Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020452.1 Corchorus olitorius cultivar O-4 contig20485, 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: 80337
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3496 original size:3 final size:3
Alignment explanation
Indices: 3490--3514 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3480 TTCATCATAA
3490 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
3515 TAAGAAACCT
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):
TCT
Found at i:4878 original size:9 final size:9
Alignment explanation
Indices: 4866--4896 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4856 CCCCCCCCCC
4866 CCCCCCAAA
1 CCCCCCAAA
4875 CCCCCCAAA
1 CCCCCCAAA
*
4884 CCCCCCAAT
1 CCCCCCAAA
4893 CCCC
1 CCCC
4897 TATTCTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.71, G:0.00, T:0.03
Consensus pattern (9 bp):
CCCCCCAAA
Found at i:4889 original size:1 final size:1
Alignment explanation
Indices: 4847--4871 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4837 TTTATCATAA
4847 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
4872 AAACCCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:17899 original size:185 final size:185
Alignment explanation
Indices: 17582--17953 Score: 726
Period size: 185 Copynumber: 2.0 Consensus size: 185
17572 ATAACAGGTA
*
17582 ATAAGTAAGCATGTATACTACTTTCCCCTCTTTTTTATCTTTTAAGATCCCAACTTCATTCACTG
1 ATAACTAAGCATGTATACTACTTTCCCCTCTTTTTTATCTTTTAAGATCCCAACTTCATTCACTG
17647 GCTCTGAGATTTGTGATGTTTGTAGAAGGTGGCCCAAGATAGAGACTTGGTAAGAAGACTATTTT
66 GCTCTGAGATTTGTGATGTTTGTAGAAGGTGGCCCAAGATAGAGACTTGGTAAGAAGACTATTTT
17712 AGTATATATATTTTGCCAGAAAACAAAGAGGCAGAGATTGATTATCGCTAACATG
131 AGTATATATATTTTGCCAGAAAACAAAGAGGCAGAGATTGATTATCGCTAACATG
17767 ATAACTAAGCATGTATACTACTTTCCCCTCTTTTTTATCTTTTAAGATCCCAACTTCATTCACTG
1 ATAACTAAGCATGTATACTACTTTCCCCTCTTTTTTATCTTTTAAGATCCCAACTTCATTCACTG
17832 GCTCTGAGATTTGTGATGTTTGTAGAAGGTGGCCCAAGATAGAGACTTGGTAAGAAGACTATTTT
66 GCTCTGAGATTTGTGATGTTTGTAGAAGGTGGCCCAAGATAGAGACTTGGTAAGAAGACTATTTT
*
17897 AGTATATATATTTTGCCAGAAAACAAAGAGGCAGAGATTGATTATCGGTAACATG
131 AGTATATATATTTTGCCAGAAAACAAAGAGGCAGAGATTGATTATCGCTAACATG
17952 AT
1 AT
17954 GCAAATGATG
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 185 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (185 bp):
ATAACTAAGCATGTATACTACTTTCCCCTCTTTTTTATCTTTTAAGATCCCAACTTCATTCACTG
GCTCTGAGATTTGTGATGTTTGTAGAAGGTGGCCCAAGATAGAGACTTGGTAAGAAGACTATTTT
AGTATATATATTTTGCCAGAAAACAAAGAGGCAGAGATTGATTATCGCTAACATG
Found at i:20896 original size:45 final size:43
Alignment explanation
Indices: 20812--20898 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 43
20802 TAGTTTTGGA
* *
20812 TTGAATATTGACACTACTAGATGGATGAAGTTTGGGAATCAGG
1 TTGAATATTGACACTACTAGATGGATGAAATTTGAGAATCAGG
20855 TTGAATATTGACACTACACTAGATGGATGAAATTTGAGAATCAG
1 TTGAATATTGACACT--ACTAGATGGATGAAATTTGAGAATCAG
20899 AAAAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 15 0.38
45 25 0.62
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (43 bp):
TTGAATATTGACACTACTAGATGGATGAAATTTGAGAATCAGG
Found at i:27083 original size:58 final size:58
Alignment explanation
Indices: 26988--27097 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
26978 ATTAATCAAA
*
26988 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * *
27046 TATCGAGTGACATGTTTTTTTATTAGATGTC-T-AAAAAAGATGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATG-CATAAAAAAAGACGTTTTAGGACC
27098 GAGGCATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 31 0.67
59 14 0.30
60 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:29291 original size:204 final size:203
Alignment explanation
Indices: 28940--29339 Score: 687
Period size: 204 Copynumber: 2.0 Consensus size: 203
28930 GCTTAATAAC
28940 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
* *
29005 GATACAGCACATTATTATTATTATACATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATTATACATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGT
*
29070 TGATTTATTGAATTAAATTAGATCAATGTACAAACAAAATTTCAAAATTATAAAAGATATTAAAG
131 TGATTTATTAAATTAAATTAGATCAATGT-CAAACAAAATTTCAAAATTATAAAAGATATT-AAG
29135 ATCTGATTTA
194 ATCTGATTTA
*
29145 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
* * * *
29209 GATACAACACATTACTATTA-TATATATAGAATTATACCAAAAAAAATTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTATTATACATAAAACTATA-CAAAAAAAAGTAGTTGAACATTAGTGG
29273 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
130 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
29338 TC
195 TC
29340 CAATTTATAT
Statistics
Matches: 186, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
202 6 0.03
203 44 0.24
204 112 0.60
205 24 0.13
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAAATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATTATACATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
CTGATTTA
Found at i:30417 original size:22 final size:22
Alignment explanation
Indices: 30390--30432 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30380 CGTAAGTAAC
30390 TGATGAAAGATAAT-TGAGTTTA
1 TGATGAAAGAT-ATCTGAGTTTA
30412 TGATGAAAGATATCTGAGTTT
1 TGATGAAAGATATCTGAGTTT
30433 GGGTTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (22 bp):
TGATGAAAGATATCTGAGTTTA
Found at i:31052 original size:2 final size:2
Alignment explanation
Indices: 31045--31082 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31035 AGAATGCGTT
31045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31083 CACAAACCAC
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):
TA
Found at i:34166 original size:23 final size:22
Alignment explanation
Indices: 34128--34191 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
34118 TTTTTAGTAT
*
34128 ATTTTTTTTAACTTT-AATTTA
1 ATTTTTTTTAAATTTAAATTTA
34149 ATTTTTTATTCAAATTTAAATTTA
1 ATTTTTT-TT-AAATTTAAATTTA
* *
34173 ATTTTGATTTATATTTAAA
1 ATTTT-TTTTAAATTTAAA
34192 ATATACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 7 0.19
22 2 0.06
23 13 0.36
24 13 0.36
25 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTTTAAATTTAAATTTA
Found at i:34175 original size:24 final size:21
Alignment explanation
Indices: 34128--34177 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 21
34118 TTTTTAGTAT
*
34128 ATTTTTTTTAACTTTAATTTA
1 ATTTTTTTTAAATTTAATTTA
34149 ATTTTTTATTCAAATTTAAATTTA
1 ATTTTTT-TT-AAATTT-AATTTA
34173 ATTTT
1 ATTTT
34178 GATTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 2 0.08
23 5 0.20
24 11 0.44
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTTTTAAATTTAATTTA
Found at i:39061 original size:21 final size:22
Alignment explanation
Indices: 39037--39084 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
39027 GAATTTCAAG
* *
39037 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATAAAATTTTGTT
39058 AACCTTCTTATAAAATTTTGTT
1 AACCTTCTTATAAAATTTTGTT
39080 AACCT
1 AACCT
39085 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (22 bp):
AACCTTCTTATAAAATTTTGTT
Found at i:39118 original size:22 final size:22
Alignment explanation
Indices: 39070--39496 Score: 80
Period size: 22 Copynumber: 19.5 Consensus size: 22
39060 CCTTCTTATA
* *
39070 AAATTTTGTTAACCTCCCTAA-G
1 AAATTTTGATAACCTCAC-AATG
* *
39092 GAATTTTGA-AGACCTCACTATG
1 AAATTTTGATA-ACCTCACAATG
* * *
39114 AAATTCTGATAACTTCCCAATG
1 AAATTTTGATAACCTCACAATG
* *
39136 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACC-TCACAATG
* * *
39159 AGATGTTGATAACGTC-CATATG
1 AAATTTTGATAACCTCACA-ATG
* * * *
39181 ATATATTGATAACCACGTC-ATG
1 AAATTTTGATAACCTC-ACAATG
* *
39203 AAAATTT-AAAACCCTC-CATATG
1 AAATTTTGATAA-CCTCACA-ATG
* * **
39225 -AATTGTT-AGTAATCGCACTCTG
1 AAATT-TTGA-TAACCTCACAATG
*
39247 AAATTTTGATAATCATCACACTATG
1 AAATTTTGATAA-CCTCACA--ATG
* * * * *
39272 AAATTGTAATAAGCTCACTATAA
1 AAATTTTGATAACCTCACAAT-G
* *
39295 AAATTTTGATAAACCTTC-CCATA
1 AAATTTTGAT-AACC-TCACAATG
* * *
39318 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCTCACAATG
*
39341 AAATTTTGATAACCTC-CTTATG
1 AAATTTTGATAACCTCAC-AATG
** *
39363 AAAGCTTGA-AAACT-AC----
1 AAATTTTGATAACCTCACAATG
* **
39379 AAATTTTGATAACCTCCCTGTG
1 AAATTTTGATAACCTCACAATG
** ** *
39401 ATTTTTTGATAACCTCATTATA
1 AAATTTTGATAACCTCACAATG
* * * *
39423 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCACAATG
* ** *
39445 AAATTTTGAAAACCAAACTATG
1 AAATTTTGATAACCTCACAATG
* *
39467 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACAATG
39487 AAATTTTGAT
1 AAATTTTGAT
39497 TACTCCATAA
Statistics
Matches: 293, Mismatches: 82, Indels: 62
0.67 0.19 0.14
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
18 1 0.00
20 13 0.04
21 16 0.05
22 161 0.55
23 66 0.23
24 11 0.04
25 14 0.05
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCACAATG
Found at i:39169 original size:45 final size:45
Alignment explanation
Indices: 39107--39195 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
39097 TTGAAGACCT
* *
39107 CACTATGAAATTCTGATAACTTCCCA-ATGAAATTTTGATAACCAA
1 CACTATGAAATTCTGATAACGT-CCATATGAAATATTGATAACCAA
* *
39152 CACTATGAGATGT-TGATAACGTCCATATGATATATTGATAACCA
1 CACTATGAAAT-TCTGATAACGTCCATATGAAATATTGATAACCA
39196 CGTCATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 34 0.89
46 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (45 bp):
CACTATGAAATTCTGATAACGTCCATATGAAATATTGATAACCAA
Found at i:39306 original size:23 final size:22
Alignment explanation
Indices: 39289--39358 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 22
39279 AATAAGCTCA
39289 CTATAAAAATTTTGATAAACCTTC
1 CTAT-AAAATTTTGATAAACC-TC
*
39313 CCATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCT-C
39336 CTATAAAATTTTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
39357 CT
1 CT
39359 TATGAAAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 3 0.07
22 6 0.14
23 31 0.72
24 3 0.07
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACCTC
Found at i:39452 original size:44 final size:43
Alignment explanation
Indices: 39379--39496 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 43
39369 TGAAAACTAC
* ** ** *
39379 AAATTTTGATAACCTCCCTGTGATTTTTTGATAACCTCATTATA
1 AAATTTTGATAATCTCCCT-TGAAATTTTGATAACCAAACTATA
* * *
39423 AAATTTTGTTAATCTCCCTATGAAATTTTGAAAACCAAACTATG
1 AAATTTTGATAATCTCCCT-TGAAATTTTGATAACCAAACTATA
39467 AAATTTTGAT-ATCCTCCC-TGAAATTTTGAT
1 AAATTTTGATAAT-CTCCCTTGAAATTTTGAT
39497 TACTCCATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 11 0.18
43 2 0.03
44 48 0.79
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (43 bp):
AAATTTTGATAATCTCCCTTGAAATTTTGATAACCAAACTATA
Found at i:39652 original size:22 final size:22
Alignment explanation
Indices: 39604--39683 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
39594 TCACATTCTG
*
39604 AAAA-TTTGATAACCTCTTTTAT
1 AAAATTTTGATAACCTC-TCTAT
* *
39626 GAAATTTCGATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* * *
39648 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
39670 GAAATTTTGATAAC
1 AAAATTTTGATAAC
39684 AACACTATGG
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 35 0.76
23 11 0.24
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:39756 original size:21 final size:24
Alignment explanation
Indices: 39703--39825 Score: 106
Period size: 22 Copynumber: 5.5 Consensus size: 24
39693 GATAACCTCG
* *
39703 CTATGAAATTTTGATAA-C-AACA
1 CTATGAAATTTTGATAATCTATCT
39725 CTATGAAATTTTGATAATCT-TCT
1 CTATGAAATTTTGATAATCTATCT
*
39748 -TAT-AAATTTTGATATTCTGATCT
1 CTATGAAATTTTGATAATCT-ATCT
*
39771 CTATGAAATTTCGATAATC-A-CT
1 CTATGAAATTTTGATAATCTATCT
*
39793 CTATGAGA-TTTGATAA-C-AT-T
1 CTATGAAATTTTGATAATCTATCT
*
39813 CTATCAAATTTTG
1 CTATGAAATTTTG
39826 GTACTCCTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 17
0.76 0.08 0.15
Matches are distributed among these distances:
20 9 0.11
21 25 0.30
22 29 0.35
23 6 0.07
24 3 0.04
25 12 0.14
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCT
Found at i:39878 original size:22 final size:21
Alignment explanation
Indices: 39860--40008 Score: 85
Period size: 22 Copynumber: 6.9 Consensus size: 21
39850 TTTTAACCTT
39860 CATATGAAATTTTGATAACCA
1 CATATGAAATTTTGATAACCA
*
39881 CACTA--AAATTTTTTTATAACCA
1 CA-TATGAAA--TTTTGATAACCA
*
39903 CACTATGAAATTTTGATAACCTCC
1 CA-TATGAAATTTTGATAA-C-CA
* *
39927 CTATATGAAATATT-ATTAACCT
1 C-ATATGAAATTTTGA-TAACCA
*
39949 C--ATGAAATTTTGTTAACCA
1 CATATGAAATTTTGATAACCA
*
39968 CACTATGAAATTCTT-ATAACCT
1 CA-TATGAAATT-TTGATAACCA
* *
39990 CGCTATGACATTTTGATAA
1 C-ATATGAAATTTTGATAA
40009 TCTCTTTGAA
Statistics
Matches: 100, Mismatches: 12, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
19 15 0.15
20 3 0.03
21 4 0.04
22 54 0.54
23 5 0.05
24 18 0.18
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (21 bp):
CATATGAAATTTTGATAACCA
Found at i:40098 original size:21 final size:23
Alignment explanation
Indices: 40065--40115 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
40055 ATTTCAATTA
40065 AAATTTCAATAACCT-TCCTAAG
1 AAATTTCAATAACCTATCCTAAG
*
40087 AAATTT-AATAACCTGATCCTATG
1 AAATTTCAATAACCT-ATCCTAAG
40110 AAATTT
1 AAATTT
40116 TGGTAACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.31
22 6 0.23
23 12 0.46
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (23 bp):
AAATTTCAATAACCTATCCTAAG
Found at i:40133 original size:22 final size:22
Alignment explanation
Indices: 40105--40259 Score: 124
Period size: 22 Copynumber: 7.0 Consensus size: 22
40095 TAACCTGATC
*
40105 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
40127 CTATGAAATTTTGATAA-CATTC-
1 CTATGAAATTTTGATAACCA--CA
*
40149 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
40172 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
40193 CTATGGAATTTTGATAATCTC-
1 CTATGAAATTTTGATAACCACA
* *
40214 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
40237 TTATGAAGTTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
40259 C
1 C
40260 AGAGACAAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
20 1 0.01
21 7 0.07
22 92 0.88
23 3 0.03
25 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:40220 original size:66 final size:65
Alignment explanation
Indices: 40086--40259 Score: 201
Period size: 66 Copynumber: 2.6 Consensus size: 65
40076 ACCTTCCTAA
*
40086 GAAATT-TAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACATTCC
1 GAAATTATAATAACC--ATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACA-TCC
40150 CAT
63 CAT
* * * *
40153 GAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAATC-TCCT
1 GAAATTATAATAACCAT-CATATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CATCC-
40216 CAT
63 CAT
* * *
40219 GAAATTATAATAACCATCTTATGAAGTTTTGATAACCACAC
1 GAAATTATAATAACCATCATATGAAATTTTGGTAACCACAC
40260 AGAGACAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
65 4 0.04
66 73 0.79
67 10 0.11
68 5 0.05
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (65 bp):
GAAATTATAATAACCATCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACATCCCAT
Found at i:40439 original size:14 final size:15
Alignment explanation
Indices: 40413--40441 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40403 TTAATTTTTT
40413 AATTGAAATTTAAAA
1 AATTGAAATTTAAAA
40428 AATTGAAA-TTAAAA
1 AATTGAAATTTAAAA
40442 GTAAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATTGAAATTTAAAA
Found at i:40461 original size:20 final size:20
Alignment explanation
Indices: 40423--40461 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40413 AATTGAAATT
40423 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
40443 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
40462 ATAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:40648 original size:21 final size:22
Alignment explanation
Indices: 40611--40654 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
40601 ATTAGAAATT
40611 GCTACCCCTAGAAAAAATTGTTG
1 GCTACCCCTAGAAAAAATT-TTG
40634 GCTACCCC-A-AAAAAATTTTG
1 GCTACCCCTAGAAAAAATTTTG
40654 G
1 G
40655 TTAAGAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 1 0.05
23 8 0.38
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (22 bp):
GCTACCCCTAGAAAAAATTTTG
Found at i:43626 original size:631 final size:632
Alignment explanation
Indices: 42415--43683 Score: 2380
Period size: 631 Copynumber: 2.0 Consensus size: 632
42405 GCAGCGAGCT
*
42415 GGAGATACAAGATGGGGATCTCATTTTCATTTTATTTGCAGCCTACTAAGGTGGTATGGACCAAC
1 GGAGATACAAGATGGGGATCTCACTTTCATTTTATTTGCAGCCTACTAAGGTGGTATGGACCAAC
42480 AAGAGCTGTTGTTGAGAACATCCTAAAGAAAGGCACATCAGGTGCTCAAAGAGGTGAAGCTCACG
66 AAGAGCTGTTGTTGAGAACATCCTAAAGAAAGGCACATCAGGTGCTCAAAGAGGTGAAGCTCACG
42545 GCATTCTTACTATATTAAATTCCTTCAATTTTGTCTTTATCTTGCATGCTATGGAAAAGATGATG
131 GCATTCTTACTATATTAAATTCCTTCAA---T-TC--T-TCTTGCATGCTATGGAAAAGATGATG
*
42610 GGAATCACTGATATTCTTTGCCACGCTTTACAAAAAAATCTCAAGATATTGTAAATGTTGTGCAT
189 GGAATCACTGATATTCTTTGCCAAGCTTTACAAAAAAATCTCAAGATATTGTAAATGTTGTGCAT
42675 CTTGTCTCTACAACCAAATCACTTATTCAAAAATTAAGGGAGGAAGGATGGGATTCATTAATTGA
254 CTTGTCTCTACAACCAAATCACTTATTCAAAAATTAAGGGAGGAAGGATGGGATTCATTAATTGA
42740 AAGTGTAGAAGCATTTTGTGTCAAATATGAAATCAGTTTTCCTGATATGAATGCTCCCTACTTTG
319 AAGTGTAGAAGCATTTTGTGTCAAATATGAAATCAGTTTTCCTGATATGAATGCTCCCTACTTTG
*
42805 TTGGTCGAGGTCGATCCCGAAAGGAGCAAAAGGATTTGACGTTGGAGAATTTTTATAGGAATGAC
384 TTGGTCGAGGTCGATCACGAAAGGAGCAAAAGGATTTGACGTTGGAGAATTTTTATAGGAATGAC
42870 ATATTTTTAACTGCAATAGATTATCAGTTGAAAGAGTTAAACAATAGATTCAATGAGCATGTATT
449 ATATTTTTAACTGCAATAGATTATCAGTTGAAAGAGTTAAACAATAGATTCAATGAGCATGTATT
*
42935 GGAGATTCTTGTTCTTAGCTCTTGTTTAAGTCCTAGAGATGGTTTCATACCATTCAAGATTGATG
514 GGAGATTCTTGTTCTTAACTCTTGTTTAAGTCCTAGAGATGGTTTCATACCATTCAAGATTGATG
43000 ACATATGTTACTTGGTTGAGAAATTTTATCATGCTGATTTTACTGTGCAAGAGG
579 ACATATGTTACTTGGTTGAGAAATTTTATCATGCTGATTTTACTGTGCAAGAGG
*
43054 GGAGATACAAGATGGGGATCTCACTTTCATTTTATTTGCAGCCTGCTAAGGTGGTATGGACCAAC
1 GGAGATACAAGATGGGGATCTCACTTTCATTTTATTTGCAGCCTACTAAGGTGGTATGGACCAAC
*
43119 AAGAGCTGTTGTTGAGAACATCCTAAAGAAAGGCACATCAGGTGCTCAAAGAGGTGAAGCTCATG
66 AAGAGCTGTTGTTGAGAACATCCTAAAGAAAGGCACATCAGGTGCTCAAAGAGGTGAAGCTCACG
43184 GCATTCTTACTATATTAAATTCCTTCAA-TC-TCTTGCATGCTATGGAAAAGATGATGGGAATCA
131 GCATTCTTACTATATTAAATTCCTTCAATTCTTCTTGCATGCTATGGAAAAGATGATGGGAATCA
43247 CTGATATTCTTTGCCAAGCTTTACAAAAAAAATCTCAAGATATTGTAAATGTTGTGCATCTTGTC
196 CTGATATTCTTTGCCAAGCTTTAC-AAAAAAATCTCAAGATATTGTAAATGTTGTGCATCTTGTC
43312 TCTACAACCAAATCACTTATTCAAAAATTAAGGGAGGAAGGATGGGATTCATTAATTGAAAGTGT
260 TCTACAACCAAATCACTTATTCAAAAATTAAGGGAGGAAGGATGGGATTCATTAATTGAAAGTGT
43377 AGAAGCATTTTGTGTCAAATATGAAATCAGTTTTCCTGATATGAATGCTCCCTACTTTGTTGGTC
325 AGAAGCATTTTGTGTCAAATATGAAATCAGTTTTCCTGATATGAATGCTCCCTACTTTGTTGGTC
*
43442 GAGGTCGATCACGAAAGGAGCAAAAGGATTTGACGTTGGAGCATTTTTATAGGAATGACATATTT
390 GAGGTCGATCACGAAAGGAGCAAAAGGATTTGACGTTGGAGAATTTTTATAGGAATGACATATTT
43507 TTAACTGCAATAGATTATCAGTTGAAAGAGTTAAACAATAGATTCAATGAGCATGTATTGGAGAT
455 TTAACTGCAATAGATTATCAGTTGAAAGAGTTAAACAATAGATTCAATGAGCATGTATTGGAGAT
43572 TCTTGTTCTTAACTCTTGTTTAAGTCCTAGAGATGGTTTCATACCATTCAAGATTGATGACATAT
520 TCTTGTTCTTAACTCTTGTTTAAGTCCTAGAGATGGTTTCATACCATTCAAGATTGATGACATAT
*
43637 GTTACTTGGTTGAGAAATTTTATCATGCTGGTTTTACTGTGCAAGAG
585 GTTACTTGGTTGAGAAATTTTATCATGCTGATTTTACTGTGCAAGAG
43684 CGAATTCATT
Statistics
Matches: 621, Mismatches: 8, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
630 56 0.09
631 408 0.66
634 2 0.00
639 155 0.25
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (632 bp):
GGAGATACAAGATGGGGATCTCACTTTCATTTTATTTGCAGCCTACTAAGGTGGTATGGACCAAC
AAGAGCTGTTGTTGAGAACATCCTAAAGAAAGGCACATCAGGTGCTCAAAGAGGTGAAGCTCACG
GCATTCTTACTATATTAAATTCCTTCAATTCTTCTTGCATGCTATGGAAAAGATGATGGGAATCA
CTGATATTCTTTGCCAAGCTTTACAAAAAAATCTCAAGATATTGTAAATGTTGTGCATCTTGTCT
CTACAACCAAATCACTTATTCAAAAATTAAGGGAGGAAGGATGGGATTCATTAATTGAAAGTGTA
GAAGCATTTTGTGTCAAATATGAAATCAGTTTTCCTGATATGAATGCTCCCTACTTTGTTGGTCG
AGGTCGATCACGAAAGGAGCAAAAGGATTTGACGTTGGAGAATTTTTATAGGAATGACATATTTT
TAACTGCAATAGATTATCAGTTGAAAGAGTTAAACAATAGATTCAATGAGCATGTATTGGAGATT
CTTGTTCTTAACTCTTGTTTAAGTCCTAGAGATGGTTTCATACCATTCAAGATTGATGACATATG
TTACTTGGTTGAGAAATTTTATCATGCTGATTTTACTGTGCAAGAGG
Found at i:44549 original size:30 final size:29
Alignment explanation
Indices: 44487--44556 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
44477 ACCGAACCGT
****
44487 CAAATAAGCCCCTGAACTTTAATTTTGGC
1 CAAATAAGCCCCTGAACTTTAAAAAAGGC
*
44516 CAAATAAGCCCCTGAAGTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACT-TTAAAAAAGGC
44546 CAAATAAGCCC
1 CAAATAAGCCC
44557 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAAAGGC
Found at i:48008 original size:7 final size:7
Alignment explanation
Indices: 47996--48020 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47986 TTATTTTCTT
47996 TCAAATC
1 TCAAATC
48003 TCAAATC
1 TCAAATC
48010 TCAAATC
1 TCAAATC
48017 TCAA
1 TCAA
48021 TCCAAAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
TCAAATC
Found at i:48775 original size:19 final size:20
Alignment explanation
Indices: 48741--48784 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
48731 ACTACCTTTC
48741 TAACTAACCATTTACAATAT
1 TAACTAACCATTTACAATAT
* *
48761 TAACTAGCC-TTTACAATTT
1 TAACTAACCATTTACAATAT
48780 TAACT
1 TAACT
48785 GATATACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (20 bp):
TAACTAACCATTTACAATAT
Found at i:53604 original size:19 final size:20
Alignment explanation
Indices: 53570--53611 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
53560 ACTACCTTTC
53570 TAACTAACCATTTACAATAT
1 TAACTAACCATTTACAATAT
* *
53590 TAACTAGCC-TTTACAATTT
1 TAACTAACCATTTACAATAT
53609 TAA
1 TAA
53612 TTGATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (20 bp):
TAACTAACCATTTACAATAT
Found at i:57208 original size:3 final size:3
Alignment explanation
Indices: 57200--57250 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
57190 CTATTGATTT
57200 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
57248 TGA
1 TGA
57251 GAAGAAGCGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:59657 original size:3 final size:3
Alignment explanation
Indices: 59643--59690 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
59633 CGGATGATAT
* * *
59643 TAA TAT TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59691 AAAGCATGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:71747 original size:25 final size:24
Alignment explanation
Indices: 71700--71751 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
71690 ATTTCATATA
71700 AAATTTAAATATTTTAATAATGTCT
1 AAATTTAAATATTTTAATAATGT-T
71725 AAATTATAAATA-TTT-ATATATGTT
1 AAATT-TAAATATTTTAATA-ATGTT
71749 AAA
1 AAA
71752 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTTAAATATTTTAATAATGTT
Found at i:71920 original size:21 final size:21
Alignment explanation
Indices: 71894--71942 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
71884 CGCTGATTAC
* *
71894 AATCTCATTTGTACAGTATCT
1 AATCTCATATGTACAGTAACT
71915 AATCTCATATGTACAGTAACT
1 AATCTCATATGTACAGTAACT
71936 AATCTCA
1 AATCTCA
71943 CCATCTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (21 bp):
AATCTCATATGTACAGTAACT
Found at i:72361 original size:18 final size:19
Alignment explanation
Indices: 72322--72361 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
72312 GTGCTCCCGT
72322 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
72343 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
72361 T
1 T
72362 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:80251 original size:68 final size:68
Alignment explanation
Indices: 80142--80277 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
80132 GCATTTAAAA
80142 TCATCAAAAGATGCAACCTTGCGAAACACCAGGCATTTAAAATCATCAAAAGCCTGGAGAGTTCA
1 TCATCAAAAGATGCAACCTTGCGAAACACCAGGCATTTAAAATCATCAAAAGCCTGGAGAGTTCA
80207 CTT
66 CTT
*
80210 TCATCAAAAGATGCAACCTTGCGAAACACCGGGCATTTAAAATCATCAAAAGCCTGGAGAGTTCA
1 TCATCAAAAGATGCAACCTTGCGAAACACCAGGCATTTAAAATCATCAAAAGCCTGGAGAGTTCA
80275 CTT
66 CTT
80278 CTTGTTCTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (68 bp):
TCATCAAAAGATGCAACCTTGCGAAACACCAGGCATTTAAAATCATCAAAAGCCTGGAGAGTTCA
CTT
Done.