Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008438.1 Hibiscus syriacus cultivar Beakdansim tig00111237_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: 406264
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:293468 original size:29 final size:29
Alignment explanation
Indices: 293383--293459 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
293373 ACAGTTTCTC
*
293383 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCTTT
*
293411 TTGAATAAAAATCTTGGAGTTTGTTCTTT
1 TTGAATAAAAATCTTTGAGTTTGTTCTTT
*
293440 TTGAATAAATATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
293460 CGTTTCTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 5 0.11
29 39 0.89
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.47
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTGTTCTTT
Found at i:293490 original size:174 final size:174
Alignment explanation
Indices: 293190--293512 Score: 594
Period size: 175 Copynumber: 1.9 Consensus size: 174
293180 ACGATTTTTG
293190 TCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAG
1 TCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAG
* *
293255 TTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTTTGAGTCTATTTATT
66 TTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTAGAAAAAATCTTTGAGTCTATTTATT
293320 TTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTC
131 TTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTC
293364 TCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
1 TCTCTTGAGACAGTTTCTCTTG-AAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGA
*
293429 GTTTGTTCTTTTTGAATAAATATCTTTGAGTCGTTTCTTTAG-AAAAATCTTTGAGTCTATTTAT
65 GTTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTAGAAAAAATCTTTGAGTCTATTTAT
*
293493 TTTGAAACAAAGTTTTGTCT
130 TTTAAAACAAAGTTTTGTCT
293513 CTCTTGAGAC
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
174 63 0.44
175 81 0.56
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (174 bp):
TCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAG
TTTGTTCCTTTTGAATAAATATCTTTGAGTCGTTTCTTTAGAAAAAATCTTTGAGTCTATTTATT
TTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTC
Found at i:293534 original size:146 final size:146
Alignment explanation
Indices: 293237--293545 Score: 402
Period size: 146 Copynumber: 2.1 Consensus size: 146
293227 TTGTTCCTTT
* * *
293237 TGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAA
1 TGAA-AAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTGTTTCTTTTGAAAAAA
*
293302 TCTTTGAGTCTATTTATTTTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTCTCT
65 TCTTTGAGTCTATTTACTTTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTCTCT
* *
293367 CTTGAGACAGTTTCTCT
130 CTTGAGACAGATTCTCG
293384 TGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTT-TGTTCTTTTTGAATAA
1 TGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTGT-TTC-TTTTGAA-AA
* * *
293448 ATATCTTTGAGTC-GTTT-CTTTAGAA-AAA-TCTTTGAGTCTATTTATTTTGAAACAAAGTTTT
63 A-ATCTTTGAGTCTATTTACTTTAAAACAAAGT-TTT--GTCTATTTATTTTAAAACAAAGTTTT
293509 GTCTCTCTTGAGACA-ATT-TCG
124 GTCTCTCTTGAGACAGATTCTCG
293530 TG--AAAAATCTTTGAGT
1 TGAAAAAAATCTTTGAGT
293546 CTGAAACAAA
Statistics
Matches: 146, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
144 14 0.10
145 2 0.01
146 54 0.37
147 19 0.13
148 46 0.32
149 11 0.08
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (146 bp):
TGAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTGTTTCTTTTGAAAAAAT
CTTTGAGTCTATTTACTTTAAAACAAAGTTTTGTCTATTTATTTTAAAACAAAGTTTTGTCTCTC
TTGAGACAGATTCTCG
Found at i:293573 original size:52 final size:53
Alignment explanation
Indices: 293495--293598 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
293485 CTATTTATTT
293495 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
293547 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
293599 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:293598 original size:26 final size:28
Alignment explanation
Indices: 293568--293626 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
293558 TTTGTCTCTC
293568 TTGAGA-CAATT-TTGTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
*** *
293594 TTGAGATTGTTTCTTTTGAAAAAAATCT
1 TTGAGATCAATTCTTGTGAAAAAAATCT
293622 TTGAG
1 TTGAG
293627 TTTGTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
28 19 0.70
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGAGATCAATTCTTGTGAAAAAAATCT
Found at i:293638 original size:27 final size:28
Alignment explanation
Indices: 293582--293719 Score: 116
Period size: 28 Copynumber: 4.5 Consensus size: 28
293572 GACAATTTTG
293582 TGAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
*
293610 TGAAAAAAATCTTTGAGTTTGTTTCTTT
1 TGAAAAAAATCTTTGAGATTGTTTCTTT
* * *
293638 GGAAACAAAATTCTTTCTCTCTTAAGATAGTTTCTTT
1 TGAAA-AAAA-------TCT-TTGAGATTGTTTCTTT
*
293675 TGAAACAAAAATCTTTGAGTTTGTTTCTTT
1 TG-AA-AAAAATCTTTGAGATTGTTTCTTT
293705 TGAAACAAAAT-TTTG
1 TGAAA-AAAATCTTTG
293720 TCTCTCTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
28 36 0.40
29 11 0.12
30 15 0.17
31 3 0.03
36 3 0.03
37 14 0.16
38 6 0.07
39 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGATTGTTTCTTT
Found at i:293680 original size:37 final size:36
Alignment explanation
Indices: 293630--293751 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
293620 CTTTGAGTTT
*
293630 GTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATT-TTTCTCTCTTAAGATA
* * * *
293667 GTTTCTTTTGAAACAAAA-----ATCT-TTGAGTTT
1 GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
293697 GTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTTGAAACAAAATTTT-TCTCTCTTAAGATA
*
293734 ATTTCTTTTGAAACAAAA
1 GTTTCTTTTGAAACAAAA
293752 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 23 0.34
31 3 0.04
36 3 0.04
37 39 0.57
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (36 bp):
GTTTCTTTTGAAACAAAATTTTTCTCTCTTAAGATA
Found at i:293693 original size:67 final size:67
Alignment explanation
Indices: 293597--293811 Score: 271
Period size: 67 Copynumber: 3.3 Consensus size: 67
293587 AAAATCTTTG
*
293597 AGATTGTTTCTTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTT-TCTCTC
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATT-TTGTCTCTC
293659 TTA
65 TTA
*
293662 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
293727 TA
66 TA
* * * * *
293729 AGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCT
*
293791 CTTG
64 CTTA
**
293795 AGACCGTTTCTTTTGAA
1 AGATAGTTTCTTTTGAA
293812 GTAAATCTTT
Statistics
Matches: 134, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
65 15 0.11
66 35 0.26
67 82 0.61
68 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (67 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
TA
Found at i:294531 original size:35 final size:36
Alignment explanation
Indices: 294502--294575 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
294492 TGTTTCTTTG
* *
294502 GAAACAAAATTACCATCTTTGA-ATCTGTTTCCCTT
1 GAAACAAAATAAACATCTTTGAGATCTGTTTCCCTT
*
294537 GAAACAAAATAAACATCTTTGAGATC-GTTTACCTT
1 GAAACAAAATAAACATCTTTGAGATCTGTTTCCCTT
294572 GAAA
1 GAAA
294576 TGAATTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 32 0.91
36 3 0.09
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (36 bp):
GAAACAAAATAAACATCTTTGAGATCTGTTTCCCTT
Found at i:294671 original size:66 final size:65
Alignment explanation
Indices: 294550--294688 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 65
294540 ACAAAATAAA
* * ** *
294550 CATCTTTGAGATCGTTTACCTTGAAATGAATTTCGTCTCATTTGAGACAATTTCCCATGAAATAC
1 CATCTTTGAGAACGTTTACCTTAAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAATAC
* * * * *
294615 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAA-TTCCCTTTAAAT
1 C-ATCTTTGAGAACGTTTACCTT-AAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAAT
*
294679 GC
64 AC
294681 CATCTTTG
1 CATCTTTG
294689 GGTTGTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
65 8 0.13
66 31 0.51
67 22 0.36
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (65 bp):
CATCTTTGAGAACGTTTACCTTAAAACAAATTTCGTCTCACTTGAGACAATTTCCCATGAAATAC
Found at i:295067 original size:46 final size:45
Alignment explanation
Indices: 294913--295418 Score: 335
Period size: 40 Copynumber: 11.8 Consensus size: 45
294903 TAGCTTCTAA
* *
294913 AGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATC-CC--
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * * *
294955 -CA-GACCAGATCTCCTTATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
* *
294996 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * * *
295041 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC--
1 -AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCA-TCACCTT
* * * *
295085 --A-GACCAGATCTCCTTATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
* *
295125 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGTCATCACC-TT
* *
295171 AGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATC-CC--
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * * *
295213 -CA-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
* *
295254 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * *
295300 AGATGGCCAGATCTCCTCATCACGTATGAGCCGTGTCATC-CC--
1 AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * *
295342 -CA-GACCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
*
295383 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 AGATGACCAGACC-TCCTCATCACGTAGGAACCGTGT
295419 TACTACCTTT
Statistics
Matches: 364, Mismatches: 61, Indels: 77
0.73 0.12 0.15
Matches are distributed among these distances:
38 2 0.01
39 6 0.02
40 115 0.32
41 6 0.02
42 8 0.02
43 108 0.30
45 14 0.04
46 101 0.28
47 4 0.01
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (45 bp):
AGATGACCAGACCTCCTCATCACGTAGGAACCGTGTCATCACCTT
Found at i:295142 original size:129 final size:129
Alignment explanation
Indices: 294912--295472 Score: 862
Period size: 129 Copynumber: 4.3 Consensus size: 129
294902 ATAGCTTCTA
* * * *
294912 AAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCAC
1 AAGATGGCCAGAAC-TCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCAC
294976 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
65 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* *
295041 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
1 AAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCACG
295106 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * * * *
295170 TAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCT-CTTCATCA
1 AAGATGGCCAGAAC-TCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTT-ATCA
295233 CGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
64 CGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCT
295298 T
129 T
* * *
295299 TAGATGGCCAGATCTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACG
1 AAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCACG
295364 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA-CTACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC-ACC-T
295428 T
129 T
* * * * * *
295429 AA-ACGACCCGAACTCTTCATCACGTATGAGCAGTGTCGTCCCCA
1 AAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCA
295473 ACAACCAAAA
Statistics
Matches: 399, Mismatches: 26, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
128 5 0.01
129 387 0.97
130 7 0.02
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (129 bp):
AAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTTATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
Found at i:295281 original size:83 final size:84
Alignment explanation
Indices: 294919--295338 Score: 372
Period size: 83 Copynumber: 4.9 Consensus size: 84
294909 CTAAAGATGG
*
294919 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTT-ATCACGTAGGAG
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCT-CTTCATCACGTAGGAG
294983 CCGTGTCA-ACCATAGATAA
65 CCGTGTCATACCATAGATAA
* * *
295002 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCTTCATCACGT
* * *
295067 ATGAGCCGTGTCATTCC-CAG---A
60 AGGAGCCGTGTCATACCATAGATAA
* * * * ** * *
295088 CCAGATC-TCCTTATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CCGTCCTCATCACGTA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC-TCTTCATCACGTA
* * * **
295151 GGAACCGTGTTATCACCTTTAGATGG
61 GGAGCCGTGTCAT-ACC-ATAGATAA
*
295177 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGC
295242 CGTGTCA-ACCATAGATAA
66 CGTGTCATACCATAGATAA
* * *
295260 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATCTCCTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCTTCATCACGT
*
295325 ATGAGCCGTGTCAT
60 AGGAGCCGTGTCAT
295339 CCCCAGACCA
Statistics
Matches: 268, Mismatches: 41, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
82 1 0.00
83 97 0.36
84 9 0.03
85 1 0.00
86 64 0.24
87 2 0.01
88 4 0.01
89 88 0.33
90 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (84 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGC
CGTGTCATACCATAGATAA
Found at i:295370 original size:258 final size:258
Alignment explanation
Indices: 294913--295429 Score: 957
Period size: 258 Copynumber: 2.0 Consensus size: 258
294903 TAGCTTCTAA
294913 AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGT
1 AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGT
294978 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAA
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAA
* * *
295043 GATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTA
131 GATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTA
295108 GGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA-TCACCTTT
196 GGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTACT-ACCTTT
295171 AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCT-CTTCATCACG
1 AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTT-ATCACG
*
295235 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
65 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTA
*
295300 AGATGGCCAGATCTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
130 AGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
295365 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTACTACCTTT
195 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTACTACCTTT
295429 A
1 A
295430 AACGACCCGA
Statistics
Matches: 252, Mismatches: 5, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
257 3 0.01
258 248 0.98
259 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (258 bp):
AGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTTATCACGT
AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAA
GATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTA
GGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTACTACCTTT
Found at i:295633 original size:3 final size:3
Alignment explanation
Indices: 295625--295681 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
295615 TTATATATAT
** *
295625 TTA TTA TTA TCG TTA TTT TTA TTA TTTA TTA TTA TTA -TA TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA
*
295671 TCA TTA TTA TT
1 TTA TTA TTA TT
295682 TACATATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:299104 original size:18 final size:19
Alignment explanation
Indices: 299065--299105 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
299055 TTTGATCATG
299065 ATATTTCAATATGCATGGAT
1 ATATTTCAATATGCAT-GAT
299085 ATATTTC-ATATGACAT-AT
1 ATATTTCAATATG-CATGAT
299103 ATA
1 ATA
299106 ATCAAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
ATATTTCAATATGCATGAT
Found at i:300011 original size:35 final size:37
Alignment explanation
Indices: 299965--300036 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
299955 TTCATTTAGG
299965 GGGGAATCGATA-CCCCCCAG-GGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGAGGGGAATCTGTTCCC
300000 GGGGAATCGATACCCCCCCAGAGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGAGGGGAATCTGTTCCC
300037 CTTACACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 12 0.34
36 8 0.23
37 15 0.43
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.17
Consensus pattern (37 bp):
GGGGAATCGATACCCCCCCAGAGGGGAATCTGTTCCC
Found at i:321338 original size:40 final size:40
Alignment explanation
Indices: 321283--321365 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
321273 CATGCCTCCT
321283 TCAAACCTGGGCCCTAAGCGGTCGCCCCCCTCGCCTACCC
1 TCAAACCTGGGCCCTAAGCGGTCGCCCCCCTCGCCTACCC
*
321323 TCAAACTTGGGCCCTAAGCGGTCGCCCCCCTCGCCTACCC
1 TCAAACCTGGGCCCTAAGCGGTCGCCCCCCTCGCCTACCC
321363 TCA
1 TCA
321366 GGGCCGGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.17
Consensus pattern (40 bp):
TCAAACCTGGGCCCTAAGCGGTCGCCCCCCTCGCCTACCC
Found at i:327787 original size:79 final size:79
Alignment explanation
Indices: 327656--327815 Score: 275
Period size: 79 Copynumber: 2.0 Consensus size: 79
327646 TTTTTTCTCG
* *
327656 TTGTTCTGCATACATTACATAGATAGCAGTTGGTTACAGTCGACAATCCAGAAATTGCTCATGAG
1 TTGTTCTGCATACATAACATAGATAGCAGTTGATTACAGTCGACAATCCAGAAATTGCTCATGAG
327721 AGTGGATTCCAAAC
66 AGTGGATTCCAAAC
* *
327735 TTGTTCTGCATACATAACATAGATAGCAGTTGATTATAGTCGGCAATCCAGAAATTGCTCATGAG
1 TTGTTCTGCATACATAACATAGATAGCAGTTGATTACAGTCGACAATCCAGAAATTGCTCATGAG
*
327800 AGTGGATTCTAAAC
66 AGTGGATTCCAAAC
327814 TT
1 TT
327816 ATGATTTCGT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (79 bp):
TTGTTCTGCATACATAACATAGATAGCAGTTGATTACAGTCGACAATCCAGAAATTGCTCATGAG
AGTGGATTCCAAAC
Found at i:331928 original size:40 final size:40
Alignment explanation
Indices: 331874--331949 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
331864 ATGACAATGA
*
331874 AAAAATACAGATCCAGTAAATCCTACTCAAAGCAAAGTAG
1 AAAAATAAAGATCCAGTAAATCCTACTCAAAGCAAAGTAG
331914 AAAAATAAAGATCCAGTAAATCCTACTCAAAGCAAA
1 AAAAATAAAGATCCAGTAAATCCTACTCAAAGCAAA
331950 ACTCAACATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.53, C:0.20, G:0.11, T:0.17
Consensus pattern (40 bp):
AAAAATAAAGATCCAGTAAATCCTACTCAAAGCAAAGTAG
Found at i:336412 original size:23 final size:23
Alignment explanation
Indices: 336386--336443 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
336376 GAATATATTT
*
336386 GTTTAATGTTCATGAACATGTTC
1 GTTTAACGTTCATGAACATGTTC
* * *
336409 GTTTAACGTTTATGAATATGTTT
1 GTTTAACGTTCATGAACATGTTC
336432 GTTTAACGTTCA
1 GTTTAACGTTCA
336444 AAAACATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (23 bp):
GTTTAACGTTCATGAACATGTTC
Found at i:341091 original size:36 final size:36
Alignment explanation
Indices: 341050--341152 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
341040 AGTTGAGTAT
341050 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* * *
341086 TATCAGTTTTGGTACATTCGTGTATCGATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
341122 TATCAGCTTTGGTATATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
341153 CCAGCACCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:349167 original size:36 final size:36
Alignment explanation
Indices: 349126--349228 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
349116 AGTTGAGTAT
*
349126 TATCAGTTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
349162 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
349198 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
349229 CCAGCACCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:352845 original size:10 final size:10
Alignment explanation
Indices: 352820--352853 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
352810 TATTTAAAAA
*
352820 AATAAAAAAT
1 AATAATAAAT
352830 AATAATAAAT
1 AATAATAAAT
352840 AATAATAAAT
1 AATAATAAAT
352850 AATA
1 AATA
352854 CTAACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AATAATAAAT
Found at i:359370 original size:2 final size:2
Alignment explanation
Indices: 359363--359404 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
359353 TAAAAATCAG
359363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
359405 TAATTTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361062 original size:72 final size:73
Alignment explanation
Indices: 360971--361110 Score: 210
Period size: 72 Copynumber: 1.9 Consensus size: 73
360961 TTTATGAATA
* * * * *
360971 ATTTTTTAGTTGTTTTTCATGTCGAATTGGCACTATGTAATTGTAGGCATTATTAGGGCCCTTTT
1 ATTTTTTAGTTGTTTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCCTTTT
361036 CATTTTTC
66 CATTTTTC
* *
361044 ATTTTTTA-TTTTTTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGGCCTTTT
1 ATTTTTTAGTTGTTTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCCTTTT
361108 CAT
66 CAT
361111 GACGGGCGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 52 0.87
73 8 0.13
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (73 bp):
ATTTTTTAGTTGTTTTTCATGTCAAATTGACAATATGTAAATGTAGGCATCATTAGGGCCCTTTT
CATTTTTC
Found at i:370602 original size:83 final size:83
Alignment explanation
Indices: 370463--370628 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
370453 GATGAAACTG
370463 TCCAACATCTTTTCATTTCTTGTTCTTTTTCGTGGGAACTTTGGAACAAAATTATCAGCTTCTGG
1 TCCAACATCTTTTCATTTCTTGTTCTTTTTCGTGGGAACTTTGGAACAAAATTATCAGCTTCTGG
370528 GATCTTTCTATAGCTCTA
66 GATCTTTCTATAGCTCTA
370546 TCCAACATCTTTTCATTTCTTGTTCTTTTTCGTGGGAACTTTGGAACAAAATTATCAGCTTCTGG
1 TCCAACATCTTTTCATTTCTTGTTCTTTTTCGTGGGAACTTTGGAACAAAATTATCAGCTTCTGG
370611 GATCTTTCTATAGCTCTA
66 GATCTTTCTATAGCTCTA
370629 CCTCGCGATC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (83 bp):
TCCAACATCTTTTCATTTCTTGTTCTTTTTCGTGGGAACTTTGGAACAAAATTATCAGCTTCTGG
GATCTTTCTATAGCTCTA
Found at i:374510 original size:24 final size:24
Alignment explanation
Indices: 374483--374530 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
374473 GGCTCGATTT
374483 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
*
374507 TCTTCTAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
374531 ATTCCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (24 bp):
TCTTCCAACAGTCAGACCTTTTAA
Found at i:374906 original size:24 final size:26
Alignment explanation
Indices: 374879--374937 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
374869 TCCTACATGG
*
374879 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
374903 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
374932 TTAATT
1 TTAATT
374938 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:375058 original size:21 final size:20
Alignment explanation
Indices: 375034--375094 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
375024 ACTTGTTATT
375034 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
375055 TTGTTTATCTAATATGTTTAA
1 TTG-TTAGGTAATCTGTTTAA
375076 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
375095 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.39
21 18 0.55
22 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:375295 original size:14 final size:14
Alignment explanation
Indices: 375278--375304 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
375268 TTTCTGTTTT
375278 TAATATGTTAGTTA
1 TAATATGTTAGTTA
375292 TAATATGTTAGTT
1 TAATATGTTAGTT
375305 TACTGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TAATATGTTAGTTA
Found at i:375348 original size:14 final size:14
Alignment explanation
Indices: 375278--375342 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
375268 TTTCTGTTTT
*
375278 TAATATGTTAGTTA
1 TAATTTGTTAGTTA
*
375292 TAATATGTTAGTT-
1 TAATTTGTTAGTTA
* * *
375305 TACTGTTTTTA-TTGC
1 TAAT-TTGTTAGTT-A
375320 TAATTTGTTAGTTA
1 TAATTTGTTAGTTA
375334 TAATTTGTT
1 TAATTTGTT
375343 TTTTATGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 5 0.12
14 31 0.76
15 5 0.12
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (14 bp):
TAATTTGTTAGTTA
Found at i:389881 original size:31 final size:29
Alignment explanation
Indices: 389841--389909 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
389831 TTATAATATA
* *
389841 TAATGATTATTTTGTAAAAACTTAATAAATT
1 TAATAATTATTTTATAAAAAC-TAA-AAATT
* *
389872 TAATAATTATTTTATAAAATCTAAAATTT
1 TAATAATTATTTTATAAAAACTAAAAATT
389901 TAATAATTA
1 TAATAATTA
389910 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.38
30 3 0.09
31 18 0.53
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (29 bp):
TAATAATTATTTTATAAAAACTAAAAATT
Done.