Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007471.1 Hibiscus syriacus cultivar Beakdansim tig00020520_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: 86040
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:521 original size:79 final size:79
Alignment explanation
Indices: 424--572 Score: 244
Period size: 79 Copynumber: 1.9 Consensus size: 79
414 ACCGTAGTGC
* *
424 TACACATAAGGTCGTGCCCACCATATAAACCGAAGCGTATTACACATAAGTTCGTGCCCACCATA
1 TACACATAAGGTCATGCCCACCATATAAACCGAAGCGTATTACACATAAGGTCGTGCCCACCATA
489 TACACCGAAGTTAT
66 TACACCGAAGTTAT
* * * *
503 TACACATAAGGTCATGCCCACCATATACATCGAGGTGTATTACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCATGCCCACCATATAAACCGAAGCGTATTACACATAAGGTCGTGCCCACCATA
568 TACAC
66 TACAC
573 TTAGTGTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (79 bp):
TACACATAAGGTCATGCCCACCATATAAACCGAAGCGTATTACACATAAGGTCGTGCCCACCATA
TACACCGAAGTTAT
Found at i:588 original size:40 final size:40
Alignment explanation
Indices: 424--572 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
414 ACCGTAGTGC
* *
424 TACACATAAGGTCGTGCCCACCATATAAACCGAAGCGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
464 TACACATAAGTTCGTGCCCACCATATACACCGAAGT-TAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
503 TACACATAAGGTCATGCCCACCATATACATCGAGGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
543 TACACATAAGGTCGTGCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
573 TTAGTGTCCT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 35 0.35
40 64 0.65
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3280 original size:14 final size:14
Alignment explanation
Indices: 3261--3308 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3251 TTTGACCCAG
3261 TCGAGTCAACTCGT
1 TCGAGTCAACTCGT
*
3275 TCGAGTCAACTTG-
1 TCGAGTCAACTCGT
*
3288 TCTAAGTCAACTCGT
1 TC-GAGTCAACTCGT
*
3303 CCGAGT
1 TCGAGT
3309 GAACCCGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.89
15 1 0.04
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (14 bp):
TCGAGTCAACTCGT
Found at i:5419 original size:96 final size:96
Alignment explanation
Indices: 5255--5454 Score: 294
Period size: 96 Copynumber: 2.1 Consensus size: 96
5245 ATCACTAATT
* * *
5255 TACTGGTTTATGAACTATGGTTACTTCAAATATGTTCTCAGGTTACCTATTTTCACTATAAAATA
1 TACTGGTTTATGAACTATGGTTACCTCAAATATGTTATCAGGTTACCTATTTTCACTAGAAAATA
*
5320 TGATCGTTCCTGATTTATGGATCATGGAATC
66 TGATCGTTCCTGATTTATGGATCATGAAATC
* * ** * *
5351 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATTTGGTTTTCC-GTTTTCACTAGAAAAT
1 TACTGGTTTATGAACTATGGTTACCTCAAATATGTTATCAGG-TTACCTATTTTCACTAGAAAAT
5415 ATGATCGTTCCTGATTTATGGATCATGAAATC
65 ATGATCGTTCCTGATTTATGGATCATGAAATC
5447 TACTGGTT
1 TACTGGTT
5455 ACTACTTGAA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
96 89 0.96
97 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (96 bp):
TACTGGTTTATGAACTATGGTTACCTCAAATATGTTATCAGGTTACCTATTTTCACTAGAAAATA
TGATCGTTCCTGATTTATGGATCATGAAATC
Found at i:8765 original size:21 final size:21
Alignment explanation
Indices: 8739--8790 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
8729 TTCCTATAAA
*
8739 GTATCGGTACCTAAGAAACAT
1 GTATCGATACCTAAGAAACAT
8760 GTATCGATACCTAAGAAACAT
1 GTATCGATACCTAAGAAACAT
8781 GTATCGATAC
1 GTATCGATAC
8791 ATGACAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (21 bp):
GTATCGATACCTAAGAAACAT
Found at i:9591 original size:449 final size:449
Alignment explanation
Indices: 8853--9767 Score: 1438
Period size: 449 Copynumber: 2.0 Consensus size: 449
8843 ATGTAAAGAA
* *
8853 TTGACAAAACCGGTTTCTATAATTGCGACTATAAAGTATCGATACACGTATGAAAAGTATCGATG
1 TTGACAAAACCGATTTCCATAATTGCGACTATAAAGTATCGATACACGTATGAAAAGTATCGATG
* *** * *
8918 CTTAATACTTCGAAATGGATTACTTTAAAGTAATAGGTAAATTTACAATAAAAGCTTTAAAATAT
66 CTTAAAACTTCGAAACCAATTACTTTAAAGTAATAGGTAAATATACAATAAAAGCTTAAAAATAT
8983 ACCGGTTTAATGACAAAATATGTTTACATAAAGTATCAATACTTTTGGTATATATATCGATACTT
131 ACCGGTTTAATGACAAAATATGTTTACATAAAGTATCAATACTTTTGGTATATATATCGATACTT
*
9048 TTTGTCCAATATGCTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTATC
196 TTTATCCAATATGCTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTATC
* *
9113 AATACATAACAATATAACAAGTTAAAAATTGATAAAACCGATTTCATTATGACAAAACCGGTAAA
261 AATACATAACAATATAACAAGTTAAAAATTGATAAAACCGATTTCAATATGACAAAACCGGCAAA
* * * ** *
9178 TAGCTACCTGTTTTGAAAAAAAATGAAACATCTTGAAAGTATCGATATTGTACATAAAAGTATTG
326 TAGCTACCGGTTTTGAAAAAAAACGAAACATCTTAAAAGTATCGATACCGTACATAAAAGTATCG
* *
9243 ATACTTCTGTAAGGGTAATGGAATTGATTAAATATAAATAACATAACAGATTCATCTTT
391 ATACTTATGTAAGGGTAATGGAATCGATTAAATATAAATAACATAACAGATTCATCTTT
* * *
9302 TTGACAAAACCGATTTCCATAATTGCGCCTATAAAGTATTGATACACGTATGAAAAGTATCGATT
1 TTGACAAAACCGATTTCCATAATTGCGACTATAAAGTATCGATACACGTATGAAAAGTATCGATG
**
9367 CTTAAAACTTCGAAACCAATTACTTTAAAGTAATAGGTAAATATACAATGTAAGCTGTAAAAATA
66 CTTAAAACTTCGAAACCAATTACTTTAAAGTAATAGGTAAATATACAATAAAAGCT-TAAAAATA
* * ** *
9432 TATCGGTTTATTGACAAAATATGTTTACATAAAGTATTGATA-TTGTTGGTATATGTATCGATAC
130 TACCGGTTTAATGACAAAATATGTTTACATAAAGTATCAATACTT-TTGGTATATATATCGATAC
9496 TTTTTATCCAA-ATGCTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTA
194 TTTTTATCCAATATGCTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTA
* * * * * *
9560 TCGATACATGACAATATAACATGTTAAAAATTGATAAAATCGGTTTCAATATGACAAAACTGGCA
259 TCAATACATAACAATATAACAAGTTAAAAATTGATAAAACCGATTTCAATATGACAAAACCGGCA
* **
9625 AATAGCTATCGGTTTTGAAAAAAAACGAAATGTCTTAAAAGTATCGATACCGTACATAAAAGTAT
324 AATAGCTACCGGTTTTGAAAAAAAACGAAACATCTTAAAAGTATCGATACCGTACATAAAAGTAT
* *
9690 CGATACTTATGTAAGGGTAATGGTATCGATTAAATATAAATAACATAACAGGTTCATCTTT
389 CGATACTTATGTAAGGGTAATGGAATCGATTAAATATAAATAACATAACAGATTCATCTTT
9751 TTGACAAAACCGATTTC
1 TTGACAAAACCGATTTC
9768 AACCGATTAC
Statistics
Matches: 424, Mismatches: 40, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
449 351 0.83
450 73 0.17
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (449 bp):
TTGACAAAACCGATTTCCATAATTGCGACTATAAAGTATCGATACACGTATGAAAAGTATCGATG
CTTAAAACTTCGAAACCAATTACTTTAAAGTAATAGGTAAATATACAATAAAAGCTTAAAAATAT
ACCGGTTTAATGACAAAATATGTTTACATAAAGTATCAATACTTTTGGTATATATATCGATACTT
TTTATCCAATATGCTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTATC
AATACATAACAATATAACAAGTTAAAAATTGATAAAACCGATTTCAATATGACAAAACCGGCAAA
TAGCTACCGGTTTTGAAAAAAAACGAAACATCTTAAAAGTATCGATACCGTACATAAAAGTATCG
ATACTTATGTAAGGGTAATGGAATCGATTAAATATAAATAACATAACAGATTCATCTTT
Found at i:9928 original size:388 final size:385
Alignment explanation
Indices: 9380--10090 Score: 1113
Period size: 388 Copynumber: 1.8 Consensus size: 385
9370 AAAACTTCGA
* *
9380 AACCAATTACTTTAAAGTAATAGGTAAATATACAATGTAAGCTGTAAAAATATATCGGTTTATTG
1 AACCAATTACTTTAAAGTAATAGGTAAATATACAATGTAAGATGT-AAAATATATCGGTTTAATG
* * ** *
9445 ACAAAATATGTTTACATAAAGTATTGATATTGTTGGTATATGTATCGATACTTTTTATCCAAATG
65 AAAAAAAACATTTACATAAAGTATCGATATTGTTGGTATATGTATCGATACTTTTTATCCAAATG
*
9510 CTTCCCAAACTAGATGCACGTAGGAAGTATCGATACCTATGACACATGTATCGATACATGACAAT
130 CTTCCCAAACTAGATGCACGTAGAAAGTATCGATACCTATGACACATGTATCGATACATGAC-AT
* * * *
9575 ATAACATGTTAAAAATTGATAAAATCGGTTTCAATATGAC-AAAACTGGCAAATAGCTA-TCGGT
194 ATAACAGGTTAAAAATTGATAAAACCGGTTTCAATATGACAAAAAC-GGCAAATAACTACT-AGT
* * * * *
9638 TTTGAAAAAAAACGAAATGTCTTAAAAGTATCGATACCGTACATAAAAGTATCGATACTTATGTA
257 TTTG-AAAAAAACGAAACGTCTCAAAAGTATCAATACCATACATAAAAGTATCGATACATATGTA
9703 AGGGTAATGGTATCGATTAAATATAAATAACATAACAGGTTCATCTTTTTGACAAAACCGATTTC
321 AGGGTAATGGTATCGATTAAATATAAATAACATAACAGGTTCATCTTTTTGACAAAACCGATTTC
*
9768 AACCGATTACTTTAAAGTAATAGGTAAATATACAATGTAAGATGT-AAATATATCGGTTTAATGA
1 AACCAATTACTTTAAAGTAATAGGTAAATATACAATGTAAGATGTAAAATATATCGGTTTAATG-
* *
9832 AAAAAAAACATTTACATAAAGTATCGATATTGTTGGTATATGTATCGATACTTTTTGTCCAGTAT
65 AAAAAAAACATTTACATAAAGTATCGATATTGTTGGTATATGTATCGATACTTTTTATCCA-AAT
*
9897 GCTTCCCAAACTAGATGCACGTAGAAAGTATCGATACCTATGACACATGTATTGATACATGACAT
129 GCTTCCCAAACTAGATGCACGTAGAAAGTATCGATACCTATGACACATGTATCGATACATGACAT
*
9962 ATAACAGGTTAAAAATTGATAAAACCGGTTTCAATATGACAAAAACGGTAAATAACTACTAGTTT
194 ATAACAGGTTAAAAATTGATAAAACCGGTTTCAATATGACAAAAACGGCAAATAACTACTAGTTT
* **
10027 TGAAAAAAACGAAACGTCTCGAAAGTATCAATTTCATACATAAAAGTATCGATACATATGTAAG
259 TGAAAAAAACGAAACGTCTCAAAAGTATCAATACCATACATAAAAGTATCGATACATATGTAAG
10091 AGTATTCAAT
Statistics
Matches: 294, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
386 71 0.24
387 111 0.38
388 112 0.38
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (385 bp):
AACCAATTACTTTAAAGTAATAGGTAAATATACAATGTAAGATGTAAAATATATCGGTTTAATGA
AAAAAAACATTTACATAAAGTATCGATATTGTTGGTATATGTATCGATACTTTTTATCCAAATGC
TTCCCAAACTAGATGCACGTAGAAAGTATCGATACCTATGACACATGTATCGATACATGACATAT
AACAGGTTAAAAATTGATAAAACCGGTTTCAATATGACAAAAACGGCAAATAACTACTAGTTTTG
AAAAAAACGAAACGTCTCAAAAGTATCAATACCATACATAAAAGTATCGATACATATGTAAGGGT
AATGGTATCGATTAAATATAAATAACATAACAGGTTCATCTTTTTGACAAAACCGATTTC
Found at i:15883 original size:10 final size:10
Alignment explanation
Indices: 15831--15886 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
15821 AGATATATTA
15831 AAATAA-AAT
1 AAATAATAAT
*
15840 AAATAATAAA
1 AAATAATAAT
* *
15850 AAAGGAAAAAT
1 AAA-TAATAAT
15861 AATATAATAAT
1 AA-ATAATAAT
*
15872 AAATAGTAAT
1 AAATAATAAT
15882 AAATA
1 AAATA
15887 TAAATATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 6 0.16
10 17 0.46
11 13 0.35
12 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (10 bp):
AAATAATAAT
Found at i:15889 original size:16 final size:18
Alignment explanation
Indices: 15860--15892 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
15850 AAAGGAAAAA
15860 TAATATAATAATAAATAG
1 TAATATAATAATAAATAG
15878 TAATA-AAT-ATAAATA
1 TAATATAATAATAAATA
15893 TAAAAGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TAATATAATAATAAATAG
Found at i:18533 original size:13 final size:13
Alignment explanation
Indices: 18515--18541 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18505 TTGAATATAA
18515 AATCTTAAAATTC
1 AATCTTAAAATTC
18528 AATCTTAAAATTC
1 AATCTTAAAATTC
18541 A
1 A
18542 TTAGTACTTT
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:31245 original size:20 final size:20
Alignment explanation
Indices: 31216--31258 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31206 ATTCCACCAC
*
31216 ATGCAACTACATGCTTCTAA
1 ATGCAACTACATGCTACTAA
* *
31236 ATGCATCTACATGGTACTAA
1 ATGCAACTACATGCTACTAA
31256 ATG
1 ATG
31259 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTACTAA
Found at i:36801 original size:21 final size:20
Alignment explanation
Indices: 36751--36802 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
36741 GAAATTAAGT
*
36751 TTTGCAAATCATAATTTTTC
1 TTTGCAAATCATAATTTTAC
*
36771 TTTTCAAAATCATCAATTTTGAC
1 TTTGC-AAATCAT-AATTTT-AC
36794 -TTGCAAATC
1 TTTGCAAATC
36803 TTTTATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 9 0.35
23 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (20 bp):
TTTGCAAATCATAATTTTAC
Found at i:40661 original size:2 final size:2
Alignment explanation
Indices: 40654--40692 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
40644 AAATGTATCG
*
40654 AC AC AC AC AC -C AC TC AC AC AC AC AC AC -C AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40693 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.51, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:40673 original size:13 final size:13
Alignment explanation
Indices: 40654--40692 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 13
40644 AAATGTATCG
40654 ACACACACACCACTC
1 ACACACACA-CAC-C
40669 ACACACACACACC
1 ACACACACACACC
40682 ACACACACACA
1 ACACACACACA
40693 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
14 3 0.12
15 9 0.38
ACGTcount: A:0.46, C:0.51, G:0.00, T:0.03
Consensus pattern (13 bp):
ACACACACACACC
Found at i:40676 original size:17 final size:17
Alignment explanation
Indices: 40654--40692 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
40644 AAATGTATCG
*
40654 ACACACACACCACTCAC
1 ACACACACACCACACAC
40671 ACACACACACCACACAC
1 ACACACACACCACACAC
40688 ACACA
1 ACACA
40693 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.51, G:0.00, T:0.03
Consensus pattern (17 bp):
ACACACACACCACACAC
Found at i:40697 original size:2 final size:2
Alignment explanation
Indices: 40692--40721 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40682 ACACACACAC
40692 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
40722 TACGTACTTA
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:40981 original size:107 final size:106
Alignment explanation
Indices: 40856--41474 Score: 333
Period size: 107 Copynumber: 5.6 Consensus size: 106
40846 ATAAAGCTTG
* * *
40856 ATAACAAATCAAGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCTCCATCAGCTTAAAT
1 ATAACAAATTAAGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCCCCATCAGCTTAAAA
* *
40921 TTTGTTAACATTTAGGTGTTACCTAATATGTTGATCATACT
66 TTTGTTAACATTTAGGCGTTACCTAATATGTTGATAATACT
* * * * * *
40962 GATAACAAATTAAGTAATTAA-CATATTTTGTTATCGTCAAATTTCAAAGGCCCCATCAGTTTTA
1 -ATAACAAATTAAGTAATTAACCA-GTTATGTTATCGTCGAATTCCTAAGGCCCCATCAG-CTTA
* ** * * * *
41026 ATAATGTGATACCTATTATGTTACATAAGCGCTACCTAATATGTT-ATTATGCT
63 A-AATTTG-T---TA--ACATT---TAGGCGTTACCTAATATGTTGATAATACT
* ** * * * * * * *
41079 -TAATTATGTTTACAGTAATTAACC-GTTATTTTATTGACGGATTTCTAAGGCTCTATCAGCTTA
1 ATAA-CA-AATTA-AGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCCCCATCAGCTTA
* * *
41142 AACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACA
63 AAATTTGTTAACA-TTTAGGCGTTACCTAATATGTTGATAATACT
* * *
41187 ATAACAAATTAAGTAATTAACCTA-TTTTGTTATCGTCGGAATTCC-AAAGCCCCATCAACTTAA
1 ATAACAAATTAAGTAATTAACC-AGTTATGTTATCGTC-GAATTCCTAAGGCCCCATCAGCTT-A
** * * * * *
41250 AAATGCGCTACCTATTACGTTATTAAGCGCTACCTAATATGTT-ATTATGCT
63 AAATTTG-T---TA--AC-AT-TTAGGCGTTACCTAATATGTTGATAATACT
* * * * * * * * *
41301 -TAATAATGTTTAGAGTAATTAACCGGTTATGTTATCTTCGGATTTCTAAGGCTCTATTAGCTTA
1 ATAACAA--ATTA-AGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCCCCATCAGCTTA
* * *
41365 AACTTTGGTAACATTTTAGGCGTTAACTAATATGTTGATAATACT
63 AAATTTGTTAACA-TTTAGGCGTTACCTAATATGTTGATAATACT
* * * *
41410 AATAACAAATTAA-TAATTAACCTA-TTTTGTTATCTTCGGATTTCC-AAAGCCCCATCAGCTTA
1 -ATAACAAATTAAGTAATTAACC-AGTTATGTTATCGTC-GAATTCCTAAGGCCCCATCAGCTTA
41472 AAA
63 AAA
41475 AGGCACTACC
Statistics
Matches: 372, Mismatches: 98, Indels: 84
0.67 0.18 0.15
Matches are distributed among these distances:
106 13 0.03
107 126 0.34
108 43 0.12
109 20 0.05
110 3 0.01
111 9 0.02
112 2 0.01
113 7 0.02
114 8 0.02
115 42 0.11
116 38 0.10
117 34 0.09
118 26 0.07
119 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (106 bp):
ATAACAAATTAAGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCCCCATCAGCTTAAAA
TTTGTTAACATTTAGGCGTTACCTAATATGTTGATAATACT
Found at i:41282 original size:22 final size:22
Alignment explanation
Indices: 41254--41296 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41244 ACTTAAAAAT
*
41254 GCGCTACCTATTACGTTATTAA
1 GCGCTACCTAATACGTTATTAA
*
41276 GCGCTACCTAATATGTTATTA
1 GCGCTACCTAATACGTTATTA
41297 TGCTTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GCGCTACCTAATACGTTATTAA
Found at i:41381 original size:223 final size:224
Alignment explanation
Indices: 40867--41560 Score: 959
Period size: 223 Copynumber: 3.1 Consensus size: 224
40857 TAACAAATCA
* * * * * * *
40867 AGTAATTAACCAGTTATGTTATCGTCGAATTCCTAAGGCTCCATCAGCTTAAATTTTGTTAACA-
1 AGTAATTAACCGGTTATGTTATCTTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
* * * *
40931 TTTAGGTGTTACCTAATATGTTGATCATACTGATAACAAATTAAGTAATTAACATATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * ** * * * * *
40996 CGTC-AAATTTCAAAGGCCCCATCAGTTTTAATAATGTGATACCTATTATGTTACATAAGCGCTA
131 CGTCGGAATTCCAAA-GCCCCATCA-ACTTAAAAATGCGCTACCTATTACGTTA-TTAAGCGCTA
*
41060 CCTAATATGTTATTATGCTTAATTATGTTTAC
193 CCTAATATGTTATTATGCTTAATAATGTTTAC
* *
41092 AGTAATTAACC-GTTATTTTAT-TGACGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACA
1 AGTAATTAACCGGTTATGTTATCT-TCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACA
41155 TTTTAGGCGTTACCTAATATGTTGATAATAC-AATAACAAATTAAGTAATTAACCTATTTTGTTA
65 TTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTA
41219 TCGTCGGAATTCCAAAGCCCCATCAACTTAAAAATGCGCTACCTATTACGTTATTAAGCGCTACC
130 TCGTCGGAATTCCAAAGCCCCATCAACTTAAAAATGCGCTACCTATTACGTTATTAAGCGCTACC
*
41284 TAATATGTTATTATGCTTAATAATGTTTAG
195 TAATATGTTATTATGCTTAATAATGTTTAC
*
41314 AGTAATTAACCGGTTATGTTATCTTCGGATTTCTAAGGCTCTATTAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCTTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
*
41379 TTTAGGCGTTAACTAATATGTTGATAATACTAATAACAAATTAA-TAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * * * * **
41443 CTTCGGATTTCCAAAGCCCCATCAGCTTAAAAAGGCACTACCTATTACGTTATATAAGCTTTACC
131 CGTCGGAATTCCAAAGCCCCATCAACTTAAAAATGCGCTACCTATTACGTTAT-TAAGCGCTACC
* * *
41508 TAATATGTTATTGTGCTTGATAATGTTTCC
195 TAATATGTTATTATGCTTAATAATGTTTAC
* *
41538 AGTAATTAAACGATTATGTTATC
1 AGTAATTAACCGGTTATGTTATC
41561 GTCTATATTT
Statistics
Matches: 422, Mismatches: 40, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
222 50 0.12
223 167 0.40
224 158 0.37
225 47 0.11
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (224 bp):
AGTAATTAACCGGTTATGTTATCTTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGGAATTCCAAAGCCCCATCAACTTAAAAATGCGCTACCTATTACGTTATTAAGCGCTACCT
AATATGTTATTATGCTTAATAATGTTTAC
Found at i:44951 original size:160 final size:160
Alignment explanation
Indices: 44687--45006 Score: 622
Period size: 160 Copynumber: 2.0 Consensus size: 160
44677 ATTAGGACAA
*
44687 CCATAAAAATTATTAGCTAAATAGGATACGCAAAAGTTTATTTTGGGATCTGTATTTGTTATGAT
1 CCATAAAAATAATTAGCTAAATAGGATACGCAAAAGTTTATTTTGGGATCTGTATTTGTTATGAT
44752 AATCTAGATCTCGTCACGTCGAGGTAATAAATTTTAATAGAAAATATATTTTATTCAATTGATTA
66 AATCTAGATCTCGTCACGTCGAGGTAATAAATTTTAATAGAAAATATATTTTATTCAATTGATTA
44817 ATATTTAATTATTTTTCTCGAATTCGTCTT
131 ATATTTAATTATTTTTCTCGAATTCGTCTT
44847 CCATAAAAATAATTAGCTAAATAGGATACGCAAAAGTTTATTTTGGGATCTGTATTTGTTATGAT
1 CCATAAAAATAATTAGCTAAATAGGATACGCAAAAGTTTATTTTGGGATCTGTATTTGTTATGAT
44912 AATCTAGATCTCGTCACGTCGAGGTAATAAATTTTAATAGAAAATATATTTTATTCAATTGATTA
66 AATCTAGATCTCGTCACGTCGAGGTAATAAATTTTAATAGAAAATATATTTTATTCAATTGATTA
*
44977 ATATTTAATTATTTTTCTGGAATTCGTCTT
131 ATATTTAATTATTTTTCTCGAATTCGTCTT
45007 GTCGGAGTGA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 158 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (160 bp):
CCATAAAAATAATTAGCTAAATAGGATACGCAAAAGTTTATTTTGGGATCTGTATTTGTTATGAT
AATCTAGATCTCGTCACGTCGAGGTAATAAATTTTAATAGAAAATATATTTTATTCAATTGATTA
ATATTTAATTATTTTTCTCGAATTCGTCTT
Found at i:45164 original size:44 final size:44
Alignment explanation
Indices: 45101--45189 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
45091 CCGGCGTTCA
*
45101 TATTGATATGTTTTTATTAAATAAAAAAAATTAAAT-GATGTGAT
1 TATTGATATATTTTTATTAAATAAAAAAAATTAAATAG-TGTGAT
* **
45145 TATTGATATATTTTTATTAAATACAAAGTATTAAATAGTGTGAT
1 TATTGATATATTTTTATTAAATAAAAAAAATTAAATAGTGTGAT
45189 T
1 T
45190 GGGAACTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (44 bp):
TATTGATATATTTTTATTAAATAAAAAAAATTAAATAGTGTGAT
Found at i:47083 original size:26 final size:26
Alignment explanation
Indices: 47047--47103 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
47037 TCGTTGTTTG
* *
47047 TCTCCTGGGAGATAAATGGACAATGA
1 TCTCCTAGGAGACAAATGGACAATGA
*
47073 TCTCCTAGGAGACAAATGGTCAATGA
1 TCTCCTAGGAGACAAATGGACAATGA
47099 TCTCC
1 TCTCC
47104 AACATGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (26 bp):
TCTCCTAGGAGACAAATGGACAATGA
Found at i:48360 original size:45 final size:46
Alignment explanation
Indices: 48311--48413 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 46
48301 TTGGTTGCGG
* * * **
48311 AAATTAAAATCAAAGA-ATTAGTTCCTTTCGATTATTGGGTTGTGA
1 AAATTAAAATCAAAAAGATTAGTTACTTTCGATTATTGGATTACGA
48356 AAATTAAAAT-AAAAAGATTAGTTACTTTCGATTATTGGATTACGA
1 AAATTAAAATCAAAAAGATTAGTTACTTTCGATTATTGGATTACGA
48401 AAATT-AAATCAAA
1 AAATTAAAATCAAA
48414 TGGTTAGTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 8 0.16
45 43 0.84
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.35
Consensus pattern (46 bp):
AAATTAAAATCAAAAAGATTAGTTACTTTCGATTATTGGATTACGA
Found at i:48826 original size:39 final size:39
Alignment explanation
Indices: 48771--48847 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
48761 GAGGATCATA
* * *
48771 TTATGCAAAAGGAAATAAATCGTTAGATTTATTGTCCTG
1 TTATGCAAAAGAAAATAAATCATTAAATTTATTGTCCTG
* *
48810 TTATGTAAAAGAAAATAAATCATTAAATTTATTTTCCT
1 TTATGCAAAAGAAAATAAATCATTAAATTTATTGTCCT
48848 TGAATATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (39 bp):
TTATGCAAAAGAAAATAAATCATTAAATTTATTGTCCTG
Found at i:48912 original size:39 final size:39
Alignment explanation
Indices: 48868--48966 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 39
48858 ATGATTTTGG
* * *
48868 TTTGTAAAAAGAAATAAATCGTAGAATTTATTTTCCAAT
1 TTTGTAAAAGGAAATAAATCGTAGAATTTAGTCTCCAAT
* * * *
48907 TTTGTAAAAGGAAATAAATTGTTGGATTTAGTCTCCTAT
1 TTTGTAAAAGGAAATAAATCGTAGAATTTAGTCTCCAAT
48946 TTTGTAAAAGGAAATAAATCG
1 TTTGTAAAAGGAAATAAATCG
48967 AAACAACTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (39 bp):
TTTGTAAAAGGAAATAAATCGTAGAATTTAGTCTCCAAT
Found at i:56276 original size:21 final size:21
Alignment explanation
Indices: 56252--56303 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
56242 TCAAATGAAC
*
56252 AGTATCGATACTGAT-TGAAG
1 AGTATCGATACTGATATAAAG
*
56272 TAGTATCCATACTGATATAAAG
1 -AGTATCGATACTGATATAAAG
56294 -GTATCGATAC
1 AGTATCGATAC
56304 CAAGGGTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTGATATAAAG
Found at i:56829 original size:15 final size:14
Alignment explanation
Indices: 56786--56844 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
56776 ATTTTATTGG
56786 TATATGAAAATGTT
1 TATATGAAAATGTT
56800 TATATGTAAATATGTT
1 TATATG-AAA-ATGTT
*
56816 ATATACGAAAATGTT
1 -TATATGAAAATGTT
*
56831 CTATGTGAAAATGT
1 -TATATGAAAATGT
56845 GCTAAGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
14 6 0.16
15 19 0.50
16 8 0.21
17 5 0.13
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (14 bp):
TATATGAAAATGTT
Found at i:56872 original size:15 final size:15
Alignment explanation
Indices: 56822--56873 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
56812 TGTTATATAC
*
56822 GAAAATGTTCTATGT
1 GAAAATGTTCTAAGT
*
56837 GAAAATGTGCTAAGT
1 GAAAATGTTCTAAGT
* *
56852 AAAAAATGTTCTACGT
1 -GAAAATGTTCTAAGT
56868 GAAAAT
1 GAAAAT
56874 ACCCTATGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (15 bp):
GAAAATGTTCTAAGT
Found at i:56872 original size:16 final size:16
Alignment explanation
Indices: 56823--56872 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
56813 GTTATATACG
*
56823 AAAATGTTCTATGTG-
1 AAAATGTTCTAAGTGA
* *
56838 AAAATGTGCTAAGTAA
1 AAAATGTTCTAAGTGA
*
56854 AAAATGTTCTACGTGA
1 AAAATGTTCTAAGTGA
56870 AAA
1 AAA
56873 TACCCTATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (16 bp):
AAAATGTTCTAAGTGA
Found at i:57044 original size:25 final size:24
Alignment explanation
Indices: 57004--57059 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
56994 GAGTCAAGGG
57004 TTCTACGTGATCCTTCAGGACAAA
1 TTCTACGTGATCCTTCAGGACAAA
* * *
57028 TTTCTACGTGGTTCTTCAGGTCAAA
1 -TTCTACGTGATCCTTCAGGACAAA
57053 TTCTACG
1 TTCTACG
57060 CGGTCCTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (24 bp):
TTCTACGTGATCCTTCAGGACAAA
Found at i:58226 original size:26 final size:28
Alignment explanation
Indices: 58174--58226 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
58164 TAGATCAAAG
*
58174 AGATTTGGCTCAGAACAGTGTATTTTTT
1 AGATTTGGCTCAGAACAGTGCATTTTTT
58202 AGATTTGG-TC-GAACAGTGGCATTTT
1 AGATTTGGCTCAGAACAGT-GCATTTT
58227 AGTGACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 8 0.35
28 8 0.35
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (28 bp):
AGATTTGGCTCAGAACAGTGCATTTTTT
Found at i:59680 original size:15 final size:16
Alignment explanation
Indices: 59660--59692 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59650 TCAATTTAAG
*
59660 TATCG-ATTTTATTTT
1 TATCGAATTTTATATT
59675 TATCGAATTTTATATT
1 TATCGAATTTTATATT
59691 TA
1 TA
59693 AGTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TATCGAATTTTATATT
Found at i:60772 original size:34 final size:35
Alignment explanation
Indices: 60734--60801 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
60724 ACGTTATTGG
* * *
60734 ATATTTACATATATCAGATG-ATTACAGTTATCAT
1 ATATTTACAGATATAAAATGTATTACAGTTATCAT
*
60768 ATATTTACAGATATAAAATGTTTTACAGTTATCA
1 ATATTTACAGATATAAAATGTATTACAGTTATCA
60802 GGCACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (35 bp):
ATATTTACAGATATAAAATGTATTACAGTTATCAT
Found at i:61313 original size:20 final size:20
Alignment explanation
Indices: 61288--61330 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
61278 TGGTTTGAAG
*
61288 TTTTAATTTTTTATTTAAAT
1 TTTTAATTTATTATTTAAAT
* *
61308 TTTTAATTTATTGTTTATAT
1 TTTTAATTTATTATTTAAAT
61328 TTT
1 TTT
61331 ATGGATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTAATTTATTATTTAAAT
Found at i:64953 original size:126 final size:126
Alignment explanation
Indices: 64715--64964 Score: 392
Period size: 126 Copynumber: 2.0 Consensus size: 126
64705 ATTTCGGATA
** *
64715 TTTGAAGTATTTGAAATCTATAAATGTGAGGGTTAATTTTAATATATTTTAAGTAATGTTTGGGT
1 TTTGAAGTATTTGAAATCTATAAATGCAAGGGTTAATTTTAATATATTTTAAGTAATGTTTGGGC
*
64780 ACGATTTTGGAGAATTTGATTAATGGGCCTTCTAAATCTGACATGTTTCATTTAGGTCGGG
66 ACGATTTTGGAGAATTTGATTAATGGGCCTTCTAAATCCGACATGTTTCATTTAGGTCGGG
* * * *
64841 TTTGACGTGTTTGAAATCTATAAATGCAAGGGTTAATTTTAATGTATTTTGAGTAATGTTTGGGC
1 TTTGAAGTATTTGAAATCTATAAATGCAAGGGTTAATTTTAATATATTTTAAGTAATGTTTGGGC
* ** *
64906 ACGATTTTGGGGAATTTGATTAATGGGCCTTCTGGATCCGACCTGTTTCATTTAGGTCG
66 ACGATTTTGGAGAATTTGATTAATGGGCCTTCTAAATCCGACATGTTTCATTTAGGTCG
64965 AGTTAAGGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 112 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (126 bp):
TTTGAAGTATTTGAAATCTATAAATGCAAGGGTTAATTTTAATATATTTTAAGTAATGTTTGGGC
ACGATTTTGGAGAATTTGATTAATGGGCCTTCTAAATCCGACATGTTTCATTTAGGTCGGG
Found at i:68390 original size:3 final size:3
Alignment explanation
Indices: 68364--68420 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
68354 TCAGAAAAAA
* * *
68364 TAT TAAT TAT ATAT TAT TAC TAT TAT TAT TAT TAT TGT TAT TTT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
68411 TAA TAT TAT T
1 TAT TAT TAT T
68421 TACATATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:71959 original size:21 final size:21
Alignment explanation
Indices: 71918--71961 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
71908 ATCTAAAAAT
* *
71918 TCGGATATTCGAAATTTCGGA
1 TCGGATATTCCAAATTCCGGA
71939 TCGGATA-TCCAAATATCCGGA
1 TCGGATATTCCAAAT-TCCGGA
71960 TC
1 TC
71962 CAAATCAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TCGGATATTCCAAATTCCGGA
Found at i:72491 original size:23 final size:24
Alignment explanation
Indices: 72445--72491 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
72435 CCATGAAGTG
*
72445 GTATCGATACTACTTTATATAGTA
1 GTATCGATACTACTTTATACAGTA
72469 GTATCGATACT-CTTT-TGACAGTA
1 GTATCGATACTACTTTAT-ACAGTA
72492 TCGATACCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 9 0.43
24 11 0.52
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (24 bp):
GTATCGATACTACTTTATACAGTA
Found at i:73164 original size:16 final size:16
Alignment explanation
Indices: 73143--73173 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73133 ATTACAGTAT
73143 TGAGATTAGACAAATA
1 TGAGATTAGACAAATA
*
73159 TGAGATTAGATAAAT
1 TGAGATTAGACAAAT
73174 CTCAAGGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (16 bp):
TGAGATTAGACAAATA
Found at i:73867 original size:16 final size:17
Alignment explanation
Indices: 73835--73868 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
73825 TTTAAATTTT
*
73835 ATTTATTTTGTAGTTAA
1 ATTTAGTTTGTAGTTAA
73852 ATTTAGTTTG-AGTTAA
1 ATTTAGTTTGTAGTTAA
73868 A
1 A
73869 AATGATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (17 bp):
ATTTAGTTTGTAGTTAA
Found at i:74463 original size:8 final size:8
Alignment explanation
Indices: 74450--74475 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
74440 CACGCTTCCG
74450 TCACTGAC
1 TCACTGAC
74458 TCACTGAC
1 TCACTGAC
74466 TCACTGAC
1 TCACTGAC
74474 TC
1 TC
74476 GATGTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (8 bp):
TCACTGAC
Found at i:78452 original size:12 final size:12
Alignment explanation
Indices: 78435--78460 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
78425 CATCGAATTC
78435 AATAAAAAAGAA
1 AATAAAAAAGAA
78447 AATAAAAAAGAA
1 AATAAAAAAGAA
78459 AA
1 AA
78461 GGGATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AATAAAAAAGAA
Done.