Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 21
Found at i:4436623 original size:44 final size:44
Alignment explanation
Indices: 4436535--4436628 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
4436525 GGCCTTGTGC
* *
4436535 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
*
4436579 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TCATAGTGT
4436623 ATCGAT
1 ATCGAT
4436629 TCATGAAGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 27 0.61
45 17 0.39
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
Found at i:4442361 original size:21 final size:21
Alignment explanation
Indices: 4442335--4442375 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4442325 TCAGTGAATC
4442335 GATGCATACCCAAGGTGCATT
1 GATGCATACCCAAGGTGCATT
4442356 GATGCATACCCAAGGTGCAT
1 GATGCATACCCAAGGTGCAT
4442376 CAAGTGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
GATGCATACCCAAGGTGCATT
Found at i:4442482 original size:64 final size:63
Alignment explanation
Indices: 4442414--4442594 Score: 222
Period size: 65 Copynumber: 2.8 Consensus size: 63
4442404 TTAGACCCTT
* *
4442414 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATAAAATGCATTCAATGTTTCA-AAATAGCCT
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-AGCCT
4442477 G
63 G
* * *
4442478 AGTGCATCGATGCATGGTTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGTCTG
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAAGCCTG
* * *
4442543 AGTGCATCGATGCATAGTATGTGCATCAATGCATGAAATGTATTCGATGTTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTTT
4442595 AATTTATTCC
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.44
65 52 0.51
66 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAAGCCTG
Found at i:4442567 original size:65 final size:65
Alignment explanation
Indices: 4442434--4442594 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 65
4442424 TGCACTAAGA
* *
4442434 GTGCATCGATGCATAAAATGCATTCAATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
*
4442498 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-AGTCTGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATAGT-
4442562 T-
64 TG
* * *
4442563 GTGCATCAATGCATGAAATGTATTCGATGTTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTT
4442595 AATTTATTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 28 0.32
65 56 0.64
66 4 0.05
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGTTG
Found at i:4442641 original size:65 final size:65
Alignment explanation
Indices: 4442434--4442641 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 65
4442424 TGCACTAAGA
* * * *
4442434 GTGCATCGATGCATAAAATGCATTCAATGTTTCAA-AATAGCCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAATAAAAGTCTGAGTGCATCGATGCATGGTTG
* *
4442498 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGTCTGAGTGCATCGATGCATAGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAATAAAAGTCTGAGTGCATCGATGCATGGT-T
4442563 -
65 G
* * * ** * *
4442563 GTGCATCAATGCATGAAATGTATTCGATG-TTTAAT-TTATTCCATG-GTGCATTGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAATAAAAGT-C-TGAGTGCATCGATGCATGG-
4442625 TTG
63 TTG
*
4442628 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
4442642 CACTTTGAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 53 0.44
65 65 0.54
66 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAATAAAAGTCTGAGTGCATCGATGCATGGTTG
Found at i:4452365 original size:18 final size:18
Alignment explanation
Indices: 4452342--4452379 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4452332 CAAATGCCAC
4452342 CCCCAGAGTACATTAGTA
1 CCCCAGAGTACATTAGTA
4452360 CCCCAGAGTACATTAGTA
1 CCCCAGAGTACATTAGTA
4452378 CC
1 CC
4452380 TCACACGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (18 bp):
CCCCAGAGTACATTAGTA
Found at i:4453407 original size:46 final size:46
Alignment explanation
Indices: 4453299--4453786 Score: 726
Period size: 46 Copynumber: 10.6 Consensus size: 46
4453289 TTAATTTCAA
* * * *
4453299 TTATGGCCT-CTTGTCATGCCTTAATACACCCGTTCATACATTTTTAG
1 TTATGGCATCCTT-TCATGCCTTAATGCATCCGTTCATGCA-TTTTAG
4453346 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* * *
4453392 TTATGACATCCTTTCATGCCTTAAAAGCACCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTT-AATGCATCCGTTCATGCATTTTAG
* * * *
4453439 TTATGACATCCTTTCATGCCGTAATTCATCCGTTCATGCATTTTAT
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
4453485 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGTATTCTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
4453531 GTATGACATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
4453577 TTATGGCATCCTTTAATGCCCTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* * * *
4453623 TTACGGCATCCTTTCATGCCTTAACGCATTCATTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
* *
4453669 TTATGACATCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
4453715 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
*
4453761 TTATGTCATCCTTTCATGCCTTAATG
1 TTATGGCATCCTTTCATGCCTTAATG
4453787 ACAACATAGT
Statistics
Matches: 399, Mismatches: 40, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
46 321 0.80
47 75 0.19
48 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAG
Found at i:4470468 original size:29 final size:27
Alignment explanation
Indices: 4470426--4470543 Score: 94
Period size: 29 Copynumber: 4.2 Consensus size: 27
4470416 TTCGGTTTTA
* *
4470426 CTATTCTGGGAATTAATTCGAAATAGGTG
1 CTATTTTGGTAATT-ATTCGAAA-AGGTG
* * *
4470455 CTATTTTAGTAATTTTTTGAAAA-GTG
1 CTATTTTGGTAATTATTCGAAAAGGTG
* * *
4470481 ATATTCTGGGAATTAATTCGAAAAGGGTG
1 CTATTTTGGTAATT-ATTCGAAAA-GGTG
**
4470510 CTATTTTGGTAATTATTTTAAAAAGGTG
1 CTATTTTGGTAATTA-TTCGAAAAGGTG
4470538 CTATTT
1 CTATTT
4470544 GTGTAAAATG
Statistics
Matches: 69, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
26 13 0.19
27 8 0.12
28 17 0.25
29 31 0.45
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (27 bp):
CTATTTTGGTAATTATTCGAAAAGGTG
Found at i:4470486 original size:55 final size:56
Alignment explanation
Indices: 4470427--4470534 Score: 175
Period size: 55 Copynumber: 1.9 Consensus size: 56
4470417 TCGGTTTTAC
*
4470427 TATTCTGGGAATTAATTCGAAATA-GGTGCTATTTTAGTAATT-TTTTGAAAAGTGA
1 TATTCTGGGAATTAATTCGAAA-AGGGTGCTATTTTAGTAATTATTTTAAAAAGTGA
*
4470482 TATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTGGTAATTATTTTAAAAAG
1 TATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTAGTAATTATTTTAAAAAG
4470535 GTGCTATTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
54 1 0.02
55 39 0.80
56 9 0.18
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (56 bp):
TATTCTGGGAATTAATTCGAAAAGGGTGCTATTTTAGTAATTATTTTAAAAAGTGA
Found at i:4470537 original size:28 final size:28
Alignment explanation
Indices: 4470450--4470543 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 28
4470440 AATTCGAAAT
* *
4470450 AGGTGCTATTTTAGTAATT-TTTTGAAA
1 AGGTGCTATTTTGGTAATTATTTTAAAA
* * * **
4470477 A-GTGATATTCTGGGAATTAATTCGAAAA
1 AGGTGCTATTTTGGTAATT-ATTTTAAAA
*
4470505 GGGTGCTATTTTGGTAATTATTTTAAAA
1 AGGTGCTATTTTGGTAATTATTTTAAAA
4470533 AGGTGCTATTT
1 AGGTGCTATTT
4470544 GTGTAAAATG
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
26 13 0.26
27 1 0.02
28 22 0.44
29 14 0.28
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (28 bp):
AGGTGCTATTTTGGTAATTATTTTAAAA
Found at i:4476289 original size:29 final size:29
Alignment explanation
Indices: 4476245--4476404 Score: 124
Period size: 29 Copynumber: 5.7 Consensus size: 29
4476235 ACCGTTGACC
* * *
4476245 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTCTTGGAATTAATTCGAATAT
*
4476274 GGTGCTATTCTTGGAATTAATTAGAAATAT
1 GGTGCTATTCTTGGAATTAATTCG-AATAT
4476304 -GTGCTATT-TTGGTAATT--TTCGAA-A-
1 GGTGCTATTCTTGG-AATTAATTCGAATAT
* * *
4476328 AGTGATATTCTGGGAATTAATTCGAA-ATT
1 GGTGCTATTCTTGGAATTAATTCGAATA-T
*
4476357 GGTGCTATT-TTGGGAATTAATTCGAA-ACG
1 GGTGCTATTCTT-GGAATTAATTCGAATA-T
4476386 GGTGCTATT-TTGGTAATTA
1 GGTGCTATTCTTGG-AATTA
4476405 TTTTAAAAAG
Statistics
Matches: 109, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.11
26 5 0.05
27 10 0.09
28 7 0.06
29 72 0.66
30 3 0.03
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTTGGAATTAATTCGAATAT
Found at i:4476337 original size:54 final size:55
Alignment explanation
Indices: 4476279--4476383 Score: 151
Period size: 54 Copynumber: 1.9 Consensus size: 55
4476269 ATTTTGGTGC
* *
4476279 TATTCTTGGAATTAATTAGAAATAT-GTGCTATTTTGGTAATT-TTCGAAAAGTGA
1 TATTCTGGGAATTAATTAGAAAT-TGGTGCTATTTTGGGAATTATTCGAAAAGTGA
*
4476333 TATTCTGGGAATTAATTCGAAATTGGTGCTATTTTGGGAATTAATTCGAAA
1 TATTCTGGGAATTAATTAGAAATTGGTGCTATTTTGGGAATT-ATTCGAAA
4476384 CGGGTGCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
53 1 0.02
54 37 0.82
56 7 0.16
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (55 bp):
TATTCTGGGAATTAATTAGAAATTGGTGCTATTTTGGGAATTATTCGAAAAGTGA
Found at i:4476391 original size:83 final size:83
Alignment explanation
Indices: 4476250--4476403 Score: 238
Period size: 83 Copynumber: 1.9 Consensus size: 83
4476240 TGACCGGTGC
** * *
4476250 TATTCTGGGAATTAATTCGATTTTGGTGCTATTCTTGGAATTAATTAGAAATATGTGCTATTTTG
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTTGGAATTAATTAGAAACAGGTGCTATTTTG
4476315 GTAATTTTCGAAAAGTGA
66 GTAATTTTCGAAAAGTGA
* *
4476333 TATTCTGGGAATTAATTCGAAATTGGTGCTATT-TTGGGAATTAATTCGAAACGGGTGCTATTTT
1 TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTT-GGAATTAATTAGAAACAGGTGCTATTTT
4476397 GGTAATT
65 GGTAATT
4476404 ATTTTAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
82 2 0.03
83 62 0.97
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (83 bp):
TATTCTGGGAATTAATTCGAAATTGGTGCTATTCTTGGAATTAATTAGAAACAGGTGCTATTTTG
GTAATTTTCGAAAAGTGA
Found at i:4476417 original size:29 final size:29
Alignment explanation
Indices: 4476245--4476424 Score: 113
Period size: 29 Copynumber: 6.3 Consensus size: 29
4476235 ACCGTTGACC
* * ****
4476245 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
4476274 GGTGCTATTCTT-GGAATTAATT-AGAAATA-
1 GGTGCTATT-TTGGGAATTAATTCA-AAA-AG
* * *
4476303 TGTGCTATTTTGGTAATT--TTCGAAAA-
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * **
4476329 -GTGATATTCTGGGAATTAATTCGAAATT
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* *
4476357 GGTGCTATTTTGGGAATTAATTCGAAACG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * *
4476386 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
4476415 GGTGCTATTT
1 GGTGCTATTT
4476425 GTGTAAAATG
Statistics
Matches: 121, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
25 14 0.12
26 1 0.01
27 12 0.10
28 2 0.02
29 91 0.75
30 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:4479279 original size:18 final size:18
Alignment explanation
Indices: 4479258--4479300 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4479248 AAAGCTAGTC
4479258 CATTAAAACTAGTTCATT
1 CATTAAAACTAGTTCATT
* * *
4479276 CATTTAAATTGGTTCATT
1 CATTAAAACTAGTTCATT
*
4479294 AATTAAA
1 CATTAAA
4479301 CTATCTCCTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (18 bp):
CATTAAAACTAGTTCATT
Found at i:4479526 original size:6 final size:6
Alignment explanation
Indices: 4479515--4479558 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
4479505 TTTCCCAGGG
* * *
4479515 ATTATT ATTATT ATTAGT AGTAGT ATTAGT ATTAGT ATTAGT AT
1 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT AT
4479559 CATTTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTAGT
Found at i:4493806 original size:8 final size:8
Alignment explanation
Indices: 4493793--4493870 Score: 58
Period size: 8 Copynumber: 10.0 Consensus size: 8
4493783 AAAGAGAATG
4493793 AATGAAAA
1 AATGAAAA
4493801 AATGAAAA
1 AATGAAAA
*
4493809 ATTG-AAA
1 AATGAAAA
4493816 AA-GAAAA
1 AATGAAAA
*
4493823 AATAAAAATA
1 AAT-GAAA-A
4493833 AATGAAAA
1 AATGAAAA
*
4493841 AA--AAAG
1 AATGAAAA
*
4493847 AATAAAAA
1 AATGAAAA
4493855 GAAT-AAAA
1 -AATGAAAA
4493863 AATGAAAA
1 AATGAAAA
4493871 GAAAAATAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
6 6 0.11
7 12 0.21
8 25 0.45
9 9 0.16
10 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (8 bp):
AATGAAAA
Found at i:4493838 original size:24 final size:21
Alignment explanation
Indices: 4493796--4493854 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 21
4493786 GAGAATGAAT
4493796 GAAAAAATGAAAAATTGAAAAA
1 GAAAAAAT-AAAAATTGAAAAA
4493818 GAAAAAATAAAAATAAATGAAAAA
1 GAAAAAATAAAAAT---TGAAAAA
4493842 -AAAAGAATAAAAA
1 GAAAA-AATAAAAA
4493855 GAATAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.18
22 8 0.24
23 4 0.12
24 15 0.45
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (21 bp):
GAAAAAATAAAAATTGAAAAA
Found at i:4493840 original size:10 final size:10
Alignment explanation
Indices: 4493819--4493875 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
4493809 ATTGAAAAAG
4493819 AAAAAAT-AA
1 AAAAAATGAA
4493828 AAATAAATGAA
1 AAA-AAATGAA
*
4493839 AAAAAAAGAA
1 AAAAAATGAA
*
4493849 TAAAAA-GAA
1 AAAAAATGAA
4493858 TAAAAAATGAA
1 -AAAAAATGAA
4493869 AAGAAAA
1 AA-AAAA
4493876 ATAGAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 6 0.15
10 22 0.55
11 12 0.30
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:4494976 original size:105 final size:105
Alignment explanation
Indices: 4494794--4495110 Score: 463
Period size: 105 Copynumber: 3.0 Consensus size: 105
4494784 TCAACAACAA
*
4494794 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
4494859 CCTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
66 CTTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
* *
4494899 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
4494964 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CTTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
* * * * *
4495004 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAT
1 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
4495069 CTGACAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
66 CT---TAAAGGAGAAG--GTTCGTAATGAGAAGAACTTGTTC
4495111 AACCTTAGCT
Statistics
Matches: 190, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
105 160 0.84
108 9 0.05
110 21 0.11
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CTTAAAGGAGAAGGTTCGTAATGAGAAGAACTTGTTCCTT
Found at i:4499541 original size:15 final size:15
Alignment explanation
Indices: 4499503--4499541 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
4499493 AATGCATACC
4499503 AATT-TTTTTCTTAA
1 AATTGTTTTTCTTAA
*
4499517 AAATGATTTTTCTTAA
1 AATTG-TTTTTCTTAA
4499533 AATTGTTTT
1 AATTGTTTT
4499542 AAAAGATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 4 0.19
16 14 0.67
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (15 bp):
AATTGTTTTTCTTAA
Found at i:4500614 original size:19 final size:19
Alignment explanation
Indices: 4500592--4500629 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4500582 TTTTTCTAAT
4500592 TTTTGTGTCATTTT-TCATC
1 TTTTGTGT-ATTTTATCATC
*
4500611 TTTTTTGTATTTTATCATC
1 TTTTGTGTATTTTATCATC
4500630 ATAACATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.66
Consensus pattern (19 bp):
TTTTGTGTATTTTATCATC
Found at i:4506382 original size:5 final size:5
Alignment explanation
Indices: 4506372--4506400 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4506362 AAAATAGACT
4506372 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
4506401 TAACCTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:4507383 original size:2 final size:2
Alignment explanation
Indices: 4507376--4507421 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4507366 CATAGTTCCC
4507376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4507418 AT AT
1 AT AT
4507422 TTTGTTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4507637 original size:26 final size:27
Alignment explanation
Indices: 4507595--4507647 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4507585 GGTGAACTTG
4507595 AAATGAATCTAACATTTTTATT-TATT
1 AAATGAATCTAACATTTTTATTATATT
*
4507621 AAATGACAT-TAATATTTTTATTATATT
1 AAATGA-ATCTAACATTTTTATTATATT
4507648 TGTTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (27 bp):
AAATGAATCTAACATTTTTATTATATT
Found at i:4510612 original size:42 final size:42
Alignment explanation
Indices: 4510541--4510669 Score: 213
Period size: 42 Copynumber: 3.1 Consensus size: 42
4510531 GTTGACTGAA
4510541 CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
1 CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
* * * * *
4510583 CTTCTATTGATTGAATTTCTATTGGGGGTGATTAAAACTAAT
1 CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
4510625 CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
1 CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
4510667 CTG
1 CTG
4510670 GCTGATTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (42 bp):
CTGCTATTGATTGAATTGCTACTGAGGGTGATTAAAACTATT
Found at i:4516190 original size:37 final size:37
Alignment explanation
Indices: 4516149--4516238 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
4516139 TTGGGTTTAC
* * **
4516149 CATCCCAAAGGATGAACCAGTCAATAATTGGATCTAT
1 CATCCTAATGGATGAACCAACCAATAATTGGATCTAT
* * *
4516186 CATCCTAATGTATGAACCAACCAATAATTTGATTTAT
1 CATCCTAATGGATGAACCAACCAATAATTGGATCTAT
4516223 CATCCTAATGGATGAA
1 CATCCTAATGGATGAA
4516239 TTTGTCGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (37 bp):
CATCCTAATGGATGAACCAACCAATAATTGGATCTAT
Found at i:4517086 original size:2 final size:2
Alignment explanation
Indices: 4517079--4517109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4517069 TTTTTAAAAC
4517079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4517110 CCCCCATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4518533 original size:18 final size:18
Alignment explanation
Indices: 4518510--4518545 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4518500 CTTCCATCCG
*
4518510 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
4518528 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
4518546 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:4519879 original size:18 final size:18
Alignment explanation
Indices: 4519856--4519940 Score: 125
Period size: 18 Copynumber: 4.7 Consensus size: 18
4519846 ACGTCGGTCA
* *
4519856 GGTCGGGTCAGGTCAACG
1 GGTCGGGTCGGGTAAACG
* *
4519874 GGTCGGGTCGGGTCAACT
1 GGTCGGGTCGGGTAAACG
*
4519892 GGTCAGGTCGGGTAAACG
1 GGTCGGGTCGGGTAAACG
4519910 GGTCGGGTCGGGTAAACG
1 GGTCGGGTCGGGTAAACG
4519928 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
4519941 TGTGACCGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.14, C:0.19, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCGGGTAAACG
Found at i:4519882 original size:23 final size:24
Alignment explanation
Indices: 4519841--4519888 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
4519831 GGTCAACATT
4519841 GGTCAACGTCGGTCAGGTCGGGTCA
1 GGTCAACG-CGGTCAGGTCGGGTCA
*
4519866 GGTCAACG-GGTCGGGTCGGGTCA
1 GGTCAACGCGGTCAGGTCGGGTCA
4519889 ACTGGTCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.15, C:0.23, G:0.44, T:0.19
Consensus pattern (24 bp):
GGTCAACGCGGTCAGGTCGGGTCA
Done.