Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016086.1 Corchorus olitorius cultivar O-4 contig16119, 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: 20507
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:420 original size:10 final size:10
Alignment explanation
Indices: 405--429 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
395 AGTCATTTCT
405 AAAAAAAAGA
1 AAAAAAAAGA
415 AAAAAAAAGA
1 AAAAAAAAGA
425 AAAAA
1 AAAAA
430 GAAAAGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:12497 original size:22 final size:22
Alignment explanation
Indices: 12467--12569 Score: 82
Period size: 22 Copynumber: 4.6 Consensus size: 22
12457 TTCAACGTAG
*
12467 AAATATTGATAATCACACTGTGA
1 AAAT-TTGATAACCACACTGTGA
* ** * *
12490 AAATTTGATAAGCTTATTATG-
1 AAATTTGATAACCACACTGTGA
* * * *
12511 GAATTTCGATAACCTCTCTTTGA
1 AAATTT-GATAACCACACTGTGA
12534 AAATTTGATAACCACACTGTGA
1 AAATTTGATAACCACACTGTGA
*
12556 AATTTTGATAACCA
1 AAATTTGATAACCA
12570 TAATCTTTTG
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
21 5 0.08
22 48 0.77
23 9 0.15
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTTGATAACCACACTGTGA
Found at i:12665 original size:22 final size:22
Alignment explanation
Indices: 12633--12844 Score: 153
Period size: 22 Copynumber: 9.7 Consensus size: 22
12623 AACCTAATCC
* *
12633 CTAT-AAATTTTGATAACCACT
1 CTATGAAATTTTGATAACCGCA
* *
12654 CTATGAAATTTTGGTAACTGCA
1 CTATGAAATTTTGATAACCGCA
*
12676 CTATGAAATTTTGGTAACCGCA
1 CTATGAAATTTTGATAACCGCA
* *
12698 CTATGAAATCTTGGTAACCGCA
1 CTATGAAATTTTGATAACCGCA
* * **
12720 CTATGAAATCTTGGTAACCATA
1 CTATGAAATTTTGATAACCGCA
* * * * *
12742 GTATTAATTTTTGATAACCTCC
1 CTATGAAATTTTGATAACCGCA
* * * * *
12764 CTAT-AAAATTTGGTTACTGGA
1 CTATGAAATTTTGATAACCGCA
* *
12785 CTATGAAATTTTGATAATCTC-
1 CTATGAAATTTTGATAACCGCA
*
12806 CTTATGAAATTTTTGATAACCTC-
1 C-TATGAAA-TTTTGATAACCGCA
12829 CTTATGAAATTTTGAT
1 C-TATGAAATTTTGAT
12845 TACCACACAA
Statistics
Matches: 154, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
21 18 0.12
22 115 0.75
23 21 0.14
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCGCA
Found at i:12774 original size:23 final size:23
Alignment explanation
Indices: 12595--12841 Score: 99
Period size: 22 Copynumber: 11.1 Consensus size: 23
12585 ACAAAAAAAA
* *
12595 TTTGATAACCTTCCTTTGAAA-T
1 TTTGATAACCTCCCTATGAAATT
*
12617 TTTAATAACCTAATCCCTAT-AAA-T
1 TTTGATAACC---TCCCTATGAAATT
* *
12641 TTTGATAACCACTCTATGAAA-T
1 TTTGATAACCTCCCTATGAAATT
* *
12663 TTTGGTAA-CTGCACTATGAAA-T
1 TTTGATAACCT-CCCTATGAAATT
* * *
12685 TTTGGTAACCGCACTATGAAA-T
1 TTTGATAACCTCCCTATGAAATT
* * * *
12707 CTTGGTAACCGCACTATGAAA-T
1 TTTGATAACCTCCCTATGAAATT
* * ** *
12729 CTTGGTAACCAT-AGTAT-TAATT
1 TTTGATAACC-TCCCTATGAAATT
*
12751 TTTGATAACCTCCCTAT-AAA-A
1 TTTGATAACCTCCCTATGAAATT
* * **
12772 TTTGGTTA-CTGGACTATGAAA-T
1 TTTGATAACCT-CCCTATGAAATT
* *
12794 TTTGATAATCTCCTTATGAAATT
1 TTTGATAACCTCCCTATGAAATT
*
12817 TTTGATAACCTCCTTATGAAATT
1 TTTGATAACCTCCCTATGAAATT
12840 TT
1 TT
12842 GATTACCACA
Statistics
Matches: 181, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.01
21 19 0.10
22 114 0.63
23 28 0.15
24 13 0.07
25 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (23 bp):
TTTGATAACCTCCCTATGAAATT
Found at i:12946 original size:22 final size:22
Alignment explanation
Indices: 12920--12969 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
12910 AATTTTCCTT
*
12920 ATGAAAGCTTGATAATCTCACC
1 ATGAAAGCTTAATAATCTCACC
* *
12942 ATGAAAGTTTAATAATCTCACT
1 ATGAAAGCTTAATAATCTCACC
12964 ATGAAA
1 ATGAAA
12970 TTTTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (22 bp):
ATGAAAGCTTAATAATCTCACC
Found at i:13580 original size:22 final size:22
Alignment explanation
Indices: 13557--14137 Score: 193
Period size: 22 Copynumber: 25.7 Consensus size: 22
13547 TATAGTGTGA
*
13557 TTATCAAAATTTCATAGGAAGA
1 TTATCAAAATTTCATAGGAAGG
* * *
13579 TTGTCAAAATTTCACA-CAGAGG
1 TTATCAAAATTTCATAGGA-AGG
* * * *
13601 TAATCAAAATTTCACATTG-TGG
1 TTATCAAAATTTCATA-GGAAGG
* *
13623 TTCTCAAAATTTCATATGGATTATG
1 TTATCAAAATTTCATA-GGA--AGG
* * * *
13648 TTATTAAAATTTTATAGAAAAG
1 TTATCAAAATTTCATAGGAAGG
* *
13670 TTATTAAAATTTCATAGTG-TGG
1 TTATCAAAATTTCATAG-GAAGG
*
13692 TTATCAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGGAAGG
* *
13714 TTATCAAAATTCCATAGCG-AGT
1 TTATCAAAATTTCATAG-GAAGG
*
13736 TTATCAAAATTTTATAAGG-AGG
1 TTATCAAAATTTCAT-AGGAAGG
*
13758 TTATCAAAGATTTCATAGTG-TGG
1 TTATCAAA-ATTTCATAG-GAAGG
* * * * **
13781 TTACCGACATTTCATAGTAATA
1 TTATCAAAATTTCATAGGAAGG
* * *
13803 TTAGAAAAATCTAAATTTCATACGAGGG
1 TT------ATCAAAATTTCATAGGAAGG
* * *
13831 TTATTAAAATTTTATAGTATA-G
1 TTATCAAAATTTCATAGGA-AGG
13853 TTATCAAAATTTCATCAGGAA-G
1 TTATCAAAATTTCAT-AGGAAGG
** * *
13875 CAATCAAAATCTCATAGAGTA-G
1 TTATCAAAATTTCATAG-GAAGG
* * *
13897 TTGGTCAAAAATTCATAGAGATCAGA
1 TT-ATCAAAATTTCATAG-GA--AGG
* * *
13923 TTACCAAAATTTCATAAGAATG
1 TTATCAAAATTTCATAGGAAGG
* * **
13945 TTATCAAAATTTTAAATCAAGG
1 TTATCAAAATTTCATAGGAAGG
**
13967 TTATCAAAATTTCCCAGTG-AGG
1 TTATCAAAATTTCATAG-GAAGG
* * **
13989 TTATGAAAAATTTTCATATTG-TTG
1 TTAT-CAAAA-TTTCATA-GGAAGG
**
14013 TTATTGAAATTTCATATGG-AGG
1 TTATCAAAATTTCATA-GGAAGG
* * *
14035 TT-TC-AAATTTCATAGTATGA
1 TTATCAAAATTTCATAGGAAGG
**
14055 TTATTTTAAATTTCATA-GAGAGG
1 TTA-TCAAAATTTCATAGGA-AGG
* * *
14078 TTAGCATAATTTCATTGGAAGG
1 TTATCAAAATTTCATAGGAAGG
**
14100 TTATTGAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGGAAGG
*
14122 TTATCGAAATTTCATA
1 TTATCAAAATTTCATA
14138 ATGTTATTAT
Statistics
Matches: 409, Mismatches: 114, Indels: 72
0.69 0.19 0.12
Matches are distributed among these distances:
19 1 0.00
20 13 0.03
21 5 0.01
22 276 0.67
23 57 0.14
24 15 0.04
25 26 0.06
26 2 0.00
28 14 0.03
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAGG
Found at i:13717 original size:44 final size:44
Alignment explanation
Indices: 13548--14734 Score: 286
Period size: 44 Copynumber: 26.7 Consensus size: 44
13538 ATATAAAAAT
* * * *
13548 ATAGTGTGATTATCAAAATTTCATAGGAAGATTGTCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* ** * * * ** * *
13592 ACACAGAGGTAATCAAAATTTCACATTGTGGTTCTCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * * ** * *
13636 ATA-TGGATTATGTTATTAAAATTTTATAGAAAAGTTATTAAAATTTC
1 ATAGT-G--T-GGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
*
13683 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTCC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * * * *
13727 ATAGCGAGTTTATCAAAATTTTATAAGGAGGTTATCAAAGATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAA-ATTTC
* * * ** ** *
13772 ATAGTGTGGTTACCGACATTTCATAGTAATATTAGAAAAATCTAAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTT------ATCAAAATTTC
* * * * *
13822 ATACGAG-GGTTATTAAAATTTTATA-GTATAGTTATCAAAATTTC
1 ATA-GTGTGGTTATCAAAATTTCATAGGGA-GGTTATCAAAATTTC
** ** * * * *
13866 ATCAG-GAAGCAATCAAAATCTCATAGAGTA-GTTGGTCAAAAATTC
1 AT-AGTGTGGTTATCAAAATTTCATAG-GGAGGTT-ATCAAAATTTC
* * * * * * *
13911 ATAGAGATCAGATTACCAAAATTTCATAAGAATGTTATCAAAATTTT
1 ATAGTG-T--GGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* ** ** * *
13958 A-AATCAAGGTTATCAAAATTTCCCAGTGAGGTTATGAAAAATTTTC
1 ATAGT-GTGGTTATCAAAATTTCATAGGGAGGTTAT-CAAAA-TTTC
* * ** *
14004 ATATTGTTGTTATTGAAATTTCATATGGAGGTT-TC-AAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * ** * * *
14046 ATAGTATGATTATTTTAAATTTCATAGAGAGGTTAGCATAATTTC
1 ATAGTGTGGTTA-TCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * ** * *
14091 ATTG-GAAGGTTATTGAAATTTCATAGGAAGGTTATCGAAATTTC
1 ATAGTG-TGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* ** * * **
14135 ATAATGTTATTATCAAAA--ACTTA--GAGTGTGGT----ATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAG-GTTATCAAAATTTC
* * * * * * *
14172 AAAGGGAGGTTATCAAAATTGCATTTGTGTGGTTA-CTAAAATTTC
1 ATAGTGTGGTTATCAAAATTTCA-TAGGGAGGTTATC-AAAATTTC
* * * * *
14217 GTA-TGAAGGTTATTAAAATTTCAAAGGG-GGACTATCAAAATTTC
1 ATAGTG-TGGTTATCAAAATTTCATAGGGAGG-TTATCAAAATTTC
* * * * *** * *
14261 ATAGGGAGGATATCAGAATTTCATATTTTA-GTTTTCAAAATTTT
1 ATAGTGTGGTTATCAAAATTTCATA-GGGAGGTTATCAAAATTTC
* *
14305 ATAG-G-GGTTATCAAAATTACATAGGGAGGTTAAC-AAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* ** *
14346 ATATTGAAGTTAATTATCGAAAA-ATCATAGGGAGGTTATCAAAA--T-
1 ATA--G-TG-TGGTTATC-AAAATTTCATAGGGAGGTTATCAAAATTTC
* * *
14391 -T--TGTGATTATCAAAATTTCATAAGGAGGTTATCAAAATTTT
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * * * * * **
14432 ATAGGGAGATTTATCAAAATTTTATATGAATTTTTATCAAAATTTC
1 ATAGTGTG-GTTATCAAAATTTCATAGGGA-GGTTATCAAAATTTC
* * * * * * *
14478 ATACTGAGATCAT-AACAATTTCATAGTGTGATTATCAAAATTTC
1 ATAGTGTGGTTATCAA-AATTTCATAGGGAGGTTATCAAAATTTC
* * * * *
14522 ACAGTGTGAATTATGATCACTAAGATTTCATAAGGAGGTTATAAAAAATATC
1 ATAGTGTG--GT-T-ATCA--AA-ATTTCATAGGGAGGTTAT-CAAAATTTC
* * * * * *
14574 ATAGTGTGCTTACCAACATTTCACATGGAGATTATCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
*
14618 ATAGTGTGGTTATCAAAATTT-A-AGTGGATGGTTATCGAAATTTC
1 ATAGTGTGGTTATCAAAATTTCATAG-GGA-GGTTATCAAAATTTC
* * * ** * *
14662 AGTAG-GAGGTCATCAAAATTTTATAGCAATGTTTTCAAAA-TTC
1 A-TAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
* * *
14705 TATAGGGAGGTTAACAAAATTTCATAGGGA
1 -ATAGTGTGGTTATCAAAATTTCATAGGGA
14735 AGTTCTTGAA
Statistics
Matches: 807, Mismatches: 251, Indels: 170
0.66 0.20 0.14
Matches are distributed among these distances:
37 21 0.03
38 26 0.03
39 2 0.00
40 4 0.00
41 15 0.02
42 38 0.05
43 36 0.04
44 331 0.41
45 131 0.16
46 50 0.06
47 61 0.08
48 28 0.03
49 3 0.00
50 25 0.03
51 22 0.03
52 14 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
ATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTC
Found at i:14425 original size:22 final size:22
Alignment explanation
Indices: 14167--14830 Score: 131
Period size: 22 Copynumber: 29.9 Consensus size: 22
14157 AGAGTGTGGT
14167 ATTTCA-AAGGGAGGTTATCAAA
1 ATTTCATAA-GGAGGTTATCAAA
* ** *
14189 ATTGCATTTGTGTGGTTA-CTAAA
1 ATTTCATAAG-GAGGTTATC-AAA
* * * *
14212 ATTTCGTATGAAGGTTATTAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
14234 ATTTCA-AAGGGGGACTATCAAA
1 ATTTCATAAGGAGG-TTATCAAA
* * *
14256 ATTTCATAGGGAGGATATCAGA
1 ATTTCATAAGGAGGTTATCAAA
*** *
14278 ATTTCATATTTTA-GTTTTCAAA
1 ATTTCATA-AGGAGGTTATCAAA
*
14300 ATTTTAT-AGG-GGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* * *
14320 ATTACATAGGGAGGTTAAC-AA
1 ATTTCATAAGGAGGTTATCAAA
* * *
14341 ATTTCATATTGAAGTTAATTATCGAAA
1 ATTTCATA-AGGAG---GTTATC-AAA
* *
14368 A-ATCATAGGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
*
14389 ATTT-GT---GA--TTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
14405 ATTTCATAAGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* * *
14427 ATTTTATAGGGAGATTTATCAAA
1 ATTTCATAAGGAG-GTTATCAAA
* * * **
14450 ATTTTATATGAATTTTTATCAAA
1 ATTTCATAAGGA-GGTTATCAAA
** * *
14473 ATTTCATACTGAGATCAT-AACA
1 ATTTCATAAGGAGGTTATCAA-A
* *
14495 ATTTCAT-AGTGTGATTATCAAA
1 ATTTCATAAG-GAGGTTATCAAA
* * **
14517 ATTTCACAGTGTGAATTATGATCACTAA
1 ATTTCATA-AG-GAGGT-T-ATCA--AA
*
14545 GATTTCATAAGGAGGTTATAAAAA
1 -ATTTCATAAGGAGGTTAT-CAAA
* * * * *
14569 ATATCAT-AGTGTGCTTACCAAC
1 ATTTCATAAG-GAGGTTATCAAA
* * *
14591 ATTTCACATGGAGATTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
*
14613 ATTTCAT-AGTGTGGTTATCAAA
1 ATTTCATAAG-GAGGTTATCAAA
* *
14635 ATTT-A-AGTGGATGGTTATCGAA
1 ATTTCATA-AGGA-GGTTATCAAA
*
14657 ATTTCAGT-AGGAGGTCATCAAA
1 ATTTCA-TAAGGAGGTTATCAAA
* * * *
14679 ATTTTAT-AGCAATGTTTTCAAA
1 ATTTCATAAG-GAGGTTATCAAA
* *
14701 A-TTCTATAGGGAGGTTAACAAA
1 ATTTC-ATAAGGAGGTTATCAAA
* * * **
14723 ATTTCATAGGGAAGTTCTTGAA
1 ATTTCATAAGGAGGTTATCAAA
* * * *
14745 ATTTGAT-TGGAAGGTTTTCGAA
1 ATTTCATAAGG-AGGTTATCAAA
* *
14767 ATTGT-AT-AGTATCGTTATCAAA
1 ATT-TCATAAGGA-GGTTATCAAA
* ** *
14789 ACTTCATAAAAATGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
14811 AGTTT-ATAAGGAGGTTATCA
1 A-TTTCATAAGGAGGTTATCA
14831 TAGGGAGATA
Statistics
Matches: 456, Mismatches: 131, Indels: 110
0.65 0.19 0.16
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
18 2 0.00
20 15 0.03
21 34 0.07
22 265 0.58
23 84 0.18
24 6 0.01
25 10 0.02
26 11 0.02
27 6 0.01
28 3 0.01
29 7 0.02
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
ATTTCATAAGGAGGTTATCAAA
Found at i:14449 original size:23 final size:22
Alignment explanation
Indices: 14397--14476 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
14387 AAATTTGTGA
* *
14397 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTTATAAGGAGT
*
14419 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAAGGAG-T
* * *
14442 TTATCAAAATTTTATATGAATTT
1 TTATCAAAATTTTATAAGGA-GT
14465 TTATCAAAATTT
1 TTATCAAAATTT
14477 CATACTGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.38
23 31 0.62
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGGAGT
Found at i:15906 original size:2 final size:2
Alignment explanation
Indices: 15901--15931 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15891 TAGTAGTAAG
15901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15932 GTTTTAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16098 original size:22 final size:21
Alignment explanation
Indices: 15987--16130 Score: 112
Period size: 22 Copynumber: 6.6 Consensus size: 21
15977 TGAGTATTTT
*
15987 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTA-CA
* *
16009 TATTAAATTTTGATAA-TCACGC
1 TATGAAATTTTGATAACT-AC-A
*
16031 TATGAAATTTTGATAATTA-A
1 TATGAAATTTTGATAACTACA
* * *
16051 CTACGAAATTATGATAAACTCCA
1 -TATGAAATTTTGAT-AACTACA
*
16074 TATGAAATTTTGATAACCTAAA
1 TATGAAATTTTGATAA-CTACA
* *
16096 TATGAAATTTTAATAAACCTTCA
1 TATGAAATTTTGAT-AA-CTACA
16119 TATGAAATTTTG
1 TATGAAATTTTG
16131 TAATCTTCCT
Statistics
Matches: 99, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
21 16 0.16
22 64 0.65
23 19 0.19
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACA
Found at i:16184 original size:22 final size:20
Alignment explanation
Indices: 16119--16191 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
16109 TAAACCTTCA
*
16119 TATGAAATTTTGTAATCTTCC
1 TATG-AATTTTGTAATCTCCC
* * *
16140 TACGATTTTTGATAACCTCCC
1 TATGAATTTTG-TAATCTCCC
*
16161 TATGAGATTTTGTTAATCTGCC
1 TATGA-ATTTTG-TAATCTCCC
16183 TAT-AATTTT
1 TATGAATTTT
16192 TTGATACTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.27
21 15 0.37
22 15 0.37
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (20 bp):
TATGAATTTTGTAATCTCCC
Found at i:16499 original size:45 final size:45
Alignment explanation
Indices: 16435--16522 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
16425 TCTAATTTGA
16435 TTTAGCTCTTATAATATGATTATACGTTTAAAAATTCAACTCCGG
1 TTTAGCTCTTATAATATGATTATACGTTTAAAAATTCAACTCCGG
* * *
16480 TTTAGTTCTTATAGTATGATTATACGTTTACAAATTCAACTCC
1 TTTAGCTCTTATAATATGATTATACGTTTAAAAATTCAACTCC
16523 TTTGAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (45 bp):
TTTAGCTCTTATAATATGATTATACGTTTAAAAATTCAACTCCGG
Found at i:16969 original size:3 final size:3
Alignment explanation
Indices: 16961--17005 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
16951 TGGGTTGGCC
16961 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
17006 AACATAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17945 original size:22 final size:22
Alignment explanation
Indices: 17919--17960 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17909 GGCAAATTTA
* *
17919 TAACCTAAATGACCCGAGAAGT
1 TAACCCAAATGACCCAAGAAGT
*
17941 TAACCCGAATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
17961 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:18474 original size:42 final size:43
Alignment explanation
Indices: 18427--18516 Score: 119
Period size: 45 Copynumber: 2.1 Consensus size: 43
18417 CATTATTTAA
* *
18427 ATTCTA-CTACATCTCTAGGGAATTCATCAATATAAAGCTAAT
1 ATTCTACCTACATCTCTAGAGAATTCATCAAAATAAAGCTAAT
* *
18469 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTACATCTCTAGAGAATTCATCAAAATAAAGCTAAT
18514 ATT
1 ATT
18517 AATTGTTGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 6 0.15
45 35 0.85
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (43 bp):
ATTCTACCTACATCTCTAGAGAATTCATCAAAATAAAGCTAAT
Done.