Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023650.1 Corchorus olitorius cultivar O-4 contig23683, 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: 43122
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:265 original size:2 final size:2
Alignment explanation
Indices: 258--291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
248 ACATGAAATC
258 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
292 TCTATAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1338 original size:478 final size:482
Alignment explanation
Indices: 435--1352 Score: 1555
Period size: 478 Copynumber: 1.9 Consensus size: 482
425 TGTGGATGCC
* *
435 CAAATACCAAGTAATTTTATTCAAACAATTATTCCAATTTAAATATTAAAATCCATTTATAAAAT
1 CAAATACCAAGTAACTTTATTCAAACAATTATTCCAATTTAAATATTAAAATACATTTATAAAAT
*
500 TTGAATTCAAAATATATAAATATAAAATTTATTTTTATTTTTAATTTTAACTATATTGGAATTCA
66 TTGAATTCAAAATATATAAATATAAAA--TA-TTTTATTTTTAATTTTAACTAGATTGGAATTCA
565 AAAGATATTGAATTTGAAATTTGTTCATTTATCTCGGAAAAAAATAGTTATTTCAAAAAATATAA
128 AAAGATATTGAATTTGAAATTTGTTCATTTATCTCGGAAAAAAATAGTTATTTCAAAAAATATAA
630 TCAACTCATATTAATTTATAAAATTGATGCTAAAAAGAAAAAAAAGTTACCATTTATTTAGATAA
193 TCAACTCATATTAATTTATAAAATTGATGCTAAAAAGAAAAAAAAGTTACCATTTATTTAGATAA
* * *
695 AATCTAAACCGTAATTTAAAAAAAAAGAAATACTACATTAAGCTCAAAATTTGTTTGAAACCAAG
258 AATCTAAACCGTAATTTAAAAAAAAAGAAATACTAAAATAAGCTCAAAATCTGTTTGAAACCAAG
* * *
760 TTTTTGTTGAAATCATGTAAATTAAAGTAAGAAATATTTCAATGTAGTTTCCAAACTCTCATAGT
323 TTTTTGTTGAAATCATATAAATCAAAGTAAGAAATATTTCAATGTAATTTCCAAACTCTCATAGT
825 AGTATTTAGATTACTAAAGCAACAAACCCAATAAATCTCAACTTATATATATTCATATGACATGT
388 AGTATTTAGATTACTAAAGCAACAAACCCAATAAATCTCAACTTATATATATTCATATGACATGT
890 AGGATTTTTCCTTGATTTTAGCGGTACTAA
453 AGGATTTTTCCTTGATTTTAGCGGTACTAA
*
920 CAAATACCAAGTAACTTTATTCAAACAATTATTCCAATTTAAATATTAAAATAGATTTATAAAAT
1 CAAATACCAAGTAACTTTATTCAAACAATTATTCCAATTTAAATATTAAAATACATTTATAAAAT
* * *
985 TTTAATTGAAAATATATAAAT-T-TAA-A-TTTATTTTTAATTTTAACTAGA-TGAGAATTCAAA
66 TTGAATTCAAAATATATAAATATAAAATATTTTATTTTTAATTTTAACTAGATTG-GAATTCAAA
*
1045 AGATATTGAATTTGAAATTTGTTCATTTCTCTCGGAAAAAAATAGTTATTTCAAAAAATATAATC
130 AGATATTGAATTTGAAATTTGTTCATTTATCTCGGAAAAAAATAGTTATTTCAAAAAATATAATC
*
1110 AACTCATATTAATTTATAAAATTGATGCTAACAAGAAACAAAAA-TTATCCATTTATTTAGA-AA
195 AACTCATATTAATTTATAAAATTGATGCTAAAAAGAAA-AAAAAGTTA-CCATTTATTTAGATAA
1173 AATCTAAACCGTAA-TTAAAAAAAAAGAAATACTAAAATAAGCTCAAAATCTGTTTGAAACCAAG
258 AATCTAAACCGTAATTTAAAAAAAAAGAAATACTAAAATAAGCTCAAAATCTGTTTGAAACCAAG
*
1237 TTTTTTGTTGAAATCATATAAATCAAGGTAAGAAATATTTCAATGTAATTTCCAAACTCTCATAG
323 -TTTTTGTTGAAATCATATAAATCAAAGTAAGAAATATTTCAATGTAATTTCCAAACTCTCATAG
* *
1302 TAGTTTTTAGATTACTAAAGCAACAAACCCAATAAATGTCAACTTATATAT
387 TAGTATTTAGATTACTAAAGCAACAAACCCAATAAATCTCAACTTATATAT
1353 TTTAATATAT
Statistics
Matches: 411, Mismatches: 18, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
477 49 0.12
478 259 0.63
479 18 0.04
480 1 0.00
483 2 0.00
484 1 0.00
485 81 0.20
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (482 bp):
CAAATACCAAGTAACTTTATTCAAACAATTATTCCAATTTAAATATTAAAATACATTTATAAAAT
TTGAATTCAAAATATATAAATATAAAATATTTTATTTTTAATTTTAACTAGATTGGAATTCAAAA
GATATTGAATTTGAAATTTGTTCATTTATCTCGGAAAAAAATAGTTATTTCAAAAAATATAATCA
ACTCATATTAATTTATAAAATTGATGCTAAAAAGAAAAAAAAGTTACCATTTATTTAGATAAAAT
CTAAACCGTAATTTAAAAAAAAAGAAATACTAAAATAAGCTCAAAATCTGTTTGAAACCAAGTTT
TTGTTGAAATCATATAAATCAAAGTAAGAAATATTTCAATGTAATTTCCAAACTCTCATAGTAGT
ATTTAGATTACTAAAGCAACAAACCCAATAAATCTCAACTTATATATATTCATATGACATGTAGG
ATTTTTCCTTGATTTTAGCGGTACTAA
Found at i:3033 original size:2 final size:2
Alignment explanation
Indices: 3026--3059 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3016 CATGATCGTA
*
3026 AT AT AT AT AC 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
3060 GTACTTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6655 original size:37 final size:37
Alignment explanation
Indices: 6614--6711 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 37
6604 ACTAAAACCT
* *
6614 GATGGGAACTTTCCCAATTCGAAAAT-TTTGAAAACTG
1 GATGGGAACTTTCCCAATTTGAAAATCTTAG-AAACTG
* *
6651 GATGGGAACTTTTCCAATTTG-AAATCTTAGAAACTT
1 GATGGGAACTTTCCCAATTTGAAAATCTTAGAAACTG
* *
6687 GTTAGGAACTTTCCCAATTTGAAAA
1 GATGGGAACTTTCCCAATTTGAAAA
6712 CTATGAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.52
37 25 0.48
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (37 bp):
GATGGGAACTTTCCCAATTTGAAAATCTTAGAAACTG
Found at i:7933 original size:22 final size:23
Alignment explanation
Indices: 7894--7938 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
7884 AATTTACTAT
7894 TTTTATATTCATGATTAAGTGTG
1 TTTTATATTCATGATTAAGTGTG
*
7917 TTTTA-ATTACAT-ATTAATTGTG
1 TTTTATATT-CATGATTAAGTGTG
7939 CGTGAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (23 bp):
TTTTATATTCATGATTAAGTGTG
Found at i:9225 original size:20 final size:21
Alignment explanation
Indices: 9202--9248 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
9192 TAATAATGCT
9202 AAATTAACCCAAA-T-AAATC
1 AAATTAACCCAAATTGAAATC
*
9221 GAAATT-ACCTAAATTGAAATC
1 -AAATTAACCCAAATTGAAATC
9242 AAATTAA
1 AAATTAA
9249 ATTCTAACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (21 bp):
AAATTAACCCAAATTGAAATC
Found at i:10057 original size:48 final size:48
Alignment explanation
Indices: 9999--10842 Score: 962
Period size: 48 Copynumber: 17.8 Consensus size: 48
9989 TTTTCTCCAA
* * * *
9999 TATTCCCGTTTTGCCCTTCCCGGCCAGAAGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
*
10047 TATT-CTCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATGTTT
1 TATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * **
10095 TATTCCTGTGTTGCCCTTCCC-ATTAGAAGGTGTTGTTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * * * *
10142 CATTCCTATTTTGCCCTTCCCGGTTGGAAGGTGTTGCTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * ** *
10190 TATTCCTGTGTTGCTCTTCCCACT-GGAAGGTGTTGTTTTCAATGTGT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * *
10237 TATTCCTGTTTTGGCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
** * * *
10285 TATTCCTGTTTTGCCCTTCCCACT-AGAACGTGTTGCTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* *
10332 TCATTCCTGTTTTTCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT
1 T-ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * *
10381 TATT-CTCGTTTTGCCCTTCCTGGTCGAAAGGTGTTGTTTTCAACGTTT
1 TATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* **
10429 TATTCCTGTGTTGCCCTTTTCGGTCGGAAGGTGTTGTTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * **
10477 TATTCCTGGTTTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATGCGT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * * * * *
10525 TATTCCTGTTTTGTCCTTCCCGATCGGAAGATTTTATTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * *
10573 TATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCATTGTGT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
** * *
10621 TATTCCTGTTTTGCCCTTCTTGGTCGGAGGGTGTTGTTTTCAATATTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* **
10669 TATTCCTGTTTTTCCCTTCCCACT-GGAAGGTGTTGTTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
* * * *
10716 TCATTCCTGTTTCGCCCTTACCGGTCAGAAGGTTTTGTTTTC-------
1 T-ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
*
10758 -ATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
** **
10805 TATTCCCATTTTGCCCTTCCCCATCGGAATGG-GTTGTT
1 TATTCCTGTTTTGCCCTTCCCGGTCGGAA-GGTGTTGTT
10843 CCTATTCCTT
Statistics
Matches: 668, Mismatches: 109, Indels: 38
0.82 0.13 0.05
Matches are distributed among these distances:
40 35 0.05
47 127 0.19
48 466 0.70
49 40 0.06
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (48 bp):
TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTT
Found at i:10762 original size:40 final size:40
Alignment explanation
Indices: 10711--10798 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
10701 TTGTTTTCAA
* *
10711 TGTTTTCATTCCTGTTTCGCCCTTACCGGTCAGAAGGTTT
1 TGTTTTCATTCCTATTTCGCCCTTACCGGTCAGAAGGTGT
* * *
10751 TGTTTTCATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCATTCCTATTTCGCCCTTACCGGTCAGAAGGTGT
10791 TGTTTTCA
1 TGTTTTCA
10799 ATGTTTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (40 bp):
TGTTTTCATTCCTATTTCGCCCTTACCGGTCAGAAGGTGT
Found at i:10842 original size:88 final size:87
Alignment explanation
Indices: 10666--10851 Score: 205
Period size: 88 Copynumber: 2.1 Consensus size: 87
10656 GTTTTCAATA
* * **
10666 TTTTATTCCTGTTTTTCCCTTCCCACTGGAAGGTGTTGTTTTCAATGTTTTCATTCCTGTTTCGC
1 TTTTATTCCTATTTTGCCCTTCCCACTGGAAGGTGTTGTTTTCAATGTTTTCATTCCCATTTCGC
** *
10731 CCTTACCGGTCAGAAGGTTTTG
66 CCTTACCCATCAGAAGGTGTTG
** *
10753 TTTTCATTCCTATTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT-ATTCCCATTTT
1 TTTT-ATTCCTATTTTGCCCTTCCCACT-GGAAGGTGTTGTTTTCAATGTTTTCATTCCCATTTC
* *
10817 GCCCTTCCCCATCGGAATGG-GTTG
64 GCCCTTACCCATCAGAA-GGTGTTG
*
10841 TTCCTATTCCT
1 TT-TTATTCCT
10852 TTATTGTCAG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
87 4 0.05
88 51 0.62
89 27 0.33
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (87 bp):
TTTTATTCCTATTTTGCCCTTCCCACTGGAAGGTGTTGTTTTCAATGTTTTCATTCCCATTTCGC
CCTTACCCATCAGAAGGTGTTG
Found at i:13285 original size:52 final size:52
Alignment explanation
Indices: 13217--13561 Score: 424
Period size: 52 Copynumber: 6.6 Consensus size: 52
13207 AAAGCAAACT
* * *** *
13217 AAAACCTGATGTGAACTTTTCCAATTTGAAAACCGGCTAAATTGAATACTTAG
1 AAAA-CTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
* * * *
13270 AAAATTGATGGGAACTTTCCCAATTTGAAAAAAAGTTAAATTAAATAATTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
* *
13322 AAAACTGATGGGAACTTTCCCGATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
* * * * * *
13374 AAAATTGATGAGAACTTTCCC-ACTTGAAAAACAGCCAAATTCAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
* * *
13425 AAGACTGATGGGAACTTTTCCCGACTTGAAAAACAA-CTAAATTGAATACTTTG
1 AAAACTGATGGGAAC-TTTCCCAATTTGAAAAA-AAGCTAAATTGAATACTTTG
* * *
13478 AAGATTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
*
13530 AAAACTGATGGGAACTTTCCCAATTTGCAAAA
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAA
13562 TTAAGTTGAT
Statistics
Matches: 253, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
51 39 0.15
52 170 0.67
53 43 0.17
54 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
Found at i:20105 original size:6 final size:6
Alignment explanation
Indices: 20094--20153 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
20084 TATATACCTG
* ** *
20094 TCGAGC TCGAGC TCGAGC TCGAAC TCGTA-- TCGAAT TCGAGC TCGAAC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCG-AGC TCGAGC TCGAGC TCGAGC
*
20141 TCGAGC TTGAGC T
1 TCGAGC TCGAGC T
20154 TGAATTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 40 0.89
7 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23
Consensus pattern (6 bp):
TCGAGC
Found at i:20111 original size:12 final size:12
Alignment explanation
Indices: 20094--20147 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
20084 TATATACCTG
*
20094 TCGAGCTCGAGC
1 TCGAGCTCGAAC
20106 TCGAGCTCGAAC
1 TCGAGCTCGAAC
*
20118 TCGTA--TCGAAT
1 TCG-AGCTCGAAC
20129 TCGAGCTCGAAC
1 TCGAGCTCGAAC
20141 TCGAGCT
1 TCGAGCT
20148 TGAGCTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
12 26 0.72
13 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (12 bp):
TCGAGCTCGAAC
Found at i:21646 original size:2 final size:2
Alignment explanation
Indices: 21639--21668 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21629 TATTGTGATG
21639 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21669 ACTAATGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24427 original size:19 final size:18
Alignment explanation
Indices: 24382--24453 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
24372 ACAACAGGTG
* *
24382 GTATTATGTATTATTAGT
1 GTATTATTTATTATTAAT
*
24400 CGTAGTATTTATTATTAAT
1 -GTATTATTTATTATTAAT
24419 GTTATTA-TTATTTATTAAT
1 G-TATTATTTA-TTATTAAT
24438 GTATTCATTTATTATT
1 GTATT-ATTTATTATT
24454 TCCGCAGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.18
19 34 0.76
20 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (18 bp):
GTATTATTTATTATTAAT
Found at i:25486 original size:45 final size:45
Alignment explanation
Indices: 25403--25489 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
25393 AGCAACAATT
*
25403 AATATTAGCTTTATTTTAATGAATTATATAGAAATGGAGTAGTAG
1 AATATTAGCTTTATTTTAATGAATTACATAGAAATGGAGTAGTAG
* * **
25448 AATATTAGCTTTATTTTGATGAATTACCTAGAGGTGGAGTAG
1 AATATTAGCTTTATTTTAATGAATTACATAGAAATGGAGTAG
25490 AATTTAGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATTACATAGAAATGGAGTAGTAG
Found at i:35987 original size:11 final size:11
Alignment explanation
Indices: 35953--36000 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
35943 TTGAAATAAT
35953 TCTTC-AATAG
1 TCTTCAAATAG
35963 TCTTC--A-AG
1 TCTTCAAATAG
**
35971 TCTTCAAATTT
1 TCTTCAAATAG
35982 TCTTCAAATAG
1 TCTTCAAATAG
35993 TCTTCAAA
1 TCTTCAAA
36001 CACGAACTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 6 0.19
11 17 0.55
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:37950 original size:13 final size:13
Alignment explanation
Indices: 37932--37956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37922 GGAATGGCCC
37932 TTTATAGATAACG
1 TTTATAGATAACG
37945 TTTATAGATAAC
1 TTTATAGATAAC
37957 ATGTATACTA
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTTATAGATAACG
Found at i:42548 original size:23 final size:24
Alignment explanation
Indices: 42502--42548 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
42492 TAGTTCTAAA
*
42502 TTTGGGTCTTGATTGTTTTATTTG
1 TTTGGGTCTTGATTATTTTATTTG
42526 TTTGGG-CTT-ATTATTTGTATTTG
1 TTTGGGTCTTGATTATTT-TATTTG
42549 GGCTCAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.11, C:0.04, G:0.23, T:0.62
Consensus pattern (24 bp):
TTTGGGTCTTGATTATTTTATTTG
Done.