Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000636.1 Hibiscus syriacus cultivar Beakdansim tig00001232_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: 81404
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1773 original size:2 final size:2
Alignment explanation
Indices: 1766--1822 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
1756 TGTTGTACCT
1766 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1807 -A TA TA CA TA CA TA TA T
1 TA TA TA TA TA TA TA TA T
1823 CATGCCTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1804 original size:27 final size:27
Alignment explanation
Indices: 1766--1822 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1756 TGTTGTACCT
* * *
1766 TATATATATATATTATATATATATATA
1 TATATATATATATAATATACATACATA
1793 TATATATATATATAATATACATACATA
1 TATATATATATATAATATACATACATA
1820 TAT
1 TAT
1823 CATGCCTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TATATATATATATAATATACATACATA
Found at i:2001 original size:28 final size:28
Alignment explanation
Indices: 1969--2035 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1959 TTCTTTAAAA
* *
1969 AGTGTTTAACCTTTTGTTTTTACTCAAC
1 AGTGTTTAACCTTTCGTTTTCACTCAAC
1997 AGTGTTTAACCTTTCGTTTTCACTCAAC
1 AGTGTTTAACCTTTCGTTTTCACTCAAC
*
2025 GGTGTTTAACC
1 AGTGTTTAACC
2036 GTTCATCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (28 bp):
AGTGTTTAACCTTTCGTTTTCACTCAAC
Found at i:2154 original size:81 final size:81
Alignment explanation
Indices: 2018--2249 Score: 338
Period size: 81 Copynumber: 2.9 Consensus size: 81
2008 TTTCGTTTTC
* * ** *
2018 ACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAATTGCATAGTT
1 ACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTT
2083 AGGCCATTATTCCTTT
66 AGGCCATTATTCCTTT
* * * *
2099 ACTCAACGGTATTAAACCGTTCATCTACCTGGCATAATTGGTATATTTCTGCCAATTGCACAATT
1 ACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTT
* *
2164 AGGCTATTATTCTTTT
66 AGGCCATTATTCCTTT
** *
2180 ACTCAACGGTATTAAATTGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTT
1 ACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTT
2245 AGGCC
66 AGGCC
2250 TTAAAGACAC
Statistics
Matches: 132, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 132 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (81 bp):
ACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTT
AGGCCATTATTCCTTT
Found at i:2309 original size:68 final size:68
Alignment explanation
Indices: 2199--2655 Score: 664
Period size: 68 Copynumber: 6.7 Consensus size: 68
2189 TATTAAATTG
* ** ** * * *
2199 TTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCTTAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2264 CCT
66 CCT
* *
2267 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAACGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2332 CCT
66 CCT
* * *
2335 TTCATATAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2400 CCT
66 CCT
* * *
2403 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCATAGTTAGGCCTCAAAGGTACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2468 CCT
66 CCT
* * *
2471 TTCATCTAACTAGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCCAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2536 CCT
66 CCT
* * *
2539 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACATTTAGGACTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
2604 CCT
66 CCT
* * * * *
2607 TTCATCTAACTGTCATAAATTACACATTTCTGTC-AATACATAGTTAGGC
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGC
2656 TTCTTAATCT
Statistics
Matches: 352, Mismatches: 37, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
67 11 0.03
68 341 0.97
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3427 original size:22 final size:22
Alignment explanation
Indices: 3390--3442 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3380 TTGGTAACGA
*
3390 TACCCTTACCATGGTATCGATAC
1 TACCC-TACCATGGTACCGATAC
*
3413 TACCCTACTATGGTACCGATAC
1 TACCCTACCATGGTACCGATAC
3435 T-CCCTACC
1 TACCCTACC
3443 GGTATGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.25, C:0.36, G:0.11, T:0.28
Consensus pattern (22 bp):
TACCCTACCATGGTACCGATAC
Found at i:3455 original size:95 final size:96
Alignment explanation
Indices: 3323--3512 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 96
3313 GATACTTCTA
* * *
3323 TACTATGGTACCGATACCCCCTTCAGGTATCGATACCAAAAATAGGTTCGATGTTGCTTGGTAAC
1 TACTATGGTACCGATACCCCCTACAGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTAAC
*
3388 GATA-CCCTTACCATGGTATCGATACTACCC
66 AATACCCCTTACCATGGTATCGATACTACCC
* * * * * *
3418 TACTATGGTACCGATACTCCCTACCGGTATGGATACCAAAATTAGATTCGATGTTTCATGGTATC
1 TACTATGGTACCGATACCCCCTACAGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTAAC
*
3483 AATACCCCTTATCATGGTATCGATACTACC
66 AATACCCCTTACCATGGTATCGATACTACC
3513 TTCTCGGTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 59 0.71
96 24 0.29
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (96 bp):
TACTATGGTACCGATACCCCCTACAGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTAAC
AATACCCCTTACCATGGTATCGATACTACCC
Found at i:5065 original size:45 final size:45
Alignment explanation
Indices: 5016--5102 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
5006 TTACATGAGA
* *
5016 ATATGATATAAGCTATGTGGTAATGACATAAGTGATTATATGAAC
1 ATATGATATAAGCTACGTGATAATGACATAAGTGATTATATGAAC
* * *
5061 ATATGATATAAGTTACGTGATAATGACTTATGTGATTATATG
1 ATATGATATAAGCTACGTGATAATGACATAAGTGATTATATG
5103 TATATGTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (45 bp):
ATATGATATAAGCTACGTGATAATGACATAAGTGATTATATGAAC
Found at i:5110 original size:16 final size:16
Alignment explanation
Indices: 5089--5144 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
5079 GATAATGACT
*
5089 TATGTGATTATATGTA
1 TATGTGATTATATGAA
*
5105 TATGTG-TGATATTGAA
1 TATGTGATTATA-TGAA
5121 CTATGTGATTATATGAA
1 -TATGTGATTATATGAA
5138 TATGTGA
1 TATGTGA
5145 AATGTGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.12
16 16 0.47
17 10 0.29
18 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (16 bp):
TATGTGATTATATGAA
Found at i:5114 original size:33 final size:33
Alignment explanation
Indices: 5077--5143 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
5067 TATAAGTTAC
*
5077 GTGATAATG-ACTTATGTGATTATATGTATATGT
1 GTGATAATGAAC-TATGTGATTATATGAATATGT
*
5110 GTGATATTGAACTATGTGATTATATGAATATGT
1 GTGATAATGAACTATGTGATTATATGAATATGT
5143 G
1 G
5144 AAATGTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.43
Consensus pattern (33 bp):
GTGATAATGAACTATGTGATTATATGAATATGT
Found at i:5254 original size:23 final size:23
Alignment explanation
Indices: 5228--5317 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
5218 GGTTCTACGC
*
5228 GGTCCTTTGGGACAATTCTGTAT
1 GGTCCTTTGGGACAATTCTATAT
* * * * **
5251 GGTCTTTTGAGATATTTCTACGT
1 GGTCCTTTGGGACAATTCTATAT
*
5274 GGTCCTTTGGGAC-ATATATATAT
1 GGTCCTTTGGGACAAT-TCTATAT
* *
5297 GGTCCTTCGGGACATTTCTAT
1 GGTCCTTTGGGACAATTCTAT
5318 GTGGCACTTC
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (23 bp):
GGTCCTTTGGGACAATTCTATAT
Found at i:5314 original size:46 final size:46
Alignment explanation
Indices: 5220--5321 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 46
5210 GAGTCGAGGG
* * * * * *
5220 TTCTACGCGGTCCTTTGGGACAATTCTGTATGGTCTTTTGAGATAT
1 TTCTACGTGGTCCTTTGGGACAATTATATATGGTCCTTCGAGACAT
*
5266 TTCTACGTGGTCCTTTGGGAC-ATATATATATGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTTGGGACAAT-TATATATGGTCCTTCGAGACAT
*
5312 TTCTATGTGG
1 TTCTACGTGG
5322 CACTTCCGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 2 0.04
46 45 0.96
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (46 bp):
TTCTACGTGGTCCTTTGGGACAATTATATATGGTCCTTCGAGACAT
Found at i:5457 original size:6 final size:6
Alignment explanation
Indices: 5446--5487 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
5436 ATGAATAGTA
* * *
5446 AATGAT AATGAT AATGAT AATGAG AATGAG AATGAG AATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
5488 GTTTTTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (6 bp):
AATGAT
Found at i:5463 original size:12 final size:12
Alignment explanation
Indices: 5446--5487 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5436 ATGAATAGTA
*
5446 AATGATAATGAT
1 AATGATAATGAG
5458 AATGATAATGAG
1 AATGATAATGAG
*
5470 AATGAGAATGAG
1 AATGATAATGAG
5482 AATGAT
1 AATGAT
5488 GTTTTTGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (12 bp):
AATGATAATGAG
Found at i:5705 original size:31 final size:32
Alignment explanation
Indices: 5659--5724 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
5649 ATGAATGAAC
* *
5659 AATGCATAATGTTATATGT-TTTTGTTGGTTA
1 AATGCATAATGTTATATATATTATGTTGGTTA
* * *
5690 AATGCATGATTTTATATATATTATGTTGTTTA
1 AATGCATAATGTTATATATATTATGTTGGTTA
5722 AAT
1 AAT
5725 ATATGATGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (32 bp):
AATGCATAATGTTATATATATTATGTTGGTTA
Found at i:5726 original size:18 final size:18
Alignment explanation
Indices: 5700--5734 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5690 AATGCATGAT
* *
5700 TTTATATATATTATGTTG
1 TTTAAATATATGATGTTG
5718 TTTAAATATATGATGTT
1 TTTAAATATATGATGTT
5735 TCTTGTACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTAAATATATGATGTTG
Found at i:9021 original size:13 final size:12
Alignment explanation
Indices: 8982--9023 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
8972 TATGTGTGCA
8982 TGTATAT-AATT
1 TGTATATGAATT
*
8993 TGTTATATGAACT
1 TG-TATATGAATT
9006 TGTATATGATATT
1 TGTATATGA-ATT
9019 TGTAT
1 TGTAT
9024 TATATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 2 0.08
12 12 0.46
13 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.52
Consensus pattern (12 bp):
TGTATATGAATT
Found at i:12998 original size:16 final size:16
Alignment explanation
Indices: 12979--13028 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 16
12969 TGCAATGTTA
12979 TACATGAGCTATGTGT
1 TACATGAGCTATGTGT
12995 TACATGTTAGACTATGTGT
1 TACATG--AG-CTATGTGT
*
13014 TACATGATCTATGTG
1 TACATGAGCTATGTG
13029 GATATATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 13 0.43
17 1 0.03
18 2 0.07
19 14 0.47
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (16 bp):
TACATGAGCTATGTGT
Found at i:13289 original size:15 final size:17
Alignment explanation
Indices: 13254--13307 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 17
13244 GACAAGGACT
*
13254 TATGTGATTATATG-TC
1 TATGTGATTATATGAAC
13270 TATGTGA-TAT-TGAAC
1 TATGTGATTATATGAAC
13285 TATGTGATTATATGAA-
1 TATGTGATTATATGAAC
13301 TATGTGA
1 TATGTGA
13308 AATGTGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 17 0.50
17 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (17 bp):
TATGTGATTATATGAAC
Found at i:13450 original size:23 final size:23
Alignment explanation
Indices: 13410--13469 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
13400 AGACAATTCC
* *
13410 ATGTGGTCCTTTGAGACATATCT
1 ATGTGGTCCTTCGGGACATATCT
* *
13433 ATGTGGTCCTTCGGGACATTTTT
1 ATGTGGTCCTTCGGGACATATCT
13456 ATGTGG-CACTTCGG
1 ATGTGGTC-CTTCGG
13470 TTCAATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (23 bp):
ATGTGGTCCTTCGGGACATATCT
Found at i:15272 original size:23 final size:23
Alignment explanation
Indices: 15246--15294 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
15236 TCAACCATAA
*
15246 TAACATAACAGGTAGCG-CTTATT
1 TAACATAACAAGTAGCGCCTT-TT
* *
15269 TAACGTAATAAGTAGCGCCTTTT
1 TAACATAACAAGTAGCGCCTTTT
15292 TAA
1 TAA
15295 ATCTTATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
TAACATAACAAGTAGCGCCTTTT
Found at i:15905 original size:131 final size:131
Alignment explanation
Indices: 15677--16153 Score: 719
Period size: 131 Copynumber: 3.6 Consensus size: 131
15667 TATACCGATA
* * * *
15677 AAAACGTTTACCATATACATTGTTAATTTAGCTATTACTTTAAAGTAATAGGTTTCGAAATTATA
1 AAAA-GTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATA
* * * * *
15742 AGTATCGATATTTTATATATGAGTATCGATACTTTGACATTTATGCCTATTTTCATTATA-CTGG
65 AGTATAGATACTTTATATATGAGTATCAATACTTGGACATTTATGTCTATTTTCATTATATC-GG
15806 TAG
129 TAG
* * *
15809 AAACGTTTACCATGTACATTGTTAATTTACCTATTA-ATTTAAAGTAATAGGTTTCGAAATTATA
1 AAAAGTTTACCATTTACATTGTTAATTTACCTATTACA-TTAAAGTAATAGGTTCCGAAATTATA
* *
15873 AGTATTGATACTTTGTATATGAGTATCAATACTTGGACATTTATGTCTATTTTCATTATATCGGT
65 AGTATAGATACTTTATATATGAGTATCAATACTTGGACATTTATGTCTATTTTCATTATATCGGT
15938 AG
130 AG
15940 AAAAGTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATAA
1 AAAAGTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATAA
* * *
16005 GTACAAATGCTTTATATAT--GTATCAATACTTGGACATTTATGTCTATTTTCATTATATCGGTA
66 GTATAGATACTTTATATATGAGTATCAATACTTGGACATTTATGTCTATTTTCATTATATCGGTA
16068 G
131 G
16069 AAAAGTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATAA
1 AAAAGTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATAA
* * *
16134 GTACAAATGCTTTATATATG
66 GTATAGATACTTTATATATG
16154 TGCATCGATA
Statistics
Matches: 323, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
129 129 0.40
131 189 0.59
132 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (131 bp):
AAAAGTTTACCATTTACATTGTTAATTTACCTATTACATTAAAGTAATAGGTTCCGAAATTATAA
GTATAGATACTTTATATATGAGTATCAATACTTGGACATTTATGTCTATTTTCATTATATCGGTA
G
Found at i:16575 original size:75 final size:74
Alignment explanation
Indices: 16445--16609 Score: 226
Period size: 75 Copynumber: 2.2 Consensus size: 74
16435 TGGGCATTTA
* * *
16445 CGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAACTGATAGGT-ATTTTAAT
1 CGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAACTGATAGGTGA--TTAAC
*
16509 GTAATAGGTAGT
64 GGAATAGGTA-T
* * *
16521 -GCCTATTTTATTTTACCATTTATATTATTAATAACCTTTAAACAAATTGGTAGGTGATTAACGG
1 CGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAACTGATAGGTGATTAACGG
16585 AATAGGTAT
66 AATAGGTAT
16594 CGCCTATTTTATTTTA
1 CGCCTATTTTATTTTA
16610 ACTGGTTAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
73 1 0.01
74 28 0.35
75 50 0.62
76 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (74 bp):
CGCCTATTTTATTTTACCATTTACATTATTAATAACCTTTAAACAAACTGATAGGTGATTAACGG
AATAGGTAT
Found at i:18824 original size:197 final size:197
Alignment explanation
Indices: 18586--18973 Score: 562
Period size: 197 Copynumber: 2.0 Consensus size: 197
18576 CGCTTTACCG
* *
18586 GTTTTGTCAAATTTCAACATGCTATATTGTCATATATCGATACATGTGTCTGAGGTATTGATACT
1 GTTTTGTCAAATTTCAACATGCTATATTGTCATATATCGATACATGTGTCTAAGGTATCGATACT
* * *
18651 TTATAGGCGCTATTATTGTAAATCTTTTAAATTCCTAAAGTACCGACACTTTGGTACATATACTT
66 TTATAGACGCTATTATTGCAAATCTTTTAAATTCCTAAAGTACCAACACTTTGGTACATATACTT
* **
18716 ATAAAAATATCGATACAAATTTCAACCATT-TTGATAGCTCTTTACCGGTTTTGTCAAATTGAAA
131 ATAAAAATATCGATACAAATTTCAACAATTCCAG-TAGCTCTTTACCGGTTTTGTCAAATTGAAA
18780 CCA
195 CCA
* * * * *
18783 GTTTTGTCAATTTTTAACATGTTATATTGTCATGTATCGATATATGTGTCTAAGGTATCGATACT
1 GTTTTGTCAAATTTCAACATGCTATATTGTCATATATCGATACATGTGTCTAAGGTATCGATACT
* * * * *
18848 TTTTAGACGCTATTATTGCAATTCTTTTAAATTTCTAAAGTATCAATACTTTGGTACATATACTT
66 TTATAGACGCTATTATTGCAAATCTTTTAAATTCCTAAAGTACCAACACTTTGGTACATATACTT
** * *
18913 ATAAATGTATCGATACAAATTTCAATAATTCCAGTTGCTCTTTACCGGTTTTGTCAAATTG
131 ATAAAAATATCGATACAAATTTCAACAATTCCAGTAGCTCTTTACCGGTTTTGTCAAATTG
18974 CAACATGTTA
Statistics
Matches: 168, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
197 167 0.99
198 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (197 bp):
GTTTTGTCAAATTTCAACATGCTATATTGTCATATATCGATACATGTGTCTAAGGTATCGATACT
TTATAGACGCTATTATTGCAAATCTTTTAAATTCCTAAAGTACCAACACTTTGGTACATATACTT
ATAAAAATATCGATACAAATTTCAACAATTCCAGTAGCTCTTTACCGGTTTTGTCAAATTGAAAC
CA
Found at i:19085 original size:177 final size:177
Alignment explanation
Indices: 18783--19106 Score: 477
Period size: 177 Copynumber: 1.8 Consensus size: 177
18773 ATTGAAACCA
* ** * * * *
18783 GTTTTGTCAATTTTTAACATGTTATATTGTCATGTATCGATATATGTGTCTAAGGTATCGATACT
1 GTTTTGTCAAATTGCAACATGTTATATTATCATGTATCGATACATATGTCTAAGATATCGATACT
* * *
18848 TTTTAGACGCTATTATTGCAATTCTTTTAAATTTCTAAAGTATCAATACTTTGGTACATATACTT
66 TTATAGACGCTATTATTGCAATTCTTTTAAATTACTAAAGTATCAATACTTTGATACATATACTT
*
18913 ATAAATGTATCGATACAAATTTCAATAATTCCAGTTGCTCTTTACCG
131 ATAAAGGTATCGATACAAATTTCAATAATTCCAGTTGCTCTTTACCG
*
18960 GTTTTGTCAAATTGCAACATGTTATATTATCATGTATCGATACATATGTGTAAGATATCGATACT
1 GTTTTGTCAAATTGCAACATGTTATATTATCATGTATCGATACATATGTCTAAGATATCGATACT
* * * * * *
19025 TTATAGGCGCTTTTGTTGCAATTCTTTTAAATTACTAAAGTTTCGATACTTTTATACATATACTT
66 TTATAGACGCTATTATTGCAATTCTTTTAAATTACTAAAGTATCAATACTTTGATACATATACTT
*
19090 ATAAAGGTATTGATACA
131 ATAAAGGTATCGATACA
19107 TGTCTACTTT
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
177 128 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (177 bp):
GTTTTGTCAAATTGCAACATGTTATATTATCATGTATCGATACATATGTCTAAGATATCGATACT
TTATAGACGCTATTATTGCAATTCTTTTAAATTACTAAAGTATCAATACTTTGATACATATACTT
ATAAAGGTATCGATACAAATTTCAATAATTCCAGTTGCTCTTTACCG
Found at i:23496 original size:6 final size:6
Alignment explanation
Indices: 23485--23511 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
23475 CGTGAGGTTA
23485 GTTTAG GTTTAG GTTTAG GTTTAG GTT
1 GTTTAG GTTTAG GTTTAG GTTTAG GTT
23512 ATTTAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (6 bp):
GTTTAG
Found at i:29937 original size:38 final size:38
Alignment explanation
Indices: 29886--30000 Score: 212
Period size: 38 Copynumber: 3.0 Consensus size: 38
29876 ATTACTCACA
*
29886 AGAATCGATTGGCTGAAAAGATAGCTCCGAAAGTGGTT
1 AGAATCGATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
29924 AGAATCGATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
1 AGAATCGATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
*
29962 AGAATCAATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
1 AGAATCGATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
30000 A
1 A
30001 TTACACCTCC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (38 bp):
AGAATCGATTGGCTGAAAAGGTAGCTCCGAAAGTGGTT
Found at i:34453 original size:8 final size:9
Alignment explanation
Indices: 34433--34464 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
34423 AAAAGGAATG
34433 AAAATGAGA
1 AAAATGAGA
34442 AAAATGAGA
1 AAAATGAGA
34451 AAAATGA-A
1 AAAATGAGA
34459 AAAATG
1 AAAATG
34465 TTGGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (9 bp):
AAAATGAGA
Found at i:34487 original size:10 final size:10
Alignment explanation
Indices: 34469--34517 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
34459 AAAATGTTGG
34469 AAAAT-AAAA
1 AAAATGAAAA
*
34478 AGAA-GAAAA
1 AAAATGAAAA
34487 AAAATGAAAA
1 AAAATGAAAA
34497 AAAATGAAAA
1 AAAATGAAAA
**
34507 ATGATGAAAA
1 AAAATGAAAA
34517 A
1 A
34518 TGAAAAGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 10 0.29
10 24 0.71
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:34506 original size:17 final size:17
Alignment explanation
Indices: 34386--34523 Score: 61
Period size: 18 Copynumber: 7.9 Consensus size: 17
34376 ATATTTCGCT
*
34386 TGAAGAAAAATGATAAAA
1 TGAAAAAAAATGA-AAAA
**
34404 TGATTAAAAATGAAATAA
1 TGAAAAAAAATGAAA-AA
*
34422 --AAAAAGGAATG-AAAA
1 TGAAAAA-AAATGAAAAA
*
34437 TG-AGAAAAATGAGAAAAA
1 TGAAAAAAAAT--GAAAAA
** *
34455 TGAAAAAATGTTGGAAAA
1 TGAAAAAA-AATGAAAAA
**
34473 T-AAAAAGAAGAAAAAAAA
1 TGAAAAA-AA-ATGAAAAA
34491 TGAAAAAAAATGAAAAA
1 TGAAAAAAAATGAAAAA
**
34508 TGATGAAAAATGAAAA
1 TGAAAAAAAATGAAAA
34524 GGAAAAAAGA
Statistics
Matches: 88, Mismatches: 20, Indels: 25
0.66 0.15 0.19
Matches are distributed among these distances:
15 5 0.06
16 8 0.09
17 32 0.36
18 33 0.38
19 9 0.10
20 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (17 bp):
TGAAAAAAAATGAAAAA
Found at i:34518 original size:10 final size:10
Alignment explanation
Indices: 34390--34520 Score: 52
Period size: 10 Copynumber: 13.9 Consensus size: 10
34380 TTCGCTTGAA
34390 GAAAAATGAT
1 GAAAAATGAT
34400 --AAAATGAT
1 GAAAAATGAT
*
34408 TAAAAATGAAAT
1 GAAAAATG--AT
* *
34420 AAAAAAAGGAAT
1 -GAAAAATG-AT
34432 G-AAAATGA-
1 GAAAAATGAT
34440 GAAAAATGA-
1 GAAAAATGAT
34449 GAAAAATGA-
1 GAAAAATGAT
*
34458 -AAAAATGTT
1 GAAAAATGAT
*
34467 G-GAAA--AT
1 GAAAAATGAT
*
34474 -AAAAA-GAA
1 GAAAAATGAT
**
34482 GAAAAAAAAT
1 GAAAAATGAT
**
34492 GAAAAAAAAT
1 GAAAAATGAT
34502 GAAAAATGAT
1 GAAAAATGAT
34512 GAAAAATGA
1 GAAAAATGA
34521 AAAGGAAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
7 4 0.04
8 17 0.18
9 25 0.26
10 39 0.41
12 5 0.05
13 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (10 bp):
GAAAAATGAT
Found at i:34529 original size:43 final size:42
Alignment explanation
Indices: 34441--34574 Score: 119
Period size: 45 Copynumber: 3.1 Consensus size: 42
34431 TGAAAATGAG
* * * *
34441 AAAAATGAGAAAAATGAAAAAATGTTGGAAAATAAAAAGAAGAAA
1 AAAAATGAAAAAAATG-AAAAATGATGAAAAATGAAAAG--GAAA
34486 AAAAATGAAAAAAAATGAAAAATGATGAAAAATGAAAAGGAAA
1 AAAAATG-AAAAAAATGAAAAATGATGAAAAATGAAAAGGAAA
* * * *
34529 AAAGA-GATAAAAATGGGAAAATGGAAGAAAAATGTAAAA-GAAA
1 AAAAATGAAAAAAAT-GAAAAAT-GATGAAAAATG-AAAAGGAAA
34572 AAA
1 AAA
34575 GGAAAAATGA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
41 7 0.09
42 7 0.09
43 25 0.32
44 4 0.05
45 26 0.34
46 8 0.10
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (42 bp):
AAAAATGAAAAAAATGAAAAATGATGAAAAATGAAAAGGAAA
Found at i:34575 original size:43 final size:41
Alignment explanation
Indices: 34496--34591 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 41
34486 AAAAATGAAA
*
34496 AAAAATGAAAAATGATGAAAAATGAAAAGGAAAAAAGAGAT
1 AAAAATGAAAAATGAAGAAAAATGAAAAGGAAAAAAGAGAT
*
34537 AAAAATGGGAAAATGGAAGAAAAATGTAAAA-GAAAAAAG-GA-
1 AAAAAT-GAAAAAT-GAAGAAAAATG-AAAAGGAAAAAAGAGAT
34578 AAAATGATGAAAAA
1 AAAA--ATGAAAAA
34592 AGAAATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
41 10 0.21
42 13 0.28
43 20 0.43
44 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (41 bp):
AAAAATGAAAAATGAAGAAAAATGAAAAGGAAAAAAGAGAT
Found at i:35844 original size:37 final size:37
Alignment explanation
Indices: 35790--35900 Score: 116
Period size: 37 Copynumber: 3.0 Consensus size: 37
35780 TCGAAACGAG
* * *
35790 TCAATCTTAAGCATTCACAAAAGAGCAGTGAATCAAT
1 TCAATCTTAAGCCTTCACAAAAGAGCAGTGAAGCAAA
** *
35827 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAAAAGAGCAGTGAAGCAAA
*** *
35864 T-AATCTATAAGCCTTCATGGAAGAGTAGTGAAGCAAA
1 TCAATCT-TAAGCCTTCACAAAAGAGCAGTGAAGCAAA
35901 CTCATTTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 5 0.08
37 61 0.92
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACAAAAGAGCAGTGAAGCAAA
Found at i:36089 original size:55 final size:54
Alignment explanation
Indices: 35919--36215 Score: 274
Period size: 55 Copynumber: 5.6 Consensus size: 54
35909 ATGAAGATAA
* * **
35919 AGTCTTATACTCTCTGAA-GAAATAGGGAGCGGACACGTTTATTGAAGA----TCG
1 AGTCTTATACTCCCTGAACG-AATAGGGAGCAGACATATTTA-TGAAGATTGTTCG
* * * **
35970 AGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGATG-A-A--GTTCG
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACATATTT-ATGAAGATTGTTCG
* *
36021 AGTCTTATACTCCCTGAACGATTAGGAAGCAGACATATTTATTGAAGATTGTTCG
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACATATTTA-TGAAGATTGTTCG
*
36076 AGT-TCTATACTCCCTGAACGAATAGGGAGC-GAACCTATTGTATGAAGATTGTTCG
1 AGTCT-TATACTCCCTGAACGAATAGGGAGCAG-ACATATT-TATGAAGATTGTTCG
* * * * *
36131 AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTGCTGAAGAATGTTAG
1 AGTCTTATACTCCCTGAACGAATAGGGAGCAGACATATTT-ATGAAGATTGTTCG
* *
36186 AGTCTTATACTTCCTGAAGGAATAGGGAGC
1 AGTCTTATACTCCCTGAACGAATAGGGAGC
36216 GGGCTCGTCA
Statistics
Matches: 210, Mismatches: 21, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
49 1 0.00
50 2 0.01
51 76 0.36
52 3 0.01
53 1 0.00
54 3 0.01
55 120 0.57
56 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (54 bp):
AGTCTTATACTCCCTGAACGAATAGGGAGCAGACATATTTATGAAGATTGTTCG
Found at i:36177 original size:110 final size:104
Alignment explanation
Indices: 35919--36216 Score: 327
Period size: 110 Copynumber: 2.8 Consensus size: 104
35909 ATGAAGATAA
* * * * *
35919 AGTCTTATACTCTCTGAAGAAATAGGGAGCGGACACGTTTATTGAAGA---TCGAGTCCTATACT
1 AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTATTGAAGATGTTCGAGTTCTATACT
* *
35981 CTCTGAAGGAATAGGGAGCAGACACGTTTGATGAAGTTCG
66 CCCTGAAGGAATAGGGAGC-GACACCTTTGATGAAGTTCG
* * * *
36021 AGTCTTATACTCCCTGAACGATTAGGAAGCAGACATATTTATTGAAGATTGTTCGAGTTCTATAC
1 AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTATTGAAGA-TGTTCGAGTTCTATAC
*
36086 TCCCTGAACGAATAGGGAGCGA-ACCTATTGTATGAAGATTGTTCG
65 TCCCTGAAGGAATAGGGAGCGACACCT-TTG-ATG-A-A--GTTCG
** *
36131 AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTGCTGAAGAATGTTAGAG-TCTTATA
1 AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTATTGAAG-ATGTTCGAGTTC-TATA
*
36195 CTTCCTGAAGGAATAGGGAGCG
64 CTCCCTGAAGGAATAGGGAGCG
36217 GGCTCGTCAT
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
102 40 0.25
104 3 0.02
105 5 0.03
106 33 0.20
107 1 0.01
108 1 0.01
109 2 0.01
110 77 0.47
111 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (104 bp):
AGTCTTATACTCCCTGAACAAATAGGGAGCAGACACATTTATTGAAGATGTTCGAGTTCTATACT
CCCTGAAGGAATAGGGAGCGACACCTTTGATGAAGTTCG
Found at i:41305 original size:22 final size:22
Alignment explanation
Indices: 41279--41329 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
41269 AAGTCCAGTG
*
41279 AATAAATTAAAAAAATTAAAAA
1 AATAAATTAAAAAAATAAAAAA
*
41301 TAT-AA-TAAAAAAATAAAAAA
1 AATAAATTAAAAAAATAAAAAA
41321 AATATAATT
1 AATA-AATT
41330 CAGTGAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
20 16 0.70
21 2 0.09
22 4 0.17
23 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
AATAAATTAAAAAAATAAAAAA
Found at i:41311 original size:11 final size:11
Alignment explanation
Indices: 41295--41328 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41285 TTAAAAAAAT
41295 TAAAAATATAA
1 TAAAAATATAA
*
41306 TAAAAAAATAA
1 TAAAAATATAA
*
41317 AAAAAATATAA
1 TAAAAATATAA
41328 T
1 T
41329 TCAGTGAGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:47019 original size:24 final size:24
Alignment explanation
Indices: 46991--47061 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
46981 ACATTACTTG
*
46991 AATTCTGTTCTGATTTCTGATATG
1 AATTCTGTTCTGATTTCTGATATA
* * *
47015 GATTCTGTTCTGATATCTGATCTA
1 AATTCTGTTCTGATTTCTGATATA
* *
47039 AATTCTGTTTTGATTTCTAATAT
1 AATTCTGTTCTGATTTCTGATAT
47062 CTCCATTTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.51
Consensus pattern (24 bp):
AATTCTGTTCTGATTTCTGATATA
Found at i:49133 original size:23 final size:23
Alignment explanation
Indices: 49075--49141 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
49065 TTAAGAGATA
* **
49075 AATTTATAAAATTTCAGGATGAGTG
1 AATTTATAAAATTTTA-GA-GAACG
*
49100 AACTTATAAAATTTTAGAGAACG
1 AATTTATAAAATTTTAGAGAACG
49123 AATTTATAAAATTTTAGAG
1 AATTTATAAAATTTTAGAG
49142 GGTAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 21 0.57
24 2 0.05
25 14 0.38
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (23 bp):
AATTTATAAAATTTTAGAGAACG
Found at i:49872 original size:16 final size:15
Alignment explanation
Indices: 49847--49887 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
49837 TTAAACATTT
49847 AAAAATCATATATAA
1 AAAAATCATATATAA
* *
49862 ACAATATCATATTTAA
1 A-AAAATCATATATAA
49878 AAAAATCATA
1 AAAAATCATA
49888 AAAATCTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATCATATATAA
Found at i:63772 original size:19 final size:19
Alignment explanation
Indices: 63748--63798 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
63738 CCTTCACTAG
63748 TGTATCGGTACACTGCATA
1 TGTATCGGTACACTGCATA
*
63767 TGTATCGGTACACTGCCTA
1 TGTATCGGTACACTGCATA
63786 TGTATCGGTACAC
1 TGTATCGGTACAC
63799 AAATTACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (19 bp):
TGTATCGGTACACTGCATA
Found at i:63915 original size:21 final size:21
Alignment explanation
Indices: 63889--63944 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
63879 AAATTGGTCT
*
63889 TAGTGTATCGGTACCCATTCA
1 TAGTGTACCGGTACCCATTCA
* *
63910 TAGTGTACCGATACCCATTTA
1 TAGTGTACCGGTACCCATTCA
63931 TAGTGTACCGGTAC
1 TAGTGTACCGGTAC
63945 ACCCTGCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (21 bp):
TAGTGTACCGGTACCCATTCA
Found at i:65803 original size:16 final size:16
Alignment explanation
Indices: 65784--65814 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65774 GAATATTTTT
65784 TTTTGTTGTTGGGATA
1 TTTTGTTGTTGGGATA
*
65800 TTTTGTTGTTTGGAT
1 TTTTGTTGTTGGGAT
65815 TGTTTGTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.61
Consensus pattern (16 bp):
TTTTGTTGTTGGGATA
Found at i:65820 original size:16 final size:16
Alignment explanation
Indices: 65785--65834 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
65775 AATATTTTTT
*
65785 TTTGTTGTTGGGATAT-
1 TTTGTTGTTTGGAT-TG
65801 TTTGTTGTTTGGATTG
1 TTTGTTGTTTGGATTG
65817 TTTG-TGTTTTGGA-TG
1 TTTGTTG-TTTGGATTG
65832 TTT
1 TTT
65835 AATTAGACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.08, C:0.00, G:0.30, T:0.62
Consensus pattern (16 bp):
TTTGTTGTTTGGATTG
Found at i:67812 original size:60 final size:59
Alignment explanation
Indices: 67713--67828 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 59
67703 AAATGATCCC
* * * *
67713 CCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTTACAAAATGGTTCT
1 CCGACTATAGGTGTTGCTTTATTGAGTCCCTGAGCTATTAAAAGTTACAAAATGGTTCT
* *
67772 CCGACTCTAGGATGTTGCTTTATTGAGTCCCTCGA-CTATTACAAGTTACAAAATGGT
1 CCGACTATAGG-TGTTGCTTTATTGAGTCCCT-GAGCTATTAAAAGTTACAAAATGGT
67829 CATCCAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 10 0.20
60 38 0.78
61 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (59 bp):
CCGACTATAGGTGTTGCTTTATTGAGTCCCTGAGCTATTAAAAGTTACAAAATGGTTCT
Found at i:67839 original size:269 final size:269
Alignment explanation
Indices: 67360--67903 Score: 1043
Period size: 269 Copynumber: 2.0 Consensus size: 269
67350 AGTTATACCG
67360 GTTAACAATTATAGGTTTTTTGACACCCTTATATATATTTTTGGGTAGCTAATATATTTTTTGTT
1 GTTAACAATTATAGGTTTTTTGACACCCTTATATATATTTTTGGGTAGCTAATATATTTTTTGTT
67425 AAAGTACATAAATGATCCCCCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTT
66 AAAGTACATAAATGATCCCCCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTT
*
67490 ACAAAATGGTTCTCCGACTCTAGGATGTTGCTTTGTTGAGTCCCCCGACTATTACAAGTTACAAA
131 ACAAAATGGTTCTCCGACTCTAGGATGTTGCTTTATTGAGTCCCCCGACTATTACAAGTTACAAA
*
67555 ATGGTCATCCAAATATTCATATATTCCAAACTTGTCATTTTCCGTTAAAATTTTGATGGCCGACT
196 ATGGTCATCCAAATATTCATATATTCCAAACTCGTCATTTTCCGTTAAAATTTTGATGGCCGACT
67620 AATATGAAT
261 AATATGAAT
67629 GTTAACAATTATAGGTTTTTTGACACCCTTATATATATTTTTGGGTAGCTAATATATTTTTTGTT
1 GTTAACAATTATAGGTTTTTTGACACCCTTATATATATTTTTGGGTAGCTAATATATTTTTTGTT
67694 AAAGTACATAAATGATCCCCCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTT
66 AAAGTACATAAATGATCCCCCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTT
*
67759 ACAAAATGGTTCTCCGACTCTAGGATGTTGCTTTATTGAGTCCCTCGACTATTACAAGTTACAAA
131 ACAAAATGGTTCTCCGACTCTAGGATGTTGCTTTATTGAGTCCCCCGACTATTACAAGTTACAAA
* *
67824 ATGGTCATCCAAATATTCATATGTTCCAAACTCGTCATTTTCCGTTAAAATTTTGATGGCCGTCT
196 ATGGTCATCCAAATATTCATATATTCCAAACTCGTCATTTTCCGTTAAAATTTTGATGGCCGACT
67889 AATATGAAT
261 AATATGAAT
67898 GTTAAC
1 GTTAAC
67904 CTGCTGATTG
Statistics
Matches: 270, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
269 270 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (269 bp):
GTTAACAATTATAGGTTTTTTGACACCCTTATATATATTTTTGGGTAGCTAATATATTTTTTGTT
AAAGTACATAAATGATCCCCCGACTATAGGTGTTTCTTTATTGAGTCTCTTAGTTATTAAAAGTT
ACAAAATGGTTCTCCGACTCTAGGATGTTGCTTTATTGAGTCCCCCGACTATTACAAGTTACAAA
ATGGTCATCCAAATATTCATATATTCCAAACTCGTCATTTTCCGTTAAAATTTTGATGGCCGACT
AATATGAAT
Found at i:73628 original size:13 final size:14
Alignment explanation
Indices: 73601--73633 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
73591 TGTGCCAAAA
73601 ATTAATAATAATAC
1 ATTAATAATAATAC
*
73615 ATTAA-AATATTAC
1 ATTAATAATAATAC
73628 ATTAAT
1 ATTAAT
73634 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTAATAATAATAC
Found at i:74534 original size:88 final size:89
Alignment explanation
Indices: 74385--74561 Score: 293
Period size: 88 Copynumber: 2.0 Consensus size: 89
74375 GTGGACCCAT
* * * *
74385 CACAAATTTTTGACGGAATAGGTGGATTTGTCAGAAATTTGTGACGGGTCCACAAATTCCGTCAC
1 CACAAATTTGTGACGAAATAGGTGGATCTGTCAGAAATTTGTGACGGGACCACAAATTCCGTCAC
74450 AAATTTAAAATAC-TTTTTCTAAA
66 AAATTTAAAATACATTTTTCTAAA
* *
74473 CACAAATTTGTGACGAAATAGGTGGATCTGTCATAAATTTGTGACGGGACCATAAATTCCGTCAC
1 CACAAATTTGTGACGAAATAGGTGGATCTGTCAGAAATTTGTGACGGGACCACAAATTCCGTCAC
74538 AAATTTAAAATACATTTTTCTAAA
66 AAATTTAAAATACATTTTTCTAAA
74562 AATAATATTT
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 72 0.88
89 10 0.12
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (89 bp):
CACAAATTTGTGACGAAATAGGTGGATCTGTCAGAAATTTGTGACGGGACCACAAATTCCGTCAC
AAATTTAAAATACATTTTTCTAAA
Found at i:75157 original size:25 final size:27
Alignment explanation
Indices: 75129--75192 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
75119 TAAAATTACA
*
75129 ATATAAAATAAAA-AAA-GATAAATGC
1 ATATAAAATAAAACAAAGGATAAATAC
75154 ATATAAAA-AAAAGCAAAGGATAAATAC
1 ATATAAAATAAAA-CAAAGGATAAATAC
75181 ATATAAATATAA
1 ATATAAA-ATAA
75193 TTGTTTACCG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 3 0.09
27 15 0.45
28 1 0.03
29 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (27 bp):
ATATAAAATAAAACAAAGGATAAATAC
Found at i:76393 original size:60 final size:59
Alignment explanation
Indices: 76291--76475 Score: 208
Period size: 60 Copynumber: 3.1 Consensus size: 59
76281 GCATCATATG
* * * * * *
76291 TCCCCAAACTATAACTTTCATTTTAGATTAGTCTTTACACTTTTGAATATTCAAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTC-CTAAACTTTTGAATATTCAAATTTCA
* * *
76351 TCCCCAAACTATGACTCTCATTCTAAATTAGCCCTAAAACTTTTGAACATTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCT-AAACTTTTGAATATTCAAATTTCA
* * * * * * *
76411 TCCCTAAACCATGACCCTCTTTCTAAATTAGTACTGAACTTTTGAATATTCCAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTAAACTTTTGAATATTCAAATTTCA
76470 TCCCCA
1 TCCCCA
76476 TATTCATCCA
Statistics
Matches: 105, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 27 0.26
60 78 0.74
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTAAACTTTTGAATATTCAAATTTCA
Found at i:76419 original size:29 final size:29
Alignment explanation
Indices: 76329--76419 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
76319 TAGTCTTTAC
* * *
76329 ACTTTTGAATATTCAAATTTCATCCCCAA
1 ACTTTTGAACATTCTAATTTCATCCCTAA
* * * *
76358 AC-TATGACTCTCATTCTAAATT-AGCCCTAAA
1 ACTTTTGA---ACATTCTAATTTCATCCCT-AA
76389 ACTTTTGAACATTCTAATTTCATCCCTAA
1 ACTTTTGAACATTCTAATTTCATCCCTAA
76418 AC
1 AC
76420 CATGACCCTC
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
28 4 0.09
29 16 0.36
30 9 0.20
31 12 0.27
32 4 0.09
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
ACTTTTGAACATTCTAATTTCATCCCTAA
Found at i:77762 original size:18 final size:19
Alignment explanation
Indices: 77721--77764 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
77711 TTTGGTTCAC
77721 GGAATATAAGATTACCAATG
1 GGAATATAAGATTACC-ATG
*
77741 GGAATGTAAGATTACC-TG
1 GGAATATAAGATTACCATG
77759 GGAATA
1 GGAATA
77765 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (19 bp):
GGAATATAAGATTACCATG
Found at i:77956 original size:2 final size:2
Alignment explanation
Indices: 77949--77976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77939 AATTCATAAA
77949 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
77977 TACAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.