Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000206.1 Hibiscus syriacus cultivar Beakdansim tig00000366_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: 74074
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2110 original size:3 final size:3
Alignment explanation
Indices: 2102--2147 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
2092 TTATTTATGT
* *
2102 TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC ATC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2148 CACACACTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:11183 original size:25 final size:27
Alignment explanation
Indices: 11123--11186 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
11113 TATATGAGAA
11123 TTTGAAAATTTTAAGAAAATATCATAAT
1 TTTG-AAATTTTAAGAAAATATCATAAT
*
11151 TTTGAAATTTT-A-AAATTATCATATAT
1 TTTGAAATTTTAAGAAAATATCATA-AT
11177 TTT-AAATTTT
1 TTTGAAATTTT
11187 TTCTTTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 17 0.50
26 6 0.18
27 7 0.21
28 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTGAAATTTTAAGAAAATATCATAAT
Found at i:17445 original size:22 final size:22
Alignment explanation
Indices: 17415--17458 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17405 CATTATTATC
**
17415 AAAAATTTATTTTTATATCTTT
1 AAAAATTTATAATTATATCTTT
*
17437 AAAATTTTATAATTATATCTTT
1 AAAAATTTATAATTATATCTTT
17459 TAGATCTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (22 bp):
AAAAATTTATAATTATATCTTT
Found at i:18138 original size:18 final size:18
Alignment explanation
Indices: 18099--18142 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18089 ATATTCTCAA
* *
18099 TAATCTTATTCCCATCGT
1 TAATCTTATTCCCACCGG
*
18117 TAATCTTATTCCCGCCGG
1 TAATCTTATTCCCACCGG
18135 TAATCTTA
1 TAATCTTA
18143 CCTTACGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (18 bp):
TAATCTTATTCCCACCGG
Found at i:22920 original size:44 final size:44
Alignment explanation
Indices: 22870--22956 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
22860 ACAAACACAA
* *
22870 CCCAATTCAGCAGTGATATATTTGTAAAATGAAGAATTTAGCAG
1 CCCAATTCAGCAGTGATATATTTGTAAAAGGAAAAATTTAGCAG
*
22914 CCCAATTCAGCAGTGATATGTTTGTAAAAGGAAAAATTTAGCA
1 CCCAATTCAGCAGTGATATATTTGTAAAAGGAAAAATTTAGCA
22957 ATAAAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (44 bp):
CCCAATTCAGCAGTGATATATTTGTAAAAGGAAAAATTTAGCAG
Found at i:30731 original size:42 final size:42
Alignment explanation
Indices: 30633--30771 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
30623 TTTATTGTAA
* * * * * *
30633 AAACACCGTAATAGAGTATAAATTTTGTGGCGTTT-TAACC-C
1 AAACGCCGCAATAGAGTATACATATAGCGGCGTTTAT-ACCAC
* * * *
30674 AAACACCACAATAGAGTGGTA-ATTTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGAGT-ATACATATAGCGGCGTTTATACCAC
* * *
30716 AAACGTCGCAATAGAGTATACATATAGCGGCGTTTATTCCTC
1 AAACGCCGCAATAGAGTATACATATAGCGGCGTTTATACCAC
30758 AAACGCCGCAATAG
1 AAACGCCGCAATAG
30772 TGTTAATCAA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 32 0.40
42 49 0.60
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTATACATATAGCGGCGTTTATACCAC
Found at i:30808 original size:41 final size:41
Alignment explanation
Indices: 30757--30876 Score: 188
Period size: 41 Copynumber: 2.9 Consensus size: 41
30747 GTTTATTCCT
30757 CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
*
30798 CAAACACCGCAATAGTGTTAATCAATAGTGGCA-TTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGG-AGTTTTTAGA
* * *
30839 CAAACGCCACAATAGTGTTAATCGATAGTGGCGTTTTT
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTT
30877 TTTTGTATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 71 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
Found at i:31022 original size:41 final size:40
Alignment explanation
Indices: 30977--31082 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 40
30967 AGAGTTGTAA
30977 TTTAGTGG-TGTTTT-TAAATAAACACCGCAATTGTATTCTCC
1 TTTAGTGGCT-TTTTGT-AATAAACACCGCAATTGTATTCT-C
* * *
31018 TTTAGTGGCTTTTTGTAATAAACTCCGTAATTGTTTTCTC
1 TTTAGTGGCTTTTTGTAATAAACACCGCAATTGTATTCTC
*
31058 TGTTAGTGGCATTTTCGTAATAAAC
1 T-TTAGTGGC-TTTTTGTAATAAAC
31083 GCCGTAATAG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
40 2 0.04
41 40 0.70
42 15 0.26
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (40 bp):
TTTAGTGGCTTTTTGTAATAAACACCGCAATTGTATTCTC
Found at i:32582 original size:16 final size:16
Alignment explanation
Indices: 32558--32592 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
32548 TGCTACCTAC
*
32558 TTTTGTGGTGTTTCAA
1 TTTTATGGTGTTTCAA
32574 TTTTATGGTGTTTCAA
1 TTTTATGGTGTTTCAA
32590 TTT
1 TTT
32593 ATTTGCCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.60
Consensus pattern (16 bp):
TTTTATGGTGTTTCAA
Found at i:39698 original size:21 final size:21
Alignment explanation
Indices: 39674--39725 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
39664 TGAAGCAAGG
39674 GAAGCAGAGAGAGCAGTAGCA
1 GAAGCAGAGAGAGCAGTAGCA
** *
39695 GAAGCAGCCAGAGCAGTAGCG
1 GAAGCAGAGAGAGCAGTAGCA
39716 GAAGCAGAGA
1 GAAGCAGAGA
39726 AAGAAGCAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.38, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAGTAGCA
Found at i:39742 original size:21 final size:21
Alignment explanation
Indices: 39718--39776 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
39708 CAGTAGCGGA
* * *
39718 AGCAGAGAAAGAAGCAGTGGC
1 AGCACAGAGAGAAGCAATGGC
39739 AGCACAGAGAGAAGCAATGGC
1 AGCACAGAGAGAAGCAATGGC
*
39760 AACACAGAGAGAAGCAA
1 AGCACAGAGAGAAGCAA
39777 CACATCAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.32, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAATGGC
Found at i:40319 original size:43 final size:43
Alignment explanation
Indices: 40189--40536 Score: 260
Period size: 43 Copynumber: 8.1 Consensus size: 43
40179 TTTTTAGCAG
* * * * * *
40189 AAACACCGCAAAACATCAATACCTACTGCGGCG--TTTGTGAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATG-AA
* * * * *
40231 AAGACGCCG-TAAAACATTAACACATACTGCGGCG-TTTTAGCGAA
1 AA-ACGCCGCT-AAATATCAACACCTATTGCGGCGTTTTTA-TGAA
* *
40275 AAATGCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTT-TGAA
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTT-TTATGAA
* * ** * * *
40318 AAATGCTGCTAAATATTTACACCTATTGCAGTGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
*
40361 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
* * * * * *
40404 AAACACTGCTAAATATCAACACATATTACGGTGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
* * * * *
40447 AAACGCCGCTAAATATCAACACCTATTACGGTGTTTGTCA-CAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTATGAA
* * *
40490 AAACGCCGCTAAATATCAATACCTATTGCAGCGTTTTTTGTGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCG-TTTTTATGAA
40534 AAA
1 AAA
40537 AACGCCGCAA
Statistics
Matches: 246, Mismatches: 47, Indels: 24
0.78 0.15 0.08
Matches are distributed among these distances:
42 5 0.02
43 218 0.89
44 20 0.08
45 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA
Found at i:40438 original size:86 final size:86
Alignment explanation
Indices: 40279--40484 Score: 290
Period size: 86 Copynumber: 2.4 Consensus size: 86
40269 AGCGAAAAAT
* ** ** *
40279 GCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTTTGAAAAATGCTGCTAAATATTTACACCTA
1 GCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTTTGAAAAACACTGCTAAATATCAACACATA
*
40343 TTGCAGTGTTTTTATGACAAAC
65 TTACAGTGTTTTTATGACAAAC
40365 GCCGCTAAATATCAACACCTATTGCGGCGTTT-TTCTGAAAAACACTGCTAAATATCAACACATA
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGTT-TGAAAAACACTGCTAAATATCAACACATA
*
40429 TTACGGTGTTTTTATGACAAAC
65 TTACAGTGTTTTTATGACAAAC
* *
40451 GCCGCTAAATATCAACACCTATTACGGTGTTTGT
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGT
40485 CACACAAACG
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
85 3 0.03
86 103 0.96
87 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (86 bp):
GCCGCTAAATATCAACACCTATTGCGGCGTTTGTTTGAAAAACACTGCTAAATATCAACACATAT
TACAGTGTTTTTATGACAAAC
Found at i:49389 original size:19 final size:19
Alignment explanation
Indices: 49365--49414 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
49355 ATGCCATCAA
49365 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
49384 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
*
49403 TACATCGATGCA
1 TGCATCGATGCA
49415 CCCCCTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:49773 original size:25 final size:25
Alignment explanation
Indices: 49718--49779 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
49708 ATAAGTCTAG
*
49718 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
49744 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
49769 ATTCATATTAT
1 ATTCATATTAT
49780 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:49871 original size:31 final size:30
Alignment explanation
Indices: 49823--49881 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
49813 TATATAAGCT
49823 ATGTGATAAAATAATGGAACATGATATGTTC
1 ATGTGATAAAATAATGGAA-ATGATATGTTC
* *
49854 ATGTGATAAAGGT-ATGGAAATTATATGT
1 ATGTGATAAA-ATAATGGAAATGATATGT
49882 CTATACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 16 0.64
32 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
ATGTGATAAAATAATGGAAATGATATGTTC
Found at i:60264 original size:36 final size:36
Alignment explanation
Indices: 60217--60331 Score: 124
Period size: 36 Copynumber: 3.2 Consensus size: 36
60207 TTTACAAATT
* **
60217 TTGAAATTGTTTTATTTGAAACAAA-ATTGATCTCAC
1 TTGAGATTGTTTTATTAAAAACAAATATTG-TCTCAC
* *
60253 TTGAGATTGTTTTCTTAAAAACAAATTTTGTCTCAC
1 TTGAGATTGTTTTATTAAAAACAAATATTGTCTCAC
** * *
60289 TTGAGAAAGTTTCTCTTAAAAACAAATTTTGTCTCAC
1 TTGAGATTGTTT-TATTAAAAACAAATATTGTCTCAC
60326 TTGAGA
1 TTGAGA
60332 CAATCTTCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
36 37 0.53
37 33 0.47
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (36 bp):
TTGAGATTGTTTTATTAAAAACAAATATTGTCTCAC
Found at i:60344 original size:37 final size:37
Alignment explanation
Indices: 60247--60331 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
60237 ACAAAATTGA
**
60247 TCTCACTTGAGATTGTTT-TCTTAAAAACAAATTTTG
1 TCTCACTTGAGAAAGTTTCTCTTAAAAACAAATTTTG
60283 TCTCACTTGAGAAAGTTTCTCTTAAAAACAAATTTTG
1 TCTCACTTGAGAAAGTTTCTCTTAAAAACAAATTTTG
60320 TCTCACTTGAGA
1 TCTCACTTGAGA
60332 CAATCTTCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 16 0.35
37 30 0.65
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
TCTCACTTGAGAAAGTTTCTCTTAAAAACAAATTTTG
Found at i:60433 original size:68 final size:67
Alignment explanation
Indices: 60297--60436 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 67
60287 ACTTGAGAAA
** * * *
60297 GTTTCTCTTAAAAACAAATTTTGTCTCACTTGAGACAATCTTCCTTAAGACACGAACATTTGAGA
1 GTTTCTCTTAAAAACAAATTTCATCTCACTTGAGACAATCTTCCCTAAAACACGAACATTTGAAA
60362 TT
66 TT
* *
60364 GTTTTTCTTAAAAAACAAATTTCATCTCACTTGAGACAGT-TTCCCCTAGAAACAC-AA-ATTCT
1 GTTTCTCTT-AAAAACAAATTTCATCTCACTTGAGACAATCTT-CCCTA-AAACACGAACATT-T
60426 GAAATT
62 GAAATT
60432 GTTTC
1 GTTTC
60437 ACTTGAAACA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
67 13 0.21
68 43 0.70
69 5 0.08
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (67 bp):
GTTTCTCTTAAAAACAAATTTCATCTCACTTGAGACAATCTTCCCTAAAACACGAACATTTGAAA
TT
Found at i:60477 original size:104 final size:105
Alignment explanation
Indices: 60351--60574 Score: 346
Period size: 104 Copynumber: 2.1 Consensus size: 105
60341 TTAAGACACG
60351 AACATTTGAGATTGTTTTTCTTAAAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCT-AGAA
1 AACATTTGAGATTGTTTTTCTT-AAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCTCA-AA
60415 ACAC-AAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT-
64 ACACAAAATTCTGAAATTGTTTCACTTGAAACAAAATTGATA
* * * * *
60455 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCGCTTGAGATAGTTTTCGCTCAAAAT
1 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCTCAAAAC
*
60520 ACAAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATA
66 ACAAAATTCTGAAATTGTTTCACTTGAAACAAAATTGATA
*
60560 AACCTTTGAGATTGT
1 AACATTTGAGATTGT
60575 GTCTCTCGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
103 38 0.35
104 58 0.53
105 14 0.13
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (105 bp):
AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCTCAAAAC
ACAAAATTCTGAAATTGTTTCACTTGAAACAAAATTGATA
Found at i:60587 original size:104 final size:103
Alignment explanation
Indices: 60351--60614 Score: 334
Period size: 104 Copynumber: 2.5 Consensus size: 103
60341 TTAAGACACG
* * * * * *
60351 AACATTTGAGATTGTTTTTCTTAAAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCTAGAAA
1 AACATTTGAGATTGTGTCTCTT-AAAAACAAATTTCATCTCGCTTGAGATAGTTTTCCCTAAAAA
60416 CACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
65 CACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
* * *
60455 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCTCGCTTGAGATAGTTTTCGCTCAAAAT
1 AACATTTGAGATTGTGTCTCTTAAAAACAAATTTCATCTCGCTTGAGATAGTTTTCCCT-AAAA-
*
60520 ACA-AAATTTTGAAATTGTTTCACTTGAAACAAAATTGAT
64 ACACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
* ** * *
60559 AAACCTTTGAGATTGTGTCTC-TCGAAACAAAGTTTCGTCTCGCTAGAGATAGTTTT
1 -AACATTTGAGATTGTGTCTCTTAAAAACAAA-TTTCATCTCGCTTGAGATAGTTTT
60615 TCTTGAAATA
Statistics
Matches: 143, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
103 33 0.23
104 68 0.48
105 42 0.29
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (103 bp):
AACATTTGAGATTGTGTCTCTTAAAAACAAATTTCATCTCGCTTGAGATAGTTTTCCCTAAAAAC
ACAAATTCTGAAATTGTTTCACTTGAAACAAAATTGAT
Found at i:60781 original size:66 final size:66
Alignment explanation
Indices: 60682--60929 Score: 320
Period size: 66 Copynumber: 3.8 Consensus size: 66
60672 GCTTGAGACA
* * * * * *
60682 GTTTCTCTTGGAACAAAGTTTTGTTTCTCTTAAGACAGATTCTCTTTAAACATAAACAATTGAGA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACATAAACAATTGAGA
60747 TT
65 TT
* * * **
60749 TTTTCCCTTGAAACAAATTTTGTCTCTCTTAAGACATTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACATAAACAATTGAGAT
60814 T
66 T
* * * * *
60815 GTTTCCCTTGAAGCAAATTTTATCTCGCTTGAGACTGTTTCTCTTGAAACATAAGCAATTGAGAT
1 GTTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACATAAACAATTGAGAT
60880 T
66 T
*
60881 GTTTCCCTTGAAACAAA--TTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 GTTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACA
60930 AATTATCCCT
Statistics
Matches: 159, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
64 30 0.19
66 115 0.72
67 14 0.09
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (66 bp):
GTTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACATAAACAATTGAGAT
T
Found at i:61096 original size:97 final size:97
Alignment explanation
Indices: 60928--61107 Score: 263
Period size: 97 Copynumber: 1.9 Consensus size: 97
60918 TCTCTTGAAA
* * *
60928 CAAATTATCCCTAAAGATGGCTAGACGTCCTCATCATGTAGGAACAATGTCATCCACCGACCAAA
1 CAAATTATCCCTAAAGACGACTAGACGTCATCATCATGTAGGAACAATGTCATCCACCGACCAAA
60993 CTTCCTCATCACATAGGAACCATGTTGTCTCC
66 CTTCCTCATCACATAGGAACCATGTTGTCTCC
* * * * *
61025 CAAATTGTCCCTAAAGACGACTAGACGTTATCTTCATGTAGGAACAATGTCGTTCACCGACCAAA
1 CAAATTATCCCTAAAGACGACTAGACGTCATCATCATGTAGGAACAATGTCATCCACCGACCAAA
*
61090 -TCTCCTCATCACGTAGGA
66 CT-TCCTCATCACATAGGA
61108 GCAGTGTCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 1 0.01
97 72 0.99
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (97 bp):
CAAATTATCCCTAAAGACGACTAGACGTCATCATCATGTAGGAACAATGTCATCCACCGACCAAA
CTTCCTCATCACATAGGAACCATGTTGTCTCC
Found at i:61378 original size:3 final size:3
Alignment explanation
Indices: 61359--61411 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
61349 AGGGTCTAAC
*
61359 TTA TTA TTG TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
61404 TTA ATA TT
1 TTA TTA TT
61412 TATTTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:66614 original size:16 final size:16
Alignment explanation
Indices: 66570--66614 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
66560 TTTAACGACC
*
66570 ACGATGAGCAACACTA
1 ACGATGAGCACCACTA
66586 ACGATGAGCACCACTA
1 ACGATGAGCACCACTA
*
66602 ACGATGAGTACCA
1 ACGATGAGCACCA
66615 ATACTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (16 bp):
ACGATGAGCACCACTA
Found at i:66684 original size:20 final size:22
Alignment explanation
Indices: 66659--66706 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
66649 GATTCAACAT
66659 ATAATT-AAG-AATTATTTAAA
1 ATAATTAAAGAAATTATTTAAA
66679 ATAATTAAAAGTAAATTATTTAAA
1 ATAATT-AAAG-AAATTATTTAAA
66703 ATAA
1 ATAA
66707 AAAGTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
22 3 0.12
24 15 0.62
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATTAAAGAAATTATTTAAA
Found at i:66711 original size:21 final size:23
Alignment explanation
Indices: 66668--66714 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
66658 TATAATTAAG
66668 AATTATTTAAAATAATTAAAAGTA
1 AATTATTTAAAATAA-TAAAAGTA
66692 AATTATTTAAAAT-A-AAAAGTA
1 AATTATTTAAAATAATAAAAGTA
66713 AA
1 AA
66715 CTATACCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.39
23 1 0.04
24 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
AATTATTTAAAATAATAAAAGTA
Found at i:68112 original size:16 final size:16
Alignment explanation
Indices: 68091--68131 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
68081 GACATCCTAA
68091 TTGTTACTGCTTCTAG
1 TTGTTACTGCTTCTAG
68107 TTGTTACTGCTTCTAG
1 TTGTTACTGCTTCTAG
68123 TTGTTACTG
1 TTGTTACTG
68132 ATAGTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (16 bp):
TTGTTACTGCTTCTAG
Found at i:68796 original size:21 final size:23
Alignment explanation
Indices: 68772--68813 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
68762 CTATATATGT
68772 AGTATAGATA-CTCTA-GGGTCA
1 AGTATAGATACCTCTATGGGTCA
*
68793 AGTATTGATACCTCTATGGGT
1 AGTATAGATACCTCTATGGGT
68814 ATCGATACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (23 bp):
AGTATAGATACCTCTATGGGTCA
Found at i:69618 original size:20 final size:21
Alignment explanation
Indices: 69579--69625 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
69569 GGCTAATTGG
*
69579 GCCCAAGACCAACCCAATTAA
1 GCCCAAGACCAACACAATTAA
69600 GCCCAAGACC-ACACAATTAA
1 GCCCAAGACCAACACAATTAA
69620 GCCCAA
1 GCCCAA
69626 CAACTTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.43, C:0.38, G:0.11, T:0.09
Consensus pattern (21 bp):
GCCCAAGACCAACACAATTAA
Found at i:71149 original size:31 final size:31
Alignment explanation
Indices: 71113--71176 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
71103 CTCGAGCTGA
71113 GTTAAACCAAAATGCAGTAGGTTCTAGATGC
1 GTTAAACCAAAATGCAGTAGGTTCTAGATGC
71144 GTTAAACCAAAATGCAGTAGGTTCTAGATGC
1 GTTAAACCAAAATGCAGTAGGTTCTAGATGC
71175 GT
1 GT
71177 CTCCTGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (31 bp):
GTTAAACCAAAATGCAGTAGGTTCTAGATGC
Found at i:72902 original size:40 final size:40
Alignment explanation
Indices: 72858--72984 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 40
72848 ATCTTGAACC
* * *
72858 TTTTTTCCTAGAGTGCCCTTTGTG-GGTTTCACTATAAGTTT
1 TTTTTTCCTAGAGCGCCCTTT-TGAGTTTTCACTCTAAG-TT
* *
72899 TTTTTTGGCTTAGGGCGCCCTTTTGAGTTTTCACTCTAA-TT
1 TTTTTT--CCTAGAGCGCCCTTTTGAGTTTTCACTCTAAGTT
* *
72940 TTTTTTCGTAGAGCGCCCTTTACGAGTTTTCACTCTAAGTT
1 TTTTTTCCTAGAGCGCCCTTT-TGAGTTTTCACTCTAAGTT
72981 TTTT
1 TTTT
72985 AACTTTAGGC
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
39 13 0.18
40 15 0.21
41 20 0.27
42 2 0.03
43 23 0.32
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (40 bp):
TTTTTTCCTAGAGCGCCCTTTTGAGTTTTCACTCTAAGTT
Done.