Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000868.1 Hibiscus syriacus cultivar Beakdansim tig00001675_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: 77078
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:324 original size:17 final size:17
Alignment explanation
Indices: 298--343 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 17
288 TGTTATGTTT
*
298 ATATTTTTTAAAATAAA
1 ATATTATTTAAAATAAA
315 ATATTATTT---A-AAA
1 ATATTATTTAAAATAAA
328 ATATTATTTAAAATAA
1 ATATTATTTAAAATAA
344 TCTAAACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 1 0.04
17 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTATTTAAAATAAA
Found at i:330 original size:13 final size:13
Alignment explanation
Indices: 312--340 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
302 TTTTTAAAAT
312 AAAATATTATTTA
1 AAAATATTATTTA
325 AAAATATTATTTA
1 AAAATATTATTTA
338 AAA
1 AAA
341 TAATCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:2567 original size:25 final size:25
Alignment explanation
Indices: 2538--2585 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2528 ACATATATGG
*
2538 TTACCCATTATTAGGGTTTTTTTTC
1 TTACCCATTATTAGGGGTTTTTTTC
2563 TTACCCATTATTAGGGGTTTTTT
1 TTACCCATTATTAGGGGTTTTTT
2586 GTCATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (25 bp):
TTACCCATTATTAGGGGTTTTTTTC
Found at i:4003 original size:25 final size:25
Alignment explanation
Indices: 3974--4031 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3964 TGTTGGCAAG
* *
3974 CTTCTCACTTCATGACCTCTACTTT
1 CTTCTAACCTCATGACCTCTACTTT
*
3999 CTTCTAACCTCATTACCTCTACTTT
1 CTTCTAACCTCATGACCTCTACTTT
4024 CTTCTAAC
1 CTTCTAAC
4032 ATACGCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.36, G:0.02, T:0.43
Consensus pattern (25 bp):
CTTCTAACCTCATGACCTCTACTTT
Found at i:4400 original size:71 final size:71
Alignment explanation
Indices: 4305--4440 Score: 238
Period size: 71 Copynumber: 1.9 Consensus size: 71
4295 TTCAGAACCA
*
4305 GACCGGTTAGCAAACCGACTATGCTACCGGTTCACTGGTTCAACCGGTCGAACCA-GTCGGAAGA
1 GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAA-CAGGTCGGAAGA
4369 AGAATCG
65 AGAATCG
*
4376 GACCGGTTAGCGAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
1 GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
4441 CCGGACGACG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 2 0.03
71 60 0.97
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (71 bp):
GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
GAATCG
Found at i:5540 original size:42 final size:43
Alignment explanation
Indices: 5466--5549 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 43
5456 GGTGCTGAAC
5466 ATTGATACACGAATGTACCAAAGCTGATATGATAACTAATAAT
1 ATTGATACACGAATGTACCAAAGCTGATATGATAACTAATAAT
*
5509 ATTGATACACGAATGT-CCAAAGCTGATATGATAACTGATAA
1 ATTGATACACGAATGTACCAAAGCTGATATGATAACTAATAA
5550 GCACTCACTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 24 0.60
43 16 0.40
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (43 bp):
ATTGATACACGAATGTACCAAAGCTGATATGATAACTAATAAT
Found at i:5681 original size:17 final size:17
Alignment explanation
Indices: 5654--5717 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
5644 TATTTGATAA
5654 CTGTAAAATATCTTATAT
1 CTGT-AAATATCTTATAT
* *
5672 CTGTAAATATATGATAAT
1 CTGTAAATATCTTAT-AT
*
5690 -TGT-TATCATCTTATAT
1 CTGTAAAT-ATCTTATAT
*
5706 CTGTAAAGATCT
1 CTGTAAATATCT
5718 GATAACTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
16 4 0.11
17 24 0.69
18 7 0.20
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (17 bp):
CTGTAAATATCTTATAT
Found at i:8559 original size:29 final size:30
Alignment explanation
Indices: 8530--8606 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
8520 ATCTATAACT
*
8530 TTTTAAAA-TTACATTTTTATCCCT-AAAC
1 TTTTAAAACTTACATTTTTAGCCCTCAAAC
* *
8558 TTTTACAAAGTT-TATATTTTAGCCCTCAAAC
1 TTTTA-AAACTTACAT-TTTTAGCCCTCAAAC
8589 TTTTAAAACTTACATTTT
1 TTTTAAAACTTACATTTT
8607 AGTCACTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.12
29 5 0.12
30 19 0.47
31 11 0.28
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTAAAACTTACATTTTTAGCCCTCAAAC
Found at i:18824 original size:17 final size:18
Alignment explanation
Indices: 18785--18831 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
18775 TATTTATGAG
18785 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
18803 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
18820 GGAATTGAAATC
1 GGAATTGAAATC
18832 CAATTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:19459 original size:33 final size:32
Alignment explanation
Indices: 19412--19510 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 32
19402 AACCCGAACC
19412 CGACCCGACTCGAATATCACACTTAAAAAAACT
1 CGACCCGAC-CGAATATCACACTTAAAAAAACT
*
19445 CGACCCGATCCGAATATCACATTTAAAAAAA-T
1 CGACCCGA-CCGAATATCACACTTAAAAAAACT
* * *
19477 CCA-AC--CCGAATATCACACTT-AAAAAACC
1 CGACCCGACCGAATATCACACTTAAAAAAACT
19505 CGACCC
1 CGACCC
19511 AACCCGAACA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
27 6 0.11
28 16 0.29
29 1 0.02
31 1 0.02
32 3 0.05
33 28 0.50
34 1 0.02
ACGTcount: A:0.42, C:0.32, G:0.08, T:0.17
Consensus pattern (32 bp):
CGACCCGACCGAATATCACACTTAAAAAAACT
Found at i:20098 original size:24 final size:24
Alignment explanation
Indices: 20059--20105 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20049 TTTTTATATA
*
20059 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
20083 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
20106 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:26938 original size:24 final size:25
Alignment explanation
Indices: 26911--26963 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
26901 TGTTTATTAA
* * *
26911 TAAACTTATTTGTTAATATATTT-T
1 TAAACTAATTTATTAATAGATTTAT
*
26935 TAAACTAATTTATTAGTAGATTTAT
1 TAAACTAATTTATTAATAGATTTAT
26960 TAAA
1 TAAA
26964 ATTGATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (25 bp):
TAAACTAATTTATTAATAGATTTAT
Found at i:28929 original size:31 final size:31
Alignment explanation
Indices: 28894--28990 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
28884 ATTTCTTAGA
28894 AGTTTAAGGACTAATTTAGAATGAGTATCAT
1 AGTTTAAGGACTAATTTAGAATGAGTATCAT
* * * * *
28925 AGTTTGAGGA-TGAAATTAGAAT-A-TTTAAA
1 AGTTTAAGGACT-AATTTAGAATGAGTATCAT
* ** * *
28954 AATTTAAATACTAATTTAAAATGAGTACCAT
1 AGTTTAAGGACTAATTTAGAATGAGTATCAT
28985 AGTTTA
1 AGTTTA
28991 GAAATATATG
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
29 17 0.37
30 4 0.09
31 25 0.54
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.36
Consensus pattern (31 bp):
AGTTTAAGGACTAATTTAGAATGAGTATCAT
Found at i:28940 original size:60 final size:60
Alignment explanation
Indices: 28808--28989 Score: 185
Period size: 60 Copynumber: 3.0 Consensus size: 60
28798 TTTGGATGAA
* * * *
28808 TTTGAGAATGAAATTCA-AA-AGTTTAAAAGTTTAGGGGCTAATTTAGAAT-ACG-CTCATAG
1 TTTGAGGATGAAATT-AGAATA-TTTAAAAGTTTAAGGACTAATTTAGAATGA-GTATCATAG
* * *
28867 TTTGAGGATGAAATT-GGATTTCTTAGAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
1 TTTGAGGATGAAATTAGAATAT-TTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
* ** * *
28927 TTTGAGGATGAAATTAGAATATTTAAAAATTTAAATACTAATTTAAAATGAGTACCATAG
1 TTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
28987 TTT
1 TTT
28990 AGAAATATAT
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
58 2 0.02
59 39 0.38
60 57 0.56
61 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (60 bp):
TTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
Found at i:34731 original size:30 final size:30
Alignment explanation
Indices: 34697--34757 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
34687 TTTTTCAAAA
*
34697 TCATACCTAAAGTTTAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
34727 TCATACCTAAAGTTAAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
34757 T
1 T
34758 TAGTACCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (30 bp):
TCATACCTAAAGTTAAATTTTTGTTTCATT
Found at i:35116 original size:121 final size:121
Alignment explanation
Indices: 34827--35133 Score: 332
Period size: 121 Copynumber: 2.5 Consensus size: 121
34817 TAACGTCAAG
* * * * * ***
34827 TTTTGAAAAAATTGAAAGTTTAGATATGAAAACGGAACAAAACTGATAGTTTAGTCACTAAACAT
1 TTTTAAAAAAATTGAAAATTTAGATATGAAAACTGAACAAAATTGATAGTTTAGACACTAAATGC
* * * ** *
34892 GTTAGGTTTTTAACGATGAGTACTAAAACGAAATAAGAACTAAATGTTAAGTATGA
66 GTTAGATTTTTAACGACGAGTACTAAAACGAAATAAAAACTAAACATCAAGTATGA
* * * * *
34948 TTTTAAAAAAACT-AAAAGTTTTGGTACGAAAA-TGAATC-AAATCTGATAGTTTAGGCACTAAA
1 TTTTAAAAAAATTGAAAA-TTTAGATATGAAAACTGAA-CAAAAT-TGATAGTTTAGACACTAAA
* * *
35010 TGCGTTAGATTTTTAACGGCGTGTACTAAAATGAAATAAAAACTAAACATCAAGTATGA
63 TGCGTTAGATTTTTAACGACGAGTACTAAAACGAAATAAAAACTAAACATCAAGTATGA
* * * *
35069 TTTTAAAAAAATTGAAAATTTCGATATTAAAACTGACCAAAATTGATAGTTTAGATACTAAATGC
1 TTTTAAAAAAATTGAAAATTTAGATATGAAAACTGAACAAAATTGATAGTTTAGACACTAAATGC
35134 ATAATTTATC
Statistics
Matches: 151, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
120 9 0.06
121 131 0.87
122 11 0.07
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (121 bp):
TTTTAAAAAAATTGAAAATTTAGATATGAAAACTGAACAAAATTGATAGTTTAGACACTAAATGC
GTTAGATTTTTAACGACGAGTACTAAAACGAAATAAAAACTAAACATCAAGTATGA
Found at i:39276 original size:30 final size:30
Alignment explanation
Indices: 39242--39302 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
39232 TTTTTCAAAA
*
39242 TCATACCTAAAGTTTAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
39272 TCATACCTAAAGTTAAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
39302 T
1 T
39303 TAGTACCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (30 bp):
TCATACCTAAAGTTAAATTTTTGTTTCATT
Found at i:39633 original size:121 final size:121
Alignment explanation
Indices: 39372--39640 Score: 315
Period size: 121 Copynumber: 2.2 Consensus size: 121
39362 TAACGTCAAG
* * * *
39372 TTTTGAAAAAATTGAAAGTTTAGATATGAAAACGGATCAAAACTGATAGTTTAGTCACTAAACAT
1 TTTTGAAAAAATTGAAAGTTTAGGTACGAAAACGAATCAAAACTGATAGTTTAGGCACTAAACAT
* * * ** * *
39437 GTTAGGTTTTTAACGATGGGTACTAAAACGAAATAAGAACTAAATGTTAAATATGA
66 GTTAGATTTTTAACGACGGGTACTAAAACGAAATAAAAACTAAACATCAAAAATGA
* * * * * **
39493 TTTTGAAAAAAACTAAAAGTTTTGGTACGAAAA-TAATCAAATCTGATAGTTTAGGCACTAAATG
1 TTTTG-AAAAAATTGAAAGTTTAGGTACGAAAACGAATCAAAACTGATAGTTTAGGCACTAAACA
* * *
39557 TGTTAGATTTTTAACGGCGTGTACTAAAATGAAATAAAAACTAAACATCAAGAAATGA
65 TGTTAGATTTTTAACGACGGGTACTAAAACGAAATAAAAACTAAACATCAA-AAATGA
*
39615 TTTTGAAAAAATTGAAAGTTTCGGTA
1 TTTTGAAAAAATTGAAAGTTTAGGTA
39641 TTAAAGCTGA
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
121 90 0.74
122 32 0.26
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.31
Consensus pattern (121 bp):
TTTTGAAAAAATTGAAAGTTTAGGTACGAAAACGAATCAAAACTGATAGTTTAGGCACTAAACAT
GTTAGATTTTTAACGACGGGTACTAAAACGAAATAAAAACTAAACATCAAAAATGA
Found at i:42841 original size:16 final size:15
Alignment explanation
Indices: 42815--42846 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
42805 TAATTTAGTC
42815 TAATATTAATATTTA
1 TAATATTAATATTTA
42830 TAATATTCAATATTTA
1 TAATATT-AATATTTA
42846 T
1 T
42847 TATTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATTAATATTTA
Found at i:42863 original size:22 final size:23
Alignment explanation
Indices: 42816--42864 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
42806 AATTTAGTCT
* *
42816 AATA-TTAATATTTATAATATTC
1 AATATTTAATATTTATAATAATA
*
42838 AATATTTATTATTTAT-ATAATA
1 AATATTTAATATTTATAATAATA
42860 AATAT
1 AATAT
42865 AAAATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTAATATTTATAATAATA
Found at i:44591 original size:4 final size:4
Alignment explanation
Indices: 44582--44612 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
44572 GATAACATAA
*
44582 AAAT AAAT AAAG AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
44613 CATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:44672 original size:17 final size:17
Alignment explanation
Indices: 44650--44684 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44640 ATCATTTCAA
44650 ATTATCAAAAATAATAT
1 ATTATCAAAAATAATAT
44667 ATTATCAAAAATAATAT
1 ATTATCAAAAATAATAT
44684 A
1 A
44685 CTGAGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTATCAAAAATAATAT
Found at i:44806 original size:14 final size:14
Alignment explanation
Indices: 44787--44841 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
44777 TAGTAAATAA
*
44787 AATATTTCAATTTT
1 AATATTTAAATTTT
* *
44801 AATATTAAAATATT
1 AATATTTAAATTTT
44815 AA-ATATTAAATTTT
1 AATAT-TTAAATTTT
44829 AATATTTTAAATT
1 AATA-TTTAAATT
44842 AACACATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 2 0.06
14 22 0.67
15 8 0.24
16 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTTAAATTTT
Found at i:47546 original size:19 final size:16
Alignment explanation
Indices: 47516--47564 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
47506 AATTGATGAC
47516 TAAATAAAATAATTAAT
1 TAAAT-AAATAATTAAT
*
47533 ATAAAAGTAAATAATTGAT
1 -T-AAA-TAAATAATTAAT
47552 TAAATAAATAATT
1 TAAATAAATAATT
47565 TATCTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 9 0.32
17 3 0.11
18 2 0.07
19 13 0.46
20 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TAAATAAATAATTAAT
Found at i:52046 original size:2 final size:2
Alignment explanation
Indices: 52037--52066 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
52027 TTAAATTTTT
52037 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52067 TGCTAAGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57966 original size:19 final size:19
Alignment explanation
Indices: 57924--57967 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
57914 AAATCAAAAC
*
57924 ATTTTTTTTCAAAATTTTCA
1 ATTTTTTTTCAAAA-TTCCA
57944 ATTTGTTTTTCAAAA-TCCA
1 ATTT-TTTTTCAAAATTCCA
57963 ATTTT
1 ATTTT
57968 GCTTCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 7 0.32
20 4 0.18
21 10 0.45
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTTTTTCAAAATTCCA
Found at i:61035 original size:10 final size:10
Alignment explanation
Indices: 61022--61095 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 10
61012 CCAACACGCT
61022 GGCCATCCGA
1 GGCCATCCGA
61032 GGCCATCCGACCGA
1 GGCCAT----CCGA
*
61046 GGCTATCCGA
1 GGCCATCCGA
*
61056 GAG-CATCTGA
1 G-GCCATCCGA
61066 GGCCATCCGA
1 GGCCATCCGA
*
61076 GAG-CATCTGA
1 G-GCCATCCGA
61086 GGCCATCCGA
1 GGCCATCCGA
61096 ACGAGCTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
9 2 0.04
10 37 0.74
11 2 0.04
14 9 0.18
ACGTcount: A:0.23, C:0.34, G:0.30, T:0.14
Consensus pattern (10 bp):
GGCCATCCGA
Found at i:61073 original size:20 final size:20
Alignment explanation
Indices: 61044--61095 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
61034 CCATCCGACC
*
61044 GAGGCTATCCGAGAGCATCT
1 GAGGCCATCCGAGAGCATCT
61064 GAGGCCATCCGAGAGCATCT
1 GAGGCCATCCGAGAGCATCT
61084 GAGGCCATCCGA
1 GAGGCCATCCGA
61096 ACGAGCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (20 bp):
GAGGCCATCCGAGAGCATCT
Found at i:61135 original size:33 final size:33
Alignment explanation
Indices: 61092--61199 Score: 189
Period size: 33 Copynumber: 3.3 Consensus size: 33
61082 CTGAGGCCAT
* *
61092 CCGAACGAGCTATGCGAGGGAATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
*
61125 TCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
61158 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
61191 CCGAGCGAG
1 CCGAGCGAG
61200 GGTAGGTCGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.26, C:0.24, G:0.41, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAG
Found at i:61236 original size:29 final size:29
Alignment explanation
Indices: 61203--61258 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
61193 GAGCGAGGGT
*
61203 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
61232 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
61259 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:61398 original size:114 final size:114
Alignment explanation
Indices: 61198--61486 Score: 551
Period size: 114 Copynumber: 2.5 Consensus size: 114
61188 CAGCCGAGCG
61198 AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTATGTG
1 AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTATGTG
61263 TTGGGACGTACATGTGCCATGCAACACGCTCATTCTCTCTGTTTGAACA
66 TTGGGACGTACATGTGCCATGCAACACGCTCATTCTCTCTGTTTGAACA
* *
61312 AGGGTAGGTCACCCGGAGTGCATGGCGATCTACAAGGTCGCCCGGAGGGCATGGCGACCTATGTG
1 AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTATGTG
61377 TTGGGACGTACATGTGCCATGCAACACGCTCATTCTCTCTGTTTGAACA
66 TTGGGACGTACATGTGCCATGCAACACGCTCATTCTCTCTGTTTGAACA
*
61426 AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAAGGCATGGCGACCTA
1 AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTA
61487 CGACCAACAC
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 170 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.20
Consensus pattern (114 bp):
AGGGTAGGTCGCCCGGAGTGCATGGCGACCTACAAGGTCGCCCGGAGGGCATGGCGACCTATGTG
TTGGGACGTACATGTGCCATGCAACACGCTCATTCTCTCTGTTTGAACA
Found at i:61477 original size:29 final size:29
Alignment explanation
Indices: 61431--61487 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
61421 GAACAAGGGT
61431 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
61460 AGGTCGCCCGGAAG-GCATGGCGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
61488 GACCAACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.21, C:0.32, G:0.35, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:62866 original size:2 final size:2
Alignment explanation
Indices: 62859--63052 Score: 130
Period size: 2 Copynumber: 100.0 Consensus size: 2
62849 AATTATTGAA
* * * *
62859 TC TC TC TC TC TC TC -C CC CC TC TC TC TC TC CC TC TC TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
62900 TC TC CC TC TC TC CC TC TC -C T- TC TC TC TC CC TC TC TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
62940 TC CC TC TC CC TC CC TC TC CC TC CC TC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * *
62982 CC TC -C TC TC TC CC TC TC CC TC -C TC -C CC TC CC CC CC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
63021 TC TC TC TC TC CC CC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
63053 ACTCATTTGT
Statistics
Matches: 150, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
1 6 0.04
2 144 0.96
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (2 bp):
TC
Found at i:62894 original size:10 final size:10
Alignment explanation
Indices: 62859--63052 Score: 174
Period size: 10 Copynumber: 18.8 Consensus size: 10
62849 AATTATTGAA
*
62859 TCTCTCTCTC
1 TCTCTCTCCC
* *
62869 TCTCCCCCCTC
1 TCTCTCTCC-C
62880 TCTCTCTCCC
1 TCTCTCTCCC
62890 TCTCTCTCCC
1 TCTCTCTCCC
* *
62900 TCTCCCTCTC
1 TCTCTCTCCC
* *
62910 TCCCTCTCCT
1 TCTCTCTCCC
62920 TCTCTCTCCC
1 TCTCTCTCCC
62930 TCTCTCTCCC
1 TCTCTCTCCC
62940 TCCCTCTCCCTCCC
1 T--CTCT--CTCCC
*
62954 TCTCCCTCCC
1 TCTCTCTCCC
62964 TCTCTCTCCC
1 TCTCTCTCCC
62974 TCTCTCTCCC
1 TCTCTCTCCC
62984 TCCTCTCTCCC
1 T-CTCTCTCCC
*
62995 TCTCCCT-CC
1 TCTCTCTCCC
* *
63004 TCCCCTCCCCC
1 T-CTCTCTCCC
* * *
63015 CCCCTCTCTC
1 TCTCTCTCCC
*
63025 TCTCTCCCCC
1 TCTCTCTCCC
*
63035 TCTCTCTCTC
1 TCTCTCTCCC
63045 TCTCTCTC
1 TCTCTCTC
63053 ACTCATTTGT
Statistics
Matches: 148, Mismatches: 28, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
9 3 0.02
10 112 0.76
11 20 0.14
12 7 0.05
14 6 0.04
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (10 bp):
TCTCTCTCCC
Found at i:76540 original size:24 final size:26
Alignment explanation
Indices: 76501--76551 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
76491 ATTACAGTGA
76501 GGAAATAAAAACATCAG-AATTATAT
1 GGAAATAAAAACATCAGAAATTATAT
76526 GGAAAT-AAAACATCAGAAATTATAT
1 GGAAATAAAAACATCAGAAATTATAT
76551 G
1 G
76552 TTAATACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24
Consensus pattern (26 bp):
GGAAATAAAAACATCAGAAATTATAT
Done.