Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022005.1 Corchorus olitorius cultivar O-4 contig22038, 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: 54597
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2057 original size:38 final size:38
Alignment explanation
Indices: 2006--2108 Score: 172
Period size: 37 Copynumber: 2.7 Consensus size: 38
1996 GATCCTCCGA
*
2006 GTCATCTTTCAGCAGTTATCAAGATCGACTGGAAACAG
1 GTCATCTTTCAGCAGTTATCAAGATCGACTAGAAACAG
*
2044 GTCATCTTTCAGCAGTTATCAAG-TTGACTAGAAACAG
1 GTCATCTTTCAGCAGTTATCAAGATCGACTAGAAACAG
*
2081 ATCATCTTTCAGCAGTTATCAAGATCGA
1 GTCATCTTTCAGCAGTTATCAAGATCGA
2109 TCTCAGAGCA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
37 34 0.57
38 26 0.43
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (38 bp):
GTCATCTTTCAGCAGTTATCAAGATCGACTAGAAACAG
Found at i:3902 original size:15 final size:16
Alignment explanation
Indices: 3880--3919 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
3870 AGAGATTGAC
3880 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
*
3895 ATAAAACAATTAAACT
1 AGAAAACAATTAAACT
3911 AGAAAACAA
1 AGAAAACAA
3920 AGCAGAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.68, C:0.12, G:0.05, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8230 original size:47 final size:47
Alignment explanation
Indices: 8179--9263 Score: 1296
Period size: 47 Copynumber: 22.8 Consensus size: 47
8169 AAACAAAGGA
* * * * *
8179 TAGTTTAATTCCAGGTAATTACACTAAATAGCAAAAGAAGAAGAGGT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* * * *
8226 TAGTTTAATTCTGGGTAATTAAACTAAATAGTGAAAGAAGAAGAGGT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* * * *
8273 TAGTTTAATTCTGGGCAATTAAACTAAAGATTAAATAGCAAAAGAAGAAGAGGT
1 TAGTTTAATTCTAGGTAATTAAACT-AAG------TAGTAAAAGAAGAAGAGAT
* *
8327 TAGTCTAATTC-AGAGCAATTAAACTAAAGAGTAAAAGAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAG-GTAATTAAAC-------T-----AAGTAGTAAAAGAAGAAGAGAT
* * *
8386 TAGTTTAATTCCAGGTAATTAAGCTAAGTAGTAGAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
*
8433 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTGAAAGAA-AAGGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAA-GAGAT
*
8480 TAGTTTAATTCTAGGTAATTAAAATAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
8527 TAGTTTAA--CTA-G-AATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
*
8570 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGGT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* * * *
8617 TAGTTTAGTTCTGGGTAATTAAACTAAATAATAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* *
8664 TAGTTTAGTTCTAGGTAATTAAACTAAGTAGTGAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* *
8711 TAGTTTAATTCTAGGTAATTAAAATAAGTATTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
8758 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
8805 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
8852 TAGTTTAATTCTAGGTAATTAAACTAAGTAGT-AAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
8898 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* **
8945 TAGTTTAATTCTAGGTAATTAAACTAAGTA-TTAAACTAGAAGAGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* *
8991 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAGAAGAAGATAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
*
9038 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAGAAGGAA-AGAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAA-GAAGAGAT
*
9085 TAGTTTAATTCTAGGTAATTAAGC----T-G---AAGAAG-AG-G-T
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
* * * * * *
9121 TAGTTTAATTCTAGGAAATTAAACTAGGTAGCAAATGAAGAACAAACAAT
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAG-A-AGA-GAT
*
9171 TAGTTCAATTCT-GAGTAATTAAACTAAAG-AGTAAAAGAAGAAGTAAACAGTAAT
1 TAGTTTAATTCTAG-GTAATTAAACT-AAGTAGTAAAAGAAGAAG-----AG--AT
* * *
9225 TAGTTTAATTCTGGGTAGTTAAACTAAATAGTAAAAGAA
1 TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAA
9264 AGAGTAAACA
Statistics
Matches: 917, Mismatches: 66, Indels: 103
0.84 0.06 0.09
Matches are distributed among these distances:
36 23 0.03
37 2 0.00
38 1 0.00
39 5 0.01
40 1 0.00
41 1 0.00
42 1 0.00
43 39 0.04
44 6 0.01
45 6 0.01
46 92 0.10
47 580 0.63
48 8 0.01
49 2 0.00
50 31 0.03
51 2 0.00
52 1 0.00
53 4 0.00
54 70 0.08
55 1 0.00
59 35 0.04
60 2 0.00
61 1 0.00
65 3 0.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (47 bp):
TAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
Found at i:9189 original size:86 final size:83
Alignment explanation
Indices: 9027--9192 Score: 201
Period size: 83 Copynumber: 2.0 Consensus size: 83
9017 AGTAGTAGAA
* * * * * *
9027 GAAGAAGATATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAGAAGGAAAGATTAGTTTA
1 GAAGAAGAGATTAGTTTAATTCTAGGAAATTAAACTAAGTAGAAGAAGAAGCAAAAATTAGTTCA
9092 ATTCTAGGTAATTAAGCT
66 ATTCTAGGTAATTAAGCT
* *
9110 GAAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAGGTAGCAAATGAAGAA-CAAACAATTAG
1 GAAGAAGAGATTAGTTTAATTCTAGGAAATTAAACTAAGTAG--AA-GAAGAAGCAAA-AATTAG
9174 TTCAATTCT-GAGTAATTAA
62 TTCAATTCTAG-GTAATTAA
9193 ACTAAAGAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
83 38 0.54
85 5 0.07
86 27 0.39
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (83 bp):
GAAGAAGAGATTAGTTTAATTCTAGGAAATTAAACTAAGTAGAAGAAGAAGCAAAAATTAGTTCA
ATTCTAGGTAATTAAGCT
Found at i:9247 original size:54 final size:54
Alignment explanation
Indices: 9168--9336 Score: 218
Period size: 54 Copynumber: 3.1 Consensus size: 54
9158 AAGAACAAAC
*
9168 AATTAGTTCAATTCTGAGTAATTAAACTAAAGAGTAAAAG-AAGAAGTAAACAGT
1 AATTAGTTTAATTCTGAGTAATTAAACTAAAGAGTAAAAGAAAG-AGTAAACAGT
* * *
9222 AATTAGTTTAATTCTGGGTAGTTAAACTAAATAGTAAAAGAAAGAGTAAACA-T
1 AATTAGTTTAATTCTGAGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAACAGT
* * * *
9275 AATTTAGTTT-AGTCTTGAGTAACTAAACTAAAGAGTAAAAGAAAGAGTGAGCAGT
1 AA-TTAGTTTAATTC-TGAGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAACAGT
9330 AATTAGT
1 AATTAGT
9337 GATTAAGCTA
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
53 6 0.06
54 88 0.88
55 6 0.06
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (54 bp):
AATTAGTTTAATTCTGAGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAACAGT
Found at i:9356 original size:36 final size:36
Alignment explanation
Indices: 9311--9385 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
9301 ACTAAAGAGT
* *
9311 AAAAGAAAGAGTGAGCAGTAATTAGTGATTAAGCTA
1 AAAAGAAAGAGTAAGCAATAATTAGTGATTAAGCTA
*
9347 AAAAGAAAGAGTAAGCAATAATTAGTGATTAGGCTA
1 AAAAGAAAGAGTAAGCAATAATTAGTGATTAAGCTA
9383 AAA
1 AAA
9386 CAAAGTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (36 bp):
AAAAGAAAGAGTAAGCAATAATTAGTGATTAAGCTA
Found at i:13698 original size:13 final size:13
Alignment explanation
Indices: 13682--13884 Score: 79
Period size: 14 Copynumber: 14.3 Consensus size: 13
13672 TTATATGAGA
13682 AAATAATATTTAG
1 AAATAATATTTAG
*
13695 AAATGATATATGTAATG
1 AAAT-A-ATAT-TTA-G
* *
13712 AAATTATAATTAG
1 AAATAATATTTAG
* * *
13725 GAATTATATTTAT
1 AAATAATATTTAG
*
13738 AAATTATATATGTAATG
1 AAA-TA-ATAT-TTA-G
* *
13755 AAATATTATTTTG
1 AAATAATATTTAG
13768 AAAATAATATTTAG
1 -AAATAATATTTAG
*
13782 AAAATATATATGTAATG
1 -AAATA-ATAT-TTA-G
*
13799 AAATTATAATTATA-
1 AAATAAT-ATT-TAG
13813 AAATAATATTTAG
1 AAATAATATTTAG
*
13826 AAATTATAAATGTTTAG
1 -AA--AT-AATATTTAG
*
13843 AAATTATATTTAG
1 AAATAATATTTAG
*
13856 --ATTATATTTAG
1 AAATAATATTTAG
13867 AAAATAATATTTAG
1 -AAATAATATTTAG
13881 AAAT
1 AAAT
13885 TATAAATGTA
Statistics
Matches: 144, Mismatches: 24, Indels: 44
0.68 0.11 0.21
Matches are distributed among these distances:
11 11 0.08
12 2 0.01
13 32 0.22
14 42 0.29
15 21 0.15
16 19 0.13
17 17 0.12
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
AAATAATATTTAG
Found at i:13793 original size:44 final size:44
Alignment explanation
Indices: 13680--13838 Score: 173
Period size: 44 Copynumber: 3.6 Consensus size: 44
13670 AATTATATGA
* *
13680 GAAAATAATATTTAG-AAATGATATATGTAATGAAAT-TATAATTA
1 GAAAATAATATTTAGAAAAT-ATATATGTAATGAAATAT-TATTTT
* * * *
13724 G-GAATTATATTTATAAATTATATATGTAATGAAATATTATTTT
1 GAAAATAATATTTAGAAAATATATATGTAATGAAATATTATTTT
* *
13767 GAAAATAATATTTAGAAAATATATATGTAATGAAATTATAATTAT
1 GAAAATAATATTTAGAAAATATATATGTAATGAAA-TATTATTTT
* *
13812 -AAAATAATATTTAGAAATTATAAATGT
1 GAAAATAATATTTAGAAAATATATATGT
13839 TTAGAAATTA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
43 31 0.32
44 59 0.61
45 7 0.07
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.40
Consensus pattern (44 bp):
GAAAATAATATTTAGAAAATATATATGTAATGAAATATTATTTT
Found at i:13871 original size:55 final size:55
Alignment explanation
Indices: 13801--13910 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
13791 ATGTAATGAA
* * *
13801 ATTATAATTATAAAATAATATTTAGAAATTATAAATGT-TTAGAAATTATATTTAG
1 ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAAT-GAAATTATAATTAG
*
13856 ATTATATTTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
1 ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
13911 GGGCATTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 49 0.98
56 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (55 bp):
ATTATAATTAGAAAATAATATTTAGAAATTATAAATGTAATGAAATTATAATTAG
Found at i:13943 original size:32 final size:32
Alignment explanation
Indices: 13907--13983 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
13897 GAAATTATAA
*
13907 TTAGGGGCATTTTAT-TTAGAAAACGCCACTAT
1 TTAGGGGCATTTTATCCTA-AAAACGCCACTAT
** * * *
13939 TTAGGGGTGTTTTCTCCTATAAACGTCACTAT
1 TTAGGGGCATTTTATCCTAAAAACGCCACTAT
13971 TTAGGGGCATTTT
1 TTAGGGGCATTTT
13984 CTCCAGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (32 bp):
TTAGGGGCATTTTATCCTAAAAACGCCACTAT
Found at i:13984 original size:32 final size:32
Alignment explanation
Indices: 13927--14068 Score: 108
Period size: 32 Copynumber: 4.4 Consensus size: 32
13917 TTTATTTAGA
**
13927 AAACGCCACTATTTAGGGGTGTTTTCTCCTAT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTAT
*
13959 AAACGTCACTATTTAGGGGCATTTTCTCC-AGT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTA-T
* * * * *
13991 AGACGCCGCTATTTAGTGGCGTTTTCTTC-AGT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTA-T
*** * * * *
14023 TGTCGCCGCTATTTAGGGGCGTTTTCTTCAAT
1 AAACGCCACTATTTAGGGGCATTTTCTCCTAT
*
14055 AAACGCCCCTATTT
1 AAACGCCACTATTT
14069 TGCAGCATTT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.01
32 90 0.98
33 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (32 bp):
AAACGCCACTATTTAGGGGCATTTTCTCCTAT
Found at i:14108 original size:21 final size:20
Alignment explanation
Indices: 14075--14124 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
14065 ATTTTGCAGC
14075 ATTTTCTGCATAATTACCAAA
1 ATTTT-TGCATAATTACCAAA
* *
14096 ATTTTTGCAATAATTGCCAGA
1 ATTTTTGC-ATAATTACCAAA
14117 ATTATTTG
1 ATT-TTTG
14125 GGGGCACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.72
22 4 0.16
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
ATTTTTGCATAATTACCAAA
Found at i:35803 original size:29 final size:29
Alignment explanation
Indices: 35742--35804 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
35732 TTTTCTGATT
* * *
35742 TTGTTTAAGTGCGGATTGTACACTTGTGT
1 TTGTTCAAGTGCGGATTGTACACTTGGGA
* **
35771 TTGTTCAAGTGTGGATTGTGTACTTGGGA
1 TTGTTCAAGTGCGGATTGTACACTTGGGA
35800 TTGTT
1 TTGTT
35805 TTGAGTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.08, G:0.30, T:0.46
Consensus pattern (29 bp):
TTGTTCAAGTGCGGATTGTACACTTGGGA
Found at i:38165 original size:2 final size:2
Alignment explanation
Indices: 38153--38183 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
38143 TCAGTAAGTA
38153 AT AT CAT 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
38184 CAAAAGCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42312 original size:28 final size:26
Alignment explanation
Indices: 42267--42319 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
42257 GTTTAAAAAA
*
42267 CAGCTTTTATTTTTTTCTTTTTTTTC
1 CAGCTTTTATTTTTTTCTTATTTTTC
42293 CAGCTTTTATATTTCTTTCTTATTTTT
1 CAGCTTTTAT-TTT-TTTCTTATTTTT
42320 AACTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 11 0.46
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (26 bp):
CAGCTTTTATTTTTTTCTTATTTTTC
Found at i:44238 original size:20 final size:21
Alignment explanation
Indices: 44206--44259 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
44196 ATAAACTTAC
44206 AAGGTTAAC-AAAAAG-TTTAAT
1 AAGGTT-ACTAAAAAGCTTT-AT
*
44227 AA-GTTACTAAAATGCTTTAT
1 AAGGTTACTAAAAAGCTTTAT
44247 AAGGTTACTAAAA
1 AAGGTTACTAAAA
44260 CCCTAACGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 15 0.52
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.31
Consensus pattern (21 bp):
AAGGTTACTAAAAAGCTTTAT
Found at i:44359 original size:21 final size:21
Alignment explanation
Indices: 44326--44370 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
44316 TAAAGTTACT
*
44326 AAAACTTAGTAAGCTTACTAA
1 AAAACTTAGTAAGCTCACTAA
*
44347 AAAACCTTA-TAAGGTCACTAA
1 AAAA-CTTAGTAAGCTCACTAA
44368 AAA
1 AAA
44371 CATATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (21 bp):
AAAACTTAGTAAGCTCACTAA
Found at i:44843 original size:9 final size:9
Alignment explanation
Indices: 44829--44854 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
44819 TTCCCAACAT
44829 AATTGTTTG
1 AATTGTTTG
44838 AATTGTTTG
1 AATTGTTTG
44847 AATTGTTT
1 AATTGTTT
44855 CTCATTCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (9 bp):
AATTGTTTG
Found at i:45345 original size:84 final size:84
Alignment explanation
Indices: 45188--45432 Score: 286
Period size: 84 Copynumber: 2.9 Consensus size: 84
45178 ACCCAATAAC
* * * * *
45188 CAAATTCCCCAAACACATTTATAACACAGGGGCAACTCTTTTTCTAAAGTCCTCAAGTACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAA-TCTCTTCCTAAAGTCCTCAAGCACATTTA
45253 TAACACAGAGGCATCTACAT
65 TAACACAGAGGCATCTACAT
*
45273 CAAAGTCCCCAAACACAATTATAAAACAGGGGCAAT-TCTTCCTAAAAGTCCTCAAGCACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTCCT-AAAGTCCTCAAGCACATTTA
* * *
45337 TAACACAGAGACATTTATAT
65 TAACACAGAGGCATCTACAT
* * *
45357 CAAAGT-CCC--AC-CAATTATAACATAGGGGC-ATCTCTCTCTCTCAAAGTCCCCAAGCACAAT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCT-TC-CT-AAAGTCCTCAAGCACATT
*
45417 TATAACACAGGGGCAT
63 TATAACACAGAGGCAT
45433 TTCTCTCTCT
Statistics
Matches: 140, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
79 2 0.01
80 19 0.14
81 4 0.03
82 32 0.23
83 8 0.06
84 43 0.31
85 32 0.23
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.24
Consensus pattern (84 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTCCTAAAGTCCTCAAGCACATTTAT
AACACAGAGGCATCTACAT
Found at i:45422 original size:45 final size:43
Alignment explanation
Indices: 45188--45471 Score: 219
Period size: 45 Copynumber: 6.7 Consensus size: 43
45178 ACCCAATAAC
* * * *
45188 CAAATTCCCCAAACACATTTATAACACAGGGGCAACTCTT-TTT
1 CAAAGTCCCCAAGCACATTTATAACACAGGGGC-ATTCTTCTCT
* * * * *
45231 CTAAAGTCCTCAAGTACATTTATAACACAGAGGCA-TCTAC-AT
1 C-AAAGTCCCCAAGCACATTTATAACACAGGGGCATTCTTCTCT
* * *
45273 CAAAGTCCCCAAACACAATTATAAAACAGGGGCAATTCTTC-CT
1 CAAAGTCCCCAAGCACATTTATAACACAGGGGC-ATTCTTCTCT
* * * * * *
45316 AAAAGTCCTCAAGCACATTTATAACACAGAGACA-T-TTATAT
1 CAAAGTCCCCAAGCACATTTATAACACAGGGGCATTCTTCTCT
* *
45357 CAAAGT-CCC-A-C-CAATTATAACATAGGGGCATCTCTCTCTCT
1 CAAAGTCCCCAAGCACATTTATAACACAGGGGCAT-TCT-TCTCT
*
45398 CAAAGTCCCCAAGCACAATTATAACACAGGGGCATTTCTCTCTCT
1 CAAAGTCCCCAAGCACATTTATAACACAGGGGCA-TTCT-TCTCT
* * *
45443 CATAGTCCTCAAGCACATTTATGACACAG
1 CAAAGTCCCCAAGCACATTTATAACACAG
45472 AAGCATCTAT
Statistics
Matches: 190, Mismatches: 37, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
37 15 0.08
38 1 0.01
39 2 0.01
40 5 0.03
41 42 0.22
42 10 0.05
43 34 0.18
44 28 0.15
45 52 0.27
46 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (43 bp):
CAAAGTCCCCAAGCACATTTATAACACAGGGGCATTCTTCTCT
Found at i:52619 original size:3 final size:3
Alignment explanation
Indices: 52552--52609 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
52542 TGCTTTTACC
* * *
52552 ATT ATT ACT AAT ATT ATT ATT ATT A-T AAT ATT ATT ACTT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT
*
52598 ATG ATT ATT ATT
1 ATT ATT ATT ATT
52610 GGGATTATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 38 0.83
4 6 0.13
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:53973 original size:2 final size:2
Alignment explanation
Indices: 53960--53993 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
53950 ATCCATTGTC
*
53960 AT AT AA 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
53994 TTGAATGAAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.