTTACAATTCCATAGCATAAATAGAATACAGAAAATA
131 ACTCACAATTCCATAGCATAAATAGAATACAGAAAATA
2582 GCATAAATTCAAAAGTAACGGCTACAAGAAACAAGCTCCTGAATCATAAACATTATACAATCAAT
1 GCATAAATTCAAAAGTAACGGCTACAAGAAACAAGCTCCTGAATCATAAACATTATACAATCAAT
2647 CACAATTTTTATGCATCATCTGTCTCTCTAGTAAGATTGGTGAAGATTGACAAAATCAAAATTGA
66 CACAATTTTTATGCATCATCTGTCTCTCTAGTAAGATTGGTGAAGATTGACAAAATCAAAATTGA
*
2712 ACTCACAATTCCATAGCATAACTAGAATACAGAAAA
131 ACTCACAATTCCATAGCATAAATAGAATACAGAAAA
2748 ATACTCAATA
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 163 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (168 bp):
GCATAAATTCAAAAGTAACGGCTACAAGAAACAAGCTCCTGAATCATAAACATTATACAATCAAT
CACAATTTTTATGCATCATCTGTCTCTCTAGTAAGATTGGTGAAGATTGACAAAATCAAAATTGA
ACTCACAATTCCATAGCATAAATAGAATACAGAAAATA
Found at i:9894 original size:11 final size:10
Alignment explanation
Indices: 9872--9914 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
9862 CGAAAGAGGT
9872 AAAAAATATA
1 AAAAAATATA
*
9882 AAAAAATATT
1 AAAAAATATA
9892 AAAAAAT-TCA
1 AAAAAATAT-A
9902 AAAAAA-ATA
1 AAAAAATATA
9911 AAAA
1 AAAA
9915 GCCATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATATA
Found at i:9998 original size:15 final size:15
Alignment explanation
Indices: 9975--10020 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
9965 AGTTAATCAA
*
9975 ATTACTTAGTTTATG
1 ATTAATTAGTTTATG
9990 ATTAATTAG--TAT-
1 ATTAATTAGTTTATG
10002 -TTAATTAGTTTATG
1 ATTAATTAGTTTATG
10016 ATTAA
1 ATTAA
10021 AATGAAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
11 8 0.31
13 6 0.23
15 12 0.46
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (15 bp):
ATTAATTAGTTTATG
Found at i:10420 original size:18 final size:18
Alignment explanation
Indices: 10394--10432 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10384 GGACCGCTTA
10394 AATTTTATATAAAATT-T
1 AATTTTATATAAAATTGT
*
10411 AATTTATATATATAATTGT
1 AATTT-TATATAAAATTGT
10430 AAT
1 AAT
10433 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTTATATAAAATTGT
Found at i:10444 original size:22 final size:22
Alignment explanation
Indices: 10419--10464 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
10409 TTAATTTATA
*
10419 TATATAATTGTAATATAAAATT
1 TATATAATCGTAATATAAAATT
*
10441 TATATTATCGTAATATAAAATT
1 TATATAATCGTAATATAAAATT
10463 TA
1 TA
10465 AATTTGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAATCGTAATATAAAATT
Found at i:17674 original size:35 final size:35
Alignment explanation
Indices: 17635--18158 Score: 849
Period size: 35 Copynumber: 15.1 Consensus size: 35
17625 TTAAGTCGAT
* *
17635 CTTAATTACCCTGAATTAAGTTGTTTACGGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
17670 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
17705 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
17740 CTTAATTACCCTGAATTAAGTTGATTACTAACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
17775 CTTAATTACCCTGAATTAAGTTTATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
17810 CTTAATTACCCTGAATTAAGCTGATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
* *
17845 CTTAATTACGCTGAATTAAGTTGATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
17880 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
* *
17915 TTTAATTACCCTGAATTAAGTTGATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
* * *
17950 CTTAATTACCCTGAATTAAATTTATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
17985 CTTAATTA-CCTGAATTAAGTTTATTA---ACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
18016 CTTAATTACCCTGAATTAAGTTGATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
* *
18051 CTTAATTACCCTGAATTAAGTTTATTACTGACTCA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
*
18086 CTTAATTACCCTGAATTAAGTTTATTACTGACTTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
* *
18121 CTTAATTACCCTGAATTAAGTTGATTATTGAATTA
1 CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
18156 CTT
1 CTT
18159 TTCCTTACTT
Statistics
Matches: 459, Mismatches: 26, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
31 12 0.03
32 17 0.04
34 17 0.04
35 413 0.90
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (35 bp):
CTTAATTACCCTGAATTAAGTTGATTACTGACTTA
Found at i:18799 original size:51 final size:50
Alignment explanation
Indices: 18616--18911 Score: 303
Period size: 51 Copynumber: 5.8 Consensus size: 50
18606 AGATTTCACT
* * * * * *
18616 TTTATTT-CACATTA-TTCAAAGATTTCATCTTTTACTTAAAAGATTTAATC
1 TTTATTTACAAATTACTTAAAAG-TTTAATCTTTCAATTAAAA-ATTCAATC
* * * * * *
18666 TTTATTTACAAAAATTACTTAAAAGTTCAATCTTTTAATCAAAGATTACATTT
1 TTTATTTAC--AAATTACTTAAAAGTTTAATCTTTCAATTAAAAATT-CAATC
*
18719 TTTATTTACAAACTTACTTAAAAGCTTAATCTTTCAATTAAAAATTCAATC
1 TTTATTTACAAA-TTACTTAAAAGTTTAATCTTTCAATTAAAAATTCAATC
* * *
18770 TTTATTCACAAATTACCTAAAAGATTTAATCTTTCACTTAAAAATTCAATC
1 TTTATTTACAAATTACTTAAAAG-TTTAATCTTTCAATTAAAAATTCAATC
*
18821 TTTATTTACAAATTACTTAAAAGCTTAATCTTTCAATTAAAAATTC-ATC
1 TTTATTTACAAATTACTTAAAAGTTTAATCTTTCAATTAAAAATTCAATC
* * * *
18870 TCTATTTACAAATTACTTGAAAGATTCATC-TTCTAATTAAAA
1 TTTATTTACAAATTACTTAAAAGTTTAATCTTTC-AATTAAAA
18912 GTCCCACTTT
Statistics
Matches: 209, Mismatches: 29, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
48 3 0.01
49 37 0.18
50 38 0.18
51 64 0.31
52 31 0.15
53 30 0.14
54 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.43
Consensus pattern (50 bp):
TTTATTTACAAATTACTTAAAAGTTTAATCTTTCAATTAAAAATTCAATC
Found at i:18933 original size:150 final size:154
Alignment explanation
Indices: 18633--19003 Score: 384
Period size: 150 Copynumber: 2.4 Consensus size: 154
18623 CACATTATTC
* *
18633 AAAGATTTCATCTTTTACTTAAAAGATTTAATCTTTATTTACAAAAATTACTTAAAAG-TTCAAT
1 AAAGATTTAATCTTTTACTTAAAA-ATTAAATCTTTATTTAC--AAATTACTTAAAAGCTT-AAT
* * * * *
18697 CTTTTAATCAAAGATTACATTTTTTATTTACAAACTTACTTAAAAGCTTAATCTTTCAATTAAAA
62 CTTTCAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAA
*
18762 ATTCAATCTTTATTCACAAATTAC-CTA
127 ATCCAATCTTTATTCACAAATTACTCTA
* *
18789 AAAGATTTAATCTTTCACTTAAAAATTCAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
1 AAAGATTTAATCTTTTACTTAAAAATTAAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
* * * *
18854 CAATTAAAAATT-CA-TCTCTATTTACAAA-TTACTTGAAAGATTCATC-TTCTAATTAAAAGTC
66 CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTC-AATTAAAAATC
* * * * *
18915 CCA-CTTTTTTTTATAAATTACTTTA
130 CAATC-TTTATTCACAAATTACTCTA
* * * * *
18940 AAA-ATTCAATCTTTTACTTAAACAA--AAATCTTTATATACACATGACTTAAAAAGCTTAAACT
1 AAAGATTTAATCTTTTACTTAAA-AATTAAATCTTTATTTACAAATTACTT-AAAAGCTTAATCT
19002 TT
64 TT
19004 GTACCAGATT
Statistics
Matches: 184, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
149 23 0.12
150 70 0.38
151 19 0.10
152 2 0.01
153 30 0.16
154 2 0.01
155 16 0.09
156 22 0.12
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (154 bp):
AAAGATTTAATCTTTTACTTAAAAATTAAATCTTTATTTACAAATTACTTAAAAGCTTAATCTTT
CAATCAAAAATTACATTCTCTATTTACAAACTTACTTAAAAGATTAATCTTTCAATTAAAAATCC
AATCTTTATTCACAAATTACTCTA
Found at i:21886 original size:27 final size:28
Alignment explanation
Indices: 21856--21923 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
21846 TTGAAGGTGT
*
21856 ACCAAAATGTCCCTAAATATGC-A-AATG
1 ACCAAAATGACCCTAAA-ATGCAAGAATG
*
21883 ACCAAAAT-ACCCT-TAATGCAAGAATG
1 ACCAAAATGACCCTAAAATGCAAGAATG
*
21909 ACCAAAATGCCCCTA
1 ACCAAAATGACCCTA
21924 TGTGACCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 16 0.47
27 12 0.35
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (28 bp):
ACCAAAATGACCCTAAAATGCAAGAATG
Found at i:36490 original size:2 final size:2
Alignment explanation
Indices: 36483--36511 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36473 AATCTTTTCC
36483 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36512 TTTTCTGGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37116 original size:47 final size:48
Alignment explanation
Indices: 37044--37136 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
37034 GCGCGTCAGA
37044 CGTCTTTTATTTTTTTTCCTAAACAATTATAG-ATACATAAAATAATCT
1 CGTCTTTTATTTTTTTTCCTAAACAATTATAGAAT-CATAAAATAATCT
37092 CGTCTTTTA-TTTTTTTCCTAAACAATTATAGAATCATAAAATAAT
1 CGTCTTTTATTTTTTTTCCTAAACAATTATAGAATCATAAAATAAT
37137 TTCTACAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 33 0.75
48 11 0.25
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (48 bp):
CGTCTTTTATTTTTTTTCCTAAACAATTATAGAATCATAAAATAATCT
Found at i:46444 original size:70 final size:70
Alignment explanation
Indices: 46331--46953 Score: 847
Period size: 70 Copynumber: 8.8 Consensus size: 70
46321 TGGATCAATC
* * * *
46331 GGAAACAACTGATGAAAAACCGCCCTGAGTCAACTGAATCGATCATTCTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
*
46396 AACAT
66 AACTT
* * * *
46401 GGAAACTACTGAAGAAATACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTGGAAT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG-AT
46466 AAAC-T
65 AAACTT
* * *
46471 GGAAAGCGACTGAAGAATGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTTGGAT
1 GGAAA-CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAT
*
46536 AAACGT
65 AAACTT
** * * * ** *
46542 GGAAACTGCTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACAAAAACTTTTATT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
46607 AACTT
66 AACTT
* *
46612 GGAAACAACTGAAGAAAGGCCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAAT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GGAT
46677 AAACTT
65 AAACTT
** * * * *
46683 -GAAAGCTTCTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGTCATAAACTTCGAA
1 GGAAA-CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GGA
46747 TAAACTT
64 TAAACTT
*
46754 GAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
46819 AA-TGT
66 AACT-T
* * * *
46824 GGAAGCTACTAAAGAAAGACCGCCCTGGGTCGACTGAATTGATCATTCTGACATAAACTTGGAAT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG-AT
46889 AAACTT
65 AAACTT
*
46895 GAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
46954 GGAGAAAGAC
Statistics
Matches: 488, Mismatches: 56, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
69 1 0.00
70 243 0.50
71 240 0.49
72 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (70 bp):
GGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATA
AACTT
Found at i:46592 original size:141 final size:141
Alignment explanation
Indices: 46333--46953 Score: 897
Period size: 141 Copynumber: 4.4 Consensus size: 141
46323 GATCAATCGG
* * * *
46333 AAACAACTGATGAAAAACCGCCCTGAGTCAACTGAATCGATCATTCTGACATAAACTTGGATAAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
* * * *
46398 CATGGAAACTACTGAAGAAATACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTGG
66 CGTGGAAACTACTAAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG
46463 AATAAACTGGA
131 AATAAACTGGA
* * * *
46474 AAGCGACTGAAGAATGACCGCCCTGGGTCGACTGAATCGATCATTCTAACATAAACTTGGATAAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
* * * * *
46539 CGTGGAAACTGCTGAAGAAAGACCACCCTGGGTCGACCGAATCGATCATTCTGACAAAAACTT-T
66 CGTGGAAACTACTAAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG
* *
46603 TATTAACTTGG-
131 AATAAAC-TGGA
* *
46614 AAACAACTGAAGAAAGGCCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GGATAA
* * * * *
46679 AC-TTGAAAGCTTCTAAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGTCATAAACTT
65 ACGTGGAAA-CTACTAAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT
* *
46743 CGAATAAACTTGA
129 GGAATAAACTGGA
46756 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
* * * *
46821 TGTGGAAGCTACTAAAGAAAGACCGCCCTGGGTCGACTGAATTGATCATTCTGACATAAACTTGG
66 CGTGGAAACTACTAAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG
*
46886 AATAAACTTGA
131 AATAAACTGGA
46897 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
46954 GGAGAAAGAC
Statistics
Matches: 429, Mismatches: 45, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
140 63 0.15
141 300 0.70
142 66 0.15
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (141 bp):
AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAA
CGTGGAAACTACTAAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGG
AATAAACTGGA
Found at i:46995 original size:35 final size:35
Alignment explanation
Indices: 46942--47012 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
46932 ATCGATCATT
* * *
46942 CTGACATAAACTGGAGAAAGACCGCCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
*
46977 CTGAAATAAACTTAAGAAAGACCACCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
47012 C
1 C
47013 CAAATCGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.15
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCACCCTGGGTCAA
Found at i:48155 original size:21 final size:21
Alignment explanation
Indices: 48131--48206 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
48121 TCATCATTCA
48131 TTTTTCTCTTTTC-CTTCTTTC
1 TTTTT-TCTTTTCTCTTCTTTC
*
48152 TTTTTTCTTTTCTTTTCTTTC
1 TTTTTTCTTTTCTCTTCTTTC
* *
48173 ATCATTTTTC-TTCCTCTTTTTTC
1 -T--TTTTTCTTTTCTCTTCTTTC
48196 TTGTTTT-TTTT
1 TT-TTTTCTTTT
48207 ACATGCACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 8 0.18
21 18 0.41
22 2 0.05
23 10 0.23
24 6 0.14
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.75
Consensus pattern (21 bp):
TTTTTTCTTTTCTCTTCTTTC
Found at i:48999 original size:44 final size:45
Alignment explanation
Indices: 48888--48999 Score: 147
Period size: 44 Copynumber: 2.5 Consensus size: 45
48878 TGCAACTTTG
* *
48888 GAAAAACCCTTTTATCAAAACCCTCTTTAAAACCATAATTCTTCTT
1 GAAAAACCATTTTATCAAAA-CCTCTTTAAAACCATAACTCTTCTT
* * *
48934 GAAAAAACATTTTATCAAAACCT-TTTGAAAACCATGACTCTTTTT
1 GAAAAACCATTTTATCAAAACCTCTTT-AAAACCATAACTCTTCTT
48979 G-AAAACCATTTTATCAAAACC
1 GAAAAACCATTTTATCAAAACC
49000 CTGACATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
44 22 0.37
45 19 0.32
46 18 0.31
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (45 bp):
GAAAAACCATTTTATCAAAACCTCTTTAAAACCATAACTCTTCTT
Found at i:49396 original size:2 final size:2
Alignment explanation
Indices: 49389--49418 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
49379 ACAGTAGAAA
49389 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49419 AAAAGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49408 original size:15 final size:15
Alignment explanation
Indices: 49388--49419 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49378 AACAGTAGAA
49388 AATATATATATATAT
1 AATATATATATATAT
49403 AATATATATATATAT
1 AATATATATATATAT
49418 AA
1 AA
49420 AAAGCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:49409 original size:13 final size:13
Alignment explanation
Indices: 49391--49416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49381 AGTAGAAAAT
49391 ATATATATATATA
1 ATATATATATATA
49404 ATATATATATATA
1 ATATATATATATA
49417 TAAAAAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Done.