Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008809.1 Hibiscus syriacus cultivar Beakdansim tig00111963_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: 55947
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:9056 original size:75 final size:75
Alignment explanation
Indices: 8872--9077 Score: 256
Period size: 74 Copynumber: 2.8 Consensus size: 75
8862 CAAAGCCAAA
* * * * **
8872 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
8937 TTGGCTCCGAG
65 TTGGCTCCGAG
* * *
8948 ATTTCCAGAATGCTCGGAGGGAACTGATT-CCCCCATAGGAGGAACCGATTCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
9012 TTGTTCCGAG
66 TGGCTCCGAG
* *
9022 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCA-AGG-GGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCT
9078 TGTTCAACGG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
74 59 0.52
75 24 0.21
76 30 0.27
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:14882 original size:21 final size:21
Alignment explanation
Indices: 14856--14895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14846 CCCCCTTTGA
*
14856 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
14877 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
14896 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:17619 original size:54 final size:54
Alignment explanation
Indices: 17532--17655 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
17522 CCCCATAGGA
* ** *
17532 GGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTCCAGAATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
* * * *
17586 GGAACCGATTCCCCCCTAAACATTTTTGTTCCGAGAATTCCAGTATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
17640 GGAACCGATTCCCCCC
1 GGAACCGATTCCCCCC
17656 CAAGGGGTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (54 bp):
GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
Found at i:20350 original size:2 final size:2
Alignment explanation
Indices: 20345--20380 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20335 ACACACACAC
20345 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
20381 TCAGGACTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23674 original size:19 final size:19
Alignment explanation
Indices: 23637--23674 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23627 CAAAATGATC
*
23637 AATAAAAATCGCAATGCGA
1 AATAAAAATCGCAACGCGA
*
23656 AATAAAAATCGTAACGCGA
1 AATAAAAATCGCAACGCGA
23675 TCTCCAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
AATAAAAATCGCAACGCGA
Found at i:23807 original size:20 final size:20
Alignment explanation
Indices: 23765--23817 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
23755 GATTTTCCAT
* *
23765 AATCACAACACGAATATGAA
1 AATCACAACGCGAACATGAA
23785 AATCACAACGCGAACAT-ATA
1 AATCACAACGCGAACATGA-A
*
23805 AATCGCAACGCGA
1 AATCACAACGCGA
23818 TTCTAACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.49, C:0.25, G:0.13, T:0.13
Consensus pattern (20 bp):
AATCACAACGCGAACATGAA
Found at i:23849 original size:41 final size:41
Alignment explanation
Indices: 23804--23999 Score: 249
Period size: 41 Copynumber: 4.8 Consensus size: 41
23794 GCGAACATAT
* *
23804 AAATCGCAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTA
1 AAATCGCAACGCGTATTCGTAA--ATCGCAACGAGAATACGTA
*
23845 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
23886 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGT-
1 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
* * * *
23926 AAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGT-
1 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
* *
23966 AAATCGCAATGCG-AATCTGTAAATCGCAACGAGA
1 AAATCGCAACGCGTATTC-GTAAATCGCAACGAGA
24000 TTCTGACTAT
Statistics
Matches: 140, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.01
40 63 0.45
41 69 0.49
42 3 0.02
43 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
Found at i:23870 original size:20 final size:20
Alignment explanation
Indices: 23803--23996 Score: 194
Period size: 20 Copynumber: 9.6 Consensus size: 20
23793 CGCGAACATA
*
23803 TAAATCGCAACGCG-ATTC-
1 TAAATCGCAACGCGAATCCG
* *
23821 TAACTATCGCAACGAGTATCCG
1 TAA--ATCGCAACGCGAATCCG
*
23843 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGAATCCG
* *
23864 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGAATCCG
* *
23884 TAAAATCGCAACGCGTATTCG
1 T-AAATCGCAACGCGAATCCG
* *
23905 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGAATCCG
* *
23925 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGAATCCG
* *
23945 TAAATCGCAATGCGAATACG
1 TAAATCGCAACGCGAATCCG
* *
23965 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGCGAATCCG
23985 TAAATCGCAACG
1 TAAATCGCAACG
23997 AGATTCTGAC
Statistics
Matches: 149, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
18 3 0.02
20 106 0.71
21 37 0.25
22 1 0.01
23 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGAATCCG
Found at i:27472 original size:34 final size:33
Alignment explanation
Indices: 27426--27526 Score: 112
Period size: 34 Copynumber: 3.0 Consensus size: 33
27416 CTTAATGTCT
*
27426 ATCGCAACGCGAAAATTACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATTACTATCGCAACGAGAAA
* * ** *
27460 ATCGCAATGCGAAATGAAAAATCGCAACGTGAAA
1 ATCGCAACGCGAAAT-TACTATCGCAACGAGAAA
* *
27494 ATCGCAACGCGGAATTACTATCGCAACGCGAAA
1 ATCGCAACGCGAAATTACTATCGCAACGAGAAA
27527 TGAAAATCGC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
33 18 0.33
34 36 0.67
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAACGCGAAATTACTATCGCAACGAGAAA
Found at i:27518 original size:19 final size:19
Alignment explanation
Indices: 27459--27543 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
27449 GCAACGAGAG
*
27459 AATCGCAATGCGAAATGAAA
1 AATCGCAACGCGAAATG-AA
27479 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
* * *
27493 AATCGCAACGCGGAATTAC
1 AATCGCAACGCGAAATGAA
*
27512 TATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
27531 AATCGCAACGCGA
1 AATCGCAACGCGA
27544 TTTTAGTTTC
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.19
15 2 0.04
16 2 0.04
18 2 0.04
19 29 0.55
20 8 0.15
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:27555 original size:19 final size:19
Alignment explanation
Indices: 27533--27574 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27523 GAAATGAAAA
27533 TCGCAACGCGATTTTAGTT
1 TCGCAACGCGATTTTAGTT
***
27552 TCGCGTTGCGATTTTAGTT
1 TCGCAACGCGATTTTAGTT
27571 TCGC
1 TCGC
27575 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
TCGCAACGCGATTTTAGTT
Found at i:27575 original size:19 final size:19
Alignment explanation
Indices: 27540--27585 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
27530 AAATCGCAAC
27540 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
27559 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
27578 GCGATTTT
1 GCGATTTT
27586 GTCGTTGCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:27597 original size:33 final size:32
Alignment explanation
Indices: 27555--27648 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 32
27545 TTTAGTTTCG
* * *
27555 CGTTGCGATTTTAGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTA-TTTCGCATTGCGATTCTCT
*
27588 CGTTGCGATTTTAATTTCTCATTGCGATTCTCT
1 CGTTGCGATTTT-ATTTCGCATTGCGATTCTCT
27621 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTT-ATTTCGCATTGCGAT
27649 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (32 bp):
CGTTGCGATTTTATTTCGCATTGCGATTCTCT
Found at i:27647 original size:19 final size:17
Alignment explanation
Indices: 27540--27648 Score: 68
Period size: 19 Copynumber: 6.3 Consensus size: 17
27530 AAATCGCAAC
27540 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGC-TT
27559 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGC-TT
*
27578 GCGA-TTT-TGTCG-TT
1 GCGATTTTATTTCGCTT
*
27592 GCGATTTTAATTTCTCATT
1 GCGATTTT-ATTTCGC-TT
* *
27611 GCGA--TTCTCTCG-TT
1 GCGATTTTATTTCGCTT
27625 GCGATTTTCATTTCGCATT
1 GCGATTTT-ATTTCGC-TT
27644 GCGAT
1 GCGAT
27649 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
14 12 0.17
15 3 0.04
16 9 0.12
17 9 0.12
18 3 0.04
19 36 0.50
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (17 bp):
GCGATTTTATTTCGCTT
Found at i:27774 original size:14 final size:14
Alignment explanation
Indices: 27755--27791 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
27745 CATCAATTAA
27755 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
27769 ACAAATCATCTTTT
1 ACAAATCAACTTTT
27783 ACAAATCAA
1 ACAAATCAA
27792 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:29178 original size:21 final size:21
Alignment explanation
Indices: 29112--29178 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
29102 GTGAATCGGG
*
29112 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
29132 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
29154 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
29175 CTCT
1 CTCT
29179 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:29197 original size:42 final size:41
Alignment explanation
Indices: 29112--29234 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
29102 GTGAATCGGG
* * * *
29112 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
29154 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
29196 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
29235 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:31118 original size:26 final size:25
Alignment explanation
Indices: 31067--31120 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
31057 ATACCAAGTT
* *
31067 AGATATACCAAAAACTACACTGTAA
1 AGATATACCAAAAACTAAACTATAA
31092 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
31118 AGA
1 AGA
31121 GTAGTAGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:31204 original size:20 final size:20
Alignment explanation
Indices: 31179--31260 Score: 96
Period size: 20 Copynumber: 4.2 Consensus size: 20
31169 TTTTGGTTGA
31179 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
31199 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
31218 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
*
31238 AATGAAAATCGCAATGAGAG
1 AATGAAAATCGCAACGAGAG
31258 AAT
1 AAT
31261 CGCGTAGCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.31
20 36 0.69
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:31241 original size:19 final size:19
Alignment explanation
Indices: 31177--31308 Score: 123
Period size: 19 Copynumber: 7.1 Consensus size: 19
31167 TCTTTTGGTT
*
31177 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
31196 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
31216 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
31236 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
* *
31253 G--A-GAGAATCGCGTA-GC
1 GAAATGAAAATCGC-AACGC
*
31269 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
31288 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
31307 GA
1 GA
31309 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
14 8 0.09
15 2 0.02
16 1 0.01
17 1 0.01
18 2 0.02
19 44 0.48
20 31 0.34
21 2 0.02
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:31367 original size:20 final size:20
Alignment explanation
Indices: 31315--31392 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
31305 GCGATTTTGG
*
31315 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
31335 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
*
31356 TTTCGTGTTGCGCTTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
31376 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
31393 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:31892 original size:20 final size:20
Alignment explanation
Indices: 31864--32098 Score: 199
Period size: 20 Copynumber: 11.7 Consensus size: 20
31854 GCTTTAAAAA
31864 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
* *
31884 TCGCATTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
* *
31904 ACGCATTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
*
31924 TCTCGTTGCGATTTACAG-AT
1 TCGCGTTGCGATTTAC-GTAT
*
31944 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
31964 T-GTCGTTGCGATTTTACGTAT
1 TCG-CGTTGCGA-TTTACGTAT
** * *
31985 TATCGTTGCAATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
* *
32005 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACGTAT
* * * *
32026 ACTCGTTGCGATAGT-CAG-AA
1 TCGCGTTGCGAT-TTAC-GTAT
** *
32046 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTACGTAT
* *
32066 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGTAT
32086 TCGCGTTGCGATT
1 TCGCGTTGCGATT
32099 CTGGAAAATC
Statistics
Matches: 175, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.02
20 133 0.76
21 39 0.22
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAT
Found at i:31924 original size:40 final size:41
Alignment explanation
Indices: 31865--32098 Score: 223
Period size: 40 Copynumber: 5.8 Consensus size: 41
31855 CTTTAAAAAT
*
31865 CGCGTTGCGATTTACGTATTCGCATTGCGA-TTTACGGATA
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTTACGGATA
* * *
31905 CGCATTGCGATTTACGTATTCTCGTTGCGA-TTTACAGATA
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTTACGGATA
*
31945 CGCGTTGCGATTTACGTATT-GTCGTTGCGATTTTACGTATTA
1 CGCGTTGCGATTTACGTATTCG-CGTTGCGATTTTACGGA-TA
* * * *
31987 -TCGTTGCAATTTACGGATACGCGTTGCGATTTTACGGATA
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTTACGGATA
* * * * *
32027 CTCGTTGCGATAGT-CAG-AATCGCGTTGCGATTTATA-TG-TT
1 CGCGTTGCGAT-TTAC-GTATTCGCGTTGCGATTT-TACGGATA
* *
32067 CGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATT
32099 CTGGAAAATC
Statistics
Matches: 161, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 91 0.57
41 62 0.39
42 7 0.04
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTACGTATTCGCGTTGCGATTTTACGGATA
Found at i:32197 original size:20 final size:19
Alignment explanation
Indices: 32148--32201 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
32138 ATTATTCATA
32148 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
32167 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
32188 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
32202 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:35510 original size:2 final size:2
Alignment explanation
Indices: 35503--35542 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
35493 TAGATCCCGA
*
35503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35543 GCATGTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40854 original size:35 final size:36
Alignment explanation
Indices: 40784--40856 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
40774 TCACCAATTT
*
40784 AGGTTTCATAAGAAATTTGGGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
*
40820 AGGTTTCATGAGAAATTTGAGTA-TTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
40855 AG
1 AG
40857 CTTAATTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
Found at i:45760 original size:14 final size:14
Alignment explanation
Indices: 45741--45770 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
45731 TTTAGATTTT
*
45741 TTAAAATTACATTA
1 TTAAAAATACATTA
45755 TTAAAAATACATTA
1 TTAAAAATACATTA
45769 TT
1 TT
45771 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:45905 original size:7 final size:7
Alignment explanation
Indices: 45850--46044 Score: 146
Period size: 7 Copynumber: 27.9 Consensus size: 7
45840 TTATGTAATA
*
45850 GGTTTAG
1 GGTTTAT
*
45857 GGTTTAG
1 GGTTTAT
*
45864 GGTTTAG
1 GGTTTAT
*
45871 GGTTTAG
1 GGTTTAT
*
45878 GGTTTAG
1 GGTTTAT
*
45885 GGTTTAG
1 GGTTTAT
45892 GGTTTAT
1 GGTTTAT
45899 GGTTTAT
1 GGTTTAT
*
45906 GATTTAT
1 GGTTTAT
* *
45913 AAG-TTAG
1 -GGTTTAT
*
45920 GGTTTGT
1 GGTTTAT
45927 GGTTTAT
1 GGTTTAT
* *
45934 GATTCAT
1 GGTTTAT
* *
45941 AAG-TTAG
1 -GGTTTAT
45948 GGTTTAT
1 GGTTTAT
45955 GGTTTAT
1 GGTTTAT
*
45962 GGTTT-G
1 GGTTTAT
*
45968 GGATTCAT
1 GG-TTTAT
45976 GGTTTAT
1 GGTTTAT
45983 GGTTTAT
1 GGTTTAT
45990 GGTTTAT
1 GGTTTAT
*
45997 GATTTAT
1 GGTTTAT
46004 GGTTTAT
1 GGTTTAT
*
46011 GGTTT-G
1 GGTTTAT
*
46017 GGATTCAT
1 GG-TTTAT
46025 GGTTTAT
1 GGTTTAT
*
46032 GATTTAT
1 GGTTTAT
46039 GGTTTA
1 GGTTTA
46045 ATTTATACAC
Statistics
Matches: 151, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
6 6 0.04
7 141 0.93
8 4 0.03
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (7 bp):
GGTTTAT
Found at i:47687 original size:16 final size:16
Alignment explanation
Indices: 47666--47696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47656 AAGTAAAATA
*
47666 AACAATCAGGATGTTT
1 AACAATCAGCATGTTT
47682 AACAATCAGCATGTT
1 AACAATCAGCATGTT
47697 ACTGTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (16 bp):
AACAATCAGCATGTTT
Found at i:48097 original size:17 final size:17
Alignment explanation
Indices: 48075--48107 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
48065 TTCGAGTTCG
48075 AGTTCGAGCTTGAATCA
1 AGTTCGAGCTTGAATCA
48092 AGTTCGAGCTTGAATC
1 AGTTCGAGCTTGAATC
48108 GGGCTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCA
Found at i:48138 original size:35 final size:35
Alignment explanation
Indices: 48092--48202 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
48082 GCTTGAATCA
* *
48092 AGTTCGAGCTTGAATCGGGCTCAAATTTGAGTTTG
1 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
48127 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
1 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
* *
48162 AGTTCGAGCTTGAATCGAGCTCGAGTCTCGAGTTTCG
1 AGTTCGAGCTTGAATCGAGCTCAAAT-TCGAGTTT-G
48199 AGTT
1 AGTT
48203 TCAATCGAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 57 0.81
36 8 0.11
37 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (35 bp):
AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
Found at i:48146 original size:11 final size:11
Alignment explanation
Indices: 48130--48182 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
48120 GAGTTTGAGT
48130 TCGAGCTTGAA
1 TCGAGCTTGAA
**
48141 TCGAGCTCAAA
1 TCGAGCTTGAA
* *
48152 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
48165 TCGAGCTTGAA
1 TCGAGCTTGAA
48176 TCGAGCT
1 TCGAGCT
48183 CGAGTCTCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:48187 original size:23 final size:23
Alignment explanation
Indices: 48066--48193 Score: 63
Period size: 23 Copynumber: 5.7 Consensus size: 23
48056 AGGTTCAAAT
*
48066 TCGAGTTCGAGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAGCTTGAA
48089 TC-A-----AGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAGCTTGAA
* * * * * *
48106 TCGGGCTCAAATTTGAGTTTGAGT
1 TCGAGCTCGAGTTCGAGCTTGA-A
* * **
48130 TCGAGCTTGA-ATCGAGCTCAAA
1 TCGAGCTCGAGTTCGAGCTTGAA
* *
48152 TTCGAGTTTGAGTTCGAGCTTGAA
1 -TCGAGCTCGAGTTCGAGCTTGAA
48176 TCGAGCTCGAGTCTCGAG
1 TCGAGCTCGAGT-TCGAG
48194 TTTCGAGTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 19
0.66 0.18 0.17
Matches are distributed among these distances:
17 16 0.21
22 1 0.01
23 37 0.49
24 21 0.28
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (23 bp):
TCGAGCTCGAGTTCGAGCTTGAA
Done.