Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008371.1 Hibiscus syriacus cultivar Beakdansim tig00111127_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: 546649
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:463844 original size:50 final size:49
Alignment explanation
Indices: 463739--463851 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 49
463729 AATAAGAAAT
* *
463739 AATAATAATAAATAAAATAATTACAATAATAATAAATGATATTAATAAAT
1 AATAATAAT-AATAAAATAATTACAATAATAATAAATGATATTAAAAAAC
* * *
463789 AATAATAATAATATAATAA-TATAATATATATATAAAT-ATTTTAAAAAAC
1 AATAATAATAATAAAATAATTACAATA-ATA-ATAAATGATATTAAAAAAC
463838 ATATAATATATAAT
1 A-ATAATA-ATAAT
463852 TTCCAAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
48 6 0.11
49 22 0.41
50 21 0.39
51 5 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (49 bp):
AATAATAATAATAAAATAATTACAATAATAATAAATGATATTAAAAAAC
Found at i:463981 original size:11 final size:11
Alignment explanation
Indices: 463965--463989 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
463955 TATAATATAT
463965 AAATGTTTTCA
1 AAATGTTTTCA
463976 AAATGTTTTCA
1 AAATGTTTTCA
463987 AAA
1 AAA
463990 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:464064 original size:25 final size:25
Alignment explanation
Indices: 464019--464066 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
464009 TCAAAAATGT
464019 TTTTCAAAACTATATATTATATACG
1 TTTTCAAAACTATATATTATATACG
*
464044 TTTTCAATA-TATATATATATATA
1 TTTTCAAAACTATATAT-TATATA
464067 TATTATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATACG
Found at i:464152 original size:39 final size:37
Alignment explanation
Indices: 463878--464152 Score: 195
Period size: 37 Copynumber: 7.4 Consensus size: 37
463868 TTTTTGAAAT
* * * ** *
463878 TATATAATATATAGATTTTAAAAAATGTTTAGAAAAAT
1 TATATATTATATATATTTT-CAAAATGTTTTCAAAAAA
* *
463916 TATATATTATATAT-TTTT-AAAATATTTTTTAAAAAA
1 TATATATTATATATATTTTCAAAAT-GTTTTCAAAAAA
* * *
463952 CTATATAATATATAAATGTTTTCAAAATGTTTTC-AAAAC
1 -TATAT-AT-TATATATATTTTCAAAATGTTTTCAAAAAA
* * *
463991 TATATATCATATAAATTTTCAAAAATGTTTTTC-AAAAC
1 TATATATTATATATATTTTC-AAAATG-TTTTCAAAAAA
** * * * * *
464029 TATATATTATATACGTTTTCAATAT-ATAT--ATATA
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAA
* * *
464063 TATATATTATATACATTTTCAAAATGTTTTCAAAGAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAAA
*
464100 TATATATTATATATATTTTTAAAATGTTTTCGAAAAAAA
1 TATATATTATATATATTTTCAAAATGTTTTC--AAAAAA
464139 TATATATTATATAT
1 TATATATTATATAT
464153 CATATAATAT
Statistics
Matches: 189, Mismatches: 35, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
34 25 0.13
35 9 0.05
36 17 0.09
37 51 0.27
38 46 0.24
39 28 0.15
40 8 0.04
41 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAAA
Found at i:465600 original size:31 final size:29
Alignment explanation
Indices: 465565--465625 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
465555 CAAATATAAG
*
465565 TCTTCTTCATTATTAAAGGCTATTTGTAC
1 TCTTCTTCACTATTAAAGGCTATTTGTAC
465594 TC-TCTTCACTATTAAAGGCTATTTGTAC
1 TCTTCTTCACTATTAAAGGCTATTTGTAC
465622 TCTT
1 TCTT
465626 TCTCTCTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 27 0.90
29 3 0.10
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.48
Consensus pattern (29 bp):
TCTTCTTCACTATTAAAGGCTATTTGTAC
Found at i:468352 original size:27 final size:27
Alignment explanation
Indices: 468322--468386 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
468312 AAAACAATGT
468322 TGAATGATTCAACACAGAAATAAATTC
1 TGAATGATTCAACACAGAAATAAATTC
* * * *
468349 TGAATGATTCACCATATAAGTAAATTC
1 TGAATGATTCAACACAGAAATAAATTC
468376 TGAATGATTCA
1 TGAATGATTCA
468387 GAGCAATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (27 bp):
TGAATGATTCAACACAGAAATAAATTC
Found at i:477232 original size:45 final size:45
Alignment explanation
Indices: 477182--477285 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
477172 TAATGTCCAG
* *** *
477182 TCCTCTGCCTTTTTATGGATTTTTAACAGATTTGATTGGTTCTGC
1 TCCTCTGCCTTTATACCCATTTTTAACAGATTTGATAGGTTCTGC
* * * *
477227 TCCTCTGCCTTTATCCCCTTTTTTAACAGTTTTGATAGTTTCTGC
1 TCCTCTGCCTTTATACCCATTTTTAACAGATTTGATAGGTTCTGC
*
477272 TCCTTTGCCTTTAT
1 TCCTCTGCCTTTAT
477286 CTGAGGAGCT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (45 bp):
TCCTCTGCCTTTATACCCATTTTTAACAGATTTGATAGGTTCTGC
Found at i:477286 original size:45 final size:45
Alignment explanation
Indices: 477201--477286 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
477191 TTTTTATGGA
*
477201 TTTTTAACAGATTTGATTGGTTCTGCTCCTCTGCCTTTATCCCCT
1 TTTTTAACAGATTTGATAGGTTCTGCTCCTCTGCCTTTATCCCCT
* * *
477246 TTTTTAACAGTTTTGATAGTTTCTGCTCCTTTGCCTTTATC
1 TTTTTAACAGATTTGATAGGTTCTGCTCCTCTGCCTTTATC
477287 TGAGGAGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.14, C:0.23, G:0.13, T:0.50
Consensus pattern (45 bp):
TTTTTAACAGATTTGATAGGTTCTGCTCCTCTGCCTTTATCCCCT
Found at i:480997 original size:27 final size:27
Alignment explanation
Indices: 480957--481011 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
480947 TGATAACATT
480957 AATAATTTTAGATACCTAAATTGAAAAA
1 AATAATTTTAGATACCTAAA-TGAAAAA
*
480985 AATAA-TTTAGATACCTTAATGAAAAA
1 AATAATTTTAGATACCTAAATGAAAAA
481011 A
1 A
481012 GACGTATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.31
27 13 0.50
28 5 0.19
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (27 bp):
AATAATTTTAGATACCTAAATGAAAAA
Found at i:483161 original size:29 final size:29
Alignment explanation
Indices: 483127--483185 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
483117 CCTAAATTAA
483127 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
483156 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
483185 T
1 T
483186 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:487843 original size:29 final size:29
Alignment explanation
Indices: 487809--487867 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
487799 CCTAAATTAA
487809 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
487838 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
487867 T
1 T
487868 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:504186 original size:131 final size:132
Alignment explanation
Indices: 503939--504194 Score: 379
Period size: 131 Copynumber: 1.9 Consensus size: 132
503929 CTAGTAATTT
* * * *
503939 TACAATACACATTTCTTTCTTTCTCTTGCATCAAAAATCCTCATGCCCACATGATAAATATCAAA
1 TACAAAACACAATTCTTTCATTCTCTTGCATCAAAAATCCTCATGCACACATGATAAATATCAAA
* *
504004 ATAAAATAACTATCAAATAGATAATTCTTCTATAAAATGGTTCAAAAATCTAGTAATGTACTTAA
66 ATAAAATAACTACCAAATAGATAATCCTTCTATAAAATGGTTCAAAAATCTAGTAATGTACTTAA
504069 AA
131 AA
* **
504071 TACAAAACACAATTCTTTCATTCTCTTGCATCAAAATTTTTCATGCACACATGAT-AATATCAAA
1 TACAAAACACAATTCTTTCATTCTCTTGCATCAAAAATCCTCATGCACACATGATAAATATCAAA
* * * * *
504135 ATAGAATAACTGCCATATAGGTAATCCTTCTATGAAATGGTTCAAAAATCTAGTAATGTA
66 ATAAAATAACTACCAAATAGATAATCCTTCTATAAAATGGTTCAAAAATCTAGTAATGTA
504195 TCTCATCACC
Statistics
Matches: 110, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 62 0.56
132 48 0.44
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (132 bp):
TACAAAACACAATTCTTTCATTCTCTTGCATCAAAAATCCTCATGCACACATGATAAATATCAAA
ATAAAATAACTACCAAATAGATAATCCTTCTATAAAATGGTTCAAAAATCTAGTAATGTACTTAA
AA
Found at i:509646 original size:90 final size:88
Alignment explanation
Indices: 509492--509679 Score: 322
Period size: 90 Copynumber: 2.1 Consensus size: 88
509482 TGATGGGATG
* *
509492 TTTTGAAAGGGTTCTGGAGATGAGGTTCACTGTTAAATCATGTGTTAATCTATCTTATTAGGGCA
1 TTTTGGAAGGGTTCTGAAGATGAGGTTCACTGTTAAATCATGTGTTAATCTATCTTATTAGGGCA
509557 CTTCCGACTCGGAGGAAGCTTAT
66 CTTCCGACTCGGAGGAAGCTTAT
* *
509580 TTTTGGAAGGGTTCTGAAGATGGGGTTTTCACTGTTAAATCATGTGTTAATCTATCTTATTCGGG
1 TTTTGGAAGGGTTCTGAAGATGAGG--TTCACTGTTAAATCATGTGTTAATCTATCTTATTAGGG
509645 CACTTCCGACTCGGAGGAAGCTTAT
64 CACTTCCGACTCGGAGGAAGCTTAT
509670 TTTTGGAAGG
1 TTTTGGAAGG
509680 CAATTGTTTG
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 22 0.23
90 72 0.77
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (88 bp):
TTTTGGAAGGGTTCTGAAGATGAGGTTCACTGTTAAATCATGTGTTAATCTATCTTATTAGGGCA
CTTCCGACTCGGAGGAAGCTTAT
Found at i:511472 original size:64 final size:63
Alignment explanation
Indices: 511387--511547 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
511377 TTATTTAAGG
* * * * *
511387 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAATCATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAACAAA-CATCGAATAGGATTTA
* *
511451 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAACAAACATCGAATAGGATTTA
*
511515 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
511548 ACCTTCTTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.69
65 24 0.28
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAACAAACATCGAATAGGATTTA
Found at i:513103 original size:22 final size:19
Alignment explanation
Indices: 513059--513128 Score: 90
Period size: 18 Copynumber: 3.6 Consensus size: 19
513049 TTAAGGAGTA
513059 GTCCTACGGGACATAA-TG
1 GTCCTACGGGACATAAGTG
513077 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--ATA-AGTG
*
513099 GTCCTTCGGGACAT-AGTG
1 GTCCTACGGGACATAAGTG
513117 GTCCTACGGGAC
1 GTCCTACGGGAC
513129 GAATACTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
18 27 0.59
20 5 0.11
21 1 0.02
22 13 0.28
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (19 bp):
GTCCTACGGGACATAAGTG
Found at i:514257 original size:127 final size:127
Alignment explanation
Indices: 514067--514728 Score: 625
Period size: 125 Copynumber: 5.2 Consensus size: 127
514057 TTCTTATAAA
* ** * *
514067 AAAAATCTAGTAATGTACTTAAAATACAAAACACAGTTCTTTTTTTCTCTTGCATCAAAATTCCT
1 AAAAATCTAGTAATGTACTT-AAATATAGGACA-TGTT-TTTCTTTCTCTTGCATCAAAATTCCT
* * *
514132 CATGCCCACATAATTATATCAAAATAGAATAATTGTCGCATAGGCAATTTTTCTATGAAAATGG-
63 CATGCCCACATGATAATATCAAAATAGAATAATTGTCACATAGGCAA-TTTTCTATG-AAATGGT
514196 TC
126 TC
* *
514198 AACAAATCTAGTTATGTACTTAAATATAGGACATG-TTTT-TTTCTCTGGCATCAAAATTCCTCA
1 AA-AAATCTAGTAATGTACTTAAATATAGGACATGTTTTTCTTTCTCTTGCATCAAAATTCCTCA
* * * * * *
514261 TGTCCACATGATAATATCAAAATAGAATAACTGCCATATATGTAATTTTCTATGAAATGGTTC
65 TGCCCACATGATAATATCAAAATAGAATAATTGTCACATAGGCAATTTTCTATGAAATGGTTC
* *
514324 AAAAATCTAATAATGTACTTAAAT-TAGGACA-GTTCTTTCTTTCTCTTACATCAAAATTCCTCA
1 AAAAATCTAGTAATGTACTTAAATATAGGACATGTT-TTTCTTTCTCTTGCATCAAAATTCCTCA
* * * * * *
514387 GGCCCACGTGATAATATCAAAATAGAAAAACTGCCATATAGGCAATTCTTCTATGAAATGGTTC
65 TGCCCACATGATAATATCAAAATAGAATAATTGTCACATAGGCAATT-TTCTATGAAATGGTTC
* * * * *
514451 AAAAATTTAGTAAAGTAATTAAA-ATACTGGATACAT-TTCTTTCTTTTTCTT-CTACCAAAATT
1 AAAAATCTAGTAATGTACTTAAATATA--GG--ACATGTT-TTTCTTTCTCTTGC-ATCAAAATT
* * * ** * **
514513 CCTCATGCCCACATGATAATACCAGAATAGAATAATTGTAACATAAACAACTCTTCTACAAAATG
60 CCTCATGCCCACATGATAATATCAAAATAGAATAATTGTCACATAGGCAA-TTTTCTATGAAATG
*
514578 ATT-
124 GTTC
* * * *
514581 AAAAA---A-T-ATGTACTTAAAACACAAGACACGGTTTTGTCTTTCTCTTGCATCAAAATTCCT
1 AAAAATCTAGTAATGTACTT-AAATATAGGACA-TGTTTT-TCTTTCTCTTGCATCAAAATTCCT
* * * *
514641 CATGCTCACATTATAATATCAAAATAGAATAACTT-TCACATAGGCTATTTTCCATGAAATGGTT
63 CATGCCCACATGATAATATCAAAATAGAATAA-TTGTCACATAGGCAATTTTCTATGAAATGGTT
514705 C
127 C
*
514706 AAAAATCTAGTAATATACTTAAA
1 AAAAATCTAGTAATGTACTTAAA
514729 ATACAAGACT
Statistics
Matches: 437, Mismatches: 67, Indels: 56
0.78 0.12 0.10
Matches are distributed among these distances:
123 4 0.01
124 22 0.05
125 99 0.23
126 83 0.19
127 99 0.23
128 4 0.01
129 7 0.02
130 14 0.03
131 87 0.20
132 18 0.04
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (127 bp):
AAAAATCTAGTAATGTACTTAAATATAGGACATGTTTTTCTTTCTCTTGCATCAAAATTCCTCAT
GCCCACATGATAATATCAAAATAGAATAATTGTCACATAGGCAATTTTCTATGAAATGGTTC
Found at i:515569 original size:130 final size:130
Alignment explanation
Indices: 515260--515581 Score: 405
Period size: 132 Copynumber: 2.5 Consensus size: 130
515250 ACTTCAATTC
* * *
515260 TGCCCACGTGATAATATCAAAATAGAATAACTGCCACATAGGTGATTCTTCTATGAAATGATTCA
1 TGCCCACGTGATAATATCAAAATAGAATAACTGCCACATAGATAATTCTTCTATGAAATGATTAA
* * *
515325 AAAATATAGTAATGTACTTAAAATACAGGACAATTCTTTCTTTCTTTTTTTGTATCAAAATTTCT
66 AAAATATAGTAATGTACTTAAAATACAGAACAATTCTTTCTTTC--TTCTTGCATCAAAATTTCT
**
515390 TG
129 CA
* *
515392 TGCCCACGTGATAATATCAAAATAGAATAATTGTCACATAGATAATTCTTCTATGAAATGATTAA
1 TGCCCACGTGATAATATCAAAATAGAATAACTGCCACATAGATAATTCTTCTATGAAATGATTAA
* * * * **
515457 AAAATCTTGTAGTGTACTTAAAATACATAACATAATTCTTTCTTTC-TCTTGCATCAATGTTT-T
66 AAAATATAGTAATGTACTTAAAATACAGAAC--AATTCTTTCTTTCTTCTTGCATCAAAATTTCT
515520 CA
129 CA
* * ***
515522 TGCCCACATGATAATATCAAAATAGAATAACTACCACATATCCAATTCTTCTATGAAATG
1 TGCCCACGTGATAATATCAAAATAGAATAACTGCCACATAGATAATTCTTCTATGAAATG
515582 GTTCAAAAGA
Statistics
Matches: 165, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
130 54 0.33
131 12 0.07
132 86 0.52
134 13 0.08
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (130 bp):
TGCCCACGTGATAATATCAAAATAGAATAACTGCCACATAGATAATTCTTCTATGAAATGATTAA
AAAATATAGTAATGTACTTAAAATACAGAACAATTCTTTCTTTCTTCTTGCATCAAAATTTCTCA
Found at i:522054 original size:41 final size:41
Alignment explanation
Indices: 521996--522081 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
521986 AATACTACTG
* *
521996 CAAAACAGATACGTTAGCACTAAC-TGTTTGGAAAAATAAAT
1 CAAAACAGATACATTAGCACTAACAT-CTTGGAAAAATAAAT
*
522037 CAAAACAGATACATTAGCACTAACATCTTGGAAAAATAATT
1 CAAAACAGATACATTAGCACTAACATCTTGGAAAAATAAAT
522078 CAAA
1 CAAA
522082 CAGTAAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (41 bp):
CAAAACAGATACATTAGCACTAACATCTTGGAAAAATAAAT
Found at i:525559 original size:35 final size:35
Alignment explanation
Indices: 525506--525580 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
525496 CCACATAAGT
* *
525506 AAGAAAATGTATGATACAAGGTATACTCCTAACAC
1 AAGAAAATGAAAGATACAAGGTATACTCCTAACAC
*
525541 AAGAAAATGAAAGGTACAAGGTATACTCCTAACAC
1 AAGAAAATGAAAGATACAAGGTATACTCCTAACAC
525576 AAGAA
1 AAGAA
525581 TCGATCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (35 bp):
AAGAAAATGAAAGATACAAGGTATACTCCTAACAC
Found at i:541435 original size:20 final size:20
Alignment explanation
Indices: 541410--541463 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
541400 AATGAACAAA
541410 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
541430 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
541450 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
541464 ATGTAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:541494 original size:21 final size:21
Alignment explanation
Indices: 541470--541536 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
541460 GAATATGTAA
*
541470 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
541491 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
** *
541512 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
541532 TCGCA
1 TCGCA
541537 ACGCGAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 10 0.25
21 30 0.75
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:541532 original size:20 final size:20
Alignment explanation
Indices: 541507--541551 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
541497 TGCGATATTC
*
541507 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
541527 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
541547 CAAAT
1 CAAAT
541552 GTTTTTACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:541708 original size:20 final size:20
Alignment explanation
Indices: 541683--541722 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
541673 CGACATCCGT
541683 CCCCATCTCCGACGAAATCC
1 CCCCATCTCCGACGAAATCC
*
541703 CCCCATTTCCGACGAAATCC
1 CCCCATCTCCGACGAAATCC
541723 GTCTATCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.47, G:0.10, T:0.17
Consensus pattern (20 bp):
CCCCATCTCCGACGAAATCC
Found at i:542003 original size:19 final size:19
Alignment explanation
Indices: 541934--541995 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
541924 AACACCAAAT
* *
541934 TCGCAACGCGAAAATGAAAA
1 TCGCAATGCGAAACT-AAAA
541954 TCGCAATGCGAAACTAAAA
1 TCGCAATGCGAAACTAAAA
541973 TCGCAATGCGAAACTAAAA
1 TCGCAATGCGAAACTAAAA
541992 TCGC
1 TCGC
541996 GTTGCGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 27 0.68
20 13 0.32
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAACTAAAA
Found at i:544154 original size:21 final size:21
Alignment explanation
Indices: 544128--544183 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
544118 TATGCTCGAT
544128 GCACCTATCATCATTCAAGAG
1 GCACCTATCATCATTCAAGAG
* *
544149 GCACCT-CCTATCGTTCAAGAG
1 GCACCTATC-ATCATTCAAGAG
*
544170 GCCCCTATCATCAT
1 GCACCTATCATCAT
544184 CGAAGAAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (21 bp):
GCACCTATCATCATTCAAGAG
Found at i:544178 original size:42 final size:42
Alignment explanation
Indices: 544131--544213 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
544121 GCTCGATGCA
* *
544131 CCTATCATCATTC-AAG-AGGCACCTCCTATCGTTCAAGAGGCC
1 CCTATCATCA-TCGAAGAAGGC-CCTCCCACCGTTCAAGAGGCC
*
544173 CCTATCATCATCGAAGAAGTCCCTCCCACCGTTCAAGAGGC
1 CCTATCATCATCGAAGAAGGCCCTCCCACCGTTCAAGAGGC
544214 TACTGTCATC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 31 0.86
43 3 0.08
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.22
Consensus pattern (42 bp):
CCTATCATCATCGAAGAAGGCCCTCCCACCGTTCAAGAGGCC
Done.