Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018437.1 Corchorus olitorius cultivar O-4 contig18470, 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: 35209
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:4634 original size:6 final size:6
Alignment explanation
Indices: 4625--4651 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4615 GATGATGATG
4625 ATGCCC ATGCCC ATGCCC ATGCCC ATG
1 ATGCCC ATGCCC ATGCCC ATGCCC ATG
4652 ATGACTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGCCC
Found at i:10661 original size:85 final size:86
Alignment explanation
Indices: 10565--10735 Score: 308
Period size: 86 Copynumber: 2.0 Consensus size: 86
10555 AAATTAAAAT
*
10565 GGTAAAAATAAAATAGTT-ATAATAATATTGAATTTAATTAAATAAAAATATATTTTTTAGTAGA
1 GGTAAAAATAAAATAGTTAATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGA
*
10629 ATAATTGTAAAAGTTTATTTC
66 ATAACTGTAAAAGTTTATTTC
*
10650 GGTAAAAATAAAATATTTAATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGA
1 GGTAAAAATAAAATAGTTAATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGA
10715 ATAACTGTAAAAGTTTATTTC
66 ATAACTGTAAAAGTTTATTTC
10736 TAAAAAAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
85 17 0.21
86 65 0.79
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (86 bp):
GGTAAAAATAAAATAGTTAATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGA
ATAACTGTAAAAGTTTATTTC
Found at i:10771 original size:14 final size:13
Alignment explanation
Indices: 10752--10790 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
10742 AAATTGTAAA
10752 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
10765 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
10779 ATTTAAAAAATT
1 ATTTAAAAAATT
10791 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:11057 original size:123 final size:125
Alignment explanation
Indices: 10779--11036 Score: 321
Period size: 132 Copynumber: 2.1 Consensus size: 125
10769 TAAGAAATAT
* *
10779 ATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAAGAAATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT---ATA-
* * * *
10844 GTATAAGGTTATTAGATTTAGTTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
62 GTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
* * *
10908 CATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 ---ATTTAAAAAATTCTAAGAAATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATATAG
*
10971 TA-AA-GATATTAGATTTAATTAAAT-AAAATTAGAGTTTTTAGTTGAATAAAACTATAAAAG
63 TATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
11031 -TTTAAA
1 ATTTAAA
11037 CAATGGCATT
Statistics
Matches: 120, Mismatches: 6, Indels: 13
0.86 0.04 0.09
Matches are distributed among these distances:
119 6 0.05
123 33 0.28
124 18 0.15
125 2 0.02
126 2 0.02
128 2 0.02
132 57 0.47
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (125 bp):
ATTTAAAAAATTCTAAGAAATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAG
Found at i:11746 original size:19 final size:20
Alignment explanation
Indices: 11724--11767 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
11714 TATTAATTAA
11724 TTATTTTA-ATATTAAATTT
1 TTATTTTATATATTAAATTT
* *
11743 TTA-TCTATATATTATATTT
1 TTATTTTATATATTAAATTT
11762 TTATTT
1 TTATTT
11768 AAAAACTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 3 0.15
19 16 0.80
20 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTATATATTAAATTT
Found at i:22758 original size:123 final size:129
Alignment explanation
Indices: 22620--22876 Score: 427
Period size: 123 Copynumber: 2.0 Consensus size: 129
22610 CATTGTTTAA
*
22620 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
22682 A-ATTTTTACCATTTTACTATTTT-AATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTACTATTTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
22743 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-C
22808 TATTTTATTTTTACCATTTTACTATTTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAA
65 TA---TATTTTTACCATTTTACTATTTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAA
22873 TAT
127 TAT
22876 A
1 A
22877 TTTCTTAAAT
Statistics
Matches: 123, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
123 55 0.45
124 3 0.02
125 2 0.02
127 2 0.02
131 22 0.18
132 4 0.03
133 35 0.28
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (129 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:23157 original size:15 final size:15
Alignment explanation
Indices: 23120--23167 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
23110 ATTCATCATT
* *
23120 TTTAAAACTTATTAA
1 TTTAAAATTTATTTA
*
23135 GTTAAAAATTTATTTA
1 -TTTAAAATTTATTTA
*
23151 TTTAAAATTTAATTA
1 TTTAAAATTTATTTA
23166 TT
1 TT
23168 GTGATTAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTAAAATTTATTTA
Found at i:25632 original size:4 final size:4
Alignment explanation
Indices: 25625--25667 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
25615 TTTTTACCGT
* *
25625 TATC TATC TATC TATC TATC TATC TATC TATC TCTC TCTC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
25668 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:25670 original size:2 final size:2
Alignment explanation
Indices: 25665--25701 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
25655 TCTCTCTCTC
25665 TA TA TA TA TA TA TA TA TA T- TA TA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25702 AAAGTACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:26934 original size:22 final size:22
Alignment explanation
Indices: 26855--27066 Score: 125
Period size: 22 Copynumber: 9.6 Consensus size: 22
26845 TAATTTTGGA
* *
26855 GGTTATCAAAA-TTCATTGTGT
1 GGTTATCAAAATTTTATAGTGT
26876 GGTTA-CTAAAATTTTATAGTGT
1 GGTTATC-AAAATTTTATAGTGT
* *
26898 AGTTGATCTCAAAATTTTATTGTGT
1 GGTT-A--TCAAAATTTTATAGTGT
*
26923 GGTTATCAAAATTTTATAGTGA
1 GGTTATCAAAATTTTATAGTGT
* * *
26945 GGTTACCAAACTTTAATAG-GT
1 GGTTATCAAAATTTTATAGTGT
* *
26966 AGGATATTAAAATTTTATAGTGT
1 -GGTTATCAAAATTTTATAGTGT
* * * * *
26989 AGTTATCACAAGTTCAT-GGGAT
1 GGTTATCAAAATTTTATAGTG-T
*
27011 -GTTATCAAAATTTCATAG-GAT
1 GGTTATCAAAATTTTATAGTG-T
* *
27032 -GTTATCAAAATTTCATA-TGGA
1 GGTTATCAAAATTTTATAGT-GT
*
27053 GGTTATTAAAATTT
1 GGTTATCAAAATTT
27067 CATAAGGAGG
Statistics
Matches: 151, Mismatches: 27, Indels: 25
0.74 0.13 0.12
Matches are distributed among these distances:
20 1 0.01
21 46 0.30
22 82 0.54
23 3 0.02
24 1 0.01
25 17 0.11
26 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGT
Found at i:27067 original size:22 final size:22
Alignment explanation
Indices: 26923--27244 Score: 242
Period size: 22 Copynumber: 14.8 Consensus size: 22
26913 TTTATTGTGT
* *
26923 GGTTATCAAAATTTTATAGTGA
1 GGTTATCAAAATTTCATAGGGA
* * * *
26945 GGTTACCAAACTTTAATAGGTA
1 GGTTATCAAAATTTCATAGGGA
* * * *
26967 GGATATTAAAATTTTATAGTGTA
1 GGTTATCAAAATTTCATAG-GGA
* *
26990 -GTTATCACAAGTTCAT-GGGA
1 GGTTATCAAAATTTCATAGGGA
*
27010 TGTTATCAAAATTTCATA-GGA
1 GGTTATCAAAATTTCATAGGGA
* *
27031 TGTTATCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGGGA
* *
27053 GGTTATTAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAGGGA
**
27075 GGTTATTGAAA-TTCAT-GGGAA
1 GGTTATCAAAATTTCATAGGG-A
* ** *
27096 GCTTATCGGAATTTCACAGGGA
1 GGTTATCAAAATTTCATAGGGA
* ****
27118 GATTA-CTAAAATTTCATACTCT
1 GGTTATC-AAAATTTCATAGGGA
*
27140 GGTTTTCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGGGA
* *
27162 GGTTAACAAAATTTCATAGGGC
1 GGTTATCAAAATTTCATAGGGA
* * * *
27184 GATTATCGAAATTTTATATGGA
1 GGTTATCAAAATTTCATAGGGA
*
27206 GGTTATCAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGGGA
*
27228 GATTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
27245 GGTGTTCTTA
Statistics
Matches: 235, Mismatches: 56, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.02
21 51 0.22
22 173 0.74
23 7 0.03
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGGA
Found at i:27196 original size:44 final size:44
Alignment explanation
Indices: 26925--28056 Score: 281
Period size: 44 Copynumber: 25.8 Consensus size: 44
26915 TATTGTGTGG
* * * * * *
26925 TTATCAAAATTTTATAGTGAGGTTACCAAACTTTAATAGGTAGGA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGA-GA
* * * * *
26970 -TATTAAAATTTTATAGTGTA-GTTATCACAAGTTCAT-GGGATG-
1 TTATCAAAATTTCATAG-GGAGGTTATCAAAATTTCATAGGGA-GA
* * *
27012 TTATCAAAATTTCATA-GGATGTTATCAAAATTTCATATGGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * ** *
27055 TTATTAAAATTTCATAAGGAGGTTATTGAAA-TTCAT-GGGAAGC
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGG-AGA
** * * **** *
27098 TTATCGGAATTTCACAGGGAGATTA-CTAAAATTTCATACTCTGG
1 TTATCAAAATTTCATAGGGAGGTTATC-AAAATTTCATAGGGAGA
* * *
27142 TTTTCAAAATTTCATAGGGAGGTTAACAAAATTTCATAGGGCGA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * *
27186 TTATCGAAATTTTATATGGAGGTTATCAAAATTTCATAGGAAGA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
*** * *
27230 TTATCAAAATTTCAT-GGTGTTCTTATAAAAATTGCATAGTGAGATAGAGTGA
1 TTATCAAAATTTCATAGG-GAGGTTATCAAAATTTCATA--G-G---GA--GA
* * ** * *
27282 GCTTATCAAAATTTCA-CGTGTCGTTACCAAAATTTCATAGTGTA-A
1 --TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GGAGA
* * ** * * *
27327 TAATCACAATTTCATA--GAGGTTAAGAAAATTTCGTGGGGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * * * *
27369 TTATCAAAATTTCACAGTGTGGTTGTC-AAATTT-TTA--TA-A
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
*** * * * * *** *
27408 -TAT-GGCATTTTAGAGGGAGAGGTTATCAAATTTTAATTTTGTG-
1 TTATCAAAATTTCATA-GG-GAGGTTATCAAAATTTCATAGGGAGA
* * ** ** * *
27451 GTAACTAAAATTTCATAATGATTTTACCAAAATTT-ATAGTGAGA
1 TTATC-AAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * * * *
27495 TTAACAAAATTTGATAGAGTGGTTCTCAAAATTTTATAGGGAGA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * *** *
27539 TTAACAAAATTTCATAGGCAAGTTATTGTAATTTTAT-GGTGTAGTTAA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGG-G-AG---A
* * * * ***
27587 TTATCAAAATTTCATTGGG-GGTTATCAAACTTTAATAGCGTTC
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * * * *
27630 TTATCAAAAATCCGTA-GGAGGTTAACAAAATTTTAT-GAGGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GGAGA
* * * * * *
27673 TAAT-AAAATGTTTATAGGGATGTTATGAAAATTTCATA-AGATGG
1 TTATCAAAAT-TTCATAGGGAGGTTATCAAAATTTCATAGGGA-GA
* * *
27717 TTATCAAAATTTCAT-GAGGTGGTTTTCAAAATTTCAT---GAGG
1 TTATCAAAATTTCATAG-GGAGGTTATCAAAATTTCATAGGGAGA
* * * *
27758 TTATCAAAATTTCAAATGGAGGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGA-GA
* * * * *
27803 TTAT-ACAATTTTCATAGTGAGG-TATCACAATTTCAT-GGTATGT
1 TTATCA-AAATTTCATAGGGAGGTTATCAAAATTTCATAGGGA-GA
* ** * * * * * * * * *
27846 TTATCAAAATTTCGTAATGTGATTACCGATATTTTATCGGAAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
* * * * * * * * *
27890 TAATCAAAATTTCGTAATGTGCGCTTACCAACATTTCATTGGGAGG
1 TTATCAAAATTTCAT-A-GGGAGGTTATCAAAATTTCATAGGGAGA
*
27936 TTATCAAAATTTCATA-GGATGGTTATCAAAATTTCATTAGGTA-A
1 TTATCAAAATTTCATAGGGA-GGTTATCAAAATTTCA-TAGGGAGA
* * * *
27980 TTATTAAAATTTTATAGGGAGTGTGA-CAAAATTTTATAGGGA-A
1 TTATCAAAATTTCATAGGGAG-GTTATCAAAATTTCATAGGGAGA
* * * *
28023 GTTAACAAAATTTCATATGGAGGTTCTCGAAATT
1 -TTATCAAAATTTCATAGGGAGGTTATCAAAATT
28057 CTATGGCATC
Statistics
Matches: 782, Mismatches: 235, Indels: 141
0.68 0.20 0.12
Matches are distributed among these distances:
37 6 0.01
38 4 0.01
39 7 0.01
40 6 0.01
41 38 0.05
42 55 0.07
43 176 0.23
44 341 0.44
45 42 0.05
46 40 0.05
47 13 0.02
48 19 0.02
50 1 0.00
51 2 0.00
52 2 0.00
53 15 0.02
54 15 0.02
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGA
Found at i:27392 original size:22 final size:22
Alignment explanation
Indices: 27284--27398 Score: 65
Period size: 22 Copynumber: 5.4 Consensus size: 22
27274 TAGAGTGAGC
* *
27284 TTATCAAAATTTCA-CGTGTCG
1 TTATCAAAATTTCATAGTGTGG
* **
27305 TTACCAAAATTTCATAGTGTAA
1 TTATCAAAATTTCATAGTGTGG
* * *
27327 TAATCACAATTTCATA--GAGG
1 TTATCAAAATTTCATAGTGTGG
** * * * *
27347 TTAAGAAAATTTCGTGGGGAGG
1 TTATCAAAATTTCATAGTGTGG
*
27369 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
27391 TTGTCAAA
1 TTATCAAA
27399 TTTTTATAAT
Statistics
Matches: 67, Mismatches: 24, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
20 11 0.16
21 13 0.19
22 43 0.64
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:27504 original size:21 final size:22
Alignment explanation
Indices: 27452--27555 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
27442 AATTTTGTGG
**
27452 TAACTAAAATTTCATA-ATGATTT
1 TAAC-AAAATTTCATAGA-GAGAT
* *
27475 TACCAAAATTT-ATAGTGAGAT
1 TAACAAAATTTCATAGAGAGAT
* * *
27496 TAACAAAATTTGATAGAGTGGT
1 TAACAAAATTTCATAGAGAGAT
** * *
27518 TCTCAAAATTTTATAGGGAGAT
1 TAACAAAATTTCATAGAGAGAT
27540 TAACAAAATTTCATAG
1 TAACAAAATTTCATAG
27556 GCAAGTTATT
Statistics
Matches: 62, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
21 16 0.26
22 43 0.69
23 3 0.05
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TAACAAAATTTCATAGAGAGAT
Found at i:27546 original size:22 final size:22
Alignment explanation
Indices: 27478--27556 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
27468 ATGATTTTAC
*
27478 CAAAA-TTTATAGTGAGATTAA
1 CAAAATTTTATAGGGAGATTAA
* * * * **
27499 CAAAATTTGATAGAGTGGTTCT
1 CAAAATTTTATAGGGAGATTAA
27521 CAAAATTTTATAGGGAGATTAA
1 CAAAATTTTATAGGGAGATTAA
*
27543 CAAAATTTCATAGG
1 CAAAATTTTATAGG
27557 CAAGTTATTG
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 5 0.11
22 39 0.89
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.33
Consensus pattern (22 bp):
CAAAATTTTATAGGGAGATTAA
Found at i:27671 original size:22 final size:21
Alignment explanation
Indices: 27587--28056 Score: 209
Period size: 22 Copynumber: 21.5 Consensus size: 21
27577 GTGTAGTTAA
* *
27587 TTATCAAAATTTCATTGGGGG
1 TTATCAAAATTTCATAGGAGG
* * ***
27608 TTATCAAACTTTAATAGCGTTC
1 TTATCAAAATTTCATAG-GAGG
* * *
27630 TTATCAAAAATCCGTAGGAGG
1 TTATCAAAATTTCATAGGAGG
* *
27651 TTAACAAAATTTTATGAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
27673 TAAT-AAAATGTTTATAGGGATG
1 TTATCAAAAT-TTCATA-GGAGG
* *
27695 TTATGAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAGGA-GG
*
27717 TTATCAAAATTTCATGAGGTGG
1 TTATCAAAATTTCAT-AGGAGG
*
27739 TTTTCAAAATTTCAT--GAGG
1 TTATCAAAATTTCATAGGAGG
*
27758 TTATCAAAATTTCAAATGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
27780 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
27802 TTTAT-ACAATTTTCATAGTGAGG
1 -TTATCA-AAATTTCATAG-GAGG
* *
27825 -TATCACAATTTCAT-GGTATGT
1 TTATCAAAATTTCATAGG-A-GG
* * * *
27846 TTATCAAAATTTCGTAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* * * * *
27868 TTACCGATATTTTATCGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* * * *
27890 TAATCAAAATTTCGTAATGTGCGC
1 TTATCAAAATTTCAT-A-G-GAGG
* * *
27914 TTACCAACATTTCATTGGGAGG
1 TTATCAAAATTTCA-TAGGAGG
27936 TTATCAAAATTTCATAGGATGG
1 TTATCAAAATTTCATAGGA-GG
*
27958 TTATCAAAATTTCATTAGGTA-A
1 TTATCAAAATTTCA-TAGG-AGG
* *
27980 TTATTAAAATTTTATAGGGAGTG
1 TTATCAAAATTTCATA-GGAG-G
* * *
28003 TGA-CAAAATTTTATAGGGAAG
1 TTATCAAAATTTCATA-GGAGG
*
28024 TTAACAAAATTTCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
28046 TTCTCGAAATT
1 TTATCAAAATT
28057 CTATGGCATC
Statistics
Matches: 330, Mismatches: 88, Indels: 61
0.69 0.18 0.13
Matches are distributed among these distances:
19 17 0.05
20 2 0.01
21 55 0.17
22 210 0.64
23 30 0.09
24 14 0.04
25 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:27945 original size:46 final size:44
Alignment explanation
Indices: 27846--27948 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 44
27836 CATGGTATGT
* * *
27846 TTATCAAAATTTCGTAATGTGATTACCGATATTTTATCGGAAGG
1 TTATCAAAATTTCGTAATGTGATTACCAACATTTCATCGGAAGG
* * * *
27890 TAATCAAAATTTCGTAATGTGCGCTTACCAACATTTCATTGGGAGG
1 TTATCAAAATTTCGTAATGT--GATTACCAACATTTCATCGGAAGG
27936 TTATCAAAATTTC
1 TTATCAAAATTTC
27949 ATAGGATGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 19 0.39
46 30 0.61
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCGTAATGTGATTACCAACATTTCATCGGAAGG
Found at i:28103 original size:22 final size:21
Alignment explanation
Indices: 28073--28139 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
28063 CATCGTCATA
*
28073 AAAACTTTATAGTGTAATTATC
1 AAAATTTTATAGTG-AATTATC
*
28095 AAAATTTTATA-TGGAGGTTATC
1 AAAATTTTATAGT-GA-ATTATC
28117 AAAATTTTATAGTG-ATTATC
1 AAAATTTTATAGTGAATTATC
28137 AAA
1 AAA
28140 TTTAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.21
21 2 0.05
22 28 0.72
23 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAATTTTATAGTGAATTATC
Found at i:28781 original size:22 final size:22
Alignment explanation
Indices: 28753--28799 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
28743 TAATTGTTGA
28753 ATTTTTGCATGACACCTTTTGC
1 ATTTTTGCATGACACCTTTTGC
* *
28775 ATTTTTGCATGGCATCTTTTGC
1 ATTTTTGCATGACACCTTTTGC
28797 ATT
1 ATT
28800 CATCCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (22 bp):
ATTTTTGCATGACACCTTTTGC
Found at i:30860 original size:20 final size:21
Alignment explanation
Indices: 30819--30865 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
30809 GAAGTTTTTA
*
30819 GGTTTTAGAAACAGAGAGA-G
1 GGTTTTAGAAACAGAGAAAGG
*
30839 GGTTTTAGAGAA-AGGGAAAGG
1 GGTTTTAGA-AACAGAGAAAGG
30860 GGTTTT
1 GGTTTT
30866 CTAGGGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (21 bp):
GGTTTTAGAAACAGAGAAAGG
Found at i:32342 original size:15 final size:15
Alignment explanation
Indices: 32313--32355 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
32303 ATCATTAAAG
* *
32313 AATAAGAGAGCAATC
1 AATAAAAGAGTAATC
*
32328 AATAAAATAGTAATC
1 AATAAAAGAGTAATC
*
32343 AGTAAAAGAGTAA
1 AATAAAAGAGTAA
32356 AGACTAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (15 bp):
AATAAAAGAGTAATC
Found at i:32363 original size:22 final size:21
Alignment explanation
Indices: 32338--32459 Score: 125
Period size: 22 Copynumber: 6.0 Consensus size: 21
32328 AATAAAATAG
32338 TAATCAGTAAAAGAGTAAAGA
1 TAATCAGTAAAAGAGTAAAGA
* * *
32359 CTAATTAGGAAAAAAGTAATAG-
1 -TAATCAGTAAAAGAGTAA-AGA
32381 TAATCAGT-AAAGAGTAAAGA
1 TAATCAGTAAAAGAGTAAAGA
32401 GTAATCAGT-AAA-A-T--AG-
1 -TAATCAGTAAAAGAGTAAAGA
32417 TAATCAGTAAAAGAGTAAAGA
1 TAATCAGTAAAAGAGTAAAGA
32438 GTAATCAGTAAAAGAGTAAAGA
1 -TAATCAGTAAAAGAGTAAAGA
32460 GTAAAAGAGT
Statistics
Matches: 84, Mismatches: 6, Indels: 20
0.76 0.05 0.18
Matches are distributed among these distances:
15 8 0.10
16 3 0.04
17 3 0.04
18 1 0.01
19 3 0.04
20 11 0.13
21 17 0.20
22 36 0.43
23 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
TAATCAGTAAAAGAGTAAAGA
Found at i:32396 original size:7 final size:7
Alignment explanation
Indices: 32386--32498 Score: 77
Period size: 7 Copynumber: 15.7 Consensus size: 7
32376 AATAGTAATC
32386 AGTAAAG
1 AGTAAAG
32393 AGTAAAG
1 AGTAAAG
**
32400 AGTAATC
1 AGTAAAG
*
32407 AGTAAAAT
1 AGT-AAAG
**
32415 AGTAATC
1 AGTAAAG
32422 AGTAAAAG
1 AGT-AAAG
32430 AGTAAAG
1 AGTAAAG
**
32437 AGTAATC
1 AGTAAAG
32444 AGTAAAAG
1 AGT-AAAG
32452 AGTAAAG
1 AGTAAAG
32459 AGTAAAAG
1 AGT-AAAG
32467 AGTAATA-
1 AGTAA-AG
***
32474 A-TAGTC
1 AGTAAAG
32480 AGTAAAG
1 AGTAAAG
32487 AGTAAAG
1 AGTAAAG
32494 AGTAA
1 AGTAA
32499 TCAAGGAAGA
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
6 3 0.04
7 56 0.68
8 23 0.28
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:32420 original size:15 final size:15
Alignment explanation
Indices: 32396--32472 Score: 71
Period size: 15 Copynumber: 5.7 Consensus size: 15
32386 AGTAAAGAGT
32396 AAAGAGTAATCAGTA
1 AAAGAGTAATCAGTA
*
32411 AAATAGTAATCAGT-
1 AAAGAGTAATCAGTA
32425 AAA-AG-----AGT-
1 AAAGAGTAATCAGTA
32433 AAAGAGTAATCAGTA
1 AAAGAGTAATCAGTA
**
32448 AAAGAGTAAAGAGTA
1 AAAGAGTAATCAGTA
32463 AAAGAGTAAT
1 AAAGAGTAAT
32473 AATAGTCAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
8 6 0.12
9 2 0.04
13 2 0.04
14 6 0.12
15 35 0.69
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (15 bp):
AAAGAGTAATCAGTA
Found at i:32429 original size:79 final size:80
Alignment explanation
Indices: 32267--32456 Score: 247
Period size: 79 Copynumber: 2.4 Consensus size: 80
32257 ATTAAAATTC
* * * * ** *
32267 AAAGAGTGAAGAGTAATCAGCACAATGGTAATAGTAATCATTAAAGAATAAGAGAGCAATCAATA
1 AAAGAGTAAAGACTAATCAGGAAAAAAGTAATAGTAATCAGTAAAGAATAAGAGAGCAATCAATA
32332 AAATAGTAATCAGTA
66 AAATAGTAATCAGTA
* * * *
32347 AAAGAGTAAAGACTAATTAGGAAAAAAGTAATAGTAATCAGTAAAGAGTAA-AGAGTAATCAGTA
1 AAAGAGTAAAGACTAATCAGGAAAAAAGTAATAGTAATCAGTAAAGAATAAGAGAGCAATCAATA
32411 AAATAGTAATCAGTA
66 AAATAGTAATCAGTA
* * *
32426 AAAGAGTAAAGAGTAATCAGTAAAAGAGTAA
1 AAAGAGTAAAGACTAATCAGGAAAAAAGTAA
32457 AGAGTAAAAG
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
79 53 0.56
80 42 0.44
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (80 bp):
AAAGAGTAAAGACTAATCAGGAAAAAAGTAATAGTAATCAGTAAAGAATAAGAGAGCAATCAATA
AAATAGTAATCAGTA
Found at i:32441 original size:94 final size:99
Alignment explanation
Indices: 32324--32542 Score: 261
Period size: 94 Copynumber: 2.3 Consensus size: 99
32314 ATAAGAGAGC
* * * * ** *
32324 AATCAATAAAATAGTAATCAGTAAAAGAGT-AAAGACTAATTAGGAAAAAAGTAATAGTAATCAG
1 AATCAGTAAAAGAGTAAACAGTAAAACAGTAAAAGACTAAAGAGGAAAAAAGTAATAATAATCAG
*
32388 TAAAGAGTAAAGAGTAATC-A-GTA-A-AATAGT
66 TAAAGAGTAAAGAGTAATCAAGGAAGAGAATAGT
* * * * * *
32418 AATCAGTAAAAGAGTAAAGAGT-AATCAGTAAAAGAGTAAAGAGTAAAAGAGTAATAATAGTCAG
1 AATCAGTAAAAGAGTAAACAGTAAAACAGTAAAAGACTAAAGAGGAAAAAAGTAATAATAATCAG
32482 TAAAGAGTAAAGAGTAATCAAGGAAGAGTAATAGT
66 TAAAGAGTAAAGAGTAATCAAGGAAGAG-AATAGT
32517 AATCAGTAAAAGAGTAAACAGTAAAA
1 AATCAGTAAAAGAGTAAACAGTAAAA
32543 TGATAATAGT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 5 0.05
94 64 0.63
95 1 0.01
96 2 0.02
97 1 0.01
99 27 0.26
100 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (99 bp):
AATCAGTAAAAGAGTAAACAGTAAAACAGTAAAAGACTAAAGAGGAAAAAAGTAATAATAATCAG
TAAAGAGTAAAGAGTAATCAAGGAAGAGAATAGT
Found at i:32527 original size:77 final size:78
Alignment explanation
Indices: 32427--32578 Score: 229
Period size: 77 Copynumber: 2.0 Consensus size: 78
32417 TAATCAGTAA
* *
32427 AAGAGTAAAGAGTAATCAGTAAAAGAGTAAAGAGTAAAA-GAGTAATAATAGTCAGTAAAGAGTA
1 AAGAGTAAAGAGTAATCAGTAAAAGAGTAAACAGTAAAATGA-TAATAATAATCAGTAAAGAGTA
32491 AA-GAGTAATCAAGG
65 AATG-GTAATCAAGG
* *
32505 AAGAGT-AATAGTAATCAGTAAAAGAGTAAACAGTAAAATGATAATAGTAATCAGTAAAGAGTAA
1 AAGAGTAAAGAGTAATCAGTAAAAGAGTAAACAGTAAAATGATAATAATAATCAGTAAAGAGTAA
32569 ATGGTAATCA
66 ATGGTAATCA
32579 GTAAAAAGAG
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
77 59 0.87
78 9 0.13
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (78 bp):
AAGAGTAAAGAGTAATCAGTAAAAGAGTAAACAGTAAAATGATAATAATAATCAGTAAAGAGTAA
ATGGTAATCAAGG
Found at i:32575 original size:21 final size:20
Alignment explanation
Indices: 32373--32604 Score: 120
Period size: 21 Copynumber: 11.9 Consensus size: 20
32363 TTAGGAAAAA
*
32373 AGTAATAGTAATCAGTAAAG
1 AGTAATGGTAATCAGTAAAG
*
32393 AGTAAAGAGTAATCAGTAAA-
1 AGTAATG-GTAATCAGTAAAG
32413 A-T-A--GTAATCAGTAAAAG
1 AGTAATGGTAATCAGT-AAAG
*
32430 AGTAAAGAGTAATCAGTAAA-
1 AGTAATG-GTAATCAGTAAAG
**
32450 AG--A--GTAAAGAGTAAAAG
1 AGTAATGGTAATCAGT-AAAG
** *
32467 AGTAATAATAGTCAGTAAAG
1 AGTAATGGTAATCAGTAAAG
* *
32487 AGTAAAGAGTAATCAAG-GAAG
1 AGTAATG-GTAATC-AGTAAAG
*
32508 AGTAATAGTAATCAGTAAA-
1 AGTAATGGTAATCAGTAAAG
*
32527 AG--A--GTAAACAGTAAA-
1 AGTAATGGTAATCAGTAAAG
*
32542 ATGATAATAGTAATCAGTAAAG
1 A-G-TAATGGTAATCAGTAAAG
32564 AGTAAATGGTAATCAGTAAAAAG
1 AGT-AATGGTAATCAGT--AAAG
*
32587 AGTATTGGTAATCAGTAA
1 AGTAATGGTAATCAGTAA
32605 TTAAAATTCA
Statistics
Matches: 165, Mismatches: 20, Indels: 54
0.69 0.08 0.23
Matches are distributed among these distances:
15 28 0.17
16 7 0.04
17 4 0.02
18 3 0.02
19 8 0.05
20 28 0.17
21 56 0.34
22 24 0.15
23 7 0.04
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTAATGGTAATCAGTAAAG
Found at i:32643 original size:10 final size:9
Alignment explanation
Indices: 32614--32652 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
32604 ATTAAAATTC
32614 AAAGAGTAA
1 AAAGAGTAA
32623 AAATG-GTAA
1 AAA-GAGTAA
*
32632 AAAGATTAA
1 AAAGAGTAA
32641 AAAGAGTAA
1 AAAGAGTAA
32650 AAA
1 AAA
32653 TGGTATCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (9 bp):
AAAGAGTAA
Found at i:32686 original size:37 final size:37
Alignment explanation
Indices: 32639--32715 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
32629 TAAAAAGATT
*
32639 AAAAAGAGTAAAAATGGTATCCAATAATTAAAGTAAA
1 AAAAAAAGTAAAAATGGTATCCAATAATTAAAGTAAA
** *
32676 AAAAAAAGTAAAAATGGTATTGAGTAATTAAAGTAAA
1 AAAAAAAGTAAAAATGGTATCCAATAATTAAAGTAAA
32713 AAA
1 AAA
32716 GGCAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (37 bp):
AAAAAAAGTAAAAATGGTATCCAATAATTAAAGTAAA
Found at i:32785 original size:26 final size:26
Alignment explanation
Indices: 32741--32806 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
32731 CCAGTAAAAA
* *
32741 AAAAAGTGTAAAAAAATGGTAATAAGT
1 AAAAAGAGT-AAAGAATGGTAATAAGT
* *
32768 AAATAGAGTAAAGAATGGTAATCAGT
1 AAAAAGAGTAAAGAATGGTAATAAGT
*
32794 AAAAAGTGTAAAG
1 AAAAAGAGTAAAG
32807 CTAATCGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 26 0.79
27 7 0.21
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (26 bp):
AAAAAGAGTAAAGAATGGTAATAAGT
Found at i:34549 original size:31 final size:31
Alignment explanation
Indices: 34511--34572 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
34501 AAACACACTT
34511 TCTAAGGCTCATTTGATCATTTTAGGTCTAC
1 TCTAAGGCTCATTTGATCATTTTAGGTCTAC
34542 TCTAAGGCTCATTTGATCATTTTAGGTCTAC
1 TCTAAGGCTCATTTGATCATTTTAGGTCTAC
34573 AGGGGCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (31 bp):
TCTAAGGCTCATTTGATCATTTTAGGTCTAC
Done.