Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006113.1 Hibiscus syriacus cultivar Beakdansim tig00014489_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: 81423
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4626 original size:23 final size:23
Alignment explanation
Indices: 4596--4642 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4586 GAATCAGTAT
4596 AATTTACTCTAAACCATTTGTAC
1 AATTTACTCTAAACCATTTGTAC
4619 AATTTACTCTAAACCATTTGTAC
1 AATTTACTCTAAACCATTTGTAC
4642 A
1 A
4643 CAAACTGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTACTCTAAACCATTTGTAC
Found at i:4772 original size:17 final size:18
Alignment explanation
Indices: 4752--4790 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
4742 TATAATTACT
4752 TTTTAAATTAATA-ATAA
1 TTTTAAATTAATATATAA
*
4769 TTTTAAATTATTATATAA
1 TTTTAAATTAATATATAA
4787 TTTT
1 TTTT
4791 TATTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATTAATATATAA
Found at i:5038 original size:3 final size:3
Alignment explanation
Indices: 5030--5069 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5020 CTTGTCTCAC
5030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5070 TTCAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5271 original size:15 final size:15
Alignment explanation
Indices: 5251--5280 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5241 TTTCTTCCTC
5251 GCACTAAATTCAGAA
1 GCACTAAATTCAGAA
5266 GCACTAAATTCAGAA
1 GCACTAAATTCAGAA
5281 TTTTGTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
GCACTAAATTCAGAA
Found at i:6947 original size:149 final size:149
Alignment explanation
Indices: 6706--6997 Score: 451
Period size: 149 Copynumber: 2.0 Consensus size: 149
6696 AAGATGTAAA
* * * * *
6706 TGATAGAATTGATGATGTGCATATGATGAGCACTGCAGAAAAAGCTTCAAAATCCGGTGAAGATG
1 TGATAGAACTGATGATGTACATATGATGAACACTGCAGAAAAAACTTCAAAATCAGGTGAAGATG
* * *
6771 ATGAAAAGGAGGGTTTTTTCCGGAACTTTTCAAGGATAAATCCGAGGAAAATAAAGACGGGAATG
66 ATGAAAAGGAGGGTTTTTTCCGGAACTTTTCAAGGATAAAACCGAGGAAAAGAAAGAAGGGAATG
6836 ATAAGAATGATGACGTAGC
131 ATAAGAATGATGACGTAGC
* ** * *
6855 TGATAGAACTGATGATGTACATATGGTGAATTCTGCTGAAAAAACTTCAAAATCAGGTGAATATG
1 TGATAGAACTGATGATGTACATATGATGAACACTGCAGAAAAAACTTCAAAATCAGGTGAAGATG
6920 ATGAAAAGGAGGG-TTTTTCCGGAAACTTTTCAAGGATAAAACCGAGGAAAAGAAAGAAGGGAAT
66 ATGAAAAGGAGGGTTTTTTCCGG-AACTTTTCAAGGATAAAACCGAGGAAAAGAAAGAAGGGAAT
6984 GATAAGAATGATGA
130 GATAAGAATGATGA
6998 TGGCGAGGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
148 9 0.07
149 120 0.93
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (149 bp):
TGATAGAACTGATGATGTACATATGATGAACACTGCAGAAAAAACTTCAAAATCAGGTGAAGATG
ATGAAAAGGAGGGTTTTTTCCGGAACTTTTCAAGGATAAAACCGAGGAAAAGAAAGAAGGGAATG
ATAAGAATGATGACGTAGC
Found at i:14692 original size:14 final size:14
Alignment explanation
Indices: 14673--14700 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14663 ATGTTATTAG
14673 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
14687 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
14701 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:17001 original size:51 final size:51
Alignment explanation
Indices: 16925--17025 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
16915 TAAGGAAAGG
* *
16925 ATAGGTTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
16976 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
17026 CTCCCCTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:17880 original size:51 final size:51
Alignment explanation
Indices: 17804--17904 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
17794 TAAGGAAAGG
* *
17804 ATAGGTTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
17855 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
17905 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:19684 original size:14 final size:14
Alignment explanation
Indices: 19665--19692 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19655 CCTGATACCA
19665 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
19679 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
19693 AAGTCTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:30437 original size:60 final size:61
Alignment explanation
Indices: 30316--30437 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 61
30306 TAACATCCAT
**
30316 GAAACTTGAAAGAAAACATTAATGGAATGTAGAGCTAACAAATTCACTCAACCAAACACAA
1 GAAACTTGAAAGAAAACAACAATGGAATGTAGAGCTAACAAATTCACTCAACCAAACACAA
* * * * *
30377 GAAACTTGAAAGCAAACAACAATGG-GTGTAGAGCTAATAAATGT-ACTCAACGAAATACAA
1 GAAACTTGAAAGAAAACAACAATGGAATGTAGAGCTAACAAAT-TCACTCAACCAAACACAA
30437 G
1 G
30438 TTCAAGTCAG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 30 0.57
61 23 0.43
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (61 bp):
GAAACTTGAAAGAAAACAACAATGGAATGTAGAGCTAACAAATTCACTCAACCAAACACAA
Found at i:50585 original size:29 final size:29
Alignment explanation
Indices: 50543--50602 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
50533 TCAGTAAAGC
50543 TTCTGTTAATGCCAATATAATGCTATTGT
1 TTCTGTTAATGCCAATATAATGCTATTGT
50572 TTCTGTTAATGCCAATATAATGCTATTGT
1 TTCTGTTAATGCCAATATAATGCTATTGT
50601 TT
1 TT
50603 GAAATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (29 bp):
TTCTGTTAATGCCAATATAATGCTATTGT
Found at i:54261 original size:16 final size:16
Alignment explanation
Indices: 54240--54284 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
54230 AATATACGGC
54240 GTGACCGGTTAAATAA
1 GTGACCGGTTAAATAA
54256 GTGACCGGTTAAATAA
1 GTGACCGGTTAAATAA
54272 GTGACCGGTTAAA
1 GTGACCGGTTAAA
54285 ATTTAGACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (16 bp):
GTGACCGGTTAAATAA
Found at i:54361 original size:23 final size:23
Alignment explanation
Indices: 54335--54382 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
54325 ATAAAGTACA
*
54335 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
54358 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
54381 AT
1 AT
54383 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:54836 original size:23 final size:23
Alignment explanation
Indices: 54800--54895 Score: 138
Period size: 23 Copynumber: 4.2 Consensus size: 23
54790 ACACTTTACA
* * *
54800 ATATAACCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATC
* * *
54823 ATATAAACGATACCTATTACATT
1 ATATAAGCGCTACCTATTACATC
54846 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATC
54869 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATC
54892 ATAT
1 ATAT
54896 GTTTACCTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATC
Found at i:55354 original size:39 final size:39
Alignment explanation
Indices: 55300--55386 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
55290 TCAAGTTGTA
*
55300 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
55339 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
55378 AATTTTGAT
1 GATTTTGAT
55387 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:55665 original size:18 final size:18
Alignment explanation
Indices: 55642--55678 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55632 CGAAATATAT
55642 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
55660 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
55678 A
1 A
55679 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:56094 original size:25 final size:25
Alignment explanation
Indices: 56066--56116 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
56056 ATTTTCCAAA
*
56066 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
56091 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
56116 T
1 T
56117 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:56406 original size:21 final size:22
Alignment explanation
Indices: 56381--56432 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
56371 ACACTTTACA
*
56381 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
56404 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
56427 ATATAA
1 ATATAA
56433 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:56417 original size:23 final size:23
Alignment explanation
Indices: 56391--56453 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
56381 ATATAACCAC
56391 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
56414 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
56437 TACCTATTACATCATAT
1 TACCTATTACATTATAT
56454 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:56852 original size:25 final size:25
Alignment explanation
Indices: 56795--56860 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
56785 CACTCAAAAG
*
56795 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
56820 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
56845 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
56861 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:60124 original size:182 final size:183
Alignment explanation
Indices: 59327--60217 Score: 1631
Period size: 183 Copynumber: 4.9 Consensus size: 183
59317 TTAAAATTAC
* *
59327 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
59392 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
59457 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
59510 CGATACTTTTTTAAATCGTATCGACACATTTTCCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
59575 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
59640 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
59693 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACTGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
59758 ATTAAAAAGTTTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
59823 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
59876 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
59941 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
60006 ATATTACAAAATTATCTATTACA-TATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
60058 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
60123 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
60188 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
60218 ATGTTGAAAG
Statistics
Matches: 688, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
182 177 0.26
183 511 0.74
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:63484 original size:17 final size:18
Alignment explanation
Indices: 63462--63504 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
63452 ATATATCCGG
63462 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
63479 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
63499 TATCAT
1 TATCAT
63505 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:63522 original size:20 final size:19
Alignment explanation
Indices: 63467--63513 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
63457 TCCGGTATCA
63467 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
63486 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
63507 TTTTACC
1 TTTTACC
63514 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:63687 original size:20 final size:18
Alignment explanation
Indices: 63635--63692 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
63625 CACTTTTAAA
63635 TTTACCGGTTTATCATTT
1 TTTACCGGTTTATCATTT
*
63653 GTTACCGGTTTTATCATATT
1 TTTACCGG-TTTATCAT-TT
* *
63673 TTTACCTGGTATATCGTTT
1 TTTACC-GGTTTATCATTT
63692 T
1 T
63693 GGATCGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 7 0.21
19 11 0.33
20 13 0.39
21 2 0.06
ACGTcount: A:0.17, C:0.16, G:0.14, T:0.53
Consensus pattern (18 bp):
TTTACCGGTTTATCATTT
Found at i:64144 original size:227 final size:226
Alignment explanation
Indices: 63744--64184 Score: 776
Period size: 227 Copynumber: 1.9 Consensus size: 226
63734 TTAAAACTGC
*
63744 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTATAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
63809 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
63874 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
63939 GTATGGACACTTTTATAAAATGATATATACTT
195 GTATGGACACTTTTATAAAATGATATATACTT
*
63971 TTTTGAAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCTACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
64035 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
64100 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAA
130 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAA
64165 GTATGGACACTTTTATAAAA
195 GTATGGACACTTTTATAAAA
64185 AGGATAGATA
Statistics
Matches: 204, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
226 32 0.16
227 145 0.71
228 27 0.13
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAATGATATATACTT
Found at i:67812 original size:54 final size:55
Alignment explanation
Indices: 67717--67826 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
67707 GAAAACTTAA
67717 ACAAAAAATGGTCCCAAGAAAACAATTGGCAACTGTGAATCAATATACGATTTAC
1 ACAAAAAATGGTCCCAAGAAAACAATTGGCAACTGTGAATCAATATACGATTTAC
**
67772 ACAAAAAATGGTCCGGAGAAAACAATTGGC-ACTGTGAATCAATATACGATTTAC
1 ACAAAAAATGGTCCCAAGAAAACAATTGGCAACTGTGAATCAATATACGATTTAC
67826 A
1 A
67827 GTGGACTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 25 0.47
55 28 0.53
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (55 bp):
ACAAAAAATGGTCCCAAGAAAACAATTGGCAACTGTGAATCAATATACGATTTAC
Found at i:71393 original size:6 final size:6
Alignment explanation
Indices: 71382--71406 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71372 CTAAATTTAG
71382 GCTGTT GCTGTT GCTGTT GCTGTT G
1 GCTGTT GCTGTT GCTGTT GCTGTT G
71407 GTGGCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (6 bp):
GCTGTT
Found at i:73751 original size:31 final size:31
Alignment explanation
Indices: 73713--73965 Score: 240
Period size: 31 Copynumber: 8.1 Consensus size: 31
73703 ACATATACAT
73713 AAGTGATGATGTGATACATGTCACATGT-TCA
1 AAGTGATGATGTGATACATGTCACATGTCT-A
* **
73744 AAGTGATGATGTGATACACGTCATGTGTCTA
1 AAGTGATGATGTGATACATGTCACATGTCTA
* * ** *
73775 AAATGACGAAATGATACATATCACATGTCTA
1 AAGTGATGATGTGATACATGTCACATGTCTA
* * * *
73806 AAGTGATTATGTGAAATATGTCATATGTCTA
1 AAGTGATGATGTGATACATGTCACATGTCTA
* * * *
73837 AAATGACGATATGATACATATCACATGTCTA
1 AAGTGATGATGTGATACATGTCACATGTCTA
* * *
73868 AAGTGATTATGTGAAATATGTCACATGTAC-A
1 AAGTGATGATGTGATACATGTCACATGT-CTA
* *
73899 TAAGTGATGATGTGATACATATCACGTGTCTA
1 -AAGTGATGATGTGATACATGTCACATGTCTA
* * * *
73931 AAGTGATGATATAATACATGTCACGTATCTA
1 AAGTGATGATGTGATACATGTCACATGTCTA
73962 AAGT
1 AAGT
73966 AATAAATAAT
Statistics
Matches: 174, Mismatches: 44, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
31 148 0.85
32 26 0.15
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (31 bp):
AAGTGATGATGTGATACATGTCACATGTCTA
Found at i:73977 original size:30 final size:30
Alignment explanation
Indices: 73913--74013 Score: 157
Period size: 30 Copynumber: 3.3 Consensus size: 30
73903 TGATGATGTG
* * * *
73913 ATACATATCACGTGTCTAAAGTGATGATATA
1 ATACATGTCACGTATCTAAAGTAAT-AAATA
73944 ATACATGTCACGTATCTAAAGTAATAAATA
1 ATACATGTCACGTATCTAAAGTAATAAATA
73974 ATACATGTCACGTATCTAAAGTAATAAATA
1 ATACATGTCACGTATCTAAAGTAATAAATA
74004 ATACATGTCA
1 ATACATGTCA
74014 TATTATTCTT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 44 0.67
31 22 0.33
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (30 bp):
ATACATGTCACGTATCTAAAGTAATAAATA
Done.