Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006941.1 Hibiscus syriacus cultivar Beakdansim tig00017835_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: 73299
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:272 original size:60 final size:59
Alignment explanation
Indices: 1--281 Score: 245
Period size: 60 Copynumber: 4.8 Consensus size: 59
* *
1 AATGCAACACTATATAATTTGAAGACTA-TTTAGAACTTTTAATAGTATAGTACTCAAC
1 AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGTATAGTAATCAAC
** ** * * * * *
59 AAAACAACACCGTATAACTTGGAGACAATTTTGTAACTATTAATAGT-TGGGAG-AATCAAC
1 AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGTAT---AGTAATCAAC
* *
119 AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGTATAGTACTCAACC
1 AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGTATAGTAATCAA-C
* * * * * * * *
179 AA-AC-ACAC-GTAT-ACTTGGAGACAATTTTGTAACTATTAATAGT-TGAGAAAATCAAC
1 AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGTAT-AG-TAATCAAC
* *
235 AATGCAACCCTATATAATTTGAAAACTATTTTATAACTTTTAATAGT
1 AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGT
282 CTATGGCTCA
Statistics
Matches: 169, Mismatches: 41, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
55 1 0.01
56 30 0.18
57 9 0.05
58 31 0.18
59 24 0.14
60 71 0.42
61 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (59 bp):
AATGCAACACTATATAATTTGAAGACTATTTTATAACTTTTAATAGTATAGTAATCAAC
Found at i:293 original size:116 final size:119
Alignment explanation
Indices: 1--281 Score: 480
Period size: 116 Copynumber: 2.4 Consensus size: 119
1 AATGCAACACTATATAATTTGAAGACTA-TTTAGAACTTTTAATAGTATAGTACTCAACAAAACA
1 AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGTATAGTACTCAACAAAACA
* *
65 ACACCGTATAACTTGGAGACAATTTTGTAACTATTAATAGTTGGGAGAATCAAC
66 ACACCGTATAACTTGGAGACAATTTTGTAACTATTAATAGTTGAGAAAATCAAC
*
119 AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGTATAGTACTCAACCAAAC-
1 AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGTATAGTACTCAACAAAACA
183 ACA-CGTAT-ACTTGGAGACAATTTTGTAACTATTAATAGTTGAGAAAATCAAC
66 ACACCGTATAACTTGGAGACAATTTTGTAACTATTAATAGTTGAGAAAATCAAC
* * *
235 AATGCAACCCTATATAATTTGAAAACTATTTTATAACTTTTAATAGT
1 AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGT
282 CTATGGCTCA
Statistics
Matches: 156, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
116 86 0.55
117 5 0.03
118 31 0.20
119 34 0.22
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (119 bp):
AATGCAACACTATATAATTTGAAGACTATTTTAGAACTTTTAATAGTATAGTACTCAACAAAACA
ACACCGTATAACTTGGAGACAATTTTGTAACTATTAATAGTTGAGAAAATCAAC
Found at i:2706 original size:12 final size:12
Alignment explanation
Indices: 2673--2711 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2663 TTACTATTTT
*
2673 TTTATTTTTAAA
1 TTTATTTTAAAA
*
2685 TATATATTTAAAA
1 TTTAT-TTTAAAA
2698 TTTATTTTAAAA
1 TTTATTTTAAAA
2710 TT
1 TT
2712 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:7702 original size:213 final size:215
Alignment explanation
Indices: 7339--7772 Score: 736
Period size: 213 Copynumber: 2.0 Consensus size: 215
7329 TAAACTATTG
7339 CAAAATGAGATCCAATTATGAAACATCGTCGACATTTCTTGATCAGAAAAGTATTGTGATAAATG
1 CAAAATGAGATCCAATTATGAAACATCGTCGACATTTCTTGATCAGAAAAGTATTGTGATAAATG
7404 TAACATGAAACGTCAAACTATAATGATAGAAAAAATTGTGTCATAAAATCAAAGGAATAAATATG
66 TAACATGAAACGTCAAACTATAATGATAGAAAAAATTGTGTCATAAAATCAAAGGAATAAATATG
7469 TAATAGAAGCAGACAAAAACAAACTCTTAAATGATATGT-AAA-AATAAAATT-AAACACTG-A-
131 TAATAGAAGCAGACAAAAACAAACTCTTAAATGATATGTAAAAGAATAAAATTAAAACACTGAAT
7529 AT-ATTATTTAGATATAAGT
196 ATAATTATTTAGATATAAGT
* *
7548 CAAAATGAGATCTAATTATGAAACATCGTCGACATTTCTTGATCAGAAGATGTATTGTGATAAAT
1 CAAAATGAGATCCAATTATGAAACATCGTCGACATTTCTTGATCAGAA-AAGTATTGTGATAAAT
* *
7613 GTAACATGAAATGTCAAACTACTACAATGATAGAAAAAATTGTGTCATAAAATCCAAGGAATAAA
65 GTAACATGAAACGTCAAACTA-T--AATGATAGAAAAAATTGTGTCATAAAATCAAAGGAATAAA
*
7678 TATGTCATAGAAGCAGACAAAAACAAACTCTTAAATGATATGTAAAAAGAATAAAATTAAAACAC
127 TATGTAATAGAAGCAGACAAAAACAAACTCTTAAATGATATGT-AAAAGAATAAAATTAAAACAC
7743 TGAATATAATTATTTAGATATAAGT
191 TGAATATAATTATTTAGATATAAGT
7768 CAAAA
1 CAAAA
7773 ATTAAATAAA
Statistics
Matches: 209, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
209 47 0.22
210 35 0.17
211 1 0.00
213 81 0.39
215 3 0.01
216 9 0.04
217 8 0.04
218 1 0.00
219 2 0.01
220 22 0.11
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (215 bp):
CAAAATGAGATCCAATTATGAAACATCGTCGACATTTCTTGATCAGAAAAGTATTGTGATAAATG
TAACATGAAACGTCAAACTATAATGATAGAAAAAATTGTGTCATAAAATCAAAGGAATAAATATG
TAATAGAAGCAGACAAAAACAAACTCTTAAATGATATGTAAAAGAATAAAATTAAAACACTGAAT
ATAATTATTTAGATATAAGT
Found at i:15795 original size:60 final size:60
Alignment explanation
Indices: 15694--15866 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
15684 AAGTATGCCC
* * * * *
15694 ATCATTTTAAATTAGTCCCTAAACTTTTAAATATTCTAATTTTATCTCCAAACTATTACT
1 ATCATTCTAAATTAGTCCCTAAACTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
* * * * *
15754 ATCATTCTAAATTATTCCTTAAATTTTTGAACATTTTAATTTCATCCCCAAACTATAACT
1 ATCATTCTAAATTAGTCCCTAAACTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
* * *
15814 TTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTCAT-CCCAAAC
1 ATCATTCTAAATTAGTCCCTAAAC-TTTTAAACATTCTAATTTCATCCCCAAAC
15867 CATACGTATA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 76 0.81
61 18 0.19
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.42
Consensus pattern (60 bp):
ATCATTCTAAATTAGTCCCTAAACTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
Found at i:16173 original size:60 final size:60
Alignment explanation
Indices: 15994--16174 Score: 170
Period size: 59 Copynumber: 3.0 Consensus size: 60
15984 GATGAAATTA
* * ** * * *
15994 GGATGAAATTGGAATATTCAAAAAGTTTAGGGACTAATTTAGAAA-GAGGGTCATAGTGTAG
1 GGATGAAATTGAAATACTC-AAAAGTTTAAAGACTAATTTA-AAATGAGGGTCATAATTTGG
* * * * **
16055 GGATGAAATTGAAAT-GTCAAATGTTTAAAGACTAGTTTAGAATGATAGTCA-AAGTTTGG
1 GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAA-TTTGG
* * *
16114 GGATGAAATTAAAATACTCAAAAGTTTAAAGACCAATTTAAAATGAGGGTTATAATTTGG
1 GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAATTTGG
16174 G
1 G
16175 ACATATGATG
Statistics
Matches: 95, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
58 3 0.03
59 40 0.42
60 36 0.38
61 16 0.17
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (60 bp):
GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAATTTGG
Found at i:19277 original size:38 final size:38
Alignment explanation
Indices: 19212--19356 Score: 182
Period size: 38 Copynumber: 3.8 Consensus size: 38
19202 AATAAAAAAG
* * * * *
19212 TAAACGAGTTTGTTAATAAACACAAACGAACGACCCGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* *
19250 TAAACGAGCTTGTCCATGAACATAAACGAATGACCTGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* *
19288 TAAACGAGCTTGTTCGTGAACATAAACGAATGACCTGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* * *
19326 TAAAGGAGCTTGTTCGTGAACATAAATGAAC
1 TAAACGAGCTTGTTCATGAACATAAACGAAC
19357 CGAACACATC
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 95 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
Found at i:22719 original size:24 final size:24
Alignment explanation
Indices: 22687--22732 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22677 AAAAACCGAG
* *
22687 TAAACGAGCTTATAAATGAGTCCA
1 TAAAAGAGCTTATAAAAGAGTCCA
22711 TAAAAGAGCTTATAAAAGAGTC
1 TAAAAGAGCTTATAAAAGAGTC
22733 AATTAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (24 bp):
TAAAAGAGCTTATAAAAGAGTCCA
Found at i:24283 original size:60 final size:60
Alignment explanation
Indices: 24163--24286 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
24153 GTCCTTGATT
* * * *
24163 TTTTAAATATTTTAATTTCATCCCTAAAGTATGATTATGATTCTAAATTAGTCCTCAAAC
1 TTTTAAATATTTTAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGCCCTCAAAC
* * *
24223 TTTTGAATATTTTGATTTCATCCCCAAACTATGGCA-T-TCATTCTAAATTGGCCC-CTAAAC
1 TTTTAAATATTTTAATTTCATCCCCAAACTAT-G-ATTATCATTCTAAATTAGCCCTC-AAAC
24283 TTTT
1 TTTT
24287 TTGAACATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 1 0.02
60 50 0.93
61 2 0.04
62 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.43
Consensus pattern (60 bp):
TTTTAAATATTTTAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGCCCTCAAAC
Found at i:24514 original size:60 final size:60
Alignment explanation
Indices: 24435--24592 Score: 158
Period size: 60 Copynumber: 2.6 Consensus size: 60
24425 GAATTTGGAT
* ** *
24435 ATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAGAAAGAGAGTCATATTTTAGGG-
1 ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTT-GGGA
* ** *
24495 ATGAAATT-ATAATGTTCAAAAGTCTAAGGATTAATTTAGAATGAGAGTCATAGTTTGGGA
1 ATGAAATTGA-AATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGA
* * * * * *
24555 ATGAAATTGGAATCTTTAAAAGTCCAAGAACCGATTTA
1 ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTA
24593 AAATGAAGGT
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 4 0.05
60 75 0.95
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (60 bp):
ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGA
Found at i:26985 original size:2 final size:2
Alignment explanation
Indices: 26978--27019 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
26968 GGCTTTGTAA
26978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27020 GTTCCACTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29767 original size:20 final size:20
Alignment explanation
Indices: 29731--29768 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29721 ATCCTATTCC
**
29731 CTGGTAATCTTTTATTCCCT
1 CTGGTAATCTTACATTCCCT
29751 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
29769 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCT
Found at i:31356 original size:102 final size:101
Alignment explanation
Indices: 31237--31460 Score: 306
Period size: 102 Copynumber: 2.2 Consensus size: 101
31227 GTGTTTCAAG
* * * * *
31237 AGAAACTGTCTCGAGAGAGATGAAATTTGTTT-AATGGAAAACAGATTTAAATATTTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAA-GGAAAACAGATTCAAAGATTTTATTTCAA
*
31301 GGGAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAA
65 GAGAAACTGTCTCAAGAGAGACAAAATTT-GTTCTAAA
* * *
31339 AGAAACTATCTCAAGAGAGACGAAATTTTTTTCAAGGAAAACAGATTCAGAGATTTTATTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTATTTCAAG
* **
31404 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACG
66 AGAAACTGTCTCAAGAGAGACAAAATTTGTTCTAAA
*
31440 AGAAAATGTCTCAAGAGAGAC
1 AGAAACTGTCTCAAGAGAGAC
31461 AAAAATAAGA
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
101 24 0.22
102 81 0.76
103 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (101 bp):
AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTATTTCAAG
AGAAACTGTCTCAAGAGAGACAAAATTTGTTCTAAA
Found at i:31457 original size:138 final size:137
Alignment explanation
Indices: 31303--31763 Score: 625
Period size: 138 Copynumber: 3.4 Consensus size: 137
31293 TGTTTCAAGG
* *
31303 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTT
1 GAAAATGTCTCAAGAGAGACAAAATTTA-TTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTA
* *
31368 TTTCAAGGAAAACAGATTCAGAGATTTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
65 TTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
31433 TTTTACGA
130 TTTTACGA
* * * * *
31441 GAAAATGTCTCAAGAGAGACAAAA---A---T--AAGAAAATGTCTCAAGATAGGCGACATTTAT
1 GAAAATGTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTAT
*
31498 TTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGT
66 TTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
31563 TTTACGA
131 TTTACGA
* * * *
31570 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTA-TTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTA
* * * * *
31635 TTTAAAGGAAAATAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTG
65 TTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
31700 TTTTAAGA
130 TTTTACGA
* * *
31708 G-AAGTCGTCTCAAGAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGAC
1 GAAAAT-GTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGAC
31764 AACACTTTAT
Statistics
Matches: 284, Mismatches: 29, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
129 118 0.42
131 1 0.00
132 1 0.00
135 1 0.00
136 1 0.00
137 27 0.10
138 135 0.48
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (137 bp):
GAAAATGTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTAT
TTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
TTTACGA
Found at i:31572 original size:36 final size:36
Alignment explanation
Indices: 31522--31765 Score: 229
Period size: 36 Copynumber: 6.9 Consensus size: 36
31512 ATTCAAAGAT
* *
31522 TTTGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
31558 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
31594 TTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
31631 TTTGTTTAAAG-GAAAATAGAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAGAAACT-G-TCTCAAGAGAGACAAAA
* * * *
31660 TTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
*
31696 TTTGTTTTAAGAG-AAGTCGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACT-GTCTCAAGAGAGACAAAA
* *
31732 TTTATTTTAAGAGAAACTATCTCAAGAGAGACAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
31766 CACTTTATTT
Statistics
Matches: 167, Mismatches: 27, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 14 0.08
30 6 0.04
31 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 9 0.05
36 98 0.59
37 35 0.21
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:31762 original size:38 final size:37
Alignment explanation
Indices: 31679--31776 Score: 96
Period size: 36 Copynumber: 2.7 Consensus size: 37
31669 AGGGAAACTG
* * *
31679 TCTC-GAGAGAAACAAAATTTGTTTTAAGAGAAGTCG
1 TCTCAGAGAGAAACAAAATTTATTTTAAGAGAACTCA
*
31715 TCTCA-AGAGAGACAAAATTTATTTTAAGAGAAACT-A
1 TCTCAGAGAGAAACAAAATTTATTTTAAGAG-AACTCA
* *
31751 TCTCA-AGAGAGACAACACTTTATTTT
1 TCTCAGAGAGAAACAA-AATTTATTTT
31777 GAGTAAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 42 0.78
37 12 0.22
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (37 bp):
TCTCAGAGAGAAACAAAATTTATTTTAAGAGAACTCA
Found at i:32147 original size:36 final size:36
Alignment explanation
Indices: 32107--32352 Score: 224
Period size: 36 Copynumber: 7.0 Consensus size: 36
32097 ATTCAGAGAT
*
32107 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
32143 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
32179 TTTATTTCTAAAAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
32216 TTTGTTTAAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
* * *
32245 TTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
32281 TTTATTTTAAGAGAAA-TCGTTTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAA
* *
32317 TTTATTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
32353 CTTTATTTTG
Statistics
Matches: 170, Mismatches: 26, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.01
29 18 0.11
30 2 0.01
31 1 0.01
32 1 0.01
33 2 0.01
34 1 0.01
35 3 0.02
36 109 0.64
37 32 0.19
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:32228 original size:138 final size:137
Alignment explanation
Indices: 32052--32348 Score: 443
Period size: 138 Copynumber: 2.2 Consensus size: 137
32042 AGTTAAAAAT
* * * * * *
32052 AAGAATCTGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAATATATTCAGAGATTTTGTTTCAA
1 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
* * *
32117 GAGAAACTATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAAT-GTCTCAAGAGAGACAAAATT
66 GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAG-AAATCGTCTCAAGAGAGACAAAATT
32181 TATTTCTAA
130 TATTT-TAA
32190 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
1 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
* * * *
32255 GGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTTTCAAGAGAGACAAAATTT
66 GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAGAGAGACAAAATTT
32320 ATTTTAA
131 ATTTTAA
*
32327 GAGAAACTGTCTCAAGAGAGAC
1 AAGAAACTGTCTCAAGAGAGAC
32349 AAAACTTTAT
Statistics
Matches: 144, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
137 28 0.19
138 116 0.81
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (137 bp):
AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAGAGAGACAAAATTT
ATTTTAA
Found at i:32571 original size:585 final size:585
Alignment explanation
Indices: 31461--32634 Score: 2105
Period size: 585 Copynumber: 2.0 Consensus size: 585
31451 CAAGAGAGAC
* *
31461 AAAAATAAGAAAATGTCTCAAGATAGGCGACATTTATTTCAAGGAAAACAGATTCAAAGATTTTG
1 AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTATTTCAAGGAAAACAGATTCAAAGATTTTG
*
31526 TTTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
66 TTTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
*
31591 AAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAATAGATTCAA
131 AAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAA
* *
31656 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTGTTTTAAGAGAAGTCGTCTCAA
196 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAA
*
31721 GAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAACACTTTATTTTGAGTAAATT
261 GAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
31786 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
326 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
31851 GTTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGT
391 GTTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGT
* * *
31916 GGATGACATGTTTGTTGTGACACTAAATCACTTCATCGGGCATGATATCATTATTTGTGAAGTTG
456 GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTG
*
31981 AAATCGTGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
521 AAATCGTGGATGGCTCATTTATTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
** * * * *
32046 AAAAATAAGAATCTGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAATATATTCAGAGATTTTG
1 AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTATTTCAAGGAAAACAGATTCAAAGATTTTG
*
32111 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
66 TTTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
* * *
32176 AAATTTATTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAA
131 AAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAA
*
32241 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTTTCAA
196 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAA
*
32306 GAGAGACAAAATTTATTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
261 GAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
32371 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
326 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
* *
32436 GTTCATGCATGTTGAAGAAATCCTTTTAGAAGCTCTAATCGTTGACTTAAGGAAGTCAAATCTGT
391 GTTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGT
* *
32501 GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCCTTCTTCGTGAAGTTG
456 GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTG
32566 AAATCGTGGATGGCTCATTTATTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
521 AAATCGTGGATGGCTCATTTATTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
32631 AAAA
1 AAAA
32635 TCCACACATG
Statistics
Matches: 562, Mismatches: 27, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
585 562 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (585 bp):
AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTATTTCAAGGAAAACAGATTCAAAGATTTTG
TTTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
AAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAA
AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAA
GAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
GTTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGT
GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTG
AAATCGTGGATGGCTCATTTATTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
Found at i:37639 original size:58 final size:60
Alignment explanation
Indices: 37515--37695 Score: 201
Period size: 60 Copynumber: 3.0 Consensus size: 60
37505 ATATATCTCC
* * * * *
37515 AAACTATAACCATCATTTTAAACTGGTCATTAAACTTTTGAATA-TCTCAATTTCATCCCC
1 AAACTATGACCCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTC-CAATTTCATCCCT
** * *
37575 AAACTATGAGTCTCATTTTAAATTAGTCCTTAAA-ATTT-AATATTCCAATTTCATCCCT
1 AAACTATGACCCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
* *
37633 AAACTATGACCCTC-TTTCTAAATTGGT-CTCCAAATTTTTGAATATTCCAATTTCATCCCT
1 AAACTATGACCCTCATTT-TAAATTGGTCCT-TAAACTTTTGAATATTCCAATTTCATCCCT
37693 AAA
1 AAA
37696 TTCATCCAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.05
58 39 0.38
59 8 0.08
60 50 0.49
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (60 bp):
AAACTATGACCCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTCCAATTTCATCCCT
Found at i:46306 original size:60 final size:60
Alignment explanation
Indices: 46195--46367 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 60
46185 AAGTATGCCC
* * * * * * *
46195 ATCATTTTAAATTGGTCCCTAAACTTTTAAATATTCTAATTTTATCTCCAAACTATTACT
1 ATCATTCTAAATTAGTCCCTAAATTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
* * * *
46255 ATCATTCTAAATTATTCCTTAAATTTTTGAACATTTTAATTTCATCCCCAAACTATAACT
1 ATCATTCTAAATTAGTCCCTAAATTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
* * *
46315 TTCATTCTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTCAT-CCCAAAC
1 ATCATTCTAAATTAGTCCCTAAA-TTTTTAAACATTCTAATTTCATCCCCAAAC
46368 CATACGTATA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 75 0.80
61 19 0.20
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (60 bp):
ATCATTCTAAATTAGTCCCTAAATTTTTAAACATTCTAATTTCATCCCCAAACTATAACT
Found at i:46675 original size:60 final size:60
Alignment explanation
Indices: 46496--46676 Score: 170
Period size: 59 Copynumber: 3.0 Consensus size: 60
46486 GATGAAATTA
* * ** * * *
46496 GGATGAAATTGGAATATTCAAAAAGTTTAGGGACTAATTTAGAAA-GAGGGTCATAGTGTAG
1 GGATGAAATTGAAATACTC-AAAAGTTTAAAGACTAATTTA-AAATGAGGGTCATAATTTGG
* * * * **
46557 GGATGAAATTGAAAT-GTCAAATGTTTAAAGACTAGTTTAGAATGATAGTCA-AAGTTTGG
1 GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAA-TTTGG
* * *
46616 GGATGAAATTAAAATACTCAAAAGTTTAAAGACCAATTTAAAATGAGGGTTATAATTTGG
1 GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAATTTGG
46676 G
1 G
46677 ACATATGATG
Statistics
Matches: 95, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
58 3 0.03
59 40 0.42
60 36 0.38
61 16 0.17
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (60 bp):
GGATGAAATTGAAATACTCAAAAGTTTAAAGACTAATTTAAAATGAGGGTCATAATTTGG
Found at i:49786 original size:38 final size:38
Alignment explanation
Indices: 49721--49865 Score: 182
Period size: 38 Copynumber: 3.8 Consensus size: 38
49711 AATAAAAAAG
* * * * *
49721 TAAACGAGTTTGTTAATAAACACAAACGAACGACCCGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* *
49759 TAAACGAGCTTGTCCATGAACATAAACGAATGACCTGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* *
49797 TAAACGAGCTTGTTCGTGAACATAAACGAATGACCTGA
1 TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
* * *
49835 TAAAGGAGCTTGTTCGTGAACATAAATGAAC
1 TAAACGAGCTTGTTCATGAACATAAACGAAC
49866 CGAACACATC
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 95 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAACGAGCTTGTTCATGAACATAAACGAACGACCTGA
Found at i:53237 original size:24 final size:24
Alignment explanation
Indices: 53210--53255 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53200 AATAACCGAG
* *
53210 TAAACGAGCTTATAAATGAGTCCA
1 TAAAAGAGCTTATAAAAGAGTCCA
53234 TAAAAGAGCTTATAAAAGAGTC
1 TAAAAGAGCTTATAAAAGAGTC
53256 AATTAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (24 bp):
TAAAAGAGCTTATAAAAGAGTCCA
Found at i:54813 original size:60 final size:60
Alignment explanation
Indices: 54693--54816 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
54683 TCCTTGATTT
* * * *
54693 TTTTAAATATTTTAATTTCATCCCTAAAGTATGATTATGATTCTAAATTAGTCCTCAAAC
1 TTTTAAATATTTTAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGCCCTCAAAC
* * *
54753 TTTTGAATATTTTGATTTCATCCCCAAACTATGGCA-T-TCATTCTAAATTGGCCC-CTAAAC
1 TTTTAAATATTTTAATTTCATCCCCAAACTAT-G-ATTATCATTCTAAATTAGCCCTC-AAAC
54813 TTTT
1 TTTT
54817 TTGAACATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 1 0.02
60 50 0.93
61 2 0.04
62 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.43
Consensus pattern (60 bp):
TTTTAAATATTTTAATTTCATCCCCAAACTATGATTATCATTCTAAATTAGCCCTCAAAC
Found at i:55047 original size:60 final size:60
Alignment explanation
Indices: 54968--55125 Score: 158
Period size: 60 Copynumber: 2.6 Consensus size: 60
54958 GAATTTGGAT
* ** *
54968 ATGAAATTGAAATATTCAAAAGTTTGGGGACCAATTTAGAAAGAGAGTCATATTTTAGGG-
1 ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTT-GGGA
* ** *
55028 ATGAAATT-ATAATGTTCAAAAGTCTAAGGATTAATTTAGAATGAGAGTCATAGTTTGGGA
1 ATGAAATTGA-AATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGA
* * * * * *
55088 ATGAAATTGGAATCTTTAAAAGTCCAAGAACCGATTTA
1 ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTA
55126 AAATGAAGGT
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 4 0.05
60 75 0.95
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (60 bp):
ATGAAATTGAAATATTCAAAAGTCTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGGGA
Found at i:58137 original size:2 final size:2
Alignment explanation
Indices: 58130--58199 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
58120 TTGTAAATAC
58130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58172 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
58200 GTTCCACTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60938 original size:20 final size:20
Alignment explanation
Indices: 60902--60939 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60892 ATCCTATTCC
**
60902 CTGGTAATCTTTTATTCCCT
1 CTGGTAATCTTACATTCCCT
60922 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
60940 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCT
Found at i:62534 original size:102 final size:101
Alignment explanation
Indices: 62407--62630 Score: 333
Period size: 102 Copynumber: 2.2 Consensus size: 101
62397 GTGTTTCAAG
* * *
62407 AGAAACTGTCTCGAGAGAGATGAAATTTGTTT-AATGGAAAACAGATTCAAATATTTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAA-GGAAAACAGATTCAAAGATTTTGTTTCAA
*
62471 GGGAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAA
65 GAGAAACTGTCTCAAGAGAGACAAAATTT-GTTCTAAA
* *
62509 AGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
* **
62574 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACG
66 AGAAACTGTCTCAAGAGAGACAAAATTTGTTCTAAA
*
62610 AGAAAATGTCTCAAGAGAGAC
1 AGAAACTGTCTCAAGAGAGAC
62631 AAAAATAAGA
Statistics
Matches: 110, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 24 0.22
102 84 0.76
103 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (101 bp):
AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAG
AGAAACTGTCTCAAGAGAGACAAAATTTGTTCTAAA
Found at i:62603 original size:36 final size:36
Alignment explanation
Indices: 62563--62934 Score: 244
Period size: 36 Copynumber: 10.9 Consensus size: 36
62553 ATTCAGAGAT
62563 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
62599 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
62635 -----AT-AAGA-AAA-TGTCTCAAGAGAGGCGACA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
62663 TTTGTTTCAAG-GAAAACAGAT-TC---AGAG-----A
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
*
62691 TTTGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
62727 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
62763 TTTAG-TTCTAAAAGAAACTGTCTCAAGAGAAACAAAA
1 TTT-GTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
62800 TTTGTTTAAAG-GAAAATAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAGAAACT-G-TCTCAAGAGAGACAAAA
* * *
62829 TTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
62865 TTTGTTTTAAGAG-AAGTCGTCTCGAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAA
* * *
62901 TTTATTTTAAGAGAAACTATCTCAAGAGAGACAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
62935 CACTTTATTT
Statistics
Matches: 263, Mismatches: 37, Indels: 72
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.00
28 36 0.14
29 18 0.07
30 9 0.03
31 6 0.02
32 1 0.00
33 6 0.02
34 4 0.02
35 12 0.05
36 135 0.51
37 35 0.13
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:62628 original size:138 final size:137
Alignment explanation
Indices: 62473--62932 Score: 643
Period size: 138 Copynumber: 3.4 Consensus size: 137
62463 TGTTTCAAGG
*
62473 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTA-TTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTG
62538 TTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
65 TTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
62603 TTTTACGA
130 TTTTACGA
* * * *
62611 GAAAATGTCTCAAGAGAGACAAAA---A---T--AAGAAAATGTCTCAAGAGAGGCGACATTTGT
1 GAAAATGTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTGT
*
62668 TTCAAGGAAAACAGATTCAGAGA-TTTGTTTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGT
66 TTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
62732 TTTACGA
131 TTTACGA
* * *
62739 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTA-TTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTG
* * * * * *
62804 TTTAAAGGAAAATAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTG
65 TTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
62869 TTTTAAGA
130 TTTTACGA
* * * *
62877 G-AAGTCGTCTCGAGAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGAC
1 GAAAAT-GTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGAC
62933 AACACTTTAT
Statistics
Matches: 286, Mismatches: 25, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
128 71 0.25
129 50 0.17
131 2 0.01
135 2 0.01
137 73 0.26
138 88 0.31
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (137 bp):
GAAAATGTCTCAAGAGAGACAAAATTTATTCTAAAAGAAACTATCTCAAGAGAGACGAAATTTGT
TTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
TTTACGA
Found at i:62706 original size:64 final size:64
Alignment explanation
Indices: 62509--62871 Score: 247
Period size: 65 Copynumber: 5.5 Consensus size: 64
62499 TAGTTCTAAA
*
62509 AGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGA-TTTGTTTCAAG
* * * * ****
62574 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAA-TG-TCTCAAGAGA---GACAAA
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAG-GAAAACAGAT-TC-AGAGATTTG-TTTC
*
62634 AATA
62 AA-G
* * *
62638 AGAAAATGTCTCAAGAGAGGCGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGATTTGTTTCAAG
* * * * *
62702 AGAAACGGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAA-TG-TCTCAAGAGAGACAAAATT
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAG-GAAAACAGAT-TC---AGAG-----ATT
*
62765 TAG-TTCTAAA
56 T-GTTTC-AAG
* * * * *
62775 AGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAATAGATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGA-TTTGTTTCAAG
* * * *
62840 GGAAACTGTCTCGAGAGAAACAAAATTTGTTT
1 AGAAACTGTCTCAAGAGAGACGAAATTTGTTT
62872 TAAGAGAAGT
Statistics
Matches: 232, Mismatches: 40, Indels: 52
0.72 0.12 0.16
Matches are distributed among these distances:
62 1 0.00
63 13 0.06
64 66 0.28
65 77 0.33
66 17 0.07
67 4 0.02
70 3 0.01
72 12 0.05
73 38 0.16
74 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (64 bp):
AGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACAGATTCAGAGATTTGTTTCAAG
Found at i:62930 original size:38 final size:36
Alignment explanation
Indices: 62848--62945 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
62838 AGGGAAACTG
* * *
62848 TCTCGAGAGAAACAAAATTTGTTTTAAGAGAAGTCG
1 TCTCGAGAGAAACAAAATTTATTTTAAGAGAACTCA
*
62884 TCTCGAGAGAGACAAAATTTATTTTAAGAGAAACT-A
1 TCTCGAGAGAAACAAAATTTATTTTAAGAG-AACTCA
* * *
62920 TCTCAAGAGAGACAACACTTTATTTT
1 TCTCGAGAGAAACAA-AATTTATTTT
62946 GAGTAAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
36 42 0.78
37 12 0.22
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (36 bp):
TCTCGAGAGAAACAAAATTTATTTTAAGAGAACTCA
Found at i:63316 original size:36 final size:36
Alignment explanation
Indices: 63276--63521 Score: 233
Period size: 36 Copynumber: 7.0 Consensus size: 36
63266 ATTCAGAGAT
*
63276 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
63312 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
63348 TTTATTTCTAAAAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
63385 TTTGTTTAAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAA
* * *
63414 TTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
63450 TTTATTTTAAGAGAAA-TCGTTTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAA
*
63486 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
63522 CTTTATTTTG
Statistics
Matches: 169, Mismatches: 27, Indels: 28
0.75 0.12 0.12
Matches are distributed among these distances:
28 1 0.01
29 18 0.11
30 2 0.01
31 1 0.01
32 1 0.01
33 2 0.01
34 1 0.01
35 3 0.02
36 108 0.64
37 32 0.19
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:63397 original size:138 final size:137
Alignment explanation
Indices: 63221--63517 Score: 461
Period size: 138 Copynumber: 2.2 Consensus size: 137
63211 AGTTAAAAAT
* * *
63221 AAGAAACTGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTTGTTTCAA
1 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
* * *
63286 GAGAAACTATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAAT-GTCTCAAGAGAGACAAAATT
66 GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAG-AAATCGTCTCAAGAGAGACAAAATT
63350 TATTTCTAA
130 TATTT-TAA
63359 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
1 AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
* * * *
63424 GGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTTTCAAGAGAGACAAAATTT
66 GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAGAGAGACAAAATTT
*
63489 GTTTTAA
131 ATTTTAA
*
63496 GAGAAACTGTCTCAAGAGAGAC
1 AAGAAACTGTCTCAAGAGAGAC
63518 AAAACTTTAT
Statistics
Matches: 146, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
137 28 0.19
138 118 0.81
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (137 bp):
AAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAA
GAGAAACTATCTCAAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAGAGAGACAAAATTT
ATTTTAA
Found at i:63801 original size:585 final size:584
Alignment explanation
Indices: 62631--63803 Score: 2130
Period size: 585 Copynumber: 2.0 Consensus size: 584
62621 CAAGAGAGAC
*
62631 AAAAATAAGAAAATGTCTCAAGAGAGGCGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTGT
1 AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTGT
*
62696 TTCAAGAGAAACGGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAA
66 TTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAA
*
62761 AATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAATAGATTCAAA
131 AATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAAA
* * *
62826 GATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTGTTTTAAGAGAAGTCGTCTCGAG
196 GATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAG
*
62891 AGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAACACTTTATTTTGAGTAAATTA
261 AGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATTA
62956 GTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTTG
326 GTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTTG
63021 TTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGTG
391 TTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGTG
* * *
63086 GATGACATGTTTGTTGTGACACTAAATCACTTCATCGGGCATGATATCATTATTTGTGAAGTTGA
456 GATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTGA
*
63151 AATCGTGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
521 AATCATGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
*
63215 AAAAATAAGAAACTGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTTG
1 AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAACAGATTCAGAGA-TTTG
*
63280 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
65 TTTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACA
* * *
63345 AAATTTATTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAA
130 AAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAA
*
63410 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTTTCAA
195 AGATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAA
* *
63475 GAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
260 GAGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATT
63540 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
325 AGTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTT
* *
63605 GTTCATGCATGTTGAAGAAATCCTTTTAGAAGCTCTAATCGTTGACTTAAGGAAGTCAAATCTGT
390 GTTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGT
* *
63670 GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCCTTCTTCGTGAAGTTG
455 GGATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTG
63735 AAATCATGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
520 AAATCATGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
63800 AAAA
1 AAAA
63804 TCCACACATG
Statistics
Matches: 565, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
584 58 0.10
585 507 0.90
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (584 bp):
AAAAATAAGAAAATGTCTCAAGAGAGACGACATTTGTTTCAAGGAAAACAGATTCAGAGATTTGT
TTCAAGAGAAACGATCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATGTCTCAAGAGAGACAA
AATTTAGTTCTAAAAGAAACTGTCTCAAGAGAAACAAAATTTGTTTAAAGGAAAACAGATTCAAA
GATTTTGTTTCAAGGGAAACTGTCTCGAGAGAAACAAAATTTATTTTAAGAGAAATCGTCTCAAG
AGAGACAAAATTTATTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTTATTTTGAGTAAATTA
GTCTTAAGCGAGACGACCCCTTGTTTCGAGAGAAACAATCTCAAAGGTGATCGATAATCTGCTTG
TTCATGCATGTTGAAGAAATCCTTTCAGAAGCTCTAATCATTGACTTAAGGAAGTCAAATCTGTG
GATGACATGTTTATTGTGACACTAAATCACTTCATCGGGCACGATATCATTATTCGTGAAGTTGA
AATCATGGATGGCTCATTTGTTGTGAAATTGAGCTTTTAATTGGATGTCCTTCGTTGTGAAGTT
Found at i:65053 original size:95 final size:93
Alignment explanation
Indices: 64888--65070 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 93
64878 ATATAAATAT
* * *
64888 CTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTAGAGGGACA
1 CTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTAGAGGGACA
64953 ACTCAAACTTTATTGTATAGTATAATCAC
66 ACTCAAACTTTATTGTATA-TATAATCAC
*
64982 CTTTATCAAGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTG-CTCTAGAGGGA
1 CTTTATCAAGCTAGCTGAATATTATCCATAAAG-CCGGGCGTTTAACCAATTGCCT-TAGAGGGA
*
65046 CAACTCAAGCTTTATTGTATATATA
64 CAACTCAAACTTTATTGTATATATA
65071 TAATATTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
94 36 0.44
95 46 0.56
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (93 bp):
CTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGGCGTTTAACCAATTGCCTTAGAGGGACA
ACTCAAACTTTATTGTATATATAATCAC
Found at i:71492 original size:15 final size:15
Alignment explanation
Indices: 71472--71501 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
71462 TGAAACCAAG
71472 TTTGAAAAATTACTC
1 TTTGAAAAATTACTC
71487 TTTGAAAAATTACTC
1 TTTGAAAAATTACTC
71502 CCCCTTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTGAAAAATTACTC
Done.