Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006050.1 Hibiscus syriacus cultivar Beakdansim tig00014311_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: 130487
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1295 original size:225 final size:225
Alignment explanation
Indices: 904--1355 Score: 841
Period size: 225 Copynumber: 2.0 Consensus size: 225
894 GAAATCGGGC
904 GAGTTTTATTTCTATAACGATTCGCCACTTTGCAGTCCGTTGCCGCCAGGCACGCCGTGGAACAA
1 GAGTTTTATTTCTATAACGATTCGCCACTTTGCAGTCCGTTGCCGCCAGGCACGCCGTGGAACAA
*
969 TATGTCAGCAGCTGAATTTGCTAGTCGAGGTGGTGTCATTGGCTTAGACAACGAGTCATTGTTTA
66 TATGTCAGCAGCTGAATTTGCTAGTCGAGGTGGTGTCATCGGCTTAGACAACGAGTCATTGTTTA
1034 GTATCCACACGGGGAACATGAGTTTAATTGGCAGTCCGTTCCCGGTCACTCCACGTAATAATCAG
131 GTATCCACACGGGGAACATGAGTTTAATTGGCAGTCCGTTCCCGGTCACTCCACGTAATAATCAG
*
1099 ACAGCGACTGAAACTACCGGGCAAAGTGGT
196 ACAGCGACTGAAACTACCAGGCAAAGTGGT
* *
1129 GAGTTTTATTTCTATAACGATTCGCCACTTTGTAGTCCGTTGCCGCCAGGCACTCCGTGGAACAA
1 GAGTTTTATTTCTATAACGATTCGCCACTTTGCAGTCCGTTGCCGCCAGGCACGCCGTGGAACAA
* *
1194 TTTGTCAGCAGCTGAATTTGCTAGTCGAGGTGGTGTCATCGGCTTAGACAACGAGTTATTGTTTA
66 TATGTCAGCAGCTGAATTTGCTAGTCGAGGTGGTGTCATCGGCTTAGACAACGAGTCATTGTTTA
*
1259 GTATCCACACGGGGAACATGAGTTTAATTGGCAGTCCGTTCCCGGTCACTCCACTTAATAATCAG
131 GTATCCACACGGGGAACATGAGTTTAATTGGCAGTCCGTTCCCGGTCACTCCACGTAATAATCAG
1324 ACAGCGACTGAAACTACCAGGCAAAGTGGT
196 ACAGCGACTGAAACTACCAGGCAAAGTGGT
1354 GA
1 GA
1356 CTCGAACGAG
Statistics
Matches: 220, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 220 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (225 bp):
GAGTTTTATTTCTATAACGATTCGCCACTTTGCAGTCCGTTGCCGCCAGGCACGCCGTGGAACAA
TATGTCAGCAGCTGAATTTGCTAGTCGAGGTGGTGTCATCGGCTTAGACAACGAGTCATTGTTTA
GTATCCACACGGGGAACATGAGTTTAATTGGCAGTCCGTTCCCGGTCACTCCACGTAATAATCAG
ACAGCGACTGAAACTACCAGGCAAAGTGGT
Found at i:3089 original size:103 final size:103
Alignment explanation
Indices: 2910--3116 Score: 414
Period size: 103 Copynumber: 2.0 Consensus size: 103
2900 TATCATAGTT
2910 AAGTTTTAAAACAAAATTTAAGGACAGCTGAGAAAGGGGAAATAAAGGATGATTTTTGTAATTAA
1 AAGTTTTAAAACAAAATTTAAGGACAGCTGAGAAAGGGGAAATAAAGGATGATTTTTGTAATTAA
2975 ACCTTTGATTCTGGACCTTAGAATTGTGGACCAGGTAA
66 ACCTTTGATTCTGGACCTTAGAATTGTGGACCAGGTAA
3013 AAGTTTTAAAACAAAATTTAAGGACAGCTGAGAAAGGGGAAATAAAGGATGATTTTTGTAATTAA
1 AAGTTTTAAAACAAAATTTAAGGACAGCTGAGAAAGGGGAAATAAAGGATGATTTTTGTAATTAA
3078 ACCTTTGATTCTGGACCTTAGAATTGTGGACCAGGTAA
66 ACCTTTGATTCTGGACCTTAGAATTGTGGACCAGGTAA
3116 A
1 A
3117 TTCACAAGTG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (103 bp):
AAGTTTTAAAACAAAATTTAAGGACAGCTGAGAAAGGGGAAATAAAGGATGATTTTTGTAATTAA
ACCTTTGATTCTGGACCTTAGAATTGTGGACCAGGTAA
Found at i:9495 original size:24 final size:23
Alignment explanation
Indices: 9468--9545 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 23
9458 AATAATATGT
9468 TTTATAATAATATATTTATAATCA
1 TTTATAATAATATATTTATAAT-A
* *
9492 TTTAT--T-AT-TTTTTAAAAT-
1 TTTATAATAATATATTTATAATA
*
9510 TATTAAAATAATATATTTTATAATA
1 T-TTATAATAATATA-TTTATAATA
*
9535 TTTTTAATAAT
1 TTTATAATAAT
9546 TAAATAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 8 0.20
21 3 0.08
22 3 0.08
23 1 0.03
24 20 0.50
25 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTATAATAATATATTTATAATA
Found at i:9559 original size:58 final size:58
Alignment explanation
Indices: 9444--9559 Score: 139
Period size: 58 Copynumber: 2.0 Consensus size: 58
9434 ATATCAATAC
* * * *
9444 TTTAAAATAATTAAAATAATATGTTTTATAATAATATATTTATAATCATTTATTATTT
1 TTTAAAATAATTAAAATAATATATTTTATAATAATATATTTATAATAAATAATTATTT
*
9502 TTTAAAATTATTAAAATAATATATTTTATAAT-AT-T-TTTAATAATTAAATAATATATTT
1 TTTAAAATAATTAAAATAATATATTTTATAATAATATATTT-ATAA-TAAATAAT-TATTT
9560 CAACATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
55 3 0.06
56 5 0.10
57 7 0.14
58 35 0.70
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (58 bp):
TTTAAAATAATTAAAATAATATATTTTATAATAATATATTTATAATAAATAATTATTT
Found at i:11699 original size:16 final size:16
Alignment explanation
Indices: 11675--11705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11665 CTTGGTGAGC
11675 TTAACGAGCAACGAGA
1 TTAACGAGCAACGAGA
*
11691 TTAATGAGCAACGAG
1 TTAACGAGCAACGAG
11706 TCGAGTAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (16 bp):
TTAACGAGCAACGAGA
Found at i:15148 original size:19 final size:19
Alignment explanation
Indices: 15124--15166 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15114 AAATTGAGAC
15124 ATTTAATTAAGTTGATTTG
1 ATTTAATTAAGTTGATTTG
* *
15143 ATTTAATTCAGTTTATTTG
1 ATTTAATTAAGTTGATTTG
15162 -TTTAA
1 ATTTAA
15167 CAGTTAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (19 bp):
ATTTAATTAAGTTGATTTG
Found at i:17365 original size:30 final size:30
Alignment explanation
Indices: 17331--17421 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
17321 AATCATTTTG
*
17331 ATTGTTTTAGCTTCTACTTGCTCTGGTACA
1 ATTGTTTTAGTTTCTACTTGCTCTGGTACA
*
17361 ATTGTTTTAATTTCTACTTGCTCTGGTACA
1 ATTGTTTTAGTTTCTACTTGCTCTGGTACA
17391 ATTGTTTTAGTTTCTACTTGCTCTGGTACA
1 ATTGTTTTAGTTTCTACTTGCTCTGGTACA
17421 A
1 A
17422 CAATTTTTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (30 bp):
ATTGTTTTAGTTTCTACTTGCTCTGGTACA
Found at i:25048 original size:58 final size:58
Alignment explanation
Indices: 24986--25104 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 58
24976 ATCAAAAGTT
* * * *
24986 TAGGGATTAATTAAGAATTAAGATAGTAGTTTGGGGATAAATTTGGAATATTTAAAAG
1 TAGGGATTAATTAAGAACTAAGATAATAGTTTGGGGATAAAATTAGAATATTTAAAAG
* *
25044 TAGGGATTAATTTAGAACTAGGATAATAGTTTGGGGATAAAATTAGAATATTTAAAAG
1 TAGGGATTAATTAAGAACTAAGATAATAGTTTGGGGATAAAATTAGAATATTTAAAAG
25102 TAG
1 TAG
25105 AGACCAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.42, C:0.01, G:0.24, T:0.34
Consensus pattern (58 bp):
TAGGGATTAATTAAGAACTAAGATAATAGTTTGGGGATAAAATTAGAATATTTAAAAG
Found at i:25081 original size:31 final size:29
Alignment explanation
Indices: 24982--25093 Score: 75
Period size: 31 Copynumber: 3.8 Consensus size: 29
24972 AATGATCAAA
* * *
24982 AGTTTAGGGATTAATTAAGAATTAAGATAGT
1 AGTTTAGGGATAAATTTAGAA-T-AGATAAT
* * ** *
25013 AGTTTGGGGATAAATTTGGAATATTTAAA
1 AGTTTAGGGATAAATTTAGAATAGATAAT
*
25042 AG--TAGGGATTAATTTAGAACTAGGATAAT
1 AGTTTAGGGATAAATTTAGAA-TA-GATAAT
* *
25071 AGTTTGGGGATAAAATTAGAATA
1 AGTTTAGGGATAAATTTAGAATA
25094 TTTAAAAGTA
Statistics
Matches: 60, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
27 14 0.23
28 2 0.03
29 10 0.17
30 3 0.05
31 31 0.52
ACGTcount: A:0.41, C:0.01, G:0.24, T:0.34
Consensus pattern (29 bp):
AGTTTAGGGATAAATTTAGAATAGATAAT
Found at i:25131 original size:58 final size:58
Alignment explanation
Indices: 25007--25139 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 58
24997 TAAGAATTAA
* * * * ** *
25007 GATAGTAGTTTGGGGATAAATTTGGAATATTTAAAAGTAGGGATTAATTTAGAACTAG
1 GATAATAGTTTGGGGATAAAATTAGAATATTTAAAAGTAGAGACCAATTTAGAACAAG
*
25065 GATAATAGTTTGGGGATAAAATTAGAATATTTAAAAGTAGAGACCAATTT-GAAACAAT
1 GATAATAGTTTGGGGATAAAATTAGAATATTTAAAAGTAGAGACCAATTTAG-AACAAG
* *
25123 GATCATAGTTTGAGGAT
1 GATAATAGTTTGGGGAT
25140 GTATGATGCC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 1 0.02
58 63 0.98
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
GATAATAGTTTGGGGATAAAATTAGAATATTTAAAAGTAGAGACCAATTTAGAACAAG
Found at i:25484 original size:24 final size:24
Alignment explanation
Indices: 25452--25498 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
25442 AAATGGCAGC
25452 TTTTTCTTCTTCCTCATCTTCAGA
1 TTTTTCTTCTTCCTCATCTTCAGA
25476 TTTTTCTTCTTCCTCATCTTCAG
1 TTTTTCTTCTTCCTCATCTTCAG
25499 CTTCAAAACC
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:0.11, C:0.30, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTTTCTTCTTCCTCATCTTCAGA
Found at i:33776 original size:57 final size:57
Alignment explanation
Indices: 33706--33996 Score: 496
Period size: 57 Copynumber: 5.1 Consensus size: 57
33696 GGAATTTTCC
* **
33706 TTTTAAATTTAACTTAAAAACAGGTGTTCTCATTACATTTTTATTTTAAATGTTTAT
1 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
33763 TTTTAAATTTAACTTAAAAAT-AATGTTCTCATTACATTTTTATTTTAAATGTTTAT
1 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
* * *
33819 TTTTTAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAACGATTAT
1 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
33876 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
1 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
* *
33933 TTTTAAATTTAACTTAAAAATAAATGTTTTCATTACATTTTTATTTTACATGTTTA-
1 TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
33989 TTTTAAAT
1 TTTTAAAT
33997 GTTGATATCG
Statistics
Matches: 222, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
56 61 0.27
57 161 0.73
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (57 bp):
TTTTAAATTTAACTTAAAAATAAATGTTCTCATTACATTTTTATTTTAAATGTTTAT
Found at i:33983 original size:13 final size:13
Alignment explanation
Indices: 33965--33999 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
33955 AATGTTTTCA
*
33965 TTACATTTTTATT
1 TTACATGTTTATT
33978 TTACATGTTTATT
1 TTACATGTTTATT
*
33991 TTAAATGTT
1 TTACATGTT
34000 GATATCGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (13 bp):
TTACATGTTTATT
Found at i:39816 original size:55 final size:55
Alignment explanation
Indices: 39754--40235 Score: 670
Period size: 55 Copynumber: 8.7 Consensus size: 55
39744 CTTCAAATGG
* * * * *
39754 CGGGTCTGCTCCCTATTCTTTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAA
* * * * *
39809 CGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCCTAA-AAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTT-C-AACAAA
*
39865 CGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
* * * * *
39920 CGTGTCTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCCTAA-AAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTT-C-AACAAA
39976 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
40031 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
40086 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
40141 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
* * * *
40196 CGTGTCTGCTCCCTATTCCTTCAAAGAGTATA-AGACTCGA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGA
40236 TCTTCATAAA
Statistics
Matches: 393, Mismatches: 24, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
54 6 0.02
55 292 0.74
56 89 0.23
57 6 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (55 bp):
CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
Found at i:40143 original size:110 final size:111
Alignment explanation
Indices: 39754--40235 Score: 674
Period size: 111 Copynumber: 4.4 Consensus size: 111
39744 CTTCAAATGG
* * * * * * *
39754 CGGGTCTGCTCCCTATTCTTTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAACGTGTCTGC
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGC
* *
39818 TCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCCTAAAAA
65 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCCTAAAAA
* * *
39865 CGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCTGCT
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
* *
39930 CCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCCTAAAAA
66 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCCTAAAAA
39976 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
*
40041 CTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTT-C-AACAAA
66 CCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCCTAA-AAA
40086 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
*
40151 CTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTT-C-AACAAA
66 CCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCCTAA-AAA
* * * *
40196 CGTGTCTGCTCCCTATTCCTTCAAAGAGTATA-AGACTCGA
1 CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGA
40236 TCTTCATAAA
Statistics
Matches: 351, Mismatches: 16, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
109 3 0.01
110 150 0.43
111 197 0.56
112 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (111 bp):
CGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCCTAAAAA
Found at i:41619 original size:18 final size:17
Alignment explanation
Indices: 41598--41656 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
41588 TTTCCTTCCC
*
41598 TTTTCCATTTTTTTCGTT
1 TTTTCCATATTTTTC-TT
41616 TTTTCCATCATTTTTCTT
1 TTTTCCAT-ATTTTTCTT
*
41634 TTTTCTCA-CTTTTTCATT
1 TTTTC-CATATTTTTC-TT
41652 TTTTC
1 TTTTC
41657 TCTTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 6 0.17
18 22 0.61
19 8 0.22
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTCCATATTTTTCTT
Found at i:41657 original size:18 final size:19
Alignment explanation
Indices: 41607--41658 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
41597 CTTTTCCATT
41607 TTTTTCGTTTTTTC-CATCA
1 TTTTTC-TTTTTTCTCATCA
41626 TTTTTCTTTTTTCTCA-C-
1 TTTTTCTTTTTTCTCATCA
41643 TTTTTCATTTTTTCTC
1 TTTTTC-TTTTTTCTC
41659 TTTTATTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.19
18 17 0.55
19 8 0.26
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTCTTTTTTCTCATCA
Found at i:45231 original size:2 final size:2
Alignment explanation
Indices: 45224--45252 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45214 AAATAAATAC
45224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45253 CATACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45278 original size:12 final size:13
Alignment explanation
Indices: 45261--45289 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
45251 TACATACAAT
45261 AATGAATG-AATG
1 AATGAATGAAATG
45273 AATGAATGAAATG
1 AATGAATGAAATG
45286 AATG
1 AATG
45290 GGAGAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
AATGAATGAAATG
Found at i:51418 original size:45 final size:47
Alignment explanation
Indices: 51351--51449 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 47
51341 TGTTATCCAC
* * *
51351 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTCA
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCATTATTCA
* *
51397 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAAGCATTTATTCG
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCA-TTATTCA
51444 AAAAAT
1 AAAAAT
51450 GAAAATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 26 0.57
46 8 0.17
47 12 0.26
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (47 bp):
AAAAATAAATCCTAACCGCATGATATCTAATTCGCAAGCATTATTCA
Found at i:53926 original size:15 final size:15
Alignment explanation
Indices: 53888--53930 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
53878 CCAAATACCA
*
53888 ACCTAAAACCAAGAT
1 ACCTAAAACCAAAAT
*
53903 --CTAAGACCAAAAT
1 ACCTAAAACCAAAAT
53916 ACCTAAAACCAAAAT
1 ACCTAAAACCAAAAT
53931 CTTACCCTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.56, C:0.26, G:0.05, T:0.14
Consensus pattern (15 bp):
ACCTAAAACCAAAAT
Found at i:57222 original size:25 final size:24
Alignment explanation
Indices: 57149--57222 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
57139 AAAGTCCAAC
57149 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
* **
57175 AAA-TGAGA-AATAATAAAAAAAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
57199 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
57223 AAAAATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:59445 original size:110 final size:111
Alignment explanation
Indices: 59251--59471 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 111
59241 ATTACAAAAA
* *
59251 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
59316 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
59362 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
59426 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
59472 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 71 0.67
111 35 0.33
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:59609 original size:12 final size:10
Alignment explanation
Indices: 59595--59634 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
59585 ACCTTAAATA
*
59595 GAGAGTATTT
1 GAGAGAATTT
59605 GAGAGAAATTT
1 GAGAG-AATTT
59616 -AGAGAATTT
1 GAGAGAATTT
59625 GAGAGAATTT
1 GAGAGAATTT
59635 TGTGTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 5 0.19
10 18 0.67
11 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:61237 original size:20 final size:20
Alignment explanation
Indices: 61214--61259 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
61204 ACATGTTCCA
*
61214 AAATCGCAACGATAATATGT
1 AAATCGCAACGAGAATATGT
* *
61234 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGAGAATATGT
61254 AAATCG
1 AAATCG
61260 AAACACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
AAATCGCAACGAGAATATGT
Found at i:61430 original size:20 final size:20
Alignment explanation
Indices: 61405--61444 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61395 ACCGATATAG
*
61405 GTAAACAGTAATATCGCAAT
1 GTAAACAGCAATATCGCAAT
*
61425 GTAAACAGCACTATCGCAAT
1 GTAAACAGCAATATCGCAAT
61445 CCGATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (20 bp):
GTAAACAGCAATATCGCAAT
Found at i:61443 original size:57 final size:57
Alignment explanation
Indices: 61323--61434 Score: 145
Period size: 57 Copynumber: 2.0 Consensus size: 57
61313 CTTTTCTGAT
* * ****
61323 TTCGCAACAGTAATTACCGATATAGGTAAACAGTATTATCGCAATGCGATTTTCAAA
1 TTCGCAACAGTAATTACCGATATAGGTAAACAGTAATATCGCAATGCAAACAGCAAA
*
61380 TTCGCAAC-GCTAATTACCGATATAGGTAAACAGTAATATCGCAATGTAAACAGCA
1 TTCGCAACAG-TAATTACCGATATAGGTAAACAGTAATATCGCAATGCAAACAGCA
61435 CTATCGCAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
56 1 0.02
57 46 0.98
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (57 bp):
TTCGCAACAGTAATTACCGATATAGGTAAACAGTAATATCGCAATGCAAACAGCAAA
Found at i:61497 original size:77 final size:77
Alignment explanation
Indices: 61348--61500 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
61338 ACCGATATAG
* * *
61348 GTAAACAGTATTATCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
1 GTAAACAGCACTATCGCAATCCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
*
61413 TAATATCGCAAT
66 CAATATCGCAAT
61425 GTAAACAGCACTATCGCAATCCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA-
1 GTAAACAGCACTATCGCAATCCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
61489 CAACTATCGCAA
66 CAA-TATCGCAA
61501 CGCGAATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
76 2 0.03
77 69 0.97
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (77 bp):
GTAAACAGCACTATCGCAATCCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAG
CAATATCGCAAT
Found at i:62153 original size:20 final size:21
Alignment explanation
Indices: 62130--62174 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
62120 AATTTGTAAA
62130 TCGCAACACAGTTTC-CAAAT
1 TCGCAACACAGTTTCGCAAAT
* *
62150 TCGCAACTCAGTTTCGGAAAT
1 TCGCAACACAGTTTCGCAAAT
62171 TCGC
1 TCGC
62175 GTTGCGATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (21 bp):
TCGCAACACAGTTTCGCAAAT
Found at i:62392 original size:20 final size:20
Alignment explanation
Indices: 62369--62418 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
62359 TGACTTCTGT
62369 GTTGCGATTTACATATT-TGC
1 GTTGCGATTTACATATTAT-C
*
62389 GTTGCGATTTGCATATTATC
1 GTTGCGATTTACATATTATC
62409 GTTGCGATTT
1 GTTGCGATTT
62419 TGGAATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (20 bp):
GTTGCGATTTACATATTATC
Found at i:65278 original size:37 final size:39
Alignment explanation
Indices: 65237--65310 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
65227 AACTTAACTT
*
65237 AAATTTTGAACG-AG-ATACTAAAATGAAACAAAAACGA
1 AAATTTTGAACGAAGAATACTAAAATAAAACAAAAACGA
* *
65274 AAATTTTTAACGACAGAATACTAAAATAAAATAAAAA
1 AAATTTTGAACGA-AGAATACTAAAATAAAACAAAAA
65311 ATTATAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 11 0.35
39 2 0.06
40 18 0.58
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.22
Consensus pattern (39 bp):
AAATTTTGAACGAAGAATACTAAAATAAAACAAAAACGA
Found at i:75147 original size:34 final size:34
Alignment explanation
Indices: 75100--75184 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
75090 CCCGAATCTA
* *
75100 AAAATATTTTATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
75134 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
75168 AAAATATTATATATATA
1 AAAATATTATATATATA
75185 TATATATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:75961 original size:31 final size:31
Alignment explanation
Indices: 75902--75961 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
75892 AACAGTTACG
*
75902 TTGGGGACCATATTGAAAACGGAATAAATGT
1 TTGGGGACCATATTGAAAACGAAATAAATGT
*
75933 TTGGGGACCATATTGCAAAC-AAACTAAAT
1 TTGGGGACCATATTGAAAACGAAA-TAAAT
75962 ATTGAGGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (31 bp):
TTGGGGACCATATTGAAAACGAAATAAATGT
Found at i:78811 original size:23 final size:23
Alignment explanation
Indices: 78785--78853 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
78775 CACCACAGCT
*
78785 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
78808 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
78831 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
78854 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:87043 original size:99 final size:99
Alignment explanation
Indices: 86856--87036 Score: 290
Period size: 99 Copynumber: 1.8 Consensus size: 99
86846 CAGGCCCAAA
* *
86856 GAAGAGGATTACTTCTATTCCAATCCAGAAGAATGCCTGCGACAACAATATGGTCAACTAAGTAG
1 GAAGAGGATTACTTCTATGCCAATCCAGAAGAATGCCTGCGACAACAATACGGTCAACTAAGTAG
86921 CTCGTGATCCCTCTCTCGTGGGATTTGTAATACC
66 CTCGTGATCCCTCTCTCGTGGGATTTGTAATACC
* * * * *
86955 GAAGAGGATTACTTGTATGCGAATTCAGAAGAATGCTTGCGACAACAATACGGTCGACTAAGTAG
1 GAAGAGGATTACTTCTATGCCAATCCAGAAGAATGCCTGCGACAACAATACGGTCAACTAAGTAG
*
87020 CTCGTGATCTCTCTCTC
66 CTCGTGATCCCTCTCTC
87037 CGGGGATAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (99 bp):
GAAGAGGATTACTTCTATGCCAATCCAGAAGAATGCCTGCGACAACAATACGGTCAACTAAGTAG
CTCGTGATCCCTCTCTCGTGGGATTTGTAATACC
Found at i:93284 original size:9 final size:10
Alignment explanation
Indices: 93268--93293 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
93258 TCAGCATCAT
93268 ATTTTTTTTC
1 ATTTTTTTTC
93278 ATTTTTTTTC
1 ATTTTTTTTC
93288 ATTTTT
1 ATTTTT
93294 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTC
Found at i:94371 original size:22 final size:21
Alignment explanation
Indices: 94339--94379 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
94329 GAAGAGGACT
* *
94339 GGAGGAGGAGGAGGATAAAATA
1 GGAGGAAGAGG-GAATAAAATA
94361 GGAGGAAGAGGGAATAAAA
1 GGAGGAAGAGGGAATAAAA
94380 ACGGGATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (21 bp):
GGAGGAAGAGGGAATAAAATA
Found at i:95961 original size:12 final size:12
Alignment explanation
Indices: 95944--95968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95934 TTCGATAAAA
95944 AAATAATATTTT
1 AAATAATATTTT
95956 AAATAATATTTT
1 AAATAATATTTT
95968 A
1 A
95969 CCGAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:95961 original size:20 final size:20
Alignment explanation
Indices: 95911--95961 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
95901 TTTTACAGGT
* *
95911 TTTTAAATAGGAAAATTAATA
1 TTTTAAATA-AAAAAATAATA
**
95932 TTTTCGATAAAAAAATAATA
1 TTTTAAATAAAAAAATAATA
95952 TTTTAAATAA
1 TTTTAAATAA
95962 TATTTTACCG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
TTTTAAATAAAAAAATAATA
Found at i:96345 original size:12 final size:11
Alignment explanation
Indices: 96321--96455 Score: 56
Period size: 12 Copynumber: 11.4 Consensus size: 11
96311 TTCAAAGAGG
96321 TTTTAT-TTAA
1 TTTTATATTAA
96331 TTTTATATTATA
1 TTTTATATTA-A
* *
96343 TTTGATTTTAA
1 TTTTATATTAA
96354 TTTTAATATTAA
1 TTTT-ATATTAA
* *
96366 TTTTTTAAATAAA
1 --TTTTATATTAA
**
96379 TTAAATATTAATA
1 TTTTATATT-A-A
96392 TTTTAATATTATA
1 TTTT-ATATTA-A
**
96405 TATAGATATTAA
1 T-TTTATATTAA
96417 TTTTAATATTAA
1 TTTT-ATATTAA
* *
96429 TTTTTAAATAAA
1 -TTTTATATTAA
**
96441 TTAAATATTAA
1 TTTTATATTAA
96452 TTTT
1 TTTT
96456 TTAAAATTAT
Statistics
Matches: 90, Mismatches: 24, Indels: 21
0.67 0.18 0.16
Matches are distributed among these distances:
10 6 0.07
11 22 0.24
12 30 0.33
13 22 0.24
14 10 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:96385 original size:24 final size:27
Alignment explanation
Indices: 96358--96484 Score: 89
Period size: 24 Copynumber: 4.4 Consensus size: 27
96348 TTTTAATTTT
96358 AATATTAATTTTTTAA-A-TAAAT-TA
1 AATATTAATTTTTTAATATTAAATATA
* *
96382 AATATTAATATTTTAATATTATATATA
1 AATATTAATTTTTTAATATTAAATATA
* *
96409 GATATTAATTTTAATATTAATTTTTAAATAAATTA
1 AATATTAA-TTT--T-TTAA-TATTAAAT--A-TA
* *
96444 AATATTAATTTTTTAAAATTATATTATA
1 AATATTAATTTTTTAATATTA-AATATA
96472 AATATTTAATTTT
1 AATA-TTAATTTT
96485 ATATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
24 15 0.19
25 1 0.01
26 4 0.05
27 9 0.11
28 8 0.10
29 9 0.11
30 4 0.05
31 10 0.12
32 7 0.09
34 4 0.05
35 9 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (27 bp):
AATATTAATTTTTTAATATTAAATATA
Found at i:96439 original size:62 final size:63
Alignment explanation
Indices: 96330--96485 Score: 228
Period size: 62 Copynumber: 2.5 Consensus size: 63
96320 GTTTTATTTA
* *
96330 ATTTT-ATATTATAT-TTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
96391 ATTTTAATATTATATATAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
* * *
96453 TTTTTAAAATTATATTATAAATATTTAATTTTA
1 ATTTTAATATTATA-TATAGATA-TTAATTTTA
96486 TATCATATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
61 5 0.06
62 45 0.52
63 27 0.31
64 9 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (63 bp):
ATTTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
Found at i:97061 original size:31 final size:31
Alignment explanation
Indices: 97002--97062 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
96992 GTAGTTGTAT
* * **
97002 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATATCAGTATTACAAAACTA
97033 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAGTATTACAAAACT
97063 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAGTATTACAAAACTA
Found at i:97365 original size:22 final size:22
Alignment explanation
Indices: 97335--97376 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
97325 AAAATGCTTT
*
97335 TAAAAATTTAATTATTTTATTA
1 TAAAAATTTAAATATTTTATTA
*
97357 TAAACATTTAAATATTTTAT
1 TAAAAATTTAAATATTTTAT
97377 AACCTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAATTTAAATATTTTATTA
Found at i:97435 original size:21 final size:22
Alignment explanation
Indices: 97405--97455 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
97395 ATTTATAAAG
97405 ATAATAATTATTCTT-TTAATC-A
1 ATAA-AATTATT-TTGTTAATCTA
*
97427 ATAAAATTATTTTGTTACTCTA
1 ATAAAATTATTTTGTTAATCTA
97449 ATAAAAT
1 ATAAAAT
97456 ATTAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 12 0.46
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAAATTATTTTGTTAATCTA
Found at i:97496 original size:2 final size:2
Alignment explanation
Indices: 97484--97522 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
97474 TATAATATTA
*
97484 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97523 ATCACGAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:100669 original size:2 final size:2
Alignment explanation
Indices: 100662--100699 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
100652 AATTTATCTA
100662 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
100700 TATTGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100834 original size:2 final size:2
Alignment explanation
Indices: 100805--100860 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
100795 TTATTTAAAT
* * * *
100805 TA TA TA AA TA TT TA -A TA AA TA AA 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
100846 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
100861 TGTGACATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:101461 original size:10 final size:10
Alignment explanation
Indices: 101446--101470 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
101436 AAAATATAGG
101446 TATTAAATTA
1 TATTAAATTA
101456 TATTAAATTA
1 TATTAAATTA
101466 TATTA
1 TATTA
101471 TATTTGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTAAATTA
Found at i:103063 original size:24 final size:24
Alignment explanation
Indices: 103036--103081 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
103026 TTAAATTACT
103036 AATTTTAATCTATTTTAATATTTA
1 AATTTTAATCTATTTTAATATTTA
* * *
103060 AATTTTTATTTCTTTTAATATT
1 AATTTTAATCTATTTTAATATT
103082 ATATTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
AATTTTAATCTATTTTAATATTTA
Found at i:103875 original size:14 final size:14
Alignment explanation
Indices: 103856--103883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
103846 CGCTGGGCAT
103856 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
103870 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
103884 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:103910 original size:20 final size:22
Alignment explanation
Indices: 103851--103913 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 22
103841 CAACACGCTG
103851 GGCATCCGAGGCCATCCGACCGA
1 GGCATCCGAGGCCATCCGA-CGA
*
103874 GGCCATCCGAAAG-CATCCGA-GA
1 GG-CATCCG-AGGCCATCCGACGA
103896 -GCATCCGAGGCCATCCGA
1 GGCATCCGAGGCCATCCGA
103914 ATGAGCTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 1 0.03
22 2 0.06
23 2 0.06
24 13 0.37
25 2 0.06
ACGTcount: A:0.25, C:0.37, G:0.29, T:0.10
Consensus pattern (22 bp):
GGCATCCGAGGCCATCCGACGA
Found at i:104032 original size:23 final size:23
Alignment explanation
Indices: 103998--104057 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
103988 CTCGGTTGCC
103998 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
104021 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
104044 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
104058 GTCAGATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:119755 original size:4 final size:4
Alignment explanation
Indices: 119710--119736 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
119700 TCACAAATAC
119710 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
119737 GCTTGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:120434 original size:29 final size:29
Alignment explanation
Indices: 120349--120434 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 29
120339 CCCAACCCAT
* ****
120349 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
**
120378 AGGTCGCCATGCACTCTGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
120407 AGGTCGCCATGCACGCCCGGCGACCAAG
1 AGGTCGCCATGCACTCCCGGCGACCAAG
120435 CTTTTAACCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:124013 original size:34 final size:34
Alignment explanation
Indices: 123969--124078 Score: 130
Period size: 35 Copynumber: 3.2 Consensus size: 34
123959 TAAATAGTCC
* * *
123969 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAA-TTCATTATAAACCCCAAATTCTAAAATAAT
* *
124004 TCAATTCATTATAAACCCTAAATTCCAAAATAAT
1 TCAATTCATTATAAACCCCAAATTCTAAAATAAT
* * *
124038 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATT-CATTATAAACCCCAAATTCTAAAATAAT
124073 TCAATT
1 TCAATT
124079 TAAGGTTTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 31 0.48
35 33 0.52
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTCATTATAAACCCCAAATTCTAAAATAAT
Found at i:126921 original size:15 final size:16
Alignment explanation
Indices: 126894--126923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
126884 CTTATTTTAT
126894 TAATATATAATTAAAA
1 TAATATATAATTAAAA
126910 TAATAT-TAATTAAA
1 TAATATATAATTAAA
126924 TATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATATAATTAAAA
Found at i:126982 original size:29 final size:30
Alignment explanation
Indices: 126933--126989 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
126923 ATATTTTTAA
126933 AAAATTATATTGAAACAAAAA-ATATTCCC
1 AAAATTATATTGAAACAAAAAGATATTCCC
**
126962 AAAATTATAATT-AAATTAAAAGATATTC
1 AAAATTAT-ATTGAAACAAAAAGATATTC
126990 TCTATGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATTATATTGAAACAAAAAGATATTCCC
Found at i:127217 original size:18 final size:18
Alignment explanation
Indices: 127194--127233 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
127184 GAAAAGAAAA
*
127194 AAATGTTGCATCATACAT
1 AAATGTTACATCATACAT
127212 AAATGTTACATCATACAT
1 AAATGTTACATCATACAT
127230 AAAT
1 AAAT
127234 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (18 bp):
AAATGTTACATCATACAT
Found at i:127369 original size:29 final size:31
Alignment explanation
Indices: 127337--127412 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
127327 GAAACAAATA
127337 GGAGGGCCAAATTGAG-T-TTTTCTTGAGTT
1 GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
*
127366 GGAGGGCAAAATTGAGTTATTTTCTTGAGTT
1 GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
*
127397 GGAGGGCCAGATTGAG
1 GGAGGGCCAAATTGAG
127413 AGAGAAATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 15 0.36
30 1 0.02
31 26 0.62
ACGTcount: A:0.24, C:0.09, G:0.34, T:0.33
Consensus pattern (31 bp):
GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
Found at i:128280 original size:17 final size:17
Alignment explanation
Indices: 128258--128291 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
128248 TAATTAGCCT
128258 CTAAATAATGAAAATAA
1 CTAAATAATGAAAATAA
128275 CTAAATAATGAAAATAA
1 CTAAATAATGAAAATAA
128292 GACGGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
CTAAATAATGAAAATAA
Done.