Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022698.1 Corchorus olitorius cultivar O-4 contig22731, 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: 74086
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:963 original size:21 final size:21
Alignment explanation
Indices: 907--963 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
897 TTTATAACAC
*
907 CTTGTTCCTGCCTCATCTCTT
1 CTTGTGCCTGCCTCATCTCTT
* ** * *
928 CTTGGGAATGTCTCATTTCTT
1 CTTGTGCCTGCCTCATCTCTT
949 CTTGTGCCTGCCTCA
1 CTTGTGCCTGCCTCA
964 GATGTTGGAT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.09, C:0.32, G:0.16, T:0.44
Consensus pattern (21 bp):
CTTGTGCCTGCCTCATCTCTT
Found at i:5206 original size:27 final size:27
Alignment explanation
Indices: 5173--5328 Score: 112
Period size: 23 Copynumber: 6.4 Consensus size: 27
5163 AAAATAATAA
*
5173 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
5200 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
5224 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
5246 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
5270 -AATAAATAGATA-AT-AAT--TAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
*
5292 TAATAAATAAAATGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
5319 AAATAGATAA
1 TAATAAATAA
5329 TAGTAAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 34
0.68 0.08 0.23
Matches are distributed among these distances:
19 2 0.02
21 8 0.08
22 4 0.04
23 39 0.39
24 4 0.04
25 8 0.08
27 30 0.30
28 5 0.05
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:5225 original size:19 final size:19
Alignment explanation
Indices: 5203--5408 Score: 84
Period size: 19 Copynumber: 11.4 Consensus size: 19
5193 GCTAAATTAA
5203 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
5222 TAAATAAATAGAT-AATAAT
1 TAAATAAAAAGATAAAT-AG
* *
5241 TAAATTAATAA-ATAAAAAG
1 TAAA-TAAAAAGATAAATAG
**
5260 ATAAATAGTAA-ATAAATAG
1 -TAAATAAAAAGATAAATAG
* * *
5279 ---ATAATAA-TTAAATTAA
1 TAAATAAAAAGATAAA-TAG
*
5295 TAAATAAAATGATAAATAG
1 TAAATAAAAAGATAAATAG
*
5314 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
5332 T-AA-AAAAA-ATAAA-A-
1 TAAATAAAAAGATAAATAG
* *
5346 -AGATAAATAG-TAAATAG
1 TAAATAAAAAGATAAATAG
* * * * *
5363 ATAGAT-AATAGTTAAAAAA
1 -TAAATAAAAAGATAAATAG
*
5382 TAAATACAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
5401 TAAATAAA
1 TAAATAAA
5409 TAATAAAAAA
Statistics
Matches: 139, Mismatches: 29, Indels: 38
0.67 0.14 0.18
Matches are distributed among these distances:
14 1 0.01
15 21 0.15
16 9 0.06
17 2 0.01
18 18 0.13
19 74 0.53
20 14 0.10
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:5229 original size:46 final size:46
Alignment explanation
Indices: 5171--5414 Score: 374
Period size: 46 Copynumber: 5.4 Consensus size: 46
5161 AAAAAATAAT
* *
5171 AATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
*
5217 AATAGTAAATAAATAGATAATAATTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
* *
5263 AATAGTAAATAAATAGATAATAATTAAATTAATAAATAAAATGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
5309 AATAGTAAATAAATAGATAATAG-TAAA--AA-AAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
* * *
5351 AATAGTAAATAGATAGATAATAGTTAAA-AAATAAATACAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
5396 AATAGTAAATAAATA-ATAA
1 AATAGTAAATAAATAGATAA
5415 AAAATCTTTT
Statistics
Matches: 186, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
42 34 0.18
43 6 0.03
44 6 0.03
45 30 0.16
46 110 0.59
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
Found at i:5370 original size:27 final size:26
Alignment explanation
Indices: 5171--5387 Score: 98
Period size: 27 Copynumber: 8.9 Consensus size: 26
5161 AAAAAATAAT
* *
5171 AATAATAAATAAATAGAT-AATAGCTA
1 AATAATAGATAAAAAGATAAATAG-TA
*
5197 AATTAATAAATAAAAAGATAAATAGTA
1 AA-TAATAGATAAAAAGATAAATAGTA
* *
5224 AATAAATAGATAATAA-TTAAAT--T-
1 AAT-AATAGATAAAAAGATAAATAGTA
5247 AAT-A-A-ATAAAAAGATAAATAGTA
1 AATAATAGATAAAAAGATAAATAGTA
* *
5270 AATAAATAGATAATAA-TTAAAT--T-
1 AAT-AATAGATAAAAAGATAAATAGTA
*
5293 AAT-A-A-ATAAAATGATAAATAGTA
1 AATAATAGATAAAAAGATAAATAGTA
* *
5316 AATAAATAGAT-AATAG-TAAA-A-AA
1 AAT-AATAGATAAAAAGATAAATAGTA
* *
5339 AATAAAAAGATAAATAG-TAAATAGATA
1 AAT-AATAGATAAAAAGATAAATAG-TA
* *
5366 GATAATAGTTAAAAA-ATAAATA
1 AATAATAGATAAAAAGATAAATA
5388 CAAAGATAAA
Statistics
Matches: 147, Mismatches: 20, Indels: 48
0.68 0.09 0.22
Matches are distributed among these distances:
19 11 0.07
20 12 0.08
21 2 0.01
22 2 0.01
23 23 0.16
24 12 0.08
25 7 0.05
26 33 0.22
27 40 0.27
28 5 0.03
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (26 bp):
AATAATAGATAAAAAGATAAATAGTA
Found at i:5385 original size:26 final size:27
Alignment explanation
Indices: 5356--5411 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5346 AGATAAATAG
* *
5356 TAAATAGATAGAT-AATAGTTAAA-AAA
1 TAAATACAAAGATAAATAG-TAAATAAA
5382 TAAATACAAAGATAAATAGTAAATAAA
1 TAAATACAAAGATAAATAGTAAATAAA
5409 TAA
1 TAA
5412 TAAAAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (27 bp):
TAAATACAAAGATAAATAGTAAATAAA
Found at i:6922 original size:17 final size:17
Alignment explanation
Indices: 6900--6932 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6890 AAAGGCCCTT
*
6900 GAACTTATACAAAATGC
1 GAACTTACACAAAATGC
6917 GAACTTACACAAAATG
1 GAACTTACACAAAATG
6933 ACCAAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (17 bp):
GAACTTACACAAAATGC
Found at i:6968 original size:18 final size:18
Alignment explanation
Indices: 6937--6972 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6927 AAAATGACCA
* *
6937 AATAAGCCCTTGAACTCT
1 AATAAACCCCTGAACTCT
6955 AATAAACCCCTGAACTCT
1 AATAAACCCCTGAACTCT
6973 TAAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.31, G:0.08, T:0.25
Consensus pattern (18 bp):
AATAAACCCCTGAACTCT
Found at i:8034 original size:19 final size:20
Alignment explanation
Indices: 8006--8043 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7996 TTTACAAAAC
8006 TTTTTATTTAATAAGATAAA
1 TTTTTATTTAATAAGATAAA
*
8026 TTTTT-TTTAATAATATAA
1 TTTTTATTTAATAAGATAA
8044 TAATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTATTTAATAAGATAAA
Found at i:8895 original size:2 final size:2
Alignment explanation
Indices: 8888--8913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8878 GTTTTTGCTC
8888 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
8914 TGAAATCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12180 original size:16 final size:16
Alignment explanation
Indices: 12159--12190 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12149 GATCCTTCAA
12159 GATCCTTCAAAATTTT
1 GATCCTTCAAAATTTT
*
12175 GATCCTTCAAGATTTT
1 GATCCTTCAAAATTTT
12191 TTGGGTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (16 bp):
GATCCTTCAAAATTTT
Found at i:14053 original size:22 final size:22
Alignment explanation
Indices: 14022--14065 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14012 TTCTTTACTG
14022 ACCTTAAATAAGAAGAATGGTA
1 ACCTTAAATAAGAAGAATGGTA
* *
14044 ACCTTGAATAAGAAGATTGGTA
1 ACCTTAAATAAGAAGAATGGTA
14066 TAACCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (22 bp):
ACCTTAAATAAGAAGAATGGTA
Found at i:14345 original size:18 final size:20
Alignment explanation
Indices: 14322--14373 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
14312 AACGTTAAAG
14322 TTATAACCTTA-A-TTTTTT
1 TTATAACCTTATAGTTTTTT
*
14340 TTATAACTTGTATAGTTTTTT
1 TTATAACCT-TATAGTTTTTT
14361 TTAGTAACCTTAT
1 TTA-TAACCTTAT
14374 TAGATGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 8 0.29
19 2 0.07
20 1 0.04
21 12 0.43
22 5 0.18
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.58
Consensus pattern (20 bp):
TTATAACCTTATAGTTTTTT
Found at i:14674 original size:20 final size:21
Alignment explanation
Indices: 14649--14689 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
14639 ATTAATAAGA
14649 GTATAGCATTTTCA-TAATCT
1 GTATAGCATTTTCAGTAATCT
*
14669 GTATAGCTTTTTCAGTAATCT
1 GTATAGCATTTTCAGTAATCT
14690 TATGTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (21 bp):
GTATAGCATTTTCAGTAATCT
Found at i:17004 original size:33 final size:33
Alignment explanation
Indices: 16966--17035 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
16956 ATGTATTTAC
16966 TAGTATATATATATAATGAGTTGTATTAAGTGT
1 TAGTATATATATATAATGAGTTGTATTAAGTGT
16999 TAGTATATATATATAATGAGTTGTATTAAGTGT
1 TAGTATATATATATAATGAGTTGTATTAAGTGT
17032 TAGT
1 TAGT
17036 TAAGATCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.46
Consensus pattern (33 bp):
TAGTATATATATATAATGAGTTGTATTAAGTGT
Found at i:21612 original size:20 final size:23
Alignment explanation
Indices: 21585--21637 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
21575 CGGCATTTAA
21585 TAAATATAT-T-CAAGAAAATTC
1 TAAATATATATCCAAGAAAATTC
*
21606 TAATATATATATCCAAGAACATTC
1 TAA-ATATATATCCAAGAAAATTC
21630 T-AATATAT
1 TAAATATAT
21638 CTCAGTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
23 2 0.07
24 11 0.39
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (23 bp):
TAAATATATATCCAAGAAAATTC
Found at i:21635 original size:24 final size:24
Alignment explanation
Indices: 21578--21637 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
21568 TTAGAAACGG
* *
21578 CATT-TAATAAATATATTCAAGAA
1 CATTCTAATATATATATCCAAGAA
*
21601 AATTCTAATATATATATCCAAGAA
1 CATTCTAATATATATATCCAAGAA
21625 CATTCTAATATAT
1 CATTCTAATATAT
21638 CTCAGTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (24 bp):
CATTCTAATATATATATCCAAGAA
Found at i:29260 original size:30 final size:31
Alignment explanation
Indices: 29212--29281 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 31
29202 AAAAAATTCT
29212 CTTATGTTTTTCTTTTGGGACAAAATAATCC
1 CTTATGTTTTTCTTTTGGGACAAAATAATCC
*
29243 CTTATGTTTTT-TTTTGGGACAAATTAATCC
1 CTTATGTTTTTCTTTTGGGACAAAATAATCC
*
29273 CTTAAGTTT
1 CTTATGTTT
29282 CAGAAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (31 bp):
CTTATGTTTTTCTTTTGGGACAAAATAATCC
Found at i:29465 original size:18 final size:18
Alignment explanation
Indices: 29426--29459 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29416 AAAAAATTCA
*
29426 AAAATTGAAAAAAATATG
1 AAAATTGAAAAAAACATG
29444 AAAATT-AAAAAAACAT
1 AAAATTGAAAAAAACAT
29460 CTAAAACAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (18 bp):
AAAATTGAAAAAAACATG
Found at i:29515 original size:3 final size:3
Alignment explanation
Indices: 29509--29533 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29499 TTTATTTCCT
29509 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
29534 CCTCCACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:33263 original size:16 final size:16
Alignment explanation
Indices: 33242--33290 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
33232 TTAGTAAGAC
33242 TTTTTCTAATTAGTAT
1 TTTTTCTAATTAGTAT
33258 TTTTTCTAATTA-TCA-
1 TTTTTCTAATTAGT-AT
33273 -TTTTCTAATTAGTAT
1 TTTTTCTAATTAGTAT
33288 TTT
1 TTT
33291 GTTATCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.41
15 2 0.07
16 15 0.52
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.63
Consensus pattern (16 bp):
TTTTTCTAATTAGTAT
Found at i:33289 original size:14 final size:14
Alignment explanation
Indices: 33243--33290 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 14
33233 TAGTAAGACT
33243 TTTTCTAATTAGTA
1 TTTTCTAATTAGTA
33257 TTTTTTCTAATTA-TCA
1 --TTTTCTAATTAGT-A
33273 TTTTCTAATTAGTA
1 TTTTCTAATTAGTA
33287 TTTT
1 TTTT
33291 GTTATCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 16 0.53
15 2 0.07
16 12 0.40
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTTCTAATTAGTA
Found at i:42656 original size:10 final size:9
Alignment explanation
Indices: 42613--42670 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
42603 TAAAAGTAAC
42613 TAAGAAAAA
1 TAAGAAAAA
*
42622 TAAACAAAAA
1 T-AAGAAAAA
42632 TAA-AAGAAA
1 TAAGAA-AAA
42641 -AAGAAAAA
1 TAAGAAAAA
42649 TAACGAAAAA
1 TAA-GAAAAA
*
42659 TAA-AAAGA
1 TAAGAAAAA
42667 TAAG
1 TAAG
42671 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:42656 original size:16 final size:17
Alignment explanation
Indices: 42627--42664 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
42617 AAAAATAAAC
42627 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
42644 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
42660 AAAAA
1 AAAAA
42665 GATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:50849 original size:11 final size:11
Alignment explanation
Indices: 50833--50865 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
50823 ACTCAATTTA
50833 TCAATGATCCT
1 TCAATGATCCT
50844 TCAATGAT-CT
1 TCAATGATCCT
50854 TCAATGATCCT
1 TCAATGATCCT
50865 T
1 T
50866 AAATCCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (11 bp):
TCAATGATCCT
Found at i:50857 original size:10 final size:10
Alignment explanation
Indices: 50833--50862 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
50823 ACTCAATTTA
50833 TCAATGATCCT
1 TCAATGAT-CT
50844 TCAATGATCT
1 TCAATGATCT
50854 TCAATGATC
1 TCAATGATC
50863 CTTAAATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (10 bp):
TCAATGATCT
Found at i:58975 original size:178 final size:178
Alignment explanation
Indices: 58605--58987 Score: 466
Period size: 178 Copynumber: 2.2 Consensus size: 178
58595 TTCCACCATA
* * * * *
58605 AGCACAAATTATATAATATTAAGTAGACCATCTATTTCCTTTAATCGAAACAACTAATCCTTTGG
1 AGCAAAAATTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATCCTTTGG
* * * *
58670 AAGCATTTTTTATACTTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTTTAGATCAT
66 AAGCATTTTTGATACTTCGAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAAATCAT
* * * *
58735 AGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGG
131 AGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* * * *
58783 AGCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAAT-TTTTCG
1 AGCAAAAATTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATCCTTT-G
* *
58847 GAAGCATTTTTGATA-TTTGAAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAAATG
65 GAAGCATTTTTGATACTTCG-AACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAAATC
* * * * * * *
58911 ATGGAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAACCGG
129 ATAGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
* *
58961 AG-AGAAAATTATATAATGTTAAATAGA
1 AGCA-AAAATTATATAATATTAAGTAGA
58988 TCGTTTAGCC
Statistics
Matches: 172, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
177 7 0.04
178 165 0.96
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (178 bp):
AGCAAAAATTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATCCTTTGG
AAGCATTTTTGATACTTCGAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAAATCAT
AGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGG
Found at i:60842 original size:66 final size:66
Alignment explanation
Indices: 60771--60910 Score: 185
Period size: 66 Copynumber: 2.1 Consensus size: 66
60761 GTGAGCAGGC
* *
60771 ATGTGAAAGTGGTGA-CAAGGATACATCCAGGCCAAT-GAAGTCAGAGGATAGAGATAACAAGCG
1 ATGTGAAAGTGGCGAGCAA-CATACATCCAGGCCAATGGAA-TCAGAGGATAGAGATAACAAGCG
60834 GAA
64 GAA
* * * * *
60837 CTGTGAAAGTGGCGAGGAACATGCATCTAGGCCAATGGAATCAGTGGATAGAGATAACAAGCGGA
1 ATGTGAAAGTGGCGAGCAACATACATCCAGGCCAATGGAATCAGAGGATAGAGATAACAAGCGGA
60902 A
66 A
60903 ATGTGAAA
1 ATGTGAAA
60911 TGGATTGAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
66 59 0.92
67 5 0.08
ACGTcount: A:0.39, C:0.14, G:0.31, T:0.16
Consensus pattern (66 bp):
ATGTGAAAGTGGCGAGCAACATACATCCAGGCCAATGGAATCAGAGGATAGAGATAACAAGCGGA
A
Found at i:61959 original size:16 final size:16
Alignment explanation
Indices: 61938--61977 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
61928 CCAAACAACC
61938 AAAAAAAAAAGA-AAG
1 AAAAAAAAAAGAGAAG
61953 AAAAAAAAAAGAGAAG
1 AAAAAAAAAAGAGAAG
61969 AAAAAAAAA
1 AAAAAAAAA
61978 GGCCATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAGAAG
Found at i:61960 original size:17 final size:16
Alignment explanation
Indices: 61938--61977 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
61928 CCAAACAACC
61938 AAAAAAAAAAGAAAGAA
1 AAAAAAAAAAG-AAGAA
*
61955 AAAAAAAAGAGAAGAA
1 AAAAAAAAAAGAAGAA
61971 AAAAAAA
1 AAAAAAA
61978 GGCCATTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAGAA
Found at i:63468 original size:19 final size:19
Alignment explanation
Indices: 63444--63500 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
63434 GGCATATGGG
63444 AACGTGATAGCACTAGTAA
1 AACGTGATAGCACTAGTAA
63463 AACGTGATAGCACTAGTAA
1 AACGTGATAGCACTAGTAA
63482 AACGTGATAGCACTAGTAA
1 AACGTGATAGCACTAGTAA
63501 GGAGTCGCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (19 bp):
AACGTGATAGCACTAGTAA
Found at i:73114 original size:16 final size:16
Alignment explanation
Indices: 73093--73125 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
73083 TCAACTTTCA
*
73093 GTGAAAGTGATGAAGC
1 GTGAAAGCGATGAAGC
73109 GTGAAAGCGATGAAGC
1 GTGAAAGCGATGAAGC
73125 G
1 G
73126 AACGAAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.39, T:0.15
Consensus pattern (16 bp):
GTGAAAGCGATGAAGC
Found at i:73661 original size:100 final size:99
Alignment explanation
Indices: 73488--73756 Score: 344
Period size: 100 Copynumber: 2.7 Consensus size: 99
73478 AAATGAGTGC
* * *
73488 TAAATTCTATAAACAATTTTTTTTATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATC
1 TAAATTCCATAAATAA-TTTTTTCATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATC
** *
73553 CGTGTCTAAATCCGCTT-TCAAATTATAATATGTAA
65 CGTGTCTAAATCCGCTTCT-AAACAATAATAAGTAA
* * *
73588 TAAATTCCATAGATAAATTTTTTCATTTCATTTGGAAACAGAATTTAACACGGAAACTACATATT
1 TAAATTCCATAAAT-AATTTTTTCATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATC
* *
73653 CGTGTCTAAATCCGCTTCTAACCAATAATAAGTAC
65 CGTGTCTAAATCCGCTTCTAAACAATAATAAGTAA
* * * *
73688 TAAATTCTATAAATAA-TTTTTCTATTTCATTTGGAAACGGAACTTAGCATGGAAACTACATATC
1 TAAATTCCATAAATAATTTTTTC-ATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATC
*
73752 TGTGT
65 CGTGT
73757 GTCGAAACGT
Statistics
Matches: 147, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
98 6 0.04
99 42 0.29
100 96 0.65
101 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (99 bp):
TAAATTCCATAAATAATTTTTTCATTTCATTTGGAAACGGAATTTAACACGGAAACTACATATCC
GTGTCTAAATCCGCTTCTAAACAATAATAAGTAA
Done.