Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009442.1 Hibiscus syriacus cultivar Beakdansim tig00113506_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: 81879
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8187 original size:20 final size:19
Alignment explanation
Indices: 8158--8198 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
8148 TACATTCGAA
8158 ATATGGAGTGTATCGATAC
1 ATATGGAGTGTATCGATAC
*
8177 ATATAGGAGTGTATCGGTAC
1 ATAT-GGAGTGTATCGATAC
8197 AT
1 AT
8199 CCCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (19 bp):
ATATGGAGTGTATCGATAC
Found at i:8627 original size:23 final size:24
Alignment explanation
Indices: 8595--8640 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
8585 ATGAAGAGAG
8595 AAAATTAAAATAAGGAAA-TAAAAT
1 AAAATTAAAATAA-GAAATTAAAAT
8619 AAAA-TAAAATAAGAAATTAAAA
1 AAAATTAAAATAAGAAATTAAAA
8641 AGAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAATTAAAATAAGAAATTAAAAT
Found at i:16720 original size:24 final size:24
Alignment explanation
Indices: 16693--16738 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16683 GTCAATTTCC
16693 TTTTACTAATATTATTAGGTTAGA
1 TTTTACTAATATTATTAGGTTAGA
* **
16717 TTTTAGTTGTATTATTAGGTTA
1 TTTTACTAATATTATTAGGTTA
16739 ATTATTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.54
Consensus pattern (24 bp):
TTTTACTAATATTATTAGGTTAGA
Found at i:16753 original size:24 final size:24
Alignment explanation
Indices: 16701--16754 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
16691 CCTTTTACTA
16701 ATATTATTAGGTTAGATTTTAGTT
1 ATATTATTAGGTTAGATTTTAGTT
*
16725 GTATTATTAGGTTA-ATTATT-GATT
1 ATATTATTAGGTTAGATT-TTAG-TT
16749 ATATTA
1 ATATTA
16755 ATATTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (24 bp):
ATATTATTAGGTTAGATTTTAGTT
Found at i:18240 original size:118 final size:118
Alignment explanation
Indices: 18031--18254 Score: 306
Period size: 118 Copynumber: 1.9 Consensus size: 118
18021 CCTAAACTTT
* ** *
18031 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTACAATGATTGAGGGACCATTTTAATTCTTT
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
* *
18096 GACTAAATAATTGGTTAAAATGAATTATGATTAATATTAGACACTTTAGTCCC
66 GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
* * ** * * *
18149 TTAATTAGGGAATGATTTGATTTGGCTCTCGCATTAAAATGCTCAAGGGACCATTTTGATTATTC
1 TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATT-
*
18214 T-ACTTAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
65 TGACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGA
18255 GCTTTCATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
118 90 0.99
119 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (118 bp):
TTAATTAGGAAATAATTCAATTTGGCTCTAGCATTAAAATGATCAAGGGACCATTTTAATTATTT
GACTAAATAATTGGTTAAAATAAATTAAGATTAATATTAGACACTTTAGTCCC
Found at i:21066 original size:35 final size:35
Alignment explanation
Indices: 21024--21093 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
21014 GCGATAATGC
*
21024 CTAAGGTGATGATGTTGAATGAAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
* *
21059 CTAAGGTGAGGATGTTGAGTGCAATAAAGGTGATA
1 CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
21094 ACACTTAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.31, T:0.27
Consensus pattern (35 bp):
CTAAGGTGAGGATGTTGAATGAAATAAAGGTGATA
Found at i:22788 original size:34 final size:33
Alignment explanation
Indices: 22712--22844 Score: 122
Period size: 34 Copynumber: 3.8 Consensus size: 33
22702 ATTGTTTTCC
* * *
22712 TTAAAACATATTTTATCTCAATTGAGATTATTTTTT
1 TTAAAATATATCTTATCTCACTTGAG---ATTTTTT
* *
22748 TCTAAAATAGATCTTATTTCACTTGAGATTTTTT
1 T-TAAAATATATCTTATCTCACTTGAGATTTTTT
* *
22782 ATTAAAACATACCTTATCTCACTTGAGATTGTTTT
1 -TTAAAATATATCTTATCTCACTTGAGATT-TTTT
* *
22817 CTTAAAATATATTTTATCTCATTTGAGA
1 -TTAAAATATATCTTATCTCACTTGAGA
22845 ATTGAGATTT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
34 31 0.39
35 28 0.35
36 1 0.01
37 20 0.25
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (33 bp):
TTAAAATATATCTTATCTCACTTGAGATTTTTT
Found at i:22834 original size:35 final size:35
Alignment explanation
Indices: 22650--22844 Score: 185
Period size: 36 Copynumber: 5.5 Consensus size: 35
22640 TCACTAAAGT
* *
22650 TTTTATCTCGCTTGAGATTGTTTTTCTTAAAGCATA
1 TTTTATCTCACTTGAGATTG-TTTTCTTAAAACATA
* ** *
22686 CTTTATCTTGCTTAAGATTGTTTTCCTTAAAACATA
1 TTTTATCTCACTTGAGATTGTTTT-CTTAAAACATA
* * * * *
22722 TTTTATCTCAATTGAGATTATTTTTTTCTAAAATAGA
1 TTTTATCTCACTTGAGATT-GTTTTCT-TAAAACATA
* * *
22759 TCTTATTTCACTTGAGATT-TTTTATTAAAACATA
1 TTTTATCTCACTTGAGATTGTTTTCTTAAAACATA
** *
22793 CCTTATCTCACTTGAGATTGTTTTCTTAAAATATA
1 TTTTATCTCACTTGAGATTGTTTTCTTAAAACATA
*
22828 TTTTATCTCATTTGAGA
1 TTTTATCTCACTTGAGA
22845 ATTGAGATTT
Statistics
Matches: 129, Mismatches: 26, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
34 24 0.19
35 36 0.28
36 42 0.33
37 27 0.21
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (35 bp):
TTTTATCTCACTTGAGATTGTTTTCTTAAAACATA
Found at i:22911 original size:36 final size:36
Alignment explanation
Indices: 22861--22993 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 36
22851 ATTTTATCTT
*
22861 ACTTGAGATTATTTTTCTTAAAACATATAATATATC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** *
22897 ACTTGAGATAATTTTTATTAAAATAGATTTTATCTC
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* * * ** * *
22933 ACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTT
1 ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
* *
22969 ACTTGAAATTGTTTTTCTTAAAACA
1 ACTTGAGATTATTTTTCTTAAAACA
22994 AATTTGTTTA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (36 bp):
ACTTGAGATTATTTTTCTTAAAACAGATAATATATC
Found at i:22979 original size:131 final size:130
Alignment explanation
Indices: 22721--22979 Score: 306
Period size: 131 Copynumber: 2.0 Consensus size: 130
22711 CTTAAAACAT
* * ** *
22721 ATTTTATCTCAATTGAGATTATTTTTTTCTAAAATAGATCTTATTTCACTTGAGATTTTTTATTA
1 ATTTTATCTCAATTGAGATTATTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATTA
* * * * *
22786 AAACATACCTTATCTCACTTGAGATTGTTTTCTTAAAATATATTTTATCTCATTTGAGAATTGAG
66 AAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGAG
* * *
22851 ATTTTATCTTACTTGAGATTATTTTTCT-TAAAACATATAATATATCACTTGAGATAATTTTTAT
1 ATTTTATCTCAATTGAGATTATTTTTCTCTAAAACAGATAATATATCACTTGAGAT--TTTTTAT
* ** * * *
22915 TAAAATAGATTTTATCTCACTGGAGATTGTTTTTCTTAAAACAGGTTTTATTTTACTTGA-AATT
64 TAAAACAGACCTTATCTCACTGGAGATTG-TTTTCTTAAAACAGATTTTATCTCACTTGAGAATT
22979 G
128 G
22980 TTTTTCTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
129 22 0.21
130 25 0.23
131 36 0.34
132 24 0.22
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (130 bp):
ATTTTATCTCAATTGAGATTATTTTTCTCTAAAACAGATAATATATCACTTGAGATTTTTTATTA
AAACAGACCTTATCTCACTGGAGATTGTTTTCTTAAAACAGATTTTATCTCACTTGAGAATTGAG
Found at i:23148 original size:13 final size:12
Alignment explanation
Indices: 23126--23159 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23116 CCTTTTACTA
23126 ATATTATTAGTTT
1 ATATTATTAG-TT
*
23139 ATATTTTTAGTT
1 ATATTATTAGTT
23151 ATATTATTA
1 ATATTATTA
23160 ATTTAACTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
ATATTATTAGTT
Found at i:23154 original size:12 final size:13
Alignment explanation
Indices: 23126--23164 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
23116 CCTTTTACTA
23126 ATATTATTAGTTT
1 ATATTATTAGTTT
*
23139 ATATTTTTAG-TT
1 ATATTATTAGTTT
*
23151 ATATTATTAATTT
1 ATATTATTAGTTT
23164 A
1 A
23165 ACTGTTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATATTATTAGTTT
Found at i:27511 original size:3 final size:3
Alignment explanation
Indices: 27503--27642 Score: 235
Period size: 3 Copynumber: 46.7 Consensus size: 3
27493 TTTTTATCCA
*
27503 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
27551 TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
27599 CAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
27643 ATTTATATTA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29079 original size:16 final size:15
Alignment explanation
Indices: 29058--29090 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29048 AAATATTTTG
*
29058 ATATATAT-TCATAA
1 ATATATATATAATAA
29072 ATATATATATAATAA
1 ATATATATATAATAA
29087 ATAT
1 ATAT
29091 TAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:29838 original size:13 final size:15
Alignment explanation
Indices: 29807--29843 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29797 TTATATGTTT
29807 TATTTTATTTGCAAA
1 TATTTTATTTGCAAA
29822 TATTTTATTT-C-AA
1 TATTTTATTTGCAAA
29835 TA-TTTATTT
1 TATTTTATTT
29844 TTATGTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAA
Found at i:40655 original size:1 final size:1
Alignment explanation
Indices: 40649--40688 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
40639 ATGCTTGAAG
*
40649 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40689 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:42571 original size:52 final size:52
Alignment explanation
Indices: 41630--42570 Score: 1660
Period size: 52 Copynumber: 18.1 Consensus size: 52
41620 TATGTGCTCA
* *
41630 ATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
41682 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
41733 ATAGCATCTTCTGGAAGTGGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGT-GTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
41785 ATAGCATCTTCTGGAAGTGATTTTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
41838 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
41889 ATAGCATCTTCTGGAAGTGGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGT-GTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
41941 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
41993 ATACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42045 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAG-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42096 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42148 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42200 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42252 ATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42304 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
42356 ATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42408 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
42460 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
42512 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
42565 A-AGCAT
1 ATAGCAT
42571 TGAGTTTAGA
Statistics
Matches: 865, Mismatches: 17, Indels: 14
0.97 0.02 0.02
Matches are distributed among these distances:
51 124 0.14
52 715 0.83
53 26 0.03
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:42651 original size:83 final size:83
Alignment explanation
Indices: 42512--42716 Score: 383
Period size: 83 Copynumber: 2.5 Consensus size: 83
42502 TGGACAGAAC
*
42512 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
42577 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
42595 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
42660 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
* *
42678 ATAGCATCTTCTGGAAGCGTTCTTTGAGTTATTTGATCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
42717 AAAGAAGTGC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 119 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
TAGAAGATGAATTTGCCA
Found at i:43642 original size:113 final size:113
Alignment explanation
Indices: 43274--43939 Score: 1021
Period size: 113 Copynumber: 5.8 Consensus size: 113
43264 GATTCAAATT
43274 CATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CATC-ATTTGATGGATCATCATTTCCAGAG-AA-AGTTCATAATGAGAAGAACTCATCTGAAGAA
43339 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* *
43390 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
43455 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* *
43506 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
43571 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* **
43619 CATCATTTGGTGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * * *
43684 AGAAGAAGTTTATAATGAGAATAACTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
43732 CATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 CATC-ATTTGATGGATCATCATTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCTGAA
* * *
43797 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
60 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* *
43851 CATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
43915 AAG-AGAAAGTTCATAATGAGAAGAA
65 AAGAAG-AAGTTCATAATGAGAAGAA
43940 CTCATCAAGA
Statistics
Matches: 520, Mismatches: 19, Indels: 25
0.92 0.03 0.04
Matches are distributed among these distances:
112 2 0.00
113 227 0.44
114 24 0.05
115 27 0.05
116 153 0.29
117 2 0.00
118 21 0.04
119 64 0.12
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
Found at i:43772 original size:229 final size:229
Alignment explanation
Indices: 43270--43941 Score: 1075
Period size: 229 Copynumber: 2.9 Consensus size: 229
43260 CAAAGATTCA
*
43270 AATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCTGA
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
43335 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
43400 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAA
131 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAA
*
43465 GTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
193 GTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTG
* * *
43502 AATCCATC-ATTTGGTGGATCATCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAACTCATCTGA
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
43564 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
*
43629 TGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * * *
43694 TATAATGAGAATAACTTGTTCAACCTTTTGCTTG
196 CATAATGAGAAGAACTTGTTCAACCTTTTACCTG
*
43728 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TCATC
* * *
43793 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATT
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATT
* * * *
43858 TGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGA
128 TGGTGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-
43921 AAGTTCATAATGAGAAGAACT
191 AAGTTCATAATGAGAAGAACT
43942 CATCAAGAGC
Statistics
Matches: 408, Mismatches: 24, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
226 61 0.15
227 22 0.05
228 3 0.01
229 148 0.36
230 2 0.00
231 26 0.06
232 146 0.36
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (229 bp):
AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTACCTG
Found at i:44197 original size:3 final size:3
Alignment explanation
Indices: 44189--44319 Score: 217
Period size: 3 Copynumber: 43.7 Consensus size: 3
44179 TTTTTATCCA
*
44189 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
44237 TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
44285 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44320 ATTTATATTA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:51743 original size:32 final size:31
Alignment explanation
Indices: 51700--51774 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
51690 ATGGGGCCTG
* * *
51700 AGAGCCTACCCAAGACAATTCTCGGGGCCAT
1 AGAGCCTACCCAAGAAAAATCTCAGGGCCAT
* *
51731 AGAGGCTTACCCAAGAAAAATCTCAGGGCCGT
1 AGA-GCCTACCCAAGAAAAATCTCAGGGCCAT
51763 AGAGCCTACCCA
1 AGAGCCTACCCA
51775 GTGGCCGCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 11 0.30
32 26 0.70
ACGTcount: A:0.32, C:0.31, G:0.23, T:0.15
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAAATCTCAGGGCCAT
Found at i:51848 original size:31 final size:31
Alignment explanation
Indices: 51793--51851 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
51783 CTTAGGTCCA
**
51793 TAAGGAATTACCAATCAGTGCTGAACCTATC
1 TAAGGAATTACCAATCAACGCTGAACCTATC
51824 TAAGGAATTACCAA-CAACGACTGAACCT
1 TAAGGAATTACCAATCAACG-CTGAACCT
51852 GCCAGAGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (31 bp):
TAAGGAATTACCAATCAACGCTGAACCTATC
Found at i:51970 original size:24 final size:24
Alignment explanation
Indices: 51919--52012 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
51909 ACAGATATAT
*
51919 CAGAAATCAAAACAGGAA-T-AGAG
1 CAGAAATCAGAACA-GAATTCAGAG
*
51942 CAGAAATCATAACAGAATTCAGAG
1 CAGAAATCAGAACAGAATTCAGAG
* *
51966 AAGAAATTAGAACAGAATTCAGAG
1 CAGAAATCAGAACAGAATTCAGAG
* * *
51990 CATAAATCAGAACAAAAATCAGA
1 CAGAAATCAGAACAGAATTCAGA
52013 TAAAATATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
22 3 0.05
23 14 0.23
24 43 0.72
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAG
Found at i:56464 original size:24 final size:24
Alignment explanation
Indices: 56385--56464 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
56375 ATCATAATTC
*
56385 ATAA-ATAAATATCCTTAGTCAAA
1 ATAACATAAATATCCTTAATCAAA
* * *
56408 ACAACATAAATGA-AC-AAATC-AA
1 ATAACATAAAT-ATCCTTAATCAAA
*
56430 ATCACAAATAAATATCCTTAATCAAA
1 AT-A-ACATAAATATCCTTAATCAAA
56456 ATAACATAA
1 ATAACATAA
56465 TTGAACTCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 13
0.65 0.14 0.21
Matches are distributed among these distances:
22 3 0.07
23 8 0.20
24 20 0.49
25 6 0.15
26 4 0.10
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (24 bp):
ATAACATAAATATCCTTAATCAAA
Found at i:58714 original size:56 final size:56
Alignment explanation
Indices: 58601--58743 Score: 187
Period size: 56 Copynumber: 2.5 Consensus size: 56
58591 CCTACCTGAA
* * *
58601 GGGATACCTTAGGTCAACAAGGACTTACCCTAATTGTAGCGTAAGAGAAAACCTAAG
1 GGGATACCTTAGGTCCATAAGGACTTA-CCTAATTATAGCGTAAGAGAAAACCTAAG
* * * * *
58658 GGGATACCTCAGGTCCATAAGGACTTACCTAATTATAGTGTATGAGCAAACTTAAG
1 GGGATACCTTAGGTCCATAAGGACTTACCTAATTATAGCGTAAGAGAAAACCTAAG
* *
58714 GGGACACCTTAGGTGCATAAGGACTTACCT
1 GGGATACCTTAGGTCCATAAGGACTTACCT
58744 TAGACCCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
56 51 0.68
57 24 0.32
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (56 bp):
GGGATACCTTAGGTCCATAAGGACTTACCTAATTATAGCGTAAGAGAAAACCTAAG
Found at i:59139 original size:23 final size:24
Alignment explanation
Indices: 59109--59158 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
59099 AATTAATAGA
59109 TATAATCA-GA-CATTTA-TAGTTT
1 TATAATCATGATCATTTAGTA-TTT
59131 TATACATCATGATCATTTAGTATTT
1 TATA-ATCATGATCATTTAGTATTT
59156 TAT
1 TAT
59159 TATATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 4 0.17
24 2 0.08
25 12 0.50
26 2 0.08
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (24 bp):
TATAATCATGATCATTTAGTATTT
Found at i:60107 original size:24 final size:24
Alignment explanation
Indices: 60073--60179 Score: 83
Period size: 24 Copynumber: 4.5 Consensus size: 24
60063 TAACGGGTAT
* * * *
60073 ATCAAAAATCAAAATAGAATTCAG
1 ATCAGAAATCATAACAGAATCCAG
* *
60097 ATCAGATATCATAACACAATCCAG
1 ATCAGAAATCATAACAGAATCCAG
*
60121 ATCAGAAATCAGAACAGAATCCATG
1 ATCAGAAATCATAACAGAATCCA-G
* * * *
60146 -TCA-AGTATCATAATAGAATTCAA
1 ATCAGA-AATCATAACAGAATCCAG
60169 ATCAGAAATCA
1 ATCAGAAATCA
60180 GATAAAATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.02
24 61 0.95
25 2 0.03
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATCCAG
Found at i:62072 original size:18 final size:18
Alignment explanation
Indices: 62049--62103 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
62039 AAGTAAATGG
62049 TCAATGGTTAACAGTTGA
1 TCAATGGTTAACAGTTGA
* *
62067 TCAATGGTTAACGGTCGA
1 TCAATGGTTAACAGTTGA
* *
62085 TCAACGGTCAACGAGTTGA
1 TCAATGGTTAAC-AGTTGA
62104 CTCAGTGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (18 bp):
TCAATGGTTAACAGTTGA
Found at i:62132 original size:14 final size:14
Alignment explanation
Indices: 62096--62144 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
62086 CAACGGTCAA
*
62096 CGAGTTGACTCAGT
1 CGAGTTGACTCACT
*
62110 -GACTTGACTCACT
1 CGAGTTGACTCACT
*
62123 CGAGTTGACTCAGCG
1 CGAGTTGACTCA-CT
62138 CGAGTTG
1 CGAGTTG
62145 GATTAGTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.38
14 10 0.34
15 8 0.28
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (14 bp):
CGAGTTGACTCACT
Found at i:64197 original size:12 final size:12
Alignment explanation
Indices: 64162--64220 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
64152 AAACGGGTAT
*
64162 ATCAGAAATCAAA
1 ATCAGAAATC-AG
*
64175 AT-AGAATTCAG
1 ATCAGAAATCAG
*
64186 ATCAGATATCAG
1 ATCAGAAATCAG
*
64198 AACA-AAATCCAG
1 ATCAGAAAT-CAG
64210 ATCAGAAATCA
1 ATCAGAAATCA
64221 TAACAGAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
11 6 0.17
12 24 0.67
13 6 0.17
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.19
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:64238 original size:24 final size:24
Alignment explanation
Indices: 64162--64268 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
64152 AAACGGGTAT
* * *
64162 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCATAACAGAATCCAG
* * *
64186 ATCAGATATCAGAACAAAATCCAG
1 ATCAGAAATCATAACAGAATCCAG
64210 ATCAGAAATCATAACAGAATCCATG
1 ATCAGAAATCATAACAGAATCCA-G
** * * *
64235 -TCAGGTATCATAACCGAATTCAA
1 ATCAGAAATCATAACAGAATCCAG
*
64258 ATCAAAAATCA
1 ATCAGAAATCA
64269 GATAAAATAT
Statistics
Matches: 65, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
24 64 0.98
25 1 0.02
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATCCAG
Found at i:66050 original size:14 final size:14
Alignment explanation
Indices: 66033--66086 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
66023 CAACGGTTAA
*
66033 CGAGTTGACCCAGT
1 CGAGTTGACTCAGT
66047 CGAGTTGACTCAGT
1 CGAGTTGACTCAGT
* *
66061 CGAGTTGGCTCAAT
1 CGAGTTGACTCAGT
*
66075 CGAGTTGGCTCA
1 CGAGTTGACTCA
66087 ATCGGGTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:67264 original size:27 final size:26
Alignment explanation
Indices: 67206--67276 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
67196 GTACCCAATG
*
67206 GTATTTCAATCATTTTAAAACCCGAT
1 GTATTTCAATCATTTTAAAACCAGAT
***
67232 GATATTTCAATCATTTTGGGACTCAGAT
1 G-TATTTCAATCATTTTAAAAC-CAGAT
*
67260 GTATTTCAGTCATTTTA
1 GTATTTCAATCATTTTA
67277 TTCAGTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.03
27 31 0.84
28 5 0.14
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (26 bp):
GTATTTCAATCATTTTAAAACCAGAT
Found at i:76505 original size:56 final size:56
Alignment explanation
Indices: 76438--76585 Score: 161
Period size: 56 Copynumber: 2.6 Consensus size: 56
76428 ATAGGATCCT
* *
76438 ACCTGAAGGGATACCTTAGTTCCACAAGGACTTACCCTAATTGTAGCGTAGGAGAAA
1 ACCT-AAGGGATACCTTAGGTCCACAAGGACTTACCCTAATTATAGCGTAGGAGAAA
* * * * * *
76495 ACCTAAGGGATACCTCAGGTCCATAAGGACTTACTCTAATTATAGTGTATGAGCAA
1 ACCTAAGGGATACCTTAGGTCCACAAGGACTTACCCTAATTATAGCGTAGGAGAAA
* * * * *
76551 ACTTAAGGGGACACCTTAGGTGCATAGGGACTTAC
1 ACCTAA-GGGATACCTTAGGTCCACAAGGACTTAC
76586 TTTAGACCCA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
56 49 0.64
57 28 0.36
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (56 bp):
ACCTAAGGGATACCTTAGGTCCACAAGGACTTACCCTAATTATAGCGTAGGAGAAA
Found at i:77582 original size:27 final size:27
Alignment explanation
Indices: 77551--77621 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
77541 GTGCCCAATG
77551 GTATTTCAATTATTTTAAAAC-CCGAT
1 GTATTTCAATTATTTTAAAACTCCGAT
* ** *
77577 GATATTTCAATCATTTTGGAACTCGGAT
1 G-TATTTCAATTATTTTAAAACTCCGAT
*
77605 GTATTTCAGTTATTTTA
1 GTATTTCAATTATTTTA
77622 TTCAGTTCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 1 0.03
27 30 0.83
28 5 0.14
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (27 bp):
GTATTTCAATTATTTTAAAACTCCGAT
Done.