Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001942.1 Hibiscus syriacus cultivar Beakdansim tig00003935_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: 81246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2265 original size:45 final size:45
Alignment explanation
Indices: 2211--2463 Score: 332
Period size: 45 Copynumber: 5.6 Consensus size: 45
2201 TTTTTTGCTG
* * * * *
2211 ATAATGCACCCATATGCATT-TCAATTATGGCATCCTCTCATGTCG
1 ATAATGCACCCATATGCATTAT-TATTTTGGCATCCTTTCATGCCT
*
2256 ATAATGCACCCATATGTATTATTATTTTGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCT
* * * *
2301 ATAATGCACTCATACT-CGTTATTATTTTGGTATCCTTTCATGACT
1 ATAATGCACCCATA-TGCATTATTATTTTGGCATCCTTTCATGCCT
*
2346 ATAATGCACCCATATGCCTTATTATTTTGGCAT-CTATTCATGCCT
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCT-TTCATGCCT
* * *
2391 ATAATGCTCCCATAAGCATTATTATTTTGGCATCCTTTCATGCTT
1 ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCT
2436 ATAATGCACCCATATGCATTATTATTTT
1 ATAATGCACCCATATGCATTATTATTTT
2464 TGTTCATTCA
Statistics
Matches: 182, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
44 3 0.02
45 175 0.96
46 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.41
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCT
Found at i:11930 original size:13 final size:12
Alignment explanation
Indices: 11906--11959 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
11896 TTTTTAAATT
11906 TTTTC-TTTTTC
1 TTTTCTTTTTTC
11917 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
11930 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
11944 TCTTCTTTTATC
1 TTTTCTTTTTTC
11956 TTTT
1 TTTT
11960 TCTCTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
13 9 0.25
14 8 0.22
15 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:11930 original size:19 final size:18
Alignment explanation
Indices: 11904--11960 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
11894 TGTTTTTAAA
11904 TTTT-TTCTTTTTCTTTT
1 TTTTCTTCTTTTTCTTTT
11921 CTTTTCTTC-TTTTCTGATTT
1 -TTTTCTTCTTTTTCT--TTT
*
11941 TTCTCTTCTTTTATCTTTT
1 TTTTCTTCTTTT-TCTTTT
11960 T
1 T
11961 CTCTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 10 0.30
19 14 0.42
20 6 0.18
21 3 0.09
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTTTCTTTT
Found at i:13021 original size:15 final size:15
Alignment explanation
Indices: 12997--13031 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12987 TGTTGAAAAG
*
12997 GCATCTTCATGGGCA
1 GCATCGTCATGGGCA
*
13012 TCATCGTCATGGGCA
1 GCATCGTCATGGGCA
13027 GCATC
1 GCATC
13032 ATTCATGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.26
Consensus pattern (15 bp):
GCATCGTCATGGGCA
Found at i:19789 original size:15 final size:17
Alignment explanation
Indices: 19765--19799 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
19755 AACGTCTTTT
19765 AAAACAATTTTAAGA-A
1 AAAACAATTTTAAGACA
19781 AAAAC-ATTTTAAGACA
1 AAAACAATTTTAAGACA
19797 AAA
1 AAA
19800 TTGGTTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.63, C:0.09, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAACAATTTTAAGACA
Found at i:21896 original size:18 final size:18
Alignment explanation
Indices: 21868--21913 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
21858 ACCAGTCATA
* *
21868 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
*
21886 ACCGGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
21904 ACCCGACCCG
1 ACCCGACCCG
21914 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:21906 original size:13 final size:13
Alignment explanation
Indices: 21890--21919 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21880 CCGTTGACCG
21890 GACCCGACCCATT
1 GACCCGACCCATT
*
21903 GACCCGACCCGTT
1 GACCCGACCCATT
21916 GACC
1 GACC
21920 GTTGATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:22640 original size:36 final size:36
Alignment explanation
Indices: 22593--22665 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
22583 AGTTCTGGAA
*
22593 TTAAGTGATAAAAGAATCAGCCATGGAAATGTAGAT
1 TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
* *
22629 TTAAGTGATAAAAGAATCATACATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
22665 T
1 T
22666 ATAATTTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
Found at i:24475 original size:24 final size:25
Alignment explanation
Indices: 24460--24550 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 25
24450 ATTTCCTACT
*
24460 TGAATTATGTTTTGATAT-ATGACC
1 TGAATTATGTTTTGATTTCATGACC
*
24484 TGAATTATGTTTTGATTTC-TGATC
1 TGAATTATGTTTTGATTTCATGACC
* * * **
24508 TGGATTCTGTTCTGATATT--TGTTC
1 TGAATTATGTTTTGAT-TTCATGACC
*
24532 TGAATTCTGTTTTGATTTC
1 TGAATTATGTTTTGATTTC
24551 GGATATCTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.18, T:0.53
Consensus pattern (25 bp):
TGAATTATGTTTTGATTTCATGACC
Found at i:26745 original size:66 final size:65
Alignment explanation
Indices: 26608--26801 Score: 201
Period size: 66 Copynumber: 2.9 Consensus size: 65
26598 AGGGATAATG
** * * * * **
26608 GTTTCAAGAGAAACCATCTCAAGAGAGACAAACTAGTTTCAAGGGAAACAGA-CTCAAAGAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGAGAAACA-ATCTCAAAG-ATGG
26672 AT
64 AT
* * *
26674 ATTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTTGTTTCAAGCGAAACAATCTCAAAGATGGG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGATGGA
26739 T
65 T
* * * * *
26740 GTTTCAAGTGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGATAAACGATCTCAAAGAT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGAGAAACAATCTCAAAGAT
26802 TTTTCAAGAG
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
66 82 0.76
67 26 0.24
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGAGAAACAATCTCAAAGATGGAT
Found at i:27063 original size:37 final size:36
Alignment explanation
Indices: 26944--27066 Score: 108
Period size: 37 Copynumber: 3.4 Consensus size: 36
26934 AAGGAAAAAA
* * *
26944 GTCTCAAGTGAGACGAAATTTGTTTTGAGAGAAA-TT
1 GTCTCAAGCGAGACAAAATTTGTTTTAAGA-AAACTT
* * *
26980 GTCCCAA-CAAGACAAAATTTGTTTTTAGCAAAAAC-T
1 GTCTCAAGCGAGACAAAATTTGTTTTAAG--AAAACTT
* * *
27016 GCCTCGAGCGAGATAAAATTTGCTTTTAAGAAAACTT
1 GTCTCAAGCGAGACAAAATTTG-TTTTAAGAAAACTT
27053 GTCTCAAGCGAGAC
1 GTCTCAAGCGAGAC
27067 GACCTTTTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
35 17 0.25
36 19 0.28
37 25 0.37
38 6 0.09
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTAAGAAAACTT
Found at i:30624 original size:24 final size:22
Alignment explanation
Indices: 30563--30624 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 22
30553 TTGTCATAAT
*
30563 CATTTTTTTGAAAAACAATTAA
1 CATTTATTTGAAAAACAATTAA
*
30585 -ATATTATTTAATAAAAACAATTATGA
1 CAT-TTATTT--GAAAAACAATTA--A
30611 CATTTATTTGAAAA
1 CATTTATTTGAAAA
30625 GTTTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
21 2 0.06
22 5 0.16
24 15 0.48
26 7 0.23
27 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (22 bp):
CATTTATTTGAAAAACAATTAA
Found at i:37099 original size:19 final size:19
Alignment explanation
Indices: 37075--37111 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37065 TAGAATGCAA
37075 AAATGGTACCGATACCATG
1 AAATGGTACCGATACCATG
**
37094 AAATGGTATTGATACCAT
1 AAATGGTACCGATACCAT
37112 AGTGCAAAGT
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:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (19 bp):
AAATGGTACCGATACCATG
Found at i:37183 original size:104 final size:104
Alignment explanation
Indices: 37052--37266 Score: 430
Period size: 104 Copynumber: 2.1 Consensus size: 104
37042 TACTACCATT
37052 AAGGCTCAGAGTCTAGAATGCAAAAATGGTACCGATACCATGAAATGGTATTGATACCATAGTGC
1 AAGGCTCAGAGTCTAGAATGCAAAAATGGTACCGATACCATGAAATGGTATTGATACCATAGTGC
37117 AAAGTATTACTGATACTCCTGAGACAGTATCGATACCAC
66 AAAGTATTACTGATACTCCTGAGACAGTATCGATACCAC
37156 AAGGCTCAGAGTCTAGAATGCAAAAATGGTACCGATACCATGAAATGGTATTGATACCATAGTGC
1 AAGGCTCAGAGTCTAGAATGCAAAAATGGTACCGATACCATGAAATGGTATTGATACCATAGTGC
37221 AAAGTATTACTGATACTCCTGAGACAGTATCGATACCAC
66 AAAGTATTACTGATACTCCTGAGACAGTATCGATACCAC
37260 AAGGCTC
1 AAGGCTC
37267 CAATGGCTAG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 111 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (104 bp):
AAGGCTCAGAGTCTAGAATGCAAAAATGGTACCGATACCATGAAATGGTATTGATACCATAGTGC
AAAGTATTACTGATACTCCTGAGACAGTATCGATACCAC
Found at i:37203 original size:19 final size:19
Alignment explanation
Indices: 37179--37215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37169 TAGAATGCAA
37179 AAATGGTACCGATACCATG
1 AAATGGTACCGATACCATG
**
37198 AAATGGTATTGATACCAT
1 AAATGGTACCGATACCAT
37216 AGTGCAAAGT
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:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (19 bp):
AAATGGTACCGATACCATG
Found at i:38075 original size:15 final size:15
Alignment explanation
Indices: 38051--38080 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38041 GGTGCCTATT
*
38051 ACATTGAAGATTCAC
1 ACATTCAAGATTCAC
38066 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
38081 TACCTGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Found at i:39889 original size:51 final size:51
Alignment explanation
Indices: 39780--39878 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
39770 AGAACTTGTT
* *
39780 GAAAAGGAAGAGGAGAAAAGAGAAGGGACACCGGAGACGGAAAAAGAGAAA
1 GAAAAGGAAGAGGAGAAAAGAGAAGGAACACCGCAGACGGAAAAAGAGAAA
* *
39831 GAAAAGGAAGAGG-GTAAAGGAGAAGGAACATCGCA-A-GGAAAAAG-GAAA
1 GAAAAGGAAGAGGAG-AAAAGAGAAGGAACACCGCAGACGGAAAAAGAGAAA
39879 AGGAGAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
48 4 0.09
49 8 0.19
50 2 0.05
51 29 0.67
ACGTcount: A:0.55, C:0.07, G:0.36, T:0.02
Consensus pattern (51 bp):
GAAAAGGAAGAGGAGAAAAGAGAAGGAACACCGCAGACGGAAAAAGAGAAA
Found at i:42299 original size:2 final size:2
Alignment explanation
Indices: 42281--42368 Score: 106
Period size: 2 Copynumber: 44.5 Consensus size: 2
42271 TCAATCTACA
* * * * *
42281 AT AT AC AT AT TT AT AT AT AT TT AT AT AT AT AT AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42323 AT AT AT -T TT AT AT TT 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
42364 AT AT A
1 AT AT A
42369 ATTTACGAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:42478 original size:85 final size:84
Alignment explanation
Indices: 42425--42606 Score: 231
Period size: 85 Copynumber: 2.1 Consensus size: 84
42415 AATGGCGTGT
* *
42425 GCTTCAATGACACGCAATATAAGTCATACATGTGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACACACAAACGTATGT
42490 CAAGCAGATTTATGACGGGG
66 -AAGCAGATTTATGACGGGG
** * * * *
42510 GCTTCAATGATGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACACACAAACGTATGT
* * *
42575 CATCTTA-ATTTATGACAGGG
66 AAGC--AGATTTATGACGGGG
42595 GCTTCAATGACA
1 GCTTCAATGACA
42607 GTTGCGCGTC
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
84 2 0.02
85 81 0.96
86 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (84 bp):
GCTTCAATGACACGCAATATAAGTCATACATGCGTGTCATAAATTTATGACACACAAACGTATGT
AAGCAGATTTATGACGGGG
Found at i:47542 original size:8 final size:8
Alignment explanation
Indices: 47531--47595 Score: 80
Period size: 8 Copynumber: 7.9 Consensus size: 8
47521 TTTTTGGCTC
47531 TTTTTTTG
1 TTTTTTTG
47539 TTTTTTTG
1 TTTTTTTG
47547 CCTTTTTTT-
1 --TTTTTTTG
47556 TTTTTTTG
1 TTTTTTTG
47564 CCTTTTTTTG
1 --TTTTTTTG
47574 -TTTTTTG
1 TTTTTTTG
47581 TTTTTTTG
1 TTTTTTTG
47589 TTTTTTT
1 TTTTTTT
47596 TGAAAAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
7 14 0.27
8 22 0.43
10 15 0.29
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:47569 original size:25 final size:25
Alignment explanation
Indices: 47531--47588 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
47521 TTTTTGGCTC
** *
47531 TTTTTTTGTTTTTTTGCCTTTTTTT
1 TTTTTTTGCCTTTTTGCCTTTTTTG
***
47556 TTTTTTTGCCTTTTTTTGTTTTTTG
1 TTTTTTTGCCTTTTTGCCTTTTTTG
47581 TTTTTTTG
1 TTTTTTTG
47589 TTTTTTTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (25 bp):
TTTTTTTGCCTTTTTGCCTTTTTTG
Found at i:47593 original size:35 final size:36
Alignment explanation
Indices: 47520--47597 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
47510 AAATTTTGGC
47520 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTTTT
1 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTTTT
* **
47556 TTTTTTTGC-CTTTTTTTG-TTTTTTGTTTTTTTGTT
1 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTT-TT
47591 TTTTTTG
1 TTTTTTG
47598 AAAAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 12 0.32
35 17 0.46
36 8 0.22
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.81
Consensus pattern (36 bp):
TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTTTT
Found at i:47597 original size:17 final size:18
Alignment explanation
Indices: 47520--47595 Score: 106
Period size: 17 Copynumber: 4.4 Consensus size: 18
47510 AAATTTTGGC
*
47520 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGC-CTTTTTTTG
47539 TTTTTTTGCCTTTTTTT-
1 TTTTTTTGCCTTTTTTTG
47556 TTTTTTTGCCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
47574 -TTTTTTG--TTTTTTTG
1 TTTTTTTGCCTTTTTTTG
47589 TTTTTTT
1 TTTTTTT
47596 TGAAAAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
15 8 0.15
16 6 0.11
17 24 0.44
18 8 0.15
19 8 0.15
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.82
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:52274 original size:8 final size:8
Alignment explanation
Indices: 52263--52325 Score: 76
Period size: 8 Copynumber: 7.8 Consensus size: 8
52253 TTTTTGGCTC
52263 TTTTTTTG
1 TTTTTTTG
52271 TTTTTTTG
1 TTTTTTTG
*
52279 CCTTTTTT-
1 -TTTTTTTG
52287 TTTTTTTG
1 TTTTTTTG
52295 CCTTTTTTTG
1 --TTTTTTTG
52305 -TTTTTTG
1 TTTTTTTG
52312 TTTTTTTG
1 TTTTTTTG
52320 TTTTTT
1 TTTTTT
52326 GAAAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
7 13 0.27
8 21 0.44
9 6 0.12
10 8 0.17
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:52290 original size:16 final size:17
Alignment explanation
Indices: 52252--52326 Score: 102
Period size: 16 Copynumber: 4.4 Consensus size: 17
52242 AAATTTTGGC
52252 TTTTTTGGCTCTTTTTTTG
1 TTTTTT-GC-CTTTTTTTG
52271 TTTTTTTGCCTTTTTTT-
1 -TTTTTTGCCTTTTTTTG
52288 TTTTTTGCCTTTTTTTG
1 TTTTTTGCCTTTTTTTG
52305 TTTTTTG--TTTTTTTG
1 TTTTTTGCCTTTTTTTG
52320 TTTTTTG
1 TTTTTTG
52327 AAAAAAAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.28
16 16 0.30
17 7 0.13
18 8 0.15
19 2 0.04
20 6 0.11
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (17 bp):
TTTTTTGCCTTTTTTTG
Found at i:52300 original size:34 final size:32
Alignment explanation
Indices: 52252--52326 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 32
52242 AAATTTTGGC
*
52252 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTTT
1 TTTTTTTGCTCTTTTTTTG-TTTTTTG--TTTTTT
52287 TTTTTTTGC-CTTTTTTTGTTTTTTGTTTTTT
1 TTTTTTTGCTCTTTTTTTGTTTTTTGTTTTTT
52318 TGTTTTTTG
1 T-TTTTTTG
52327 AAAAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 7 0.18
32 7 0.18
33 7 0.18
34 9 0.24
35 8 0.21
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (32 bp):
TTTTTTTGCTCTTTTTTTGTTTTTTGTTTTTT
Found at i:57000 original size:8 final size:8
Alignment explanation
Indices: 56989--57054 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
56979 TTTTTGGCTC
56989 TTTTTTTG
1 TTTTTTTG
56997 TTTTTTTG
1 TTTTTTTG
*
57005 CCTTTTTTTT
1 --TTTTTTTG
57015 TTTTTTTG
1 TTTTTTTG
*
57023 CCTTTTTTG
1 -TTTTTTTG
57032 -TTTTTTG
1 TTTTTTTG
57039 TTTTTTTG
1 TTTTTTTG
57047 TTTTTTTG
1 TTTTTTTG
57055 AAAAAAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
7 7 0.14
8 30 0.59
9 7 0.14
10 7 0.14
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:57000 original size:18 final size:17
Alignment explanation
Indices: 56978--57052 Score: 84
Period size: 15 Copynumber: 4.4 Consensus size: 17
56968 AAATTTTGGC
56978 TTTTTTGGCTCTTTTTTTG
1 TTTTTT-GC-CTTTTTTTG
*
56997 TTTTTTTGCCTTTTTTTTT
1 -TTTTTTGCC-TTTTTTTG
57016 TTTTTTGCC-TTTTTTG
1 TTTTTTGCCTTTTTTTG
57032 TTTTTTG--TTTTTTTG
1 TTTTTTGCCTTTTTTTG
57047 TTTTTT
1 TTTTTT
57053 TGAAAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
15 13 0.25
16 13 0.25
18 10 0.20
19 9 0.18
20 6 0.12
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (17 bp):
TTTTTTGCCTTTTTTTG
Found at i:57000 original size:19 final size:18
Alignment explanation
Indices: 56978--57052 Score: 86
Period size: 18 Copynumber: 4.3 Consensus size: 18
56968 AAATTTTGGC
56978 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
* *
56997 TTTTTTTGCCTTTTTTTT
1 TTTTTTGGCCTTTTTTTG
*
57015 TTTTTTTGCC-TTTTTTG
1 TTTTTTGGCCTTTTTTTG
57032 TTTTTT-G--TTTTTTTG
1 TTTTTTGGCCTTTTTTTG
57047 TTTTTT
1 TTTTTT
57053 TGAAAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
15 13 0.25
16 1 0.02
17 12 0.23
18 18 0.35
19 8 0.15
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:62719 original size:17 final size:17
Alignment explanation
Indices: 62697--62731 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
62687 AGAGACTATA
62697 ATGAATAAATGAAAAAT
1 ATGAATAAATGAAAAAT
62714 ATGAATAAATGAAAAAT
1 ATGAATAAATGAAAAAT
62731 A
1 A
62732 CAGTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (17 bp):
ATGAATAAATGAAAAAT
Found at i:63634 original size:5 final size:5
Alignment explanation
Indices: 63624--63670 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
63614 TTAAATATTT
*
63624 TTTTA TTTTA TTTTA TTTCTA GTTTA TTCTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTT-TA TTTTA TT-TTA -TTTTA TTTTA TTTT
63671 TTTAACTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 25 0.68
6 10 0.27
7 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:63658 original size:17 final size:16
Alignment explanation
Indices: 63630--63670 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
63620 ATTTTTTTAT
63630 TTTATTTTATTTCTAG
1 TTTATTTTATTTCTAG
* *
63646 TTTATTCTTATTTTTAT
1 TTTATT-TTATTTCTAG
63663 TTTATTTT
1 TTTATTTT
63671 TTTAACTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTCTAG
Found at i:63738 original size:10 final size:9
Alignment explanation
Indices: 63706--63756 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
63696 ACTTTATTCA
63706 TTTTATTTT
1 TTTTATTTT
* *
63715 CTTTA-GTT
1 TTTTATTTT
63723 TTTTATTTT
1 TTTTATTTT
63732 TTATTATTTT
1 TT-TTATTTT
63742 TGTTTATTTT
1 T-TTTATTTT
63752 CTTTT
1 -TTTT
63757 TTTACTAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 6 0.18
9 8 0.24
10 18 0.53
11 2 0.06
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTATTTT
Found at i:64498 original size:17 final size:18
Alignment explanation
Indices: 64466--64499 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
64456 ATTCATATAT
*
64466 TTTATTCCTTCGTGTGAA
1 TTTATTCCTCCGTGTGAA
64484 TTTATT-CTCCGTGTGA
1 TTTATTCCTCCGTGTGA
64500 GCATATGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTATTCCTCCGTGTGAA
Found at i:65585 original size:14 final size:15
Alignment explanation
Indices: 65559--65589 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
65549 TACTTAAACA
65559 TATTTTGCATTTTTT
1 TATTTTGCATTTTTT
65574 TATTTT-CATTTTTT
1 TATTTTGCATTTTTT
65588 TA
1 TA
65590 CATTCGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTTGCATTTTTT
Found at i:67964 original size:20 final size:20
Alignment explanation
Indices: 67939--68058 Score: 116
Period size: 20 Copynumber: 6.4 Consensus size: 20
67929 TGAGATAGTT
67939 TCTCTTGAAACAAATTTGTC
1 TCTCTTGAAACAAATTTGTC
67959 TCTCTTGAAACAAATTTGTC
1 TCTCTTGAAACAAATTTGTC
* *
67979 TCTCTTGAGAC--AGTT-TC
1 TCTCTTGAAACAAATTTGTC
*
67996 -C-CTTGAAACAAATTTTATC
1 TCTCTTGAAACAAA-TTTGTC
*
68015 TCTCTTGAGAC-AA-TT-TC
1 TCTCTTGAAACAAATTTGTC
68032 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAA-TTTGTC
68051 TCTCTTGA
1 TCTCTTGA
68059 GACAGTTTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
15 14 0.17
16 4 0.05
17 5 0.06
18 9 0.11
19 4 0.05
20 34 0.41
21 12 0.15
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTGTC
Found at i:67984 original size:55 final size:57
Alignment explanation
Indices: 67909--68027 Score: 179
Period size: 55 Copynumber: 2.1 Consensus size: 57
67899 AATTTACTCA
* * *
67909 AAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA-TTTGTCTCTCTTG
1 AAACAAAG-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
67966 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
1 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
*
68022 AGACAA
1 AAACAA
68028 TTTCCCTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 33 0.58
56 17 0.30
57 7 0.12
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (57 bp):
AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
Found at i:68024 original size:36 final size:36
Alignment explanation
Indices: 67962--68144 Score: 240
Period size: 36 Copynumber: 5.3 Consensus size: 36
67952 ATTTGTCTCT
67962 CTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* *
67997 CTTGAAACAAATTTTATCTCTCTTGAGACAATTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
68033 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* * *
68069 CTTGAAACAAA------ATCT-TTGA-ATATGTTTTC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACA-GTTTCC
*
68098 CTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
68134 CTTGAAACAAA
1 CTTGAAACAAA
68145 ATCTTTGAAT
Statistics
Matches: 126, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.02
29 19 0.15
30 3 0.02
35 14 0.11
36 86 0.68
37 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:68095 original size:29 final size:29
Alignment explanation
Indices: 68063--68171 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 29
68053 TCTTGAGACA
68063 GTTTCCCTTGAAACAAAATCTTTGAATAT
1 GTTTCCCTTGAAACAAAATCTTTGAATAT
* * * *
68092 GTTTTCCTTAAAACAAATTTTGTCTCTCTTGAGACA-
1 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATAT
68128 GTTTCCCTTGAAACAAAATCTTTGAATAT
1 GTTTCCCTTGAAACAAAATCTTTGAATAT
*
68157 GTTTTCCTTGAAACA
1 GTTTCCCTTGAAACA
68172 GATTTTGTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
28 2 0.03
29 33 0.53
30 3 0.05
35 3 0.05
36 19 0.31
37 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (29 bp):
GTTTCCCTTGAAACAAAATCTTTGAATAT
Found at i:68113 original size:65 final size:65
Alignment explanation
Indices: 68032--68197 Score: 296
Period size: 65 Copynumber: 2.6 Consensus size: 65
68022 AGACAATTTC
68032 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
*
68097 CCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
* * *
68162 CCTTGAAACAGATTTTGTCTCCCTTGAGACAATTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
68198 TTTTGGAACT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (65 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
Found at i:68226 original size:37 final size:36
Alignment explanation
Indices: 68159--68367 Score: 231
Period size: 36 Copynumber: 5.8 Consensus size: 36
68149 TTGAATATGT
* *
68159 TTTC-CTTGAAACAGATTTTGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * * * *
68194 TTTCTTTTGGAACTAAGTCTTGTCTCTCTTGAGACAT
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAA
* * *
68231 TTTTTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* **
68267 TTTCCCTCAAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAA
* *
68304 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * *
68340 TTTCCCTTTAAACAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCT
68368 ATACAGTTTC
Statistics
Matches: 143, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
35 4 0.03
36 80 0.56
37 59 0.41
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:68290 original size:73 final size:72
Alignment explanation
Indices: 68158--68367 Score: 267
Period size: 73 Copynumber: 2.9 Consensus size: 72
68148 TTTGAATATG
* * * * ** ** *
68158 TTTTCCTTGAAACAGATTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTCTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAGTTTTGTCTCTCT
*
68223 TGAGACAT
65 TGAGACAA
* *
68231 TTTTTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTCAAAACAAAGTTTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAGTTTTGTCTCTCT
68296 TGAGACAA
65 TGAGACAA
* * *
68304 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTTAAACAAGTTTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAGTTTTGTCTCTCT
68368 ATACAGTTTC
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 15 0.13
73 104 0.87
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (72 bp):
TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAGTTTTGTCTCTCTT
GAGACAA
Found at i:68492 original size:34 final size:33
Alignment explanation
Indices: 68438--68589 Score: 261
Period size: 33 Copynumber: 4.6 Consensus size: 33
68428 TTTGGAGACA
68438 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
68471 GTTTCTCATGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
68504 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
68537 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAACAC-AAAAAACCTTTG-AAATC
68571 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
68590 GACCTTCGAG
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
33 82 0.72
34 28 0.25
35 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:68753 original size:82 final size:82
Alignment explanation
Indices: 68586--68823 Score: 306
Period size: 82 Copynumber: 3.0 Consensus size: 82
68576 TCTTGAAACA
* * *
68586 CAAAGACCTTCGAGTTCGACTACACTCAGCTTTGAGGGAAC-ATCATTTGCAGCATAACTCAAGG
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGCAGCATAGCTCAAGG
*
68650 CTAGAAGGGTTATCTAC
66 CTAAAAGGGTTATCTAC
* * *
68667 CAAAGACCTTTGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGTAGCATAGCTCAGGG
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGCAGCATAGCTCAAGG
*
68732 CTAAAAGGGTTATCTGC
66 CTAAAAGGGTTATCTAC
* * * * **
68749 CAAAGACCTTCGAGTTCGATTCCATTCAGC-TC-AAGGCA-TATCATTCACAGCATAGCTCAAGG
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGCAGCATAGCTCAAGG
68811 -TAAGAAGGGTTAT
66 CTAA-AAGGGTTAT
68824 TTGTCAACGA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
78 3 0.02
79 29 0.21
80 5 0.04
81 40 0.29
82 61 0.44
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (82 bp):
CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGCAGCATAGCTCAAGG
CTAAAAGGGTTATCTAC
Found at i:70102 original size:9 final size:8
Alignment explanation
Indices: 70090--70154 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 8
70080 TTTTTTTACG
70090 TTATTCATT
1 TTATT-ATT
*
70099 TTATTTTCT
1 TTATTAT-T
70108 TTATTA-T
1 TTATTATT
70115 TTATTATT
1 TTATTATT
70123 TTATTTATT
1 TTA-TTATT
*
70132 TTGTTTATT
1 TT-ATTATT
* *
70141 TTCTTTTT
1 TTATTATT
70149 TTATTA
1 TTATTA
70155 ACTTTTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.16
8 13 0.29
9 25 0.56
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:70159 original size:13 final size:13
Alignment explanation
Indices: 70075--70160 Score: 54
Period size: 13 Copynumber: 6.7 Consensus size: 13
70065 AACTAACCCT
70075 TTTACTTTTTTTA
1 TTTACTTTTTTTA
* *
70088 CGTTA-TTCATTTTA
1 -TTTACTT-TTTTTA
* *
70102 TTTTC-TTTATTA
1 TTTACTTTTTTTA
*
70114 TTTA-TTATTTTA
1 TTTACTTTTTTTA
70126 TTTA-TTTTGTTTA
1 TTTACTTTT-TTTA
*
70139 TTTTCTTTTTTTA
1 TTTACTTTTTTTA
*
70152 TTAACTTTT
1 TTTACTTTT
70161 AATTATCTCT
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
12 19 0.35
13 23 0.43
14 12 0.22
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTACTTTTTTTA
Found at i:72298 original size:35 final size:35
Alignment explanation
Indices: 72252--72328 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
72242 AACATAATCA
72252 TCAATTATATTCTAAACCCCAAAGTCCAAAATACT
1 TCAATTATATTCTAAACCCCAAAGTCCAAAATACT
* * * *
72287 TCAATTATATTCTAAATCTCAAATTCTAAAATACT
1 TCAATTATATTCTAAACCCCAAAGTCCAAAATACT
*
72322 TTAATTA
1 TCAATTA
72329 CATGCCCAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAAGTCCAAAATACT
Found at i:72553 original size:3 final size:3
Alignment explanation
Indices: 72534--72594 Score: 74
Period size: 3 Copynumber: 20.3 Consensus size: 3
72524 CTACATAAAC
72534 ATT A-T ATT ATAT ATT ATT ATT ATAT ATT ATT A-T ATT ATT ATAT ATT
1 ATT ATT ATT AT-T ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT
72580 ATT ATT A-T ATT ATT A
1 ATT ATT ATT ATT ATT A
72595 ATTTATAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.12
3 37 0.71
4 9 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:72556 original size:13 final size:12
Alignment explanation
Indices: 72534--72594 Score: 74
Period size: 13 Copynumber: 5.1 Consensus size: 12
72524 CTACATAAAC
72534 ATTA-TATTATAT
1 ATTATTATTAT-T
72546 ATTATTATTATAT
1 ATTATTATTAT-T
72559 ATTATTA-TATT
1 ATTATTATTATT
72570 ATTATATATTATT
1 ATTAT-TATTATT
72583 ATTA-TATTATT
1 ATTATTATTATT
72594 A
1 A
72595 ATTTATAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
11 14 0.30
12 9 0.20
13 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:72557 original size:18 final size:18
Alignment explanation
Indices: 72534--72592 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
72524 CTACATAAAC
72534 ATTATATTATATATTATT
1 ATTATATTATATATTATT
72552 ATTATA-TAT-TATTA-T
1 ATTATATTATATATTATT
72567 A-T-TATTATATATTATT
1 ATTATATTATATATTATT
72583 ATTATATTAT
1 ATTATATTAT
72593 TAATTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.06
14 4 0.11
15 7 0.19
16 7 0.19
17 4 0.11
18 12 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATATTATATATTATT
Found at i:73409 original size:23 final size:23
Alignment explanation
Indices: 73374--73446 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
73364 ATACTTTACA
*
73374 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
73397 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
73420 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
73443 ATAT
1 ATAT
73447 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:73490 original size:22 final size:22
Alignment explanation
Indices: 73464--73508 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
73454 TATTATATTG
*
73464 AAAGTGTCCATACTTTTTATAA
1 AAAGTATCCATACTTTTTATAA
* *
73486 AAAGTATCGATACTTTTTTTAA
1 AAAGTATCCATACTTTTTATAA
73508 A
1 A
73509 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
AAAGTATCCATACTTTTTATAA
Found at i:73898 original size:23 final size:23
Alignment explanation
Indices: 73865--73937 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
73855 ATACTTTACA
73865 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
73888 ATATAAACACTATCTATTACATT
1 ATATAAGCACTACCTATTACATT
** *
73911 ATATAAGTGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
73934 ATAT
1 ATAT
73938 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:74307 original size:488 final size:489
Alignment explanation
Indices: 72972--74773 Score: 3241
Period size: 491 Copynumber: 3.7 Consensus size: 489
72962 TTATAATATG
*
72972 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
73037 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
73101 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
*
73166 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* *
73231 ACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACT
* *
73296 CAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAATACGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGA
73361 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
73426 GTGCTACCTATTACATCATATTTTTACCTATTATA
455 GTGCTACCTATTACATCATATTTTTACCTATTATA
73461 TTGAAAGTGTCCATACTTTTTAT-AAAAAGTATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAG-ATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
73525 TTCAATTTTTTTGTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCACTTG
65 TTCAA-TTTTTT-TAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
73590 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
128 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
*
73655 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
193 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAT
* * *
73720 ATACCGTAACATAAAAAATAAATCATTAAATACATATAATTACTAAATTGATATCTTAAAACTCA
258 ATACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
*
73785 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAT
323 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAG
* *
73850 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTATCTATTACATTATAT
388 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
73915 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
453 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
73952 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
74017 TCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
74081 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAGCAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
74146 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * * * *
74211 TCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTC
*
74276 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
*
74341 AGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
*
74406 CGCTACCTATTACATCATATTTTTACCTATTATA
456 TGCTACCTATTACATCATATTTTTACCTATTATA
74440 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATAC-TTTTTTTAAAGTTATGTAATTTATGT
*
74505 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* * *
74570 ACAAAAAATTATTTGATTGTTTTGAAATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
* *
74635 TTAACCAAAGATAGTAATAAATATGTAATATATATGTTTATTGATTTTAATTTAATAATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* * *
74700 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
259 TACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
74765 TCAAAAGAT
324 TCAAAAGAT
74774 GTACATACCT
Statistics
Matches: 1271, Mismatches: 34, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
487 6 0.00
488 481 0.38
489 51 0.04
490 5 0.00
491 722 0.57
492 6 0.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
TGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:74339 original size:979 final size:980
Alignment explanation
Indices: 72972--74773 Score: 3304
Period size: 979 Copynumber: 1.8 Consensus size: 980
72962 TTATAATATG
*
72972 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
73037 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
73102 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
*
73167 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * *
73232 CCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCACTC
261 CCATAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTC
* * *
73297 AAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAATACGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
*
73362 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
*
73427 TGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTAT-AAAAAGT
456 CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAAG-
73491 ATCGATAC-TTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTGTAATAGTGTTTCATGTT
520 ATCGATACTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTT-TAATAGTGTTTCATGTT
* *
73555 TTCCACCTACAATATTAATTTAATAATTTCACTTGCACAAAAAATTATTTGATTGTTTTGATATT
584 TTCCACCTACAATATTAATTTAATAATTTCACTTACACAAAAAATTATTTGATTGTTTTGAAATT
73620 TTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAAT
649 TTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAAT
* *
73685 ATATATGTTTATTGTTTTTAATTTAATGATAATATATACCGTAACATAAAAAATAAATCATTAAA
714 ATATATGTTTATTGATTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAAA
* *
73750 TACATATAATTACTAAATTGATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
779 CACATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
73815 CACAGTGAAATAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACCT
844 CACAGTGAAATAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACCT
73880 ATTACATTATATAAACACTATCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACC
909 ATTACATTATATAAACACTATCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACC
73945 TATTATA
974 TATTATA
73952 TTGAAAGTGTCCATAC-TTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
74016 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
66 TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
*
74081 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAGCAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
74146 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * * *
74211 TCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCATAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTC
74276 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
74341 AGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
74406 CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
456 CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
74471 TCGATACTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTT
521 TCGATACTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTT
*
74536 CCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGAAATTTT
586 CCACCTACAATATTAATTTAATAATTTCACTTACACAAAAAATTATTTGATTGTTTTGAAATTTT
* * *
74601 ATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGATAGTAATAAATATGTAATAT
651 ATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATAT
* * *
74666 ATATGTTTATTGATTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACG
716 ATATGTTTATTGATTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAAACA
*
74731 CCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
781 CATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGAT
74774 GTACATACCT
Statistics
Matches: 791, Mismatches: 29, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
979 732 0.93
980 59 0.07
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (980 bp):
TTGAAAGTGTCCATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCATAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAAGA
TCGATACTTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTT
CCACCTACAATATTAATTTAATAATTTCACTTACACAAAAAATTATTTGATTGTTTTGAAATTTT
ATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATAT
ATATGTTTATTGATTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTAAACA
CATATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCA
CAGTGAAATAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTACCTAT
TACATTATATAAACACTATCTATTACATTATATAAGTGCTACCTATTACATCATATTTTTACCTA
TTATA
Found at i:74388 original size:23 final size:23
Alignment explanation
Indices: 74362--74425 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
74352 AACATAAGCA
74362 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
74385 CTACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
74408 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
74426 TTTTACCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:75905 original size:12 final size:12
Alignment explanation
Indices: 75888--75912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75878 CTAAATGCAT
75888 ATTTATCATCAA
1 ATTTATCATCAA
75900 ATTTATCATCAA
1 ATTTATCATCAA
75912 A
1 A
75913 CAAGAAACCC
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTATCATCAA
Found at i:77026 original size:198 final size:200
Alignment explanation
Indices: 76424--77161 Score: 1302
Period size: 200 Copynumber: 3.7 Consensus size: 200
76414 TTATATACCA
* *
76424 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACAATATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
76489 ATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
76554 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
76619 GACCT
196 GACCT
* *
76624 ATTTTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACCT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
76689 TTGGGTTTCGATGTTTATGTGG-TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACC
66 TTGGGTTTCGATGTTTATG-GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACC
*
76753 CTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACATATTATTT
130 CTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTT
76818 AGACCT
195 AGACCT
*
76824 ATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
76889 TTGGTTTTCGATGTTTATGGGATCGACAC-TTTT-TATATGGATCGACACTGTATGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* * *
76952 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTTGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
77017 GACCT
196 GACCT
* *
77022 ATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
77087 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGTACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
77152 TGTTTGCCAT
131 TGTTTGCCAT
77162 ATTGTAAATT
Statistics
Matches: 512, Mismatches: 22, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
198 185 0.36
199 10 0.02
200 315 0.62
201 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACCT
Found at i:77119 original size:398 final size:400
Alignment explanation
Indices: 76424--77161 Score: 1313
Period size: 398 Copynumber: 1.9 Consensus size: 400
76414 TTATATACCA
*
76424 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACAATATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTT
*
76489 ATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTGTATGGTTGCACCC
76554 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
* *
76619 GACCTATTTTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTA
196 GACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACATATTACATTA
76684 TACCTTTGGGTTTCGATGTTTATGTGGTCGACACTTTTTATATATGGATCGACACTTTATGGTTG
261 TACCTTTGGGTTTCGATGTTTATGTGGTCGACACTTTTTATATATGGATCGACACTTTATGGTTG
76749 CACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACATATT
326 CACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACATATT
76814 ATTTAGACCT
391 ATTTAGACCT
* *
76824 ATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTT
*
76889 -TTGGTTTTCGATGTTTATGGGATCGACAC-TTTT-TATATGGATCGACACTGTATGGTTGCACC
66 ATGGGTTTT-GATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTGTATGGTTGCACC
* * *
76951 CTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACTACAAAAGTGTTGATACATTATTT
130 CTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTT
*
77016 AGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATT
195 AGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACATATTACATT
*
77081 ATACTTTTGGGTTTCGATGTTTATG-GGATCGACACTTTTTATATATGGATCGACACTTTATGGT
260 ATACCTTTGGGTTTCGATGTTTATGTGG-TCGACACTTTTTATATATGGATCGACACTTTATGGT
*
77145 TGTACCCTGTTTGCCAT
324 TGCACCCTGTTTGCCAT
77162 ATTGTAAATT
Statistics
Matches: 323, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
397 2 0.01
398 228 0.71
399 11 0.03
400 82 0.25
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (400 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACAATATACTT
ATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTGTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACATATTACATTA
TACCTTTGGGTTTCGATGTTTATGTGGTCGACACTTTTTATATATGGATCGACACTTTATGGTTG
CACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACATATT
ATTTAGACCT
Found at i:77297 original size:19 final size:19
Alignment explanation
Indices: 77273--77322 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
77263 ATTATATTCA
77273 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
*
77292 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
77311 TATACAAAATTA
1 TATACAAAATTA
77323 ACCCTACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:78761 original size:18 final size:17
Alignment explanation
Indices: 78728--78781 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
78718 CATCGACTTC
*
78728 CTTCCTCCTCATTTCTT
1 CTTCCTCCTCTTTTCTT
*
78745 C--CAT-CTCTTCTTCTT
1 CTTCCTCCTCTT-TTCTT
78760 CTTCCTCCCTCTTTTCTT
1 CTTCCT-CCTCTTTTCTT
78778 CTTC
1 CTTC
78782 ATATTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
17 3 0.10
18 9 0.31
19 5 0.17
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTCCTCCTCTTTTCTT
Found at i:78776 original size:15 final size:15
Alignment explanation
Indices: 78728--78778 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
78718 CATCGACTTC
*
78728 CTTCCT-CCTCATTT
1 CTTCCTCCCTCTTTT
*
78742 CTTCCATCTCTTCTTCTT
1 CTTCC-TC-CCTCTT-TT
78760 CTTCCTCCCTCTTTT
1 CTTCCTCCCTCTTTT
78775 CTTC
1 CTTC
78779 TTCATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 5 0.17
17 6 0.20
18 7 0.23
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTCCTCCCTCTTTT
Found at i:79083 original size:21 final size:21
Alignment explanation
Indices: 79058--79122 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
79048 CCCTTTATGC
* *
79058 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
79079 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
79100 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
79121 CT
1 CT
79123 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Done.