Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018995.1 Corchorus olitorius cultivar O-4 contig19028, 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: 38096
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1881 original size:4 final size:4
Alignment explanation
Indices: 1872--1897 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1862 TCATGAATAA
1872 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1898 GGCTTTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:13950 original size:19 final size:19
Alignment explanation
Indices: 13910--13946 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13900 AATTTTTAAG
13910 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
13929 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
13947 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:14807 original size:132 final size:132
Alignment explanation
Indices: 14638--14892 Score: 365
Period size: 132 Copynumber: 1.9 Consensus size: 132
14628 TCATTTATCC
* * *
14638 AAATTTTAATATATCTAAGATTTTTAATTAAATTAGTAAAATGATAAAAA-TAAATTAAG-TATA
1 AAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAAATGATAAAAATTAAATT--GTTATA
* * *
14701 AGGATATAAGATTTAATTAAATAAAAAAATAGAG-TTTTTAGTTGAGTAAAACTATAAAAGTATA
64 AAGATATAAGATTTAAGTAAAT--AAAAATAGAGTTTTTTAGTTGAATAAAACTATAAAAGTATA
14765 TTTAAA
127 TTTAAA
*
14771 AAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATTGTTATAAA
1 AAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAAATGATAAAAATTAAATTGTTATAAA
* *
14835 GATATTAGATTTAAGTAAATAAAAATAGAGTTTTTTAGTTGAATAAAATTATAAAAGT
66 GATATAAGATTTAAGTAAATAAAAATAGAGTTTTTTAGTTGAATAAAACTATAAAAGT
14893 TTAAACAATG
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
130 10 0.09
131 26 0.24
132 51 0.46
133 23 0.21
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (132 bp):
AAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAAATGATAAAAATTAAATTGTTATAAA
GATATAAGATTTAAGTAAATAAAAATAGAGTTTTTTAGTTGAATAAAACTATAAAAGTATATTTA
AA
Found at i:16820 original size:21 final size:20
Alignment explanation
Indices: 16774--16821 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16764 ATTCAAAATA
**
16774 AAATAAAAACTACCCATTTT
1 AAATAAAAACTACCCATTAG
*
16794 AAATAAAAACTACCCGTTAG
1 AAATAAAAACTACCCATTAG
16814 AAGATAAA
1 AA-ATAAA
16822 TATAATACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (20 bp):
AAATAAAAACTACCCATTAG
Found at i:20748 original size:36 final size:35
Alignment explanation
Indices: 20706--20783 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
20696 TTAAAACTGG
*
20706 AAAAATTCATGACCACCGGCAAAAATTCTCTAAACT
1 AAAAATT-ATGACCACCAGCAAAAATTCTCTAAACT
* ***
20742 AAAAATTTTGATTTCCAGCAAAAATTCTCTAAACT
1 AAAAATTATGACCACCAGCAAAAATTCTCTAAACT
20777 AAAAATT
1 AAAAATT
20784 TTGATTTCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 30 0.81
36 7 0.19
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.28
Consensus pattern (35 bp):
AAAAATTATGACCACCAGCAAAAATTCTCTAAACT
Found at i:20765 original size:35 final size:35
Alignment explanation
Indices: 20724--20794 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
20714 ATGACCACCG
20724 GCAAAAATTCTCTAAACTAAAAATTTTGATTTCCA
1 GCAAAAATTCTCTAAACTAAAAATTTTGATTTCCA
20759 GCAAAAATTCTCTAAACTAAAAATTTTGATTTCCA
1 GCAAAAATTCTCTAAACTAAAAATTTTGATTTCCA
20794 G
1 G
20795 AATCTAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (35 bp):
GCAAAAATTCTCTAAACTAAAAATTTTGATTTCCA
Found at i:22433 original size:20 final size:21
Alignment explanation
Indices: 22389--22435 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
22379 AAGAAAAGAA
*
22389 TAAAAAATAAAAAAATTAGAG
1 TAAAAAATAAAAAAATCAGAG
*
22410 -AAAAAATAATAAAATCA-AG
1 TAAAAAATAAAAAAATCAGAG
22429 TAAAAAA
1 TAAAAAA
22436 AGTAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (21 bp):
TAAAAAATAAAAAAATCAGAG
Found at i:33648 original size:7 final size:7
Alignment explanation
Indices: 33636--33660 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33626 TCACTACTAC
33636 TTGAATA
1 TTGAATA
33643 TTGAATA
1 TTGAATA
33650 TTGAATA
1 TTGAATA
33657 TTGA
1 TTGA
33661 TACTACTTTA
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
TTGAATA
Found at i:35058 original size:2 final size:2
Alignment explanation
Indices: 35051--35135 Score: 68
Period size: 2 Copynumber: 48.5 Consensus size: 2
35041 CCGTTTAGTA
*
35051 AT AT AT AT A- AT -T AA AT AT AT AT -T AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35088 AT -T AG AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35124 AT A- AT AT AT AT A
1 AT AT AT AT AT AT A
35136 ATTATTAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
1 12 0.18
2 55 0.82
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:35070 original size:12 final size:13
Alignment explanation
Indices: 35049--35139 Score: 102
Period size: 12 Copynumber: 7.2 Consensus size: 13
35039 GACCGTTTAG
35049 TAATATATATAAT
1 TAATATATATAAT
35062 TAA-ATATAT-AT
1 TAATATATATAAT
35073 TATATATATAATAAT
1 TA-ATATAT-ATAAT
* *
35088 ATTAGATATATAAT
1 -TAATATATATAAT
35102 T-ATATATATAA-
1 TAATATATATAAT
35113 TAATATATATAA-
1 TAATATATATAAT
35125 TAATATATATAAT
1 TAATATATATAAT
35138 TA
1 TA
35140 TTAAACAGCC
Statistics
Matches: 68, Mismatches: 3, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
11 5 0.07
12 38 0.56
13 10 0.15
14 7 0.10
15 7 0.10
16 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (13 bp):
TAATATATATAAT
Found at i:35839 original size:57 final size:56
Alignment explanation
Indices: 35769--35956 Score: 243
Period size: 57 Copynumber: 3.3 Consensus size: 56
35759 TTTAAATACT
* * * *
35769 CCAAAATTTGGGGTTTGACCATATATATATAATAAAATGTTTTTTGTGGTTTCACTA
1 CCAAACTTTGGGGTTTGACCATACATATACAAT-AAATGTTTTTTGTGGTTTGACTA
* *
35826 CCAAACTTTGGGGTTTGACCATACATGTACAAT-GATGTTTTTTGTGGTTTGACTA
1 CCAAACTTTGGGGTTTGACCATACATATACAATAAATGTTTTTTGTGGTTTGACTA
* * *
35881 TCAAACTTTGGGGTTTGACCATGCATATACAATGAAATGTTTTTTGTGGTTTGACCA
1 CCAAACTTTGGGGTTTGACCATACATATACAAT-AAATGTTTTTTGTGGTTTGACTA
* * *
35938 TCGAATTTTGGGGTTTGAC
1 CCAAACTTTGGGGTTTGAC
35957 AATCATCATT
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
55 50 0.43
57 66 0.57
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (56 bp):
CCAAACTTTGGGGTTTGACCATACATATACAATAAATGTTTTTTGTGGTTTGACTA
Found at i:35887 original size:55 final size:55
Alignment explanation
Indices: 35770--36076 Score: 240
Period size: 57 Copynumber: 5.2 Consensus size: 55
35760 TTAAATACTC
* * * * * * *
35770 CAAAATTTGGGGTTTGACCATATATATATAATAAAATGTTTTTTGTGGTTTCACTAC
1 CAAACTTTGGGGTTTGACCATACATGTACAAT--GATGTTTTTTGTGGTTTGACTAT
35827 CAAACTTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGTGGTTTGACTAT
1 CAAACTTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGTGGTTTGACTAT
* * *
35882 CAAACTTTGGGGTTTGACCATGCATATACAATGAAATGTTTTTTGTGGTTTGACCAT
1 CAAACTTTGGGGTTTGACCATACATGTACAATG--ATGTTTTTTGTGGTTTGACTAT
* * * *
35939 CGAATTTTGGGGTTTGACAATCATCATTTGGGGTTTGACCATGTATGTACAATGATGTTTTGTGG
1 CAAACTTTGGGGTTTGACCAT-A-CA--T---G--T-ACAATG-ATG-----T--T-TTTTGTGG
36004 TTTGACTAGT
47 TTTGACTA-T
* *
36014 -GAACTTT-GGGTTTAACCATACATGTACAATGATGTTTTTTGTGGTTTGACTAT
1 CAAACTTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGTGGTTTGACTAT
36067 CAAACTTTGG
1 CAAACTTTGG
36077 TATTTAACCA
Statistics
Matches: 204, Mismatches: 23, Indels: 48
0.74 0.08 0.17
Matches are distributed among these distances:
53 1 0.00
54 22 0.11
55 53 0.26
57 68 0.33
59 2 0.01
61 1 0.00
62 3 0.01
63 5 0.02
64 1 0.00
66 5 0.02
67 5 0.02
69 1 0.00
71 3 0.01
72 1 0.00
73 11 0.05
74 21 0.10
75 1 0.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (55 bp):
CAAACTTTGGGGTTTGACCATACATGTACAATGATGTTTTTTGTGGTTTGACTAT
Found at i:35952 original size:21 final size:19
Alignment explanation
Indices: 35922--35980 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
35912 ATGAAATGTT
*
35922 TTTTGTGGTTTGACCATCGAA
1 TTTTGGGGTTTGACCATC--A
*
35943 TTTTGGGGTTTGACAATCA
1 TTTTGGGGTTTGACCATCA
35962 TCATTTGGGGTTTGACCAT
1 T--TTTGGGGTTTGACCAT
35981 GTATGTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.06
21 31 0.94
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (19 bp):
TTTTGGGGTTTGACCATCA
Found at i:36042 original size:52 final size:53
Alignment explanation
Indices: 35943--36087 Score: 152
Period size: 54 Copynumber: 2.7 Consensus size: 53
35933 GACCATCGAA
* * * * **
35943 TTTTGGGGTTTGACAATC-ATCATTTGGGGTTTGACCATGTATGTACAATGATG-
1 TTTTGTGGTTTGACTATCAAAC-TTT-GGGTTTAACCATACATGTACAATGATGT
*
35996 TTTTGTGGTTTGACTAGT-GAACTTTGGGTTTAACCATACATGTACAATGATGTT
1 TTTTGTGGTTTGACTA-TCAAACTTTGGGTTTAACCATACATGTACAATGATG-T
*
36050 TTTTGTGGTTTGACTATCAAACTTTGGTATTTAACCAT
1 TTTTGTGGTTTGACTATCAAACTTTGG-GTTTAACCAT
36088 CATCCTTTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
52 24 0.31
53 18 0.23
54 27 0.35
55 9 0.12
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (53 bp):
TTTTGTGGTTTGACTATCAAACTTTGGGTTTAACCATACATGTACAATGATGT
Found at i:36181 original size:53 final size:55
Alignment explanation
Indices: 36100--36273 Score: 181
Period size: 55 Copynumber: 3.2 Consensus size: 55
36090 TCCTTTAAAC
* * *
36100 TTTGACCATACATGTATAATAATATTTTTT-T-GTTTCACTACCAAACTTTGGAG
1 TTTGACCATGCATGTACAATGATATTTTTTGTGGTTTCACTACCAAACTTTGGAG
* * * * * *
36153 TTTGACCATGCATGTACAATGGTTTTTTTTGTGGTTTGATTATCAAACTTTGGGG
1 TTTGACCATGCATGTACAATGATATTTTTTGTGGTTTCACTACCAAACTTTGGAG
* * * * * *
36208 TTTGACCATGCATATACAATGAAATGCTTTTTGTGGTTTGACTATCGAACTTTGGGG
1 TTTGACCATGCATGTACAATGATAT--TTTTTGTGGTTTCACTACCAAACTTTGGAG
36265 TTTGACCAT
1 TTTGACCAT
36274 CATTATTTGG
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
53 25 0.25
54 1 0.01
55 39 0.38
57 37 0.36
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (55 bp):
TTTGACCATGCATGTACAATGATATTTTTTGTGGTTTCACTACCAAACTTTGGAG
Found at i:36214 original size:55 final size:56
Alignment explanation
Indices: 36131--36273 Score: 189
Period size: 55 Copynumber: 2.6 Consensus size: 56
36121 ATATTTTTTT
* * * * * **
36131 GTTTCACTACCAAACTTTGGAGTTTGACCATGCATGTACAATG-GTTTTTTTTGTG
1 GTTTGACTATCAAACTTTGGGGTTTGACCATGCATATACAATGAATGCTTTTTGTG
*
36186 GTTTGATTATCAAACTTTGGGGTTTGACCATGCATATACAATGAAATGCTTTTTGTG
1 GTTTGACTATCAAACTTTGGGGTTTGACCATGCATATACAATG-AATGCTTTTTGTG
*
36243 GTTTGACTATCGAACTTTGGGGTTTGACCAT
1 GTTTGACTATCAAACTTTGGGGTTTGACCAT
36274 CATTATTTGG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
55 38 0.50
57 38 0.50
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (56 bp):
GTTTGACTATCAAACTTTGGGGTTTGACCATGCATATACAATGAATGCTTTTTGTG
Found at i:36216 original size:129 final size:128
Alignment explanation
Indices: 35839--36216 Score: 432
Period size: 128 Copynumber: 2.9 Consensus size: 128
35829 AACTTTGGGG
*
35839 TTTGACCATACATGTACAATGATGTTTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATG
1 TTTGACCATACATGTACAATGATGTTTTTT-T-GTTTGACTACCAAACTTT-GGGTTTGACCATG
* * * * * *
35904 CATATACAATGAAATGTTTTTTGTGGTTTGACCATCGAATTTTGGGGTTTGACAATCATCATTTG
63 CATGTACAATG--ATGTTTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATCATCATTTA
***
35969 GGG
126 AAC
** * * *** * *
35972 TTTGACCATGTATGTACAATGATGTTTTGTGGTTTGACTAGTGAACTTTGGGTTTAACCATACAT
1 TTTGACCATACATGTACAATGATGTTTTTTTGTTTGACTACCAAACTTTGGGTTTGACCATGCAT
** * *
36037 GTACAATGATGTTTTTTGTGGTTTGACTATCAAACTTTGGTATTTAACCATCATCCTTTAAAC
66 GTACAATGATGTTTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATCATCATTTAAAC
* * * *
36100 TTTGACCATACATGTATAATAATATTTTTTTGTTTCACTACCAAACTTTGGAGTTTGACCATGCA
1 TTTGACCATACATGTACAATGATGTTTTTTTGTTTGACTACCAAACTTTGG-GTTTGACCATGCA
* * *
36165 TGTACAATGGTTTTTTTTGTGGTTTGATTATCAAACTTTGGGGTTTGACCAT
65 TGTACAATGATGTTTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCAT
36217 GCATATACAA
Statistics
Matches: 203, Mismatches: 41, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
128 83 0.41
129 57 0.28
130 21 0.10
131 15 0.07
133 27 0.13
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (128 bp):
TTTGACCATACATGTACAATGATGTTTTTTTGTTTGACTACCAAACTTTGGGTTTGACCATGCAT
GTACAATGATGTTTTTTGTGGTTTGACTATCAAACTTTGGGGTTTGACCATCATCATTTAAAC
Found at i:36266 original size:21 final size:20
Alignment explanation
Indices: 36258--36315 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 20
36248 ACTATCGAAC
36258 TTTGGGGTTTGACCATCATTA
1 TTTGGGGTTTGACCATCA-TA
36279 TTTGGGGTTTGACCATCATCA
1 TTTGGGGTTTGACCATCAT-A
*
36300 TATGGGGTTTGACCAT
1 TTTGGGGTTTGACCAT
36316 GCATGTACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (20 bp):
TTTGGGGTTTGACCATCATA
Found at i:36367 original size:95 final size:97
Alignment explanation
Indices: 36203--36389 Score: 297
Period size: 95 Copynumber: 1.9 Consensus size: 97
36193 TATCAAACTT
*
36203 TGGGGTTTGACCATGCATATACAATGAAATGCTTTTTGTGGTTTGACTATCGAACTTTGGGGTTT
1 TGGGGTTTGACCATGCATATACAATG-AATGC-TTTTGTGGTTTGACTATCGAACTTTGGGGTTC
* *
36268 GACCATCATTATTTGGGGTTTGACCATCATCATA
64 GACCATCATCAATTGGGGTTTGACCATCATCATA
* *
36302 TGGGGTTTGACCATGCATGTACAATG-ATG-TTTTGTGGTTTGACTATTGAACTTTGGGGTTCGA
1 TGGGGTTTGACCATGCATATACAATGAATGCTTTTGTGGTTTGACTATCGAACTTTGGGGTTCGA
36365 CCATCATCAATTGGGGTTTGACCAT
66 CCATCATCAATTGGGGTTTGACCAT
36390 ATATGTACAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
95 55 0.66
97 3 0.04
99 25 0.30
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (97 bp):
TGGGGTTTGACCATGCATATACAATGAATGCTTTTGTGGTTTGACTATCGAACTTTGGGGTTCGA
CCATCATCAATTGGGGTTTGACCATCATCATA
Found at i:36758 original size:22 final size:23
Alignment explanation
Indices: 36714--36760 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
36704 TTGGCAAAAT
*
36714 GAACCCGAAACTCGCCCGAACCC
1 GAACCCGAAACCCGCCCGAACCC
*
36737 GAACCCG-AACCCGCCCGGACCC
1 GAACCCGAAACCCGCCCGAACCC
36759 GA
1 GA
36761 GTTGACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.28, C:0.49, G:0.21, T:0.02
Consensus pattern (23 bp):
GAACCCGAAACCCGCCCGAACCC
Found at i:36793 original size:6 final size:6
Alignment explanation
Indices: 36782--36848 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 6
36772 AAGTCAACGT
**
36782 CCCGAA CCCGAA CCCGAA AAC--A CCCGAA CCCGAGGCA GCCCGAA CCCGAA
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGA---A -CCCGAA CCCGAA
36832 CCCG-A CCCGAA CCCGAA
1 CCCGAA CCCGAA CCCGAA
36849 ATAATTTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 5 0.10
6 36 0.72
7 1 0.02
9 1 0.02
10 5 0.10
ACGTcount: A:0.33, C:0.48, G:0.19, T:0.00
Consensus pattern (6 bp):
CCCGAA
Found at i:36808 original size:16 final size:16
Alignment explanation
Indices: 36787--36849 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
36777 AACGTCCCGA
36787 ACCCGAACCCGAAAAC
1 ACCCGAACCCGAAAAC
**
36803 ACCCGAACCCG-AGGC
1 ACCCGAACCCGAAAAC
**
36818 AGCCCGAACCCGAACCC
1 A-CCCGAACCCGAAAAC
36835 GACCCGAACCCGAAA
1 -ACCCGAACCCGAAA
36850 TAATTTGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.08
16 21 0.54
17 14 0.36
18 1 0.03
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (16 bp):
ACCCGAACCCGAAAAC
Found at i:37122 original size:34 final size:35
Alignment explanation
Indices: 37073--37148 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
37063 CTAAAAAGTC
* *
37073 TAAACAAATAAAGAGTCTA-GAAAGAGGTTTACTAA
1 TAAA-AAACAAAGAGTCTACAAAAGAGGTTTACTAA
37108 TAAAAAACAAAGAGTCTACAAAAGAGGTTTACTAA
1 TAAAAAACAAAGAGTCTACAAAAGAGGTTTACTAA
37143 TAAAAA
1 TAAAAA
37149 CAATTACATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 13 0.34
35 25 0.66
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.21
Consensus pattern (35 bp):
TAAAAAACAAAGAGTCTACAAAAGAGGTTTACTAA
Done.