Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020307.1 Corchorus olitorius cultivar O-4 contig20340, 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: 53238
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1651 original size:22 final size:22
Alignment explanation
Indices: 1609--1651 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1599 TTTTTAATTA
**
1609 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
1631 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
1652 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:9410 original size:50 final size:49
Alignment explanation
Indices: 9351--9782 Score: 393
Period size: 50 Copynumber: 8.6 Consensus size: 49
9341 GATTAAAAGA
* * * * *
9351 TGAAACTTTTAAGCAATTTGTCAATAAAGATTGAATTTGTAAGTGGAAAT
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAA-TGAAAAT
* * * *
9401 TGAAGCTTTTAAGTAATTTGTAAATAAATATTGGATTTTTAATTAAAAGAT
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAA-TGAAA-AT
* * * * * *
9452 TAAACCTTTTAAGCAATTTGTGAATAAAGATTGGATTTTTAATTAAAAGA
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATGAAAA-T
*
9502 TAAACCTTTTAAGTAATTTGTGAAA-AAAGATTGAATTTTTAAGTGAAAAT
1 TGAACCTTTTAAGTAATTTGT-AAATAAAGATTGAATTTTTAA-TGAAAAT
* * * *
9552 TGAAACTTTTAAGTAATTTGTAAATAAATATTGGATTTTTTAATTAAAAGAT
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATT-GAATTTTTAA-TGAAA-AT
* * * * * * *
9604 TAAACCTTGTAAGCAATTTGTAAATAAA-AATGAGATTTTTGATTAAAAGA
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGA-ATTTTTAATGAAAA-T
* * *
9654 TGAAGCTTTTAAGTAATTTATGAATAAAGATTGAATTTTTAAGTGAAAGA-
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAA-TGAAA-AT
* * *
9704 TGAAACTTTTAAGTAATCTGTAAATAAAGATTGGATTTTTAATGAAAAGAT
1 TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATG-AAA-AT
* *
9755 TAAACCTTTTAAGCAATTTGTAAATAAA
1 TGAACCTTTTAAGTAATTTGTAAATAAA
9783 AGGGGAAATC
Statistics
Matches: 314, Mismatches: 54, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
49 7 0.02
50 181 0.58
51 99 0.32
52 27 0.09
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.38
Consensus pattern (49 bp):
TGAACCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATGAAAAT
Found at i:9668 original size:152 final size:150
Alignment explanation
Indices: 9335--9783 Score: 704
Period size: 151 Copynumber: 3.0 Consensus size: 150
9325 TAAAAATTTA
* * * *
9335 ATTTTTGATTAAAAGATGAAACTTTTAAGCAATTTGTCAATAAAGATTGAATTTGTAAGTGGAAA
1 ATTTTTGATTAAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAAGTGAAAA
*
9400 TTGAAGCTTTTAAGTAATTTGTAAATAAATATTGGATTTTTAATTAAAAGATTAAACCTTTTAAG
66 TTGAAACTTTTAAGTAATTTGTAAATAAATATTGGATTTTTAATTAAAAGATTAAACCTTTTAAG
* *
9465 CAATTTGTGAATAAAGATTGG
131 CAATTTGTAAATAAA-AATGG
* *
9486 ATTTTTAATTAAAAGAT-AAACCTTTTAAGTAATTTGTGAAAAAAGATTGAATTTTTAAGTGAAA
1 ATTTTTGATTAAAAGATGAAA-CTTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAAGTGAAA
*
9550 ATTGAAACTTTTAAGTAATTTGTAAATAAATATTGGATTTTTTAATTAAAAGATTAAACCTTGTA
65 ATTGAAACTTTTAAGTAATTTGTAAATAAATATTGGA-TTTTTAATTAAAAGATTAAACCTTTTA
9615 AGCAATTTGTAAATAAAAATGAG
129 AGCAATTTGTAAATAAAAATG-G
* *
9638 ATTTTTGATTAAAAGATGAAGCTTTTAAGTAATTTATGAATAAAGATTGAATTTTTAAGTGAAAG
1 ATTTTTGATTAAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAAGTGAAA-
* * *
9703 A-TGAAACTTTTAAGTAATCTGTAAATAAAGATTGGATTTTTAATGAAAAGATTAAACCTTTTAA
65 ATTGAAACTTTTAAGTAATTTGTAAATAAATATTGGATTTTTAATTAAAAGATTAAACCTTTTAA
9767 GCAATTTGTAAATAAAA
130 GCAATTTGTAAATAAAA
9784 GGGGAAATCT
Statistics
Matches: 275, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
150 3 0.01
151 136 0.49
152 133 0.48
153 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (150 bp):
ATTTTTGATTAAAAGATGAAACTTTTAAGTAATTTGTGAATAAAGATTGAATTTTTAAGTGAAAA
TTGAAACTTTTAAGTAATTTGTAAATAAATATTGGATTTTTAATTAAAAGATTAAACCTTTTAAG
CAATTTGTAAATAAAAATGG
Found at i:10500 original size:48 final size:48
Alignment explanation
Indices: 10375--11060 Score: 921
Period size: 48 Copynumber: 14.2 Consensus size: 48
10365 TAAATCGAAA
10375 ATTCCTGTTTTGCCCTTCCCGG-CTGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTC-GGAAGGTGTTGTTTTCAATGTTTT
* * * *
10423 CATTCATGTTTTGCCCTTCCTGGTCGGAAGGTGATGTTTTCAATATTTT
1 -ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * *
10472 ATTCCTGTTTTGCCATTCCAGGTTGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* ** * *
10520 ATTTCTACTTTGCCCTTCCCGGCCGGAAGGTGTTGTCTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
*
10568 CATTCCTGTTTTGCCATT-CCGGTCGGAAGGTGTTGTTTTCAATGTTTT
1 -ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * *
10616 ATTCCTGTTTTGCCCTTCCCGGCCAGAAGGTGTTGTTTTCAATATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * *
10664 ATTCATGTTTTGCCATTCCC-GACAGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTC-GGAAGGTGTTGTTTTCAATGTTTT
* * *
10712 CATTCTTGTTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCATTGTTTT
1 -ATTCCTG-TTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* *
10762 ATTCATGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* *
10810 ATTCTTGTTTTGCTCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
*
10858 ATTCATGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * * *
10906 ATT-CTCGTTTTACCCTTCCTGGTCGGAAGGTGTTGTCTTCAACGTTTT
1 ATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* ** * *
10954 ATTCCCGTTTTGCCCTTTTCGATTGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * * *
11002 ATTCATGTTTTGTCTTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
11050 ATTCCTGTTTT
1 ATTCCTGTTTT
11061 CAATGTTTTA
Statistics
Matches: 558, Mismatches: 70, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
47 19 0.03
48 433 0.78
49 68 0.12
50 36 0.06
51 2 0.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (48 bp):
ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
Found at i:11060 original size:20 final size:20
Alignment explanation
Indices: 11035--11080 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
11025 CGGAAGGTGT
11035 TGTTTTCAATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
11055 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
11075 CGTTTT
1 TGTTTT
11081 GCCCTTCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:11118 original size:163 final size:164
Alignment explanation
Indices: 10891--11194 Score: 459
Period size: 163 Copynumber: 1.9 Consensus size: 164
10881 CGGAAGGTGT
*
10891 TGTTTTCAATGTTTTATTCTCGTTTTACCCTTCCTGGTCGGAAGGTGTTGTCTTCAACGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTACCCTTCCTGGTCGGAAGGTGTTGTCTTCAACGTTTTAT
** * ** *
10956 TCCCGTTTTGCCCTTTTCGATTGGAAGGTGTTGTTTTCAATGTTTTATTCAT-GTTTTGTCTTTC
66 TCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAACATTTTATTC-TCGTTTTGTCATTC
**
11020 CCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCC
130 CCCATCGGAAGGTGTTGTTTTCAATATTTTATTCC
* * *
11055 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCC-GGTCGGAAGGTGTTGTCTTTAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTACCCTTCCTGGTCGGAAGGTGTTGTCTTCAACGTTTTAT
* *
11119 TCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCTCGTTTTGTCATTCC
66 TCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAACATTTTATTCTCGTTTTGTCATTCC
11184 CCATCGGAAGG
131 CCATCGGAAGG
11195 AGTAGTTCCT
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 1 0.01
163 92 0.74
164 32 0.26
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (164 bp):
TGTTTTCAATGTTTTATTCCCGTTTTACCCTTCCTGGTCGGAAGGTGTTGTCTTCAACGTTTTAT
TCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAACATTTTATTCTCGTTTTGTCATTCC
CCATCGGAAGGTGTTGTTTTCAATATTTTATTCC
Found at i:11119 original size:67 final size:68
Alignment explanation
Indices: 10987--11127 Score: 214
Period size: 67 Copynumber: 2.1 Consensus size: 68
10977 TGGAAGGTGT
* * *
10987 TGTTTTCAATGTTTTATTCATGTTTTGTCTTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
1 TGTTTTCAATGTTTTATTCACGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
11052 TCC
66 TCC
* *
11055 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTT-CCGGTCGGAAGGTGTTGTCTTT-AATGTTTTA
1 TGTTTTCAATGTTTTATTCACGTTTTGCCCTTCCCGGTCGGAAGGTGTTGT-TTTCAATATTTTA
11118 TTCC
65 TTCC
11122 TGTTTT
1 TGTTTT
11128 GCCCTTCCCG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 36 0.54
68 31 0.46
ACGTcount: A:0.13, C:0.16, G:0.18, T:0.52
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCACGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTAT
TCC
Found at i:11165 original size:48 final size:48
Alignment explanation
Indices: 11055--11194 Score: 178
Period size: 48 Copynumber: 2.9 Consensus size: 48
11045 ATTTTATTCC
*
11055 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTT-CCGGTCGGAAGGTGT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
11102 TGTCTTT-AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGT-TTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
** * * **
11150 TGTTTTCAACATTTTATT-CTCGTTTTGTCATTCCCCATCGGAAGG
1 TGTTTTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGG
11195 AGTAGTTCCT
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
47 32 0.39
48 50 0.61
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (48 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
Found at i:11175 original size:115 final size:116
Alignment explanation
Indices: 10943--11168 Score: 357
Period size: 115 Copynumber: 2.0 Consensus size: 116
10933 AGGTGTTGTC
* *
10943 TTCAACGTTTTATTCCCGTTTTGCCCTTTTCGATTGGAAGGTGTTGTTTTCAATGTTTTATTCAT
1 TTCAACGTTTTATTCCCGTTTTGCCCTTTCCGATCGGAAGGTGTTGTTTTCAATGTTTTATTCAT
* * *
11008 GTTTTGTCTTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTT
66 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTGTT
* * *
11059 TTCAATGTTTTATTCCCGTTTTGCCC-TTCCGGTCGGAAGGTGTTGTCTTT-AATGTTTTATTCC
1 TTCAACGTTTTATTCCCGTTTTGCCCTTTCCGATCGGAAGGTGTTGT-TTTCAATGTTTTATTCA
11122 TGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTC
65 TGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTC
11169 TCGTTTTGTC
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
115 73 0.72
116 28 0.28
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (116 bp):
TTCAACGTTTTATTCCCGTTTTGCCCTTTCCGATCGGAAGGTGTTGTTTTCAATGTTTTATTCAT
GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAACATTTTATTCCTGTT
Found at i:14171 original size:15 final size:16
Alignment explanation
Indices: 14143--14172 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14133 ATTTATCTTC
14143 TATCTTCATTTGTTTT
1 TATCTTCATTTGTTTT
14159 TATCTTC-TTTGTTT
1 TATCTTCATTTGTTT
14173 GCCTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.13, G:0.07, T:0.70
Consensus pattern (16 bp):
TATCTTCATTTGTTTT
Found at i:19878 original size:25 final size:25
Alignment explanation
Indices: 19844--19948 Score: 129
Period size: 25 Copynumber: 4.1 Consensus size: 25
19834 ACATTATTTG
*
19844 GTGCAAAAAGGAATGCAAATGTAGA
1 GTGCAAAAAGAAATGCAAATGTAGA
*
19869 GTGCAAAAAGGAATGCAAATGTAGA
1 GTGCAAAAAGAAATGCAAATGTAGA
* * *
19894 TTGCAAACAGAAATGCAAATGTATA
1 GTGCAAAAAGAAATGCAAATGTAGA
*
19919 ATGCAAAAAAAAGAAATGCAAATGTAGA
1 GTGC---AAAAAGAAATGCAAATGTAGA
19947 GT
1 GT
19949 ACAACTACCA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
25 49 0.71
28 20 0.29
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (25 bp):
GTGCAAAAAGAAATGCAAATGTAGA
Found at i:20514 original size:28 final size:28
Alignment explanation
Indices: 20477--20570 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
20467 TTGAGGTGAC
20477 CCAAAATGCCCCTGGATGTGCAAAATGA
1 CCAAAATGCCCCTGGATGTGCAAAATGA
**
20505 CCAAAATGCCCCTGGACATGCAAAATGA
1 CCAAAATGCCCCTGGATGTGCAAAATGA
* * *
20533 CCAAAATGCCCTTAG-TGT-AAAAATGA
1 CCAAAATGCCCCTGGATGTGCAAAATGA
20559 CCAAAATGCCCC
1 CCAAAATGCCCC
20571 ATTAGGTGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.31
27 1 0.02
28 39 0.67
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (28 bp):
CCAAAATGCCCCTGGATGTGCAAAATGA
Found at i:21089 original size:36 final size:34
Alignment explanation
Indices: 21012--21104 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 34
21002 ACCTTTAAAG
*
21012 ATGCTACACTGAGTCATCTGAATTCATCCATTGAAG
1 ATGCTACACTGAGTCATCT-AATTCAT-CATTGAAA
*
21048 ATGCTACACTGAGTCATCTACATTCAAT-TTTGAAA
1 ATGCTACACTGAGTCATCTA-ATTC-ATCATTGAAA
* *
21083 ATTGCTACACCGAGCCATCTAA
1 A-TGCTACACTGAGTCATCTAA
21105 ATTCCTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
35 8 0.16
36 40 0.80
37 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (34 bp):
ATGCTACACTGAGTCATCTAATTCATCATTGAAA
Found at i:32952 original size:9 final size:9
Alignment explanation
Indices: 32938--32964 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
32928 CAATAAACAT
32938 CAAAACAAA
1 CAAAACAAA
32947 CAAAACAAA
1 CAAAACAAA
32956 CAAAACAAA
1 CAAAACAAA
32965 GCAACTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAACAAA
Found at i:37124 original size:12 final size:12
Alignment explanation
Indices: 37107--37149 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
37097 CATTATTTGG
37107 TGCAAAAAGGAA
1 TGCAAAAAGGAA
*
37119 TGC-AAATGTAGAA
1 TGCAAAAAG--GAA
37132 TGCAAAAAGGAA
1 TGCAAAAAGGAA
37144 TGCAAA
1 TGCAAA
37150 TGCAGATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 6 0.23
14 4 0.15
ACGTcount: A:0.53, C:0.09, G:0.23, T:0.14
Consensus pattern (12 bp):
TGCAAAAAGGAA
Found at i:37134 original size:13 final size:13
Alignment explanation
Indices: 37116--37207 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
37106 GTGCAAAAAG
37116 GAATGCAAATGTA
1 GAATGCAAATGTA
*
37129 GAATGCAAA--AA
1 GAATGCAAATGTA
*
37140 GGAATGCAAATGCA
1 -GAATGCAAATGTA
* *
37154 GATTGCAAA--CA
1 GAATGCAAATGTA
37165 GAAATGCAAATGTA
1 G-AATGCAAATGTA
* ***
37179 TAATGCAAAAAAA
1 GAATGCAAATGTA
37192 GAAATGCAAATGTA
1 G-AATGCAAATGTA
37206 GA
1 GA
37208 GTACAACCAC
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
11 4 0.07
12 16 0.27
13 27 0.46
14 12 0.20
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (13 bp):
GAATGCAAATGTA
Found at i:37141 original size:25 final size:25
Alignment explanation
Indices: 37107--37207 Score: 130
Period size: 25 Copynumber: 4.0 Consensus size: 25
37097 CATTATTTGG
*
37107 TGCAAAAAGGAATGCAAATGTAGAA
1 TGCAAAAAGAAATGCAAATGTAGAA
* * *
37132 TGCAAAAAGGAATGCAAATGCAGAT
1 TGCAAAAAGAAATGCAAATGTAGAA
* *
37157 TGCAAACAGAAATGCAAATGTATAA
1 TGCAAAAAGAAATGCAAATGTAGAA
37182 TGCAAAAAAAGAAATGCAAATGTAGA
1 TGC--AAAAAGAAATGCAAATGTAGA
37208 GTACAACCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
25 46 0.71
27 19 0.29
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (25 bp):
TGCAAAAAGAAATGCAAATGTAGAA
Found at i:37774 original size:28 final size:28
Alignment explanation
Indices: 37737--37830 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
37727 CTGAGGTGAC
*
37737 CCAAAATGCCCCTGGATATGGAAAATGA
1 CCAAAATGCCCCTGGATATGAAAAATGA
* *
37765 CCAAAATGCCCCTGGACATGCAAAATGA
1 CCAAAATGCCCCTGGATATGAAAAATGA
* * *
37793 CCAAAATGCCCTTTG-TGT-AAAAATGA
1 CCAAAATGCCCCTGGATATGAAAAATGA
37819 CCAAAATGCCCC
1 CCAAAATGCCCC
37831 CCTTAGGTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.31
27 1 0.02
28 39 0.67
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (28 bp):
CCAAAATGCCCCTGGATATGAAAAATGA
Found at i:46403 original size:15 final size:17
Alignment explanation
Indices: 46383--46415 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
46373 CGTTCAAATG
46383 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
46398 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
46415 T
1 T
46416 GAGTCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:48724 original size:49 final size:47
Alignment explanation
Indices: 48649--48789 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 47
48639 CAAGCAATCC
*** *
48649 TTTACTTTTTACTGCACTTTTTCTCAATTTTTACTTCAAAGTTGAACT
1 TTTA-TTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
*
48697 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTAC-TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
* * *
48746 TTTAATTTTCACTGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTT-ATTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGA
48790 TTGGCACGCT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
47 18 0.22
48 23 0.28
49 34 0.41
50 7 0.09
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (47 bp):
TTTATTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:50548 original size:16 final size:16
Alignment explanation
Indices: 50527--50562 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
50517 GGGTTGATTT
* *
50527 GGTTTGGGTCATTTTG
1 GGTTTGGGACATTTCG
50543 GGTTTGGGACATTTCG
1 GGTTTGGGACATTTCG
50559 GGTT
1 GGTT
50563 GTTTGGATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.08, G:0.39, T:0.44
Consensus pattern (16 bp):
GGTTTGGGACATTTCG
Found at i:50613 original size:16 final size:17
Alignment explanation
Indices: 50594--50630 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
50584 CCCAAAAATC
50594 TGGGTCA-TTTCTGGGT
1 TGGGTCAGTTTCTGGGT
*
50610 TGGGTCAGTTTTTGGGT
1 TGGGTCAGTTTCTGGGT
50627 TGGG
1 TGGG
50631 CGGATTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.05, C:0.08, G:0.43, T:0.43
Consensus pattern (17 bp):
TGGGTCAGTTTCTGGGT
Done.