Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018262.1 Corchorus olitorius cultivar O-4 contig18295, 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: 42013
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3221 original size:34 final size:29
Alignment explanation
Indices: 3145--3268 Score: 117
Period size: 33 Copynumber: 4.0 Consensus size: 29
3135 CAATCTTGGG
3145 ATGACAACTTCTGGTGTC-AATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAAATAATTT--T---C
*
3178 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAA-ATAAT--TTT--C
3212 ATGACAACTTCTGGTGTC-AATAATTTTC
1 ATGACAACTTCTGGTGTCAAATAATTTTC
*
3240 ATGACAACTTCTGGTGTCAATTAAATTTT
1 ATGACAACTTCTGGTGTCAAAT-AATTTT
3269 AAAAATAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
28 18 0.22
29 2 0.03
30 9 0.11
32 5 0.06
33 19 0.24
34 19 0.24
35 6 0.08
37 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (29 bp):
ATGACAACTTCTGGTGTCAAATAATTTTC
Found at i:5227 original size:27 final size:27
Alignment explanation
Indices: 5192--5257 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
5182 AAAAATACAC
*
5192 AAAATTATATTTTAATAATGGCATAGTT
1 AAAAATATATTTTAATAATGGCA-AGTT
* *
5220 -AAAATATATTTTAATAATGGTAATTT
1 AAAAATATATTTTAATAATGGCAAGTT
5246 AAAAATATATTT
1 AAAAATATATTT
5258 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (27 bp):
AAAAATATATTTTAATAATGGCAAGTT
Found at i:5388 original size:2 final size:2
Alignment explanation
Indices: 5381--5413 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5371 TTCGTAATTT
*
5381 TA TA TA TA -A TA TA GA 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
5414 CTAGTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:6234 original size:14 final size:13
Alignment explanation
Indices: 6215--6253 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
6205 AAATTGTAAA
6215 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
6228 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
6242 ATTTAAAAAATT
1 ATTTAAAAAATT
6254 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:6482 original size:122 final size:128
Alignment explanation
Indices: 6239--6492 Score: 403
Period size: 122 Copynumber: 2.0 Consensus size: 128
6229 ATTTAAGAAA
6239 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT---AATAAAA
* *
6304 TAGATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
6369 G
128 G
*
6370 TATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A-AAAAT-C
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
*
6431 ATA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
6492 T
1 T
6493 TTAAACAATG
Statistics
Matches: 119, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
122 55 0.46
123 2 0.02
124 3 0.03
125 5 0.04
126 1 0.01
130 46 0.39
131 7 0.06
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAATAAAATAC
ATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:7985 original size:16 final size:16
Alignment explanation
Indices: 7966--8007 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
7956 TTAATATTCC
7966 ATGGAATTAAAATATG
1 ATGGAATTAAAATATG
* *
7982 ATGG-GTTACTAATATG
1 ATGGAATTA-AAATATG
7998 ATGGAATTAA
1 ATGGAATTAA
8008 CATTCTTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 4
0.71 0.14 0.14
Matches are distributed among these distances:
15 3 0.15
16 14 0.70
17 3 0.15
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.33
Consensus pattern (16 bp):
ATGGAATTAAAATATG
Found at i:13320 original size:2 final size:2
Alignment explanation
Indices: 13313--13341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13303 ATTTATCAAA
13313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13342 ACAACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13430 original size:19 final size:18
Alignment explanation
Indices: 13406--13452 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
13396 TTCTGTTTAG
*
13406 TTATTTACTCATTTTTCAC
1 TTATTTACTCATTTGT-AC
*
13425 TTATTTATTCATTTGTAC
1 TTATTTACTCATTTGTAC
13443 TTAGTTTACT
1 TTA-TTTACT
13453 AGCGTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.21, C:0.15, G:0.04, T:0.60
Consensus pattern (18 bp):
TTATTTACTCATTTGTAC
Found at i:13539 original size:52 final size:52
Alignment explanation
Indices: 13457--13556 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
13447 TTTACTAGCG
*
13457 TTTGTTCTTATTAACACTCTTTAATAAGGAGAACACAGGACATTGGGTATCA
1 TTTGTTCTTATTAACACTCTTTAATAAGGAGAACAAAGGACATTGGGTATCA
*
13509 TTTGTTCTTATTAACACTCTTTAATGAGGAGAACAAAGGACATTGGGT
1 TTTGTTCTTATTAACACTCTTTAATAAGGAGAACAAAGGACATTGGGT
13557 GGTAGAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (52 bp):
TTTGTTCTTATTAACACTCTTTAATAAGGAGAACAAAGGACATTGGGTATCA
Found at i:22685 original size:22 final size:23
Alignment explanation
Indices: 22660--22708 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
22650 AATAGACCCT
* *
22660 ACTATTTTA-CCAAAAGAAAAGA
1 ACTATTTTACCCAAAAAAAAAAA
22682 ACTATTTTACCCAAAAAAAAAAA
1 ACTATTTTACCCAAAAAAAAAAA
22705 ACTA
1 ACTA
22709 GACCCTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.22
Consensus pattern (23 bp):
ACTATTTTACCCAAAAAAAAAAA
Found at i:29301 original size:22 final size:22
Alignment explanation
Indices: 29225--29304 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
29215 GATAATTTCT
29225 CTATGAAATTTTGGT-ATCCTCC
1 CTATGAAATTTTGGTAAT-CTCC
* *
29247 TTATTG-AATTCTGGTAATCT-C
1 CTA-TGAAATTTTGGTAATCTCC
*
29268 CTAATGAAATTTTGGTAATTTCC
1 CT-ATGAAATTTTGGTAATCTCC
29291 CTATGAAATTTTGG
1 CTATGAAATTTTGG
29305 ATTCCATGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 4 0.08
22 37 0.77
23 7 0.15
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGGTAATCTCC
Found at i:29817 original size:21 final size:22
Alignment explanation
Indices: 29787--29846 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
29777 TCTGGACCCC
*
29787 CTATGAAATTTTGGTGACCTCT
1 CTATGAAATTTTGGTAACCTCT
29809 CTATG-AATTTTGGTAACCTCT
1 CTATGAAATTTTGGTAACCTCT
*
29830 CTATGAAATTTTAGTAA
1 CTATGAAATTTTGGTAA
29847 TACGCTGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCTCT
Found at i:29934 original size:22 final size:22
Alignment explanation
Indices: 29887--30136 Score: 134
Period size: 22 Copynumber: 11.3 Consensus size: 22
29877 GTTTTCTTTT
* * *
29887 TGAAATTTTGGTAACCACAC-TG
1 TGAAATTCTGGTAACCTC-CGTA
*
29909 TGAAA-TCATGGTTACCTCCGTA
1 TGAAATTC-TGGTAACCTCCGTA
*
29931 TGAAATTCTGGTAACCTCCTTA
1 TGAAATTCTGGTAACCTCCGTA
* ** * *
29953 TGAAAATCTAATAATCTCCATA
1 TGAAATTCTGGTAACCTCCGTA
** * *
29975 TGAAATTCTAATAATCTCCATA
1 TGAAATTCTGGTAACCTCCGTA
** *
29997 TGAAATTCTGGTAATGTCCCTA
1 TGAAATTCTGGTAACCTCCGTA
* * *
30019 TGAAAGTTCTGGTAACGTTCTTA
1 TGAAA-TTCTGGTAACCTCCGTA
* * *
30042 TGAAATTATCGTAACCTCCTTA
1 TGAAATTCTGGTAACCTCCGTA
* * *
30064 TGAAAGTT-TAGTAACATTCC-AA
1 TGAAA-TTCTGGTAAC-CTCCGTA
*
30086 TGAAATTTTGGTAACCTCTC-TA
1 TGAAATTCTGGTAACCTC-CGTA
**
30108 TGAAAGTT-TGGTAACCTCCCCA
1 TGAAA-TTCTGGTAACCTCCGTA
30130 TGAAATT
1 TGAAATT
30137 TTTGATAACA
Statistics
Matches: 188, Mismatches: 30, Indels: 21
0.79 0.13 0.09
Matches are distributed among these distances:
21 9 0.05
22 151 0.80
23 28 0.15
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
TGAAATTCTGGTAACCTCCGTA
Found at i:30066 original size:89 final size:88
Alignment explanation
Indices: 29909--30126 Score: 221
Period size: 89 Copynumber: 2.5 Consensus size: 88
29899 AACCACACTG
* * * *
29909 TGAAA-TCATGGTTACCTCCGTATGAAA-TTCTGGTAACCTCCTTATGAAAATCTAATAATCTCC
1 TGAAATTC-TGGTAACCTCCCTATGAAAGTTCTGGTAACCTCCTTATGAAAATATAATAACCTCC
29972 ATATGAAA-TTCTAATAATC-TCCATA
65 ATATGAAAGTT-TAATAA-CATCCA-A
** * * * ** *
29997 TGAAATTCTGGTAATGTCCCTATGAAAGTTCTGGTAACGTTCTTATGAAATTATCGTAACCTCCT
1 TGAAATTCTGGTAACCTCCCTATGAAAGTTCTGGTAACCTCCTTATGAAAATATAATAACCTCCA
*
30062 TATGAAAGTTTAGTAACATTCCAA
66 TATGAAAGTTTAATAACA-TCCAA
* *
30086 TGAAATTTTGGTAACCTCTCTATGAAAGTT-TGGTAACCTCC
1 TGAAATTCTGGTAACCTCCCTATGAAAGTTCTGGTAACCTCC
30127 CCATGAAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
88 30 0.28
89 70 0.66
90 6 0.06
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (88 bp):
TGAAATTCTGGTAACCTCCCTATGAAAGTTCTGGTAACCTCCTTATGAAAATATAATAACCTCCA
TATGAAAGTTTAATAACATCCAA
Found at i:30089 original size:111 final size:111
Alignment explanation
Indices: 29929--30159 Score: 254
Period size: 111 Copynumber: 2.1 Consensus size: 111
29919 GTTACCTCCG
* * *
29929 TATGAAATTCTGGTAACCTCCTTATGAAAATCTAATAATCTCCATATGAAATTCTAATAATCTC-
1 TATGAAATTATCGTAACCTCCTTATGAAAATCTAATAATCTCCATATGAAATTCTAATAACCTCT
** * * *
29993 CATATGAAA-TTCTGGTAATGTCCCTATGAAAGTTCTGGTAACGTTCT
66 C-TATGAAAGTT-TGGTAACCTCCCCATGAAAGTTCTGATAACATTCT
* * * * **
30040 TATGAAATTATCGTAACCTCCTTATGAAAGTTTAGTAA-CATTCCA-ATGAAATTTTGGTAACCT
1 TATGAAATTATCGTAACCTCCTTATGAAAATCTAATAATC--TCCATATGAAATTCTAATAACCT
* *
30103 CTCTATGAAAGTTTGGTAACCTCCCCATGAAATTTTTGATAACATTCT
64 CTCTATGAAAGTTTGGTAACCTCCCCATGAAAGTTCTGATAACATTCT
30151 TATGAAATT
1 TATGAAATT
30160 TTGATAACCC
Statistics
Matches: 100, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
110 1 0.01
111 92 0.92
112 7 0.07
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (111 bp):
TATGAAATTATCGTAACCTCCTTATGAAAATCTAATAATCTCCATATGAAATTCTAATAACCTCT
CTATGAAAGTTTGGTAACCTCCCCATGAAAGTTCTGATAACATTCT
Found at i:30136 original size:44 final size:45
Alignment explanation
Indices: 30017--30186 Score: 141
Period size: 44 Copynumber: 3.8 Consensus size: 45
30007 GTAATGTCCC
* * ** * *
30017 TATGAAAGTTCTGGTAACGTTCTTATGAAATTATCGTAACCTC-CT
1 TATGAAAGTT-TGGTAACCTCCCCATGAAATTTTGGTAACCTCTCT
* * * *
30062 TATGAAAGTTTAGTAACATTCCAATGAAATTTTGGTAACCTCTC-
1 TATGAAAGTTTGGTAACCTCCCCATGAAATTTTGGTAACCTCTCT
* *
30106 TATGAAAGTTTGGTAACCTCCCCATGAAATTTTTGATAACAT-TCT
1 TATGAAAGTTTGGTAACCTCCCCATGAAA-TTTTGGTAACCTCTCT
* *
30151 TATGAAATTTTGATAACC-CCACACTATGAAATTTTG
1 TATGAAAGTTTGGTAACCTCC-C-C-ATGAAATTTTG
30187 ATTACCTCCC
Statistics
Matches: 105, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
44 55 0.52
45 38 0.36
46 6 0.06
47 6 0.06
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (45 bp):
TATGAAAGTTTGGTAACCTCCCCATGAAATTTTGGTAACCTCTCT
Found at i:30145 original size:23 final size:22
Alignment explanation
Indices: 30085--30196 Score: 91
Period size: 22 Copynumber: 5.0 Consensus size: 22
30075 TAACATTCCA
* * *
30085 ATGAAATTTTGGTAACCTCTCT
1 ATGAAATTTTGATAACCTCCCC
* *
30107 ATGAAAGTTTGGTAACCTCCCC
1 ATGAAATTTTGATAACCTCCCC
* * **
30129 ATGAAATTTTTGATAACATTCTT
1 ATGAAA-TTTTGATAACCTCCCC
30152 ATGAAATTTTGATAACC-CCACAC
1 ATGAAATTTTGATAACCTCC-C-C
*
30175 TATGAAATTTTGATTACCTCCC
1 -ATGAAATTTTGATAACCTCCC
30197 TATTAATTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.01
22 35 0.49
23 16 0.23
24 17 0.24
25 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCC
Found at i:30164 original size:22 final size:22
Alignment explanation
Indices: 30017--30167 Score: 83
Period size: 22 Copynumber: 6.8 Consensus size: 22
30007 GTAATGTCCC
* * *
30017 TATGAAAGTTCTGGTAACGTTCT
1 TATGAAA-TTTTGATAACATTCT
* * *
30040 TATGAAATTATCG-TAACCTCCT
1 TATGAAATT-TTGATAACATTCT
* *
30062 TATGAAAGTTT-AGTAACATTCC
1 TATGAAATTTTGA-TAACATTCT
* * *
30084 AATGAAATTTTGGTAAC-CTCT
1 TATGAAATTTTGATAACATTCT
* * * * *
30105 CTATGAAAGTTTGGTAACCTCCC
1 -TATGAAATTTTGATAACATTCT
*
30128 CATGAAATTTTTGATAACATTCT
1 TATGAAA-TTTTGATAACATTCT
30151 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
30168 CCCACACTAT
Statistics
Matches: 95, Mismatches: 26, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
21 3 0.03
22 67 0.71
23 25 0.26
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACATTCT
Found at i:30241 original size:56 final size:59
Alignment explanation
Indices: 30147--30262 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 59
30137 TTTGATAACA
* * *
30147 TTCTTATGAAATTTTGATAACCCCACACTATGAAATTTTGATTACCTCCCTAT-TAATT
1 TTCTTATGAAATTTTGATAACACCACACTATAAAATTTTGATAACCTCCCTATGTAATT
* * *
30205 TTCTTATGAAGTTTTGA-AA-ACCACACTATAAAATTTTGGTAAGCTCCCTATGTAATT
1 TTCTTATGAAATTTTGATAACACCACACTATAAAATTTTGATAACCTCCCTATGTAATT
30262 T
1 T
30263 GGTAACGTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
56 27 0.53
57 8 0.16
58 16 0.31
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (59 bp):
TTCTTATGAAATTTTGATAACACCACACTATAAAATTTTGATAACCTCCCTATGTAATT
Found at i:30305 original size:26 final size:26
Alignment explanation
Indices: 30254--30307 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
30244 TAAGCTCCCT
* *
30254 ATGTAATTTGGTAACGTCGCTAAGAA
1 ATGTAATTTGGTAACATCACTAAGAA
*
30280 ATGTAATTTGGTAACATCACTGAGAA
1 ATGTAATTTGGTAACATCACTAAGAA
30306 AT
1 AT
30308 TTTGATAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (26 bp):
ATGTAATTTGGTAACATCACTAAGAA
Found at i:30347 original size:22 final size:22
Alignment explanation
Indices: 30286--30348 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
30276 AGAAATGTAA
* *
30286 TTTGGTAACATCACTGA-GAAAT
1 TTTGGTAACCTC-CTTATGAAAT
* *
30308 TTTGATAACCT-TTCTATGAAAT
1 TTTGGTAACCTCCT-TATGAAAT
30330 TTTGGTAACCTCCTTATGA
1 TTTGGTAACCTCCTTATGA
30349 CATAAAACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 29 0.91
23 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTGGTAACCTCCTTATGAAAT
Found at i:30520 original size:22 final size:21
Alignment explanation
Indices: 30480--30519 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30470 TTACTAGGTC
30480 TAATCTCTTATGAAATTTTGA
1 TAATCTCTTATGAAATTTTGA
30501 TAATCTCATTAT-AAATTTT
1 TAATCTC-TTATGAAATTTT
30520 TTTTTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TAATCTCTTATGAAATTTTGA
Found at i:41915 original size:2 final size:2
Alignment explanation
Indices: 41894--41933 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
41884 TTGGACGAGA
* * *
41894 AT AT AT AA AT AA AT AA 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 AT AT AT
41934 TTATTGAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Done.