Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008203.1 Hibiscus syriacus cultivar Beakdansim tig00110824_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: 117312
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6013 original size:17 final size:17
Alignment explanation
Indices: 5991--6048 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
5981 TCTAAACCGG
*
5991 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
6008 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
6025 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
6042 GTTGACC
1 GTTGACC
6049 GTTGACCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:6048 original size:7 final size:7
Alignment explanation
Indices: 6038--6074 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
6028 GACCCGACCC
6038 GACCGTT
1 GACCGTT
6045 GACCGTT
1 GACCGTT
6052 GACCG-T
1 GACCGTT
6058 GACCGTT
1 GACCGTT
6065 GACCGTT
1 GACCGTT
6072 GAC
1 GAC
6075 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:6062 original size:13 final size:13
Alignment explanation
Indices: 6038--6070 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6028 GACCCGACCC
6038 GACCGTTGACCGTT
1 GACCG-TGACCGTT
6052 GACCGTGACCGTT
1 GACCGTGACCGTT
6065 GACCGT
1 GACCGT
6071 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:13008 original size:13 final size:13
Alignment explanation
Indices: 12990--13032 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
12980 GTCAAAGAAA
12990 GTCAACGGTCACG
1 GTCAACGGTCACG
13003 GTCAACGGTCACG
1 GTCAACGGTCACG
13016 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
13030 GTC
1 GTC
13033 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.79
14 6 0.21
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:13010 original size:7 final size:7
Alignment explanation
Indices: 12990--13032 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
12980 GTCAAAGAAA
12990 GTCAACG
1 GTCAACG
12997 GTC-ACG
1 GTCAACG
13003 GTCAACG
1 GTCAACG
13010 GTC-ACG
1 GTCAACG
13016 GTCAACG
1 GTCAACG
13023 GTCAACG
1 GTCAACG
13030 GTC
1 GTC
13033 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:13023 original size:20 final size:19
Alignment explanation
Indices: 12994--13032 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
12984 AAGAAAGTCA
12994 ACGGTCACGGTCAACGGTC
1 ACGGTCACGGTCAACGGTC
13013 ACGGTCAACGGTCAACGGTC
1 ACGGTC-ACGGTCAACGGTC
13033 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (19 bp):
ACGGTCACGGTCAACGGTC
Found at i:13044 original size:17 final size:17
Alignment explanation
Indices: 13022--13062 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
13012 CACGGTCAAC
*
13022 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
13039 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
13056 GGTCAAC
1 GGTCAAC
13063 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:13094 original size:20 final size:19
Alignment explanation
Indices: 13056--13146 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
13046 AGTCGGGTCG
*
13056 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
13075 GGTCAAACCGGTTCTTGACC
1 GGTCAAACCGGTTC-AGACC
*
13095 AGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* * *
13114 GGTTAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
13134 GGTCAAACCGGTT
1 GGTCAAACCGGTT
13147 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.02
19 28 0.47
20 31 0.52
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:13115 original size:10 final size:10
Alignment explanation
Indices: 13058--13146 Score: 69
Period size: 9 Copynumber: 9.1 Consensus size: 10
13048 TCGGGTCGGG
*
13058 TCAACCCGGT
1 TCAAACCGGT
*
13068 TCAGACCGG-
1 TCAAACCGGT
13077 TCAAACCGGT
1 TCAAACCGGT
** *
13087 TCTTGACCAG-
1 TC-AAACCGGT
13097 TCAAACCGGT
1 TCAAACCGGT
*
13107 TCGAACCGGT
1 TCAAACCGGT
13117 T-AAACCGGT
1 TCAAACCGGT
*
13126 TCAAAACTGG-
1 TC-AAACCGGT
13136 TCAAACCGGT
1 TCAAACCGGT
13146 T
1 T
13147 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 26 0.43
10 24 0.40
11 10 0.17
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:13139 original size:39 final size:39
Alignment explanation
Indices: 13056--13146 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
13046 AGTCGGGTCG
* ***
13056 GGTCAACCCGGTTCAGACCGGTCAAACCGGTTCTTGACC
1 GGTCAAACCGGTTCAGACCGGTCAAACCGGTTCAAAACC
* * *
13095 AGTCAAACCGGTTC-GAACCGGTTAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAG-ACCGGTCAAACCGGTTCAAAACC
13134 GGTCAAACCGGTT
1 GGTCAAACCGGTT
13147 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 42 0.98
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (39 bp):
GGTCAAACCGGTTCAGACCGGTCAAACCGGTTCAAAACC
Found at i:14034 original size:2 final size:2
Alignment explanation
Indices: 14027--14052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14017 AGCTCAGGTT
14027 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
14053 ACCCACCACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15572 original size:27 final size:27
Alignment explanation
Indices: 15534--15585 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
15524 ACCATAAGTT
*
15534 AGGTTACGCTTACTTGATGATTGTTGG
1 AGGTTACGCTTACTTAATGATTGTTGG
* *
15561 AGGTTATGCTTACTTAATGCTTGTT
1 AGGTTACGCTTACTTAATGATTGTT
15586 TCAATCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (27 bp):
AGGTTACGCTTACTTAATGATTGTTGG
Found at i:18127 original size:15 final size:15
Alignment explanation
Indices: 18107--18135 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18097 TCGCAGCCGC
18107 AGCAGCCTTCTTCTG
1 AGCAGCCTTCTTCTG
18122 AGCAGCCTTCTTCT
1 AGCAGCCTTCTTCT
18136 TGCTGGCGTC
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:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
AGCAGCCTTCTTCTG
Found at i:21314 original size:30 final size:30
Alignment explanation
Indices: 21275--21445 Score: 107
Period size: 30 Copynumber: 5.7 Consensus size: 30
21265 AAATAGTAAT
*
21275 AACAGAAATTTACAGGACTAAAACAACAAA
1 AACAGAAATTTAAAGGACTAAAACAACAAA
** * * *
21305 AATGGAAATTTAAATGACTAAAATAATAAA
1 AACAGAAATTTAAAGGACTAAAACAACAAA
* *
21335 AACAGAAAGTTAAAGGACTAAAATAGA-AAA
1 AACAGAAATTTAAAGGACTAAAACA-ACAAA
* * ** **
21365 AACATAATTTTAAATGG--TTGAACAGTAAA
1 AACAGAAATTTAAA-GGACTAAAACAACAAA
* * * * *
21394 AAAAGAAACTAAAAGGACTAAAACAATAAT
1 AACAGAAATTTAAAGGACTAAAACAACAAA
*
21424 TACA-AACATTTAAAGGACTAAA
1 AACAGAA-ATTTAAAGGACTAAA
21446 TAGTAAAAAT
Statistics
Matches: 105, Mismatches: 30, Indels: 12
0.71 0.20 0.08
Matches are distributed among these distances:
28 2 0.02
29 18 0.17
30 82 0.78
31 3 0.03
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (30 bp):
AACAGAAATTTAAAGGACTAAAACAACAAA
Found at i:21377 original size:60 final size:59
Alignment explanation
Indices: 21265--21380 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 59
21255 ATAAGATACT
* * * * *
21265 AAATAGTAATAACAGAAATTTACAGGACTAAAACAACAAAAATGGAAATTTAAATGACTA
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAACAAAAAAAAT-GAAATTTAAATGACTA
* *
21325 AAATAATAAAAACAGAAAGTTAAAGGACTAAAATAGAAAAAACAT-AATTTTAAATG
1 AAATAATAAAAACAGAAAGTTAAAGGACTAAAACA-AAAAAA-ATGAAATTTAAATG
21381 GTTGAACAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 40 0.85
61 5 0.11
62 2 0.04
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (59 bp):
AAATAATAAAAACAGAAAGTTAAAGGACTAAAACAAAAAAAATGAAATTTAAATGACTA
Found at i:22268 original size:17 final size:18
Alignment explanation
Indices: 22214--22268 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
22204 CTCTCTTTAC
22214 TTTTC-TTTCTTTGTTGTTT
1 TTTTCTTTTCTTTGTTG--T
22233 TTCTTCTTTTCGATTTGTTG-
1 TT-TTCTTTTC--TTTGTTGT
22253 TTTTCTTTTCTTTGTT
1 TTTTCTTTTCTTTGTT
22269 ATTCTCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 6 0.19
19 10 0.31
20 5 0.16
21 4 0.12
23 7 0.22
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTTGTTGT
Found at i:22766 original size:9 final size:10
Alignment explanation
Indices: 22755--22809 Score: 62
Period size: 9 Copynumber: 5.6 Consensus size: 10
22745 GTAAAATGCA
22755 AATAAATAA-
1 AATAAATAAT
*
22764 AATTAATAAT
1 AATAAATAAT
22774 AAT-AATAAT
1 AATAAATAAT
22783 AATAACGATAAT
1 AATAA--ATAAT
22795 AAT-AATAAT
1 AATAAATAAT
22804 AATAAA
1 AATAAA
22810 AAGACCCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 25 0.62
10 6 0.15
11 1 0.03
12 8 0.20
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:22775 original size:3 final size:3
Alignment explanation
Indices: 22767--22808 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
22757 TAAATAAAAT
**
22767 TAA TAA TAA TAA TAA TAA TAA CGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
22809 AAAGACCCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:34799 original size:132 final size:133
Alignment explanation
Indices: 34555--34826 Score: 372
Period size: 132 Copynumber: 2.0 Consensus size: 133
34545 AAATATCTAC
* * *
34555 TTTTAAACATTATTTCCCAAAATATTTTTTTTCTAAAGTATCTTTACACCATTAAATGTTAAGTT
1 TTTT-AACATTATTTCCCAAAATA-TTTTTTTCGAAAGTATCTCTACACCATTAAATGTCAAGTT
* *
34620 GGTTAATTGAAAATGTTTGTATCATTAACTTTTGAATCTCTTGAGATTATT-TTCCTTAATTATT
64 GGTTAATTGAAAATGCTTGTATCATTAACTTTTGAATCTCTGGAGATTATTCTT-CTTAATTATT
34684 CATAAA
128 CATAAA
* *
34690 TTTTAACATTATTTCCCAAAATA-TTTTTTGGAAAGTATCTCTACACCCA-TAAATGTCAGGTT-
1 TTTTAACATTATTTCCCAAAATATTTTTTTCGAAAGTATCTCTACA-CCATTAAATGTCAAGTTG
* * * *
34752 GTTGTATTGAAAATGCTTGTATCTTTAATTTTTGAATCTCTGGAGATTGTTCTTCTTAATTATTC
65 GTT-AATTGAAAATGCTTGTATCATTAACTTTTGAATCTCTGGAGATTATTCTTCTTAATTATTC
34817 ATAAA
129 ATAAA
34822 TTTTA
1 TTTTA
34827 TTCATTGAAG
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
131 3 0.02
132 92 0.75
133 5 0.04
134 19 0.15
135 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (133 bp):
TTTTAACATTATTTCCCAAAATATTTTTTTCGAAAGTATCTCTACACCATTAAATGTCAAGTTGG
TTAATTGAAAATGCTTGTATCATTAACTTTTGAATCTCTGGAGATTATTCTTCTTAATTATTCAT
AAA
Found at i:37029 original size:13 final size:13
Alignment explanation
Indices: 37011--37036 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37001 TATTAATAAC
37011 AATAAATATTATA
1 AATAAATATTATA
37024 AATAAATATTATA
1 AATAAATATTATA
37037 TTATAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAAATATTATA
Found at i:38234 original size:2 final size:2
Alignment explanation
Indices: 38229--38267 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
38219 CTCTGCTCTT
*
38229 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38268 TAACACACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39360 original size:2 final size:2
Alignment explanation
Indices: 39353--39387 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39343 TTAGAGATAA
39353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39388 ATTATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55238 original size:35 final size:36
Alignment explanation
Indices: 55192--55272 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
55182 AACACAATCA
* *
55192 TCAATTACATTCTAGACCCCAAATTCC-AAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
55227 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
55263 TCAATTACAT
1 TCAATTACAT
55273 GCCCAAACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 25 0.60
36 17 0.40
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:55286 original size:36 final size:34
Alignment explanation
Indices: 55209--55288 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 34
55199 CATTCTAGAC
* * *
55209 CCCAAATTCCAAAATGCTTCAATTACATTCTAAA
1 CCCAAATTCCAAAATACTTCAATTACATCCCAAA
55243 CCTCAAATTCCAAAAATACTTCAATTACATGCCCAAA
1 CC-CAAATTCC-AAAATACTTCAATTACAT-CCCAAA
55280 CCCAAATTC
1 CCCAAATTC
55289 ATAATTCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 2 0.05
35 8 0.20
36 24 0.60
37 6 0.15
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.26
Consensus pattern (34 bp):
CCCAAATTCCAAAATACTTCAATTACATCCCAAA
Found at i:55960 original size:148 final size:149
Alignment explanation
Indices: 55773--56051 Score: 461
Period size: 148 Copynumber: 1.9 Consensus size: 149
55763 AAACTATTTA
* * * *
55773 AATTAGAATAAAATAATATTGTAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAAAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* **
55838 AATTCAATTCAATTTGACTTGATTTAAAATTTATAAACTCAAATAG-AAAAAAGTTTGAGTCAAC
66 AATTCAATTCAATTCGACTTGATTTAAAATTTATAAACTCAAATAGAAAAAAAAATTGAGTCAAC
55902 TATTTTATAAACTAAACTG
131 TATTTTATAAACTAAACTG
*
55921 AATTAAAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAAAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
55986 AATTCAATTTAATTCGACTTGATTTAAATTTTATAAACTCAAATAGAAAAAAAAATTGAGTCAAC
66 AATTCAATTCAATTCGACTTGATTTAAAATTTATAAACTCAAATAGAAAAAAAAATTGAGTCAAC
56051 T
131 T
56052 CAAATCGAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 103 0.86
149 17 0.14
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (149 bp):
AATTAAAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAAATTTATAAACTCAAATAGAAAAAAAAATTGAGTCAAC
TATTTTATAAACTAAACTG
Found at i:56051 original size:27 final size:27
Alignment explanation
Indices: 56021--56105 Score: 127
Period size: 27 Copynumber: 3.1 Consensus size: 27
56011 AAATTTTATA
* *
56021 AACTCAAATAGAAAAAAAAATT-GAGTC
1 AACTCAAATCG-AAAAAATATTCGAGTC
*
56048 AACTCAAATCGAAAAAATATTCAAGTC
1 AACTCAAATCGAAAAAATATTCGAGTC
56075 AACTCAAATCGAAAAAATATTCGAGTC
1 AACTCAAATCGAAAAAATATTCGAGTC
56102 AACT
1 AACT
56106 ATTTTATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.17
27 44 0.83
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.21
Consensus pattern (27 bp):
AACTCAAATCGAAAAAATATTCGAGTC
Found at i:60647 original size:6 final size:6
Alignment explanation
Indices: 60636--60696 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
60626 GACACGTATT
* * *
60636 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
60684 ACCACG ACCACG A
1 ACCACG ACCACG A
60697 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:60704 original size:5 final size:5
Alignment explanation
Indices: 60694--60747 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
60684 ACCACGACCA
* * * *
60694 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
60744 CGAG
1 CGAG
60748 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:66612 original size:6 final size:6
Alignment explanation
Indices: 66601--66661 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
66591 GACACGTATT
* *
66601 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
66649 ACCACG ACCACG A
1 ACCACG ACCACG A
66662 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:66669 original size:5 final size:5
Alignment explanation
Indices: 66659--66712 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
66649 ACCACGACCA
* * * *
66659 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
66709 CGAG
1 CGAG
66713 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:72585 original size:6 final size:6
Alignment explanation
Indices: 72574--72634 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
72564 GACACGTATT
* *
72574 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
72622 ACCACG ACCACG A
1 ACCACG ACCACG A
72635 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:72642 original size:5 final size:5
Alignment explanation
Indices: 72632--72685 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
72622 ACCACGACCA
* * * *
72632 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
72682 CGAG
1 CGAG
72686 ACGGACGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:73940 original size:6 final size:6
Alignment explanation
Indices: 73929--73977 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
73919 GAAGACACGT
73929 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC
1 ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC ATTACC
73977 A
1 A
73978 CGACCACGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTACC
Found at i:73983 original size:6 final size:6
Alignment explanation
Indices: 73974--74076 Score: 197
Period size: 6 Copynumber: 17.2 Consensus size: 6
73964 CATTACCATT
73974 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
74022 ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
74070 ACCACG A
1 ACCACG A
74077 GCCGAGCCGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:74084 original size:5 final size:5
Alignment explanation
Indices: 74074--74127 Score: 90
Period size: 5 Copynumber: 10.8 Consensus size: 5
74064 ACCACGACCA
* *
74074 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
74124 CGAG
1 CGAG
74128 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.20, C:0.37, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:76109 original size:28 final size:29
Alignment explanation
Indices: 76076--76133 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
76066 TTAATTCTTA
76076 TTTATTAAAAATTTTAAAAT-TATATTTG
1 TTTATTAAAAATTTTAAAATATATATTTG
* **
76104 TTTATTAAAATTTTTAGGATATATATTTG
1 TTTATTAAAAATTTTAAAATATATATTTG
76133 T
1 T
76134 ATTTGTACGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTATTAAAAATTTTAAAATATATATTTG
Found at i:78434 original size:27 final size:27
Alignment explanation
Indices: 78393--78458 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
78383 TGCCAAGAGA
78393 AAGGCACCCAATAGACACCTAAGGATAT
1 AAGGCA-CCAATAGACACCTAAGGATAT
78421 AAGGCACCAATAGACACCTAAGGATAT
1 AAGGCACCAATAGACACCTAAGGATAT
78448 AAGGCACCAAT
1 AAGGCACCAAT
78459 TACAGAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 32 0.84
28 6 0.16
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (27 bp):
AAGGCACCAATAGACACCTAAGGATAT
Found at i:93162 original size:3 final size:3
Alignment explanation
Indices: 93156--93269 Score: 129
Period size: 3 Copynumber: 37.0 Consensus size: 3
93146 CATCATCATC
* * * *
93156 ATT ATT ATT ATC ATT ATT ATT ATT GTT TTT ATT ATT ATC ATT ATT AGTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * *
93205 TTT AATT CTT CTT ATT ATT ATT ATC ATT CATT ATT ATT ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
93252 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
93270 CATTGAATCA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
3 88 0.93
4 7 0.07
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:96452 original size:10 final size:9
Alignment explanation
Indices: 96419--96453 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
96409 TTTAATCAAT
*
96419 AAATCTATC
1 AAATCTGTC
96428 AAATCTGTC
1 AAATCTGTC
96437 AAATCTGTC
1 AAATCTGTC
96446 GAAATCTG
1 -AAATCTG
96454 GGATTTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (9 bp):
AAATCTGTC
Found at i:105805 original size:323 final size:317
Alignment explanation
Indices: 105219--105858 Score: 1000
Period size: 323 Copynumber: 2.0 Consensus size: 317
105209 AGCCTGATCG
* * *
105219 AATTGAGGTTAATGAAGCATTAGAACTTCAAAATAGGATCATTGTACTGGAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
*
105284 ATGTGATAGCAAGGTGCATGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGTT
66 ATGTGATAGCAAGGTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGTT
*
105349 CCGAGAAAGAAAAAGCTAGTTTGAAGCAGAAGCAGTTTTATGATAAAATTCAAGATTTGCAGTGT
131 CCGAGAAAGAAAAAGCTAGTTTGAAGCAGAAGCAGTTTTATGAGAAAATTCAAGATTTGCAGTGT
* * *
105414 CAGCTCGATACAGCCCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAAGCAATTG
196 CAACTCGATACAGCCCAAAGAGAAATTGTGGAGATGAAACTAGAGCTTGCTGAGAGAAGCAATTG
* *
105479 CATTAAAGTCTTGAATGAA-AGCCTTGAGACTTCAAAATCGGAGAGCAACAGGCTTAA
261 CATTAAAGTCTTAAATGAAGA-CCTTGAGACTTCAAAATCGGAAAGCAACAGGCTTAA
105536 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
* * * *
105601 TTGTTGATAGCAAGAG-GCAGGCATTGTTGGAAGAGTTATGTATTACTAAAGAAATGCTCTAGTG
66 ATG-TGATAGCAAG-GTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAG
*
105665 TTCCGAGAAAGAAAATGCTAG-TTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATT
129 TTCCGAGAAAGAAAAAGCTAGTTTGAAG-----C-AGAAGCAGTTTTATGAGAAAATTCAAGATT
*
105729 TGCAGTGTCAACTCGATAC-GTCTCAAAGAGAAATTGTGGAGATGAAACTAGAGCTTGCTGAGAG
188 TGCAGTGTCAACTCGATACAG-CCCAAAGAGAAATTGTGGAGATGAAACTAGAGCTTGCTGAGAG
* *
105793 AAGCAGTTGCATTAAAGTCTTAAATGAAGACCTTGAGACTTCAAAATCGGAAAGCAACGGGCTTA
252 AAGCAATTGCATTAAAGTCTTAAATGAAGACCTTGAGACTTCAAAATCGGAAAGCAACAGGCTTA
105858 A
317 A
105859 GAGCAATATG
Statistics
Matches: 295, Mismatches: 18, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
317 70 0.24
318 74 0.25
319 1 0.00
322 2 0.01
323 147 0.50
324 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (317 bp):
AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAATGTACTGGAGAAAGAAAATCAAC
ATGTGATAGCAAGGTGCAGGCATTGTTGGAAGAGTTAAGTATTACTAAAGAAATGCTCGAGAGTT
CCGAGAAAGAAAAAGCTAGTTTGAAGCAGAAGCAGTTTTATGAGAAAATTCAAGATTTGCAGTGT
CAACTCGATACAGCCCAAAGAGAAATTGTGGAGATGAAACTAGAGCTTGCTGAGAGAAGCAATTG
CATTAAAGTCTTAAATGAAGACCTTGAGACTTCAAAATCGGAAAGCAACAGGCTTAA
Found at i:115479 original size:94 final size:98
Alignment explanation
Indices: 115374--115549 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 98
115364 CGGGTCGGGT
*
115374 TTTTTTAAGTGTGATATTC-GGATC-AGTCGGGTCGGGTT-TTTAA-GTGATATTCGAGTC-GGT
1 TTTTTTAAGTGTGATATTCAGG-TCGAGTCGGGTCGGATTGTTTAAGGTGATATTCGAGTCGGGT
*
115434 CGGGTTTTTAAGTGTGATATTCGGGTCAATCGAG
65 AGGGTTTTTAAGTGTGATATTCGGGTCAATCGAG
* * * *
115468 TTTTTTGAGTGTGATATTCAGGTCGGGTCGGGTCTGATTGTTTAAGTGTGATATTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGATTGTTTAAG-GTGATATTCGAGTCGGGT
*
115533 ATGGTTTTTAAGTGTGA
65 AGGGTTTTTAAGTGTGA
115550 CAATTGGGTC
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
94 20 0.29
95 13 0.19
96 5 0.07
98 13 0.19
99 18 0.26
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.41
Consensus pattern (98 bp):
TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGATTGTTTAAGGTGATATTCGAGTCGGGTA
GGGTTTTTAAGTGTGATATTCGGGTCAATCGAG
Found at i:115546 original size:31 final size:31
Alignment explanation
Indices: 115363--115563 Score: 141
Period size: 31 Copynumber: 6.4 Consensus size: 31
115353 CATATTTTGA
115363 TCGGGTCGGGT-T--TTTTTAAGTGTGATAT
1 TCGGGTCGGGTCTGGTTTTTAAGTGTGATAT
*
115391 TCGGATCAGTCGGGTCGGGTTTTTAA--GTGATAT
1 TCGG----GTCGGGTCTGGTTTTTAAGTGTGATAT
* *
115424 TCGAGTC-GGTCGGGTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCTGGTTTTTAAGTGTGATAT
** *
115454 TCGGGTC-AATC-GAGTTTTTTGAGTGTGATATT
1 TCGGGTCGGGTCTG-G-TTTTTAAGTGTGATA-T
*
115486 CAGGTCGGGTCGGGTCTGATTGTTTAAGTGTGATAT
1 ----TCGGGTCGGGTCTGGTT-TTTAAGTGTGATAT
* *
115522 TCGGGTCGGGTATGGTTTTTAAGTGTGACAAT
1 TCGGGTCGGGTCTGGTTTTTAAGTGTGA-TAT
115554 T-GGGTCGGGT
1 TCGGGTCGGGT
115564 TTAGGGTGAA
Statistics
Matches: 140, Mismatches: 13, Indels: 37
0.74 0.07 0.19
Matches are distributed among these distances:
28 18 0.13
29 4 0.03
30 16 0.11
31 34 0.24
32 26 0.19
33 10 0.07
35 7 0.05
36 10 0.07
37 14 0.10
38 1 0.01
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.39
Consensus pattern (31 bp):
TCGGGTCGGGTCTGGTTTTTAAGTGTGATAT
Done.