Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001839.1 Hibiscus syriacus cultivar Beakdansim tig00003723_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: 159195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1756 original size:17 final size:16
Alignment explanation
Indices: 1734--1766 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1724 ATCAATAATC
*
1734 AAAAAATTGTTTTCCA
1 AAAAAAATGTTTTCCA
1750 AAAAAAATGTTTTCCA
1 AAAAAAATGTTTTCCA
1766 A
1 A
1767 CTATCAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (16 bp):
AAAAAAATGTTTTCCA
Found at i:4852 original size:32 final size:32
Alignment explanation
Indices: 4816--4878 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
4806 TAAGTTAATC
4816 TAAAATC-ACAAATAATTGATGATAATTTCTCT
1 TAAAATCTAC-AATAATTGATGATAATTTCTCT
* * *
4848 TAAAATCTTCTATAATTGATGATACTTTCTC
1 TAAAATCTACAATAATTGATGATAATTTCTC
4879 AAAACTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.41
Consensus pattern (32 bp):
TAAAATCTACAATAATTGATGATAATTTCTCT
Found at i:5073 original size:19 final size:19
Alignment explanation
Indices: 5051--5090 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5041 ATAATGATTA
5051 ATTTTTCAAATA-AAATTTT
1 ATTTTT-AAATATAAATTTT
*
5070 ATTTTTAAATATATATTTT
1 ATTTTTAAATATAAATTTT
5089 AT
1 AT
5091 AAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTAAATATAAATTTT
Found at i:6174 original size:31 final size:30
Alignment explanation
Indices: 6139--6209 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
6129 AAATATTAAT
*
6139 ATTTTGTTACAAATCGATAAAGTTAATGATC
1 ATTTTGTTACAAATCGATAAAATTAAT-ATC
*
6170 ATTTTGTTAGAAATCGATAAAATTAATATC
1 ATTTTGTTACAAATCGATAAAATTAATATC
* *
6200 AATTTATTAC
1 ATTTTGTTAC
6210 TTTTTAAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (30 bp):
ATTTTGTTACAAATCGATAAAATTAATATC
Found at i:17038 original size:16 final size:17
Alignment explanation
Indices: 17017--17060 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
17007 TTTCATACAT
17017 AAATAAAATATAA-TGA
1 AAATAAAATATAATTGA
*
17033 AAAT-AAATGTAATTGA
1 AAATAAAATATAATTGA
17049 AAATACAAATAT
1 AAATA-AAATAT
17061 TAACATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
18 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (17 bp):
AAATAAAATATAATTGA
Found at i:17598 original size:76 final size:75
Alignment explanation
Indices: 17511--17674 Score: 204
Period size: 76 Copynumber: 2.2 Consensus size: 75
17501 GGAAAATAAG
* ** ** *
17511 GACTAAAATAAAAGATTTATAAATGTGGTGGCCATATTCGAATATCAAAG-AAACATACATGAAA
1 GACTAAAATAAAAGATTTAAAAAACTCATGGCCATATTCGAATAGCAAAGAAAACATACA--AAA
17575 TATTAAATCAGT
64 TATTAAATCAGT
* * * * *
17587 GACTAAAATAAAATATTTAAAAAACTCATGGTCATATTTGAATAGCAAGGAAAATATACAAAATA
1 GACTAAAATAAAAGATTTAAAAAACTCATGGCCATATTCGAATAGCAAAGAAAACATACAAAATA
17652 TTAAATCAGT
66 TTAAATCAGT
17662 GACTAAAATAAAA
1 GACTAAAATAAAA
17675 CTATTACAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
75 28 0.37
76 40 0.53
77 8 0.11
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (75 bp):
GACTAAAATAAAAGATTTAAAAAACTCATGGCCATATTCGAATAGCAAAGAAAACATACAAAATA
TTAAATCAGT
Found at i:18972 original size:3 final size:3
Alignment explanation
Indices: 18943--19003 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
18933 TGTAATATAT
* **
18943 TAA TAA CAA TAA TTAA TAA GCA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18988 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
19004 TACAATTAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19059 original size:2 final size:2
Alignment explanation
Indices: 19052--19076 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19042 CTACACCTTG
19052 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19077 GCATGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19542 original size:2 final size:2
Alignment explanation
Indices: 19535--19560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19525 ATGTATTCAC
19535 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19561 ATTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19756 original size:16 final size:16
Alignment explanation
Indices: 19737--19768 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19727 TATCTCTTAA
19737 AATTTTATAAATTATC
1 AATTTTATAAATTATC
19753 AATTTTATAAATTATC
1 AATTTTATAAATTATC
19769 TCTTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTATAAATTATC
Found at i:21022 original size:31 final size:29
Alignment explanation
Indices: 20972--21183 Score: 122
Period size: 30 Copynumber: 6.9 Consensus size: 29
20962 GATACTAATG
* *
20972 ATTAA-TTCAAAAAAAATATTTTATTTTTT
1 ATTAACTT-AAAAAATATATTTTATTTTGT
* *
21001 ATCTTAACTTTAAAAGTATATTTTATTTTGT
1 A--TTAACTTAAAAAATATATTTTATTTTGT
* *
21032 ATTAACTTAAAAAATATATTTT-TTATAT
1 ATTAACTTAAAAAATATATTTTATTTTGT
* *
21060 CTTAACTTCATATATATATATATATATATTATTCTTTT
1 ATTAACTT-A-A-A-A-A-ATATAT-T-TTATT-TTGT
* *
21098 ATTAACTTAACAAATATATTTTATTATTAT
1 ATTAACTTAAAAAATATATTTTATT-TTGT
* * * * * *
21128 TTTAACTTCAAATATTTTTTTTATTCTTCT
1 ATTAACTTAAAAAATATATTTTATT-TTGT
*
21158 ATTAACTTAAAAATAAATATTTTATT
1 ATTAACTTAAAAA-ATATATTTTATT
21184 ATTAACTTAA
Statistics
Matches: 140, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
28 11 0.08
29 21 0.15
30 41 0.29
31 33 0.24
32 9 0.06
33 2 0.01
34 7 0.05
35 1 0.01
36 3 0.02
37 3 0.02
38 9 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTAACTTAAAAAATATATTTTATTTTGT
Found at i:21106 original size:66 final size:61
Alignment explanation
Indices: 20972--21185 Score: 190
Period size: 60 Copynumber: 3.4 Consensus size: 61
20962 GATACTAATG
* * * * * *
20972 ATTAA-TTCAAAAAAAATATTTTATTTTTTATCTTAACTTTAAA-AGTATAT-TTTATT-TTGT
1 ATTAACTT-AAAAAATATATTTTA--TTATATCTTAACTTCAAATATTTTATATTTATTCTTCT
21032 ATTAACTTAAAAAATATATTTT-TTATATCTTAACTTCATATATATATATATATATATTATTCTT
1 ATTAACTTAAAAAATATATTTTATTATATCTTAACTTCA-A-ATAT-T-T-TATAT-TTATTCTT
*
21096 TT
60 CT
* *
21098 ATTAACTTAACAAATATATTTTATTATTATTTTAACTTCAAATATTTT-T-TTTATTCTTCT
1 ATTAACTTAAAAAATATATTTTATTA-TATCTTAACTTCAAATATTTTATATTTATTCTTCT
*
21158 ATTAACTTAAAAATAAATATTTTATTAT
1 ATTAACTTAAAAA-ATATATTTTATTAT
21186 TAACTTAAGT
Statistics
Matches: 130, Mismatches: 11, Indels: 26
0.78 0.07 0.16
Matches are distributed among these distances:
57 14 0.11
58 1 0.01
59 1 0.01
60 41 0.32
61 16 0.12
62 1 0.01
63 4 0.03
64 2 0.02
65 6 0.05
66 28 0.22
67 4 0.03
68 12 0.09
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (61 bp):
ATTAACTTAAAAAATATATTTTATTATATCTTAACTTCAAATATTTTATATTTATTCTTCT
Found at i:21286 original size:24 final size:22
Alignment explanation
Indices: 21239--21281 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21229 AGTTAATAAC
*
21239 AAAATATATTTTTTAAGTTAAT
1 AAAATATATTTTTAAAGTTAAT
21261 AAAATATATTTTTAAAGTTAA
1 AAAATATATTTTTAAAGTTAA
21282 GATAAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
AAAATATATTTTTAAAGTTAAT
Found at i:21303 original size:52 final size:53
Alignment explanation
Indices: 21205--21360 Score: 151
Period size: 53 Copynumber: 2.9 Consensus size: 53
21195 TTAATAAAAG
* * * * * * *
21205 AATAAAATATATTGTTTGAAGATAAGTTAATAACAAAATATATTTTTTAAGT-T
1 AATAAAATATATT-TTTAAAGTTAAGATAAGAATAAAATATATTTTTTAAATAA
21258 AATAAAATATATTTTTAAAGTTAAGATAAGAATAAAATATA-TTTTTAAATAAA
1 AATAAAATATATTTTTAAAGTTAAGATAAGAATAAAATATATTTTTTAAAT-AA
* *
21311 AATAAAATATA-TTTAATAAGTT-AGAT-AGAAAGTAAAATATATATTTTAAA
1 AATAAAATATATTTTTA-AAGTTAAGATAAG-AA-TAAAATATATTTTTTAAA
21361 AATTAAGATA
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
51 10 0.11
52 33 0.38
53 38 0.43
54 7 0.08
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (53 bp):
AATAAAATATATTTTTAAAGTTAAGATAAGAATAAAATATATTTTTTAAATAA
Found at i:21314 original size:23 final size:24
Alignment explanation
Indices: 21278--21324 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
21268 ATTTTTAAAG
*
21278 TTAAGATAAGAATAAAATATATTT
1 TTAAGATAAAAATAAAATATATTT
21302 TTAA-ATAAAAATAAAATATATTT
1 TTAAGATAAAAATAAAATATATTT
21325 AATAAGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
TTAAGATAAAAATAAAATATATTT
Found at i:22684 original size:81 final size:81
Alignment explanation
Indices: 22549--22713 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
22539 ATTAAACGAA
*
22549 TATATTCACAAATATTAAACAAACATATTCGTGAATGTTGAATAAACAAACACAAACACCTTAAA
1 TATATTCACAAATATTAAACAAACATATTCGCGAATGTTGAATAAACAAACACAAACACCTTAAA
*
22614 AAATAAACACCATTTC
66 AAAGAAACACCATTTC
22630 TATATTCACAAATATTAAACAAACATATTCGCGAATGTTGAATAAACAAACACAAACACCTTAAA
1 TATATTCACAAATATTAAACAAACATATTCGCGAATGTTGAATAAACAAACACAAACACCTTAAA
22695 AAAGAAACACCATTTC
66 AAAGAAACACCATTTC
22711 TAT
1 TAT
22714 CTAAGCCATA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.25
Consensus pattern (81 bp):
TATATTCACAAATATTAAACAAACATATTCGCGAATGTTGAATAAACAAACACAAACACCTTAAA
AAAGAAACACCATTTC
Found at i:32381 original size:20 final size:20
Alignment explanation
Indices: 32295--32426 Score: 149
Period size: 21 Copynumber: 6.5 Consensus size: 20
32285 CAGTTTCCAG
32295 ATTCGCAACGCGATAGTCCAA
1 ATTCGCAACGCGATAGT-CAA
* * * *
32316 AATCACAACGTGATAGTGGAA
1 ATTCGCAACGCGATAGT-CAA
32337 ATTCGCAACGCGATAGTCGAA
1 ATTCGCAACGCGATAGTC-AA
32358 ATTCGCAACGCGATAGTCAA
1 ATTCGCAACGCGATAGTCAA
* *
32378 ATTCGCAATGCGAAAGTCAA
1 ATTCGCAACGCGATAGTCAA
* *
32398 ATTTGCAACACAGA-AGTCAA
1 ATTCGCAACGC-GATAGTCAA
32418 ATTCGCAAC
1 ATTCGCAAC
32427 TTAATTATCT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
20 42 0.45
21 52 0.55
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATTCGCAACGCGATAGTCAA
Found at i:33497 original size:26 final size:25
Alignment explanation
Indices: 33444--33504 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
33434 TGAGTTGGTG
* *
33444 TTTAGGTTTTAAGATAGATTAAGGA
1 TTTAGGTTTTAAGAGAGATTAAGAA
* *
33469 TTTAGGGTTTTAAGAGAGGTTTAGAA
1 TTTA-GGTTTTAAGAGAGATTAAGAA
33495 TTTAAGGTTT
1 TTT-AGGTTT
33505 AGGATGATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.13
26 25 0.83
27 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (25 bp):
TTTAGGTTTTAAGAGAGATTAAGAA
Found at i:35410 original size:21 final size:20
Alignment explanation
Indices: 35324--35481 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
35314 AAATGACCAA
**
35324 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
35343 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
35363 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
35383 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
35404 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
35425 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
35445 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
35466 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
35482 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:35510 original size:20 final size:20
Alignment explanation
Indices: 35448--35641 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
35438 CGATTTTCCA
* ** *
35448 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
35468 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
35488 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35508 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
35528 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
35548 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35568 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
35588 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
35608 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
35629 AAATCGCAACGCG
1 AAATCGCAACGCG
35642 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:35532 original size:60 final size:60
Alignment explanation
Indices: 35448--35641 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
35438 CGATTTTCCA
* ** * *
35448 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
35508 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
35568 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
35629 AAATCGCAACGCG
1 AAATCGCAACGCG
35642 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:36059 original size:32 final size:32
Alignment explanation
Indices: 36021--36089 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
36011 ATTTCACTTA
*
36021 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
36053 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
36085 GATTT
1 GATTT
36090 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:36070 original size:18 final size:18
Alignment explanation
Indices: 36021--36070 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
36011 ATTTCACTTA
*
36021 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
36039 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
36053 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
36071 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:36216 original size:20 final size:20
Alignment explanation
Indices: 36172--36281 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
36162 TGCAGAAGAG
*
36172 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
36193 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
36213 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
36234 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
36248 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
36267 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
36282 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:36229 original size:41 final size:38
Alignment explanation
Indices: 36165--36281 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
36155 TTCAATTTGC
* *
36165 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
36203 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
36244 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
36277 AGAAT
1 AGAAT
36282 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:36251 original size:14 final size:14
Alignment explanation
Indices: 36232--36288 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
36222 GAGAAATGAA
36232 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
36246 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
36265 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36279 AATCGCAACG
1 AATCGCAACG
36289 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:36264 original size:33 final size:33
Alignment explanation
Indices: 36224--36304 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
36214 CGCAACGAGA
36224 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
36257 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
36290 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
36305 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:36347 original size:33 final size:33
Alignment explanation
Indices: 36305--36419 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
36295 CAAAATCGCA
*
36305 TTGCGATTTTCATTTCGCGTTGCGATTCTCCCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
36338 TTGCGATTTTCATTTCGCGTTTCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
36371 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36404 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
36420 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:36363 original size:19 final size:19
Alignment explanation
Indices: 36300--36397 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
36290 GAAACCAAAA
*
36300 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36319 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
36333 TCCCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36352 TCGCGTTTCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
36366 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
36385 TCGCGTTGCGATT
1 TCGCGTTGCGATT
36398 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36377 original size:14 final size:14
Alignment explanation
Indices: 36319--36411 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 14
36309 GATTTTCATT
36319 TCGCGTTGCGATTC
1 TCGCGTTGCGATTC
*
36333 TCCCGTTGCGATTTTC
1 TCGCGTTGCGA--TTC
*
36349 ATTTCGCGTTTCGATTC
1 ---TCGCGTTGCGATTC
*
36366 TCTCGTTGCGATTGTC
1 TCGCGTTGCGA-T-TC
36382 ATTTCGCGTTGCGATTC
1 ---TCGCGTTGCGATTC
*
36399 TCTCGTTGCGATT
1 TCGCGTTGCGATT
36412 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 31 0.50
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 19 0.31
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
TCGCGTTGCGATTC
Found at i:38276 original size:93 final size:93
Alignment explanation
Indices: 38117--38492 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
38107 TAGATTGCTT
*
38117 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38182 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
38210 AGTAAATTTGTTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38275 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38303 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38368 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38396 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38461 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38488 AGTAA
1 AGTAA
38493 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 274 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:38580 original size:19 final size:19
Alignment explanation
Indices: 38540--38667 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
38530 TAGTTTACTT
* *
38540 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
38560 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
38579 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
38597 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
38611 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
38630 TCGCAA--C--AA-CAAGA
1 TCGCAACGCGAAACCAAAA
38644 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38663 TCGCA
1 TCGCA
38668 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 5 0.06
17 1 0.01
18 12 0.14
19 36 0.41
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:38636 original size:33 final size:32
Alignment explanation
Indices: 38576--38667 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
38566 CGCGAAACCA
** *
38576 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACAAC
38607 AGAATCGCAACGCGAAACCAAAATCGCAACAAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACAAC
38640 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
38668 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 38 0.69
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACAAC
Found at i:38685 original size:19 final size:19
Alignment explanation
Indices: 38663--38797 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
38653 GAAACCAAAA
*
38663 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38682 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
38698 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
38715 TCGCATTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
38731 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
38748 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
38767 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
38787 TCGTGTTGCGA
1 TCGCGTTGCGA
38798 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.15
16 12 0.12
17 12 0.12
19 46 0.47
20 12 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38704 original size:14 final size:14
Alignment explanation
Indices: 38685--38741 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
38675 TTTCATTTCG
38685 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
38699 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
38716 CGCATTGCGATTCTTT
1 CG--TTGCGATTCTTT
38732 CGTTGCGATT
1 CGTTGCGATT
38742 TTCATTTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.42
16 8 0.21
17 8 0.21
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:38710 original size:33 final size:33
Alignment explanation
Indices: 38668--38760 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
38658 CAAAATCGCA
38668 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
38701 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
38734 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
38761 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:40739 original size:14 final size:14
Alignment explanation
Indices: 40720--40755 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40710 ATTGTTTAAT
40720 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
40734 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
40748 TGATTTGT
1 TGATTTGT
40756 GTAATTGATG
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:40878 original size:19 final size:19
Alignment explanation
Indices: 40862--40956 Score: 137
Period size: 19 Copynumber: 5.2 Consensus size: 19
40852 AAAAATGACT
40862 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40881 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
40900 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40914 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40933 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
40953 ATCG
1 ATCG
40957 TAACGAGAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.57
20 13 0.19
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40991 original size:53 final size:53
Alignment explanation
Indices: 40862--40977 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
40852 AAAAATGACT
40862 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
40914 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
40967 ATCGCAATGCG
1 ATCGCAATGCG
40978 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:41030 original size:19 final size:19
Alignment explanation
Indices: 41006--41170 Score: 180
Period size: 19 Copynumber: 9.4 Consensus size: 19
40996 GATTCTCTCG
41006 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41025 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
41044 TTGC-A-ATTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41058 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41077 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41096 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41110 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
41130 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
41144 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41163 TTGCGATT
1 TTGCGATT
41171 CTCTCGTTGC
Statistics
Matches: 122, Mismatches: 8, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
14 21 0.17
15 1 0.01
16 16 0.13
17 13 0.11
18 4 0.03
19 55 0.45
20 12 0.10
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41041 original size:52 final size:52
Alignment explanation
Indices: 40984--41142 Score: 300
Period size: 52 Copynumber: 3.0 Consensus size: 52
40974 TGCGTTTATA
40984 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
41036 ATTTCGCATTGCAATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
41088 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
41141 AT
1 AT
41143 GTTGGGATTT
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 87 0.84
53 17 0.16
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:41192 original size:33 final size:33
Alignment explanation
Indices: 40984--41184 Score: 212
Period size: 33 Copynumber: 5.9 Consensus size: 33
40974 TGCGTTTATA
40984 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
41017 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC
* * *
41048 AATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
41088 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
41121 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
41155 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
41185 GTAATTTCCG
Statistics
Matches: 139, Mismatches: 15, Indels: 28
0.76 0.08 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 62 0.45
34 29 0.21
35 7 0.05
36 3 0.02
37 1 0.01
38 11 0.08
39 4 0.03
40 7 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:43485 original size:12 final size:12
Alignment explanation
Indices: 43468--43492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43458 TCTTCGGGGA
43468 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43480 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43492 C
1 C
43493 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:43701 original size:24 final size:24
Alignment explanation
Indices: 43667--43713 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43657 CTGAAACATC
43667 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43691 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43714 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44424 original size:20 final size:20
Alignment explanation
Indices: 44396--44625 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
44386 AAATTTCAGT
* * *
44396 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44416 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
44436 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44456 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
44476 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44496 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
44516 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
44536 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
44556 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
44576 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
44596 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
44616 GTTGCGATTT
1 GTTGCGATTT
44626 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44642 original size:21 final size:21
Alignment explanation
Indices: 44612--44694 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
44602 ATTTTCATAT
*
44612 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
44633 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
44654 TCGCATTGCGATTTT-AAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
44675 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
44695 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:44685 original size:42 final size:43
Alignment explanation
Indices: 44592--44690 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44582 ATTTATGTGT
* *
44592 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGAAAAA
**
44633 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-AAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGAAA-AA
*
44675 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44691 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGAAAAA
Found at i:46036 original size:18 final size:18
Alignment explanation
Indices: 45995--46055 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
45985 AAAATTAATC
*
45995 AAATAATATATATTAAAATA
1 AAATAATATATA--AAATTA
*
46015 AAATAATA-ATACTAATTA
1 AAATAATATATA-AAATTA
*
46033 AAATATTATATAAAATTA
1 AAATAATATATAAAATTA
46051 AAATA
1 AAATA
46056 TATTTAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 21 0.60
19 6 0.17
20 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATATATAAAATTA
Found at i:47398 original size:3 final size:3
Alignment explanation
Indices: 47390--47508 Score: 139
Period size: 3 Copynumber: 39.0 Consensus size: 3
47380 TTATTTATTA
*
47390 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * *
47437 TAT TAT AAT AAT AAT AAT ACT AAT ACT AAT ACT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
47485 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
47509 TTTAAATAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
3 92 0.94
4 6 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:47893 original size:76 final size:76
Alignment explanation
Indices: 47641--48510 Score: 1605
Period size: 76 Copynumber: 11.4 Consensus size: 76
47631 GAAATGTTGA
47641 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
47706 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
47717 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
47782 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
47794 AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
47859 AGGCTTTTTGG
66 AGGCTTTTTGG
47870 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
47935 AGGCTTTTTGG
66 AGGCTTTTTGG
47946 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48011 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48022 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48087 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48098 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48163 AGGCTTTTTTGG
66 AGGC-TTTTTGG
48175 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48240 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48251 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48316 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
48327 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
48392 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
48404 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAAGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48469 AGGCTTTTTTGG
66 AGGC-TTTTTGG
48481 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
48511 TGGGAAATAG
Statistics
Matches: 771, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
76 514 0.67
77 257 0.33
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:48174 original size:229 final size:228
Alignment explanation
Indices: 47641--48510 Score: 1614
Period size: 229 Copynumber: 3.8 Consensus size: 228
47631 GAAATGTTGA
47641 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
47706 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCA
*
47771 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
47836 TGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
47870 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
47935 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
48000 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
* *
48065 GAAAACATCAAAAAGCTCCTGAAGGCTTTTTGG
196 GAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
*
48098 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48163 AGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
66 AGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
48228 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
48293 TGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
48327 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGCTCCCG
* *
48392 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAAGATTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
48457 AAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
130 AAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
48511 TGGGAAATAG
Statistics
Matches: 625, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
228 176 0.28
229 384 0.61
230 65 0.10
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (228 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
GAAAATATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:48254 original size:153 final size:152
Alignment explanation
Indices: 47641--48510 Score: 1605
Period size: 153 Copynumber: 5.7 Consensus size: 152
47631 GAAATGTTGA
47641 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
47706 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCA
47771 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
* *
47794 AAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
47859 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
47924 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
47946 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48011 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
48076 AAAGCTCCTGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
48098 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48163 AGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
66 AGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
48228 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
*
48251 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
48316 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCA
48381 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
* *
48404 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAAGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48469 AGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
66 AGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
48511 TGGGAAATAG
Statistics
Matches: 698, Mismatches: 16, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
152 298 0.43
153 363 0.52
154 37 0.05
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:51889 original size:115 final size:114
Alignment explanation
Indices: 51575--51915 Score: 551
Period size: 114 Copynumber: 3.0 Consensus size: 114
51565 GATCATGCAG
* * * * * *
51575 TTCA-TCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 TTCATTCTTT-AAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
51639 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
51689 TTCATTTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATTCTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
51754 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
51803 TTCA-TCTTTAGAATCCAATGATTGCTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATTCTTTA-AATCCAATGATTG-GTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
51867 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
64 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
51916 CGTGGCACTT
Statistics
Matches: 213, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
113 5 0.02
114 117 0.55
115 91 0.43
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATTCTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:59571 original size:18 final size:18
Alignment explanation
Indices: 59530--59590 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
59520 AAAATTAATC
*
59530 AAATAATATATATTAAAATA
1 AAATAATATATA--AAATTA
*
59550 AAATAATA-ATACTAATTA
1 AAATAATATATA-AAATTA
*
59568 AAATATTATATAAAATTA
1 AAATAATATATAAAATTA
59586 AAATA
1 AAATA
59591 TATTTAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 21 0.60
19 6 0.17
20 8 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATATATAAAATTA
Found at i:61010 original size:3 final size:3
Alignment explanation
Indices: 61002--61117 Score: 124
Period size: 3 Copynumber: 38.0 Consensus size: 3
60992 TTATTTATTA
* *
61002 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAAT AAT TAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * * * *
61049 TAT TAT TAT AAT AAT AAT AAT ACT AAT ACT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
61097 AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
61118 TTTAAATAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
3 91 0.94
4 6 0.06
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:61319 original size:32 final size:32
Alignment explanation
Indices: 61249--61600 Score: 496
Period size: 32 Copynumber: 11.1 Consensus size: 32
61239 GTCGAAGTAC
* *
61249 TACCTATGT-TCTTCGGGACATATGAAC-AGAT
1 TACCTATGTCT-TTCGGGACATATGGACAATAT
* *
61280 TACCTATGTCTTTCGGGATATATGGACAGTAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
*
61312 TACCTATGTCTTTCGGGACATATGGACATTAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
*
61344 TACCTATGTCTTTCAGGACATATGGACAATAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
61376 TACCTATGTCTTTCGGGACATATGGACAATAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
* * *
61408 TACATATGTTTTTCGGGACATATGAACAATAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
* **
61440 TTCCTATGTCTTTCGGGACATATGGACGGTAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
* **
61472 TACCTATGTCTTTCGGGATATATGGACGGTAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
*
61504 TACATATGTCTTTCGGGACATATGGACAATAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
* *
61536 TATCTATGTCTTTCGGGACATATGAACAATAT
1 TACCTATGTCTTTCGGGACATATGGACAATAT
61568 TACCTATGT-TCTTCGGGACATATGGACAA-AT
1 TACCTATGTCT-TTCGGGACATATGGACAATAT
61599 TA
1 TA
61601 TTATACGAGC
Statistics
Matches: 289, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
31 28 0.10
32 261 0.90
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (32 bp):
TACCTATGTCTTTCGGGACATATGGACAATAT
Found at i:65894 original size:14 final size:15
Alignment explanation
Indices: 65869--65897 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65859 TTATAAATAT
65869 AATAATATTTTAAAA
1 AATAATATTTTAAAA
65884 AATAA-ATTTTAAAA
1 AATAATATTTTAAAA
65898 CCACTAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATATTTTAAAA
Found at i:67161 original size:31 final size:32
Alignment explanation
Indices: 67115--67182 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
67105 AGATCGGTTA
*
67115 ATTTTTGGTTCGGGTCAATA-CGAATCGATTG
1 ATTTTTAGTTCGGGTCAATATCGAATCGATTG
* *
67146 ATTTTTAGTTTGGGTCAGTATCGAATCGATTG
1 ATTTTTAGTTCGGGTCAATATCGAATCGATTG
67178 ATTTT
1 ATTTT
67183 CGATTCGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (32 bp):
ATTTTTAGTTCGGGTCAATATCGAATCGATTG
Found at i:67249 original size:20 final size:20
Alignment explanation
Indices: 67203--67249 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
67193 CAACCTTTGG
*
67203 ATCGGGCCAATTTGGGTTAA
1 ATCGGGTCAATTTGGGTTAA
67223 ATCGGGTCAATTTGGGTTAA
1 ATCGGGTCAATTTGGGTTAA
67243 ATCGGGT
1 ATCGGGT
67250 ATGAGTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (20 bp):
ATCGGGTCAATTTGGGTTAA
Found at i:72127 original size:11 final size:11
Alignment explanation
Indices: 72104--72140 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
72094 TGTAATTAAT
72104 TATTTATATATA
1 TATTTA-ATATA
72116 TATTTAATATA
1 TATTTAATATA
72127 TATTTAATATA
1 TATTTAATATA
72138 TAT
1 TAT
72141 AATAATGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAATATA
Found at i:72161 original size:3 final size:3
Alignment explanation
Indices: 72139--72222 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
72129 TTTAATATAT
* *
72139 ATA ATA ATG ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
72187 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
72223 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:73121 original size:112 final size:112
Alignment explanation
Indices: 72536--73322 Score: 1144
Period size: 113 Copynumber: 7.0 Consensus size: 112
72526 TGATAGTATC
*
72536 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
72600 TCATTATGAACTTTCTCTGGAAAGGCTGATCCATCAATTGATGAATTT
66 TCATTATGAAC-TTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
*** *
72648 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** *** * * * *
72713 TCATTATGAACTTTCTCTGAAAAAAATAATCCATCCAGTGATGAATTC
66 TCATTATGAAC-TTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* ** * *
72761 AGATTAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*** * * *
72826 TCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
66 TCATTATGAA-CTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
72874 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
72939 TCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAAC-TTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
72987 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
73052 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGGATTT
66 TCATTATGAACTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
*
73099 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
73164 TCATTATGAACTTATCTGGCAATGTTAATCCATCAAATGATGGATTT
66 TCATTATGAACTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
73211 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAGCTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
73276 TCATTATGAACTTATCTGGCAATGTTGATCCATCAAATGATGGATTT
66 TCATTATGAACTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
73323 GAATCTTTGC
Statistics
Matches: 632, Mismatches: 40, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
112 256 0.41
113 375 0.59
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:74021 original size:83 final size:83
Alignment explanation
Indices: 73875--74340 Score: 762
Period size: 83 Copynumber: 5.6 Consensus size: 83
73865 CACTTCTTCA
* *
73875 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCATATTCAT-TTGCCAAA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTTATCTT-CCAAA
73938 TTCAATGATTGATTCTGTCC
64 TTCAATGATTGATTCTGTCC
* * *
73958 AACAAGATCAGATAACTCACAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTTCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCCAAATT
*
74023 CAATGATTGATTTTGTCC
66 CAATGATTGATTCTGTCC
* *
74041 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGGGC-AATTTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTT-ATCTTCCAAAT
74105 TCAATGATTGATTCTGTCC
65 TCAATGATTGATTCTGTCC
*
74124 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGC-AATTTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTT-ATCTTCCAAAT
74188 TCAATGATTGATTCTGTCC
65 TCAATGATTGATTCTGTCC
* *
74207 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-GCAAATTCATCTTCCTAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCCAAATT
74271 CAATGATTGATTCTGTCC
66 CAATGATTGATTCTGTCC
74289 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATT
74341 CATTTGTTCT
Statistics
Matches: 360, Mismatches: 18, Indels: 10
0.93 0.05 0.03
Matches are distributed among these distances:
82 80 0.22
83 276 0.77
84 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCCAAATT
CAATGATTGATTCTGTCC
Found at i:75138 original size:19 final size:20
Alignment explanation
Indices: 75114--75155 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
75104 AATAGAAAAG
75114 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATTTCCAATA
75133 AATAAATTGAATTTCCAATA
1 AATAAATTGAATTTCCAATA
75153 AAT
1 AAT
75156 TGAACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
AATAAATTGAATTTCCAATA
Found at i:75502 original size:10 final size:10
Alignment explanation
Indices: 75489--75522 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
75479 TTGACCCCCC
75489 TTTTTTTTCT
1 TTTTTTTTCT
75499 TTTTTTTTCT
1 TTTTTTTTCT
75509 TTTTTTTTCT
1 TTTTTTTTCT
75519 TTTT
1 TTTT
75523 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:87519 original size:212 final size:214
Alignment explanation
Indices: 87150--87579 Score: 828
Period size: 212 Copynumber: 2.0 Consensus size: 214
87140 ATTTATCCTA
87150 AATATATTATTTTAATATAAAGGATTAAAATAAAAGAAATTAAAATTCGAAGACTGAATTAAAAA
1 AATATATTATTTTAATATAAAGGATTAAAATAAAAGAAATTAAAATTCGAAGACTGAATT-AAAA
87215 TATTATAAATTCATTTAGTGACTAAAATGTAAAGTTTACAATTACGGAGGACTGCGGACGGGGTT
65 TATTATAAATTCATTTAGTGACTAAAATGTAAAGTTTACAATTACGGAGGACTGCGGACGGGGTT
87280 TAACTATTTCATAATTACGCGCATAGTCCTTCCCGAAACGACATCGTTCGGGAAGGAC-TATATG
130 TAACTATTTCATAATTACGCGCATAGTCCTTCCCGAAACGACATCGTTCGGGAAGGACATATATG
87344 GTCCAAAACCGGCTGGCCCG
195 GTCCAAAACCGGCTGGCCCG
87364 AATATATTATTTTAATATAAAGGATTAAAATAAAAGAAATTAAAATTCGAAGACTGAATT-AAAT
1 AATATATTATTTTAATATAAAGGATTAAAATAAAAGAAATTAAAATTCGAAGACTGAATTAAAAT
87428 ATTATAAATTCATTTAGTGACTAAAATGTAAAGTTTACAATTACGGAGGACTGCGGACGGGGTTT
66 ATTATAAATTCATTTAGTGACTAAAATGTAAAGTTTACAATTACGGAGGACTGCGGACGGGGTTT
87493 AACTATTTCATAATTACGCGCATAGTCCTTCCCGAAACGACATCGTTCGGGAAGGACTATATATG
131 AACTATTTCATAATTACGCGCATAGTCCTTCCCGAAACGACATCGTTCGGGAAGGAC-ATATATG
87558 GTCCAAAACCGGCTGGCCCG
195 GTCCAAAACCGGCTGGCCCG
87578 AA
1 AA
87580 GGGCCAGCTT
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
212 126 0.59
214 88 0.41
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (214 bp):
AATATATTATTTTAATATAAAGGATTAAAATAAAAGAAATTAAAATTCGAAGACTGAATTAAAAT
ATTATAAATTCATTTAGTGACTAAAATGTAAAGTTTACAATTACGGAGGACTGCGGACGGGGTTT
AACTATTTCATAATTACGCGCATAGTCCTTCCCGAAACGACATCGTTCGGGAAGGACATATATGG
TCCAAAACCGGCTGGCCCG
Found at i:88487 original size:11 final size:11
Alignment explanation
Indices: 88466--88500 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
88456 TGTAATTAAT
88466 TATTT-ATATA
1 TATTTAATATA
88476 TATTTAATATA
1 TATTTAATATA
88487 TATTTAATATA
1 TATTTAATATA
88498 TAT
1 TAT
88501 AATAATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAATATA
Found at i:88521 original size:3 final size:3
Alignment explanation
Indices: 88499--88576 Score: 129
Period size: 3 Copynumber: 26.0 Consensus size: 3
88489 TTTAATATAT
* * *
88499 ATA ATA ATG ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
88547 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
88577 TGGATAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:90621 original size:22 final size:23
Alignment explanation
Indices: 90589--90640 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
90579 TATCAGTGTT
* *
90589 TTTTTTAGTTT-TAATTTTCTTC
1 TTTTTTAGTTTAAAATTTTATTC
90611 TATTTTT-GTTTAAAATTTTATTC
1 T-TTTTTAGTTTAAAATTTTATTC
90634 TTTTTTA
1 TTTTTTA
90641 CTTGTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTTAGTTTAAAATTTTATTC
Found at i:91966 original size:21 final size:21
Alignment explanation
Indices: 91942--91984 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
91932 TATTTGAATT
*
91942 AATTAATATATACCAAACATA
1 AATTAATAAATACCAAACATA
* *
91963 AATTTATAAATATCAAACATA
1 AATTAATAAATACCAAACATA
91984 A
1 A
91985 TATGAAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAATAAATACCAAACATA
Found at i:92148 original size:22 final size:23
Alignment explanation
Indices: 92092--92151 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
92082 TCACTAAATC
*
92092 AAAT-ATATATTTCATAACATTA
1 AAATAATATATTTCATAAAATTA
92114 ATTAATAAATATATTTCA-AAAATTA
1 A--AAT-AATATATTTCATAAAATTA
92139 AAATAATATATTT
1 AAATAATATATTT
92152 GAATCAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 10 0.30
23 3 0.09
24 3 0.09
25 7 0.21
26 10 0.30
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAATATATTTCATAAAATTA
Found at i:92861 original size:28 final size:28
Alignment explanation
Indices: 92830--92885 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
92820 CATTTACGAG
*
92830 ATATATCTTCAAAATATTC-TAAAATAAT
1 ATATATC-TAAAAATATTCATAAAATAAT
92858 ATATATCTAAAAATATTCATAAAATAAT
1 ATATATCTAAAAATATTCATAAAATAAT
92886 CTAGATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATATCTAAAAATATTCATAAAATAAT
Found at i:93856 original size:30 final size:29
Alignment explanation
Indices: 93822--93891 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
93812 AATCTACCCT
* *
93822 TTTAATTTTGTCCATCAGACCATCTAACTA
1 TTTAATTTTGTCAATCAAACCA-CTAACTA
*
93852 TTTAATTGTTTTCAATCAAACCACTAACTA
1 TTTAATT-TTGTCAATCAAACCACTAACTA
93882 -TTAATATTTG
1 TTTAAT-TTTG
93892 ACGAAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.21
30 15 0.44
31 12 0.35
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTAATTTTGTCAATCAAACCACTAACTA
Found at i:95502 original size:46 final size:46
Alignment explanation
Indices: 95435--95526 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
95425 GTTCTACAAG
*
95435 GACAATCGGGGGTGCCATGATGGTCATTTAGTCCAATACTAAGCTT
1 GACAATCGGAGGTGCCATGATGGTCATTTAGTCCAATACTAAGCTT
* *
95481 GACAATCGGAGGTGCTATGATGGTCATTTAGTCCAGTACTAAGCTT
1 GACAATCGGAGGTGCCATGATGGTCATTTAGTCCAATACTAAGCTT
95527 TCTTTTCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (46 bp):
GACAATCGGAGGTGCCATGATGGTCATTTAGTCCAATACTAAGCTT
Found at i:95555 original size:2 final size:2
Alignment explanation
Indices: 95548--95592 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
95538 TTCTGCTAAA
95548 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
95590 AT A
1 AT A
95593 ATTTAGAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105474 original size:31 final size:31
Alignment explanation
Indices: 105436--105500 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
105426 TCCTTGGAAG
105436 TAAGAGAAAATGAGCGGAAAATCATTGCATA
1 TAAGAGAAAATGAGCGGAAAATCATTGCATA
105467 TAAGAGAAAATGAGCGGAAAATCATTGCATA
1 TAAGAGAAAATGAGCGGAAAATCATTGCATA
105498 TAA
1 TAA
105501 TTTTATCGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (31 bp):
TAAGAGAAAATGAGCGGAAAATCATTGCATA
Found at i:106079 original size:29 final size:29
Alignment explanation
Indices: 106015--106081 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
106005 CAGAACAAAA
*
106015 TGGATTGAGGATTGAGTTGTGAAAGGCTAG
1 TGGA-TGAAGATTGAGTTGTGAAAGGCTAG
*
106045 TAGATGAAGATTGAGTTGTGAAAGG-TCAG
1 TGGATGAAGATTGAGTTGTGAAAGGCT-AG
106074 TGGATGAA
1 TGGATGAA
106082 CTAACGAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 29 0.88
30 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.37, T:0.28
Consensus pattern (29 bp):
TGGATGAAGATTGAGTTGTGAAAGGCTAG
Found at i:115408 original size:19 final size:20
Alignment explanation
Indices: 115386--115439 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
115376 TTATGAGTTT
*
115386 TTTTAAATTGTT-TTTAAAA
1 TTTTAAATTATTATTTAAAA
115405 TTTTAAATTATTATTTAAAAA
1 TTTTAAATTATTATTT-AAAA
*
115426 TATTAAAATTATTA
1 T-TTTAAATTATTA
115440 AAATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 5 0.17
22 11 0.37
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAAATTATTATTTAAAA
Found at i:115962 original size:31 final size:30
Alignment explanation
Indices: 115914--115971 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
115904 ATGGACCACA
* *
115914 AATGTACAAAATATATTTTATTTTTATTTT
1 AATGTAAAAAATATATTTTATCTTTATTTT
115944 AATGTAAAAATATATATTTTATCTTTAT
1 AATGTAAAAA-ATATATTTTATCTTTAT
115972 CATCACTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (30 bp):
AATGTAAAAAATATATTTTATCTTTATTTT
Found at i:116870 original size:25 final size:24
Alignment explanation
Indices: 116836--116883 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
116826 TGTAAATAAA
**
116836 ATAAATATTATTTTATTATCATATT
1 ATAAATATTAAATT-TTATCATATT
116861 ATAAATATTAAATTTTATCATAT
1 ATAAATATTAAATTTTATCATAT
116884 AAATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAAATATTAAATTTTATCATATT
Found at i:116894 original size:17 final size:19
Alignment explanation
Indices: 116872--116910 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
116862 TAAATATTAA
*
116872 ATTTTAT-CA-TATAAATT
1 ATTTTATACATTATAAAAT
116889 ATTTTATACATTATAAAAT
1 ATTTTATACATTATAAAAT
116908 ATT
1 ATT
116911 AAGAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTATACATTATAAAAT
Found at i:126784 original size:19 final size:19
Alignment explanation
Indices: 126760--126816 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 19
126750 TGCAAAAGAT
126760 ATAAATAATCATATTAATA
1 ATAAATAATCATATTAATA
*
126779 ATAAATAATACTAATAATAATA
1 ATAAATAAT-C--ATATTAATA
126801 ATAAATAATCA-ATTAA
1 ATAAATAATCATATTAA
126817 AACTAGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 1 0.03
21 1 0.03
22 17 0.52
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATAATCATATTAATA
Found at i:130051 original size:18 final size:20
Alignment explanation
Indices: 130028--130064 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
130018 CTCATAAAAA
130028 ATACTAAA-A-ATAGTTTAG
1 ATACTAAATATATAGTTTAG
130046 ATACTAAATATATAGTTTA
1 ATACTAAATATATAGTTTA
130065 CTCTAAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (20 bp):
ATACTAAATATATAGTTTAG
Found at i:131257 original size:153 final size:153
Alignment explanation
Indices: 131034--131332 Score: 427
Period size: 153 Copynumber: 2.0 Consensus size: 153
131024 TAGGAAGCGG
* * * * *
131034 CTGGTTCTTGTTCTGTCGGTCTTTTGAAGGAGGGTCCTCCATCGAACGGTGCTGTTTATGTTGAT
1 CTGGTTCTGGTACTGTCGATCTTTTGAAGAAGGGTCCTCCATCGAACGGTGCTGTTTACGTTGAT
** * **
131099 AATCATGTTTTGACGGAATTACTCCATTGATGAGTTGTTTATTTTTTTCTGGTTGCTCCACGTTC
66 AATCATGTTTTGAAAGAATTACTCCATTGATGACTTGTTTACCTTTTTCTGGTTGCTCCACGTTC
*
131164 CGAGATGGAGGCGGCGGTTGGTT
131 CGAGATGAAGGCGGCGGTTGGTT
* * *
131187 CTGGTTCTGGTACTTTCGATCTTTTGAAGAAGGGTCCTCCATCGGACGTTGCTGTTTACGTTGAT
1 CTGGTTCTGGTACTGTCGATCTTTTGAAGAAGGGTCCTCCATCGAACGGTGCTGTTTACGTTGAT
* * * *
131252 GATCATGTTTTGAAAGAATTACTCCGTTGATGTCTTGTTTACCTTTTTCTGGTTGCTCCACTTTC
66 AATCATGTTTTGAAAGAATTACTCCATTGATGACTTGTTTACCTTTTTCTGGTTGCTCCACGTTC
*
131317 CGAGCTGAAGGCGGCG
131 CGAGATGAAGGCGGCG
131333 ACGCCTCTGC
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
153 127 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (153 bp):
CTGGTTCTGGTACTGTCGATCTTTTGAAGAAGGGTCCTCCATCGAACGGTGCTGTTTACGTTGAT
AATCATGTTTTGAAAGAATTACTCCATTGATGACTTGTTTACCTTTTTCTGGTTGCTCCACGTTC
CGAGATGAAGGCGGCGGTTGGTT
Found at i:131521 original size:2 final size:2
Alignment explanation
Indices: 131514--131572 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
131504 CGCTTTCCAC
131514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
131556 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
131573 TATTAAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:134584 original size:29 final size:28
Alignment explanation
Indices: 134535--134597 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
134525 TTATAAAAGT
*
134535 ACCTTTTAAAAAATATAATTTTAA-AAA
1 ACCTTTTAAAAAATAAAATTTTAATAAA
*
134562 ACCTTTTACAAATCATAAAATTTTAATAAA
1 ACCTTTTA-AAA-AATAAAATTTTAATAAA
*
134592 ATCTTT
1 ACCTTT
134598 GTATTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 8 0.27
28 3 0.10
29 11 0.37
30 8 0.27
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (28 bp):
ACCTTTTAAAAAATAAAATTTTAATAAA
Found at i:135313 original size:30 final size:30
Alignment explanation
Indices: 135277--135335 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
135267 CAGTGACCAT
*
135277 CATAGGTATCCAGGAGCACATGGCGACCTC
1 CATAGGTATCCAGGAGCACACGGCGACCTC
* * *
135307 CATAGGTCTCTAGGAGCACACGGTGACCT
1 CATAGGTATCCAGGAGCACACGGCGACCT
135336 ATGGAGCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (30 bp):
CATAGGTATCCAGGAGCACACGGCGACCTC
Found at i:135437 original size:19 final size:19
Alignment explanation
Indices: 135415--135451 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
135405 TTGGAGACTA
135415 ATGGAGCACTTGACGACCT
1 ATGGAGCACTTGACGACCT
* *
135434 ATGGATCACTTGGCGACC
1 ATGGAGCACTTGACGACC
135452 AATGAGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (19 bp):
ATGGAGCACTTGACGACCT
Found at i:137584 original size:38 final size:38
Alignment explanation
Indices: 137509--137585 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
137499 GTTAGAAAAT
* *
137509 ATTTATATATATTTTTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATATTTTTTTTAAAAATTGAAAATCATAAA
137547 ATTTATATA-ATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATA-TTTTTTTTA-AAAATTGAAAATCATAAA
137585 A
1 A
137586 AGGTTTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 1 0.03
38 24 0.69
39 10 0.29
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (38 bp):
ATTTATATATATTTTTTTTAAAAATTGAAAATCATAAA
Found at i:138555 original size:32 final size:31
Alignment explanation
Indices: 138464--138561 Score: 110
Period size: 31 Copynumber: 3.1 Consensus size: 31
138454 TAGCTTAATA
* *
138464 ATTAAATTTATCAAATTATTATAAAATAATC
1 ATTAAATTTATCAAAATATTATAAAATGATC
*
138495 ATTAAATTTATCAAAATATT-TAATAAATGGTC
1 ATTAAATTTATCAAAATATTAT-A-AAATGATC
* *
138527 ATTAAAATTTATCAAACTGTTATAAAATGAT-
1 ATT-AAATTTATCAAAATATTATAAAATGATC
138558 ATTA
1 ATTA
138562 TAATAATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
30 2 0.04
31 23 0.40
32 15 0.26
33 16 0.28
34 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (31 bp):
ATTAAATTTATCAAAATATTATAAAATGATC
Found at i:145602 original size:25 final size:23
Alignment explanation
Indices: 145554--145614 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
145544 ATATTATATT
*
145554 TTTTTGTTATTTTTTAGATTTTTGG
1 TTTTTGTT-TTTTTTACATTTTT-G
*
145579 TTTTTGTTTTTTTTACTTTCTTTG
1 TTTTTGTTTTTTTTACATT-TTTG
*
145603 TTATT-TTTTTTT
1 TTTTTGTTTTTTT
145615 CTTTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.22
24 14 0.44
25 11 0.34
ACGTcount: A:0.08, C:0.03, G:0.10, T:0.79
Consensus pattern (23 bp):
TTTTTGTTTTTTTTACATTTTTG
Found at i:145619 original size:28 final size:27
Alignment explanation
Indices: 145579--145634 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
145569 AGATTTTTGG
*
145579 TTTTTGTTTTTTTTAC-TTTCTTTGTTA
1 TTTTTGTTTTTTTT-CTTTTATTTGTTA
*
145606 TTTTTTTTTCTTTTTCTTTTATTTGTTA
1 TTTTTGTTT-TTTTTCTTTTATTTGTTA
145634 T
1 T
145635 ATTATTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (27 bp):
TTTTTGTTTTTTTTCTTTTATTTGTTA
Found at i:145627 original size:21 final size:21
Alignment explanation
Indices: 145579--145629 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
145569 AGATTTTTGG
*
145579 TTTTTGTTTTTTTTACTTTCT
1 TTTTTATTTTTTTTACTTTCT
* *
145600 TTGTTATTTTTTTTTCTTT-T
1 TTTTTATTTTTTTTACTTTCT
145620 TCTTTTATTT
1 T-TTTTATTT
145630 GTTATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTTTTTACTTTCT
Found at i:145725 original size:15 final size:17
Alignment explanation
Indices: 145707--145738 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
145697 CATAATATAA
145707 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
145722 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
145739 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:145855 original size:24 final size:24
Alignment explanation
Indices: 145823--145869 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
145813 TAAAAATATT
145823 AAAAACTCAAACAACATTTTAACC
1 AAAAACTCAAACAACATTTTAACC
145847 AAAAACTCAAACAACATTTTAAC
1 AAAAACTCAAACAACATTTTAAC
145870 TAACAACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAAACTCAAACAACATTTTAACC
Found at i:146961 original size:101 final size:103
Alignment explanation
Indices: 146720--147025 Score: 519
Period size: 101 Copynumber: 3.0 Consensus size: 103
146710 TATGGATACA
* * *
146720 AAGAAGAAGAACAAAATACAATACCATCGGAGTAACTAGCAATTACCATTGAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
146785 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
*
146823 AAGAAGAAGAACAAAAT-CAGTACCATCGGAGTAACTAACAATTACCATACAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
* *
146887 CCAAATGCAGA-TTGAAGAAGGAACAAAACTAACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
*
146924 AAGAAGAA-AACAAAATACAGTACAATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
1 AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
*
146988 CCAAACGCAGATTTTAAGAAGGAACAAAACTCACCAAG
66 CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
147026 CATAAACAAA
Statistics
Matches: 190, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
100 8 0.04
101 87 0.46
102 78 0.41
103 17 0.09
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (103 bp):
AAGAAGAAGAACAAAATACAGTACCATCGGAGTAACTAACAATTACCATTCAAGACCAGTTCAAA
CCAAATGCAGATTTTAAGAAGGAACAAAACTCACCAAG
Done.