Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005947.1 Hibiscus syriacus cultivar Beakdansim tig00013962_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: 75471
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:1769 original size:14 final size:13
Alignment explanation
Indices: 1717--1801 Score: 57
Period size: 13 Copynumber: 6.4 Consensus size: 13
1707 ATTTAAACAA
* *
1717 TATTTATTATTTT
1 TATTTTTTATTAT
* *
1730 TATATTTAATTAT
1 TATTTTTTATTAT
*
1743 ATATATTTGTATTAT
1 -TAT-TTTTTATTAT
1758 CTATTTTTTATTAT
1 -TATTTTTTATTAT
*
1772 TATTTGTTTACT-T
1 TATTT-TTTATTAT
*
1785 T-TTTATTATTAT
1 TATTTTTTATTAT
1797 TATTT
1 TATTT
1802 ATTCTTTCGT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
11 4 0.07
12 5 0.09
13 19 0.35
14 17 0.31
15 10 0.18
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTTTATTAT
Found at i:1799 original size:25 final size:27
Alignment explanation
Indices: 1732--1801 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 27
1722 ATTATTTTTA
*
1732 TATTTAATTA-TATATATTTGTATTATC
1 TATTTTATTATTAT-TATTTGTATTATC
1759 TATTTT-TTATTATTATTTGT-TTA-C
1 TATTTTATTATTATTATTTGTATTATC
*
1783 TTTTTTATTATTATTATTT
1 TATTTTATTATTATTATTT
1802 ATTCTTTCGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 6 0.15
25 15 0.38
26 10 0.26
27 8 0.21
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (27 bp):
TATTTTATTATTATTATTTGTATTATC
Found at i:1866 original size:16 final size:16
Alignment explanation
Indices: 1847--1902 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1837 TATATATATA
1847 TATATATTATCACTAT
1 TATATATTATCACTAT
* *
1863 TATATATT-TTATTAT
1 TATATATTATCACTAT
1878 TACTATATTTATCACTAT
1 TA-TATA-TTATCACTAT
1896 GTATATA
1 -TATATA
1903 CTTTTGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 2 0.06
18 9 0.28
19 2 0.06
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.54
Consensus pattern (16 bp):
TATATATTATCACTAT
Found at i:1866 original size:18 final size:17
Alignment explanation
Indices: 1845--1902 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
1835 TATATATATA
1845 TATATATATTATCACTAT
1 TATATAT-TTATCACTAT
*
1863 TATATATTT-T-ATTAT
1 TATATATTTATCACTAT
1878 TACTATATTTATCACTAT
1 TA-TATATTTATCACTAT
1896 GTATATA
1 -TATATA
1903 CTTTTGATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 6 0.18
16 8 0.24
17 3 0.09
18 15 0.44
19 2 0.06
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (17 bp):
TATATATTTATCACTAT
Found at i:1869 original size:2 final size:2
Alignment explanation
Indices: 1819--1853 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1809 CGTCATTTTA
1819 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1854 TATCACTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7451 original size:30 final size:30
Alignment explanation
Indices: 7415--7473 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
7405 AGTTAAGGCA
*
7415 TGAGACATTATATTGTTGAGTTAGTGTTAG
1 TGAGACATTATATTGTTGAGTCAGTGTTAG
7445 TGAGACATTATATTGTTGAGTCAGTGTTA
1 TGAGACATTATATTGTTGAGTCAGTGTTA
7474 AAAAGCAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.42
Consensus pattern (30 bp):
TGAGACATTATATTGTTGAGTCAGTGTTAG
Found at i:8025 original size:16 final size:16
Alignment explanation
Indices: 8006--8047 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
7996 AATTTAGCGA
8006 AACCGAAATCAA-TCAG
1 AACCGAAATCAATTC-G
*
8022 AACCGAAATTAATTCG
1 AACCGAAATCAATTCG
8038 AACCGAAATC
1 AACCGAAATC
8048 GAAATCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.17
Consensus pattern (16 bp):
AACCGAAATCAATTCG
Found at i:8054 original size:38 final size:37
Alignment explanation
Indices: 8003--8116 Score: 156
Period size: 38 Copynumber: 3.0 Consensus size: 37
7993 CAAAATTTAG
* **
8003 CGAAACCGAAATCAATCAGAACCGAAATTAATTCGAAC
1 CGAAACCGAAATCAA-CAGAATCGAAATTAACCCGAAC
*
8041 CGAAATCGAAATCAACCAGAATCGAAATTAACCCGAAC
1 CGAAACCGAAATCAA-CAGAATCGAAATTAACCCGAAC
* *
8079 CGAAACCGAAATTAACCGAATCGAAATTAACCCGAAC
1 CGAAACCGAAATCAACAGAATCGAAATTAACCCGAAC
8116 C
1 C
8117 AAAAAAACTA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
37 22 0.32
38 46 0.68
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.14
Consensus pattern (37 bp):
CGAAACCGAAATCAACAGAATCGAAATTAACCCGAAC
Found at i:8079 original size:22 final size:22
Alignment explanation
Indices: 8063--8104 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
8053 CAACCAGAAT
8063 CGAAATTAACCCGAACCGAAAC
1 CGAAATTAACCCGAACCGAAAC
*
8085 CGAAATTAA-CCGAATCGAAA
1 CGAAATTAACCCGAACCGAAA
8105 TTAACCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.26, G:0.14, T:0.12
Consensus pattern (22 bp):
CGAAATTAACCCGAACCGAAAC
Found at i:8113 original size:16 final size:16
Alignment explanation
Indices: 8044--8114 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 16
8034 TTCGAACCGA
* *
8044 AATCGAAATCAACCAG
1 AATCGAAATTAACCCG
8060 AATCGAAATTAACCCGAACCG
1 AATCGAAATTAA--C---CCG
*
8081 AAACCGAAATTAA-CCG
1 -AATCGAAATTAACCCG
8097 AATCGAAATTAACCCG
1 AATCGAAATTAACCCG
8113 AA
1 AA
8115 CCAAAAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
15 11 0.25
16 19 0.43
18 1 0.02
21 2 0.05
22 11 0.25
ACGTcount: A:0.48, C:0.25, G:0.13, T:0.14
Consensus pattern (16 bp):
AATCGAAATTAACCCG
Found at i:8918 original size:32 final size:31
Alignment explanation
Indices: 8877--8972 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 31
8867 CCTAAATTGA
* *
8877 AAATCAACCGATCTGATATTGACCCTACCCG
1 AAATCAACCGATCTGGTATTGACCCGACCCG
* * ** *
8908 AAATCTAACCGATCAGGTATTAACTAGACCCAA
1 AAATC-AACCGATCTGGTATTGACCCGACCC-G
8941 AAATCAACCGATCTGGTATTGACCCGACCCG
1 AAATCAACCGATCTGGTATTGACCCGACCCG
8972 A
1 A
8973 TATTGATCAA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
31 6 0.12
32 40 0.78
33 5 0.10
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (31 bp):
AAATCAACCGATCTGGTATTGACCCGACCCG
Found at i:10287 original size:314 final size:314
Alignment explanation
Indices: 9491--10428 Score: 1739
Period size: 310 Copynumber: 3.0 Consensus size: 314
9481 CGTTGTGATC
9491 TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTC--TGACGAGGATAAGAGTAAATACGAGATTG
1 TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTCTATGACGAGGATAAGAGTAAATACGAGATTG
* *
9554 TCTATTTCTTAGGGACCACAACCCTTTATATAGTTGATTTAATAATAAGTTATTGTCTTCATCGA
66 TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
9619 ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
131 ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
9684 TTTATAACATAATCGATCACTTAATTTATGCTATA-TTTATGATAACAATATGCATTATAAACAT
196 TTTATAACATAATCGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
* * *
9748 ATGCCTATAATTATGGATTTTAATCCTACAATCTTCCATTTGGGAAAAATATGT
261 ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
*
9802 TTCCAAGAAGATAGAGTCCCTTAAGTAT-AACTCTATGACGGGGAT-A-AGTAAATACGAGATTG
1 TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTCTATGACGAGGATAAGAGTAAATACGAGATTG
9864 TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
66 TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
9929 ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
131 ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
*
9994 TTTATAACATAATTGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
196 TTTATAACATAATCGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
10059 ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
261 ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
*
10113 TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTCTATGACGAGGATAAGAGTAAATACAAGATTG
1 TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTCTATGACGAGGATAAGAGTAAATACGAGATTG
10178 TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
66 TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
*
10243 AATATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
131 ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
10308 -TT-TAACATAATCGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
196 TTTATAACATAATCGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
10371 ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
261 ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
10425 TTCC
1 TTCC
10429 TAGTAAATGT
Statistics
Matches: 610, Mismatches: 11, Indels: 11
0.97 0.02 0.02
Matches are distributed among these distances:
310 183 0.30
311 137 0.22
312 143 0.23
313 3 0.00
314 144 0.24
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (314 bp):
TTCCAAGAAGATAGAGTCCCTTAAGTATAAACTCTATGACGAGGATAAGAGTAAATACGAGATTG
TCTATTTCTTGGGGACCACAACCCTTTATATAGTTGATTTAAGAATAAGTTATTGTCTTCATCGA
ATTATAAATACAATTTTAATAGTATCTACACTTTTATTTCCATGACACTTCTAATACCTTATGAC
TTTATAACATAATCGATCACTTAATTTATGCTATATTTTATGATAACAATATGCATTATAAACAT
ATGCCCATAATTATGGATTTTAATCCTACAATCTTCCACTTGGGCAAAATATGT
Found at i:13247 original size:2 final size:2
Alignment explanation
Indices: 13240--13305 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
13230 ATTTGTTTCA
13240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13282 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
13306 TCTATTAACC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16045 original size:18 final size:17
Alignment explanation
Indices: 16020--16053 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16010 AGGAAAAGGA
*
16020 AAAGAAAATAACAAAAG
1 AAAGAAAAAAACAAAAG
16037 AAAGTAAAAAAACAAAA
1 AAAG-AAAAAAACAAAA
16054 ACAACAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAGAAAAAAACAAAAG
Found at i:16779 original size:20 final size:20
Alignment explanation
Indices: 16754--16791 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16744 AAGAATTGCT
*
16754 ATTAGGGCACTCAATTAAAG
1 ATTAGGGAACTCAATTAAAG
16774 ATTAGGGAACTCAATTAA
1 ATTAGGGAACTCAATTAA
16792 TTTCCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTAGGGAACTCAATTAAAG
Found at i:21328 original size:41 final size:42
Alignment explanation
Indices: 21203--21485 Score: 437
Period size: 42 Copynumber: 6.8 Consensus size: 42
21193 GATAGTCGAG
* * *
21203 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCAATAGTCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
* * *
21245 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCAATAGTCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
21287 GTTCGCGTTGCGATTCATTCC-AATTCGTTGCGACAGGCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
* *
21328 GTTCGCATTGCGATTCATTCC-AATTTGTTGCGACAGGCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
* * *
21369 GTTCGCATTGCAATTCA-TCCCAATTCGTTGCGACAGGCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
21410 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
*
21452 GTTCGCGTTGCGATTCATTCCAAATTCGCTGCGA
1 GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGA
21486 TAGTCCAAAT
Statistics
Matches: 228, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 3 0.01
41 106 0.46
42 119 0.52
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (42 bp):
GTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGGCGAA
Found at i:22266 original size:6 final size:6
Alignment explanation
Indices: 22255--22279 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22245 TCGTCCCGTC
22255 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
22280 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:22423 original size:41 final size:41
Alignment explanation
Indices: 22360--22562 Score: 334
Period size: 41 Copynumber: 4.9 Consensus size: 41
22350 ATTTGGACTA
22360 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGCCTG
*
22402 TCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTG
1 TCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
*
22443 TCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTG
1 TCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
* * *
22484 TCGCAACGAATTAGAATGAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
*
22525 TCGCAACGAATTTGGAATGAATCGCAACGTGAACTTCG
1 TCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCG
22563 ACTATCGCGT
Statistics
Matches: 153, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
41 118 0.77
42 35 0.23
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (41 bp):
TCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTG
Found at i:22569 original size:21 final size:20
Alignment explanation
Indices: 22503--22570 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
22493 ATTAGAATGA
22503 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * *
22524 ATCGCAAC-GAATTTGGAAT
1 ATCGCAACGGAACTTCGACT
22543 GAATCGCAACGTGAACTTCGACT
1 --ATCGCAACG-GAACTTCGACT
22566 ATCGC
1 ATCGC
22571 GTTGCGAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 8 0.22
21 21 0.57
23 8 0.22
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAACGGAACTTCGACT
Found at i:33967 original size:23 final size:24
Alignment explanation
Indices: 33910--33975 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
33900 AATATCATAC
*
33910 TCGTTTATATGTTCACGAATATAT
1 TCGTTTATATATTCACGAATATAT
* * *
33934 TCGTTTATATATTTACGAATGTGT
1 TCGTTTATATATTCACGAATATAT
33958 TC-TTTATATATTCACGAA
1 TCGTTTATATATTCACGAA
33976 CGAATTCGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.41
24 22 0.59
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (24 bp):
TCGTTTATATATTCACGAATATAT
Found at i:43496 original size:59 final size:59
Alignment explanation
Indices: 43380--43499 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 59
43370 TAGGGGTCAA
* *
43380 TTAGAAAAAGATTATAATTTAAGGATGAAATTAGAATGTTTAAAAATATTAAAACTAAT
1 TTAGAAAAAGATCATAATTTAAGGATAAAATTAGAATGTTTAAAAATATTAAAACTAAT
* * *
43439 TTAGAATAAGAGTCATAATTTGAA-GATAAAATTA-AATG-TTAAAAATTTTAACGACTAAT
1 TTAGAAAAAGA-TCATAATTT-AAGGATAAAATTAGAATGTTTAAAAATATTAA-AACTAAT
43498 TT
1 TT
43500 TAAAATGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 12 0.23
59 22 0.42
60 17 0.32
61 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (59 bp):
TTAGAAAAAGATCATAATTTAAGGATAAAATTAGAATGTTTAAAAATATTAAAACTAAT
Found at i:43517 original size:60 final size:60
Alignment explanation
Indices: 43390--43517 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 60
43380 TTAGAAAAAG
* *
43390 ATTATAATTTAAGGATGAAATTAGAATGTTTAAAAATATTAAAACTAATTTAGAATAAGA
1 ATTATAATTTAAGGATAAAATTAGAATGTTTAAAAATATTAAAACTAATTTAAAATAAGA
* * * * * *
43450 GTCATAATTTGAA-GATAAAATTA-AATG-TTAAAAATTTTAACGACTAATTTTAAAATGATA
1 ATTATAATTT-AAGGATAAAATTAGAATGTTTAAAAATATTAA-AACTAA-TTTAAAATAAGA
43510 ATTATAAT
1 ATTATAAT
43518 GGGATGCATT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
58 12 0.22
59 9 0.16
60 32 0.58
61 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (60 bp):
ATTATAATTTAAGGATAAAATTAGAATGTTTAAAAATATTAAAACTAATTTAAAATAAGA
Found at i:46042 original size:45 final size:45
Alignment explanation
Indices: 45993--46248 Score: 293
Period size: 45 Copynumber: 5.7 Consensus size: 45
45983 ACTCTAACAT
* *
45993 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATACA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* * * *
46038 CTTTTATGTTGATAATGTACCCATATACATCTT-AACCATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCAT-TTCAACTATAGTATA
* * * * *
46083 TTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* *
46128 CTTTTCTGTTGATAATGCACTCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* * * **
46173 CTTTTCTGTTGATAATGCACCTATATGCATTTCAACTCTGGCGT-
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
*
46217 CTTTTCAT-TCTAATAATGCACCCATATGCATT
1 CTTTTC-TGT-TGATAATGCACCCATATGCATT
46249 ATTTTGTTAT
Statistics
Matches: 184, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
44 9 0.05
45 173 0.94
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
Found at i:46105 original size:90 final size:90
Alignment explanation
Indices: 45950--46209 Score: 296
Period size: 90 Copynumber: 2.9 Consensus size: 90
45940 GTAACCTCCA
* * **
45950 TTTATGATT-ATAATACA-CCATTATACATTTTAAACTCTAACAT-CTTTTCTGTTGATAATGCA
1 TTTATG-TTGATAATGCACCCA-TATACA-TTTCAACTCTAGTATACTTTTCTGTTGATAATGCA
*
46012 CCCATATGCATTTCAACTATAATACACT
63 CCCATATGCATTTCAACTATAACACACT
* * *
46040 TTTATGTTGATAATGTACCCATATACATCTT-AAC-CATAGTATATTTTTCTGTTGATAATGTAC
1 TTTATGTTGATAATGCACCCATATACAT-TTCAACTC-TAGTATACTTTTCTGTTGATAATGCAC
* * * *
46103 CCATATACATTTCAACTCTAGCATACT
64 CCATATGCATTTCAACTATAACACACT
* * * *
46130 TTTCTGTTGATAATGCACTCATATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCT
1 TTTATGTTGATAATGCACCCATATACATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCC
46195 ATATGCATTTCAACT
66 ATATGCATTTCAACT
46210 CTGGCGTCTT
Statistics
Matches: 144, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
88 1 0.01
89 12 0.08
90 127 0.88
91 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (90 bp):
TTTATGTTGATAATGCACCCATATACATTTCAACTCTAGTATACTTTTCTGTTGATAATGCACCC
ATATGCATTTCAACTATAACACACT
Found at i:46315 original size:79 final size:79
Alignment explanation
Indices: 46219--46409 Score: 294
Period size: 79 Copynumber: 2.4 Consensus size: 79
46209 TCTGGCGTCT
* * * *
46219 TTTCATTCTAATAATGCACCCATATGCATTATT-TTGTTATACCGATAATATACCCATATACATA
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTT-TTATACCAATAATATAACCATATACATA
46283 TCAGCTAAGGTATCC
65 TCAGCTAAGGTATCC
* * * *
46298 TTTTATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCAATAATGTAACCATATACATAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATACCAATAATATAACCATATACATAT
46363 CAGCTAAGGTATCC
66 CAGCTAAGGTATCC
46377 TTTCATGCCAATAATGCACCCATATGCATTATT
1 TTTCATGCCAATAATGCACCCATATGCATTATT
46410 ATTCTATTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 99 0.98
80 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (79 bp):
TTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATACCAATAATATAACCATATACATAT
CAGCTAAGGTATCC
Found at i:51452 original size:45 final size:45
Alignment explanation
Indices: 51397--51568 Score: 238
Period size: 45 Copynumber: 3.8 Consensus size: 45
51387 ACTCTAACAT
* *
51397 CTTTTCTGTTGATAAT-TCACCCATATGCGTTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGT-ACCCATATACATTTCAACTATAGTATA
* * * *
51442 CTTTTATGTTGATAATGTACCCATATACATCTCAACCATAATATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* *
51487 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
* *
51532 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACT
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACT
51569 CTGACATCCT
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 111 0.99
46 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
Found at i:51569 original size:45 final size:45
Alignment explanation
Indices: 51386--51607 Score: 236
Period size: 45 Copynumber: 5.0 Consensus size: 45
51376 ATACATTTTA
* * *
51386 AACTCTAACAT-CTTTTCTGTTGATAATTCACCCATATGCGTTTC
1 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
* * * * * *
51430 AACTATAGTATACTTTTATGTTGATAATGTACCCATATACATCTC
1 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
** * *
51475 AAC-CATAATATACTTTTCTGTTGATAATGTACCCATATACATTTC
1 AACTC-TAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
51520 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
* ***
51565 AACTCT-GACAT-CCTTTCATGCCAATAATGCACCCATATGCATT
1 AACTCTAG-CATACTTTTC-TGTTGATAATGCACCCATATGCATT
51608 ATTTTGTTAT
Statistics
Matches: 152, Mismatches: 21, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
44 14 0.09
45 137 0.90
46 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (45 bp):
AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
Found at i:51673 original size:79 final size:79
Alignment explanation
Indices: 51571--51771 Score: 314
Period size: 79 Copynumber: 2.5 Consensus size: 79
51561 TTTCAACTCT
* *
51571 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATT-TTGTTATGCCGATAATATACTCAT
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTT-TTATGCCAATAATATACCCAT
51635 ATACATATCAGCTAA
65 ATACATATCAGCTAA
* * *
51650 GGCATCCTTTCATGCCACTAATGCACCCATATGCATTATTCTTTTATGCCAATAATGTACCCATA
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCAATAATATACCCATA
51715 TACATATCAGCTAA
66 TACATATCAGCTAA
* * *
51729 GACATCCTTTTATGCCAATAATGTACCCATATGCATAATTCTT
1 GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTT
51772 CTATTCATTA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 109 0.98
80 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (79 bp):
GACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCAATAATATACCCATA
TACATATCAGCTAA
Found at i:53190 original size:14 final size:14
Alignment explanation
Indices: 53171--53200 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53161 AAATTTCCAT
*
53171 AAAATATATTTTAA
1 AAAATATACTTTAA
53185 AAAATATACTTTAA
1 AAAATATACTTTAA
53199 AA
1 AA
53201 CAAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATACTTTAA
Found at i:55009 original size:23 final size:23
Alignment explanation
Indices: 54983--55027 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
54973 CACCATAGCT
*
54983 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
55006 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
55028 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:55265 original size:149 final size:149
Alignment explanation
Indices: 54995--55309 Score: 524
Period size: 149 Copynumber: 2.1 Consensus size: 149
54985 TATAATTGCA
*
54995 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAA
*
55059 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
* * *
55124 CCACATAATATATATATATC
130 CCAAAGAATATACATATATC
**
55144 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
55209 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
*
55274 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
55293 TCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
55310 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
148 1 0.01
149 154 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:55429 original size:14 final size:14
Alignment explanation
Indices: 55410--55437 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55400 AACTTGTAAT
55410 TCACGTATCACATA
1 TCACGTATCACATA
55424 TCACGTATCACATA
1 TCACGTATCACATA
55438 GTTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:56840 original size:21 final size:21
Alignment explanation
Indices: 56816--56860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56806 TGTTGTTCGT
* *
56816 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
56837 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
56858 TTG
1 TTG
56861 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:59335 original size:23 final size:22
Alignment explanation
Indices: 59311--59355 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59301 CTTCGATATT
59311 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
59335 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
59356 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:60843 original size:3 final size:3
Alignment explanation
Indices: 60837--60902 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
60827 TATTATTTTT
* * * * * *
60837 TAA TAA TAA TAA T-A TATA TTA TAA TTA TTA TTA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
60882 TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
60903 ATAAAAATGG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.93
4 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
TAA
Found at i:61333 original size:112 final size:109
Alignment explanation
Indices: 61133--61438 Score: 361
Period size: 112 Copynumber: 2.8 Consensus size: 109
61123 TAGAGTCATT
* * *
61133 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTT-TT-TT-TT-AGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * * *
61194 GAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 GAACTTACTCTGGAAAAGCTAATCCATCAAATGATGAATTTAAA
*
61238 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCAT
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGAT---GAGTTCTTCTCAT
* * *
61303 TATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAA
63 TATGAACT-TACTCTGGAAAAGCTAATCCATCAAATGATGAATTTAAA
* *
61350 CAAAAGGTTGAACAAGTTCTTCTCCTTATGAACTTTTTCTGCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAA---TTTCT-TCTTCTTCAGATGAGTTCTTCTCA
*
61415 TTATGAACTTTCTCTGGAAAAGCT
62 TTATGAACTTACTCTGGAAAAGCT
61439 GATGCTAATC
Statistics
Matches: 168, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
105 31 0.18
106 2 0.01
107 2 0.01
108 2 0.01
109 4 0.02
112 80 0.48
113 31 0.18
115 5 0.03
116 11 0.07
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (109 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTACTCTGGAAAAGCTAATCCATCAAATGATGAATTTAAA
Found at i:61566 original size:36 final size:39
Alignment explanation
Indices: 61492--61582 Score: 134
Period size: 36 Copynumber: 2.4 Consensus size: 39
61482 TGAAATAAGC
* *
61492 TCTTCTCATTGTAAACTTTTTCTTCTCCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTTTCTTCTCCTTCAGATGAGT
*
61531 TGTTCTCATTATGAACTTTTTC-T-T-CTTCAGATGAGT
1 TCTTCTCATTATGAACTTTTTCTTCTCCTTCAGATGAGT
61567 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
61583 CTCTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
36 27 0.56
37 1 0.02
38 1 0.02
39 19 0.40
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (39 bp):
TCTTCTCATTATGAACTTTTTCTTCTCCTTCAGATGAGT
Found at i:61840 original size:113 final size:113
Alignment explanation
Indices: 61528--62004 Score: 540
Period size: 113 Copynumber: 4.2 Consensus size: 113
61518 CCTTCAGATG
*
61528 AGTTGTTCTCATTATGAAC--TTT-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAACCTCT--
1 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCTAA
* * * * * *
61587 CTGGAAAAGTTGATCCA-TCAAGTGAT-AGATTTGAGTAAAAATTTGAACA
65 CTGGTAATGTTGATCCATTGAA-TGATGA-ATTTAAGCAAAAAGTTGAACA
*
61636 AATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
1 AGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTC
* * * ** * *
61700 TACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
62 TAACTGGTAATGTTGATCCATTGAATGATGAATTTAAGCAAAAAGTTGAACA
* * * * *
61752 AGTTCTTCTCCTTATGAACTTTTTATGCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGAAC
1 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
*
61817 TGGTAATGTTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACA
66 TGGTAATGTTGATCCATTGAATGATGAATTTAAGCAAAAAGTTGAACA
* * * *
61865 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGGTGAGTTCTTCTTATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* ** * * *
61930 TGGTACTACTGTTCCACTGAGTGATGAATTTAAGCAAAAAGTTGAACA
66 TGGTAATGTTGATCCATTGAATGATGAATTTAAGCAAAAAGTTGAACA
61978 AGTTCTTCTCATTATGAACTTTGTTCT
1 AGTTCTTCTCATTATGAACTTT-TTCT
62005 GGAAAAGCTG
Statistics
Matches: 312, Mismatches: 43, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
108 16 0.05
109 1 0.00
110 2 0.01
111 2 0.01
112 11 0.04
113 183 0.59
114 8 0.03
115 19 0.06
116 64 0.21
117 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
TGGTAATGTTGATCCATTGAATGATGAATTTAAGCAAAAAGTTGAACA
Found at i:62866 original size:115 final size:115
Alignment explanation
Indices: 62700--63014 Score: 524
Period size: 115 Copynumber: 2.7 Consensus size: 115
62690 GATCATGCAG
* * * * * *
62700 TTCATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
62764 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATCTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATCTCTACTATGAGCACA
* *
62814 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATATCAAACTAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
62879 AACACTTCCAGAAAATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATCTCTACTATGAGCACA
62929 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
62994 AACACTTCCAAAAGATGCTAT
66 AACACTTCCAGAAGATGCTAT
63015 GAGCACATTC
Statistics
Matches: 186, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
114 23 0.12
115 163 0.88
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATCTCTACTATGAGCACA
Found at i:63077 original size:93 final size:93
Alignment explanation
Indices: 62918--63208 Score: 546
Period size: 93 Copynumber: 3.1 Consensus size: 93
62908 CTTATTTCTA
*
62918 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAG
*
62983 ATAACTCAAAGAACACTTCCAAAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
63011 CTATGAGCACATTCATCTTTCAAATCCAATGATGGGTTTTTAGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAG
63076 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
63104 CTATGAGCACATTCATCTTTTAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAG
63169 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
63197 CTATGAGCACAT
1 CTATGAGCACAT
63209 GGCACTTGTT
Statistics
Matches: 193, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 193 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:64211 original size:14 final size:14
Alignment explanation
Indices: 64188--64270 Score: 81
Period size: 14 Copynumber: 6.3 Consensus size: 14
64178 TCTTGACCCC
*
64188 CTTTTTTCTTTTTT
1 CTTTTCTCTTTTTT
64202 CTTTTCTCTTTTTT
1 CTTTTCTCTTTTTT
64216 -TCTTTCTCTTTTTT
1 CT-TTTCTCTTTTTT
*
64230 C-CTT-T-TTTTTT
1 CTTTTCTCTTTTTT
64241 CTTTT-TC-TTTTT
1 CTTTTCTCTTTTTT
64253 CTTGTTCT-TTTTTT
1 CTT-TTCTCTTTTTT
64267 CTTT
1 CTTT
64271 CTTCAAGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
11 7 0.12
12 12 0.20
13 6 0.10
14 34 0.58
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (14 bp):
CTTTTCTCTTTTTT
Found at i:64235 original size:36 final size:36
Alignment explanation
Indices: 64188--64270 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
64178 TCTTGACCCC
64188 CTTTTTTCTTTTTTCTTTTC-TCTT-TTTTTCTT-TCT
1 CTTTTTTCTTTTTT-TTTTCTTCTTCTTTTTCTTGT-T
* *
64223 CTTTTTTCCTTTTTTTTTCTTTTTCTTTTTCTTGTT
1 CTTTTTTCTTTTTTTTTTCTTCTTCTTTTTCTTGTT
64259 CTTTTTTTCTTT
1 C-TTTTTTCTTT
64271 CTTCAAGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 5 0.12
35 16 0.39
36 10 0.24
37 10 0.24
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (36 bp):
CTTTTTTCTTTTTTTTTTCTTCTTCTTTTTCTTGTT
Found at i:64271 original size:18 final size:16
Alignment explanation
Indices: 64191--64273 Score: 78
Period size: 18 Copynumber: 4.8 Consensus size: 16
64181 TGACCCCCTT
64191 TTTTCTTTTTTCTTTTC
1 TTTT-TTTTTTCTTTTC
*
64208 -TCTTTTTTTCTTTCTC
1 TTTTTTTTTTCTTT-TC
*
64224 TTTTTTCCTTTTTTTTTC
1 TTTTTT--TTTTCTTTTC
64242 TTTTTCTTTTTCTTGTTC
1 TTTTT-TTTTTCTT-TTC
64260 TTTTTTTCTTTCTT
1 TTTTTTT-TTTCTT
64274 CAAGAATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
15 10 0.18
16 4 0.07
17 12 0.22
18 21 0.38
19 8 0.15
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTC
Found at i:64272 original size:12 final size:12
Alignment explanation
Indices: 64189--64273 Score: 81
Period size: 12 Copynumber: 7.1 Consensus size: 12
64179 CTTGACCCCC
64189 TTTTTTCTTT-T
1 TTTTTTCTTTCT
64200 TTCTTTTC--TCT
1 TT-TTTTCTTTCT
64211 TTTTTTCTTTCT
1 TTTTTTCTTTCT
*
64223 CTTTTTTCCTT-T
1 -TTTTTTCTTTCT
64235 TTTTTTCTTT-T
1 TTTTTTCTTTCT
64246 TCTTTTTCTTGTTCT
1 T-TTTTTC-T-TTCT
64261 TTTTTTCTTTCT
1 TTTTTTCTTTCT
64273 T
1 T
64274 CAAGAATAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
10 6 0.10
11 16 0.25
12 20 0.32
13 11 0.17
14 8 0.13
15 2 0.03
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:71589 original size:15 final size:15
Alignment explanation
Indices: 71566--71596 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71556 TGAAATGAAT
71566 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
71581 AATGTATGTATGCAA
1 AATGAATGTATGCAA
71596 A
1 A
71597 GAGGTATTGA
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:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (15 bp):
AATGAATGTATGCAA
Done.