Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002181.1 Hibiscus syriacus cultivar Beakdansim tig00004444_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: 42264
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15313 original size:32 final size:31
Alignment explanation
Indices: 15245--15333 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 31
15235 ATGACCACTA
* * *
15245 TCCATATGTTCCAAAGAACATAGGT-AGCTG
1 TCCATATGTCCCGAAGGACATAGGTAAGCTG
*
15275 TCCATATGTCCCGAAGGACATAGGTAATCATG
1 TCCATATGTCCCGAAGGACATAGGTAAGC-TG
15307 TCCATATGTCCCGAAGGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
15334 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.42
31 2 0.04
32 29 0.55
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAGCTG
Found at i:15628 original size:2 final size:2
Alignment explanation
Indices: 15621--15646 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15611 TTATGTAAAC
15621 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
15647 CACTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18878 original size:20 final size:19
Alignment explanation
Indices: 18831--18881 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
18821 CTTATTAATG
* *
18831 ATGTGATTTAAACATTTAA
1 ATGTAATTTAAAAATTTAA
* *
18850 ATTTTATTTAACAAATTTAA
1 ATGTAATTTAA-AAATTTAA
18870 ATGTAATTTAAA
1 ATGTAATTTAAA
18882 CATCATTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (19 bp):
ATGTAATTTAAAAATTTAA
Found at i:23255 original size:18 final size:20
Alignment explanation
Indices: 23232--23272 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
23222 CTCCTAAAAA
23232 TTTAAA-ATTATC-ATATAT
1 TTTAAATATTATCTATATAT
*
23250 TTTAAATTTTATCTATATAT
1 TTTAAATATTATCTATATAT
23270 TTT
1 TTT
23273 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 9 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAATATTATCTATATAT
Found at i:24061 original size:14 final size:14
Alignment explanation
Indices: 24042--24097 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
24032 CGTTCGTGAA
24042 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
24056 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
24069 --TT-GTTTATGTT
1 CGTTCGATTATGTT
24080 CGTTCGATTATGTT
1 CGTTCGATTATGTT
24094 CGTT
1 CGTT
24098 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:24076 original size:24 final size:24
Alignment explanation
Indices: 24049--24118 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
24039 GAACGTTCGA
*
24049 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
24073 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
24097 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
24119 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:24857 original size:10 final size:10
Alignment explanation
Indices: 24842--24900 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
24832 GGGTCTCCAA
24842 CGTTTATGTT
1 CGTTTATGTT
24852 CGTTTATGTT
1 CGTTTATGTT
24862 CG----TGTT
1 CGTTTATGTT
24868 CGTTTATGTT
1 CGTTTATGTT
24878 CG----TGTT
1 CGTTTATGTT
24884 CGTTTATGTT
1 CGTTTATGTT
24894 CGTTTAT
1 CGTTTAT
24901 TTATTAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
6 12 0.29
10 29 0.71
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:24869 original size:16 final size:16
Alignment explanation
Indices: 24848--24896 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
24838 CCAACGTTTA
24848 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24864 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24880 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24896 T
1 T
24897 TTATTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:24893 original size:26 final size:26
Alignment explanation
Indices: 24842--24900 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
24832 GGGTCTCCAA
* *
24842 CGTTTATGTTCGTTTATGTTCGTGTT
1 CGTTTATGTTCGTTTACGTTCATGTT
*
24868 CGTTTATGTTCGTGTT-CGTTTATGTT
1 CGTTTATGTTCGT-TTACGTTCATGTT
24894 CGTTTAT
1 CGTTTAT
24901 TTATTAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (26 bp):
CGTTTATGTTCGTTTACGTTCATGTT
Found at i:24987 original size:16 final size:16
Alignment explanation
Indices: 24966--24998 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24956 AAAAAAAATT
24966 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24982 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24998 T
1 T
24999 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:29396 original size:18 final size:19
Alignment explanation
Indices: 29373--29415 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
29363 CAGTAATCCT
29373 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
29391 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
29411 ATTCC
1 ATTCC
29416 GTGAACCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:29403 original size:20 final size:20
Alignment explanation
Indices: 29378--29415 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29368 ATCCTATTCC
29378 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
29398 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
29416 GTGAACCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:29407 original size:662 final size:654
Alignment explanation
Indices: 28115--29434 Score: 1989
Period size: 662 Copynumber: 2.0 Consensus size: 654
28105 TAATTTTGCA
* ** * * ****
28115 CTTAGGGGTATTTGGATGGGGATGTGATATTCTTATGGGAATGGAATTCACATTTTTTCGTTTGG
1 CTTAGGGGTATTTGGATGGGGATGTGAGATTCCCATGGGAATGAAATCCACATTCCCCCGTTTGG
* * * * * *
28180 TTAGCTCGGGAATCTCATTCCTGGTAATGTAAGATTACTAATAGTGGATTTTTGGGGTATATTAC
66 TTAGCCCGGGAATCCCATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTGGGATATATTAC
* * *
28245 CGAGAATGTCATTACCTCCATTTCTTTAGATATTGTTGGATTACAGGCATTTTGGACTAAAATGT
131 CGAGAATGTCATTACCTCCATTTCCTTAGATATTATTGGATTACA-GCATTTTGGACTAAAATGA
*
28310 CTTTAATTTTTTTTTCTTTCAAAAATATCATTATTCTCTCATTGAATAATAAAAATTCTACAAAG
195 CTTTAAATTTTTTTTCTTTCAAAAATATCATTATTCTCTCATTGAATAATAAAAATTCTACAAAG
*
28375 GTTAAATTACAAATTTATTCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTT
260 GTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTT
*
28440 TATATGAAGTTCAGGGGTTAAAAAAATTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTG
325 TATATGAAGTTCAGGGGTTAAAAAAATTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTA
*
28505 TAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCAAAC
390 TAAAAAAATTATATAAAATTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCAAAC
* *
28570 TTGTTAAAAAAACAAATACATAATAAGGACAATTTGGTCAAATATACATTCCAATAATCTTTTAT
455 TTGTTAAAAAAACAAATACATAATAAGGACAATTTGATCAAATATACATTCAAATAATCTTTTAT
* * *
28635 TCTTTTAACCAAACATGGTAATCTTACATTCCTGCTAAGCCAACCAACCACAAAATACAACATTC
520 TCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTC
* ** *
28700 CCAGTAATCTTATTCCCTGATAATCTTACATTCTTATTGGTAATCTTACATTCCGTGAACCAAAC
585 CCAGTAATCCTATTCCCTGATAATCTTACATTCCCACTGGTAATCTTACATTCCGTGAACCAAAC
28765 GCACC
650 GCACC
* *
28770 CTTAGGGGGTGTTTGGATGGGGAATGTGGGATTCCCATGGGAATGAAATCCACATTCCCCCGTTT
1 CTTA-GGGGTATTTGGATGGGG-ATGTGAGATTCCCATGGGAATGAAATCCACATTCCCCCGTTT
28835 GGTTAGCCCGGGAATCCCATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTTGGGATATAT
64 GGTTAGCCCGGGAATCCCATTCCCGGTAATGTAAGATTACCAATAGTAGA-TTTTTGGGATATAT
* * * * *
28900 TACCGGGAATGTTATTACCTCCCTTTCCTTAGGTATTATTGGATTATC-GCGTTTTGGACTAAAA
128 TACCGAGAATGTCATTACCTCCATTTCCTTAGATATTATTGGATTA-CAGCATTTTGGACTAAAA
* * * * * *
28964 TGGAC-TTAAATTTTTTTTCTTTCAAAAATATTATTCTTTTTTCATTGAATAATAAAAATTTTAT
192 T-GACTTTAAATTTTTTTTCTTTCAAAAATATCATTATTCTCTCATTGAATAATAAAAATTCTAC
* ** *
29028 GAATTTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAGTCTATAATTAAA
256 AAAGGTTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAA
* *
29093 ATTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTATCTTTTCATTAAACC-TTTTATATTTTC
321 ATTTTATATGAAGTTCAGGGGTT-AAA-AAAA-TTTACCCTTTCATTAAACCTTTTTATATTTTC
29157 AATTTTATAAAAAAAAAATTATATAAAATTTATGAATTTAAATTTTTTAAAGAAAATATATAAAT
383 AATTTTAT---AAAAAAATTATATAAAATTTATGAATTTAAATTTTTTAAAGAAAATATATAAAT
*
29222 ATTTTCAAACTTGTTAAAAAAACAAATATATAATAAGGACAATTTGATCAAATATACATTCAAAT
445 ATTTTCAAACTTGTTAAAAAAACAAATACATAATAAGGACAATTTGATCAAATATACATTCAAAT
* * * * *
29287 AATCTTTTATTCCTTTAACTAAACACGGTATTCTTACATTCTTGCTAAGCTAATCAAACACAAAA
510 AATCTTTTATTCCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAA
*
29352 TACAACATTCCCAGTAATCCTATTCCCTGGTAATCTTACATTCCCACTGGTAATCTTACATTCCG
575 TACAACATTCCCAGTAATCCTATTCCCTGATAATCTTACATTCCCACTGGTAATCTTACATTCCG
*
29417 TGAACCAAGCGCACC
640 TGAACCAAACGCACC
29432 CTT
1 CTT
29435 TCAACTTTTT
Statistics
Matches: 596, Mismatches: 58, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
655 4 0.01
656 16 0.03
657 228 0.38
658 58 0.10
659 24 0.04
660 17 0.03
662 249 0.42
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (654 bp):
CTTAGGGGTATTTGGATGGGGATGTGAGATTCCCATGGGAATGAAATCCACATTCCCCCGTTTGG
TTAGCCCGGGAATCCCATTCCCGGTAATGTAAGATTACCAATAGTAGATTTTTGGGATATATTAC
CGAGAATGTCATTACCTCCATTTCCTTAGATATTATTGGATTACAGCATTTTGGACTAAAATGAC
TTTAAATTTTTTTTCTTTCAAAAATATCATTATTCTCTCATTGAATAATAAAAATTCTACAAAGG
TTAAATTACAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTT
ATATGAAGTTCAGGGGTTAAAAAAATTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTAT
AAAAAAATTATATAAAATTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCAAACT
TGTTAAAAAAACAAATACATAATAAGGACAATTTGATCAAATATACATTCAAATAATCTTTTATT
CCTTTAACCAAACACGGTAATCTTACATTCCTGCTAAGCCAACCAAACACAAAATACAACATTCC
CAGTAATCCTATTCCCTGATAATCTTACATTCCCACTGGTAATCTTACATTCCGTGAACCAAACG
CACC
Found at i:37157 original size:6 final size:6
Alignment explanation
Indices: 37146--37198 Score: 56
Period size: 6 Copynumber: 8.5 Consensus size: 6
37136 GACACGTATT
37146 ACCACG ACCACG ACCACG TATTACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ----ACCACG ACCACG ACCACG ACCACG ACCACG
37196 ACC
1 ACC
37199 CGAGACGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.23
6 27 0.63
10 6 0.14
ACGTcount: A:0.30, C:0.49, G:0.15, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:37166 original size:22 final size:22
Alignment explanation
Indices: 37138--37185 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
37128 GTGTCGAAGA
37138 CACGTATTACCACGACCACGAC
1 CACGTATTACCACGACCACGAC
37160 CACGTATTACCACGACCACGAC
1 CACGTATTACCACGACCACGAC
37182 CACG
1 CACG
37186 ACCCGACCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.42, G:0.15, T:0.12
Consensus pattern (22 bp):
CACGTATTACCACGACCACGAC
Found at i:37716 original size:6 final size:6
Alignment explanation
Indices: 37695--37797 Score: 192
Period size: 6 Copynumber: 17.5 Consensus size: 6
37685 TCTCGTCTCG
37695 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37741 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
37789 GGTCGT GGT
1 GGTCGT GGT
37798 AATACGTGTC
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.10
6 87 0.90
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:37838 original size:22 final size:22
Alignment explanation
Indices: 37810--38020 Score: 225
Period size: 20 Copynumber: 10.0 Consensus size: 22
37800 TACGTGTCTT
37810 CGATTCTTGGAAGATCGCGTTG
1 CGATTCTTGGAAGATCGCGTTG
37832 CGATTCTTGGAAGATCGCGTTG
1 CGATTCTTGGAAGATCGCGTTG
* *
37854 CGATT-TTCTG-A-ATGGCGTTG
1 CGATTCTT-GGAAGATCGCGTTG
37874 CGATTCTTGG-A-ATCGCGTTG
1 CGATTCTTGGAAGATCGCGTTG
*
37894 CGATT-TTCTG-A-ATCGCGTTG
1 CGATTCTT-GGAAGATCGCGTTG
*
37914 CGATTCTTGGAAGATCGCATTG
1 CGATTCTTGGAAGATCGCGTTG
*
37936 CGATT-TTCTG-A-ATCGCGTTG
1 CGATTCTT-GGAAGATCGCGTTG
37956 CGATTCTTGGAAGATCGCGTTG
1 CGATTCTTGGAAGATCGCGTTG
* *
37978 CGATT-TT--ATGAATCGCATTG
1 CGATTCTTGGAAG-ATCGCGTTG
37998 CGATTCTTGGAAGATCGCGTTG
1 CGATTCTTGGAAGATCGCGTTG
38020 C
1 C
38021 AATCTTCTTT
Statistics
Matches: 161, Mismatches: 14, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.02
20 72 0.45
21 18 0.11
22 65 0.40
23 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (22 bp):
CGATTCTTGGAAGATCGCGTTG
Found at i:37873 original size:20 final size:19
Alignment explanation
Indices: 37823--38085 Score: 181
Period size: 20 Copynumber: 12.8 Consensus size: 19
37813 TTCTTGGAAG
*
37823 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTTG-A
37844 GATCGCGTTGCGATTTTCTGA
1 -ATCGCGTTGCGATTTT-TGA
* *
37865 ATGGCGTTGCGATTCTTGGA
1 ATCGCGTTGCGATT-TTTGA
37885 ATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTTT-TGA
*
37905 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTTG-A
*
37926 GATCGCATTGCGATTTTCTGA
1 -ATCGCGTTGCGATTTT-TGA
*
37947 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTTG-A
37968 GATCGCGTTGCGATTTTATGA
1 -ATCGCGTTGCGATTTT-TGA
* *
37989 ATCGCATTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTTG-A
*
38010 GATCGCGTTGCAATCTTCTT--
1 -ATCGCGTTGCGAT-TT-TTGA
* * * *
38030 TTCAACGTTGCGCTTTTCTAA
1 ATC-GCGTTGCGATTTT-TGA
*
38051 ATCGCGTTGCG-GTTTTGA
1 ATCGCGTTGCGATTTTTGA
38069 TATCGCGTTGCGATTTT
1 -ATCGCGTTGCGATTTT
38086 GTTGGTCATT
Statistics
Matches: 194, Mismatches: 25, Indels: 46
0.73 0.09 0.17
Matches are distributed among these distances:
18 3 0.02
19 21 0.11
20 90 0.46
21 22 0.11
22 56 0.29
23 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (19 bp):
ATCGCGTTGCGATTTTTGA
Found at i:37960 original size:82 final size:84
Alignment explanation
Indices: 37823--38020 Score: 346
Period size: 82 Copynumber: 2.4 Consensus size: 84
37813 TTCTTGGAAG
*
37823 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATGGCGTTGCGATTCTTGG-A-A
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGA
*
37886 TCGCGTTGCGATTTTCTGA
66 TCGCGTTGCGATTTTATGA
*
37905 ATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGA
37970 TCGCGTTGCGATTTTATGA
66 TCGCGTTGCGATTTTATGA
*
37989 ATCGCATTGCGATTCTTGGAAGATCGCGTTGC
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGC
38021 AATCTTCTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
82 59 0.54
83 1 0.01
84 49 0.45
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (84 bp):
ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGA
TCGCGTTGCGATTTTATGA
Found at i:38041 original size:42 final size:42
Alignment explanation
Indices: 37823--38020 Score: 346
Period size: 42 Copynumber: 4.8 Consensus size: 42
37813 TTCTTGGAAG
37823 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
37865 ATGGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
37905 ATCGCGTTGCGATTCTTGGAAGATCGCATTGCGATTTTCTGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
37947 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGA
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
*
37989 ATCGCATTGCGATTCTTGGAAGATCGCGTTGC
1 ATCGCGTTGCGATTCTTGGAAGATCGCGTTGC
38021 AATCTTCTTT
Statistics
Matches: 148, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
40 38 0.26
41 2 0.01
42 108 0.73
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (42 bp):
ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGA
Found at i:41754 original size:28 final size:29
Alignment explanation
Indices: 41656--41751 Score: 90
Period size: 28 Copynumber: 3.3 Consensus size: 29
41646 GTTTGAATAA
*
41656 TTTAAGTACCTATTTTGA-CATAAA-ATAC
1 TTTAGGTACCTATTTTGACCA-AAAGATAC
* * *
41684 TTTAGGCACCTATTTTGACAAAAATGAAAAC
1 TTTAGGTACCTATTTTGACCAAAA-G-ATAC
* *
41715 TTTATGTACTTATTTTGACCAAAAGATA-
1 TTTAGGTACCTATTTTGACCAAAAGATAC
41743 TTTAGGTAC
1 TTTAGGTAC
41752 TTAAATAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 27 0.50
29 3 0.06
30 1 0.02
31 23 0.43
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (29 bp):
TTTAGGTACCTATTTTGACCAAAAGATAC
Done.