Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009507.1 Corchorus capsularis cultivar CVL-1 contig09528, 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: 42464
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:593 original size:2 final size:2
Alignment explanation
Indices: 586--611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
576 ATTGGAATAC
586 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
612 TTTCGATGAA
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:1992 original size:2 final size:2
Alignment explanation
Indices: 1966--2015 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
1956 GTTTATGAAT
* * *
1966 TA TA TT TA TA TT TA TA CTA -A TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
2008 T- TA TA TA T
1 TA TA TA TA T
2016 TATTTGTGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2358 original size:24 final size:26
Alignment explanation
Indices: 2331--2397 Score: 93
Period size: 24 Copynumber: 2.7 Consensus size: 26
2321 AGTCAATACC
2331 ATATATGACAACTAGCTCCTTTC-A-
1 ATATATGACAACTAGCTCCTTTCAAG
*
2355 ATATATTACAACTAGCTCCTTTCAAG
1 ATATATGACAACTAGCTCCTTTCAAG
* *
2381 AAAAATGACAACTAGCT
1 ATATATGACAACTAGCT
2398 GTACTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 22 0.59
25 1 0.03
26 14 0.38
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (26 bp):
ATATATGACAACTAGCTCCTTTCAAG
Found at i:7448 original size:113 final size:115
Alignment explanation
Indices: 7229--7468 Score: 324
Period size: 113 Copynumber: 2.1 Consensus size: 115
7219 AAATATTTTC
*
7229 AGTCGACTGAAAATTATTTTCAACACTTGTTACAATTGACTGAAAGTTCAATCAGTCTATTCAAG
1 AGTCGACTGAAAATGATTTTCAACACTTGTTACAATTGACTGAAAGTTCAATCAGTCTATTCAAG
**
7294 AAAAGTGGCAGTGTTGACGACCAAGAGACTGCAGTTTCAACACCAAGGAT
66 AAAAGTGGCAGTGTTGACGACCAAGAGACTGCAGTTTCAACACCAACCAT
* * * * * * * *
7344 AGTTGACTGAAAGTGATTTTCAACACTT-TCTATAGTTGACTGAAATTTTAATCAGTC-CTTC-C
1 AGTCGACTGAAAATGATTTTCAACACTTGT-TACAATTGACTGAAAGTTCAATCAGTCTATTCAA
* * *
7406 TAAAAGTGGCAGTGTTGACGACCACGCGACTGCAGTTTCAACACCAACCAT
65 GAAAAGTGGCAGTGTTGACGACCAAGAGACTGCAGTTTCAACACCAACCAT
7457 AGTCGACTGAAA
1 AGTCGACTGAAA
7469 CTCACTATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
113 57 0.52
114 4 0.04
115 48 0.44
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (115 bp):
AGTCGACTGAAAATGATTTTCAACACTTGTTACAATTGACTGAAAGTTCAATCAGTCTATTCAAG
AAAAGTGGCAGTGTTGACGACCAAGAGACTGCAGTTTCAACACCAACCAT
Found at i:10828 original size:2 final size:2
Alignment explanation
Indices: 10821--10845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10811 CCATTGGACC
10821 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 T
10846 TCACATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10936 original size:4 final size:4
Alignment explanation
Indices: 10927--10954 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
10917 ACCAAAAACA
10927 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
10955 GGGACTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:11155 original size:17 final size:17
Alignment explanation
Indices: 11133--11184 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
11123 CTGTATCACA
11133 ATATAAATATTACATAT
1 ATATAAATATTACATAT
*
11150 ATATAAATATTACCACA-
1 ATATAAATATTA-CATAT
11167 ATATAAATATTACATAT
1 ATATAAATATTACATAT
11184 A
1 A
11185 CTATCAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.10
17 25 0.81
18 3 0.10
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAAATATTACATAT
Found at i:15196 original size:22 final size:21
Alignment explanation
Indices: 15140--15769 Score: 207
Period size: 22 Copynumber: 28.9 Consensus size: 21
15130 GTCTCTGTGT
* *
15140 GGTTATCAAATTTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
15161 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
15184 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
15206 GGTTACCAAAATTTCATACGGA
1 GGTTATCAAAATTTCATA-GGA
* * * *
15228 AGTTATCATATTTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
15250 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
15272 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
15296 AGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
15318 GGTTATTGAAATTTCATAGTA
1 GGTTATCAAAATTTCATAGGA
* * * *
15339 --CTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GA
*
15359 GGTTATC--AA----AGA-GA
1 GGTTATCAAAATTTCATAGGA
* **
15373 GATTATCAAAACATCATAGCGA
1 GGTTATCAAAATTTCATAG-GA
15395 GGTTAT-AAGAATTTCATAGTGTA
1 GGTTATCAA-AATTTCATAG-G-A
**
15418 -GTTAAAAAAATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGGA
* *
15439 GGTTA-CTAATATTTCATGGGGA
1 GGTTATC-AAAATTTCAT-AGGA
*
15461 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
** *
15483 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
15505 GGTTGTCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GGA
* *
15527 GGTTATAAAAGTCTCAATTTCATATG-
1 GGTTAT-CAA-----AATTTCATAGGA
* * * *
15553 GAG-TACCGAAATTTGATAGAA
1 G-GTTATCAAAATTTCATAGGA
*
15574 GGTTATC-AAATCTCATA-GA
1 GGTTATCAAAATTTCATAGGA
*
15593 GTGATTATCGAAATTTCATAGAGATCA
1 G-G-TTATCAAAATTTCATAG-G---A
*
15620 GATTATCAAAATTT-ATAGGAA
1 GGTTATCAAAATTTCATAGG-A
* * *
15641 GATTATCAAAATTTCATAATGT
1 GGTTATCAAAATTTCAT-AGGA
* * * *
15663 TGTTATCGAAATTTTAAAGCGA
1 GGTTATCAAAATTTCATAG-GA
*
15685 GGTTATCAAAATTACATAATGTGA
1 GGTTATCAAAATTTCAT-A-G-GA
* *
15709 -TTTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAG-GA
* * *
15730 GGTCAACAAAATTTTATAGAGA
1 GGTTATCAAAATTTCATAG-GA
*
15752 GGTTATTAAAATTTCATA
1 GGTTATCAAAATTTCATA
15770 AAGAAATTAT
Statistics
Matches: 447, Mismatches: 110, Indels: 102
0.68 0.17 0.15
Matches are distributed among these distances:
14 7 0.02
16 4 0.01
19 14 0.03
20 23 0.05
21 37 0.08
22 279 0.62
23 32 0.07
24 24 0.05
25 12 0.03
26 3 0.01
27 3 0.01
28 9 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:15643 original size:21 final size:24
Alignment explanation
Indices: 15595--15658 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 24
15585 CTCATAGAGT
*
15595 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
15620 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
15641 GATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
15659 ATGTTGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 15 0.41
22 3 0.08
23 2 0.05
24 4 0.11
25 13 0.35
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:15985 original size:22 final size:21
Alignment explanation
Indices: 15914--15993 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
15904 TCAGGGAGGA
**
15914 TATCAAAATTTCATA-TGAAGG
1 TATCAAAATTTCATAGTTTA-G
15935 CTATCAAAATTTCATAGTTTAG
1 -TATCAAAATTTCATAGTTTAG
*
15957 TTTTCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAGT-T-TAG
15981 -ATCAAAATTTCAT
1 TATCAAAATTTCAT
15994 TGGGAGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 44 0.88
23 3 0.06
24 3 0.06
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (21 bp):
TATCAAAATTTCATAGTTTAG
Found at i:16111 original size:23 final size:22
Alignment explanation
Indices: 16059--16166 Score: 110
Period size: 22 Copynumber: 4.8 Consensus size: 22
16049 CAAATTTGTA
* *
16059 GTTAT-AAGATTTCATAAGGAG
1 GTTATCAAAATTTCATAGGGAG
*
16080 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
* *
16102 GTTTATCAAAATTTTAGAGGGAAG
1 G-TTATCAAAATTTCATAGGG-AG
**
16126 GTTTATCAAAATTTCATAATGAG
1 G-TTATCAAAATTTCATAGGGAG
*
16149 GTTATCACAATTTCATAG
1 GTTATCAAAATTTCATAG
16167 TGTGATTGTG
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
21 5 0.07
22 29 0.39
23 21 0.28
24 19 0.26
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGAG
Found at i:16132 original size:24 final size:23
Alignment explanation
Indices: 16076--16139 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
16066 GATTTCATAA
*
16076 GGAGG-TTATCAAAATTTTATAG
1 GGAGGTTTATCAAAATTTTAGAG
16098 GGAGGTTTATCAAAATTTTAGAG
1 GGAGGTTTATCAAAATTTTAGAG
16121 GGAAGGTTTATCAAAATTT
1 GG-AGGTTTATCAAAATTT
16140 CATAATGAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 5 0.13
23 18 0.46
24 16 0.41
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (23 bp):
GGAGGTTTATCAAAATTTTAGAG
Found at i:20824 original size:3 final size:3
Alignment explanation
Indices: 20816--20854 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
20806 TTTTAATGAC
20816 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20855 CATCATCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20859 original size:3 final size:3
Alignment explanation
Indices: 20853--20878 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20843 TATTATTATT
20853 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
20879 GGCAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:21390 original size:22 final size:21
Alignment explanation
Indices: 21321--21483 Score: 86
Period size: 22 Copynumber: 7.7 Consensus size: 21
21311 ATAACCACAT
* * *
21321 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAA-CACTC
* *
21343 TATAAAATTTTGATCTACA-TAC
1 TATGAAATTTTGAT-AACACT-C
21365 TATGAAATTTTGATAACACTC
1 TATGAAATTTTGATAACACTC
* **
21386 TTATGAAATTTTGAAAACTAAAC
1 -TATGAAATTTTGATAAC-ACTC
* *
21409 TATAAAATTTCGATAAC-CTTC
1 TATGAAATTTTGATAACAC-TC
*
21430 ATATGAAATTTTGATATC-CTC
1 -TATGAAATTTTGATAACACTC
** *
21451 CCTG-AATTTTGATATC-CTCC
1 TATGAAATTTTGATAACACT-C
21471 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
21484 TACTCCATAA
Statistics
Matches: 111, Mismatches: 21, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
19 16 0.14
20 12 0.11
21 7 0.06
22 73 0.66
23 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACACTC
Found at i:21395 original size:44 final size:41
Alignment explanation
Indices: 21321--21444 Score: 113
Period size: 44 Copynumber: 2.9 Consensus size: 41
21311 ATAACCACAT
* * * *
21321 TATGAAATTTTGTTAATCTCCCTATAAAATTTTGATCTACATAC
1 TATGAAATTTTGATAACCT-CATATGAAATTTTGATCTA-A-AC
* *
21365 TATGAAATTTTGATAACACTCTTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAAC-CTCATATGAAATTTTG--ATCTAAAC
* *
21409 TATAAAATTTCGATAACCTTCATATGAAATTTTGAT
1 TATGAAATTTTGATAACC-TCATATGAAATTTTGAT
21445 ATCCTCCCTG
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 58 0.87
45 3 0.04
46 4 0.06
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (41 bp):
TATGAAATTTTGATAACCTCATATGAAATTTTGATCTAAAC
Found at i:21489 original size:19 final size:20
Alignment explanation
Indices: 21433--21483 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
21423 AACCTTCATA
21433 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
21453 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
21472 TGAAATTTTGAT
1 TGAAATTTTGAT
21484 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:21751 original size:25 final size:22
Alignment explanation
Indices: 21701--21796 Score: 76
Period size: 21 Copynumber: 4.4 Consensus size: 22
21691 GAACACAATA
*
21701 AAATTTTGATAAT-CTTTCTAT
1 AAATTTTGATAATCCTCTCTAT
21722 AAATTTTGATAATCCGATCTCTAT
1 AAATTTTGATAATCC--TCTCTAT
*
21746 GAAATTTCGATAATCC-CTCTAT
1 -AAATTTTGATAATCCTCTCTAT
* *
21768 GAGA-TTTGATAA-CCT-TCTACC
1 -AAATTTTGATAATCCTCTCTA-T
21789 AAATTTTG
1 AAATTTTG
21797 GTACTTCTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
20 8 0.13
21 24 0.39
22 10 0.16
24 6 0.10
25 14 0.23
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAATCCTCTCTAT
Found at i:21768 original size:22 final size:22
Alignment explanation
Indices: 21564--21796 Score: 81
Period size: 22 Copynumber: 10.6 Consensus size: 22
21554 AGAAATACCA
*
21564 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATC-CCT
*
21587 -TCTGAAATTTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCC-CT
* * * * *
21608 TTATAAAATTTTGTTTA-CGACT
1 CTATGAAATTTTGATAATC-CCT
*
21630 CTAT-AAATTTCTGATAATCACAT
1 CTATGAAATTT-TGATAATC-CCT
* * *
21653 -TATGTAATTTTCATAA-CCTCA
1 CTATGAAATTTTGATAATCC-CT
* *** *
21674 CTTTGAAATTTTGATAAGAACA
1 CTATGAAATTTTGATAATCCCT
* * **
21696 CAATAAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCCCT
21718 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAATCC---CT
*
21742 CTATGAAATTTCGATAATCCCT
1 CTATGAAATTTTGATAATCCCT
* *
21764 CTATGAGA-TTTGATAA-CCTT
1 CTATGAAATTTTGATAATCCCT
**
21784 CTACCAAATTTTG
1 CTATGAAATTTTG
21797 GTACTTCTTA
Statistics
Matches: 155, Mismatches: 40, Indels: 32
0.68 0.18 0.14
Matches are distributed among these distances:
20 10 0.06
21 39 0.25
22 80 0.52
23 7 0.05
24 5 0.03
25 14 0.09
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCCCT
Found at i:21848 original size:22 final size:22
Alignment explanation
Indices: 21837--21959 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
21827 CCTTCATATG
21837 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
** * *
21859 AAATTTTGATAACTTCCCCATGA
1 AAATTTTGATAACCACACTAT-A
* * *
21882 AAATATT-AGTAACCTC-CTAATG
1 AAATTTTGA-TAACCACACT-ATA
* *
21904 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCACACTATA
* * * *
21926 AAATTTTTATTACCTCGCTATA
1 AAATTTTGATAACCACACTATA
*
21948 ACATTTTGATAA
1 AAATTTTGATAA
21960 TCTATTTGGT
Statistics
Matches: 76, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
22 59 0.78
23 17 0.22
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:21882 original size:44 final size:44
Alignment explanation
Indices: 21834--22145 Score: 100
Period size: 44 Copynumber: 7.2 Consensus size: 44
21824 TAACCTTCAT
21834 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTCCCC
1 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTCCCC
* * * * ** * *
21878 ATGAAAATATT-AGTAACCTC-CTAATGAAATTTTGTTAACCACACT
1 ATG-AAATTTTGA-TAACCACACT-ATAAAATTTTGATAACTTCCCC
* * * * *
21923 ATGAAATTTTTATTACCTCGCTATAACATTTTGATAA--T---C
1 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTCCCC
* *** *
21962 -T---A-TTTGGTAACCTTTCTATAAAATTGTGATAA-TTAACCACCC
1 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTT---C-CCC
** * *
22004 TATGAAATTTCAATAACCA-ACCTA-AGAAATTTTGATAACCTGAT-TCT
1 -ATGAAATTTTGATAACCACA-CTATA-AAATTTTGATAA-CT--TCCCC
* * **
22051 AAGAAATTTTGGTAACCACACTATGAAAA-TTTGATAACTTCCAT
1 ATGAAATTTTGATAACCACACTAT-AAAATTTTGATAACTTCCCC
* * ** *
22095 ATGAAATTTTGGTAACCACATTATGGAATTTTGATAACTTCCTC
1 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTCCCC
22139 ATGAAAT
1 ATGAAAT
22146 CATAATAACC
Statistics
Matches: 196, Mismatches: 42, Indels: 60
0.66 0.14 0.20
Matches are distributed among these distances:
34 23 0.12
35 2 0.01
38 1 0.01
42 1 0.01
43 3 0.02
44 74 0.38
45 36 0.18
46 25 0.13
47 7 0.04
48 22 0.11
50 1 0.01
52 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (44 bp):
ATGAAATTTTGATAACCACACTATAAAATTTTGATAACTTCCCC
Found at i:22041 original size:22 final size:22
Alignment explanation
Indices: 21995--22088 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
21985 TTGTGATAAT
* * **
21995 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTTGA
22017 TAACCAACCTAAGAAATTTTGA
1 TAACCAACCTAAGAAATTTTGA
** *
22039 TAACCTGATTCTAAGAAATTTTGG
1 TAACC--AACCTAAGAAATTTTGA
* *
22063 TAACC-ACACTATGAAAATTTGA
1 TAACCAAC-CTAAGAAATTTTGA
22085 TAAC
1 TAAC
22089 TTCCATATGA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
22 38 0.67
24 19 0.33
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTTGA
Found at i:22097 original size:22 final size:22
Alignment explanation
Indices: 22072--22145 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
22062 GTAACCACAC
*
22072 TATGAAAATTTGATAACTTCCA
1 TATGAAATTTTGATAACTTCCA
*
22094 TATGAAATTTTGGTAAC--CACA
1 TATGAAATTTTGATAACTTC-CA
*
22115 TTATGGAATTTTGATAACTTCC-
1 -TATGAAATTTTGATAACTTCCA
22137 TCATGAAAT
1 T-ATGAAAT
22146 CATAATAACC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
22 36 0.86
23 1 0.02
24 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTCCA
Found at i:22155 original size:44 final size:44
Alignment explanation
Indices: 22063--22177 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
22053 GAAATTTTGG
* * ** **
22063 TAACCACACTATGAAAATTTGATAACTTCCATATGAAATTTTGG
1 TAACCACATTATGAAATTTTGATAACTTCCATATGAAATCATAA
*
22107 TAACCACATTATGGAATTTTGATAACTTCC-TCATGAAATCATAA
1 TAACCACATTATGAAATTTTGATAACTTCCAT-ATGAAATCATAA
*
22151 TAACCATC-TTATGAAATTTTCATAACT
1 TAACCA-CATTATGAAATTTTGATAACT
22178 ACATAGAGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 1 0.02
44 58 0.97
45 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (44 bp):
TAACCACATTATGAAATTTTGATAACTTCCATATGAAATCATAA
Found at i:22381 original size:19 final size:20
Alignment explanation
Indices: 22350--22387 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
22340 TATTGACATT
22350 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
22369 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
22388 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:22517 original size:26 final size:27
Alignment explanation
Indices: 22469--22528 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
22459 TGAAAATTTT
* **
22469 AATTAATTTTTAAATAATTAATAAT-G
1 AATTAATTTATAAATAAAAAATAATGG
*
22495 AATTAATTTATAATTAAAAAATAATGG
1 AATTAATTTATAAATAAAAAATAATGG
22522 AA-TAATT
1 AATTAATT
22529 AAAATATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
AATTAATTTATAAATAAAAAATAATGG
Found at i:22591 original size:31 final size:31
Alignment explanation
Indices: 22556--22615 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
22546 TGGCAATTTA
*
22556 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATGTTTCAAAAAAAAGGGTACAATTG
*
22587 GAAATATGTTTCAAAAATAAGGGTACAAT
1 GAAATATGTTTCAAAAAAAAGGGTACAAT
22616 CGAAAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTCAAAAAAAAGGGTACAATTG
Found at i:23815 original size:30 final size:30
Alignment explanation
Indices: 23779--23840 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
23769 TTTTAATGTC
23779 ATTTCACTTCTCCCTTTTATTGTTTGTTAT
1 ATTTCACTTCTCCCTTTTATTGTTTGTTAT
23809 ATTTCACTTCTCCCTTTTATTGTTTGTTAT
1 ATTTCACTTCTCCCTTTTATTGTTTGTTAT
23839 AT
1 AT
23841 AATTTATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (30 bp):
ATTTCACTTCTCCCTTTTATTGTTTGTTAT
Found at i:25414 original size:12 final size:11
Alignment explanation
Indices: 25385--25415 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
25375 GGCAAAGCTC
25385 TGGATACCGGA
1 TGGATACCGGA
25396 TGGATACCGGA
1 TGGATACCGGA
25407 TGGGATACC
1 T-GGATACC
25416 AAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (11 bp):
TGGATACCGGA
Found at i:28443 original size:15 final size:15
Alignment explanation
Indices: 28423--28452 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28413 TGCTTTATTC
28423 ATAGAATTTACGAAT
1 ATAGAATTTACGAAT
*
28438 ATAGAATTTATGAAT
1 ATAGAATTTACGAAT
28453 CTCAAAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (15 bp):
ATAGAATTTACGAAT
Found at i:28720 original size:21 final size:22
Alignment explanation
Indices: 28670--28740 Score: 99
Period size: 21 Copynumber: 3.2 Consensus size: 22
28660 AGTTTGGTTC
*
28670 ATAAATCTTCTTAATATGTTAT
1 ATAAATCTTCTTAATATATTAT
*
28692 AAAAATCTTCTTAATATATT-T
1 ATAAATCTTCTTAATATATTAT
*
28713 ATAAATCTTCTTAATATGTTACT
1 ATAAATCTTCTTAATATATTA-T
28736 ATAAA
1 ATAAA
28741 AAAAAAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.44
22 18 0.42
23 6 0.14
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (22 bp):
ATAAATCTTCTTAATATATTAT
Found at i:40150 original size:438 final size:434
Alignment explanation
Indices: 39257--40564 Score: 1513
Period size: 438 Copynumber: 3.0 Consensus size: 434
39247 CCCGTTTATA
* * *
39257 ATAAACAAATCATTTTTTGATGGTTTATTTATCAAATGATCCATATACTTTTATGTTTTATGCTA
1 ATAAACAAATAATTTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGTTTTATGCTA
* * *
39322 TTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACGTTTCACCTTTGATTCTTTTATTTTTTG
66 TTTAGTCCCTCACAAATTATGGGTTGGACGATTGAACGTTTCA-CTTTAATTCTTTTATTTTTTG
* *
39387 TTTTGTTTGTCCGATGAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTC
130 TTTT-TTTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
** * * **
39452 CATTCAGGATTCAAAAGTCAATTTTGATGTTTTGATT-AAAAAAAAACTTCTGAAATTTTGTGGT
194 CATGAAGGATCCAAAAGTCAA-TTTAATGTTTTGATTCAAAAAAATGCTT-TGAAATTTTGTGGT
* *
39516 CTTGATTGCCGGTCTATTTGATATCGTATAAATTTTGGTCCACTTGTCCGATTGAGGTTGTTCAA
257 CTTGATTGCCGGTCTATTTAATATTGTAT-AATTTTGGTCCACTTGTCCGATTGAGGTTGTTCAA
* ** *
39581 GTGTCGGTTAAAAGGTTATTGCATGATCTATGACTTTCGTTAAGGGCCTGAAAGTTGAATTTGAT
321 GTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTTAAGGGCCTGAAAACTAAATTTGAT
*
39646 TAATGAGTTTCGTGGAGGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
386 TAATGAGTTTCGTGGAAGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
* * * **
39695 ATAGACAAATAATTTTTTGCTGGAATATTTATCAAATGATCCCTATACTTTTATAATTTATGCTA
1 ATAAACAAATAATTTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGTTTTATGCTA
*
39760 TTTAGTCCCTCACAAATTCTGGGTTGGACGATTGAACGTTTCAGCTTTAATTCTTTTATTTTTTG
66 TTTAGTCCCTCACAAATTATGGGTTGGACGATTGAACGTTTCA-CTTTAATTCTTTTATTTTTTG
39825 TTTTTCTTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
130 TTTTT-TTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTT
39890 CATGAAGGATCCAAAAGTCAATCTTAATGTTTTGATTCAAAAAAATGCTCTTGAAATTTTGTGGT
194 CATGAAGGATCCAAAAGTCAAT-TTAATGTTTTGATTCAAAAAAATGCT-TTGAAATTTTGTGGT
* *
39955 CTCT-ATTGCCGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGTTTGTTTA
257 CT-TGATTGCCGGTCTATTTAATATTGTATAATTTT-GGTCCACTTGTCCGATTGAGGTTGTTCA
* * * * * *
40019 TGTGT-GGATTAATAGGTTATTGTATTATCTACGACTTTTGTTAAGGGCTTGAAAACTAAATTTG
320 AGTGTCGG-TTAAAAGGTTATTGCATGATCTACGACTTTCGTTAAGGGCCTGAAAACTAAATTTG
*
40083 ATTAATGAGTTTCGTGGAAGGTTCGAG-AGAGAATTTTTATGTTTGGTCTCC
384 ATTAATGAGTTTCGTGGAAGGTTCAAGAAG-GAATTTTTATGTTTGGTCTCC
* * * * *
40134 ATAAACAAATATTTTTTTTCGCTGGATTATCTATTAAATGATCCTTATACTTTTATGTTTTATAC
1 ATAAACAAATA-ATTTTTT-GCTGGATTATTTATCAAATGATCCATATACTTTTATGTTTTATGC
* * * * * * *
40199 TATTTAATCCTTTA-AAATTATGGGTTGAACGATTTAACGCTTTGACTTTTATT-TTTGT-TTTT
64 TATTTAGTCCCTCACAAATTATGGGTTGGACGATTGAACG-TTTCACTTTAATTCTTT-TATTTT
* ** * * * **
40261 TCTATTCTGGTTGTGCGATCAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAA
127 T-TGTT-TTTTTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA
* * * * ** * * * *
40326 CTTTCATGAATGA-CTCAGAAGCCAA-ATAATGTTTAAATTCTAAAAAATGATTTTTAAATTTCG
190 CTTTCATGAAGGATC-CAAAAGTCAATTTAATGTTTTGATTCAAAAAAATG-CTTTGAAATTTTG
* * * * * * *
40389 TTGTTTTGATTGCCGGTCTATTTAATATTGTATAATTTTTGCTCAACTTGTTCGATTGAAGTTAT
253 TGGTCTTGATTGCCGGTCTATTTAATATTGTATAA-TTTTGGTCCACTTGTCCGATTGAGGTTGT
* * * ** * * * ** * *** *
40454 TCAAGTGTCAGTTAAAATGTTAATGTGTAATCCATGACTTTCACTAAGGGCTTGAATGTTGAATT
317 TCAAGTGTCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTTAAGGGCCTGAAAACTAAATT
* *
40519 TGATTCATGAGTTTCAT-GAAGGGTTCAA-AAGGTAATTTTTATGTTT
382 TGATTAATGAGTTTCGTGGAA-GGTTCAAGAAGG-AATTTTTATGTTT
40565 CATCTCTATC
Statistics
Matches: 749, Mismatches: 99, Indels: 44
0.84 0.11 0.05
Matches are distributed among these distances:
437 7 0.01
438 381 0.51
439 196 0.26
440 111 0.15
441 54 0.07
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (434 bp):
ATAAACAAATAATTTTTTGCTGGATTATTTATCAAATGATCCATATACTTTTATGTTTTATGCTA
TTTAGTCCCTCACAAATTATGGGTTGGACGATTGAACGTTTCACTTTAATTCTTTTATTTTTTGT
TTTTTTGTCCGATCAAGGTGATTTAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
TGAAGGATCCAAAAGTCAATTTAATGTTTTGATTCAAAAAAATGCTTTGAAATTTTGTGGTCTTG
ATTGCCGGTCTATTTAATATTGTATAATTTTGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTC
GGTTAAAAGGTTATTGCATGATCTACGACTTTCGTTAAGGGCCTGAAAACTAAATTTGATTAATG
AGTTTCGTGGAAGGTTCAAGAAGGAATTTTTATGTTTGGTCTCC
Found at i:41037 original size:30 final size:29
Alignment explanation
Indices: 40995--41093 Score: 130
Period size: 30 Copynumber: 3.4 Consensus size: 29
40985 AAAATGATAA
40995 AAAATGAG-TTTTTTTTTGGCAATAGATT
1 AAAATGAGTTTTTTTTTTGGCAATAGATT
*
41023 AAAATGAG-TTTTTTTTTGCACCAATAGATT
1 AAAATGAGTTTTTTTTTTG--GCAATAGATT
**
41053 AAAATGAGGGTTTTTTTTGGCAATAAGATT
1 AAAATGAGTTTTTTTTTTGGCAAT-AGATT
41083 AAAATGAGTTT
1 AAAATGAGTTT
41094 ATGAGGTGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 18 0.29
29 4 0.06
30 31 0.50
31 9 0.15
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (29 bp):
AAAATGAGTTTTTTTTTTGGCAATAGATT
Found at i:41387 original size:52 final size:52
Alignment explanation
Indices: 41304--41408 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
41294 TCCACTAAAA
* *
41304 GATCCAGGTGTTTCTTCTTCGGCCGAAACTTAGCCAGGTGTTAACTGAGCAT
1 GATCCAAGTGTTTCTTCTTCGGCCCAAACTTAGCCAGGTGTTAACTGAGCAT
* * * *
41356 GATCCAAGTGTTTCTT-TTTGGCCCAAGACTTAGGCAGGTGTTGATTGAGCAT
1 GATCCAAGTGTTTCTTCTTCGGCCCAA-ACTTAGCCAGGTGTTAACTGAGCAT
41408 G
1 G
41409 CAAAAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 8 0.17
52 38 0.83
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (52 bp):
GATCCAAGTGTTTCTTCTTCGGCCCAAACTTAGCCAGGTGTTAACTGAGCAT
Done.