Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008544.1 Hibiscus syriacus cultivar Beakdansim tig00111433_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: 84437
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:1543 original size:39 final size:38
Alignment explanation
Indices: 1499--1583 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
1489 ACAAATTCGC
*
1499 GTTGCGATTTACAGATTCGCATTGCCAA-TTGACTTCA-GT
1 GTTGCGATTGAC-GA-TCGCATTGCCAATTTGACTT-ATGT
* *
1538 GTTGCGAATTGACTATCGCATTGCGAATTTGACTTATGT
1 GTTGCG-ATTGACGATCGCATTGCCAATTTGACTTATGT
1577 GTTGCGA
1 GTTGCGA
1584 ATTTGACTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 13 0.32
39 22 0.55
40 5 0.12
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (38 bp):
GTTGCGATTGACGATCGCATTGCCAATTTGACTTATGT
Found at i:1543 original size:59 final size:59
Alignment explanation
Indices: 1455--1641 Score: 177
Period size: 59 Copynumber: 3.1 Consensus size: 59
1445 AATTTGACTA
* * *
1455 TCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTGCGATTTACAGAT
1 TCGC-TTGCCAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATAT
* * * * *
1515 TCGCATTGCCAA-TTGACTTCAGTGTTGCGAATTGAC-TA-TCGCATTGCGAATTTGACTTAT
1 TCGC-TTGCCAATTTGACTTCTGTGTTGCG-ATTTACAAATTCGCGTTGCG-ATTT-ACATAT
* * *
1575 GT-G-TTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGCGTTCCGATTTACATAT
1 -TCGCTTGCCAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATAT
1633 TCGCGTTGC
1 TCGC-TTGC
1642 GACTTGGAAA
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
57 1 0.01
58 26 0.26
59 41 0.41
60 31 0.31
61 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (59 bp):
TCGCTTGCCAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGATTTACATAT
Found at i:1571 original size:20 final size:20
Alignment explanation
Indices: 1444--1591 Score: 80
Period size: 20 Copynumber: 7.5 Consensus size: 20
1434 TTCAGTGTGT
1444 GAATTTGACTATCGCGTTGC
1 GAATTTGACTATCGCGTTGC
* **
1464 AAATTTGACT-TCTGTATTGC
1 GAATTTGACTATC-GCGTTGC
*
1484 G-ATTT-ACAAATTCGCGTTGC
1 GAATTTGAC-TA-TCGCGTTGC
* *
1504 G-ATTT-ACAGATTCGCATTGC
1 GAATTTGAC-TA-TCGCGTTGC
* *
1524 CAA-TTGACT-TCAGTGTTGC
1 GAATTTGACTATC-GCGTTGC
*
1543 GAA-TTGACTATCGCATTGC
1 GAATTTGACTATCGCGTTGC
*
1562 GAATTTGACTTAT-GTGTTGC
1 GAATTTGAC-TATCGCGTTGC
1582 GAATTTGACT
1 GAATTTGACT
1592 TCTGTGTTGC
Statistics
Matches: 100, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.04
19 28 0.28
20 60 0.60
21 8 0.08
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
GAATTTGACTATCGCGTTGC
Found at i:1584 original size:39 final size:39
Alignment explanation
Indices: 1515--1591 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
1505 ATTTACAGAT
1515 TCGCATTGCCAATTGACTTCAGTGTTGCGAA-TTGACTA
1 TCGCATTGCCAATTGACTTCAGTGTTGCGAATTTGACTA
*
1553 TCGCATTGCGAATTTGACTT-ATGTGTTGCGAATTTGACT
1 TCGCATTGCCAA-TTGACTTCA-GTGTTGCGAATTTGACT
1592 TCTGTGTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 12 0.34
39 17 0.49
40 6 0.17
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (39 bp):
TCGCATTGCCAATTGACTTCAGTGTTGCGAATTTGACTA
Found at i:1592 original size:20 final size:20
Alignment explanation
Indices: 1527--1603 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
1517 GCATTGCCAA
1527 TTGACTTCA-GTGTTGCGAA-
1 TTGACTT-ATGTGTTGCGAAT
**
1546 TTGAC-TATCGCATTGCGAAT
1 TTGACTTAT-GTGTTGCGAAT
1566 TTGACTTATGTGTTGCGAAT
1 TTGACTTATGTGTTGCGAAT
*
1586 TTGACTTCTGTGTTGCGA
1 TTGACTTATGTGTTGCGA
1604 TTTACAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 13 0.27
20 31 0.63
21 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (20 bp):
TTGACTTATGTGTTGCGAAT
Found at i:1626 original size:20 final size:20
Alignment explanation
Indices: 1601--1639 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1591 TTCTGTGTTG
*
1601 CGATTTACAAATTTGCGTTC
1 CGATTTACAAATTCGCGTTC
*
1621 CGATTTACATATTCGCGTT
1 CGATTTACAAATTCGCGTT
1640 GCGACTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTC
Found at i:1660 original size:118 final size:118
Alignment explanation
Indices: 1444--1663 Score: 291
Period size: 118 Copynumber: 1.9 Consensus size: 118
1434 TTCAGTGTGT
*
1444 GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTGCGATTT
1 GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATTT
** *
1509 ACAGATTCGCATTGCCAATTGACTTCAGTGTTGCGAATTGACTATCGCATTGC
66 ACAGATTCGCATTGCCAATTGACAACAGGGTTGCGAATTGACTATCGCATTGC
* * * *
1562 GAATTTGACTTAT-GTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGCGTTCCGATT
1 GAATTTGAC-TATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATT
* * * * *
1626 TACATATTCGCGTTGCGACTTGGA-AACTGGGTTGCGAA
65 TACAGATTCGCATTGCCAATT-GACAACAGGGTTGCGAA
1664 ATTGGAGTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
118 82 0.94
119 5 0.06
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (118 bp):
GAATTTGACTATCGCGTTGCAAATTTGACTTCTGTATTGCGATTTACAAATTCGCGTTCCGATTT
ACAGATTCGCATTGCCAATTGACAACAGGGTTGCGAATTGACTATCGCATTGC
Found at i:3169 original size:356 final size:357
Alignment explanation
Indices: 2480--3191 Score: 1365
Period size: 356 Copynumber: 2.0 Consensus size: 357
2470 CAATTACGTG
2480 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
1 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
2545 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
66 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
2610 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
131 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
2675 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
196 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
2740 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
261 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
2805 CTATTAAATTTTCGATCGATTTAAAGAAACCTA
326 CTATTAAA-TTTCGATCGATTTAAAGAAACCTA
*
2838 GAATTAATTATTG-TGAACTTGAATTGGTTGTGAT-AAAAGGTCAGTAAACTGAATAAGACTCAA
1 GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
2901 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
66 ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
2966 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
131 ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
*
3031 AAAAAATTACAAAAATATCATATGTGGTACAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
196 AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
* *
3096 GATTGTCCTTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
261 GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
3161 CTATTAAATTTCGATCGATTTAAAGAAACCT
326 CTATTAAATTTCGATCGATTTAAAGAAACCT
3192 TGATAATAAT
Statistics
Matches: 350, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
355 23 0.07
356 294 0.84
357 20 0.06
358 13 0.04
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (357 bp):
GAATTAATTATTGTTGAACTTGAACTGGTTGTGATAAAAAGGTCAGTAAACTGAATAAGACTCAA
ATGACTCCTATAAGAAATTGGAAGATCGATAATAAATTCAAGTTCAGTGATTAATCAGTAAATCA
ATTGACCTTAAGATTTGTAATTCTGATTACTTTTGTTAAATGCTAGATGTTGGAATGCTCGGATA
AAAAAATTACAAAAATATCATATGTGGTAAAATTATGAAAATGTCTTGTACTGTAAAAAAGACAA
GACTGTCCCTGAAAGTGAGAAAAACCTGAAAAGTCATACTCGATTCAATAAAACTATCGTTTCAC
CTATTAAATTTCGATCGATTTAAAGAAACCTA
Found at i:15676 original size:18 final size:15
Alignment explanation
Indices: 15641--15673 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
15631 ACGATTCCGT
15641 TAACAACAACTCCAA
1 TAACAACAACTCCAA
*
15656 TAACAACAACTCCGA
1 TAACAACAACTCCAA
15671 TAA
1 TAA
15674 TAATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.30, G:0.03, T:0.15
Consensus pattern (15 bp):
TAACAACAACTCCAA
Found at i:18172 original size:7 final size:7
Alignment explanation
Indices: 18160--18197 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
18150 TCTCTCATTT
18160 CTTCTTC
1 CTTCTTC
18167 CTTCTTC
1 CTTCTTC
18174 CTTCTTC
1 CTTCTTC
*
18181 CTTCAT-
1 CTTCTTC
18187 CTTCTT-
1 CTTCTTC
18193 CTTCT
1 CTTCT
18198 CCCAAACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (7 bp):
CTTCTTC
Found at i:19357 original size:23 final size:23
Alignment explanation
Indices: 19312--19359 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19302 ATAGCACTAT
**
19312 GGTGCATTTCTACGTGGCACTTC
1 GGTGCATTTCTACACGGCACTTC
19335 GGTGCATTTCTACACGGTC-CTTC
1 GGTGCATTTCTACACGG-CACTTC
19358 GG
1 GG
19360 GAAAAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACACGGCACTTC
Found at i:19390 original size:24 final size:24
Alignment explanation
Indices: 19319--19391 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
19309 TATGGTGCAT
*
19319 TTCTACGTGGCACTTCGGTGC-AT
1 TTCTACGTGGCACTTCGGTGCAAA
** *
19342 TTCTACACGGTC-CTTCGG-GAAAAA
1 TTCTACGTGG-CACTTCGGTG-CAAA
19366 TTCTACGTGGCACTTCGGTGCAAA
1 TTCTACGTGGCACTTCGGTGCAAA
19390 TT
1 TT
19392 TATACGAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
22 1 0.03
23 15 0.39
24 21 0.55
25 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (24 bp):
TTCTACGTGGCACTTCGGTGCAAA
Found at i:19941 original size:11 final size:11
Alignment explanation
Indices: 19927--19961 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19917 CGTTTTACGG
*
19927 AGTACTATAGC
1 AGTACTATAAC
19938 AGTACTATAAC
1 AGTACTATAAC
*
19949 AGTACTGTAAC
1 AGTACTATAAC
19960 AG
1 AG
19962 GGGAATCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (11 bp):
AGTACTATAAC
Found at i:20468 original size:18 final size:18
Alignment explanation
Indices: 20423--20472 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
20413 ATGAACTTGA
*
20423 AAATAAGATATGAATATG
1 AAATAAGTTATGAATATG
*
20441 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATATG
20460 AAATAAGTTATGA
1 AAATAAGTTATGA
20473 GTTCGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATAAGTTATGAATATG
Found at i:20481 original size:19 final size:18
Alignment explanation
Indices: 20423--20487 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
20413 ATGAACTTGA
* **
20423 AAATAAGATATGAATATG
1 AAATAAGTTATGAATCGG
*
20441 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATCGG
*
20460 AAATAAGTTATGAGTTCGG
1 AAATAAGTTATGA-ATCGG
*
20479 AAACAAGTT
1 AAATAAGTT
20488 CTAAAATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
18 13 0.32
19 27 0.68
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (18 bp):
AAATAAGTTATGAATCGG
Found at i:20533 original size:13 final size:13
Alignment explanation
Indices: 20509--20568 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
20499 AAATAAAGAT
*
20509 TATGAAAATGAAA
1 TATGAAAGTGAAA
*
20522 TGTGAAAGTG-AA
1 TATGAAAGTGAAA
20534 TATGAAAGTGAAA
1 TATGAAAGTGAAA
* * *
20547 GATGAAAATGAGA
1 TATGAAAGTGAAA
20560 TATGAAAGT
1 TATGAAAGT
20569 TTTGTATATG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (13 bp):
TATGAAAGTGAAA
Found at i:20636 original size:39 final size:39
Alignment explanation
Indices: 20593--20675 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
20583 AAAAAGAATA
* *
20593 TGATATGACTGTTATGTATGATATTGTTTATCTTGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
*
20632 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
20671 TGATA
1 TGATA
20676 AAATCATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:22913 original size:25 final size:25
Alignment explanation
Indices: 22879--22953 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
22869 GAGTCGAGGG
22879 TTCTACGTGGTCCTTCGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
*
22904 TTCTACGTGGTCCTTTGGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
* *
22929 TTCTACATGGTCCTTCAGGACAAAT
1 TTCTACGTGGTCCTTCGGGACAAAT
22954 CTATGTGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (25 bp):
TTCTACGTGGTCCTTCGGGACAAAT
Found at i:27396 original size:21 final size:23
Alignment explanation
Indices: 27372--27421 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
27362 TTTTGTATTA
*
27372 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
27393 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
27414 TTATTATT
1 ATATTATT
27422 TAAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:28472 original size:3 final size:3
Alignment explanation
Indices: 28466--28512 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
28456 TATATTACGT
* *
28466 TTA TTA TATA TAA TATA T-A TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28512 T
1 T
28513 ACGTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39852 original size:48 final size:49
Alignment explanation
Indices: 39775--39868 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
39765 AATACTTCGC
* ** * *
39775 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGGAAAAA-AAAAACAT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAACAT
*
39823 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
39869 AGAGGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 34 0.87
49 5 0.13
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (49 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAACAT
Found at i:40841 original size:105 final size:105
Alignment explanation
Indices: 40655--41383 Score: 1323
Period size: 105 Copynumber: 6.9 Consensus size: 105
40645 AGGTTTTACC
40655 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
40720 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
40760 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
40825 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
40865 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
40930 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
40970 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
41035 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
41075 CAGAGCCAATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
41140 ACGAAGGGACCGCTGGTTGTCTACAAGCATTTCTCAAATC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
*
41180 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
41245 ATGAAGGGACCGCTGGTTGTCAGCAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
* * *
41285 CAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
41350 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
41384 CCAATTTCAG
Statistics
Matches: 599, Mismatches: 24, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 594 0.99
106 5 0.01
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
Found at i:41489 original size:20 final size:20
Alignment explanation
Indices: 41451--41492 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41441 TCAGAACTCT
*
41451 GAGTTCGATTTCGACTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
41471 GAGTTCGATTTTAATTTCAC
1 GAGTTCGATTTCAACTTCAC
41491 GA
1 GA
41493 CGAAGGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:41739 original size:21 final size:23
Alignment explanation
Indices: 41715--41764 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
41705 TTTTGTATTA
*
41715 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
41736 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
41757 TTATTATT
1 ATATTATT
41765 TAAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:42947 original size:18 final size:18
Alignment explanation
Indices: 42917--42983 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
42907 TTTACCATTT
*
42917 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
42935 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
42953 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
*
42971 TTTTTTAT-TTATT
1 TTATTTATATTATT
42984 CATGTAATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 5 0.13
18 33 0.87
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:44784 original size:17 final size:18
Alignment explanation
Indices: 44750--44790 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
44740 TATTCTAAAT
44750 AAAAATAAAATAAGTTAA
1 AAAAATAAAATAAGTTAA
*
44768 AAAAATGAAATAA-TTAA
1 AAAAATAAAATAAGTTAA
*
44785 TAAAAT
1 AAAAAT
44791 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAATAAAATAAGTTAA
Found at i:50033 original size:7 final size:7
Alignment explanation
Indices: 50017--50069 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
50007 TTTAGTGGTC
*
50017 AAAATAT
1 AAAATTT
50024 AAAATTT
1 AAAATTT
* *
50031 AAAGTAT
1 AAAATTT
50038 AAAATTT
1 AAAATTT
*
50045 AAAATAT
1 AAAATTT
50052 AAAATTT
1 AAAATTT
50059 AAAATTT
1 AAAATTT
50066 AAAA
1 AAAA
50070 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
AAAATTT
Found at i:50040 original size:14 final size:14
Alignment explanation
Indices: 50017--50069 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
50007 TTTAGTGGTC
50017 AAAATATAAAATTT
1 AAAATATAAAATTT
*
50031 AAAGTATAAAATTT
1 AAAATATAAAATTT
50045 AAAATATAAAATTT
1 AAAATATAAAATTT
*
50059 AAAATTTAAAA
1 AAAATATAAAA
50070 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
AAAATATAAAATTT
Found at i:53726 original size:63 final size:64
Alignment explanation
Indices: 53591--53748 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 64
53581 TTCAAGGTAC
* * * * * *
53591 ATCGATGCACATGAAGTGCATCAATGCACTCCTTTAAAATAAAAACATTGAATTCCATCAGTGT
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATTGAATACCATCAGTGT
* ** *
53655 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATTGAATAGGATTTA-TGT
1 ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATTGAATACCA-TCAGTGT
*
53718 ATCGATGCA-TAGATAGTGCATCGATGCACCC
1 ATCGATGCACAAG-TAGTGCATCGATGCACCC
53749 GTCAAGGGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
62 2 0.02
63 47 0.58
64 32 0.40
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATTGAATACCATCAGTGT
Found at i:54482 original size:23 final size:23
Alignment explanation
Indices: 54391--54474 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
54381 CAATCTTATA
*
54391 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
54414 CGGCAGTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
54437 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
54460 TGGCACTTCTGTGCA
1 TGGCACTTCGGTGCA
54475 TTTATACGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:61388 original size:23 final size:23
Alignment explanation
Indices: 61335--61393 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
61325 CAATCTTATA
* *
61335 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
61358 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
61381 TGGCACTTCGGTG
1 TGGCACTTCGGTG
61394 TATTTATACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:61403 original size:23 final size:23
Alignment explanation
Indices: 61336--61403 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
61326 AATCTTATAT
* * *
61336 GGCACTACAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTATACGC
* *
61359 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTATACGC
* *
61382 GGCACTTCGGTGTATTTATACG
1 GGCACTTCGGTGCAATTATACG
61404 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:62988 original size:35 final size:35
Alignment explanation
Indices: 62937--63018 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
62927 CTACCCTATG
*
62937 TATCGATGCATCCCTAGACGGGTGCATCGAAGCAC
1 TATCTATGCATCCCTAGACGGGTGCATCGAAGCAC
62972 TATCTATGCATCCCTAGACGGGTGCATCGAAGCAC
1 TATCTATGCATCCCTAGACGGGTGCATCGAAGCAC
63007 TATCTATGCATC
1 TATCTATGCATC
63019 GGTGCACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (35 bp):
TATCTATGCATCCCTAGACGGGTGCATCGAAGCAC
Found at i:63078 original size:63 final size:63
Alignment explanation
Indices: 62991--63152 Score: 186
Period size: 63 Copynumber: 2.6 Consensus size: 63
62981 ATCCCTAGAC
* * **
62991 GGGTGCATCGAAGCACTATCTATGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTT-AG
1 GGGTGCATCGATGCACTATCTATGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAG
* * * *
63053 GGGATGCATCGATGCACT-CCTTATGCATCGATGCACCAATCGCATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTATC-TATGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAG
* *
63117 GGGTGCATCGATGCACT-TCCTGTGCATCGATACACA
1 GGGTGCATCGATGCACTAT-CTATGCATCGATGCACA
63153 CTGAACAATT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
62 4 0.05
63 75 0.89
64 5 0.06
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (63 bp):
GGGTGCATCGATGCACTATCTATGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAG
Found at i:64517 original size:18 final size:18
Alignment explanation
Indices: 64494--64534 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
64484 ATATCCCTAT
64494 TTCTTATACAAAAATTTA
1 TTCTTATACAAAAATTTA
* *
64512 TTCTTATACATAACTTTA
1 TTCTTATACAAAAATTTA
64530 TTCTT
1 TTCTT
64535 TATCATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (18 bp):
TTCTTATACAAAAATTTA
Found at i:67328 original size:44 final size:44
Alignment explanation
Indices: 67247--67346 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
67237 GCACTATCTA
* **
67247 TGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTT-AGGGG
1 TGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAGGGG
* * *
67290 ATGTATCGATGCACCAATCCCATTCGATGTTTCCATTTTAATGGG
1 -TGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAGGGG
67335 TGCATCGATGCA
1 TGCATCGATGCA
67347 TTTCCTGTGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 44 0.92
45 4 0.08
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (44 bp):
TGCATCGATGCACAAATCCCATTCGATGTTTCCATTTTAAGGGG
Found at i:77620 original size:5 final size:5
Alignment explanation
Indices: 77591--77659 Score: 93
Period size: 5 Copynumber: 13.8 Consensus size: 5
77581 GTCCGTCCGT
* * * * *
77591 CTCGT CTCGT CTCGG CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
77641 CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCG
77660 TGGTCGTGGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.04, C:0.41, G:0.36, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:77668 original size:6 final size:6
Alignment explanation
Indices: 77657--77705 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
77647 TCGGCTCGGC
* *
77657 TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
77705 T
1 T
77706 AATACGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:83575 original size:5 final size:5
Alignment explanation
Indices: 83551--83610 Score: 66
Period size: 5 Copynumber: 12.0 Consensus size: 5
83541 GTCCGTCCGT
* * * * * *
83551 CTCGT CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
83601 CTCGG CTCGG
1 CTCGG CTCGG
83611 TTCGTGGTCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.07, C:0.40, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:83623 original size:6 final size:6
Alignment explanation
Indices: 83612--83666 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
83602 TCGGCTCGGT
*
83612 TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
83660 TCGTGG T
1 TCGTGG T
83667 AATACGTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:83940 original size:22 final size:22
Alignment explanation
Indices: 83915--83969 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
83905 TCAGGAGTTA
* *
83915 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
83937 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
83959 CGGGAGTTATA
1 CAGGAGTTATA
83970 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Done.