Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001347.1 Hibiscus syriacus cultivar Beakdansim tig00002625_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: 89292
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1404 original size:28 final size:28
Alignment explanation
Indices: 1361--1419 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1351 CGAACTTATT
1361 CATGCATTTACCAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
* *
1389 CATGTATTTACGAACTATCAATGTGTAC
1 CATGCATTTACCAACTATCAATGTGTAC
1417 CAT
1 CAT
1420 AAGCATACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (28 bp):
CATGCATTTACCAACTATCAATGTGTAC
Found at i:3179 original size:21 final size:20
Alignment explanation
Indices: 3137--3179 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3127 TGTCATGTCA
* *
3137 TTTTTATTTTACTTATTTAT
1 TTTTTATGTTACTTATTAAT
*
3157 TTTTTATAGTTACTTGTTAAT
1 TTTTTAT-GTTACTTATTAAT
3178 TT
1 TT
3180 CCTTGTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTATGTTACTTATTAAT
Found at i:4504 original size:13 final size:13
Alignment explanation
Indices: 4486--4512 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4476 AGTAACCACG
4486 AAGACCATGCTAC
1 AAGACCATGCTAC
4499 AAGACCATGCTAC
1 AAGACCATGCTAC
4512 A
1 A
4513 TCCATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.15
Consensus pattern (13 bp):
AAGACCATGCTAC
Found at i:6363 original size:22 final size:22
Alignment explanation
Indices: 6312--6402 Score: 110
Period size: 22 Copynumber: 4.1 Consensus size: 22
6302 CGCCAACCGA
* * *
6312 CCACCGTCGGTCACTATTCTGC
1 CCACCGTCAGTCACTATTCCGG
* *
6334 CCATCGTCGGTCACTATTCCGG
1 CCACCGTCAGTCACTATTCCGG
* *
6356 CCACCGTCAGTTACTATTCCGA
1 CCACCGTCAGTCACTATTCCGG
*
6378 CCACCGTCAGTTACTATTCCGG
1 CCACCGTCAGTCACTATTCCGG
6400 CCA
1 CCA
6403 TACTATTCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.18, C:0.38, G:0.18, T:0.26
Consensus pattern (22 bp):
CCACCGTCAGTCACTATTCCGG
Found at i:6897 original size:25 final size:25
Alignment explanation
Indices: 6863--6915 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
6853 TTTACTGGAA
6863 GCTACTGGAATTTCAACATGTAGGG
1 GCTACTGGAATTTCAACATGTAGGG
*
6888 GCTACTGGAATTTCAACGTGTAGGG
1 GCTACTGGAATTTCAACATGTAGGG
6913 GCT
1 GCT
6916 GCTGTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (25 bp):
GCTACTGGAATTTCAACATGTAGGG
Found at i:11147 original size:11 final size:12
Alignment explanation
Indices: 11131--11159 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11121 ATATAAGGAT
11131 ATAAAAT-AAAA
1 ATAAAATAAAAA
11142 ATAAAATAAAAA
1 ATAAAATAAAAA
11154 ATAAAA
1 ATAAAA
11160 GAATTGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:11773 original size:31 final size:31
Alignment explanation
Indices: 11738--11807 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
11728 CTTTCCGACT
11738 GAAATAATAAGAATATGATAACTCTTACCAA
1 GAAATAATAAGAATATGATAACTCTTACCAA
11769 GAAATAATAAGAATATGATAACTCTTACCAA
1 GAAATAATAAGAATATGATAACTCTTACCAA
11800 GAAATAAT
1 GAAATAAT
11808 TTGATATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (31 bp):
GAAATAATAAGAATATGATAACTCTTACCAA
Found at i:12000 original size:2 final size:2
Alignment explanation
Indices: 11993--12022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11983 TTAACCTTTC
11993 AT AT 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 AT AT
12023 TAATGTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13095 original size:22 final size:22
Alignment explanation
Indices: 13070--13121 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
13060 ATCATGGGAT
* *
13070 GAATAGTGACCGACGGTGGCTG
1 GAATAGTGACAGACGGTGGCTA
*
13092 GAATAGTAACAGACGGTGGCTA
1 GAATAGTGACAGACGGTGGCTA
*
13114 AAATAGTG
1 GAATAGTG
13122 TCTGAGGGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (22 bp):
GAATAGTGACAGACGGTGGCTA
Found at i:13697 original size:2 final size:2
Alignment explanation
Indices: 13690--13717 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13680 AGTCACATTA
13690 AT 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 AT
13718 GTTATTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23159 original size:20 final size:20
Alignment explanation
Indices: 23130--23169 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
23120 ATTATCCTAT
*
23130 TCACTAATAATCTTTTATTC
1 TCACTAATAATCTTATATTC
*
23150 TCACTGATAATCTTATATTC
1 TCACTAATAATCTTATATTC
23170 CATAAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (20 bp):
TCACTAATAATCTTATATTC
Found at i:23453 original size:31 final size:31
Alignment explanation
Indices: 23381--23482 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
23371 TCAATTGTTG
* * *
23381 ATGTTACACATACCACGTCATT-TTTTAATA
1 ATGTGACATATACAACGTCATTATTTTAATA
* * *
23411 ATATGATATATACAACGTCATTATTTTAATG
1 ATGTGACATATACAACGTCATTATTTTAATA
** *
23442 ATGTGACATATACAATATCATCATTTTTAATA
1 ATGTGACATATACAACGTCATTA-TTTTAATA
23474 ATGTGACAT
1 ATGTGACAT
23483 TTTCTTGATA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
30 17 0.29
31 25 0.43
32 16 0.28
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (31 bp):
ATGTGACATATACAACGTCATTATTTTAATA
Found at i:24550 original size:24 final size:24
Alignment explanation
Indices: 24504--24555 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
24494 AACAAACTCG
**
24504 TTTAACTACTCGTTTATTGGCTCC
1 TTTAACTACTCGTTTATAAGCTCC
* *
24528 TTTAACTATTCGTTTATAAGCTCG
1 TTTAACTACTCGTTTATAAGCTCC
24552 TTTA
1 TTTA
24556 CCCTGTTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTAACTACTCGTTTATAAGCTCC
Found at i:26625 original size:18 final size:18
Alignment explanation
Indices: 26602--26637 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
26592 ATGTACCCTT
26602 TTGAATTTAAAGTACCTA
1 TTGAATTTAAAGTACCTA
26620 TTGAATTTAAAGTACCTA
1 TTGAATTTAAAGTACCTA
26638 GAGAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TTGAATTTAAAGTACCTA
Found at i:32436 original size:2 final size:2
Alignment explanation
Indices: 32429--32461 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
32419 GATGATTGTA
32429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32462 TTTAGATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33332 original size:60 final size:59
Alignment explanation
Indices: 33239--33396 Score: 169
Period size: 60 Copynumber: 2.6 Consensus size: 59
33229 TTTAGTGATA
* ** * *
33239 AAATTGGAATATTCAAAAGTTTGGGGACCAATTTAGAAA-G-AGTGATA-TAGTTTACGGATG
1 AAATTAGAATATTCAAAAGTTTAAGGACCAATTTA-AAAGGAAGTCATACT--TTGA-GGATG
* ** *
33299 AAATTAGAATTTTCAAAAGTTTAAGGATGAATTTAAAATGGAAGTCCTACTTTGAGGATG
1 AAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAA-GGAAGTCATACTTTGAGGATG
33359 AAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAA
1 AAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAA
33397 TGAGAGTTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 3 0.04
60 69 0.84
61 4 0.05
62 5 0.06
63 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (59 bp):
AAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAAGGAAGTCATACTTTGAGGATG
Found at i:35371 original size:85 final size:86
Alignment explanation
Indices: 35255--35411 Score: 228
Period size: 85 Copynumber: 1.8 Consensus size: 86
35245 TCTTTTGACT
* * * * *
35255 GTCTTCTATATTCATATATATTGTTGGAGTTGCCTAATTAATACATATGGCACTAGTGAAATCTC
1 GTCTTCTACATTCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAACTGAAATATC
35320 -AATTTGGCATTTTTATGGCA
66 TAATTTGGCATTTTTATGGCA
* *
35340 GTCTTCTACATGT-ATATATATTGTTAGAGTTGCCTGATTAATCCATATGGCACAACTGAAATAT
1 GTCTTCTACAT-TCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAACTGAAATAT
35404 CTAATTTG
65 CTAATTTG
35412 ACATAATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
85 56 0.89
86 7 0.11
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (86 bp):
GTCTTCTACATTCATATATATTGTTAGAGTTGCCTAATTAATACATATGGCACAACTGAAATATC
TAATTTGGCATTTTTATGGCA
Found at i:40975 original size:22 final size:22
Alignment explanation
Indices: 40945--40986 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40935 TAATTAAAAA
40945 TGTTAATGAACAATTAAAATCT
1 TGTTAATGAACAATTAAAATCT
* *
40967 TGTTTATGAACATTTAAAAT
1 TGTTAATGAACAATTAAAAT
40987 ACAAAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
TGTTAATGAACAATTAAAATCT
Found at i:53968 original size:29 final size:29
Alignment explanation
Indices: 53837--53971 Score: 117
Period size: 29 Copynumber: 4.6 Consensus size: 29
53827 CTTTTTTAAA
* * * *
53837 TAATTACCAAAATAGCACCCTTTTTGAAT
1 TAATTCCCAGAATAGCACCCATTTCGAAT
* * *
53866 TAATTCCCATAATAGTACCAATTTCGAAT
1 TAATTCCCAGAATAGCACCCATTTCGAAT
* ** * *
53895 TAATTCCCAGAATATCACCTTTTTCAAAAA
1 TAATTCCCAGAATAGCACCCATTTC-GAAT
* * *
53925 AAATTACCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAGAATAGCACCCATTTCGAAT
*
53954 TAATTCCCCGAATAGCAC
1 TAATTCCCAGAATAGCAC
53972 TAAACCGAAT
Statistics
Matches: 80, Mismatches: 25, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
29 59 0.74
30 21 0.26
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (29 bp):
TAATTCCCAGAATAGCACCCATTTCGAAT
Found at i:54055 original size:26 final size:25
Alignment explanation
Indices: 53998--54057 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
53988 CCAAAATAAC
*
53998 ACCGGTCAACGGTCAACGGGTCGGG
1 ACCGGTCAACGGTAAACGGGTCGGG
* * *
54023 TCGGGTCAACGGGTAAACGGGTCGTG
1 ACCGGTCAAC-GGTAAACGGGTCGGG
54049 ACCGGTCAA
1 ACCGGTCAA
54058 ATCGGTCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (25 bp):
ACCGGTCAACGGTAAACGGGTCGGG
Found at i:61398 original size:10 final size:10
Alignment explanation
Indices: 61379--61411 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
61369 GATCGTGACT
61379 GGTC-AAACC
1 GGTCAAAACC
61388 GGTCAAAACC
1 GGTCAAAACC
61398 GGTTCAAAACC
1 GG-TCAAAACC
61409 GGT
1 GGT
61412 TTCCAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 8 0.36
11 10 0.45
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.15
Consensus pattern (10 bp):
GGTCAAAACC
Found at i:61406 original size:11 final size:11
Alignment explanation
Indices: 61383--61412 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61373 GTGACTGGTC
61383 AAACCGG-TCA
1 AAACCGGTTCA
61393 AAACCGGTTCA
1 AAACCGGTTCA
61404 AAACCGGTT
1 AAACCGGTT
61413 TCCAGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:73782 original size:20 final size:21
Alignment explanation
Indices: 73748--73787 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
73738 TATAATTTTA
**
73748 TTTTTTTAACTTTAT-ATAAT
1 TTTTTTTAAAATTATCATAAT
73768 TTTTTTTAAAATTATCATAA
1 TTTTTTTAAAATTATCATAA
73788 CGTGAAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTTTAAAATTATCATAAT
Found at i:74608 original size:21 final size:22
Alignment explanation
Indices: 74557--74609 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
74547 TCCTTTTTCC
*
74557 TTATTTT-CTTTTTCTTCCTTT
1 TTATTTTCCTTTTTCTTCCTTG
* *
74578 TTCTTCTCCTTTTTC-TCCTTG
1 TTATTTTCCTTTTTCTTCCTTG
74599 TTATTTTCCTT
1 TTATTTTCCTT
74610 GTCGTCGTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATTTTCCTTTTTCTTCCTTG
Found at i:75974 original size:27 final size:29
Alignment explanation
Indices: 75928--75981 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
75918 AACATATTTA
75928 TTGAGTATTTAAACTATTATTTTTTTATT
1 TTGAGTATTTAAACTATTATTTTTTTATT
*
75957 TTGA-TATTTAAA-TTTTATTTTTTTA
1 TTGAGTATTTAAACTATTATTTTTTTA
75982 AATCATACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 12 0.50
28 8 0.33
29 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (29 bp):
TTGAGTATTTAAACTATTATTTTTTTATT
Found at i:76207 original size:25 final size:26
Alignment explanation
Indices: 76179--76227 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
76169 TAATTTTGAA
*
76179 AAAAATAA-AATTTAGGTACCAAAAC
1 AAAAATAATAATTTAGATACCAAAAC
* *
76204 AAAAGTAATATTTTAGATACCAAA
1 AAAAATAATAATTTAGATACCAAA
76228 TGTGTAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.24
Consensus pattern (26 bp):
AAAAATAATAATTTAGATACCAAAAC
Found at i:76569 original size:30 final size:30
Alignment explanation
Indices: 76494--76569 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
76484 ACGATTTAAC
* *
76494 AGTTCAGTGGTATAATTGAAATGGAAATCAA
1 AGTTCAGTGGTATAATTGAAA-GAAAATAAA
*
76525 AGTTCAGTGCTATAATTGAAA-AAAACTAAA
1 AGTTCAGTGGTATAATTGAAAGAAAA-TAAA
*
76555 AGTTTAGTGGTATAA
1 AGTTCAGTGGTATAA
76570 ACGATACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.08
30 16 0.41
31 20 0.51
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (30 bp):
AGTTCAGTGGTATAATTGAAAGAAAATAAA
Found at i:81586 original size:16 final size:18
Alignment explanation
Indices: 81565--81597 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
81555 AATAACACAC
81565 ATAAA-TAT-TAAAATAA
1 ATAAATTATATAAAATAA
81581 ATAAATTATATAAAATA
1 ATAAATTATATAAAATA
81598 TCCAACTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAATTATATAAAATAA
Found at i:81752 original size:14 final size:14
Alignment explanation
Indices: 81735--81761 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
81725 TTTCTATTCA
81735 TCTAAACCCTAAAC
1 TCTAAACCCTAAAC
81749 TCTAAACCCTAAA
1 TCTAAACCCTAAA
81762 AAAAATCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TCTAAACCCTAAAC
Found at i:84776 original size:34 final size:32
Alignment explanation
Indices: 84717--84783 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
84707 ACTTAAAGTA
* *
84717 TTTTTTGGTCAAAATAAGTATCTAAAGTTACTTT
1 TTTTTTGGTCAAAATAAGCACCTAAA-TTA-TTT
*
84751 TTTTTTTGTCAAAATAAGCACCTAAATTATTT
1 TTTTTTGGTCAAAATAAGCACCTAAATTATTT
84783 T
1 T
84784 ATCAAATAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 3 0.10
34 23 0.77
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (32 bp):
TTTTTTGGTCAAAATAAGCACCTAAATTATTT
Found at i:84925 original size:29 final size:30
Alignment explanation
Indices: 84889--84975 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 30
84879 ATTGAATATG
*
84889 TTAGGTACATATTTTGACTAAAAAAT-ACT
1 TTAGGTACTTATTTTGACTAAAAAATAACT
* *
84918 TTAGGTACTTATTTTAACAAAGAAAAATATAACT
1 TTAGGTACTTATTTTGAC---TAAAAA-ATAACT
84952 TTAGGTACTTATTTTGA-TAAAAAA
1 TTAGGTACTTATTTTGACTAAAAAA
84976 AATACCTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
29 17 0.35
30 5 0.10
32 5 0.10
33 2 0.04
34 19 0.40
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (30 bp):
TTAGGTACTTATTTTGACTAAAAAATAACT
Found at i:84955 original size:34 final size:32
Alignment explanation
Indices: 84908--84979 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 32
84898 TATTTTGACT
84908 AAAAA-ATACTTTAGGTACTTATTTTAACAAA
1 AAAAATATACTTTAGGTACTTATTTTAACAAA
* *
84939 GAAAAATATAACTTTAGGTACTTATTTTGATAAA
1 -AAAAATAT-ACTTTAGGTACTTATTTTAACAAA
84973 AAAAATA
1 AAAAATA
84980 CCTTAAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 5 0.14
33 9 0.25
34 22 0.61
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (32 bp):
AAAAATATACTTTAGGTACTTATTTTAACAAA
Found at i:87250 original size:31 final size:31
Alignment explanation
Indices: 87212--87340 Score: 142
Period size: 31 Copynumber: 4.3 Consensus size: 31
87202 GAGTTGAGGG
* *
87212 TTACCTATGTCTTTCGAGACATATGTACATA
1 TTACCTATGTCTTTCGAGACATATGGACAAA
*
87243 TTACCTATGTCTTTCGAGATATATGGACAAA
1 TTACCTATGTCTTTCGAGACATATGGACAAA
****
87274 TTACCTATGTCTTTCGAG--ATATGGATGGT
1 TTACCTATGTCTTTCGAGACATATGGACAAA
* *
87303 TTACCTATGTCCTTAG-GACATATGGAC--A
1 TTACCTATGTCTTTCGAGACATATGGACAAA
87331 TTACCTATGT
1 TTACCTATGT
87341 TCTTCGGAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
28 11 0.13
29 21 0.25
30 7 0.08
31 46 0.54
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (31 bp):
TTACCTATGTCTTTCGAGACATATGGACAAA
Found at i:87355 original size:57 final size:59
Alignment explanation
Indices: 87212--87356 Score: 140
Period size: 57 Copynumber: 2.4 Consensus size: 59
87202 GAGTTGAGGG
* * * *
87212 TTACCTATGTCTTTCGAGACAT--ATGTACATATTACCTATGTCTTTCGAGATATATGGACAAA
1 TTACCTATGTCTTTCGAGACATGGATG---GT-TTACCTATGTCCTTAGAGACATATGGAC-AA
*
87274 TTACCTATGTCTTTCGAGATATGGATGGTTTACCTATGTCCTTAG-GACATATGGAC-A
1 TTACCTATGTCTTTCGAGACATGGATGGTTTACCTATGTCCTTAGAGACATATGGACAA
87331 TTACCTATGT-TCTTCG-GAACATGGAT
1 TTACCTATGTCT-TTCGAG-ACATGGAT
87357 AGTGGTCATT
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
56 2 0.03
57 22 0.30
59 10 0.14
60 14 0.19
61 1 0.01
62 21 0.29
64 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (59 bp):
TTACCTATGTCTTTCGAGACATGGATGGTTTACCTATGTCCTTAGAGACATATGGACAA
Done.