Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014885.1 Corchorus capsularis cultivar CVL-1 contig14906, 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: 54482
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4102 original size:2 final size:2
Alignment explanation
Indices: 4095--4127 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4085 TAATTGCCTA
4095 AT AT 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 AT AT A
4128 GCCTTGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5161 original size:15 final size:15
Alignment explanation
Indices: 5141--5173 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5131 TAGTTTATGG
5141 TTATTTTCTTTGCCT
1 TTATTTTCTTTGCCT
5156 TTATTTTCTTTGCCT
1 TTATTTTCTTTGCCT
5171 TTA
1 TTA
5174 ACTGGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.18, G:0.06, T:0.67
Consensus pattern (15 bp):
TTATTTTCTTTGCCT
Found at i:8116 original size:2 final size:2
Alignment explanation
Indices: 8105--8141 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
8095 TTAAGTCTTT
8105 TA TA TA -A TA TA TA TA TA TA 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 TA TA
8142 AAGTTTATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11579 original size:15 final size:15
Alignment explanation
Indices: 11559--11589 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11549 AATTATCGTT
11559 ATCAAAAGATTTTGG
1 ATCAAAAGATTTTGG
11574 ATCAAAAGATTTTGG
1 ATCAAAAGATTTTGG
11589 A
1 A
11590 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
ATCAAAAGATTTTGG
Found at i:14225 original size:11 final size:11
Alignment explanation
Indices: 14195--14237 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
14185 TGCTTCTACC
*
14195 AAAAGAAATGA
1 AAAAGAAAAGA
**
14206 AAATTAAAAGA
1 AAAAGAAAAGA
14217 AAAAGAAAAAGA
1 AAAAG-AAAAGA
14229 AAAAGAAAA
1 AAAAGAAAA
14238 AACAAAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:14238 original size:6 final size:6
Alignment explanation
Indices: 14211--14251 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
14201 AATGAAAATT
14211 AAAAGA AAAAGA AAAAGA AAAAGA AAAA-A CAAAAGGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAA-GA AAAA
14252 CCAAAAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 26 0.81
7 4 0.12
8 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:14256 original size:13 final size:13
Alignment explanation
Indices: 14222--14266 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
14212 AAAGAAAAAG
* *
14222 AAAAAGAAAAAGA
1 AAAAACAAAAGGA
14235 AAAAACAAAAGGA
1 AAAAACAAAAGGA
*
14248 AAAACCAAAAGGCA
1 AAAAACAAAAGG-A
14262 AAAAA
1 AAAAA
14267 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAGGA
Found at i:15645 original size:17 final size:17
Alignment explanation
Indices: 15623--15657 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15613 TGTTTCATTC
15623 AAGTCCTAGGAGATGGA
1 AAGTCCTAGGAGATGGA
15640 AAGTCCTAGGAGATGGA
1 AAGTCCTAGGAGATGGA
15657 A
1 A
15658 TATTTTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.17
Consensus pattern (17 bp):
AAGTCCTAGGAGATGGA
Found at i:16735 original size:30 final size:30
Alignment explanation
Indices: 16699--16757 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
16689 AGGGGTGCGA
*
16699 CCGAATTCCGATTAAGGCGATTCTAGCAGT
1 CCGAATTCCAATTAAGGCGATTCTAGCAGT
*
16729 CCGAATTCTAATTAAGGCGATTCTAGCAG
1 CCGAATTCCAATTAAGGCGATTCTAGCAG
16758 CATTTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (30 bp):
CCGAATTCCAATTAAGGCGATTCTAGCAGT
Found at i:17052 original size:48 final size:49
Alignment explanation
Indices: 16968--17060 Score: 179
Period size: 48 Copynumber: 1.9 Consensus size: 49
16958 AATCGAATGG
16968 TCAGGGAGGTGAGAAAAAAAAAAACAATCGAAAACTTTCAGATATCGGA
1 TCAGGGAGGTGAGAAAAAAAAAAACAATCGAAAACTTTCAGATATCGGA
17017 TCAGGGAGGTGAG-AAAAAAAAAACAATCGAAAACTTTCAGATAT
1 TCAGGGAGGTGAGAAAAAAAAAAACAATCGAAAACTTTCAGATAT
17061 AGAGTCAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 31 0.70
49 13 0.30
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.17
Consensus pattern (49 bp):
TCAGGGAGGTGAGAAAAAAAAAAACAATCGAAAACTTTCAGATATCGGA
Found at i:17085 original size:178 final size:174
Alignment explanation
Indices: 16788--17134 Score: 579
Period size: 178 Copynumber: 2.0 Consensus size: 174
16778 GAAGAATCAG
* *
16788 ATGGTCAGAGAGGTGAGGAAAAAAAACAATCGAAAACTTTCAGATATCGGATCATGGAGGTGAGG
1 ATGGTCAGAGAGGTGAGAAAAAAAAACAATCGAAAACTTTCAGATATCGGATCAGGGAGGTGAGG
* *
16853 AAAAAAAAAACAATCGAAAACTTTCAGATTCGAGTCAAATTTAAAAGTTTGACTAGAAGGTATGG
66 AAAAAAAAAACAATCGAAAACTTTCAGATTAGAGTCAAATTTAAAAGTTTGACTAGAAGGTACGG
16918 TCTTATTCGGCATTGAAACAGATATGTCACTATTTGAAGGAATCGA
131 TCTTATTCGGCATTGAAACAG--ATGTCACTATTTGAAGGAATCGA
*
16964 ATGGTCAGGGAGGTGAGAAAAAAAAAAACAATCGAAAACTTTCAGATATCGGATCAGGGAGGTGA
1 ATGGTCAGAGAGGTGAG--AAAAAAAAACAATCGAAAACTTTCAGATATCGGATCAGGGAGGTGA
*
17029 -GAAAAAAAAAACAATCGAAAACTTTCAGATATAGAGTCAAATTTAAAAGTTTGACTAGAAGGTG
64 GGAAAAAAAAAACAATCGAAAACTTTCAGAT-TAGAGTCAAATTTAAAAGTTTGACTAGAAGGTA
*
17093 CGGTCTTATTCGGCATTGGAACAGATGTCACTATTTGAAGGA
128 CGGTCTTATTCGGCATTGAAACAGATGTCACTATTTGAAGGA
17135 TGCTAGATCT
Statistics
Matches: 161, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
176 34 0.21
177 30 0.19
178 97 0.60
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (174 bp):
ATGGTCAGAGAGGTGAGAAAAAAAAACAATCGAAAACTTTCAGATATCGGATCAGGGAGGTGAGG
AAAAAAAAAACAATCGAAAACTTTCAGATTAGAGTCAAATTTAAAAGTTTGACTAGAAGGTACGG
TCTTATTCGGCATTGAAACAGATGTCACTATTTGAAGGAATCGA
Found at i:17612 original size:27 final size:28
Alignment explanation
Indices: 17568--17623 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
17558 TCTCGTTTTT
17568 AAAAGTTAAGGGACCAATTTGTCCAAAA
1 AAAAGTTAAGGGACCAATTTGTCCAAAA
*
17596 AAAAGTTAAGGGA-CAATTTGTCCCAAA
1 AAAAGTTAAGGGACCAATTTGTCCAAAA
17623 A
1 A
17624 TGGATAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.21
Consensus pattern (28 bp):
AAAAGTTAAGGGACCAATTTGTCCAAAA
Found at i:24634 original size:7 final size:7
Alignment explanation
Indices: 24622--24649 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
24612 TTTGCTCTCA
24622 CTTGTTT
1 CTTGTTT
24629 CTTGTTT
1 CTTGTTT
24636 CTTGTTT
1 CTTGTTT
24643 CTTGTTT
1 CTTGTTT
24650 GTTTGTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.71
Consensus pattern (7 bp):
CTTGTTT
Found at i:28405 original size:17 final size:17
Alignment explanation
Indices: 28364--28416 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
28354 CCCCTAAATT
28364 ACTGGTGATATAAGATC
1 ACTGGTGATATAAGATC
* * *
28381 ATTAGTGATGTAAGATC
1 ACTGGTGATATAAGATC
*
28398 ACTGGTGATATTAGATC
1 ACTGGTGATATAAGATC
28415 AC
1 AC
28417 CTGGATTTAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (17 bp):
ACTGGTGATATAAGATC
Found at i:29967 original size:138 final size:137
Alignment explanation
Indices: 29717--29992 Score: 455
Period size: 138 Copynumber: 2.0 Consensus size: 137
29707 ACCCATCGCA
*
29717 ATTTAACATGGAATAAGGAGATGGTAGTTTACTCCAAAAAACTGGTAATGGGTGAAGATGTTGAA
1 ATTTAACATGAAATAAGGAGATGGTAGTTTACTCCAAAAAACTGGTAATGGGTGAAGATGTTGAA
* * **
29782 ACCTATAAAACTTTTTGTGATTTTTGAAACTAAGAGGTTTCATAATTGGTGAAATTTTTTTGAGA
66 ACCTATAAAACTTTTTGTGATTTTTAAAACTAAGAGGTTTCAGAATT-GTGAAAAGTTTTTGAGA
*
29847 TATAGGAG
130 TACAGGAG
* *
29855 ATTTAACTTGAAATAAGGAGATGGTGGTTTAC-CCTAAAAAACTGGTAATGGGTGAAGATGTTGA
1 ATTTAACATGAAATAAGGAGATGGTAGTTTACTCC-AAAAAACTGGTAATGGGTGAAGATGTTGA
29919 AACCTATAAAACTTTTTGTGATTTTTAAAACTAAGAGGTTTCAGAATTGTGAAAAGTTTTTGAGA
65 AACCTATAAAACTTTTTGTGATTTTTAAAACTAAGAGGTTTCAGAATTGTGAAAAGTTTTTGAGA
29984 TACAGGAG
130 TACAGGAG
29992 A
1 A
29993 GAGTAGGACA
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
137 25 0.19
138 104 0.81
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (137 bp):
ATTTAACATGAAATAAGGAGATGGTAGTTTACTCCAAAAAACTGGTAATGGGTGAAGATGTTGAA
ACCTATAAAACTTTTTGTGATTTTTAAAACTAAGAGGTTTCAGAATTGTGAAAAGTTTTTGAGAT
ACAGGAG
Found at i:33203 original size:5 final size:5
Alignment explanation
Indices: 33193--33232 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
33183 GATAATGTTT
33193 TTTTG TTTTG TTTTG TTTTG TTTTTG TTTTG TTTT- TTTTG
1 TTTTG TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG TTTTG
33233 CGATAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:33217 original size:11 final size:11
Alignment explanation
Indices: 33192--33228 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
33182 AGATAATGTT
33192 TTTTTGTTTTG
1 TTTTTGTTTTG
33203 -TTTTGTTTTG
1 TTTTTGTTTTG
33213 TTTTTGTTTTG
1 TTTTTGTTTTG
33224 TTTTT
1 TTTTT
33229 TTTGCGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:33218 original size:21 final size:20
Alignment explanation
Indices: 33192--33232 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
33182 AGATAATGTT
33192 TTTTTGTTTTGTTTTGTTTTG
1 TTTTTGTTTTGTTTT-TTTTG
33213 TTTTTGTTTTGTTTTTTTTG
1 TTTTTGTTTTGTTTTTTTTG
33233 CGATAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (20 bp):
TTTTTGTTTTGTTTTTTTTG
Found at i:34618 original size:30 final size:31
Alignment explanation
Indices: 34582--34650 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
34572 GTGCAAATGG
*
34582 GTCCCTAAAGTGAACTT-AGTGAGTAATTGA
1 GTCCCTAAAGTGAACTTAAGTGAGCAATTGA
* * * *
34612 GTCCCTAAAGTGGAGTTAATTGAGCAATTGG
1 GTCCCTAAAGTGAACTTAAGTGAGCAATTGA
34643 GTCCCTAA
1 GTCCCTAA
34651 CTCATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (31 bp):
GTCCCTAAAGTGAACTTAAGTGAGCAATTGA
Found at i:34647 original size:31 final size:30
Alignment explanation
Indices: 34574--34650 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
34564 GGACAAATGT
*
34574 GCAAATGGGTCCCTAAAGTGAACTTAGTGA
1 GCAATTGGGTCCCTAAAGTGAACTTAGTGA
* * * * *
34604 GTAATTGAGTCCCTAAAGTGGAGTTAATTGA
1 GCAATTGGGTCCCTAAAGTGAACTT-AGTGA
34635 GCAATTGGGTCCCTAA
1 GCAATTGGGTCCCTAA
34651 CTCATTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (30 bp):
GCAATTGGGTCCCTAAAGTGAACTTAGTGA
Found at i:42260 original size:25 final size:24
Alignment explanation
Indices: 42215--42261 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
42205 TATTCAAAGT
**
42215 ATGATTTAATATTATCTAAATTAA
1 ATGATTTAATATTATAAAAATTAA
*
42239 ATGATTTCATTATTATAAAAATT
1 ATGATTT-AATATTATAAAAATT
42262 CTCAAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
ATGATTTAATATTATAAAAATTAA
Found at i:44160 original size:30 final size:31
Alignment explanation
Indices: 44106--44170 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
44096 AACTTTATAT
*
44106 TTTCCGATTGTATCCTTATTTTTAAAACATA
1 TTTCCAATTGTATCCTTATTTTTAAAACATA
44137 TTTCCAATTGTATCCTT-TTTTTAAAACATA
1 TTTCCAATTGTATCCTTATTTTTAAAACATA
44167 TTTC
1 TTTC
44171 TAAATTGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTCCAATTGTATCCTTATTTTTAAAACATA
Found at i:44177 original size:31 final size:31
Alignment explanation
Indices: 44112--44177 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 31
44102 ATATTTTCCG
*
44112 ATTGTATCCTTATTTTTAAAACATATTTCCA
1 ATTGTATCCTTATTTTTAAAACATATTTCAA
44143 ATTGTATCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTATCCTTATTTTTAAAACATATTTC-AA
44174 ATTG
1 ATTG
44178 CTATTACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (31 bp):
ATTGTATCCTTATTTTTAAAACATATTTCAA
Found at i:44943 original size:22 final size:22
Alignment explanation
Indices: 44918--45093 Score: 149
Period size: 22 Copynumber: 7.9 Consensus size: 22
44908 TCTCTCTATG
**
44918 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGTA
* * *
44940 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGTA
*
44963 -GGTTATCAAAATTCCATAGTA
1 TGGTTATCAAAATTTCATAGTA
*
44984 TGGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAGTA
* * *
45006 TGGTTACCAAAATTTCATAATG
1 TGGTTATCAAAATTTCATAGTA
* * *
45028 TAGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGTA
* *
45050 TCAGGTTATTAAAATTTCTTAGGT-
1 T--GGTTATCAAAATTTCATA-GTA
**
45074 TGGTTATTGAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
45094 GGTGGTTAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.03
22 104 0.83
23 2 0.02
24 15 0.12
25 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGTA
Found at i:44987 original size:44 final size:44
Alignment explanation
Indices: 44919--45944 Score: 178
Period size: 44 Copynumber: 23.8 Consensus size: 44
44909 CTCTCTATGT
* *
44919 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGAG-GA
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCAT-AGTGA
* ** *
44963 GGTTATCAAAATTCCATAGTATGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
* ** * * *
45007 GGTTACCAAAATTTCATAATGTAGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATA-G-TGA
* * *** ** * *
45053 GGTTATTAAAATTTCTTAGGTTGGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
* * * **
45097 GG-T-T---AA-TT-ATCACAAT-TTTATAGAAAATTT-ATCAAAGA
1 GGTTATCAAAATTTCAT-AAAATGGTTAT-CAAAATTTCAT-AGTGA
* * ** *
45135 GATTATCAAAATGTCATAGCGA-GGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAAAATTTCATA-AAATGGTTATCAA-AATTTCATAGTGA
* * ** * * *
45179 GGTTAACAGAATTTCATTAGGA-GGTTACTC-ATATTTCATGGGGA
1 GGTTATCAAAATTTCA-TAAAATGGTTA-TCAAAATTTCATAGTGA
* ****
45223 GGTTATCAAAATTTTATAGTGCGGTTATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTG-A
* * * * * * **
45267 GGTTATGAAAGTCTCAATTTCATAATGAG-TACCAAAATTTGATA-AAA
1 GGTTATCAAAATTTC-A--T-AAAATG-GTTATCAAAATTTCATAGTGA
* * * * * *
45314 GGTTATC-AAATCTCATATAGTGATTATCGAAATTTCATAGCGA
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
* * * *
45357 TGGAGTTATCAAAATTT-ATAGTAA-GATTATCGAAATTTCATAGTGT
1 --G-GTTATCAAAATTTCATA-AAATGGTTATCAAAATTTCATAGTGA
* * * *
45403 TGTTATCAAAATTTCA-AAGCAA-GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAA--AATGGTTATCAAAATTTCATAGTGA
* * * ** * * *
45447 GATTATCAGAATTTCATAGAGGGGTCAACAAAA-TTCTATAAAT-A
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTC-AT-AGTGA
* * *
45491 GGTTATCAAAATTTCATAAAGA-GGTTATC-AAATTCTCAAAATGT
1 GGTTATCAAAATTTCATAAA-ATGGTTATCAAAATT-TCATAGTGA
* * * *
45535 GATTA-CAAAAATTTCAT--AGTGG---T----ATTT--TGGGGA
1 GGTTATC-AAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
** * *
45568 GGTTATCAAAATTTCATAGTATGATTA-CCAAA--T--TAG-GAA
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTG-A
* * ** * *
45607 GGTTATTAAACTTT--TATTATGGAGTAATCAAAATTTC--AGGGA
1 GGTTATCAAAATTTCATAAAAT-G-GTTATCAAAATTTCATAGTGA
* * * *
45649 GGATATCAAAATTTCATAAGAA-AGTTATCAAAATTCCATAGTTTA
1 GGTTATCAAAATTTCATAA-AATGGTTATCAAAATTTCATAG-TGA
* * *
45694 -GTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGT-A
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
* * ** * * * *
45736 TGTAGATCAAAATTTCATAGGGA-GATTAACAAAATTTCATAATAA
1 GGT-TATCAAAATTTCATA-AAATGGTTATCAAAATTTCATAGTGA
* * ** **
45781 TGTTACCAAAAAATCATAGGGA-GGTTATCAAAA-TT--T-GT-A
1 GGTTATCAAAATTTCATA-AAATGGTTATCAAAATTTCATAGTGA
* * * *
45820 -GTTATCAAAATTTCGTAAGAA-AGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTCATAA-AATGGTTATCAAAATTTCATAGTGA
* *
45863 GGTTTATCAAAATTTTATAGGAAGAT--TTATCAAAATTTCATAGCGA
1 GG-TTATCAAAATTTCATA--AA-ATGGTTATCAAAATTTCATAGTGA
** *
45909 GGTTATCAAAATTTCATAATGTGATTATCAAAATTT
1 GGTTATCAAAATTTCATAAAATGGTTATCAAAATTT
45945 GAAAGTGTGA
Statistics
Matches: 721, Mismatches: 170, Indels: 182
0.67 0.16 0.17
Matches are distributed among these distances:
33 15 0.02
34 1 0.00
35 3 0.00
36 3 0.00
37 12 0.02
38 39 0.05
39 25 0.03
40 6 0.01
41 3 0.00
42 51 0.07
43 48 0.07
44 333 0.46
45 62 0.09
46 87 0.12
47 17 0.02
48 15 0.02
49 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAAATGGTTATCAAAATTTCATAGTGA
Found at i:45162 original size:22 final size:22
Alignment explanation
Indices: 45137--46125 Score: 233
Period size: 22 Copynumber: 44.7 Consensus size: 22
45127 ATCAAAGAGA
* *
45137 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
45159 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
45181 TTAACAGAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
45203 TTACTC-ATATTTCATGGGGAGG
1 TTA-TCAAAATTTCATAGTGAGG
* *
45225 TTATCAAAATTTTATAGTGCGG
1 TTATCAAAATTTCATAGTGAGG
45247 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
45269 TTATGAAAGTCTCAATTTCATAATGA-G
1 TTAT-CAA-----AATTTCATAGTGAGG
* * **
45296 -TACCAAAATTTGATA-AAAGG
1 TTATCAAAATTTCATAGTGAGG
*
45316 TTATC-AAATCTCATA-T-AGTG
1 TTATCAAAATTTCATAGTGAG-G
* *
45336 ATTATCGAAATTTCATAGCGATGGAG
1 -TTATCAAAATTTCATAGTGA--G-G
* *
45362 TTATCAAAATTT-ATAGTAAGA
1 TTATCAAAATTTCATAGTGAGG
* **
45383 TTATCGAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* **
45405 TTATCAAAATTTCAAAGCAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
45427 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
45449 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * *
45471 TCAACAAAA-TTCTATAAAT-AGG
1 TTATCAAAATTTC-AT-AGTGAGG
**
45493 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
45515 TTATC-AAATTCTCAAAATGTGA
1 TTATCAAAATT-TCATAGTGAGG
*
45537 TTA-CAAAAATTTCATAGTG-GTA
1 TTATC-AAAATTTCATAGTGAG-G
* ** ** * * ***
45559 TTTTGGGGAGGTTATCAAAAT-TTC
1 TTAT--CAAAATT-TCATAGTGAGG
* ** *
45583 ATAGT-ATGATTACCAAATTAG-GAAGG
1 TTA-TCAAAATT-TC--A-TAGTG-AGG
* * *
45609 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
* *
45631 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
45651 ATATCAAAATTTCATAAG-AAAG
1 TTATCAAAATTTCAT-AGTGAGG
* *
45673 TTATCAAAATTCCATAGTTTA-G
1 TTATCAAAATTTCATAG-TGAGG
* *
45695 TTTTCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
*
45717 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * *
45738 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* * * *
45761 TTAACAAAATTTCATAATAATG
1 TTATCAAAATTTCATAGTGAGG
* ** *
45783 TTACCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
45805 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
* * *
45821 TTATCAAAATTTCGTAAG-AAAG
1 TTATCAAAATTTCAT-AGTGAGG
* *
45843 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
45865 TTTATCAAAATTTTATAG-GAAGAT
1 -TTATCAAAATTTCATAGTG-AG-G
*
45889 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
45911 TTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* * * *
45933 TTATCAAAATTTGAAAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
*
45955 TTA-CTAACAA-TTCATA-TGGACG
1 TTATC-AA-AATTTCATAGT-GAGG
* * * ** *
45977 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
45999 TTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * *
46021 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AGG
* *
46044 TTATCAAAATTTCATTG-GAAAG
1 TTATCAAAATTTCATAGTG-AGG
*
46066 TTATCAAAATTTCATATTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
46088 -TATTCAAAATTCCTTAGGGAGG
1 TTA-TCAAAATTTCATAGTGAGG
*
46110 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
46126 AGAAGGTTAA
Statistics
Matches: 695, Mismatches: 190, Indels: 164
0.66 0.18 0.16
Matches are distributed among these distances:
16 10 0.01
17 3 0.00
18 1 0.00
19 6 0.01
20 32 0.05
21 55 0.08
22 448 0.64
23 85 0.12
24 12 0.02
25 21 0.03
26 9 0.01
27 1 0.00
28 10 0.01
29 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:45873 original size:23 final size:23
Alignment explanation
Indices: 45843--45922 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
45833 CGTAAGAAAG
45843 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
45866 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
45889 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
45911 TTATCAAAATTT
1 TTATCAAAATTT
45923 CATAATGTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 12 0.24
23 39 0.76
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:45915 original size:45 final size:44
Alignment explanation
Indices: 45633--46213 Score: 226
Period size: 44 Copynumber: 13.3 Consensus size: 44
45623 TTATGGAGTA
* *
45633 ATCAAAATTTC--AGGGAGGATATCAAAATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGTT
* ** * **
45675 ATCAAAATTCCATAGTTTA-GTTTTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAG-CGAGGTTATCAAAATTTCATAAGAAAGTT
* * * **
45719 ATCAAAATTTCATAG-TATGTAGATCAAAATTTCAT-AGGGAGATT
1 ATCAAAATTTCATAGCGAGGT-TATCAAAATTTCATAAGAAAG-TT
* *** * * ** * * *
45763 AACAAAATTTCATAATAATGTTACCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGTT
* *
45807 ATCAAAA-TT--T-G-TA-GTTATCAAAATTTCGTAAGAAAGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGTT
* * * * *
45845 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGCGAGG-TTATCAAAATTTCATAAGAA-AGTT
**
45891 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAATGTGA-TT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAA-GAAAGTT
* * * * * * * *
45935 ATCAAAATTTGAAAGTGTGATTA-CTAACAA-TTCATATGGACGTT
1 ATCAAAATTTCATAGCGAGGTTATC-AA-AATTTCATAAGAAAGTT
* * * * * * * * * *
45979 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGTT
* * * * **
46023 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGAAAGTT
1 ATCAAAATTTCATAGCG-AGGTTATCAAAATTTCATAAGAAAGTT
** * * * * *
46068 ATCAAAATTTCATATTGAGG-TATTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGCGAGGTTA-TCAAAATTTCATAAGAAAGTT
* * ** *
46112 AACAAAATTTCATAAG-AAGGTTAAAAAAAATTT-ATAAAAAAGTT
1 ATCAAAATTTCAT-AGCGAGGTT-ATCAAAATTTCATAAGAAAGTT
* * * * ** *
46156 CTCAAAATTTCATAG-TATCGTTATTAAAATTTCATTGGAAAATT
1 ATCAAAATTTCATAGCGA-GGTTATCAAAATTTCATAAGAAAGTT
*
46200 ATCAAATTTTCATA
1 ATCAAAATTTCATA
46214 ATGGGATCAT
Statistics
Matches: 402, Mismatches: 108, Indels: 56
0.71 0.19 0.10
Matches are distributed among these distances:
38 25 0.06
39 3 0.01
41 2 0.00
42 13 0.03
43 25 0.06
44 224 0.56
45 87 0.22
46 23 0.06
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAAAGTT
Found at i:46132 original size:22 final size:22
Alignment explanation
Indices: 46107--46169 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
46097 TTCCTTAGGG
*
46107 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAAA
*
46129 AGGTTAAAAAAAATTT-ATAAAA
1 AGGTT-AACAAAATTTCATAAAA
* **
46151 AAGTTCTCAAAATTTCATA
1 AGGTTAACAAAATTTCATA
46170 GTATCGTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.21
22 17 0.52
23 9 0.27
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:49853 original size:2 final size:2
Alignment explanation
Indices: 49848--49880 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49838 CACTCCCCCC
49848 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 T
49881 CTCCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51052 original size:13 final size:13
Alignment explanation
Indices: 51034--51058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51024 TTTCCTACTT
51034 CAGTCCATTTTTC
1 CAGTCCATTTTTC
51047 CAGTCCATTTTT
1 CAGTCCATTTTT
51059 GTTGGGTCCG
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:53017 original size:112 final size:112
Alignment explanation
Indices: 52820--53044 Score: 414
Period size: 112 Copynumber: 2.0 Consensus size: 112
52810 CCACCATGTG
* *
52820 TCAACAGAAAAACATAGTGCCATAAGTCACTAAATTAGGATGCCACAACTGAGAGAAAAAGGCTA
1 TCAACAGAAAAACATAGTGCCATAAGTCACCAAATTAGGATGCCACAACTAAGAGAAAAAGGCTA
52885 GATACGTGTTTGACATACACCCCTCGGGATTGCTTCTCTTGGAAAGA
66 GATACGTGTTTGACATACACCCCTCGGGATTGCTTCTCTTGGAAAGA
* *
52932 TCAACAGAAAATCATAGTGCCATAAGTCACCAAATTAGGATGCCACAGCTAAGAGAAAAAGGCTA
1 TCAACAGAAAAACATAGTGCCATAAGTCACCAAATTAGGATGCCACAACTAAGAGAAAAAGGCTA
52997 GATACGTGTTTGACATACACCCCTCGGGATTGCTTCTCTTGGAAAGA
66 GATACGTGTTTGACATACACCCCTCGGGATTGCTTCTCTTGGAAAGA
53044 T
1 T
53045 TAAATTAAAT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (112 bp):
TCAACAGAAAAACATAGTGCCATAAGTCACCAAATTAGGATGCCACAACTAAGAGAAAAAGGCTA
GATACGTGTTTGACATACACCCCTCGGGATTGCTTCTCTTGGAAAGA
Done.