Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002910.1 Hibiscus syriacus cultivar Beakdansim tig00006017_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: 61078
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1334 original size:19 final size:19
Alignment explanation
Indices: 1281--1330 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1271 ATTCAGTTTT
*
1281 AATTTGACAAAACGATTGG
1 AATTTGACAAAACGATTGC
* *
1300 AAATTGACAAAACGATTTC
1 AATTTGACAAAACGATTGC
1319 AATTTGA-AAAAC
1 AATTTGACAAAAC
1331 CGATAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (19 bp):
AATTTGACAAAACGATTGC
Found at i:1614 original size:25 final size:25
Alignment explanation
Indices: 1586--1663 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
1576 TTTAGGAATT
1586 TAAAGAATTGCAATAATAGCGCCTA
1 TAAAGAATTGCAATAATAGCGCCTA
* ** *
1611 TAAA-ATATTG--ATACTTTAG-GAATT
1 TAAAGA-ATTGCAATA--ATAGCGCCTA
1635 TAAAGAATTGCAATAATAGCGCCTA
1 TAAAGAATTGCAATAATAGCGCCTA
1660 TAAA
1 TAAA
1664 ATATCGATAC
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
23 3 0.08
24 14 0.37
25 18 0.47
26 3 0.08
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (25 bp):
TAAAGAATTGCAATAATAGCGCCTA
Found at i:1639 original size:49 final size:49
Alignment explanation
Indices: 1567--1678 Score: 206
Period size: 49 Copynumber: 2.3 Consensus size: 49
1557 TGCACCTAAG
1567 TATTGATACTTTAGGAATTTAAAGAATTGCAATAATAGCGCCTATAAAA
1 TATTGATACTTTAGGAATTTAAAGAATTGCAATAATAGCGCCTATAAAA
1616 TATTGATACTTTAGGAATTTAAAGAATTGCAATAATAGCGCCTATAAAA
1 TATTGATACTTTAGGAATTTAAAGAATTGCAATAATAGCGCCTATAAAA
* *
1665 TATCGATACCTTAG
1 TATTGATACTTTAG
1679 ACACATTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (49 bp):
TATTGATACTTTAGGAATTTAAAGAATTGCAATAATAGCGCCTATAAAA
Found at i:1644 original size:24 final size:24
Alignment explanation
Indices: 1568--1644 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
1558 GCACCTAAGT
1568 ATTGATACTTTAGGAATTTAAAGA
1 ATTGATACTTTAGGAATTTAAAGA
* ** *
1592 ATTGCA-A-TAATAGCGCCTATAAA-A
1 ATTG-ATACT-TTAG-GAATTTAAAGA
1616 TATTGATACTTTAGGAATTTAAAGA
1 -ATTGATACTTTAGGAATTTAAAGA
1641 ATTG
1 ATTG
1645 CAATAATAGC
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
23 1 0.03
24 20 0.53
25 16 0.42
26 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (24 bp):
ATTGATACTTTAGGAATTTAAAGA
Found at i:4903 original size:23 final size:23
Alignment explanation
Indices: 4876--4922 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
4866 ACCGAATTCG
4876 ACGCC-CCCTATTCTTGAATTTTA
1 ACGCCTCCC-ATTCTTGAATTTTA
*
4899 ACGCCTCCCATTCTTGACTTTTA
1 ACGCCTCCCATTCTTGAATTTTA
4922 A
1 A
4923 TAATCTCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.38
Consensus pattern (23 bp):
ACGCCTCCCATTCTTGAATTTTA
Found at i:9379 original size:17 final size:17
Alignment explanation
Indices: 9353--9410 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
9343 TTTACCTGTT
*
9353 GACCCAACCGTTGACCC
1 GACCCGACCGTTGACCC
9370 GACCCGACCGTTGACCC
1 GACCCGACCGTTGACCC
**
9387 GAATCGACCCGTTGACCC
1 GACCCGA-CCGTTGACCC
9405 GACCCG
1 GACCCG
9411 TTGACCGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 21 0.60
18 14 0.40
ACGTcount: A:0.21, C:0.45, G:0.22, T:0.12
Consensus pattern (17 bp):
GACCCGACCGTTGACCC
Found at i:9409 original size:13 final size:13
Alignment explanation
Indices: 9391--9416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9381 TGACCCGAAT
9391 CGACCCGTTGACC
1 CGACCCGTTGACC
9404 CGACCCGTTGACC
1 CGACCCGTTGACC
9417 GTTGACCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:9540 original size:29 final size:29
Alignment explanation
Indices: 9508--9563 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
9498 GTTTGAAAAA
9508 GGTGATATTCTGGGAATTAATACGAAATT
1 GGTGATATTCTGGGAATTAATACGAAATT
* * *
9537 GGTGCTATTTTGGGAATTAATTCGAAA
1 GGTGATATTCTGGGAATTAATACGAAA
9564 AGGGTGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
GGTGATATTCTGGGAATTAATACGAAATT
Found at i:9569 original size:29 final size:29
Alignment explanation
Indices: 9424--9583 Score: 139
Period size: 28 Copynumber: 5.7 Consensus size: 29
9414 ACCGTTGACC
* ***
9424 GGTGTTATTTTGGGAATTAATTCG-GTTT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
* **
9452 AGTGCTATTCGGGGAATTAATTCG-AAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
* * * *
9480 GGTGCTATTTTGGTAATT-GTTTGAAAAA
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
* * * *
9508 GGTGATATTCTGGGAATTAATACGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
*
9537 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAAAT
*
9566 GGTGCT-TTTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
9584 TTTAAACAAA
Statistics
Matches: 102, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
27 3 0.03
28 64 0.63
29 35 0.34
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAT
Found at i:9583 original size:57 final size:56
Alignment explanation
Indices: 9457--9569 Score: 154
Period size: 56 Copynumber: 2.0 Consensus size: 56
9447 GGTTTAGTGC
* * * * *
9457 TATTCGGGGAATTAATTCGAAATGGTGCTATTTTGGTAATTGTTTGAAAAAGGTGA
1 TATTCTGGGAATTAATACGAAATGGTGCTATTTTGGGAATTATTCGAAAAAGGTGA
*
9513 TATTCTGGGAATTAATACGAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTG
1 TATTCTGGGAATTAATACGAAA-TGGTGCTATTTTGGGAATT-ATTCGAAAAAGGTG
9570 CTTTTTGGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
56 20 0.41
57 18 0.37
58 11 0.22
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (56 bp):
TATTCTGGGAATTAATACGAAATGGTGCTATTTTGGGAATTATTCGAAAAAGGTGA
Found at i:11294 original size:17 final size:17
Alignment explanation
Indices: 11272--11312 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
11262 CGTATCGCCG
*
11272 ATAAAATTTTACTATTC
1 ATAAAATTTCACTATTC
11289 ATAAAA-TTCACTATTC
1 ATAAAATTTCACTATTC
11305 ATATAAAT
1 ATA-AAAT
11313 AGTAACCTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAAATTTCACTATTC
Found at i:12094 original size:12 final size:13
Alignment explanation
Indices: 12067--12095 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12057 TTAATTAAGA
12067 TTTAAGATATTAT
1 TTTAAGATATTAT
12080 TTTAA-ATATTAT
1 TTTAAGATATTAT
12092 TTTA
1 TTTA
12096 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTAAGATATTAT
Found at i:12697 original size:18 final size:18
Alignment explanation
Indices: 12674--12716 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12664 CTTTAGATTA
*
12674 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
12692 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
12710 TTTATTT
1 TTTATTT
12717 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:12841 original size:21 final size:21
Alignment explanation
Indices: 12815--12882 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
12805 AACACTTCTT
12815 TTTTTATTTTATTTAGTTTTA
1 TTTTTATTTTATTTAGTTTTA
** *
12836 TTTTTATTTTA-CCA---CT-
1 TTTTTATTTTATTTAGTTTTA
*
12852 TTTTTATTTTATTTTGTTTTA
1 TTTTTATTTTATTTAGTTTTA
12873 TTTTTATTTT
1 TTTTTATTTT
12883 CTCTTTTAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
16 11 0.31
17 1 0.03
20 2 0.06
21 21 0.60
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTATTTAGTTTTA
Found at i:12882 original size:16 final size:16
Alignment explanation
Indices: 12816--12882 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
12806 ACACTTCTTT
*
12816 TTTTA-TTTTATTTAG
1 TTTTATTTTTATTTTG
*
12831 TTTTATTTTTATTTTACCAC
1 TTTTATTTTTATTTT----G
*
12851 TTTTTTATTTTATTTTG
1 TTTTAT-TTTTATTTTG
12868 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
12883 CTCTTTTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
15 5 0.12
16 17 0.41
17 5 0.12
20 5 0.12
21 9 0.22
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTATTTTG
Found at i:12970 original size:33 final size:34
Alignment explanation
Indices: 12868--12976 Score: 96
Period size: 40 Copynumber: 3.0 Consensus size: 34
12858 TTTTATTTTG
*
12868 TTTTATTTTTATTTTCTCTTTTAACATTTTTTATA
1 TTTTA-TTTTATTTTTTCTTTTAACATTTTTTATA
* *
12903 TTTTATTATTTTTCTTTTCTGAAATTTAATATTTTTT-TCA
1 TTTTATT-TTATT-TTTTCT----TTTAACATTTTTTAT-A
12943 -TTTATTTTATTTTTTCTTTTAACATTTTTATATA
1 TTTTATTTTATTTTTTCTTTTAACATTTTT-TATA
12977 ACATTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
33 11 0.18
34 4 0.07
35 10 0.17
36 5 0.08
37 6 0.10
38 4 0.07
39 7 0.12
40 13 0.22
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (34 bp):
TTTTATTTTATTTTTTCTTTTAACATTTTTTATA
Found at i:20264 original size:86 final size:86
Alignment explanation
Indices: 20137--20344 Score: 328
Period size: 86 Copynumber: 2.4 Consensus size: 86
20127 AGGAGTCACT
* * * *
20137 TGAAGAATATACCACATGACTTTCTCGTGAAGAGGAGTCATCCAAAGATCATCTCACCTGGTTCA
1 TGAAGAATATACCACAAGACTTTCCCGTGAAGGGGAATCATCCAAAGATCATCTCACCTGGTTCA
*
20202 GACTCGCGAAGGGGAACCACC
66 GACTCACGAAGGGGAACCACC
*
20223 TGAAGAATATACCACAAGACTTTCCCGTGAAGGGGAATCATCCAAATATCATCTCACCTGGTTCA
1 TGAAGAATATACCACAAGACTTTCCCGTGAAGGGGAATCATCCAAAGATCATCTCACCTGGTTCA
20288 GACTCACGAAGGGGAACCACC
66 GACTCACGAAGGGGAACCACC
**
20309 TGAAGAATATACCACTTGGA-TTTCCCGTGAAGGGGA
1 TGAAGAATATACCAC-AAGACTTTCCCGTGAAGGGGA
20345 GTCAACTAAA
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
86 111 0.98
87 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (86 bp):
TGAAGAATATACCACAAGACTTTCCCGTGAAGGGGAATCATCCAAAGATCATCTCACCTGGTTCA
GACTCACGAAGGGGAACCACC
Found at i:20785 original size:200 final size:199
Alignment explanation
Indices: 20411--21191 Score: 942
Period size: 200 Copynumber: 3.9 Consensus size: 199
20401 AGAGGAACCG
* * * * * *
20411 TTTATAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAACAAAACTTTTGAATTCGATTCCAATC
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
* * * ** * * *
20476 AGCTCAAAGGCATATTAACCGCATTGTAGCAATGATAAACTACTTTCCGGTTAAATTTTAAACCA
66 AGCTCAAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACCG
* * * * * *
20541 ATGTCTTTAAGTCAAGAAGAAGACATAGGTTGGTTGCAATTTAGCAATAAGGAACTATCTCACAG
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTC-CAG
*
20606 CCGAG
195 CCGAA
* * * *
20611 TTTACAACATAACTCAAGGCGAGAAGGGCTATCTTTCAACAAAACTTTCGAGTTCGATTCCTTTC
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
* *
20676 ATCTCGAAA-GCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACT
66 AGCTC-AAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACC
* *
20740 GAGGTCTTTAAGTCAAGAAGAAGACCTAGATTGGGTGCGATTTAGCAACAAGAAACTATCTCCAT
130 GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCCA-
20805 GCCGAA
194 GCCGAA
* * *
20811 TGTACAGCGTAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTTCATTC
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
* * *
20876 AGCTCAAAGGCTTATCAACCGCATGGTAGCAACGAGGAACTATTTTCCGGTTGAAGTTTAAATCG
66 AGCTCAAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACCG
* * * *
20941 AGGTCTTTAAGT---TAAGAAGACCTAGGTTAGCTGCGATTTAGTAACAAGAAACTATCTCCCAA
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCT-CCAG
*
21003 CTGAA
195 CCGAA
** * * *
21008 TTTACAGCATAGCTCAAGGCGAGAAATGATATTTGTCAACAAAACTTTCAAGTTCGATTCCATTC
1 TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
* * * * * * * *
21073 AGCTCGAAGACATATCAGCCGCATGGTAGCATCAAGGAACAACTTTTCGGTTGAATTTTCAAACC
66 AGCTCAAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTT-AAACC
* * ** * *
21138 GAGGTCTTTAA-ACTAAGAAGAAGACCAAGGTTAACTACGATTTGGCAACAAGAA
130 GAGGTCTTTAAGTC-AAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAA
21192 GCCATCTTCC
Statistics
Matches: 499, Mismatches: 73, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
197 150 0.30
198 18 0.04
199 5 0.01
200 291 0.58
201 35 0.07
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (199 bp):
TTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
AGCTCAAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACCG
AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCCAGC
CGAA
Found at i:22199 original size:22 final size:21
Alignment explanation
Indices: 22178--22264 Score: 52
Period size: 22 Copynumber: 4.0 Consensus size: 21
22168 CACTTCTTTC
22178 TTTCTTTTATTTTTTTA-TTT
1 TTTCTTTTATTTTTTTATTTT
* *
22198 TCTCACTTTATTTTATTTTATTTT
1 TTTC-TTTTA-TTT-TTTTATTTT
* **
22222 ATT-TTTTATTTTAATATTTT
1 TTTCTTTTATTTTTTTATTTT
* *
22242 TTCTATTTTATTATTTTTCTTTT
1 TT-TCTTTTATT-TTTTTATTTT
22265 ATGAAATTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
20 11 0.22
21 8 0.16
22 14 0.29
23 12 0.24
24 4 0.08
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTATTTTTTTATTTT
Found at i:22230 original size:17 final size:16
Alignment explanation
Indices: 22208--22259 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
22198 TCTCACTTTA
22208 TTTTATTTTATTTTATT
1 TTTTATTTTATTTT-TT
*
22225 TTTTATTTTAATATTTT
1 TTTTATTTT-ATTTTTT
*
22242 TTCTATTTTATTATTTT
1 TTTTATTTTATT-TTTT
22259 T
1 T
22260 CTTTTATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.80
18 4 0.13
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTTT
Found at i:22239 original size:25 final size:25
Alignment explanation
Indices: 22211--22258 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
22201 CACTTTATTT
*
22211 TATTTTATTTTATTTT-TTATTTTAA
1 TATTTT-TTCTATTTTATTATTTTAA
22236 TATTTTTTCTATTTTATTATTTT
1 TATTTTTTCTATTTTATTATTTT
22259 TCTTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (25 bp):
TATTTTTTCTATTTTATTATTTTAA
Found at i:22248 original size:9 final size:8
Alignment explanation
Indices: 22182--22259 Score: 59
Period size: 8 Copynumber: 9.2 Consensus size: 8
22172 TCTTTCTTTC
22182 TTTTATTT
1 TTTTATTT
22190 TTTTATTT
1 TTTTATTT
* *
22198 TCTCACTTT
1 TTTTA-TTT
22207 ATTTTATTT
1 -TTTTATTT
22216 TATTT-TATT
1 T-TTTAT-TT
22225 TTTTATTT
1 TTTTATTT
**
22233 TAATATTT
1 TTTTATTT
22241 TTTCTATTT
1 TTT-TATTT
*
22250 TATTATTT
1 TTTTATTT
22258 TT
1 TT
22260 CTTTTATGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
8 31 0.57
9 20 0.37
10 3 0.06
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:22264 original size:14 final size:15
Alignment explanation
Indices: 22220--22266 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
22210 TTATTTTATT
*
22220 TTATTTTTTATTTTA
1 TTATTTTTTCTTTTA
*
22235 ATATTTTTTCTATTTTA
1 TTATTTTTTC--TTTTA
22252 TTA-TTTTTCTTTTA
1 TTATTTTTTCTTTTA
22266 T
1 T
22267 GAAATTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
16 6 0.22
17 7 0.26
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTTTCTTTTA
Found at i:28786 original size:21 final size:21
Alignment explanation
Indices: 28760--28799 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28750 AAAAAACTGT
*
28760 TTTTTATTAATTTTTTTTATA
1 TTTTTATTAAATTTTTTTATA
28781 TTTTTATTAAATTTTTTTA
1 TTTTTATTAAATTTTTTTA
28800 AATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTAAATTTTTTTATA
Found at i:28800 original size:10 final size:11
Alignment explanation
Indices: 28760--28802 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
28750 AAAAAACTGT
28760 TTTTTATT-AA
1 TTTTTATTAAA
* *
28770 TTTTTTTTATA
1 TTTTTATTAAA
28781 TTTTTATTAAA
1 TTTTTATTAAA
28792 TTTTT-TTAAA
1 TTTTTATTAAA
28802 T
1 T
28803 AATTAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTATTAAA
Found at i:38562 original size:3 final size:3
Alignment explanation
Indices: 38506--38550 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
38496 CCTTTTTCTT
* *
38506 TTA TTA TTA TTA TTA ATA ATA TGTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
38551 TATAAATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:40842 original size:46 final size:46
Alignment explanation
Indices: 40772--40859 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
40762 GATTTCATTT
* * *
40772 TTTTTCTAAACAAAGCATGGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCAAACAAAGCATGAAACTAGAAAGCATG-AGGTTAGGTTAA
40818 TTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGG
40860 ACTTATACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.03
46 37 0.97
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (46 bp):
TTTTTCCAAACAAAGCATGAAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:42570 original size:8 final size:7
Alignment explanation
Indices: 42546--42586 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
42536 TTTTCATACA
42546 TGCA-TT
1 TGCATTT
42552 TGCATTT
1 TGCATTT
42559 TGCATCTT
1 TGCAT-TT
42567 TGCATTT
1 TGCATTT
*
42574 T-TATTT
1 TGCATTT
42580 TGCATTT
1 TGCATTT
42587 GTATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 9 0.30
7 14 0.47
8 7 0.23
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:42581 original size:13 final size:13
Alignment explanation
Indices: 42550--42593 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
42540 CATACATGCA
*
42550 TTTGCATTTTGCAT
1 TTTGCATTTT-TAT
42564 CTTTGCATTTTTAT
1 -TTTGCATTTTTAT
*
42578 TTTGCATTTGTAT
1 TTTGCATTTTTAT
42591 TTT
1 TTT
42594 TATGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 2 0.07
15 10 0.37
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (13 bp):
TTTGCATTTTTAT
Found at i:42685 original size:35 final size:34
Alignment explanation
Indices: 42646--42715 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
42636 CATTCACATA
* *
42646 TTTACATTTGTATTTGCATTTTGCATCTTTGCATT
1 TTTACATTTATATTTACATTTT-CATCTTTGCATT
* *
42681 TTTACGTTTATATTTACATTTTCATTTTTGCATT
1 TTTACATTTATATTTACATTTTCATCTTTGCATT
42715 T
1 T
42716 GCATATTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (34 bp):
TTTACATTTATATTTACATTTTCATCTTTGCATT
Found at i:45172 original size:71 final size:72
Alignment explanation
Indices: 45090--45223 Score: 207
Period size: 72 Copynumber: 1.9 Consensus size: 72
45080 ACACAATAAA
* *
45090 GCTTGAGTTAT-CCCTTAAAACAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGT
1 GCTTGAATTATCCCCCTAAAACAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGT
45154 CTGTTAT
66 CTGTTAT
* * * *
45161 GCTTGAATTATCCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTA
1 GCTTGAATTATCCCCCTAAAACAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTA
45224 ACTTATTATA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
71 10 0.18
72 46 0.82
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (72 bp):
GCTTGAATTATCCCCCTAAAACAATAGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGT
CTGTTAT
Found at i:47636 original size:75 final size:75
Alignment explanation
Indices: 47512--47679 Score: 212
Period size: 75 Copynumber: 2.2 Consensus size: 75
47502 TAGCAAGAAA
* * * *
47512 CAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATTGACACATTTTAAATG
1 CAAATGATGGGGCATGCTAAAAGCCCATTTCAATCAGAATCAGAAATATTAACACATTTTAAACG
47577 TTTGCATCAG
66 TTTGCATCAG
* * * *
47587 TAAATGATGGGGCATGCTAAAAGCCCATTTCAATCAGAAAT-TGAAATATTAACTCATTTTGAAC
1 CAAATGATGGGGCATGCTAAAAGCCCATTTCAATCAG-AATCAGAAATATTAACACATTTTAAAC
* *
47651 GTTTGTATTAG
65 GTTTGCATCAG
* *
47662 CAAATGTTGGGTCATGCT
1 CAAATGATGGGGCATGCT
47680 GAAGACTCAT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 76 0.96
76 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (75 bp):
CAAATGATGGGGCATGCTAAAAGCCCATTTCAATCAGAATCAGAAATATTAACACATTTTAAACG
TTTGCATCAG
Found at i:48622 original size:54 final size:54
Alignment explanation
Indices: 48553--48754 Score: 271
Period size: 54 Copynumber: 3.7 Consensus size: 54
48543 TTCACTGGCA
** * *
48553 AACATCTGTGTAGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTATTACG
1 AACATCTGTACAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACG
* *
48607 AACATCTGTACAGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTTACA
1 AACATCTGTACAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACG
* * * * * *
48661 AACATCTATGCATAAACCACATGAAATGATGAATGTGTTGTCAAATGTTTTATG
1 AACATCTGTACAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACG
*
48715 AACATCTG-AGCAGAAGCAACAGGAAATGATGAATGTGTTG
1 AACATCTGTA-CAGAAGCCACAGGAAATGATGAATGTGTTG
48755 CCAGATATTT
Statistics
Matches: 127, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
54 127 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (54 bp):
AACATCTGTACAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACG
Found at i:48740 original size:108 final size:108
Alignment explanation
Indices: 48551--48754 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 108
48541 GCTTCACTGG
* * *
48551 CAAACATCTGTGTAGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTATTACGAACATCTGT
1 CAAACATCTATGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTATTACGAACATCTGT
48616 ACAGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTTA
66 ACAGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTTA
* * *
48659 CAAACATCTATGCATAAACCACATGAAATGATGAATGTGTTGTCAAATGTTTTATGAACATCTG-
1 CAAACATCTATGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTATTACGAACATCTGT
48723 AGCAGAAG-CAACAGGAAATGATGAATGTGTTG
66 A-CAGAAGAC-ACAGGAAATGATGAATGTGTTG
48755 CCAGATATTT
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 2 0.02
108 86 0.98
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (108 bp):
CAAACATCTATGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGTATTACGAACATCTGT
ACAGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTTA
Found at i:49096 original size:211 final size:214
Alignment explanation
Indices: 48698--49110 Score: 562
Period size: 211 Copynumber: 1.9 Consensus size: 214
48688 GATGAATGTG
* * *
48698 TTGTCAAATGTTTTATGAACATCTGAGCAGAAGCAACAGGAAATGATGAATGTGTTGCCAGATAT
1 TTGTCAAATGTTTTACGAACATCTGAGCAGAAACAACAGGAAATGATGAATGTGTTGCCAAATAT
** * *
48763 TTTATGAACCAGTGATTATGGTGCTGAACCAATGTTGCAATCATATGGTATTTCCATTTATGGAC
66 TTTACAAACCAG-GATTATGATGCTGAACCAATGCTGCAATCATATGGTATTTCCATTTATGGAC
*** * *
48828 CCAAGATGAATTTTGACTTCTTCAATCCCAAGGTTAGAAGTGAGATATGATGAAGATTTCTTTCC
130 CCAAGATGAAGCCTGACATCTTCAACCCCAAGGTTAGAAGTGAGATATGATGAAGATTTCTTTCC
48893 ACAGAAGGGAAATTGAAATT
195 ACAGAAGGGAAATTGAAATT
* * * * *
48913 TTGTCAAATGTTTTACGAACATCTTAGCAGAAACCACATGAAATGATGAATGTGTTGTCAAATGT
1 TTGTCAAATGTTTTACGAACATCTGAGCAGAAACAACAGGAAATGATGAATGTGTTGCCAAATAT
* * * * * **
48978 TTTACAAATCA-G-TTATGATGTTGAACCAATGCTGCGATCATATGGTGTTTCCATTT-TTGATT
66 TTTACAAACCAGGATTATGATGCTGAACCAATGCTGCAATCATATGGTATTTCCATTTATGGACC
* *
49040 CAAGATGAAGCCTGTCATCTTCAACCCCAAGGTTAGAAGTGAGATATGATGAAGATTTCTTTCTA
131 CAAGATGAAGCCTGACATCTTCAACCCCAAGGTTAGAAGTGAGATATGATGAAGATTTCTTTCCA
49105 CAGAAG
196 CAGAAG
49111 TGAATCCCAA
Statistics
Matches: 172, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
211 67 0.39
212 39 0.23
213 1 0.01
215 65 0.38
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (214 bp):
TTGTCAAATGTTTTACGAACATCTGAGCAGAAACAACAGGAAATGATGAATGTGTTGCCAAATAT
TTTACAAACCAGGATTATGATGCTGAACCAATGCTGCAATCATATGGTATTTCCATTTATGGACC
CAAGATGAAGCCTGACATCTTCAACCCCAAGGTTAGAAGTGAGATATGATGAAGATTTCTTTCCA
CAGAAGGGAAATTGAAATT
Found at i:50185 original size:45 final size:45
Alignment explanation
Indices: 50088--50676 Score: 1000
Period size: 45 Copynumber: 13.1 Consensus size: 45
50078 GGGAGCTTTT
*
50088 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50132 TGATGTTTTCAAAGCATTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50177 TGATGTTTTCAAAGCATTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50222 TGATGTTTTCAAAGCCTTCGGGTCATATGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
50267 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
50312 TGATGTTTTTAAAGCCTTCAGGTCATCTTTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
50357 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
50402 TGATGTTTTCAAAGCCTTCGGGTCATATGTAATCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50447 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
50492 TGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
50537 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAACCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50582 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
50627 TGATGTTTTCAAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
50672 AGATG
1 TGATG
50677 ATAAGACCTT
Statistics
Matches: 513, Mismatches: 31, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
44 31 0.06
45 482 0.94
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:50840 original size:3 final size:3
Alignment explanation
Indices: 50832--50876 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
50822 CCTTTTTCTT
* * *
50832 TTA TTA TTA TTA ATA ATA TGTA TTA TTA TTA TTA TTA TAA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
50877 GTCGTAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:51418 original size:23 final size:24
Alignment explanation
Indices: 51389--51446 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
51379 TTTTTCTAAA
51389 AAAAAGATTAATATATA-TTATTT
1 AAAAAGATTAATATATATTTATTT
* * *
51412 ATAAAGATATGATATTTATTTATTT
1 AAAAAGAT-TAATATATATTTATTT
*
51437 AAAAATATTA
1 AAAAAGATTA
51447 GAACTGGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 7 0.26
24 8 0.30
25 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
AAAAAGATTAATATATATTTATTT
Found at i:51671 original size:27 final size:26
Alignment explanation
Indices: 51615--51692 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
51605 ACTTTTTTTA
*
51615 ATATTTTAAAAATAAATAAATATTAT
1 ATATTTTAAAAATAAATAAATAATAT
*
51641 -TATTTTATAAAATTAATAAATAATAT
1 ATATTTTA-AAAATAAATAAATAATAT
*
51667 ATATTAATAAAAATAAA-ATAATAATA
1 ATATT-TTAAAAATAAATA-AATAATA
51693 ATAATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
25 7 0.16
26 17 0.39
27 18 0.41
28 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATTTTAAAAATAAATAAATAATAT
Found at i:51704 original size:9 final size:9
Alignment explanation
Indices: 51680--51749 Score: 56
Period size: 9 Copynumber: 7.4 Consensus size: 9
51670 TTAATAAAAA
51680 TAAAATAA-
1 TAAAATAAT
51688 TAATAATAAT
1 TAA-AATAAT
51698 TAAAAT-AT
1 TAAAATAAT
51706 TAAACAT-AT
1 TAAA-ATAAT
51715 TAAAATATATT
1 TAAAATA-A-T
*
51726 TAAACAATAAC
1 T-AA-AATAAT
51737 TAAAATAAT
1 TAAAATAAT
51746 TAAA
1 TAAA
51750 CTATAGTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
8 11 0.21
9 25 0.48
10 6 0.12
11 3 0.06
12 3 0.06
13 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAATAAT
Found at i:51748 original size:20 final size:20
Alignment explanation
Indices: 51680--51750 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
51670 TTAATAAAAA
*
51680 TAAAATAA-T-AATAATAAT
1 TAAAATAATTAAACAATAAT
51698 TAAAAT-ATTAAAC-AT-AT
1 TAAAATAATTAAACAATAAT
*
51715 TAAAATATATTTAAACAATAAC
1 TAAAATA-A-TTAAACAATAAT
51737 TAAAATAATTAAAC
1 TAAAATAATTAAAC
51751 TATAGTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
17 9 0.20
18 9 0.20
19 3 0.07
20 12 0.27
21 3 0.07
22 8 0.18
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATAATTAAACAATAAT
Found at i:53150 original size:29 final size:28
Alignment explanation
Indices: 53127--53190 Score: 96
Period size: 26 Copynumber: 2.3 Consensus size: 28
53117 GTAATATGTA
53127 ATAATAATATTTATTATTAATAATCAAAT
1 ATAATAATA-TTATTATTAATAATCAAAT
*
53156 ATAATAATATTATTATT-ATAA-CAATT
1 ATAATAATATTATTATTAATAATCAAAT
53182 ATAATAATA
1 ATAATAATA
53191 ATAAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 13 0.38
27 4 0.12
28 8 0.24
29 9 0.26
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAATAATATTATTATTAATAATCAAAT
Found at i:53191 original size:29 final size:30
Alignment explanation
Indices: 53125--53193 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
53115 CTGTAATATG
53125 TAATAATAATATTTATTATTAATAATCAAA
1 TAATAATAATATTTATTATTAATAATCAAA
53155 T-ATAATAATA-TTATTATT-ATAA-CAATTA
1 TAATAATAATATTTATTATTAATAATCAA--A
53183 TAATAATAATA
1 TAATAATAATA
53194 AAAATAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.08
27 4 0.11
28 10 0.28
29 18 0.50
30 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TAATAATAATATTTATTATTAATAATCAAA
Found at i:53448 original size:17 final size:17
Alignment explanation
Indices: 53426--53481 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
53416 GTTGAACAAA
53426 TTCTTCTTATTATGAAC
1 TTCTTCTTATTATGAAC
* *
53443 TTCTTCTTTTTCA-GATGAG
1 TTCTTCTTATT-ATGA--AC
*
53462 TTCTTCTCATTATGAAC
1 TTCTTCTTATTATGAAC
53479 TTC
1 TTC
53482 CTCTGAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
17 16 0.53
18 2 0.07
19 12 0.40
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.52
Consensus pattern (17 bp):
TTCTTCTTATTATGAAC
Found at i:53685 original size:112 final size:112
Alignment explanation
Indices: 53556--54096 Score: 881
Period size: 113 Copynumber: 4.8 Consensus size: 112
53546 GCTAAGGTCA
*
53556 AACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
*
53621 ACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
66 ACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
*
53668 AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * * *
53733 ACCTGGCAATGCTAATCCATCTAGTGATGAATTTGAGAAAAAGGTTG
66 ACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
53780 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
53845 TACCAGGCAATGATGATCGATCGAGTGATGAATTCGAGCAAAAGGTTG
65 TACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
*
53893 AACAAGTTCTTCTCATTATGAACTTC-T-T-CTTCTTCAGATGAGTTCTTCTCATTATGAAGTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * *
53955 AACTGGCAATGCTAATCCATCGAGTGATGAATTTGAGCAAAAGGTTG
66 ACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
* * *
54002 AACAAGTTCTTCTCATTATGAACTTTTTCTTTCTTCTTCAGATGAGTTCTTCTCATTACGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
54067 TACCTGGCAATGTTGATCCATCGAGTGATG
65 TACCTGGCAATGCTGATCCATCGAGTGATG
54097 GATTTAAATC
Statistics
Matches: 396, Mismatches: 28, Indels: 9
0.91 0.06 0.02
Matches are distributed among these distances:
109 99 0.25
110 2 0.01
112 136 0.34
113 159 0.40
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (112 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
ACCTGGCAATGCTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTG
Found at i:53710 original size:23 final size:22
Alignment explanation
Indices: 53676--53720 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
53666 TGAACAAGTT
53676 CTTCTCATTATGAACTTCTTCTC
1 CTTCTCATTATG-ACTTCTTCTC
*
53699 CTTCTTCA-TATGAGTTCTTCTC
1 CTTC-TCATTATGACTTCTTCTC
53721 ATTATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.49
Consensus pattern (22 bp):
CTTCTCATTATGACTTCTTCTC
Found at i:53984 original size:222 final size:225
Alignment explanation
Indices: 53556--54096 Score: 946
Period size: 222 Copynumber: 2.4 Consensus size: 225
53546 GCTAAGGTCA
*
53556 AACAAGCTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
53620 TACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATT
66 TACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATT
* *
53685 ATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTAATC
131 ATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTAATC
*
53750 CATCTAGTGATGAATTTGAGAAAAAGGTTG
196 CATCGAGTGATGAATTTGAGAAAAAGGTTG
53780 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
53845 TACCAGGCAATGATGATCGATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATT
66 TACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATT
*
53910 ATGAACTTC-T-T-CTTCTTCAGATGAGTTCTTCTCATTATGAAGTCTAACTGGCAATGCTAATC
131 ATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTAATC
*
53972 CATCGAGTGATGAATTTGAGCAAAAGGTTG
196 CATCGAGTGATGAATTTGAGAAAAAGGTTG
* * *
54002 AACAAGTTCTTCTCATTATGAACTTTTTCTTTCTTCTTCAGATGAGTTCTTCTCATTACGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
54067 TACCTGGCAATGTTGATCCATCGAGTGATG
66 TACCTGGCAATGTTGATCCATCGAGTGATG
54097 GATTTAAATC
Statistics
Matches: 301, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
222 165 0.55
223 1 0.00
224 29 0.10
225 106 0.35
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (225 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTAATC
CATCGAGTGATGAATTTGAGAAAAAGGTTG
Found at i:54503 original size:22 final size:22
Alignment explanation
Indices: 54452--54505 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
54442 AATAAAACTT
*
54452 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
54474 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
54496 TCATCTTTGA
1 TCATCTTTGA
54506 GGAATGTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:58635 original size:72 final size:72
Alignment explanation
Indices: 58518--58652 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
58508 TATAATAGGT
*
58518 TAGCTGAATATTATCCATAAAGCCGGGGCAATTAACCAATTGCTTTAAAGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTGCTTTAAAGGGACAACTCAAGCAT
58583 AACAAAC
66 AACAAAC
* ** *
58590 TAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTGCTTTAAAGGGACAACTCAAGC
58653 TTTATTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGCCAGGGCAATTAACCAATTGCTTTAAAGGGACAACTCAAGCAT
AACAAAC
Done.