Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008423.1 Hibiscus syriacus cultivar Beakdansim tig00111206_pilon, 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: 1633377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1574900 original size:33 final size:33
Alignment explanation
Indices: 1574853--1574947 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1574843 GACAAGTTGG
*
1574853 AAAATTCATCTTGGTTGGTGGCCAACTTAT-TT
1 AAAATTCATCTTGGTTGGTGGCCAACTTATATA
*
1574885 GAAATGTCATCTTGGTTGGTGGCCAACTTATATA
1 AAAAT-TCATCTTGGTTGGTGGCCAACTTATATA
*
1574919 AAAATTCATCTTTGGTAGGTGGCCAACTT
1 AAAATTCATC-TTGGTTGGTGGCCAACTT
1574948 TGCACATGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.07
33 30 0.54
34 22 0.39
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (33 bp):
AAAATTCATCTTGGTTGGTGGCCAACTTATATA
Found at i:1581601 original size:25 final size:25
Alignment explanation
Indices: 1581564--1581615 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1581554 ATTTCCAGCT
*
1581564 TTGATTTCCAGCCACCAA-ATTTGAC
1 TTGATTTACAGCC-CCAACATTTGAC
* *
1581589 TTGATTTATAGCCCCAACTTTTGAC
1 TTGATTTACAGCCCCAACATTTGAC
1581614 TT
1 TT
1581616 CCAACACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
TTGATTTACAGCCCCAACATTTGAC
Found at i:1584126 original size:5 final size:5
Alignment explanation
Indices: 1584118--1584143 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1584108 GGGGTTTCTC
1584118 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
1584144 GTTTAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:1590314 original size:5 final size:5
Alignment explanation
Indices: 1590304--1590343 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
1590294 TGATGTAGGA
1590304 TTTCT TTTCT TTTCT TTTCT TTTCT TTT-T GTTT-T TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTTCT T
1590344 ATTTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:1592124 original size:22 final size:22
Alignment explanation
Indices: 1592094--1592144 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1592084 CATGGCCCTA
* *
1592094 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACATT
*
1592116 ATGGACCTATTTGTAAGACATT
1 ATGGACCTAGTTGTAAGACATT
1592138 ATGGACC
1 ATGGACC
1592145 CTAAGGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACATT
Found at i:1593920 original size:3 final size:3
Alignment explanation
Indices: 1593912--1593960 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
1593902 ATTAATGGCA
1593912 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
1593958 ATT
1 ATT
1593961 CACTACATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1594875 original size:14 final size:15
Alignment explanation
Indices: 1594854--1594945 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 15
1594844 ATGATAATTA
1594854 ATATACTTTATATTT
1 ATATACTTTATATTT
1594869 A-ATAC-TTATATTT
1 ATATACTTTATATTT
* *
1594882 ATATACTTGAATACTT
1 ATATACTT-TATATTT
*** *
1594898 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
*
1594913 AT-TACTTTACA-TT
1 ATATACTTTATATTT
*
1594926 ATATACTTTATATAT
1 ATATACTTTATATTT
1594941 ATATA
1 ATATA
1594946 TATAGATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 13 0.22
14 20 0.34
15 17 0.29
16 9 0.15
ACGTcount: A:0.38, C:0.12, G:0.01, T:0.49
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:1594949 original size:19 final size:19
Alignment explanation
Indices: 1594925--1594964 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1594915 TACTTTACAT
*
1594925 TATATACTTTATATATATA
1 TATATACATTATATATATA
* *
1594944 TATATAGATTATATATGTA
1 TATATACATTATATATATA
1594963 TA
1 TA
1594965 CAAATTGAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TATATACATTATATATATA
Found at i:1595080 original size:25 final size:24
Alignment explanation
Indices: 1595033--1595078 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1595023 TGATGAGGGA
1595033 TGAAATTGAATTAATTATAAAATT
1 TGAAATTGAATTAATTATAAAATT
*
1595057 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
1595079 ATGGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATT
Found at i:1595982 original size:24 final size:25
Alignment explanation
Indices: 1595932--1595994 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1595922 ATTGAAACAA
* * *
1595932 TTATAATATATATATATATATGTATG
1 TTATGATA-ATATGTATATATGAATG
1595958 -TATGTATAATATGTATA-ATGAATG
1 TTATG-ATAATATGTATATATGAATG
1595982 TTATGATAATATG
1 TTATGATAATATG
1595995 ATGCATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 14 0.44
25 15 0.47
26 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (25 bp):
TTATGATAATATGTATATATGAATG
Found at i:1596011 original size:20 final size:21
Alignment explanation
Indices: 1595940--1596009 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
1595930 AATTATAATA
*
1595940 TATATATATATATGTATGTATG
1 TATATATATATATG-ATGAATG
* *
1595962 TATA-ATATGTATAATGAATG
1 TATATATATATATGATGAATG
*
1595982 T-TATGATA-ATATGATGCATG
1 TATAT-ATATATATGATGAATG
1596002 TATATATA
1 TATATATA
1596010 ATGTACATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 20 0.51
21 13 0.33
22 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (21 bp):
TATATATATATATGATGAATG
Found at i:1596057 original size:20 final size:20
Alignment explanation
Indices: 1596029--1596067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1596019 ATACTTTATG
*
1596029 TATATATATATACATATACA
1 TATACATATATACATATACA
*
1596049 TATACATATATACTTATAC
1 TATACATATATACATATAC
1596068 TTTATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
TATACATATATACATATACA
Found at i:1596128 original size:589 final size:567
Alignment explanation
Indices: 1594965--1596599 Score: 2301
Period size: 589 Copynumber: 2.9 Consensus size: 567
1594955 TATATGTATA
* *
1594965 CAAATTGAACAAACATGAAATTGAAAATAAAAAATTGAATAAATTACA-CAAAACACATTGATGA
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTA-AGCAACACACATTGATGA
* * * *
1595029 GGGATGAAATTGAATTAATTATAAAATTTGAAGTTGATATTAATATAAAAATGGACGAAATTGCA
65 GGGATGAAATTGAATTAATTATAAAATGTGAA-CTAATATTAATATAAAAATGGACTAAATTGCA
*
1595094 TACATTTAAAAAGTTGGTGAACATAATTTGAAAATAAATTTATTATGTGATTTACATTTTATA-G
129 TACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGG
* *
1595158 G---GTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCATATACAAATATACTT
194 GTTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATT
*
1595220 TGAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATACAATAAACAACATAAA
259 TGAAGGAATAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATA-AATAAACAACATAAA
1595285 AGGATCAAATAAAAAAAAGTGTAAAATGTGAGGAAAATTGTAAAA-GAACTGAATTGCATTAATT
323 AGGATCAAAT-AAAAAAA-TGTAAAATGTGAGGAAAATTGTAAAATGAACTGAATTGCATTAATT
1595349 TCAAAAGTTGGAGAAAATT-AA-AA--A-AAT-TATA-ATATATA-T-TTATG------TT-TAA
386 TCAAAAGTTGGAGAAAATTAAACAATTATAATATATATATATATATTATTATGTATATATTATAA
*
1595398 TGAATGTTATGATAATATGATGCATGTATATCTAATGTACATTATACTTTATATATATAGATATA
451 TGAATGTTATGATAATATGATGCATGTATATATAATGTACATTATACTTTATATATATAGATATA
*
1595463 CACATATGCATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
516 CACATATACATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
*
1595515 CAAATTGAGCAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
*
1595580 GGATGAAATTGAATTAATTATAAAATGTGAACCATATATTAATATAAAAATGGACTAAATTGCAT
66 GGATGAAATTGAATTAATTATAAAATGTGAACTA-ATATTAATATAAAAATGGACTAAATTGCAT
* * *
1595645 ACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGGG
130 ACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGGG
*
1595710 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCGGATACAAATATAATTT
195 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATTT
* * *
1595775 GAAGGAATAAATTGAACAAATATGAAATTA-AAAATAAAATTTTAAATAAATTAAAGAACACAAA
260 GAAGGAATAAATTGAACAAATATGAAATTACAAATTAAAA-TTTAAATAAA-TAAACAACATAAA
* * * * * * * *
1595839 TGGATTAAATCGAAATAATTGTAAAATGTTAAGAAAATGTGTAAAATTAACTAAATTGCATTAAT
323 AGGATCAAAT--AAAAAAATGTAAAATGTGAGGAAAAT-TGTAAAATGAACTGAATTGCATTAAT
* *
1595904 TTCAAAAGTTAAGAAAAAATTGAAACAATTATAATATATATATATATATGTATGTATGTATAATA
385 TTCAAAAGTT-GGAGAAAATT-AAACAATTATAATATATATATATATAT-TAT-TATGTAT-ATA
1595969 TGTATAATGAATGTTATGATAATATGATGCATGTATATATAATGTACATTATACTTTATGTATAT
445 T-TATAATGAATGTTATGATAATATGATGCATGTATATATAATGTACATTATACTTTA--TATAT
* * *
1596034 ATATATACATATACATATACATATATACTTATACTTTATAGTTTATAGTTTATATATGTATATAA
507 ATAGAT--ATACACATATACATATATACTTATAC-------TTTATAGTTCATATATGTATATAA
1596099 AGTAC
563 AGTAC
1596104 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
* *
1596169 GGATGAAATTGAATTAATTATAAAATGTGAAACTAATATTAATATAAAAATGGAATAAATTGGAT
66 GGATGAAATTGAATTAATTATAAAATGTG-AACTAATATTAATATAAAAATGGACTAAATTGCAT
* * *
1596234 ATATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTGTGTGATTTATATTTTATAGGG
130 ACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGGG
* * **
1596299 TTTGTTTTAAGTAAATTACTAAAATATAAATAAGGATGGGTCAATTTCAGATATGAATATAATTT
195 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATTT
* * *
1596364 GAA-GAACTAAATTGAACAAATCTGAAATTACAAATTTAAATTTAAATAAAATAAATAACATAAA
260 GAAGGAA-TAAATTGAACAAATATGAAATTACAAATTAAAATTTAAAT-AAATAAACAACATAAA
* * *
1596428 AGGATCAAATAAAAAAATGTAAAATGTGAGGGAAAATTATAAAATGGATTGAATTGCATTAATTT
323 AGGATCAAATAAAAAAATGTAAAATGTGA-GGAAAATTGTAAAATGAACTGAATTGCATTAATTT
* * *
1596493 CAAAAATTGGGGAAAATTAAAACAATTATAATATATATATATATATATATATATATATATATATA
387 CAAAAGTTGGAGAAAATT-AAACAATTATAATATATATATATATAT-TAT-TATGTATATAT-TA
*
1596558 TAATGAATGTTATAATAATATGATGCATGTATATATAATGTA
448 TAATGAATGTTATGATAATATGATGCATGTATATATAATGTA
1596600 AAATATAAGT
Statistics
Matches: 960, Mismatches: 76, Indels: 63
0.87 0.07 0.06
Matches are distributed among these distances:
549 1 0.00
550 177 0.18
551 2 0.00
553 10 0.01
554 132 0.14
555 12 0.01
556 26 0.03
557 8 0.01
559 2 0.00
560 2 0.00
562 1 0.00
563 3 0.00
564 4 0.00
565 7 0.01
567 1 0.00
568 1 0.00
569 4 0.00
576 1 0.00
577 1 0.00
578 53 0.06
580 10 0.01
582 24 0.03
585 47 0.05
586 43 0.04
587 46 0.05
588 9 0.01
589 319 0.33
590 14 0.01
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (567 bp):
CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
GGATGAAATTGAATTAATTATAAAATGTGAACTAATATTAATATAAAAATGGACTAAATTGCATA
CATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGGGT
TTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCAGATACAAATATAATTTG
AAGGAATAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATAAACAACATAAAAGG
ATCAAATAAAAAAATGTAAAATGTGAGGAAAATTGTAAAATGAACTGAATTGCATTAATTTCAAA
AGTTGGAGAAAATTAAACAATTATAATATATATATATATATTATTATGTATATATTATAATGAAT
GTTATGATAATATGATGCATGTATATATAATGTACATTATACTTTATATATATAGATATACACAT
ATACATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
Found at i:1596530 original size:2 final size:2
Alignment explanation
Indices: 1596519--1597268 Score: 135
Period size: 2 Copynumber: 377.0 Consensus size: 2
1596509 TTAAAACAAT
1596519 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA
* * * * *
1596560 -A TGA -A TG T- TA TA -A TA -A TA TGA TG CA TG TA TA TA TA -A TG
1 TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
* * * * *
1596598 TA -A AA TA TA -A GTA TA TA TA TA AA GTG TA AA CTA TA AA GTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* * * * *
1596640 TA TA CTT TA AA GTA TA AA GTG TA TA TA TA TA TA TA TA TA TA AA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
1596683 CTA TA AA GTA TA AA GTA TA -A GTA TA T- TA TA -A GTA 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
* * * * * *
1596725 AA T- TA TA AA GTA TA TA TA CTT TT TA CTA -A AA CTT 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
* * * * * *
1596767 T- TA TA AA CT- TA TA TA TA TA AA GTA TA -A T- TA TA AA GA CA AA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
1596807 AA TA TA TA -A GTA TA TA TA TA AA GTA TA TA -A GTA TA TA TA CA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * *
1596848 TA TA AA GTA -A AA GTA TA -A CA TA AA TA TA TA CTA 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
* * *
1596889 TA TA TA TA TA TA TA TA TA GT- TC TA GTA TA AA T- TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
*
1596931 TA TA TA -A TA -A TA TA AA CTA TA -A GTA TA T- TA 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 TA
* * * * * *
1596971 TA TA TA TA CTC TA T- TC TT TA TA TA TA TA CTT TA T- TC TT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
1597013 -A T- TA TA CTC TA TT TA TA TG TA TA -A TA TA CT- TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
1597052 TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA GTA 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 TA
* * *
1597094 TA TA CTT TA TA GTA TA TA TA TA TA CTT TA TA T- TC T- TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
1597135 CT- TG TA TA TT TA -A TA CT- TA TA TA T- TT TA TA T- TA TA TA CT-
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
1597174 TA GA TA CTT TA TA T- TA TA TGA T- TA TA TA CTT TA TC TT TA TA
1 TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA
* *
1597215 -A T- TA TA CTA TA TA TA TA TA TA TT TA TA CTT TA TA T- TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
1597255 TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA
1597269 CTTTATACTA
Statistics
Matches: 542, Mismatches: 108, Indels: 196
0.64 0.13 0.23
Matches are distributed among these distances:
1 51 0.09
2 440 0.81
3 51 0.09
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1596639 original size:23 final size:23
Alignment explanation
Indices: 1596613--1596664 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1596603 TATAAGTATA
*
1596613 TATATAAAGTGTAAACTATAAAG
1 TATATAAACTGTAAACTATAAAG
* * *
1596636 TATATATACTTTAAAGTATAAAG
1 TATATAAACTGTAAACTATAAAG
*
1596659 TGTATA
1 TATATA
1596665 TATATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (23 bp):
TATATAAACTGTAAACTATAAAG
Found at i:1596643 original size:37 final size:36
Alignment explanation
Indices: 1596602--1596726 Score: 95
Period size: 37 Copynumber: 3.6 Consensus size: 36
1596592 ATAATGTAAA
*
1596602 ATATA-AGTATATA-TATAAAGTGTAAACTATAAAGT
1 ATATATAGTATAAACTATAAAGTGTAAA-TATAAAGT
* * * *
1596637 ATATATACTTTAAAGTATAAAGTGT--ATATATA-T
1 ATATATAGTATAAACTATAAAGTGTAAATATAAAGT
*
1596670 ATATATA-TATAAACTATAAAGTATAAAGTAT-AAGT
1 ATATATAGTATAAACTATAAAGTGTAAA-TATAAAGT
*
1596705 ATATTATAAGTATATA-TATAAA
1 ATA-TAT-AGTATAAACTATAAA
1596727 TTATAAAGTA
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
32 14 0.19
33 8 0.11
34 7 0.10
35 13 0.18
36 8 0.11
37 17 0.24
38 5 0.07
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (36 bp):
ATATATAGTATAAACTATAAAGTGTAAATATAAAGT
Found at i:1596714 original size:11 final size:12
Alignment explanation
Indices: 1596660--1596742 Score: 62
Period size: 11 Copynumber: 7.8 Consensus size: 12
1596650 AGTATAAAGT
1596660 GTATATATAT-A
1 GTATATATATAA
1596671 -TATATATATAA
1 GTATATATATAA
*
1596682 --A-CTATA-AA
1 GTATATATATAA
*
1596690 GTATAAAGTATAA
1 GTATATA-TATAA
1596703 GTATAT-TATAA
1 GTATATATATAA
1596714 GTATATATATAA
1 GTATATATATAA
1596726 --AT-TATA-AA
1 GTATATATATAA
1596734 GTATATATA
1 GTATATATA
1596743 CTTTTTACTA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
8 4 0.07
9 8 0.14
10 15 0.26
11 17 0.29
12 7 0.12
13 7 0.12
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (12 bp):
GTATATATATAA
Found at i:1596781 original size:15 final size:14
Alignment explanation
Indices: 1596761--1596835 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 14
1596751 TAAAACTTTA
*
1596761 TATATATTATAAAC
1 TATATATTATAAAG
1596775 T-TATATATATAAAG
1 TATATAT-TATAAAG
1596789 TATA-ATTATAAAG
1 TATATATTATAAAG
* * *
1596802 -ACAAAAATATATAAG
1 TA-TATATTATA-AAG
1596817 TATATA-TATAAAG
1 TATATATTATAAAG
1596830 TATATA
1 TATATA
1596836 AGTATATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 1 0.02
13 22 0.44
14 19 0.38
15 7 0.14
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (14 bp):
TATATATTATAAAG
Found at i:1597145 original size:119 final size:115
Alignment explanation
Indices: 1596958--1597171 Score: 263
Period size: 119 Copynumber: 1.8 Consensus size: 115
1596948 TATAAGTATA
* *
1596958 TTATATATATATATATATATACTCTATTCTTTATATATATACTTTATTCTTTATAATTATACTCT
1 TTATATATATATATATATATACTCTATACTATATATATATACTTTATTCTTTATAATTATA--CT
1597023 ATTT-ATA-TGTATAATATACTTATATTATATATTATTATATATGTATATATACT
64 ATTTAATACT-TAT-ATAT-CTTATATTATATATTATTATATATGTATATATACT
* * * *
1597076 TTATAGTATATATATATATATACTTTATAGTATATATATATACTTTATATTCTTATATACTTGTA
1 TTATA-TATATATATATATATACTCTATACTATATATATATAC-TT-TATTCTT-TATAATTATA
*
1597141 -TATTTAATACTTATATATTTTATATTATATA
62 CTATTTAATACTTATATATCTTATATTATATA
1597172 CTTAGATACT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
118 17 0.20
119 42 0.51
120 8 0.10
121 8 0.10
122 8 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (115 bp):
TTATATATATATATATATATACTCTATACTATATATATATACTTTATTCTTTATAATTATACTAT
TTAATACTTATATATCTTATATTATATATTATTATATATGTATATATACT
Found at i:1597247 original size:84 final size:81
Alignment explanation
Indices: 1597037--1597259 Score: 213
Period size: 84 Copynumber: 2.7 Consensus size: 81
1597027 ATATGTATAA
* * * *
1597037 TATACTTATATTATA-TATTATTATATATGTATATATACTTTATAGTATATATATATATATACTT
1 TATATTTATATTATACTA-TA-TATATATATATTTATACTTTATA-T-TATATATATAGATACTT
1597101 TATAGTATATATATATACTT
62 TATAGTATATATATATACTT
* * *
1597121 TATATTCT-TA-TATACT-TGTATATTTAATACTTATATATTTTATATTATATACT-TAGATACT
1 TATATT-TATATTATACTATATATATAT-ATA-TT-TATACTTTATATTATATA-TATAGATACT
*
1597182 TTATATTATATGATTATATACTT
61 TTATAGTATAT-A-TATATACTT
*
1597205 TATCTTTATAATTATACTATATATATATATATTTATACTTTATATTATTATATAT
1 TATATTTAT-ATTATACTATATATATATATATTTATACTTTATATTA-TATATAT
1597260 GTATATATAC
Statistics
Matches: 113, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
81 6 0.05
82 26 0.23
83 9 0.08
84 47 0.42
85 9 0.08
86 9 0.08
87 7 0.06
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (81 bp):
TATATTTATATTATACTATATATATATATATTTATACTTTATATTATATATATAGATACTTTATA
GTATATATATATACTT
Found at i:1597352 original size:15 final size:15
Alignment explanation
Indices: 1597332--1597362 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1597322 TTACACACAC
1597332 ACATATATATTGTAT
1 ACATATATATTGTAT
*
1597347 ACATATATATTTTAT
1 ACATATATATTGTAT
1597362 A
1 A
1597363 TTATATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (15 bp):
ACATATATATTGTAT
Found at i:1597362 original size:22 final size:23
Alignment explanation
Indices: 1597337--1597382 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1597327 CACACACATA
*
1597337 TATATTGTATACATATATA-TTT
1 TATATTATATACATATATACTTT
*
1597359 TATATTATATACTTATATACTTT
1 TATATTATATACATATATACTTT
1597382 T
1 T
1597383 GTCTCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATTATATACATATATACTTT
Found at i:1597478 original size:28 final size:25
Alignment explanation
Indices: 1597438--1597539 Score: 73
Period size: 26 Copynumber: 3.9 Consensus size: 25
1597428 TAAAAGTATG
1597438 TATATATATATATAATTTATAGTTTA
1 TATATATATATATAATTTATA-TTTA
*
1597464 TATATATACTCATATACTTTATATTTA
1 TATATATA-T-ATATAATTTATATTTA
* * **
1597491 AACTATATAATTTATAA-TTATACATA
1 TA-TATAT-ATATATAATTTATATTTA
*
1597517 -ATATATAAATATAAGTTGTATAT
1 TATATATATATATAA-TT-TATAT
1597540 ATTTAAATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
23 6 0.10
24 5 0.08
25 2 0.03
26 19 0.32
27 10 0.17
28 17 0.28
29 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (25 bp):
TATATATATATATAATTTATATTTA
Found at i:1597559 original size:21 final size:22
Alignment explanation
Indices: 1597513--1597561 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1597503 TATAATTATA
1597513 CATA-ATATATAAATATAAGTT
1 CATATATATATAAATATAAGTT
* *
1597534 -GTATATATTTAAATATAA-TT
1 CATATATATATAAATATAAGTT
1597554 CATATATA
1 CATATATA
1597562 ATTCATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
CATATATATATAAATATAAGTT
Found at i:1597562 original size:11 final size:11
Alignment explanation
Indices: 1597546--1597614 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
1597536 ATATATTTAA
1597546 ATATAATTCAT
1 ATATAATTCAT
1597557 ATATAATTCAT
1 ATATAATTCAT
**
1597568 AT-TAATAAACT
1 ATATAATTCA-T
*
1597579 ATATAATTTAT
1 ATATAATTCAT
*
1597590 ATATAGTT--T
1 ATATAATTCAT
*
1597599 A-ATAGTTCAT
1 ATATAATTCAT
1597609 ATATAA
1 ATATAA
1597615 AGTCTATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 7 0.15
11 27 0.57
12 5 0.11
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (11 bp):
ATATAATTCAT
Found at i:1597638 original size:2 final size:2
Alignment explanation
Indices: 1597631--1597795 Score: 87
Period size: 2 Copynumber: 83.0 Consensus size: 2
1597621 TAGTTCATGG
* *
1597631 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA 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 TA
* * * * *
1597673 TA GTT TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TT TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* *
1597714 TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA CTT TA TA TA TA CTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
1597754 TA TA TA -A TT TA TA TG TA GTT TA TA TA TA GTA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
1597796 ATTGTTTAAA
Statistics
Matches: 122, Mismatches: 24, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
1 9 0.07
2 104 0.85
3 9 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1597723 original size:5 final size:5
Alignment explanation
Indices: 1597713--1597737 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1597703 TAGTTTATTT
1597713 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
1597738 TACTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1597749 original size:11 final size:11
Alignment explanation
Indices: 1597733--1597791 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
1597723 ATATAATATA
1597733 ATATATACTTT
1 ATATATACTTT
1597744 ATATATACTTT
1 ATATATACTTT
1597755 ATATA-A-TTT
1 ATATATACTTT
* *
1597764 ATATGTAGTTT
1 ATATATACTTT
* *
1597775 ATATATAGTAT
1 ATATATACTTT
1597786 ATATAT
1 ATATAT
1597792 TATAATTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
9 7 0.16
10 2 0.05
11 34 0.79
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (11 bp):
ATATATACTTT
Found at i:1599462 original size:80 final size:80
Alignment explanation
Indices: 1599328--1599623 Score: 443
Period size: 80 Copynumber: 3.7 Consensus size: 80
1599318 CAATAAAAAG
* * * * *
1599328 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTAACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* *
1599392 TTAAGCACACAGCTAA
65 TTATGCACACAGCAAA
*
1599408 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1599473 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* *
1599488 GGGAACCAACCTAAGGATATACCTTGGTACCTACCCAAGATATCCTTAGGTCCGTAAGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1599553 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
1599568 CGGAACCAACCTAAGGATATGCCTTGGGGCCT-CCCTAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCC-AAGATATCCTTAGGTCCGTA
1599624 ATGACTTACA
Statistics
Matches: 199, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
79 3 0.02
80 186 0.93
81 10 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:1604259 original size:16 final size:17
Alignment explanation
Indices: 1604226--1604269 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1604216 CCGGTTTCGG
1604226 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
1604243 TTTTTAAAAAACC-G-T
1 TTTTAAAAAAACCGGTT
*
1604258 TTATAAAAAAAC
1 TTTTAAAAAAAC
1604270 TGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 1 0.04
17 12 0.50
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1605459 original size:32 final size:33
Alignment explanation
Indices: 1605363--1605461 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1605353 AACTCAACAT
* * *
1605363 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
1605396 AATCCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1605429 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1605461 A
1 A
1605462 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 12 0.20
33 49 0.80
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1607913 original size:19 final size:20
Alignment explanation
Indices: 1607884--1607922 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1607874 GTTAAAATAA
*
1607884 CCGGTTTAAAAAAATCCGAT
1 CCGGTTTAAAAAAAACCGAT
1607904 CCGG-TTAAAAAAAACCGAT
1 CCGGTTTAAAAAAAACCGAT
1607923 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
CCGGTTTAAAAAAAACCGAT
Found at i:1611627 original size:23 final size:23
Alignment explanation
Indices: 1611545--1611619 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1611535 TTTATTATTT
*
1611545 TATTAATTAGGATTCTAGTTTGT
1 TATTAATTAGGATTCTAGTTTGC
*
1611568 TATTAATTAGGATTCTAATTTGC
1 TATTAATTAGGATTCTAGTTTGC
1611591 TATT-ATGTAGGATTCTAGTTTGC
1 TATTAAT-TAGGATTCTAGTTTGC
1611614 TATTAA
1 TATTAA
1611620 ATACGATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 2 0.04
23 44 0.94
24 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (23 bp):
TATTAATTAGGATTCTAGTTTGC
Found at i:1611941 original size:25 final size:24
Alignment explanation
Indices: 1611910--1611966 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 24
1611900 TTTTATCTTT
*
1611910 GTATTTTATTTTAAATAGGTTTTA
1 GTATTTTAGTTTAAATAGGTTTTA
1611934 GGTATTTTAGTTTAAATAGGTTTTA
1 -GTATTTTAGTTTAAATAGGTTTTA
1611959 GTATTTTA
1 GTATTTTA
1611967 ATTAGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 8 0.26
25 23 0.74
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (24 bp):
GTATTTTAGTTTAAATAGGTTTTA
Found at i:1612749 original size:19 final size:19
Alignment explanation
Indices: 1612725--1612765 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1612715 TATTTATTAT
*
1612725 TTTATTATTTTCCT-TTTTA
1 TTTATTATTAT-CTATTTTA
1612744 TTTATTATTATCTATTTTA
1 TTTATTATTATCTATTTTA
1612763 TTT
1 TTT
1612766 TACTAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTATTATCTATTTTA
Found at i:1618220 original size:5 final size:5
Alignment explanation
Indices: 1618194--1618252 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
1618184 ACCCATTTCG
* * * *
1618194 TTTTA -TTT- TTTTA TTTCA TTTTA TTTTCG TTCTA TTTCA TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA -TTTTA
1618244 TTTTA TTTT
1 TTTTA TTTT
1618253 TAGAAAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 6 0.14
5 28 0.67
6 8 0.19
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1618221 original size:11 final size:11
Alignment explanation
Indices: 1618202--1618252 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
1618192 CGTTTTATTT
1618202 TTTTA-TTTCA
1 TTTTATTTTCA
*
1618212 TTTTATTTTCG
1 TTTTATTTTCA
*
1618223 TTCTA-TTTCA
1 TTTTATTTTCA
*
1618233 TTTTATTTTTA
1 TTTTATTTTCA
1618244 TTTTATTTT
1 TTTTATTTT
1618253 TAGAAAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 13 0.38
11 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:1618230 original size:16 final size:16
Alignment explanation
Indices: 1618202--1618252 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1618192 CGTTTTATTT
*
1618202 TTTTATTTC-ATTTTA
1 TTTTAGTTCTATTTTA
* *
1618217 TTTTCGTTCTATTTCA
1 TTTTAGTTCTATTTTA
* *
1618233 TTTTATTTTTATTTTA
1 TTTTAGTTCTATTTTA
1618249 TTTT
1 TTTT
1618253 TAGAAAACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTAGTTCTATTTTA
Found at i:1618231 original size:21 final size:18
Alignment explanation
Indices: 1618188--1618242 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 18
1618178 GAGGCAACCC
*
1618188 ATTTCGTTTTATTTTTTT
1 ATTTCATTTTATTTTTTT
1618206 ATTTCATTTTATTTTCGTTCT
1 ATTTCATTTTATTTT--TT-T
1618227 ATTTCATTTTATTTTT
1 ATTTCATTTTATTTTT
1618243 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 14 0.42
19 1 0.03
20 2 0.06
21 16 0.48
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTCATTTTATTTTTTT
Found at i:1618250 original size:21 final size:21
Alignment explanation
Indices: 1618202--1618251 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1618192 CGTTTTATTT
*
1618202 TTTTATTTCATTTTATTTTCG
1 TTTTATTTCATTTTATTTTCA
* *
1618223 TTCTATTTCATTTTATTTTTA
1 TTTTATTTCATTTTATTTTCA
1618244 TTTTATTT
1 TTTTATTT
1618252 TTAGAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTCATTTTATTTTCA
Found at i:1618253 original size:11 final size:11
Alignment explanation
Indices: 1618194--1618254 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
1618184 ACCCATTTCG
*
1618194 TTTTATTTTTT
1 TTTTATTTTAT
1618205 TATTTCATTTTAT
1 T-TTT-ATTTTAT
** *
1618218 TTTCGTTCTA-
1 TTTTATTTTAT
*
1618228 TTTCATTTTAT
1 TTTTATTTTAT
1618239 TTTTATTTTAT
1 TTTTATTTTAT
1618250 TTTTA
1 TTTTA
1618255 GAAAACTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 8 0.20
11 20 0.50
12 5 0.12
13 7 0.17
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:1618279 original size:15 final size:15
Alignment explanation
Indices: 1618261--1618303 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1618251 TTTAGAAAAC
*
1618261 TTTATTTTCTTTCTA
1 TTTATTTTATTTCTA
1618276 TTTATTTTATTT-TA
1 TTTATTTTATTTCTA
* *
1618290 ATTATTTTTTTTCT
1 TTTATTTTATTTCT
1618304 GAACAGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTATTTCTA
Found at i:1619979 original size:19 final size:19
Alignment explanation
Indices: 1619955--1619992 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1619945 ATTTGTATTT
*
1619955 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
1619974 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
1619993 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:1620002 original size:43 final size:42
Alignment explanation
Indices: 1619954--1620084 Score: 102
Period size: 43 Copynumber: 3.3 Consensus size: 42
1619944 TATTTGTATT
1619954 TTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATT-AGTTTTAGGATA
* * *
1619997 TTATTTT-TATA---TTT--TA-TCT--TT-GTTTTAGGTATT
1 TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGG-ATA
* * **
1620030 TTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATAATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATTA-GTTTTAGGATA
1620073 TTATTTTAAATA
1 TTATTTTAAATA
1620085 TTATTTTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
32 8 0.12
33 8 0.12
34 5 0.08
36 2 0.03
37 5 0.08
39 5 0.08
40 2 0.03
42 5 0.08
43 20 0.31
44 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (42 bp):
TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGGATA
Found at i:1620827 original size:15 final size:18
Alignment explanation
Indices: 1620803--1620855 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
1620793 CTATTACTAT
1620803 TTAT-TATTTTATTATT-
1 TTATCTATTTTATTATTA
1620819 TT-TCT-TTTTATTTATTA
1 TTATCTATTTTA-TTATTA
1620836 TTATCTATTTTATT-TTA
1 TTATCTATTTTATTATTA
1620853 TTA
1 TTA
1620856 AATCTTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.19
16 8 0.25
17 8 0.25
18 5 0.16
19 5 0.16
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATCTATTTTATTATTA
Found at i:1620834 original size:19 final size:20
Alignment explanation
Indices: 1620806--1620855 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1620796 TTACTATTTA
*
1620806 TTATTTTATTATTTTTCT-TT
1 TTATTTTATTA-TTATCTATT
1620826 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
1620845 TTATTTTATTA
1 TTATTTTATTA
1620856 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:1623313 original size:28 final size:29
Alignment explanation
Indices: 1623253--1623314 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
1623243 GCTATTCTGG
**
1623253 TAATTATTTGGAAAAGGGTGTCATTCTGG
1 TAATTATTTGGAAAAGGGTGTCATTCTCA
* * *
1623282 TAATTATTTTGAAAA-GGTGTTATTTTCA
1 TAATTATTTGGAAAAGGGTGTCATTCTCA
1623310 TAATT
1 TAATT
1623315 GTAAAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (29 bp):
TAATTATTTGGAAAAGGGTGTCATTCTCA
Found at i:1623416 original size:29 final size:27
Alignment explanation
Indices: 1623325--1623416 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 27
1623315 GTAAAAAAAA
*
1623325 TCGTAATTTTTTAAAAAAATGATATTTT
1 TCGTAATTTTTTAAAAATATGATA-TTT
* *
1623353 TAGTAATTATTTTGAAAATAGTGATATTT
1 TCGTAATT-TTTTAAAAATA-TGATATTT
* *
1623382 TGGTAATTGTTTTAAAAATGATGTTATTT
1 TCGTAATT-TTTTAAAAAT-ATGATATTT
1623411 TCGTAA
1 TCGTAA
1623417 AATGGTTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.13
29 40 0.75
30 6 0.11
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (27 bp):
TCGTAATTTTTTAAAAATATGATATTT
Found at i:1631215 original size:20 final size:20
Alignment explanation
Indices: 1631190--1631227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1631180 CCCCCTTTGA
*
1631190 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1631210 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1631228 TGGGGTTCTA
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:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1631633 original size:25 final size:26
Alignment explanation
Indices: 1631584--1631633 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1631574 AGAATTTTTC
*
1631584 AAAAAAATTTTTAAATTTTCGAAATA
1 AAAAAAATTGTTAAATTTTCGAAATA
1631610 AAAAAAATGTGTT-AATTTTC-AAAT
1 AAAAAAAT-TGTTAAATTTTCGAAAT
1631634 TATTGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 15 0.68
27 3 0.14
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (26 bp):
AAAAAAATTGTTAAATTTTCGAAATA
Done.