Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008904.1 Hibiscus syriacus cultivar Beakdansim tig00112184_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: 372056
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 3 of 3
Found at i:311681 original size:12 final size:12
Alignment explanation
Indices: 311664--311689 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
311654 TTAGTAACAC
311664 TGTTTTGTCTTT
1 TGTTTTGTCTTT
311676 TGTTTTGTCTTT
1 TGTTTTGTCTTT
311688 TG
1 TG
311690 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:311762 original size:19 final size:19
Alignment explanation
Indices: 311691--311780 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 19
311681 TGTCTTTTGG
311691 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
311710 TTTCGCGTTACGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
311726 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
311743 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
311762 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
311781 AAGTTCCAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.16
16 3 0.05
17 3 0.05
19 26 0.47
21 14 0.25
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:313668 original size:14 final size:14
Alignment explanation
Indices: 313649--313684 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
313639 ATTGTTTAAT
313649 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
313663 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
313677 TGATTTGT
1 TGATTTGT
313685 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:313807 original size:19 final size:19
Alignment explanation
Indices: 313791--313835 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
313781 AAAAATGACT
313791 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
313810 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
313829 ATCGCAA
1 ATCGCAA
313836 CGACAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:313888 original size:19 final size:19
Alignment explanation
Indices: 313862--314012 Score: 107
Period size: 19 Copynumber: 8.7 Consensus size: 19
313852 CGAAACTAAA
313862 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
313881 TTCACGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
313896 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
313914 TTTGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
313929 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
313947 TTCGTGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
313962 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
313980 TTCGCGTTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
313999 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
314013 AGACATTAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 27 0.27
16 9 0.09
17 9 0.09
19 45 0.45
20 11 0.11
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:313904 original size:14 final size:14
Alignment explanation
Indices: 313885--313974 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
313875 TTTCATTTCA
313885 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
313899 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
*
313917 GCATTGCGATTCTCT
1 -CGTTGCGATTCTCT
*
313932 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
313949 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
313965 CGTTGCGATT
1 CGTTGCGATT
313975 TTCATTTCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 24 0.40
15 2 0.03
16 9 0.15
17 9 0.15
18 2 0.03
19 14 0.23
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:313908 original size:33 final size:33
Alignment explanation
Indices: 313866--313992 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
313856 ACTAAATTCG
*
313866 CGTTGCGATTTTCATTTCACGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
313899 CGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
313932 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
313965 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
313993 AGTCATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:314007 original size:20 final size:20
Alignment explanation
Indices: 313965--314058 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
313955 GCGATTCTCT
**
313965 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
313984 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
314004 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
314023 ATGGTTGCGA-ACGTCATTTCCG
1 --CGTTGCGATA-GTCATTTCCG
*
314045 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
314059 AATGATTGCC
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
19 18 0.31
20 27 0.46
21 11 0.19
22 3 0.05
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:316556 original size:24 final size:24
Alignment explanation
Indices: 316522--316575 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
316512 CTGAAACATC
*
316522 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
316546 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
316570 ATCAAA
1 ATCAAA
316576 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:317483 original size:20 final size:20
Alignment explanation
Indices: 317309--317482 Score: 224
Period size: 20 Copynumber: 8.7 Consensus size: 20
317299 GATTCTGTAT
* *
317309 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
317329 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
317349 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
317369 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
317389 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
317409 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
317429 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
317450 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
317470 TATCGCATTGCGA
1 TATCGCGTTGCGA
317483 TTTTCCAAAT
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
19 3 0.02
20 122 0.87
21 14 0.10
22 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:317502 original size:41 final size:41
Alignment explanation
Indices: 317334--317504 Score: 141
Period size: 40 Copynumber: 4.2 Consensus size: 41
317324 GTCAGAATCT
* * * *** *
317334 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGA-ATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
* * *** *
317374 CGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTC-AGTATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
* * ** *
317414 CGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
317455 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCG
*
317496 CATTGCGAT
1 CGTTGCGAT
317505 TTTCCAAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
40 65 0.57
41 47 0.41
42 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
Found at i:317537 original size:20 final size:21
Alignment explanation
Indices: 317472--317544 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
317462 ATAGTCAGTA
317472 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
317493 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
317514 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
317534 TCGCATTGCGA
1 TCGCATTGCGA
317545 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 17 0.35
21 32 0.65
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:317559 original size:41 final size:42
Alignment explanation
Indices: 317471--317559 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
317461 GATAGTCAGT
* * *
317471 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
* ** **
317513 TTCGCATTGCGA-TTTACTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
317554 ATCGCA
1 ATCGCA
317560 ACACGAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (42 bp):
ATCGCATTGCGATTTTACAAATTCGCATTGCGAATTGCCAAA
Found at i:322251 original size:20 final size:20
Alignment explanation
Indices: 322212--322251 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
322202 AGATTATTAA
322212 TGGGAATAAAAGATTACCAG
1 TGGGAATAAAAGATTACCAG
*
322232 TGGGAATAAAATATTACCAG
1 TGGGAATAAAAGATTACCAG
322252 AGAATAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (20 bp):
TGGGAATAAAAGATTACCAG
Found at i:322424 original size:15 final size:15
Alignment explanation
Indices: 322406--322436 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
322396 AAATTTTAAA
322406 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
322421 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
322436 T
1 T
322437 CTATATGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:322490 original size:21 final size:21
Alignment explanation
Indices: 322466--322506 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
322456 TACTTGAGTA
322466 TTTAATTAT-ATTATATATTAT
1 TTTAATTATAATTA-ATATTAT
*
322487 TTTAATTTTAATTAATATTA
1 TTTAATTATAATTAATATTA
322507 AATTTTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATTATAATTAATATTAT
Found at i:324537 original size:27 final size:27
Alignment explanation
Indices: 324471--324525 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
324461 CCAAGGCTGG
324471 ACAAAGCATTCTAAATGCAACTCATAA
1 ACAAAGCATTCTAAATGCAACTCATAA
*
324498 ACAAAGCATTCTAAATGCAACTCTTAA
1 ACAAAGCATTCTAAATGCAACTCATAA
324525 A
1 A
324526 TTTATCATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (27 bp):
ACAAAGCATTCTAAATGCAACTCATAA
Found at i:327521 original size:60 final size:59
Alignment explanation
Indices: 327428--327589 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 59
327418 AAATAGACCC
* * *
327428 GAAGTTGTTTTGTTGAGTCTTTCGACTGTTAAAAGTTACAAATTGATCCTCAGATTATAG
1 GAAGTTGCTTTGTTGAGTCTCTCGACTGTTAAAAGTTACAAATTG-TCCTCAGACTATAG
*
327488 GAAGTTGCTTTGTTGAGTCTCTCGACTGTTAAAAGTTACAAAATTGTCCTCCGACTATAG
1 GAAGTTGCTTTGTTGAGTCTCTCGACTGTTAAAAGTTAC-AAATTGTCCTCAGACTATAG
* * * * *
327548 GGAGTTACTTTGTTGAATCTCTTGACTATTAAAAGTTACAAA
1 GAAGTTGCTTTGTTGAGTCTCTCGACTGTTAAAAGTTACAAA
327590 ATAGTCACTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 3 0.03
60 83 0.90
61 6 0.07
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (59 bp):
GAAGTTGCTTTGTTGAGTCTCTCGACTGTTAAAAGTTACAAATTGTCCTCAGACTATAG
Found at i:328036 original size:28 final size:28
Alignment explanation
Indices: 327996--328081 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 28
327986 ATATATCGAT
327996 AATTT-AGAGATAAAATTAAAATGTTCAA
1 AATTTGAG-GATAAAATTAAAATGTTCAA
* * *
328024 AATTTCG-GGATAAATTTAGAATGATGATCAT
1 AATTT-GAGGATAAAATTA-AA--ATGTTCAA
* *
328055 AATTTGAGGATGAAATTAGAATGTTCA
1 AATTTGAGGATAAAATTAAAATGTTCA
328082 CAACTTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
28 20 0.44
29 3 0.07
30 2 0.04
31 20 0.44
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (28 bp):
AATTTGAGGATAAAATTAAAATGTTCAA
Found at i:328771 original size:21 final size:22
Alignment explanation
Indices: 328742--328782 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
328732 TTTGATTGGG
*
328742 ATTAATATATA-TATTATATTT
1 ATTAATATATACTATAATATTT
*
328763 ATTATTATATACTATAATAT
1 ATTAATATATACTATAATAT
328783 GATGATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAATATATACTATAATATTT
Found at i:328796 original size:3 final size:3
Alignment explanation
Indices: 328790--328816 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
328780 TATGATGATG
328790 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
328817 TTACAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:342533 original size:18 final size:17
Alignment explanation
Indices: 342502--342540 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
342492 GTATTATGCT
*
342502 TGAAGAAAAAGAAAAAA
1 TGAAAAAAAAGAAAAAA
342519 TGAAAAAAAATGAAAAAA
1 TGAAAAAAAA-GAAAAAA
342537 TGAA
1 TGAA
342541 GAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (17 bp):
TGAAAAAAAAGAAAAAA
Found at i:343638 original size:136 final size:135
Alignment explanation
Indices: 343394--343864 Score: 651
Period size: 136 Copynumber: 3.5 Consensus size: 135
343384 GGAGGTGAAC
*
343394 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * ** *
343459 ATGAGAAGAGTTTGTTCGACCTATCACTCGATTCACGGCATTTCAAATCAGTGATGCCTCGCTTG
65 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTG
343524 AGGGAT
130 AGGGAT
* * * **
343530 CAACATTTCCAGTGAAAAGTTCATAATGAGAAGAACTCATCCAACAGAACGAGAAGAAGTTCATA
1 CAACATTTCCAATG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
*
343595 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGCCATTTCGAATCAGTGACACCTCACTTG
65 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTG
343660 AGGGAT
130 AGGGAT
**
343666 TGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAA-TGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* *
343731 ATGAGAATAGCTTGTTTGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTC-CATT
65 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCAC-TT
343795 ----G--
129 GAGGGAT
* *
343796 --ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCTGAAAGA-GG-G-AGAAGTTCATA
1 CAACATTTCCAA-TGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
343856 ATGAGAAGA
65 ATGAGAAGA
343865 ACTTATTCAA
Statistics
Matches: 307, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
125 19 0.06
126 1 0.00
127 2 0.01
128 44 0.14
132 1 0.00
135 2 0.01
136 236 0.77
137 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (135 bp):
CAACATTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCACTTGA
GGGAT
Found at i:350120 original size:21 final size:22
Alignment explanation
Indices: 350082--350130 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
350072 CAATATATAT
350082 TATTTTAAAATTTAAATA-TGA
1 TATTTTAAAATTTAAATATTGA
*
350103 TATTTT-AAGTTTATAATATTGA
1 TATTTTAAAATTTA-AATATTGA
*
350125 TTTTTT
1 TATTTT
350131 GTATTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 10 0.42
22 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TATTTTAAAATTTAAATATTGA
Found at i:354863 original size:136 final size:136
Alignment explanation
Indices: 354618--354966 Score: 524
Period size: 136 Copynumber: 2.6 Consensus size: 136
354608 TTGTTAGATT
* * * *
354618 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTC-TTTT-GGATGAGTTTTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * ** * *
354681 CTTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTG
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTC-ATGAATCGAGTG
354745 ATAGGTC
130 ATAGGTC
354752 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * * *
354817 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
354882 TAGGTC
131 TAGGTC
* *
354888 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
354953 CTCCATTGAAAATG
66 CTCCATTGAAAATG
354967 CTGATCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 31 0.16
135 4 0.02
136 159 0.82
137 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:355950 original size:10 final size:10
Alignment explanation
Indices: 355937--355993 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
355927 TCCTTCTTCA
355937 TTTTTCTTTC
1 TTTTTCTTTC
*
355947 TTTTTTTTTC
1 TTTTTCTTTC
*
355957 TTTTTTTTTC
1 TTTTTCTTTC
*
355967 TTCTT-TTT-
1 TTTTTCTTTC
*
355975 TTTTTCATTTT
1 TTTTTC-TTTC
355986 TTTTTCTT
1 TTTTTCTT
355994 CAAGCATAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 4 0.10
9 3 0.07
10 28 0.68
11 6 0.15
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:355957 original size:24 final size:24
Alignment explanation
Indices: 355930--355993 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 24
355920 TGAACCCTCC
355930 TTCTTCATTTTTCTTTCTTTTTTT
1 TTCTTCATTTTTCTTTCTTTTTTT
**
355954 TTCTTTTTTTTTC-TTC-TTTTTT
1 TTCTTCATTTTTCTTTCTTTTTTT
*
355976 TT-TTCATTTTTTTTTCTT
1 TTCTTCATTTTTCTTTCTT
355994 CAAGCATAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 7 0.21
22 11 0.33
23 4 0.12
24 11 0.33
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (24 bp):
TTCTTCATTTTTCTTTCTTTTTTT
Found at i:355995 original size:14 final size:12
Alignment explanation
Indices: 355937--355990 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 12
355927 TCCTTCTTCA
355937 TTTTTCTTTCTTTT
1 TTTTTC-TT-TTTT
355951 TTTTTCTTTTTT
1 TTTTTCTTTTTT
355963 TTTCTTC-TTTTT
1 TTT-TTCTTTTTT
355975 TTTTTCATTTTTT
1 TTTTTC-TTTTTT
355988 TTT
1 TTT
355991 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.08
12 15 0.41
13 13 0.35
14 6 0.16
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTTTT
Done.