Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008026.1 Hibiscus syriacus cultivar Beakdansim tig00110502_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: 525378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 4 of 4
Found at i:466130 original size:28 final size:27
Alignment explanation
Indices: 466099--466161 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
466089 AGTTGATACA
*
466099 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
466127 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
466155 ATATTTT
1 ATATTTT
466162 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:466261 original size:16 final size:18
Alignment explanation
Indices: 466240--466273 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
466230 ATTTCTTATT
466240 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
466256 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
466274 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:466420 original size:21 final size:21
Alignment explanation
Indices: 466396--466438 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
466386 TATTACCTTA
466396 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
466417 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
466438 A
1 A
466439 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:466456 original size:35 final size:35
Alignment explanation
Indices: 466407--466492 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
466397 ATTGAAGTAT
** * *
466407 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
466442 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
466477 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
466493 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:470503 original size:4 final size:4
Alignment explanation
Indices: 470494--470535 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
470484 TCCCTTCAAT
**
470494 TAAA TAAA TAAA TAAA TAAA TTCA -AAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
470536 TCCATAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 1 0.03
4 32 0.97
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:470523 original size:19 final size:19
Alignment explanation
Indices: 470499--470586 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 19
470489 TCAATTAAAT
470499 AAATAAATAAATAAATTCA
1 AAATAAATAAATAAATTCA
470518 AAATAAATAAATAAA-T-A
1 AAATAAATAAATAAATTCA
* *
470535 ATCCAT-AATAAAT-TATTACAA
1 A--AATAAATAAATAAATT-C-A
470556 AAATAAATAAAGT--ATTCA
1 AAATAAATAAA-TAAATTCA
470574 AAATAAATAAATA
1 AAATAAATAAATA
470587 TTTCAAAGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
17 4 0.07
18 21 0.37
19 20 0.35
20 9 0.16
21 3 0.05
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (19 bp):
AAATAAATAAATAAATTCA
Found at i:475924 original size:4 final size:4
Alignment explanation
Indices: 475915--475997 Score: 51
Period size: 4 Copynumber: 19.0 Consensus size: 4
475905 TCCCTTCAAT
*
475915 TAAA TAAA TAATT TAAAA TAAA TAAA TAAA TAAA TTTGAAA TAAA TAAA
1 TAAA TAAA TAA-A T-AAA TAAA TAAA TAAA TAAA --T-AAA TAAA TAAA
* * *
475964 TAAT TCATAA TAAA TTAT TACAA -AAA TAAA TAAA
1 TAAA T-A-AA TAAA TAAA TA-AA TAAA TAAA TAAA
475998 ATATTCAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
3 2 0.03
4 46 0.74
5 6 0.10
6 5 0.08
7 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:475956 original size:23 final size:22
Alignment explanation
Indices: 475915--475966 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
475905 TCCCTTCAAT
475915 TAAATAAATAATTTAAAATAAA
1 TAAATAAATAATTTAAAATAAA
*
475937 TAAATAAATAAATTTGAAATAAA
1 TAAATAAAT-AATTTAAAATAAA
475960 TAAATAA
1 TAAATAA
475967 TTCATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATAAATAATTTAAAATAAA
Found at i:475997 original size:20 final size:18
Alignment explanation
Indices: 475934--476016 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
475924 AATTTAAAAT
* **
475934 AAATAAATAAATAAATTTG
1 AAATAAATAAAT-TATTCA
*
475953 AAATAAATAAATAATTC-
1 AAATAAATAAATTATTCA
475970 --AT-AATAAATTATTACAA
1 AAATAAATAAATTATT-C-A
*
475987 AAATAAATAAAATATTCA
1 AAATAAATAAATTATTCA
*
476005 AAATAAGTAAAT
1 AAATAAATAAAT
476017 ATTTCAAAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.19
15 3 0.06
18 15 0.28
19 15 0.28
20 10 0.19
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATAAATAAATTATTCA
Found at i:476018 original size:17 final size:19
Alignment explanation
Indices: 475972--476024 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
475962 AATAATTCAT
* *
475972 AATAAATTATTACAAAAATA
1 AATAAAATATTTC-AAAATA
475992 AATAAAATA-TTCAAAATA
1 AATAAAATATTTCAAAATA
*
476010 AGT-AAATATTTCAAA
1 AATAAAATATTTCAAA
476025 GTAATTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 14 0.48
19 2 0.07
20 8 0.28
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (19 bp):
AATAAAATATTTCAAAATA
Found at i:476710 original size:36 final size:36
Alignment explanation
Indices: 476645--476729 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
476635 TTAATATCAA
* * *
476645 TTTAAAATTAAAATAATACACGCCGATTAATATGGG
1 TTTAAAATTAAAACAATACACACCAATTAATATGGG
** * *
476681 TTTAAAATTAAAACAATACGTACCAATTAATATTGT
1 TTTAAAATTAAAACAATACACACCAATTAATATGGG
476717 TTTAAAATTAAAA
1 TTTAAAATTAAAA
476730 TGATGTATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (36 bp):
TTTAAAATTAAAACAATACACACCAATTAATATGGG
Found at i:478272 original size:13 final size:13
Alignment explanation
Indices: 478254--478281 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
478244 CTAATCGATT
478254 ATATATTCATGAG
1 ATATATTCATGAG
478267 ATATATTCATGAG
1 ATATATTCATGAG
478280 AT
1 AT
478282 CAATATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
ATATATTCATGAG
Found at i:482035 original size:15 final size:16
Alignment explanation
Indices: 482004--482037 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
481994 TTGTTAGGAA
482004 TTAAGAGTTAGAATATT
1 TTAAGAGTTA-AATATT
482021 TTAAGAGTT-AATATT
1 TTAAGAGTTAAATATT
482036 TT
1 TT
482038 TTTATTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
TTAAGAGTTAAATATT
Found at i:491511 original size:241 final size:242
Alignment explanation
Indices: 491088--491570 Score: 959
Period size: 241 Copynumber: 2.0 Consensus size: 242
491078 TTCTGGCTTT
491088 TCTTTTGCTTTAGGTTTTCAGTTTAATAAAAATATTTTTTCTTCATCTTTTTTTTCTACACGCTT
1 TCTTTTGCTTTAGGTTTTCAGTTTAATAAAAATATTTTTTCTTCATCTTTTTTTTCTACACGCTT
491153 GGATAAACTTTTCTTTAACTGATAGCTAAGAGAAGACTCGATCCATTCTCGTGAGAATTGCAAAT
66 GGATAAACTTTTCTTTAACTGATAGCTAAGAGAAGACTCGATCCATTCTCGTGAGAATTGCAAAT
491218 GTACTTCAAATCTTTAGATTTTTTTCTTGATTTTCAGCATAAAGGGGAGGCAATCAACATTTCTT
131 GTACTTCAAATCTTTAGATTTTTTTCTTGATTTTCAGCATAAAGGGGAGGCAATCAACATTTCTT
491283 TAAACATCTCAACATTTTCAATCC-AAGAGTGCACATTAGCTTGATC
196 TAAACATCTCAACATTTTCAATCCAAAGAGTGCACATTAGCTTGATC
491329 TCTTTTGCTTTAGGTTTTCAGTTTAATAAAAATATTTTTTCTTCATCTTTTTTTTCTACACGCTT
1 TCTTTTGCTTTAGGTTTTCAGTTTAATAAAAATATTTTTTCTTCATCTTTTTTTTCTACACGCTT
491394 GGATAAACTTTTCTTTAACTGATAGCTAAGAGAAGACTCGATCCATTCTCGTGAGAATTGCAAAT
66 GGATAAACTTTTCTTTAACTGATAGCTAAGAGAAGACTCGATCCATTCTCGTGAGAATTGCAAAT
491459 GTACTTCAAATCTTTAGATTTTTTTCTTGATTTTCAGCATAAAGGGGAGGCAATCAACATTTCTT
131 GTACTTCAAATCTTTAGATTTTTTTCTTGATTTTCAGCATAAAGGGGAGGCAATCAACATTTCTT
491524 TAAACATCTCAACATTTTCAATCCAAAGAGTGCACATTAGCTTGATC
196 TAAACATCTCAACATTTTCAATCCAAAGAGTGCACATTAGCTTGATC
491571 GACGTTGTGA
Statistics
Matches: 241, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
241 219 0.91
242 22 0.09
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (242 bp):
TCTTTTGCTTTAGGTTTTCAGTTTAATAAAAATATTTTTTCTTCATCTTTTTTTTCTACACGCTT
GGATAAACTTTTCTTTAACTGATAGCTAAGAGAAGACTCGATCCATTCTCGTGAGAATTGCAAAT
GTACTTCAAATCTTTAGATTTTTTTCTTGATTTTCAGCATAAAGGGGAGGCAATCAACATTTCTT
TAAACATCTCAACATTTTCAATCCAAAGAGTGCACATTAGCTTGATC
Found at i:494593 original size:23 final size:23
Alignment explanation
Indices: 494567--494611 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
494557 AATAATATTT
494567 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
494590 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
494612 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:494963 original size:14 final size:14
Alignment explanation
Indices: 494935--494978 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
494925 CCGGAAATGT
* *
494935 AATTCATTTTTCAG
1 AATTCAATTTCCAG
*
494949 AATTTAATTTCCAG
1 AATTCAATTTCCAG
*
494963 AATTCAATTTCTAG
1 AATTCAATTTCCAG
494977 AA
1 AA
494979 AACCAATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:499080 original size:3 final size:3
Alignment explanation
Indices: 499072--499140 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
499062 CCTATTGTTT
* * *
499072 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TCA TTA TTA TCA -CA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
**
499119 TT- TTA TTA TTA CCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
499141 TTTTGATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:499354 original size:4 final size:4
Alignment explanation
Indices: 499345--499379 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
499335 TTTTATTATT
*
499345 TTTA TTTA TTTA TTTA TTATC TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TT
499380 GTTATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:499356 original size:17 final size:17
Alignment explanation
Indices: 499336--499394 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
499326 TTTTCTTCAT
*
499336 TTTA-TTATTTTTATTTA
1 TTTATTTATTATT-TTTA
*
499353 TTTATTTATTATCTTTA
1 TTTATTTATTATTTTTA
* *
499370 TTTATTTATTGTTATTA
1 TTTATTTATTATTTTTA
499387 TTT-TTTAT
1 TTTATTTAT
499395 ATACTTTCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 5 0.14
17 25 0.69
18 6 0.17
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTATTTATTATTTTTA
Found at i:499362 original size:21 final size:22
Alignment explanation
Indices: 499334--499391 Score: 91
Period size: 21 Copynumber: 2.6 Consensus size: 22
499324 CATTTTCTTC
499334 ATTTTATTATTTTTATTTATTT
1 ATTTTATTATTTTTATTTATTT
*
499356 A-TTTATTATCTTTATTTATTT
1 ATTTTATTATTTTTATTTATTT
499377 ATTGTTATTATTTTT
1 ATT-TTATTATTTTT
499392 TATATACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 20 0.62
22 2 0.06
23 10 0.31
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTATTATTTTTATTTATTT
Found at i:504855 original size:286 final size:287
Alignment explanation
Indices: 504339--504861 Score: 763
Period size: 286 Copynumber: 1.8 Consensus size: 287
504329 TTTGTTTGAA
* *
504339 ATTGGATTTTAATTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAAGGGGCTT
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAAGGGGCTT
* *
504404 CTCAATTTCATTTAGAGCCAAATTCAACTTTACGACGAAGGATATTGGACTCGAAACAATACAAA
66 CTCAATTTCATTCAGAGCCAAATTCAACTTCACGACGAAGGATATTGGACTCGAAACAATACAAA
*
504469 CTTGGATTTCAACTTCACGATGAAGGATATTGAAGTCAAGGCTCAACTTCACGACGAAGGGGCCA
131 CTTGGATTTCAACTTCACGATGAAGGATATTGAAGTCAAGGCTCAACTTCACAACGAAGGGGCCA
*
504534 TCCACGATTTCAACTCCACGACAGAGGATATCGTGCCCACAAATCCACGATTTCAACTTAACGGC
196 TCCACGATTTCAACTCCACGACAGAGGATATCGTGCACACAAATCCACGATTTCAACTTAACGGC
504599 GAAGGATATCATGCCTATCTACACAAG
261 GAAGGATATCATGCCTATCTACACAAG
*
504626 ATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAAGGGGCTT
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAAGGGGCTT
* * ** * * **
504691 C-CAGTTTCATTCAGAGCCAATTTCAACTTCACGGTGAATGATATTGGACTCGAAGC-A-ACATT
66 CTCAATTTCATTCAGAGCCAAATTCAACTTCACGACGAAGGATATTGGACTCGAAACAATACAAA
* * *
504753 CATTGGATTTCAACTTCACGATGAATGATATCT-AATTCCACGGCTCAACTTCACAACGAAGGGG
131 C-TTGGATTTCAACTTCACGATGAAGGATAT-TGAAGT-CAAGGCTCAACTTCACAACGAAGGGG
* *
504817 TCATCCACGGA-TTCAACTTCACGAC-GAAGGGA-ATCGTGCACACAA
193 CCATCCAC-GATTTCAACTCCACGACAG-A-GGATATCGTGCACACAA
504862 GCATATTATA
Statistics
Matches: 210, Mismatches: 20, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
284 4 0.02
285 33 0.16
286 105 0.50
287 68 0.32
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (287 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGAAGGGGCTT
CTCAATTTCATTCAGAGCCAAATTCAACTTCACGACGAAGGATATTGGACTCGAAACAATACAAA
CTTGGATTTCAACTTCACGATGAAGGATATTGAAGTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGATTTCAACTCCACGACAGAGGATATCGTGCACACAAATCCACGATTTCAACTTAACGGC
GAAGGATATCATGCCTATCTACACAAG
Found at i:505412 original size:36 final size:34
Alignment explanation
Indices: 505339--505838 Score: 224
Period size: 36 Copynumber: 14.4 Consensus size: 34
505329 TTGAATATGT
* * *
505339 TTTCCTTGAAACAAATTTCT-TCTCCCTTGAGATAG
1 TTTCTTTGAAAC-AATTT-TGTCTCTCTTGAGACAG
505374 TTTCTTT-AGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTTTGA-AAC-AA-TTTTGTCTCTCTTGAGACAG
*
505410 TTTCTCTTGAAACAA-ATTGTCTCTCTTGAGACAG
1 TTTCT-TTGAAACAATTTTGTCTCTCTTGAGACAG
*
505444 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTT-CTTTGAAAC-AATTTTGTCTCTCTTGAGACAG
* ** *
505480 TTTCCCTTGAAACAA-----AATCT-TTGA-ATATG
1 TTT-CTTTGAAACAATTTTGTCTCTCTTGAGACA-G
* * *
505509 TTTTACATT-AAACAAATTTCGTCTCCCTTGAGACAG
1 -TTT-CTTTGAAAC-AATTTTGTCTCTCTTGAGACAG
* *
505545 TTTCTTTTGGAACTAAATTTTGTCTCTCTTGAAACA-
1 TTTC-TTTGAAAC--AATTTTGTCTCTCTTGAGACAG
** * *
505581 AAT-TTTG--TC---TTTGTCTCTCATGAGACAG
1 TTTCTTTGAAACAATTTTGTCTCTCTTGAGACAG
*
505609 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACGG
1 TTTCT-TTGAAAC-AATTTTGTCTCTCTTGAGACAG
* ** *
505645 TTTCACTTGAAACAA-----AATCT-TTGA-ATATG
1 TTTC-TTTGAAACAATTTTGTCTCTCTTGAGACA-G
* *
505674 TTTTACATT-AAACAAATTTTGTCTCCCTTGAGACAG
1 -TTT-CTTTGAAAC-AATTTTGTCTCTCTTGAGACAG
* *
505710 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTC-TTTGAAAC-AA-TTTTGTCTCTCTTGAGACAG
*
505747 TTTCTCTTTAAACAAATTTTGTCTTTGTCTCTCTTGAGACAG
1 TTTCT-TTGAAAC-AA-----T-TTTGTCTCTCTTGAGACAG
505789 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCT-TTGAAAC-AATTTTGTCTCTCTTGAGACAG
*
505825 TTTCCCTTGAAACA
1 TTT-CTTTGAAACA
505839 CCAACCTTTG
Statistics
Matches: 361, Mismatches: 52, Indels: 104
0.70 0.10 0.20
Matches are distributed among these distances:
27 16 0.04
28 4 0.01
29 19 0.05
30 24 0.07
31 1 0.00
32 2 0.01
34 35 0.10
35 34 0.09
36 131 0.36
37 59 0.16
38 1 0.00
41 2 0.01
42 33 0.09
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (34 bp):
TTTCTTTGAAACAATTTTGTCTCTCTTGAGACAG
Found at i:505417 original size:15 final size:15
Alignment explanation
Indices: 505397--505453 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
505387 AAGTTTTGTC
505397 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
* *
505412 TCTCTTGAAACAAATTGTC
1 TCTCTTGAGAC--A--GTT
505431 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
*
505446 TCCCTTGA
1 TCTCTTGA
505454 AACAAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 19 0.58
17 2 0.06
19 12 0.36
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (15 bp):
TCTCTTGAGACAGTT
Found at i:505436 original size:19 final size:19
Alignment explanation
Indices: 505412--505474 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
505402 TGAGACAGTT
505412 TCTCTTGAAACAAATTGTC
1 TCTCTTGAAACAAATTGTC
* *
505431 TCTCTTGAGAC-AGTT-TC
1 TCTCTTGAAACAAATTGTC
505448 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAA--TTGTC
505467 TCTCTTGA
1 TCTCTTGA
505475 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 7 0.21
16 2 0.06
17 2 0.06
18 5 0.15
19 12 0.35
20 1 0.03
21 5 0.15
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (19 bp):
TCTCTTGAAACAAATTGTC
Found at i:505658 original size:165 final size:169
Alignment explanation
Indices: 505256--505856 Score: 713
Period size: 165 Copynumber: 3.5 Consensus size: 169
505246 ACAAGGGGTC
* * * *
505256 GTCTCTCTTGAGACTAATTTACTC--AAAACAAAGTTTTGTCTCTTTTGAGACAGTTTCCATTGA
1 GTCTCTCTTGAGAC-AGTTT-CTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * * *
505319 AACAAAATCTTTGAATATGTTTT-CCTTGAAACAAATTTCTTCTCCCTTGAGATAGTTTC-TTTA
63 AACAAAATCTTTGAATATGTTTTACATT-AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
* * ** * *
505382 GAACTAAGTTTTGTCTCTC-T-T-G-AGACAGTTTCTCTTGAAACAAATT
127 GAACTAAATTTTGTCTCTCTTATAGTAAACA-AAT-T-TTG--TC--TTT
*
505428 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
505493 AAAATCTTTGAATATGTTTTACATTAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATCTTTGAATATGTTTTACATTAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
505558 TAAATTTTGTCTCTC-T-T-G-AAACAAATTTTGTCTTT
131 TAAATTTTGTCTCTCTTATAGTAAACAAATTTTGTCTTT
* * *
505593 GTCTCTCATGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCACTTGAAAC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
*
505658 AAAATCTTTGAATATGTTTTACATTAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATCTTTGAATATGTTTTACATTAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
*
505723 TAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTTAAACAAATTTTGTCTTT
131 TAAATTTTGTCTCTCTT---ATAG--------TAAACAAATTTTGTCTTT
505773 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* *
505838 ACCAACCTTTGAATATGTT
66 A-AAATCTTTGAATATGTT
505857 ACTCTTGGAA
Statistics
Matches: 383, Mismatches: 26, Indels: 31
0.87 0.06 0.07
Matches are distributed among these distances:
165 141 0.37
166 1 0.00
167 1 0.00
169 3 0.01
170 4 0.01
171 86 0.22
172 52 0.14
180 80 0.21
181 15 0.04
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (169 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATCTTTGAATATGTTTTACATTAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAATTTTGTCTCTCTTATAGTAAACAAATTTTGTCTTT
Found at i:505775 original size:42 final size:42
Alignment explanation
Indices: 505691--505838 Score: 156
Period size: 42 Copynumber: 3.8 Consensus size: 42
505681 TTAAACAAAT
* * * *
505691 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAA----GT-
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
* *
505728 TTTGTCTCTCTTGAGATAGTTTCTCTTTAAACAAATTTTGTC
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
505770 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA-----T-
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
*
505806 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
505839 CCAACCTTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
36 32 0.33
37 30 0.31
41 2 0.02
42 33 0.34
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTC
Found at i:505828 original size:78 final size:79
Alignment explanation
Indices: 505691--505838 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 79
505681 TTAAACAAAT
* * * * * *
505691 TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
505756 AAACAAATTTTGTC
66 AAACAAATTTTGTC
*
505770 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
505834 AAACA
66 AAACA
505839 CCAACCTTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 33 0.53
79 29 0.47
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (79 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAATTTTGTC
Found at i:505931 original size:34 final size:34
Alignment explanation
Indices: 505892--505977 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 34
505882 CTGGAGACAA
*
505892 TTTCTCTTGAAACACAAAAAAACCTTT-GAAATCG
1 TTTCTCTTGAAACACAAAAAAACCTTTAAAAAT-G
* *
505926 TTTCTCCTGAAACATAAAAAAACCTTTAAAAATG
1 TTTCTCTTGAAACACAAAAAAACCTTTAAAAATG
505960 TTTCTCTTGAAACACAAA
1 TTTCTCTTGAAACACAAA
505978 GACCTTCGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 42 0.91
35 4 0.09
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (34 bp):
TTTCTCTTGAAACACAAAAAAACCTTTAAAAATG
Found at i:507941 original size:23 final size:21
Alignment explanation
Indices: 507893--507950 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 21
507883 TTATTATTAT
507893 TATTATTATTATTATTACCATA
1 TATT-TTATTATTATTACCATA
*
507915 TATTTTATCATTATTATCGCATA
1 TATTTTATTATTATTA-C-CATA
507938 TATTTTATTATTA
1 TATTTTATTATTA
507951 CCTTTATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 11 0.34
22 5 0.16
23 16 0.50
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTTTATTATTATTACCATA
Found at i:507950 original size:3 final size:3
Alignment explanation
Indices: 507883--507931 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
507873 CCTATTGTTT
** *
507883 TTA TTA TTA TTA TTA TTA TTA TTA TTA CCA TATA TT- TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
507928 TTA T
1 TTA T
507932 CGCATATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:508209 original size:17 final size:16
Alignment explanation
Indices: 508168--508221 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
508158 TTTTCTTCTT
*
508168 TTTATTTATTTCTTTA
1 TTTATTTATTTTTTTA
*
508184 TTATCTTTATTATTTTTA
1 TT-TATTTATT-TTTTTA
*
508202 TTTATTTATTGTTATTA
1 TTTATTTATT-TTTTTA
508219 TTT
1 TTT
508222 TTTCTATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 2 0.06
17 22 0.71
18 7 0.23
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTTTTA
Found at i:508210 original size:23 final size:22
Alignment explanation
Indices: 508180--508223 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
508170 TATTTATTTC
508180 TTTATTATCT-TTATTATTTTTA
1 TTTATTAT-TGTTATTATTTTTA
508202 TTTATTTATTGTTATTATTTTT
1 TTTA-TTATTGTTATTATTTTT
508224 TCTATACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTATTATTGTTATTATTTTTA
Found at i:508219 original size:26 final size:25
Alignment explanation
Indices: 508167--508224 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
508157 ATTTTCTTCT
*
508167 TTTTATTTATTTCTTTATTATCTTTA
1 TTTT-TTTATTTATTTATTATCTTTA
*
508193 TTATTTTTATTTATTTATTGT-TATTA
1 TT-TTTTTATTTATTTATTATCT-TTA
508219 TTTTTT
1 TTTTTT
508225 CTATACTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.18
26 21 0.75
27 2 0.07
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTTTTATTTATTTATTATCTTTA
Found at i:508756 original size:42 final size:42
Alignment explanation
Indices: 508691--508777 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
508681 ACCGAATTAA
* **
508691 ACGGGGATGGGGGAAAATTGTTTATGCTAAACGGGGACGGGG
1 ACGGGGATGGGGAAAAACCGTTTATGCTAAACGGGGACGGGG
*
508733 ACGGGGATGGGGAAAAACCGTTTATGTTAAACGGGGACGGGG
1 ACGGGGATGGGGAAAAACCGTTTATGCTAAACGGGGACGGGG
508775 ACG
1 ACG
508778 AGTTTGGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.11, G:0.44, T:0.17
Consensus pattern (42 bp):
ACGGGGATGGGGAAAAACCGTTTATGCTAAACGGGGACGGGG
Found at i:508916 original size:37 final size:39
Alignment explanation
Indices: 508846--508931 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 39
508836 TATTAAAAAT
*
508846 AATTATTATATATATATATATATTAATAAATTTAATTTA
1 AATTAATATATATATATATATATTAATAAATTTAATTTA
* *
508885 AATTAATA-ATATATATA-ATATTTATATATTTAATTTA
1 AATTAATATATATATATATATATTAATAAATTTAATTTA
508922 AA-T-ATATATA
1 AATTAATATATA
508932 CCCGGCCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 3 0.07
36 4 0.09
37 20 0.47
38 9 0.21
39 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
AATTAATATATATATATATATATTAATAAATTTAATTTA
Found at i:516180 original size:22 final size:22
Alignment explanation
Indices: 516141--516208 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
516131 GTTTTTGTTC
*
516141 AAAGTCAAAGGTCA-GACCGGTT
1 AAAGTCAACGGT-ATGACCGGTT
* * * *
516163 AAATTCAATGGTATGACCAGTC
1 AAAGTCAACGGTATGACCGGTT
* *
516185 AAAGTCAACGGTCTGACTGGTT
1 AAAGTCAACGGTATGACCGGTT
516207 AA
1 AA
516209 CAAAAGTTCG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (22 bp):
AAAGTCAACGGTATGACCGGTT
Found at i:520325 original size:22 final size:22
Alignment explanation
Indices: 520299--520347 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
520289 TTCGATCATA
* * *
520299 GTCAAAGTCAATGGTCATACCG
1 GTCAAACTCAACGGTCAGACCG
520321 GTCAAACTCAACGGTCAGACCG
1 GTCAAACTCAACGGTCAGACCG
*
520343 ATCAA
1 GTCAA
520348 CCGTTCGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (22 bp):
GTCAAACTCAACGGTCAGACCG
Found at i:520439 original size:17 final size:17
Alignment explanation
Indices: 520417--520454 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
520407 AGACCACCAC
520417 GCGCACTGACGGCGCGT
1 GCGCACTGACGGCGCGT
520434 GCGCACTGACGGCGCGT
1 GCGCACTGACGGCGCGT
520451 GCGC
1 GCGC
520455 CTGCGGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.37, G:0.42, T:0.11
Consensus pattern (17 bp):
GCGCACTGACGGCGCGT
Found at i:521553 original size:2 final size:2
Alignment explanation
Indices: 521546--521572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
521536 GTAGGCAATC
521546 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
521573 ACATGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:522023 original size:21 final size:21
Alignment explanation
Indices: 521969--522021 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
521959 TAGTCAAATT
*
521969 ACCC-ATGAGTTTCGACCCGA
1 ACCCAATGAGTTTAGACCCGA
*
521989 ACCCAATGAATTTAGACCCGA
1 ACCCAATGAGTTTAGACCCGA
*
522010 A-CCTATGAGTTT
1 ACCCAATGAGTTT
522022 TATCAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
ACCCAATGAGTTTAGACCCGA
Found at i:523559 original size:15 final size:15
Alignment explanation
Indices: 523539--523568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
523529 AATTACCAAT
*
523539 TTCCATTGAAATATC
1 TTCCATTAAAATATC
523554 TTCCATTAAAATATC
1 TTCCATTAAAATATC
523569 CATAGTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCCATTAAAATATC
Done.