Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010437.1 Corchorus capsularis cultivar CVL-1 contig10458, 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: 48351
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:2380 original size:18 final size:19
Alignment explanation
Indices: 2357--2394 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2347 GAAATAGGAT
2357 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
2375 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
2394 T
1 T
2395 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:5943 original size:26 final size:26
Alignment explanation
Indices: 5910--5961 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5900 TTATAAATTT
5910 TTTTTGTTTTATTGATTAATCTATAG
1 TTTTTGTTTTATTGATTAATCTATAG
*
5936 TTTTTGTTTTATTGATTAATTTATAG
1 TTTTTGTTTTATTGATTAATCTATAG
5962 AGAAATGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (26 bp):
TTTTTGTTTTATTGATTAATCTATAG
Found at i:9274 original size:13 final size:13
Alignment explanation
Indices: 9240--9274 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
9230 AAATAAAATT
9240 AAAAGAAAACAAAC
1 AAAA-AAAACAAAC
*
9254 GAAAAAAACAAAC
1 AAAAAAAACAAAC
9267 AAAAAAAA
1 AAAAAAAA
9275 TACCTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:12103 original size:19 final size:21
Alignment explanation
Indices: 12067--12108 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12057 TTTCTTCTAT
12067 TTTAATTACTTGCAA-TTTAG
1 TTTAATTACTTGCAATTTTAG
*
12087 TTTAATTA-TTTCAATTTTAG
1 TTTAATTACTTGCAATTTTAG
12107 TT
1 TT
12109 CATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTACTTGCAATTTTAG
Found at i:17746 original size:44 final size:46
Alignment explanation
Indices: 17671--17800 Score: 119
Period size: 45 Copynumber: 2.9 Consensus size: 46
17661 TTAACATTCT
* *
17671 TATGAAATTTTGTTAA-TCTCCCTAAGGAATTTTGA-AGACC-ACAA
1 TATGAAATTTTGATAACTCTCCCTAAGAAATTTTGATA-ACCAACAA
*
17715 TATGAAATTTTGATAACT-TCCC-AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACTCTCCCTAA-GAAATTTTGATAACCAACAA
* * * * * *
17760 TATGAGATGTTGATAAC-CTCCATATGATATATTGATAACCA
1 TATGAAATTTTGATAACTCTCCCTAAGAAATTTTGATAACCA
17801 CGCTATGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
43 2 0.03
44 31 0.44
45 37 0.52
46 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (46 bp):
TATGAAATTTTGATAACTCTCCCTAAGAAATTTTGATAACCAACAA
Found at i:17794 original size:22 final size:22
Alignment explanation
Indices: 17671--18105 Score: 167
Period size: 22 Copynumber: 20.0 Consensus size: 22
17661 TTAACATTCT
* * *
17671 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCA
* * * *
17693 TAAGGAATTTTGA-AGACCACAA
1 TATGAAATTTTGATA-ACCTCCA
*
17715 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
17738 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
17759 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * *
17782 TATGATATATTGATAACCACGC-
1 TATGAAATTTTGATAACCTC-CA
* * * *
17804 TATGAAAATTTAAAAACCTCTA
1 TATGAAATTTTGATAACCTCCA
17826 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
*
17847 CTCTGAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
17869 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
*
17892 TATGAAATTTTGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCA
* *
17915 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * *
17938 TATAAAATTTTGATAACTTTC-
1 TATGAAATTTTGATAACCTCCA
*
17959 TCATGAAATCTTGATAA--T---
1 T-ATGAAATTTTGATAACCTCCA
* *
17977 TA-CAAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCTCCA
** *
17998 TATGATTTTTTGATAATCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
18019 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * * *
18042 TATGATA-TTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
* *
18063 TACGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
*
18085 TATGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
18106 CCGAATTTTG
Statistics
Matches: 313, Mismatches: 68, Indels: 64
0.70 0.15 0.14
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 2 0.01
20 3 0.01
21 25 0.08
22 204 0.65
23 61 0.19
24 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:17922 original size:23 final size:23
Alignment explanation
Indices: 17852--17953 Score: 109
Period size: 23 Copynumber: 4.5 Consensus size: 23
17842 TCACACTCTG
* * * *
17852 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
17874 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
17896 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
17919 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
17942 AAATTTTGATAA
1 AAATTTTGATAA
17954 CTTTCTCATG
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 27 0.40
23 41 0.60
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:17974 original size:45 final size:45
Alignment explanation
Indices: 17852--17975 Score: 123
Period size: 45 Copynumber: 2.8 Consensus size: 45
17842 TCACACTCTG
* * *
17852 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
17896 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
*
17942 AAATTTTGAT-AA-CTTTCTCATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCT-ATGAAAT-TTGATAA
17976 TTACAAATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
44 16 0.24
45 29 0.43
46 23 0.34
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:18025 original size:60 final size:61
Alignment explanation
Indices: 17919--18036 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 61
17909 TCTTCCTATA
*
17919 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTCATGAAATCTTGATAATTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTCTCTCATGAAATCTTGATAATTAC
* * ** * * *
17980 AAATTTTGAT-AACCTCCTTATGATTTTTTGATAA-TCTCATTATGAAATTTTGTTAAT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTCTC-TCATGAAATCTTGATAAT
18037 CTCCCTATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 3 0.06
60 35 0.73
61 10 0.21
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.44
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTCTCTCATGAAATCTTGATAATTAC
Found at i:18162 original size:19 final size:19
Alignment explanation
Indices: 18090--18156 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
18080 CCTCTTATGA
*
18090 AATTTTGATATCCTCCCCG
1 AATTTTGATATCCTCCCTG
18109 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
18128 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
18147 AAATTTTGAT
1 -AATTTTGAT
18157 TACTCCATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 37 0.80
20 9 0.20
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:18263 original size:22 final size:22
Alignment explanation
Indices: 18235--18409 Score: 128
Period size: 22 Copynumber: 8.0 Consensus size: 22
18225 CCATAAATAC
18235 CACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* ** *
18257 CATTATGAAATTTTCTTAATCT
1 CACTATGAAATTTTGATAACCT
* * * *
18279 CCCTATGATATTTTGATCTACGT
1 CACTATGAAATTTTGAT-AACCT
18302 -ACTATGAAATTTTGATAACCCT
1 CACTATGAAATTTTGATAA-CCT
* *
18324 C-TTATGAAATTTTGA-AAACT
1 CACTATGAAATTTTGATAACCT
* *
18344 AAACTATGAAATTTTGATAACTTT
1 -CACTATGAAATTTTGATAAC-CT
* *
18368 CA-TATGAAATTTTGGTATCCT
1 CACTATGAAATTTTGATAACCT
* *
18389 C-C-CTGAAATTTTGATATCCT
1 CACTATGAAATTTTGATAACCT
18409 C
1 C
18410 TATAATAAAA
Statistics
Matches: 117, Mismatches: 28, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
20 19 0.16
21 5 0.04
22 87 0.74
23 5 0.04
24 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:18351 original size:66 final size:66
Alignment explanation
Indices: 18236--18361 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
18226 CATAAATACC
** * ** *
18236 ACTATGAAATTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTTGATCTACG
1 ACTATGAAATTTTGATAACCTCATTATGAAATTTTCGAAAACTAACTATGAAATTTTGATCTACG
18301 T
66 T
18302 ACTATGAAATTTTGATAACCCTC-TTATGAAATTTT-GAAAACTAAACTATGAAATTTTGAT
1 ACTATGAAATTTTGATAA-CCTCATTATGAAATTTTCGAAAACT-AACTATGAAATTTTGAT
18362 AACTTTCATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.08
66 44 0.85
67 4 0.08
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (66 bp):
ACTATGAAATTTTGATAACCTCATTATGAAATTTTCGAAAACTAACTATGAAATTTTGATCTACG
T
Found at i:18374 original size:66 final size:66
Alignment explanation
Indices: 18236--18381 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
18226 CATAAATACC
** * ** * *
18236 ACTATGAAATTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTTGATCTACG
1 ACTATGAAATTTTGATAACCTCATTATGAAATTTTCGAAAACTAACTATGAAATTTTGATCAACG
18301 T
66 T
18302 ACTATGAAATTTTGATAACCCTC-TTATGAAATTTT-GAAAACTAAACTATGAAATTTTGAT-AA
1 ACTATGAAATTTTGATAA-CCTCATTATGAAATTTTCGAAAACT-AACTATGAAATTTTGATCAA
*
18364 CTT
64 CGT
*
18367 TCATATGAAATTTTG
1 AC-TATGAAATTTTG
18382 GTATCCTCCC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 8 0.12
66 56 0.82
67 4 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
ACTATGAAATTTTGATAACCTCATTATGAAATTTTCGAAAACTAACTATGAAATTTTGATCAACG
T
Found at i:18397 original size:20 final size:20
Alignment explanation
Indices: 18372--18409 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18362 AACTTTCATA
*
18372 TGAAATTTTGGTATCCTCCC
1 TGAAATTTTGATATCCTCCC
18392 TGAAATTTTGATATCCTC
1 TGAAATTTTGATATCCTC
18410 TATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:18455 original size:248 final size:240
Alignment explanation
Indices: 18005--18496 Score: 725
Period size: 248 Copynumber: 2.0 Consensus size: 240
17995 CCTTATGATT
* *
18005 TTTTGATAATCTCATTATGAAATTTTGTTAATCTCCCTATGATATTTGATCTACATACTACGAAA
1 TTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTGATCTACATACTACGAAA
** * * *
18070 TTTTGATAACCCTCTTATGAAATTTTGATATCCTCCCCGAATTTTGATATCCTCCCTGAATTTTG
66 TTTTGATAACCCTCTTATGAAATTTTGATAAACTCCACGAATTTTGATAACCTCCATGAATTTTG
18135 ATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACC
131 ATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACC
*
18200 ATACTATGAAATTTTGATAACCTCCCCATAAATACCACTATGAAA
196 ATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
* *
18245 TTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTTGATCTACGTACTATGAA
1 TTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATA-TTTGATCTACATACTACGAA
* * * *
18310 ATTTTGATAACCCTCTTATGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACTTTCATATG
65 ATTTTGATAACCCTCTTATGAAATTTTGATAAACT---CCACG-AATTTTGATAAC-CTC-CATG
* * *
18374 AAATTTTGGTATCCTCCCTGAAATTTTGATATCCTCTATAATAAAAGTTTAATAACCTTCCTAAT
124 -AATTTTGATATCCTCCCTGAAATTTTGAT-TACTCCATAATAAAAGTTTAATAACCTTCCTAAT
* *
18439 TTGGTAACCATACTATGAAATTTTGATAAACTCCCCATAAGTACTACTATGAAA
187 TTGGTAACCATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
18493 TTTT
1 TTTT
18497 TGTAATCACA
Statistics
Matches: 224, Mismatches: 19, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
240 45 0.20
241 47 0.21
243 2 0.01
244 11 0.05
245 2 0.01
246 2 0.01
247 28 0.12
248 87 0.39
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (240 bp):
TTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTGATCTACATACTACGAAA
TTTTGATAACCCTCTTATGAAATTTTGATAAACTCCACGAATTTTGATAACCTCCATGAATTTTG
ATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACC
ATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
Found at i:18543 original size:22 final size:22
Alignment explanation
Indices: 18516--18859 Score: 186
Period size: 22 Copynumber: 15.6 Consensus size: 22
18506 ATTTTAAAAA
*
18516 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
18538 TTTGATAACCTCTTTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
18560 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * * * *
18582 TCTAATAATCACAT-TATGTAAT
1 TTTGATAACCTC-TCTATGAAAT
*
18604 TTTGATAACCTCGCCT-TGAAAT
1 TTTGATAACCTC-TCTATGAAAT
* *
18626 TTTGATAATCTTTCTAT-AAAT
1 TTTGATAACCTCTCTATGAAAT
*
18647 TTTGATAATCTGATCTCTATGAAAT
1 TTTGATAA-C--CTCTCTATGAAAT
* * * *
18672 TTAGATAATCACTCTATGAGA-
1 TTTGATAACCTCTCTATGAAAT
*
18693 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
* **
18714 TTTGGT-ATTTCT-TATGAAAT
1 TTTGATAACCTCTCTATGAAAT
** *
18734 TCAGACTTTTACCT-TCATATGAAAT
1 TTTGA---TAACCTCTC-TATGAAAT
* * *
18759 TTTGATAACCACACTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
18781 TTTGATAACCTCCCCATGAAAT
1 TTTGATAACCTCTCTATGAAAT
*
18803 ATT-AGTAACCTC-CTAATGAAAT
1 TTTGA-TAACCTCTCT-ATGAAAT
* * * *
18825 TTTGTTAACCACACTATGACAT
1 TTTGATAACCTCTCTATGAAAT
*
18847 TTTGATAATCTCT
1 TTTGATAACCTCT
18860 TTGATAACCT
Statistics
Matches: 237, Mismatches: 65, Indels: 40
0.69 0.19 0.12
Matches are distributed among these distances:
20 18 0.08
21 30 0.13
22 152 0.64
23 7 0.03
24 8 0.03
25 22 0.09
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:18626 original size:248 final size:246
Alignment explanation
Indices: 18005--18632 Score: 643
Period size: 248 Copynumber: 2.6 Consensus size: 246
17995 CCTTATGATT
* * * * ** * * * * **
18005 TTTTGATAATCTCATTATGAAATTTTGTTAATCTCCCTATGATA-TTTGATCTACATACTACGAA
1 TTTTGATAACCACATTATAAAAATTTCATAACCTCCCTATGAAATTTTGATCAACCTACTATAAA
* ** *** *
18069 ATTTTGATAACCCTCTTATGAAATTTTGATATCCT---CCCCG-AATTTTGATATCCTCCC-TG-
66 ATTTTGATAACCCTCTTATGAAATTCTGA-AAACTAAACTATGAAATTTTGATAACCTCCCTTGA
18128 AATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTT
130 AATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTT
*
18193 GGTAACCATACTATGAAATTTTGATAACCTCCCCATAAATACCACTATGAAA
195 GGTAACCATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
* * * * * * * * *
18245 TTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGATATTTTGATCTACGTACTATGAA
1 TTTTGATAACCACATTATAAAAATTTCATAACCTCCCTATGAAATTTTGATCAACCTACTATAAA
* * * *
18310 ATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACTTTCATATGA
66 ATTTTGATAACCCTCTTATGAAATTCTGAAAACTAAACTATGAAATTTTGATAACCTCCCT-TGA
* * *
18375 AATTTTGGTATCCTCCCTGAAATTTTGATATCCTCTATAATAAAAGTTTAATAACCTTCCTAATT
130 AATTTTGATATCCTCCCTGAAATTTTGAT-TACTCCATAATAAAAGTTTAATAACCTTCCTAATT
* *
18440 TGGTAACCATACTATGAAATTTTGATAAACTCCCCATAAGTACTACTATGAAA
194 TGGTAACCATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
* * * **
18493 TTTTTG-TAATCACATTTTAAAAATTTGATAACCTCTTTATGAAATTTTGAT-AACCT-CTTTAT
1 -TTTTGATAACCACATTATAAAAATTTCATAACCTCCCTATGAAATTTTGATCAACCTAC--TAT
* * * * *
18555 AAAATTTTGTTGACCC-CTCTATGAAATTCT-AATAA-TCACATTATGTAATTTTGATAACCTCG
63 AAAATTTTGATAACCCTCT-TATGAAATTCTGAA-AACT-AAACTATGAAATTTTGATAACCTC-
18617 CCTTGAAATTTTGATA
124 CCTTGAAATTTTGATA
18633 ATCTTTCTAT
Statistics
Matches: 329, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
240 45 0.14
241 47 0.14
243 2 0.01
244 13 0.04
246 3 0.01
247 36 0.11
248 176 0.53
249 7 0.02
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (246 bp):
TTTTGATAACCACATTATAAAAATTTCATAACCTCCCTATGAAATTTTGATCAACCTACTATAAA
ATTTTGATAACCCTCTTATGAAATTCTGAAAACTAAACTATGAAATTTTGATAACCTCCCTTGAA
ATTTTGATATCCTCCCTGAAATTTTGATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTG
GTAACCATACTATGAAATTTTGATAAACTCCCCATAAATACCACTATGAAA
Found at i:18976 original size:22 final size:20
Alignment explanation
Indices: 18937--19017 Score: 53
Period size: 22 Copynumber: 4.0 Consensus size: 20
18927 ATTTTGATTC
* *
18937 TATGAAATTTTGGCAACCACAT
1 TATGAAA-TTTAGTAACCAC-T
18959 TATGAAATTCTAGTAACC-C-
1 TATGAAATT-TAGTAACCACT
*
18978 -ATGAAATTATAATAACCATCT
1 TATGAAATT-TAGTAACCA-CT
18999 TATGAAATTT-GATAACCAC
1 TATGAAATTTAG-TAACCAC
19018 ATAAAGACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 15 0.31
20 2 0.04
21 10 0.21
22 21 0.44
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (20 bp):
TATGAAATTTAGTAACCACT
Found at i:18993 original size:18 final size:18
Alignment explanation
Indices: 18960--18994 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18950 CAACCACATT
* *
18960 ATGAAATTCTAGTAACCC
1 ATGAAATTATAATAACCC
18978 ATGAAATTATAATAACC
1 ATGAAATTATAATAACC
18995 ATCTTATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (18 bp):
ATGAAATTATAATAACCC
Found at i:20179 original size:262 final size:262
Alignment explanation
Indices: 19714--20488 Score: 1507
Period size: 262 Copynumber: 3.0 Consensus size: 262
19704 GGAAGCCTAA
19714 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
1 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
19779 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
66 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
19844 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
131 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
19909 TATCTCAAGCCCTAATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTGATCCAGAGC
196 TATCTCAAGCCCTAATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTGATCCAGAGC
19974 TC
261 TC
19976 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
1 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
20041 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
66 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
20106 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
131 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
20171 TATCTCAAGCCCCT-ATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTGATCCAGAG
196 TATCTCAAG-CCCTAATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTGATCCAGAG
20235 CTC
260 CTC
20238 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
1 AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
20303 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
66 TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
20368 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
131 AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
* * *
20433 TATCTCAAGACCTAATTCTGCCGTTTCAGTGGATGATTTTGCCCTTGTAATTTCTG
196 TATCTCAAGCCCTAATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTG
20489 GACAAAATTG
Statistics
Matches: 508, Mismatches: 3, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
261 3 0.01
262 501 0.99
263 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (262 bp):
AGAAAGAATCCAAGTCCAATCAGTAATTATGATGCGATAATGATTCAGCCATGATGCAGCATTGT
TAAATCATATTGAAAGGAGAACTTCACCAGAGCAGTTTTAGAAGAAAATTCATAACTTTTGATCC
AGAGCTCAGAAAAATGCAAATGATGTACTGTTGGAAAGATGATTCTAAGATCTACAACTTTATGT
TATCTCAAGCCCTAATTCTGTCGTTTCGGTGGATGATTTTGCCCTTGTAATTTCTGATCCAGAGC
TC
Found at i:21185 original size:31 final size:31
Alignment explanation
Indices: 21147--21212 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
21137 TGGCAATTTA
* * *
21147 GAAATATATTTTTTAAAA-AGGGGTACAATTG
1 GAAATATA-TTTTAAAAATAAGGGTACAATCG
21178 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
21209 GAAA
1 GAAA
21213 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:25794 original size:15 final size:15
Alignment explanation
Indices: 25762--25809 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
25752 ATTCACTTAT
25762 TATGTAGTTGTATATAA
1 TATGTAGTTG--TATAA
25779 TATGTAGTTGTATAA
1 TATGTAGTTGTATAA
25794 TATGTAGTTGTATAA
1 TATGTAGTTGTATAA
25809 T
1 T
25810 TTAATGATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 21 0.68
17 10 0.32
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (15 bp):
TATGTAGTTGTATAA
Found at i:41680 original size:31 final size:31
Alignment explanation
Indices: 41644--41812 Score: 196
Period size: 31 Copynumber: 5.5 Consensus size: 31
41634 GTGTCCGACA
* *
41644 TGGCATGCCACATGTAACAAAAAGTGACATG
1 TGGCATGCCACATGTACCAAAAAGTGACACG
* * *
41675 TGGCATGCCATATATACCAAAAAGTGACACA
1 TGGCATGCCACATGTACCAAAAAGTGACACG
* * *
41706 TGTCACT-CCACGTGTACCAAAAAGTGACATG
1 TGGCA-TGCCACATGTACCAAAAAGTGACACG
*
41737 TGGCACGCCACATGTACCAAAAAGTGACACG
1 TGGCATGCCACATGTACCAAAAAGTGACACG
* ** *
41768 TGACATGCCACATGTTTCAAAAAGTGGCACG
1 TGGCATGCCACATGTACCAAAAAGTGACACG
*
41799 TGGCATGTCACATG
1 TGGCATGCCACATG
41813 CACAAAAGGA
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (31 bp):
TGGCATGCCACATGTACCAAAAAGTGACACG
Found at i:44540 original size:15 final size:16
Alignment explanation
Indices: 44520--44563 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
44510 TGTCAAAGCA
*
44520 TAATTTTTTA-AATTT
1 TAATTTTATATAATTT
44535 TAATTTTATATAATTT
1 TAATTTTATATAATTT
44551 T--TTTTATATAATT
1 TAATTTTATATAATT
44564 AAAGGTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 12 0.44
15 9 0.33
16 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTTATATAATTT
Found at i:46367 original size:119 final size:121
Alignment explanation
Indices: 46232--46476 Score: 284
Period size: 124 Copynumber: 2.0 Consensus size: 121
46222 ATAAAAAAAA
* * *
46232 TTACATAATATATAAT-C-C-ATCAAACTAACTAGTTAAA-TC-TACAGTAGAACTTGAATCTAA
1 TTACATAATATATAATCCACTATCAAACAAACTAGCTAAACACGTACAGTAGAACTTGAATCTAA
* * * *
46292 AATTTCAAAATTTAGATCATACCATACATACGTTGGTTGAGTTGACAACATGGGTGTTG
66 AACTTCAAAATGTAGAT-AT--CATACATACGTTGGTTAAGTTGACAACACGGGTGTTG
* * *
46351 TTACATTATATATAATCCATCTATCAAACAAATTAGCTAAACCCACGTACTGTAGAACTTGAATC
1 TTACATAATATATAATCCA-CTATCAAACAAACTAGCTAAA--CACGTACAGTAGAACTTGAATC
* * *
46416 TAAAACTTCAAAATGTAGGTATCATACATATGTTGGTTAAGTTGATAACACGGGTGTTG
63 TAAAACTTCAAAATGTAGATATCATACATACGTTGGTTAAGTTGACAACACGGGTGTTG
46475 TT
1 TT
46477 TAATTAGCTA
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
119 15 0.14
120 1 0.01
122 1 0.01
123 16 0.15
124 35 0.33
126 3 0.03
127 34 0.32
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (121 bp):
TTACATAATATATAATCCACTATCAAACAAACTAGCTAAACACGTACAGTAGAACTTGAATCTAA
AACTTCAAAATGTAGATATCATACATACGTTGGTTAAGTTGACAACACGGGTGTTG
Done.