Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006767.1 Hibiscus syriacus cultivar Beakdansim tig00017099_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: 61007
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:427 original size:24 final size:24
Alignment explanation
Indices: 398--508 Score: 114
Period size: 24 Copynumber: 4.6 Consensus size: 24
388 GAATGTTTTA
*
398 TCTGATTTCTGATTTGAATTATGT
1 TCTGATTTCTGATATGAATTATGT
* * *
422 TCTGATTTCTAATCTGAATTTTGT
1 TCTGATTTCTGATATGAATTATGT
* * *
446 TATGATTTCTAATATGGATTATGT
1 TCTGATTTCTGATATGAATTATGT
* * * *
470 TCTGATATATGATATAAATTCTGT
1 TCTGATTTCTGATATGAATTATGT
*
494 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
509 CTCTGTTTAT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTATGT
Found at i:500 original size:48 final size:48
Alignment explanation
Indices: 400--508 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
390 ATGTTTTATC
* * * * * *
400 TGATTTCTGATTTGAATTATGTTCTGATTTCTAATCTGAATTTTGTTA
1 TGATTTCTGATATGAATTATGTTCTGATATATAATATAAATTCTGTTA
* * * *
448 TGATTTCTAATATGGATTATGTTCTGATATATGATATAAATTCTGTTT
1 TGATTTCTGATATGAATTATGTTCTGATATATAATATAAATTCTGTTA
496 TGATTTCTGATAT
1 TGATTTCTGATAT
509 CTCTGTTTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (48 bp):
TGATTTCTGATATGAATTATGTTCTGATATATAATATAAATTCTGTTA
Found at i:9042 original size:22 final size:21
Alignment explanation
Indices: 9000--9039 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8990 AAGACAATTT
9000 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
9021 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
9040 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:12095 original size:10 final size:10
Alignment explanation
Indices: 12080--12116 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
12070 ACTACCTAAG
12080 ACTGTTGACT
1 ACTGTTGACT
12090 ACTGTTGACT
1 ACTGTTGACT
12100 A---TTGACT
1 ACTGTTGACT
12107 ACTGTTGACT
1 ACTGTTGACT
12117 GTTGATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.29
10 17 0.71
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (10 bp):
ACTGTTGACT
Found at i:12099 original size:17 final size:17
Alignment explanation
Indices: 12079--12121 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
12069 CACTACCTAA
12079 GACTGTTGACTACTGTT
1 GACTGTTGACTACTGTT
*
12096 GACTATTGACTACTGTT
1 GACTGTTGACTACTGTT
12113 GACTGTTGA
1 GACTGTTGA
12122 TCGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (17 bp):
GACTGTTGACTACTGTT
Found at i:12172 original size:21 final size:21
Alignment explanation
Indices: 12143--12183 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12133 TAACCGCATT
*
12143 GACCGTTGACCGCCGTTGACG
1 GACCGTTGACCGACGTTGACG
*
12164 GACCTTTGACCGACGTTGAC
1 GACCGTTGACCGACGTTGAC
12184 TATCGTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (21 bp):
GACCGTTGACCGACGTTGACG
Found at i:14466 original size:24 final size:24
Alignment explanation
Indices: 14411--14512 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 24
14401 GTGTTTTATC
* * * * *
14411 TGATTTCCAATTTCAATTATGTTC
1 TGATTTCTAATATGAATTCTGTTT
* *
14435 TGATTTCTAATCTGAATTCTGTTA
1 TGATTTCTAATATGAATTCTGTTT
*
14459 TGATTTCTAATATGGATTCTGTTT
1 TGATTTCTAATATGAATTCTGTTT
* * *
14483 TGATATATGATATGAATTCTGTTT
1 TGATTTCTAATATGAATTCTGTTT
14507 TGATTT
1 TGATTT
14513 TTGATATCTC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.52
Consensus pattern (24 bp):
TGATTTCTAATATGAATTCTGTTT
Found at i:34273 original size:109 final size:108
Alignment explanation
Indices: 34024--34288 Score: 356
Period size: 108 Copynumber: 2.4 Consensus size: 108
34014 TCCATCATAG
* * * * * *
34024 AAGGAGGTGGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTTGCCTAATGAATAAGTTC
1 AAGGAAGTGGATCAACATTTCCATAAGAGTTCATAATGAGAAGAACTCGCCCAAAGAAAAAGTTC
* * * *
34089 ATGATGAGAATAACTTGTTTGGTTTCTTTCAAATACATCACAA
66 ATAATGAGAATAACTTATTTGATTTATTTCAAATACATCACAA
*
34132 AAGGAGGTGGATCAACATTTCCATAAGAGTTCATAATGAGAAGAACTCGCCCAAAGAAGAAAGTT
1 AAGGAAGTGGATCAACATTTCCATAAGAGTTCATAATGAGAAGAACTCGCCCAAAGAA-AAAGTT
*
34197 CATAATGAGAATAACTTATTCT-ATTTATTTCAAATTCATCACAA
65 CATAATGAGAATAACTTATT-TGATTTATTTCAAATACATCACAA
*
34241 AA-GAAGTGGATCAACATGTT-CAGTAAGTGTTCATAATGAGAAGAACTC
1 AAGGAAGTGGATCAACAT-TTCCA-TAAGAGTTCATAATGAGAAGAACTC
34289 ATCCCAATAA
Statistics
Matches: 141, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
108 70 0.50
109 70 0.50
110 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (108 bp):
AAGGAAGTGGATCAACATTTCCATAAGAGTTCATAATGAGAAGAACTCGCCCAAAGAAAAAGTTC
ATAATGAGAATAACTTATTTGATTTATTTCAAATACATCACAA
Found at i:34452 original size:3 final size:3
Alignment explanation
Indices: 34444--34546 Score: 116
Period size: 3 Copynumber: 34.0 Consensus size: 3
34434 TTACCTAACC
* * * * * * *
34444 TTA TTA TTA TTTA ATA CTA TTA GTA TTA TTG TTG TTG TTA TTG TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
34490 TTG TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34538 TTA TTA TTA
1 TTA TTA TTA
34547 AATAAAAGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 84 0.97
4 3 0.03
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39224 original size:443 final size:439
Alignment explanation
Indices: 38387--39665 Score: 1312
Period size: 443 Copynumber: 2.9 Consensus size: 439
38377 ACAATATCAA
* * * * * * * * * * *
38387 ACATAATTCTACATGTAAGATTATGCATTTCAGTCATATCCTTTTTTACATGTGTGGAATTATGC
1 ACATAATTCTACAAGTAAAACTAAGCATTTCAGACGTATTCATTTTTATACGTGTAGAATTATGC
*
38452 GTAAATCTTCACTTCACTTTTTTCCTTGTTTCTCCCT-GAGACTCTATTCCTCTTAAATTACTCA
66 GTAAATCTTCACTTCACTTTTTTCCTTGTTTCTCCATCGA-ACTCTATTCCTCTTAAATTACTCA
* * * *
38516 CGATGTGAAAATATAGGGATACTT-A-GTAGGTTCCA-GTGGGGTGCCTTATATTCGGGTCAAGG
130 CGATGTGAAAATA-AGGGACACTTAACG-AGTTTCAATG-GGGGTGCCTTATATTTGGGT-AAGG
* * * *
38578 TCGGGTGGGTAAAACTCATACCCAACCCATGTGTATCCCTATGACTATCTTAGATTGATACTTAC
191 TCGGGTGGGTAAAAATCAAACCCAACCCATGTGCATCCCTAGGACTATCTTAGATTGATACTTAC
* * * *
38643 AAGTGTAATCATGTGAATTAGGTTTATACTTAAAAGTATAAGCATGTGAATCAAGAGTTTTCTTC
256 AAGTGTAATCCTG-GAATTAGGTTGATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTC
* ** * *
38708 CTTATACTAAAGCTCATGACTAATAGTCATGAG-TTTGTATTTGAACGCTTAGGCTCATAATTGT
320 CTTATACTAAAGCTCAGGACTAAGGGTCAGGAGCTTT-TATTTGAACACTTAGGCTCATAATTGT
* *
38772 TTCTCCATCGGAATCTTGATAGAGGAATCCACCAACTCGTCTGAACCATATAAAAC
384 TTCTCCATCGGAATCTTGATAGAGGAATCCACCAAATCGTCTAAACCATATAAAAC
* * *
38828 ACATAATTCTACAAGTAAAACT-AGACATTTCATG-TGTATTCATTTTTTTCACGTTTAGAATTA
1 ACATAATTCTACAAGTAAAACTAAG-CATTTCA-GACGTATTCATTTTTAT-ACGTGTAGAATTA
* * * **
38891 TGTGTAAATCTTCACTTCAGTTTTTTCCTTGTTTC-CCATCGAACTCTATTTCTCTTAAATTGGT
63 TGCGTAAATCTTCACTTCACTTTTTTCCTTGTTTCTCCATCGAACTCTATTCCTCTTAAATTACT
* **
38955 CACGATGTGACAATAAGAGGACACTTAACGAGTTTCAATGGGGGTGCCTTATATTTGGGTTTGGA
128 CACGATGTGAAAATAAG-GGACACTTAACGAGTTTCAATGGGGGTGCCTTATATTTGGGTAAGG-
* *
39020 TCGGGTGGGGTAAAAATCAAAACCAACCCATGTGCATCCCTAGGACTATCTTAGATTTATACTTA
191 TCGGGT-GGGTAAAAATCAAACCCAACCCATGTGCATCCCTAGGACTATCTTAGATTGATACTTA
* *
39085 GAAGTGTAATCCTCGGAATTAGGTTGATACTTAAATGTGTAAGCATGAGAATCAAGAGTTTTCTT
255 CAAGTGTAATCCT-GGAATTAGGTTGATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTT
* * * **
39150 CCTTATACTAAAGATC-GAGACTAAGGGCCAGGAGCTTTTATTTGAACACTTTGGCTCATGCTTG
319 CCTTATACTAAAGCTCAG-GACTAAGGGTCAGGAGCTTTTATTTGAACACTTAGGCTCATAATTG
* * * * * * ** *
39214 TTTTTCCATCGGAATTTTGATGGAGGAATCTATCAAATGGTCTAAACCATATTTAAT
383 TTTCTCCATCGGAATCTTGATAGAGGAATCCACCAAATCGTCTAAACCATATAAAAC
* ** * * * *
39271 ACATTATTCTACATTTAAAATTAAGCATTTTAGACGTATTTATTTTTATACGTGTAGAAGTATGC
1 ACATAATTCTACAAGTAAAACTAAGCATTTCAGACGTATTCATTTTTATACGTGTAGAATTATGC
* * ** * * ** * *
39336 GTAAATATACACTTCACTTTTAGCCTTGTTTCTCCACCAAACTCTATTCCTCTTAAATTTTTTAG
66 GTAAATCTTCACTTCACTTTTTTCCTTGTTTCTCCATCGAACTCTATTCCTCTTAAATTACTCAC
* * * * * * * * * **
39401 GATATGATAATAGGGGGATC-CTTAGC-AGATTCCAGTGGTGGTGCCTTGTATTCT-AGTCGGGG
131 GATGTGAAAATA-AGGGA-CACTTAACGAG-TTTCAATGGGGGTGCCTTATATT-TGGGT-AAGG
*** * * * *
39463 TCAATTAGGGTAAAAATTAGACCCAACCCATGTACATCCCTAGGACTATCTTAGGTTGATACTTA
191 TCGGGT-GGGTAAAAATCAAACCCAACCCATGTGCATCCCTAGGACTATCTTAGATTGATACTTA
* *
39528 CAAGTGTAATCCTAGAATTAGGTTGATACTTAAAAGTGTAATCAT-AGGAATCAAGAGTTTTCTT
255 CAAGTGTAATCCTGGAATTAGGTTGATACTTAAAAGTGTAAGCATGA-GAATCAAGAGTTTTCTT
* * * *
39592 CCTTATTCTAAAGCTCAGGACTATGGGTC-GCGAGCATTTATTTGAACGA-ATAGGCTCATACA-
319 CCTTATACTAAAGCTCAGGACTAAGGGTCAG-GAGCTTTTATTTGAAC-ACTTAGGCTCATA-AT
39654 TGTTTCTCCATC
381 TGTTTCTCCATC
39666 AAAATCTAAA
Statistics
Matches: 695, Mismatches: 117, Indels: 51
0.81 0.14 0.06
Matches are distributed among these distances:
440 3 0.00
441 82 0.12
442 224 0.32
443 375 0.54
444 11 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (439 bp):
ACATAATTCTACAAGTAAAACTAAGCATTTCAGACGTATTCATTTTTATACGTGTAGAATTATGC
GTAAATCTTCACTTCACTTTTTTCCTTGTTTCTCCATCGAACTCTATTCCTCTTAAATTACTCAC
GATGTGAAAATAAGGGACACTTAACGAGTTTCAATGGGGGTGCCTTATATTTGGGTAAGGTCGGG
TGGGTAAAAATCAAACCCAACCCATGTGCATCCCTAGGACTATCTTAGATTGATACTTACAAGTG
TAATCCTGGAATTAGGTTGATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTCCTTATA
CTAAAGCTCAGGACTAAGGGTCAGGAGCTTTTATTTGAACACTTAGGCTCATAATTGTTTCTCCA
TCGGAATCTTGATAGAGGAATCCACCAAATCGTCTAAACCATATAAAAC
Found at i:44727 original size:3 final size:3
Alignment explanation
Indices: 44719--44754 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
44709 TCCTCAATAA
*
44719 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
44755 GAGATGGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44763 original size:12 final size:12
Alignment explanation
Indices: 44719--44766 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
44709 TCCTCAATAA
*
44719 AAGAAGAAGAAG
1 AAGAAGGAGAAG
*
44731 AAGAAGAAGAAG
1 AAGAAGGAGAAG
44743 AAGAAGGAGAAG
1 AAGAAGGAGAAG
* *
44755 GAGATGGAGAAG
1 AAGAAGGAGAAG
44767 TCGAGCGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (12 bp):
AAGAAGGAGAAG
Found at i:52315 original size:14 final size:14
Alignment explanation
Indices: 52298--52338 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
52288 TGAAAAAAGT
52298 GAAAAAAAATAGAA
1 GAAAAAAAATAGAA
52312 GAAAAAAAATTAG-A
1 GAAAAAAAA-TAGAA
52326 GAAAAAAAA-AGAA
1 GAAAAAAAATAGAA
52339 AAAGAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 1 0.04
14 19 0.76
15 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (14 bp):
GAAAAAAAATAGAA
Found at i:54598 original size:42 final size:41
Alignment explanation
Indices: 54527--54617 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
54517 AAGCGCTACA
* * *
54527 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCG
1 GGCCATCTGTCAGTCTTTCGAGCAAGATGA-TAAATCATTCG
* * *
54569 GGTCATCTGTCAGTCTTTCGAGTAAGATGATAAGTCATTCG
1 GGCCATCTGTCAGTCTTTCGAGCAAGATGATAAATCATTCG
54610 GGCCATCT
1 GGCCATCT
54618 ATAAGACCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 17 0.40
42 25 0.60
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
GGCCATCTGTCAGTCTTTCGAGCAAGATGATAAATCATTCG
Found at i:54719 original size:17 final size:16
Alignment explanation
Indices: 54689--54723 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54679 AGTTTCTCAT
54689 TAAAATTTTCAAAAAA
1 TAAAATTTTCAAAAAA
**
54705 TAAAATTTTTGAAAAA
1 TAAAATTTTCAAAAAA
54721 TAA
1 TAA
54724 GAAATCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAAAATTTTCAAAAAA
Found at i:54827 original size:42 final size:41
Alignment explanation
Indices: 54780--54872 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 41
54770 AGGTAAGTCA
*
54780 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
1 TCGGGCCATCAGTAAGTCTTTCGAGCAAGATGA-TAAATCCT
* * * *
54822 TCGGGCCATCTGTCAGTCTTTCGAGCAAGATTATAAGTCCT
1 TCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCCT
*
54863 TCGAGCCATC
1 TCGGGCCATC
54873 TATAAGACCT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.30
Consensus pattern (41 bp):
TCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCCT
Found at i:54967 original size:16 final size:15
Alignment explanation
Indices: 54946--54976 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
54936 AATTTCTCAT
54946 TAAAATTTTCAGAAAA
1 TAAAATTTTC-GAAAA
54962 TAAAATTTTCGAAAA
1 TAAAATTTTCGAAAA
54977 GTAAGAAATC
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:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
TAAAATTTTCGAAAA
Found at i:55160 original size:258 final size:260
Alignment explanation
Indices: 54374--55339 Score: 1419
Period size: 257 Copynumber: 3.8 Consensus size: 260
54364 CCAGAACATT
* * * * **
54374 AAGATGATTTCATATGATAATTTGAAAAATGAGAAAGTGGTTTTCAAAGTTTCTCATTTAGTATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* * *
54439 TTCAGAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* * *
54504 TTCCAAAATTGGTAAG-CGCTACAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
*
54568 GGGTCATCTGTCAGTCTTTCGAGTAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
196 GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* ** *
54633 AAGATTCTTGAATATGATAATTTGAAAAATGAGAAA-CGATTTTCAAAGTTTCTCA-TTAAAATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* *
54696 TTCAAAAAATAAAATTTTTGAAAAATAAGAAATCAATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* *
54761 TTCCAAAATAGGTAAGTCA--TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
* * * * *
54824 GGGCCATCTGTCAGTCTTTCGAGCAAGATTATAAGTCCTTCGAGCCATCTATAAGACCTTCGGAC
196 GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* * *
54889 AAGATGCTTTCATATGATAATCTGAAAACTAAGAAAGCGATTTTCAAAATTTCTCA-TTAAAATT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* *
54953 TTCAGAAAATAAAATTTTCGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* ** * * * *
55018 TTCCAAAATTGGTAAG-CACTTTAGATCATCAGTAAATCTTTTGAGCATCATAATTAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
55082 GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
196 GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
* ** *
55147 AAGATGCTTTCATATTATAATTTGAAAAATAAGAAATTGATTTTCAAAGTTTCTCATTTAAATTT
1 AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
* * * **
55212 TTCAAAAAATGAAATTTGTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTGGCCTAGTAAACTAT
66 TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
* * *
55277 TTTCAAAATTGGTAAGTC-CTTTAGGCCATCAGTAAGTCTTTCGAGCAAGATGA-TAAATCCTTC
131 TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
55340 AGAGTTGTTT
Statistics
Matches: 630, Mismatches: 71, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
256 132 0.21
257 183 0.29
258 174 0.28
259 140 0.22
260 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (260 bp):
AAGATGCTTTCATATGATAATTTGAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAAAATT
TTCAAAAAATAAAATTTTTGAAAAGTAAGAAATCGATTTCCAAAGTTTCTTACCTAGTAAACTAT
TTCCAAAATTGGTAAGTCACTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
GGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGC
Found at i:55462 original size:3 final size:3
Alignment explanation
Indices: 55454--55487 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55444 CCCAGATCTT
55454 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55488 AGGCCCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.