Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017652.1 Corchorus olitorius cultivar O-4 contig17685, 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: 98359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:837 original size:55 final size:56
Alignment explanation
Indices: 749--861 Score: 167
Period size: 55 Copynumber: 2.0 Consensus size: 56
739 TATCCGTTTC
*
749 CTTTCACACAATAAATATTAAAATAAATTCTATCCC-ATATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTAAAATAAATCCTATCCCTATATCTCTACTTAATTATT
* * *
804 CTTTCACAC-ATAAAATGTTATAATAAATCCTATCCCTCTATCTCTACTTAATTATT
1 CTTTCACACAAT-AAATATTAAAATAAATCCTATCCCTATATCTCTACTTAATTATT
860 CT
1 CT
862 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 2 0.04
55 30 0.58
56 20 0.38
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATATTAAAATAAATCCTATCCCTATATCTCTACTTAATTATT
Found at i:952 original size:21 final size:21
Alignment explanation
Indices: 928--994 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
918 AAGGATAAAG
928 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
** * *
949 ATTT-A-TAAAGAATTTTCTATG
1 ATTTGAGTTGAGTA-TTTCT-TA
970 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
991 ATTT
1 ATTT
995 ACAGAAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 14 0.41
22 6 0.18
23 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:3282 original size:13 final size:13
Alignment explanation
Indices: 3245--3356 Score: 77
Period size: 13 Copynumber: 8.3 Consensus size: 13
3235 CTGAGACATG
*
3245 TTTGTAA-TTATT
1 TTTGTAAGTAATT
* *
3257 ATTGTATGTAATT
1 TTTGTAAGTAATT
*
3270 TTTATAAGTAATT
1 TTTGTAAGTAATT
*
3283 TTT-TATGTTAATT
1 TTTGTAAG-TAATT
*
3296 ATTAGTGTATGTAATT
1 -TT--TGTAAGTAATT
3312 TTTGTAAGTAATATTT
1 TTTGTAAGT-A-A-TT
3328 TTTGTAAGTAATT
1 TTTGTAAGTAATT
*
3341 TTT-TTAGTAATT
1 TTTGTAAGTAATT
3353 TTTG
1 TTTG
3357 CCGCCCATGG
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
12 19 0.23
13 33 0.41
14 4 0.05
15 4 0.05
16 17 0.21
17 4 0.05
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (13 bp):
TTTGTAAGTAATT
Found at i:3295 original size:42 final size:43
Alignment explanation
Indices: 3249--3329 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
3239 GACATGTTTG
*
3249 TAATTATTATTGTATGTAATTTTTATAAGTAAT-TTTTTATGT
1 TAATTATTAGTGTATGTAATTTTTATAAGTAATATTTTTATGT
*
3291 TAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTT
1 TAATTATTAGTGTATGTAATTTTTATAAGTAATATTTTT
3330 TGTAAGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (43 bp):
TAATTATTAGTGTATGTAATTTTTATAAGTAATATTTTTATGT
Found at i:3329 original size:16 final size:15
Alignment explanation
Indices: 3310--3350 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 15
3300 GTGTATGTAA
3310 TTTTTGTAAGTAATAT
1 TTTTTGTAAGTAAT-T
3326 TTTTTGTAAGTAATT
1 TTTTTGTAAGTAATT
3341 TTTTTAGTAA
1 TTTTT-GTAA
3351 TTTTTGCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTTTGTAAGTAATT
Found at i:3333 original size:29 final size:27
Alignment explanation
Indices: 3268--3355 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 27
3258 TTGTATGTAA
* *
3268 TTTTTATAAGTAATTTTTTATGTTAATT
1 TTTTTGTAAGTAATTTTTTAAG-TAATT
** *
3296 ATTAGTGTATGTAATTTTTGTAAGTAATAT
1 -TTTTTGTAAGTAATTTTT-TAAGTAAT-T
*
3326 TTTTTGTAAGTAATTTTTTTAGTAATT
1 TTTTTGTAAGTAATTTTTTAAGTAATT
3353 TTT
1 TTT
3356 GCCGCCCATG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.08
28 7 0.15
29 33 0.69
30 4 0.08
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.60
Consensus pattern (27 bp):
TTTTTGTAAGTAATTTTTTAAGTAATT
Found at i:26142 original size:15 final size:15
Alignment explanation
Indices: 26122--26152 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26112 GATCATGAAT
*
26122 ACTATGAGATTAACA
1 ACTATGAAATTAACA
26137 ACTATGAAATTAACA
1 ACTATGAAATTAACA
26152 A
1 A
26153 TCTAAGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (15 bp):
ACTATGAAATTAACA
Found at i:31051 original size:10 final size:10
Alignment explanation
Indices: 31037--31121 Score: 125
Period size: 10 Copynumber: 8.5 Consensus size: 10
31027 ATTTAGTATA
*
31037 GATATTTACA
1 GATATTTACG
*
31047 GATATTTACA
1 GATATTTACG
*
31057 GATACTTACG
1 GATATTTACG
31067 GATATTTACG
1 GATATTTACG
*
31077 GATATTTATG
1 GATATTTACG
*
31087 GATACTTACG
1 GATATTTACG
31097 GATATTTACG
1 GATATTTACG
31107 GATATTTACG
1 GATATTTACG
31117 GATAT
1 GATAT
31122 ATCGAGAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 68 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (10 bp):
GATATTTACG
Found at i:31073 original size:30 final size:30
Alignment explanation
Indices: 31037--31120 Score: 141
Period size: 30 Copynumber: 2.8 Consensus size: 30
31027 ATTTAGTATA
* *
31037 GATATTTACAGATATTTACAGATACTTACG
1 GATATTTACGGATATTTACGGATACTTACG
*
31067 GATATTTACGGATATTTATGGATACTTACG
1 GATATTTACGGATATTTACGGATACTTACG
31097 GATATTTACGGATATTTACGGATA
1 GATATTTACGGATATTTACGGATA
31121 TATCGAGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (30 bp):
GATATTTACGGATATTTACGGATACTTACG
Found at i:31161 original size:20 final size:20
Alignment explanation
Indices: 31120--31183 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
31110 ATTTACGGAT
*
31120 ATATCGAGAATATATCGA--G
1 ATATCGATAA-ATATCGACGG
31139 ATATCGATAAATATCGACGG
1 ATATCGATAAATATCGACGG
*
31159 ATACACGGAT--ATATCGACGG
1 ATA-TC-GATAAATATCGACGG
31179 ATATC
1 ATATC
31184 CGGTGACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 17 0.45
21 1 0.03
22 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (20 bp):
ATATCGATAAATATCGACGG
Found at i:32023 original size:30 final size:32
Alignment explanation
Indices: 31989--32057 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
31979 TAAAAATAAA
31989 AAAAAATCATTTTTTCCTTT-TTTTCTGTTT-
1 AAAAAATCATTTTTTCCTTTCTTTTCTGTTTG
* * * *
32019 AAAAAAACATTTTTTCTTTTCTTTTTTTTTTG
1 AAAAAATCATTTTTTCCTTTCTTTTCTGTTTG
32051 AAAAAAT
1 AAAAAAT
32058 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 18 0.56
31 8 0.25
32 6 0.19
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (32 bp):
AAAAAATCATTTTTTCCTTTCTTTTCTGTTTG
Found at i:32786 original size:30 final size:31
Alignment explanation
Indices: 32750--32818 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
32740 GTGCAAATGG
32750 GTCCCTGAAATGAACGT-AGTGAGCAATTGA
1 GTCCCTGAAATGAACGTAAGTGAGCAATTGA
* * * *
32780 GTCCCTGAAGTGAAGGTAATTGAGCAATTGG
1 GTCCCTGAAATGAACGTAAGTGAGCAATTGA
32811 GTCCCTGA
1 GTCCCTGA
32819 CTTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.44
31 19 0.56
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (31 bp):
GTCCCTGAAATGAACGTAAGTGAGCAATTGA
Found at i:32848 original size:12 final size:13
Alignment explanation
Indices: 32823--32855 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
32813 CCCTGACTTT
32823 TTTTTTAAATATA
1 TTTTTTAAATATA
32836 TTTTTTAAA-ATA
1 TTTTTTAAATATA
32848 TTTTTTAA
1 TTTTTTAA
32856 TCAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:35675 original size:2 final size:2
Alignment explanation
Indices: 35670--35696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35660 TAGGATTAAC
35670 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35697 TCTTAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36470 original size:7 final size:7
Alignment explanation
Indices: 36460--36495 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
36450 GAAAATTATC
36460 AACAGAA
1 AACAGAA
36467 AACAGAA
1 AACAGAA
36474 AACAGAA
1 AACAGAA
*
36481 AACGGAA
1 AACAGAA
*
36488 AACGGAA
1 AACAGAA
36495 A
1 A
36496 CGAACTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.67, C:0.14, G:0.19, T:0.00
Consensus pattern (7 bp):
AACAGAA
Found at i:57794 original size:13 final size:13
Alignment explanation
Indices: 57755--57795 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
57745 TTTTCTTTTT
57755 GAAAAAAA-AAAA
1 GAAAAAAAGAAAA
57767 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
* *
57780 GAAAAAGAGAGAA
1 GAAAAAAAGAAAA
57793 GAA
1 GAA
57796 GACAGGCGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:61073 original size:131 final size:132
Alignment explanation
Indices: 60869--61202 Score: 607
Period size: 132 Copynumber: 2.5 Consensus size: 132
60859 GAAATCGAGT
*
60869 TGCATTGACTTATATGGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
1 TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
*
60934 GGGACCATTGAGTCCTAACTAA-TTGAAATCGAGTTGCATTGACTTTGAAACTAAAGTGTATCTA
66 GGGACCATTGAGTCCTAACTAATTTGAAATCGAGTTGCATTGACTTTGAAACTAAAGTGCATCTA
60998 GA
131 GA
61000 TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
1 TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
* * *
61065 GGGACCATTGAGTCCTCATTAATTTGAAATCGAGTTGCATTGACTTTGGAACTAAAGTGCATCTA
66 GGGACCATTGAGTCCTAACTAATTTGAAATCGAGTTGCATTGACTTTGAAACTAAAGTGCATCTA
61130 GA
131 GA
61132 TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
1 TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
*
61197 TGGACC
66 GGGACC
61203 TCAAACCGGA
Statistics
Matches: 196, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
131 84 0.43
132 112 0.57
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (132 bp):
TGCATTGACTTATATTGAACTAAACTGCATCTAGATGCATTGACTAACACGGAATTGAACCGCGT
GGGACCATTGAGTCCTAACTAATTTGAAATCGAGTTGCATTGACTTTGAAACTAAAGTGCATCTA
GA
Found at i:73667 original size:6 final size:6
Alignment explanation
Indices: 73653--73706 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
73643 TTAAAACTAT
73653 AAAAA- AAAAAC AAAAAC AAAAAC AAAAATC -AAAA- AAAAA- AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA-C AAAAAC AAAAAC AAAAAC
73698 -AAAAC AAAA
1 AAAAAC AAAA
73707 CTACAAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 19 0.43
6 24 0.55
7 1 0.02
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:76520 original size:19 final size:19
Alignment explanation
Indices: 76496--76572 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
76486 TTAAATAGCA
*
76496 ACTGTACTGATGAGATTAC
1 ACTGTACCGATGAGATTAC
* *
76515 ACTGTACCGATTAGATTATGT
1 ACTGTACCGATGAGATTA--C
**
76536 ACTGTACATATGAGATTAC
1 ACTGTACCGATGAGATTAC
*
76555 ACTGTACCGATTAGATTA
1 ACTGTACCGATGAGATTA
76573 TGTACTGTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 31 0.67
21 15 0.33
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (19 bp):
ACTGTACCGATGAGATTAC
Found at i:76541 original size:21 final size:21
Alignment explanation
Indices: 76515--76582 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
76505 ATGAGATTAC
76515 ACTGTACCGATTAGATTATGT
1 ACTGTACCGATTAGATTATGT
** * *
76536 ACTGTACATATGAGATTA--C
1 ACTGTACCGATTAGATTATGT
76555 ACTGTACCGATTAGATTATGT
1 ACTGTACCGATTAGATTATGT
76576 ACTGTAC
1 ACTGTAC
76583 ATATGAGATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.41
21 22 0.59
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (21 bp):
ACTGTACCGATTAGATTATGT
Found at i:76551 original size:40 final size:40
Alignment explanation
Indices: 76496--76593 Score: 180
Period size: 40 Copynumber: 2.5 Consensus size: 40
76486 TTAAATAGCA
76496 ACTGTAC-TGATGAGATTACACTGTACCGATTAGATTATGT
1 ACTGTACAT-ATGAGATTACACTGTACCGATTAGATTATGT
76536 ACTGTACATATGAGATTACACTGTACCGATTAGATTATGT
1 ACTGTACATATGAGATTACACTGTACCGATTAGATTATGT
76576 ACTGTACATATGAGATTA
1 ACTGTACATATGAGATTA
76594 TTAGAGCAGC
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 56 0.98
41 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (40 bp):
ACTGTACATATGAGATTACACTGTACCGATTAGATTATGT
Found at i:76591 original size:21 final size:21
Alignment explanation
Indices: 76527--76594 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
76517 TGTACCGATT
76527 AGATTATGTACTGTACATATG
1 AGATTATGTACTGTACATATG
* ** *
76548 AGATTA--CACTGTACCGATT
1 AGATTATGTACTGTACATATG
76567 AGATTATGTACTGTACATATG
1 AGATTATGTACTGTACATATG
76588 AGATTAT
1 AGATTAT
76595 TAGAGCAGCG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.41
21 22 0.59
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (21 bp):
AGATTATGTACTGTACATATG
Found at i:77086 original size:57 final size:57
Alignment explanation
Indices: 76993--77108 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
76983 TATCCATTTC
*
76993 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
*
77050 CTTTTACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
77107 CT
1 CT
77109 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.40
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
Found at i:77199 original size:21 final size:21
Alignment explanation
Indices: 77175--77241 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
77165 AAGGATCATG
77175 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** * *
77196 ATTT-A-CAAAGAATTTTCTATG
1 ATTTGAGTTGAGTA-TTTCT-TA
77217 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
77238 ATTT
1 ATTT
77242 ACAGAGAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 14 0.44
22 6 0.19
23 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:77231 original size:42 final size:42
Alignment explanation
Indices: 77172--77254 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
77162 GTTAAGGATC
77172 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
*
77214 ATGATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
77255 AAGACTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:80759 original size:29 final size:29
Alignment explanation
Indices: 80658--80758 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
80648 GCTTATTGCT
* *
80658 CAAAAAGGCCCCTGAAC-TTACACAAAACGGC
1 CAAAAAAGCCCCTAAACTTTA-A-AAAA-GGC
* * *
80689 CAAATAAGCCCCTAAACTTTAATTACA-GC
1 CAAAAAAGCCCCTAAACTTTAA-AAAAGGC
80718 CAAAAAAGCCCCTAAACTCTTAAAAAAGGC
1 CAAAAAAGCCCCTAAACT-TTAAAAAAGGC
80748 CAAAAAAGCCC
1 CAAAAAAGCCC
80759 TTTTTGACGG
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
29 21 0.36
30 17 0.29
31 17 0.29
32 3 0.05
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.14
Consensus pattern (29 bp):
CAAAAAAGCCCCTAAACTTTAAAAAAGGC
Found at i:86154 original size:34 final size:34
Alignment explanation
Indices: 86110--86177 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
86100 AATTTATCCA
*
86110 AACACTCTGTTAGTCTTTAATTTTAGGTATCAGT
1 AACACACTGTTAGTCTTTAATTTTAGGTATCAGT
86144 AACACACTGTTAGTCTTTAATTTTAGGTATCAGT
1 AACACACTGTTAGTCTTTAATTTTAGGTATCAGT
86178 GACTTGTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (34 bp):
AACACACTGTTAGTCTTTAATTTTAGGTATCAGT
Found at i:87736 original size:10 final size:10
Alignment explanation
Indices: 87721--87760 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
87711 GAAGTCAATT
*
87721 TACATATACA
1 TACATATATA
87731 TACATATATA
1 TACATATATA
87741 TACATATATA
1 TACATATATA
*
87751 TATATATATA
1 TACATATATA
87761 AATAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
TACATATATA
Found at i:87743 original size:14 final size:14
Alignment explanation
Indices: 87724--87756 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
87714 GTCAATTTAC
87724 ATATACATACATAT
1 ATATACATACATAT
*
87738 ATATACATATATAT
1 ATATACATACATAT
87752 ATATA
1 ATATA
87757 TATAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATACATACATAT
Found at i:90366 original size:13 final size:13
Alignment explanation
Indices: 90339--90372 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
90329 AGTTTTAAAC
90339 ATATCATTTAAAAA
1 ATAT-ATTTAAAAA
90353 ATATATTTAAAAA
1 ATATATTTAAAAA
90366 ATTATAT
1 A-TATAT
90373 ATATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATTTAAAAA
Found at i:96091 original size:16 final size:16
Alignment explanation
Indices: 96067--96098 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96057 TGATTGGTAT
96067 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
96083 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
96099 ATCTCCTTTT
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:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Done.