Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023552.1 Corchorus olitorius cultivar O-4 contig23585, 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: 13426
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6387 original size:107 final size:103
Alignment explanation
Indices: 6269--6559 Score: 415
Period size: 107 Copynumber: 2.8 Consensus size: 103
6259 TGGTTTTTTA
* *
6269 TTATAGAGTTTTAGAAATAAAATATAAAACAAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTT
6334 ATTATTATTTTAAGGGAAAATGT-CAAAATTAATAATTTATTG
65 ATT-TTATTTTAAGGGAAAAT-TCCAAAATTAATAA--TATTG
* *
6376 TTATAGGGTTTTAGAAATAAAATAAAAAACTAATTTTACTAAGTTTAGTCCCAAATTAAAATTTT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTT
* *
6441 ATTCTTATTTTAAGGGTAAATTCCATAATTAATAATATTG
65 ATT-TTATTTTAAGGGAAAATTCCAAAATTAATAATATTG
* **
6481 TTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT-TT
6545 ATTTTATTTTAAGGG
65 ATTTTATTTTAAGGG
6560 TTAGAAAAAT
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
103 26 0.15
104 16 0.09
105 36 0.21
106 1 0.01
107 90 0.53
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (103 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTA
TTTTATTTTAAGGGAAAATTCCAAAATTAATAATATTG
Found at i:6789 original size:88 final size:88
Alignment explanation
Indices: 6640--6816 Score: 318
Period size: 88 Copynumber: 2.0 Consensus size: 88
6630 TTGATACGTC
* *
6640 AGGAAGGAGAATTGTGTGGAACAAAATGGAGGGACGTGTAGCAAAATTCATAATATTTTTCACTT
1 AGGAAGGAGAATTGTGTGGAACAAAATGAAGGGACGTGTACCAAAATTCATAATATTTTTCACTT
6705 GCATAGTTTATCAGGCCATTAAT
66 GCATAGTTTATCAGGCCATTAAT
* *
6728 AGGAAGGAGAATTGTGTGGAATAAAATGAAGGGACGTGTACCAAAATTCATGATATTTTTCACTT
1 AGGAAGGAGAATTGTGTGGAACAAAATGAAGGGACGTGTACCAAAATTCATAATATTTTTCACTT
6793 GCATAGTTTATCAGGCCATTAAT
66 GCATAGTTTATCAGGCCATTAAT
6816 A
1 A
6817 AATTGTTTAC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (88 bp):
AGGAAGGAGAATTGTGTGGAACAAAATGAAGGGACGTGTACCAAAATTCATAATATTTTTCACTT
GCATAGTTTATCAGGCCATTAAT
Found at i:8159 original size:18 final size:18
Alignment explanation
Indices: 8136--8172 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
8126 ATCACAATTT
*
8136 GGGGGTGAGCAATTTATG
1 GGGGGTGAGCAATTCATG
8154 GGGGGTGAGCAATTCATG
1 GGGGGTGAGCAATTCATG
8172 G
1 G
8173 AGTGAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.08, G:0.46, T:0.24
Consensus pattern (18 bp):
GGGGGTGAGCAATTCATG
Found at i:8679 original size:112 final size:110
Alignment explanation
Indices: 8467--8686 Score: 327
Period size: 110 Copynumber: 2.0 Consensus size: 110
8457 GTTGTTTTAA
* *
8467 CATTACGTCAACATGAAGAAATTCTTTTCGATGTTGTAGTCTCTGAAAAGGATAATGAGATTTTT
1 CATTACCTCAACATGAAGAAATTCTTTTCGATGTTGTAGTCTCTGAAAAGCATAATGAGATTTTT
8532 TTTTGTTCAAGAGGATAATGGGATATTGGGAATTCTAAACAAAGG
66 TTTTGTTCAAGAGGATAATGGGATATTGGGAATTCTAAACAAAGG
* **
8577 CATTACCTCAACATGGAA-AATTTCTTTTCGATGTTGTAGTCTCTGGTAAGCATAATG-GTAATT
1 CATTACCTCAACAT-GAAGAAATTCTTTTCGATGTTGTAGTCTCTGAAAAGCATAATGAG--A-T
* *
8640 TTTTTTTTTTTCAAGAGGATAATGGGATATTGGGAATTCTACACAAA
62 TTTTTTTTGTTCAAGAGGATAATGGGATATTGGGAATTCTAAACAAA
8687 TGCAATTAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
109 1 0.01
110 48 0.48
111 4 0.04
112 46 0.46
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (110 bp):
CATTACCTCAACATGAAGAAATTCTTTTCGATGTTGTAGTCTCTGAAAAGCATAATGAGATTTTT
TTTTGTTCAAGAGGATAATGGGATATTGGGAATTCTAAACAAAGG
Found at i:10444 original size:16 final size:16
Alignment explanation
Indices: 10404--10438 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
10394 AATAAAAAAA
*
10404 AGATAAATAGGTATAG
1 AGATAAATAGATATAG
10420 AGATAAATAGATATAG
1 AGATAAATAGATATAG
10436 AGA
1 AGA
10439 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (16 bp):
AGATAAATAGATATAG
Found at i:10485 original size:4 final size:4
Alignment explanation
Indices: 10476--10677 Score: 97
Period size: 4 Copynumber: 52.8 Consensus size: 4
10466 AGATAATAAT
* ** *
10476 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * *
10522 AGTA AATA AATA GAT- AATA ATTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
10568 AGTA AATA AATA GATA ATAGTT AA-A AATA AATA AATA GATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA
* ** * * *
10616 AATA AATA GAT- AATA GTTA AAAA AATA AA-A AA-A AATA AAT- AGTG
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
10660 AATA AAT- AATA AAAA AAT
1 AATA AATA AATA AATA AAT
10678 CTTTTTGGTC
Statistics
Matches: 143, Mismatches: 39, Indels: 32
0.67 0.18 0.15
Matches are distributed among these distances:
3 29 0.20
4 106 0.74
5 6 0.04
6 2 0.01
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:10500 original size:19 final size:20
Alignment explanation
Indices: 10390--10642 Score: 117
Period size: 19 Copynumber: 12.8 Consensus size: 20
10380 TTTAAAAATA
*
10390 AAATA-ATAAA-AAAAAGAT
1 AAATAGATAAATAAATAGAT
10408 AAATAGGTATAGAGATAAATAGAT
1 AAATA-G-ATA-A-ATAAATAGAT
* * *
10432 ATAGAGA-ATAATAAATAAAT
1 AAATAGATA-AATAAATAGAT
** *
10452 AGGTAGCTAAA-AAA-AGAT
1 AAATAGATAAATAAATAGAT
10470 AATAATA-ATAAATAAATAGAT
1 -A-AATAGATAAATAAATAGAT
* * *
10491 -AATAGCTAAATTAATAAAT
1 AAATAGATAAATAAATAGAT
* * *
10510 AAAAAGATAAAT-AGTAAAT
1 AAATAGATAAATAAATAGAT
10529 AAATAGAT-AAT-AAT---T
1 AAATAGATAAATAAATAGAT
*
10544 AAATTA-ATAAATAAAAAGAT
1 AAA-TAGATAAATAAATAGAT
10564 AAATAG-TAAATAAATAGAT
1 AAATAGATAAATAAATAGAT
*
10583 AATAGTTAAAAATAAATAAATAGAT
1 AA-A--T--AGATAAATAAATAGAT
10608 AAATAG-TAAATAAATAGAT
1 AAATAGATAAATAAATAGAT
* *
10627 -AATAGTTAAAAAAATA
1 AAATAGATAAATAAATA
10643 AAAAAAAATA
Statistics
Matches: 182, Mismatches: 26, Indels: 53
0.70 0.10 0.20
Matches are distributed among these distances:
15 6 0.03
16 5 0.03
17 2 0.01
18 22 0.12
19 70 0.38
20 34 0.19
21 10 0.05
22 4 0.02
23 2 0.01
24 12 0.07
25 15 0.08
ACGTcount: A:0.64, C:0.01, G:0.10, T:0.25
Consensus pattern (20 bp):
AAATAGATAAATAAATAGAT
Found at i:10505 original size:27 final size:27
Alignment explanation
Indices: 10475--10584 Score: 103
Period size: 27 Copynumber: 4.4 Consensus size: 27
10465 AAGATAATAA
*
10475 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
10502 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
10526 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
10548 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
10575 AAATAGATAA
1 TAATAAATAA
10585 TAGTTAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
19 1 0.01
21 4 0.06
22 2 0.03
23 20 0.30
24 2 0.03
25 4 0.06
27 29 0.43
28 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:10547 original size:46 final size:46
Alignment explanation
Indices: 10462--10671 Score: 304
Period size: 46 Copynumber: 4.6 Consensus size: 46
10452 AGGTAGCTAA
* *
10462 AAAAAGATAATAATAATAAATAAATAGATAATAGCTAAATTAATAAAT
1 AAAAAGAT-A-AATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
*
10510 AAAAAGATAAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
10556 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAA--AATAAAT
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
* **
10600 AAATAGATAAATAGTAAATAAATAGATAATAGTTAAAAAAATAAA-
1 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
*
10645 AAAAA-ATAAATAGTGAATAAATA-ATAA
1 AAAAAGATAAATAGTAAATAAATAGATAA
10672 AAAAATCTTT
Statistics
Matches: 153, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
43 4 0.03
44 60 0.39
45 4 0.03
46 76 0.50
47 1 0.01
48 8 0.05
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (46 bp):
AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
Found at i:12329 original size:54 final size:54
Alignment explanation
Indices: 12198--12509 Score: 300
Period size: 54 Copynumber: 5.8 Consensus size: 54
12188 TCAACCACAA
* * *
12198 TGGATCAT-TTAAGATTCAAC-CTTGATCATGGAAACCTTTCTTGGAATGA-TCGCAC
1 TGGATCATCTGAAGA-TCAACTC-TGATCATCGAAAAC-TTCTTGGAATGACT-GCAC
* *
12253 TGGATCGAAT-TGAAAATCAACTCTGATCATCGAAAACTTATTGGAATGACTGCAC
1 TGGATC--ATCTGAAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACTGCAC
* * * * * *
12308 TGTATCAAT-TGAAGATCAACTCTGATCATTGAAAATTTCTTGAAAAGACCGCAC
1 TGGATC-ATCTGAAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACTGCAC
* * * *
12362 TAGATCATCT--TGATCAACTCTGATC-TCTAAAAACTTCTTGGAATAACTGCAC
1 TGGATCATCTGAAGATCAACTCTGATCATC-GAAAACTTCTTGGAATGACTGCAC
** * *
12414 TGGATCATCTGGGGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCAC
1 TGGATCATCTGAAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACTGCAC
*
12468 TGGATCATCT-AGGGATCAACTCTGATCATCGAAAACTTCTTG
1 TGGATCATCTGA-AGATCAACTCTGATCATCGAAAACTTCTTG
12510 AAACGAGATC
Statistics
Matches: 216, Mismatches: 31, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
51 1 0.00
52 41 0.19
53 2 0.01
54 120 0.56
55 27 0.12
56 18 0.08
57 7 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
TGGATCATCTGAAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACTGCAC
Found at i:12395 original size:106 final size:107
Alignment explanation
Indices: 12268--12505 Score: 320
Period size: 106 Copynumber: 2.2 Consensus size: 107
12258 CGAATTGAAA
* * *
12268 ATCAACTCTGATCATCGAAAACTTATTGGAATGACTGCACTGTATCAAT-TGAAGATCAACTCTG
1 ATCAACTCTGATCATCAAAAACTTATTGGAATAACTGCACTGGATC-ATCTGAAGATCAACTCTG
* *
12332 ATCATTGAAAATTTCTTGAAAAGACCGCACTAGATCATCT-TG
65 ATCATTGAAAACTTCTTGAAAAGACCGCACTAGATCATCTAGG
* **
12374 ATCAACTCTGATC-TCTAAAAACTTCTTGGAATAACTGCACTGGATCATCTGGGGATCAACTCTG
1 ATCAACTCTGATCATC-AAAAACTTATTGGAATAACTGCACTGGATCATCTGAAGATCAACTCTG
* * *
12438 ATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGG
65 ATCATTGAAAACTTCTTGAAAAGACCGCACTAGATCATCTA-GG
*
12482 ATCAACTCTGATCATCGAAAACTT
1 ATCAACTCTGATCATCAAAAACTT
12506 CTTGAAACGA
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
105 4 0.03
106 88 0.77
108 21 0.18
109 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (107 bp):
ATCAACTCTGATCATCAAAAACTTATTGGAATAACTGCACTGGATCATCTGAAGATCAACTCTGA
TCATTGAAAACTTCTTGAAAAGACCGCACTAGATCATCTAGG
Found at i:12561 original size:142 final size:142
Alignment explanation
Indices: 12373--12636 Score: 433
Period size: 142 Copynumber: 1.9 Consensus size: 142
12363 AGATCATCTT
* * * *
12373 GATCAACTCTGATCTCTAAAAACTTCTTGGAATAACTGCACTGGATCATCTGGGGATCAACTCTG
1 GATCAACTATGATCTATAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGAGATCAACTCTG
*
12438 ATCAT-TGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAA
66 ATC-TCTAAAAACTTCTTGGAATGACCGCACTGGATCAT-TAGGGATCAACTCTGATCATCGAAA
12502 ACTTCTTGAAACGA
129 ACTTCTTGAAACGA
*
12516 GATCAACTATGATC-ATAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTG
1 GATCAACTATGATCTATAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGAGATCAACTCTG
*
12580 ATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATTTGGGATCAACTCTGATCA
66 ATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATTAGGGATCAACTCTGATCA
12637 AAGAGAACTA
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
141 19 0.17
142 81 0.72
143 13 0.12
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (142 bp):
GATCAACTATGATCTATAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGAGATCAACTCTG
ATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATTAGGGATCAACTCTGATCATCGAAAAC
TTCTTGAAACGA
Found at i:12577 original size:88 final size:89
Alignment explanation
Indices: 12427--12597 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 89
12417 ATCATCTGGG
* *
12427 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTG
1 GATCAACTATGATCATTAAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTG
*
12492 ATCATC-GAAAACTTCTTGAAACGA
66 ATC-TCTAAAAACTTCTTGAAACGA
12516 GATCAACTATGATCA-TAAAAACTTCTTGGAATGACCGCACTGGATCATCT-GGAGATCAACTCT
1 GATCAACTATGATCATTAAAAACTTCTTGGAATGACCGCACTGGATCATCTAGG-GATCAACTCT
12579 GATCTCTAAAAACTTCTTG
65 GATCTCTAAAAACTTCTTG
12598 GAATGACCGC
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
87 4 0.05
88 59 0.77
89 14 0.18
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (89 bp):
GATCAACTATGATCATTAAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTG
ATCTCTAAAAACTTCTTGAAACGA
Found at i:12599 original size:54 final size:53
Alignment explanation
Indices: 12516--12702 Score: 263
Period size: 54 Copynumber: 3.5 Consensus size: 53
12506 CTTGAAACGA
* *
12516 GATCAACTATGATC-ATAAAAACTTCTTGGAATGACCGCACTGGATCATCTGG
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGG
*
12568 AGATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATTTGG
1 -GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGG
* * *
12622 GATCAACTCTGA--TCAAAGAGAACTACTTGAAATGACCGCACTGGATCATCTAGG
1 GATCAACTCTGATCTCTAA-A-AACTTCTTGGAATGACCGCACTGGATCATCT-GG
12676 GATCAACTCTGATCTCTAAAAACTTCT
1 GATCAACTCTGATCTCTAAAAACTTCT
12703 ATGAAAGACC
Statistics
Matches: 119, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
51 4 0.03
52 1 0.01
53 53 0.45
54 56 0.47
55 1 0.01
56 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (53 bp):
GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGG
Found at i:12663 original size:195 final size:196
Alignment explanation
Indices: 12320--12708 Score: 579
Period size: 195 Copynumber: 2.0 Consensus size: 196
12310 TATCAATTGA
* * * *
12320 AGATCAACTCTGATCATTGAAAATTTCTTGAAAAGACCGCACTAGATCATCTTGATCAACTCTGA
1 AGATCAACTATGATCATTAAAAACTTCTTGAAAAGACCGCACTAGATCATCTAGATCAACTCTGA
* **
12385 TCTCTAAAAACTTCTTGGAATAACTGCACTGGATCATCTGGGGATCAACTCTGATCATTGAAAAC
66 TCTCTAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGGGATCAACTCTGATCAAAGAAAAC
* * *
12450 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATC-GAAAACTTCT-TGAAA
131 TACTTGAAATGACCGCACTGGATCATCTAGGGATCAACTCTGATC-TCTAAAAACTTCTATGAAA
12513 CG
195 CG
* * *
12515 AGATCAACTATGATCA-TAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCT
1 AGATCAACTATGATCATTAAAAACTTCTTGAAAAGACCGCACTAGATCATCT--AGATCAACTCT
* * *
12579 GATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCAT-TTGGGATCAACTCTGATCAAAGAGA
64 GATCTCTAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGGGATCAACTCTGATCAAAGAAA
12643 ACTACTTGAAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTATGAA
129 ACTACTTGAAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTATGAA
12708 A
194 A
12709 GACCACACAG
Statistics
Matches: 174, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
194 32 0.18
195 90 0.52
196 52 0.30
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (196 bp):
AGATCAACTATGATCATTAAAAACTTCTTGAAAAGACCGCACTAGATCATCTAGATCAACTCTGA
TCTCTAAAAACTTCTTGGAATAACCGCACTGGATCATCTGGGGATCAACTCTGATCAAAGAAAAC
TACTTGAAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTATGAAAC
G
Found at i:12735 original size:54 final size:53
Alignment explanation
Indices: 12676--13041 Score: 455
Period size: 54 Copynumber: 6.8 Consensus size: 53
12666 ATCATCTAGG
* * *
12676 GATCAACTCTGATCTCTAAAAACTTCTATGAAAGACCACACAGGGTTATCTGATA
1 GATCAACT-TAATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGA-A
* * * * *
12731 -ATCAACATAGATCTTTGAAAGCTTTTATGAAAGACTGCACAGGGTTATCTGAA
1 GATCAACTTA-ATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
* * *
12784 GAACAACTTAAATTTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTAAA
1 GATCAACTT-AATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
* * *
12838 GATCAACTTAAACTTCTGAAAACTTCTATGAAAAACCGCACAGGGTCATCTGAA
1 GATCAACTTAATC-TCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
* *
12892 GATCAACTTAAATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGAA
1 GATCAACTT-AATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
* * * *
12946 GATCAACTTAAACTTCTAAAAACTTCTATGAAAGACCGCACAGGGTCATCTAAA
1 GATCAACTTAATC-TCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
* *
13000 GGTCAACTTAAATCTCTGAAAACTTCTATGAAAAACCGCACA
1 GATCAACTT-AATCTCTGAAAACTTCTATGAAAGACCGCACA
13042 AGGTGCCTGA
Statistics
Matches: 269, Mismatches: 35, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
53 7 0.03
54 255 0.95
55 7 0.03
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (53 bp):
GATCAACTTAATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTGAA
Found at i:12807 original size:303 final size:303
Alignment explanation
Indices: 12235--12816 Score: 637
Period size: 303 Copynumber: 1.9 Consensus size: 303
12225 ATGGAAACCT
* *
12235 TTCTTGGAATGATCGCACTGGATCGAATTGAAAATCAACTCTGATCATCGAAAACTTATTGGAAT
1 TTCTTGGAATGACCGCACTGGATC-AATTGAAAATCAACTCTGATCATCAAAAACTTATTGGAAT
* * ** * *
12300 GACTGCACTGTATCAATTGAAGATCAACTCTGATCATTGAAAATTTCTTGAAAAGACCGCACTAG
65 GACCGCACTGGATCAATTGAAGATCAACTCTGATCAAAGAAAACTACTTGAAAAGACCGCACTAG
* ** * * *
12365 ATCATCTTGATCAACTCTGATCTCTAAAAACTTCTTGGAATAACTGCACTGGATCATCTGGGGAT
130 ATCATCTGGATCAACTCTGATCTCTAAAAACTTCTTGGAATAACCACACAGGATCATCTGAGAAT
* * * * * *
12430 CAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATC
195 CAACTCAGATCATTGAAAACTTCTTGGAAAGACCGCACAGGATCATCTAGAGAACAACTCTAATC
12495 ATCGAAAACTTCT-TGAAACGAGATCAACTATGATCATAAAAAC
260 ATCGAAAACTTCTATGAAACGAGATCAACTATGATCATAAAAAC
* * *
12538 TTCTTGGAATGACCGCACTGGATC-ATCTGGAGATCAACTCTGATC-TCTAAAAACTTCTTGGAA
1 TTCTTGGAATGACCGCACTGGATCAAT-TGAAAATCAACTCTGATCATC-AAAAACTTATTGGAA
* * * * *
12601 TGACCGCACTGGATCATTTG-GGATCAACTCTGATCAAAGAGAACTACTTGAAATGACCGCACTG
64 TGACCGCACTGGATCAATTGAAGATCAACTCTGATCAAAGAAAACTACTTGAAAAGACCGCACTA
* *
12665 GATCATCTAGGGATCAACTCTGATCTCTAAAAACTTCTAT-GAA-AGACCACACAGGGTTATCTG
129 GATCATCT--GGATCAACTCTGATCTCTAAAAACTTCT-TGGAATA-ACCACACAGGATCATCTG
* * * * * * *
12728 ATAATCAACAT-AGATCTTTGAAAGCTT-TTATGAAAGACTGCACAGGGTTATCT-GAAGAACAA
190 AGAATCAAC-TCAGATCATTGAAAACTTCTT-GGAAAGACCGCACAGGATCATCTAG-AGAACAA
*
12790 CT-TAAAT-TTCTGAAAACTTCTATGAAA
252 CTCT-AATCATC-GAAAACTTCTATGAAA
12817 GACCGCACAG
Statistics
Matches: 229, Mismatches: 38, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
301 48 0.21
302 53 0.23
303 121 0.53
304 7 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (303 bp):
TTCTTGGAATGACCGCACTGGATCAATTGAAAATCAACTCTGATCATCAAAAACTTATTGGAATG
ACCGCACTGGATCAATTGAAGATCAACTCTGATCAAAGAAAACTACTTGAAAAGACCGCACTAGA
TCATCTGGATCAACTCTGATCTCTAAAAACTTCTTGGAATAACCACACAGGATCATCTGAGAATC
AACTCAGATCATTGAAAACTTCTTGGAAAGACCGCACAGGATCATCTAGAGAACAACTCTAATCA
TCGAAAACTTCTATGAAACGAGATCAACTATGATCATAAAAAC
Found at i:12826 original size:108 final size:108
Alignment explanation
Indices: 12687--13041 Score: 516
Period size: 108 Copynumber: 3.3 Consensus size: 108
12677 ATCAACTCTG
* * * *
12687 ATCTCTAAAAACTTCTATGAAAGACCACACAGGGTTATCTGATA-ATCAACATAGATCTT-TGAA
1 ATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGA-AGATCAACTTA-AACTTCTGAA
* * * * *
12750 AGCTTTTATGAAAGACTGCACAGGGTTATCTGAAGAACAACTTAA
64 AACTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
* * * *
12795 ATTTCTGAAAACTTCTATGAAAGACCGCACAGGGTTATCTAAAGATCAACTTAAACTTCTGAAAA
1 ATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGAAGATCAACTTAAACTTCTGAAAA
*
12860 CTTCTATGAAAAACCGCACAGGGTCATCTGAAGATCAACTTAA
66 CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
*
12903 ATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGAAGATCAACTTAAACTTCTAAAAA
1 ATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGAAGATCAACTTAAACTTCTGAAAA
* *
12968 CTTCTATGAAAGACCGCACAGGGTCATCTAAAGGTCAACTTAA
66 CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
*
13011 ATCTCTGAAAACTTCTATGAAAAACCGCACA
1 ATCTCTGAAAACTTCTATGAAAAACCACACA
13042 AGGTGCCTGA
Statistics
Matches: 224, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
107 5 0.02
108 219 0.98
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (108 bp):
ATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATCTGAAGATCAACTTAAACTTCTGAAAA
CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
Found at i:12924 original size:162 final size:162
Alignment explanation
Indices: 12649--13041 Score: 531
Period size: 162 Copynumber: 2.4 Consensus size: 162
12639 GAGAACTACT
* * ** * * *
12649 TGAAATGACCGCACTGGATCATCTAGGGATCAACTCT-GATCTCTAAAAACTTCTATGAAAGACC
1 TGAAA-GACCGCACAGGGTCATCTAAAGATCAACT-TAAATCTCTGAAAACTTCTATGAAAAACC
* * * * * * * **
12713 ACACAGGGTTATCTGATAATCAACATAGATCTTTGAAAGCTTTTATGAAAGACTGCACAGGGTTA
64 GCACAGGGTCATCTGATAATCAACATAAATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTA
* *
12778 TCTGAAGAACAACTTAAATTTCTGAAAACTTCTA
129 TCTGAAGAACAACTTAAACTTCTAAAAACTTCTA
*
12812 TGAAAGACCGCACAGGGTTATCTAAAGATCAACTTAAA-CTTCTGAAAACTTCTATGAAAAACCG
1 TGAAAGACCGCACAGGGTCATCTAAAGATCAACTTAAATC-TCTGAAAACTTCTATGAAAAACCG
*
12876 CACAGGGTCATCTGA-AGATCAACTTAAATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTA
65 CACAGGGTCATCTGATA-ATCAACATAAATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTA
*
12940 TCTGAAGATCAACTTAAACTTCTAAAAACTTCTA
129 TCTGAAGAACAACTTAAACTTCTAAAAACTTCTA
*
12974 TGAAAGACCGCACAGGGTCATCTAAAGGTCAACTTAAATCTCTGAAAACTTCTATGAAAAACCGC
1 TGAAAGACCGCACAGGGTCATCTAAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAAACCGC
13039 ACA
66 ACA
13042 AGGTGCCTGA
Statistics
Matches: 203, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
161 3 0.01
162 194 0.96
163 6 0.03
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (162 bp):
TGAAAGACCGCACAGGGTCATCTAAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAAACCGC
ACAGGGTCATCTGATAATCAACATAAATCTCTGAAAACTTCTATGAAAAACCACACAGGGTTATC
TGAAGAACAACTTAAACTTCTAAAAACTTCTA
Done.