Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011448.1 Corchorus capsularis cultivar CVL-1 contig11469, 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: 58984
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:415 original size:60 final size:59
Alignment explanation
Indices: 308--441 Score: 155
Period size: 60 Copynumber: 2.3 Consensus size: 59
298 TCTTACAAGA
* * * * *
308 GGGAC-ATTTCCCCCCTAAATTTTATTTTGAAACTTTTAGTCATTAAACTATCAAAATC
1 GGGACAATTTCCCCCCTAAATTCTAATTTGAAACTTTCAGCCATTAAACCATCAAAATC
* * *
366 GGGACAATTTCCCCCTTAAACTTCTAATTTGAAACTTTCA-CCCTCTAAACCATCAAAATT
1 GGGACAATTTCCCCCCTAAA-TTCTAATTTGAAACTTTCAGCCAT-TAAACCATCAAAATC
*
426 GGGACAATTTCTCCCC
1 GGGACAATTTCCCCCC
442 AAGAAATGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 5 0.08
59 15 0.24
60 43 0.68
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (59 bp):
GGGACAATTTCCCCCCTAAATTCTAATTTGAAACTTTCAGCCATTAAACCATCAAAATC
Found at i:11934 original size:2 final size:2
Alignment explanation
Indices: 11927--11956 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11917 GTTAAAAATA
11927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11957 TAGAGCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15011 original size:43 final size:44
Alignment explanation
Indices: 14955--15057 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
14945 TATAGTTAGG
* * * * * *
14955 TTATCAAAGTTTCATATGGAGTTTATCACAATTTCAT-AGGTAA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATAA
* *
14998 TTATCAAAATTTCATAGGGTGGTTATCAAAATTTAATAAGATAG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATAA
15042 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
15058 AAACTATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 31 0.61
44 20 0.39
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTAATAAGATAA
Found at i:15058 original size:22 final size:22
Alignment explanation
Indices: 14954--15058 Score: 115
Period size: 22 Copynumber: 4.8 Consensus size: 22
14944 TTATAGTTAG
* *
14954 GTTATCAAAGTTTCATATGG-A
1 GTTATCAAAATTTCATAAGGTA
*
14975 GTTTATCACAATTTCAT-AGGTA
1 G-TTATCAAAATTTCATAAGGTA
* * *
14997 ATTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTCATAAGGTA
* *
15019 GTTATCAAAATTTAATAAGATA
1 GTTATCAAAATTTCATAAGGTA
15041 GTTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
15059 AACTATTAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.25
22 51 0.75
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGTA
Found at i:15569 original size:22 final size:22
Alignment explanation
Indices: 15509--15748 Score: 135
Period size: 22 Copynumber: 10.8 Consensus size: 22
15499 TTCTTGGGAT
**
15509 GTTATCAAAATTTCATAAGGTT
1 GTTATCAAAATTTCATAAGGAG
* ** *
15531 ATTAAAATAGAATTTCATAAGGAT
1 GTTATCA-A-AATTTCATAAGGAG
* *
15555 GTTATCAAAATTTCATATGGAA
1 GTTATCAAAATTTCATAAGGAG
*
15577 GTTATCAGAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* * * *
15599 GCTATCGAAA-TTCATGAGAAG
1 GTTATCAAAATTTCATAAGGAG
* * *
15620 GTTAACAAAATTTCACAGGGAG
1 GTTATCAAAATTTCATAAGGAG
****
15642 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAAGGAG
** *
15664 ACTATCAAAATTTCCATAGGGAG
1 GTTATCAAAATTT-CATAAGGAG
* * * *
15687 GCTAACAAAATTTCATATGGCG
1 GTTATCAAAATTTCATAAGGAG
* * *
15709 ATTATCGAAATTTGAT-AGGAAG
1 GTTATCAAAATTTCATAAGG-AG
*
15731 ATTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
15749 TGTGCTTATA
Statistics
Matches: 162, Mismatches: 48, Indels: 15
0.72 0.21 0.07
Matches are distributed among these distances:
21 19 0.12
22 106 0.65
23 20 0.12
24 17 0.10
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:15878 original size:22 final size:23
Alignment explanation
Indices: 15831--15925 Score: 85
Period size: 22 Copynumber: 4.4 Consensus size: 23
15821 TAGTTTAACA
*
15831 ATCACAATTTCAT-A-G-AGGTT
1 ATCAAAATTTCATGAGGCAGGTT
*
15851 AACAAAATTTCATG-GGCAGGTT
1 ATCAAAATTTCATGAGGCAGGTT
* *
15873 ATCAAAATTTTA-GAGGGAGGTT
1 ATCAAAATTTCATGAGGCAGGTT
* * *
15895 ATCAAAATTTCATAATG-TGGTT
1 ATCAAAATTTCATGAGGCAGGTT
15917 ATCAAAATT
1 ATCAAAATT
15926 GGCTAAAATC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.18
21 2 0.03
22 46 0.75
23 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (23 bp):
ATCAAAATTTCATGAGGCAGGTT
Found at i:16289 original size:22 final size:22
Alignment explanation
Indices: 16237--16608 Score: 135
Period size: 22 Copynumber: 17.0 Consensus size: 22
16227 GAGGGAGAGC
* * * *
16237 TTATCAAATTTTCATTGTGTGG
1 TTATCAAAATTTCATAGTGAGT
* * *
16259 TAATTAAAATTTCATAATGAGT
1 TTATCAAAATTTCATAGTGAGT
*
16281 TTATCAAAATTT-ATAGTGAGA
1 TTATCAAAATTTCATAGTGAGT
* * * *
16302 TTAACAAAATTTGATAGTGTGG
1 TTATCAAAATTTCATAGTGAGT
* * * *
16324 TTCTCAAAATTTTATAGGGAGA
1 TTATCAAAATTTCATAGTGAGT
* *
16346 TTAACAAAATTTCATAGGTAAG-
1 TTATCAAAATTTCATA-GTGAGT
* * *
16368 TTATCATAATTTTATGGTGTAGTT
1 TTATCAAAATTTCATAGTG-AG-T
* * * *
16392 AATTATCAAAATTACATTG-GGGG
1 --TTATCAAAATTTCATAGTGAGT
* * *
16415 TTACCAAAATTTAATAGTG-TT
1 TTATCAAAATTTCATAGTGAGT
*
16436 CTTATCAAAATTTCATAG-GAGA
1 -TTATCAAAATTTCATAGTGAGT
* * * *
16458 TTAACACAATTTTATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGT
* *
16480 TTATAAAAAATTT-ATAGGGA-T
1 TTAT-CAAAATTTCATAGTGAGT
16501 GTTATCAAAATTTCATGAAGTG-GT
1 -TTATCAAAATTTCAT--AGTGAGT
*
16525 TT-TCAAAATTTC--A-TGAGG
1 TTATCAAAATTTCATAGTGAGT
* *
16543 TTATCAAAATTTCA-AATGGAGG
1 TTATCAAAATTTCATAGT-GAGT
* * *
16565 TTGTCAAAATTTTAAAAG-GAGGT
1 TTATCAAAA-TTTCATAGTGA-GT
*
16588 TTATAAAAATTTCATAGTGAG
1 TTATCAAAATTTCATAGTGAG
16609 GCATCACAAT
Statistics
Matches: 258, Mismatches: 65, Indels: 54
0.68 0.17 0.14
Matches are distributed among these distances:
17 2 0.01
18 4 0.02
19 10 0.04
20 1 0.00
21 56 0.22
22 140 0.54
23 25 0.10
24 6 0.02
25 1 0.00
26 13 0.05
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGT
Found at i:16632 original size:107 final size:106
Alignment explanation
Indices: 16437--16645 Score: 244
Period size: 107 Copynumber: 2.0 Consensus size: 106
16427 AATAGTGTTC
* * *
16437 TTATCAAAATTTCATAGGAGATTAACACAATTTTATAAGGAGGTTATAAAAAATTTATAGGGATG
1 TTATCAAAATTTCAAAGGAGATTAACAAAATTTTAAAAGGAGGTTATAAAAAATTTATAGGGATG
** *
16502 TTATCAAAATTTCATGAAGTGGTTTTCAAAATTTCATGAGG
66 GCATCAAAATTTCATGAAGTGGTTATCAAAATTTCATGAGG
* ** *
16543 TTATCAAAATTTCAAATGGAGGTTGTCAAAATTTTAAAAGGAGGTT-TATAAAAATTTCATAGTG
1 TTATCAAAATTTCAAA-GGAGATTAACAAAATTTTAAAAGGAGGTTATA-AAAAATTT-ATAGGG
* * *
16607 A-GGCATCACAATTTTATGGTA-TGGTTATCAAAATTTCAT
63 ATGGCATCAAAATTTCAT-GAAGTGGTTATCAAAATTTCAT
16646 AATGTGATTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
106 17 0.20
107 61 0.71
108 8 0.09
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (106 bp):
TTATCAAAATTTCAAAGGAGATTAACAAAATTTTAAAAGGAGGTTATAAAAAATTTATAGGGATG
GCATCAAAATTTCATGAAGTGGTTATCAAAATTTCATGAGG
Found at i:16730 original size:22 final size:22
Alignment explanation
Indices: 16704--16775 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
16694 GCTTACCATC
*
16704 ATTTCACTCGGAGGTTATCAAA
1 ATTTCACTAGGAGGTTATCAAA
* * *
16726 ATTTCATTAGGTGGTTATTAAA
1 ATTTCACTAGGAGGTTATCAAA
* * *
16748 ATTTTA-TAGGGAAGTTAACAAA
1 ATTTCACTA-GGAGGTTATCAAA
16770 ATTTCA
1 ATTTCA
16776 TATGTAGTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTTCACTAGGAGGTTATCAAA
Found at i:17700 original size:44 final size:44
Alignment explanation
Indices: 17637--17723 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
17627 AAAACTACAG
*
17637 TCGGCCAACATGGTCAATAATCGGATAAAAACCGGTTAGACCGA
1 TCGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGA
17681 TCGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCG
1 TCGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCG
17724 GCAGTTGGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (44 bp):
TCGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGA
Found at i:17857 original size:101 final size:101
Alignment explanation
Indices: 17682--17883 Score: 377
Period size: 101 Copynumber: 2.0 Consensus size: 101
17672 TTAGACCGAT
17682 CGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGGCAGTTGGACCGGATTCTGATCG
1 CGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGGCAGTTGGACCGGATTCTGATCG
*
17747 GATAGAACCGGTTTGATGTCCGACCGATTCAACCGG
66 GATAGAACCGATTTGATGTCCGACCGATTCAACCGG
* *
17783 CGGCCAACATGGTCAATAATCGGATAAAAGCCGATTAGACCGGCAGTTGGACCGGGTTCTGATCG
1 CGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGGCAGTTGGACCGGATTCTGATCG
17848 GATAGAACCGATTTGATGTCCGACCGATTCAACCGG
66 GATAGAACCGATTTGATGTCCGACCGATTCAACCGG
17884 GAACCGATGG
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (101 bp):
CGGCCAACATGGTCAATAATCGGATAAAAACCGATTAGACCGGCAGTTGGACCGGATTCTGATCG
GATAGAACCGATTTGATGTCCGACCGATTCAACCGG
Found at i:25816 original size:18 final size:18
Alignment explanation
Indices: 25793--25829 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25783 TCATATGTCA
25793 AACTGAACTGGAAAACAG
1 AACTGAACTGGAAAACAG
*
25811 AACTGAATTGGAAAACAG
1 AACTGAACTGGAAAACAG
25829 A
1 A
25830 CAAACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (18 bp):
AACTGAACTGGAAAACAG
Found at i:32423 original size:29 final size:29
Alignment explanation
Indices: 32386--32459 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
32376 CAAACTATTG
* *
32386 AATCGAGGACGTTTTGTCTCATGAACTT-CA
1 AATC-AGGACATTTTG-CCCATGAACTTCCA
* *
32416 AATCAGGATATTTTGCCCCTGAACTTCCA
1 AATCAGGACATTTTGCCCATGAACTTCCA
32445 AATTCAGGACATTTT
1 AA-TCAGGACATTTT
32460 ACCCCCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 9 0.24
29 13 0.35
30 15 0.41
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (29 bp):
AATCAGGACATTTTGCCCATGAACTTCCA
Found at i:32459 original size:30 final size:28
Alignment explanation
Indices: 32407--32464 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
32397 TTTTGTCTCA
* *
32407 TGAACTTCAAATCAGGATATTTTGCCCC
1 TGAACTTCAAATCAGGACATTTTACCCC
32435 TGAACTTCCAAATTCAGGACATTTTACCCC
1 TGAACTT-CAAA-TCAGGACATTTTACCCC
32465 CTAAACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 4 0.15
30 15 0.58
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
TGAACTTCAAATCAGGACATTTTACCCC
Found at i:32472 original size:31 final size:28
Alignment explanation
Indices: 32409--32472 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
32399 TTGTCTCATG
* * *
32409 AACTTCAAATCAGGATATTTTGCCCCTG
1 AACTTCAAATCAGGACATTTTCCCCCTA
32437 AACTTCCAAATTCAGGACATTTTACCCCCTA
1 AACTT-CAAA-TCAGGACATTTT-CCCCCTA
32468 AACTT
1 AACTT
32473 TCAGAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 5 0.17
29 4 0.13
30 11 0.37
31 10 0.33
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
AACTTCAAATCAGGACATTTTCCCCCTA
Found at i:34292 original size:20 final size:20
Alignment explanation
Indices: 34267--34316 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
34257 ATTTGTTGGT
34267 GCTTAGGCTTTGGGCAATTA
1 GCTTAGGCTTTGGGCAATTA
34287 GCTTAGGCTTTGGGCAATTA
1 GCTTAGGCTTTGGGCAATTA
34307 GCTTAGGCTT
1 GCTTAGGCTT
34317 GAACTATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (20 bp):
GCTTAGGCTTTGGGCAATTA
Found at i:44908 original size:2 final size:2
Alignment explanation
Indices: 44897--44935 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
44887 GATTTGATAG
44897 AT AT AT -T AT AT AT AT AT AT AT AT AT 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
44936 TGCTCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:45556 original size:16 final size:16
Alignment explanation
Indices: 45535--45654 Score: 55
Period size: 16 Copynumber: 7.4 Consensus size: 16
45525 GGCAGTTTTC
45535 TCGGGTCATTTGGGTT
1 TCGGGTCATTTGGGTT
45551 TCGGGTCATCTT-GGTAAT
1 TCGGGTCAT-TTGGGT--T
* * * *
45569 TCTGGTTATTTGAGTC
1 TCGGGTCATTTGGGTT
* *
45585 TCGGGTCATTCGGGTC
1 TCGGGTCATTTGGGTT
* **
45601 TCAGGTCATACGGGTT
1 TCGGGTCATTTGGGTT
* * * *
45617 CCGGGTCGTTCGGGTC
1 TCGGGTCATTTGGGTT
* *
45633 TCGGATC-TACTGGGTT
1 TCGGGTCAT-TTGGGTT
45649 TCGGGT
1 TCGGGT
45655 TGGGCGGGTT
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
15 1 0.01
16 62 0.81
17 4 0.05
18 10 0.13
ACGTcount: A:0.10, C:0.19, G:0.34, T:0.37
Consensus pattern (16 bp):
TCGGGTCATTTGGGTT
Found at i:45654 original size:32 final size:32
Alignment explanation
Indices: 45585--45654 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
45575 TATTTGAGTC
45585 TCGGGTCATTCGGGTCTCAGGTCATACGGGTT
1 TCGGGTCATTCGGGTCTCAGGTCATACGGGTT
* *
45617 CCGGGTCGTTCGGGTCTC-GGATC-TACTGGGTT
1 TCGGGTCATTCGGGTCTCAGG-TCATAC-GGGTT
45649 TCGGGT
1 TCGGGT
45655 TGGGCGGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (32 bp):
TCGGGTCATTCGGGTCTCAGGTCATACGGGTT
Found at i:46757 original size:11 final size:11
Alignment explanation
Indices: 46743--46780 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
46733 ATTCATAACA
46743 AATTTATAATT
1 AATTTATAATT
46754 AATTTATAATT
1 AATTTATAATT
46765 -ATTTGATAATT
1 AATTT-ATAATT
*
46776 GATTT
1 AATTT
46781 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:47069 original size:16 final size:16
Alignment explanation
Indices: 47048--47181 Score: 126
Period size: 16 Copynumber: 8.4 Consensus size: 16
47038 GTTAACTTCA
*
47048 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
47064 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
*
47080 TCGGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
* *
47096 ACGGGTCATTCGAGTT
1 TCGGGTCATTCGGGTT
*
47112 TCGAGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
47128 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
* *
47144 TCGAGTCATTTGGGTT
1 TCGGGTCATTCGGGTT
* * *
47160 GCAGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
47176 TCGGGT
1 TCGGGT
47182 TGGGCGGGTT
Statistics
Matches: 90, Mismatches: 26, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
15 2 0.02
16 86 0.96
17 2 0.02
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:47084 original size:32 final size:32
Alignment explanation
Indices: 47048--47181 Score: 153
Period size: 32 Copynumber: 4.2 Consensus size: 32
47038 GTTAACTTCA
* * *
47048 TCGGGTTATTCGGGTTTCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTTACGGGTCATTCGGGTC
* * *
47080 TCGGGTCACTCGGGTTACGGGTCATTCGAGTT
1 TCGGGTCATTCGGGTTACGGGTCATTCGGGTC
*
47112 TCGAGTCA-TCTGGGTTACGGGTCATTCGGGTC
1 TCGGGTCATTC-GGGTTACGGGTCATTCGGGTC
* * * *
47144 TCGAGTCATTTGGGTTGCAGGTCATTCGGGTC
1 TCGGGTCATTCGGGTTACGGGTCATTCGGGTC
47176 TCGGGT
1 TCGGGT
47182 TGGGCGGGTT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.02
32 84 0.97
33 1 0.01
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (32 bp):
TCGGGTCATTCGGGTTACGGGTCATTCGGGTC
Found at i:47457 original size:31 final size:31
Alignment explanation
Indices: 47386--47450 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
47376 AACTTTATGT
*
47386 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
47417 TTTCCAATTGTACCCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
47447 TTTC
1 TTTC
47451 TTAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:47752 original size:22 final size:22
Alignment explanation
Indices: 47727--47865 Score: 70
Period size: 22 Copynumber: 6.3 Consensus size: 22
47717 TGTCTCTATG
47727 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
47749 TGGTTAT-TATATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
47771 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
47792 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
47814 TCAAGTTATTAAAATTTC-TTAGA
1 T--GGTTATCAAAATTTCATAAGA
** * *
47837 TTGGTTATTGAAATTTCATAGGG
1 -TGGTTATCAAAATTTCATAAGA
47860 TGGTTA
1 TGGTTA
47866 ATTATCACAA
Statistics
Matches: 86, Mismatches: 22, Indels: 18
0.68 0.17 0.14
Matches are distributed among these distances:
20 1 0.01
21 13 0.15
22 53 0.62
23 6 0.07
24 13 0.15
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:48030 original size:22 final size:22
Alignment explanation
Indices: 48002--48236 Score: 89
Period size: 22 Copynumber: 10.5 Consensus size: 22
47992 CAAATTTGAT
48002 AGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
* *
48024 AGGTTATAAAAGTCTCAATTTCATATGG
1 AGGTTAT-CAA-----AATTTCATATGA
*
48052 A-G-TA-CAAAAATTTGATA-GA
1 AGGTTATC-AAAATTTCATATGA
*
48071 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* * *
48090 AGTGATTATCGAAATTTAATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
48115 TAGGATTATCAAAATTT-ATATGA
1 -AGG-TTATCAAAATTTCATATGA
* *
48138 AGATTATCAAATTTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
48160 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
48182 AGGTTATCAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* * *
48204 TGATTATCAAAATTTCATA-AA
1 AGGTTATCAAAATTTCATATGA
48225 GAGGTTATCAAA
1 -AGGTTATCAAA
48237 TTTTTAAAAT
Statistics
Matches: 160, Mismatches: 28, Indels: 50
0.67 0.12 0.21
Matches are distributed among these distances:
19 4 0.03
20 20 0.12
21 20 0.12
22 71 0.44
23 8 0.05
24 5 0.03
25 15 0.09
26 4 0.03
27 1 0.01
28 12 0.08
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:48082 original size:20 final size:21
Alignment explanation
Indices: 48058--48157 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 21
48048 ATGGAGTACA
48058 AAAATTTGATAGAAGG-TTATC
1 AAAATTT-ATAGAAGGATTATC
*
48079 -AAATCTCATAG-AGTGATTATC
1 AAAAT-TTATAGAAG-GATTATC
*
48100 GAAATTTAATAAAGATAGGATTATC
1 AAAATTT-AT--AGA-AGGATTATC
48125 AAAATTTATATGAA-GATTATC
1 AAAATTTATA-GAAGGATTATC
*
48146 AAATTTTCATAG
1 AAAATTT-ATAG
48158 TGTTGTTATC
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
19 2 0.03
20 9 0.14
21 21 0.33
22 11 0.17
23 2 0.03
24 4 0.06
25 13 0.20
26 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (21 bp):
AAAATTTATAGAAGGATTATC
Found at i:48123 original size:25 final size:26
Alignment explanation
Indices: 48093--48141 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
48083 CTCATAGAGT
*
48093 GATTATCGAAATTTA-ATAAAGATAG
1 GATTATCAAAATTTATATAAAGATAG
*
48118 GATTATCAAAATTTATATGAAGAT
1 GATTATCAAAATTTATATAAAGAT
48142 TATCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (26 bp):
GATTATCAAAATTTATATAAAGATAG
Found at i:48144 original size:21 final size:23
Alignment explanation
Indices: 48118--48222 Score: 94
Period size: 22 Copynumber: 4.8 Consensus size: 23
48108 ATAAAGATAG
48118 GATTATCAAAATTT-ATA-TGAA
1 GATTATCAAAATTTCATAGTGAA
* **
48139 GATTATCAAATTTTCATAGTGTT
1 GATTATCAAAATTTCATAGTGAA
* *
48162 G-TTATCAAAATTTCAAAGCG-A
1 GATTATCAAAATTTCATAGTGAA
* * * *
48183 GGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCATAGTGAA
48205 GATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
48223 AAGAGGTTAT
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
21 14 0.21
22 50 0.75
23 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGAA
Found at i:48211 original size:44 final size:44
Alignment explanation
Indices: 48118--48266 Score: 157
Period size: 44 Copynumber: 3.4 Consensus size: 44
48108 ATAAAGATAG
*
48118 GATTATCAAAATTT-ATATGAAGA--TTATCAAATTTTCATAGTGTT
1 GATTATCAAAATTTCATA--AAGAGGTTATCAAATTTTCATAATG-T
* * *
48162 G-TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCATAATGT
* *
48205 GATTATCAAAATTTCATAAAGAGGTTATCAAATTTTTAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGT
48249 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
48267 GTGGTATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 14
0.79 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 16 0.18
44 68 0.76
45 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGT
Found at i:48378 original size:19 final size:19
Alignment explanation
Indices: 48348--48414 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
48338 TGATGGAGTA
48348 ATCAAAATTTCAAG-GAGGAT
1 ATCAAAA-TTC-AGTGAGGAT
*
48368 ACCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGTGAGGAT
*
48387 ATCGAAATTCAGTGAGGAT
1 ATCAAAATTCAGTGAGGAT
48406 ATCAAAATT
1 ATCAAAATT
48415 TCATATGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 2 0.05
19 34 0.81
20 6 0.14
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAGTGAGGAT
Found at i:48644 original size:23 final size:23
Alignment explanation
Indices: 48596--48658 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
48586 CATAAGAAAG
* **
48596 TTATCAAAATTTTATAGGGATGT
1 TTATCAAAATTTTATAGGAAAAT
*
48619 TTATTAAAATTTTATAGGAAAAT
1 TTATCAAAATTTTATAGGAAAAT
*
48642 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
48659 CGAGGTTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAAAT
Found at i:48693 original size:26 final size:26
Alignment explanation
Indices: 48649--48700 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
48639 AATTTATCAA
* *
48649 AATTTCATAGCGAGGTTATCACAATT
1 AATTTCATAGCGAGATTATCAAAATT
* *
48675 AATTTCATAGTGTGATTATCAAAATT
1 AATTTCATAGCGAGATTATCAAAATT
48701 TTAAAGTGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (26 bp):
AATTTCATAGCGAGATTATCAAAATT
Found at i:48925 original size:22 final size:22
Alignment explanation
Indices: 48894--48945 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
48884 AAGATTCTTG
* * * *
48894 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
48916 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
48938 AAATTTCA
1 AAATTTCA
48946 AAATTTCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:50680 original size:16 final size:16
Alignment explanation
Indices: 50659--50693 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
50649 TGGGTCCGTC
50659 CCACCTAATAATTTCT
1 CCACCTAATAATTTCT
50675 CCACCTAATAATTTCT
1 CCACCTAATAATTTCT
50691 CCA
1 CCA
50694 GTTGCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (16 bp):
CCACCTAATAATTTCT
Found at i:58866 original size:19 final size:20
Alignment explanation
Indices: 58820--58867 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
58810 TGCGGCACGC
*
58820 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
58842 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
58861 CACATGT
1 CACATGT
58868 CACGCCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:58872 original size:53 final size:53
Alignment explanation
Indices: 58787--58889 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
58777 GACGTGGCAC
* **
58787 GCCACGTGTACCAAAAAGTGACATGCGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACACGGCACGCCACATGTACCAAAAAGTCGT
* * **
58840 GCCACATGTACCAAAAAGTGACACATGTCACGCCATGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACACGGCACGCCACATGTACCAAAAAGT
58890 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACACGGCACGCCACATGTACCAAAAAGTCGT
Found at i:58917 original size:31 final size:31
Alignment explanation
Indices: 58839--58937 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
58829 CAAAAAGTCG
* *
58839 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* **
58870 CGCCATGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * *
58901 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
58932 TGCCAC
1 TGCCAC
58938 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Done.