Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004612.1 Hibiscus syriacus cultivar Beakdansim tig00010317_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: 79459
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1359 original size:190 final size:193
Alignment explanation
Indices: 1022--1558 Score: 765
Period size: 190 Copynumber: 2.7 Consensus size: 193
1012 TATTTAAATT
*
1022 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTACACATATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATT-AAAAAGTGTCGATACATGTTG-----ATATTCTCTCATAAAATCAG-
*
1087 ATATTTATACCTGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
59 -TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
1152 GGATCGATACATTTTATAAATGTATCGACACTTTATGGTT-CCCCCCTTTTAGCATTCATTCGGG
123 GGATCGATACATTTTATAAATGTATCGACACTTTATGGTTGCACCCCTTTTAGCATTCATTCGGG
1216 ACC-AA
188 ACCAAA
*
1221 CGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGATATTCTCTCATAAAATC-GTATTTAT
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGATATTCTCTCATAAAATCAGTATTTAT
* * *
1285 ATCGGTTACATTGAAAATTTATCTATTACATTATACTTATGGATGCATATGTTTCTAGGATCGAT
66 ACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGGATCGAT
* * * * *
1350 ACTTTTTATAAATGTATCGACACTTTATTGTTGCACCCTTTTTGGCATTCATTCTGGACCAAA
131 ACATTTTATAAATGTATCGACACTTTATGGTTGCACCCCTTTTAGCATTCATTCGGGACCAAA
* *
1413 AGTATCGACACAAAATTTAAAAAGTGCCAATACATGTTGTAGACCTATTCTCTCATAAAATCAAT
1 AGTATCGACACAAAA-TTAAAAAGTGTCGATACATG-T-T-GA--TATTCTCTCATAAAATC-A-
*
1478 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
58 GTATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
1543 GGATCGATAAATTTTA
123 GGATCGATACATTTTA
1559 CCTATTATAT
Statistics
Matches: 307, Mismatches: 20, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
190 98 0.32
191 23 0.07
192 17 0.06
193 36 0.12
194 1 0.00
195 1 0.00
196 2 0.01
198 38 0.12
199 16 0.05
201 75 0.24
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (193 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGATATTCTCTCATAAAATCAGTATTTAT
ACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTGGGATCGAT
ACATTTTATAAATGTATCGACACTTTATGGTTGCACCCCTTTTAGCATTCATTCGGGACCAAA
Found at i:3690 original size:33 final size:33
Alignment explanation
Indices: 3644--3709 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3634 CATATTAAGA
*
3644 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
3677 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
3710 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:3768 original size:21 final size:21
Alignment explanation
Indices: 3743--3786 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3733 CCCCTTATGC
3743 CTCTCAAGTGTATCTTCAACT
1 CTCTCAAGTGTATCTTCAACT
* * *
3764 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCAACT
3785 CT
1 CT
3787 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCAACT
Found at i:3889 original size:15 final size:15
Alignment explanation
Indices: 3869--3901 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3859 ACTCTGTTTT
3869 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
*
3884 CCCTCACTGTCATCC
1 CCCTCACCGTCATCC
3899 CCC
1 CCC
3902 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.61, G:0.06, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:6386 original size:182 final size:182
Alignment explanation
Indices: 6013--6432 Score: 540
Period size: 182 Copynumber: 2.3 Consensus size: 182
6003 GGTAGCGCTT
* * *
6013 TACCGGTTTTATAATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTATAAAATATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCG
6078 ACACTTTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
66 ACACTTTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
* * ** *
6143 TACCGACACTTTAAATATATCTGGTAGCTCTTTATCGATTTTATCATTTCGA
131 TACCGACACGTTAAATATATCCGGTAGCGATTTATCGATATTATCATTTCGA
* * * *
6195 TATCGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATTGATACATTTTTATAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCG
* * * * * *
6260 ACACTTTATAGGCGTTAAAATTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAACG
66 ACACTTTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
* * * * *
6325 TATCGACACGTTCAATATATCCGGTAAG-GATTTA-CAGGTATTGTCTTTTCG-
131 TACCGACACGTTAAATATATCCGGT-AGCGATTTATC-GATATTATCATTTCGA
* * * *
6376 TGACCGGTTTTATCGATATTTTTACCTGTTATATTGATATGAATCGATACATTTTTA
1 T-ACCGGTTTTATC-ATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTA
6433 ATTTGGATCG
Statistics
Matches: 204, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
181 2 0.01
182 163 0.80
183 39 0.19
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCG
ACACTTTATAAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
TACCGACACGTTAAATATATCCGGTAGCGATTTATCGATATTATCATTTCGA
Found at i:7289 original size:20 final size:20
Alignment explanation
Indices: 7264--7301 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7254 GGTAGCGCTT
*
7264 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATAATTTTGA
7284 TACCGGTTTTATAATTTT
1 TACCGGTTTTATAATTTT
7302 TTTACCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (20 bp):
TACCGGTTTTATAATTTTGA
Found at i:7307 original size:20 final size:20
Alignment explanation
Indices: 7262--7307 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
7252 CCGGTAGCGC
*
7262 TTTACCGGTTTTATCATTTT
1 TTTACCGGTTTTATAATTTT
**
7282 GATACCGGTTTTATAATTTT
1 TTTACCGGTTTTATAATTTT
7302 TTTACC
1 TTTACC
7308 TGTTATATCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATAATTTT
Found at i:7470 original size:182 final size:182
Alignment explanation
Indices: 7236--7703 Score: 634
Period size: 182 Copynumber: 2.6 Consensus size: 182
7226 TGAAAGTATA
* * * *
7236 GACACTTTAAACATATCCGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTTTATAATTT
1 GACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATAATAT
* *
7301 TTTTACCTGTTATATCGTTTTGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
66 TTTTACATGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
*
7366 AAACTGCTTT-TCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACC
131 AAACTG-TTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
* * * *
7418 GACACTTTAAATATATTCGGTAACTCTTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATAT
1 GACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATAATAT
* * * * *
7483 TTTTACTTGTTATATCATTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGTTA
66 TTTTACATGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
* *
7548 AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTAGATTAAAGTATC
131 AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
* * * * * * * * *
7600 GACACGTTCAATATATCCGGTAAGGATTTACCGGTATTGTCTTTTCG-TGGCCGGTTTTATCGAT
1 GACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCGAT-ACCGGTTTTAT-AAT
* *
7664 ATTTTTACATGTTATATTGATATGGATCGATACATTTTTA
64 ATTTTTACATGTTATATCGTTATGGATCGATACATTTTTA
7704 ATTTGGATCG
Statistics
Matches: 250, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
181 4 0.02
182 209 0.84
183 37 0.15
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (182 bp):
GACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCGATACCGGTTTTATAATAT
TTTTACATGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
AAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTAGATTAAAGTACC
Found at i:8748 original size:20 final size:20
Alignment explanation
Indices: 8701--8748 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
8691 ATCCGGTAGC
8701 TCTTTACCGGTTTTATCATT
1 TCTTTACCGGTTTTATCATT
**
8721 TCAATACCGGTTTTATCATAT
1 TCTTTACCGGTTTTATCAT-T
8742 T-TTTACC
1 TCTTTACC
8749 TGTTATATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.50
Consensus pattern (20 bp):
TCTTTACCGGTTTTATCATT
Found at i:8817 original size:182 final size:182
Alignment explanation
Indices: 8487--8962 Score: 686
Period size: 182 Copynumber: 2.6 Consensus size: 182
8477 CGTACTTATG
* ** *
8487 AAAGTATCAACACTTTAAATATATTTGGTAGCGCTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATACCGGTTT
* *
8552 TATCATATTTTTACATGTTATATCGTTGTGGATCGATGCATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
*
8617 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGGTACTTATATT
131 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * *
8669 AAAGTACCGACACTTTAAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATACCGGTTT
8734 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* * * *
8799 AGGCGTTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
131 AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * * * **
8851 AAAGTATCGACACATTCAATATATCCGGTAAG-GATTTACCGGTATTGTC-TTTTTGTGACCGGT
1 AAAGTATCGACACTTTAAATATATCCGGT-AGCGCTTTACCGGTTTTATCATTTTAAT-ACCGGT
* * * *
8914 TTTATCGATATTTTTACCTATTATATTGATATGGATCGATACATTTTTA
64 TTTATC-ATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTA
8963 ATTTAGATCG
Statistics
Matches: 263, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 4 0.02
182 219 0.83
183 40 0.15
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
AAGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
Found at i:9939 original size:3 final size:3
Alignment explanation
Indices: 9931--9995 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
9921 GAGACCATTA
9931 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
9979 TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TT
9996 ATTTTATTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:23044 original size:7 final size:8
Alignment explanation
Indices: 22989--23043 Score: 56
Period size: 9 Copynumber: 6.2 Consensus size: 8
22979 GAAAAAATTG
22989 AAATGAAAA
1 AAAT-AAAA
22998 AAATCAAAA
1 AAAT-AAAA
23007 AGAATAAAA
1 A-AATAAAA
*
23016 AGAAGAATAA
1 A-AATAA-AA
23026 AAATAAAA
1 AAATAAAA
23034 AAATAAAA
1 AAATAAAA
23042 AA
1 AA
23044 TGAGGAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 12 0.29
9 23 0.56
10 6 0.15
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (8 bp):
AAATAAAA
Found at i:23061 original size:18 final size:19
Alignment explanation
Indices: 23040--23080 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
23030 AAAAAAATAA
*
23040 AAAATGAGGAAAAG-AAAG
1 AAAATGAGAAAAAGAAAAG
23058 AAAA-GAGAAAAAGAAAAG
1 AAAATGAGAAAAAGAAAAG
23076 AAAAT
1 AAAAT
23081 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (19 bp):
AAAATGAGAAAAAGAAAAG
Found at i:24676 original size:134 final size:134
Alignment explanation
Indices: 24380--24703 Score: 427
Period size: 135 Copynumber: 2.4 Consensus size: 134
24370 GCAAATCGAA
* * * * * *
24380 CTCATTTCAATGTTCCCTAAAGAATAGTAGAATGAATCAACATTTCCAAATCTAATTTTCCTTGA
1 CTCAATTCAATATTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGATCTGATTTTCCTTGA
** ** *
24445 AGAAACAGCTGAACAAATCCCTTGTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTAGAACAAG
66 AGAAACAGAGGAACAAATCCC-TAATTTTCCAGATTTGATCTTCCCTGAAGAACAGTAGAACAAG
*
24510 TCTGT
130 TCTGC
* * *
24515 CTCAATTCAATCTTCCCTGAAGAACAGT-GAAGTGAATCAACATCTCTAGATCTGATTTTCCTTG
1 CTCAATTCAATATTCCCTGAAGAACAGTAGAA-TGAATCAACATTTCCAGATCTGATTTTCCTTG
* * * *
24579 AAGAATCAGAGGAACAGATCCC-AATTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGGACAA
65 AAGAAACAGAGGAACAAATCCCTAATTTTCCAGATTTGATCTTCCCTGAAGAA-CAGTAGAACAA
24643 GTCTGC
129 GTCTGC
*
24649 CTCAATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGA
1 CTCAATTCAATATTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGATCTGA
24704 CCTACCCTGA
Statistics
Matches: 165, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
133 27 0.16
134 65 0.39
135 73 0.44
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (134 bp):
CTCAATTCAATATTCCCTGAAGAACAGTAGAATGAATCAACATTTCCAGATCTGATTTTCCTTGA
AGAAACAGAGGAACAAATCCCTAATTTTCCAGATTTGATCTTCCCTGAAGAACAGTAGAACAAGT
CTGC
Found at i:28619 original size:3 final size:3
Alignment explanation
Indices: 28613--28643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28603 AAAAAAAAAT
28613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28644 ATTAACTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28701 original size:17 final size:17
Alignment explanation
Indices: 28676--28709 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28666 AGGAGAGAAG
28676 AAAAGAAAAAAATAAAT
1 AAAAGAAAAAAATAAAT
* *
28693 AAAATAAAAAGATAAAT
1 AAAAGAAAAAAATAAAT
28710 TGAAAAATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAGAAAAAAATAAAT
Found at i:30111 original size:3 final size:3
Alignment explanation
Indices: 30103--30169 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
30093 TTAAATAAGA
* * *
30103 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30148 AAAT AAT AAT AAT AAT -AT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT A
30170 GTATAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30169 original size:33 final size:33
Alignment explanation
Indices: 30103--30189 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 33
30093 TTAAATAAGA
*
30103 AATAATAATAATAAATAAAATAATTACACTAAT
1 AATAATAATAATAAATAAAATAATAACACTAAT
*
30136 AATAATAATAATAAATAATAATAATAATA-TAAT
1 AATAATAATAATAAATAA-AATAATAACACTAAT
30169 AGTATAATATATATATAAATA
1 A--ATAATA-ATA-ATAAATA
30190 TTTTTTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 23 0.49
34 8 0.17
35 6 0.13
36 3 0.06
37 7 0.15
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (33 bp):
AATAATAATAATAAATAAAATAATAACACTAAT
Found at i:30175 original size:13 final size:14
Alignment explanation
Indices: 30104--30179 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 14
30094 TAAATAAGAA
30104 ATAATAATAATAAAT
1 ATAATAATAAT-AAT
*
30119 AAAATAATTACACTAAT
1 ATAATAA-TA-A-TAAT
30136 AATAATAATAATAA-
1 -ATAATAATAATAAT
30150 ATAATAATAATAAT
1 ATAATAATAATAAT
*
30164 ATAATAGT-ATAAT
1 ATAATAATAATAAT
30177 ATA
1 ATA
30180 TATATAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 21 0.40
14 7 0.13
15 9 0.17
16 3 0.06
17 6 0.11
18 7 0.13
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:30259 original size:35 final size:35
Alignment explanation
Indices: 30171--30259 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 35
30161 AATATAATAG
30171 TATAATATATATAT--AAATATTTTTTAAAAAACA
1 TATAATATATATATAAAAATATTTTTTAAAAAACA
* * ** **
30204 TATAATATATAATTTCAAAAATGTTTTTTTTAAATTA
1 TATAATATAT-ATAT-AAAAATATTTTTTAAAAAACA
30241 TATAATATATATATAAAAA
1 TATAATATATATATAAAAA
30260 AAATGCTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
33 10 0.22
34 3 0.07
35 5 0.11
36 3 0.07
37 24 0.53
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (35 bp):
TATAATATATATATAAAAATATTTTTTAAAAAACA
Found at i:30313 original size:19 final size:20
Alignment explanation
Indices: 30280--30319 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
30270 AAAAAAAATT
*
30280 ATATATTATATATTTTTAAA
1 ATATATTATACATTTTTAAA
30300 ATATA-TATACATTTTTAAA
1 ATATATTATACATTTTTAAA
30319 A
1 A
30320 ACTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTATACATTTTTAAA
Found at i:30350 original size:11 final size:11
Alignment explanation
Indices: 30334--30358 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30324 TATAATATAT
30334 AAATGTTTTCA
1 AAATGTTTTCA
30345 AAATGTTTTCA
1 AAATGTTTTCA
30356 AAA
1 AAA
30359 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:30422 original size:38 final size:39
Alignment explanation
Indices: 30311--30449 Score: 132
Period size: 38 Copynumber: 3.6 Consensus size: 39
30301 TATATATACA
* *
30311 TTTTTAAAAACTATATA-ATATATAAATGTTTT-CAAAATG
1 TTTTTCAAAACTATATATATATAT-AA-GTTTTAAAAAATG
*
30350 -TTTTCAAAACTATATATCATATA-AA-TTTTCAAAAAAGG
1 TTTTTCAAAACTATATAT-ATATATAAGTTTT-AAAAAATG
*
30388 TTTTTCAAAACTATATAT-TATATACGTTTTAAAAAATG
1 TTTTTCAAAACTATATATATATATAAGTTTTAAAAAATG
*
30426 CTTTT-AAATA-TATATATATATATA
1 TTTTTCAAA-ACTATATATATATATA
30450 TATATATATA
Statistics
Matches: 85, Mismatches: 6, Indels: 19
0.77 0.05 0.17
Matches are distributed among these distances:
36 4 0.05
37 14 0.16
38 41 0.48
39 21 0.25
40 5 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (39 bp):
TTTTTCAAAACTATATATATATATAAGTTTTAAAAAATG
Found at i:30438 original size:2 final size:2
Alignment explanation
Indices: 30433--30472 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
30423 ATGCTTTTAA
30433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30473 CATTTTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30473 original size:61 final size:58
Alignment explanation
Indices: 30399--30512 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 58
30389 TTTTCAAAAC
* *
30399 TATATATTATATACGTTTTAAAAAATGCTTTT-AAATA-TATATATATATATATATATATA
1 TATATATTATATACATTTT-AAAAATG-TTTTCAAAGACTATATAT-TATATATATATATA
*
30458 TATATATATATTATACATTTTCAAAATGTTTTCAAAGACTATATATTATATATAT
1 TATATAT-TA-TATACATTTTAAAAATGTTTTCAAAGACTATATATTATATATAT
30513 TTTTAAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
59 11 0.23
60 21 0.44
61 16 0.33
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (58 bp):
TATATATTATATACATTTTAAAAATGTTTTCAAAGACTATATATTATATATATATATA
Found at i:31360 original size:81 final size:81
Alignment explanation
Indices: 31201--31894 Score: 723
Period size: 81 Copynumber: 8.4 Consensus size: 81
31191 TTATTGACAA
* * * * * * * * * *
31201 ATAACCCTTCTTGTCTTGAGCTATGTTGTAAACGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
** *
31266 CGGGGGTC-CTTGGCAG
65 CGAAGGTCTTTTGGCAG
* *
31282 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
31347 GAAGGTCTTTTGGCGACAG
66 GAAGGTCTTTT-G-G-CAG
* * * * *
31366 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
* ** *
31431 TGGGGGTC-CTTGGCAG
65 CGAAGGTCTTTTGGCAG
* * *
31447 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
*
31512 AAAGGTCTTTTGTTAGCAG
66 GAAGGTCTTTTG---GCAG
* * * *
31531 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGT-GATCGAAC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG-TCGAAC
**
31595 TCGGGGGTC-TTTGGCAG
64 TCGAAGGTCTTTTGGCAG
* *
31612 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
31677 GAAGGTCTTTTGGTCACAG
66 GAAGGTCTTTTGG---CAG
* * * * * * * *
31696 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTCGAACT
**
31761 CGGGGGTC-TTTGGCAG
65 CGAAGGTCTTTTGGCAG
* * *
31777 ATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCTTCGAAGCTGAGCGTAGTCGAACT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGTCGAACT
*
31842 CAAAGGTCTTTTGTTAGCAG
65 CGAAGGTCTTTTG---GCAG
* *
31862 ATAACCCTTCTTGACTTAAGTTATACTGCAAAT
1 ATAACCCTTCTTGACTTAAGCTATGCTGCAAAT
31895 AGTTTGTTAA
Statistics
Matches: 505, Mismatches: 86, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
80 80 0.16
81 180 0.36
82 6 0.01
83 2 0.00
84 126 0.25
85 111 0.22
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
ATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTTGGCAG
Found at i:31473 original size:165 final size:164
Alignment explanation
Indices: 31196--31894 Score: 1067
Period size: 165 Copynumber: 4.2 Consensus size: 164
31186 TAATTTTATT
* * * * ** * * * * *
31196 GACAAATAACCCTTCTTGTCTTGAGCTATGTTGTAAACGATATGACCTCGAAGTTGAGTGTAATC
1 GACAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
*
31261 GAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTG
66 GAACTCGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
*
31326 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGC
131 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-GC
31361 GACAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
1 GACAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
*
31426 GAACTTGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
66 GAACTCGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
*
31491 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
131 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGC
* *
31525 TAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTGAT
1 GA-CAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* *
31590 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTT
65 CGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
31655 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG-
130 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGC
* * * * *
31689 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 G--ACAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* *
31754 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCT
64 TCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
* *
31819 TCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
129 T-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGC
*
31856 TAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
1 GA-CAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
31895 AGTTTGTTAA
Statistics
Matches: 490, Mismatches: 38, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
164 2 0.00
165 424 0.87
166 64 0.13
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
GACAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
GAACTCGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGC
Found at i:31628 original size:330 final size:331
Alignment explanation
Indices: 31241--31894 Score: 1177
Period size: 330 Copynumber: 2.0 Consensus size: 331
31231 AACGATATGA
*
31241 CCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
31306 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-CGACAGATAA
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC-ACAGATAA
* *
31370 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
130 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
* *
31435 GGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GGAGCTGAG
195 GGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCTTCGAAGCTGAG
31499 CGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
260 CGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
31564 GATGTGC
325 GATGTGC
* *
31571 CCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
31636 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAAC
* * * *
31701 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGG
131 CCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGG
*
31766 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCTTCGAAGCTGAGC
196 GTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCTTCGAAGCTGAGC
31831 GTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
261 GTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAAT
31895 AGTTTGTTAA
Statistics
Matches: 310, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
330 236 0.76
331 74 0.24
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (331 bp):
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAAC
CCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGG
GTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATCCTGCAAATGATGTGCCTTCGAAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
ATGTGC
Found at i:35281 original size:18 final size:19
Alignment explanation
Indices: 35241--35285 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
35231 AGTTAATGTG
35241 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
35260 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
35278 AATGCAAA
1 AATGCAAA
35286 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:37001 original size:3 final size:3
Alignment explanation
Indices: 36995--37022 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
36985 AAAAAAAAAT
36995 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
37023 ATTAACTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:37080 original size:17 final size:17
Alignment explanation
Indices: 37055--37088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
37045 AGGAGAGAAG
37055 AAAAGAAAAAAATAAAT
1 AAAAGAAAAAAATAAAT
* *
37072 AAAATAAAAAGATAAAT
1 AAAAGAAAAAAATAAAT
37089 TGAAAAATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAGAAAAAAATAAAT
Found at i:37159 original size:17 final size:18
Alignment explanation
Indices: 37134--37176 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
37124 GTAAAAAAAC
37134 AAAATAAACAA-AAGTAAT
1 AAAATAAACAATAA-TAAT
37152 AAAA-AAACAATAATAAT
1 AAAATAAACAATAATAAT
37169 AAAATAAA
1 AAAATAAA
37177 TTTAGGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAACAATAATAAT
Found at i:37206 original size:16 final size:15
Alignment explanation
Indices: 37185--37225 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
37175 AATTTAGGGC
37185 AAATAAGATAAAAATG
1 AAATAA-ATAAAAATG
*
37201 AAATAAATAAAAATA
1 AAATAAATAAAAATG
37216 ATAATAAATA
1 A-AATAAATA
37226 TACTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
AAATAAATAAAAATG
Found at i:37216 original size:10 final size:11
Alignment explanation
Indices: 37185--37256 Score: 53
Period size: 12 Copynumber: 6.6 Consensus size: 11
37175 AATTTAGGGC
37185 AAATAAGATA-A
1 AAATAA-ATATA
*
37196 AAATGAA-AT-
1 AAATAAATATA
*
37205 AAATAAAAATA
1 AAATAAATATA
37216 ATAATAAATATA
1 A-AATAAATATA
* *
37228 CTAATAAATATG
1 -AAATAAATATA
37240 AAATAAA-ATA
1 AAATAAATATA
37250 AAATAAA
1 AAATAAA
37257 CAACATGAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
9 7 0.14
10 12 0.24
11 12 0.24
12 18 0.37
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (11 bp):
AAATAAATATA
Found at i:38488 original size:3 final size:3
Alignment explanation
Indices: 38480--38540 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
38470 TTAAATAAGA
* * *
38480 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
38526 AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
38541 GTATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38546 original size:13 final size:14
Alignment explanation
Indices: 38481--38555 Score: 77
Period size: 13 Copynumber: 5.5 Consensus size: 14
38471 TAAATAAGAA
38481 ATAATAATAATAA-
1 ATAATAATAATAAT
* *
38494 ATAA-AATAATTAC
1 ATAATAATAATAAT
38507 ACTAATAATAATAAT
1 A-TAATAATAATAAT
38522 A-AATAATAATAAT
1 ATAATAATAATAAT
*
38535 ATAATAGT-ATAAT
1 ATAATAATAATAAT
38548 ATATATAA
1 ATA-ATAA
38556 ATATTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
12 7 0.13
13 26 0.50
14 11 0.21
15 8 0.15
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:38681 original size:19 final size:20
Alignment explanation
Indices: 38648--38687 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
38638 AAAAAAAATT
*
38648 ATATATTATATATTTTTAAA
1 ATATATTATACATTTTTAAA
38668 ATATA-TATACATTTTTAAA
1 ATATATTATACATTTTTAAA
38687 A
1 A
38688 ACTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTATACATTTTTAAA
Found at i:38718 original size:11 final size:11
Alignment explanation
Indices: 38702--38726 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38692 TATAATATAT
38702 AAATGTTTTCA
1 AAATGTTTTCA
38713 AAATGTTTTCA
1 AAATGTTTTCA
38724 AAA
1 AAA
38727 CTATATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:38773 original size:35 final size:36
Alignment explanation
Indices: 38686--38807 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 36
38676 ACATTTTTAA
*
38686 AAACTATATAATATATAAATGTTTTC--AAAATGTTTTC
1 AAACTATAT-ATATATAAA--TTTTCAAAAAAGGTTTTC
*
38723 AAAACTATAT-CATATAAATTTTCAAAAAAGGTTTTC
1 -AAACTATATATATATAAATTTTCAAAAAAGGTTTTC
** *
38759 AAACTATAT-TATATACGTTTT-AAAAAATGCTTTT-
1 AAACTATATATATATAAATTTTCAAAAAA-GGTTTTC
38793 AAA-TATATATATATA
1 AAACTATATATATATA
38808 TATATATATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
33 5 0.07
34 20 0.27
35 23 0.31
36 17 0.23
38 9 0.12
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (36 bp):
AAACTATATATATATAAATTTTCAAAAAAGGTTTTC
Found at i:38800 original size:2 final size:2
Alignment explanation
Indices: 38795--38838 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
38785 ATGCTTTTAA
38795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38836 AT A
1 AT A
38839 CATTTTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41634 original size:15 final size:15
Alignment explanation
Indices: 41610--41640 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41600 TGTTTGGTTT
*
41610 GTGGTGGGAGCTTGG
1 GTGGTAGGAGCTTGG
41625 GTGGTAGGAGCTTGG
1 GTGGTAGGAGCTTGG
41640 G
1 G
41641 GCTCCTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.58, T:0.26
Consensus pattern (15 bp):
GTGGTAGGAGCTTGG
Found at i:42460 original size:2 final size:2
Alignment explanation
Indices: 42455--42651 Score: 87
Period size: 2 Copynumber: 101.0 Consensus size: 2
42445 AAAAAATACA
* *
42455 AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * * *
42497 AT A- AT -T AT -T AT A- AG CT AT AT AT AT AA AT -T AT GT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42534 AT GA- ACT AT AT AT AT AA AT -T AT AT AT AT AT AA AT -T AT AT AT
1 AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
42575 GT AT AA ACT AT AA AA AGT AT AT AGT TT AT AA ACT AT A- AT TT AT
1 AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT
42618 AT -T A- 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
42652 TAGTGAATGG
Statistics
Matches: 147, Mismatches: 27, Indels: 42
0.68 0.12 0.19
Matches are distributed among these distances:
1 13 0.09
2 127 0.86
3 7 0.05
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:42499 original size:13 final size:13
Alignment explanation
Indices: 42455--42586 Score: 68
Period size: 15 Copynumber: 9.2 Consensus size: 13
42445 AAAAAATACA
*
42455 ATATATATATA-T
1 ATATATATAAACT
*
42467 ATATATAATATAAGT
1 ATATAT-ATA-AACT
*
42482 TTATATATAAACT
1 ATATATATAAACT
42495 ATATAATTATTATAAGCT
1 ATAT-A-TA-TA-AA-CT
*
42513 ATATATATAAATT
1 ATATATATAAACT
* *
42526 ATGTGTATATGAACT
1 A--TATATATAAACT
*
42541 ATATATATAAATTAT
1 ATATATATAAA--CT
*
42556 ATATATATAAATT
1 ATATATATAAACT
42569 ATATATGTATAAACT
1 ATATA--TATAAACT
42584 ATA
1 ATA
42587 AAAAGTATAT
Statistics
Matches: 93, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
12 6 0.06
13 25 0.27
14 7 0.08
15 42 0.45
16 4 0.04
17 3 0.03
18 6 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:42549 original size:15 final size:14
Alignment explanation
Indices: 42455--42648 Score: 88
Period size: 13 Copynumber: 13.8 Consensus size: 14
42445 AAAAAATACA
42455 ATATATATAT-A-T
1 ATATATATATAACT
*
42467 ATATATAATATAAGT
1 ATATAT-ATATAACT
*
42482 TTATATATA-AACT
1 ATATATATATAACT
42495 ATATAATTATTATAAGCT
1 ATAT-A-TA-TATAA-CT
*
42513 ATATATATA-AATT
1 ATATATATATAACT
* *
42526 ATGTGTATATGAACT
1 ATATATATAT-AACT
*
42541 ATATATATA-AATT
1 ATATATATATAACT
*
42554 ATATATATATAAATT
1 ATATATATAT-AACT
*
42569 ATATATGTATAA--
1 ATATATATATAACT
*
42581 ACTATA-A-A-AAGT
1 A-TATATATATAACT
*
42593 ATATAGTTTATAAACT
1 ATATA-TATAT-AACT
*
42609 ATAATTTATATTAA-T
1 AT-ATATATA-TAACT
42624 ATATATATATATA-T
1 ATATATATATA-ACT
42638 ATATATATATA
1 ATATATATATA
42649 TATTAGTGAA
Statistics
Matches: 142, Mismatches: 17, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
10 2 0.01
11 5 0.04
12 8 0.06
13 36 0.25
14 29 0.20
15 36 0.25
16 14 0.10
17 6 0.04
18 6 0.04
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (14 bp):
ATATATATATAACT
Found at i:42550 original size:28 final size:28
Alignment explanation
Indices: 42455--42574 Score: 109
Period size: 28 Copynumber: 4.2 Consensus size: 28
42445 AAAAAATACA
* *
42455 ATATATATATA-TATATATA-ATATAAGT
1 ATATATATAAATTATATATATATA-AACT
* * *
42482 TTATATATAAACTATATAATTATTATAAGCT
1 ATATATATAAATTATAT-A-TA-TATAAACT
* * *
42513 ATATATATAAATTATGTGTATATGAACT
1 ATATATATAAATTATATATATATAAACT
*
42541 ATATATATAAATTATATATATATAAATT
1 ATATATATAAATTATATATATATAAACT
42569 ATATAT
1 ATATAT
42575 GTATAAACTA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
27 9 0.12
28 41 0.55
29 3 0.04
30 2 0.03
31 16 0.22
32 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (28 bp):
ATATATATAAATTATATATATATAAACT
Found at i:42742 original size:19 final size:20
Alignment explanation
Indices: 42718--42755 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42708 TTGATTTTAT
42718 TTGGG-AATTTAGAGGGAAA
1 TTGGGAAATTTAGAGGGAAA
*
42737 TTGGGAAATTTAGATGGAA
1 TTGGGAAATTTAGAGGGAA
42756 TAGAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGGGAAATTTAGAGGGAAA
Found at i:43183 original size:21 final size:21
Alignment explanation
Indices: 43145--43206 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
43135 AGTTTATAGA
*
43145 AACCTTAAA-CCTTAAACTATG
1 AACCCTAAACCCTT-AACTATG
* *
43166 AACCCTAAACCCTTAACTCTT
1 AACCCTAAACCCTTAACTATG
* * *
43187 AATCCTAATCCCTGAACTAT
1 AACCCTAAACCCTTAACTAT
43207 ATATGTAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (21 bp):
AACCCTAAACCCTTAACTATG
Found at i:43265 original size:13 final size:13
Alignment explanation
Indices: 43247--43271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43237 ACTATGTATA
43247 ATATATATATAAC
1 ATATATATATAAC
43260 ATATATATATAA
1 ATATATATATAA
43272 ACTATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATATAAC
Found at i:43277 original size:13 final size:15
Alignment explanation
Indices: 43247--43279 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43237 ACTATGTATA
43247 ATATATATATAACAT
1 ATATATATATAACAT
43262 ATATATATA-AAC-T
1 ATATATATATAACAT
43275 ATATA
1 ATATA
43280 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 3 0.17
15 9 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATATATATAACAT
Found at i:43530 original size:34 final size:34
Alignment explanation
Indices: 43491--43573 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
43481 TATGTAACAT
* *
43491 TAACCTATAGTCTATAAACAATAGTTAATATATA
1 TAACCTATAGTATATAAACAATAATTAATATATA
43525 TAACCTATAGTATATAAACAATAATTAATATATA
1 TAACCTATAGTATATAAACAATAATTAATATATA
43559 TAACCTATAGTATAT
1 TAACCTATAGTATAT
43574 GTATACATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (34 bp):
TAACCTATAGTATATAAACAATAATTAATATATA
Found at i:43538 original size:16 final size:16
Alignment explanation
Indices: 43519--43573 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
43509 CAATAGTTAA
43519 TATATATAACCTATAG
1 TATATATAACCTATAG
* *
43535 TATATA-AACAATAATTAA
1 TATATATAAC-CT-A-TAG
43553 TATATATAACCTATAG
1 TATATATAACCTATAG
43569 TATAT
1 TATAT
43574 GTATACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.10
16 14 0.45
17 2 0.06
18 9 0.29
19 3 0.10
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (16 bp):
TATATATAACCTATAG
Found at i:43634 original size:20 final size:21
Alignment explanation
Indices: 43590--43656 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
43580 ATATAAACTA
* *
43590 TATATGTAAATTATAGTACATG
1 TATATATAAATTATA-TATATG
*
43612 TATGTATAAATTATATATA-G
1 TATATATAAATTATATATATG
* *
43632 TATATATAAACTATATATATA
1 TATATATAAATTATATATATG
43653 TATA
1 TATA
43657 ACCTATAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 18 0.47
21 7 0.18
22 13 0.34
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (21 bp):
TATATATAAATTATATATATG
Found at i:43668 original size:20 final size:20
Alignment explanation
Indices: 43518--43676 Score: 67
Period size: 20 Copynumber: 8.4 Consensus size: 20
43508 ACAATAGTTA
43518 ATATATATAACCTATAGTAT
1 ATATATATAACCTATAGTAT
* *
43538 ATA-A-ACAA--TA-ATTA-
1 ATATATATAACCTATAGTAT
43552 ATATATATAACCTATAG--T
1 ATATATATAACCTATAGTAT
* * *
43570 ATATGTAT-ACATATA-AACT
1 ATATATATAACCTATAGTA-T
* **
43589 ATATATGTAAATTATAGTACAT
1 ATATATATAACCTATAGT--AT
* * **
43611 GTATGTATAAATTATA-TAT
1 ATATATATAACCTATAGTAT
*
43630 AGTATATATAAAC--TA-TAT
1 A-TATATATAACCTATAGTAT
43648 ATATATATAACCTATAGTAT
1 ATATATATAACCTATAGTAT
43668 ATATATATA
1 ATATATATA
43677 CAATCTCTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 34
0.67 0.12 0.22
Matches are distributed among these distances:
14 3 0.03
15 4 0.04
16 5 0.05
17 16 0.15
18 18 0.17
19 13 0.12
20 29 0.28
21 1 0.01
22 14 0.13
23 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATATATAACCTATAGTAT
Found at i:45508 original size:14 final size:14
Alignment explanation
Indices: 45432--45510 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 14
45422 TTTTATAATG
*
45432 AACCCTAAATCCTA
1 AACCCTAAACCCTA
* *
45446 AATCCT-AACCATA
1 AACCCTAAACCCTA
*
45459 AACCATAAACCCTA
1 AACCCTAAACCCTA
* * ***
45473 AAACATAAATTATA
1 AACCCTAAACCCTA
**
45487 AAGTCTAAACCCTA
1 AACCCTAAACCCTA
45501 AACCCTAAAC
1 AACCCTAAAC
45511 TATACTTACC
Statistics
Matches: 46, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
13 9 0.20
14 37 0.80
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.20
Consensus pattern (14 bp):
AACCCTAAACCCTA
Found at i:45622 original size:21 final size:21
Alignment explanation
Indices: 45561--45615 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
45551 TATCTTTGTA
* **
45561 ATAAACCCTAAACCCTATTCT
1 ATAAACCTTAAACCCTAAACT
*
45582 ATAAACTTTAAACCCTAAACT
1 ATAAACCTTAAACCCTAAACT
45603 ATAAACCTTAAAC
1 ATAAACCTTAAAC
45616 ACCAAACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAACCTTAAACCCTAAACT
Found at i:48000 original size:16 final size:16
Alignment explanation
Indices: 47979--48015 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
47969 CTTGGTGCTC
47979 TGTCTCTTGTTTTGTG
1 TGTCTCTTGTTTTGTG
47995 TGTCTCTTGTTTTGTG
1 TGTCTCTTGTTTTGTG
48011 TGTCT
1 TGTCT
48016 GCAGGGCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.24, T:0.62
Consensus pattern (16 bp):
TGTCTCTTGTTTTGTG
Found at i:48528 original size:17 final size:17
Alignment explanation
Indices: 48506--48542 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
48496 ATTCGAGTTT
48506 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
48523 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
48540 GAG
1 GAG
48543 CTCAAAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:50451 original size:27 final size:27
Alignment explanation
Indices: 50341--50443 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
50331 CTTGGATGAG
* ** **
50341 AAATTATGAAAATACTTTTATTAGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
*
50368 AAATTATGAAAATACCCTTATGGGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
*
50395 AAATTACGAAAATAACCTTATGGGGTA
1 AAATTACGAAAATACCCTTATGGGGTA
50422 AAATTACGAAAATACCCTTATG
1 AAATTACGAAAATACCCTTATG
50444 TTGTAAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (27 bp):
AAATTACGAAAATACCCTTATGGGGTA
Found at i:54702 original size:24 final size:24
Alignment explanation
Indices: 54657--54743 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
54647 ATGGGTACAT
* ** *
54657 GTGTGCGCGTGCACATGAGTGTGC
1 GTGTGCGTGTGCATGTGTGTGTGC
54681 GTGTGCGTGTGCATGTGTGTGTGCAC
1 GTGTGCGTGTGCATGTGTGTGTG--C
* * *
54707 GTGTGTGTGTCTGCATGGGTGCGTGC
1 GTGTGCGTG--TGCATGTGTGTGTGC
*
54733 GTGTGTGTGTG
1 GTGTGCGTGTG
54744 TGTGAGAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
24 21 0.40
26 19 0.37
28 12 0.23
ACGTcount: A:0.07, C:0.15, G:0.45, T:0.33
Consensus pattern (24 bp):
GTGTGCGTGTGCATGTGTGTGTGC
Found at i:54721 original size:28 final size:28
Alignment explanation
Indices: 54681--54744 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
54671 ATGAGTGTGC
* * * *
54681 GTGTGCGTGTGCATGTGTGTGTGCACGT
1 GTGTGTGTCTGCATGGGTGCGTGCACGT
**
54709 GTGTGTGTCTGCATGGGTGCGTGCGTGT
1 GTGTGTGTCTGCATGGGTGCGTGCACGT
54737 GTGTGTGT
1 GTGTGTGT
54745 GTGAGAGAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.05, C:0.12, G:0.45, T:0.38
Consensus pattern (28 bp):
GTGTGTGTCTGCATGGGTGCGTGCACGT
Found at i:55709 original size:16 final size:17
Alignment explanation
Indices: 55659--55710 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
55649 AAAAAAATTA
55659 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
55676 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
55691 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
55707 AATT
1 AATT
55711 AAATCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:68843 original size:23 final size:24
Alignment explanation
Indices: 68802--68861 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
68792 TGGTACATTA
68802 GTGTACATTCTACGCGGCAC-TTAT
1 GTGTA-ATTCTACGCGGCACTTTAT
* * *
68826 GTTTAATTCTATGTGGCACTTTAT
1 GTGTAATTCTACGCGGCACTTTAT
68850 GTGTAATTCTAC
1 GTGTAATTCTAC
68862 TATTTGTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (24 bp):
GTGTAATTCTACGCGGCACTTTAT
Found at i:73175 original size:6 final size:7
Alignment explanation
Indices: 73159--73188 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
73149 CTATCATTGC
73159 TTTGTTT
1 TTTGTTT
73166 TTTG-TT
1 TTTGTTT
73172 TTTGTTT
1 TTTGTTT
73179 TTTGTTT
1 TTTGTTT
73186 TTT
1 TTT
73189 TTACATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTGTTT
Found at i:73177 original size:13 final size:13
Alignment explanation
Indices: 73159--73187 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
73149 CTATCATTGC
73159 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
73172 TTTGTTTTTTGTT
1 TTTGTTTTTTGTT
73185 TTT
1 TTT
73188 TTTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTGTTTTTTGTT
Found at i:75267 original size:34 final size:34
Alignment explanation
Indices: 75228--75294 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
75218 TGAACATATA
* *
75228 TAAACGAACATGTTCACGAATGTTAAATGAACAC
1 TAAACGAACATGCTCACGAATGTTAAACGAACAC
* **
75262 TAAACGAACGTGCTCGTGAATGTTAAACGAACA
1 TAAACGAACATGCTCACGAATGTTAAACGAACA
75295 TGTTCGCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (34 bp):
TAAACGAACATGCTCACGAATGTTAAACGAACAC
Found at i:75365 original size:23 final size:23
Alignment explanation
Indices: 75337--75404 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
75327 ACTTTTAAAC
*
75337 GAACATTAAACAAACATGTTCAT
1 GAACATTAAACGAACATGTTCAT
* *
75360 GAACATCCAAACGAATATGTTCAT
1 GAACAT-TAAACGAACATGTTCAT
*
75384 GAACATTAAACGAACACGTTC
1 GAACATTAAACGAACATGTTC
75405 GCAAACTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (23 bp):
GAACATTAAACGAACATGTTCAT
Found at i:78752 original size:26 final size:26
Alignment explanation
Indices: 78714--78773 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
78704 TTATATTGTA
*
78714 GCACAGAGGTGCTCAATCATCTTAAT
1 GCACAGAGCTGCTCAATCATCTTAAT
78740 GCACAGAGCTGCTCAATCATCTTAAT
1 GCACAGAGCTGCTCAATCATCTTAAT
*
78766 GCATAGAG
1 GCACAGAG
78774 GTGTCAGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (26 bp):
GCACAGAGCTGCTCAATCATCTTAAT
Found at i:78856 original size:55 final size:55
Alignment explanation
Indices: 78740--79085 Score: 356
Period size: 55 Copynumber: 6.3 Consensus size: 55
78730 TCATCTTAAT
* * * * * * * *
78740 GCACAGAGCTGCTCAATCA-TCTTA-ATGCATAGAGGTGTCAGATCCTAGATTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCT-CTCGGTTGAA
* * * *
78794 GCACAGAGGTGCTCAATCAATGTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
* * * * * * *
78849 GTACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
* *
78904 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCCGCTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
* * * ** * *
78959 GTACAGAGGTGCTCAGTCATTTTTAATTGCACAGAGGTGTCAGTTCTCGGTTGAA
1 GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
* * * * *
79014 GCACAGAGGTGCTCAATTC-GTTTTAGCTACATAGAGGTGTCAGCTTTTGATTGAT
1 GCACAGAGGTGCTCAA-TCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
79069 GCACAGAGGTGCTCAAT
1 GCACAGAGGTGCTCAAT
79086 TGCTAATTCT
Statistics
Matches: 240, Mismatches: 49, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
54 19 0.08
55 204 0.85
56 17 0.07
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (55 bp):
GCACAGAGGTGCTCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCGGTTGAA
Found at i:78883 original size:28 final size:26
Alignment explanation
Indices: 78851--79002 Score: 78
Period size: 28 Copynumber: 5.5 Consensus size: 26
78841 TGGCTGAAGT
78851 ACAGAGGTGCTCAGTCATTTTTAACTGC
1 ACAGAGGTG-TCAGTCATTTTTAA-TGC
* *
78879 ACAGAGGTGTCAGTTC-TCGATTGAA-GC
1 ACAGAGGTGTCAG-TCAT--TTTTAATGC
* * * *
78906 ACAGAGGTGCTCAATCAGTTTTAGCTAC
1 ACAGAGGTG-TCAGTCATTTTTA-ATGC
** * *
78934 ACAGAGGTGTCAGCTC-TCCGCTGAA-GT
1 ACAGAGGTGTCAG-TCAT--TTTTAATGC
78961 ACAGAGGTGCTCAGTCATTTTTAATTGC
1 ACAGAGGTG-TCAGTCATTTTTAA-TGC
78989 ACAGAGGTGTCAGT
1 ACAGAGGTGTCAGT
79003 TCTCGGTTGA
Statistics
Matches: 90, Mismatches: 20, Indels: 29
0.65 0.14 0.21
Matches are distributed among these distances:
26 6 0.07
27 37 0.41
28 41 0.46
29 6 0.07
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (26 bp):
ACAGAGGTGTCAGTCATTTTTAATGC
Found at i:78907 original size:27 final size:26
Alignment explanation
Indices: 78877--79024 Score: 88
Period size: 27 Copynumber: 5.4 Consensus size: 26
78867 ATTTTTAACT
78877 GCACAGAGGTGTCAGTTCTCGATTGAA
1 GCACAGAGGTGTCAGTTCTCG-TTGAA
* * **
78904 GCACAGAGGTGCTCA-ATC-AGTTTTA
1 GCACAGAGGTG-TCAGTTCTCGTTGAA
* *
78929 GCTACACAGAGGTGTCAGCTCTCCGCTGAA
1 G---CACAGAGGTGTCAGTTCT-CGTTGAA
* * *
78959 GTACAGAGGTGCTCAG-TCAT-TTTTAA
1 GCACAGAGGTG-TCAGTTC-TCGTTGAA
78985 TTGCACAGAGGTGTCAGTTCTCGGTTGAA
1 --GCACAGAGGTGTCAGTTCTC-GTTGAA
79014 GCACAGAGGTG
1 GCACAGAGGTG
79025 CTCAATTCGT
Statistics
Matches: 91, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
25 4 0.04
26 4 0.04
27 43 0.47
28 32 0.35
29 4 0.04
30 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (26 bp):
GCACAGAGGTGTCAGTTCTCGTTGAA
Found at i:78914 original size:110 final size:109
Alignment explanation
Indices: 78742--79083 Score: 481
Period size: 110 Copynumber: 3.1 Consensus size: 109
78732 ATCTTAATGC
* * * * * *
78742 ACAGAGCTGCTCAATCA-TCTTAATGCATAGAGGTGTCAGATCCTAGATTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAATGCACAGAGGTGTCAG-TTCTCGATTGAAGCACAGAGGTGC
* *
78806 TCAATCAATGTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
65 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
78851 ACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAA-TGCACAGAGGTGTCAGTTCTCGATTGAAGCACAGAGGTGC
**
78916 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTCCGCTGAAGT
65 TCAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
*
78961 ACAGAGGTGCTCAGTCATTTTTAATTGCACAGAGGTGTCAGTTCTCGGTTGAAGCACAGAGGTGC
1 ACAGAGGTGCTCAGTCATTTTTAA-TGCACAGAGGTGTCAGTTCTCGATTGAAGCACAGAGGTGC
* * ** * *
79026 TCAATTC-GTTTTAGCTACATAGAGGTGTCAGCTTTTGATTGATGC
65 TCAA-TCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
79071 ACAGAGGTGCTCA
1 ACAGAGGTGCTCA
79084 ATTGCTAATT
Statistics
Matches: 210, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
109 15 0.07
110 178 0.85
111 17 0.08
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (109 bp):
ACAGAGGTGCTCAGTCATTTTTAATGCACAGAGGTGTCAGTTCTCGATTGAAGCACAGAGGTGCT
CAATCAGTTTTAGCTACACAGAGGTGTCAGCTCTTGGCTGAAGT
Done.