Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000639.1 Hibiscus syriacus cultivar Beakdansim tig00001238_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: 58440
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1779 original size:42 final size:47
Alignment explanation
Indices: 1723--1835 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 47
1713 GTTTAAACAC
*
1723 ACTAACAAATTAATTAATATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
*
1765 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTTATATAATAT-ATATATAACTTAA
1815 ACTAACAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
1836 AACTTAAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
42 15 0.25
43 1 0.02
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 4 0.07
50 23 0.39
51 3 0.05
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.41
Consensus pattern (47 bp):
ACTAACAAACTAATTAATATTTTTTATATAATATATATATAACTTAA
Found at i:1835 original size:28 final size:30
Alignment explanation
Indices: 1795--1857 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1785 ATTTTTTATA
1795 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1825 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1853 TAATA
1 TAATA
1858 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1864 original size:28 final size:28
Alignment explanation
Indices: 1799--1864 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1789 TTTATATAAT
1799 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
1827 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
1855 ATAATTTATA
1 ATAATATATA
1865 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:1867 original size:21 final size:21
Alignment explanation
Indices: 1834--1882 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1824 CTAATATAAT
1834 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1855 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1876 ATTAACT
1 A-TAACT
1883 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2361 original size:17 final size:17
Alignment explanation
Indices: 2339--2375 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2329 GGATGCAGAG
2339 GGTTAAAGCTTGGTCGT
1 GGTTAAAGCTTGGTCGT
2356 GGTTAAAGCTTGGTCGT
1 GGTTAAAGCTTGGTCGT
2373 GGT
1 GGT
2376 GCAGAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.38, T:0.35
Consensus pattern (17 bp):
GGTTAAAGCTTGGTCGT
Found at i:2496 original size:11 final size:11
Alignment explanation
Indices: 2482--2514 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2472 CATGCACAGC
2482 TCCCACATGCA
1 TCCCACATGCA
2493 TCCCACA-GC-
1 TCCCACATGCA
2502 TCCCACATGCA
1 TCCCACATGCA
2513 TC
1 TC
2515 ACTCCTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 7 0.35
10 4 0.20
11 9 0.45
ACGTcount: A:0.24, C:0.48, G:0.09, T:0.18
Consensus pattern (11 bp):
TCCCACATGCA
Found at i:2501 original size:20 final size:20
Alignment explanation
Indices: 2476--2514 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2466 ATGACCCATG
2476 CACAGCTCCCACATGCATCC
1 CACAGCTCCCACATGCATCC
2496 CACAGCTCCCACATGCATC
1 CACAGCTCCCACATGCATC
2515 ACTCCTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.49, G:0.10, T:0.15
Consensus pattern (20 bp):
CACAGCTCCCACATGCATCC
Found at i:2534 original size:31 final size:31
Alignment explanation
Indices: 2493--2556 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2483 CCCACATGCA
2493 TCCCACAGCTCCCACATGCATCACTCCTTGG
1 TCCCACAGCTCCCACATGCATCACTCCTTGG
*
2524 TCCCATAGCTCCCACATGCATCACTCCTTGG
1 TCCCACAGCTCCCACATGCATCACTCCTTGG
2555 TC
1 TC
2557 GCCCGGAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.44, G:0.12, T:0.25
Consensus pattern (31 bp):
TCCCACAGCTCCCACATGCATCACTCCTTGG
Found at i:21908 original size:19 final size:19
Alignment explanation
Indices: 21871--21909 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21861 ACTTCTTAAT
* *
21871 TTTATTAGATTTTATAATA
1 TTTATTAGATTTAAAAATA
*
21890 TTTATTTGATTTAAAAATA
1 TTTATTAGATTTAAAAATA
21909 T
1 T
21910 AATTAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTATTAGATTTAAAAATA
Found at i:22830 original size:29 final size:29
Alignment explanation
Indices: 22793--22874 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
22783 AAACTAAATT
*
22793 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
22822 GATGCCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
22851 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
22875 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:24186 original size:15 final size:15
Alignment explanation
Indices: 24163--24192 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24153 ACGAGGCTGG
24163 AATTACAACAATAAC
1 AATTACAACAATAAC
*
24178 AATTCCAACAATAAC
1 AATTACAACAATAAC
24193 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:27594 original size:29 final size:29
Alignment explanation
Indices: 27559--27640 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
27549 AAACTAAATT
27559 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAATTAAA
*
27588 GATGTCATTACTTACATCATTTAATTAAT
1 GATGTCATTACTTACATCATTTAATTAAA
*
27617 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
27641 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAATTAAA
Found at i:32315 original size:511 final size:512
Alignment explanation
Indices: 29279--32755 Score: 4359
Period size: 513 Copynumber: 6.8 Consensus size: 512
29269 ATATACGGTG
* * *
29279 ATAGAGGATCCCC-TGGCGAATACCTCTTTCAGGACTAAAAGAA-TCTGAATAAATTCCATTCCA
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAA-AAGTCTGAATAACTTCCATTCCA
* * * * * *
29342 TTGAAGCTGGAAAGTTGAAGAAGTAATACATTGCATGATAATGAGAGGGAAACCTGGAAGGAAAC
65 TTGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAAC
* ** * * *
29407 ATGCGTCAACCAAAGAGTCGAGAATGAAATCCCATTTTAGTCAGTCAAAAGCTTTCTCAAAATCC
130 TTGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCC
* * *
29472 ACTTTAATTGTCATCCACCCTTGCTTGCTTTTGTTGAGACGCATGGAATG-AAAGCTTCCTGATT
195 ACTTTAA-T-T-ATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATT
* * *
29536 AATTATAATATTTTCCGTAATAGATCTGCCTAATAAAAAGTTAGTTTGAGTCGGTTTAATGATCA
257 AATTATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCA
* * * * *
29601 TGGGCATAATTGTCTTCAAAAGATGAACAATAATCTTGGTAAGCAGTTTATAAGGAACAATGCAT
322 TGAGCATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCAT
* * * * *
29666 AGACTAATAGGCCGAAAATTCGA-AAAAGTTTCAGGCGCATTAGTTTTGGGAATAAGGGCCAGGA
387 AGACTAATAGGCCAAAAATTCGAGAAAA-TTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGA
* * * * *
29730 TCCTTTTTTTAAAAAATTGGATCCAACATACCACCTGCAAAAACATGTTTAATGGCTTTGCAA
451 TCGTTTTGTT-CAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
* * *
29793 ATAGAGGAT-CCCTTGGCGAATACCTCTTTCA-AGACTAAAAGAGTCGGAATAACTTCCATT-C-
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGA-ACTAAAAAAGTCTGAATAACTTCCATTCCA
** * * *
29854 TTGAAGTTGGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGGGAAA-CC----TG---C
65 TTGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAAC
** * * *
29911 --G--TCAACCAAAGGGTCGAGAATGAAATCCTATTTTAGTCGGTCAAAAGCTTTCTCCAAATCC
130 TTGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCC
** * **
29972 ACTTTAATTGCCATTAACCCTTGCTTGCTTTTGGTGAGGCGCATGGAA-CCAAAGCTTCCTGATT
195 ACTTTAATT---ATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATT
* * * * * * * *
30036 AATTATAATATTTTCTGTAATAGATATGCCCGATAAAAAGTTAATTT-AATCATGTTTGATGAGC
257 AATTATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTC-GGTTTAATGAGC
* * * * * * * * * * *
30100 AAGGGCATAATTGTCTTCAAAAGATGAAAAATAATATTGCTGAGCAGTTTATGAGGAAGAGTGAA
321 ATGAGCATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCA
* * * * *
30165 TAAACTATTAGGCCGAAAATTCGAGAAAATTTCAGGCGCATCAATTTTGGGAATAAGGGCGAAGA
386 TAGACTAATAGGCCAAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGA
* * * *
30230 TCGTTTTGTTTAAATTTGGATCCAATATACCATATGC-AAAACATGTTTAATAGCTTTGCAA
451 TCGTTTTGTTCAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
* * * * *
30291 ATAGAGGATCTCCTTAGCGAATACCTCTTTCAGGACTAAAAGAGTCTGAATAACTTCCATTCCAT
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTCCATTCCAT
* * * * * * *
30356 TGAAGCTGGAAAGCTGCATAAGTAATACATTGCATGATAATGCGAGGGAAACCCGGAGGGAAACC
66 TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAACT
** * *
30421 TGCGTCAACCAAAGAGTCGAGAATGAAATCCCATTTTAGTCAGTCAAAAGCTTTCTCCAAATCCA
131 TGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCCA
* * * **
30486 CTTTAATTGTCATCCACCCTTGCTTGCTTTTGGTGAGGCACATGCAATG-AAAGCTTTATGATTA
196 CTTTAA-T-T-ATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTA
* * * * *
30550 ATTATAATATTTTCTGTAATAGATCTGCCCAATAATAAGTTAGTTTGAGCCAGTTTAATGAGCAT
258 ATTATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCAT
* * * *
30615 -AGGCATAATTATCTTCAAAAGGCAAACAATAATCTTGGTGAGCAGTTTATAAGGAACAGTGCAT
323 GA-GCATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCAT
* * * *
30679 AGACTAATAGGCCAAAAAATT-GAGAAAGTTTCAAGCACATCAATTTTGAGAATATGGGCCAAGA
387 AGACTAATAGGCC-AAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGA
*
30743 TCGTTTTGTTCAAATTTGGAT-CAACATACCACATGCAAAAACATGTTTAATGGGTTTGCAA
451 TCGTTTTGTTCAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
* * * ** * * *
30804 ATAAAGGATCCCCTTGGTGAATATATCTTTCAGAACTAAAAGTGTCTGAATAAGTTTCATTCCAC
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTCCATTCCAT
* * * *
30869 TAAACCTAAAAAGTTGAAGAAGTAATACATTGCATGATAATGCAAGTGAAA-CCTGAGGGAAACT
66 TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAACT
** * *
30933 TGTATCAACCAAAGAATCGAGAATGATGT-CCATTTTAGTCGGTCAAAAACTTTCTCCAAAACCA
131 TGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCCA
*
30997 CTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTAAAT
196 CTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTAATT
* ** *
31062 ATAATATTTTCTGTAATAGATCTGCCTTATAAAAAGATAGTTTGAGTTGGTTTAATGAGCATGAG
261 ATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCATGAG
* * *
31127 CATAATTATCTTCAAATGACGAACAATAATTTTGGTGAGCATTTTATAAGGAACAATGCATATAC
326 CATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCATAGAC
* *
31192 TAATATGCCAAAAATTCGAGAAAATTTCAGGTC-CATCAATTTTGGGAATAAAGGCCAAGATCGT
391 TAATAGGCCAAAAATTCGAGAAAATTTCAGG-CACATCAATTTTGGGAATAAGGGCCAAGATCGT
* * * *
31256 TTTGTTCAAATTTGGATCCAACATACCACCTGCAAAAACATGATAAATGGCTTTGTAA
455 TTTGTTCAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
* *
31314 ATAGAGGATCCCCTTGACGAATATCTCTTTCAGAACTAAAAAAAAGTCTGAATAAGTTCCATT-C
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACT--AAAAAAGTCTGAATAACTTCCATTCC
* * *
31378 AGTTAAACCTAGAAAGTTGAAGAAGTGATACATTGCATGATAATGCGAGTGAAACCCGGAGGAAA
64 A-TTGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAA
* *
31443 ACTTGTATCAACC--AGAATCGAGAATGAAGTCCCATTTTAGTCGGTCAAAAACGTTT-TCCAAA
128 ACTTGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAAC-TTTCTCCAAA
* * *
31505 TCCACTTTAATTATCCACCCTTGCTTGTTTTTGGTGGGGCACATCGAATGAAAAGCTTCCTGATT
192 TCCACTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATT
* * * * * * *
31570 AATTATAATATTTTTCGTAATAGATATGTCCGATAAAAAGATAATTTGAATAGGTTTAATGAGCA
257 AATTATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCA
* * * *
31635 TGAGCATAATTATCTTCAAACGATGAACAATAATTTTGGTGAGAAATTTATAAGGAACAATGCAT
322 TGAGCATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCAT
* * * *
31700 AGACTAATAGGCCAAAAAAATGGAGAAAATTTCAAGCACATCAATTTTGGGAATAAGGGTCAAGA
387 AGACTAATAGGCC-AAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGA
* * * * * * * * **
31765 TCATTTTGTT-TAATTTAGATCAAACATATCAAATGCAAAAAACATGTTGAATAGCTTTTAAA
451 TCGTTTTGTTCAAATTTGGATCCAACATACCACATGC-AAAAACATGTTTAATGGCTTTGCAA
*
31827 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTTCATTCCAT
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTCCATTCCAT
* *
31892 TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCAGAGGGAAACA
66 TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAACT
* * * **
31957 TGTATCAACCAAATAATTGAGAATGAAGTCTAATTTTAGTCAGTCAAAAACTTTCTCCAAATCCA
131 TGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCCA
* * * * *
32022 TTTTAATTATCCACCATTACTTGCTTTTGGTGGGGCGCACGGAATGAAAAGATT-CTGATTAATT
196 CTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTAATT
* * * *
32086 ATAATATTTTCCGTAATAGATATGCCCAATAAAAA-ATAGTTTGATTTGGTTTACTGAGCATGAG
261 ATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCATGAG
* * * *
32150 CATAATTTTCTTCAAACGACGAACAATAATTTTGGTGAGTAGTATATAAGGAACAATGCATAGAC
326 CATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCATAGAC
* *
32215 TAATAGACCAAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCTAGATCGTT
391 TAATAGGCCAAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGATCGTT
* * * *
32280 TTGTTCAAATTTGGATCCAACATACCACCTGCAAAAACATGTTGAATGGATTTGTAA
456 TTGTTCAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
* * * * * *
32337 ATAGAAGATCCCATTGGCGAATATCACTTTTAAAACTAAAAAAGTCTGAATAAATTCCATTCCAT
1 ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTCCATTCCAT
* * * *
32402 TGAACCTATAAAGTTGAAGAAGTAATACATTGCATGATAATGTGAGTTAAACCTGGAGGGAAACT
66 TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAACT
* *
32467 TGTATCAAACAAAGAATCGATAATGAAATCCCATTTTAGTC-GATCAAAAACTTTCTCCAAATCC
131 TGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAG-TCAAAAACTTTCTCCAAATCC
* *
32531 ACTTTAATTATCCACCTTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCGTCCTGATTAAT
195 ACTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTAAT
* * ** * *
32596 AATAATATTTTCCGTAAAAGATCTGCCTGATAAAAAGATAATTTGAGTCGGTTTAATGAGCATGG
260 TATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCATGA
* * *
32661 GCATAATTATCTTCAAACG-CTGAACAATAATTTTGGTGAGCAGTTTATAAAGAACAATGCATAT
325 GCATAATTATCTTCAAAAGAC-GAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCATAG
*
32725 ACTAATACGCCAAAAATTCGAGAAAATTTCA
389 ACTAATAGGCCAAAAATTCGAGAAAATTTCA
32756 TGTGTAATCA
Statistics
Matches: 2602, Mismatches: 307, Indels: 110
0.86 0.10 0.04
Matches are distributed among these distances:
498 33 0.01
499 72 0.03
500 280 0.11
501 52 0.02
502 3 0.00
504 1 0.00
506 1 0.00
507 1 0.00
508 42 0.02
509 197 0.08
510 368 0.14
511 305 0.12
512 559 0.21
513 629 0.24
514 58 0.02
515 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (512 bp):
ATAGAGGATCCCCTTGGCGAATATCTCTTTCAGAACTAAAAAAGTCTGAATAACTTCCATTCCAT
TGAACCTAGAAAGTTGAAGAAGTAATACATTGCATGATAATGCGAGTGAAACCCGGAGGGAAACT
TGTATCAACCAAAGAATCGAGAATGAAATCCCATTTTAGTCAGTCAAAAACTTTCTCCAAATCCA
CTTTAATTATCCACCCTTGCTTGCTTTTGGTGGGGCGCATGGAATGAAAAGCTTCCTGATTAATT
ATAATATTTTCCGTAATAGATCTGCCCAATAAAAAGATAGTTTGAGTCGGTTTAATGAGCATGAG
CATAATTATCTTCAAAAGACGAACAATAATTTTGGTGAGCAGTTTATAAGGAACAATGCATAGAC
TAATAGGCCAAAAATTCGAGAAAATTTCAGGCACATCAATTTTGGGAATAAGGGCCAAGATCGTT
TTGTTCAAATTTGGATCCAACATACCACATGCAAAAACATGTTTAATGGCTTTGCAA
Found at i:45996 original size:17 final size:17
Alignment explanation
Indices: 45971--46017 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
45961 TTAATTAAAG
*
45971 CATGTTTGGGTAGATAT
1 CATGATTGGGTAGATAT
45988 CATGATTGGGTAGATAT
1 CATGATTGGGTAGATAT
*
46005 CATGATTTGGTAG
1 CATGATTGGGTAG
46018 GTGTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (17 bp):
CATGATTGGGTAGATAT
Found at i:49357 original size:5 final size:5
Alignment explanation
Indices: 49347--49436 Score: 90
Period size: 5 Copynumber: 17.6 Consensus size: 5
49337 TTCATCGATT
*
49347 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATATA TTACA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA TTATA TTATA
* * * * * * *
49399 TTACA TTACA TTACA TTACA TTACA TTACA TTACA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
49437 CATTTGCATT
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
5 74 0.93
6 2 0.03
7 4 0.05
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (5 bp):
TTATA
Found at i:49362 original size:10 final size:10
Alignment explanation
Indices: 49347--49587 Score: 173
Period size: 10 Copynumber: 24.3 Consensus size: 10
49337 TTCATCGATT
*
49347 TTATATTATA
1 TTATATTACA
*
49357 TTATATTATA
1 TTATATTACA
*
49367 TTATATTATA
1 TTATATTACA
49377 TTATATT--A
1 TTATATTACA
49385 -TATATTACA
1 TTATATTACA
49394 TTATATTACA
1 TTATATTACA
*
49404 TTACATTACA
1 TTATATTACA
*
49414 TTACATTACA
1 TTATATTACA
*
49424 TTACATTACA
1 TTATATTACA
* *
49434 TTACATTTGCA
1 TTATA-TTACA
** *
49445 TTGCATTGCA
1 TTATATTACA
** *
49455 TTGCATTGCA
1 TTATATTACA
**
49465 TTGCATTACA
1 TTATATTACA
*
49475 TTACATTACA
1 TTATATTACA
* *
49485 TTACATTGCA
1 TTATATTACA
* *
49495 TTAGATTGCA
1 TTATATTACA
* *
49505 TTACATTGCA
1 TTATATTACA
* *
49515 TTACATTCCA
1 TTATATTACA
*
49525 TTACATTACA
1 TTATATTACA
*
49535 TTACATTACA
1 TTATATTACA
*
49545 TTACATTACA
1 TTATATTACA
*
49555 TTACATTACA
1 TTATATTACA
*
49565 TTACATTACA
1 TTATATTACA
*
49575 TTATATTATA
1 TTATATTACA
49585 TTA
1 TTA
49588 AATATATCAT
Statistics
Matches: 215, Mismatches: 12, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
7 6 0.03
8 1 0.00
9 1 0.00
10 199 0.93
11 8 0.04
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (10 bp):
TTATATTACA
Found at i:49367 original size:15 final size:15
Alignment explanation
Indices: 49347--49587 Score: 205
Period size: 15 Copynumber: 15.9 Consensus size: 15
49337 TTCATCGATT
* *
49347 TTATATTATATTATA
1 TTATATTACATTACA
* *
49362 TTATATTATATTATA
1 TTATATTACATTACA
*
49377 TTATATTATATATTACA
1 TTATA-T-TACATTACA
49394 TTATATTACATTACA
1 TTATATTACATTACA
*
49409 TTACATTACATTACA
1 TTATATTACATTACA
*
49424 TTACATTACATTACA
1 TTATATTACATTACA
* *
49439 TT-TGCATTGCATTGCA
1 TTAT--ATTACATTACA
** * *
49455 TTGCATTGCATTGCA
1 TTATATTACATTACA
*
49470 TTACATTACATTACA
1 TTATATTACATTACA
* * *
49485 TTACATTGCATTAGA
1 TTATATTACATTACA
** *
49500 TTGCATTACATTGCA
1 TTATATTACATTACA
* *
49515 TTACATTCCATTACA
1 TTATATTACATTACA
*
49530 TTACATTACATTACA
1 TTATATTACATTACA
*
49545 TTACATTACATTACA
1 TTATATTACATTACA
*
49560 TTACATTACATTACA
1 TTATATTACATTACA
*
49575 TTATATTATATTA
1 TTATATTACATTA
49588 AATATATCAT
Statistics
Matches: 199, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
15 173 0.87
16 13 0.07
17 13 0.07
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (15 bp):
TTATATTACATTACA
Found at i:49437 original size:5 final size:5
Alignment explanation
Indices: 49388--49587 Score: 265
Period size: 5 Copynumber: 39.8 Consensus size: 5
49378 TATATTATAT
*
49388 ATTAC ATTAT ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
* * * * * *
49438 ATTTGC ATTGC ATTGC ATTGC ATTGC ATTGC ATTAC ATTAC ATTAC ATTAC
1 A-TTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
* * * * *
49489 ATTGC ATTAG ATTGC ATTAC ATTGC ATTAC ATTCC ATTAC ATTAC ATTAC
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC
* *
49539 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAT ATTAT ATTA
1 ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTAC ATTA
49588 AATATATCAT
Statistics
Matches: 179, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
5 175 0.98
6 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (5 bp):
ATTAC
Found at i:49739 original size:18 final size:18
Alignment explanation
Indices: 49697--49739 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
49687 AAATTACGAT
*
49697 CGCGACACCCGCAGCGAA
1 CGCGATACCCGCAGCGAA
*
49715 CGTGATACCCGCAGCGAA
1 CGCGATACCCGCAGCGAA
*
49733 TGCGATA
1 CGCGATA
49740 ACATCTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.35, G:0.28, T:0.09
Consensus pattern (18 bp):
CGCGATACCCGCAGCGAA
Done.