Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010960.1 Corchorus capsularis cultivar CVL-1 contig10981, 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: 108982
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1694 original size:199 final size:199
Alignment explanation
Indices: 1340--1961 Score: 904
Period size: 199 Copynumber: 3.1 Consensus size: 199
1330 AAATTTGAGT
*
1340 GTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATTTGTATTAATATTAAATATTTAATT
1 GTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
* * *
1405 ATTTATGAAATGAAGTATGTGCCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACA
66 AATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACA
* * *
1470 GTGTATTTTATAATAATCCTATAAGAACATTTATACAATGCACCGTCAGTGGAGTTTAGCAGACT
131 GTGTATTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
*
1535 GCAT
196 GCAC
* * * * *
1539 GTGCAGGGTTTAAGGGTTGGCATATGTCCCCTTAGGGAATATGTATTAATATTATATATTTAATT
1 GTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
* * * *
1604 AATGATGAAATGAGGTATGTGTCAACTTCTTAACCCACTTATAGAGTTCAAAATTTACATTGACA
66 AATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACA
* * * * * *
1669 -TGTGTTGTATAATAATCCTTATAAGAAAAATTATATAATATACCGTTAGTGGATTTTAGCAGAC
131 GTGTATTGTATAATAATCC-TATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGAC
*
1733 TACAC
195 TGCAC
*
1738 GTGCGGGGTTTAAGGTTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
1 GTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
* * *** *
1803 AATTATGAAATGTGGTATATGTCAACTTCTTAATGTGCTTATGGAGTCCAAAATTTACATTGATA
66 AATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACA
* * *
1868 GTGTATTGTATAATAATCCTATAAGAACAATTATACAATACACCATCAATGAAGTTTAGCAGACT
131 GTGTATTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
*
1933 GTAC
196 GCAC
*
1937 GTGCGGGCTTTAAGGGTTGACATGT
1 GTGCGGGGTTTAAGGGTTGACATGT
1962 CCTATTTTAT
Statistics
Matches: 368, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
198 16 0.04
199 335 0.91
200 17 0.05
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (199 bp):
GTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
AATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACA
GTGTATTGTATAATAATCCTATAAGAACAATTATACAATACACCGTCAGTGGAGTTTAGCAGACT
GCAC
Found at i:2004 original size:171 final size:170
Alignment explanation
Indices: 1794--2132 Score: 495
Period size: 171 Copynumber: 2.0 Consensus size: 170
1784 TAATATTAAA
* *
1794 TATTTAATTAATTATGAAATGTGGTATATGTCAACTTCTTAA-TGTGCTTATGGAGTCCAAAATT
1 TATTTAATTAATTATGAAATGGGGTATATGTCAACTTCTTAACT-CGCTTATGGAGTCCAAAATT
* *
1858 TACATTGATAGTGTATTGTATAATAATCCTATAAGAACA-ATTATACAATACACCATCAATGAAG
65 TACACTGACAGTGTATTGTATAATAATCCTATAAGAA-AGATTATACAATACACCATCAATGAAG
*
1922 TTTAGCAGACTGTACGTGC-GGGCTTTAAGGGTTGACATGTCC
129 TTTAGCAGACTGCACGTGCAGGG-TTTAAGGGTTGACATGTCC
* *
1964 TATTTTATTAATTATGAAATGGGGGTATATGTCAACTTCTTAACTCGCTTATGGAGTCCAAATTT
1 TATTTAATTAATTATGAAAT-GGGGTATATGTCAACTTCTTAACTCGCTTATGGAGTCCAAAATT
* ** * * *
2029 TACACTGACAGTGTATTGTATAATAATCTTATAAGAAAGATTATATTATACACCGTCAGTGGAGT
65 TACACTGACAGTGTATTGTATAATAATCCTATAAGAAAGATTATACAATACACCATCAATGAAGT
*
2094 TTAGCATACTGCACGTGCAGGGTTTAAGGGTTGACATGT
130 TTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGT
2133 TTCCCCTAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
170 20 0.13
171 127 0.84
172 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (170 bp):
TATTTAATTAATTATGAAATGGGGTATATGTCAACTTCTTAACTCGCTTATGGAGTCCAAAATTT
ACACTGACAGTGTATTGTATAATAATCCTATAAGAAAGATTATACAATACACCATCAATGAAGTT
TAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTCC
Found at i:2343 original size:194 final size:195
Alignment explanation
Indices: 1964--2331 Score: 479
Period size: 194 Copynumber: 1.9 Consensus size: 195
1954 TGACATGTCC
* * * * * *
1964 TATTTTATTAATTATGAAATGGGGGTATATGTCAACTTCTTAACTCGCTTATGGAGTCCAAATTT
1 TATTTAATTAATGATGAAATGGAGGTATATGTCAACTTATTAACCCGCTTATGGAGTCCAAAATT
* * * * ** * * *
2029 TACACTGACAGTGTATTGTATAATAATCTTATAAGAAAGATTATATTATACACCGTCAGTGGAGT
66 TACACTGACAATGTATTGCATAATAATCCTATAAGAAAAATTATACAATACACAGTCAGTCGAGC
* * * *
2094 TTAGCATACTGCACGTGCAGGGTTTAAGGGTTGACATGTTTCCCCTAAAGGAATATGTAACTATA
131 TTAGCAGACTGCACGTGCAGGGTTTAAGGGCTCACATGTGTCCCCTAAAGGAATATGTAACTATA
* *
2159 TATTTAATTAATGATGAAAT-GAGGTATATGTTAACTTATTAACCCGCTTATGGAGTTCAAAATT
1 TATTTAATTAATGATGAAATGGAGGTATATGTCAACTTATTAACCCGCTTATGGAGTCCAAAATT
* *
2223 TACATTGACAATGTATTGCATAGTAATCCCTATAAGAAAAATTATACAATACA-AGTCAGTCGAG
66 TACACTGACAATGTATTGCATAATAAT-CCTATAAGAAAAATTATACAATACACAGTCAGTCGAG
** *
2287 CTTAGTGGACTGCACGTGCGGGGTTTAAGGGCTCACATGTGTCCC
130 CTTAGCAGACTGCACGTGCAGGGTTTAAGGGCTCACATGTGTCCC
2332 TTTAGGGAAT
Statistics
Matches: 146, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
194 107 0.73
195 39 0.27
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (195 bp):
TATTTAATTAATGATGAAATGGAGGTATATGTCAACTTATTAACCCGCTTATGGAGTCCAAAATT
TACACTGACAATGTATTGCATAATAATCCTATAAGAAAAATTATACAATACACAGTCAGTCGAGC
TTAGCAGACTGCACGTGCAGGGTTTAAGGGCTCACATGTGTCCCCTAAAGGAATATGTAACTATA
Found at i:3767 original size:198 final size:198
Alignment explanation
Indices: 3193--4006 Score: 1087
Period size: 198 Copynumber: 4.1 Consensus size: 198
3183 TAGTATATAT
* * *
3193 ATATTTAATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATC
1 ATATTTAATTAATTATGAAATG-GGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATT
* * ** * * *
3258 TACACTGACAGTGTATTGTATAATAATAC-AGTAAGAAATTTTATTCAATACACGGTTAGTGGAG
65 TACACTGACAATGTATTGTATAATAATCCTA-TAAGAAAAATTATACAATACACCGTCAGTGGAG
* *
3322 TTTAGCAGACTGCACGTGCGGGATTTAAGGGTTGACATGTATCCCCTTAGGGAATATGTATTAAT
129 TTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAAT
3387 ATTAA
194 ATTAA
* *
3392 ATATTTAATTAATTATGAAATAAGGTATGTGTCAACTTCTTAACCGGCCCGCTTATGGAGTCCAA
1 ATATTTAATTAATTATGAAAT-GGGTATGTGTCAACCTCTTAA----CCCGCTTATGGAGTCCAA
* * * *
3457 AATTTACACTGAC-A-GTGTTGGATAATAATCTCTATAAGGAAAATTATACAACACACCGTCAGT
61 AATTTACACTGACAATGTATTGTATAATAATC-CTATAAGAAAAATTATACAATACACCGTCAG-
** *
3520 TTTAGTTTAGCAGACTGCACGTGTGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTA
124 TGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTA
3585 TTAATATTAA
189 TTAATATTAA
* * *
3595 ATATTTAATTAATTATGAAATGCGTATGTGTCAACCTCTTAACCCTCTTATAGAGTCCAAAATTT
1 ATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTT
** * *
3660 ACACT-ACAATGTATTGTATAATAATCCCTATAAGAAAAATTATACAATACACCACCAATGAAGT
66 ACACTGACAATGTATTGTATAATAAT-CCTATAAGAAAAATTATACAATACACCGTCAGTGGAGT
* * * * * *
3724 TTAGTAGACTACACGTGTGGGGTTTAAGGGCTGGCATGTGTCCCCTTAGGCAATATGTATTAATA
130 TTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATA
3789 TTAA
195 TTAA
*
3793 ATATTTAATTAATTATGAAATGGGTATATGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTT
1 ATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTT
* * * * *
3858 ACACTTACAGTGTATTATATAATAATCATATAAGAAAAATTATACAATACACCGTCGGTGGAGTT
66 ACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTT
* * * * ** *
3923 TAGTAGACTGCACGCGCAGGGTTTAAGGGTTGACATATGTCGGCTTAGGGAATATGTGTTAATAT
131 TAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATAT
3988 TAA
196 TAA
3991 ATATTTAATTAATTAT
1 ATATTTAATTAATTAT
4007 AAAAAAGCTC
Statistics
Matches: 542, Mismatches: 61, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
197 2 0.00
198 267 0.49
199 98 0.18
200 1 0.00
201 13 0.02
202 40 0.07
203 121 0.22
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (198 bp):
ATATTTAATTAATTATGAAATGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTT
ACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTT
TAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATAT
TAA
Found at i:10553 original size:10 final size:10
Alignment explanation
Indices: 10538--10562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10528 CTTAGAAACA
10538 TGAAAGAAAT
1 TGAAAGAAAT
10548 TGAAAGAAAT
1 TGAAAGAAAT
10558 TGAAA
1 TGAAA
10563 ATACCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
TGAAAGAAAT
Found at i:12405 original size:24 final size:24
Alignment explanation
Indices: 12377--12429 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
12367 TTCCATCACT
12377 TTATAACCTCATAAATCATATTTA
1 TTATAACCTCATAAATCATATTTA
*** *
12401 TTATATTGTTATAAATCATATTTA
1 TTATAACCTCATAAATCATATTTA
12425 TTATA
1 TTATA
12430 TTTAAATCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATAACCTCATAAATCATATTTA
Found at i:13270 original size:26 final size:28
Alignment explanation
Indices: 13226--13277 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
13216 AGTTGAGCTT
*
13226 TTTTTTGGACCTTATTAAACTTTTTTCC
1 TTTTCTGGACCTTATTAAACTTTTTTCC
*
13254 TTTTCTGG-CCTTA-TAAAGTTTTTT
1 TTTTCTGGACCTTATTAAACTTTTTT
13278 TAGTCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 5 0.23
28 7 0.32
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.58
Consensus pattern (28 bp):
TTTTCTGGACCTTATTAAACTTTTTTCC
Found at i:13332 original size:21 final size:22
Alignment explanation
Indices: 13263--13334 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
13253 CTTTTCTGGC
* * *
13263 CTTATAAAGTTTTTTTAGTCAT
1 CTTATTAAGTATTTTTAGTAAT
* * *
13285 CTTATTAAGTGTTTTTACCTAAC
1 CTTATTAAGTATTTTTA-GTAAT
13308 CTTATTAAG-ATTTTTAGTAAT
1 CTTATTAAGTATTTTTAGTAAT
13329 CTTATT
1 CTTATT
13335 GTGGATTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.22
22 21 0.51
23 11 0.27
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (22 bp):
CTTATTAAGTATTTTTAGTAAT
Found at i:15218 original size:28 final size:28
Alignment explanation
Indices: 15136--15206 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
15126 AGTAAGTATA
15136 AAAATTAAGGATACTAATTGTGGTAATT
1 AAAATTAAGGATACTAATTGTGGTAATT
15164 AAAATTAAGGATACTAATTGTGGTAATT
1 AAAATTAAGGATACTAATTGTGGTAATT
15192 AAAATTAAGGATACT
1 AAAATTAAGGATACT
15207 TAATGTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (28 bp):
AAAATTAAGGATACTAATTGTGGTAATT
Found at i:15962 original size:20 final size:21
Alignment explanation
Indices: 15925--15963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15915 TATAAAGCTT
*
15925 TATTTTAGTAATTTTATTAAG
1 TATTCTAGTAATTTTATTAAG
15946 TATTCTAGTAA-TTTATTA
1 TATTCTAGTAATTTTATTA
15964 TTAAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTCTAGTAATTTTATTAAG
Found at i:17112 original size:2 final size:2
Alignment explanation
Indices: 17105--17130 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17095 TCCAAATGAC
17105 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
17131 CACCACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18063 original size:191 final size:191
Alignment explanation
Indices: 17831--18214 Score: 741
Period size: 191 Copynumber: 2.0 Consensus size: 191
17821 AATAATTAAA
17831 AATTAACTTTCATCAAAATCAATTTGTAAGATTAATTAATTAAAATCAATATATAAGATACGTTT
1 AATTAACTTTCATCAAAATCAATTTGTAAGATTAATTAATTAAAATCAATATATAAGATACGTTT
17896 GAAAAAAGAAATCAATCATATATATTCTATTATTATAACTTAAAAACCCATGAAATATTCAATTT
66 GAAAAAAGAAATCAATCATATATATTCTATTATTATAACTTAAAAACCCATGAAATATTCAATTT
* *
17961 AGCAAATTTTTAGGTGAATTAGAATTTCGTATTATAATAGTTTAATTTTAATCATAACAAT
131 AGCAAAATTTTAGGTGAATTAGAATTTCATATTATAATAGTTTAATTTTAATCATAACAAT
18022 AATTAACTTTCATCAAAATCAATTTGTAAGATTAATTAATTAAAATCAATATATAAGATACGTTT
1 AATTAACTTTCATCAAAATCAATTTGTAAGATTAATTAATTAAAATCAATATATAAGATACGTTT
*
18087 GAAAAAAGAAATCAATCATATATATTCTATTATTATAACTTTAAAACCCATGAAATATTCAATTT
66 GAAAAAAGAAATCAATCATATATATTCTATTATTATAACTTAAAAACCCATGAAATATTCAATTT
18152 AGCAAAATTTTAGGTGAATTAGAATTTCATATTATAATAGTTTAATTTTAATCATAACAAT
131 AGCAAAATTTTAGGTGAATTAGAATTTCATATTATAATAGTTTAATTTTAATCATAACAAT
18213 AA
1 AA
18215 CAGTATGGTA
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 190 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (191 bp):
AATTAACTTTCATCAAAATCAATTTGTAAGATTAATTAATTAAAATCAATATATAAGATACGTTT
GAAAAAAGAAATCAATCATATATATTCTATTATTATAACTTAAAAACCCATGAAATATTCAATTT
AGCAAAATTTTAGGTGAATTAGAATTTCATATTATAATAGTTTAATTTTAATCATAACAAT
Found at i:21311 original size:2 final size:2
Alignment explanation
Indices: 21272--21300 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21262 ATTGTTTTAA
21272 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
21301 AAAGATATAT
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:21969 original size:16 final size:17
Alignment explanation
Indices: 21948--21981 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21938 TTGAAGGATA
*
21948 TTTAAAA-ATGTATTTT
1 TTTAAAAGATCTATTTT
21964 TTTAAAAGATCTATTTT
1 TTTAAAAGATCTATTTT
21981 T
1 T
21982 GAATGATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAAAGATCTATTTT
Found at i:41351 original size:78 final size:78
Alignment explanation
Indices: 41254--41409 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
41244 GAGCTCGTCT
41254 TGCTATAACTACATCTACATGTGTCATGTTACGACTAGCTTGTGCAATCTGATAATCATCCAATG
1 TGCTATAACTACATCTACATGTGTCATGTTACGACTAGCTTGTGCAATCTGATAATCATCCAATG
41319 GAGATACCAATCA
66 GAGATACCAATCA
*
41332 TGCTATAACTACATCTACATGTGTCATGTTACGACTAGCTTGTGCAATCTGATGATCATCCAATG
1 TGCTATAACTACATCTACATGTGTCATGTTACGACTAGCTTGTGCAATCTGATAATCATCCAATG
41397 GAGATACCAATCA
66 GAGATACCAATCA
41410 GAAGGATTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (78 bp):
TGCTATAACTACATCTACATGTGTCATGTTACGACTAGCTTGTGCAATCTGATAATCATCCAATG
GAGATACCAATCA
Found at i:43585 original size:11 final size:10
Alignment explanation
Indices: 43567--43600 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
43557 AATTGTCTTC
43567 AAATCTTCAA
1 AAATCTTCAA
43577 AATATCTTCAA
1 AA-ATCTTCAA
43588 GAAATCTTCAA
1 -AAATCTTCAA
43599 AA
1 AA
43601 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:44394 original size:33 final size:33
Alignment explanation
Indices: 44347--44427 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
44337 AGAAGCCGCG
*
44347 CACCACCGGCCACATAACTCGGCCATGCCCGGA
1 CACCACCGGCCACATAACTCAGCCATGCCCGGA
* * *
44380 CACCACCGGACACATGACTCAGCCATGCCCGGC
1 CACCACCGGCCACATAACTCAGCCATGCCCGGA
*
44413 CACAACCGGCCACAT
1 CACCACCGGCCACAT
44428 GATCCTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.26, C:0.46, G:0.20, T:0.09
Consensus pattern (33 bp):
CACCACCGGCCACATAACTCAGCCATGCCCGGA
Found at i:45464 original size:9 final size:9
Alignment explanation
Indices: 45433--45465 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
45423 ACTTATATCG
45433 AAAAATAAA
1 AAAAATAAA
*
45442 AAAATTAAA
1 AAAAATAAA
45451 AAAAATAAA
1 AAAAATAAA
45460 AAAAAT
1 AAAAAT
45466 TTCGACCAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:50892 original size:33 final size:33
Alignment explanation
Indices: 50852--50949 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
50842 AGAAGCCGCG
50852 CACCACCGGCCACATGACTCGGCCATGCCCGGA
1 CACCACCGGCCACATGACTCGGCCATGCCCGGA
50885 CACCACCGGCCACATGACTCGGCCATGCCCGGA
1 CACCACCGGCCACATGACTCGGCCATGCCCGGA
*
50918 CACCACCGGACACATGACTCGGCCATGCCCGG
1 CACCACCGGCCACATGACTCGGCCATGCCCGG
50950 CCACATGATC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.09
Consensus pattern (33 bp):
CACCACCGGCCACATGACTCGGCCATGCCCGGA
Found at i:52585 original size:30 final size:24
Alignment explanation
Indices: 52509--52574 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
52499 GGCTTTTTTA
52509 ACGACCACCATGTGGTCGATTCTC
1 ACGACCACCATGTGGTCGATTCTC
52533 ACGACCACCATGTGGTCGATTCTC
1 ACGACCACCATGTGGTCGATTCTC
52557 ACGACCACCATGTGGTCG
1 ACGACCACCATGTGGTCG
52575 TTTGAAATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (24 bp):
ACGACCACCATGTGGTCGATTCTC
Found at i:54586 original size:12 final size:12
Alignment explanation
Indices: 54569--54595 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54559 CCGAATCCCG
54569 AAACATTCAACA
1 AAACATTCAACA
54581 AAACATTCAACA
1 AAACATTCAACA
54593 AAA
1 AAA
54596 AGACCCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACATTCAACA
Found at i:73382 original size:15 final size:15
Alignment explanation
Indices: 73362--73400 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
73352 GCAGTAATTA
73362 ATTTTTTAATTACTT
1 ATTTTTTAATTACTT
*
73377 ATTTTTTAATTATTT
1 ATTTTTTAATTACTT
*
73392 AATTTTTAA
1 ATTTTTTAA
73401 GTTATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTAATTACTT
Found at i:73405 original size:16 final size:15
Alignment explanation
Indices: 73359--73405 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
73349 GTTGCAGTAA
*
73359 TTAATTTTTTAATTAC
1 TTAA-TTTTTAATTAT
*
73375 TTATTTTTTAATTAT
1 TTAATTTTTAATTAT
73390 TTAATTTTTAAGTTAT
1 TTAATTTTTAA-TTAT
73406 GAAATTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TTAATTTTTAATTAT
Found at i:77328 original size:15 final size:15
Alignment explanation
Indices: 77308--77337 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
77298 ATTTTTAATT
77308 TATTGGTATTGATGA
1 TATTGGTATTGATGA
77323 TATTGGTATTGATGA
1 TATTGGTATTGATGA
77338 AGATTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (15 bp):
TATTGGTATTGATGA
Found at i:78090 original size:44 final size:45
Alignment explanation
Indices: 78042--78130 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
78032 TAACGTATAT
78042 GATAATGGA-TTTTGTAGATAT-TGCTATCATTAACAAGTCCTAAC
1 GATAATGGATTTTTGTAGAT-TCTGCTATCATTAACAAGTCCTAAC
* * * *
78086 GATAATGGATTTTTGTAGGTTCTGTTATCTTTAATAAGTCCTAAC
1 GATAATGGATTTTTGTAGATTCTGCTATCATTAACAAGTCCTAAC
78131 ATTCAGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 10 0.26
45 29 0.74
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (45 bp):
GATAATGGATTTTTGTAGATTCTGCTATCATTAACAAGTCCTAAC
Found at i:80230 original size:25 final size:25
Alignment explanation
Indices: 80196--80250 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
80186 TGAGAACAAT
*
80196 TTCTCACATTCTTCATATTTTATTG
1 TTCTCACATTCTTCATATTTTATTC
80221 TTCTCACATTCTTCATATTTTATTC
1 TTCTCACATTCTTCATATTTTATTC
80246 TTCTC
1 TTCTC
80251 CATATTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (25 bp):
TTCTCACATTCTTCATATTTTATTC
Found at i:80274 original size:16 final size:16
Alignment explanation
Indices: 80253--80283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
80243 TTCTTCTCCA
80253 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
80269 TATTCTCTTGTCTTT
1 TATTCTATTGTCTTT
80284 TCCATACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:80810 original size:23 final size:23
Alignment explanation
Indices: 80765--80810 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
80755 CAATTATTTG
* *
80765 TAATTATTAATTAACTAAGATAA
1 TAATTATTAATTAAATAAAATAA
80788 TAATTATT-ATATAAATAAAATAA
1 TAATTATTAAT-TAAATAAAATAA
80811 AGCACATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATTATTAATTAAATAAAATAA
Found at i:83558 original size:45 final size:45
Alignment explanation
Indices: 83507--83592 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
83497 ACTTCTCTAG
83507 CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAC
1 CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAC
*
83552 CTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
83593 AACTCTGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (45 bp):
CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAC
Found at i:90470 original size:2 final size:2
Alignment explanation
Indices: 90463--90490 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
90453 CTCACAAACA
90463 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
90491 TTACCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:91020 original size:18 final size:16
Alignment explanation
Indices: 90982--91020 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
90972 TCTTAAAATA
90982 GCAAATAACCTAATCC
1 GCAAATAACCTAATCC
*
90998 CCAAATAACCTCCAATCC
1 GCAAATAACCT--AATCC
91016 GCAAA
1 GCAAA
91021 CTTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.44, C:0.36, G:0.05, T:0.15
Consensus pattern (16 bp):
GCAAATAACCTAATCC
Found at i:93513 original size:175 final size:175
Alignment explanation
Indices: 93194--93518 Score: 460
Period size: 175 Copynumber: 1.9 Consensus size: 175
93184 GTGTTAGATT
93194 CAAATCCACCTTTGAGACACGCCAAAGATCAACTTGAAACACCAAAACTTCTAGACTTGTAGTAG
1 CAAATCCACCTTTGAGACACGCCAAAGATCAACTTGAAACACCAAAACTTCTAGACTTGTAG-AG
* * ** * *
93259 TCGATAAACCTAACCTAGTCTTTTTCTTCGTTCGTCGGCCTTAAGCTCTCAATTAGACCTGCAAT
65 TCGACAAACCTAACCTAGTATCCTCCTTCGTTCGTCGGCCTTAAGCCCTCAATTAGACCTGCAAT
*
93324 TGAACACTTAAGATCACAAGTGATACGAATCTAGTTGCAATCGGTC
130 TGAACACCTAAGATCACAAGTGATACGAATCTAGTTGCAATCGGTC
* *
93370 CAAATCCACCTTTGAGACCCGCCAAAGATCAACTTGAATCACC-AAACTTCTAGACTTGTA-AGT
1 CAAATCCACCTTTGAGACACGCCAAAGATCAACTTGAAACACCAAAACTTCTAGACTTGTAGAGT
* * * *
93433 CGACAATCTTCA-CTAGATAAATCCTCCTTCGTTCGTCGG-CTTTAGACCCTCAATTAGACCTGC
66 CGACAAACCTAACCTAG-T--ATCCTCCTTCGTTCGTCGGCCTTAAG-CCCTCAATTAGACCTGC
93496 AATTGAACACCTAAGATCACAAG
127 AATTGAACACCTAAGATCACAAG
93519 ATTCACAAAC
Statistics
Matches: 132, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
172 4 0.03
173 12 0.09
174 5 0.04
175 70 0.53
176 41 0.31
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (175 bp):
CAAATCCACCTTTGAGACACGCCAAAGATCAACTTGAAACACCAAAACTTCTAGACTTGTAGAGT
CGACAAACCTAACCTAGTATCCTCCTTCGTTCGTCGGCCTTAAGCCCTCAATTAGACCTGCAATT
GAACACCTAAGATCACAAGTGATACGAATCTAGTTGCAATCGGTC
Found at i:100505 original size:30 final size:30
Alignment explanation
Indices: 100471--100530 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
100461 TGCCCGGCCT
* * *
100471 TGTGCGATTGGTCCTTGCCATGGCCGGTCA
1 TGTGCGATTGCTCCATGCAATGGCCGGTCA
100501 TGTGCGATTGCTCCATGCAATGGCCGGTCA
1 TGTGCGATTGCTCCATGCAATGGCCGGTCA
100531 CATGCGATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.13, C:0.27, G:0.32, T:0.28
Consensus pattern (30 bp):
TGTGCGATTGCTCCATGCAATGGCCGGTCA
Found at i:100537 original size:30 final size:30
Alignment explanation
Indices: 100473--100538 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
100463 CCCGGCCTTG
* * * **
100473 TGCGATTGGTCCTTGCCATGGCCGGTCATG
1 TGCGATTGCTCCATGCAATGGCCGGTCACA
100503 TGCGATTGCTCCATGCAATGGCCGGTCACA
1 TGCGATTGCTCCATGCAATGGCCGGTCACA
100533 TGCGAT
1 TGCGAT
100539 CCCATCTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.27
Consensus pattern (30 bp):
TGCGATTGCTCCATGCAATGGCCGGTCACA
Done.