Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008362.1 Hibiscus syriacus cultivar Beakdansim tig00111101_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: 636979
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 3 of 3
Found at i:555771 original size:165 final size:165
Alignment explanation
Indices: 555499--555884 Score: 763
Period size: 165 Copynumber: 2.3 Consensus size: 165
555489 ATAACCCTTC
*
555499 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
555564 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
66 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
555629 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
131 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
555664 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
555729 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
66 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
555794 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
131 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
555829 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
1 ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
555885 AGTTTGTTTA
Statistics
Matches: 220, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 220 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (165 bp):
ACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
Found at i:562485 original size:35 final size:35
Alignment explanation
Indices: 562446--562738 Score: 187
Period size: 36 Copynumber: 8.2 Consensus size: 35
562436 CAAAATGCTT
* * *
562446 TTTTAAAACTATATATTATACATGTTTTTAAAACG
1 TTTTAAAACTATATATTATATATATTTTTAAAATG
* *
562481 TTTTAAAA--AT-T-TTATAATATATTTTCAGAAACG
1 TTTTAAAACTATATATTAT-ATATATTTTTA-AAATG
* *
562514 GTTTAAAAAT-TATA-TATATATATTTTTAAAATG
1 TTTTAAAACTATATATTATATATATTTTTAAAATG
* * **
562547 TTTTTCAAAAATTATATATT-TA-ATGTTTTTAAAAAA
1 -TTTT--AAAACTATATATTATATATATTTTTAAAATG
* *
562583 ATTCAAAAC-ATATATTATATA-ATTTTTCAAAAATG
1 TTTTAAAACTATATATTATATATATTTTT--AAAATG
562618 ATTTTAAAAACTATATATTATATATATATTTTCTAAAATG
1 -TTTT-AAAACTATATA-T-TATATATATTTT-TAAAATG
** *
562658 TTTTAAAAACTATATA--ATATATAGTTTCAACAAATAT
1 TTTT-AAAACTATATATTATATATA-TTTTTA-AAAT-G
* *
562695 TTTTAAAACTATATATTATATACATTTTCAAAATG
1 TTTTAAAACTATATATTATATATATTTTTAAAATG
562730 TTTTCAAAA
1 TTTT-AAAA
562739 ATTATGTATA
Statistics
Matches: 204, Mismatches: 26, Indels: 55
0.72 0.09 0.19
Matches are distributed among these distances:
31 4 0.02
32 16 0.08
33 29 0.14
34 15 0.07
35 30 0.15
36 44 0.22
37 19 0.09
38 12 0.06
39 17 0.08
40 12 0.06
41 5 0.02
42 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAACTATATATTATATATATTTTTAAAATG
Found at i:562519 original size:33 final size:34
Alignment explanation
Indices: 562476--562565 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
562466 CATGTTTTTA
* *
562476 AAACGTTTTAAAAATTTTATA-ATATATTTTCAG
1 AAACGGTTTAAAAATTATATATATATATTTTCAG
*
562509 AAACGGTTTAAAAATTATATATATATATTTTTA-
1 AAACGGTTTAAAAATTATATATATATATTTTCAG
* *
562542 AAATGTTTTTCAAAAATTATATAT
1 AAACG-GTTT-AAAAATTATATAT
562566 TTAATGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 23 0.47
34 13 0.27
35 13 0.27
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (34 bp):
AAACGGTTTAAAAATTATATATATATATTTTCAG
Found at i:563631 original size:2 final size:2
Alignment explanation
Indices: 563616--563656 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
563606 ATAATTTCTA
*
563616 AT AT AT GT AT -T 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
563657 TATTTGAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:568057 original size:21 final size:20
Alignment explanation
Indices: 568031--568070 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
568021 AAAATGATAA
568031 ATTAGGGTTAGAGATATTAAT
1 ATTAGGGTTAGAGAT-TTAAT
* *
568052 ATTAGGTTTAGGGATTTAA
1 ATTAGGGTTAGAGATTTAA
568071 GTTTGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTAGGGTTAGAGATTTAAT
Found at i:582676 original size:19 final size:19
Alignment explanation
Indices: 582644--582710 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
582634 TTATTTTACT
582644 TAAATTATTATTATTA-TTA
1 TAAA-TATTATTATTATTTA
582663 TAAATATTATT-TATATTTA
1 TAAATATTATTAT-TATTTA
*
582682 TATATATTATTATTATTTAA
1 TAAATATTATTATTATTT-A
582702 TAAATATTA
1 TAAATATTA
582711 CAAACCCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.02
18 9 0.21
19 22 0.52
20 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATATTATTATTATTTA
Found at i:584048 original size:3 final size:3
Alignment explanation
Indices: 584030--584091 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
584020 TATTTTAATC
* *
584030 ATT ATTT ATT -TT ATT ATT ATT ATT TTT ATT GTT -TT AATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
*
584075 -TC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
584092 CATAAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
2 5 0.10
3 39 0.80
4 5 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:584415 original size:30 final size:28
Alignment explanation
Indices: 584369--584424 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
584359 TCATTTTCTG
584369 ATATTTTTAAATAAATAAATATTTTATTT
1 ATATTTTTAAATAAATAAAT-TTTTATTT
* *
584398 ATATTTTATATATAAATATATTTTTAT
1 ATATTTT-TAAATAAATAAATTTTTAT
584425 ATAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATTTTTAAATAAATAAATTTTTATTT
Found at i:584432 original size:26 final size:26
Alignment explanation
Indices: 584383--584433 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
584373 TTTTAAATAA
* *
584383 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
584409 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
584434 ACTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:587496 original size:34 final size:34
Alignment explanation
Indices: 587458--587525 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
587448 TCACAACCAC
*
587458 TTAAATACTAATGTGGT-ATATATTA-TATTAACAA
1 TTAAATAC--ATGTGGTAATATATTACTAATAACAA
587492 TTAAATACATGTGGTAATATATTACTAATAACAA
1 TTAAATACATGTGGTAATATATTACTAATAACAA
587526 AATATTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.23
33 8 0.26
34 16 0.52
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (34 bp):
TTAAATACATGTGGTAATATATTACTAATAACAA
Found at i:589119 original size:22 final size:22
Alignment explanation
Indices: 589082--589124 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
589072 CTAAACCAAT
589082 TAATTATTAATAAAAT-TTAAA
1 TAATTATTAATAAAATATTAAA
*
589103 TAATTACTTAATCAAATATTAA
1 TAATTA-TTAATAAAATATTAA
589125 TAACATTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATTATTAATAAAATATTAAA
Found at i:604011 original size:18 final size:18
Alignment explanation
Indices: 603988--604023 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
603978 CTGTCATGGT
603988 ACATTGATCCACACACCG
1 ACATTGATCCACACACCG
604006 ACATTGATCCACACACCG
1 ACATTGATCCACACACCG
604024 TTGTCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.39, G:0.11, T:0.17
Consensus pattern (18 bp):
ACATTGATCCACACACCG
Found at i:605587 original size:20 final size:20
Alignment explanation
Indices: 605562--605718 Score: 100
Period size: 20 Copynumber: 7.8 Consensus size: 20
605552 GTTTCTGAAA
* *
605562 TCGCAACGCGAATTTGGTAT
1 TCGCAACACGAATTTCGTAT
*
605582 TCGCAACACGGAATTTCTGAAT
1 TCGCAACAC-GAATTTC-GTAT
** * *
605604 TCGCAACGTGAATTTCTTTT
1 TCGCAACACGAATTTCGTAT
* * * * *
605624 TTGGAACGCGAATTTCTTTT
1 TCGCAACACGAATTTCGTAT
* **
605644 TCGCAACAAG-ATTTTTTAAT
1 TCGCAACACGAATTTCGT-AT
* *
605664 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTCGTAT
* * *
605684 TCGCAACTCGATTTTCATAT
1 TCGCAACACGAATTTCGTAT
605704 TCGCAACACGAATTT
1 TCGCAACACGAATTT
605719 TAATTTAGCA
Statistics
Matches: 106, Mismatches: 27, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
19 6 0.06
20 71 0.67
21 19 0.18
22 10 0.09
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (20 bp):
TCGCAACACGAATTTCGTAT
Found at i:605608 original size:22 final size:21
Alignment explanation
Indices: 605522--605718 Score: 90
Period size: 20 Copynumber: 9.8 Consensus size: 21
605512 GAACTCCAAT
*
605522 TTCGCAACAC-AATTT-TAAA
1 TTCGCAACACGAATTTCTGAA
* * *
605541 TTCGGAACTC-AGTTTCTGAA
1 TTCGCAACACGAATTTCTGAA
* * * *
605561 ATCGCAACGCGAATTT-GGTA
1 TTCGCAACACGAATTTCTGAA
605581 TTCGCAACACGGAATTTCTGAA
1 TTCGCAACAC-GAATTTCTGAA
** **
605603 TTCGCAACGTGAATTTCT-TT
1 TTCGCAACACGAATTTCTGAA
* * * **
605623 TTTGGAACGCGAATTTCT-TT
1 TTCGCAACACGAATTTCTGAA
* * *
605643 TTCGCAACAAG-ATTTTTTAA
1 TTCGCAACACGAATTTCTGAA
**
605663 TTCGCAACACGAATTT-TGTT
1 TTCGCAACACGAATTTCTGAA
* *
605683 TTCGCAACTCG-ATTT-TCATA
1 TTCGCAACACGAATTTCTGA-A
605703 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
605719 TAATTTAGCA
Statistics
Matches: 133, Mismatches: 37, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
19 22 0.17
20 75 0.56
21 26 0.20
22 10 0.08
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (21 bp):
TTCGCAACACGAATTTCTGAA
Found at i:605616 original size:21 final size:20
Alignment explanation
Indices: 605553--605620 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
605543 CGGAACTCAG
*
605553 TTTCTGAAATCGCAACGCGAA
1 TTTCTGAATTCGCAACG-GAA
* *
605574 TTT-GGTATTCGCAACACGGAA
1 TTTCTGAATTCGC-A-ACGGAA
605595 TTTCTGAATTCGCAACGTGAA
1 TTTCTGAATTCGCAACG-GAA
605616 TTTCT
1 TTTCT
605621 TTTTTGGAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
20 9 0.24
21 19 0.50
22 10 0.26
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (20 bp):
TTTCTGAATTCGCAACGGAA
Found at i:605676 original size:40 final size:40
Alignment explanation
Indices: 605632--605750 Score: 122
Period size: 40 Copynumber: 3.0 Consensus size: 40
605622 TTTTGGAACG
605632 CGAATTTCT-TTTTCGCAACAAGATTTTTTAATTCGCAACA
1 CGAATTT-TATTTTCGCAACAAGATTTTTTAATTCGCAACA
* ** *
605672 CGAATTTTGTTTTCGCAACTCGA-TTTTCATATTCGCAACA
1 CGAATTTTATTTTCGCAACAAGATTTTTTA-ATTCGCAACA
* *
605712 CGAATTTTAATTTAGCAACAA-ATTTTATT--TTCGCAACA
1 CGAATTTTATTTTCGCAACAAGATTTT-TTAATTCGCAACA
605750 C
1 C
605751 AAATGTTTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
38 10 0.15
39 7 0.11
40 48 0.73
41 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (40 bp):
CGAATTTTATTTTCGCAACAAGATTTTTTAATTCGCAACA
Found at i:605729 original size:20 final size:20
Alignment explanation
Indices: 605642--605750 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
605632 CGAATTTCTT
* *
605642 TTTCGCAACAAGATTTTTTAA
1 TTTCGCAACACGA-ATTTTAA
**
605663 -TTCGCAACACGAATTTTGT
1 TTTCGCAACACGAATTTTAA
* *
605682 TTTCGCAACTCG-ATTTTCA
1 TTTCGCAACACGAATTTTAA
605701 TATTCGCAACACGAATTTTAA
1 T-TTCGCAACACGAATTTTAA
* *
605722 TTTAGCAACA--AATTTTAT
1 TTTCGCAACACGAATTTTAA
605740 TTTCGCAACAC
1 TTTCGCAACAC
605751 AAATGTTTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
18 16 0.22
19 10 0.14
20 39 0.54
21 7 0.10
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTCGCAACACGAATTTTAA
Found at i:605737 original size:18 final size:18
Alignment explanation
Indices: 605714--605749 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
605704 TCGCAACACG
605714 AATTTTAATTTAGCAACA
1 AATTTTAATTTAGCAACA
* *
605732 AATTTTATTTTCGCAACA
1 AATTTTAATTTAGCAACA
605750 CAAATGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (18 bp):
AATTTTAATTTAGCAACA
Found at i:610128 original size:15 final size:16
Alignment explanation
Indices: 610108--610145 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
610098 TTAATTAAAT
610108 TATATTAATT-TCATA
1 TATATTAATTATCATA
*
610123 TATATTAATTATCATT
1 TATATTAATTATCATA
610139 TATATTA
1 TATATTA
610146 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTAATTATCATA
Found at i:610896 original size:19 final size:19
Alignment explanation
Indices: 610855--610897 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
610845 TCAATTTACA
*
610855 ATTATAATTGTAAATCTTC
1 ATTATAATTGTAAATATTC
* *
610874 ATTATAATTTTAAATATTT
1 ATTATAATTGTAAATATTC
610893 ATTAT
1 ATTAT
610898 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTATAATTGTAAATATTC
Found at i:614095 original size:39 final size:39
Alignment explanation
Indices: 614051--614130 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
614041 TTACAAAAGT
*
614051 ATTAAACATAAAAGATGAG-TTTACAGTAGTTTGTATAAA
1 ATTAAACATAAAAGA-GAGTTTTACAATAGTTTGTATAAA
* *
614090 ATTAAACATATAAGAGAGTTTTACAATAGTTTTTATAAA
1 ATTAAACATAAAAGAGAGTTTTACAATAGTTTGTATAAA
614129 AT
1 AT
614131 AAAGAGGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 3 0.08
39 34 0.92
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (39 bp):
ATTAAACATAAAAGAGAGTTTTACAATAGTTTGTATAAA
Found at i:614189 original size:18 final size:18
Alignment explanation
Indices: 614166--614202 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
614156 GTTAGTGGGT
614166 AAAAATTGAGTGAAAGTA
1 AAAAATTGAGTGAAAGTA
614184 AAAAATTGAGTGAAAGTA
1 AAAAATTGAGTGAAAGTA
614202 A
1 A
614203 GTATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAAATTGAGTGAAAGTA
Found at i:617655 original size:17 final size:17
Alignment explanation
Indices: 617635--617668 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
617625 CCACCTGATC
617635 AAAATACCATGTTACCG
1 AAAATACCATGTTACCG
617652 AAAATACCATGTTACCG
1 AAAATACCATGTTACCG
617669 GCAGCAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAATACCATGTTACCG
Found at i:623569 original size:40 final size:40
Alignment explanation
Indices: 623525--623601 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
623515 ATATAAATGA
*
623525 TAGTGACACATAATTTATTGCACCCTTA-AAAATCATATGC
1 TAGTGAAACATAATTTATTGCACCC-TAGAAAATCATATGC
** *
623565 TAGTGAAAGGTAATTTATTGCGCCCTAGAAAATCATA
1 TAGTGAAACATAATTTATTGCACCCTAGAAAATCATA
623602 AAGATAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (40 bp):
TAGTGAAACATAATTTATTGCACCCTAGAAAATCATATGC
Found at i:624614 original size:25 final size:25
Alignment explanation
Indices: 624586--624672 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
624576 ATTAGTCTTT
624586 TAATC-TCATCAAAAAAAGCAATCAG
1 TAATCATCATC-AAAAAAGCAATCAG
* * ** * **
624611 TAATCGTCACCCGTAAAAGTAATCTTT
1 TAATCATCA-TCAAAAAAGCAATC-AG
*
624638 TAATC-TCATCAGAAAAGCAATCAG
1 TAATCATCATCAAAAAAGCAATCAG
624662 TAATCATCATC
1 TAATCATCATC
624673 CGTAGAAAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
24 5 0.11
25 20 0.43
26 15 0.33
27 6 0.13
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (25 bp):
TAATCATCATCAAAAAAGCAATCAG
Found at i:624676 original size:51 final size:52
Alignment explanation
Indices: 624571--624676 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 52
624561 AAGTTACCAT
* * *
624571 GTAAAATTAGTCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCGTCACCC
1 GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
* *
624623 GTAAAAGTAATCTTTTAATCTCATC-AGAAAAGCAATCAGTAATCATCATCC
1 GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
624674 GTA
1 GTA
624677 GAAAACAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 26 0.53
52 23 0.47
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (52 bp):
GTAAAAGTAATCTTTTAATCTCATCAAAAAAAGCAATCAGTAATCATCACCC
Found at i:625762 original size:34 final size:34
Alignment explanation
Indices: 625724--625803 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
625714 TATTTCAATG
625724 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
1 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
625758 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
1 AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
*
625792 AATAAATTTTAA
1 AATTAATTTTAA
625804 ATAACTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (34 bp):
AATTAATTTTAAGCGTGTACTTGTTTTATTAAAT
Found at i:631830 original size:30 final size:31
Alignment explanation
Indices: 631785--631845 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
631775 AGAGAAAGTG
631785 TTTAATTGATTTAATTTAAAAATTCAATTAA
1 TTTAATTGATTTAATTTAAAAATTCAATTAA
* * *
631816 TTTAATT-TTTTAATTTAAAAGTTGAATTAA
1 TTTAATTGATTTAATTTAAAAATTCAATTAA
631846 GTGTAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTAATTGATTTAATTTAAAAATTCAATTAA
Found at i:634439 original size:15 final size:17
Alignment explanation
Indices: 634414--634445 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
634404 TATAGCCAAG
634414 TTTAGATCTGA-TCAAT
1 TTTAGATCTGATTCAAT
634430 TTTA-ATCTGATTCAAT
1 TTTAGATCTGATTCAAT
634446 CTTATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (17 bp):
TTTAGATCTGATTCAAT
Found at i:636590 original size:2 final size:2
Alignment explanation
Indices: 636585--636614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
636575 TCTCTCTCTC
636585 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
636615 TCATCAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.