Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002549.1 Hibiscus syriacus cultivar Beakdansim tig00005176_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: 52408
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:321 original size:33 final size:34
Alignment explanation
Indices: 260--335 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
250 GCAACTTTCG
* *
260 CGTTGCAATTTTCATTTTTGCATTGTGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGTGATTCACT
*
294 CGTTGCGATTTTCA-TTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGTGATTCACT
327 CGTTGCGAT
1 CGTTGCGAT
336 AGTCATCCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGTGATTCACT
Found at i:366 original size:20 final size:19
Alignment explanation
Indices: 327--430 Score: 132
Period size: 20 Copynumber: 5.7 Consensus size: 19
317 GTGATTCTCT
327 CGTTGCGATAGTCA-TCCG
1 CGTTGCGATAGTCATTCCG
345 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTC-ATTCCG
365 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCA-TTCCG
*
385 TGTTGCGATAGTCATT-CG
1 CGTTGCGATAGTCATTCCG
403 CGTTGCG--A-T--TTCCG
1 CGTTGCGATAGTCATTCCG
417 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
431 ATGAATGTCT
Statistics
Matches: 75, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
13 2 0.03
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 21 0.28
19 4 0.05
20 35 0.47
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (19 bp):
CGTTGCGATAGTCATTCCG
Found at i:378 original size:38 final size:37
Alignment explanation
Indices: 327--432 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 37
317 GTGATTCTCT
327 CGTTGCGATAGTCATCCGCGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATCCGCGTTGCGATAGTCAATT-CG
*
365 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCA--TCCGCGTTGCGATAGTCAATTCG
403 CGTTGCGAT--T--TCCGCGTTGCGATAGTCAAT
1 CGTTGCGATAGTCATCCGCGTTGCGATAGTCAAT
433 GAATGTCTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
32 16 0.25
33 2 0.03
36 1 0.02
38 25 0.40
39 3 0.05
40 16 0.25
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (37 bp):
CGTTGCGATAGTCATCCGCGTTGCGATAGTCAATTCG
Found at i:2874 original size:24 final size:24
Alignment explanation
Indices: 2840--2893 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2830 CTGAAAAATC
2840 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2864 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2888 ATCAAA
1 ATCAAA
2894 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2907 original size:24 final size:24
Alignment explanation
Indices: 2840--2907 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2830 CTGAAAAATC
* * *
2840 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2864 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2888 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2908 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3758 original size:41 final size:40
Alignment explanation
Indices: 3713--3821 Score: 134
Period size: 40 Copynumber: 2.7 Consensus size: 40
3703 CAGAAATCGA
*
3713 GTTGCGAATTTGA-AATTCAGTATTGCGATAGTCAGAATCTC
1 GTTGCGAATTT-ACAATTC-GCATTGCGATAGTCAGAATCTC
*
3754 GTTGCG-ATTTACGTATTCGCATTGCGATAGTCAGAATCTC
1 GTTGCGAATTTAC-AATTCGCATTGCGATAGTCAGAATCTC
*
3794 GTTGCG-ATTTACGTATTCGCATTGCGAT
1 GTTGCGAATTTAC-AATTCGCATTGCGAT
3822 TTACGTTCCA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.02
40 53 0.83
41 10 0.16
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (40 bp):
GTTGCGAATTTACAATTCGCATTGCGATAGTCAGAATCTC
Found at i:3760 original size:20 final size:20
Alignment explanation
Indices: 3735--3801 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
3725 AAATTCAGTA
3735 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
3755 TTGCGAT--TTACGTAT-TCG
1 TTGCGATAGTCA-GAATCTCG
3773 CATTGCGATAGTCAGAATCTCG
1 --TTGCGATAGTCAGAATCTCG
3795 TTGCGAT
1 TTGCGAT
3802 TTACGTATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 21 0.57
21 3 0.08
22 5 0.14
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:3781 original size:40 final size:40
Alignment explanation
Indices: 3734--3866 Score: 187
Period size: 40 Copynumber: 3.2 Consensus size: 40
3724 GAAATTCAGT
3734 ATTGCGATAGTCAGAATCTCGTTGCGATTTACGTATTCGC
1 ATTGCGATAGTCAGAATCTCGTTGCGATTTACGTATTCGC
3774 ATTGCGATAGTCAGAATCTCGTTGCGATTTACGTATTCGC
1 ATTGCGATAGTCAGAATCTCGTTGCGATTTACGTATTCGC
*
3814 ATTGCGATTTACGTTCCA-AATTCGCGTTGCGATTTACGTATTCGC
1 ATTGCGA--TA-G-T-CAGAA-TCTCGTTGCGATTTACGTATTCGC
*
3859 GTTGCGAT
1 ATTGCGAT
3867 TTATGTATTC
Statistics
Matches: 85, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
40 47 0.55
42 2 0.02
43 2 0.02
44 3 0.04
45 31 0.36
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCTCGTTGCGATTTACGTATTCGC
Found at i:3818 original size:20 final size:20
Alignment explanation
Indices: 3755--3885 Score: 124
Period size: 20 Copynumber: 6.3 Consensus size: 20
3745 CAGAATCTCG
3755 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
3775 TTGCGATAGT-CAGAATCTCG--
1 TTGCGAT-TTAC-GTAT-TCGCA
3795 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
3815 TTGCGATTTACGTTCCAAATTCGCG
1 TTGCGATTTACG-T----ATTCGCA
*
3840 TTGCGATTTACGTATTCGCG
1 TTGCGATTTACGTATTCGCA
*
3860 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATTCGCA
3880 TTGCGA
1 TTGCGA
3886 ATTAGGAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.03
19 4 0.04
20 59 0.63
21 5 0.05
22 3 0.03
24 1 0.01
25 18 0.19
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:3918 original size:20 final size:21
Alignment explanation
Indices: 3882--3926 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3872 TATTCGCATT
3882 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3903 GCGAATTTGG-AAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3923 GCGA
1 GCGA
3927 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:10579 original size:34 final size:34
Alignment explanation
Indices: 10537--10605 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
10527 TCTCCAGCTG
10537 TGTGGGGAAAAAACACTCAATGAAAACACCTAAC
1 TGTGGGGAAAAAACACTCAATGAAAACACCTAAC
10571 TGTGGGGAAAAAACACTCAATGAAAACACCTAAC
1 TGTGGGGAAAAAACACTCAATGAAAACACCTAAC
10605 T
1 T
10606 ATGTGCCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.16
Consensus pattern (34 bp):
TGTGGGGAAAAAACACTCAATGAAAACACCTAAC
Found at i:14976 original size:28 final size:28
Alignment explanation
Indices: 14893--14965 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
14883 ACTGACGTTG
14893 CTTTCAAGCACTAGT-TCGACAGTATAAT
1 CTTTCAAGCACTA-TCTCGACAGTATAAT
*
14921 CTTTCAAGCACTAACTCGACAGTATAAT
1 CTTTCAAGCACTATCTCGACAGTATAAT
14949 CTTTCAAGCACTATCTC
1 CTTTCAAGCACTATCTC
14966 CACAATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (28 bp):
CTTTCAAGCACTATCTCGACAGTATAAT
Found at i:16209 original size:60 final size:60
Alignment explanation
Indices: 16085--16225 Score: 135
Period size: 60 Copynumber: 2.4 Consensus size: 60
16075 ATATGTTTCT
* * * * *
16085 AAACTACAATCCTCGTTTTAAATTAGTCTTTAAACTCTTGAATATTTAAATTTCATACTC
1 AAACTACGACCCTCATTCTAAACTAGTCTTTAAACTCTTGAATATTTAAATTTCATACTC
* * * * *
16145 AAACTATGACTCTCATTCTAAACTAGTCTTTAAACT-TTTAA-ATGTTATAATTTTAT-CCC
1 AAACTACGACCCTCATTCTAAACTAGTCTTTAAACTCTTGAATAT-TTA-AATTTCATACTC
*
16204 TAAACTACGACCCTCTTTCTAA
1 -AAACTACGACCCTCATTCTAA
16226 GTTGGTCCCC
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
58 2 0.03
59 9 0.14
60 54 0.83
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (60 bp):
AAACTACGACCCTCATTCTAAACTAGTCTTTAAACTCTTGAATATTTAAATTTCATACTC
Found at i:16483 original size:59 final size:60
Alignment explanation
Indices: 16391--16529 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 60
16381 GTGTATATGT
* * * *
16391 ATAGTTTGGGATGAAAATGGAATGTTCAAAAAGTATGGGGGC-AATTTAGAATGA-AGTTC
1 ATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTATGAGGACTAATTTAGAATGATAG-TC
* *
16450 ATAGTTTGGGGATGAAATTGAAATTTTC-AAAAGTTTGAGGACTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTCAAAAAGTATGAGGACTAATTTAGAATGATAGTC
*
16510 ATAATTTAGGGATGAAATTG
1 ATAGTTT-GGGATGAAATTG
16530 GAATATTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 18 0.26
60 49 0.71
61 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATGTTCAAAAAGTATGAGGACTAATTTAGAATGATAGTC
Found at i:16557 original size:60 final size:59
Alignment explanation
Indices: 16432--16558 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 59
16422 AGTATGGGGG
* * * *
16432 CAATTTAGAATGAAGTTCATAGTTTGGGGATGAAATTGAAATTTTCAAAAGTTTGAGGA
1 CAATTTAGAATGAAGTTCATAATTTAGGGATGAAATTGAAATTTTCAAAAATTTAAGGA
*
16491 CTAATTTAGAATGATAG-TCATAATTTAGGGATGAAATTGGAATATTT-AAAAATTTAAGGA
1 C-AATTTAGAATGA-AGTTCATAATTTAGGGATGAAATTGAAAT-TTTCAAAAATTTAAGGA
16551 TCAATTTA
1 -CAATTTA
16559 AAATAAGGAC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
59 1 0.02
60 52 0.88
61 6 0.10
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (59 bp):
CAATTTAGAATGAAGTTCATAATTTAGGGATGAAATTGAAATTTTCAAAAATTTAAGGA
Found at i:17385 original size:20 final size:22
Alignment explanation
Indices: 17352--17396 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
17342 ATTGAGTTAT
17352 TAAAAAATATTAATATTTTAAG
1 TAAAAAATATTAATATTTTAAG
17374 TAAAAAA-A-TAATATTTTAAG
1 TAAAAAATATTAATATTTTAAG
17394 TAA
1 TAA
17397 TATTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.65
21 1 0.04
22 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAAAAATATTAATATTTTAAG
Found at i:20301 original size:27 final size:27
Alignment explanation
Indices: 20271--20324 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20261 TCGAACCATC
*
20271 GCAAACCTCACCTTCGACAAGATGGAT
1 GCAAACCTCACCGTCGACAAGATGGAT
20298 GCAAACCTCACCGTCGACAAGATGGAT
1 GCAAACCTCACCGTCGACAAGATGGAT
20325 ATCAACGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (27 bp):
GCAAACCTCACCGTCGACAAGATGGAT
Found at i:23592 original size:18 final size:18
Alignment explanation
Indices: 23566--23600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23556 TCGAAAGGAC
*
23566 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
23584 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
23601 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:25909 original size:32 final size:31
Alignment explanation
Indices: 25873--25948 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
25863 CGGGCCGTGA
*
25873 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
25905 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
25936 AGCCTACCTAAGA
1 GGCCTACCTAAGA
25949 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:26852 original size:17 final size:17
Alignment explanation
Indices: 26830--26867 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
26820 AACGGTCAAC
* *
26830 GGTCAACGGTCGGGTTG
1 GGTCAACAGTCGGGTCG
26847 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
26864 GGTC
1 GGTC
26868 GGGTCAGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:32515 original size:32 final size:31
Alignment explanation
Indices: 32479--32554 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
32469 CGGGCCGTGA
*
32479 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
32511 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
32542 AGCCTACCTAAGA
1 GGCCTACCTAAGA
32555 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:33437 original size:7 final size:7
Alignment explanation
Indices: 33425--33455 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
33415 GTCAAAGGAA
33425 GTCAACG
1 GTCAACG
33432 GTCAACG
1 GTCAACG
33439 GTCAACG
1 GTCAACG
33446 GTCAACG
1 GTCAACG
33453 GTC
1 GTC
33456 GGGTTGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:33467 original size:17 final size:17
Alignment explanation
Indices: 33445--33516 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
33435 AACGGTCAAC
* *
33445 GGTCAACGGTCGGGTTG
1 GGTCAACAGTCGGGTCG
33462 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
33479 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
33496 GGT---CAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
33510 GGTCAAC
1 GGTCAAC
33517 CCGGTTCAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
14 14 0.28
17 36 0.72
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:33485 original size:34 final size:31
Alignment explanation
Indices: 33445--33516 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 31
33435 AACGGTCAAC
* *
33445 GGTCAACGGTCGGGTTGGGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGT---CAGTCGGGTCG
33479 GGTCAACAGTCGGGTCGGGTCAGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCAGTCGGGTCG
33510 GGTCAAC
1 GGTCAAC
33517 CCGGTTCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 18 0.50
34 18 0.50
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.19
Consensus pattern (31 bp):
GGTCAACAGTCGGGTCGGGTCAGTCGGGTCG
Found at i:33504 original size:14 final size:14
Alignment explanation
Indices: 33468--33514 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 14
33458 GTTGGGTCAA
33468 CAGTCGGGTCGGGT
1 CAGTCGGGTCGGGT
33482 CAACAGTCGGGTCGGGT
1 ---CAGTCGGGTCGGGT
33499 CAGTCGGGTCGGGT
1 CAGTCGGGTCGGGT
33513 CA
1 CA
33515 ACCCGGTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.53
17 14 0.47
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (14 bp):
CAGTCGGGTCGGGT
Found at i:33555 original size:20 final size:19
Alignment explanation
Indices: 33510--33561 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
33500 AGTCGGGTCG
* *
33510 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
* *
33529 GGCCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
33549 GGTCAAACCGGTT
1 GGTCAAACCGGTT
33562 TTCCAGCAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:40785 original size:25 final size:24
Alignment explanation
Indices: 40756--40832 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
40746 ACAGTTTATT
40756 AATTAAATTTTATAATTATAATTAA
1 AATTAAA-TTTATAATTATAATTAA
* * *
40781 AATTAAATATTGTAATATAAAAGTAA
1 AATTAAAT-TTATAAT-TATAATTAA
* *
40807 AATTTTAA-TTATAATTATAATGAA
1 AA-TTAAATTTATAATTATAATTAA
40831 AA
1 AA
40833 AATTAGCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
24 9 0.22
25 19 0.46
26 9 0.22
27 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATTAAATTTATAATTATAATTAA
Found at i:40801 original size:20 final size:19
Alignment explanation
Indices: 40769--40820 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
40759 TAAATTTTAT
* *
40769 AATTATAAT-TAAAATTAA
1 AATTGTAATATAAAAGTAA
40787 ATATTGTAATATAAAAGTAA
1 A-ATTGTAATATAAAAGTAA
*
40807 AATTTTAATTATAA
1 AATTGTAA-TATAA
40821 TTATAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 13 0.46
20 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATTGTAATATAAAAGTAA
Found at i:42090 original size:15 final size:16
Alignment explanation
Indices: 42070--42100 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42060 CAATACATAA
42070 ATATTTAAAAA-TATT
1 ATATTTAAAAACTATT
42085 ATATTTAAAAACTATT
1 ATATTTAAAAACTATT
42101 GTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTAAAAACTATT
Found at i:45598 original size:21 final size:21
Alignment explanation
Indices: 45551--45598 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
45541 AACCGAATTT
45551 ATAAAATTACAAGTCGAGTTA
1 ATAAAATTACAAGTCGAGTTA
*
45572 AAAAAATTGAC-A-TCGAGTTCA
1 ATAAAATT-ACAAGTCGAGTT-A
45593 ATAAAA
1 ATAAAA
45599 AATTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (21 bp):
ATAAAATTACAAGTCGAGTTA
Found at i:46453 original size:2 final size:2
Alignment explanation
Indices: 46446--46470 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46436 TTTTCAATCA
46446 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
46471 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:49537 original size:17 final size:17
Alignment explanation
Indices: 49515--49551 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
49505 TTACTATGTT
49515 TCCTCTTCAATCGTTCA
1 TCCTCTTCAATCGTTCA
49532 TCCTCTTCAATCGTTCA
1 TCCTCTTCAATCGTTCA
49549 TCC
1 TCC
49552 ATAGGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.38, G:0.05, T:0.41
Consensus pattern (17 bp):
TCCTCTTCAATCGTTCA
Done.