Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004083.1 Hibiscus syriacus cultivar Beakdansim tig00008934_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: 163643
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:418 original size:197 final size:195
Alignment explanation
Indices: 56--740 Score: 664
Period size: 197 Copynumber: 3.5 Consensus size: 195
46 TAAATCGATA
* * * **
56 TATTTATACC-GTAACATTGCAAATTTACCTATTACATTATTATTATCGGTTACGATGTTTTTTA
1 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTA-TATTATCGGTTTCGATGTTTTTGG
* ** * **
120 GAACGATACAATTT-T-AATGTATCTACACTTTAT-GTTGCACCTGGTTGGGCATTCATATTTCA
65 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT--TT-----TTGGTA-TTCA
* * * *
182 TTCTGGAAAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGACATATTCTCTC
122 TTCTGGACAAAAGTATCGACACAAATTAACAA-GTGTCGATACATTATGTTAGACCTATTTTCTC
*
246 ATAAAATCGG
186 ATAAAACCGG
* *
256 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTAT-GGTTTCGATGTTTTCGG
1 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATA-TTATCGGTTTCGATGTTTTTGG
320 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGTATTCATTCTGGA
65 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTTTTTGGTATTCATTCTGGA
* * * *
385 CCAAAAGTATCGACACAAATTTAGCAAGTGTCGATACTTTATGCTA-ACCTATTTTATCATAAAA
129 -CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTAGACCTATTTTCTCATAAAA
*
449 CCGA
192 CCGG
* *
453 TATCTTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTTTCGA---TTTT
1 TA--TTTATACCGGTTACATTGTAAATTTACCTATTACATTAT-ATTATCGGTTTCGATGTTTTT
* ** * *
515 GGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TGCACCTCGTTGTGCATTCATCCT
63 GGGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTGCACCTTTTTG-GTATTCATTCT
* * * * *
579 GGACATAACTATCGACACAAATTACACAAGTGTCGATACATTATGTT-GACCTGTTTTCTAAT-T
126 GGACAAAAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTAGACCTATTTTCTCATAA
642 AACCGG
190 AACCGG
* * * * *
648 TATATTTATATCGGTTAGATTGTTAATTTACCTATTACATTA-ATTATTGGTTTTTGATGTTTTT
1 --TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTATCGG-TTTCGATG-TTTT
*
712 TGGG-TCGATAC-TTGTATAAAATGTATCGA
62 TGGGATCGATACTTTTTAT-AAATGTATCGA
741 ACATATTTAG
Statistics
Matches: 412, Mismatches: 48, Indels: 53
0.80 0.09 0.10
Matches are distributed among these distances:
193 7 0.02
194 5 0.01
195 43 0.10
196 67 0.16
197 130 0.32
198 15 0.04
199 40 0.10
200 45 0.11
201 32 0.08
202 19 0.05
203 6 0.01
204 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (195 bp):
TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCGATGTTTTTGGG
ATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTTTTTGGTATTCATTCTGGACA
AAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTAGACCTATTTTCTCATAAAACCGG
Found at i:3639 original size:197 final size:199
Alignment explanation
Indices: 3304--3765 Score: 596
Period size: 200 Copynumber: 2.3 Consensus size: 199
3294 TACCTATTTC
* * * * * * *
3304 ATTTCGATATTTTCG-GTATCGATACTTTTAATAAATATATCGACACTTTGTGCGTTAATCCTTT
1 ATTTCGATATTTTTGCG-ATCGACACTCTTAATAAATGTATCGACACTTTATGCGTTCACCCTTT
* * *
3368 TTGGCATACATTCTGGAAAAAAGTATCGACACAAATTTAACAAGTGTCGCTACATGTTATAGACA
65 TTGACATACATTCTGGAAAAAAGTATCGACACAAATTTAACAAGTGTCGATACATATTATAGACA
** *
3433 TATTCTCTCA-AAAACAGGTAT-T-TATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
130 TATTCTCTCATAAAACAGGTATATGTATACCGGTTACATTACAAAATTACCTATTACATTATAAT
3495 TAT-G
195 TATGG
* * *
3499 AGTTTCGATGTTTTTGGGATCGACACTGCTTGA-AAATGTATCGACACTTTATGCGTTCACCCTT
1 A-TTTCGATATTTTTGCGATCGACACT-CTTAATAAATGTATCGACACTTTATGCGTTCACCCTT
* * *
3563 TTTGACATCCATTCTGGACAAAAATTATCGACAC-AATATTAAGAAGTGTCGATACATATTATAG
64 TTTGACATACATTCTGGA-AAAAAGTATCGACACAAAT-TTAACAAGTGTCGATACATATTATAG
* * *
3627 ACCTATTCTCTCATAAAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACATTAT
127 ACATATTCTCTCATAAAACAGGTATATGTATACCGGTTACATTACAAAATTACCTATTACATTAT
3692 AATTATGG
192 AATTATGG
* * *
3700 ATTTCGATATTTTTGCGATCGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCCTTT
1 ATTTCGATATTTTTGCGATCGACACTCTTAATAAATGTATCGACACTTTATGCGTTC-ACCCTTT
3765 T
65 T
3766 GGATCGACAC
Statistics
Matches: 229, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
195 1 0.00
196 66 0.29
197 53 0.23
198 10 0.04
199 4 0.02
200 85 0.37
201 10 0.04
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (199 bp):
ATTTCGATATTTTTGCGATCGACACTCTTAATAAATGTATCGACACTTTATGCGTTCACCCTTTT
TGACATACATTCTGGAAAAAAGTATCGACACAAATTTAACAAGTGTCGATACATATTATAGACAT
ATTCTCTCATAAAACAGGTATATGTATACCGGTTACATTACAAAATTACCTATTACATTATAATT
ATGG
Found at i:4000 original size:249 final size:252
Alignment explanation
Indices: 3510--3962 Score: 675
Period size: 249 Copynumber: 1.8 Consensus size: 252
3500 GTTTCGATGT
3510 TTTTGGGATCGACACTGCTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
1 TTTTGGGATCGACACTGCTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
* * * * *
3575 TCTGGACAAAAATTATCGACACAATATTAAGAAGTGTCGATACATATTATAGACCTATTCTCTCA
66 TCTGGACAAAAAGTATCGACACAATACTAAGAAGTGTCAATAAATATTATAGACATATTCTCTCA
* *
3640 TAAAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTC
131 TAAAACCGGTATATGTATACCGGTTACATTACAAAATTACCCATTACATTATAATTATGGATTTC
*
3705 GATATTTTTGCGATCGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCC
196 GATATTTTTGCGATCGACACTTTTAATAAATGGATCGAAACTTTATGCGTGCAACCC
* *
3762 TTTT-GGATCGACACT-CTATGAAAATGTATCGACACTTTGTAG-GTTCACCCTTTTTGGCATCC
1 TTTTGGGATCGACACTGCT-TGAAAATGTATCGACACTTTAT-GCGTTCACCCTTTTTGACATCC
* * * * *
3824 ATTCTGGAC-AAAAGTATCGACACAATACTAATAAGTGTCAATAAATGTTGTAGATATATT-TTT
64 ATTCTGGACAAAAAGTATCGACACAATACTAAGAAGTGTCAATAAATATTATAGACATATTCTCT
* *
3887 CATAAAACCGGTATATTTATACCGGTTACATTGA-AAAATTACCCATTACATTATAATTATGGGT
129 CATAAAACCGGTATATGTATACCGGTTACATT-ACAAAATTACCCATTACATTATAATTATGGAT
*
3951 TTCGATGTTTTT
193 TTCGATATTTTT
3963 TGGGTCGTTA
Statistics
Matches: 181, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
249 71 0.39
250 45 0.25
251 60 0.33
252 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (252 bp):
TTTTGGGATCGACACTGCTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGACATCCAT
TCTGGACAAAAAGTATCGACACAATACTAAGAAGTGTCAATAAATATTATAGACATATTCTCTCA
TAAAACCGGTATATGTATACCGGTTACATTACAAAATTACCCATTACATTATAATTATGGATTTC
GATATTTTTGCGATCGACACTTTTAATAAATGGATCGAAACTTTATGCGTGCAACCC
Found at i:6904 original size:19 final size:19
Alignment explanation
Indices: 6880--6931 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
6870 CATAATTATA
6880 CTTATACAAAATTATAAAT
1 CTTATACAAAATTATAAAT
6899 CTTATACAAAATTATAAAT
1 CTTATACAAAATTATAAAT
*
6918 CTTATAAAAAATTA
1 CTTATACAAAATTA
6932 ACCCTACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
CTTATACAAAATTATAAAT
Found at i:8727 original size:33 final size:33
Alignment explanation
Indices: 8690--8753 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
8680 TCTTAAGATC
*
8690 ACCCCTTAACACCTCAACTTCTTTCACCACTTT
1 ACCCCTCAACACCTCAACTTCTTTCACCACTTT
* *
8723 ACCCCTCAACACCTCTACTTCTTTCATCACT
1 ACCCCTCAACACCTCAACTTCTTTCACCACT
8754 CCATCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (33 bp):
ACCCCTCAACACCTCAACTTCTTTCACCACTTT
Found at i:8811 original size:21 final size:21
Alignment explanation
Indices: 8787--8851 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
8777 CCCTTTATGC
* * *
8787 CTCTCAAGTGTATCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
8808 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
8829 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
8850 CT
1 CT
8852 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:0.15, C:0.31, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:11122 original size:22 final size:22
Alignment explanation
Indices: 11086--11142 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
11076 CGCTTTATCG
11086 GTTTTATC--ATTTTGATACCA
1 GTTTTATCATATTTTGATACCA
*
11106 GTTTTATCATATTTTGATACCG
1 GTTTTATCATATTTTGATACCA
11128 GTTTTATCATATTTT
1 GTTTTATCATATTTT
11143 ACATGTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 8 0.24
22 26 0.76
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (22 bp):
GTTTTATCATATTTTGATACCA
Found at i:11327 original size:20 final size:19
Alignment explanation
Indices: 11282--11339 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
11272 CCGATAGCTC
11282 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
* *
11301 TGATACCGGTTTTGTCATATT
1 T-TTACCGGTTTTATCAT-TT
* *
11322 TTTACCTGTTATATCATT
1 TTTACCGGTTTTATCATT
11340 GTGGATCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 2 0.06
20 26 0.84
21 3 0.10
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:11453 original size:182 final size:182
Alignment explanation
Indices: 11101--11541 Score: 568
Period size: 182 Copynumber: 2.4 Consensus size: 182
11091 ATCATTTTGA
* * *
11101 TACCAGTTTTATCATATTTTGATACCGGTTTTATCATA-TTTTACATGTTATATCGTTGTGGATC
1 TACCGGTTTTATC--ATTTTGATACCGGTTTTATCATATTTTTACCTGTTATATCATTGTGGATC
*
11165 GATACATTTTTATAAAGTATTGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAA
64 GATACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAA
* ** **
11230 AGTGTCGATACTTATATTAAAGTACCGACACTTTAAATATATCCGAT-AGCTCTT
129 AGTGTCGATACTTATATTAAAGAACCGACAAGTTAAATATATCCGATAAG-GATT
* *
11284 TACCGGTTTTATCATTTTGATACCGGTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCAA
1 TACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTTTACCTGTTATATCATTGTGGATCGA
* *
11349 TACATTTTTATAAAGTATCGACACTTTATAGGCGTTAAAATTGCTTCTCTTTTAAATTCACAAAG
66 TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAG
* * * * * *
11414 TGTCGATCCTTATATTAAAGAATCGATAAGTTCAATATATCTGGTAAGGATT
131 TGTCGATACTTATATTAAAGAACCGACAAGTTAAATATATCCGATAAGGATT
* * * * *
11466 TACCGGTATTGTC-TTTTCG-TGACCGATTTTATCGATATTTTTACCTGTTATATTGA-TATGGA
1 TACCGGTTTTATCATTTT-GAT-ACCGGTTTTATC-ATATTTTTACCTGTTATA-TCATTGTGGA
11528 TCGATACATTTTTA
62 TCGATACATTTTTA
11542 ATTTGGATCG
Statistics
Matches: 226, Mismatches: 26, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
181 27 0.12
182 147 0.65
183 50 0.22
184 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (182 bp):
TACCGGTTTTATCATTTTGATACCGGTTTTATCATATTTTTACCTGTTATATCATTGTGGATCGA
TACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAG
TGTCGATACTTATATTAAAGAACCGACAAGTTAAATATATCCGATAAGGATT
Found at i:12275 original size:20 final size:21
Alignment explanation
Indices: 12211--12296 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 21
12201 AAATGACCAA
*
12211 CAAATTCGCAACGCGAATA-TG
1 CAAATTCGCAACGCG-ATAGTC
** **
12232 CAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGATAGTC
12252 CAAATTCGCAACGCGATAGT-
1 CAAATTCGCAACGCGATAGTC
* *
12272 CAAATTCACAACGCGAAAGT-
1 CAAATTCGCAACGCGATAGTC
12292 CAAAT
1 CAAAT
12297 GTTTTTACGC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.04
20 36 0.68
21 15 0.28
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (21 bp):
CAAATTCGCAACGCGATAGTC
Found at i:12449 original size:22 final size:22
Alignment explanation
Indices: 12424--12474 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12414 CTACGGCGAC
*
12424 ATCCGTCACCATCTCCGACAAA
1 ATCCATCACCATCTCCGACAAA
* * *
12446 ATCCATCCCCATTTCCGACGAA
1 ATCCATCACCATCTCCGACAAA
12468 ATCCATC
1 ATCCATC
12475 TATCTCCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.41, G:0.08, T:0.22
Consensus pattern (22 bp):
ATCCATCACCATCTCCGACAAA
Found at i:12770 original size:19 final size:20
Alignment explanation
Indices: 12730--12772 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12720 AACACCAAAT
12730 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
12750 TCGCAACGTGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
12769 TCGC
1 TCGC
12773 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:12810 original size:20 final size:20
Alignment explanation
Indices: 12769--12810 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12759 GAAACTAAAA
* * *
12769 TCGCGTTGCGATTTTTATTT
1 TCGCGTTGCGAATTTAAGTT
12789 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
12809 TC
1 TC
12811 ATAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:16865 original size:39 final size:39
Alignment explanation
Indices: 16806--16892 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
16796 TCAAGTTGTA
*
16806 GATTATGATTTCCTTTTGCTTTG-CACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGC-TTGACACCATATGAGATTTG
*
16845 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
16884 GATTTTGAT
1 GATTTTGAT
16893 GAGCATCGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 3 0.07
39 42 0.93
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:17223 original size:18 final size:18
Alignment explanation
Indices: 17200--17236 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17190 CGAAATTTAT
17200 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
17218 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
17236 A
1 A
17237 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:17657 original size:11 final size:13
Alignment explanation
Indices: 17622--17672 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
17612 ATATTATTTT
17622 TCCAAATAATGTA
1 TCCAAATAATGTA
*
17635 TCCATAACAATGT-
1 TCCA-AATAATGTA
17648 T-CAAATAATGTA
1 TCCAAATAATGTA
*
17660 CCCACAATAATGT
1 TCCA-AATAATGT
17673 TTAGTTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 7 0.23
12 2 0.06
13 7 0.23
14 15 0.48
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (13 bp):
TCCAAATAATGTA
Found at i:17658 original size:25 final size:25
Alignment explanation
Indices: 17624--17673 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17614 ATTATTTTTC
* *
17624 CAAATAATGTATCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
17649 CAAATAATGTACCCACAATAATGTT
1 CAAATAATGTACCCACAACAATGTT
17674 TAGTTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:17874 original size:20 final size:20
Alignment explanation
Indices: 17808--17877 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
17798 CGGTTTGCGA
17808 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * * *
17828 TATCGCATTACGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
*
17848 TTTCGCGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
17868 TTTCGCGTTG
1 TTTCGCGTTG
17878 ATCGCAACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:19528 original size:21 final size:21
Alignment explanation
Indices: 19490--19529 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19480 GAATCTACAA
*
19490 AATCATATACATAAGAAATAT
1 AATCATATAAATAAGAAATAT
* *
19511 AATCATTTAAATATGAAAT
1 AATCATATAAATAAGAAAT
19530 GCATGCAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
AATCATATAAATAAGAAATAT
Found at i:20279 original size:12 final size:12
Alignment explanation
Indices: 20262--20286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20252 TCTTCGGGGA
20262 CTTATTCTTCTT
1 CTTATTCTTCTT
20274 CTTATTCTTCTT
1 CTTATTCTTCTT
20286 C
1 C
20287 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTATTCTTCTT
Found at i:21168 original size:19 final size:19
Alignment explanation
Indices: 21144--21189 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
21134 AACCTGTTGT
21144 GAATTTGAAATTCAATTGC
1 GAATTTGAAATTCAATTGC
21163 GAATTTGAAATTCAATTGC
1 GAATTTGAAATTCAATTGC
21182 GAATTTGA
1 GAATTTGA
21190 CTTTCGCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GAATTTGAAATTCAATTGC
Found at i:21203 original size:20 final size:20
Alignment explanation
Indices: 21178--21248 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
21168 TGAAATTCAA
21178 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
21198 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
* * *
21218 TTGAGAATTTGACTATCGCA
1 TTGCGAATTTGACTTTCGCG
21238 TTGCGAATTTG
1 TTGCGAATTTG
21249 GAAAATCACA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:21266 original size:21 final size:21
Alignment explanation
Indices: 21240--21289 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
21230 CTATCGCATT
*
21240 GCGAATTTGGAAAATCACAAC
1 GCGAATTTAGAAAATCACAAC
* *
21261 GCGAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCACAAC
21282 GCG-ATTTA
1 GCGAATTTA
21290 CATATTCGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGAATTTAGAAAATCACAAC
Found at i:24505 original size:32 final size:27
Alignment explanation
Indices: 24460--24553 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 27
24450 TAGTGTATAA
*
24460 ATATTTAACTTAAATTCATAATATTATTAT
1 ATATTTAACTTAAAAT-AT-ATATT-TTAT
24490 ATATATTAACTTTAAAATATATA-TTT-T
1 ATAT-TTAAC-TTAAAATATATATTTTAT
*
24517 ATA-TTAACTTATTAA-ATATATTTTAT
1 ATATTTAACTTA-AAATATATATTTTAT
24543 -TA-TTAACTTAA
1 ATATTTAACTTAA
24554 TTTATTTTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
24 8 0.14
25 20 0.36
26 1 0.02
27 4 0.07
28 2 0.04
29 1 0.02
30 7 0.12
31 7 0.12
32 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (27 bp):
ATATTTAACTTAAAATATATATTTTAT
Found at i:24524 original size:25 final size:25
Alignment explanation
Indices: 24491--24551 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
24481 TATTATTATA
24491 TATATTAACTTTA-AAATATATATTT
1 TATATTAACTTTATAAA-ATATATTT
*
24516 TATATTAAC-TTATTAAATATATTT
1 TATATTAACTTTATAAAATATATTT
24540 TATTATTAACTT
1 TA-TATTAACTT
24552 AATTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 13 0.41
25 18 0.56
26 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATTAACTTTATAAAATATATTT
Found at i:24553 original size:22 final size:21
Alignment explanation
Indices: 24508--24561 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
24498 ACTTTAAAAT
24508 ATATATTTTATATTAACTTATTAA
1 ATATATTTTATATTAAC-T-TT-A
24532 ATATATTTTATTATTAAC-TTA
1 ATATATTTTA-TATTAACTTTA
*
24553 ATTTATTTT
1 ATATATTTT
24562 CAAAGTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
24 10 0.36
25 7 0.25
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATATTAACTTTA
Found at i:24624 original size:30 final size:30
Alignment explanation
Indices: 24569--24644 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
24559 TTTCAAAGTA
* *
24569 TATATTTTTATCTTAATTTACTAAATACAT
1 TATATTATTATCTTAAATTACTAAATACAT
* * *
24599 TATATTATTATTTTAAATTATTAAATATAT
1 TATATTATTATCTTAAATTACTAAATACAT
* *
24629 TTTATTCTTATCTTAA
1 TATATTATTATCTTAA
24645 CTTTAAAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATTATTATCTTAAATTACTAAATACAT
Found at i:27189 original size:29 final size:28
Alignment explanation
Indices: 27155--27225 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
27145 TTTATTTAAT
* **
27155 TAAGATATGATTACTGATTTCAAAAAATG
1 TAAGATATG-TCACTGATTTCAAAAAACA
27184 TAAGATATTGTCACTGATTTCAAAAAACA
1 TAAGATA-TGTCACTGATTTCAAAAAACA
27213 TAAGATATTGTCA
1 TAAGATA-TGTCA
27226 TTTTCGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.34
Consensus pattern (28 bp):
TAAGATATGTCACTGATTTCAAAAAACA
Found at i:27251 original size:31 final size:31
Alignment explanation
Indices: 27213--27271 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
27203 TCAAAAAACA
*
27213 TAAGATATTGTCATTTTCGTTTTTATTTTGT
1 TAAGATATTGTCACTTTCGTTTTTATTTTGT
27244 TAAGATATTGTCACTTTCGTTTTTATTT
1 TAAGATATTGTCACTTTCGTTTTTATTT
27272 AATTAAGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.59
Consensus pattern (31 bp):
TAAGATATTGTCACTTTCGTTTTTATTTTGT
Found at i:27278 original size:31 final size:31
Alignment explanation
Indices: 27213--27279 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
27203 TCAAAAAACA
* **
27213 TAAGATATTGTCATTTTCGTTTTTATTTTGT
1 TAAGATATTGTCACTTTCGTTTTTATTTAAT
27244 TAAGATATTGTCACTTTCGTTTTTATTTAAT
1 TAAGATATTGTCACTTTCGTTTTTATTTAAT
27275 TAAGA
1 TAAGA
27280 CGTGATCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (31 bp):
TAAGATATTGTCACTTTCGTTTTTATTTAAT
Found at i:34489 original size:55 final size:55
Alignment explanation
Indices: 34416--34786 Score: 428
Period size: 55 Copynumber: 6.7 Consensus size: 55
34406 TCTTTGAATG
* *
34416 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAA
1 ACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAACAATCTTCATCAA
* * *
34471 ACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATATTCATCAA
1 ACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAACAATCTTCATCAA
** *
34526 ACGTTTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATCAA
* * * * * *
34581 ACGGGTTTGCTCTCTATTTC-TTCAGAGAGTATAGGACTTGAACAATCTTCAACAA
1 ACGGGTCTGCTCCCTA-TTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATCAA
*
34636 ACGGGT-TCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
1 ACGGGTCT-GCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATCAA
* * * * * *
34691 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAA
1 ACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATCAA
* * * * *
34746 ATGGGTCCGCTCTCTCTTAC-TTCAGAGAGTATAGAACTCGA
1 ACGGGTCTGCTCCCTATT-CGTTCAGGGAGTATAGAACTCGA
34787 TCTTCATAAA
Statistics
Matches: 277, Mismatches: 33, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
54 4 0.01
55 268 0.97
56 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (55 bp):
ACGGGTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATCAA
Found at i:34624 original size:110 final size:109
Alignment explanation
Indices: 34423--34786 Score: 473
Period size: 110 Copynumber: 3.3 Consensus size: 109
34413 ATGACGGGTC
** * *
34423 CGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTA
1 CGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCTGCTCTCTA
* * * * *
34487 -TTCATTCAGGGAGTATAAGACTCGAACAATATTCATCAAACGTTT
65 TTTC-TTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGTT
*
34532 CTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTTTGCTCTCTA
1 C-GCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCTCTA
*
34597 TTTCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGGGTT
65 TTTCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAAC-GGTT
*
34643 CGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTAT
1 CGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCTCTAT
* * * * *
34708 TCCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAAATGGGTC
66 TTCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAA-CGGTT
* * *
34753 CGCTCTCTCTTAC-TTCAGAGAGTATAGAACTCGA
1 CGCTCCCTATT-CGTTCAGGGAGTATAGAACTCGA
34787 TCTTCATAAA
Statistics
Matches: 227, Mismatches: 22, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
109 1 0.00
110 217 0.96
111 9 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (109 bp):
CGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCTGCTCTCTAT
TTCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGTT
Found at i:34723 original size:165 final size:165
Alignment explanation
Indices: 34416--34786 Score: 480
Period size: 165 Copynumber: 2.2 Consensus size: 165
34406 TCTTTGAATG
* * * * *
34416 ACGGGTCCGCTCCCTATT-CGTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCTG
1 ACGGGTCCGCTCTCTATTAC-TTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTG
* ** *
34480 CTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATATTCATCAAACGTTTCTGCTCCCTATTC
65 CTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATATTCATAAAACGGGTCCGCTCCCTATTC
* *
34545 GTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AA
130 CTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAA
** * *
34581 ACGGGTTTGCTCTCTATTTCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGGGT-TCG
1 ACGGGTCCGCTCTCTATTACTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCT-G
* * *
34645 CTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
65 CTCCCTATTCATTCAGGGAGTATAAG-ACTCGAACAATATTCATAAAACGGGTCCGCTCCCTATT
*
34709 CCTTCAGAGAGTATAGAACTCGAATAATCTTCAACAA
129 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
34746 ATGGGTCCGCTCTCTCTTACTTCAGAGAGTATAGAACTCGA
1 ACGGGTCCGCTCTCTATTACTTCAGAGAGTATAGGACTCGA
34787 TCTTCATAAA
Statistics
Matches: 177, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
164 4 0.02
165 172 0.97
166 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (165 bp):
ACGGGTCCGCTCTCTATTACTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCTGC
TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATATTCATAAAACGGGTCCGCTCCCTATTCC
TTCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:36193 original size:19 final size:19
Alignment explanation
Indices: 36153--36194 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
36143 TTGAACCCCC
*
36153 TTTTATTTTTCTCTATTTT
1 TTTTATTTTTCTCTATTAT
36172 TTTTATTTTTCTCT-TTCAT
1 TTTTATTTTTCTCTATT-AT
36191 TTTT
1 TTTT
36195 TTCTCCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTCTCTATTAT
Found at i:36281 original size:15 final size:14
Alignment explanation
Indices: 36250--36288 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
36240 CCATCATTTA
*
36250 TCTCATTTTCCTTT
1 TCTCATTTTTCTTT
*
36264 TCTTATTTTTCTTCT
1 TCTCATTTTTCTT-T
36279 TCTCATTTTT
1 TCTCATTTTT
36289 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTCATTTTTCTTT
Found at i:36305 original size:9 final size:9
Alignment explanation
Indices: 36293--36331 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
36283 ATTTTTATTA
36293 TTTTTTTCT
1 TTTTTTTCT
36302 TTTTTTTC-
1 TTTTTTTCT
*
36310 TTTTTCTCT
1 TTTTTTTCT
*
36319 TTTATTTCT
1 TTTTTTTCT
36328 TTTT
1 TTTT
36332 CAAGCGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:36313 original size:17 final size:17
Alignment explanation
Indices: 36264--36332 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
36254 ATTTTCCTTT
* *
36264 TCTTATTTTTCTTCTTC
1 TCTTTTTTTTCTTTTTC
* * *
36281 TCATTTTTATTATTTTTT
1 TC-TTTTTTTTCTTTTTC
36299 TCTTTTTTTTCTTTTTC
1 TCTTTTTTTTCTTTTTC
*
36316 TCTTTTATTTCTTTTTC
1 TCTTTTTTTTCTTTTTC
36333 AAGCGAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTTTTTCTTTTTC
Found at i:46069 original size:47 final size:46
Alignment explanation
Indices: 45971--46081 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 46
45961 CCATGCTTTG
* *
45971 TTATTCATAAAAAGAAATCCTAACCGCATGATATCTAATTTGCATGT
1 TTATTCA-AAAAAGAAATCCTAACCGCATGATATCTAATTCGAATGT
* *
46018 TTATTCAAAAAATAAAT-CTAACCGCATGATATCTAGTTCGAATGCAT
1 TTATTCAAAAAAGAAATCCTAACCGCATGATATCTAATTCGAATG--T
*
46065 TTATTCGAAAAACGAAA
1 TTATTC-AAAAAAGAAA
46082 ATAAATAACT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 24 0.44
46 9 0.16
47 14 0.25
48 8 0.15
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (46 bp):
TTATTCAAAAAAGAAATCCTAACCGCATGATATCTAATTCGAATGT
Found at i:57018 original size:32 final size:32
Alignment explanation
Indices: 56981--57043 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
56971 ACAACCTAAT
* *
56981 GGAGTATATTGGGGCCTTAGAACCTACCCAAA
1 GGAGTAGATTGGGGCCTAAGAACCTACCCAAA
*
57013 GGAGTAGATTGGGGCCTAAGAGCCTACCCAA
1 GGAGTAGATTGGGGCCTAAGAACCTACCCAA
57044 GGGTCACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (32 bp):
GGAGTAGATTGGGGCCTAAGAACCTACCCAAA
Found at i:60834 original size:19 final size:18
Alignment explanation
Indices: 60806--60841 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
60796 TTTCACTAAT
*
60806 AGAGGAAATATTACAAAG
1 AGAGGAAATAGTACAAAG
60824 AGAGAGAAATAGTACAAA
1 AGAG-GAAATAGTACAAA
60842 TAGCCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (18 bp):
AGAGGAAATAGTACAAAG
Found at i:65019 original size:15 final size:15
Alignment explanation
Indices: 64999--65027 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64989 AATCTAACAT
64999 TTGTCACAGCATTTC
1 TTGTCACAGCATTTC
65014 TTGTCACAGCATTT
1 TTGTCACAGCATTT
65028 TTCTAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (15 bp):
TTGTCACAGCATTTC
Found at i:65679 original size:35 final size:35
Alignment explanation
Indices: 65633--65745 Score: 158
Period size: 35 Copynumber: 3.2 Consensus size: 35
65623 AAAACATTCC
*
65633 TCAATTTCATTCTAAACCTCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCTCAAATTCCAAAATAAT
65668 TCAATTTCATTCTAAACC-CTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCTC-AAATTCCAAAATAAT
* * *
65703 TCAATTACATTCTAAAACCT-AAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCTCAAATTCCAAAATAAT
65738 TCAATTTC
1 TCAATTTC
65746 TGTCTTTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
34 1 0.01
35 64 0.91
36 5 0.07
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCTCAAATTCCAAAATAAT
Found at i:66826 original size:35 final size:34
Alignment explanation
Indices: 66771--66882 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
66761 ATTCCTCCTT
* *
66771 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
* * *
66806 TAATTGATTTTTTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
66841 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
66876 AAATTGA
1 AAATTGA
66883 GGAATGTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
35 63 0.95
36 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.44
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:72013 original size:109 final size:109
Alignment explanation
Indices: 71822--72033 Score: 424
Period size: 109 Copynumber: 1.9 Consensus size: 109
71812 TCTTTTTTGC
71822 TCGTCCGAAGCGGCTCCTGATGAGGAGATCCTTCAAGCCATTGATCGATGCGTTTTTCAGAGTGA
1 TCGTCCGAAGCGGCTCCTGATGAGGAGATCCTTCAAGCCATTGATCGATGCGTTTTTCAGAGTGA
71887 TAATGATTTGCTTTGCCGACCATTTTCCGCGGAGGAGGGAGTGA
66 TAATGATTTGCTTTGCCGACCATTTTCCGCGGAGGAGGGAGTGA
71931 TCGTCCGAAGCGGCTCCTGATGAGGAGATCCTTCAAGCCATTGATCGATGCGTTTTTCAGAGTGA
1 TCGTCCGAAGCGGCTCCTGATGAGGAGATCCTTCAAGCCATTGATCGATGCGTTTTTCAGAGTGA
71996 TAATGATTTGCTTTGCCGACCATTTTCCGCGGAGGAGG
66 TAATGATTTGCTTTGCCGACCATTTTCCGCGGAGGAGG
72034 TCACCAGTGC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (109 bp):
TCGTCCGAAGCGGCTCCTGATGAGGAGATCCTTCAAGCCATTGATCGATGCGTTTTTCAGAGTGA
TAATGATTTGCTTTGCCGACCATTTTCCGCGGAGGAGGGAGTGA
Found at i:82946 original size:38 final size:38
Alignment explanation
Indices: 82896--82970 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
82886 TCCTCCGAAA
*
82896 CAAATTCTGAAAGGCACCACTTCGCTATTATATCCGAC
1 CAAATTCCGAAAGGCACCACTTCGCTATTATATCCGAC
*
82934 CAAATTCCGAAAGGCACCCCTTCGCTATTATATCCGA
1 CAAATTCCGAAAGGCACCACTTCGCTATTATATCCGA
82971 TCGGAACGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.25
Consensus pattern (38 bp):
CAAATTCCGAAAGGCACCACTTCGCTATTATATCCGAC
Found at i:86669 original size:24 final size:24
Alignment explanation
Indices: 86634--86688 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
86624 CGTTCGATTA
*
86634 TATGTTCGTTTATGTTCATTCATT
1 TATGTTCATTTATGTTCATTCATT
*
86658 TATGTTCATTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCATTCATT
86682 TATGTTC
1 TATGTTC
86689 GAACAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (24 bp):
TATGTTCATTTATGTTCATTCATT
Found at i:86689 original size:14 final size:14
Alignment explanation
Indices: 86637--86689 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
86627 TCGATTATAT
*
86637 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
*
86651 ATTCATTTA---T-
1 GTTCATTTATGTTC
86661 GTTCATTTATGTTC
1 GTTCATTTATGTTC
86675 GTTCATTTATGTTC
1 GTTCATTTATGTTC
86689 G
1 G
86690 AACAAAGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.25
11 1 0.03
13 1 0.03
14 22 0.69
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:87101 original size:16 final size:16
Alignment explanation
Indices: 87058--87102 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
87048 AAAATTTGTT
*
87058 CATTTATGTTCATGTC
1 CATTTATGTTCGTGTC
87074 CATTTATGTTCGTGTC
1 CATTTATGTTCGTGTC
*
87090 CGTTTATGTTCGT
1 CATTTATGTTCGT
87103 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.51
Consensus pattern (16 bp):
CATTTATGTTCGTGTC
Found at i:87911 original size:31 final size:31
Alignment explanation
Indices: 87875--87933 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
87865 AACTTAAAAG
* * *
87875 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
87906 AGTTTTACAATAATGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
87934 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:87983 original size:22 final size:22
Alignment explanation
Indices: 87958--88000 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
87948 TAATAAATTA
*
87958 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATCAATCCATAT
87980 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
88001 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:88009 original size:22 final size:22
Alignment explanation
Indices: 87960--88008 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
87950 ATAAATTATT
* **
87960 TAAAATAAATTAATCCATATTT
1 TAAAATAAATCAATCCATATAA
87982 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
88005 TAAA
1 TAAA
88009 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:88012 original size:54 final size:54
Alignment explanation
Indices: 87948--88364 Score: 426
Period size: 54 Copynumber: 7.6 Consensus size: 54
87938 ACAACTACAA
*
87948 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
88002 TAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--C
* * * * *
88062 TAAAATAAATCAATTCATAA-AAATAAAT---TA-TTTAAAATAAATCAATCTATAC
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
88114 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
88168 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
88222 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
88275 T-AT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
88334 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
88365 CTAATAAATT
Statistics
Matches: 301, Mismatches: 31, Indels: 60
0.77 0.08 0.15
Matches are distributed among these distances:
48 16 0.05
49 8 0.03
50 15 0.05
52 4 0.01
53 4 0.01
54 159 0.53
55 9 0.03
56 3 0.01
57 10 0.03
58 27 0.09
59 3 0.01
60 4 0.01
62 15 0.05
63 8 0.03
64 16 0.05
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:88068 original size:22 final size:22
Alignment explanation
Indices: 88012--88080 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
88002 TAATAAATTA
88012 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AC
* *
88037 TATAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAC
*
88060 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
88081 AAAATAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 15 0.38
23 5 0.13
25 4 0.10
26 15 0.38
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAC
Found at i:88107 original size:112 final size:112
Alignment explanation
Indices: 87980--88365 Score: 547
Period size: 112 Copynumber: 3.5 Consensus size: 112
87970 TAATCCATAT
87980 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAA
88045 TAAATCAATCCATATTTTAAAATAAATCAATTCATAAAAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAATCAATTCATAAAAATAAATTA
* * *
88092 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAA
* * * * * *
88153 TAAATCAATTCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATA
66 TAAATCAATCCATATTTTAAAATAAATCAATTCATAA-AAATAAAT---TA
*
88199 TTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATA
* * *
88264 ATAAATCAATCTATATTTTAAAATAAATCAATCCATACAAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATCAATTCATAAAAATAAATTA
88312 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
88366 TAATAAATTA
Statistics
Matches: 238, Mismatches: 22, Indels: 28
0.83 0.08 0.10
Matches are distributed among these distances:
103 6 0.03
104 14 0.06
106 1 0.00
107 2 0.01
108 66 0.28
109 5 0.02
111 4 0.02
112 119 0.50
113 2 0.01
114 1 0.00
116 14 0.06
117 4 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (112 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAA
TAAATCAATCCATATTTTAAAATAAATCAATTCATAAAAATAAATTA
Found at i:88150 original size:22 final size:22
Alignment explanation
Indices: 88124--88166 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
88114 TAATAAATTA
88124 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
88146 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
88167 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:88175 original size:22 final size:22
Alignment explanation
Indices: 88126--88174 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
88116 ATAAATTATT
**
88126 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
88148 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
88171 TAAA
1 TAAA
88175 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:88204 original size:22 final size:22
Alignment explanation
Indices: 88178--88220 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
88168 TAATAAATTA
88178 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
88200 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
88221 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:88229 original size:22 final size:22
Alignment explanation
Indices: 88180--88228 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
88170 ATAAATTATT
**
88180 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
88202 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
88225 TAAA
1 TAAA
88229 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:88253 original size:32 final size:32
Alignment explanation
Indices: 88060--88376 Score: 276
Period size: 32 Copynumber: 11.0 Consensus size: 32
88050 CAATCCATAT
* **
88060 TTTAAAATAAATCAATTCATAAAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
88092 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88124 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
88146 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88178 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88200 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
88232 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
88262 --T--AATAAATCAATCTATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
88287 -------TAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88312 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88344 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
88376 T
1 T
88377 ACTTCATCCA
Statistics
Matches: 238, Mismatches: 15, Indels: 64
0.75 0.05 0.20
Matches are distributed among these distances:
22 45 0.19
23 8 0.03
24 2 0.01
25 5 0.02
26 21 0.09
28 7 0.03
30 3 0.01
31 5 0.02
32 142 0.60
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:88284 original size:80 final size:80
Alignment explanation
Indices: 88183--88333 Score: 284
Period size: 80 Copynumber: 1.9 Consensus size: 80
88173 AATTATTTAA
*
88183 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
88248 CCATACAACTACAAT
66 CCATACAACTACAAT
*
88263 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
88328 CCATAC
66 CCATAC
88334 TAATAAATTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:88336 original size:220 final size:220
Alignment explanation
Indices: 87948--88364 Score: 780
Period size: 220 Copynumber: 1.9 Consensus size: 220
87938 ACAACTACAA
*
87948 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
88013 TTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATATTTTAAAATAAATCAATTC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
88078 ATAAAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCA
131 ATAAAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
88143 TATTTTAAAATAAATCAATTCATAC
196 TATTTTAAAATAAATCAATTCATAC
88168 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
88233 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
88298 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
131 ATAAAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
88363 TA
196 TA
88365 CTAATAAATT
Statistics
Matches: 191, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 191 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (220 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATAAAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
TATTTTAAAATAAATCAATTCATAC
Found at i:89154 original size:33 final size:35
Alignment explanation
Indices: 89098--89200 Score: 126
Period size: 33 Copynumber: 3.1 Consensus size: 35
89088 TGCACTATTT
* *
89098 GAACAGT-AGA-AAACAACATTACAATTTTGATTC
1 GAACAGTGAGAGAAACAACAATACAATTTTGGTTC
* *
89131 GAACAGTGA-A-AAATAGCAATACAATTTTGGTTC
1 GAACAGTGAGAGAAACAACAATACAATTTTGGTTC
*
89164 -AATAGTGAGAGAAACAACAATACAATTTTGGTTC
1 GAACAGTGAGAGAAACAACAATACAATTTTGGTTC
89198 GAA
1 GAA
89201 TAGCAGTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 7 0.12
33 28 0.47
34 22 0.37
35 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (35 bp):
GAACAGTGAGAGAAACAACAATACAATTTTGGTTC
Found at i:91063 original size:23 final size:23
Alignment explanation
Indices: 91012--91067 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
91002 TCTAGGCAGC
* ** *
91012 GCTGACGTGGTGATGATGTGGCA
1 GCTGACGTGGTGATAACATGACA
*
91035 GTTGACGTGGTGATAACATGACA
1 GCTGACGTGGTGATAACATGACA
91058 GCTGACGTGG
1 GCTGACGTGG
91068 CATATGACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.25
Consensus pattern (23 bp):
GCTGACGTGGTGATAACATGACA
Found at i:91876 original size:11 final size:11
Alignment explanation
Indices: 91854--91890 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
91844 TTTTACCATA
91854 TTAAATTTTATT
1 TTAAA-TTTATT
91866 TTAAATTTATT
1 TTAAATTTATT
91877 TTAAATTT-TT
1 TTAAATTTATT
91887 TTAA
1 TTAA
91891 TCTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 6 0.24
11 14 0.56
12 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:93368 original size:17 final size:17
Alignment explanation
Indices: 93346--93379 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
93336 AAATGTTTAT
93346 TTTCCTTTTTCAACTCG
1 TTTCCTTTTTCAACTCG
93363 TTTCCTTTTTCAACTCG
1 TTTCCTTTTTCAACTCG
93380 CCTTGCTTGA
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:0.12, C:0.29, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTCCTTTTTCAACTCG
Found at i:97351 original size:33 final size:33
Alignment explanation
Indices: 97274--97388 Score: 167
Period size: 33 Copynumber: 3.5 Consensus size: 33
97264 AAGGTCTTTA
*
97274 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTTTTTG
*
97308 TGTTTCAAGAGGAACAATTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
* * **
97341 CGTTTTAAGAGAAACAATTTCAAATATTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
97374 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
97389 TGTTTCCAGG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 48 0.67
34 24 0.33
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:97489 original size:35 final size:35
Alignment explanation
Indices: 97440--97580 Score: 153
Period size: 35 Copynumber: 4.0 Consensus size: 35
97430 CAAAGGTTGG
97440 TGTTTCAAGAGAAACTGTCTC-AGAGAGACAAAATT
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAATT
**
97475 TGTTTCAAAGGAAACCATCTCAAGAGAGACAAAATT
1 TGTTTC-AAGGAAACTGTCTCAAGAGAGACAAAATT
97511 TGTTTCAA-G-AACTGTCTCAAGAGAGACAAAATCTT
1 TGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA--TT
** ** *
97546 TGTTTTGAGAGAAACCATCTCAAGCGAGACAAAAT
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAAT
97581 CTTTTGTTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
33 20 0.22
34 1 0.01
35 25 0.28
36 24 0.27
37 1 0.01
38 19 0.21
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:97534 original size:33 final size:36
Alignment explanation
Indices: 97440--97542 Score: 144
Period size: 36 Copynumber: 3.0 Consensus size: 36
97430 CAAAGGTTGG
97440 TGTTTC-AAGAGAAACTGTCTC-AGAGAGACAAAATT
1 TGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAATT
**
97475 TGTTTCAAAGGAAACCATCTCAAGAGAGACAAAATT
1 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATT
97511 TGTTTC-AA-G-AACTGTCTCAAGAGAGACAAAAT
1 TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAAT
97543 CTTTGTTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 21 0.34
34 1 0.02
35 17 0.27
36 23 0.37
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (36 bp):
TGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:97576 original size:38 final size:38
Alignment explanation
Indices: 97447--97607 Score: 142
Period size: 36 Copynumber: 4.4 Consensus size: 38
97437 TGGTGTTTCA
** *
97447 AGAGAAACTGTCTC-AGAGAGACAAAA--TTTG-TTTC
1 AGAGAAACCATCTCAAGAGAGACAAAATCTTTGTTTTG
* *
97481 AAAGGAAACCATCTCAAGAGAGACAAAA--TTTG-TTTC
1 AGA-GAAACCATCTCAAGAGAGACAAAATCTTTGTTTTG
**
97517 A-AG-AACTGTCTCAAGAGAGACAAAATCTTTGTTTTG
1 AGAGAAACCATCTCAAGAGAGACAAAATCTTTGTTTTG
* *
97553 AGAGAAACCATCTCAAGCGAGACAAAATCTTTTGTTTCG
1 AGAGAAACCATCTCAAGAGAGACAAAATC-TTTGTTTTG
* *
97592 AGGGAAACAATCTCAA
1 AGAGAAACCATCTCAA
97608 AGGCGACCGA
Statistics
Matches: 107, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
33 20 0.19
34 3 0.03
35 14 0.13
36 25 0.23
37 2 0.02
38 21 0.20
39 22 0.21
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (38 bp):
AGAGAAACCATCTCAAGAGAGACAAAATCTTTGTTTTG
Found at i:100748 original size:21 final size:21
Alignment explanation
Indices: 100706--100748 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
100696 TTTCTGGGCT
* *
100706 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
100727 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
100748 A
1 A
100749 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:102312 original size:103 final size:103
Alignment explanation
Indices: 102087--102304 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
102077 GTCGAGGGTC
* * * *
102087 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGATGAGACACATAC
* *
102152 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
102190 TATGTGGTCCTTCGGGACATATATGTATTCTTTTAAACATGTGTGAAGTCTGATGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGATGAGACACATAC
*
102255 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
102293 TATGTGGTCCTT
1 TATGTGGTCCTT
102305 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGATGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:102354 original size:23 final size:23
Alignment explanation
Indices: 102321--102388 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
102311 ATTATTATAT
102321 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
102344 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
102367 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
102389 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:106027 original size:23 final size:22
Alignment explanation
Indices: 105983--106027 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
105973 AATCTCATAG
*
105983 GGGAACCAATTCCCCCACAGGA
1 GGGAACCAATTCCCCCAAAGGA
*
106005 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCAATTCCCCC-AAAGGA
106028 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.11
Consensus pattern (22 bp):
GGGAACCAATTCCCCCAAAGGA
Found at i:107499 original size:101 final size:101
Alignment explanation
Indices: 107317--107529 Score: 347
Period size: 101 Copynumber: 2.1 Consensus size: 101
107307 GTCGAGGGTC
*
107317 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAATACATAC
1 TATGTGG-TCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATAC
* *
107382 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
107420 TATGTGGTCATTCGGGAC-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTC-TTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACT
*
107484 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
107521 TATGTGGTC
1 TATGTGGTC
107530 CTTATGGACA
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
101 87 0.84
102 2 0.02
103 15 0.14
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (101 bp):
TATGTGGTCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:107582 original size:23 final size:23
Alignment explanation
Indices: 107549--107611 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
107539 ATTATTATAT
*
107549 GGCACTACGGTGCAATTCTATGC
1 GGCACTCCGGTGCAATTCTATGC
* *
107572 GGCGCTCCGGTGCAATTCTATGT
1 GGCACTCCGGTGCAATTCTATGC
* *
107595 GGCATTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
107612 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTATGC
Found at i:111930 original size:7 final size:7
Alignment explanation
Indices: 111918--111956 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
111908 GTGGGCCTAT
111918 AAAAATA
1 AAAAATA
111925 AAAAATAA
1 AAAAAT-A
111933 AAAAATA
1 AAAAATA
111940 AAAAAT-
1 AAAAATA
*
111946 AATAATA
1 AAAAATA
111953 AAAA
1 AAAA
111957 TAATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:111938 original size:15 final size:15
Alignment explanation
Indices: 111918--111947 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
111908 GTGGGCCTAT
111918 AAAAATAAAAAATAA
1 AAAAATAAAAAATAA
111933 AAAAATAAAAAATAA
1 AAAAATAAAAAATAA
111948 TAATAAAAAT
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:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:111957 original size:12 final size:12
Alignment explanation
Indices: 111916--111965 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
111906 TGGTGGGCCT
*
111916 ATAAAAATAAAAA
1 ATAAAAAT-AATA
111929 ATAAAAA-AAT-
1 ATAAAAATAATA
111939 A-AAAAATAATA
1 ATAAAAATAATA
*
111950 ATAAAAATAATT
1 ATAAAAATAATA
111962 ATAA
1 ATAA
111966 TAGTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 5 0.16
10 4 0.12
11 3 0.09
12 13 0.41
13 7 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:122300 original size:30 final size:30
Alignment explanation
Indices: 122266--122326 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
122256 CGTCGTAAGG
122266 ATGAAGAAGTGTTGGAAGGGTTGAAACCTC
1 ATGAAGAAGTGTTGGAAGGGTTGAAACCTC
*
122296 ATGAAGAAGTGTTGGAAGGGTTGGAACCTC
1 ATGAAGAAGTGTTGGAAGGGTTGAAACCTC
122326 A
1 A
122327 CTCAAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.34, T:0.23
Consensus pattern (30 bp):
ATGAAGAAGTGTTGGAAGGGTTGAAACCTC
Found at i:135204 original size:16 final size:16
Alignment explanation
Indices: 135183--135214 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
135173 TACTATTCAA
135183 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
135199 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
135215 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
GTGAATAGTGAAATTT
Found at i:142200 original size:60 final size:60
Alignment explanation
Indices: 142123--142237 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
142113 AATAATTGGG
*
142123 TGATAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACATCCTATAGAAAAA
1 TGATAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAGAAAAA
* * * * **
142183 TGATCATTTTGTAACTTTTGATAGTTGAGAGACTCCACAAAGTAACACCCTATAG
1 TGATAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAG
142238 TCGAGGGACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (60 bp):
TGATAATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAACAACACCCTATAGAAAAA
Found at i:146500 original size:19 final size:21
Alignment explanation
Indices: 146478--146534 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
146468 ATAACCCCAG
146478 GGGGGTATCGATTCCCC-T-A
1 GGGGGTATCGATTCCCCTTAA
* * *
146497 GGGGGAATTGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTT-AA
146519 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
146535 TCTGCCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 14 0.48
20 1 0.03
22 14 0.48
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTTAA
Found at i:157330 original size:19 final size:19
Alignment explanation
Indices: 157306--157343 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
157296 ATTGGAATCG
157306 AATATTAAAATATTGATTT
1 AATATTAAAATATTGATTT
* *
157325 AATATTGAAATGTTGATTT
1 AATATTAAAATATTGATTT
157344 GGACTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
AATATTAAAATATTGATTT
Found at i:161585 original size:19 final size:19
Alignment explanation
Indices: 161558--161595 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
161548 ATTGGAATCA
161558 AATAGTAAAATATTGATTT
1 AATAGTAAAATATTGATTT
* *
161577 AATATTAAAATGTTGATTT
1 AATAGTAAAATATTGATTT
161596 TGGACTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
AATAGTAAAATATTGATTT
Done.