Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014775.1 Corchorus olitorius cultivar O-4 contig14808, 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: 59054
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--36 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 TAG
4 TA TA 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 TA TA T
37 GCAGAGTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:395 original size:103 final size:106
Alignment explanation
Indices: 264--530 Score: 368
Period size: 107 Copynumber: 2.6 Consensus size: 106
254 AATTTTAATT
* *
264 TTAATTT-GGGCTAAACTTGGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAACAAT-A
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAA
*
326 TTATTAATTATAG-AATTTATCCT-TAAAATAAAAA-AAAA-A
66 TTATTAATT-TAGAAATTTACCCTAT-AAATAAAAATAAAATA
* *
365 TTAATTTGGGGCTAAACATAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATGA
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAAT-A
* *
430 ATTATTAATTTTGAAATTTACCCTATAAATAAAAATAAAATT
65 ATTATTAATTTAGAAATTTACCCTATAAATAAAAATAAAATA
* * *
472 TTAATTTGGGACTAAACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
531 TAAAAAAAAA
Statistics
Matches: 146, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
101 7 0.05
102 13 0.09
103 37 0.25
104 2 0.01
105 28 0.19
106 5 0.03
107 54 0.37
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAA
TTATTAATTTAGAAATTTACCCTATAAATAAAAATAAAATA
Found at i:511 original size:107 final size:103
Alignment explanation
Indices: 241--530 Score: 372
Period size: 103 Copynumber: 2.8 Consensus size: 103
231 AATTTTTCTA
*** * *
241 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTGGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAA-AAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTAT
305 TTCTAAAACCCTATAACAATATTATTAATTATAGAATTT
65 TTCTAAAACCCTATAACAATATTATTAATTATAGAATTT
* * * *
344 ATCCTTAAAATAAAAAAAAA-ATTAATTTGGGGCTAAACATAGTGAAATTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAAAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTAT
*
408 TTCTAAAACCCTATAACAATGAATTATTAATT-TTGAAATTT
65 TTCTAAAACCCTATAACAAT--ATTATTAATTATAG-AATTT
*
449 ACCC-TATAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAATGAAATTAGTTTTATATTTT
1 ACCCTTA-AAATAAAAA-AAAATTTTAATTTGGG-CTAAACTTAGTGAAATTAGTTTTATATTTT
*
513 ATTTCTAAAACTCTATAA
63 ATTTCTAAAACCCTATAA
531 TAAAAAAAAA
Statistics
Matches: 162, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
101 7 0.04
102 15 0.09
103 51 0.31
104 4 0.02
105 27 0.17
106 7 0.04
107 51 0.31
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (103 bp):
ACCCTTAAAATAAAAAAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
TCTAAAACCCTATAACAATATTATTAATTATAGAATTT
Found at i:1035 original size:20 final size:20
Alignment explanation
Indices: 1010--1049 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1000 AATTACAAAC
1010 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
1030 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
1050 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:3673 original size:22 final size:22
Alignment explanation
Indices: 3648--3735 Score: 167
Period size: 22 Copynumber: 4.0 Consensus size: 22
3638 GAAACAACGG
*
3648 TAAACATAGTAATGACATGAAT
1 TAAACATAGTAATAACATGAAT
3670 TAAACATAGTAATAACATGAAT
1 TAAACATAGTAATAACATGAAT
3692 TAAACATAGTAATAACATGAAT
1 TAAACATAGTAATAACATGAAT
3714 TAAACATAGTAATAACATGAAT
1 TAAACATAGTAATAACATGAAT
3736 CAATAAAATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.27
Consensus pattern (22 bp):
TAAACATAGTAATAACATGAAT
Found at i:3730 original size:11 final size:11
Alignment explanation
Indices: 3650--3731 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
3640 AACAACGGTA
3650 AACATAGTAAT
1 AACATAGTAAT
*
3661 GACAT-G-AATT
1 AACATAGTAA-T
3671 AAACATAGTAAT
1 -AACATAGTAAT
3683 AACAT-G-AATT
1 AACATAGTAA-T
3693 AAACATAGTAAT
1 -AACATAGTAAT
3705 AACAT-G-AATT
1 AACATAGTAA-T
3715 AAACATAGTAAT
1 -AACATAGTAAT
3727 AACAT
1 AACAT
3732 GAATCAATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
9 6 0.11
10 6 0.11
11 33 0.58
12 6 0.11
13 6 0.11
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (11 bp):
AACATAGTAAT
Found at i:9078 original size:20 final size:20
Alignment explanation
Indices: 9043--9080 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9033 ATTACTCATT
*
9043 AAGTTGGTGACGATTCAAAA
1 AAGTTGGTGACAATTCAAAA
*
9063 AAGTTGGTGATAATTCAA
1 AAGTTGGTGACAATTCAA
9081 CTCATGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (20 bp):
AAGTTGGTGACAATTCAAAA
Found at i:11865 original size:16 final size:16
Alignment explanation
Indices: 11847--11939 Score: 91
Period size: 16 Copynumber: 5.8 Consensus size: 16
11837 AATTTTGGGT
*
11847 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
11863 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
11878 ACCCGAACCCCGAAAATG
1 ACCCGAA-CCCG-AAATG
*
11896 ACCC-AAACCGAAAATG
1 ACCCGAACCCG-AAATG
* *
11912 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
11928 ACCCGAACCCGA
1 ACCCGAACCCGA
11940 TCAACCCGAC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
15 10 0.16
16 39 0.62
17 6 0.10
18 8 0.13
ACGTcount: A:0.42, C:0.39, G:0.13, T:0.06
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Found at i:13622 original size:15 final size:17
Alignment explanation
Indices: 13589--13624 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
13579 CCGAAAACGA
13589 CCGAACCCAGAATTGAC
1 CCGAACCCAGAATTGAC
13606 CCGAACCCA-AA-TGAC
1 CCGAACCCAGAATTGAC
13621 CCGA
1 CCGA
13625 CATTTAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.36, C:0.39, G:0.17, T:0.08
Consensus pattern (17 bp):
CCGAACCCAGAATTGAC
Found at i:16225 original size:141 final size:141
Alignment explanation
Indices: 15840--16226 Score: 460
Period size: 141 Copynumber: 2.7 Consensus size: 141
15830 AGAGATGTCA
* * * * * * **
15840 AGCTTGACAATAAATTGGAGGAAATGTTCCCACTGAATTGGTTC-CAAGAGAGGTCTAGAAGGTT
1 AGCTTGACAATAAATCGCAAGAGATGGTCCCACTGAATTGATTCAC-AGAGAGGTCTAGAACTTT
* * * *
15904 GAGAGAAGTCCAATTGTTCAAGCATTGAGGAAGGTTTCCTTCAAGACTATTACCCTGAAGAACCA
65 AAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCAAGACTATTACCCTGAAGAACCA
15969 ACCATTGAAGAG
130 ACCATTGAAGAG
* * * * * *
15981 AGCTAGACAACAAATCGCAAGGGATGGTCCCACCGAATAGATTCAAAGAGAGGTCTAGAACTTTA
1 AGCTTGACAATAAATCGCAAGAGATGGTCCCACTGAATTGATTCACAGAGAGGTCTAGAACTTTA
* * * ** *
16046 AGAGAAATCGAATTGTTTAAGCATGGAGGAAGATTTCCTTCGAAG-CTATTAGTGCT-AAGAATC
66 AGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTC-AAGACTATTA-CCCTGAAGAACC
16109 AACTC-TTGAAGAG
129 AAC-CATTGAAGAG
*
16122 AAG-TTGACAATAAATCGCAAGAGATGGTCCCATTGAATTGATTCACAGAGAGGTCTAGAACTTT
1 -AGCTTGACAATAAATCGCAAGAGATGGTCCCACTGAATTGATTCACAGAGAGGTCTAGAACTTT
*
16186 AAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGGTTCCTT
65 AAGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTT
16227 GGAGATCATA
Statistics
Matches: 207, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
141 199 0.96
142 8 0.04
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (141 bp):
AGCTTGACAATAAATCGCAAGAGATGGTCCCACTGAATTGATTCACAGAGAGGTCTAGAACTTTA
AGAGAAGTCAAATTGTTTAAGCATGGAGGAAGGTTTCCTTCAAGACTATTACCCTGAAGAACCAA
CCATTGAAGAG
Found at i:18548 original size:5 final size:5
Alignment explanation
Indices: 18538--18581 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
18528 ATAATAAGTA
*
18538 TATCT TATCT TATCT TATCT TATTT TA-C- TATCT TATCT TATCT T
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT T
18582 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 32 0.91
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TATCT
Found at i:18573 original size:23 final size:23
Alignment explanation
Indices: 18543--18586 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
18533 AAGTATATCT
18543 TATCTTATCTTATCTTATTTTAC
1 TATCTTATCTTATCTTATTTTAC
*
18566 TATCTTATCTTATCTTTTTTT
1 TATCTTATCTTATCTTATTTT
18587 TTTTTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (23 bp):
TATCTTATCTTATCTTATTTTAC
Found at i:24908 original size:5 final size:5
Alignment explanation
Indices: 24898--24971 Score: 97
Period size: 5 Copynumber: 16.0 Consensus size: 5
24888 CGTATACCCC
*
24898 TCTTA TCTTA TCTTA TATTA TCTTA -C-TA TCTTA TCTTA TCTTA -C-TA
1 TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA
24944 TCTTA -C-TA TCTTA TCTTA TCTTA TCTTA
1 TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA
24972 CTACTATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
3 6 0.10
4 6 0.10
5 49 0.80
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (5 bp):
TCTTA
Found at i:24929 original size:18 final size:18
Alignment explanation
Indices: 24906--24971 Score: 78
Period size: 18 Copynumber: 3.4 Consensus size: 18
24896 CCTCTTATCT
24906 TATCTTATATTATCTTAC
1 TATCTTATATTATCTTAC
*
24924 TATCTTATCTTATCTTAC
1 TATCTTATATTATCTTAC
24942 TATCTTACTATCTTATCTTATC
1 TATCTTA-TA--TTATCTTA-C
24964 TTATCTTA
1 -TATCTTA
24972 CTACTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
18 24 0.59
19 1 0.02
21 8 0.20
22 1 0.02
23 7 0.17
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (18 bp):
TATCTTATATTATCTTAC
Found at i:24976 original size:26 final size:28
Alignment explanation
Indices: 24898--24978 Score: 125
Period size: 26 Copynumber: 3.0 Consensus size: 28
24888 CGTATACCCC
*
24898 TCTTATCTTATCTTATATTATCTTACTA
1 TCTTATCTTATCTTATCTTATCTTACTA
24926 TCTTATCTTATCTTA-C-TATCTTACTA
1 TCTTATCTTATCTTATCTTATCTTACTA
24952 TCTTATCTTATCTTATCTTA-C-TACTA
1 TCTTATCTTATCTTATCTTATCTTACTA
24978 T
1 T
24979 ATAAAAGCAC
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
26 31 0.62
27 2 0.04
28 17 0.34
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (28 bp):
TCTTATCTTATCTTATCTTATCTTACTA
Found at i:31747 original size:2 final size:2
Alignment explanation
Indices: 31740--31773 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31730 TCTCTTATTC
31740 AT 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
31774 GAATTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33352 original size:2 final size:2
Alignment explanation
Indices: 33345--33373 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33335 TTATTAGAAC
33345 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
33374 TATTGGTTTT
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:34423 original size:15 final size:15
Alignment explanation
Indices: 34403--34432 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34393 TAAGTTGATG
*
34403 GTCAAACATTTACGA
1 GTCAAAAATTTACGA
34418 GTCAAAAATTTACGA
1 GTCAAAAATTTACGA
34433 ATACAAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (15 bp):
GTCAAAAATTTACGA
Found at i:34832 original size:93 final size:93
Alignment explanation
Indices: 34729--34913 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
34719 TTGTTTAAAT
* *
34729 TTTTATAGTTTTAGTCAACTAAA-AACTCTATTTTTATTTACTTAAATCTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAACAA-TCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
* *
34793 ATTTTATTTTTACCATTTTACTATTTTAC
65 ATTTTATTTTTACCATATTACTAATTTAC
* *
34822 TTTTATAGTTTTACTCAACTAAACAATCTATTTTTATTTAATTAAATTTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAACAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
34887 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
34914 ATTAAAAAAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 82 0.98
94 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAACAATCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:39338 original size:43 final size:40
Alignment explanation
Indices: 39291--39379 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 40
39281 AAAAAAATTG
39291 TAGGAAGATTAACAAAATCTCACA-GAGAGATTATCAAAAATCA
1 TAGGAAGATT-ACAAAAT-TCACAGGA-AGATTA-CAAAAATCA
* * * *
39334 TAGGAAGGTTACAAAATTCATAGGAAGGTTACAAAATTCA
1 TAGGAAGATTACAAAATTCACAGGAAGATTACAAAAATCA
39374 TAGGAA
1 TAGGAA
39380 AGTTTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 14 0.34
41 9 0.22
42 9 0.22
43 9 0.22
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.22
Consensus pattern (40 bp):
TAGGAAGATTACAAAATTCACAGGAAGATTACAAAAATCA
Found at i:39354 original size:20 final size:20
Alignment explanation
Indices: 39325--39379 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
39315 GAGAGATTAT
*
39325 CAAAAATCATAGGAAGGTTA
1 CAAAATTCATAGGAAGGTTA
39345 CAAAATTCATAGGAAGGTTA
1 CAAAATTCATAGGAAGGTTA
39365 CAAAATTCATAGGAA
1 CAAAATTCATAGGAA
39380 AGTTTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAAATTCATAGGAAGGTTA
Found at i:39453 original size:21 final size:22
Alignment explanation
Indices: 39427--39481 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
39417 CTTATGGATC
* *
39427 TTATCACAATTTTATA-GGTGA
1 TTATCAAAATTTAATAGGGTGA
39448 TTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTAATAGGGTGA
39470 TTATCAAAATTT
1 TTATCAAAATTT
39482 CATAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGTGA
Found at i:43223 original size:11 final size:11
Alignment explanation
Indices: 43209--43233 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43199 CAAATAACTT
43209 TAAAATATAGG
1 TAAAATATAGG
43220 TAAAATATAGG
1 TAAAATATAGG
43231 TAA
1 TAA
43234 GATAATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (11 bp):
TAAAATATAGG
Found at i:50729 original size:79 final size:79
Alignment explanation
Indices: 50641--50799 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
50631 GCCTCAGAGT
* *
50641 AAACACTTGCGTAATTTATATTTAGTAAATTAAAGTGCCTGATTAATTCTAATTATATATATTCA
1 AAACACTTGCGTAACTTATATTTAGTAAATTAAAGTGCCTGATTAATTCTAATAATATATATTCA
*
50706 TTCAGATCTTGACA
66 ATCAGATCTTGACA
50720 AAACACTTGCGTAACTTATATTTAGTAAATTAAAGTGCCTGATTAATTCTAATAATATATATTCA
1 AAACACTTGCGTAACTTATATTTAGTAAATTAAAGTGCCTGATTAATTCTAATAATATATATTCA
50785 ATCAGATCTTGACA
66 ATCAGATCTTGACA
50799 A
1 A
50800 TTTCGAATAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (79 bp):
AAACACTTGCGTAACTTATATTTAGTAAATTAAAGTGCCTGATTAATTCTAATAATATATATTCA
ATCAGATCTTGACA
Found at i:50835 original size:68 final size:68
Alignment explanation
Indices: 50755--50891 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
50745 TAAATTAAAG
50755 TGCCTGATTAATTCTAATAATATATATTCAATCAGATCTTGACAATTTCGAATATTAACGAAGAA
1 TGCCTGATTAATTCTAATAATATATATTCAATCAGATCTTGACAATTTCGAATATTAACGAAGAA
50820 ATA
66 ATA
50823 TGCCTGATTAATTCTAATAATATATATTCAATCAGATCTTGACAATTTCGAATATTAACGAAGAA
1 TGCCTGATTAATTCTAATAATATATATTCAATCAGATCTTGACAATTTCGAATATTAACGAAGAA
50888 ATA
66 ATA
50891 T
1 T
50892 AATGGCCATC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (68 bp):
TGCCTGATTAATTCTAATAATATATATTCAATCAGATCTTGACAATTTCGAATATTAACGAAGAA
ATA
Found at i:52366 original size:21 final size:21
Alignment explanation
Indices: 52342--52408 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
52332 AATTCTCTGT
52342 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
52363 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
52384 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
52405 AAAT
1 AAAT
52409 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:52389 original size:42 final size:42
Alignment explanation
Indices: 52330--52409 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
52320 CCAAGTCTTC
52330 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
*
52372 AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
52410 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
Found at i:52549 original size:57 final size:58
Alignment explanation
Indices: 52475--52592 Score: 177
Period size: 57 Copynumber: 2.0 Consensus size: 58
52465 TTTATTTTGT
* *
52475 AGAATAATTAAGTAGAGATATGGGGGATAGGAATTATT-T-TGACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATA-GGGGGATAGGAATTATTATATAACATTTATTATGTGAA
*
52532 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATCATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATAGGAATTATTAT-ATAACATTTATTATGTGAA
52591 AG
1 AG
52593 GAAATGCATA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
56 16 0.29
57 21 0.38
59 18 0.33
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (58 bp):
AGAATAATTAAGTAGAGATAGGGGGATAGGAATTATTATATAACATTTATTATGTGAA
Done.