Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001692.1 Hibiscus syriacus cultivar Beakdansim tig00003380_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: 59239
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:684 original size:20 final size:19
Alignment explanation
Indices: 628--693 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 19
618 GAGACACTAG
*
628 TTTTTTTTTTTTTCATTTATTA
1 TTTTATTTTTTTT-A-TTA-TA
** *
650 TTTTATTACTATTATATATA
1 TTTTATTTTTTTTAT-TATA
670 TTTTATTTTTTTTATTAATA
1 TTTTATTTTTTTTATT-ATA
690 TTTT
1 TTTT
694 TATTATTACA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.03
20 22 0.63
21 3 0.09
22 9 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTTTTTTATTATA
Found at i:2014 original size:35 final size:36
Alignment explanation
Indices: 1971--2041 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
1961 ACTATTATTA
1971 TTATTTAGTCATGTAAATATATATATAAATA-ATAT
1 TTATTTAGTCATGTAAATATATATATAAATATATAT
* *
2006 TTATTTAGTCATGTAAATATATCTATATATATATAT
1 TTATTTAGTCATGTAAATATATATATAAATATATAT
2042 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (36 bp):
TTATTTAGTCATGTAAATATATATATAAATATATAT
Found at i:2034 original size:2 final size:2
Alignment explanation
Indices: 2022--2052 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2012 AGTCATGTAA
*
2022 AT AT AT CT 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
2053 AATAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5350 original size:113 final size:111
Alignment explanation
Indices: 5148--5477 Score: 447
Period size: 113 Copynumber: 3.0 Consensus size: 111
5138 CAGAAAAGAT
*
5148 TCAAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTTGATGGATCAACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
*
5213 AGAAGGAAGAGGAAGTTCAAAATGAGAAGAATTTGTTCAACCTTTCGC
66 AGAAGGAAGA--AAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGC
* *
5261 TCGAATTCATCACTTGATGGATCAACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATTCATCACTTGATGGATCAACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
5326 AGAAGGAAGAATAAATTCATAATGAAAAGAATTTGTTCAACCTTTCGC
66 AGAAGGAAG-A-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGC
* * * * *
5374 TCAAATTCATCACTCGATGGATCATCATT-TCCAAAG-AAAG-TCATAATGAGAAGAACTTATCT
1 TCAAATTCATCACTTGATGGATCAACATTGT-C-AGGTAGAGTTCATAATGAGAAGAACTCATCT
* *
5436 G-AG-AGGAAG-AAGTTCATAATGAGAAGAACTTGTTCAGCCTTT
64 GAAGAAGGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
5478 TGCATTACTC
Statistics
Matches: 196, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
107 29 0.15
110 6 0.03
111 2 0.01
112 22 0.11
113 134 0.68
114 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
TCAAATTCATCACTTGATGGATCAACATTGTCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTCGC
Found at i:5952 original size:3 final size:3
Alignment explanation
Indices: 5946--6005 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
5936 TTTTTTCATT
* *
5946 TTA TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
5991 ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
6006 CAAACAGGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17483 original size:23 final size:23
Alignment explanation
Indices: 17431--17484 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
17421 CAATCTTATA
*
17431 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
17454 CGACACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
17477 TGGCACTT
1 TGGCACTT
17485 TGATGCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:17491 original size:23 final size:23
Alignment explanation
Indices: 17442--17491 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17432 GGCACTACGG
*
17442 TGCAATTCTACGCGACACTTCGG
1 TGCAATTCTACGCGACACTTCGA
* * *
17465 TGCAATTCTACGTGGCACTTTGA
1 TGCAATTCTACGCGACACTTCGA
17488 TGCA
1 TGCA
17492 TTTATACGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCAATTCTACGCGACACTTCGA
Found at i:18742 original size:3 final size:3
Alignment explanation
Indices: 18734--18770 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
18724 AATATAAATT
*
18734 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
18771 ATAGGCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:18758 original size:19 final size:19
Alignment explanation
Indices: 18734--18773 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
18724 AATATAAATT
*
18734 TAATAATAATAATAATAAA
1 TAATAATAATAAAAATAAA
18753 TAATAATAATAAAAATAAA
1 TAATAATAATAAAAATAAA
18772 TA
1 TA
18774 GGCAAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAATAATAAAAATAAA
Found at i:19004 original size:39 final size:39
Alignment explanation
Indices: 18949--19754 Score: 676
Period size: 39 Copynumber: 20.5 Consensus size: 39
18939 AGGTTGAATA
*
18949 AGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* ** * *
18988 AGTTCTTCAAATTATGACCTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * * *
19027 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGATG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * * *
19066 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGACGTT
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGA--TG
*** * * *** ***** * *
19107 A-TTCTATCTCCTTCTACCGATAGAATCAAGTAAAAGGTTGA-ATA
1 AGTTCT-TC-AGAT-TA-TGA-A-ATTCTTCT-TCCTCTTCAGATG
*
19151 AGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* *
19190 AGTTCTTCAAACTATGAAATTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
*
19229 AGTTCTTCAGATTATG-AACTCATTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * *
19268 AGTTCTTCATATTAT-AAACTCCTTTTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAAA-TTCTTCTTCCTCTTCAGATG
* *
19307 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * *
19346 AGTTCTTCAGATTATG-AACTCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * *
19385 AGTTCTTCAGATTATG-AACTCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * * * *
19424 AGTTCTTCAGATTATGAACTCCTTCTTCCTTTTCATACG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * * * * *
19463 AGTTCTTCAGACTATGAACTCCTTCTCCCTTTTCAGACG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * * * *
19502 AGTTCTTCAGATTATG-AACTCTTTTTTTCTTTTCAGACG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * * * **
19541 AGTTCTTCAGATTGTGAACTCCTTTTTCCTCTTCAGACA
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* *
19580 AGTTCTTCAGATTATG-AACTCATTCTTCCTCTTCAGAAG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * *
19619 AGTTCTTCAGATTATG-AACTCATTTTTCCTCTTCATATG
1 AGTTCTTCAGATTATGAAATTC-TTCTTCCTCTTCAGATG
* * * * *
19658 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGACG
1 AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
* * * *
19697 AGTTCTTCAGATTATGAACTCCCTTTTTCCTCTTCAGATA
1 AGTTCTTCAGATTATGAAAT-TCTTCTTCCTCTTCAGATG
19737 AGTTCTTCAGATTATGAA
1 AGTTCTTCAGATTATGAA
19755 CTCCTTTTGG
Statistics
Matches: 639, Mismatches: 106, Indels: 43
0.81 0.13 0.05
Matches are distributed among these distances:
38 14 0.02
39 549 0.86
40 48 0.08
41 6 0.01
42 3 0.00
43 2 0.00
44 6 0.01
45 5 0.01
46 3 0.00
47 3 0.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (39 bp):
AGTTCTTCAGATTATGAAATTCTTCTTCCTCTTCAGATG
Found at i:19080 original size:78 final size:78
Alignment explanation
Indices: 18949--19762 Score: 916
Period size: 78 Copynumber: 10.3 Consensus size: 78
18939 AGGTTGAATA
* * * * * *
18949 AGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCAAATTATGACCTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
19014 TCCTCTTCAGACG
66 TCCTCTTCAGACG
*
19027 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
*
19092 TCCTCTTTAGACG
66 TCCTCTTCAGACG
* *** ****** * * *
19105 TTATTCTATCTCCTTCTACCGA-TA-GAA-TCAAGTAAAAGGTTGA-ATAAGTTCTTCAGACTAT
1 --A----GT-T-CTTC-A--GATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTAT
* * *
19166 GAAATTCTTCTTCCTCTTCAGATG
55 GAACTCCTTCTTCCTCTTCAGACG
* * * * * *
19190 AGTTCTTCAAACTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
*
19255 TCCTCTTCAGATG
66 TCCTCTTCAGACG
* * *
19268 AGTTCTTCATATTATAAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTTCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
19333 TCCTCTTCAGACG
66 TCCTCTTCAGACG
* * * *
19346 AGTTCTTCAGATTATGAACTCTTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
19411 TCCTCTTCAGACG
66 TCCTCTTCAGACG
* * * * *
19424 AGTTCTTCAGATTATGAACTCCTTCTTCCTTTTCATACGAGTTCTTCAGACTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
* *
19489 CCCTTTTCAGACG
66 TCCTCTTCAGACG
* * * * * *
19502 AGTTCTTCAGATTATGAACTCTTTTTTTCTTTTCAGACGAGTTCTTCAGATTGTGAACTCCTTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
*
19567 TCCTCTTCAGACA
66 TCCTCTTCAGACG
* * * * *
19580 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGAAGAGTTCTTCAGATTATGAACTCATTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
* *
19645 TCCTCTTCATATG
66 TCCTCTTCAGACG
* * *
19658 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCCTTT
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACT-CCTTC
**
19723 TTCCTCTTCAGATA
65 TTCCTCTTCAGACG
19737 AGTTCTTCAGATTATGAACTCCTTTT
1 AGTTCTTCAGATTATGAACTCCTTTT
19763 GGAAATGTTT
Statistics
Matches: 624, Mismatches: 96, Indels: 31
0.83 0.13 0.04
Matches are distributed among these distances:
74 1 0.00
75 2 0.00
76 4 0.01
77 8 0.01
78 508 0.81
79 43 0.07
80 1 0.00
83 1 0.00
84 1 0.00
85 37 0.06
86 10 0.02
87 4 0.01
88 2 0.00
89 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (78 bp):
AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
TCCTCTTCAGACG
Found at i:19270 original size:202 final size:201
Alignment explanation
Indices: 18910--19300 Score: 647
Period size: 202 Copynumber: 1.9 Consensus size: 201
18900 GATGTTGTTT
*
18910 TATCTCCTTCTGCAATAGAATCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGAAATTCTTCT
1 TATCTCCTTCTCCAATAGAATCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGAAATTCTTCT
* **
18975 TCCTCTTCAGATGAGTTCTTCAAATTATGACCTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATT
66 TCCTCTTCAGATGAGTTCTTCAAACTATGAAATCCTTCTTCCTCTTCAGACGAGTTCTTCAGATT
* * * *
19040 ATGAACTCCTTTTTTCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGACG
131 ATGAACTCATTCTTCCTCTTCAGATGAGTTCTTCAGATTATAAACTCCTTCTTCCTCTTTAGACG
19105 TTATTC
196 TTATTC
* *
19111 TATCTCCTTCTACCGATAGAATCAAGTAAAAGGTTGAATAAGTTCTTCAGACTATGAAATTCTTC
1 TATCTCCTTCT-CCAATAGAATCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGAAATTCTTC
* *
19176 TTCCTCTTCAGATGAGTTCTTCAAACTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCAGAT
65 TTCCTCTTCAGATGAGTTCTTCAAACTATGAAATCCTTCTTCCTCTTCAGACGAGTTCTTCAGAT
* *
19241 TATGAACTCATTCTTCCTCTTCAGATGAGTTCTTCATATTATAAACTCCTTTTTCCTCTT
130 TATGAACTCATTCTTCCTCTTCAGATGAGTTCTTCAGATTATAAACTCCTTCTTCCTCTT
19301 CAGATGAGTT
Statistics
Matches: 175, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
201 11 0.06
202 164 0.94
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (201 bp):
TATCTCCTTCTCCAATAGAATCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGAAATTCTTCT
TCCTCTTCAGATGAGTTCTTCAAACTATGAAATCCTTCTTCCTCTTCAGACGAGTTCTTCAGATT
ATGAACTCATTCTTCCTCTTCAGATGAGTTCTTCAGATTATAAACTCCTTCTTCCTCTTTAGACG
TTATTC
Found at i:19323 original size:117 final size:117
Alignment explanation
Indices: 18949--19762 Score: 945
Period size: 117 Copynumber: 6.9 Consensus size: 117
18939 AGGTTGAATA
* * * * * * *
18949 AGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCAAATTATGACCTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
*
19014 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGATG
66 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* *
19066 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGACGTTATTCTATCTCCTTCTACCGA-TA-
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG--A----GT-T-CTTC-A--GATTAT
* ****** * ** * * * *
19129 GAA-TCAAGT-AAAAGGTTGA-ATAAGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATG
55 GAACTC-ATTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* * * * *
19190 AGTTCTTCAAACTATGAAATTCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * *
19255 TCCTCTTCAGATGAGTTCTTCATATTATAAACTCCTTTTTCCTCTTCAGATG
66 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* * *
19307 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* *
19372 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTTTCCTCTTCAGACG
66 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* * * *
19424 AGTTCTTCAGATTATGAACTCCTTCTTCCTTTTCATACGAGTTCTTCAGACTATGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * * * * *
19489 CCCTTTTCAGACGAGTTCTTCAGATTATGAACTCTTTTTTTCTTTTCAGACG
66 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* * *
19541 AGTTCTTCAGATTGTGAACTCCTTTTTCCTCTTCAGACAAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
* * *
19606 TCCTCTTCAGAAGAGTTCTTCAGATTATGAACTCATTTTTCCTCTTCATATG
66 TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
* * * *
19658 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCCTTT
1 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACT-CATTC
**
19723 TTCCTCTTCAGATAAGTTCTTCAGATTATGAACTCCTTTT
65 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTT
19763 GGAAATGTTT
Statistics
Matches: 589, Mismatches: 90, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
113 2 0.00
114 2 0.00
115 6 0.01
116 9 0.02
117 441 0.75
118 41 0.07
119 1 0.00
122 1 0.00
123 1 0.00
124 69 0.12
125 9 0.02
126 4 0.01
127 2 0.00
128 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (117 bp):
AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCATTCT
TCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGATG
Found at i:19761 original size:39 final size:39
Alignment explanation
Indices: 19151--19762 Score: 837
Period size: 39 Copynumber: 15.7 Consensus size: 39
19141 AGGTTGAATA
* * * * *
19151 AGTTCTTCAGACTATGAAATTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * * * * *
19190 AGTTCTTCAAACTATGAAATTCTTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19229 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19268 AGTTCTTCATATTATAAACTCCTTTTTCCTCTTCAGATG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* *
19307 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
*
19346 AGTTCTTCAGATTATGAACTCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
*
19385 AGTTCTTCAGATTATGAACTCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19424 AGTTCTTCAGATTATGAACTCCTTCTTCCTTTTCATACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * * *
19463 AGTTCTTCAGACTATGAACTCCTTCTCCCTTTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19502 AGTTCTTCAGATTATGAACTCTTTTTTTCTTTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* *
19541 AGTTCTTCAGATTGTGAACTCCTTTTTCCTCTTCAGACA
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19580 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGAAG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
* * *
19619 AGTTCTTCAGATTATGAACTCATTTTTCCTCTTCATATG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
*
19658 AGTTCTTCAGATTATGAACTCCTTTTTTCTCTTCAGACG
1 AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
**
19697 AGTTCTTCAGATTATGAACTCCCTTTTTCCTCTTCAGATA
1 AGTTCTTCAGATTATGAACT-CCTTTTTCCTCTTCAGACG
19737 AGTTCTTCAGATTATGAACTCCTTTT
1 AGTTCTTCAGATTATGAACTCCTTTT
19763 GGAAATGTTT
Statistics
Matches: 522, Mismatches: 50, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
39 486 0.93
40 36 0.07
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACG
Found at i:20075 original size:45 final size:45
Alignment explanation
Indices: 19811--20344 Score: 618
Period size: 45 Copynumber: 11.7 Consensus size: 45
19801 TTGCTATTTC
* * * *
19811 AAAACATCCGGCACTGAAGATCTTATGGATGACCCGAAGACTTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAG--GTTTTG
* * * *
19858 AAAACTTCCTGCACTGTAGGTCTTATGGATGACCCGAAGACTTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAG--GTTTTG
* * *
19905 AAAACATCTTGCACTGTAGGTCTTATGGATGACCCGAAGGCTCTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGG-T-TTTG
* * *
19952 AAGACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGG--TTTTG
* * * * *
19999 AAAATATCCTGCACTGTAGGTATTATGGATGACCCGAAGGCTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* * *
20044 AAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGATTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* * *
20089 AAAACATCCTGCACTGAAGGTCTTACAGATGACTCAAAGGTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* *
20134 AAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* *
20179 AAAACATCATGCACTGAAGGTCTTATAGATAACCCGAAGGTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* * * *
20224 AAAATATCATGCACTGTAGGTCTTATAGATGACCCGAAGGTTTTA
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* * * * * *
20269 AAAATATCATGCACTGTAGGTCTTATGGATTACCCAAAGGTTTTG
1 AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
* * *
20314 AAAACATCATACACTGAAGGTCTTACAGATG
1 AAAACATCCTGCACTGAAGGTCTTATAGATG
20345 TGGGAAATAG
Statistics
Matches: 439, Mismatches: 45, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
45 274 0.62
46 1 0.00
47 163 0.37
48 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
AAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTG
Found at i:20933 original size:22 final size:22
Alignment explanation
Indices: 20908--20967 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
20898 AATAAAGCTT
20908 TCATCTTTGAAAAGAT-AATCTA
1 TCATCTTTGAAAA-ATGAATCTA
*
20930 TCATCTTTGAAGAATGAATCTA
1 TCATCTTTGAAAAATGAATCTA
*
20952 TCATCTTTGAAGAATG
1 TCATCTTTGAAAAATG
20968 TAGATGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 2 0.06
22 34 0.94
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAATGAATCTA
Found at i:24049 original size:20 final size:20
Alignment explanation
Indices: 24026--24086 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 20
24016 TTGATTCAAT
24026 TTTTTTCTTCTTTCATTTTC
1 TTTTTTCTTCTTTCATTTTC
* *
24046 TTTTTTTTTCTTTC-TTCTC
1 TTTTTTCTTCTTTCATTTTC
* *
24065 -TTTTTCATCTCT-ATTTTC
1 TTTTTTCTTCTTTCATTTTC
24083 TTTT
1 TTTT
24087 CTGATGAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 13 0.39
19 7 0.21
20 13 0.39
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTCTTCTTTCATTTTC
Found at i:24060 original size:24 final size:24
Alignment explanation
Indices: 24025--24070 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
24015 CTTGATTCAA
24025 TTTTTTTCTTCTT-TCATTTTCTT
1 TTTTTTTCTTCTTCTCATTTTCTT
*
24048 TTTTTTTCTTTCTTCTCTTTTTC
1 TTTTTTTC-TTCTTCTCATTTTC
24071 ATCTCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTCTTCTTCTCATTTTCTT
Found at i:26516 original size:14 final size:14
Alignment explanation
Indices: 26497--26629 Score: 57
Period size: 14 Copynumber: 9.4 Consensus size: 14
26487 AATGTAATTG
* *
26497 TGCAAAGATGTAAA
1 TGCAAAAATGAAAA
26511 TGCAAAAATGAAAA
1 TGCAAAAATGAAAA
* *
26525 TG--TAAATAAAAA
1 TGCAAAAATGAAAA
* *
26537 CGTAAAAATGCAAAGA
1 TGCAAAAATG-AAA-A
**
26553 T--ACGAATGCAAAA
1 TGCAAAAATG-AAAA
26566 TG--AAAATGCAAAGA
1 TGCAAAAATG-AAA-A
26580 TGC-AAAATGAAAA
1 TGCAAAAATGAAAA
26593 TGCAAAAAATGTAGAAA
1 TGC-AAAAATG-A-AAA
26610 TGCAAAAAT-AAGAA
1 TGCAAAAATGAA-AA
26624 TGCAAA
1 TGCAAA
26630 TTGCGCAATG
Statistics
Matches: 95, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
12 9 0.09
13 15 0.16
14 42 0.44
15 15 0.16
16 8 0.08
17 6 0.06
ACGTcount: A:0.59, C:0.08, G:0.17, T:0.17
Consensus pattern (14 bp):
TGCAAAAATGAAAA
Found at i:26575 original size:13 final size:14
Alignment explanation
Indices: 26557--26599 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
26547 CAAAGATACG
26557 AATGCAAAATG-AA
1 AATGCAAAATGCAA
26570 AATGCAAAGATGCAA
1 AATGCAAA-ATGCAA
26585 AATG-AAAATGCAA
1 AATGCAAAATGCAA
26598 AA
1 AA
26600 AATGTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.57
14 6 0.21
15 6 0.21
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.14
Consensus pattern (14 bp):
AATGCAAAATGCAA
Found at i:26582 original size:21 final size:21
Alignment explanation
Indices: 26558--26598 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
26548 AAAGATACGA
26558 ATGCAAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
26579 ATGCAAAATGAAAATGCAAA
1 ATGCAAAATGAAAATGCAAA
26599 AAATGTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (21 bp):
ATGCAAAATGAAAATGCAAAG
Found at i:26592 original size:27 final size:28
Alignment explanation
Indices: 26541--26599 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
26531 TAAAAACGTA
*
26541 AAAATGCAAAGATACGAATGCAAAATG-
1 AAAATGCAAAGATACAAATGCAAAATGC
*
26568 AAAATGCAAAGATGCAAAATG-AAAATGC
1 AAAATGCAAAGATAC-AAATGCAAAATGC
26596 AAAA
1 AAAA
26600 AATGTAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (28 bp):
AAAATGCAAAGATACAAATGCAAAATGC
Found at i:26601 original size:15 final size:15
Alignment explanation
Indices: 26583--26629 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
26573 GCAAAGATGC
26583 AAAATGAAAATGCAA
1 AAAATGAAAATGCAA
26598 AAAATGTAGAAATGC-A
1 AAAATG-A-AAATGCAA
26614 AAAAT-AAGAATGCAA
1 AAAATGAA-AATGCAA
26629 A
1 A
26630 TTGCGCAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.04
14 6 0.21
15 8 0.29
16 7 0.25
17 6 0.21
ACGTcount: A:0.64, C:0.06, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAATGAAAATGCAA
Found at i:26618 original size:8 final size:7
Alignment explanation
Indices: 26557--26599 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
26547 CAAAGATACG
26557 AATGCAA
1 AATGCAA
26564 AATG-AA
1 AATGCAA
26570 AATGCAA
1 AATGCAA
26577 AGATGCAA
1 A-ATGCAA
26585 AATG-AA
1 AATGCAA
26591 AATGCAA
1 AATGCAA
26598 AA
1 AA
26600 AATGTAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.36
7 14 0.42
8 7 0.21
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.14
Consensus pattern (7 bp):
AATGCAA
Found at i:30432 original size:3 final size:3
Alignment explanation
Indices: 30424--30476 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
30414 AATATAAATT
30424 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
30471 AAA TAA
1 TAA TAA
30477 ATGGGCAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:30867 original size:12 final size:12
Alignment explanation
Indices: 30850--30874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30840 AATGTCATGC
30850 TTTATATATATA
1 TTTATATATATA
30862 TTTATATATATA
1 TTTATATATATA
30874 T
1 T
30875 ATGTGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATATATA
Found at i:33108 original size:65 final size:65
Alignment explanation
Indices: 33036--33197 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 65
33026 AATTAAATTT
* * *
33036 AACATCGAATGTC-TTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTAT
1 AACATCGAATG-CATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-T
33098 GAA
64 G-A
* * * *
33101 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATTCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
*
33165 AACATCGAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
33198 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
64 33 0.39
65 49 0.58
66 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:33195 original size:17 final size:19
Alignment explanation
Indices: 33167--33215 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
33157 TATTTTGAAA
33167 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
33185 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
33204 CACCGATGCACT
1 CATCGATGCACT
33216 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:41793 original size:65 final size:64
Alignment explanation
Indices: 41715--41869 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 64
41705 AATTAAATTG
* * * *
41715 AACATCGACTGCATTTCATGCATCGATACACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATACAC-CAGCCATGCACCGATGCACTCAGGATATTT-TG
41778 AA
64 -A
* * * * * *
41780 AACATCAAATGCATTTGATGTATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATACACCAGCCATGCACCGATGCACTCAGGATATTTTGA
*
41844 AACATCGAATGCACTTGATGCATCGA
1 AACATCGAATGCATTTGATGCATCGA
41870 CGCACTCTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 25 0.33
65 47 0.63
66 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATACACCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:53769 original size:21 final size:22
Alignment explanation
Indices: 53726--53769 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
53716 CAACAATGAT
*
53726 CTATTTTTAGCTTAAATAATTAA
1 CTATTTTTA-CTTAAAGAATTAA
*
53749 CTATTTTTA-TTAAAGATTTAA
1 CTATTTTTACTTAAAGAATTAA
53770 AAGATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
CTATTTTTACTTAAAGAATTAA
Found at i:53835 original size:22 final size:22
Alignment explanation
Indices: 53791--53835 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53781 ATACAATATG
* *
53791 ATTTTAGCTCTTAAATTTAATT
1 ATTTTAACTCTTAAATCTAATT
*
53813 ATTTTAACTCTTAAATCTCATT
1 ATTTTAACTCTTAAATCTAATT
53835 A
1 A
53836 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTAACTCTTAAATCTAATT
Done.