Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009332.1 Hibiscus syriacus cultivar Beakdansim tig00113099_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: 474123
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:424861 original size:6 final size:6
Alignment explanation
Indices: 424832--424972 Score: 183
Period size: 6 Copynumber: 22.5 Consensus size: 6
424822 ATTGATGAAC
* *
424832 ATGGAGA ATGGAC ATGGAGA ATGGAC ATGGAGA ATGGAA ATGGAGA ATGGAA
1 ATGGA-A ATGGAA ATGGA-A ATGGAA ATGGA-A ATGGAA ATGGA-A ATGGAA
* * *
424884 ATGAAA ATGGAA ATGGAA ATGGAG ATGGAG ATGGAGA ATGGAA ATGGAA
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGA-A ATGGAA ATGGAA
424933 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGAGA ATG
1 ATGGAA ATGGAA ATGGAA ATGGAA ATGGAA ATGGA-A ATG
424973 ATTGATGTTG
Statistics
Matches: 121, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
6 91 0.75
7 30 0.25
ACGTcount: A:0.45, C:0.01, G:0.37, T:0.16
Consensus pattern (6 bp):
ATGGAA
Found at i:426705 original size:15 final size:15
Alignment explanation
Indices: 426687--426720 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
426677 GGAAGAGGAA
426687 GAAGTGGAATAAGAT
1 GAAGTGGAATAAGAT
426702 GAAGTGGAATAAGAT
1 GAAGTGGAATAAGAT
426717 GAAG
1 GAAG
426721 ATAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (15 bp):
GAAGTGGAATAAGAT
Found at i:432067 original size:26 final size:27
Alignment explanation
Indices: 432015--432072 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
432005 GACACTATAA
*
432015 TTTATATTAAAGATTAAATTTATAAAT
1 TTTAAATTAAAGATTAAATTTATAAAT
432042 TTTAAATTAAA-A-TAAATTTATAAAAT
1 TTTAAATTAAAGATTAAATTTAT-AAAT
432068 TTTAA
1 TTTAA
432073 CAAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.31
26 10 0.34
27 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTAAATTAAAGATTAAATTTATAAAT
Found at i:435999 original size:20 final size:19
Alignment explanation
Indices: 435948--435999 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
435938 GTGCGACAAC
*
435948 GGTTTACCTGAAAATTTAAA
1 GGTTGACCT-AAAATTTAAA
* **
435968 GATTGATTTAAAATTCTAAA
1 GGTTGACCTAAAATT-TAAA
435988 GGTTGACCTAAA
1 GGTTGACCTAAA
436000 TTGACCAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
GGTTGACCTAAAATTTAAA
Found at i:436448 original size:27 final size:27
Alignment explanation
Indices: 436410--436463 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
436400 AATCATCGAT
436410 AACTTATACACTTCACATTTTGAACAC
1 AACTTATACACTTCACATTTTGAACAC
436437 AACTTATACACTTCACATTTTGAACAC
1 AACTTATACACTTCACATTTTGAACAC
436464 TTTACATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (27 bp):
AACTTATACACTTCACATTTTGAACAC
Found at i:436463 original size:16 final size:16
Alignment explanation
Indices: 436417--436481 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
436407 GATAACTTAT
436417 ACACTTCACATTTTGA
1 ACACTTCACATTTTGA
* *
436433 ACAC--AAC-TTAT--
1 ACACTTCACATTTTGA
436444 ACACTTCACATTTTGA
1 ACACTTCACATTTTGA
*
436460 ACACTTTACATTTTGA
1 ACACTTCACATTTTGA
*
436476 TCACTT
1 ACACTT
436482 AATAGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
11 4 0.11
13 5 0.13
14 5 0.13
16 24 0.63
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
ACACTTCACATTTTGA
Found at i:438582 original size:2 final size:2
Alignment explanation
Indices: 438577--438629 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
438567 ATTTACGTGA
438577 AT AT AT AT AT AT 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 AT AT AT AT AT AT
438619 AT AT AT AT AT A
1 AT AT AT AT AT A
438630 CTTTAAGTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:440151 original size:3 final size:3
Alignment explanation
Indices: 440143--440172 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
440133 CGACGCTACA
440143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
440173 TATACAGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:450734 original size:62 final size:63
Alignment explanation
Indices: 450617--450738 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 63
450607 TTTTATTCAC
* **
450617 TTTTGCATTTTATTTTGTTTTAATTTTTGACATGATGCTTTGTTTGTTTATATTTTAGCCCTA
1 TTTTGCATTTTATTTTATTTTAATTTTTGACATGATGCTTTGCATGTTTATATTTTAGCCCTA
* *
450680 TTTT-CATTTTATTTTATTTTAATTTTTG-CATGTTGC-TTGCATGTTATTTCATTTTAGCC
1 TTTTGCATTTTATTTTATTTTAATTTTTGACATGATGCTTTGCATGTT-TAT-ATTTTAGCC
450739 ATTAATTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 7 0.13
61 9 0.17
62 32 0.62
63 4 0.08
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (63 bp):
TTTTGCATTTTATTTTATTTTAATTTTTGACATGATGCTTTGCATGTTTATATTTTAGCCCTA
Found at i:451417 original size:131 final size:131
Alignment explanation
Indices: 451172--451537 Score: 457
Period size: 131 Copynumber: 2.8 Consensus size: 131
451162 ATCGGTATTG
* * * * * *
451172 AGAATAGTAATATCTTTTCATTTCGATTGGAGTAATGAATAACTTCATTAAGGCATGAGAGGTCA
1 AGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * * **
451237 TTTATTCTCGATTGAAAATAATTAGACATTATCGTTTTCTGTCAAATCAATATTG-ATTTCTAAG
66 TTTATTATCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTT-TAAG
451301 AC
130 AC
* *
451303 GGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCA
1 AGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * *
451368 TTTATTATCGATTGGAAATCATTAGATATTATCTTTTTCACTCAGATCAATATTGAATTTTAAGA
66 TTTATTATCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGA
451433 C
131 C
* * * * * * *
451434 AAAATAGTGATATATCTTCGTTTCAATTGGAGTAATAAATGTCTGCTTTAAGGCATGAGAAGTTA
1 AGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * * *
451499 TTTA-TACCCGATTAGAAATAATTAGATAGTATTGTTTTC
66 TTTATTA-TCGATTGGAAATAATTAGATATTATCGTTTTC
451538 TCTCTTAAAA
Statistics
Matches: 202, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
130 2 0.01
131 196 0.97
132 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (131 bp):
AGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
TTTATTATCGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGA
C
Found at i:457063 original size:97 final size:97
Alignment explanation
Indices: 456895--457074 Score: 306
Period size: 97 Copynumber: 1.9 Consensus size: 97
456885 TTTCCTAGTA
* * *
456895 TATGAACTATGGTTACTTGAAATGTGTTATCAGGTATCCTGTTTTCACTGGGAAATATGATCGTT
1 TATGAACTATAGTTACCTGAAATGTGTTATCAGGTATCCTGTTTTCACTGGAAAATATGATCGTT
456960 ACTGATTTATGGATCATGGAACCTACTGGTTT
66 ACTGATTTATGGATCATGGAACCTACTGGTTT
* *
456992 TATGAACTATAGTTACCTGAAATGTGTTATCGGGTTTCCTGTTTTCACTGGAAAATATGATCGTT
1 TATGAACTATAGTTACCTGAAATGTGTTATCAGGTATCCTGTTTTCACTGGAAAATATGATCGTT
*
457057 ATTGATTTATGGATCATG
66 ACTGATTTATGGATCATG
457075 AAATCTATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 77 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (97 bp):
TATGAACTATAGTTACCTGAAATGTGTTATCAGGTATCCTGTTTTCACTGGAAAATATGATCGTT
ACTGATTTATGGATCATGGAACCTACTGGTTT
Found at i:459923 original size:30 final size:29
Alignment explanation
Indices: 459873--459971 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 29
459863 TCTTATTTTA
* * *
459873 ATTTATATCTTAATTACAAAAATATATTTT
1 ATTTTTATTTTAAATACAAAAATATA-TTT
459903 ATTTTTATTTTAAATACAAAAATATA--T
1 ATTTTTATTTTAAATACAAAAATATATTT
*
459930 ATTTTTATTTGAAAT--AAAAA-ATATTT
1 ATTTTTATTTTAAATACAAAAATATATTT
*
459956 ATTTTAATTTTAAATA
1 ATTTTTATTTTAAATA
459972 TTATAAGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
24 3 0.05
25 5 0.08
26 14 0.23
27 15 0.25
30 23 0.38
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTTTTATTTTAAATACAAAAATATATTT
Found at i:459949 original size:26 final size:27
Alignment explanation
Indices: 459873--459971 Score: 110
Period size: 26 Copynumber: 3.6 Consensus size: 27
459863 TCTTATTTTA
* * *
459873 ATTTATATCTTAATTACAAAAATATATTTT
1 ATTTTTATTTTAAATACAAAAATATA---T
459903 ATTTTTATTTTAAATACAAAAATATAT
1 ATTTTTATTTTAAATACAAAAATATAT
* *
459930 ATTTTTATTTGAAATA-AAAAATATTT
1 ATTTTTATTTTAAATACAAAAATATAT
*
459956 ATTTTAATTTTAAATA
1 ATTTTTATTTTAAATA
459972 TTATAAGAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 23 0.37
27 16 0.26
30 23 0.37
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTTTATTTTAAATACAAAAATATAT
Found at i:460013 original size:31 final size:31
Alignment explanation
Indices: 459961--460051 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 31
459951 TATTTATTTT
**
459961 AATTTTAAA-TATTATAAGAATAAAATATAA
1 AATTTTAAATTAAAATAAGAATAAAATATAA
* ** *
459991 AATTTTAAGTTAAGGTAAGAATAAAATATAT
1 AATTTTAAATTAAAATAAGAATAAAATATAA
*
460022 ATTTTTAAATTAAAATAAGAATAAAATATA
1 AATTTTAAATTAAAATAAGAATAAAATATA
460052 TTTTTGAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
30 8 0.16
31 43 0.84
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (31 bp):
AATTTTAAATTAAAATAAGAATAAAATATAA
Found at i:460052 original size:31 final size:31
Alignment explanation
Indices: 459974--460056 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
459964 TTTAAATATT
* * * *
459974 ATAAGAATAAAATATAAAATTTTAAGTTAAG
1 ATAAGAATAAAATATATATTTTTAAATTAAA
*
460005 GTAAGAATAAAATATATATTTTTAAATTAAA
1 ATAAGAATAAAATATATATTTTTAAATTAAA
460036 ATAAGAATAAAATATAT-TTTT
1 ATAAGAATAAAATATATATTTT
460057 GAGTTAAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 4 0.09
31 42 0.91
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (31 bp):
ATAAGAATAAAATATATATTTTTAAATTAAA
Found at i:460063 original size:29 final size:29
Alignment explanation
Indices: 459974--460106 Score: 140
Period size: 29 Copynumber: 4.4 Consensus size: 29
459964 TTTAAATATT
*
459974 ATAAGAATAAAATATAAAATTTTAAGTTAAG
1 ATAAGAATAAAATAT--ATTTTTAAGTTAAG
* * *
460005 GTAAGAATAAAATATATATTTTTAAATTAAA
1 ATAAGAAT-AAA-ATATATTTTTAAGTTAAG
*
460036 ATAAGAATAAAATATATTTTTGAGTTAAG
1 ATAAGAATAAAATATATTTTTAAGTTAAG
* * *
460065 ATAATAATAAATTATATTTAATAAGTTAAG
1 ATAAGAATAAAATATATTT-TTAAGTTAAG
*
460095 ATAAAAATAAAA
1 ATAAGAATAAAA
460107 GTTTTTAATG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 32 0.38
30 21 0.25
31 25 0.29
32 3 0.04
33 4 0.05
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (29 bp):
ATAAGAATAAAATATATTTTTAAGTTAAG
Found at i:460685 original size:7 final size:7
Alignment explanation
Indices: 460673--460710 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
460663 TCAAAGGAGT
460673 ACTTCCA
1 ACTTCCA
460680 ACTTCCA
1 ACTTCCA
460687 ACTTCCA
1 ACTTCCA
460694 ACTTCCA
1 ACTTCCA
460701 ACTTCCA
1 ACTTCCA
460708 ACT
1 ACT
460711 AGGCACTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (7 bp):
ACTTCCA
Found at i:461491 original size:14 final size:13
Alignment explanation
Indices: 461462--461494 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
461452 GATTTAATAA
461462 TTTTAT-ATTTAT
1 TTTTATAATTTAT
461474 TTTTATAATTTCAT
1 TTTTATAATTT-AT
461488 TTTTATA
1 TTTTATA
461495 CTATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 4 0.21
14 9 0.47
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATAATTTAT
Found at i:461568 original size:28 final size:27
Alignment explanation
Indices: 461500--461602 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 27
461490 TTATACTATA
* *
461500 ATATTAAATATTAAATTTAATATAACTAGAA
1 ATATTAAAT-TTAATTTTAAAAT-A-TA-AA
461531 ATATTAAATTTAATTTTAAAATATAAA
1 ATATTAAATTTAATTTTAAAATATAAA
* *
461558 TATATTAAATTTAGTTATAAAATATAAAA
1 -ATATTAAATTTAATTTTAAAATAT-AAA
461587 ATATTAAATTT-ATTTT
1 ATATTAAATTTAATTTT
461603 GATTGTAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.08
28 35 0.55
29 4 0.06
30 11 0.17
31 9 0.14
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTAAATTTAATTTTAAAATATAAA
Found at i:464468 original size:9 final size:9
Alignment explanation
Indices: 464449--464511 Score: 56
Period size: 9 Copynumber: 6.6 Consensus size: 9
464439 AATTGGACCT
464449 AAAATAGAAA
1 AAAATA-AAA
464459 AAAATTAAAA
1 AAAA-TAAAA
*
464469 TTAAA-AAAA
1 -AAAATAAAA
*
464478 CAAATAAATA
1 AAAATAAA-A
464488 AATAATAAAA
1 AA-AATAAAA
464498 AAAATAAAA
1 AAAATAAAA
464507 AAAAT
1 AAAAT
464512 GTTTTCGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 3 0.07
9 19 0.42
10 12 0.27
11 11 0.24
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:464576 original size:29 final size:29
Alignment explanation
Indices: 464543--464608 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
464533 AACTATATAT
464543 ATTATATAAATTTTCAAAAACGTTTT-AAA
1 ATTATATAAATTTTC-AAAACGTTTTCAAA
* *
464572 ATTATATATATTTTCAAAATGTTTTCAAA
1 ATTATATAAATTTTCAAAACGTTTTCAAA
*
464601 ACTATATA
1 ATTATATA
464609 TTATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTATATAAATTTTCAAAACGTTTTCAAA
Found at i:464633 original size:76 final size:74
Alignment explanation
Indices: 464572--464889 Score: 480
Period size: 76 Copynumber: 4.3 Consensus size: 74
464562 ACGTTTTAAA
464572 ATTATATATATTTTCAAAATGTTTTC-AAAACTATATATTATATATATTTTCAAAATGTTTTCAA
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAA
464636 AAACTATAT
66 AAACTATAT
*
464645 ATTATATATATTTTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTA
1 ATTATATATA--TTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTC
464710 AAAAACTATAT
64 AAAAACTATAT
* * * *
464721 A-TATATATATATTCGAAAGGTTTTAAAAAACTATATATTATATATATTTTTTCAAAATGTTTTC
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATA--TTTTCAAAATGTTTTC
464785 AAAAACTATAT
64 AAAAACTATAT
* * * *
464796 ATTATATATATTTTCAAATTTTTTTCAAAAACTATATATCATATACATTTTTTCAAAATGTTTTC
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATATAT--TATATATATTTTCAAAATGTTTTC
464861 -AAAACTATAT
64 AAAAACTATAT
464871 ATTATATATATTTTCAAAA
1 ATTATATATATTTTCAAAA
464890 AAATTTATAT
Statistics
Matches: 222, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
73 43 0.19
75 79 0.36
76 94 0.42
78 6 0.03
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (74 bp):
ATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAA
AAACTATAT
Found at i:464661 original size:39 final size:38
Alignment explanation
Indices: 464572--464889 Score: 465
Period size: 37 Copynumber: 8.5 Consensus size: 38
464562 ACGTTTTAAA
464572 ATTATATATA-TTTTCAAAATGTTTTC-AAAACTATAT
1 ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
464608 ATTATATATA-TTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
464645 ATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATA-TTTTTCAAAATGTTTTCAAAAACTATAT
*
464684 ATTATATATA-TTTTCAAAATGTTTTAAAAAACTATAT
1 ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
* * * *
464721 A-TATATATA-TATTCGAAAGGTTTTAAAAAACTATAT
1 ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
464757 ATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATA-TTTTTCAAAATGTTTTCAAAAACTATAT
* *
464796 ATTATATATA-TTTTCAAATTTTTTTCAAAAACTATAT
1 ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
* *
464833 ATCATATACATTTTTTCAAAATGTTTTC-AAAACTATAT
1 ATTATATATA-TTTTTCAAAATGTTTTCAAAAACTATAT
464871 ATTATATATA-TTTTCAAAA
1 ATTATATATATTTTTCAAAA
464890 AAATTTATAT
Statistics
Matches: 258, Mismatches: 16, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
36 68 0.26
37 88 0.34
38 18 0.07
39 84 0.33
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (38 bp):
ATTATATATATTTTTCAAAATGTTTTCAAAAACTATAT
Found at i:464703 original size:112 final size:112
Alignment explanation
Indices: 464572--464884 Score: 495
Period size: 112 Copynumber: 2.8 Consensus size: 112
464562 ACGTTTTAAA
464572 ATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAA
1 ATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAA
464637 AACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
66 AACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
* * * * *
464684 ATTATATATATTTTCAAAATGTTTTAAAAAACTATATA-TATATATATATTCGAAAGGTTTTAAA
1 ATTATATATATTTTCAAAATGTTTT-CAAAACTATATATTATATATATTTTCAAAATGTTTTCAA
464748 AAACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
65 AAACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
* * * *
464796 ATTATATATATTTTCAAATTTTTTTCAAAAACTATATATCATATACATTTTTTCAAAATGTTTTC
1 ATTATATATATTTTCAAAATGTTTTC-AAAACTATATAT--TATATATATTTTCAAAATGTTTTC
464861 -AAAACTATATATTATATATATTTT
63 AAAAACTATATATTATATATATTTT
464885 CAAAAAAATT
Statistics
Matches: 182, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
112 129 0.71
113 11 0.06
114 24 0.13
115 18 0.10
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (112 bp):
ATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAA
AACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
Found at i:464893 original size:39 final size:37
Alignment explanation
Indices: 464572--464889 Score: 480
Period size: 39 Copynumber: 8.5 Consensus size: 37
464562 ACGTTTTAAA
464572 ATTATATATATTTTCAAAATGTTTTC-AAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
464608 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
464645 ATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATA--TTTTCAAAATGTTTTCAAAAACTATAT
*
464684 ATTATATATATTTTCAAAATGTTTTAAAAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
* * * *
464721 A-TATATATATATTCGAAAGGTTTTAAAAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
464757 ATTATATATATTTTTTCAAAATGTTTTCAAAAACTATAT
1 ATTATATATA--TTTTCAAAATGTTTTCAAAAACTATAT
* *
464796 ATTATATATATTTTCAAATTTTTTTCAAAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
* *
464833 ATCATATACATTTTTTCAAAATGTTTTC-AAAACTATAT
1 AT--TATATATATTTTCAAAATGTTTTCAAAAACTATAT
464871 ATTATATATATTTTCAAAA
1 ATTATATATATTTTCAAAA
464890 AAATTTATAT
Statistics
Matches: 258, Mismatches: 16, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
36 74 0.29
37 82 0.32
38 12 0.05
39 90 0.35
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (37 bp):
ATTATATATATTTTCAAAATGTTTTCAAAAACTATAT
Done.