Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009124.1 Hibiscus syriacus cultivar Beakdansim tig00112614_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: 858217
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:797296 original size:17 final size:17
Alignment explanation
Indices: 797270--797311 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
797260 TTAATTTGAA
797270 AATTTGGAGATTTTGAT-G
1 AATTT-GAGA-TTTGATCG
797288 AATTTGAGATTTGATCG
1 AATTTGAGATTTGATCG
797305 AATTTGA
1 AATTTGA
797312 AGCCACCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (17 bp):
AATTTGAGATTTGATCG
Found at i:797388 original size:15 final size:17
Alignment explanation
Indices: 797370--797401 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
797360 GTTTAAAACA
797370 ATTTT-AAGA-AAAAAT
1 ATTTTAAAGACAAAAAT
797385 ATTTTAAAGACAAAAAT
1 ATTTTAAAGACAAAAAT
797402 TGGTCTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
ATTTTAAAGACAAAAAT
Found at i:798689 original size:12 final size:12
Alignment explanation
Indices: 798667--798691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
798657 TCTTTTTCGA
798667 TATTTTTTTCTT
1 TATTTTTTTCTT
798679 TATTTTTTTCTT
1 TATTTTTTTCTT
798691 T
1 T
798692 CGAATTCTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTTCTT
Found at i:801677 original size:19 final size:19
Alignment explanation
Indices: 801653--801690 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
801643 TTAGTAAGTT
801653 CCCAGTACCATGTTTCGGG
1 CCCAGTACCATGTTTCGGG
801672 CCCAGTACCATGTTTCGGG
1 CCCAGTACCATGTTTCGGG
801691 GAATAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (19 bp):
CCCAGTACCATGTTTCGGG
Found at i:809351 original size:24 final size:22
Alignment explanation
Indices: 809311--809375 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 22
809301 TATTTTTTAA
809311 TAAAAATATTAATTATTAAAATATT
1 TAAAAATA-T-ATTATTAAAA-ATT
*
809336 TAAAAATATATGTATTAATAATT
1 TAAAAATATAT-TATTAAAAATT
*
809359 TAAATAATATAATATTA
1 TAAA-AATATATTATTA
809376 TATTTTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 14 0.39
24 14 0.39
25 8 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAATATATTATTAAAAATT
Found at i:809380 original size:21 final size:21
Alignment explanation
Indices: 809331--809399 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
809321 AATTATTAAA
*
809331 ATATTTAAA-AATATATGTATT
1 ATATTTAAATAATATA-ATATT
809352 AATAATTTAAATAATATAATATT
1 -AT-ATTTAAATAATATAATATT
** * *
809375 ATATTTTTATATTATAATAAT
1 ATATTTAAATAATATAATATT
809396 ATAT
1 ATAT
809400 CAAGTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 19 0.47
22 4 0.10
23 11 0.28
24 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
ATATTTAAATAATATAATATT
Found at i:809430 original size:23 final size:23
Alignment explanation
Indices: 809379--809432 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
809369 AATATTATAT
* *
809379 TTTTATATTATAATAATATATCA
1 TTTTATATCATAAGAATATATCA
** *
809402 AGTTATATCATAAGAATATATGA
1 TTTTATATCATAAGAATATATCA
809425 TTTTATAT
1 TTTTATAT
809433 TTTTATTATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (23 bp):
TTTTATATCATAAGAATATATCA
Found at i:810176 original size:19 final size:19
Alignment explanation
Indices: 810152--810217 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
810142 TTAACTATCA
810152 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
810171 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
810193 CAACGAATTTGAAAAATCG
1 CAACGAATTTGGAAAATCG
810212 CAACGA
1 CAACGA
810218 CAACTGTAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 18 0.51
20 2 0.06
21 2 0.06
22 13 0.37
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:810190 original size:41 final size:41
Alignment explanation
Indices: 810145--810258 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
810135 TATTTTTTTA
810145 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
* *
810186 ACTATCGCAACGAATTTGAAAAATCGCAACGACAACTGTAG
1 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
* *
810227 AATATCACAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCACAA--CGAATTTGGAAAATCGCAACG
810259 CGAAATAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 47 0.72
42 14 0.22
43 4 0.06
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (41 bp):
ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:810194 original size:22 final size:22
Alignment explanation
Indices: 810167--810238 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
810157 AATTTGGAAA
*
810167 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGAAT
** *
810189 ATCGCAACGA-ATTTG-A-AAA
1 ATCGCAACGACAACTGTAGAAT
810208 ATCGCAACGACAACTGTAGAAT
1 ATCGCAACGACAACTGTAGAAT
*
810230 ATCACAACG
1 ATCGCAACG
810239 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGAAT
Found at i:810259 original size:20 final size:20
Alignment explanation
Indices: 810234--810431 Score: 101
Period size: 21 Copynumber: 9.8 Consensus size: 20
810224 TAGAATATCA
*
810234 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGCAAAATCG
*
810254 CAACGCGAAAT-AAAAATCG
1 CAACGCGAAATGCAAAATCG
* *** * *
810273 CAACCCGCTTTTCAACTATCG
1 CAACGCGAAATGCAA-AATCG
* *
810294 CACCGCGAAATGGAAAATCG
1 CAACGCGAAATGCAAAATCG
* ** * *
810314 CAACGTGATTTTCAACTATCG
1 CAACGCGAAATGCAA-AATCG
* * *
810335 CAACGCTAAATGGAAAAGCG
1 CAACGCGAAATGCAAAATCG
** * *
810355 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGCAA-AATCG
* *
810376 CAACACGAAATGAAAAATCG
1 CAACGCGAAATGCAAAATCG
** * *
810396 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGCAA-AATCG
810417 CAACGCGAAATGCAA
1 CAACGCGAAATGCAA
810432 CGCGAAGTGA
Statistics
Matches: 121, Mismatches: 52, Indels: 9
0.66 0.29 0.05
Matches are distributed among these distances:
19 14 0.12
20 53 0.44
21 54 0.45
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
CAACGCGAAATGCAAAATCG
Found at i:810271 original size:19 final size:20
Alignment explanation
Indices: 810202--810403 Score: 84
Period size: 20 Copynumber: 9.9 Consensus size: 20
810192 GCAACGAATT
*
810202 TGAAAAATCGCAACGAC-AAC
1 TGAAAAATCGCAACG-CGAAA
* *
810222 TGTAGAATATCACAACGCGAAA
1 TG-A-AAAATCGCAACGCGAAA
*
810244 TGGAAAATCGCAACGCGAAA
1 TGAAAAATCGCAACGCGAAA
* ***
810264 T-AAAAATCGCAACCCGCTTT
1 TGAAAAATCGCAACGCG-AAA
* ** *
810284 TCAACTATCGCACCGCGAAA
1 TGAAAAATCGCAACGCGAAA
* * **
810304 TGGAAAATCGCAACGTGATTT
1 TGAAAAATCGCAACGCGA-AA
* ** *
810325 TCAACTATCGCAACGCTAAA
1 TGAAAAATCGCAACGCGAAA
* * **
810345 TGGAAAAGCGCAACGCGATTT
1 TGAAAAATCGCAACGCGA-AA
* ** *
810366 TCAACTATCGCAACACGAAA
1 TGAAAAATCGCAACGCGAAA
810386 TGAAAAATCGCAACGCGA
1 TGAAAAATCGCAACGCGA
810404 TTTTCAACTA
Statistics
Matches: 121, Mismatches: 54, Indels: 14
0.64 0.29 0.07
Matches are distributed among these distances:
19 13 0.11
20 57 0.47
21 37 0.31
22 14 0.12
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (20 bp):
TGAAAAATCGCAACGCGAAA
Found at i:810326 original size:41 final size:41
Alignment explanation
Indices: 810250--810428 Score: 270
Period size: 41 Copynumber: 4.4 Consensus size: 41
810240 GAAATGGAAA
* *
810250 ATCGCAACGCGAAAT-AAAAATCGCAACCCGCTTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
* * *
810290 ATCGCACCGCGAAATGGAAAATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
* * *
810331 ATCGCAACGCTAAATGGAAAAGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
*
810372 ATCGCAACACGAAATGAAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
810413 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
810429 CAACGCGAAG
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 14 0.11
41 110 0.89
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACT
Found at i:812426 original size:23 final size:23
Alignment explanation
Indices: 812383--812426 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
812373 TAACTAGGTT
*
812383 TTAAAATATTAATGGGTTTAATG
1 TTAAAATATTAATAGGTTTAATG
*
812406 TTAAAAT-TTACTAGGTCTTAA
1 TTAAAATATTAATAGGT-TTAA
812427 GACTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAGGTTTAATG
Found at i:814552 original size:64 final size:64
Alignment explanation
Indices: 814471--814654 Score: 216
Period size: 64 Copynumber: 2.9 Consensus size: 64
814461 TCAATGGATA
* *
814471 AATTGAAACATCGAATGCATTCTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAT-TT
1 AATTGAAACATCGAATGCATT-TATGCATCGATGCACTCTCCATGCATCGATGCACTCGGATATT
* * *
814535 AATTAAAACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCGGCTAT
1 AATTGAAACATCGAATGCATTT-ATGCATCGATGCACTC-TCCATGCATCGATGCACTCGGATAT
814599 T
64 T
* * *
814600 --TTGAAACATCGAATGCACTTGATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AATTGAAACATCGAATGCA-TTTATGCATCGATGCACTCTCCA-TGCATCGATGCACT
814655 AAGGGTCCAA
Statistics
Matches: 104, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
62 1 0.01
63 45 0.43
64 56 0.54
65 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (64 bp):
AATTGAAACATCGAATGCATTTATGCATCGATGCACTCTCCATGCATCGATGCACTCGGATATT
Found at i:814634 original size:17 final size:19
Alignment explanation
Indices: 814606--814654 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
814596 TATTTTGAAA
814606 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
814624 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
814643 CACCGATGCACT
1 CATCGATGCACT
814655 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:821075 original size:453 final size:443
Alignment explanation
Indices: 820205--821536 Score: 1474
Period size: 453 Copynumber: 3.0 Consensus size: 443
820195 GAAACTCAAT
* * * * * * * *
820205 CTCCAGACGAGGAAGA-GACTATGATCCTAAGAAGACATCTGAAATAGAGAAGTCTGAGATGGTT
1 CTCCAGATGAGGAAGATAACAATGATCCTAAGAAGACAGCTGAAAAAGAGAAGTCCGAGTTGATT
* ** * * * * * *
820269 GAATTGAGTCATAAAGTTGATATATTTGTAGAAGTGGAACACGCCAGCCATGATTTCACTCAACA
66 GAATTGACTCATAAAGCAGAAACATTTGTAGAAGTGGAACATGTCAGCCATGATTCCATTCAACA
** * * * * * *
820334 TGGGAGTCCAATTGCCTCAGAGAAAATAACAAATGAAACAGATCTTGAGAGGGCAGTTGTTAGCA
131 TGGGAGTCCAATTGCCTTGGAGAATAGAACAAATGAAACTGATCCTGAGAAGGCAGTTGGTAGCA
* *
820399 AGGATTCTGACTTCGGTGAACCAACGTTGAAGCATGGTGGCTTGAAAAAGAAAGCAA-ACAAAAG
196 AGAATTCTGACTTTGGTG-ACCAACGTTG-AG--TGGTGGCTTGAAAAAGAAAGCAAGA-AAAAG
* * * * * * *
820463 GAAGAAAC-ACTTTACAGTATAACCGTGATGAAGGCCGATCCTTCCAACTCCAAAAATGATTTGG
256 GAAGAAACAACTTTCCAGTAGAGCCATGATGAAGGCTGATCCTTCTAA-TTCAAAAATGATTTGG
* ** * * * *
820527 TTGGTGAAAATAGTAGTGTCCCAAAGAATGTTGATGAGATGGAAAATGAAA-AGGAGTGTAATGC
320 TTGGGGAAAATAGTAGTGTCCGGAAGAATGTTGAGGAGA-CGAAAATGAAAGAAGAATGTAATGC
* * * * *
820591 CACATCCTGTTGCCAAACCGAAAGGCAGTACTGCTT-TTGTGGAAGTTGAAATCTCTGGAGCAGC
384 CACATCCTGCTGCCAAACCAAAAGGCAGTACTGCTTCTT-CGAAAGTGGAAATCTC-----C-GC
820655 AG
442 AG
* *
820657 CTCCAGATGAGGAAGATAACAATGATCCCAAGAAAACAGCTGAAAAAGAGAAGTCCGAGTTGATT
1 CTCCAGATGAGGAAGATAACAATGATCCTAAGAAGACAGCTGAAAAAGAGAAGTCCGAGTTGATT
** * * * *
820722 GGGTTGACTCGTAAAGCAGAAACATTTGTAGATGTGGAACATGTCGGCCACGATTCCATTCAACA
66 GAATTGACTCATAAAGCAGAAACATTTGTAGAAGTGGAACATGTCAGCCATGATTCCATTCAACA
** *
820787 TGGGAGTCCAATTGCCTTGGAGAATAGAATGAATGTAA-TGATCCTGAGAAGGCAGTTGGTAGCA
131 TGGGAGTCCAATTGCCTTGGAGAATAGAACAAATGAAACTGATCCTGAGAAGGCAGTTGGTAGCA
* * * *
820851 AGAACTCCGACTTTGGTAGACCAACGTTGAGGTTTTGTGGCTTGAAAAAGAAAGCAAGAAAAACG
196 AGAATTCTGACTTTGGT-GACCAACGTTGA-G--TGGTGGCTTGAAAAAGAAAGCAAGAAAAAGG
* * *
820916 AAGAAACAACTTTCCAGTAGAGTCATGATGAAGGCTGATCCTTCTAGTTCTAAAATGATTTGGTT
257 AAGAAACAACTTTCCAGTAGAGCCATGATGAAGGCTGATCCTTCTAATTCAAAAATGATTTGGTT
* * * * *
820981 GGGGAAGATAGTAGTATCCGGATGAATG-TGAGGAGACAGAAAATGAAACGAAGAATGTCATGCT
322 GGGGAAAATAGTAGTGTCCGGAAGAATGTTGAGGAGAC-GAAAATGAAA-GAAGAATGTAATGCC
* *
821045 ACTTCCTGCTGCCAAACCAAAAGGCAGTACTGCTTCTTCGAAAGTGGAAATCTCCGCTG
385 ACATCCTGCTGCCAAACCAAAAGGCAGTACTGCTTCTTCGAAAGTGGAAATCTCCGCAG
* ** *
821104 CTCCAGATGAGGAAGATGAA-AATTATGGTAAGAAGACAGCTGAAAATGAGAAG-CCTGAGTTGA
1 CTCCAGATGAGGAAGAT-AACAATGATCCTAAGAAGACAGCTGAAAAAGAGAAGTCC-GAGTTGA
*
821167 TTGAATTGACTCATAAAACAGAAACATTTGTAGAAGTGGAACATGTCAGCCATGATTCCATTCAA
64 TTGAATTGACTCATAAAGCAGAAACATTTGTAGAAGTGGAACATGTCAGCCATGATTCCATTCAA
* * *
821232 CATGGGAGTCCAATTGCATTGGACAATAGAACAAATGAAACTGATCCTGAGAAGACAGTTGGTAG
129 CATGGGAGTCCAATTGCCTTGGAGAATAGAACAAATGAAACTGATCCTGAGAAGGCAGTTGGTAG
* * * * * * *
821297 TAATAATTCTGACTTTGATG-TCAA-G-T--GTGGTAGCTTGAAAAAGAAAGCAAGCAAAAGGGA
194 CAAGAATTCTGACTTTGGTGACCAACGTTGAGTGGTGGCTTGAAAAAGAAAGCAAGAAAAAGGAA
* *
821357 GAAACAGCCTTCCAGTAGAGCCATGATGAAGGCTGATCCTTCTAATTCCAAAAATGATTTGGTTG
259 GAAACAACTTTCCAGTAGAGCCATGATGAAGGCTGATCCTTCTAATT-CAAAAATGATTTGGTTG
* * *
821422 GGGAAAATAGTAGTGTCCGGAAGAATGTTGAGGAGACGAAATATGAAAAGGAGAATGTAAAGCCG
323 GGGAAAATAGTAGTGTCCGGAAGAATGTTGAGGAGACGAAA-ATG-AAAGAAGAATGTAATGCCA
* * *
821487 CATCCCGCTCCCAAACCAAAAGGCAGAACTG---CTTCGAAAGTGGAAATCTC
386 CATCCTGCTGCCAAACCAAAAGGCAGTACTGCTTCTTCGAAAGTGGAAATCTC
821537 TGGGGCAACT
Statistics
Matches: 744, Mismatches: 120, Indels: 46
0.82 0.13 0.05
Matches are distributed among these distances:
438 19 0.03
439 71 0.10
440 44 0.06
441 51 0.07
442 3 0.00
444 1 0.00
445 1 0.00
446 5 0.01
447 148 0.20
448 40 0.05
451 18 0.02
452 133 0.18
453 208 0.28
454 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (443 bp):
CTCCAGATGAGGAAGATAACAATGATCCTAAGAAGACAGCTGAAAAAGAGAAGTCCGAGTTGATT
GAATTGACTCATAAAGCAGAAACATTTGTAGAAGTGGAACATGTCAGCCATGATTCCATTCAACA
TGGGAGTCCAATTGCCTTGGAGAATAGAACAAATGAAACTGATCCTGAGAAGGCAGTTGGTAGCA
AGAATTCTGACTTTGGTGACCAACGTTGAGTGGTGGCTTGAAAAAGAAAGCAAGAAAAAGGAAGA
AACAACTTTCCAGTAGAGCCATGATGAAGGCTGATCCTTCTAATTCAAAAATGATTTGGTTGGGG
AAAATAGTAGTGTCCGGAAGAATGTTGAGGAGACGAAAATGAAAGAAGAATGTAATGCCACATCC
TGCTGCCAAACCAAAAGGCAGTACTGCTTCTTCGAAAGTGGAAATCTCCGCAG
Found at i:830015 original size:7 final size:7
Alignment explanation
Indices: 830003--830027 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
829993 ACGTGCCCAC
830003 CCTCAAA
1 CCTCAAA
830010 CCTCAAA
1 CCTCAAA
830017 CCTCAAA
1 CCTCAAA
830024 CCTC
1 CCTC
830028 GATAACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTCAAA
Found at i:835473 original size:136 final size:136
Alignment explanation
Indices: 835227--835576 Score: 517
Period size: 136 Copynumber: 2.6 Consensus size: 136
835217 TTGTTAGATT
* * * *
835227 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTC-TTTT-GGATGAGTTTTTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAG-TTCTTCTCATTATGAAC
* * ** * *
835290 TCTTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGT
65 TCTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTC-ATGAATCGAGT
835354 GATAGGTC
129 GATAGGTC
835362 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * * *
835427 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
835492 TAGGTC
131 TAGGTC
* *
835498 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
835563 CTCCATTGAAAATG
66 CTCCATTGAAAATG
835577 CTGATCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
135 31 0.16
136 156 0.80
137 8 0.04
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:836558 original size:14 final size:12
Alignment explanation
Indices: 836541--836606 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 12
836531 TGAACCCTCC
836541 TTCTTCATTTTTCT
1 TTCTTC-TTTTT-T
836555 TTCTT-TTTTTT
1 TTCTTCTTTTTT
836566 TTCTT-TTTTTT
1 TTCTTCTTTTTT
836577 TTCTTCTTTTTTT
1 TTCTTC-TTTTTT
*
836590 TTCAT-TTTTTT
1 TTCTTCTTTTTT
836601 TTCTTC
1 TTCTTC
836607 AAGCATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
11 27 0.57
12 5 0.11
13 10 0.21
14 5 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTCTTTTTT
Found at i:836568 original size:11 final size:11
Alignment explanation
Indices: 836548--836605 Score: 80
Period size: 11 Copynumber: 5.1 Consensus size: 11
836538 TCCTTCTTCA
*
836548 TTTTTCTTTCT
1 TTTTTTTTTCT
836559 TTTTTTTTTCT
1 TTTTTTTTTCT
836570 TTTTTTTTTCTT
1 TTTTTTTTTC-T
*
836582 CTTTTTTTTTCA
1 -TTTTTTTTTCT
836594 TTTTTTTTTCT
1 TTTTTTTTTCT
836605 T
1 T
836606 CAAGCATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 31 0.74
12 1 0.02
13 10 0.24
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:836568 original size:15 final size:14
Alignment explanation
Indices: 836548--836591 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
836538 TCCTTCTTCA
836548 TTTTTCTTTCTTTTT
1 TTTTTCTTT-TTTTT
836563 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
*
836577 TTCTTCTTTTTTTT
1 TTTTTCTTTTTTTT
836591 T
1 T
836592 CATTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 19 0.68
15 9 0.32
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:836570 original size:25 final size:24
Alignment explanation
Indices: 836541--836606 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
836531 TGAACCCTCC
*
836541 TTCTTCATTTTTCTTTCTTTTTTTT
1 TTCTTCATTTTT-TTTCTTCTTTTT
836566 TTCTT--TTTTTTTTCTTCTTTTT
1 TTCTTCATTTTTTTTCTTCTTTTT
836588 TT-TTCATTTTTTTTTCTTC
1 TTCTTCA-TTTTTTTTCTTC
836607 AAGCATAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.05
22 13 0.35
23 5 0.14
24 12 0.32
25 5 0.14
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (24 bp):
TTCTTCATTTTTTTTCTTCTTTTT
Found at i:836607 original size:14 final size:13
Alignment explanation
Indices: 836558--836607 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
836548 TTTTTCTTTC
836558 TTTTTTTTTTC--
1 TTTTTTTTTTCAT
836569 TTTTTTTTTTC-T
1 TTTTTTTTTTCAT
836581 TCTTTTTTTTTCAT
1 T-TTTTTTTTTCAT
836595 TTTTTTTTCTTCA
1 TTTTTTTT-TTCA
836608 AGCATAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.31
12 1 0.03
13 17 0.49
14 6 0.17
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTCAT
Found at i:853753 original size:26 final size:22
Alignment explanation
Indices: 853698--853755 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
853688 ATATGTCACA
*
853698 TTTTAATAATTTTAAAATTTTAT
1 TTTTAA-AAATTTAAAATTTTAT
853721 TTTTAAAAATTTAAAATATATTAT
1 TTTTAAAAATTTAAAAT-T-TTAT
*
853745 ATTTATAAAAT
1 TTTTA-AAAAT
853756 AATTATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.33
23 7 0.23
24 8 0.27
25 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTAAAATTTTAT
Done.