Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008106.1 Hibiscus syriacus cultivar Beakdansim tig00110641_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: 540947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:459205 original size:26 final size:26
Alignment explanation
Indices: 459176--459485 Score: 253
Period size: 26 Copynumber: 12.5 Consensus size: 26
459166 TGAATATTAT
*
459176 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
459202 TAATGA-TTAGTAATAAT--TTATAA
1 TAATGATTTAATAATAATCATTATAA
*
459225 TAATGA-TT--TAATAATGATT-T--
1 TAATGATTTAATAATAATCATTATAA
* * * *
459245 TAAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
*
459271 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
459297 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
459323 TAATGATTTAATGATAAT-A--ATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
459346 TAAT-A-ATAATAATAATAATAATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
459370 TAAT-A-ATAATAATAATAATAATAA
1 TAATGATTTAATAATAATCATTATAA
459394 TAATGATTTAATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
459420 TAATGATTTAATAGTAATGATT-TAG
1 TAATGATTTAATAATAATCATTATAA
* * *
459445 TAATGATTTTATAATAATGATTTAATAC
1 TAATGATTTAATAATAATCA-TT-ATAA
459473 TAATGATTTAATA
1 TAATGATTTAATA
459486 GTTATTACTA
Statistics
Matches: 240, Mismatches: 25, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.00
20 6 0.03
21 16 0.07
22 4 0.02
23 25 0.10
24 40 0.17
25 37 0.15
26 91 0.38
27 6 0.03
28 14 0.06
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:459299 original size:3 final size:3
Alignment explanation
Indices: 459281--459423 Score: 139
Period size: 3 Copynumber: 48.7 Consensus size: 3
459271 TAATGATTTG
* * * * * * * *
459281 ATA ATA ATC ATT ATA ATA ATG AT- TTA GTA ATA ATC ATT ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
459328 AT- TTA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
459375 ATA ATA ATA ATA ATA ATA ATA ATG AT- TTA ATA ATA ATC ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
459422 AT
1 AT
459424 GATTTAATAG
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
2 3 0.03
3 113 0.97
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:459477 original size:39 final size:40
Alignment explanation
Indices: 459079--459485 Score: 175
Period size: 38 Copynumber: 10.3 Consensus size: 40
459069 TATTAATATT
** * *
459079 TAATGATTTGGTAGTAATGATTTAGTAAT--T-ATTACTAA
1 TAATGATTTAATAATAATGATTTAATAATAATCATTA-TAA
* * * *
459117 TAATGAAATT-ATAATAATGATTTAATAATGAT-TTTAATATT
1 TAATG-ATTTAATAATAATGATTTAATAATAATCATT-ATA-A
*
459158 TAATGATTTGAATATTATTAATGATTTGATAATAATCATTATAA
1 TAATGATTT-AATA--A-TAATGATTTAATAATAATCATTATAA
* *
459202 TAATGA-TTAGTAAT-A--ATTT-ATAATAATGATT-TAA
1 TAATGATTTAATAATAATGATTTAATAATAATCATTATAA
* * *
459236 TAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTTGATAA
1 TAATGA-TTTAATA-ATAATGATTT-A--A--TAATAATCA-TT-ATAA
* *
459285 TAATCA-TT-ATAATAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATGATTTAATAATAATCATTATAA
* *
459323 TAATGATTTAATGATAAT-A-ATAATAATAAT-A--ATAA
1 TAATGATTTAATAATAATGATTTAATAATAATCATTATAA
* * * *
459358 TAAT-A-ATAATAATAAT-A-ATAATAATAATAATAATAA
1 TAATGATTTAATAATAATGATTTAATAATAATCATTATAA
* * *
459394 TAATGATTTAATAATAATCA-TT-ATAATAATGATTTAATAG
1 TAATGATTTAATAATAATGATTTAATAATAATCA-TT-ATAA
* * * *
459434 TAATGA-TT--TAGTAATGATTTTATAATAATGATTTAATAC
1 TAATGATTTAATAATAATGATTTAATAATAATCA-TT-ATAA
459473 TAATGATTTAATA
1 TAATGATTTAATA
459486 GTTATTACTA
Statistics
Matches: 293, Mismatches: 35, Indels: 78
0.72 0.09 0.19
Matches are distributed among these distances:
33 21 0.07
34 11 0.04
35 19 0.06
36 17 0.06
37 10 0.03
38 62 0.21
39 37 0.13
40 38 0.13
41 6 0.02
42 8 0.03
43 2 0.01
44 9 0.03
45 28 0.10
46 13 0.04
47 4 0.01
49 8 0.03
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (40 bp):
TAATGATTTAATAATAATGATTTAATAATAATCATTATAA
Found at i:459479 original size:14 final size:14
Alignment explanation
Indices: 459114--459485 Score: 214
Period size: 14 Copynumber: 27.1 Consensus size: 14
459104 TAATTATTAC
*
459114 TAATAATGAAATT-A
1 TAATAATG-ATTTAA
459128 TAATAATGATTTAA
1 TAATAATGATTTAA
*
459142 TAATGAT--TTTAA
1 TAATAATGATTTAA
*
459154 TATTTAATGATTTGAA
1 TA-ATAATGATTT-AA
*
459170 TATTATTAATGATTTGA
1 TA--A-TAATGATTTAA
*
459187 TAATAATCA-TT-A
1 TAATAATGATTTAA
*
459199 TAATAATGA-TTAG
1 TAATAATGATTTAA
459212 TAAT-A--ATTT-A
1 TAATAATGATTTAA
459222 TAATAATGATTTAA
1 TAATAATGATTTAA
*
459236 TAATGAT--TTTAA
1 TAATAATGATTTAA
*
459248 TATTTAATGATTTGATGA
1 TA-ATAATGATTT-A--A
* *
459266 TTTAGTAATGATTTGA
1 --TAATAATGATTTAA
*
459282 TAATAATCA-TT-A
1 TAATAATGATTTAA
*
459294 TAATAATGATTTAG
1 TAATAATGATTTAA
*
459308 TAATAATCA-TT-A
1 TAATAATGATTTAA
459320 TAATAATGATTTAA
1 TAATAATGATTTAA
* *
459334 TGATAAT-A-ATAA
1 TAATAATGATTTAA
* *
459346 TAATAATAATAATAA
1 TAATAATGAT-TTAA
* *
459361 TAATAATAATAATAA
1 TAATAATGAT-TTAA
* *
459376 TAATAATAATAATAA
1 TAATAATGAT-TTAA
459391 TAATAATGATTTAA
1 TAATAATGATTTAA
*
459405 TAATAATCA-TT-A
1 TAATAATGATTTAA
459417 TAATAATGATTTAA
1 TAATAATGATTTAA
*
459431 TAGTAATGA-TT--
1 TAATAATGATTTAA
* *
459442 TAGTAATGATTTTA
1 TAATAATGATTTAA
459456 TAATAATGATTTAA
1 TAATAATGATTTAA
*
459470 TACTAATGATTTAA
1 TAATAATGATTTAA
459484 TA
1 TA
459486 GTTATTACTA
Statistics
Matches: 292, Mismatches: 33, Indels: 66
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.02
11 12 0.04
12 63 0.22
13 35 0.12
14 96 0.33
15 50 0.17
16 6 0.02
17 4 0.01
18 10 0.03
19 9 0.03
20 2 0.01
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (14 bp):
TAATAATGATTTAA
Found at i:459634 original size:24 final size:22
Alignment explanation
Indices: 459603--459661 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
459593 TGATTTGATA
*
459603 TTAATGATTTAATAATTATTAT
1 TTAATGATTTAATAATTAATAT
*
459625 TAATAATGATTT-ATTATTAATAT
1 T--TAATGATTTAATAATTAATAT
*
459648 TTAATTATTTAATA
1 TTAATGATTTAATA
459662 CTAATGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 8 0.27
22 3 0.10
23 10 0.33
24 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (22 bp):
TTAATGATTTAATAATTAATAT
Found at i:459655 original size:17 final size:17
Alignment explanation
Indices: 459615--459656 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
459605 AATGATTTAA
459615 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
459632 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
459649 TAATTATT
1 TAATTATT
459657 TAATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:459690 original size:59 final size:56
Alignment explanation
Indices: 459572--459698 Score: 130
Period size: 59 Copynumber: 2.2 Consensus size: 56
459562 TCGAATTTAT
* * **
459572 TAATGATTTTTAAATATTTAATGATTTGATATTAATGATTTAATAATTATTATTAA
1 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTAATAATTAAAATTAA
* *
459628 TAATGATTTATTATTAATATTTAATTATTTAATACTAATGATTACTAGTAA-TAAAATTATAA
1 TAATGATTT-TTA--AATATTTAATGATTTAATACTAATGATT--TAATAATTAAAA-T-TAA
459690 TAATGATTT
1 TAATGATTT
459699 GATACTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 25 0.43
60 3 0.05
61 6 0.10
62 12 0.21
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTAATAATTAAAATTAA
Found at i:462001 original size:22 final size:22
Alignment explanation
Indices: 461976--462024 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
461966 ACAACTAATA
* *
461976 AACTATTCTTTAATATAACTTT
1 AACTATTCTCTAATATAACTCT
461998 AACTATTCTCTAATATAACTCT
1 AACTATTCTCTAATATAACTCT
462020 AACTA
1 AACTA
462025 ATAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (22 bp):
AACTATTCTCTAATATAACTCT
Found at i:462002 original size:30 final size:29
Alignment explanation
Indices: 461968--462060 Score: 110
Period size: 30 Copynumber: 3.4 Consensus size: 29
461958 TCCCTTAAAC
461968 AACTAATAAACTATTCTTTAATATAAC-T
1 AACTAATAAACTATTCTTTAATATAACTT
*
461996 ---T--T-AACTATTCTCTAATATAACTCT
1 AACTAATAAACTATTCTTTAATATAACT-T
462020 AACTAATAAACTATTCTTTAATATAACTT
1 AACTAATAAACTATTCTTTAATATAACTT
462049 AAACTAATAAAC
1 -AACTAATAAAC
462061 GATTTTAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
22 18 0.33
23 1 0.02
24 1 0.02
25 1 0.02
27 1 0.02
29 2 0.04
30 30 0.56
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (29 bp):
AACTAATAAACTATTCTTTAATATAACTT
Found at i:462293 original size:21 final size:21
Alignment explanation
Indices: 462269--462308 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
462259 TTTTTATATG
*
462269 ATATAACTTAAACTTACAATA
1 ATATAACTTAAACTAACAATA
462290 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
462309 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:462537 original size:54 final size:56
Alignment explanation
Indices: 462406--462537 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 56
462396 TTATTCTTTT
* * * *
462406 ATATAACTTAAACTAATAAACT-ATTTTTTATTATAATAAAACTTAAACTACTAATA
1 ATATAACTT-AACTATTTAACTAATTTTTTATTATAATAAAACTTAAACAACCAATA
*
462462 A-ACTAA-TTAACTATTTAACTAATTTTTTA-TATAATATAAA-TTCAACAACCAA-A
1 ATA-TAACTTAACTATTTAACTAATTTTTTATTATAATA-AAACTTAAACAACCAATA
462515 ATATAACTTAACTATTTAACTAA
1 ATATAACTTAACTATTTAACTAA
462538 CTACAAACTA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
53 5 0.08
54 43 0.65
55 14 0.21
56 4 0.06
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (56 bp):
ATATAACTTAACTATTTAACTAATTTTTTATTATAATAAAACTTAAACAACCAATA
Found at i:462557 original size:27 final size:29
Alignment explanation
Indices: 462522--462586 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
462512 AAAATATAAC
*
462522 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
462549 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
462577 TTAATTATTT
1 TTAAATATTT
462587 TTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:462714 original size:21 final size:21
Alignment explanation
Indices: 462640--462700 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
462630 TGTATGTATG
462640 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
462661 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
462682 ATATAGCTTAAACTAACAA
1 ATATAACTTAAACTAACAA
462701 ACTAATTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:462742 original size:31 final size:31
Alignment explanation
Indices: 462699--462764 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
462689 TTAAACTAAC
* *
462699 AAACTAATTAACTAAAATTTTGTTTTACCTT
1 AAACTAACTAACTAAAATTTTATTTTACCTT
462730 AAACTAACTAACTAAAATTTTATTTTACCTT
1 AAACTAACTAACTAAAATTTTATTTTACCTT
462761 AAAC
1 AAAC
462765 CATAAACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.41
Consensus pattern (31 bp):
AAACTAACTAACTAAAATTTTATTTTACCTT
Found at i:462813 original size:9 final size:9
Alignment explanation
Indices: 462781--462818 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
462771 CTAACAAACT
462781 AATAATTTAA
1 AATAA-TTAA
462791 AATAA-TAA
1 AATAATTAA
*
462799 ACTAATTAA
1 AATAATTAA
462808 AATAATTAA
1 AATAATTAA
462817 AA
1 AA
462819 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:463029 original size:23 final size:23
Alignment explanation
Indices: 462998--463081 Score: 116
Period size: 23 Copynumber: 3.6 Consensus size: 23
462988 GAGCTGAAGG
462998 GCTGCAATAATGCAACAATAAGT
1 GCTGCAATAATGCAACAATAAGT
*
463021 GCTGGAATAATGCAGTA-AATAAGT
1 GCTGCAATAATGCA--ACAATAAGT
* *
463045 GTTGCAATAATACAACAATAAGT
1 GCTGCAATAATGCAACAATAAGT
463068 GCTGCAATAATGCA
1 GCTGCAATAATGCA
463082 GATGAATTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 18 0.35
25 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (23 bp):
GCTGCAATAATGCAACAATAAGT
Found at i:463286 original size:38 final size:38
Alignment explanation
Indices: 463235--463307 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
463225 TACCCATGTG
463235 CACCGAACATTGCATGAGCCATGCACAACACCACACAA
1 CACCGAACATTGCATGAGCCATGCACAACACCACACAA
*
463273 CACCGAACGTTGCATGAGCCATGCACAACACCACA
1 CACCGAACATTGCATGAGCCATGCACAACACCACA
463308 TAGGTCGCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.37, C:0.37, G:0.15, T:0.11
Consensus pattern (38 bp):
CACCGAACATTGCATGAGCCATGCACAACACCACACAA
Found at i:463348 original size:27 final size:25
Alignment explanation
Indices: 463291--463342 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
463281 GTTGCATGAG
*
463291 CCATGCACAACACCACATAGGTCGC
1 CCATGCACAACACCACACAGGTCGC
*
463316 CCATGCAGAACACCACACAGGTCGC
1 CCATGCACAACACCACACAGGTCGC
463341 CC
1 CC
463343 GGATGCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.42, G:0.17, T:0.10
Consensus pattern (25 bp):
CCATGCACAACACCACACAGGTCGC
Found at i:463370 original size:29 final size:29
Alignment explanation
Indices: 463337--463417 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
463327 ACCACACAGG
*
463337 TCGCCCGGATGCCATGGCGACCTCTAAGC
1 TCGCCCGGATGCCATGGCGACCTCCAAGC
* * *
463366 TCGCCCAGATGCCATGTCAACCTCCAAGC
1 TCGCCCGGATGCCATGGCGACCTCCAAGC
*
463395 TCGCCCGGATGGCATGGCGACCT
1 TCGCCCGGATGCCATGGCGACCT
463418 ACAACTCACT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (29 bp):
TCGCCCGGATGCCATGGCGACCTCCAAGC
Found at i:466638 original size:18 final size:18
Alignment explanation
Indices: 466612--466646 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
466602 AACCTAATTA
466612 ATAAATAAAAATAAAAAC
1 ATAAATAAAAATAAAAAC
*
466630 ATAACTAAAAATAAAAA
1 ATAAATAAAAATAAAAA
466647 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAATAAAAATAAAAAC
Found at i:468378 original size:135 final size:133
Alignment explanation
Indices: 468128--468407 Score: 373
Period size: 135 Copynumber: 2.1 Consensus size: 133
468118 GTGAAACGAG
* ** *
468128 ATTAGAAATGTTAATCCCTCAAGTGAGATTTTGCTAATTTGAAATACTAAGAATCGAGCAAAGGT
1 ATTAGAAATGTTAATCCCTCAAGTGAGATGTTGCTAATTCAAAATACCAAGAATCGAGCAAAGGT
* * * *
468193 TGAACAAGTTCTTCTCATTGGAAACTTTTTCTCCCTATATAGGATGAGTTCTTCTCATTATGAAA
66 TGAACAAGTTATTCTCATTCGAAACTTCTTCTCCCTATATAGGATAAGTTCTTCTCA-TATGAAA
468258 TCTCC
130 TCT-C
* * * ** *
468263 ATTAGAAATGTTAATCCCTCAAGTGAGGTGTTGCTGATTCAAAATGCCGTGAATTGAGCAAAGGT
1 ATTAGAAATGTTAATCCCTCAAGTGAGATGTTGCTAATTCAAAATACCAAGAATCGAGCAAAGGT
* *
468328 TGAACAAGTTATTCTCATTACG-AACTTCTTCTCCCTATATCGGATAAGTTCTTCTCATATGAAC
66 TGAACAAGTTATTCTCATT-CGAAACTTCTTCTCCCTATATAGGATAAGTTCTTCTCATATGAAA
468392 TCTC
130 TCTC
*
468396 ATTGGAAATGTT
1 ATTAGAAATGTT
468408 GATCAGTTTA
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 12 0.09
134 9 0.07
135 105 0.83
136 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (133 bp):
ATTAGAAATGTTAATCCCTCAAGTGAGATGTTGCTAATTCAAAATACCAAGAATCGAGCAAAGGT
TGAACAAGTTATTCTCATTCGAAACTTCTTCTCCCTATATAGGATAAGTTCTTCTCATATGAAAT
CTC
Found at i:480227 original size:25 final size:25
Alignment explanation
Indices: 480199--480255 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
480189 ACCTAATTAA
480199 ATAAATAAAAAATAGA-AAACAT-AAC
1 ATAAATAAAAAATA-ATAAA-ATAAAC
*
480224 ATAAATAATAAATAATAAAATAAAC
1 ATAAATAAAAAATAATAAAATAAAC
480249 ATAAATA
1 ATAAATA
480256 TCATGATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.10
25 26 0.90
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (25 bp):
ATAAATAAAAAATAATAAAATAAAC
Found at i:490236 original size:20 final size:20
Alignment explanation
Indices: 490211--490264 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
490201 ATCGGAGGGA
490211 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
490231 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
*
490251 ACCAATTCCCCCCA
1 ACCGATTCCCCCCA
490265 CTGTTCAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.15
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:501406 original size:20 final size:20
Alignment explanation
Indices: 501378--501430 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
501368 AGTACATTTT
* *
501378 GGATCGATCTCTTCAAAAAA
1 GGATTGATCCCTTCAAAAAA
* *
501398 GGATTGATCCCTTTAGAAAA
1 GGATTGATCCCTTCAAAAAA
501418 GGATTGATCCCTT
1 GGATTGATCCCTT
501431 GACCAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (20 bp):
GGATTGATCCCTTCAAAAAA
Found at i:504188 original size:22 final size:21
Alignment explanation
Indices: 504160--504213 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
504150 TACTCGGGGT
* *
504160 AGTATCAATACCCCAGTAGAGG
1 AGTATCAATACCCCAATA-AAG
* *
504182 AGTATCAGTACTCCAATAAAG
1 AGTATCAATACCCCAATAAAG
504203 AGTATCAATAC
1 AGTATCAATAC
504214 TACCTGGTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTATCAATACCCCAATAAAG
Found at i:510071 original size:15 final size:15
Alignment explanation
Indices: 510030--510071 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
510020 CTCGAACAAC
*
510030 TTCTTTCTTCTTCTA
1 TTCTTTCTTTTTCTA
*
510045 TTCTTT-TATTTTCTT
1 TTCTTTCT-TTTTCTA
510060 TTCTTTCTTTTT
1 TTCTTTCTTTTT
510072 TCGAGCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.04
15 21 0.91
16 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:522862 original size:84 final size:83
Alignment explanation
Indices: 522680--522863 Score: 223
Period size: 84 Copynumber: 2.2 Consensus size: 83
522670 TATCTCTATG
* * *
522680 AATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTTATTATATTTT
1 AATTTAAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTA-TATATATT
*
522745 ATCTTATCTTTGTTTTAGA
65 ATCTTAGCTTTGTTTTAGA
* *
522764 AATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATATTA-TTTTA-ATA-ATTA
1 AATTTAAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATATATATTA
*
522826 TCTTTAGC-TTGTTTTTAGG
66 TC-TTAGCTTTG-TTTTAGA
522845 AATTTGAAGGTTATAAATA
1 AATTT-AA-GTT-TAAATA
522864 CCTTCTCAGG
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
80 8 0.09
81 18 0.20
82 1 0.01
83 8 0.09
84 54 0.61
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.53
Consensus pattern (83 bp):
AATTTAAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATATATATTA
TCTTAGCTTTGTTTTAGA
Found at i:532144 original size:18 final size:18
Alignment explanation
Indices: 532118--532162 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
532108 GATGAGTTGA
*
532118 GAAAAAAATGATAGGATC
1 GAAATAAATGATAGGATC
532136 GAAATAAATGATAGGATC
1 GAAATAAATGATAGGATC
*
532154 GAAGTAAAT
1 GAAATAAAT
532163 TTCAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (18 bp):
GAAATAAATGATAGGATC
Found at i:532871 original size:163 final size:164
Alignment explanation
Indices: 532563--532889 Score: 647
Period size: 163 Copynumber: 2.0 Consensus size: 164
532553 AGATAAAAAA
532563 TAAAAAGATTGTCGATTTTCATTTAGAAACCTTAAGGAATGCTAAATCTATGAAGATTATTTTAA
1 TAAAAAGATTGTCGATTTTCATTTAGAAACCTTAAGGAATGCTAAATCTATGAAGATTATTTTAA
532628 AAGTTTTTTTTTTCTTATTCCTCAAAATTGTCCGTCCAGCTCAGTTGGTAGAGAGCAAGGCTCTT
66 AAGTTTTTTTTTTCTTATTCCTCAAAATTGTCCGTCCAGCTCAGTTGGTAGAGAGCAAGGCTCTT
532693 AACCTTGTGGTCGTGAGATTGAGTCCCATGGTGG
131 AACCTTGTGGTCGTGAGATTGAGTCCCATGGTGG
532727 TAAAAAGATTGTCGATTTTCATTTAGAAACCTTAAGGAATGCTAAATCTATGAAGATTATTTTAA
1 TAAAAAGATTGTCGATTTTCATTTAGAAACCTTAAGGAATGCTAAATCTATGAAGATTATTTTAA
532792 AAG-TTTTTTTTTCTTATTCCTCAAAATTGTCCGTCCAGCTCAGTTGGTAGAGAGCAAGGCTCTT
66 AAGTTTTTTTTTTCTTATTCCTCAAAATTGTCCGTCCAGCTCAGTTGGTAGAGAGCAAGGCTCTT
532856 AACCTTGTGGTCGTGAGATTGAGTCCCATGGTGG
131 AACCTTGTGGTCGTGAGATTGAGTCCCATGGTGG
532890 GCAATTTATA
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 95 0.58
164 68 0.42
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (164 bp):
TAAAAAGATTGTCGATTTTCATTTAGAAACCTTAAGGAATGCTAAATCTATGAAGATTATTTTAA
AAGTTTTTTTTTTCTTATTCCTCAAAATTGTCCGTCCAGCTCAGTTGGTAGAGAGCAAGGCTCTT
AACCTTGTGGTCGTGAGATTGAGTCCCATGGTGG
Found at i:534185 original size:24 final size:25
Alignment explanation
Indices: 534154--534200 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
534144 TTCAAATTAG
534154 TTGATTTTTT-TAAAAAATAAAAAA
1 TTGATTTTTTATAAAAAATAAAAAA
534178 TTGATTTTTTATAAAAAATAAAA
1 TTGATTTTTTATAAAAAATAAAA
534201 TAACAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TTGATTTTTTATAAAAAATAAAAAA
Found at i:540017 original size:30 final size:30
Alignment explanation
Indices: 539983--540050 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
539973 TTTTGTTTTA
* * *
539983 ATTCATTGGCATTGACTTCACTTTGCATAC
1 ATTCATTCGCATTCACTTCACTTTGCACAC
* *
540013 ATTCATTCTCTTTCACTTCACTTTGCACAC
1 ATTCATTCGCATTCACTTCACTTTGCACAC
*
540043 TTTCATTC
1 ATTCATTC
540051 TCTTCCAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTCATTCGCATTCACTTCACTTTGCACAC
Found at i:540051 original size:30 final size:30
Alignment explanation
Indices: 539997--540054 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
539987 ATTGGCATTG
*
539997 ACTTCACTTTGCATACATTCATTCTCTTTC
1 ACTTCACTTTGCACACATTCATTCTCTTTC
*
540027 ACTTCACTTTGCACACTTTCATTCTCTT
1 ACTTCACTTTGCACACATTCATTCTCTT
540055 CCAATGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (30 bp):
ACTTCACTTTGCACACATTCATTCTCTTTC
Done.