Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009734.1 Corchorus capsularis cultivar CVL-1 contig09755, 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: 16463
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:368 original size:13 final size:13
Alignment explanation
Indices: 350--376 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
340 CCGGTAGTGG
350 ATTAAATAAATAT
1 ATTAAATAAATAT
363 ATTAAATAAATAT
1 ATTAAATAAATAT
376 A
1 A
377 AAAATTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAAATAAATAT
Found at i:905 original size:16 final size:16
Alignment explanation
Indices: 886--916 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
876 TCTCGCTTCT
886 CTCTCGTCGAACAGAA
1 CTCTCGTCGAACAGAA
902 CTCTCGTCGAACAGA
1 CTCTCGTCGAACAGA
917 GTTCTTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (16 bp):
CTCTCGTCGAACAGAA
Found at i:2146 original size:19 final size:19
Alignment explanation
Indices: 2110--2147 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2100 ATTTTAATGT
*
2110 GTTCTTAATGATGAATTAA
1 GTTCTTAATAATGAATTAA
2129 GTTCATTAATAATG-ATTAA
1 GTTC-TTAATAATGAATTAA
2148 CCATTAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
GTTCTTAATAATGAATTAA
Found at i:5043 original size:24 final size:24
Alignment explanation
Indices: 5016--5072 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
5006 TCAAGTAGAG
* *
5016 GATTCCAACCTCAGTCAAATCCAA
1 GATTGCAACCTCAATCAAATCCAA
5040 GATTGCAACCTCAATCAAATCCAA
1 GATTGCAACCTCAATCAAATCCAA
5064 GATTGCAAC
1 GATTGCAAC
5073 GACAGCCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.21
Consensus pattern (24 bp):
GATTGCAACCTCAATCAAATCCAA
Found at i:7048 original size:45 final size:45
Alignment explanation
Indices: 6960--7047 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 45
6950 GTTGTATATT
*
6960 TTGGGGAAAATATACGAATTGAATGTTAAAAACTTAAGAAAAAAA
1 TTGGGGAAAATATACGAATTGAACGTTAAAAACTTAAGAAAAAAA
*
7005 TTGGGGAAAATATA-TAA-T-AACGTATAAAAACTTAAGAAAAAAA
1 TTGGGGAAAATATACGAATTGAACGT-TAAAAACTTAAGAAAAAAA
7048 ATTTGTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 4 0.10
43 20 0.50
44 2 0.05
45 14 0.35
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.24
Consensus pattern (45 bp):
TTGGGGAAAATATACGAATTGAACGTTAAAAACTTAAGAAAAAAA
Found at i:10528 original size:22 final size:21
Alignment explanation
Indices: 10503--10598 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 21
10493 TATTCATACG
10503 AAATTATGATAACCTTCCTATT
1 AAATTATGATAA-CTTCCTATT
10525 AAATTATGATAA-TTACACTATT
1 AAATTATGATAACTT-C-CTATT
* * *
10547 ---TT-TGATGACATCCTTATG
1 AAATTATGATAACTTCC-TATT
* *
10565 AAATTTTGATAACCTTCCTATA
1 AAATTATGATAA-CTTCCTATT
10587 AAATTATGATAA
1 AAATTATGATAA
10599 TTACACTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
17 1 0.02
18 9 0.16
19 3 0.05
20 2 0.03
21 3 0.05
22 36 0.62
23 4 0.07
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTATGATAACTTCCTATT
Found at i:10599 original size:62 final size:62
Alignment explanation
Indices: 10502--10673 Score: 290
Period size: 62 Copynumber: 2.8 Consensus size: 62
10492 ATATTCATAC
* * *
10502 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
1 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTGATGACATACTTAT
* *
10564 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTGATGGCATATTTAT
1 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTGATGACATACTTAT
*
10626 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTT
1 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTT
10674 ATAATTTTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 104 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTGATGACATACTTAT
Found at i:10796 original size:23 final size:22
Alignment explanation
Indices: 10770--10823 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
10760 AATGAAATTC
*
10770 TGATAACCAACACTATGAGATGT
1 TGATAACCAACA-TATGAGATAT
** *
10793 TGATAACCTCCATATGATATAT
1 TGATAACCAACATATGAGATAT
10815 TGATAACCA
1 TGATAACCA
10824 CTTTATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (22 bp):
TGATAACCAACATATGAGATAT
Found at i:10887 original size:22 final size:22
Alignment explanation
Indices: 10853--10908 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
10843 CCTCCATATG
* *
10853 AATTGTTAGTAATCACACTTTAA
1 AATTGTGA-TAATCACACTATAA
* *
10876 AATTTTGATAATCACACTATGA
1 AATTGTGATAATCACACTATAA
10898 AATTGTGATAA
1 AATTGTGATAA
10909 CCTTGCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTGTGATAATCACACTATAA
Found at i:10945 original size:23 final size:23
Alignment explanation
Indices: 10873--10998 Score: 82
Period size: 22 Copynumber: 5.6 Consensus size: 23
10863 AATCACACTT
*
10873 TAAAATTTTGAT-AATC-ACACTA
1 TAAAATTTTGATAAATCTTC-CTA
* * * *
10895 TGAAATTGTGAT-AACCTTGCTA
1 TAAAATTTTGATAAATCTTCCTA
*
10917 TGAAATTTTGATAAATCTTCCTA
1 TAAAATTTTGATAAATCTTCCTA
* * *
10940 TAAAATTATAATAAA-CCTCCATA
1 TAAAATTTTGATAAATCTTCC-TA
* *
10963 TAAAATTTTGATAACT-TTCTTA
1 TAAAATTTTGATAAATCTTCCTA
* *
10985 TGAAATCTTGATAA
1 TAAAATTTTGATAA
10999 CTACAAATTT
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
22 45 0.56
23 36 0.44
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (23 bp):
TAAAATTTTGATAAATCTTCCTA
Found at i:11053 original size:22 final size:22
Alignment explanation
Indices: 11028--11100 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
11018 CCCTATGATT
11028 TTTTGATTACATCATTATGAAA
1 TTTTGATTACATCATTATGAAA
11050 TTTTG-TTA-ATC-TCCCTATGAAA
1 TTTTGATTACATCAT---TATGAAA
** *
11072 TTCCGATCTACAT-ACTATGAAA
1 TTTTGAT-TACATCATTATGAAA
11094 TTTTGAT
1 TTTTGAT
11101 AGCCCTCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 3 0.08
22 27 0.69
23 1 0.03
24 2 0.05
25 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTTGATTACATCATTATGAAA
Found at i:11091 original size:44 final size:44
Alignment explanation
Indices: 11003--11101 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
10993 TGATAACTAC
** ** *
11003 AAATTTTGATAAGCTCCCTATGATTTTTTGATTACATCATTATG
1 AAATTTTGATAAGCTCCCTATGAAATTCCGATTACATCACTATG
* *
11047 AAATTTTGTTAATCTCCCTATGAAATTCCGATCTACAT-ACTATG
1 AAATTTTGATAAGCTCCCTATGAAATTCCGAT-TACATCACTATG
11091 AAATTTTGATA
1 AAATTTTGATA
11102 GCCCTCTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (44 bp):
AAATTTTGATAAGCTCCCTATGAAATTCCGATTACATCACTATG
Found at i:11211 original size:19 final size:19
Alignment explanation
Indices: 11158--11211 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
11148 CTTCATATGA
*
11158 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
*
11177 AATTTCGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
11196 AATTTTGGTATCCTCC
1 AATTTTGATATCCTCC
11212 ATCATAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:11404 original size:42 final size:42
Alignment explanation
Indices: 11286--11454 Score: 155
Period size: 44 Copynumber: 3.9 Consensus size: 42
11276 AGAAATACCA
* * *
11286 CTATGAAATTTTTG-TAATTACATTTTGAAAATTTGATAACCTC
1 CTATGAAA-TTTTGATAA-CACATTATGAAATTTTGATAACCTC
* * * *
11329 TTTATGAAATTTTGATAACATCTTTATAAAATTTTG-TCGACCT-
1 -CTATGAAATTTTGATAACA-CATTATGAAATTTTGAT-AACCTC
*
11372 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTC
1 CTATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCTC
* *
11415 GCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 -CTATGAAATTTTGATAAC-ACATTATGAAATTTTGATAA
11455 TCTTCAAATA
Statistics
Matches: 102, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
42 32 0.31
43 11 0.11
44 59 0.58
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (42 bp):
CTATGAAATTTTGATAACACATTATGAAATTTTGATAACCTC
Found at i:11447 original size:86 final size:86
Alignment explanation
Indices: 11286--11450 Score: 217
Period size: 86 Copynumber: 1.9 Consensus size: 86
11276 AGAAATACCA
* * * *
11286 CTATGAAATTTTTGTAATTACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
11351 TTTATAAAATTTTGTCGACCT
66 ACTATAAAATTTTGTCGACCT
* *
11372 CTATGAAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACA
1 CTATGAAATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
*
11435 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
11451 ATAATCTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 5 0.07
86 61 0.90
87 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (86 bp):
CTATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTCGACCT
Found at i:11529 original size:20 final size:22
Alignment explanation
Indices: 11439--11536 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 22
11429 ATAACAACAC
*
11439 TATGAAATTTTGATAATC-TTCA
1 TATGAAATTTCGATAATCATT-A
* * *
11461 AAT-AAATTTTGATAATCCTATCTT
1 TATGAAATTTCGATAAT-C-AT-TA
11485 TATGAAATTTCGATAATCATTA
1 TATGAAATTTCGATAATCATTA
* *
11507 TATGAGATTT-GATAA-CCTTA
1 TATGAAATTTCGATAATCATTA
*
11527 TATCAAATTT
1 TATGAAATTT
11537 TGGTACTCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.19
21 18 0.29
22 13 0.21
23 2 0.03
24 4 0.06
25 13 0.21
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
TATGAAATTTCGATAATCATTA
Found at i:11592 original size:22 final size:22
Alignment explanation
Indices: 11311--11671 Score: 139
Period size: 22 Copynumber: 16.3 Consensus size: 22
11301 AATTACATTT
* *
11311 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
11333 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* *
11355 TAAAATTTTG-TCGACC-TC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
11375 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
11397 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
11419 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
11441 TGAAATTTTGATAATCTTCAAA
1 TGAAATTTTGATAACCTTCATA
*
11463 T-AAATTTTGATAATCCTATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
* *
11487 TGAAATTTCGATAATCATT-ATA
1 TGAAATTTTGATAA-CCTTCATA
*
11509 TGAGA-TTTGATAACCTT-ATA
1 TGAAATTTTGATAACCTTCATA
* * *
11529 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
11554 TTGAAACTTTT-ACAACCTTCATA
1 -TGAAA-TTTTGATAACCTTCATA
*
11577 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
11599 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
*
11621 TGAAATATT-AGTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
11643 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
11665 TGAAATT
1 TGAAATT
11672 CGTATAACCT
Statistics
Matches: 258, Mismatches: 49, Indels: 64
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.00
20 24 0.09
21 36 0.14
22 154 0.60
23 8 0.03
24 4 0.02
25 20 0.08
26 7 0.03
27 4 0.02
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:11769 original size:22 final size:22
Alignment explanation
Indices: 11737--11784 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
11727 TTGTGATAAT
* *
11737 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
*
11759 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
11781 TAAC
1 TAAC
11785 TTGATCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:11821 original size:22 final size:22
Alignment explanation
Indices: 11791--11900 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
11781 TAACTTGATC
* * * *
11791 CTATAAAATTTTGTTAACTACT
1 CTATGAAATTTTGATAACCACA
*
11813 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
11835 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
11856 CTCATGGAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
11879 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
11901 TAGAGACAAG
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.04
22 66 0.93
23 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:12208 original size:30 final size:31
Alignment explanation
Indices: 12174--12238 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
12164 TGGCAATTTA
* *
12174 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
12204 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
12235 GAAA
1 GAAA
12239 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:14667 original size:199 final size:198
Alignment explanation
Indices: 14040--16185 Score: 2548
Period size: 199 Copynumber: 10.8 Consensus size: 198
14030 CACTTTATAG
* * * * * *
14040 AATTTTTCTTATAGGAGTATAATACAATACACTTTTCAGTGTAAATTTTACACTCTATAAGCGAG
1 AATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTT-GACTCCATAAGCGGG
* * * * *
14105 TTAAGAAGCTGACACATATCCCATTTCATAATCAATTAAATATTTAATATTAATATATATTCCTT
64 TTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCT
** * * * * * * *
14170 AAGGGGATTCATGT--GCTCTTAAACCCTGTATGTGCAGTCTGCTAAATTCGACTGACGGTATAT
129 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
14233 AGTAT
194 AGTAT
* * * *
14238 AATTTTTCTTATAAGATTATTATACAATCCACTGTCAGTATAAATTTTGGACTTCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTT-GACTCCATAAGCGGGT
* *
14303 TAAGAAGTTGACATATACCCTATTTCATAATTAATTAAATATTTAATATTAATATTAATACATAT
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATT-AA-A--T-AT-TTAATATTAATACATAT
* * * *
14368 TCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGTAGTCTGCTAAAATTCACTGACGG
124 TCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGG
14433 TGTATTA-TAT
189 TGTA-TAGTAT
* ** * * *
14443 AATTTTTCTTATAGGATTATTATACAACACGTTGTCAGTGTAAATATTAGACTCTATAAGTGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAAT-TTTGACTCCATAAGCGGGT
* * * * * * *
14508 TAAAAAGTTGATACATACCTCATTTCATCATCAATTAAATATATAATATTAATACACATTCCCTA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* * * * * *
14573 AGAGGACACATGTCAACCCTTAAACCCTGAACGTGAAGT-TAGCTAAACTCCATTTATGGTGTAT
130 AGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCT-GCTAAACTCCACTGACGGTGTAT
14637 AGTAT
194 AGTAT
* * * * *
14642 AATTTTTCTTACAGGATTGTTATACAATAAACTGTTAGTGTAAATCTTGGACTCCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAAT-TTTGACTCCATAAGCGGGT
* * ** * * * *
14707 TAAGAAGTTGATATATACATCATCTCATAATAAATTAAATATTTAATATTAATACATATTTCTTA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* * * *
14772 AGGAGACACATGTCAACCCTTAAACTCCT-CACGTGCAGTATGCTAAACTCGACTGACAATGTGT
130 AGGGGACACATGTCAACCCTTAAAC-CCTGCACGTGCAGTCTGCTAAACTCCACTGAC--GGTGT
14836 ATAGTAT
192 ATAGTAT
* * *
14843 AATTTTTCTTATAGAATTATTATACAAAACACAT-TCAGTGTAAATTTTGGACTCCACAAGCGGG
1 AATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTT-GACTCCATAAGCGGG
* * * * *
14907 TTAAGAAATTGACACATACCTCATTTCATAATTAATAAAATATTTAAGATTAAAACATA-TCCCA
64 TTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCC-
* * * *
14971 TAAGGTGAAACATGTTAACCCTTATACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
128 TAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
*
15036 TTGTAT
193 TAGTAT
* * * **
15042 AATTGTTCTTATATGATTATTATACAATAAACTG-CAAAGTAAATTTTGAACTCCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGT
* * * * *
15106 CAATAAGTTGACGCATACCCCA-TTCTATAATTGATTAAATATTTAATATTAATACATATTCCTT
65 TAAGAAGTTGACACATACCCCATTTC-ATAATTAATTAAATATTTAATATTAATACATATTCCCT
* * *
15170 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAACTCGACTGACGGTGTAT
129 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
15235 AGTAT
194 AGTAT
* * *
15240 AATTTTTCTTATATGATTATTATACAATACACTGTCAGTGTAAATTTGTGACTGCATAAGCGGTT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTT-TGACTCCATAAGCGGGT
* *
15305 TAAGAAGTTGACACATACCCCATTTCATAATTAATAAAATATTTAATATTAATATATATTCCCTA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
*
15370 AGGGGACACATGTCAACCCTTAAAGCCC-GCACGTTCAGTCTGCTAAACTCCACTGACGGTGTAT
130 AGGGGACACATGTCAACCCTTAAA-CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* *
15434 TGTGT
194 AGTAT
* * * * *
15439 AATTGTTCTTGTAGGATTATAATACAATATACTGTCAATGTAAATTTTGGACTCCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTT-GACTCCATAAGCGGGT
* *
15504 TAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATA-TAATACATATTCCATA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* *** * *
15568 AGGGGACACATGTCAACCATT---CCCCAAACGTGCAGTCTGCTAAAATCCACTGATGGTGTATA
130 AGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATA
15630 GTAT
195 GTAT
*
15634 AATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGT
* * * *
15699 TAAGAAGTTGATACATACCCCATTTCATAACTAATAAAATATTTAATGTTAATACATATTCCCTA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* * *
15764 AGGGGACACATGTCAACCCTTAAAGCCC-GCACGTTCAGTTTGCTAAACTCCACTGACGGTGGAT
130 AGGGGACACATGTCAACCCTTAAA-CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
**
15828 TTTAT
194 AGTAT
* * * * *
15833 AATTGTTCTTGTAGGATTATTTTACAATACACTGTCAATGTAAATTTTGTACTTCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGT
* * *
15898 TAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTTCCAA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
** * * * * *
15963 AGGGGACATGTGTCAACCCTT---CCAC-GCACGTGCAGTCTGCTAAAATCCATTGATGATATAT
130 AGGGGACACATGTCAACCCTTAAACC-CTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
16024 AGTAT
194 AGTAT
* * * * *
16029 AATTTTTCTTATAGGATTATTATACAATAGACTATCAGTGTAAATTTTGAATTCCATAAGTGGAT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTG-ACTCCATAAGCGGGT
* * * *
16094 TAAGAAGTTGACACATACCTCATTTCATAATAAATTAAATATTTAATTTTAATACATATTCCTTA
65 TAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTA
* * *
16159 AGGGTACATATGTCAACCCTTTAACCC
130 AGGGGACACATGTCAACCCTTAAACCC
16186 CAGTATTATT
Statistics
Matches: 1665, Mismatches: 243, Indels: 80
0.84 0.12 0.04
Matches are distributed among these distances:
194 4 0.00
195 138 0.08
196 198 0.12
197 61 0.04
198 235 0.14
199 678 0.41
200 24 0.01
201 163 0.10
202 3 0.00
203 33 0.02
204 2 0.00
205 122 0.07
206 4 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (198 bp):
AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGACTCCATAAGCGGGTT
AAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA
GGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAG
TAT
Found at i:15736 original size:394 final size:396
Alignment explanation
Indices: 14040--16185 Score: 2638
Period size: 394 Copynumber: 5.4 Consensus size: 396
14030 CACTTTATAG
* * * * *
14040 AATTTTTCTTATAGGAGTATAATACAATACACTTTTCAGTGTAAATTTT-ACACTCTATAAGCGA
1 AATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTGA-ACTCCATAAGCGG
* * * * *
14104 GTTAAGAAGCTGACACATATCCCATTTCATAATCAATTAAATATTTAATATTAATATATATTCCT
64 GTTAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCC
** * * * * * * *
14169 TAAGGGGATTCATGT--GCTCTTAAACCCTGTATGTGCAGTCTGCTAAATTCGACTGACGGTATA
129 TAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
* * * ** * * *
14232 TAGTATAATTTTTCTTATAAGATTATTATACAATCCACTGTCAGTATAAATTTTGGACTTCATAA
194 TTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAA
*
14297 GCGGGTTAAGAAGTTGACATATACCCTATTTCATAATTAATTAAATATTTAATATTAATATTAAT
259 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATT-AA-A--T-AT-TTAATATTAAT
* * *
14362 ACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGTAGTCTGCTAAAATTCAC
318 ACATATTCCATAAGGGGACACATGTCAACCCTT--ACCCCGCACGTGCAGTCTGCTAAAATCCAC
*
14427 TGACGGTGTATTA-TAT
381 TGATGGTGTA-TAGTAT
* ** * * *
14443 AATTTTTCTTATAGGATTATTATACAACACGTTGTCAGTGTAAATATT-AGACTCTATAAGTGGG
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGA-ACTCCATAAGCGGG
* * * * * * *
14507 TTAAAAAGTTGATACATACCTCATTTCATCATCAATTAAATATATAATATTAATACACATTCCCT
65 TTAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCCT
* * * * * *
14572 AAGAGGACACATGTCAACCCTTAAACCCTGAACGTGAAGT-TAGCTAAACTCCATTTATGGTGTA
130 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCT-GCTAAACTCCACTGACGGTGTA
* * * * * * *
14636 TAGTATAATTTTTCTTACAGGATTGTTATACAATAAACTGTTAGTGTAAATCTTGGACTCCATAA
194 TTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAA
* ** * *
14701 GCGGGTTAAGAAGTTGATATATACATCATCTCATAATAAATTAAATATTTAATATTAATACATAT
259 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* * * * * * * *
14766 TTCTTAAGGAGACACATGTCAACCCTTAAACTCCTCACGTGCAGTATGCTAAACTCGACTGACAA
324 TCCATAAGGGGACACATGTCAACCCTT--ACCCCGCACGTGCAGTCTGCTAAAATCCACTG---A
14831 T-GTGTATAGTAT
384 TGGTGTATAGTAT
* * * *
14843 AATTTTTCTTATAGAATTATTATACAAAACACAT-TCAGTGTAAATTTTGGACTCCACAAGCGGG
1 AATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTGAACTCCATAAGCGGG
* * * * *
14907 TTAAGAAATTGACACATACCTCATTTCATAATTAATAAAATATTTAAGATTAAAACATA-TCCCA
65 TTAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCC-
* * * *
14971 TAAGGTGAAACATGTTAACCCTTATACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
129 TAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
* * *
15036 TTGTATAATTGTTCTTATATGATTATTATACAATAAACTG-CAAAGTAAATTTTGAACTCCATAA
194 TTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAA
* * ** *
15100 GCGGGTCAATAAGTTGACGCATACCCCA-TTCTATAATTGATTAAATATTTAATATTAATACATA
259 GCGGGTTAAGAAGTTGACATATACCCCATTTC-ATAATTAATTAAATATTTAATATTAATACATA
* * * * *
15164 TTCCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTTTGCTAAACTCGACTGACG
323 TTCCATAAGGGGACACATGTCAACCCTT--ACCCCGCACGTGCAGTCTGCTAAAATCCACTGATG
15229 GTGTATAGTAT
386 GTGTATAGTAT
* * *
15240 AATTTTTCTTATATGATTATTATACAATACACTGTCAGTGTAAATTTGTG-ACTGCATAAGCGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTT-TGAACTCCATAAGCGGG
* *
15304 TTAAGAAGTTGACACATACCCCATTTCATAATTAATAAAATATTTAATATTAATATATATTCCCT
65 TTAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCCT
*
15369 AAGGGGACACATGTCAACCCTTAAAGCCC-GCACGTTCAGTCTGCTAAACTCCACTGACGGTGTA
130 AAGGGGACACATGTCAACCCTTAAA-CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
* * * *
15433 TTGTGTAATTGTTCTTGTAGGATTATAATACAATATACTGTCAATGTAAATTTTGGACTCCATAA
194 TTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAA
15498 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATA-TAATACATAT
259 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
* **
15562 TCCATAAGGGGACACATGTCAACCATT-CCCCAAACGTGCAGTCTGCTAAAATCCACTGATGGTG
324 TCCATAAGGGGACACATGTCAACCCTTACCCCGCACGTGCAGTCTGCTAAAATCCACTGATGGTG
15626 TATAGTAT
389 TATAGTAT
*
15634 AATTTTTCTTATAGGATTATTATACAATACACTGTCAATGTAAATTTTGAACTCCATAAGCGGGT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGT
* *
15699 TAAGAAGTTGATACATACCCCATTTCATAA-CTAATAAAATATTTAATGTTAATACATATTCCCT
66 TAAGAAGTTGACACATACCCCATTTCATAATC-AATAAAATATTTAATATTAATACATATTCCCT
* * *
15763 AAGGGGACACATGTCAACCCTTAAAGCCC-GCACGTTCAGTTTGCTAAACTCCACTGACGGTGGA
130 AAGGGGACACATGTCAACCCTTAAA-CCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA
* * * * * *
15827 TTTTATAATTGTTCTTGTAGGATTATTTTACAATACACTGTCAATGTAAATTTTGTACTTCATAA
194 TTGTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAA
15892 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATAT
259 GCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATA-
** * * *
15957 TTCCA-AAGGGGACATGTGTCAACCCTT-CCACGCACGTGCAGTCTGCTAAAATCCATTGATGAT
323 TTCCATAAGGGGACACATGTCAACCCTTACCCCGCACGTGCAGTCTGCTAAAATCCACTGATGGT
*
16020 ATATAGTAT
388 GTATAGTAT
* * * * *
16029 AATTTTTCTTATAGGATTATTATACAATAGACTATCAGTGTAAATTTTGAATTCCATAAGTGGAT
1 AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGT
* * * * *
16094 TAAGAAGTTGACACATACCTCATTTCATAATAAATTAAATATTTAATTTTAATACATATTCCTTA
66 TAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCCTA
* * *
16159 AGGGTACATATGTCAACCCTTTAACCC
131 AGGGGACACATGTCAACCCTTAAACCC
16186 CAGTATTATT
Statistics
Matches: 1527, Mismatches: 192, Indels: 57
0.86 0.11 0.03
Matches are distributed among these distances:
393 2 0.00
394 333 0.22
395 205 0.13
396 7 0.00
397 244 0.16
398 146 0.10
399 138 0.09
400 198 0.13
401 3 0.00
402 94 0.06
403 30 0.02
404 127 0.08
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (396 bp):
AATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGT
TAAGAAGTTGACACATACCCCATTTCATAATCAATAAAATATTTAATATTAATACATATTCCCTA
AGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATT
GTATAATTGTTCTTATAGGATTATTATACAATAAACTGTCAATGTAAATTTTGGACTCCATAAGC
GGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
CATAAGGGGACACATGTCAACCCTTACCCCGCACGTGCAGTCTGCTAAAATCCACTGATGGTGTA
TAGTAT
Found at i:16364 original size:59 final size:58
Alignment explanation
Indices: 16272--16390 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 58
16262 TTTGGTACAC
*
16272 CATTATTGTAGAGATTTTTTTGGTGAAGATTATTGTAGAAATTTTGAGTTACTAAGAT
1 CATTATTGTAGAGATTTTTTTGGTGAAGATTATTGTAGAAATTTCGAGTTACTAAGAT
* *
16330 CATTATTGTAGAGAATTTTTTTGGTGGAGATTATTGTTGAAATTTCGAGTTACTAAGAT
1 CATTATTGTAGAG-ATTTTTTTGGTGAAGATTATTGTAGAAATTTCGAGTTACTAAGAT
16389 CA
1 CA
16391 GCTCCTCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
58 13 0.23
59 44 0.77
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (58 bp):
CATTATTGTAGAGATTTTTTTGGTGAAGATTATTGTAGAAATTTCGAGTTACTAAGAT
Done.