Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022908.1 Corchorus olitorius cultivar O-4 contig22941, 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: 48696
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1389 original size:28 final size:25
Alignment explanation
Indices: 1328--1389 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1318 TAACTAGCAT
*
1328 TTGGAAGACGATTTCATCAAATAGA
1 TTGGAAGACGACTTCATCAAATAGA
* *
1353 TCGGAAGACGACTTCATCAGAGATGGAA
1 TTGGAAGACGACTTCATCA-A-ATAG-A
1381 TTGGAAGAC
1 TTGGAAGAC
1390 AATTCGAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 17 0.57
26 1 0.03
27 3 0.10
28 9 0.30
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (25 bp):
TTGGAAGACGACTTCATCAAATAGA
Found at i:1436 original size:50 final size:50
Alignment explanation
Indices: 1373--1749 Score: 445
Period size: 50 Copynumber: 7.5 Consensus size: 50
1363 ACTTCATCAG
* * *
1373 AGATGGAATTGGAAGACAATTCGAAGGATAAGCGGAAAACGATCCTTTTA
1 AGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* *
1423 GGATTGAATTGGAACGACAGTTCGAAGGATAATCGGAAGACGATCCTTTTA
1 AGATTGAATTGGAA-GACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* * * * *
1474 AAATTAAATTGGAAGACAATTCGAAGGATAAG-TGAAGACGACCCTTTTA
1 AGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* * * *
1523 AGATTGAATTGGAAGACAGTTTGAAGGATAATCAGAAGATGATCCTTTTA
1 AGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* * *
1573 AAATTGAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* * *
1623 AGATTGAATTGG-AGAACAGTTCGAAGGATAAGTGGAAGACGGTCCTTCTA
1 AGATTGAATTGGAAG-ACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
* * * *
1673 AGATTGAATTGGAAGACAGTTTGAAGAAGTTGATCGGAAGACGATCC-TTTA
1 AGATTGAATTGGAAGACAGTTCGAAG--GATAAGCGGAAGACGATCCTTTTA
* ** *
1724 TGATTGAATCAGAAGACATTTCGAAG
1 AGATTGAATTGGAAGACAGTTCGAAG
1750 AAACTGATCG
Statistics
Matches: 278, Mismatches: 43, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
49 44 0.16
50 150 0.54
51 70 0.25
52 14 0.05
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.25
Consensus pattern (50 bp):
AGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTA
Found at i:2033 original size:26 final size:26
Alignment explanation
Indices: 1997--2054 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1987 GCATTTTGTC
1997 AATTTAATACTATAATACTAGAATTT
1 AATTTAATACTATAATACTAGAATTT
2023 AATTTAATACTATAATACTAGAATTT
1 AATTTAATACTATAATACTAGAATTT
*
2049 ATTTTA
1 AATTTA
2055 GTAGTTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (26 bp):
AATTTAATACTATAATACTAGAATTT
Found at i:4648 original size:33 final size:33
Alignment explanation
Indices: 4606--4671 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4596 CTTCCCTTTC
4606 AATTTAATCCTTCAGCTTAAGAGATTCATGTGA
1 AATTTAATCCTTCAGCTTAAGAGATTCATGTGA
4639 AATTTAATCCTTCAGCTTAAGAGATTCATGTGA
1 AATTTAATCCTTCAGCTTAAGAGATTCATGTGA
4672 TTTGGTGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
AATTTAATCCTTCAGCTTAAGAGATTCATGTGA
Found at i:6759 original size:45 final size:45
Alignment explanation
Indices: 6628--6759 Score: 156
Period size: 45 Copynumber: 2.9 Consensus size: 45
6618 AACATTTTTA
* * ** * *
6628 AAGTAATTACAAAAGAAGATTTTTCAAAGTAAAAGTTTTTTATTT
1 AAGTAACTCCAAAAGAAGATTTTGGAAAGTAAAAGTTTTTAATTC
* * *
6673 AAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAATTTTTAATTC
1 AAGTAACTCCAAAAGAAGATTTTGGAAAGTAAAAGTTTTTAATTC
* * *
6718 AAGTACCTCCAAAAGAAGATTTTGGAAAGTTAAAGTCTTTAA
1 AAGTAACTCCAAAAGAAGATTTTGGAAAGTAAAAGTTTTTAA
6760 GAAATCCAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (45 bp):
AAGTAACTCCAAAAGAAGATTTTGGAAAGTAAAAGTTTTTAATTC
Found at i:8451 original size:2 final size:2
Alignment explanation
Indices: 8446--8483 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8436 TCATATATTC
8446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8484 TCATTCATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10448 original size:31 final size:28
Alignment explanation
Indices: 10409--10485 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
10399 TAAATACCCG
*
10409 AAAA-AATCCCTTATGTTTTTCTTTTGGGAC
1 AAAATAATCCCTCATG-TTTT-TTTT-GGAC
*
10439 AAAATAATCCCTCGTGTTTTTTTTGGAC
1 AAAATAATCCCTCATGTTTTTTTTGGAC
* *
10467 AAATTAATCCCTCACGTTT
1 AAAATAATCCCTCATGTTT
10486 CAAAAGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 20 0.49
29 4 0.10
30 8 0.20
31 9 0.22
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (28 bp):
AAAATAATCCCTCATGTTTTTTTTGGAC
Found at i:15329 original size:132 final size:132
Alignment explanation
Indices: 15156--15393 Score: 368
Period size: 132 Copynumber: 1.8 Consensus size: 132
15146 ATATCTAACA
* * * * *
15156 CAACAACTTATTTTGTCGTTTCAAAAGTAGTTATGTTTTTTGGAGCAACTTTCAAAGTCGCTGTG
1 CAACAACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGGAGCAACTTTCAAAGTCGCTGCG
* *
15221 AAAATTAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCATTGCGAAAAGAGTAGGATTT
66 AAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGCGAAAAGAGTAGGATTT
15286 TG
131 TG
* * * *
15288 CAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAGGTCGCTGCG
1 CAACAACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGGAGCAACTTTCAAAGTCGCTGCG
*
15353 AAAATCAATTTATAAAATATATTAAGCACCGACTAACAAAA
66 AAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAA
15394 TTCGTTTTCG
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 94 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (132 bp):
CAACAACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGGAGCAACTTTCAAAGTCGCTGCG
AAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGCGAAAAGAGTAGGATTT
TG
Found at i:15463 original size:132 final size:128
Alignment explanation
Indices: 15154--15441 Score: 335
Period size: 132 Copynumber: 2.2 Consensus size: 128
15144 TAATATCTAA
* * * * * * *
15154 CACAACAACTTATTTTGTCGTTTCAAAAGTAGTTATGTTTTTTGGAGCAACTTTCAAAGTCGCTG
1 CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAAGTCGCTG
* * *
15219 TGAAAATTAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCATTGCGAAAAGAGTAGGAT
66 CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGC----AGAGTAGGAT
15284 TT
127 TT
** *
15286 TGCAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAGGTCGCTG
1 CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAAGTCGCTG
* * * * *
15351 CGAAAATCAATTTATAAAATATATTAAGCACCGACTAACAAAATTCGTTTTC-GAGTATGATTT
66 CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTC-ATTGCAGAGTAGGATTT
* * *
15414 CACAATGACTTAATTTGTTGTTTCAAAA
1 CACAACGACTTAATTTGTCGTTACAAAA
15442 AGAATTCTGT
Statistics
Matches: 132, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
128 33 0.25
132 96 0.73
133 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (128 bp):
CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAAGTCGCTG
CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGCAGAGTAGGATTT
Found at i:15470 original size:132 final size:128
Alignment explanation
Indices: 15154--15520 Score: 319
Period size: 132 Copynumber: 2.8 Consensus size: 128
15144 TAATATCTAA
* * * * * * * *
15154 CACAACAACTTATTTTGTCGTTTCAAAAGTAGTTATGTTTTTTGGAGCAACTTTCAAAGTCGCTG
1 CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAACGACTTTCAAAGTCGCTG
* * *
15219 TGAAAATTAATTTGTAAAATATATTAAGCAACGACTAACAAAAGTCATTGCGAAAAGAGTAGGAT
66 CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGC----AGAGTAGGAT
15284 TT
127 TT
** * *
15286 TGCAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAGCGACTTTCAAGGTCGCTG
1 CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAACGACTTTCAAAGTCGCTG
* * * * *
15351 CGAAAATCAATTTATAAAATATATTAAGCACCGACTAACAAAATTCGTTTTC-GAGTATGATTT
66 CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTC-ATTGCAGAGTAGGATTT
* * * * * * *
15414 CACAATGACTTAATTTGTTGTTTCAAAAAG-AATTCTGTTTTTTTTTTGTAATGACTTT-AAATA
1 CACAACGACTTAATTTGTCGTTAC-AAAAGTAA---T-TATATTTTTTGTAACGACTTTCAAA-G
* * * *
15477 TCGTTGCGAAATTCAATTTGA-AAACTATATTAAACAACGACTAA
60 TCGCTGCGAAAATCAATTT-ATAAAATATATTAAGCAACGACTAA
15521 TATAAATCAT
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
128 31 0.16
129 5 0.03
131 3 0.02
132 150 0.78
133 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (128 bp):
CACAACGACTTAATTTGTCGTTACAAAAGTAATTATATTTTTTGTAACGACTTTCAAAGTCGCTG
CGAAAATCAATTTATAAAATATATTAAGCAACGACTAACAAAAGTCATTGCAGAGTAGGATTT
Found at i:17128 original size:30 final size:31
Alignment explanation
Indices: 17081--17155 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
17071 AAAATTACTA
17081 ATTGACCCCACTAAAATGAAAGGTTTATTCC
1 ATTGACCCCACTAAAATGAAAGGTTTATTCC
* * ***
17112 ATTGA-CCCATTAAAATGAAAGTTTTATAGT
1 ATTGACCCCACTAAAATGAAAGGTTTATTCC
17142 ATTGACCCCACTAA
1 ATTGACCCCACTAA
17156 TAATTTGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (31 bp):
ATTGACCCCACTAAAATGAAAGGTTTATTCC
Found at i:17692 original size:32 final size:32
Alignment explanation
Indices: 17656--17725 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
17646 CTTATAAGGA
* *
17656 ATTATTTCATTGCAATGAGATTTGAATATTGT
1 ATTATTTCATTGCAATAACATTTGAATATTGT
17688 ATTATTTCATTGCAATAACATTTGAATATTGT
1 ATTATTTCATTGCAATAACATTTGAATATTGT
17720 ATTATT
1 ATTATT
17726 CTAAATGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (32 bp):
ATTATTTCATTGCAATAACATTTGAATATTGT
Found at i:28025 original size:22 final size:22
Alignment explanation
Indices: 28000--28041 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27990 GACAAACCCG
*
28000 TAACCCGAATGACCCGAGAAGT
1 TAACCCGAATGACCCAAGAAGT
* *
28022 TAACTCGGATGACCCAAGAA
1 TAACCCGAATGACCCAAGAA
28042 TTGAACTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (22 bp):
TAACCCGAATGACCCAAGAAGT
Found at i:28525 original size:24 final size:23
Alignment explanation
Indices: 28495--28549 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
28485 TAAAATAAAA
*
28495 AAAAAATTGAAGAA-TAAAGTATT
1 AAAAAATTGAAGAATTAAA-CATT
*
28518 AAATAAATTTAAGAATTAAACATT
1 AAA-AAATTGAAGAATTAAACATT
28542 AAAAAATT
1 AAAAAATT
28550 TAAGGCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (23 bp):
AAAAAATTGAAGAATTAAACATT
Found at i:28719 original size:16 final size:16
Alignment explanation
Indices: 28672--28721 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
28662 CAGACTGAAG
*
28672 ACCCGAATGACCTG-A
1 ACCCGAATGACCCGAA
*
28687 ACCCAGAGATGAGCCGAA
1 ACCC-GA-ATGACCCGAA
28705 ACCCGAATGACCCGAA
1 ACCCGAATGACCCGAA
28721 A
1 A
28722 AAATTACCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 4 0.14
16 12 0.41
17 8 0.28
18 5 0.17
ACGTcount: A:0.38, C:0.32, G:0.22, T:0.08
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:29768 original size:21 final size:22
Alignment explanation
Indices: 29742--29782 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29732 GACAAACCCG
29742 TAACCCAAATGA-CCAAGAAGT
1 TAACCCAAATGACCCAAGAAGT
*
29763 TAACCCGAATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
29783 TATTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:30476 original size:16 final size:15
Alignment explanation
Indices: 30431--30473 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
30421 GACCCAGCAG
*
30431 ACCCGAATGACCTAA
1 ACCCGAATGACCGAA
30446 ACCC-AGATGAGCCGAA
1 ACCCGA-ATGA-CCGAA
30462 ACCCGAATGACC
1 ACCCGAATGACC
30474 CGAGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.37, C:0.35, G:0.19, T:0.09
Consensus pattern (15 bp):
ACCCGAATGACCGAA
Found at i:31916 original size:27 final size:27
Alignment explanation
Indices: 31885--31940 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
31875 TACTATATTC
31885 AAATAGGCAAAACAATCTTGATAAAAA
1 AAATAGGCAAAACAATCTTGATAAAAA
31912 AAATAGGCAAAACAATCTTGATAAAAA
1 AAATAGGCAAAACAATCTTGATAAAAA
31939 AA
1 AA
31941 TAAAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (27 bp):
AAATAGGCAAAACAATCTTGATAAAAA
Found at i:32734 original size:54 final size:53
Alignment explanation
Indices: 32645--32815 Score: 281
Period size: 54 Copynumber: 3.2 Consensus size: 53
32635 GATCAAATTG
*
32645 GAGATCAACTCTGATCATCGAAAACTTCTTG-AACGACCACACTGGATCATCT
1 GAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACTGGATCATCT
* *
32697 AGAGATCAACTTTGATCTTCGAAAACTTCTTGAAACGACCACACCGGATCATCT
1 -GAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACTGGATCATCT
32751 GAAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACTGGATCATCT
1 G-AGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACTGGATCATCT
32805 GGAGATCAACT
1 -GAGATCAACT
32816 TTGAAAACTT
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
53 30 0.27
54 79 0.72
55 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (53 bp):
GAGATCAACTCTGATCTTCGAAAACTTCTTGAAACGACCACACTGGATCATCT
Found at i:32864 original size:26 final size:26
Alignment explanation
Indices: 32818--32868 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
32808 GATCAACTTT
32818 GAAAACTTCTCGGAAGAACCGCACTC
1 GAAAACTTCTCGGAAGAACCGCACTC
* * *
32844 GAAAACTTCTTGTAAGGACCGCACT
1 GAAAACTTCTCGGAAGAACCGCACT
32869 AGATCATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (26 bp):
GAAAACTTCTCGGAAGAACCGCACTC
Found at i:32928 original size:54 final size:54
Alignment explanation
Indices: 32845--33347 Score: 629
Period size: 54 Copynumber: 9.3 Consensus size: 54
32835 ACCGCACTCG
* * * * *
32845 AAAACTTCTTGTAAGGACCGCACTAGATCATTTG-GAGATCAACTCTAATCATCA
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAG-GATCAACTCTGATCATTA
* * *
32899 AAAACTTCTTCTAATGACCGCACTGGATCATCTGAGGATCAAATCTGATCATTG
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* * *
32953 AAAACTTCTTGGATTGACCGCACTGGATCATCTGAGGATCAACTTTGATCATTA
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* * * * * * *
33007 TAAGCTTCTTGGAATGACCACACTGGATCATTTGAGGATCAACTCTGACCATTG
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* *
33061 AAAACTTCTTGGT-ATCATCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
1 AAAACTTCTT-GTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* *
33115 AAAACTTCTTGTAAGGACCGCACTGGATCATCTG-GAGATCAACTTTGATCATTA
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAG-GATCAACTCTGATCATTA
* * *
33169 AAAACTTCTGGTAAGGACCGCACTGGATCATCTG-GAGATCAACTCTGATCATCA
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAG-GATCAACTCTGATCATTA
* *
33223 AAAACTTCTTCG-AATGACCGCACTGGATCATCTAAGGATCAACTCTGATCATTG
1 AAAACTTCTT-GTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
* * * * *
33277 AAAACTTCTTGGAATGACCACACTGGATCATCTTAGGATCAACTCTGACCATTG
1 AAAACTTCTTGTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
*
33331 AAAACTTCTTGGAATGA
1 AAAACTTCTTGTAATGA
33348 GATCAACTCT
Statistics
Matches: 396, Mismatches: 46, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.01
54 388 0.98
55 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (54 bp):
AAAACTTCTTGTAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATTA
Found at i:33353 original size:35 final size:35
Alignment explanation
Indices: 33313--33861 Score: 741
Period size: 35 Copynumber: 15.8 Consensus size: 35
33303 ATCATCTTAG
* * * *
33313 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
33348 GATCAACTCTGATCATCAAAAATTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
33383 GATCAACTCTGATCATCGAAAACTTCTTGAAAGCGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAA-CGA
* * *
33419 GATCAACTCTAATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* **
33454 GATAAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* ***
33489 GATCAACTCTGGT-AAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
***
33523 GATCAACTCTGAT-AAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
33557 GATCAACTCTGATCATCGAAAAGTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
33592 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* * *
33627 GATCAACTTTGATCATCGAAAACTTCTTAAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
** *
33662 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
33697 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
33732 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
33767 GATCAACTCTGATC-T-TAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
33800 GATCAACTCTGATCAT--AAAAGTATCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACT-TCTTGAAACGA
33834 GATCAACTCTGATCATCGAAAACTTCTT
1 GATCAACTCTGATCATCGAAAACTTCTT
33862 ATGAAAGACC
Statistics
Matches: 463, Mismatches: 45, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.08
34 94 0.20
35 296 0.64
36 38 0.08
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
Found at i:33939 original size:54 final size:54
Alignment explanation
Indices: 33851--34050 Score: 267
Period size: 54 Copynumber: 3.7 Consensus size: 54
33841 TCTGATCATC
* ** * * *
33851 GAAAACTTCTTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAGATTTCT
1 GAAAACTTC-TATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATTTCT
* * *
33906 GAAAACTTCTATGAAAGACCACATTGGGTCATCTTAAGATCTGTTTAGATCTCT
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATTTCT
*
33960 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGAACTATTTAGATCTT-T
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGAT-TTCT
* *
34014 GAAAACTTCTATGAAAGACCATACTGGGTCATTTTAA
1 GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
34051 ACACATGTAC
Statistics
Matches: 129, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
54 119 0.92
55 10 0.08
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (54 bp):
GAAAACTTCTATGAAAGACCACACTGGGTCATCTTAAGATCTATTTAGATTTCT
Found at i:35160 original size:37 final size:39
Alignment explanation
Indices: 35084--35162 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 39
35074 ATCTTTTTGA
** * *
35084 AAAACATTTTTTCTCTTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
35123 AAAACA-TTTTT-TCTTTTGAAAAGATCACACCTAGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
35160 AAA
1 AAA
35163 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 25 0.69
38 5 0.14
39 6 0.17
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
Found at i:35382 original size:21 final size:22
Alignment explanation
Indices: 35335--35385 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
35325 TCATCCTTTC
35335 CTTTGTCTTTTGCTTTTTCAACT
1 CTTT-TCTTTTGCTTTTTCAACT
*
35358 -TTTTCTTTT-CTTTTTCAATT
1 CTTTTCTTTTGCTTTTTCAACT
35378 CTTTTCTT
1 CTTTTCTT
35386 CTTTCTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 10 0.38
21 13 0.50
22 3 0.12
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.69
Consensus pattern (22 bp):
CTTTTCTTTTGCTTTTTCAACT
Found at i:35884 original size:21 final size:21
Alignment explanation
Indices: 35858--35899 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35848 AATCAGTCCA
35858 TTTCTTTTTTCATTTTTTGCT
1 TTTCTTTTTTCATTTTTTGCT
**
35879 TTTCTTTTTTTTTTTTTTGCT
1 TTTCTTTTTTCATTTTTTGCT
35900 GATGGGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTTCATTTTTTGCT
Found at i:44258 original size:22 final size:22
Alignment explanation
Indices: 44224--44306 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
44214 ATAGGAAGGT
* *
44224 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGTTAGA
* * *
44246 TTATCAAAGTTTCATA-TGGAGT
1 TTATCAAAATTTCATAGT-TAGA
* * *
44268 TTATCACAATTTCATAGGTAAA
1 TTATCAAAATTTCATAGTTAGA
44290 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
44307 CAAAATTTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:44270 original size:44 final size:44
Alignment explanation
Indices: 44191--44305 Score: 119
Period size: 44 Copynumber: 2.6 Consensus size: 44
44181 TTATCGAAAA
* *
44191 TCATAGG-AAAGTTA-CAAAACTTCATA-GGAAGGTTTATTAAAATT
1 TCATAGGTAAA-TTATCAAAATTTCATATGG-A-GTTTATCAAAATT
* ** * *
44235 TCATAGTTAGGTTATCAAAGTTTCATATGGAGTTTATCACAATT
1 TCATAGGTAAATTATCAAAATTTCATATGGAGTTTATCAAAATT
44279 TCATAGGTAAATTATCAAAATTTCATA
1 TCATAGGTAAATTATCAAAATTTCATA
44306 GCAAAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
44 43 0.75
45 12 0.21
46 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TCATAGGTAAATTATCAAAATTTCATATGGAGTTTATCAAAATT
Found at i:44310 original size:13 final size:13
Alignment explanation
Indices: 44294--44318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44284 GGTAAATTAT
44294 CAAAATTTCATAG
1 CAAAATTTCATAG
44307 CAAAATTTCATA
1 CAAAATTTCATA
44319 AAACTATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
CAAAATTTCATAG
Found at i:44312 original size:22 final size:22
Alignment explanation
Indices: 44268--44313 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
44258 CATATGGAGT
* **
44268 TTATCACAATTTCATAGGTAAA
1 TTATCAAAATTTCATAGCAAAA
44290 TTATCAAAATTTCATAGCAAAA
1 TTATCAAAATTTCATAGCAAAA
44312 TT
1 TT
44314 TCATAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCAAAA
Found at i:46456 original size:52 final size:52
Alignment explanation
Indices: 46399--46523 Score: 232
Period size: 52 Copynumber: 2.4 Consensus size: 52
46389 CTCTATTTTG
46399 ATCTCGTCTCAGGATGTTAAATCAACTCTCTGCGAGTTTTACTTCTCTTTCA
1 ATCTCGTCTCAGGATGTTAAATCAACTCTCTGCGAGTTTTACTTCTCTTTCA
46451 ATCTCGTCTCAGGATGTTAAATCAACTCTCTGCGAGTTTTACTTCTCTTTCA
1 ATCTCGTCTCAGGATGTTAAATCAACTCTCTGCGAGTTTTACTTCTCTTTCA
* *
46503 ATCTCGTCTCAAGACGTTAAA
1 ATCTCGTCTCAGGATGTTAAA
46524 ACATTTGTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (52 bp):
ATCTCGTCTCAGGATGTTAAATCAACTCTCTGCGAGTTTTACTTCTCTTTCA
Found at i:48621 original size:21 final size:22
Alignment explanation
Indices: 48586--48643 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
48576 AGTCGCTATT
*
48586 TACCGTCC-CCTTTTTGCTAAA
1 TACCGCCCTCCTTTTTGCTAAA
*
48607 TATCGCCCTCCTTTTTGCTAAA
1 TACCGCCCTCCTTTTTGCTAAA
48629 TACCGCCCTCCTTTT
1 TACCGCCCTCCTTTT
48644 GACAATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 6 0.18
22 27 0.82
ACGTcount: A:0.16, C:0.36, G:0.09, T:0.40
Consensus pattern (22 bp):
TACCGCCCTCCTTTTTGCTAAA
Done.