Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001830.1 Hibiscus syriacus cultivar Beakdansim tig00003700_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: 86082
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3275 original size:20 final size:20
Alignment explanation
Indices: 3250--3292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3240 TCTAAGAGCA
*
3250 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
3270 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
3290 CAT
1 CAT
3293 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:17837 original size:31 final size:31
Alignment explanation
Indices: 17802--17864 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
17792 CTTTGACTTA
* *
17802 TGGAAGATGATAAGGTTGAGGTGTCTTGGTT
1 TGGAAGATGATAAGGTTGAGGTGCCATGGTT
* * *
17833 TGGAATATTATAAGGTTTAGGTGCCATGGTT
1 TGGAAGATGATAAGGTTGAGGTGCCATGGTT
17864 T
1 T
17865 AATGGTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.05, G:0.33, T:0.38
Consensus pattern (31 bp):
TGGAAGATGATAAGGTTGAGGTGCCATGGTT
Found at i:19601 original size:52 final size:52
Alignment explanation
Indices: 19500--19608 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
19490 AGGGAACTAA
* *
19500 GTGTATTATGGTGGACACGACCTTATGTGTATTATGGTCTGCACGACCTTAT
1 GTGTATTATGGTGGACACGACCTTATGTGTATTATGGTCGGCACAACCTTAT
* * * *
19552 GTGTATTATGGTTGACACGACCTTATGTGTATTATGGTGGGTATAACCTTAT
1 GTGTATTATGGTGGACACGACCTTATGTGTATTATGGTCGGCACAACCTTAT
19604 GTGTA
1 GTGTA
19609 AGCACTACGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.39
Consensus pattern (52 bp):
GTGTATTATGGTGGACACGACCTTATGTGTATTATGGTCGGCACAACCTTAT
Found at i:19608 original size:26 final size:26
Alignment explanation
Indices: 19500--19591 Score: 150
Period size: 26 Copynumber: 3.5 Consensus size: 26
19490 AGGGAACTAA
19500 GTGTATTATGGTGGACACGACCTTAT
1 GTGTATTATGGTGGACACGACCTTAT
*
19526 GTGTATTATGGTCTG-CACGACCTTAT
1 GTGTATTATGGT-GGACACGACCTTAT
*
19552 GTGTATTATGGTTGACACGACCTTAT
1 GTGTATTATGGTGGACACGACCTTAT
19578 GTGTATTATGGTGG
1 GTGTATTATGGTGG
19592 GTATAACCTT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
25 2 0.03
26 59 0.95
27 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (26 bp):
GTGTATTATGGTGGACACGACCTTAT
Found at i:33260 original size:20 final size:20
Alignment explanation
Indices: 33232--33282 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
33222 TTTTTGGGGG
33232 GTATCGATACTGTATAGGCA
1 GTATCGATACTGTATAGGCA
*
33252 GTATTGATACTGTATAGGCA
1 GTATCGATACTGTATAGGCA
*
33272 GTATCGGTACT
1 GTATCGATACT
33283 ACCCTTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (20 bp):
GTATCGATACTGTATAGGCA
Found at i:33457 original size:19 final size:19
Alignment explanation
Indices: 33430--33469 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33420 TATTTGAAAT
*
33430 AATCGAATATAATAAT-TTA
1 AATCAAATATAA-AATCTTA
33449 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
33468 AA
1 AA
33470 ATTACTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:37114 original size:26 final size:26
Alignment explanation
Indices: 37078--37134 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
37068 AGGGCACTAA
37078 GTGTATTATGGTAGGCACGACCTTAT
1 GTGTATTATGGTAGGCACGACCTTAT
*
37104 GTGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTAGGCACGACCTTAT
37130 GTGTA
1 GTGTA
37135 ATCACTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
GTGTATTATGGTAGGCACGACCTTAT
Found at i:44018 original size:14 final size:17
Alignment explanation
Indices: 43989--44035 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
43979 GCCTTCAGGC
* *
43989 TATATAAATAATAATAT
1 TATATATATAATATTAT
44006 T-TATAATATAATATTAT
1 TATAT-ATATAATATTAT
44023 TATATATATAATA
1 TATATATATAATA
44036 ACACATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATAATATTAT
Found at i:44509 original size:71 final size:71
Alignment explanation
Indices: 44393--44529 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 71
44383 GTTTAGACTC
* *
44393 AAACTTGGATTACTCCACTACTCTTCCATGAAGTTCTCATACTTTGC-AAAAAAATATGTTCCAC
1 AAACTTGGATTACTCCACAACTCTTCCATGAAGCTCTCATACTTTGCTAAAAAAAT-TGTTCCAC
44457 TAGATTA
65 TAGATTA
* *
44464 AAACTTGGATTACTTCACAACTCTTCCGTGAAGCTCTCATACTTTGCTAAAAAAATTGTTCCACT
1 AAACTTGGATTACTCCACAACTCTTCCATGAAGCTCTCATACTTTGCTAAAAAAATTGTTCCACT
44529 A
66 A
44530 CTCTTTCGTG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 53 0.87
72 8 0.13
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (71 bp):
AAACTTGGATTACTCCACAACTCTTCCATGAAGCTCTCATACTTTGCTAAAAAAATTGTTCCACT
AGATTA
Found at i:45375 original size:22 final size:22
Alignment explanation
Indices: 45350--45399 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
45340 AAAGCTTTCG
*
45350 TCTTTGAAAAGATAATCTATAA
1 TCTTTGAAAAGAGAATCTATAA
*
45372 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATAA
45394 TCTTTG
1 TCTTTG
45400 CAGAATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATAA
Found at i:45409 original size:22 final size:22
Alignment explanation
Indices: 45384--45430 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
45374 TTTGAAAAGA
* *
45384 GAATCTATCATCTTTGCAGAAT
1 GAATCTATCATCCTTACAGAAT
45406 GAATCTATCATCCTTACAGAAT
1 GAATCTATCATCCTTACAGAAT
45428 GAA
1 GAA
45431 GATATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (22 bp):
GAATCTATCATCCTTACAGAAT
Found at i:46165 original size:42 final size:42
Alignment explanation
Indices: 46060--46167 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 42
46050 TCCTTTTTGT
* * * * *
46060 CTGAAATAAGCCTTCACCACGCCCTACATATATTATTTTTTA
1 CTGAAATGAGCCTTCACCATGCCCTACATAGATTATTTCTGA
* * * *
46102 CAGAAATGGGCCTTCAGCATGCCCTACATGGATTATTTCTGA
1 CTGAAATGAGCCTTCACCATGCCCTACATAGATTATTTCTGA
* *
46144 CTGAAATGTGCCTTCATCATGCCC
1 CTGAAATGAGCCTTCACCATGCCC
46168 CAGCATTCTA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (42 bp):
CTGAAATGAGCCTTCACCATGCCCTACATAGATTATTTCTGA
Found at i:54445 original size:20 final size:20
Alignment explanation
Indices: 54391--54448 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
54381 GGCTTGGGTT
*
54391 AAACTTGTAATTGGG-CTCC
1 AAACTTATAATTGGGCCTCC
* *
54410 CAAGTTATCAATTGGGCCTCC
1 AAACTTAT-AATTGGGCCTCC
*
54431 AAACTTATAAATGGGCCT
1 AAACTTATAATTGGGCCT
54449 TCAGGCTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.16
20 16 0.52
21 10 0.32
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (20 bp):
AAACTTATAATTGGGCCTCC
Found at i:54477 original size:12 final size:12
Alignment explanation
Indices: 54456--54514 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
54446 CCTTCAGGCT
*
54456 ATATAAATAATA
1 ATATATATAATA
*
54468 ATATTTATAAT-
1 ATATATATAATA
* *
54479 ATA-ATATTATT
1 ATATATATAATA
54490 ATATATATAATA
1 ATATATATAATA
*
54502 ACATATATAATA
1 ATATATATAATA
54514 A
1 A
54515 ACGTCTCTCG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 5 0.13
11 6 0.16
12 27 0.71
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATAATA
Found at i:54484 original size:17 final size:17
Alignment explanation
Indices: 54457--54513 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
54447 CTTCAGGCTA
54457 TATAA-ATAATAATATT
1 TATAATATAATAATATT
*
54473 TATAATATAATATTA-T
1 TATAATATAATAATATT
* *
54489 TATATATATAATAACATA
1 TATA-ATATAATAATATT
54507 TATAATA
1 TATAATA
54514 AACGTCTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.29
17 20 0.59
18 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAATATAATAATATT
Found at i:54744 original size:35 final size:35
Alignment explanation
Indices: 54698--54796 Score: 162
Period size: 35 Copynumber: 2.8 Consensus size: 35
54688 CCACCATATA
54698 CACTAAGTGTCTTGGGTACACACTCTAGCGTTATG
1 CACTAAGTGTCTTGGGTACACACTCTAGCGTTATG
*
54733 CACTAAGTGTCTTGGGTACACACTCTAGTGTTATG
1 CACTAAGTGTCTTGGGTACACACTCTAGCGTTATG
* *
54768 CACTAAGTGTCTGTGGATATACACTCTAG
1 CACTAAGTGTCT-TGGGTACACACTCTAG
54797 TGCTAAATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 46 0.77
36 14 0.23
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (35 bp):
CACTAAGTGTCTTGGGTACACACTCTAGCGTTATG
Found at i:58893 original size:15 final size:15
Alignment explanation
Indices: 58857--58895 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
58847 TAAAGAGTAT
58857 TTTTCAAAAGTTCAA
1 TTTTCAAAAGTTCAA
* * *
58872 GTATCAAAATTTCAA
1 TTTTCAAAAGTTCAA
58887 TTTTCAAAA
1 TTTTCAAAA
58896 CTTAGGTGTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (15 bp):
TTTTCAAAAGTTCAA
Found at i:60468 original size:61 final size:61
Alignment explanation
Indices: 60337--60473 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
60327 GTGTGTAAGG
* * * * * *
60337 AAACTTAGTACAGGTGGTGGGCACAACCTTATGTTTCATATCTGGATCAACAGTAGAGTGT
1 AAACCTAGTGCAGGTGGTGGGCACAACCTTATGTTTCATATCCGAATCAACACTAGAGAGT
* ** * *
60398 AAACCTAGTGTAGGTGGTGGGCATGACCTTATTTTTCATATCCGAATCAGCACTAGAGAGT
1 AAACCTAGTGCAGGTGGTGGGCACAACCTTATGTTTCATATCCGAATCAACACTAGAGAGT
* *
60459 AAGCTTAGTGCAGGT
1 AAACCTAGTGCAGGT
60474 TTAACACTAC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (61 bp):
AAACCTAGTGCAGGTGGTGGGCACAACCTTATGTTTCATATCCGAATCAACACTAGAGAGT
Found at i:61792 original size:144 final size:143
Alignment explanation
Indices: 61485--61792 Score: 411
Period size: 144 Copynumber: 2.1 Consensus size: 143
61475 AGTTTCGGCC
* *
61485 ATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTCCTTATATGAAGTGATATATCACCATTG
1 ATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTCCTTATATGAAGTGATATATCACCACTG
* ** *
61550 AAAATTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACAA
66 AAAAGTTTTCTGAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACAA
* ***
61615 AAAAGTTTCTGCC
131 AAAAGTTGCTAAA
* * *
61628 ATGGTGCGTTATTTTGCCTATGAGAAATACATGTTTTTCTTATATGAAGTGATATATCACCACTG
1 ATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTCCTTATATGAAGTGATATATCACCACTG
* *
61693 AAAAACGTTTTCT-AAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGTCAT
66 -AAAA-GTTTTCTGAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCAC
** *
61757 TGAATAGTTGCTAAA
129 AAAAAAGTTGCTAAA
* *
61772 ATGGTGCATTATATTACCTAT
1 ATGGTGCATTATTTTGCCTAT
61793 AAAAAATTCA
Statistics
Matches: 142, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
143 60 0.42
144 76 0.54
145 6 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (143 bp):
ATGGTGCATTATTTTGCCTATGAGAAATACACGTTTTCCTTATATGAAGTGATATATCACCACTG
AAAAGTTTTCTGAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACAA
AAAAGTTGCTAAA
Found at i:61837 original size:144 final size:142
Alignment explanation
Indices: 61485--61847 Score: 332
Period size: 144 Copynumber: 2.5 Consensus size: 142
61475 AGTTTCGGCC
* * * * * * * * * *
61485 ATGGTGCATTATTTTGCCTATGAGAAATGCACGT-TTTCCTTATATGAAGTGATATATCACCATT
1 ATGGTGCATTATATTACCTATAAAAAATACACATCTTT-CTAATACGAAGTCATATATCACCACT
* ** *
61549 GAAAATTTTTCTGAAATGAGTTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACA
65 GAAAAGTTTTCT-AAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACA
* ***
61614 AAAAAGTTTCTGCC
129 AAAAAGTTGCTAAA
* * * * * ** * * * *
61628 ATGGTGCGTTATTTTGCCTATGAGAAATACATGTTTTTCTTATATGAAGTGATATATCACCACTG
1 ATGGTGCATTATATTACCTATAAAAAATACACATCTTTCTAATACGAAGTCATATATCACCACTG
* **
61693 AAAAACGTTTTCTAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGTCATT
66 -AAAA-GTTTTCTAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACA
* *
61758 GAATAGTTGCTAAA
129 AAAAAGTTGCTAAA
* * * * *
61772 ATGGTGCATTATATTACCTATAAAAAATTCACATCTTTGTAATACGAATTCATATTTCACTACTG
1 ATGGTGCATTATATTACCTATAAAAAATACACATCTTTCTAATACGAAGTCATATATCACCACTG
61837 AAAAGTTTTCT
66 AAAAGTTTTCT
61848 CAAATGAGTT
Statistics
Matches: 184, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
142 7 0.04
143 61 0.33
144 110 0.60
145 6 0.03
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (142 bp):
ATGGTGCATTATATTACCTATAAAAAATACACATCTTTCTAATACGAAGTCATATATCACCACTG
AAAAGTTTTCTAAAAAAATTGATATATCACTGAAAAGTTGTTGAAGATGATTAATTGGGCACAAA
AAAGTTGCTAAA
Found at i:65124 original size:19 final size:19
Alignment explanation
Indices: 65097--65138 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
65087 ATCTTCATTA
*
65097 ACAACAGTTCTTTGACAA-T
1 ACAACAGTTCATTG-CAACT
*
65116 ACAAGAGTTCATTGCAACT
1 ACAACAGTTCATTGCAACT
65135 ACAA
1 ACAA
65139 AGACCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (19 bp):
ACAACAGTTCATTGCAACT
Found at i:68460 original size:16 final size:16
Alignment explanation
Indices: 68439--68472 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
68429 CTTTGACGTT
*
68439 TGGGGCGTTGATTTTA
1 TGGGGCATTGATTTTA
68455 TGGGGCATTGATTTTA
1 TGGGGCATTGATTTTA
68471 TG
1 TG
68473 AGACCGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.35, T:0.44
Consensus pattern (16 bp):
TGGGGCATTGATTTTA
Found at i:73508 original size:20 final size:20
Alignment explanation
Indices: 73483--73524 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
73473 CTAAGAGCCT
*
73483 ATTTAGAATCATATAGATGC
1 ATTTAGAAGCATATAGATGC
* *
73503 ATTTAGGAGCATATAGGTGC
1 ATTTAGAAGCATATAGATGC
73523 AT
1 AT
73525 GTGGTGGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (20 bp):
ATTTAGAAGCATATAGATGC
Found at i:75094 original size:20 final size:21
Alignment explanation
Indices: 75069--75109 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
75059 ATATTACCAT
*
75069 CATTTCA-TTTCCACAACATC
1 CATTTCACTTGCCACAACATC
75089 CATTTCAGCTTGCCACAACAT
1 CATTTCA-CTTGCCACAACAT
75110 TCTTATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (21 bp):
CATTTCACTTGCCACAACATC
Found at i:76079 original size:29 final size:29
Alignment explanation
Indices: 76004--76063 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
75994 CAAATTTTGG
**
76004 TTAGTGACCAAAATATATTTTTTGAAAGT
1 TTAGTGACCAAAATATAAGTTTTGAAAGT
76033 TTAGTGACCAAAATATAAGTTTTGAAAGT
1 TTAGTGACCAAAATATAAGTTTTGAAAGT
76062 TT
1 TT
76064 GGTTACAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (29 bp):
TTAGTGACCAAAATATAAGTTTTGAAAGT
Found at i:82113 original size:14 final size:11
Alignment explanation
Indices: 82074--82102 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
82064 ATGCTCCATT
82074 TAGCTCCAATA
1 TAGCTCCAATA
82085 TAGCTCCAATA
1 TAGCTCCAATA
82096 TAGCTCC
1 TAGCTCC
82103 CAAGTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (11 bp):
TAGCTCCAATA
Found at i:82169 original size:2 final size:2
Alignment explanation
Indices: 82162--82196 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
82152 GTGTATGAAC
82162 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82197 CAAGATAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:84726 original size:12 final size:11
Alignment explanation
Indices: 84696--84730 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
84686 AGAAAGGAAT
*
84696 ATGATTAATAA
1 ATGAATAATAA
84707 ATGAATAATAA
1 ATGAATAATAA
84718 ATGGAATAATAA
1 AT-GAATAATAA
84730 A
1 A
84731 GATAAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (11 bp):
ATGAATAATAA
Done.