Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000866.1 Hibiscus syriacus cultivar Beakdansim tig00001672_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: 60199
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6454 original size:3 final size:3
Alignment explanation
Indices: 6446--6476 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6436 AATTTATCCT
*
6446 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6477 AATGCAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16592 original size:10 final size:11
Alignment explanation
Indices: 16561--16594 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
16551 GACACATATT
16561 ACCACGACCACG
1 ACCACGACC-CG
16573 ACCACGACCCG
1 ACCACGACCCG
16584 ACC-CGACCCG
1 ACCACGACCCG
16594 A
1 A
16595 GACGGCGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:16818 original size:20 final size:20
Alignment explanation
Indices: 16793--16986 Score: 199
Period size: 20 Copynumber: 9.4 Consensus size: 20
16783 CTATCTTTTT
16793 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTCTCTAAATCG
16813 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTCTCTAAATCG
*
16833 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
16853 CGTTGCGGTTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
* *
16873 CATTGCGGTTTTCTTCTAAATCG
1 CGTTGC-G-ATTC-TCTAAATCG
* *
16896 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
16916 CATTGCGATTATATAAATCG
1 CGTTGCGATTCTCTAAATCG
* * *
16936 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTAAATCG
*
16956 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTAAATCG
16979 CGTTGCGA
1 CGTTGCGA
16987 ACTTGGAAGC
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
20 111 0.76
21 3 0.02
22 7 0.05
23 26 0.18
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTAAATCG
Found at i:16852 original size:40 final size:40
Alignment explanation
Indices: 16795--16986 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
16785 ATCTTTTTCG
* *
16795 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * *
16835 TTGCGATTCTCTCAATCGCGTTGCGGTTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
16875 TTGCGGTTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGC-G-ATTC-TCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
16918 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
16958 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCGTTGCGA
16987 ACTTGGAAGC
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 72 0.57
41 3 0.02
42 6 0.05
43 46 0.36
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:16957 original size:83 final size:83
Alignment explanation
Indices: 16804--16986 Score: 267
Period size: 83 Copynumber: 2.2 Consensus size: 83
16794 GTTGCGATTC
* * * * * * * *
16804 TCTAAATCGCGTTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCGTTGCGGTTCTCTCA
1 TCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATCA
* *
16869 GTCGCATTGCGGTTTTCT
66 ATCGCATTGCGATTTTCT
*
16887 TCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATCA
1 TCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATCA
16952 ATCGCATTGCGATTTTCT
66 ATCGCATTGCGATTTTCT
16970 TCTAAATCGCGTTGCGA
1 TCTAAATCGCGTTGCGA
16987 ACTTGGAAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (83 bp):
TCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATCA
ATCGCATTGCGATTTTCT
Found at i:17063 original size:20 final size:20
Alignment explanation
Indices: 16793--17090 Score: 179
Period size: 20 Copynumber: 14.6 Consensus size: 20
16783 CTATCTTTTT
*
16793 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*
16813 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
16833 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
16853 CGTTGCGGTTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
16873 CATTGCGGTTTTCTTCTAAATCG
1 CGTTGC-G-ATT-TTCTAAATCG
* * *
16896 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
16916 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
16936 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
16956 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
16979 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
17000 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
17018 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
17040 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
17060 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
17079 CGTTGCGATTTT
1 CGTTGCGATTTT
17091 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 156 0.70
21 15 0.07
22 7 0.03
23 26 0.12
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:17080 original size:19 final size:20
Alignment explanation
Indices: 17040--17090 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
17030 TTCTTTTTAA
*
17040 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
17060 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
17079 CGTTGCGATTTT
1 CGTTGCGATTTT
17091 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:30408 original size:31 final size:33
Alignment explanation
Indices: 30373--30446 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
30363 TCGTTAGGAG
* * * *
30373 TATTTTATCATAGTTTGAT-AA-ATTTTATTAT
1 TATTTTATAATAATTTAATAAAGATTTAATTAT
30404 TATTTTATAATAATTTAATAAAGATTTAATTAT
1 TATTTTATAATAATTTAATAAAGATTTAATTAT
*
30437 CATTTTATAA
1 TATTTTATAA
30447 ATATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 16 0.44
32 2 0.06
33 18 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TATTTTATAATAATTTAATAAAGATTTAATTAT
Found at i:33949 original size:7 final size:7
Alignment explanation
Indices: 33907--33956 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
33897 GCCCTCCGAT
33907 TATATATA
1 TATATA-A
33915 TATATAA
1 TATATAA
* *
33922 TATTTTA
1 TATATAA
33929 TAT-TAA
1 TATATAA
33935 T-TAT-A
1 TATATAA
33940 TATATAA
1 TATATAA
33947 TATATAA
1 TATATAA
33954 TAT
1 TAT
33957 TTTTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
5 3 0.08
6 7 0.19
7 20 0.56
8 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATATAA
Found at i:33962 original size:34 final size:32
Alignment explanation
Indices: 33907--33983 Score: 120
Period size: 34 Copynumber: 2.4 Consensus size: 32
33897 GCCCTCCGAT
33907 TATATAT-ATATATAATATTTTATATTAATTA
1 TATATATAATATATAATATTTTATATTAATTA
33938 TATATATAATATATAATATTTTTTATATTAATTA
1 TATATATAATATATAATA--TTTTATATTAATTA
*
33972 TATATAAAATAT
1 TATATATAATAT
33984 TTTCGGGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 7 0.17
32 10 0.24
34 25 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATATAATATATAATATTTTATATTAATTA
Found at i:39137 original size:20 final size:20
Alignment explanation
Indices: 39112--39169 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
39102 GTTTGGTTCA
39112 GAGAATGTAAGATTACCAAT
1 GAGAATGTAAGATTACCAAT
39132 GAGAATGTAAGATTACCAAT
1 GAGAATGTAAGATTACCAAT
39152 G-GAAATGTAAGATTACCA
1 GAG-AATGTAAGATTACCA
39170 GAGAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (20 bp):
GAGAATGTAAGATTACCAAT
Found at i:39399 original size:36 final size:37
Alignment explanation
Indices: 39327--39400 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
39317 GTTGGAAAAT
* *
39327 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
39364 ATTTATA-ATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATTGAAAATCATAAA
39400 A
1 A
39401 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:40183 original size:14 final size:14
Alignment explanation
Indices: 40166--40215 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
40156 TAAACGAACA
*
40166 TAAACGAACGGATG
1 TAAACGAACGAATG
*
40180 TAAACGAAC-ACA-A
1 TAAACGAACGA-ATG
*
40193 TAAACGAAAGAATG
1 TAAACGAACGAATG
40207 TAAACGAAC
1 TAAACGAAC
40216 ACAAATGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (14 bp):
TAAACGAACGAATG
Found at i:40207 original size:27 final size:28
Alignment explanation
Indices: 40165--40228 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
40155 ATAAACGAAC
* *
40165 ATAAACGAACGGATGTAAACGAACAC-A
1 ATAAACGAAAGAATGTAAACGAACACAA
40192 ATAAACGAAAGAATGTAAACGAACACAA
1 ATAAACGAAAGAATGTAAACGAACACAA
*
40220 ATGAACGAA
1 ATAAACGAA
40229 CATAAACCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (28 bp):
ATAAACGAAAGAATGTAAACGAACACAA
Found at i:40486 original size:20 final size:20
Alignment explanation
Indices: 40461--40701 Score: 170
Period size: 20 Copynumber: 11.8 Consensus size: 20
40451 AATGACCAAC
40461 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* **
40481 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
40501 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
40521 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* ***
40542 AAGAATCGCAATGCGAGGCA-
1 AA-AATCGCAACGCGATTTAG
* *
40562 AAGAATCGCAATGCGATCTTCG
1 AA-AATCGCAACGCGAT-TTAG
*
40584 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTTAG
40605 AAAATCGCAACGCGATTTCA-
1 AAAATCGCAACGCGATTT-AG
* *
40625 ATAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
40645 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
40665 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
40685 AAAATCGCAATGCGATT
1 AAAATCGCAACGCGATT
40702 CCAAGAATCG
Statistics
Matches: 179, Mismatches: 29, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 136 0.76
21 11 0.06
22 29 0.16
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:40639 original size:40 final size:40
Alignment explanation
Indices: 40519--40714 Score: 261
Period size: 40 Copynumber: 4.8 Consensus size: 40
40509 AACGGTCAAA
* *
40519 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GG
1 AGAAAATCGCAACGCGAT-TT-CAAGAATCGCAACGCGATTG
*
40560 CA-AAGAATCGCAATGCGATCTTCGAAGAATCGCAACGCGATTG
1 -AGAA-AATCGCAACGCGAT-TTC-AAGAATCGCAACGCGATTG
*
40603 AGAAAATCGCAACGCGATTTCAATAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTG
*
40643 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTG
* *
40683 AGAAAATCGCAATGCGATTCCAAGAATCGCAA
1 AGAAAATCGCAACGCGATTTCAAGAATCGCAA
40715 AACGGCAAAA
Statistics
Matches: 142, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
40 87 0.61
41 6 0.04
42 46 0.32
43 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AGAAAATCGCAACGCGATTTCAAGAATCGCAACGCGATTG
Found at i:40711 original size:60 final size:59
Alignment explanation
Indices: 40523--40714 Score: 192
Period size: 60 Copynumber: 3.1 Consensus size: 59
40513 GTCAAAAGAA
* *
40523 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GGCAAAGAATCGCAATGCGATCTTCGAAG
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTG-AAA-AATCGCAATGCGA--TTCGAAG
* * * * * *
40587 AATCGCAACGCGATT-GAGAAAATCGCAACGCGATTTCAATAATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGA-TTGAAAAATCGCAATGCGATTCGA-AG
*
40647 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAAAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGA-AAAATCGCAATGCGATTCGAAG
40707 AATCGCAA
1 AATCGCAA
40715 AACGGCAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
59 5 0.05
60 56 0.53
61 3 0.03
62 27 0.25
63 2 0.02
64 13 0.12
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (59 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAAAAATCGCAATGCGATTCGAAG
Found at i:40836 original size:6 final size:6
Alignment explanation
Indices: 40825--40957 Score: 266
Period size: 6 Copynumber: 22.2 Consensus size: 6
40815 GACACGTATT
40825 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40873 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40921 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
40958 GAAGGCGGCG
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 127 1.00
ACGTcount: A:0.34, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:41708 original size:6 final size:6
Alignment explanation
Indices: 41699--41735 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
41689 CGCCGCCGTC
41699 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
41736 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:41795 original size:20 final size:20
Alignment explanation
Indices: 41770--41849 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
41760 GCGGATACTA
41770 TCTTTTTAGCATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
* *
41790 TCTTTTCAACATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
*** * *
41810 TCTAAATCGCGTTGCGATTT
1 TCTTTTTAGCATTGCGATTT
* *
41830 T-TGTTTCGCATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
41849 T
1 T
41850 GTTGGTCATT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.50
Consensus pattern (20 bp):
TCTTTTTAGCATTGCGATTT
Found at i:42001 original size:14 final size:14
Alignment explanation
Indices: 41982--42038 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
41972 ATATTGGGTA
41982 AACATAAATGAACG
1 AACATAAATGAACG
41996 AAC----AT-AACG
1 AACATAAATGAACG
* * *
42005 AACAGAAGTAAACG
1 AACATAAATGAACG
42019 AACATAAATGAACG
1 AACATAAATGAACG
42033 AACATA
1 AACATA
42039 TTATCGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
13 1 0.03
14 24 0.71
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:43291 original size:27 final size:28
Alignment explanation
Indices: 43239--43312 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
43229 TACTTATTAT
* *
43239 AAAAATAAGTGTTTAAATTTTATTTTTA
1 AAAAATAAGTGTCTAAAATTTATTTTTA
*
43267 AAAAATAA-TGTCTAAAGATTTTTTTTTA
1 AAAAATAAGTGTCTAAA-ATTTATTTTTA
* *
43295 TTAAAAATTAGTGGCTAA
1 --AAAAATAAGTGTCTAA
43313 CGTTATCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 7 0.19
28 17 0.46
30 7 0.19
31 6 0.16
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (28 bp):
AAAAATAAGTGTCTAAAATTTATTTTTA
Found at i:43292 original size:28 final size:28
Alignment explanation
Indices: 43239--43294 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
43229 TACTTATTAT
*
43239 AAAAATAAGTGTTTAAATTTTATTTTTA
1 AAAAATAAGTGTTAAAATTTTATTTTTA
43267 AAAAATAA-TGTCTAAAGATTTT-TTTTTA
1 AAAAATAAGTGT-TAAA-ATTTTATTTTTA
43295 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 17 0.68
29 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (28 bp):
AAAAATAAGTGTTAAAATTTTATTTTTA
Found at i:43815 original size:23 final size:23
Alignment explanation
Indices: 43771--43815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43761 GACGACCATT
*
43771 GAAGGGGGAAAGTTGGGAAGGGA
1 GAAGGGGGAAAGTCGGGAAGGGA
*
43794 GAAGGAGGGAAA-TCGGGTAGGG
1 GAAGG-GGGAAAGTCGGGAAGGG
43816 GCTGCAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.56, T:0.09
Consensus pattern (23 bp):
GAAGGGGGAAAGTCGGGAAGGGA
Found at i:45723 original size:17 final size:18
Alignment explanation
Indices: 45696--45730 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
45686 CCTTTCTCCT
45696 CTAACTGTGTTCATAGAA
1 CTAACTGTGTTCATAGAA
45714 CTAA-TGTGTTCATAGAA
1 CTAACTGTGTTCATAGAA
45731 AAAGCTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
CTAACTGTGTTCATAGAA
Found at i:46995 original size:29 final size:30
Alignment explanation
Indices: 46948--47019 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
46938 AAAATATATT
* *
46948 TTTATCTCTTTAAATTTTTATAAGTTTAAA
1 TTTATCTCTTTAAAATTTTATAAATTTAAA
46978 TTTAT-TCTTTAAAATTTTATAAATTTAAA
1 TTTATCTCTTTAAAATTTTATAAATTTAAA
*
47007 TTTATCCCTTTAA
1 TTTATCTCTTTAA
47020 TATAAAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTATCTCTTTAAAATTTTATAAATTTAAA
Found at i:48234 original size:2 final size:2
Alignment explanation
Indices: 48227--48256 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
48217 AATAGACCAC
48227 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48257 GTTGATCTAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48353 original size:19 final size:19
Alignment explanation
Indices: 48329--48367 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
48319 AATTAAAATA
*
48329 TAACTCATAATAATATTTT
1 TAACTCACAATAATATTTT
48348 TAACTCACAATAATATTTT
1 TAACTCACAATAATATTTT
48367 T
1 T
48368 TTTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (19 bp):
TAACTCACAATAATATTTT
Found at i:48524 original size:7 final size:7
Alignment explanation
Indices: 48504--48541 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
48494 TGGTATTATG
48504 TTTAGGA
1 TTTAGGA
48511 TTTTAGGA
1 -TTTAGGA
*
48519 TTTAGGG
1 TTTAGGA
48526 TTTAGGA
1 TTTAGGA
48533 TTTAGGA
1 TTTAGGA
48540 TT
1 TT
48542 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGA
Found at i:52464 original size:15 final size:15
Alignment explanation
Indices: 52444--52472 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52434 CTGAATATAA
52444 TGGATAATTTTAAAT
1 TGGATAATTTTAAAT
52459 TGGATAATTTTAAA
1 TGGATAATTTTAAA
52473 AATTAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TGGATAATTTTAAAT
Done.