Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013736.1 Corchorus capsularis cultivar CVL-1 contig13757, 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: 8893
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:79 original size:22 final size:22
Alignment explanation
Indices: 17--86 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
7 TCATATGGAA
*
17 GTTATCAAAATTTCATA-GTATG
1 GTTACCAAAATTTCATAGGT-TG
*
39 GTTACCAAAATTTCTTAGGTTG
1 GTTACCAAAATTTCATAGGTTG
*** *
61 GTTATTGAAATTTCATAGGGTG
1 GTTACCAAAATTTCATAGGTTG
83 GTTA
1 GTTA
87 ATTTTCACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 38 0.95
23 2 0.05
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGGTTG
Found at i:176 original size:22 final size:22
Alignment explanation
Indices: 151--244 Score: 55
Period size: 22 Copynumber: 4.2 Consensus size: 22
141 AGGTTATAAG
*
151 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGAGGTTAACAA
* *
173 AATTTTATTAGGAGAGGTT-ACTAA
1 AATTTCA-TA-GTGAGGTTAAC-AA
* * * * *
197 TATTTCATGGGGAGATTATCAA
1 AATTTCATAGTGAGGTTAACAA
* * *
219 AATTTTATAGTGTGGTTATCAA
1 AATTTCATAGTGAGGTTAACAA
241 AATT
1 AATT
245 CAATATGAAG
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
22 34 0.64
23 6 0.11
24 13 0.25
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTAACAA
Found at i:338 original size:22 final size:23
Alignment explanation
Indices: 308--540 Score: 132
Period size: 22 Copynumber: 10.5 Consensus size: 23
298 GAAGGTTATT
* *
308 AAATCTCATAGAG-TGATTATCG
1 AAATTTCATAGAGATGATTATCA
330 AAATTTCATAGAGATTAGATTATCA
1 AAATTTCATAGAGA-T-GATTATCA
* *
355 AAATTT-ATAG-GAAGATTGTCA
1 AAATTTCATAGAGATGATTATCA
* * *
376 AAATTCCATAGTGTTG-TTATCA
1 AAATTTCATAGAGATGATTATCA
* * *
398 AAATTTCAAAGTGA-GGTTATCA
1 AAATTTCATAGAGATGATTATCA
*
420 AAATTACATA-ATG-TGATTATCA
1 AAATTTCATAGA-GATGATTATCA
* * * * *
442 GAATTTCATAGAG-GGGTCAACA
1 AAATTTCATAGAGATGATTATCA
* *
464 AAATTTTATAAAGATG-TTATCA
1 AAATTTCATAGAGATGATTATCA
* *
486 AAATTTCATAAAGA-GGTTATCA
1 AAATTTCATAGAGATGATTATCA
* *
508 AATTTTCAGA-ATG-TGATTA-CAA
1 AAATTTCATAGA-GATGATTATC-A
530 AAATTTCATAG
1 AAATTTCATAG
541 TTGTATTTCT
Statistics
Matches: 163, Mismatches: 33, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
21 16 0.10
22 123 0.75
23 6 0.04
24 5 0.03
25 13 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATTTCATAGAGATGATTATCA
Found at i:440 original size:44 final size:45
Alignment explanation
Indices: 324--1047 Score: 153
Period size: 44 Copynumber: 16.4 Consensus size: 45
314 CATAGAGTGA
* * *
324 TTATCGAAATTTCATAGA-GATTAGATTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATA-ATGA-T-GATTATCAAAATTTCAAAGAG-AGG
* * * * *
370 TTGTCAAAATTCCATAGTGTTG-TTATCAAAATTTCAAAGTGAGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * *
414 TTATCAAAATTACATAATG-TGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * *
458 TCAACAAAATTTTATAAAGATG-TTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCA-AAGAGAGG
* *
502 TTATCAAATTTTCAGAATG-TGATTA-CAAAAATTTCATAGTTGTATTTCTGAGGAGG
1 TTATCAAAATTTCATAATGATGATTATC-AAAATTTCA-A-----A-----GA-GAGG
* * * *
558 TTATCAAAATTTCATAGT-ATGGTTA-CCAAA-TT--AGGA-AGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * * * *
597 TTATTAAACTTTTATTATG--GAGTAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAATGATGA-TTATCAAAATTTCAAAGAGAGG
* * * * *
639 ATATCAAACA-TTCATAGT-TTAATTTTCAAAATTTCATAAGAG-GG
1 TTATCAAA-ATTTCATAATGATGATTATCAAAATTTCA-AAGAGAGG
* * * * *
683 TTATCAAAATTTCATAGT-ATGCA-GATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAATGATG-ATTATCAAAATTTCAAAGAGAGG
* * * ** * *
727 TTAACAAAATTTTATAATGA-GGTTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * *
771 TTATCAAAA-TT--T-GT-A-G-TTATCAAGATTTCATAAGA-AAG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCA-AAGAGAGG
* ** * * * * *
809 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAG-GAAGAT
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAG-AG-G
** * * * * * *
855 TTATCAAAATTTCATAGCGA-GGTTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
* * * *
899 TTATCAAAATTTCAGAGTG-TGATTACCAACAA-TTCATATG-GAGG
1 TTATCAAAATTTCATAATGATGATTATCAA-AATTTCA-AAGAGAGG
* * * * * * *
943 TTTTTAAATTTTCATAATG-T-AGTTACCAATATATCATATG-GAGG
1 TTATCAAAATTTCATAATGATGA-TTATCAAAATTTCA-AAGAGAGG
* * * * * ** *
987 TTATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGAGAAG
1 TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
1032 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1048 TTGAGGTCTT
Statistics
Matches: 499, Mismatches: 121, Indels: 117
0.68 0.16 0.16
Matches are distributed among these distances:
38 23 0.05
39 24 0.05
40 5 0.01
41 7 0.01
42 26 0.05
43 27 0.05
44 249 0.50
45 72 0.14
46 33 0.07
49 1 0.00
51 1 0.00
54 2 0.00
55 4 0.01
56 25 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (45 bp):
TTATCAAAATTTCATAATGATGATTATCAAAATTTCAAAGAGAGG
Found at i:466 original size:88 final size:88
Alignment explanation
Indices: 374--540 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
364 GGAAGATTGT
** * * *
374 CAAAATTCCATAGTGTTGTTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTCCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAGAATGTGATT
*
438 ATC-AGAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
** * *
462 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAGAATGTGATTA
1 CAAAATTCCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAGAATGTGATTA
527 CAAAAATTTCATAG
66 CAAAAATTTCATAG
541 TTGTATTTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 64 0.96
89 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (88 bp):
CAAAATTCCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAGAATGTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:689 original size:22 final size:21
Alignment explanation
Indices: 664--912 Score: 125
Period size: 22 Copynumber: 11.5 Consensus size: 21
654 AGTTTAATTT
664 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCAT-AGAGGGTTA
* ***
686 TCAAAATTTCATAGTATGCAGA
1 TCAAAATTTCATAG-AGGGTTA
708 TCAAAATTTCATAG-GGAGATTA
1 TCAAAATTTCATAGAGG-G-TTA
* *
730 ACAAAATTTTATA-ATGAGGTTA
1 TCAAAATTTCATAGA-G-GGTTA
** *
752 TCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
*
774 TCAAAATTT-GT--A--GTTA
1 TCAAAATTTCATAGAGGGTTA
* **
790 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCAT-AGAGGGTTA
* *
812 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA--GAGGGTTA
* **
835 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATA-G-AGGGTTA
*
858 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGAG-GGTTA
* * *
880 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGAG-GGTTA
902 TCAAAATTTCA
1 TCAAAATTTCA
913 GAGTGTGATT
Statistics
Matches: 174, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
20 2 0.01
21 5 0.03
22 115 0.66
23 38 0.22
24 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TCAAAATTTCATAGAGGGTTA
Found at i:837 original size:23 final size:23
Alignment explanation
Indices: 787--1085 Score: 120
Period size: 22 Copynumber: 13.4 Consensus size: 23
777 AAATTTGTAG
* * * *
787 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
809 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
832 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
855 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * * *
877 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* * * *
899 TTATCAAAATTTCAGAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGT
* *
921 TTACCAACAA-TTCATATGGAGGT
1 TTATCAA-AATTTCATAGGGAGGT
* * * *
944 TT-TTAAATTTTCATAATGTA-G-
1 TTATCAAAATTTCAT-AGGGAGGT
* * * *
965 TTACCAATATATCATATGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
* * **
987 TTATCAACATCTCATAGTGTTGG-
1 TTATCAAAATTTCATAG-GGAGGT
* * *
1010 TTATCAAAATTTCATTGAGAAG-
1 TTATCAAAATTTCATAGGGAGGT
**
1032 TTATCAAAATTTCATATTGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
1055 CT-TCAAAATTCCTTAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
*
1077 TAAT-AAAAT
1 TTATCAAAAT
1086 AAAATTTCAT
Statistics
Matches: 210, Mismatches: 56, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
21 8 0.04
22 135 0.64
23 67 0.32
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:881 original size:45 final size:44
Alignment explanation
Indices: 664--1064 Score: 175
Period size: 44 Copynumber: 9.2 Consensus size: 44
654 AGTTTAATTT
* * * * ***
664 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG-TATGCAGA
1 TCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGA-GGTTA
* * * **
708 TCAAAATTTCATAGGGAGATTAACAAAATTTTATAATGAGGTTA
1 TCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTTA
** * * *
752 TCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TA-GTTA
1 TCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTTA
* * * *
790 TCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGG-TTA
*
835 TCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGTTA
* * * * * *
880 TCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTGTGATTA
1 TCAAAATTTCATAG-GAAGATTATCAAAATTTCATAGCGAGGTTA
* * * * * **
924 CCAACAA-TTCATATGG-AGGTTTTTAAATTTTCATAATGTA-GTTA
1 TCAA-AATTTCATA-GGAAGATTATCAAAATTTCATAGCG-AGGTTA
* * * * * * * *
968 CCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-GGAAGATTATCAAAATTTCATAGCG-AGGTTA
* **
1013 TCAAAATTTCATTGAGAAG-TTATCAAAATTTCATATTGAGGTCT-
1 TCAAAATTTCATAG-GAAGATTATCAAAATTTCATAGCGAGGT-TA
1057 TCAAAATT
1 TCAAAATT
1065 CCTTAGGGAG
Statistics
Matches: 273, Mismatches: 65, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
38 25 0.09
39 3 0.01
41 2 0.01
42 1 0.00
43 4 0.01
44 145 0.53
45 69 0.25
46 24 0.09
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
TCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTTA
Found at i:917 original size:22 final size:22
Alignment explanation
Indices: 640--1047 Score: 116
Period size: 22 Copynumber: 18.7 Consensus size: 22
630 TCAGGGAGGA
* *
640 TATCAAACA-TTCATAGTTTAAT
1 TATCAAA-ATTTCATAGTGTGAT
* * *
662 TTTCAAAATTTCATAAGAG-GGT
1 TATCAAAATTTCAT-AGTGTGAT
*
684 TATCAAAATTTCATAGTATGCA-
1 TATCAAAATTTCATAGTGTG-AT
* * *
706 GATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATAGTGTGAT
* * * * *
728 TAACAAAATTTTATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
** * * *
750 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
772 TATCAAAA-TT--T-GT-AG-T
1 TATCAAAATTTCATAGTGTGAT
* * **
788 TATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
810 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
833 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* * *
856 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
878 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
900 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
*
922 TACCAACAA-TTCATA-TG-GAGGT
1 TATCAA-AATTTCATAGTGTGA--T
* * * *
944 TTTTAAATTTTCATAATGT-AGT
1 TATCAAAATTTCATAGTGTGA-T
* * *
966 TACCAATATATCATA-TG-GAGGT
1 TATCAAAATTTCATAGTGTGA--T
* * *
988 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-TGAT
*
1011 TATCAAAATTTCAT--TGAGAAGT
1 TATCAAAATTTCATAGTGTG-A-T
1033 TATCAAAATTTCATA
1 TATCAAAATTTCATA
1048 TTGAGGTCTT
Statistics
Matches: 290, Mismatches: 66, Indels: 59
0.70 0.16 0.14
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
18 1 0.00
19 2 0.01
20 4 0.01
21 13 0.04
22 198 0.68
23 58 0.20
24 1 0.00
25 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:1378 original size:30 final size:30
Alignment explanation
Indices: 1343--1401 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1333 ATATTTTCCG
* *
1343 ATTGTACCCTTATTTTTAAAACATATTTCA
1 ATTGTACCATTATCTTTAAAACATATTTCA
* *
1373 ATTGTACCATTGTCTTTAAAACGTATTTC
1 ATTGTACCATTATCTTTAAAACATATTTC
1402 TAAATTGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTGTACCATTATCTTTAAAACATATTTCA
Found at i:1543 original size:37 final size:36
Alignment explanation
Indices: 1490--1578 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 36
1480 TAAGAAAGTC
*
1490 AATTTGGCTTT-T-TTTGTTTCCAA-CGTCCTATTT
1 AATTTTGCTTTGTCTTTGTTTCCAATCGTCCTATTT
**
1523 AATTTTGTCTTTTGTCTTTGTTTCCAATCGTTGTATTT
1 AATTTTG-C-TTTGTCTTTGTTTCCAATCGTCCTATTT
1561 AATTTTGCTTTGTCTTTG
1 AATTTTGCTTTGTCTTTG
1579 GTCTTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 3 0.06
36 11 0.23
37 12 0.25
38 15 0.31
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.58
Consensus pattern (36 bp):
AATTTTGCTTTGTCTTTGTTTCCAATCGTCCTATTT
Found at i:1742 original size:19 final size:20
Alignment explanation
Indices: 1715--1752 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1705 TACTATTATT
1715 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
1735 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
1753 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:1974 original size:22 final size:21
Alignment explanation
Indices: 1916--2003 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 21
1906 TTGTCTCTAT
*
1916 GTGGTTATCAAAATTTCATAAG
1 GTGGTTACCAAAATTTCAT-AG
* ** *
1938 ATGGTTAGTATAATTTCATGAG
1 GTGGTTACCAAAATTTCAT-AG
*
1960 GTGGTTACCAAAATTCCATAG
1 GTGGTTACCAAAATTTCATAG
*
1981 TGTCGTTACCAAAATTTCATAG
1 -GTGGTTACCAAAATTTCATAG
2003 G
1 G
2004 AGCAGGTTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
21 3 0.06
22 50 0.94
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
GTGGTTACCAAAATTTCATAG
Found at i:2138 original size:56 final size:56
Alignment explanation
Indices: 2078--2206 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 56
2068 TTTATAAAAA
2078 GGTTATCAAAGAGATT-ATCAAA-ATGTCATAGCAAGGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAAA-A-ATTCATCAAATATGTCATAGCAAGGTTATCAA-AATTTCATAGTGT
* * * * * ** *
2134 GGTTAACAAAATTTCATTAAATATTTCATGGGGAGGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAAATTCATCAAATATGTCATAGCAAGGTTATCAAAATTTCATAGTGT
*
2190 GGTTATCAAAATTTCAT
1 GGTTATCAAAAATTCAT
2207 ATGAAGGTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
54 2 0.03
55 6 0.10
56 51 0.84
57 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (56 bp):
GGTTATCAAAAATTCATCAAATATGTCATAGCAAGGTTATCAAAATTTCATAGTGT
Found at i:2215 original size:22 final size:22
Alignment explanation
Indices: 2167--2409 Score: 89
Period size: 22 Copynumber: 10.9 Consensus size: 22
2157 TTTCATGGGG
*
2167 AGGTTATCAAAATTTTATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
2189 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
2211 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* *
2236 AGGATTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
*
2258 AGGTTATC-AAATCTCATA--A
1 AGGTTATCAAAATTTCATATGA
**
2277 AGTGATTATCGTAATTTCATA-GA
1 AG-G-TTATCAAAATTTCATATGA
2300 GATCGGATTATCAAAATTT-ATA-GAA
1 -A--GG-TTATCAAAATTTCATATG-A
*
2325 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
2347 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
2369 AGGTTATCAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* * *
2391 TGATTATCAGAATTTCATA
1 AGGTTATCAAAATTTCATA
2410 GAGGGGTCAA
Statistics
Matches: 170, Mismatches: 27, Indels: 49
0.69 0.11 0.20
Matches are distributed among these distances:
19 3 0.02
20 10 0.06
21 29 0.17
22 85 0.50
23 3 0.02
24 9 0.05
25 19 0.11
26 8 0.05
27 4 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:2398 original size:44 final size:45
Alignment explanation
Indices: 2305--2407 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 45
2295 ATAGAGATCG
* * *
2305 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
** *
2349 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
*
2392 GATTATCAGAATTTCA
1 GATTATCAAAATTTCA
2408 TAGAGGGGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 14 0.28
44 36 0.72
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
Found at i:2608 original size:22 final size:22
Alignment explanation
Indices: 2557--3136 Score: 150
Period size: 22 Copynumber: 26.6 Consensus size: 22
2547 TTATGGAGTA
* *
2557 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATGAAGGTT
2577 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* **
2599 ATTAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
2621 TTCAAAATTTCACAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2643 AT-AAAAGTTTCATA-GTATGTAG
1 ATCAAAA-TTTCATATGAAGGT-T
* * *
2665 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
* *
2687 AACAAAAATTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * **
2709 ATCAAAAAATCATAGGGGGGTT
1 ATCAAAATTTCATATGAAGGTT
*
2731 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2747 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2769 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* * *
2792 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGAAG-GTT
* *
2815 ATCAAAATTTCATA-GCGAGATT
1 ATCAAAATTTCATATG-AAGGTT
* * *
2837 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
2859 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
2881 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * *
2903 -TTAAAATTTTCATAACG-TGGTT
1 ATCAAAA-TTTCAT-ATGAAGGTT
* *
2925 ATCAATATATCATATTG-AGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* * **
2947 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
2970 ATCAAAATTTCAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
*
2992 ATCAAAATTTCATATTG-AGATCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
3015 -TCAAAATTCCTTACGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
3036 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
** * ** *
3058 AAAAAAAATT-ATAAAAAGGTC
1 ATCAAAATTTCATATGAAGGTT
* * * **
3079 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
3101 ATTAAAATTTGATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
3123 ATCAAAATTTCATA
1 ATCAAAATTTCATA
3137 ATGGGATCAT
Statistics
Matches: 414, Mismatches: 104, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.02
17 1 0.00
18 2 0.00
20 16 0.04
21 35 0.08
22 275 0.66
23 74 0.18
24 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:2839 original size:45 final size:45
Alignment explanation
Indices: 2745--3005 Score: 132
Period size: 45 Copynumber: 5.8 Consensus size: 45
2735 AAATTTGTAG
* * * * *
2745 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGA
*
2790 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-GA
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGA
* * * * *
2835 TTATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTG-TGA
1 TTATCAAAATTTCATAG-GAAGATTATCAAAATTTCATAGCGAGGA
* * * *
2879 TTA-CTAACAA-TTCATATGG-AGGTT-TTAAAATTTTCATAACGTGG-
1 TTATC-AA-AATTTCATA-GGAAGATTATCAAAA-TTTCATAGCGAGGA
* * * * * * * *
2923 TTATCAATATATCATATTG-AGGTTATCAACATCTCATAGTGTTGG-
1 TTATCAAAATTTCATA-GGAAGATTATCAAAATTTCATAGCG-AGGA
*
2968 TTATCAAAATTTCATTGGGAAG-TTATCAAAATTTCATA
1 TTATCAAAATTTCA-TAGGAAGATTATCAAAATTTCATA
3006 TTGAGATCTT
Statistics
Matches: 168, Mismatches: 34, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
43 7 0.04
44 64 0.38
45 74 0.44
46 23 0.14
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGA
Found at i:3741 original size:12 final size:12
Alignment explanation
Indices: 3721--3764 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3711 TTGGTTAGAC
*
3721 TTTTCTTTTCTT
1 TTTTTTTTTCTT
*
3733 TTTTTTTTTCCT
1 TTTTTTTTTCTT
3745 TTTTTTTTTCATT
1 TTTTTTTTTC-TT
3758 TTTTTTT
1 TTTTTTT
3765 GTTCGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTCTT
Done.