Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010831.1 Corchorus olitorius cultivar O-4 contig10863, 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: 36112
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1080 original size:13 final size:13
Alignment explanation
Indices: 1064--1088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1054 TTAACCATTC
1064 TCTTTAGATTTTA
1 TCTTTAGATTTTA
1077 TCTTTAGATTTT
1 TCTTTAGATTTT
1089 GACCATCCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
TCTTTAGATTTTA
Found at i:2635 original size:20 final size:20
Alignment explanation
Indices: 2606--2643 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2596 GGAAGTTAAC
* *
2606 AAAATTAAAATTGGAGAAGG
1 AAAATAAAAATTGAAGAAGG
2626 AAAATAAAAATTGAAGAA
1 AAAATAAAAATTGAAGAA
2644 ATTAGGCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATTGAAGAAGG
Found at i:2737 original size:40 final size:40
Alignment explanation
Indices: 2682--3318 Score: 475
Period size: 40 Copynumber: 15.6 Consensus size: 40
2672 CAATTCCAGC
* ** * *
2682 TTAAA-TCCCACTTTGCCCTTCCTTACTGAAAGGTGTTGT
1 TTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* *
2721 TTAAATTCCCAATTTGCCCTTCCCCACCGGAAGATGTTGT
1 TTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
** *
2761 TTACTTTTCCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGT
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
** *
2802 TTTGATTCCCAGTTTGCCCTTCCCCACTGGAAGGTGTTGT
1 TTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
** *
2842 TTACTTTTCCCGGTTTGCCCTTCCCCACCGGAAGGTGTTGT
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* * *
2883 TTTAATTCCC-GTTTTGCCCTTCCCCACCAGAAGGTATTG-
1 TTAAATTCCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGT
* ** * * *
2922 TCACTTTTCCTAGTTTTCGATCCCTTCCCAACCGAAAGGTGTTGT
1 TTA-AATTCCCAG-TTT-G--CCCTTCCCCACCGGAAGGTGTTGT
** *
2967 TTACTTTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTG-
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
** * *
3007 TTACTTTTCCCAGTTCGCCCTTCCCCATCGGAAGGTGTTG-
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
**
3047 TTACTTTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* *
3088 TTTAATTCTC-GTTTTGCCCTTCCCCACCGGAAGGTGTTG-
1 TTAAATTCCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGT
** *
3127 TTACTTTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGT
1 TTA-AATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* * * *
3168 TTAAA-TCCCTTGTTTAAATCCCTAGTTTGCCCTCCTGGAAGGTGTTGT
1 TTAAATTCCC-AGTTT---GCCC----TTCCCCACC-GGAAGGTGTTGT
* * * *
3216 TT-ACTTATCCAGTTTGCCCTTCCCCACGGGAAGGTGTTAT
1 TTAAATT-CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* *** * * **
3256 CTCTTTTCCCAGTTTGTCGTTCCCCACTAGAAGGTGTTGT
1 TTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
* *
3296 TT-TATTTCCAGTATTGCCCTTCC
1 TTAAATTCCCAGT-TTGCCCTTCC
3319 GGTCGGAAGA
Statistics
Matches: 489, Mismatches: 81, Indels: 55
0.78 0.13 0.09
Matches are distributed among these distances:
39 22 0.04
40 290 0.59
41 108 0.22
42 1 0.00
43 4 0.01
44 22 0.04
45 14 0.03
47 7 0.01
48 19 0.04
49 2 0.00
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (40 bp):
TTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT
Found at i:2799 original size:81 final size:82
Alignment explanation
Indices: 2687--3318 Score: 584
Period size: 81 Copynumber: 7.7 Consensus size: 82
2677 CCAGCTTAAA
* ** * * * *
2687 TCCCACTTTGCCCTTCCTTACTGAAAGGTGTTGTTTA-AATTCCCAATTTGCCCTTCCCCACCGG
1 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGTTTGCCCTTCCCCACCGG
*
2751 AAGATGTTGTTTACTTT
66 AAGGTGTTGTTTACTTT
* *
2768 TCCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTTT--TGATTCCCAGTTTGCCCTTCCCCACTG
1 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACT-ATTCCCAGTTTGCCCTTCCCCACCG
2831 GAAGGTGTTGTTTACTTT
65 GAAGGTGTTGTTTACTTT
*
2849 TCCCGGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT--TAATTCCC-GTTTTGCCCTTCCCCACC
1 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACT-ATTCCCAG-TTTGCCCTTCCCCACC
* * *
2911 AGAAGGTATTG-TCACTTT
64 GGAAGGTGTTGTTTACTTT
* * * *
2929 TCCTAGTTTTCGATCCCTTCCCAACCGAAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTCCCCA
1 TCCCAG-TTT-G--CCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGTTTGCCCTTCCCCA
*
2994 TCGGAAGGTGTTG-TTACTTT
62 CCGGAAGGTGTTGTTTACTTT
* * *
3014 TCCCAGTTCGCCCTTCCCCATCGGAAGGTGTTG-TTACTTTTCCCAGTTTGCCCTTCCCCACCGG
1 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGTTTGCCCTTCCCCACCGG
*
3078 AAGGTGTTGTTT--TAAT
66 AAGGTGTTGTTTACT-TT
* * *
3094 TCTC-GTTTTGCCCTTCCCCACCGGAAGGTGTTG-TTACTTTTCCCAGTTTGCCCTTCCCCATCG
1 TCCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGTTTGCCCTTCCCCACCG
**
3157 GAAGGTGTTGTTTA--AA
65 GAAGGTGTTGTTTACTTT
* * * *
3173 TCCCTTGTTTAAATCCCTAGTTTGCCCTCCTGGAAGGTGTTGTTTACT-TAT-CCAGTTTGCCCT
1 TCCC-AGTTT---GCCC----TTCCCCACC-GGAAGGTGTTGTTTACTAT-TCCCAGTTTGCCCT
* * *
3236 TCCCCACGGGAAGGTGTTATCT-CTTT
56 TCCCCACCGGAAGGTGTTGTTTACTTT
* * ** *
3262 TCCCAGTTTGTCGTTCCCCACTAGAAGGTGTTGTTT--TATTTCCAGTATTGCCCTTCC
1 TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGT-TTGCCCTTCC
3319 GGTCGGAAGA
Statistics
Matches: 465, Mismatches: 56, Indels: 61
0.80 0.10 0.10
Matches are distributed among these distances:
78 2 0.00
79 12 0.03
80 147 0.32
81 167 0.36
82 1 0.00
83 4 0.01
84 26 0.06
85 41 0.09
86 2 0.00
87 7 0.02
88 46 0.10
89 10 0.02
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.38
Consensus pattern (82 bp):
TCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTATTCCCAGTTTGCCCTTCCCCACCGG
AAGGTGTTGTTTACTTT
Found at i:3079 original size:80 final size:80
Alignment explanation
Indices: 2726--3318 Score: 557
Period size: 80 Copynumber: 7.2 Consensus size: 80
2716 GTTGTTTAAA
* * *
2726 TTCCCAATTTGCCCTTCCCCACCGGAAGATGTTGTTTACTTTTCCCAGTTTGCCCTTCCCCACCA
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG-TTACTTTTCCCAGTTTGCCCTTCCCCACCG
2791 GAAGGTGTTGTT--TT
65 GAAGGTGTTGTTACTT
* *
2805 GATTCCCAGTTTGCCCTTCCCCACTGGAAGGTGTTGTTTACTTTTCCCGGTTTGCCCTTCCCCAC
1 --TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTG-TTACTTTTCCCAGTTTGCCCTTCCCCAC
2870 CGGAAGGTGTTGTT--TT
63 CGGAAGGTGTTGTTACTT
* * * *
2886 AATTCCC-GTTTTGCCCTTCCCCACCAGAAGGTATTGTCACTTTTCCTAGTTTTCGATCCCTTCC
1 --TTCCCAG-TTTGCCCTTCCCCACCGGAAGGTGTTGTTACTTTTCCCAG-TTT-G--CCCTTCC
* *
2950 CAACCGAAAGGTGTTGTTTACTT
59 CCACCGGAAGGTGTTG-TTACTT
* * *
2973 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTACTTTTCCCAGTTCGCCCTTCCCCATCGG
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTACTTTTCCCAGTTTGCCCTTCCCCACCGG
3038 AAGGTGTTGTTACTT
66 AAGGTGTTGTTACTT
*
3053 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT--TTAATTCTC-GTTTTGCCCTTCCCCAC
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTACTT--TTCCCAG-TTTGCCCTTCCCCAC
3115 CGGAAGGTGTTGTTACTT
63 CGGAAGGTGTTGTTACTT
* ** * *
3133 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTT--TAAATCCCTTGTTTAAATCCCTAGTTT
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTACT-TTTCCC-AGTTT---GCCC----TT
* *
3196 GCCCTCCTGGAAGGTGTTGTTTACTT
57 CCCCACC-GGAAGGTGTTG-TTACTT
* * * * * **
3222 AT-CCAGTTTGCCCTTCCCCACGGGAAGGTGTTATCT-CTTTTCCCAGTTTGTCGTTCCCCACTA
1 TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGT-TACTTTTCCCAGTTTGCCCTTCCCCACCG
3285 GAAGGTGTTGTT--TT
65 GAAGGTGTTGTTACTT
*
3299 ATTTCCAGTATTGCCCTTCC
1 -TTCCCAGT-TTGCCCTTCC
3319 GGTCGGAAGA
Statistics
Matches: 434, Mismatches: 49, Indels: 59
0.80 0.09 0.11
Matches are distributed among these distances:
77 2 0.00
78 3 0.01
79 11 0.03
80 146 0.34
81 134 0.31
82 1 0.00
83 4 0.01
84 23 0.05
85 43 0.10
86 1 0.00
87 9 0.02
88 44 0.10
89 12 0.03
90 1 0.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (80 bp):
TTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTACTTTTCCCAGTTTGCCCTTCCCCACCGG
AAGGTGTTGTTACTT
Found at i:3182 original size:13 final size:13
Alignment explanation
Indices: 3164--3195 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3154 TCGGAAGGTG
3164 TTGTTTAAATCCC
1 TTGTTTAAATCCC
3177 TTGTTTAAATCCC
1 TTGTTTAAATCCC
*
3190 TAGTTT
1 TTGTTT
3196 GCCCTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.50
Consensus pattern (13 bp):
TTGTTTAAATCCC
Found at i:4323 original size:30 final size:30
Alignment explanation
Indices: 4284--4340 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4274 GCTCATTGAT
* *
4284 CTCCTTGATAAG-CTCTTGGCGCATCATTCC
1 CTCCATGATAAGACT-TGGGCGCATCATTCC
4314 CTCCATGATAAGACTTGGGCGCATCAT
1 CTCCATGATAAGACTTGGGCGCATCAT
4341 AAGGACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (30 bp):
CTCCATGATAAGACTTGGGCGCATCATTCC
Found at i:5304 original size:23 final size:23
Alignment explanation
Indices: 5270--5314 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5260 GACAACCAAG
5270 AACACATCAAACACAGAAAAAAA
1 AACACATCAAACACAGAAAAAAA
* *
5293 AACACATTAAACCCAGAAAAAA
1 AACACATCAAACACAGAAAAAA
5315 CTAGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.22, G:0.04, T:0.07
Consensus pattern (23 bp):
AACACATCAAACACAGAAAAAAA
Found at i:15268 original size:40 final size:39
Alignment explanation
Indices: 15174--15495 Score: 241
Period size: 40 Copynumber: 8.2 Consensus size: 39
15164 AAAAAACTTT
* **
15174 TTGATGGGAACTTTCCCTAAATTGAAAAC-TAAAACCAAAGC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAA--AAA-C
* *
15215 -TGACGGGAACTTTCCCTAAATTGAAAACTTTTGAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAAC-TTTGAAAAAC
* *
15254 ATGATGGGATCTTTCCCTAAATTGAAAACTTTAAAAAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTT---GAAAAAC
* * ** **
15296 TTGACGAGATCTTTCCC-ATTTTGAAAAC--T--AAGGC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAC
* * *
15330 -GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTG---AAAAAC
*
15371 TTGATGGGATCTTTCGCTAAATTGAAAACTTTGAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAC
****
15410 TTGATGGGATCTTTCCCTAAATTGAAAACTAACTAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAC
* * * * *
15449 -TGACGACGA-CTTCCCCTAAATTGAAGACTTTGAAAAAT
1 TTGATG-GGATCTTTCCCTAAATTGAAAACTTTGAAAAAC
15487 TTGATGGGA
1 TTGATGGGA
15496 ACTTCCCCGC
Statistics
Matches: 224, Mismatches: 40, Indels: 37
0.74 0.13 0.12
Matches are distributed among these distances:
33 13 0.06
34 12 0.05
36 1 0.00
38 28 0.12
39 51 0.23
40 56 0.25
41 12 0.05
42 51 0.23
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (39 bp):
TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAC
Found at i:15341 original size:115 final size:113
Alignment explanation
Indices: 15216--15441 Score: 321
Period size: 115 Copynumber: 2.0 Consensus size: 113
15206 AACCAAAGCT
15216 GACGGGAACTTTCCCTAAATTGAAAACTTTTG-AAAAACATGATGGGATCTTTCCCTAAATTGAA
1 GACGGGAACTTTCCCTAAATTGAAAAC-TTTGAAAAAACATGATGGGATCTTTCCCTAAATTGAA
**
15280 AACTTTAAAAAAAAACTTGACGAGATCTTTCCC-ATTTTGAAAACTAAGGCG
65 AACTTT---AAAAAACTTGACGAGATCTTTCCCTAAATTGAAAACTAAGGCG
* *
15331 GACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACTTGATGGGATCTTTCGCTAAATTGA
1 GACGGGAACTTTCCCTAAATTGAAAACTTTG--AAAAAACATGATGGGATCTTTCCCTAAATTGA
* * *
15396 AAACTTTGAAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTAA
64 AAACTTTAAAAAACTTGACGAGATCTTTCCCTAAATTGAAAACTAA
15442 CTAAAACTGA
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
114 25 0.25
115 39 0.39
117 36 0.36
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (113 bp):
GACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAACATGATGGGATCTTTCCCTAAATTGAAA
ACTTTAAAAAACTTGACGAGATCTTTCCCTAAATTGAAAACTAAGGCG
Found at i:15365 original size:43 final size:42
Alignment explanation
Indices: 15330--15485 Score: 139
Period size: 39 Copynumber: 3.9 Consensus size: 42
15320 AAACTAAGGC
15330 GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACT
1 GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACT
* * * *
15372 TGATGGGATCTTTCGCTAAATTGAAAACTTTG---AAAAACT
1 GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACT
* * * **
15411 TGATGGGATCTTTCCCTAAATTGAAAAC--T-AACTAAAACT
1 GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACT
* * *
15450 -GACGACG-ACTTCCCCTAAATTGAAGACTTTGAAAAA
1 GGACG-GGAACTTTCCCTAAATTGAAAACTTTGAAAAA
15486 TTTGATGGGA
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
37 1 0.01
38 20 0.21
39 41 0.44
40 1 0.01
41 3 0.03
42 28 0.30
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (42 bp):
GGACGGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACT
Found at i:15419 original size:39 final size:40
Alignment explanation
Indices: 15334--15439 Score: 169
Period size: 39 Copynumber: 2.6 Consensus size: 40
15324 TAAGGCGGAC
*
15334 GGGAACTTTCCCTAAATTGAAAACTTTGAAAAAAAACTTGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTG--AAAAAACTTGAT
*
15376 GGGATCTTTCGCTAAATTGAAAACTTTG-AAAAACTTGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAAAACTTGAT
15415 GGGATCTTTCCCTAAATTGAAAACT
1 GGGATCTTTCCCTAAATTGAAAACT
15440 AACTAAAACT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 35 0.57
42 26 0.43
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (40 bp):
GGGATCTTTCCCTAAATTGAAAACTTTGAAAAAACTTGAT
Found at i:15564 original size:7 final size:7
Alignment explanation
Indices: 15532--15566 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
15522 GGAATTCTTC
*
15532 TTTTGAT
1 TTTTGAA
15539 TTTTGAA
1 TTTTGAA
15546 TTTTGAA
1 TTTTGAA
*
15553 TTTTGGA
1 TTTTGAA
15560 TTTTGAA
1 TTTTGAA
15567 AAGGACCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (7 bp):
TTTTGAA
Found at i:16091 original size:18 final size:20
Alignment explanation
Indices: 16049--16096 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
16039 GTCTTTTTAT
*
16049 TTAAACTTAATCTATTGATAA
1 TTAAAC-TAAACTATTGATAA
16070 TTAAACTAAACTA-TGA-AA
1 TTAAACTAAACTATTGATAA
16088 TTAAACTAA
1 TTAAACTAA
16097 TTCTAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 6 0.23
21 6 0.23
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (20 bp):
TTAAACTAAACTATTGATAA
Found at i:17836 original size:40 final size:40
Alignment explanation
Indices: 17776--17870 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
17766 AAAAAACTTT
* * *
17776 TTGAAGGGAACTTTCCCTAAATTGAAAACATTTGAAAAAC
1 TTGAAGGGATCTTTCACTAAATCGAAAACATTTGAAAAAC
* * * *
17816 TTGATGGGATCTTTCACTAAATCGAAAACTTTTTAAAAAG
1 TTGAAGGGATCTTTCACTAAATCGAAAACATTTGAAAAAC
*
17856 TTGACGGGATCTTTC
1 TTGAAGGGATCTTTC
17871 CCAGTTTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
TTGAAGGGATCTTTCACTAAATCGAAAACATTTGAAAAAC
Found at i:22565 original size:29 final size:30
Alignment explanation
Indices: 22513--22572 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
22503 GAAGTTCGTG
* *
22513 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGACT-ATTGAAGAATTATTTCAAGA
22544 TTTGAAGACT-TTGAAGAATTATTTCAAGA
1 TTTGAAGACTATTGAAGAATTATTTCAAGA
22573 GGAAACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTGAAGACTATTGAAGAATTATTTCAAGA
Found at i:34328 original size:26 final size:26
Alignment explanation
Indices: 34280--34331 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
34270 AAAATAGGCA
*
34280 AATTAAACTAGAAAACAATAAAATAG
1 AATTAAACTAGAAAACAAGAAAATAG
* **
34306 AATTAAACTAGAGATTAAGAAAATAG
1 AATTAAACTAGAAAACAAGAAAATAG
34332 TTTGAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (26 bp):
AATTAAACTAGAAAACAAGAAAATAG
Done.