Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002267.1 Hibiscus syriacus cultivar Beakdansim tig00004612_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: 65234
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1646 original size:2 final size:2
Alignment explanation
Indices: 1641--1679 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1631 ATTTTTTAAT
1641 TA TA TA -A TA TA 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
1680 ATGATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4783 original size:45 final size:46
Alignment explanation
Indices: 4727--4827 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 46
4717 CATTAAAGTG
* *
4727 CCACATAGAAATGTCCCGAAGGACCACATAGTATTGTC-CAAAGGA
1 CCACGTAGAAATGTCCCGAAGGACCACATAGAATTGTCTCAAAGGA
* * *
4772 CCACGTAGAAATGTCCCGAAGGACTACGTAGAATTGTCTCGAAGGA
1 CCACGTAGAAATGTCCCGAAGGACCACATAGAATTGTCTCAAAGGA
*
4818 CCGCGTAGAA
1 CCACGTAGAA
4828 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 34 0.69
46 15 0.31
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (46 bp):
CCACGTAGAAATGTCCCGAAGGACCACATAGAATTGTCTCAAAGGA
Found at i:4824 original size:23 final size:23
Alignment explanation
Indices: 4727--4827 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
4717 CATTAAAGTG
*
4727 CCACATAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
* * * *
4750 CCACATAGTATTGT-CCAAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
4772 CCACGTAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
* * *
4795 CTACGTAGAATTGTCTCGAAGGA
1 CCACGTAGAAATGTCCCGAAGGA
*
4818 CCGCGTAGAA
1 CCACGTAGAA
4828 CCCTCGACTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 18 0.28
23 47 0.72
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCGAAGGA
Found at i:5009 original size:45 final size:45
Alignment explanation
Indices: 4946--5072 Score: 164
Period size: 45 Copynumber: 2.8 Consensus size: 45
4936 ATAGATCATT
* * *
4946 TCACATAGCTTATATCACATTTTCATATAATCACGTAGTTCAATA
1 TCACATAGATTATATCACATTTTCATATAATCACATAGGTCAATA
* * * *
4991 TTACATATATTATATCACATTTTCATTTAATCACATAGGTCAATG
1 TCACATAGATTATATCACATTTTCATATAATCACATAGGTCAATA
* * *
5036 TCACATAGCTTATATCATATTATCATATAATCACATA
1 TCACATAGATTATATCACATTTTCATATAATCACATA
5073 AATCATGTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (45 bp):
TCACATAGATTATATCACATTTTCATATAATCACATAGGTCAATA
Found at i:5104 original size:19 final size:16
Alignment explanation
Indices: 5057--5117 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
5047 ATATCATATT
5057 ATCATATAATCACATAA
1 ATCATATAA-CACATAA
*
5074 ATCATGTAACACATAA
1 ATCATATAACACATAA
*
5090 GATGACATATAACACATAG
1 -AT--CATATAACACATAA
5109 ATCATATAA
1 ATCATATAA
5118 ATAGTGCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 2 0.05
19 12 0.32
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (16 bp):
ATCATATAACACATAA
Found at i:13786 original size:60 final size:60
Alignment explanation
Indices: 13646--13786 Score: 144
Period size: 60 Copynumber: 2.4 Consensus size: 60
13636 TGAAACATTC
* * * * *
13646 AAAAAGTTTGGGGACCAATTTAGAATGAAGATCACAATTTGGGGATGAAAATGAAATGTT
1 AAAAAGTTTAGGGACCAATTTAGAATGAAGACCACAATTTAGAGATGAAAATAAAATGTT
* * * * *
13706 CAAAAGTTTAAGGG-CTAATTTAGAGTGATAG-CCATAGTTTAGAGAT-AAAATTAAAATGTT
1 AAAAAGTTT-AGGGACCAATTTAGAATGA-AGACCACAATTTAGAGATGAAAA-TAAAATGTT
13766 AAAAAGTTTAGGGACCAATTT
1 AAAAAGTTTAGGGACCAATTT
13787 GAAATAAAGG
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
59 8 0.12
60 52 0.80
61 5 0.08
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (60 bp):
AAAAAGTTTAGGGACCAATTTAGAATGAAGACCACAATTTAGAGATGAAAATAAAATGTT
Found at i:18966 original size:23 final size:23
Alignment explanation
Indices: 18936--18986 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
18926 TTAGAATTTT
18936 GAATATTTTCACTTTTTTAATAA
1 GAATATTTTCACTTTTTTAATAA
18959 GAATATTTTCACTTTTTTAATAA
1 GAATATTTTCACTTTTTTAATAA
18982 GAATA
1 GAATA
18987 ACGGCTAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (23 bp):
GAATATTTTCACTTTTTTAATAA
Found at i:20394 original size:16 final size:16
Alignment explanation
Indices: 20357--20398 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
20347 AACAGCTACC
*
20357 CCTAAAACAAACCATT
1 CCTAAAGCAAACCATT
**
20373 TTTAAAGCAAACCATT
1 CCTAAAGCAAACCATT
20389 CCTAAAGCAA
1 CCTAAAGCAA
20399 TGAAACCAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.05, T:0.21
Consensus pattern (16 bp):
CCTAAAGCAAACCATT
Found at i:20637 original size:22 final size:22
Alignment explanation
Indices: 20609--20653 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20599 CCGGACCTAA
*
20609 GATCCATATCCGATCCAGACTC
1 GATCCATACCCGATCCAGACTC
*
20631 GATCCATACCCGATCCATACTC
1 GATCCATACCCGATCCAGACTC
20653 G
1 G
20654 GCGCATGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.38, G:0.13, T:0.22
Consensus pattern (22 bp):
GATCCATACCCGATCCAGACTC
Found at i:27375 original size:16 final size:16
Alignment explanation
Indices: 27354--27391 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
27344 TCAAGAAAAT
*
27354 ATACATCAATACATAC
1 ATACATCAACACATAC
27370 ATACATCAACACATAC
1 ATACATCAACACATAC
27386 ATACAT
1 ATACAT
27392 GATATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
ATACATCAACACATAC
Found at i:27947 original size:66 final size:67
Alignment explanation
Indices: 27876--28046 Score: 236
Period size: 66 Copynumber: 2.6 Consensus size: 67
27866 ATTTCAAAGC
27876 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCATTGAGTATGTTTC-CTTAAAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCATTGAGTATGTTTCTCTTAAAA
27940 CA
66 CA
* * ** * *
27942 AAGTTTTGTCTCTCTTGAGACAATTTATCTTGAAAGAAATGTCTTTGAGTATGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCATTGAGTATGTTTCTCTTAAAA
28007 CA
66 CA
* * * * *
28009 ATGTTTTATCTCTCTTGAGACAGTTTCCCTTAAAACAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAA
28047 GTTTTGTCTC
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 52 0.57
67 39 0.43
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (67 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCATTGAGTATGTTTCTCTTAAAA
CA
Found at i:28045 original size:37 final size:36
Alignment explanation
Indices: 27994--28147 Score: 142
Period size: 36 Copynumber: 4.4 Consensus size: 36
27984 CTTTGAGTAT
*
27994 GTTTCTCTTGAAACAATGTTTTATCTCTCTTGAGACA
1 GTTTCCCTTGAAACAA-GTTTTATCTCTCTTGAGACA
* * * *
28031 GTTTCCCTTAAAACAAGTTTTGTCTCTTTTGAGACT
1 GTTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACA
* *
28067 GTTTCCCTTGAAACAA-----A-CAACT-TTGAGACT
1 GTTTCCCTTGAAACAAGTTTTATC-TCTCTTGAGACA
* * *
28097 GTTTCCCTTGAAACAAGTTTTGTCTCCCTTAAGACA
1 GTTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACA
*
28133 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
28148 CAACAACTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 17
0.75 0.11 0.13
Matches are distributed among these distances:
30 25 0.26
31 2 0.02
35 1 0.01
36 53 0.56
37 14 0.15
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTATCTCTCTTGAGACA
Found at i:28053 original size:103 final size:102
Alignment explanation
Indices: 27928--28147 Score: 264
Period size: 103 Copynumber: 2.1 Consensus size: 102
27918 CATTGAGTAT
* * ***
27928 GTTT-CCTTAAAACAAAGTTTTGTCTCTCTTGAGACAATTTATCTTGAAAGAAATGTCTTTGAGT
1 GTTTCCCTTAAAAC-AAGTTTTGTCTCTCTTGAGACAATTTACCTTGAAACAAACAACTTTGAG-
* * *
27992 A-TGTTTCTCTTGAAACAATGTTTTATCTCTCTTGAGACA
64 ACTGTTTCCCTTGAAACAA-GTTTTATCTCCCTTAAGACA
* ** *
28031 GTTTCCCTTAAAACAAGTTTTGTCTCTTTTGAGACTGTTTCCCTTGAAACAAACAACTTTGAGAC
1 GTTTCCCTTAAAACAAGTTTTGTCTCTCTTGAGACAATTTACCTTGAAACAAACAACTTTGAGAC
*
28096 TGTTTCCCTTGAAACAAGTTTTGTCTCCCTTAAGACA
66 TGTTTCCCTTGAAACAAGTTTTATCTCCCTTAAGACA
* *
28133 GTTTCTCTTGAAACA
1 GTTTCCCTTAAAACA
28148 CAACAACTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
102 31 0.31
103 60 0.60
104 9 0.09
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
GTTTCCCTTAAAACAAGTTTTGTCTCTCTTGAGACAATTTACCTTGAAACAAACAACTTTGAGAC
TGTTTCCCTTGAAACAAGTTTTATCTCCCTTAAGACA
Found at i:28255 original size:65 final size:65
Alignment explanation
Indices: 28023--28345 Score: 334
Period size: 65 Copynumber: 4.9 Consensus size: 65
28013 TTTATCTCTC
* * * *
28023 TTGAGA-CAGTTTCCCTTAAAACAAGTTTTGTCTCTTTTGAGACTGTTTCCCTTGAAACAAACA-
1 TTGAGATCA-TTTCCCTTGAAACAA-TTTTGTCTCTTTTGAGACAGTTTCTCTTGAAAC-ATCAT
28086 ACT
63 ACT
* ** *
28089 TTGAGA-CTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACA-CAAC
1 TTGAGATC-ATTTCCCTTGAAACAA-TTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATC-A-
*
28152 AACT
62 TACT
* ** * * * *
28156 TTGACATTGTTTCCCTTGAAACAAAATTAGTCTCTTTTTAGACAATTTCTCTTGAAACATCATA-
1 TTGAGATCATTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATCATAC
28220 T
65 T
* *
28221 TTGATATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCAT-C
1 TTGAGATCATTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATCATAC
28285 T
65 T
* *
28286 TTGAGATCATTTCCCTTTAAACGAATTTTGTCTCTTTCGAGACAGTTTCTCTTGAAACAT
1 TTGAGATCATTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAT
28346 TTATCCCTAA
Statistics
Matches: 220, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
64 1 0.00
65 114 0.52
66 51 0.23
67 51 0.23
68 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (65 bp):
TTGAGATCATTTCCCTTGAAACAATTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATCATACT
Found at i:31161 original size:16 final size:17
Alignment explanation
Indices: 31135--31171 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
31125 ATAGACCAAT
31135 TTTTGTCTTAAAAATGA
1 TTTTGTCTTAAAAATGA
*
31152 TTTT-TCTTAAAAATTA
1 TTTTGTCTTAAAAATGA
31168 TTTT
1 TTTT
31172 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTTGTCTTAAAAATGA
Found at i:32060 original size:28 final size:28
Alignment explanation
Indices: 32012--32080 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
32002 ATAAATGAAT
*
32012 AAATAAATAAAAACTAGAAAAGAGAAA-A
1 AAATAAATAAAAACTAAAAAAG-GAAATA
*
32040 AAATACAATAAATA-TAAAAAAGGAAATA
1 AAATA-AATAAAAACTAAAAAAGGAAATA
32068 AAA-AAATTAAAAA
1 AAATAAA-TAAAAA
32081 AGTATATACA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
28 16 0.46
29 7 0.20
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.14
Consensus pattern (28 bp):
AAATAAATAAAAACTAAAAAAGGAAATA
Found at i:32104 original size:3 final size:3
Alignment explanation
Indices: 32096--32175 Score: 78
Period size: 3 Copynumber: 27.3 Consensus size: 3
32086 ATACAATGAC
* **
32096 AAT AAT AAT AAT AAT AAA AAT -AT AA- AAT AA- AAT -AT ATAT GTT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
32138 AAT AAT AAT GAAT AAT AAT AAT AAT AAT AAT TAT AAT A
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A
32176 TATATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
2 8 0.13
3 50 0.79
4 5 0.08
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:32132 original size:14 final size:15
Alignment explanation
Indices: 32099--32204 Score: 60
Period size: 18 Copynumber: 6.8 Consensus size: 15
32089 CAATGACAAT
32099 AATA-ATAATAATAA
1 AATATATAATAATAA
32113 AA-ATATAA-AATAA
1 AATATATAATAATAA
*
32126 AATATATATGTTAATAA
1 AATATATA--ATAATAA
32143 TAATGA-ATAATAATAA
1 -AAT-ATATAATAATAA
*
32159 TAATA-ATAATTATAA
1 -AATATATAATAATAA
*
32174 TATATATATATATATATA
1 AATATATA-ATA-ATA-A
*
32192 TATATATATATAA
1 AATATATA-ATAA
32205 ACTAGTGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
13 8 0.11
14 14 0.18
15 13 0.17
16 12 0.16
17 9 0.12
18 19 0.25
19 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AATATATAATAATAA
Found at i:32151 original size:22 final size:22
Alignment explanation
Indices: 32097--32175 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
32087 TACAATGACA
*
32097 ATAATAATAATAATAA-AAAT-
1 ATAATAATAATAATAATGAATA
* *
32117 ATAA-AATAAAATATATATG-TTA
1 ATAATAATAATA-ATA-ATGAATA
32139 ATAATAATGAATAATAAT-AATA
1 ATAATAAT-AATAATAATGAATA
*
32161 ATAATAATTATAATA
1 ATAATAATAATAATA
32176 TATATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 6 0.13
20 7 0.15
21 8 0.17
22 16 0.35
23 6 0.13
24 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
ATAATAATAATAATAATGAATA
Found at i:32180 original size:2 final size:2
Alignment explanation
Indices: 32169--32203 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
32159 TAATAATAAT
32169 TA TA -A TA 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
32204 AACTAGTGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33334 original size:34 final size:34
Alignment explanation
Indices: 33278--33620 Score: 216
Period size: 36 Copynumber: 9.6 Consensus size: 34
33268 AAAAAAATTG
* *
33278 TTTTAAAACTATATATAATATATATTTCAAAGATA
1 TTTTAAAACTATATATTATATA-ATTTCAAAAATA
* * *
33313 TTTTCAAAACCATATATTATATAATTTTAAAAATG
1 TTTT-AAAACTATATATTATATAATTTCAAAAATA
* * **
33348 TTTTCAAACTATAGATTATAGT--TTTCAAAAACG
1 TTTTAAAACTATATATTATA-TAATTTCAAAAATA
** * *
33381 TTTTAAAAC--TATATTATATGTTTTTAAAAATGTT
1 TTTTAAAACTATATATTATATAATTTCAAAAA--TA
*
33415 TTTTTAAACTATATATTATATAGATTTC-AAAATGA
1 TTTTAAAACTATATATTATATA-ATTTCAAAAAT-A
33450 TTTTAAAACTATATATTATATAAGTTTTC-AAAATGA
1 TTTTAAAACTATATATTATATAA--TTTCAAAAAT-A
* *
33486 TTTTAAAATTATATATTATATATTTTTTCTAAAAATA
1 TTTTAAAACTATATATTATATA--ATTTC-AAAAATA
* * **
33523 TTTTGAAATATTATATATTATATAGTTTTCAAAGGTA
1 TTTT-AAA-ACTATATATTATATA-ATTTCAAAAATA
* *
33560 TTTTTAAAA--ACTATATTAAATACATTTTCAAAATGTA
1 -TTTTAAAACTA-TATATTATATA-A-TTTCAAAA-ATA
*
33597 TTTTTAAAAATCATATATTATATA
1 -TTTTAAAACT-ATATATTATATA
33621 CATATTTTTC
Statistics
Matches: 252, Mismatches: 31, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.00
31 8 0.03
32 8 0.03
33 17 0.07
34 24 0.10
35 49 0.19
36 74 0.29
37 28 0.11
38 17 0.07
39 25 0.10
40 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
TTTTAAAACTATATATTATATAATTTCAAAAATA
Found at i:33563 original size:74 final size:71
Alignment explanation
Indices: 33278--33620 Score: 189
Period size: 74 Copynumber: 4.8 Consensus size: 71
33268 AAAAAAATTG
* * ** *
33278 TTTT-AAAACTATA-TATAATATATATTTCAAAGATATTTTCAAAACCATATATTATATAATTTT
1 TTTTAAAAACTATATTA-AATACAT-TTTCAAAAATATTTT-AAAATTATATATTATATAGTTTT
*
33341 AAAAATG--
63 CAAAATGAT
* * ** *
33348 TTTT-CAAACTATAGATT--ATA-GTTTTCAAAAACGTTTTAAAA--CTATATTATAT-GTTTTT
1 TTTTAAAAACTAT--ATTAAATACATTTTCAAAAATATTTTAAAATTATATATTATATAG-TTTT
*
33406 AAAAATG-T
63 CAAAATGAT
** * * *
33414 TTTTTTAAACTATATATTATATAGA-TTTC-AAAATGATTTTAAAACTATATATTATATAAGTTT
1 TTTTAAAAAC--TATATTAAATACATTTTCAAAAAT-ATTTTAAAATTATATATTATAT-AGTTT
33477 TCAAAATGA-
62 TCAAAATGAT
* **
33486 TTTTAAAATTA-TATATTATATATTTTTTCTAAAAATATTTTGAAATATTATATATTATATAGTT
1 TTTTAAAA--ACTATATTAAATACATTTTC-AAAAATATTTT-AAA-ATTATATATTATATAGTT
*
33550 TTC-AAAGGTAT
61 TTCAAAATG-AT
* *
33561 TTTTAAAAACTATATTAAATACATTTTCAAAATGTATTTTTAAAAATCATATATTATATA
1 TTTTAAAAACTATATTAAATACATTTTCAAAA-ATA-TTTT-AAAATTATATATTATATA
33621 CATATTTTTC
Statistics
Matches: 219, Mismatches: 25, Indels: 54
0.73 0.08 0.18
Matches are distributed among these distances:
65 21 0.10
66 4 0.02
67 11 0.05
68 16 0.07
69 19 0.09
70 14 0.06
71 21 0.10
72 21 0.10
73 16 0.07
74 48 0.22
75 28 0.13
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (71 bp):
TTTTAAAAACTATATTAAATACATTTTCAAAAATATTTTAAAATTATATATTATATAGTTTTCAA
AATGAT
Found at i:33660 original size:2 final size:2
Alignment explanation
Indices: 33649--33689 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
33639 TTTTGTGAAC
* *
33649 TA TA TA -A TA TA TG TA TA GA 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
33690 AAATAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:39463 original size:136 final size:136
Alignment explanation
Indices: 39228--39709 Score: 449
Period size: 136 Copynumber: 3.5 Consensus size: 136
39218 TTGAACAAGT
* * * *
39228 TCTTCTCATTATGAAATTCTTCT-CCTTTATCGGATAAGATCTTCTCATTAAGAACTCTCCACTG
1 TCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
* * * *** *
39292 GAAATGTTAATCCCTCAAGCCAGGTGTTACTGATTCGAAGTGTTGTGAATCGAGCAATAGGTCGA
66 GAAATGTCAATCCCTCAAGCCAGGTGTCACTGATTCGAAATACCGTGAATCAAGCAATAGGTCGA
39357 ACAAAC
131 ACAAAC
* * * *
39363 TCTTCTCATTATGAACCTCTTCTCCCTCTT-TCAGATGAGTTCTTCTCATTATGATCTCTTCATC
1 TCTTCTCATTATGAACTTCTTCTCCCT-TTATCGGATGAGTTCTTCTCATTATGAACTCTCCA-C
* * **
39427 T-GAAATGTCATTCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCAAGTGATAGGTC
64 TGGAAATGTCAATCCCTCAAGCCAGGTGTCACTGATTCGAAATACCGTGAATCAAGCAATAGGTC
*
39491 GAACAAGC
129 GAACAAAC
* * *
39499 TCTTCTCATTATGATCTTTTTCTCCCTTTGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
1 TCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
** * *** ** * * *
39564 GAAATGTTGATCCCTCGATTGAGGTGTTGCTGATTC-AACTCCATA-TGTGATTAATCGAGCTA-
66 GAAATGTCAATCCCTCAAGCCAGGTGTCACTGATTCGAA----ATACCGTG---AATCAAGCAAT
* *
39626 AGATTGAAC-AAC
124 AGGTCGAACAAAC
** * * *
39638 TTCTTCTCATTATGAACTTCTTCTATC-TTATCGGATGAGTTATTCTCATTTTGAACTCTCCATT
1 -TCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
39702 GGAAATGT
65 GGAAATGT
39710 TGATTGGTTT
Statistics
Matches: 285, Mismatches: 49, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
135 27 0.09
136 169 0.59
137 4 0.01
138 3 0.01
139 46 0.16
140 29 0.10
141 7 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (136 bp):
TCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGTCAATCCCTCAAGCCAGGTGTCACTGATTCGAAATACCGTGAATCAAGCAATAGGTCGA
ACAAAC
Found at i:40709 original size:20 final size:20
Alignment explanation
Indices: 40676--40792 Score: 56
Period size: 20 Copynumber: 5.7 Consensus size: 20
40666 AAAACATCAT
* *
40676 GCCCGAAGGTCTTATGGATG
1 GCCCGAAAGACTTATGGATG
* *
40696 GCCCGAAAGACTTAT-CATCTT
1 GCCCGAAAGACTTATGGA--TG
* *
40717 GCTCGAAAGACTTATAGATG
1 GCCCGAAAGACTTATGGATG
* * * * * *
40737 ACCCGAAGGATTTAAGCATCAT
1 GCCCGAAAGACTTATGGAT--G
* *
40759 GCTCGAAAGACTTATTGATG
1 GCCCGAAAGACTTATGGATG
*
40779 GCCCGAAGGACTTA
1 GCCCGAAAGACTTA
40793 CTCATCAAGA
Statistics
Matches: 67, Mismatches: 25, Indels: 10
0.66 0.25 0.10
Matches are distributed among these distances:
19 1 0.01
20 38 0.57
21 15 0.22
22 13 0.19
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (20 bp):
GCCCGAAAGACTTATGGATG
Found at i:40799 original size:42 final size:41
Alignment explanation
Indices: 40670--40799 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 41
40660 ATGTTGAAAA
* * * * *
40670 CATCATGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAT
* * * *
40711 CATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTT-AT
*
40753 CATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTACT
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTA-T
40795 CATCA
1 CATCA
40800 AGAAACCCTT
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
41 32 0.44
42 41 0.56
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAT
Found at i:40939 original size:52 final size:54
Alignment explanation
Indices: 40794--41106 Score: 249
Period size: 54 Copynumber: 5.8 Consensus size: 54
40784 AAGGACTTAC
* * * * * **
40794 TCATCAAGAAAC-CCTTGAAAATCAAGCTTAGTTTCTTAAAAATTTCGTTTATAGTTA
1 TCATCAAGAAACTCC-TAAAAATCAGGCTTAATTTCTTTAAAA-TTCATTTA-A-AAA
* * * *
40851 TCATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTT-GAAA
1 TCATCAAGAAACTCCTAAAAATCAGGCTTAATTTCTTTAAAATTCATTTAAAAA
* ** * *
40904 -CATCAAGAAACTCCTGAAAAA-CAGTCTTAGCTTCTTTCAAATTCATTTGAAAA
1 TCATCAAGAAACTCCT-AAAAATCAGGCTTAATTTCTTTAAAATTCATTTAAAAA
* * * * *
40957 -CGTCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTTAAAGTTCTTTTAAAAA
1 TCATCAAGAAACTCCTAAAAATCAGGCTTAATTTC-TTTAAAATTCATTTAAAAA
* * * *
41011 TCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAATCATTTAAAAA
1 TCATCAAGAAACTCCTAAAAATCAGGCTTAATTTCTTTAAAATTCATTTAAAAA
* * * * * * *
41065 TCGTCAAGAAACTTCTGAAAATTAGACTTAGTTTATTTAAAA
1 TCATCAAGAAACTCCTAAAAATCAGGCTTAATTTCTTTAAAA
41107 ACTCATTAGC
Statistics
Matches: 210, Mismatches: 40, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
52 41 0.20
53 31 0.15
54 69 0.33
55 28 0.13
56 6 0.03
57 33 0.16
58 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (54 bp):
TCATCAAGAAACTCCTAAAAATCAGGCTTAATTTCTTTAAAATTCATTTAAAAA
Found at i:40990 original size:105 final size:109
Alignment explanation
Indices: 40854--41094 Score: 321
Period size: 108 Copynumber: 2.2 Consensus size: 109
40844 ATAGTTATCA
*
40854 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAA-TTCATTT-GAAA-CATCAAGAAACT
1 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAAGTTCATTTAAAAATCATCAAGAAACT
* * * *
40916 CCTGAAAAA-CAGTCTTAGCTTCTTTCAAATTCATTTGAAAA-CG
66 CCT-AAAAATCAGACTTAGCTTCTTTAAAAATCATTTAAAAATCG
* *
40959 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTTAAAGTTCTTTTAAAAATCATCAAGAAACT
1 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAAGTTCATTTAAAAATCATCAAGAAACT
* *
41024 TCTAAAAATCAGACTTAGTTTCTTTAAAAATCATTTAAAAATCG
66 CCTAAAAATCAGACTTAGCTTCTTTAAAAATCATTTAAAAATCG
** * *
41068 TCAAGAAACTTCTGAAAATTAGACTTA
1 TCAAGAAACCCCTAAAAATTAGGCTTA
41095 GTTTATTTAA
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
105 38 0.32
106 6 0.05
107 8 0.07
108 41 0.35
109 25 0.21
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (109 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAAGTTCATTTAAAAATCATCAAGAAACT
CCTAAAAATCAGACTTAGCTTCTTTAAAAATCATTTAAAAATCG
Found at i:41107 original size:54 final size:53
Alignment explanation
Indices: 40852--41106 Score: 253
Period size: 54 Copynumber: 4.8 Consensus size: 53
40842 TTATAGTTAT
* * * * *
40852 CATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTT-GAAA
1 CATCAAGAAACTCCTAAAAATTAGACTTAGTTTCTTTAAAATTCATTTAAAAA
* * * * *
40904 CATCAAGAAACTCCTGAAAAA-CAGTCTTAGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACTCCT-AAAAATTAGACTTAGTTTCTTTAAAATTCATTTAAAAA
* * * * * *
40957 CGTCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTTAAAGTTCTTTTAAAAA
1 CATCAAGAAACTCCTAAAAATTAGACTTAGTTTC-TTTAAAATTCATTTAAAAA
* * *
41011 TCATCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAATCATTTAAAAA
1 -CATCAAGAAACTCCTAAAAATTAGACTTAGTTTCTTTAAAATTCATTTAAAAA
* * * *
41065 TCGTCAAGAAACTTCTGAAAATTAGACTTAGTTTATTTAAAA
1 -CATCAAGAAACTCCTAAAAATTAGACTTAGTTTCTTTAAAA
41107 ACTCATTAGC
Statistics
Matches: 168, Mismatches: 30, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
52 41 0.24
53 30 0.18
54 69 0.41
55 28 0.17
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (53 bp):
CATCAAGAAACTCCTAAAAATTAGACTTAGTTTCTTTAAAATTCATTTAAAAA
Found at i:41291 original size:4 final size:4
Alignment explanation
Indices: 41274--41313 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
41264 CTGTATGAAA
* *
41274 TATG TATA TATG TATG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
41314 AATACACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:41291 original size:12 final size:12
Alignment explanation
Indices: 41274--41313 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
41264 CTGTATGAAA
41274 TATGTATATATG
1 TATGTATATATG
41286 TATGTATATATG
1 TATGTATATATG
*
41298 TATGTATGTATG
1 TATGTATATATG
41310 TATG
1 TATG
41314 AATACACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (12 bp):
TATGTATATATG
Found at i:43607 original size:9 final size:9
Alignment explanation
Indices: 43593--43636 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
43583 TATATCTTCT
43593 TTTTTTTCC
1 TTTTTTTCC
43602 -TTTTTTCC
1 TTTTTTTCC
*
43610 TATTTTTCC
1 TTTTTTTCC
43619 TTTCTTTTACC
1 TTT-TTTT-CC
43630 TTTTTTT
1 TTTTTTT
43637 ATTTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.27
9 9 0.30
10 8 0.27
11 5 0.17
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:43641 original size:8 final size:8
Alignment explanation
Indices: 43630--43704 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 8
43620 TTCTTTTACC
43630 TTTTTTTA
1 TTTTTTTA
43638 TTTTTTTTA
1 -TTTTTTTA
*
43647 TTTTTTATT
1 TTTTTT-TA
43656 TTTTCTTTA
1 TTTT-TTTA
*
43665 TTTTTTCA
1 TTTTTTTA
*
43673 TTTTTTTC
1 TTTTTTTA
*
43681 TTCTTTTTT
1 TT-TTTTTA
*
43690 TCTTTTTTC
1 T-TTTTTTA
43699 TTTTTT
1 TTTTTT
43705 CTTTCTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 22 0.40
9 30 0.55
10 3 0.05
ACGTcount: A:0.07, C:0.08, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:43652 original size:11 final size:11
Alignment explanation
Indices: 43630--43714 Score: 75
Period size: 11 Copynumber: 7.5 Consensus size: 11
43620 TTCTTTTACC
*
43630 TTTTTTTATTT
1 TTTTTTTCTTT
43641 TTTTTATT-TTT
1 TTTTT-TTCTTT
43652 TATTTTTTCTTT
1 T-TTTTTTCTTT
*
43664 ATTTTTTCATTT
1 TTTTTTTC-TTT
*
43676 TTTTCTTCTTT
1 TTTTTTTCTTT
43687 TTTTCTTT-TTT
1 TTTT-TTTCTTT
*
43698 CTTTTTTCTTT
1 TTTTTTTCTTT
43709 CTTTTT
1 -TTTTT
43715 GTGTGTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 3 0.05
11 34 0.56
12 24 0.39
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:43698 original size:18 final size:17
Alignment explanation
Indices: 43589--43714 Score: 96
Period size: 18 Copynumber: 7.1 Consensus size: 17
43579 GTTTTATATC
*
43589 TTCTTTTTTTTCCTTTT
1 TTCTTTTTTTTTCTTTT
43606 TTCCTATTTTTCCTTTC-TTT
1 TT-CT-TTTTT--TTTCTTTT
* * *
43626 TAC-CTTTTTTTATTTT
1 TTCTTTTTTTTTCTTTT
* *
43642 TT-TTATTTTTTATTTT
1 TTCTTTTTTTTTCTTTT
43658 TTCTTTATTTTTTCATTTTT
1 TTCTTT-TTTTTTC--TTTT
43678 TTCTTCTTTTTTTCTTTT
1 TTCTT-TTTTTTTCTTTT
43696 TTCTTTTTTCTTTCTTTT
1 TTCTTTTTT-TTTCTTTT
43714 T
1 T
43715 GTGTGTTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
15 3 0.03
16 17 0.19
17 12 0.14
18 26 0.30
19 6 0.07
20 20 0.23
21 4 0.05
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTTTTTTTTTCTTTT
Found at i:43724 original size:1 final size:1
Alignment explanation
Indices: 43630--43714 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
43620 TTCTTTTACC
* * * * * ** * * *
43630 TTTTTTTATTTTTTTTATTTTTTATTTTTTCTTTATTTTTTCATTTTTTTCTTCTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
43695 TTTCTTTTTTCTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTT
43715 GTGTGTTTTT
Statistics
Matches: 59, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:45073 original size:20 final size:20
Alignment explanation
Indices: 45045--45097 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
45035 CGCTGTATAT
*
45045 ATGCTAATGCAAAGATGCTC
1 ATGCAAATGCAAAGATGCTC
45065 ATGCAAATGCAAAGATGCTC
1 ATGCAAATGCAAAGATGCTC
45085 ATGCAAATGCAAA
1 ATGCAAATGCAAA
45098 AATGGAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
ATGCAAATGCAAAGATGCTC
Found at i:45108 original size:20 final size:20
Alignment explanation
Indices: 45045--45130 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
45035 CGCTGTATAT
* * **
45045 ATGCTAATGCAAAGATGCTC
1 ATGCAAATGCAAAAATGCAA
* **
45065 ATGCAAATGCAAAGATGCTC
1 ATGCAAATGCAAAAATGCAA
*
45085 ATGCAAATGCAAAAATGGAA
1 ATGCAAATGCAAAAATGCAA
*
45105 ATGCAAAATGC-AAAATGTAA
1 ATGC-AAATGCAAAAATGCAA
45125 ATGCAA
1 ATGCAA
45131 CAAAGGAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.03
20 51 0.86
21 6 0.10
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
ATGCAAATGCAAAAATGCAA
Found at i:47476 original size:2 final size:2
Alignment explanation
Indices: 47469--47532 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
47459 TGAAACACGC
47469 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
47511 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
47533 TCATGGGAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57700 original size:60 final size:60
Alignment explanation
Indices: 57628--57789 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 60
57618 AACTATAAAG
*
57628 TGTTACTTTGTTGAGTCCCTTATCTATTAAAAGTTACAAAATAATCCTTTGATTATATGA
1 TGTTACTTTGTTGAGTCCCTTATCTATTAAAAGTTACAAAATAATCCTTTGATTATAGGA
* * * *
57688 TGTTTCTTTGTTGAGT-CCTCTATCTATCAAAAGTTACAAAATAGTCCTTTGATTATCGGA
1 TGTTACTTTGTTGAGTCCCT-TATCTATTAAAAGTTACAAAATAATCCTTTGATTATAGGA
**
57748 TGTTACTTTGTTGAGTTCCCCGA-CTATTAAACA-TTACAAAAT
1 TGTTACTTTGTTGAG-TCCCTTATCTATTAAA-AGTTACAAAAT
57790 GATCACTCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 3 0.03
60 81 0.91
61 3 0.03
62 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (60 bp):
TGTTACTTTGTTGAGTCCCTTATCTATTAAAAGTTACAAAATAATCCTTTGATTATAGGA
Found at i:59848 original size:21 final size:21
Alignment explanation
Indices: 59797--59849 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
59787 ATTATGACTA
*
59797 TCGCAATGCGATTTTCTAATT
1 TCGCAATGCGATTTTCCAATT
**
59818 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
59839 TCGCAATGCGA
1 TCGCAATGCGA
59850 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:59864 original size:20 final size:21
Alignment explanation
Indices: 59839--59890 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
59829 TTTTCCCAAT
*
59839 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
59859 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
59880 TCGCAATGCGA
1 TCGCAATGCGA
59891 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:59904 original size:20 final size:20
Alignment explanation
Indices: 59879--60013 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
59869 AATTTGGAAA
*
59879 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
59899 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
59920 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * **
59940 TTCGTAACGCGATTTTGACT
1 ATCGCAACGCGATACTGACT
* *
59960 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
59980 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
60000 ATCGCAACGAGATA
1 ATCGCAACGCGATA
60014 ATACAGAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 79 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:60256 original size:12 final size:12
Alignment explanation
Indices: 60239--60263 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60229 ATATAATCCT
60239 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60251 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60263 G
1 G
60264 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:60513 original size:20 final size:20
Alignment explanation
Indices: 60488--60543 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
60478 CAACGGGGAA
*
60488 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
60508 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
60528 ATCGCAACGAGAAAAT
1 ATCGCAACGAGAAAAT
60544 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGGCT
Found at i:60586 original size:14 final size:14
Alignment explanation
Indices: 60567--60620 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
60557 GAAAATCGCA
60567 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
60581 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
60598 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
60614 TTGCGAT
1 TTGCGAT
60621 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:60586 original size:33 final size:33
Alignment explanation
Indices: 60549--60619 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
60539 AAAATCGCAA
*
60549 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
60582 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
60615 TGCGA
1 TGCGA
60620 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:62241 original size:41 final size:42
Alignment explanation
Indices: 62196--62286 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
62186 CCTCTTCAAC
* *
62196 GATGACAGTGGCCTCTTGAAC-AGTGGGGGGGACTCTTGAGA
1 GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
* * *
62237 GATGATAGAGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
62279 GATGACAG
1 GATGACAG
62287 GTGAGTCGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 19 0.44
42 24 0.56
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
Found at i:62694 original size:19 final size:19
Alignment explanation
Indices: 62669--62715 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
62659 GGAAATGGCT
*
62669 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATAAAA
* *
62688 ATTGCAATGCGAAATAAAA
1 ATCGCAACGCGAAATAAAA
62707 ATCGCAACG
1 ATCGCAACG
62716 ACAAAATCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATAAAA
Found at i:62730 original size:33 final size:33
Alignment explanation
Indices: 62685--62778 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
62675 ACGCGAAATG
*
62685 AAAATTGCAATGCGAAATAAAAATCGCAACGAC
1 AAAATCGCAATGCGAAATAAAAATCGCAACGAC
* * *
62718 AAAATCGTAATGCGAAATGAAAACCGCAACGAC
1 AAAATCGCAATGCGAAATAAAAATCGCAACGAC
* * *
62751 AAAATCGCAACGCGAAACACAAATCGCA
1 AAAATCGCAATGCGAAATAAAAATCGCA
62779 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATAAAAATCGCAACGAC
Found at i:62796 original size:19 final size:19
Alignment explanation
Indices: 62774--62870 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
62764 GAAACACAAA
62774 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
62793 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
62809 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
62826 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
62842 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
62859 TCGCATTGCGAT
1 TCGCATTGCGAT
62871 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:62815 original size:14 final size:14
Alignment explanation
Indices: 62796--62854 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
62786 TTTCATTTCG
62796 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
62810 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
62827 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
62843 CGTTGCGATTTT
1 CGTTGCGATTTT
62855 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62821 original size:33 final size:33
Alignment explanation
Indices: 62779--62870 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
62769 ACAAATCGCA
*
62779 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62812 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62845 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
62871 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:62889 original size:20 final size:19
Alignment explanation
Indices: 62855--62909 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
62845 TTGCGATTTT
*
62855 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
62874 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
62894 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
62910 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:63473 original size:18 final size:18
Alignment explanation
Indices: 63450--63497 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
63440 CGGGTCGATC
63450 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
63468 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
63486 AGGTGATGGCTC
1 AGGTGATGGCTC
63498 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:64829 original size:20 final size:20
Alignment explanation
Indices: 64804--64876 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
64794 GTTTCTGAAA
*
64804 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACGCG
**
64824 AAAATGACTATCGCAACGCG
1 AAAATGAAAATCGCAACGCG
** **
64844 AATTTGACTATCGCAACGCG
1 AAAATGAAAATCGCAACGCG
*
64864 AAACT-AAAATCGC
1 AAAATGAAAATCGC
64877 GTTGCGATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 6 0.14
20 38 0.86
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATGAAAATCGCAACGCG
Done.