Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005775.1 Corchorus capsularis cultivar CVL-1 contig05793, 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: 17453
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Found at i:1246 original size:10 final size:10
Alignment explanation
Indices: 1231--1314 Score: 60
Period size: 10 Copynumber: 7.7 Consensus size: 10
1221 TATCCGCGCA
1231 CCATGCCCGG
1 CCATGCCCGG
1241 CCATGCCCGG
1 CCATGCCCGG
* *
1251 CCATATCCGCGCA
1 CCAT-GCC-CG-G
1264 CCATGCCCGG
1 CCATGCCCGG
* *
1274 CCATATCCGCGCA
1 CCAT-GCC-CG-G
*
1287 CCATGCCCCG
1 CCATGCCCGG
1297 CCATGCCCGG
1 CCATGCCCGG
1307 CCAATGCC
1 CC-ATGCC
1315 ATGCCATCCG
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
10 29 0.51
11 12 0.21
12 8 0.14
13 8 0.14
ACGTcount: A:0.15, C:0.50, G:0.23, T:0.12
Consensus pattern (10 bp):
CCATGCCCGG
Found at i:1253 original size:33 final size:33
Alignment explanation
Indices: 1207--1277 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
1197 TCGACACCAA
*
1207 GCCATGCCTGGCCATATCCGCGCACCATGCCCG
1 GCCATGCCCGGCCATATCCGCGCACCATGCCCG
1240 GCCATGCCCGGCCATATCCGCGCACCATGCCCG
1 GCCATGCCCGGCCATATCCGCGCACCATGCCCG
1273 GCCAT
1 GCCAT
1278 ATCCGCGCAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.15, C:0.46, G:0.24, T:0.14
Consensus pattern (33 bp):
GCCATGCCCGGCCATATCCGCGCACCATGCCCG
Found at i:1267 original size:23 final size:23
Alignment explanation
Indices: 1241--1300 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1231 CCATGCCCGG
1241 CCATGCCCGGCCATATCCGCGCA
1 CCATGCCCGGCCATATCCGCGCA
1264 CCATGCCCGGCCATATCCGCGCA
1 CCATGCCCGGCCATATCCGCGCA
*
1287 CCATGCCCCGCCAT
1 CCATGCCCGGCCAT
1301 GCCCGGCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (23 bp):
CCATGCCCGGCCATATCCGCGCA
Found at i:6850 original size:21 final size:19
Alignment explanation
Indices: 6820--6861 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
6810 TTCATTGTGT
*
6820 GGTTATCAAAATTTGTATGAA
1 GGTTACCAAAATTT-TAT-AA
6841 GGTTACCAAAATTTTATAA
1 GGTTACCAAAATTTTATAA
6860 GG
1 GG
6862 AAGTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (19 bp):
GGTTACCAAAATTTTATAA
Found at i:7104 original size:22 final size:22
Alignment explanation
Indices: 7023--7098 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
7013 TATAAATAAC
7023 TTCATATGGAA-ATTATCAAAAT
1 TTCATA-GGAAGATTATCAAAAT
* * *
7045 TTTATTGTG-TGATTATCAAAAT
1 TTCATAG-GAAGATTATCAAAAT
*
7067 TTCATAGGAAGATTATCGAAAT
1 TTCATAGGAAGATTATCAAAAT
*
7089 TTTATAGGAA
1 TTCATAGGAA
7099 AGTTATAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.05
22 41 0.95
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCATAGGAAGATTATCAAAAT
Found at i:7110 original size:22 final size:21
Alignment explanation
Indices: 7057--7127 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
7047 TATTGTGTGA
*
7057 TTATCAAAATTTCATAGGAAG
1 TTATAAAAATTTCATAGGAAG
** *
7078 ATTATCGAAATTTTATAGGAAAG
1 -TTATAAAAATTTCATAGG-AAG
7101 TTATAAAAA--TCATAGGGAAG
1 TTATAAAAATTTCATA-GGAAG
7121 TTATAAA
1 TTATAAA
7128 TATCTTAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 14 0.33
21 2 0.05
22 23 0.55
23 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (21 bp):
TTATAAAAATTTCATAGGAAG
Found at i:7110 original size:44 final size:44
Alignment explanation
Indices: 7012--7110 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 44
7002 CCATACTTTT
* * **
7012 TTATAAATAACTTCATATGGAAATTATCAAAATTTTATTGTGTGA
1 TTATAAA-AATTTCATATGGAAATTATCAAAATTTTATAGTGAAA
* *
7057 TTATCAAAATTTCATA-GGAAGATTATCGAAATTTTATAG-GAAA
1 TTATAAAAATTTCATATGGAA-ATTATCAAAATTTTATAGTGAAA
7100 GTTATAAAAAT
1 -TTATAAAAAT
7111 CATAGGGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
43 6 0.13
44 33 0.73
45 6 0.13
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (44 bp):
TTATAAAAATTTCATATGGAAATTATCAAAATTTTATAGTGAAA
Found at i:7160 original size:21 final size:22
Alignment explanation
Indices: 7139--7210 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
7129 ATCTTAGTTT
7139 ATAAACAACATATGAAATTTTA
1 ATAAACAACATATGAAATTTTA
* ** *
7161 ATAACCTTCCTATGAAATTTT-
1 ATAAACAACATATGAAATTTTA
* *
7182 -TAGAACCACACTATGAAATTTTG
1 ATA-AACAACA-TATGAAATTTTA
7205 ATAAAC
1 ATAAAC
7211 TCCCTCTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 28 0.74
23 3 0.08
24 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (22 bp):
ATAAACAACATATGAAATTTTA
Found at i:7174 original size:22 final size:22
Alignment explanation
Indices: 7149--7208 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
7139 ATAAACAACA
*
7149 TATGAAATTTTAATAACCTTC-C
1 TATGAAATTTTAATAACC-ACAC
* *
7171 TATGAAATTTTTAGAACCACAC
1 TATGAAATTTTAATAACCACAC
*
7193 TATGAAATTTTGATAA
1 TATGAAATTTTAATAA
7209 ACTCCCTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTAATAACCACAC
Found at i:7320 original size:22 final size:22
Alignment explanation
Indices: 7294--7529 Score: 167
Period size: 22 Copynumber: 10.8 Consensus size: 22
7284 GTAACCTCTT
* *
7294 TATGAAATTTTGTTAAACACAC
1 TATGAAATTTTGATAACCACAC
* *
7316 TATGAAATTTTG-TATCCTC-C
1 TATGAAATTTTGATAACCACAC
*
7336 ATATGAAATTTTGATAATCACAC
1 -TATGAAATTTTGATAACCACAC
* * *
7359 TGTGAAATGTTGATAACCTCAC
1 TATGAAATTTTGATAACCACAC
***
7381 TATGAAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACCACAC
* * *
7403 TTTGAAAGTTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * *
7424 TTCTGGAATTTTGATAACTACAC
1 -TATGAAATTTTGATAACCACAC
* * *
7447 TATGAAAATTTGATAATC-CTC
1 TATGAAATTTTGATAACCACAC
* ** *
7468 TGTGAGGTTTTGATAACC-CCC
1 TATGAAATTTTGATAACCACAC
* * *
7489 TTATGAAATTTTGAGAACTACAG
1 -TATGAAATTTTGATAACCACAC
7512 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
7530 TCCTTATAAC
Statistics
Matches: 164, Mismatches: 43, Indels: 14
0.74 0.19 0.06
Matches are distributed among these distances:
20 1 0.01
21 34 0.21
22 126 0.77
23 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:7409 original size:44 final size:44
Alignment explanation
Indices: 7254--7467 Score: 165
Period size: 44 Copynumber: 4.9 Consensus size: 44
7244 ATTTACACTT
*
7254 TGAAATTTTGATAACCTATCA-TG-G-AA-TTTCG-TAACCTCTTTA
1 TGAAATTTTGATAACC-A-CACTGTGAAAGTTT-GATAACCTCCTTA
* * * * * *
7296 TGAAATTTTGTTAAACACACTATGAAATTTTG-TATCCTCCATA
1 TGAAATTTTGATAACCACACTGTGAAAGTTTGATAACCTCCTTA
*
7339 TGAAATTTTGATAATCACACTGTGAAA-TGTTGATAACCTCAC-TA
1 TGAAATTTTGATAACCACACTGTGAAAGT-TTGATAACCTC-CTTA
*** * *
7383 TGAAATTTTGATAACCTTGCTTTGAAAGTTTGATAACCTCCTTC
1 TGAAATTTTGATAACCACACTGTGAAAGTTTGATAACCTCCTTA
* * * *
7427 TGGAATTTTGATAACTACACTATGAAAATTTGATAATCCTC
1 TGAAATTTTGATAACCACACTGTGAAAGTTTGATAA-CCTC
7468 TGTGAGGTTT
Statistics
Matches: 139, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 16 0.12
43 39 0.28
44 74 0.53
45 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (44 bp):
TGAAATTTTGATAACCACACTGTGAAAGTTTGATAACCTCCTTA
Found at i:7508 original size:65 final size:64
Alignment explanation
Indices: 7361--7531 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 64
7351 AATCACACTG
* * * * * *
7361 TGAAATGTTGATAACCT-CACTATGAAATTTTGATAACCTTGCTTTGAAAG-TTTGATAACCTCC
1 TGAAATTTTGAGAA-CTACACTATGAAAATTTGATAACC-T-CTGTG-AGGTTTTGATAACCCCC
*
7424 TTC
62 TTA
* *
7427 TGGAATTTTGATAACTACACTATGAAAATTTGATAATCCTCTGTGAGGTTTTGATAACCCCCTTA
1 TGAAATTTTGAGAACTACACTATGAAAATTTGATAA-CCTCTGTGAGGTTTTGATAACCCCCTTA
* *
7492 TGAAATTTTGAGAACTACAGTATGAAATTTTGATAACCTC
1 TGAAATTTTGAGAACTACACTATGAAAATTTGATAACCTC
7532 CTTATAACCT
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
64 6 0.07
65 52 0.57
66 31 0.34
67 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (64 bp):
TGAAATTTTGAGAACTACACTATGAAAATTTGATAACCTCTGTGAGGTTTTGATAACCCCCTTA
Found at i:7737 original size:44 final size:44
Alignment explanation
Indices: 7683--7767 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
7673 TTATAATCTT
*
7683 CCTATGAAATTTT-GTTAACCA-CACTATGAAATTTTGATAATACC
1 CCTATAAAATTTTAG-TAACCACCA-TATGAAATTTTGATAATACC
*
7727 CCTATAAAATTTTAGTAACCTCCATATGAAATTTTGATAAT
1 CCTATAAAATTTTAGTAACCACCATATGAAATTTTGATAAT
7768 TACACTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (44 bp):
CCTATAAAATTTTAGTAACCACCATATGAAATTTTGATAATACC
Found at i:7776 original size:22 final size:22
Alignment explanation
Indices: 7684--7785 Score: 93
Period size: 22 Copynumber: 4.6 Consensus size: 22
7674 TATAATCTTC
* *
7684 CTATGAAATTTTGTTAACCACA
1 CTATGAAATTTTGATAACTACA
*
7706 CTATGAAATTTTGATAA-TACCC
1 CTATGAAATTTTGATAACTA-CA
* *
7728 CTATAAAATTTT-AGTAACCTCCA
1 CTATGAAATTTTGA-TAA-CTACA
*
7751 -TATGAAATTTTGATAATTACA
1 CTATGAAATTTTGATAACTACA
*
7772 CTATGAAAATTTGA
1 CTATGAAATTTTGA
7786 ATTAGTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.08
22 56 0.88
23 2 0.03
24 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACTACA
Found at i:8208 original size:22 final size:21
Alignment explanation
Indices: 8180--8827 Score: 278
Period size: 22 Copynumber: 30.0 Consensus size: 21
8170 TTTCAACAAG
8180 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
8201 TTATGAAAATTCGATTACCACAC
1 -TATGAAATTTTGATAACCTC-C
*
8224 TATGAAATTTTGGT-ACCTTCC
1 TATGAAATTTTGATAACC-TCC
* *
8245 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTC-C
* * *
8267 TATGAAATTTTAATTA-TTACAC
1 TATGAAATTTTGATAACCT-C-C
*
8289 TATGAAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACC-TCC
*
8311 TGTGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * * * *
8333 TATTAAAATTTAATAATCACAC
1 TATGAAATTTTGATAACCTC-C
** *
8355 TATGAAATTTTGATAAATTAGC
1 TATGAAATTTTGATAACCT-CC
* ** *
8377 TATGAAATTTTGGTTTCTTCAC
1 TATGAAATTTTGATAACCTC-C
**
8399 TATGAAATTTTGATAATTTCCC
1 TATGAAATTTTGATAACCT-CC
* ** *
8421 TATGAAGTTTTGGGAACCACAC
1 TATGAAATTTTGATAACCTC-C
* *
8443 CATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTC-C
*
8465 TATGAAATTTTGATAATCTGCCC
1 TATGAAATTTTGATAACCT--CC
*
8488 TATGAAATTCTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* *
8510 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTC-C
* *
8532 TATGAAATTTTGATAGCCTCAG
1 TATGAAATTTTGATAACCTC-C
*
8554 TATG-AATTTTTATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
*
8575 TATGAAATTTTTGATAACC-AC
1 TATGAAA-TTTTGATAACCTCC
* ** *
8596 TTTGATAACCTCG-T-A-----
1 TATGA-AATTTTGATAACCTCC
* * *
8611 -ATGAAATTTCGATAGCCACAC
1 TATGAAATTTTGATAACCTC-C
*
8632 TATGAAATTTTGGT-ACCTCC
1 TATGAAATTTTGATAACCTCC
* * *
8652 ATATGAAATTTCGATAACCACAT
1 -TATGAAATTTTGATAACCTC-C
* *
8675 TATGAAATTTTGATAATCTTGC
1 TATGAAATTTTGATAA-CCTCC
* **
8697 TATGAAATTTTGATAACTTTTT
1 TATGAAATTTTGATAAC-CTCC
** * * *
8719 TATGACCTTTTTTATAATCTGCA
1 TATGA-AATTTTGATAACCT-CC
** * * *
8742 TACAAAAGTTTGATAACCACAT
1 TATGAAATTTTGATAACCTC-C
* **
8764 TATGAAATTATGATAAATTTCC
1 TATGAAATTTTGAT-AACCTCC
**
8786 TATGAAATTTTGATAAATTACC
1 TATGAAATTTTGATAACCT-CC
8808 TATGAAATTTTGATAACCTC
1 TATGAAATTTTGATAACCTC
8828 TCCACACTAT
Statistics
Matches: 465, Mismatches: 121, Indels: 81
0.70 0.18 0.12
Matches are distributed among these distances:
13 5 0.01
14 4 0.01
19 1 0.00
20 2 0.00
21 67 0.14
22 339 0.73
23 44 0.09
24 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:8563 original size:21 final size:22
Alignment explanation
Indices: 8180--8593 Score: 329
Period size: 22 Copynumber: 18.8 Consensus size: 22
8170 TTTCAACAAG
8180 TATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * *
8201 TTATGAAAATTCGATTACCACAC
1 -TATGAAATTTTGATAACCTCAC
*
8224 TATGAAATTTTGGT-ACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
* *
8245 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTCAC
* * *
8267 TATGAAATTTTAATTA-TTACAC
1 TATGAAATTTTGATAACCT-CAC
**
8289 TATGAAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACCTCAC
* *
8311 TGTGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * * * *
8333 TATTAAAATTTAATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
8355 TATGAAATTTTGATAA-ATTAGC
1 TATGAAATTTTGATAACCTCA-C
* ** *
8377 TATGAAATTTTGGTTTCTTCAC
1 TATGAAATTTTGATAACCTCAC
** *
8399 TATGAAATTTTGATAATTTCCC
1 TATGAAATTTTGATAACCTCAC
* ** *
8421 TATGAAGTTTTGGGAACCACAC
1 TATGAAATTTTGATAACCTCAC
* *
8443 CATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCAC
* *
8465 TATGAAATTTTGATAATCTGCCC
1 TATGAAATTTTGATAACCT-CAC
*
8488 TATGAAATTCTGATAACCTTC-C
1 TATGAAATTTTGATAACC-TCAC
* *
8510 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTCAC
* *
8532 TATGAAATTTTGATAGCCTCAG
1 TATGAAATTTTGATAACCTCAC
* *
8554 TATG-AATTTTTATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
8575 TATGAAATTTTTGATAACC
1 TATGAAA-TTTTGATAACC
8594 ACTTTGATAA
Statistics
Matches: 304, Mismatches: 75, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
21 37 0.12
22 233 0.77
23 33 0.11
24 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:8650 original size:78 final size:77
Alignment explanation
Indices: 8518--8672 Score: 195
Period size: 78 Copynumber: 2.0 Consensus size: 77
8508 CCTATGAAAT
* * * * * *
8518 TTTGATAACCACATTATGAAATTTTGATAGCCTCAGTATGAATTTTTATAACCTCCCTATGAAAT
1 TTTGATAACCACATAATGAAATTTCGATAGCCACACTATGAATTTTGATAACCTCCATATGAAA-
*
8583 TTTTGATAACCAC
65 TTTCGATAACCAC
* * *
8596 TTTGATAACCTCGTAATGAAATTTCGATAGCCACACTATGAAATTTTGGT-ACCTCCATATGAAA
1 TTTGATAACCACATAATGAAATTTCGATAGCCACACTATG-AATTTTGATAACCTCCATATGAAA
8660 TTTCGATAACCAC
65 TTTCGATAACCAC
8673 ATTATGAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
77 12 0.18
78 47 0.71
79 7 0.11
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (77 bp):
TTTGATAACCACATAATGAAATTTCGATAGCCACACTATGAATTTTGATAACCTCCATATGAAAT
TTCGATAACCAC
Found at i:8679 original size:100 final size:99
Alignment explanation
Indices: 8498--8690 Score: 239
Period size: 100 Copynumber: 1.9 Consensus size: 99
8488 TATGAAATTC
* *
8498 TGATAACCTTCCTATGAAATTTTGATAACCACATTATGAAATTTTGATAGCCTCAGTATGAATTT
1 TGATAACCTTCCTATGAAATTTCGATAACCACACTATGAAATTTTGATAGCCTCAGTATGAATTT
** * *
8563 TTATAACCTCCCTATGAAATTTTTGATAACCACTT
66 CGATAACCACACTATGAAA-TTTTGATAACCACTT
* * *
8598 TGATAACC-TCGTAATGAAATTTCGATAGCCACACTATGAAATTTTGGTA-CCTCCA-TATGAAA
1 TGATAACCTTCCT-ATGAAATTTCGATAACCACACTATGAAATTTTGATAGCCT-CAGTATG-AA
*
8660 TTTCGATAACCACATTATGAAATTTTGATAA
63 TTTCGATAACCACACTATGAAATTTTGATAA
8691 TCTTGCTATG
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
99 19 0.24
100 61 0.76
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (99 bp):
TGATAACCTTCCTATGAAATTTCGATAACCACACTATGAAATTTTGATAGCCTCAGTATGAATTT
CGATAACCACACTATGAAATTTTGATAACCACTT
Found at i:10604 original size:21 final size:22
Alignment explanation
Indices: 10574--10697 Score: 101
Period size: 22 Copynumber: 5.7 Consensus size: 22
10564 TAAATATTTT
* *
10574 TATGACATTTTGATAACTACCC
1 TATGAAATTTTGATAACCACCC
10596 TAT-AAATTTTGATAACCACCC
1 TATGAAATTTTGATAACCACCC
* ** *
10617 TATGAAAATTTGATAATTA-TC
1 TATGAAATTTTGATAACCACCC
* * * *
10638 TATGAAATTATGATAAACGCCA
1 TATGAAATTTTGATAACCACCC
* *
10660 TATGAAACTTTGATAACCTA-AC
1 TATGAAATTTTGATAACC-ACCC
*
10682 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
10698 ACTTTCCTCT
Statistics
Matches: 78, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
21 34 0.44
22 44 0.56
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCC
Found at i:10631 original size:22 final size:22
Alignment explanation
Indices: 10582--10677 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 22
10572 TTTATGACAT
* *
10582 TTTGATAACTACCCTAT-AAAT
1 TTTGATAACCACCCTATGAAAA
10603 TTTGATAACCACCCTATGAAAA
1 TTTGATAACCACCCTATGAAAA
** *
10625 TTTGATAATTA-TCTATG-AAA
1 TTTGATAACCACCCTATGAAAA
* * * *
10645 TTATGATAAACGCCATATGAAAC
1 TT-TGATAACCACCCTATGAAAA
10668 TTTGATAACC
1 TTTGATAACC
10678 TAACTATGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.08
21 27 0.46
22 23 0.39
23 4 0.07
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (22 bp):
TTTGATAACCACCCTATGAAAA
Found at i:10646 original size:43 final size:44
Alignment explanation
Indices: 10582--10699 Score: 125
Period size: 43 Copynumber: 2.7 Consensus size: 44
10572 TTTATGACAT
* * *
10582 TTTGATAA-CTACCCTAT-AAATTTTGATAACCACCCTATGAAAA
1 TTTGATAACCTA-ACTATGAAATTTTGATAAACACCATATGAAAA
* * * * *
10625 TTTGATAA-TTATCTATGAAATTATGATAAACGCCATATGAAAC
1 TTTGATAACCTAACTATGAAATTTTGATAAACACCATATGAAAA
*
10668 TTTGATAACCTAACTATGAAATTTTAATAAAC
1 TTTGATAACCTAACTATGAAATTTTGATAAAC
10700 TTTCCTCTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 4 0.06
43 39 0.63
44 19 0.31
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (44 bp):
TTTGATAACCTAACTATGAAATTTTGATAAACACCATATGAAAA
Found at i:15574 original size:3 final size:3
Alignment explanation
Indices: 15524--15554 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15514 ACAAGATGGT
15524 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15555 GACCAGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.