Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000948.1 Hibiscus syriacus cultivar Beakdansim tig00001896_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: 104288
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:550 original size:92 final size:92
Alignment explanation
Indices: 385--635 Score: 316
Period size: 92 Copynumber: 2.7 Consensus size: 92
375 CCGAAGTGCT
* * * *
385 TACCATATCA-CTGAGTGTCTTTACACACCA-AGTGTTGCACTAAGGATCCTTACACACTACATT
1 TACCATATGACCTAAGTGTCCTTACACACCATAGTGTTGCACTAAGG-TCCTTACACAATACA-T
448 GTTATATAAGTGTCCTTACA-CACTATAG
64 GTTATATAAGTGTCCTTACACCACTATAG
*
476 TACCATATGCACC-AAGTGTCC-TACACACCATAGTGTTGCACTGAGAGTCCTTACACAATACAT
1 TACCATATG-ACCTAAGTGTCCTTACACACCATAGTGTTGCACTAAG-GTCCTTACACAATACAT
*
539 GTTGTACTAAGTGTCCTTACACCACTATAG
64 GTTATA-TAAGTGTCCTTACACCACTATAG
* * * *
569 TACCATATGACCTAAGTGTCCTTACACACCATAATGCTACACTAAGTGTCCTTACAC-ATATATG
1 TACCATATGACCTAAGTGTCCTTACACACCATAGTGTTGCACTAAG-GTCCTTACACAATACATG
633 TTA
65 TTA
636 ATCCGATTAT
Statistics
Matches: 139, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
91 23 0.17
92 51 0.37
93 35 0.25
94 30 0.22
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (92 bp):
TACCATATGACCTAAGTGTCCTTACACACCATAGTGTTGCACTAAGGTCCTTACACAATACATGT
TATATAAGTGTCCTTACACCACTATAG
Found at i:3722 original size:367 final size:357
Alignment explanation
Indices: 3059--3789 Score: 1196
Period size: 367 Copynumber: 2.0 Consensus size: 357
3049 CAAGAATCTG
** *
3059 ATTTCAATAAAACCTCTTCCTCAAGAGTAAATTATTCATTTATGGAATAATTTTTTTGGGAAAAT
1 ATTTCAATAAAACCTCAACCTCAAGAGTAAATTATCCATTTATGGAATAATTTTTTTGGGAAAAT
* *
3124 TACCACTTAGCTCCCTAAACTTTTCCTAATTTTTTACTTTGGCCACTAAACTTTCAAAATTTACA
66 TACCACTTAGCTCCCTAAACTTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAATTTACA
* * *
3189 TTTTAGTCACTAACCAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCATGGAAGGTTAAGA
131 TTTTAGCCACTAACAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGTTAAGA
*
3254 ATGAAGCATCTCCATGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGTC
196 ATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGTC
3319 CTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGGG
261 CTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGGG
3384 CATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
326 CATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
3416 ATTTCAATAAAACCTCAACCTCAAGAGTAAATTATCCATTTATGGAATAAAAATTCTTTTTGGGA
1 ATTTCAATAAAACCTCAACCTCAAGAGTAAATTATCCATTTATGGAAT---AATT-TTTTTGGGA
* ** *
3481 AACTTATTACTTAGTTCCCTAAACGTTTTCC-AATTTTATACTTTAGCCACTAAACTTT-AAAAT
62 AAATTACCACTTAGCTCCCTAAAC-TTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAAT
3544 TTACATTTTAGCCACTAACAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGT
126 TTACATTTTAGCCACTAACAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGT
* *
3609 TAAGAATGAAGCATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTGCGTGCAGCCTGAAG
191 T---AA-G-A--ATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAG
3674 CATCTCATCGTCCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCAT
249 CATCTCATCGTCCTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCAT
*
3739 GAGAATTGTGGGCATTGAAGTGAGCTTGCGCAAGCTTTAGAGTC
314 GAGAATTGTGGGCATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
3783 ATTTCAA
1 ATTTCAA
3790 CCAGCACAAC
Statistics
Matches: 346, Mismatches: 16, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
357 45 0.13
360 72 0.21
361 54 0.16
362 6 0.02
363 2 0.01
364 1 0.00
365 1 0.00
367 165 0.48
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (357 bp):
ATTTCAATAAAACCTCAACCTCAAGAGTAAATTATCCATTTATGGAATAATTTTTTTGGGAAAAT
TACCACTTAGCTCCCTAAACTTTTCCTAATTTTATACTTTAGCCACTAAACTTTCAAAATTTACA
TTTTAGCCACTAACAAAATTTTGGGGTATTACACGTGCACTCCTTGCAGCCAAGGAAGGTTAAGA
ATGAAGCATCTCCAAGGTAGCGGCAATTGCGGCCATGTACGTGCAACCTGAAGCATCTCATCGTC
CTTTTACGGGCCAAATTGTTCATGCATTAAGGCTAATATGCAATGAATTTCATGAGAATTGTGGG
CATTGAAGGGAGCTTGCGCAAGCTTTAGAGTC
Found at i:5829 original size:26 final size:27
Alignment explanation
Indices: 5769--5832 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
5759 TTTAATTTTT
5769 TAAAATTTTATAAATTTACTCATAACG
1 TAAAATTTTATAAATTTACTCATAACG
5796 TAAAATTTTATAAATTTACTCAT-ACG
1 TAAAATTTTATAAATTTACTCATAACG
5822 TAAAATTTTAT
1 TAAAATTTTAT
5833 GTACGTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 14 0.38
27 23 0.62
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (27 bp):
TAAAATTTTATAAATTTACTCATAACG
Found at i:6607 original size:16 final size:15
Alignment explanation
Indices: 6586--6616 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
6576 TGTATATAAA
6586 ATTTTTAAAATAATAT
1 ATTTTTAAAA-AATAT
6602 ATTTTTAAAAAATAT
1 ATTTTTAAAAAATAT
6617 TGATGGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTAAAAAATAT
Found at i:7983 original size:2 final size:2
Alignment explanation
Indices: 7976--8008 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7966 TATTATCTTC
7976 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 A
8009 AACATGCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10788 original size:29 final size:29
Alignment explanation
Indices: 10746--10804 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
10736 TAACTCTTTG
*
10746 ACGTAATCATAAACAGATTCATATTATCT
1 ACGTAATCATAAACAAATTCATATTATCT
10775 ACGTAATCATAAACAAATTCATATTATCT
1 ACGTAATCATAAACAAATTCATATTATCT
10804 A
1 A
10805 TAATATAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (29 bp):
ACGTAATCATAAACAAATTCATATTATCT
Found at i:20232 original size:22 final size:22
Alignment explanation
Indices: 20197--20247 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20187 AAACGTTTTT
*
20197 ATGAACAGTGCTGTGAACAATA
1 ATGAACAGTACTGTGAACAATA
* *
20219 ATGAATAGTACTGTGAACAGTA
1 ATGAACAGTACTGTGAACAATA
*
20241 ATTAACA
1 ATGAACA
20248 ATACCATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (22 bp):
ATGAACAGTACTGTGAACAATA
Found at i:21041 original size:31 final size:31
Alignment explanation
Indices: 21003--21098 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
20993 TATAATAATC
*
21003 TGTCCATATGTCCCGAAGAACATAGGTTACA
1 TGTCCATATGTCCCGAAGAACATAGGTAACA
*
21034 TGTCCATATGTCCCGAAGAACATAGGTAATA
1 TGTCCATATGTCCCGAAGAACATAGGTAACA
*
21065 TGTCCATATGTCCCGAAGAACATAGGTAATA
1 TGTCCATATGTCCCGAAGAACATAGGTAACA
21096 TGT
1 TGT
21099 AACATATATA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAACA
Found at i:26325 original size:4 final size:4
Alignment explanation
Indices: 26310--26348 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
26300 AATCAAAACC
26310 ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
26349 TATATGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 31 0.94
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:29962 original size:2 final size:2
Alignment explanation
Indices: 29955--29982 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29945 TATGTTTGGT
29955 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29983 GGTTCATATT
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):
TA
Found at i:30592 original size:25 final size:25
Alignment explanation
Indices: 30558--30606 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
30548 GCTGCAGGTG
*
30558 CTCGAGTCAATTGGGATTTTATTTA
1 CTCGAGTCAATTCGGATTTTATTTA
30583 CTCGAGTCAATTCGGATTTTATTT
1 CTCGAGTCAATTCGGATTTTATTT
30607 GCTTTTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (25 bp):
CTCGAGTCAATTCGGATTTTATTTA
Found at i:46365 original size:65 final size:65
Alignment explanation
Indices: 46205--46365 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
46195 TTGTTTAAGG
* * * * *
46205 TGCATCGATGCACATGCAGTGTATCGATGCAT-GA-ATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCACA-TTAAATAGAAAACATCGAATAGGATTT
46268 A
65 A
*
46269 TGCATCGATGCATAAGGAGTGCATCGATGCATCCACATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCACATTAAATAGAAAACATCGAATAGGATTTA
*
46333 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
46366 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.71
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCACATTAAATAGAAAACATCGAATAGGATTTA
Found at i:47025 original size:2 final size:2
Alignment explanation
Indices: 47018--47049 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47008 CAGATTAGAT
47018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47050 AAGAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47980 original size:149 final size:149
Alignment explanation
Indices: 47806--48120 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
47796 GAGTCGAGGG
47806 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
47871 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
47936 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
47955 TTTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
*
48020 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
48085 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
48104 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
48121 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:48121 original size:23 final size:23
Alignment explanation
Indices: 48088--48132 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
48078 ATTATTATAT
*
48088 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
48111 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
48133 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:51243 original size:64 final size:65
Alignment explanation
Indices: 51158--51318 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 65
51148 TTGTTTAAGG
* * * *
51158 TGCATTGATGCACA-TGCAGTGCATCGATGCAT-GA-ATTTAAATAGAAAACATCGAATAGGATT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCATCCACA-TTAAATA-AAAACATCGAATAGGATT
51220 TA
64 TA
*
51222 TGCATCGATGCATAAG-G-AGTGCATCGATGCATCCACATTAAATACAAACATCGAATAGGATTT
1 TGCATCGATGCAT-AGTGTAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATAGGATTT
51285 A
65 A
*
51286 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCAT
51319 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
63 1 0.01
64 59 0.69
65 25 0.29
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAGTGTAGTGCATCGATGCATCCACATTAAATAAAAACATCGAATAGGATTTA
Found at i:52917 original size:149 final size:149
Alignment explanation
Indices: 52743--53057 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
52733 GAGTCGAGGG
52743 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
52808 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
52873 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
52892 TTTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
* * * *
52957 ATATGATCCCTAGCATATGTATATTATTCTTAAGGAATTTTATGTGGTCCTTATGGATATTATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
53022 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
53041 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
53058 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:63188 original size:21 final size:22
Alignment explanation
Indices: 63149--63214 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
63139 CTCGTATAAA
63149 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
63171 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
63192 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
63214 T
1 T
63215 ATGTCCATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.49
22 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:63475 original size:30 final size:31
Alignment explanation
Indices: 63434--63493 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
63424 TAGACATAGT
*
63434 ATTTCCATACCTTTAAAACATAG-GCATATC
1 ATTTACATACCTTTAAAACATAGTGCATATC
**
63464 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAAAACATAGTGCATAT
63494 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAAAACATAGTGCATATC
Found at i:63997 original size:66 final size:68
Alignment explanation
Indices: 63851--64022 Score: 194
Period size: 67 Copynumber: 2.6 Consensus size: 68
63841 TTTTTCTCAT
* * * *
63851 GGGGGAATCGGTT-CCCCCCTTAGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGAGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
63915 TGA
66 TGA
* * * *
63918 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATT-CCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTTCCCCCCCTGAGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
63980 TTGA
66 -TGA
*
63984 GGGGGTATCGGTT--CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCCTG-A-GGGTACCGATTCCCCT
64023 AACCCAGAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
64 6 0.07
65 1 0.01
66 29 0.32
67 37 0.41
68 17 0.19
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGAGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGA
Found at i:70078 original size:22 final size:22
Alignment explanation
Indices: 70061--70127 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
70051 CTCGTATAAA
70061 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70083 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70105 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
70127 T
1 T
70128 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:70388 original size:30 final size:31
Alignment explanation
Indices: 70347--70406 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
70337 TAGACATAGT
*
70347 ATTTCCATACCTTTAAAACATAG-GCATATC
1 ATTTACATACCTTTAAAACATAGTGCATATC
**
70377 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAAAACATAGTGCATAT
70407 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAAAACATAGTGCATATC
Found at i:70915 original size:67 final size:69
Alignment explanation
Indices: 70764--70917 Score: 197
Period size: 68 Copynumber: 2.2 Consensus size: 69
70754 TTTTTCTCAT
* * *
70764 GGGGGAATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTAGAATTTCATATAC
1 GGGGGTATCGGTT-CCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATAC
70829 GATGA
65 GATGA
* * * * *
70834 GGGGGTATCGGTTCCCCCCC-TGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATACG
70896 ATTGA
66 A-TGA
70901 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
70918 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
66 1 0.01
67 22 0.29
68 33 0.44
69 7 0.09
70 12 0.16
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATACG
ATGA
Found at i:70928 original size:67 final size:67
Alignment explanation
Indices: 70764--70939 Score: 178
Period size: 67 Copynumber: 2.6 Consensus size: 67
70754 TTTTTCTCAT
* * * *
70764 GGGGGAATCGGTTCCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTAGAATTTCATATAC
1 GGGGGTATCGGTT--CCCCCC-TGGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATAC
70829 GATGA
63 GATGA
* * * *
70834 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATACGA
70897 TTGA
65 -TGA
* *
70901 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
70940 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
65 6 0.06
66 1 0.01
67 34 0.37
68 33 0.35
69 7 0.08
70 12 0.13
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTAGAAATTCATATACGAT
GA
Found at i:72028 original size:60 final size:60
Alignment explanation
Indices: 71964--72078 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
71954 GAAACGCAAA
*** *
71964 TTTCTTTCTCGCAACGTGATTTTCGAAATTCGCAACTCG-ATTTCT-TTTTCGCAACACAAG
1 TTTCTTTCTCGCAACAAAATTTTCGAAA-TCGCAACACGAATTT-TATTTTCGCAACACAAG
* *
72024 TTTCTTTTTCGCAACAAAATTTTCTAAATCGCAACACGAATTTTATTTTCGCAAC
1 TTTCTTTCTCGCAACAAAATTTTCGAAATCGCAACACGAATTTTATTTTCGCAAC
72079 TCGATTTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 10 0.21
60 37 0.79
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.39
Consensus pattern (60 bp):
TTTCTTTCTCGCAACAAAATTTTCGAAATCGCAACACGAATTTTATTTTCGCAACACAAG
Found at i:72029 original size:20 final size:19
Alignment explanation
Indices: 71992--72078 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
71982 ATTTTCGAAA
* *
71992 TTCGCAACTCGATTTCTTT
1 TTCGCAACACAATTTCTTT
72011 TTCGCAACACAAGTTTCTTT
1 TTCGCAACACAA-TTTCTTT
* **
72031 TTCGCAACAAAATTTTCTAA
1 TTCGCAACACAA-TTTCTTT
*
72051 ATCGCAACACGAATTT-TATT
1 TTCGCAACAC-AATTTCT-TT
72071 TTCGCAAC
1 TTCGCAAC
72079 TCGATTTTCG
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 11 0.20
20 41 0.76
21 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (19 bp):
TTCGCAACACAATTTCTTT
Found at i:72086 original size:40 final size:40
Alignment explanation
Indices: 71992--72118 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
71982 ATTTTCGAAA
**
71992 TTCGCAACTCGA-TTTCTTTTTCGCAACAC-AAGTTTCT-TT
1 TTCGCAACTCGATTTTCTAATTCGCAACACGAA-TTT-TATT
*** *
72031 TTCGCAACAAAATTTTCTAAATCGCAACACGAATTTTATT
1 TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTATT
* *
72071 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAAT
1 TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTATT
72111 TTCGCAAC
1 TTCGCAAC
72119 AGTTTTTATT
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 10 0.14
40 61 0.84
41 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTATT
Found at i:72114 original size:20 final size:20
Alignment explanation
Indices: 72052--72144 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
72042 ATTTTCTAAA
*
72052 TCGCAACACGAATTTTATTT
1 TCGCAACACGAATTTTAATT
*
72072 TCGCAACTCG-ATTTTCGAA-T
1 TCGCAACACGAATTTT--AATT
72092 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTAATT
* *
72112 TCGCAACA-G-TTTTTATTT
1 TCGCAACACGAATTTTAATT
*
72130 TCGCAACACAAATTT
1 TCGCAACACGAATTT
72145 ATTGGGTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
18 15 0.25
19 8 0.13
20 31 0.52
21 6 0.10
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (20 bp):
TCGCAACACGAATTTTAATT
Found at i:72129 original size:17 final size:18
Alignment explanation
Indices: 72104--72137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72094 GCAACACGAA
72104 TTTTAA-TTTCGCAACAG
1 TTTTAATTTTCGCAACAG
*
72121 TTTTTATTTTCGCAACA
1 TTTTAATTTTCGCAACA
72138 CAAATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (18 bp):
TTTTAATTTTCGCAACAG
Found at i:72292 original size:14 final size:15
Alignment explanation
Indices: 72273--72310 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
72263 TCCCCATCTC
72273 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
72287 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
72303 TAATTTTT
1 TAATTTTT
72311 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:73096 original size:24 final size:24
Alignment explanation
Indices: 73064--73117 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
73054 GTATTCGAAA
*
73064 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTAAATACCCGGAC
* * *
73088 TTTGATCTTGTTAAATACTCGGAT
1 TTTGATCTTGGTAAATACCCGGAC
73112 TTTGAT
1 TTTGAT
73118 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCGGAC
Found at i:73123 original size:24 final size:24
Alignment explanation
Indices: 73077--73123 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
73067 GATCTTGGTC
*
73077 AATACCCGGACTTTGATCTTGTTA
1 AATACCCGGACTTTGATCATGTTA
* * *
73101 AATACTCGGATTTTGATGATGTT
1 AATACCCGGACTTTGATCATGTT
73124 TCAGAATAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
AATACCCGGACTTTGATCATGTTA
Found at i:75719 original size:16 final size:15
Alignment explanation
Indices: 75698--75732 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
75688 TGTAGATTGA
*
75698 AATTAAACAACAAAT
1 AATTAAACAAAAAAT
75713 CAATTAAACAAAAAAT
1 -AATTAAACAAAAAAT
75729 AATT
1 AATT
75733 CTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AATTAAACAAAAAAT
Found at i:77147 original size:21 final size:21
Alignment explanation
Indices: 77122--77219 Score: 146
Period size: 21 Copynumber: 4.7 Consensus size: 21
77112 GTGAATCGGG
*
77122 CTCTTGAAC-AGTGTGAGGGGC
1 CTCTTGAACGA-TGAGAGGGGC
77143 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
77164 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
77185 CTCTTGAACGAT-AGAAGTGGC
1 CTCTTGAACGATGAG-AGGGGC
77206 CTCTTGAACGATGA
1 CTCTTGAACGATGA
77220 CAGATGAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.03
21 68 0.94
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:77530 original size:21 final size:21
Alignment explanation
Indices: 77500--77554 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
77490 ATAAAACAAT
* * *
77500 ATCACTTAAAGCGGCTACCTC
1 ATCACGTAAAGCAGATACCTC
*
77521 ATCACGTAAAGTAGATACCTC
1 ATCACGTAAAGCAGATACCTC
* *
77542 ACCACGTAGAGCA
1 ATCACGTAAAGCA
77555 TCATTGTCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCACGTAAAGCAGATACCTC
Found at i:77650 original size:21 final size:21
Alignment explanation
Indices: 77624--77676 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
77614 TGCACCATTG
*
77624 TCGTCACGTAAAGTACCGACC
1 TCGTCACGTAAAGCACCGACC
* *
77645 TCGTCACGCAAAGCACTGACC
1 TCGTCACGTAAAGCACCGACC
*
77666 TCATCACGTAA
1 TCGTCACGTAA
77677 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (21 bp):
TCGTCACGTAAAGCACCGACC
Found at i:77866 original size:42 final size:42
Alignment explanation
Indices: 77791--77888 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
77781 GTGATAGAAT
** * * *
77791 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGACCCGATC
1 AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
* * *
77833 AGGTGATGGCTCTCAATTTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
77875 AGGTGATGGCTCTC
1 AGGTGATGGCTCTC
77889 GAAGTAGGGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCAATGTCGAGCTGTAGAATCGACCCGATC
Found at i:79789 original size:22 final size:22
Alignment explanation
Indices: 79761--79811 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
79751 GATAGAGGGG
*
79761 GTCGTCGGATATAGGGACGGAT
1 GTCGTCGGAGATAGGGACGGAT
* *
79783 GTCGTCGGAGATGGGGATGGAT
1 GTCGTCGGAGATAGGGACGGAT
79805 GTCGTCG
1 GTCGTCG
79812 TAGAGAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.24
Consensus pattern (22 bp):
GTCGTCGGAGATAGGGACGGAT
Found at i:79999 original size:20 final size:20
Alignment explanation
Indices: 79976--80015 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
79966 TTTGACTTCT
79976 GCGTTACGAATTACAAATTC
1 GCGTTACGAATTACAAATTC
* * *
79996 GCGTTGCGATTTACATATTC
1 GCGTTACGAATTACAAATTC
80016 ATGTTGCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
GCGTTACGAATTACAAATTC
Found at i:80301 original size:5 final size:5
Alignment explanation
Indices: 80287--80320 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
80277 GTCAACCTCA
*
80287 CTTTG ATTTG CTTTG CTTTG CTTTG CTTTG CTTT
1 CTTTG CTTTG CTTTG CTTTG CTTTG CTTTG CTTT
80321 TTCTCTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (5 bp):
CTTTG
Found at i:85498 original size:36 final size:36
Alignment explanation
Indices: 85447--85528 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
85437 TTGTTTGTCT
*
85447 GGACATTCATCTCGTATTGCTTGTCTCGTATGTTGA
1 GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
* *
85483 GGATATTCAACTCGTATTGTTTGTCTCGTATGTTGA
1 GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
85519 GGACATTCAA
1 GGACATTCAA
85529 TGTGAAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (36 bp):
GGACATTCAACTCGTATTGCTTGTCTCGTATGTTGA
Found at i:86073 original size:36 final size:36
Alignment explanation
Indices: 86032--86110 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
86022 TTAAAAAAAT
86032 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
1 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
86068 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
1 TATAATTTAAATATTTATTATTCCGTTAAACTAACG
86104 TATAATT
1 TATAATT
86111 ATATTTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (36 bp):
TATAATTTAAATATTTATTATTCCGTTAAACTAACG
Found at i:87003 original size:19 final size:18
Alignment explanation
Indices: 86975--87011 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
86965 TTTATTTGTA
86975 AATATAATAGTAAAATAT
1 AATATAATAGTAAAATAT
86993 AATATTAATAGTAAAATAT
1 AATA-TAATAGTAAAATAT
87012 TTTAATGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AATATAATAGTAAAATAT
Done.