Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015389.1 Corchorus capsularis cultivar CVL-1 contig15410, 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: 75869
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:601 original size:28 final size:28
Alignment explanation
Indices: 569--625 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
559 TCTTTTTACT
569 ATTCATAAACATGAAAATGGATCACATA
1 ATTCATAAACATGAAAATGGATCACATA
597 ATTCATAAACATGAAAATGGATCACATA
1 ATTCATAAACATGAAAATGGATCACATA
625 A
1 A
626 CATGAGACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (28 bp):
ATTCATAAACATGAAAATGGATCACATA
Found at i:825 original size:50 final size:50
Alignment explanation
Indices: 745--848 Score: 190
Period size: 50 Copynumber: 2.1 Consensus size: 50
735 TATATACTAG
745 AATAGTTTTATATACTCATGATTAGCAAAATCTTAGTTATAAAAACAAAA
1 AATAGTTTTATATACTCATGATTAGCAAAATCTTAGTTATAAAAACAAAA
* *
795 AATAGTTTTATATACTCATGATTAGTAAAATCTTAGTTATAAAAACAAAG
1 AATAGTTTTATATACTCATGATTAGCAAAATCTTAGTTATAAAAACAAAA
845 AATA
1 AATA
849 ATAAACTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (50 bp):
AATAGTTTTATATACTCATGATTAGCAAAATCTTAGTTATAAAAACAAAA
Found at i:22140 original size:3 final size:3
Alignment explanation
Indices: 22134--22187 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
22124 TTAGAAAAAA
22134 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
22182 AGAG AA
1 A-AG AA
22188 TTAATAAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23103 original size:7 final size:7
Alignment explanation
Indices: 23091--23115 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23081 TTTTTTTCAA
23091 TGAGAAT
1 TGAGAAT
23098 TGAGAAT
1 TGAGAAT
23105 TGAGAAT
1 TGAGAAT
23112 TGAG
1 TGAG
23116 GGAAATTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (7 bp):
TGAGAAT
Found at i:25325 original size:31 final size:31
Alignment explanation
Indices: 25290--25348 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
25280 AGTTTTGAGA
* **
25290 AACTTTTGAAATGTCTATTACATCCTTATTT
1 AACTTTTAAAATACCTATTACATCCTTATTT
*
25321 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTACATCCTTA
25349 CATATCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTACATCCTTATTT
Found at i:26211 original size:105 final size:108
Alignment explanation
Indices: 26090--26302 Score: 326
Period size: 109 Copynumber: 2.0 Consensus size: 108
26080 ATAATGTAAA
* * * *
26090 AATTAATTAACAATATCATT-ATCAATTTTTTTGTTTT-TTTTTT-CGAATATCTCAG-CTTTAT
1 AATTAATTAAAAATATCATTAATCAATTTTTTGGTTTTCTTTTTTCCGAATATCCCAGTC-TTAA
*
26151 AATTTATAATGTAAAGTCGGATTATTTTGTTTAAGAATTAATAT
65 AATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
*
26195 AATTAATTAAAAATATCCTTAAATCAATTTTTTGGTTTTCTTTTTTCCGAATATCCCAGTCTTAA
1 AATTAATTAAAAATATCATT-AATCAATTTTTTGGTTTTCTTTTTTCCGAATATCCCAGTCTTAA
26260 AATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATA
65 AATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATA
26303 CATCCGATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
105 18 0.19
107 16 0.16
108 6 0.06
109 56 0.58
110 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (108 bp):
AATTAATTAAAAATATCATTAATCAATTTTTTGGTTTTCTTTTTTCCGAATATCCCAGTCTTAAA
ATTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATAT
Found at i:26384 original size:17 final size:17
Alignment explanation
Indices: 26362--26394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26352 TACTATACAT
*
26362 TAATATGGATGAAATTC
1 TAATATAGATGAAATTC
26379 TAATATAGATGAAATT
1 TAATATAGATGAAATT
26395 TTATACTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.36
Consensus pattern (17 bp):
TAATATAGATGAAATTC
Found at i:26681 original size:31 final size:31
Alignment explanation
Indices: 26641--26699 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
26631 ACGGTGTCCG
26641 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
26672 ATGTGGCACGCCACATGTACCAAAAAGT
1 ACGTGGCACGCCACGTGTACCAAAAAGT
26700 CGTGCCACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:26735 original size:53 final size:53
Alignment explanation
Indices: 26650--26752 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
26640 GACGTGGCAC
** *
26650 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
* **
26703 GCCACGTGTACCAAAAAGTGACACATGTCACGCCATGTATACCAAAAAGT
1 GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGT
26753 GACACGTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
Found at i:27063 original size:32 final size:32
Alignment explanation
Indices: 27027--27089 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
27017 TATGTCACAT
27027 GGAAAAATTATTTGGTGGGACTGACCCATCAA
1 GGAAAAATTATTTGGTGGGACTGACCCATCAA
27059 GGAAAAATTATTTGGTGGGACTGACCCATCA
1 GGAAAAATTATTTGGTGGGACTGACCCATCA
27090 TGTTAGTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (32 bp):
GGAAAAATTATTTGGTGGGACTGACCCATCAA
Found at i:27879 original size:6 final size:6
Alignment explanation
Indices: 27868--27914 Score: 69
Period size: 6 Copynumber: 7.7 Consensus size: 6
27858 GATTTTACTA
27868 TTGTTT TTGTTT TTGTTT TTGTTTT TTGTTTT TTGTTT TT-TTT TTGT
1 TTGTTT TTGTTT TTGTTT TTG-TTT TTG-TTT TTGTTT TTGTTT TTGT
27915 GTGTGTGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.13
6 21 0.54
7 13 0.33
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTGTTT
Found at i:27883 original size:12 final size:12
Alignment explanation
Indices: 27868--27914 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
27858 GATTTTACTA
27868 TTGTTTTTGTTT
1 TTGTTTTTGTTT
27880 TTGTTTTTGTTTT
1 TTGTTTTTG-TTT
27893 TTGTTTTTTGTTT
1 TTG-TTTTTGTTT
27906 TT-TTTTTGT
1 TTGTTTTTGT
27915 GTGTGTGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.21
12 9 0.27
13 11 0.33
14 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (12 bp):
TTGTTTTTGTTT
Found at i:27887 original size:7 final size:7
Alignment explanation
Indices: 27871--27912 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
27861 TTTACTATTG
27871 TTTTTG-
1 TTTTTGT
27877 TTTTTG-
1 TTTTTGT
27883 TTTTTGT
1 TTTTTGT
27890 TTTTTGT
1 TTTTTGT
27897 TTTTTGT
1 TTTTTGT
27904 TTTTT-T
1 TTTTTGT
27910 TTT
1 TTT
27913 GTGTGTGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 16 0.46
7 19 0.54
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:34226 original size:16 final size:16
Alignment explanation
Indices: 34205--34238 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
34195 ATCGTGACGC
34205 GGTGCCGAAAAACGTG
1 GGTGCCGAAAAACGTG
34221 GGTGCCGAAAAACGTG
1 GGTGCCGAAAAACGTG
34237 GG
1 GG
34239 GACGACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.41, T:0.12
Consensus pattern (16 bp):
GGTGCCGAAAAACGTG
Found at i:37889 original size:31 final size:31
Alignment explanation
Indices: 37832--37890 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
37822 AAAATGGCTG
* *
37832 AAATCTCAACTTGGTACCAAAGCTTTTAAGA
1 AAATCTCAACTTAGTACCAAACCTTTTAAGA
**
37863 AAATCTCAACTTAGTATGAAACCTTTTA
1 AAATCTCAACTTAGTACCAAACCTTTTA
37891 TTTCGGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (31 bp):
AAATCTCAACTTAGTACCAAACCTTTTAAGA
Found at i:44788 original size:10 final size:10
Alignment explanation
Indices: 44765--44794 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
44755 GCAAAAAAAA
44765 AAACAATAAAT
1 AAACAAT-AAT
44776 AAACAATAAT
1 AAACAATAAT
44786 AAACAATAA
1 AAACAATAA
44795 AATCTGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (10 bp):
AAACAATAAT
Found at i:52008 original size:22 final size:21
Alignment explanation
Indices: 51983--52033 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
51973 TAATATACAG
51983 TTTTATTCTAATAAAAATTC-TA
1 TTTTATT-TAAT-AAAATTCATA
*
52005 TTTTCATTTAATTAAATTCAATA
1 TTTT-ATTTAATAAAATTC-ATA
52028 TTTTAT
1 TTTTAT
52034 AATTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTTAATAAAATTCATA
Found at i:53320 original size:22 final size:22
Alignment explanation
Indices: 53295--53917 Score: 158
Period size: 22 Copynumber: 27.9 Consensus size: 22
53285 TTTATCTCTG
53295 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
53317 TGGTTATTATGATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
53340 -GGTTATCAAAA-TTCA-ATAGTG
1 TGGTTATCAAAATTTCATA-AG-A
* *
53361 TGGTTA-CCAAATTCTCATATGGA
1 TGGTTATCAAAATT-TCATA-AGA
* *
53384 -AGTTATCAAAATTTCATACTG-
1 TGGTTATCAAAATTTCATA-AGA
* * *
53405 TGGTTACCAAAATTTCTTAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
53427 TCAGCTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
53451 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
* *
53473 TGGTTAATTATCACAATTTTAT-AGAA
1 TGG----TTATCAAAATTTCATAAG-A
* * *
53499 AGGTTATCAAAATGTCATAGCGA
1 TGGTTATCAAAATTTCATA-AGA
*
53522 -GG-TACTAAAAATTTCAT-AGTA
1 TGGTTA-TCAAAATTTCATAAG-A
* *
53543 TGGTTAGCAAAATTTCATCAGGA
1 TGGTTATCAAAATTTCAT-AAGA
**
53566 -GGTTA-CAAATATTTCATGGGGA
1 TGGTTATCAAA-ATTTCAT-AAGA
*
53588 -GGTTATCAAAATTTTATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
53609 TGATTATCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAAGA
* *
53631 AGGTTATAAAAGTCTCATTTTCATAAG-
1 TGGTTATCAAA-----A-TTTCATAAGA
* *
53658 -GAG-TACCAAAATTTGAT-AGA
1 TG-GTTATCAAAATTTCATAAGA
* *
53678 AGGTTATC-AAATCTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* *
53698 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCATA-AGA
53722 TCGGATTATCAAAATTT-AT-AGAA
1 T-GG-TTATCAAAATTTCATAAG-A
* *
53745 AGATTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
53765 TGTTGTTATCAAAATTTCAAAACGA
1 TG--GTTATCAAAATTTCATAA-GA
*
53790 -GGTTATCAAAATTACATAATG-
1 TGGTTATCAAAATTTCATAA-GA
*
53811 TGATTATCAGAAA-TTCAT-AGA
1 TGGTTATCA-AAATTTCATAAGA
* * * * *
53832 GGGGTCAACAAAATTTTATAAAA
1 -TGGTTATCAAAATTTCATAAGA
*
53855 AGGTTATCAAAATTTCATAAAGA
1 TGGTTATCAAAATTTCAT-AAGA
*
53878 -GGTTATCAAATTTTCA-AA-A
1 TGGTTATCAAAATTTCATAAGA
53897 TGTGATTA-CAAAAATTTCATA
1 TG-G-TTATC-AAAATTTCATA
53918 GTGGTATTTC
Statistics
Matches: 445, Mismatches: 91, Indels: 129
0.67 0.14 0.19
Matches are distributed among these distances:
19 4 0.01
20 23 0.05
21 46 0.10
22 268 0.60
23 32 0.07
24 31 0.07
25 12 0.03
26 19 0.04
27 2 0.00
28 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:53825 original size:88 final size:87
Alignment explanation
Indices: 53725--53918 Score: 203
Period size: 88 Copynumber: 2.2 Consensus size: 87
53715 ATAGAGATCG
* * *****
53725 GATTATCAAAATTTATAGAAAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAACG
1 GATTATCAAAATTTATAGAAAGATCAACAAAATTTCATAAAAAGGTTATCAAAATTTCATAAA-G
*
53789 AGGTTATCAAAATTACATAATGT
65 AGGTTATCAAAATTACAAAATGT
* ** * *
53812 GATTATCAGAAATTCATAGAGGGGTCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAAAG
1 GATTATCA-AAATTTATAGAAAGATCAACAAAATTTCATAAAAAGGTTATCAAAATTTCATAAAG
* *
53877 AGGTTATCAAATTTTCAAAATGT
65 AGGTTATCAAAATTACAAAATGT
53900 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTT-ATAG
53919 TGGTATTTCT
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
87 14 0.16
88 70 0.80
89 3 0.03
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (87 bp):
GATTATCAAAATTTATAGAAAGATCAACAAAATTTCATAAAAAGGTTATCAAAATTTCATAAAGA
GGTTATCAAAATTACAAAATGT
Found at i:54029 original size:19 final size:19
Alignment explanation
Indices: 53999--54046 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
53989 TTATGGAGTA
53999 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAAGGAGGAT
* *
54019 ATCAAAATTCAGGGATGAT
1 ATCAAAATTCAAGGAGGAT
54038 ATCAAAATT
1 ATCAAAATT
54047 TCATATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:54189 original size:21 final size:22
Alignment explanation
Indices: 53999--54407 Score: 157
Period size: 22 Copynumber: 18.8 Consensus size: 22
53989 TTATGGAGTA
*
53999 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
54019 ATCAAAA-TTC--AGGGATGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
54038 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
54060 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
54082 TTCAAAATGTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
54104 ATCAAAAATTTCATA-GTATGTAG
1 ATC-AAAATTTCATAGGGAGGT-T
*
54127 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
54149 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
54171 ATCAAAA-ATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
54192 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
54208 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
54230 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* * * *
54253 ATCAAAATTTCATAGTGTGATA
1 ATCAAAATTTCATAGGGAGGTT
* * *
54275 ATCAAAATTTCAGAGTGTGTGATT
1 ATCAAAATTTCATAG-G-GAGGTT
* *
54299 A-CTAACACAATTCATATGGAGGTT
1 ATC-AA-A-ATTTCATAGGGAGGTT
* * * ** *
54323 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
54345 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
54367 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
54390 ATTAAAATTTCATTGGGA
1 ATCAAAATTTCATAGGGA
54408 CAAATTGAGG
Statistics
Matches: 286, Mismatches: 79, Indels: 46
0.70 0.19 0.11
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
18 1 0.00
19 18 0.06
20 11 0.04
21 21 0.07
22 147 0.51
23 53 0.19
24 14 0.05
25 2 0.01
26 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:54586 original size:22 final size:22
Alignment explanation
Indices: 54558--54601 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54548 GATCATAAAA
54558 AATAGTGTA-ATTATCATAATTT
1 AATAGTG-AGATTATCATAATTT
*
54580 AATAGTGAGGTTATCATAATTT
1 AATAGTGAGATTATCATAATTT
54602 CATATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
AATAGTGAGATTATCATAATTT
Found at i:56137 original size:2 final size:2
Alignment explanation
Indices: 56130--56185 Score: 64
Period size: 2 Copynumber: 28.5 Consensus size: 2
56120 ATTATATGAC
*
56130 AT AT AT AT AT AT AT AT AT AT GT AT GAT AT AT A- AT AT A- AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T
56172 AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
56186 AAGAATCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 3 0.06
2 40 0.85
3 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:56186 original size:19 final size:20
Alignment explanation
Indices: 56130--56186 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 20
56120 ATTATATGAC
56130 ATATATATATATATATATATGT
1 ATATATATA-ATATA-ATATGT
56152 ATGATATATAATATAATA-GT
1 AT-ATATATAATATAATATGT
56172 ATATATATAATATAA
1 ATATATATAATATAA
56187 AGAATCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.38
20 4 0.12
21 3 0.09
22 7 0.21
23 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATATATAATATAATATGT
Found at i:62405 original size:15 final size:15
Alignment explanation
Indices: 62385--62413 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62375 TTACTACTTG
62385 CTCTGTCTCAAATTC
1 CTCTGTCTCAAATTC
62400 CTCTGTCTCAAATT
1 CTCTGTCTCAAATT
62414 ATCTGACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.41
Consensus pattern (15 bp):
CTCTGTCTCAAATTC
Found at i:64457 original size:60 final size:59
Alignment explanation
Indices: 64371--64532 Score: 157
Period size: 60 Copynumber: 2.7 Consensus size: 59
64361 CTATTTGCTT
* * * * *
64371 AAATAA-GAGCCTAACGTTTGTCAAAATGCTTAAATAAGGGTCTGATTTTTTAATTTGGCC
1 AAATAAGGA-CCTAACGTTT-TGAAAATGCTTAAATAAGGGCCCGATCTTTTAATTTGACC
* *
64431 AAATAAGGACCTAACGTTATTGAAAATG-TTCAAATAAGGACCCGATCTTTTAGTTTGACC
1 AAATAAGGACCTAACGTT-TTGAAAATGCTT-AAATAAGGGCCCGATCTTTTAATTTGACC
* * * * *
64491 AAACAAGGGCCAAACGTTGTCGAAAATGCTCAAATAAGGGCC
1 AAATAAGGACCTAACGTT-TTGAAAATGCTTAAATAAGGGCC
64533 TAGTGTCAGT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
59 2 0.02
60 78 0.93
61 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (59 bp):
AAATAAGGACCTAACGTTTTGAAAATGCTTAAATAAGGGCCCGATCTTTTAATTTGACC
Found at i:64668 original size:59 final size:59
Alignment explanation
Indices: 64575--64734 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 59
64565 CAACTCCAGG
* *
64575 CCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGG-CAAATCAAAAGATC-GA
1 CCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGGTCAAATCAAAAGATCAGA
* * *
64633 GTCCTTATTTGAGCATTTTGGAAAATATTAGGCCCTTATTTGGTCAAATTAAAAGATCAGA
1 -CCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGGTCAAATCAAAAGATCAGA
**
64694 CCCTTA-TTGAAGCATTTTGACAAACATTAGATCCTTATTTG
1 CCCTTATTTG-AGCATTTTGA-AAACATTAGGCCCTTATTTG
64735 AACAATTAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
59 42 0.48
60 43 0.49
61 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTGAAAACATTAGGCCCTTATTTGGTCAAATCAAAAGATCAGA
Found at i:64710 original size:60 final size:58
Alignment explanation
Indices: 64574--64734 Score: 191
Period size: 59 Copynumber: 2.7 Consensus size: 58
64564 TCAACTCCAG
* *
64574 GCCCTTATTTGAGCATTTTCGACAACGTTAGGCCCTTATTTGGCAAATCAAAAGATCGA
1 GCCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGGCAAATCAAAAGATCGA
* * *
64633 GTCCTTATTTGAGCATTTTGGAAAATATTAGGCCCTTATTTGGTCAAATTAAAAGATC-A
1 GCCCTTATTTGAGCATTTT-GAAAACATTAGGCCCTTATTTGG-CAAATCAAAAGATCGA
**
64692 GACCCTTA-TTGAAGCATTTTGACAAACATTAGATCCTTATTTG
1 G-CCCTTATTTG-AGCATTTTGA-AAACATTAGGCCCTTATTTG
64735 AACAATTAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
59 45 0.51
60 43 0.49
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (58 bp):
GCCCTTATTTGAGCATTTTGAAAACATTAGGCCCTTATTTGGCAAATCAAAAGATCGA
Found at i:64763 original size:2 final size:2
Alignment explanation
Indices: 64752--64793 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
64742 AGCCAGATTA
*
64752 AT AT -T AT AT AT AT AT AT AT AT AT AT AA 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
64793 A
1 A
64794 GCCAGATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65956 original size:2 final size:2
Alignment explanation
Indices: 65949--66048 Score: 128
Period size: 2 Copynumber: 50.0 Consensus size: 2
65939 CATGCCTGTC
* * * * *
65949 TG TG TG TG TG TG TG TG TG TA TG TT TG TC TG TC TG TG TG TG TC
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
65991 TG TG CG TC TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
66033 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
66049 AGCAAATGAA
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.02, C:0.05, G:0.43, T:0.50
Consensus pattern (2 bp):
TG
Found at i:71120 original size:11 final size:11
Alignment explanation
Indices: 71104--71146 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
71094 TATACTATAT
71104 CTAATTAATAG
1 CTAATTAATAG
*
71115 CTAATTAATAT
1 CTAATTAATAG
71126 CTAATTAATAG
1 CTAATTAATAG
*
71137 TTAATTAATA
1 CTAATTAATA
71147 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:71128 original size:22 final size:22
Alignment explanation
Indices: 71100--71146 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
71090 CCATTATACT
71100 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
71122 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
71144 ATA
1 ATA
71147 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.