Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017333.1 Corchorus olitorius cultivar O-4 contig17366, 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: 62741
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3194 original size:24 final size:26
Alignment explanation
Indices: 3148--3200 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
3138 TATCCTTTTT
* * *
3148 ATATTTCACAATTTATATTTTAATTA
1 ATATTTCACAATTTACATATTAAATA
3174 ATATTT-AC-ATTTACATATTAAATA
1 ATATTTCACAATTTACATATTAAATA
3198 ATA
1 ATA
3201 AAAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.67
25 2 0.08
26 6 0.25
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTTCACAATTTACATATTAAATA
Found at i:5200 original size:21 final size:21
Alignment explanation
Indices: 5161--5200 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5151 CCCGGTTAAG
**
5161 TAGGGTTAGGATATTGTATAA
1 TAGGGTTAGGATAGGGTATAA
*
5182 TAGGGTTAGGGTAGGGTAT
1 TAGGGTTAGGATAGGGTAT
5201 GTGTAGTGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
TAGGGTTAGGATAGGGTATAA
Found at i:5315 original size:19 final size:19
Alignment explanation
Indices: 5295--5331 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5285 AATTAATTAT
5295 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
5313 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
5332 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:5342 original size:19 final size:19
Alignment explanation
Indices: 5301--5342 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5291 TTATTTTAAT
* * *
5301 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
5320 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
5339 ATTA
1 ATTA
5343 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:7672 original size:75 final size:76
Alignment explanation
Indices: 7522--7665 Score: 168
Period size: 75 Copynumber: 1.9 Consensus size: 76
7512 ATGCAATAGG
* *
7522 AACAATTCCTATAAGTTCTGCAAATAGTATGAACCTGTGAATAGTGTTCCTTCTCAATACATCAA
1 AACAATTCCTATAAGTTCTGCAAACAGAATGAACCTGTGAATAGTGTTCCTTCTCAATACATCAA
**
7587 TGGTCAATGGT
66 TAATCAATGGT
* * * * *
7598 AACAGTTCCTGTAAGTTCTGCTAACA-AATGAACCTGTGAAT-GTTTTTCCTTCTCAGA-ATATC
1 AACAATTCCTATAAGTTCTGCAAACAGAATGAACCTGTGAATAG-TGTTCCTTCTCA-ATACATC
7660 AATAAT
64 AATAAT
7666 TGATGGTCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
74 1 0.02
75 33 0.58
76 23 0.40
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (76 bp):
AACAATTCCTATAAGTTCTGCAAACAGAATGAACCTGTGAATAGTGTTCCTTCTCAATACATCAA
TAATCAATGGT
Found at i:12929 original size:18 final size:19
Alignment explanation
Indices: 12906--12944 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
12896 TGTTCATTAA
12906 AAAGGTATTT-AA-GTTATC
1 AAAGGT-TTTGAATGTTATC
12924 AAAGGTTTTGAATGTTATC
1 AAAGGTTTTGAATGTTATC
12943 AA
1 AA
12945 TAAATTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (19 bp):
AAAGGTTTTGAATGTTATC
Found at i:13404 original size:12 final size:12
Alignment explanation
Indices: 13389--13415 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13379 TATAGTTATA
13389 TATATAAAAGGT
1 TATATAAAAGGT
13401 TATATAAAAGGT
1 TATATAAAAGGT
13413 TAT
1 TAT
13416 GAATCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (12 bp):
TATATAAAAGGT
Found at i:14148 original size:58 final size:58
Alignment explanation
Indices: 14049--14163 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
14039 ATTAATCAAA
*
14049 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * * * *
14107 TATCGAGTGACATATTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACAT-GTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGC
14164 ATGATGCTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 35 0.70
59 15 0.30
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:14255 original size:31 final size:31
Alignment explanation
Indices: 14214--14412 Score: 182
Period size: 31 Copynumber: 6.5 Consensus size: 31
14204 TAAGGCTAAT
*
14214 TGCTCAAATAAGGGCCTAACGTT-TGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTAT-CGAAAA
* * * * * *
14245 TGATCAAATAATGGCCCGATC-TT-T-TAATA
1 TGCTCAAATAA-GGGCCTAACGTTATCGAAAA
14274 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
* * * **
14305 TGCTCAAATAAGGGTCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA
14334 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA
14365 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
14396 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
14413 GGCATCAGTT
Statistics
Matches: 134, Mismatches: 22, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
28 10 0.07
29 28 0.21
30 10 0.07
31 76 0.57
32 10 0.07
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATCGAAAA
Found at i:14312 original size:60 final size:60
Alignment explanation
Indices: 14218--14380 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
14208 GCTAATTGCT
* * *
14218 CAAATAAGGGCCTAACGTT-TGCCAAAATGATCAAATAATGGCCCGATCTTTTAATATGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
* *
14278 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
14338 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
14381 TAACGTTATC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
Found at i:14493 original size:31 final size:30
Alignment explanation
Indices: 14453--14618 Score: 121
Period size: 31 Copynumber: 5.5 Consensus size: 30
14443 TTGATGCCAT
14453 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GCAAACGTTAG
* ** * *
14484 GCTCTTATTTG-GCCAAATT--AAA-ATATCG
1 GCCCTTATTTGAG-CATTTTGCAAACGT-TAG
14512 GCGCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GC-CCTTATTTGAGCATTTT-GCAAACGTTAG
** * *
14544 GCCCTTATTTG-GCCAAATT--AAAAGATCAG
1 GCCCTTATTTGAG-CATTTTGCAAACG-TTAG
*
14573 ACCCTTATTTGAGCATTTTGACAAACGTTAG
1 GCCCTTATTTGAGCATTTTG-CAAACGTTAG
14604 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
14619 ATTAGCCTAT
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
27 1 0.01
28 11 0.11
29 29 0.29
30 4 0.04
31 44 0.44
32 11 0.11
33 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTGCAAACGTTAG
Found at i:14528 original size:60 final size:60
Alignment explanation
Indices: 14454--14614 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
14444 TGATGCCATG
* * *
14454 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAATATC-GG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
14513 CGCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 C-CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
*
14574 CCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
14615 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
59 1 0.01
60 93 0.97
61 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:15904 original size:36 final size:36
Alignment explanation
Indices: 15864--15933 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
15854 TTTAATAACC
* *
15864 TTACATCTTTT-GTGATTTTGGTTATCATATTTCTTA
1 TTACAT-TTTTGGTAATTTTGATTATCATATTTCTTA
15900 TTACATTTTTGGTAATTTTGATTATCATATTTCT
1 TTACATTTTTGGTAATTTTGATTATCATATTTCT
15934 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59
Consensus pattern (36 bp):
TTACATTTTTGGTAATTTTGATTATCATATTTCTTA
Found at i:16538 original size:3 final size:3
Alignment explanation
Indices: 16530--16558 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16520 GATACAACAC
16530 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
16559 ATATATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16989 original size:25 final size:24
Alignment explanation
Indices: 16955--17001 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
16945 ACGTTTGCAC
16955 AAATATCTAAGAATTTGAATTAAAA
1 AAATATCTAAGAATTT-AATTAAAA
16980 AAATATCTAAGAATTTAATTAA
1 AAATATCTAAGAATTTAATTAA
17002 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATATCTAAGAATTTAATTAAAA
Found at i:17038 original size:39 final size:40
Alignment explanation
Indices: 16992--17072 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
16982 ATATCTAAGA
16992 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATTAATATTAC
* *
17031 ATTTAATTAATGTAAGTATTTTAGTTATTATTTATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATTAATATTAC
17071 AT
1 AT
17073 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATTAATATTAC
Found at i:17060 original size:21 final size:21
Alignment explanation
Indices: 16997--17060 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
16987 TAAGAATTTA
16997 ATTAATGTAAGTATTTCAGTT
1 ATTAATGTAAGTATTTCAGTT
* *
17018 ATT-A--TAA-TATTACATTT
1 ATTAATGTAAGTATTTCAGTT
*
17035 AATTAATGTAAGTATTTTAGTT
1 -ATTAATGTAAGTATTTCAGTT
17057 ATTA
1 ATTA
17061 TTTATATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 1 0.03
20 1 0.03
21 10 0.30
22 7 0.21
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (21 bp):
ATTAATGTAAGTATTTCAGTT
Found at i:18761 original size:40 final size:40
Alignment explanation
Indices: 18706--18783 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
18696 AAGAAACCCT
18706 CCACTTCAATTGGTATTCTTTCACAAAAACAAAACATGCC
1 CCACTTCAATTGGTATTCTTTCACAAAAACAAAACATGCC
* **
18746 CCACTTCAATTGGTATTTTTTCATGAAAACAAAACATG
1 CCACTTCAATTGGTATTCTTTCACAAAAACAAAACATG
18784 AGATAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (40 bp):
CCACTTCAATTGGTATTCTTTCACAAAAACAAAACATGCC
Found at i:23747 original size:10 final size:10
Alignment explanation
Indices: 23728--23766 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
23718 TGAAAGCTAA
23728 TTAT-TATAT
1 TTATATATAT
23737 TTATATATAT
1 TTATATATAT
23747 TTATATTATAT
1 TTATA-TATAT
23758 GTTATATAT
1 -TTATATAT
23767 GTATAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.15
10 10 0.37
11 8 0.30
12 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTATATATAT
Found at i:24416 original size:30 final size:31
Alignment explanation
Indices: 24371--24447 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
24361 CATGGCATGT
24371 CACGTGTACCAAAAAGCAACATGTGGCACAC
1 CACGTGTACCAAAAAGCAACATGTGGCACAC
* *
24402 CACGTGTA-CAAAAAGCGACATGTGGCACGC
1 CACGTGTACCAAAAAGCAACATGTGGCACAC
*
24432 CACGTGTATCAAAAAG
1 CACGTGTACCAAAAAG
24448 TGACACGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 28 0.65
31 15 0.35
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (31 bp):
CACGTGTACCAAAAAGCAACATGTGGCACAC
Found at i:24462 original size:31 final size:31
Alignment explanation
Indices: 24371--24530 Score: 160
Period size: 31 Copynumber: 5.2 Consensus size: 31
24361 CATGGCATGT
* ** * *
24371 CACGTGTACCAAAAAGCAACATGTGGCACAC
1 CACGTGTATCAAAAAGTGACACGTGGCACGC
* *
24402 CACGTGTA-CAAAAAGCGACATGTGGCACGC
1 CACGTGTATCAAAAAGTGACACGTGGCACGC
**
24432 CACGTGTATCAAAAAGTGACACGTAACACGC
1 CACGTGTATCAAAAAGTGACACGTGGCACGC
* * * * *
24463 CATGTGTACCCAGAAGTGACACGTGGCATGC
1 CACGTGTATCAAAAAGTGACACGTGGCACGC
* * *
24494 CATGTGTTTCAAAAAGTGACACGTGGCATGC
1 CACGTGTATCAAAAAGTGACACGTGGCACGC
24525 CACGTG
1 CACGTG
24531 CACAAAAGGA
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
30 28 0.25
31 82 0.75
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (31 bp):
CACGTGTATCAAAAAGTGACACGTGGCACGC
Found at i:26609 original size:12 final size:13
Alignment explanation
Indices: 26583--26615 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
26573 TAAACTAATT
26583 ACAAACTAAACAA
1 ACAAACTAAACAA
*
26596 ACAAA-TAAATAA
1 ACAAACTAAACAA
26608 ACAAACTA
1 ACAAACTA
26616 TTAAACCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (13 bp):
ACAAACTAAACAA
Found at i:29036 original size:529 final size:529
Alignment explanation
Indices: 28235--29294 Score: 2120
Period size: 529 Copynumber: 2.0 Consensus size: 529
28225 TAAATGTTAT
28235 AATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACCTCTCTTCGGGCCTTTCATGTCCATAT
1 AATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACCTCTCTTCGGGCCTTTCATGTCCATAT
28300 GAAAAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGGAAACAAAATTGA
66 GAAAAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGGAAACAAAATTGA
28365 AGCTATTGCACATATCCATGTAAAATCTAATATTTACTATTTATTGTTAACTTTAGGGCATATGC
131 AGCTATTGCACATATCCATGTAAAATCTAATATTTACTATTTATTGTTAACTTTAGGGCATATGC
28430 TCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTTAAATGATAGTACTTTCGAAATTT
196 TCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTTAAATGATAGTACTTTCGAAATTT
28495 TCTACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAAGTAGATTTCTAAAGATCCA
261 TCTACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAAGTAGATTTCTAAAGATCCA
28560 CTTGTATTATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAATAAGCACACATACAAAAC
326 CTTGTATTATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAATAAGCACACATACAAAAC
28625 AAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTATTATTAATTGTGTTGTTTATTCA
391 AAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTATTATTAATTGTGTTGTTTATTCA
28690 ATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGTAATGAACTATTGGATTTAAA
456 ATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGTAATGAACTATTGGATTTAAA
28755 GAAAAATAC
521 GAAAAATAC
28764 AATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACCTCTCTTCGGGCCTTTCATGTCCATAT
1 AATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACCTCTCTTCGGGCCTTTCATGTCCATAT
28829 GAAAAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGGAAACAAAATTGA
66 GAAAAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGGAAACAAAATTGA
28894 AGCTATTGCACATATCCATGTAAAATCTAATATTTACTATTTATTGTTAACTTTAGGGCATATGC
131 AGCTATTGCACATATCCATGTAAAATCTAATATTTACTATTTATTGTTAACTTTAGGGCATATGC
28959 TCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTTAAATGATAGTACTTTCGAAATTT
196 TCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTTAAATGATAGTACTTTCGAAATTT
29024 TCTACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAAGTAGATTTCTAAAGATCCA
261 TCTACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAAGTAGATTTCTAAAGATCCA
29089 CTTGTATTATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAATAAGCACACATACAAAAC
326 CTTGTATTATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAATAAGCACACATACAAAAC
29154 AAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTATTATTAATTGTGTTGTTTATTCA
391 AAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTATTATTAATTGTGTTGTTTATTCA
29219 ATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGTAATGAACTATTGGATTTAAA
456 ATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGTAATGAACTATTGGATTTAAA
29284 GAAAAATAC
521 GAAAAATAC
29293 AA
1 AA
29295 GCACCAAAAT
Statistics
Matches: 531, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
529 531 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (529 bp):
AATAAATCCTATCCCCCTTAATTATCTAGAATTGTAACCTCTCTTCGGGCCTTTCATGTCCATAT
GAAAAAGAGAGTAAACTTAGTTTTTGTTTAAGTGCTACACACTTTAGAGGAGGAAACAAAATTGA
AGCTATTGCACATATCCATGTAAAATCTAATATTTACTATTTATTGTTAACTTTAGGGCATATGC
TCAATGTTAATAGTATAGCCTTTTAAAGATGCAACACATTTTAAATGATAGTACTTTCGAAATTT
TCTACGTATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAAGTAGATTTCTAAAGATCCA
CTTGTATTATTATTAATTGTGTGGTTTATTCAATTGAACATATTAAATAAGCACACATACAAAAC
AAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTATTATTAATTGTGTTGTTTATTCA
ATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGTAATGAACTATTGGATTTAAA
GAAAAATAC
Found at i:39091 original size:6 final size:6
Alignment explanation
Indices: 39080--39107 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39070 TATCGGGTCC
39080 CAATTT CAATTT CAATTT CAATTT CAAT
1 CAATTT CAATTT CAATTT CAATTT CAAT
39108 GTTTTTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (6 bp):
CAATTT
Found at i:41663 original size:23 final size:23
Alignment explanation
Indices: 41625--41668 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41615 CGAATATTTT
*
41625 TATGAAATTTTAATAACTACCAA
1 TATGAAATTTCAATAACTACCAA
* *
41648 TATGAAATTTCGATAATTACC
1 TATGAAATTTCAATAACTACC
41669 TATAAAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
TATGAAATTTCAATAACTACCAA
Found at i:45499 original size:27 final size:26
Alignment explanation
Indices: 45450--45501 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
45440 AATTTTCTAT
45450 TTTAATAATGGAATAATTAAAATATTA
1 TTTAATAATGGAAT-ATTAAAATATTA
45477 TTTAATAATGGCAAT-TTAGAAATAT
1 TTTAATAATGG-AATATTA-AAATAT
45502 ATTAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (26 bp):
TTTAATAATGGAATATTAAAATATTA
Found at i:46025 original size:142 final size:139
Alignment explanation
Indices: 45824--46090 Score: 335
Period size: 142 Copynumber: 1.9 Consensus size: 139
45814 ATTTTTATAG
*
45824 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAATTTAATATCCTAATAATTATTTAATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAA-TTAATATCCTAATAACTATTTAATTT
* * * *
45889 TTACCATTTTACTATTTTAATAAAAAAAACT-TATATATATTAGAATTTTTGAAATATACTTTTA
65 TTACCATTTTACTAATTTAAT-AAAAAAACTAAAAATATATTAGAATTTTTAAAATATACTTTTA
45953 TAGTTTTACAC
129 TAGTTTTACAC
* *
45964 TTTTACTCAATTAAAAACCTCTATTTTTTATTTAA-TT-A-TAATATCCTTATTTATACCTATTT
1 TTTTACTCAACTAAAAA-CTCTA-TTTTTATTTAATTTAATTAATATCC-TA---ATAACTATTT
* * * *
46026 TATTTTTATCATTTTACTAATTTAATTAAAAAGCTAAAAATATATTAGAATTTTTAAAATATACT
60 AATTTTTACCATTTTACTAATTTAATAAAAAAACTAAAAATATATTAGAATTTTTAAAATATACT
46091 CCCTCCGTCC
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
138 8 0.07
139 2 0.02
140 17 0.16
141 14 0.13
142 68 0.62
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (139 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAATTAATATCCTAATAACTATTTAATTTT
TACCATTTTACTAATTTAATAAAAAAACTAAAAATATATTAGAATTTTTAAAATATACTTTTATA
GTTTTACAC
Found at i:48724 original size:41 final size:41
Alignment explanation
Indices: 48679--49125 Score: 601
Period size: 41 Copynumber: 10.9 Consensus size: 41
48669 TTTTCGTTTG
**
48679 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
48720 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTAACAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
48761 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
48802 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
48843 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
48884 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
48925 TTCAAGATTGAGTCATCGAGACCCTTAAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
48966 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * * *
49007 TTCAAGAACAAGTTATCGAGACTCTTGAATTGAATTATTAACAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATT-AA--ATTATCAA
* * * * * *
49051 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTTAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
49092 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
49126 CAAATCAAAC
Statistics
Matches: 368, Mismatches: 34, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
40 14 0.04
41 316 0.86
42 4 0.01
43 1 0.00
44 33 0.09
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:50934 original size:61 final size:62
Alignment explanation
Indices: 50867--51042 Score: 255
Period size: 61 Copynumber: 2.8 Consensus size: 62
50857 ATAACCCAAG
* * *
50867 AAAAAAAAAGCTCGCTAAGTTGAAAATCCTATAAAGGACAGCTTAGGCAAAAGTTAGAGCG-
1 AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAACGA
* * * *
50928 ATAAAAAAGGCTCACTAAGTTGAAAATCCTGTAAAGGATGGCTTAGGCAAAAGTTAGAACGA
1 AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAACGA
* *
50990 AAAAAAAAAGTCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGACAAAA
1 AAAAAAAAAG-CTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAA
51043 TTTGGAGCAC
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 54 0.54
62 8 0.08
63 38 0.38
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (62 bp):
AAAAAAAAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAACGA
Found at i:51759 original size:16 final size:16
Alignment explanation
Indices: 51738--51772 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
51728 ACAATTCAGA
51738 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
51754 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
51770 AAG
1 AAG
51773 TATTTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:51896 original size:41 final size:41
Alignment explanation
Indices: 51836--52241 Score: 555
Period size: 41 Copynumber: 9.9 Consensus size: 41
51826 TTTTCGTTTG
*
51836 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
* ***
51877 TTTAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
***
51918 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
51959 TTCAAGAACATGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
*** *
52000 TTCAAGATTGAGTCATCGAGATCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
52041 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
52082 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
52123 TTCAAGAACAAGTCATCGAGACTCTTGAATCGAATTATTATCAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * * *
52167 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATTGTTAA
1 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
52208 TTCAAGACCAAGTCATTC-A-ACCCTTGAATCAAAT
1 TTCAAGAACAAGTCA-TCGAGACCCTTGAATTAAAT
52242 CAAATCGAAC
Statistics
Matches: 331, Mismatches: 30, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
40 13 0.04
41 279 0.84
42 4 0.01
43 1 0.00
44 34 0.10
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (41 bp):
TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:56044 original size:13 final size:13
Alignment explanation
Indices: 56014--56054 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
56004 TCGGCCGAGT
*
56014 AAAAAGTAAA-AA
1 AAAAAATAAATAA
56026 AAAAAATAAATAA
1 AAAAAATAAATAA
56039 ATAAAAA-AAATAA
1 A-AAAAATAAATAA
56052 AAA
1 AAA
56055 TTTATATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 10 0.38
14 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAAATAAATAA
Found at i:56046 original size:17 final size:16
Alignment explanation
Indices: 56020--56052 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
56010 GAGTAAAAAG
56020 TAAAAAAAAAAATAAA
1 TAAAAAAAAAAATAAA
56036 TAAATAAAAAAAATAAA
1 TAAA-AAAAAAAATAAA
56053 AATTTATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
TAAAAAAAAAAATAAA
Found at i:59421 original size:75 final size:75
Alignment explanation
Indices: 59244--59443 Score: 265
Period size: 75 Copynumber: 2.7 Consensus size: 75
59234 ACTAATAAAT
* * ** * * *
59244 TGAGAAAATACCAAAACGGCGCGAAAACAATCTCCAACATTAAAAGTTGATGGGAGCTATCAGTA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCCACGTTAAAAGTTGAAGGGAGCTATCAGTA
*
59309 AATTCCAGAG
66 AATTCCAAAG
* * **
59319 TGAGAAAAGACCAAAACGGGGCGAAAAGGCTCTCCCACGTTAAAAGTTGAAGGGAGTTATTGGTA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCCACGTTAAAAGTTGAAGGGAGCTATCAGTA
59384 AATTCCAAAG
66 AATTCCAAAG
* * *
59394 TGAGAAAAGATCAAAACGGGGCGAAAAGGTTCACCCACGTTAAAAGTTGA
1 TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCCACGTTAAAAGTTGA
59444 TGAGAGTCTT
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 110 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (75 bp):
TGAGAAAAGACCAAAACGGGGCGAAAAGGATCTCCCACGTTAAAAGTTGAAGGGAGCTATCAGTA
AATTCCAAAG
Done.