Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013724.1 Corchorus capsularis cultivar CVL-1 contig13745, 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: 37862
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8460 original size:31 final size:31
Alignment explanation
Indices: 8425--8483 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
8415 ATGTTTTCCG
8425 ATTGTACCCTTATT-TTTAAAAAATATTTTCA
1 ATTGTACCCTT-TTCTTTAAAAAATATTTTCA
*
8456 ATTGTACCCTTTTCTTTAAAATATATTT
1 ATTGTACCCTTTTCTTTAAAAAATATTT
8484 CTAAATTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTGTACCCTTTTCTTTAAAAAATATTTTCA
Found at i:8830 original size:19 final size:21
Alignment explanation
Indices: 8798--8840 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
8788 TTCTTTACTA
8798 TTACTTTTTGAATTT-AATATT
1 TTACTTTTTGAATTTCAAT-TT
8819 TTAC-TTTT-AATTTCAATTT
1 TTACTTTTTGAATTTCAATTT
8838 TTA
1 TTA
8841 AATGTCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (21 bp):
TTACTTTTTGAATTTCAATTT
Found at i:9024 original size:22 final size:22
Alignment explanation
Indices: 8998--9137 Score: 113
Period size: 22 Copynumber: 6.3 Consensus size: 22
8988 TGTCTATAAG
*
8998 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
9020 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
9043 -AGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
9064 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
9086 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
9110 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
9132 TGGTTA
1 TGGTTA
9138 ATTATCACAA
Statistics
Matches: 93, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
21 3 0.03
22 70 0.75
23 3 0.03
24 17 0.18
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:9264 original size:22 final size:22
Alignment explanation
Indices: 9239--9286 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
9229 TTCATTAAAT
*
9239 ATTTAATGGGGAGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
* * *
9261 ATTTTATAGTGTGGTTATCAAA
1 ATTTAATAGGGAGGTTATCAAA
9283 ATTT
1 ATTT
9287 CGTATGAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (22 bp):
ATTTAATAGGGAGGTTATCAAA
Found at i:9298 original size:22 final size:22
Alignment explanation
Indices: 9249--9583 Score: 132
Period size: 22 Copynumber: 15.0 Consensus size: 22
9239 ATTTAATGGG
*
9249 GAGGTTATCAAAATTTTATAGT
1 GAGGTTATCAAAATTTCATAGT
* *
9271 GTGGTTATCAAAATTTCGTA-T
1 GAGGTTATCAAAATTTCATAGT
* *
9292 GAAGGTTATAAAAGTCTCAATTTCATAGG
1 G-AGGTTAT-CAA-----AATTTCATAGT
* *
9321 GA-G-TACCAAAATTTGATAG-
1 GAGGTTATCAAAATTTCATAGT
* *
9340 AAGGTTATC-AAATCTCATAGAAT
1 GAGGTTATCAAAATTTCATAG--T
* * *
9363 GA--TTATCGAAATTTTATAGA
1 GAGGTTATCAAAATTTCATAGT
*
9383 GATCGGATTATCAAAATTT-ATAGA
1 GA--GG-TTATCAAAATTTCATAGT
* *
9407 AAGATTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
** * *
9429 GTTGTTATCAAAATTTCAAAGC
1 GAGGTTATCAAAATTTCATAGT
*
9451 GAGGTTATCAAAATTAT-ATAAT
1 GAGGTTATCAAAATT-TCATAGT
* * * * *
9473 GTGATTATCAGAATTTTATAGA
1 GAGGTTATCAAAATTTCATAGT
* * * * **
9495 GGGGTCAACAAAATTTTATAAA
1 GAGGTTATCAAAATTTCATAGT
**
9517 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAGT
* * *
9539 GAGGTTATCAAATTTTCAAAAT
1 GAGGTTATCAAAATTTCATAGT
* *
9561 GTGATTA-CAAAAATTTCATAGT
1 GAGGTTATC-AAAATTTCATAGT
9583 G
1 G
9584 GTATTTCTCG
Statistics
Matches: 234, Mismatches: 56, Indels: 46
0.70 0.17 0.14
Matches are distributed among these distances:
19 1 0.00
20 21 0.09
21 24 0.10
22 152 0.65
23 4 0.02
24 6 0.03
25 13 0.06
26 2 0.01
27 1 0.00
28 9 0.04
29 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:9481 original size:44 final size:45
Alignment explanation
Indices: 9388--9578 Score: 155
Period size: 44 Copynumber: 4.4 Consensus size: 45
9378 ATAGAGATCG
* * * *
9388 GATTATCAAAATTT-ATAGAAAGATTATCAAAA-TTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTCATAATG-T
* *
9432 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTAT-ATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTCATAATGT
* * * * * * * *
9475 GATTATCAGAATTTTATAGAGGGGTCAACAAAATTTT-ATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTCATAATGT
* *
9519 GGTTATCAAAATTTCATAA-AGAGGTTATC-AAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTTCATAATGT
9563 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
9579 TAGTGGTATT
Statistics
Matches: 114, Mismatches: 27, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
43 22 0.19
44 89 0.78
45 3 0.03
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTCATAATGT
Found at i:9772 original size:44 final size:42
Alignment explanation
Indices: 9662--9802 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 42
9652 CTATGGAGTA
* **
9662 ATCAAAATTTCA-AGTATG-ATATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCATAGTATGTAGATCAAAATTTCAAAGAGGAT
* *
9701 ATCAAAATTTCATAGT-T-TAGTTTTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATAGTATGTAG--ATCAAAATTTCA-AAGA-GGAT
* *
9745 ATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTATGTAGATCAAAATTTCAAAGAG-GA-T
*
9789 AACAAAATTTCATA
1 ATCAAAATTTCATA
9803 ATGAGATTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
39 14 0.17
40 3 0.04
41 6 0.07
42 5 0.06
43 5 0.06
44 44 0.54
45 1 0.01
46 3 0.04
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (42 bp):
ATCAAAATTTCATAGTATGTAGATCAAAATTTCAAAGAGGAT
Found at i:9794 original size:22 final size:22
Alignment explanation
Indices: 9681--10107 Score: 154
Period size: 22 Copynumber: 19.7 Consensus size: 22
9671 TCAAGTATGA
9681 TATCAAAA-TTC--AGGGAGGA-
1 TATCAAAATTTCATAGGGA-GAT
**
9700 TATCAAAATTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-GGAGAT
* *
9722 TTTCAAAATTTCACAAGAGG-G-T
1 TATCAAAATTTCA-TAG-GGAGAT
*
9744 TATCAAAATTTCATA-GTATG-T
1 TATCAAAATTTCATAGGGA-GAT
*
9765 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGGAGAT
* **
9788 TAACAAAATTTCATAATGAGAT
1 TATCAAAATTTCATAGGGAGAT
** *
9810 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGGAGAT
*
9832 TATCAAAA-TT--T--GTAG-T
1 TATCAAAATTTCATAGGGAGAT
* * *
9848 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGGGAGA-T
* *
9870 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGA-GAT
* * *
9893 TAGCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGGAGA-T
* *
9916 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGGAGAT
* * * *
9938 TATCACAATTTCATAGTGTGGT
1 TATCAAAATTTCATAGGGAGAT
* * *
9960 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGAGAT
* *
9982 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATAGGGAGAT
* * * ** * *
10004 TTTTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAGGGAGAT
* * * *
10026 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAGGGAGAT
* * ** *
10048 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GGAGAT
* *
10071 CATCAAAATTTCATTGGGA-AGT
1 TATCAAAATTTCATAGGGAGA-T
10093 TATCAAAATTTCATA
1 TATCAAAATTTCATA
10108 TTGAGGTCTT
Statistics
Matches: 302, Mismatches: 80, Indels: 49
0.70 0.19 0.11
Matches are distributed among these distances:
16 8 0.03
17 5 0.02
19 11 0.04
20 4 0.01
21 6 0.02
22 207 0.69
23 61 0.20
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAGGGAGAT
Found at i:9899 original size:23 final size:23
Alignment explanation
Indices: 9873--9938 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
9863 AGAAAGTTAT
9873 CAAAATTTTATAGGGAGGTTTAG
1 CAAAATTTTATAGGGAGGTTTAG
* * *
9896 CAAAATTTTATAGGAAGATTTAT
1 CAAAATTTTATAGGGAGGTTTAG
* *
9919 CAAAATTTCATAGCGAGGTT
1 CAAAATTTTATAGGGAGGTT
9939 ATCACAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.35
Consensus pattern (23 bp):
CAAAATTTTATAGGGAGGTTTAG
Found at i:10095 original size:45 final size:44
Alignment explanation
Indices: 10046--10138 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
10036 TCATATGGAG
* *
10046 GTTATCAACATCTCATAGTGTTGGTCATCAAAATTTCATT-GGGAA
1 GTTATCAAAATCTCATAGTG-AGGTCATCAAAA-TTCATTAGGGAA
* * * *
10091 GTTATCAAAATTTCATATTGAGGTCTTCAAAATTCCTTAGGGAA
1 GTTATCAAAATCTCATAGTGAGGTCATCAAAATTCATTAGGGAA
10135 GTTA
1 GTTA
10139 ACCAAATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.12
44 19 0.46
45 17 0.41
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (44 bp):
GTTATCAAAATCTCATAGTGAGGTCATCAAAATTCATTAGGGAA
Found at i:10134 original size:44 final size:44
Alignment explanation
Indices: 10068--10151 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
10058 TCATAGTGTT
*
10068 GGTCATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGA
1 GGTCATCAAAATTTCATTGGGAAGTTAACAAAATTTCATATTGA
* * *
10112 GGTCTTCAAAA-TTCCTTAGGGAAGTTAACCAAATTTCATA
1 GGTCATCAAAATTTCATT-GGGAAGTTAACAAAATTTCATA
10152 AGAAGGTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.14
44 30 0.86
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (44 bp):
GGTCATCAAAATTTCATTGGGAAGTTAACAAAATTTCATATTGA
Found at i:10210 original size:22 final size:22
Alignment explanation
Indices: 10185--10240 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
10175 AAGGTTCTCG
* *
10185 AAATTCCATAATATCGTTATTA
1 AAATTTCATAATAACGTTATTA
** *
10207 AAATTTCATAGGAAGGTTATTA
1 AAATTTCATAATAACGTTATTA
10229 AAATTTCATAAT
1 AAATTTCATAAT
10241 GGGATCATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTCATAATAACGTTATTA
Found at i:10686 original size:1 final size:1
Alignment explanation
Indices: 10680--10706 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
10670 ACTGTTAGGG
10680 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
10707 GTGGTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14615 original size:65 final size:65
Alignment explanation
Indices: 14511--14640 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
14501 GTAACCCATT
14511 TTCCTTGTACTTGGTTAACAATACGAAACCTTTTGAGTTTTCATAAACTTTTGTCTGTTTCCTTA
1 TTCCTTGTACTTGGTTAACAATACGAAACCTTTTGAGTTTTCATAAACTTTTGTCTGTTTCCTTA
14576 TTCCTTGTACTTGGTTAACAATACGAAACCTTTTGAGTTTTCATAAACTTTTGTCTGTTTCCTTA
1 TTCCTTGTACTTGGTTAACAATACGAAACCTTTTGAGTTTTCATAAACTTTTGTCTGTTTCCTTA
14641 CATTGATTGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (65 bp):
TTCCTTGTACTTGGTTAACAATACGAAACCTTTTGAGTTTTCATAAACTTTTGTCTGTTTCCTTA
Found at i:15318 original size:21 final size:21
Alignment explanation
Indices: 15286--15326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15276 GTCACATTAA
15286 AATTTACACAACTTCAGAGAC
1 AATTTACACAACTTCAGAGAC
*
15307 AATTT-CACCAACTTGAGAGA
1 AATTTACA-CAACTTCAGAGA
15327 GGGGGCCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (21 bp):
AATTTACACAACTTCAGAGAC
Found at i:19173 original size:12 final size:12
Alignment explanation
Indices: 19156--19180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19146 TTGTATAATC
19156 GATCGGGTTAGG
1 GATCGGGTTAGG
19168 GATCGGGTTAGG
1 GATCGGGTTAGG
19180 G
1 G
19181 TAGGGTATGG
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:0.16, C:0.08, G:0.52, T:0.24
Consensus pattern (12 bp):
GATCGGGTTAGG
Found at i:19300 original size:19 final size:18
Alignment explanation
Indices: 19272--19313 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
19262 AATTAATTGT
19272 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
19290 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
19309 CTTAA
1 TTTAA
19314 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:24123 original size:13 final size:13
Alignment explanation
Indices: 24105--24129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24095 AATAAGTTAC
24105 TCTTTTTTTGGCT
1 TCTTTTTTTGGCT
24118 TCTTTTTTTGGC
1 TCTTTTTTTGGC
24130 AATCAAATCC
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:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (13 bp):
TCTTTTTTTGGCT
Found at i:26698 original size:17 final size:18
Alignment explanation
Indices: 26662--26700 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
26652 TTTCCTTAGA
26662 GAAATATTCAAAGAAATG
1 GAAATATTCAAAGAAATG
*
26680 GAAATATTC-AAGAATTG
1 GAAATATTCAAAGAAATG
26697 GAAA
1 GAAA
26701 AATGGACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (18 bp):
GAAATATTCAAAGAAATG
Found at i:26828 original size:73 final size:73
Alignment explanation
Indices: 26709--26883 Score: 287
Period size: 73 Copynumber: 2.4 Consensus size: 73
26699 AAAATGGACA
26709 ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGTCCATTCTGCATAAACAGT
1 ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGTCCATTCTGCATAAACAGT
* *
26774 GAATTGCC
66 AAAATGCC
* * *
26782 ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGTCTGTTGTGTCCTTTCTGTATAAACAGT
1 ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGTCCATTCTGCATAAACAGT
26847 AAAATGCC
66 AAAATGCC
* *
26855 ATTTCAGTCGACTGAAACTGAAGTTGAAA
1 ATTTCAGTCGACTAAAACAGAAGTTGAAA
26884 TGACCCGGGT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (73 bp):
ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGTCCATTCTGCATAAACAGT
AAAATGCC
Found at i:28886 original size:15 final size:15
Alignment explanation
Indices: 28866--28909 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28856 CAGCCCGCCG
28866 CAGCAGCTGCAGATC
1 CAGCAGCTGCAGATC
** * *
28881 CAGCAGCCCCAGCTG
1 CAGCAGCTGCAGATC
28896 CAGCAGCTGCAGAT
1 CAGCAGCTGCAGAT
28910 GTCCAGCAGA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.36, G:0.27, T:0.11
Consensus pattern (15 bp):
CAGCAGCTGCAGATC
Found at i:29879 original size:15 final size:16
Alignment explanation
Indices: 29854--29883 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29844 CTATGAGGCA
29854 ATGTGTAGAAAGCCAC
1 ATGTGTAGAAAGCCAC
29870 ATGT-TAGAAAGCCA
1 ATGTGTAGAAAGCCA
29884 TAATTCAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (16 bp):
ATGTGTAGAAAGCCAC
Found at i:29966 original size:11 final size:10
Alignment explanation
Indices: 29952--29982 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
29942 AGCAAAAATT
29952 AAAAAAAAAG
1 AAAAAAAAAG
29962 AAAAAAAAAG
1 AAAAAAAAAG
29972 AAAAAGAAAAG
1 AAAAA-AAAAG
29983 CTCCAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.75
11 5 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:29975 original size:16 final size:15
Alignment explanation
Indices: 29952--29981 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
29942 AGCAAAAATT
29952 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
29967 AAAAGAAAAAGAAAA
1 AAAA-AAAAAGAAAA
29982 GCTCCAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:33915 original size:3 final size:3
Alignment explanation
Indices: 33909--33956 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
33899 TTATTATTAA
33909 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33953 AAT A
1 AAT A
33957 TGTTCAACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:33941 original size:5 final size:5
Alignment explanation
Indices: 33913--33957 Score: 63
Period size: 5 Copynumber: 8.4 Consensus size: 5
33903 TATTAAAATA
33913 ATAAT AATAAT AATAAT AATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT AT
33958 GTTCAACCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 22 0.56
6 17 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:37553 original size:16 final size:17
Alignment explanation
Indices: 37532--37565 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
37522 TCCTTGAGCT
37532 TCTATATCTAT-CTATA
1 TCTATATCTATACTATA
37548 TCTATATCTATACTATA
1 TCTATATCTATACTATA
37565 T
1 T
37566 TAAAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTATATCTATACTATA
Found at i:37856 original size:78 final size:78
Alignment explanation
Indices: 37653--37858 Score: 326
Period size: 78 Copynumber: 2.6 Consensus size: 78
37643 TTGTTTAGGT
* * * *
37653 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTCTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
* *
37717 ATTTTATTTTACCA
65 ATTATACTTTACCA
37731 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
37796 TTATACTTTACCA
66 TTATACTTTACCA
37809 TTTTACTATTTT-CTTCAACTAAAAACTCTATTTTTATATAATTAAATCTA
1 TTTTACTATTTTAC-TCAACTAAAAACTCTATTTTTATATAATTAAATCTA
37859 TTAA
Statistics
Matches: 120, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
77 1 0.01
78 117 0.98
79 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATACTTTACCA
Done.