Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011642.1 Corchorus capsularis cultivar CVL-1 contig11663, 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: 59770
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA T
36 TCATACTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1177 original size:20 final size:20
Alignment explanation
Indices: 1152--1192 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1142 TCATTAAAGA
1152 ATGCAAAAACATCAATATTT
1 ATGCAAAAACATCAATATTT
1172 ATGCAAAAACATCAATATTT
1 ATGCAAAAACATCAATATTT
1192 A
1 A
1193 GTTGATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (20 bp):
ATGCAAAAACATCAATATTT
Found at i:2002 original size:33 final size:33
Alignment explanation
Indices: 1940--2027 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
1930 CTTTTACATT
* * *
1940 GAGCCTCCCTACT-AGGACGGCTCAGCCACGGCG
1 GAGCCTCCCCACTGGGGA-GGCTCAACCACGGCG
* *
1973 GAGCTTCCCCAGTGGGGAGGCTCAACCACGGCG
1 GAGCCTCCCCACTGGGGAGGCTCAACCACGGCG
*
2006 GAGCCTCCCCACTGGGGCGGCT
1 GAGCCTCCCCACTGGGGAGGCT
2028 TGCCGTGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 43 0.93
34 3 0.07
ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12
Consensus pattern (33 bp):
GAGCCTCCCCACTGGGGAGGCTCAACCACGGCG
Found at i:3586 original size:87 final size:89
Alignment explanation
Indices: 3440--3610 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 89
3430 TTTTTGTTTG
* *
3440 AAGTTTTAGTCTTTATTTCCTACACAAAATAATTTCAATTGTGTAATAATAAGATTTTGTT-TTT
1 AAGTTTCAGTCTTTATTTCCTACACAAAATAATTTCAATTGTGTAATAATAAGATTTTGTTGTGT
*
3504 TTTTATT-TAAAAAAGATACATAT
66 TTTTATTGAAAAAAAGATACATAT
*
3527 AAGTTTCAGTCTTTATTTCCTACACAAAATAATTTCAATTGTGTAATATTAAGATTTTGTTGTGT
1 AAGTTTCAGTCTTTATTTCCTACACAAAATAATTTCAATTGTGTAATAATAAGATTTTGTTGTGT
3592 TTTTATTGAAAAAAAGATA
66 TTTTATTGAAAAAAAGATA
3611 AACATCAGAC
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 59 0.76
88 9 0.12
89 10 0.13
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (89 bp):
AAGTTTCAGTCTTTATTTCCTACACAAAATAATTTCAATTGTGTAATAATAAGATTTTGTTGTGT
TTTTATTGAAAAAAAGATACATAT
Found at i:4735 original size:2 final size:2
Alignment explanation
Indices: 4717--4756 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
4707 ATATTTTTTT
4717 TA TA -A TA TA CTA GTA 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 TA TA TA TA TA TA T
4757 GTCCTGGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
1 1 0.03
2 30 0.86
3 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5084 original size:22 final size:22
Alignment explanation
Indices: 5034--5085 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5024 CTTGTCGCAC
*
5034 GTCGTCGCAATTGATTTATTTG
1 GTCGTCGCAATTGATTTATATG
*
5056 GTAGTCGCAATTG-TTTATAATG
1 GTCGTCGCAATTGATTTAT-ATG
*
5078 TTCGTCGC
1 GTCGTCGC
5086 TGTTTGTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (22 bp):
GTCGTCGCAATTGATTTATATG
Found at i:9182 original size:8 final size:7
Alignment explanation
Indices: 9150--9183 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
9140 ACATACTTCC
9150 CAAAATA
1 CAAAATA
9157 CAAAATA
1 CAAAATA
9164 CAAAATA
1 CAAAATA
9171 CAAAAGTA
1 CAAAA-TA
9179 CAAAA
1 CAAAA
9184 AATAGAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.12
Consensus pattern (7 bp):
CAAAATA
Found at i:13988 original size:24 final size:25
Alignment explanation
Indices: 13954--14000 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
13944 AGCCATTGCT
13954 TCTTTCTAATTAAATGCATGTTTGA
1 TCTTTCTAATTAAATGCATGTTTGA
13979 TCTTT-TAATTAAATGCATGTTT
1 TCTTTCTAATTAAATGCATGTTT
14001 CAAGAAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (25 bp):
TCTTTCTAATTAAATGCATGTTTGA
Found at i:18881 original size:2 final size:2
Alignment explanation
Indices: 18876--18904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18866 GTACTGGTAT
18876 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18905 GATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19776 original size:10 final size:10
Alignment explanation
Indices: 19748--19777 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
19738 CCCACCGCAA
*
19748 ATATATATAT
1 ATATATATGT
19758 ATATATATGT
1 ATATATATGT
19768 ATATATATGT
1 ATATATATGT
19778 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:19780 original size:2 final size:2
Alignment explanation
Indices: 19775--19799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19765 TGTATATATA
19775 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
19800 ATGTATCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:23262 original size:32 final size:32
Alignment explanation
Indices: 23212--23306 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
23202 AGTTTTGTAA
*
23212 AACTTTTGAAATGTCTATTGTACCCTTATTTT
1 AACTTTTGAAACGTCTATTGTACCCTTATTTT
* *
23244 AATTTTTGAAACGCCTATTGTACCCTTA-TTT
1 AACTTTTGAAACGTCTATTGTACCCTTATTTT
* *
23275 AACTTTTGAAACGTCTATTATATCCTTATTTT
1 AACTTTTGAAACGTCTATTGTACCCTTATTTT
23307 TCTAATATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 27 0.49
32 28 0.51
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.48
Consensus pattern (32 bp):
AACTTTTGAAACGTCTATTGTACCCTTATTTT
Found at i:23282 original size:31 final size:31
Alignment explanation
Indices: 23212--23305 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
23202 AGTTTTGTAA
*
23212 AACTTTTGAAATGTCTATTGTACCCTTATTTT
1 AACTTTTGAAACGTCTATTGTACCCTTA-TTT
* *
23244 AATTTTTGAAACGCCTATTGTACCCTTATTT
1 AACTTTTGAAACGTCTATTGTACCCTTATTT
* *
23275 AACTTTTGAAACGTCTATTATATCCTTATTT
1 AACTTTTGAAACGTCTATTGTACCCTTATTT
23306 TTCTAATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 30 0.55
32 25 0.45
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.48
Consensus pattern (31 bp):
AACTTTTGAAACGTCTATTGTACCCTTATTT
Found at i:23476 original size:130 final size:132
Alignment explanation
Indices: 23331--23593 Score: 422
Period size: 130 Copynumber: 2.0 Consensus size: 132
23321 AAACTGCCAT
* * *
23331 TATATAATTATTTTTTAATTTTTTTAATTTACATTTAATTAAATCTACGAAATATGTATCTCAAA
1 TATATAATTATTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATATCAAA
*
23396 TTTAGTTTTTATAGATTTCAACTTC-A-AACGATTCTAATAGACTAATAGCATTTAATTAAATCC
66 TTTAGTTTTTATAGATTTCAACTTCTACAAAGATTCTAATAGACTAATAGCATTTAATTAAATCC
23459 AA
131 AA
*
23461 TATATAATTATTTTTTAATTTTGTTAATTTGCATTTAATTAAATCTACGAAATATATATATCAAA
1 TATATAATTATTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATATCAAA
*
23526 TTTAGTTTTTATAGATTTCAACTTCTTGAACCAAAGTTTCTAATAGACTAATAGCATTTAATTAA
66 TTTAGTTTTTATAGATTTCAACTTC-T--A-CAAAGATTCTAATAGACTAATAGCATTTAATTAA
23591 ATC
127 ATC
23594 TACGAAATAT
Statistics
Matches: 121, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
130 86 0.71
134 1 0.01
136 34 0.28
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (132 bp):
TATATAATTATTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATATCAAA
TTTAGTTTTTATAGATTTCAACTTCTACAAAGATTCTAATAGACTAATAGCATTTAATTAAATCC
AA
Found at i:26392 original size:12 final size:12
Alignment explanation
Indices: 26375--26408 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
26365 GGAGCGTATT
26375 ATTTATTAATTA
1 ATTTATTAATTA
26387 ATTTATTAATTA
1 ATTTATTAATTA
26399 ATTTATTAAT
1 ATTTATTAAT
26409 GTTAAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTATTAATTA
Found at i:30077 original size:15 final size:14
Alignment explanation
Indices: 30057--30113 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
30047 CCCTATTTAC
30057 AAATTACAAATAAAT
1 AAATTACAAA-AAAT
*
30072 AAATTACAAAAAAA
1 AAATTACAAAAAAT
30086 AAATTCACACAAACAAAT
1 AAATT---ACAAA-AAAT
30104 AAATTACAAA
1 AAATTACAAA
30114 GAAAACTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 8 0.22
15 15 0.42
17 5 0.14
18 8 0.22
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATTACAAAAAAT
Found at i:30486 original size:149 final size:144
Alignment explanation
Indices: 30216--30508 Score: 505
Period size: 149 Copynumber: 2.0 Consensus size: 144
30206 CTGGTATTAA
*
30216 CAGTGTGTTTGGATTGAGGGACTAGTAAGAAACGGGATGGGACGGGACGGGAGGTCTTTTTGGTT
1 CAGTGTGTTTGGATTGAGGGACCAGTAAGAAACGGGATGGGACGGGACGGGAGGTCTTTTTGGTT
30281 AGTGACCCATGTTTGGATTGGAAATTAGATTTGGTCCATGGGTTTTGAAGGACCAATTTTGGTCC
66 AGTGACCCATGTTTGGATTGGAAATTAGATTTGGTCCATGGGTTTTGAAGGACCAATTTTGGTCC
30346 TTCTTGATCCTTAT
131 TTCTTGATCCTTAT
* *
30360 CAGTTTGTTTGGATTGAGGGACCAGTAAGGAACGGGATGGGACGGGACAGGACGGGAGGTCTTTT
1 CAGTGTGTTTGGATTGAGGGACCAGTAAGAAACGGGATGGGAC--G---GGACGGGAGGTCTTTT
*
30425 TGGTTAGTGACCCATGTTTGGATTGGAAATTAGATTTGGTCCATGGGTTTTGGAGGACCAATTTT
61 TGGTTAGTGACCCATGTTTGGATTGGAAATTAGATTTGGTCCATGGGTTTTGAAGGACCAATTTT
30490 GGTCCTTCTTGATCCTTAT
126 GGTCCTTCTTGATCCTTAT
30509 AAGTCCATAT
Statistics
Matches: 140, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
144 40 0.29
146 1 0.01
149 99 0.71
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.33
Consensus pattern (144 bp):
CAGTGTGTTTGGATTGAGGGACCAGTAAGAAACGGGATGGGACGGGACGGGAGGTCTTTTTGGTT
AGTGACCCATGTTTGGATTGGAAATTAGATTTGGTCCATGGGTTTTGAAGGACCAATTTTGGTCC
TTCTTGATCCTTAT
Found at i:30781 original size:221 final size:220
Alignment explanation
Indices: 30533--30950 Score: 730
Period size: 221 Copynumber: 1.9 Consensus size: 220
30523 TGGTACTCCA
* *
30533 ACTCCAAGTTGGAGTACCAACAAGGACCAAC-AAAGCTTTTATTTATAAAATGTTAGGTGATCCC
1 ACTCCAAATTGGAGTACCAACAAGGACCAACGAAA-CTTTTATTTAGAAAATGTTAGGTGATCCC
* *
30597 TCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGGATTGGTCCTTCCCTTCCTTTCCT
65 TCATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGAATTGGTCATTCCCTTCCTTTCCT
* *
30662 TTAAAAATCCCTCCTTTCCCATCCTATCCTGTCCTTTACTGATCCCTCGAAAAATTTATCCAAAC
130 TTAAAAATCCCTCATTTCCCATCCTATCCTGTCCTTTACTGATCCCT-AAAAAATTTATCCAAAC
30727 ACACTGTATAAGTCCATATTTTTTGGT
194 ACACTGTATAAGTCCATATTTTTTGGT
*
30754 ACTCCAAATTGGAGTACCAACAAGGACCAACGAAACTTTTATTTAGAAAATGTTAGGTGGTCCCT
1 ACTCCAAATTGGAGTACCAACAAGGACCAACGAAACTTTTATTTAGAAAATGTTAGGTGATCCCT
*
30819 CATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGAATTGGTCATTCCCTTCGTTTCCTT
66 CATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGAATTGGTCATTCCCTTCCTTTCCTT
*
30884 TAAAAATCCCTCATTTCCCATCCTATCCTGTCCTTTATTGATCCCTAAAAAATTTATCCAAACAC
131 TAAAAATCCCTCATTTCCCATCCTATCCTGTCCTTTACTGATCCCTAAAAAATTTATCCAAACAC
30949 AC
196 AC
30951 AGCCAGCACT
Statistics
Matches: 187, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
220 20 0.11
221 164 0.88
222 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (220 bp):
ACTCCAAATTGGAGTACCAACAAGGACCAACGAAACTTTTATTTAGAAAATGTTAGGTGATCCCT
CATGTTCCTTACTTTTTATATTTTAAACAATCCAAACAAGAATTGGTCATTCCCTTCCTTTCCTT
TAAAAATCCCTCATTTCCCATCCTATCCTGTCCTTTACTGATCCCTAAAAAATTTATCCAAACAC
ACTGTATAAGTCCATATTTTTTGGT
Found at i:31416 original size:14 final size:14
Alignment explanation
Indices: 31397--31424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31387 TCAAATGGGG
31397 AAGCATCATAAACA
1 AAGCATCATAAACA
31411 AAGCATCATAAACA
1 AAGCATCATAAACA
31425 TCTTTGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.07, T:0.14
Consensus pattern (14 bp):
AAGCATCATAAACA
Found at i:33804 original size:129 final size:128
Alignment explanation
Indices: 33575--33824 Score: 455
Period size: 129 Copynumber: 1.9 Consensus size: 128
33565 AAGGCACTGG
* *
33575 GAGGATAGTGAACTTCACCAAGAGGTAATTATCTTGCTATGTTGGTAAGGTTTATCAGATCCTTA
1 GAGGATAATGAACTTCACCAAGAGGTAATTATCTTGCTATGTTGGTAAGGTTCATCAGATCCTTA
33640 AGACTCTCTTCTGCTTCCTTGCAGCAATTGCTAAAATGAATTTCTACTCAAGTTCCCCATTGA
66 AGACTCTCTTCTGCTTCCTTGCAGCAATTGCTAAAATGAATTTCTACTCAAGTTCCCCATTGA
*
33703 GAGGATAATGAACTTCACCAAGAGGTAATTATCTTTGCTATGTTGGTAAGGTTCATCGGATCCTT
1 GAGGATAATGAACTTCACCAAGAGGTAATTATC-TTGCTATGTTGGTAAGGTTCATCAGATCCTT
*
33768 ACGACTCTCTTCTGCTTCCTTGCAGCAATTGCTAAAATGAATTTCTACTCAAGTTCC
65 AAGACTCTCTTCTGCTTCCTTGCAGCAATTGCTAAAATGAATTTCTACTCAAGTTCC
33825 TCAGTAATAA
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
128 32 0.27
129 85 0.73
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (128 bp):
GAGGATAATGAACTTCACCAAGAGGTAATTATCTTGCTATGTTGGTAAGGTTCATCAGATCCTTA
AGACTCTCTTCTGCTTCCTTGCAGCAATTGCTAAAATGAATTTCTACTCAAGTTCCCCATTGA
Found at i:40096 original size:14 final size:13
Alignment explanation
Indices: 40074--40116 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
40064 CAATATGAAA
40074 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
*
40087 CTTTTTTTTCTTTT
1 -TTCTTTTTCTTTT
*
40101 TTCTTTTTATTTT
1 TTCTTTTTCTTTT
40114 TTC
1 TTC
40117 AAAGTATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:40103 original size:21 final size:20
Alignment explanation
Indices: 40077--40116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40067 TATGAAATTC
*
40077 TTTTTCTTTTCTTTTTTTTCT
1 TTTTTCTTTT-TATTTTTTCT
40098 TTTTTCTTTTTATTTTTTC
1 TTTTTCTTTTTATTTTTTC
40117 AAAGTATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTTATTTTTTCT
Found at i:42116 original size:4 final size:4
Alignment explanation
Indices: 42107--42135 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42097 TATATTTATG
42107 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
42136 ATAACCTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:46307 original size:35 final size:33
Alignment explanation
Indices: 46240--46325 Score: 138
Period size: 35 Copynumber: 2.6 Consensus size: 33
46230 CTTTCTGCCC
46240 TTGCTTAGATGGATTTAC-TTTTTTTTCTTTCA
1 TTGCTTAGATGGATTTACTTTTTTTTTCTTTCA
*
46272 TTGCTTAGATGGATTTACTTTTTTTTTTTTGTTCA
1 TTGCTTAGATGGATTTAC-TTTTTTTTTCT-TTCA
46307 TTGCTTAGATGGATTTACT
1 TTGCTTAGATGGATTTACT
46326 AATTTACTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 18 0.36
34 10 0.20
35 22 0.44
ACGTcount: A:0.16, C:0.10, G:0.15, T:0.58
Consensus pattern (33 bp):
TTGCTTAGATGGATTTACTTTTTTTTTCTTTCA
Found at i:46933 original size:30 final size:29
Alignment explanation
Indices: 46899--46984 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
46889 GCATCCGACG
46899 TGGCATGCCACGTGTACAAAAAATGCCACA
1 TGGCATGCCACGTGTAC-AAAAATGCCACA
* * *
46929 TGGCATGCCACGTGTACAAAAAGGACATA
1 TGGCATGCCACGTGTACAAAAATGCCACA
*
46958 TGGCACGCCACGTGT-CAAAAATGCCAC
1 TGGCATGCCACGTGTACAAAAATGCCAC
46985 GTGCCATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 9 0.18
29 23 0.47
30 17 0.35
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (29 bp):
TGGCATGCCACGTGTACAAAAATGCCACA
Found at i:52702 original size:16 final size:16
Alignment explanation
Indices: 52676--52714 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
52666 TTCCTTCTCC
52676 CAAATTCTTTAACTCAT
1 CAAA-TCTTTAACTCAT
52693 CAAATCTTTAACTCAT
1 CAAATCTTTAACTCAT
52709 CAAATC
1 CAAATC
52715 GCTCCATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (16 bp):
CAAATCTTTAACTCAT
Found at i:56278 original size:44 final size:45
Alignment explanation
Indices: 56192--56280 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
56182 TAATAGAGTA
56192 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
*
56237 GTGGAATTACTAAAAGATCCCT-CCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
56281 AGAAGTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 21 0.49
45 22 0.51
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
Found at i:56959 original size:166 final size:166
Alignment explanation
Indices: 56590--56989 Score: 554
Period size: 167 Copynumber: 2.4 Consensus size: 166
56580 TAAAGTTTAA
*
56590 ACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAGACTTTTTGGTCATTTCTCA
1 ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGTCATTTCTCA
* * * * * * * ** *
56655 ATTGACTTTAATAGAGTAGTGGAATTACTAAAAGGTCCCTACCAAGACTTGCTTTTGGAGTTAGA
65 ATGGACTTGAATAGAGTAGTGGAACTAATAAAAGATCCCCACCAAGACTTGATGATGGAGCTAGA
* * *
56720 GAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATC
130 GAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATC
* *
56757 ACTTAAATGTCCA-AACTTTTGATTCTTGAGGGGATTAAACAAGTAATCTTTTTGGTCATTTCTC
1 ACTTAAATGT-CATAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTCTC
*
56821 AATGGACTTGAATAGAGTAGTGGAACTAATAAAAGATCCCCATCAAGGA-TTGATGAT-GAGCTA
64 AATGGACTTGAATAGAGTAGTGGAACTAATAAAAGATCCCCACCAA-GACTTGATGATGGAGCTA
*
56884 GAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATT
128 GAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATC
* *
56923 ACTTAAATGTCATAACTTTTGATTCTTAAAGGGATTAAATAACTAAACTTTTTGGTCATTTCTCA
1 ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTCA
56988 AT
65 AT
56990 TGAAAAGTGA
Statistics
Matches: 206, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
165 2 0.01
166 98 0.48
167 103 0.50
168 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (166 bp):
ACTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAA
TGGACTTGAATAGAGTAGTGGAACTAATAAAAGATCCCCACCAAGACTTGATGATGGAGCTAGAG
AACTAATCTTTTTCGTCTTTACCTACTTGGCAGATC
Found at i:58557 original size:438 final size:435
Alignment explanation
Indices: 57660--58666 Score: 1294
Period size: 438 Copynumber: 2.3 Consensus size: 435
57650 TTTCAAAAGT
* * *
57660 ATTTTTTAGAATTGAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAAA
* * * * *
57725 TTACCTTTTAATAAACACCTGAATTACCTTAATTGGACAAATAGAACAAAAAAAAATA-AAAAAG
66 TTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAG---GAAAAAAAATACAAAAAT
*
57789 AAATGAAGCGTTAAATCGAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAAAAAAGT
128 AAAT--A-CGTTAAATCGAATAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAAAAAAGT
* *
57854 ATGAGGGTCATTTGATAACAATTCAAATAAGAAAATATTTCTTAATGGATATCTTGAAACATAAA
190 ATGAGGGTCATTTGATAACAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
* * * *
57919 AATTTCCTTTTAAACCCTTCATGAAACTCGTAGATCAAATTAACTTTTGGGTTCTTCATGAAAGT
255 AAATCCCTTTTAAACCCTTCATGAAACTCGCAGATCAAATTAACTTTTGGGTCCTTCATGAAAGT
* * * * *
57984 CGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGAAATGTGGATCGAAA
320 CGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATCAAAA
* * * *
58049 ATTATATGATATTAAATAGACCAACAATCGAAACGACCAAATTTAGGAAGC
385 ATTATACGAAATTAAATAGACCAACAATCAAAACCACCAAATTTAGGAAGC
* * *
58100 ATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAAA
* * *
58165 TTACTTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGGAAAAAGAATACAAAAATAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGGAAAAAAAATACAAAAATAAA
* *
58230 T-C-TTAAA-CGCTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAA-TA
131 TACGTTAAATCG--A-A-TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATA-AAAAAGTA
* * * *
58291 TGAGGGTCATTTGATAAATAATCCAAGTAAGAAAATGTTTCTTAATGGAGATCTTGAAGCATAAA
191 TGAGGGTCATTTGAT-AACAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
* * *
58356 AAATCCCTTTTAAACCCTTCATGAAATTTGCAGATCAAATTTAGCTTTCT-GGTCCTTCATGAAA
255 AAATCCCTTTTAAACCCTTCATGAAACTCGCAGATCAAA-TTAACTTT-TGGGTCCTTCATGAAA
* * *
58420 GTCGTAAATCATGCAATAACCTTTTAACTGACACTTCAATAACTTCAATCGGACATGTGGA-CAA
318 GTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATC-A
* ** *
58484 AAAATTATACGAAATTAAATTGACCGGCAATCAAAACCA-CAAACTTTCGGAAGC
382 AAAATTATACGAAATTAAATAGACCAACAATCAAAACCACCAAA-TTTAGGAAGC
* * * * * * * *
58538 CTTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCGTGAAAATTGTAGATCATCAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAAA
* **
58603 TTACCTTTTAATAGACACTTGAATCACCTTAATCAGACAAATA-GAAAAAAAATACAAAAATAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGGAAAAAAAATACAAAAATAAA
58667 ATGCAACGCG
Statistics
Matches: 495, Mismatches: 61, Indels: 25
0.85 0.10 0.04
Matches are distributed among these distances:
432 2 0.00
433 5 0.01
434 2 0.00
435 1 0.00
436 52 0.11
437 116 0.23
438 218 0.44
439 1 0.00
440 98 0.20
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (435 bp):
ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATAAAA
TTACCTTTTAATAGACACATGAATCACCTTAATTGGACAAATAGGAAAAAAAATACAAAAATAAA
TACGTTAAATCGAATAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAAAAAAGTATGAGG
GTCATTTGATAACAATCCAAATAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAAATCC
CTTTTAAACCCTTCATGAAACTCGCAGATCAAATTAACTTTTGGGTCCTTCATGAAAGTCGTAAA
TCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATCAAAAATTATA
CGAAATTAAATAGACCAACAATCAAAACCACCAAATTTAGGAAGC
Done.