Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020209.1 Corchorus olitorius cultivar O-4 contig20242, 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: 64728
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:4000 original size:19 final size:18
Alignment explanation
Indices: 3976--4011 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
3966 GGCCTAGCCC
3976 ATAAGAAATAAGAAAAAGA
1 ATAAGAAA-AAGAAAAAGA
3995 ATAAGAAAAAGAAAAAG
1 ATAAGAAAAAGAAAAAG
4012 GGCCTAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (18 bp):
ATAAGAAAAAGAAAAAGA
Found at i:4008 original size:6 final size:6
Alignment explanation
Indices: 3978--4011 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3968 CCTAGCCCAT
*
3978 AAGAAA TAAGAAA AAGAAT AAGAAA AAGAAA AAG
1 AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAG
4012 GGCCTAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:4048 original size:9 final size:9
Alignment explanation
Indices: 4027--4076 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
4017 AGCCCATAAC
4027 GAAGAAGAAA
1 GAAGAA-AAA
4037 GAAGAAAAA
1 GAAGAAAAA
4046 GAAGAAAGAA
1 GAAGAAA-AA
4056 -AAG-AAAA
1 GAAGAAAAA
*
4063 GAAAAGAAAA
1 GAAGA-AAAA
4073 GAAG
1 GAAG
4077 GAAATTTGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.06
8 4 0.12
9 13 0.38
10 15 0.44
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:4049 original size:16 final size:17
Alignment explanation
Indices: 4028--4075 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
4018 GCCCATAACG
*
4028 AAGAAGAAAGAAGA-AA
1 AAGAAGAAAGAAAAGAA
4044 AAGAAGAAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
4061 AAG-A-AAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
4076 GGAAATTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 11 0.37
16 14 0.47
17 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAGAAAAGAA
Found at i:4058 original size:47 final size:46
Alignment explanation
Indices: 3949--4057 Score: 150
Period size: 46 Copynumber: 2.3 Consensus size: 46
3939 TAAATAAAAC
*
3949 AAAAG-AAAAGAAAAAGGGGCCTAGCCCATAAGAAATAAGAAAAAGA
1 AAAAGAAAAAGAAAAA-GGGCCTAGCCCATAAGAAAGAAGAAAAAGA
*
3995 ATAAGAAAAAGAAAAAGGGCCTAGCCCATAACG-AAGAAGAAAGAAGA
1 AAAAGAAAAAGAAAAAGGGCCTAGCCCATAA-GAAAGAAGAAA-AAGA
4042 AAAAGAAGAAAGAAAA
1 AAAAGAA-AAAGAAAA
4058 GAAAAGAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
46 27 0.48
47 21 0.38
48 8 0.14
ACGTcount: A:0.62, C:0.10, G:0.22, T:0.06
Consensus pattern (46 bp):
AAAAGAAAAAGAAAAAGGGCCTAGCCCATAAGAAAGAAGAAAAAGA
Found at i:4060 original size:5 final size:5
Alignment explanation
Indices: 4038--4075 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
4028 AAGAAGAAAG
*
4038 AAGAA AA-AG AAG-A AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
4076 GGAAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:5301 original size:12 final size:13
Alignment explanation
Indices: 5256--5312 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
5246 CCCGTTGAGG
5256 AAATGTTTTAT-T
1 AAATGTTTTATAT
* *
5268 ACA-GTTTTACAT
1 AAATGTTTTATAT
*
5280 AAATGATTTATA-
1 AAATGTTTTATAT
5292 AAATGTTTTA-AT
1 AAATGTTTTATAT
5304 AAATGTTTT
1 AAATGTTTT
5313 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
11 7 0.19
12 23 0.64
13 6 0.17
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (13 bp):
AAATGTTTTATAT
Found at i:6888 original size:30 final size:29
Alignment explanation
Indices: 6850--6914 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 29
6840 TTTAGACCAA
6850 ACTATTATTTAGTTTAGTATGTTTTCC-TT
1 ACTATTATTTA-TTTAGTATGTTTTCCTTT
*
6879 --TAGTA-TTATTTAGTATGTTTTCCTTT
1 ACTATTATTTATTTAGTATGTTTTCCTTT
6905 ACTATTATTT
1 ACTATTATTT
6915 TTTGAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
25 15 0.50
26 5 0.17
27 4 0.13
28 4 0.13
29 2 0.07
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (29 bp):
ACTATTATTTATTTAGTATGTTTTCCTTT
Found at i:6891 original size:25 final size:25
Alignment explanation
Indices: 6862--6914 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
6852 TATTATTTAG
*
6862 TTTAGTATGTTTTCCTTTAGTATTA
1 TTTAGTATGTTTTCCTTTACTATTA
6887 TTTAGTATGTTTTCCTTTACTATTA
1 TTTAGTATGTTTTCCTTTACTATTA
6912 TTT
1 TTT
6915 TTTGAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (25 bp):
TTTAGTATGTTTTCCTTTACTATTA
Found at i:6951 original size:20 final size:20
Alignment explanation
Indices: 6914--6952 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6904 TACTATTATT
6914 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
6934 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
6953 AATATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:7149 original size:22 final size:22
Alignment explanation
Indices: 7124--7329 Score: 134
Period size: 22 Copynumber: 9.3 Consensus size: 22
7114 TTTTTCTGTG
*
7124 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
7146 TGGTTATTATATTTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
7169 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
7190 TGCTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* * **
7213 -AGTTAACAAAATTTCACGGGA
1 TGGTTATCAAAATTTCATAGGA
* *
7234 AGGTTATCAAAATTTCATTGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
7256 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
7278 TCAAGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* **
7302 AGGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
7324 TGGTTA
1 TGGTTA
7330 CAATTTTATA
Statistics
Matches: 141, Mismatches: 32, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
21 6 0.04
22 112 0.79
23 6 0.04
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:7202 original size:66 final size:66
Alignment explanation
Indices: 7168--7330 Score: 182
Period size: 68 Copynumber: 2.4 Consensus size: 66
7158 TTTCATGAGG
* *
7168 AGGTTATCAAAATTCCATAGTGTGCTTACCAAAATTTCATATGGAAGTTAACAAAATTTCACGGG
1 AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATAGAAGTTAACAAAATTTCACGGG
7233 A
66 A
* * * * ** ***
7234 AGGTTATCAAAATTTCATTGTGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTCTTA
1 AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATA-TA-GAAGTTAACAAAATTTCACG
7299 GGA
64 GGA
** *
7302 AGGTTATTGAAATTTCATAGTGTGGTTAC
1 AGGTTATCAAAATTCCATAGTGTGGTTAC
7331 AATTTTATAG
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 38 0.47
68 43 0.53
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (66 bp):
AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATAGAAGTTAACAAAATTTCACGGG
A
Found at i:7496 original size:22 final size:22
Alignment explanation
Indices: 7358--7782 Score: 156
Period size: 22 Copynumber: 18.9 Consensus size: 22
7348 ATTAAAGAGA
* *
7358 TTATCAAAATATCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
7380 TTAT-AAGAGTTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* * *
7402 TTAACAAAATTCACATAAGGAGAGG
1 TTATCAAAATT-TCAT-A-GTGAGG
* * *
7427 TTATACTAATATTTCATGGGGAGG
1 TTAT-C-AAAATTTCATAGTGAGG
* *
7451 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
7473 TTATCAGAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
7495 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * ** *
7520 AGTACCAACATTGGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
*
7542 TTATC-AAATATCATAAGATGA--
1 TTATCAAAATTTCAT-AG-TGAGG
*
7563 TTATCGAAATTTCATAGAGATGATCGG
1 TTATCAAAATTTCAT--AG-TGA--GG
*
7590 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
* **
7612 TTATTAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
7634 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
7656 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
7678 TTATCAAAATTTCATAGATG-GG
1 TTATCAAAATTTCATAG-TGAGG
* * * *
7700 TCAAC-AAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
7721 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
7743 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
7765 TTATCAAAA-TTCATAGTG
1 TTATCAAAATTTCATAGTG
7783 GTATTTCTGG
Statistics
Matches: 295, Mismatches: 76, Indels: 65
0.68 0.17 0.15
Matches are distributed among these distances:
20 6 0.02
21 50 0.17
22 165 0.56
23 19 0.06
24 11 0.04
25 14 0.05
26 9 0.03
27 10 0.03
28 11 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:7683 original size:44 final size:43
Alignment explanation
Indices: 7589--8287 Score: 210
Period size: 44 Copynumber: 15.9 Consensus size: 43
7579 GAGATGATCG
* * * *
7589 GATTATCAAAATTT-ATAGGAAGATTATTAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGG-AGGTTATCAAAATTTCATAATG-T
*
7633 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAG-GAGGTTATCAAAATTTCATAATGT
* * * * *
7676 GATTATCAAAATTTCATA-GATGGGTCAAC-AAATTTTATAGA-GA
1 GATTATCAAAATTTCAAAGGA--GGTTATCAAAATTTCATA-ATGT
* * * *
7719 GGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATAATGT
* *
7763 GATTATCAAAA-TTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCATAGTAT
1 GATTATCAAAATTTCA-A-----A-------GGAGGTTATCAAAATTTCATAATGT
* * * * * *
7818 GGTTA-CCAAA-TT---AGGAAGGTTATTAAACTTTTATTATG-
1 GATTATCAAAATTTCAAAGG-AGGTTATCAAAATTTCATAATGT
* ** * *
7856 GACTAATCAAAATTTC-AAGGAGGACATCAAATTTTCAT-ATGAA
1 GA-TTATCAAAATTTCAAAGGAGGTTATCAAAATTTCATAATG-T
*
7899 GGTTATCAAAATTTCATAA-GAGAGTTATCAAAATTTCATAGTATGT
1 GATTATCAAAATTTCA-AAGGAG-GTTATCAAAATTTCATA--ATGT
* * * *
7945 -A-GATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAATGA
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATAATGT
* * ** * * *
7987 GGTTATAAAAAAATCATAGGGAGATTATCAAAATTT--T--T-A
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATAATGT
* *
8026 G-TTATCAAGATTTCATAAGGAGGTTATCAAAATTTTAT-ATG-
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATAATGT
* * ** *
8067 GAGGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGCGA
1 GA---TTATCAAAATTTCAAAGG-AGG-TTATCAAAATTTCATAATGT
* * * ** * * *
8115 GGTTATCACAATTTCATAGTTTGATTATCAAAATTTCAGAGTGT
1 GATTATCAAAATTTCAAAG-GAGGTTATCAAAATTTCATAATGT
** * * * *
8159 GATTA-CTAACAA-TTCATGTGGAGGTTTTTAAATTTTCATAACGT
1 GATTATC-AA-AATTTCA-AAGGAGGTTATCAAAATTTCATAATGT
* * * * *
8203 GGTTATCAATATTTCATATGGAGGTTATCAACATCTCATAATGTT
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATAATG-T
* ** *
8248 GGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 GATTATCAAAATTTCA-AAGGAGGTTATCAAAATTTCATA
8288 GTGAGGTCTT
Statistics
Matches: 489, Mismatches: 108, Indels: 115
0.69 0.15 0.16
Matches are distributed among these distances:
38 31 0.06
39 20 0.04
40 6 0.01
41 7 0.01
42 31 0.06
43 59 0.12
44 208 0.43
45 77 0.16
46 14 0.03
47 4 0.01
48 2 0.00
54 6 0.01
55 24 0.05
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (43 bp):
GATTATCAAAATTTCAAAGGAGGTTATCAAAATTTCATAATGT
Found at i:7685 original size:87 final size:87
Alignment explanation
Indices: 7589--7780 Score: 212
Period size: 87 Copynumber: 2.2 Consensus size: 87
7579 GAGATGATCG
* * **
7589 GATTATCAAAATTTATAGGA-AGATTATTA-AAATTTCATAGTGTTGTTATCAAAATTTCA-AAG
1 GATTATCAAAATTTATAGGATAGATCA--ACAAATTTCATAGAGAGGTTATCAAAATTTCATAA-
* *
7651 CGAGGTTATCAAAATTACATAATGT
63 AGAGGTTATCAAAATTACAAAATGT
* * *
7676 GATTATCAAAATTTCATA-GATGGGTCAACAAATTTTATAGAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTT-ATAGGATAGATCAACAAATTTCATAGAGAGGTTATCAAAATTTCATAAAG
* *
7740 AGGTTATCAAATTTTCAAAATGT
65 AGGTTATCAAAATTACAAAATGT
*
7763 GATTATCAAAATTCATAG
1 GATTATCAAAATTTATAG
7781 TGGTATTTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
86 4 0.05
87 76 0.86
88 8 0.09
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (87 bp):
GATTATCAAAATTTATAGGATAGATCAACAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGA
GGTTATCAAAATTACAAAATGT
Found at i:7751 original size:43 final size:43
Alignment explanation
Indices: 7633--7779 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
7623 TCATAGTGTT
* ** *
7633 GTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTG
1 GTTATCAAAATTTCATAA-AGAGGTTATC-AAATTTTATAATGAG
* * * *
7677 ATTATCAAAATTTCATAGATG-GGTCAACAAATTTTATAGA-GAG
1 GTTATCAAAATTTCATA-AAGAGGTTATCAAATTTTATA-ATGAG
* *
7720 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTG
1 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTT-ATAATGAG
*
7764 ATTATCAAAA-TTCATA
1 GTTATCAAAATTTCATA
7780 GTGGTATTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
42 2 0.02
43 45 0.54
44 33 0.40
45 2 0.02
46 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTATAATGAG
Found at i:8079 original size:23 final size:21
Alignment explanation
Indices: 7861--8340 Score: 276
Period size: 22 Copynumber: 22.0 Consensus size: 21
7851 TTATGGACTA
**
7861 ATCAAAATTTCA-AGGAGGAC
1 ATCAAAATTTCATAGGAGGTT
* *
7881 ATCAAATTTTCATATGAAGGTT
1 ATCAAAATTTCATA-GGAGGTT
*
7903 ATCAAAATTTCATAAGAGAGTT
1 ATCAAAATTTCATAGGAG-GTT
* * *
7925 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
7947 ATCAAAATTTCATAGGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* *
7969 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* ** *
7991 ATAAAAAAATCATAGGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
*
8013 ATCAAAATTT--T--TA-GTT
1 ATCAAAATTTCATAGGAGGTT
*
8029 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
8051 ATCAAAATTTTATATGGAGGTTT
1 ATCAAAATTTCATA-GGAGG-TT
*
8074 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGG-AGG-TT
8097 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* ** *
8119 ATCACAATTTCATAGTTTGATT
1 ATCAAAATTTCATAG-GAGGTT
* * *
8141 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
*
8163 A-CTAACAA-TTCATGTGGAGGTT
1 ATC-AA-AATTTCAT-AGGAGGTT
* * * * *
8185 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
8207 ATCAATATTTCATATGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* * **
8229 ATCAACATCTCATAATGTTGGTT
1 ATCAAAATTTCAT-A-GGAGGTT
* *
8252 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCA-TAGGAGGTT
8274 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAG-GAGGT-T
* * *
8297 -TCAAAATTCCTTAGGGTGGTT
1 ATCAAAATTTCATA-GGAGGTT
* *
8318 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
8340 A
1 A
8341 GAAACAATTT
Statistics
Matches: 353, Mismatches: 77, Indels: 58
0.72 0.16 0.12
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
20 12 0.03
21 14 0.04
22 245 0.69
23 67 0.19
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:8085 original size:60 final size:60
Alignment explanation
Indices: 7966--8084 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
7956 TCATAGGGAG
*
7966 GTTAACAAAATTTCATAATGAGGTTATAAAAAAATCATAGGGAGATTATCAAAATTTTTA
1 GTTAACAAAATTTCATAAGGAGGTTATAAAAAAATCATAGGGAGATTATCAAAATTTTTA
* * * ** * * *
8026 GTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATATGGAGGTTTATCAAAATTTT
1 GTTAACAAAATTTCATAAGGAGGTTATAAAAAAATCATAGGGA-GATTATCAAAATTTT
8085 ATAGGAAGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 35 0.71
61 14 0.29
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (60 bp):
GTTAACAAAATTTCATAAGGAGGTTATAAAAAAATCATAGGGAGATTATCAAAATTTTTA
Found at i:8104 original size:104 final size:105
Alignment explanation
Indices: 7921--8128 Score: 226
Period size: 104 Copynumber: 2.0 Consensus size: 105
7911 TTCATAAGAG
* * *
7921 AGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAATG
1 AGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAAGG
*
7986 AGGTTATAAAAAAA-TCATAGGGAGATTATCAAAATTTTT
66 AGGTTATAAAAAAATTCATAGCGAGATTATCAAAATTTTT
* * * * * *
8025 AGTTATCAAGATTTCATAAGGAGGT-TATCAAAATTTTATATGGAGGTTTATCAAAATTTTAT-A
1 AGTTATCAAAATTTCAT-AGGAGGTAGATCAAAATTTCATAGGGAGG-TTAACAAAATTTCATAA
* * * *
8088 GGAAGGTT-TATCAAAATTTCATAGCGAGGTTATCACAATTT
64 GG-AGGTTATA-AAAAAATTCATAGCGAGATTATCAAAATTT
8129 CATAGTTTGA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
104 38 0.45
105 27 0.32
106 20 0.24
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (105 bp):
AGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGGGAGGTTAACAAAATTTCATAAGG
AGGTTATAAAAAAATTCATAGCGAGATTATCAAAATTTTT
Found at i:8434 original size:22 final size:22
Alignment explanation
Indices: 8392--8434 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8382 TTATTAAACC
* *
8392 TTCATAGGAAGATTATTAAAAT
1 TTCATAGGAAGATCATAAAAAT
8414 TTCATAAGG-AGATCATAAAAA
1 TTCAT-AGGAAGATCATAAAAA
8435 ATAATGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (22 bp):
TTCATAGGAAGATCATAAAAAT
Found at i:8583 original size:2 final size:2
Alignment explanation
Indices: 8539--8571 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8529 CTAAAACTAG
8539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8572 GCAAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12474 original size:16 final size:14
Alignment explanation
Indices: 12442--12475 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
12432 ACAAACTTAG
12442 ATATGAATTATGAA
1 ATATGAATTATGAA
12456 ATATGTAATTATGGAA
1 ATATG-AATTAT-GAA
12472 ATAT
1 ATAT
12476 TATGAACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 6 0.33
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (14 bp):
ATATGAATTATGAA
Found at i:12598 original size:18 final size:16
Alignment explanation
Indices: 12551--12598 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
12541 TCTTTTGGAC
*
12551 TTGAAGTACATGTAAA
1 TTGAAGTACATTTAAA
*
12567 TTGAAATAGCATTTGAAA
1 TTGAAGTA-CATTT-AAA
12585 TTGAAGTACTATTT
1 TTGAAGTAC-ATTT
12599 TTTTATCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 14 0.54
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38
Consensus pattern (16 bp):
TTGAAGTACATTTAAA
Found at i:15151 original size:7 final size:7
Alignment explanation
Indices: 15139--15164 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
15129 TAGACCCCTT
15139 TTATTAA
1 TTATTAA
15146 TTATTAA
1 TTATTAA
15153 TTATTAA
1 TTATTAA
15160 TTATT
1 TTATT
15165 TACTTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:17804 original size:11 final size:11
Alignment explanation
Indices: 17761--17798 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17751 TTTATATATA
*
17761 AAATAAATTAT
1 AAATTAATTAT
17772 CAAA-TAATTAT
1 -AAATTAATTAT
17783 AAATTAATTAT
1 AAATTAATTAT
17794 AAATT
1 AAATT
17799 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:20397 original size:31 final size:32
Alignment explanation
Indices: 20359--20425 Score: 127
Period size: 31 Copynumber: 2.1 Consensus size: 32
20349 GTAGCTAGTA
20359 TTTGGCAAATAATTCTAAATT-TGTGGTCCTC
1 TTTGGCAAATAATTCTAAATTGTGTGGTCCTC
20390 TTTGGCAAATAATTCTAAATTGTGTGGTCCTC
1 TTTGGCAAATAATTCTAAATTGTGTGGTCCTC
20422 TTTG
1 TTTG
20426 AAGACCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (32 bp):
TTTGGCAAATAATTCTAAATTGTGTGGTCCTC
Found at i:25842 original size:35 final size:37
Alignment explanation
Indices: 25803--25883 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 37
25793 CAAATACATG
25803 TACATG-C-CTTTTGAATAAAGACAACATTAAATAGA
1 TACATGTCTCTTTTGAATAAAGACAACATTAAATAGA
* *
25838 TACATGTCTTTCTCTTTTGGATAAAGACAACTTTAAATAGA
1 TACATG----TCTCTTTTGAATAAAGACAACATTAAATAGA
25879 TACAT
1 TACAT
25884 ATATTTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 6 0.16
40 1 0.03
41 31 0.82
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (37 bp):
TACATGTCTCTTTTGAATAAAGACAACATTAAATAGA
Found at i:25992 original size:29 final size:29
Alignment explanation
Indices: 25953--26020 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
25943 GAATAATCAC
25953 ATTATTCATTAATGTCTTTTTATCAACTAA
1 ATTA-TCATTAATGTCTTTTTATCAACTAA
25983 ATTATCATTAATGTCTTTTTATCAACTAA
1 ATTATCATTAATGTCTTTTTATCAACTAA
26012 ATTATCATT
1 ATTATCATT
26021 GGTAAATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (29 bp):
ATTATCATTAATGTCTTTTTATCAACTAA
Found at i:32777 original size:9 final size:9
Alignment explanation
Indices: 32763--32788 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
32753 AAAAATGTCT
32763 ATTTCATTC
1 ATTTCATTC
32772 ATTTCATTC
1 ATTTCATTC
32781 ATTTCATT
1 ATTTCATT
32789 TGGTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTTCATTC
Found at i:32876 original size:11 final size:11
Alignment explanation
Indices: 32857--32888 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
32847 ACTAGACATC
*
32857 TTTTCTTTTCT
1 TTTTTTTTTCT
32868 TTTTTTTTTCT
1 TTTTTTTTTCT
32879 TTTTTTTTTC
1 TTTTTTTTTC
32889 AGGAACTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:32878 original size:16 final size:15
Alignment explanation
Indices: 32857--32887 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
32847 ACTAGACATC
32857 TTTTCTTTTCTTTTTT
1 TTTTCTTTT-TTTTTT
32873 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
32888 CAGGAACTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:35597 original size:41 final size:41
Alignment explanation
Indices: 35540--35624 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
35530 CAAAGAAGAG
35540 TTTTGTGCTTGATTGAAAATGGCATAAAGGCAAGGGGACCA
1 TTTTGTGCTTGATTGAAAATGGCATAAAGGCAAGGGGACCA
35581 TTTTGTGCTTGATTGAAAATGGCATAAAGGCAAGGGGACCA
1 TTTTGTGCTTGATTGAAAATGGCATAAAGGCAAGGGGACCA
35622 TTT
1 TTT
35625 GGCAATTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (41 bp):
TTTTGTGCTTGATTGAAAATGGCATAAAGGCAAGGGGACCA
Found at i:35709 original size:19 final size:19
Alignment explanation
Indices: 35685--35721 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35675 CCGTTACTTC
35685 ATTTTCTTCATTTGTGTTA
1 ATTTTCTTCATTTGTGTTA
*
35704 ATTTTCTTCATTTTTGTT
1 ATTTTCTTCATTTGTGTT
35722 TTCTCCACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.08, T:0.68
Consensus pattern (19 bp):
ATTTTCTTCATTTGTGTTA
Found at i:37618 original size:12 final size:13
Alignment explanation
Indices: 37586--37632 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
37576 CTATTTTATT
37586 ATTGTTTTATTAA
1 ATTGTTTTATTAA
37599 ATTGTTTTA-TAA
1 ATTGTTTTATTAA
*
37611 A-TGTTTTTAAATAA
1 ATTG-TTTT-ATTAA
37625 ATTGTTTT
1 ATTGTTTT
37633 GGGTGCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 10 0.33
14 8 0.27
15 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (13 bp):
ATTGTTTTATTAA
Found at i:42139 original size:41 final size:41
Alignment explanation
Indices: 42055--42139 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
42045 CAAAGAAGAG
*
42055 TTTTGTGCTTGATTGAAAATGGCATAAAAGCAAGGGGAACA
1 TTTTGTGCTTGATTGAAAATGGCATAAAAGCAAGCGGAACA
* * *
42096 TTTTGTGCTTGATTGAAAATGGCATAAAGGCGAGCGGACCA
1 TTTTGTGCTTGATTGAAAATGGCATAAAAGCAAGCGGAACA
42137 TTT
1 TTT
42140 GGCAATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (41 bp):
TTTTGTGCTTGATTGAAAATGGCATAAAAGCAAGCGGAACA
Found at i:42224 original size:19 final size:19
Alignment explanation
Indices: 42200--42236 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42190 CCGTTACTTC
42200 ATTTTCTTCATTTGTGTTA
1 ATTTTCTTCATTTGTGTTA
*
42219 ATTTTCTTCATTTTTGTT
1 ATTTTCTTCATTTGTGTT
42237 TTCTCCACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.08, T:0.68
Consensus pattern (19 bp):
ATTTTCTTCATTTGTGTTA
Found at i:44142 original size:12 final size:13
Alignment explanation
Indices: 44110--44156 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
44100 CTATTTTATT
44110 ATTGTTTTATTAA
1 ATTGTTTTATTAA
44123 ATTGTTTTA-TAA
1 ATTGTTTTATTAA
*
44135 A-TGTTTTTAAATAA
1 ATTG-TTTT-ATTAA
44149 ATTGTTTT
1 ATTGTTTT
44157 GGGTTCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 8 0.27
13 10 0.33
14 8 0.27
15 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (13 bp):
ATTGTTTTATTAA
Found at i:48387 original size:21 final size:21
Alignment explanation
Indices: 48314--48387 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
48304 TGGATATTTG
48314 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTA-CC
* **
48336 TATTAAATTTTGATAACCAACC
1 TATGAAATTTTGATAA-TTACC
* *
48358 TACGAAATTTTGATAATTATC
1 TATGAAATTTTGATAATTACC
48379 TATGAAATT
1 TATGAAATT
48388 GCGATAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
21 10 0.24
22 31 0.74
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:48467 original size:21 final size:23
Alignment explanation
Indices: 48422--48471 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
48412 GATCACCTAA
48422 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
48445 CTATGAAATTTT-GTAAA-CTTC
1 CTATGAAATTTTAATAAACCTTC
48466 CTATGA
1 CTATGA
48472 TTTTTGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
22 4 0.15
23 12 0.46
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Found at i:48484 original size:42 final size:43
Alignment explanation
Indices: 48438--48520 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
48428 AATTTTAATA
* * *
48438 AACCTTCCTATGAA-ATTTTG-TAAACTTCCTATGATTTTTGAT
1 AACCTCCCTAT-AAGATTTTGTTAAACTCCCTATAATTTTTGAT
* *
48480 AACCTCCCTGTAAGATTTTGTTAATCTCCCTATAATTTTTG
1 AACCTCCCTATAAGATTTTGTTAAACTCCCTATAATTTTTG
48521 GTACTATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.06
42 15 0.44
43 17 0.50
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.45
Consensus pattern (43 bp):
AACCTCCCTATAAGATTTTGTTAAACTCCCTATAATTTTTGAT
Found at i:49333 original size:2 final size:2
Alignment explanation
Indices: 49320--49349 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
49310 AAAGCCACAC
*
49320 TA TA TC 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
49350 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50379 original size:25 final size:24
Alignment explanation
Indices: 50337--50398 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
50327 ATTCGTACTT
* *
50337 TTATAT-ATAGTATAGATATAGATA
1 TTATATAATA-TATAGATATACAAA
*
50361 TGTATATAATATATGGATATACAAA
1 T-TATATAATATATAGATATACAAA
50386 TTATATTAATATA
1 TTATA-TAATATA
50399 ATATATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 5 0.16
25 24 0.75
26 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.42
Consensus pattern (24 bp):
TTATATAATATATAGATATACAAA
Found at i:50604 original size:90 final size:92
Alignment explanation
Indices: 50447--50717 Score: 483
Period size: 90 Copynumber: 3.0 Consensus size: 92
50437 ATGCTAGCAT
50447 AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
1 AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
50512 TAGGCAACATCTCAAAGTTCAGCG-A-
66 TAGGCAACATCTCAAAGTTCAGCGAAG
*
50537 AGGTGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
1 AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
*
50602 TAGGCAACATCTCAAAGTTCAACGAAGG
66 TAGGCAACATCTCAAAGTTCAGCGAA-G
* *
50630 AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATTGGTACACCTT
1 AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
50695 TAGGCAACATCTCAAAGTTCAGC
66 TAGGCAACATCTCAAAGTTCAGC
50718 AACTGCGACG
Statistics
Matches: 172, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
90 87 0.51
91 1 0.01
93 84 0.49
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.22
Consensus pattern (92 bp):
AGGAGGTGGTGGAACATCTGCTGATGTACGAGTGCTTGGCCCCGATGGAGGAATCGGCACACCTT
TAGGCAACATCTCAAAGTTCAGCGAAG
Found at i:51433 original size:2 final size:2
Alignment explanation
Indices: 51428--51453 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51418 AAAAAAGGCA
51428 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
51454 TCCCTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53625 original size:14 final size:14
Alignment explanation
Indices: 53581--53627 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
53571 TGAAAAATAG
53581 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
53595 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
53608 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
53622 TAAAAT
1 TAAAAT
53628 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:53814 original size:149 final size:150
Alignment explanation
Indices: 53443--54047 Score: 1063
Period size: 149 Copynumber: 4.0 Consensus size: 150
53433 TGTCAATCAC
* * *
53443 AATAACCTTTTGAATAAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
53508 AAAATAGAGTTTTTAGTAGAATTAAACTATATATTAAAAAATTTTAATATATCCAAG-TTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
53572 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGT-AAATGGTAAA
53593 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
53658 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTCAATATATCCAAGTTTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
53723 GAAAAATAGT-AATGGTAAA
131 GAAAAATAGTAAATGGTAAA
*
53742 AATAAACTTTTAAATTAAAATGGTAAAAACAAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
* *
53807 AAAATAGAGTTTTTAGTATAATCAAACTATATATTAAAAAATTTTAATATAACCAAGTTTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
*
53872 GAAAAATAGT-AATGATAAA
131 GAAAAATAGTAAATGGTAAA
* *
53891 AATAAAATTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAAATTAATTAAATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
*
53956 AAAATAGAGTTTTTACTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
66 AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
54021 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGT-AAATGGTAAA
54042 AATAAA
1 AATAAA
54048 GTAATTATAA
Statistics
Matches: 435, Mismatches: 17, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
149 287 0.66
150 117 0.27
151 31 0.07
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (150 bp):
AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATG
AAAATAGAGTTTTTAGTAGAATCAAACTATATATTAAAAAATTTTAATATATCCAAGTTTTTAAT
GAAAAATAGTAAATGGTAAA
Found at i:64620 original size:30 final size:29
Alignment explanation
Indices: 64581--64663 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 29
64571 TTTGTTTTCT
* *
64581 TTCAGATTTCACAACTTCAAGAAATTTCCC
1 TTCATATTTCACAACTTCAAGAAA-TCCCC
64611 TTCATATTTCACAACTTCCAAGAAATCCCC
1 TTCATATTTCACAACTT-CAAGAAATCCCC
*
64641 TTCATATTTCCCAACTTCAAGAA
1 TTCATATTTCACAACTTCAAGAA
64664 TTGGCTGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.12
30 36 0.73
31 7 0.14
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
TTCATATTTCACAACTTCAAGAAATCCCC
Done.