Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009360.1 Corchorus capsularis cultivar CVL-1 contig09381, 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: 40989
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:7175 original size:5 final size:6
Alignment explanation
Indices: 7146--7173 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7136 GCGTGTCTTT
7146 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
7174 CATTTATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:13803 original size:2 final size:2
Alignment explanation
Indices: 13796--13837 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
13786 CTTTTTGCGC
*
13796 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
13838 TTTGCAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:17230 original size:18 final size:18
Alignment explanation
Indices: 17209--17269 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
17199 AATCTAATAA
17209 TAAATTACAAATACAAAC
1 TAAATTACAAATACAAAC
* *
17227 TAAATT-CTCAAT-CTAATAA
1 TAAATTAC-AAATAC-AA-AC
17246 TAAATTACAAATACAAAC
1 TAAATTACAAATACAAAC
17264 TAAATT
1 TAAATT
17270 CTCCTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 2 0.06
18 18 0.53
19 12 0.35
20 2 0.06
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATTACAAATACAAAC
Found at i:17248 original size:37 final size:37
Alignment explanation
Indices: 17198--17272 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
17188 AACGGACAAA
17198 CAATCTAATAATAAATTACAAATACAAACTAAATTCT
1 CAATCTAATAATAAATTACAAATACAAACTAAATTCT
17235 CAATCTAATAATAAATTACAAATACAAACTAAATTCT
1 CAATCTAATAATAAATTACAAATACAAACTAAATTCT
17272 C
1 C
17273 CTTAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.29
Consensus pattern (37 bp):
CAATCTAATAATAAATTACAAATACAAACTAAATTCT
Found at i:17251 original size:19 final size:19
Alignment explanation
Indices: 17198--17253 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
17188 AACGGACAAA
17198 CAATCTAATAATAAATTAC
1 CAATCTAATAATAAATTAC
* *
17217 AAATAC-AA-ACTAAATT-C
1 CAAT-CTAATAATAAATTAC
17234 TCAATCTAATAATAAATTAC
1 -CAATCTAATAATAAATTAC
17254 AAATACAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
19 12 0.43
20 2 0.07
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (19 bp):
CAATCTAATAATAAATTAC
Found at i:17281 original size:24 final size:23
Alignment explanation
Indices: 17254--17306 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
17244 AATAAATTAC
17254 AAATACAAACTAAATTCTCCTTAA
1 AAATA-AAACTAAATTCTCCTTAA
*
17278 AAATAATACTAAATTCTCCTTAA
1 AAATAAAACTAAATTCTCCTTAA
17301 AAATAA
1 AAATAA
17307 TCCAAACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAAAACTAAATTCTCCTTAA
Found at i:17290 original size:23 final size:23
Alignment explanation
Indices: 17262--17307 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17252 ACAAATACAA
17262 ACTAAATTCTCCTTAAAAATAAT
1 ACTAAATTCTCCTTAAAAATAAT
17285 ACTAAATTCTCCTTAAAAATAAT
1 ACTAAATTCTCCTTAAAAATAAT
17308 CCAAACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (23 bp):
ACTAAATTCTCCTTAAAAATAAT
Found at i:17969 original size:166 final size:166
Alignment explanation
Indices: 17656--17985 Score: 414
Period size: 166 Copynumber: 2.0 Consensus size: 166
17646 TCATTTGTCA
* * *
17656 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAAAATAAAAAATTAGGACATTTAA
* * * * * ** * * *
17721 GTAATATGCTAAGTAGGTAAAAACGAAAAATGTTAGTTCTCTAACTCATCATCAATCCTTGATGG
66 GTAATATGCCAAGTAGGAAAAAACGAAAAATATAAGTTATCTAACTCAAAAACAAGCCTTGATAG
* *
17786 GGATTATTTATTAATTCCACTAC-TCTATTCAAGTCC
131 GGATTATTTAGTAATTCCAC-ACTTCTATTAAAGTCC
* * *
17822 ATTGAGAAATGACCAGAAAGATTACTTATTTAATCCCCTCAAAAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAAAATAAAAAATTAGGACATTTAA
* * *
17887 GTAATCTGCCAAGTAGGAAAAAACGAAAAA-ATAAGTTATCTAACTCCAAAAACAAGGCTTGGTA
66 GTAATATGCCAAGTAGGAAAAAACGAAAAATATAAGTTATCTAACT-CAAAAACAAGCCTTGATA
*
17951 GGTATCT-TTTAGTAATTCCACACTTCTATTAAAGT
130 GGGAT-TATTTAGTAATTCCACACTTCTATTAAAGT
17986 TTAGGACATT
Statistics
Matches: 139, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
165 14 0.10
166 124 0.89
167 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (166 bp):
ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAAAATAAAAAATTAGGACATTTAA
GTAATATGCCAAGTAGGAAAAAACGAAAAATATAAGTTATCTAACTCAAAAACAAGCCTTGATAG
GGATTATTTAGTAATTCCACACTTCTATTAAAGTCC
Found at i:18610 original size:2 final size:2
Alignment explanation
Indices: 18603--18629 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18593 CTACTTAATA
18603 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 A
18630 AAGCTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18827 original size:50 final size:50
Alignment explanation
Indices: 18688--18816 Score: 212
Period size: 46 Copynumber: 2.6 Consensus size: 50
18678 TTTTTTTTTC
*
18688 TTTTTCTTTTTTTCCGTTTTCTTAGTTGTTCTTTCCTGTATTTACCATAAG
1 TTTTT-TTTTTTTTCGTTTTCTTAGTTGTTCTTTCCTGTATTTACCATAAG
18739 ----TTTTTTTTTCGTTTTCTTAGTTGTTCTTTCCTGTATTTACCATAAG
1 TTTTTTTTTTTTTCGTTTTCTTAGTTGTTCTTTCCTGTATTTACCATAAG
18785 TTTTTTTTTTTTTCGTTTTCTTAGTTGTTCTT
1 TTTTTTTTTTTTTCGTTTTCTTAGTTGTTCTT
18817 GCTTGCATTT
Statistics
Matches: 73, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
46 44 0.60
47 1 0.01
50 28 0.38
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.65
Consensus pattern (50 bp):
TTTTTTTTTTTTTCGTTTTCTTAGTTGTTCTTTCCTGTATTTACCATAAG
Found at i:20300 original size:19 final size:19
Alignment explanation
Indices: 20271--20316 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20261 AATATGAAGA
* *
20271 ATATACAAAAAAAGTTGTAT
1 ATATATAAAAAAA-TTATAT
20291 ATATATAAAAAAATTATAT
1 ATATATAAAAAAATTATAT
20310 ATATATA
1 ATATATA
20317 TATAAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
ATATATAAAAAAATTATAT
Found at i:29305 original size:108 final size:108
Alignment explanation
Indices: 29116--29325 Score: 393
Period size: 108 Copynumber: 1.9 Consensus size: 108
29106 AATTATAAAT
29116 ATATTAGATTTAATTGATTAAAAATAAAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATG
1 ATATTAGATTTAATTGATTAAAAATAAAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATG
29181 ACATTTAAGAAATATGTTTGAATAATAAGGGTACAATCGAAAG
66 ACATTTAAGAAATATGTTTGAATAATAAGGGTACAATCGAAAG
*
29224 ATATTAGATTTAATTGATTAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATG
1 ATATTAGATTTAATTGATTAAAAATAAAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATG
**
29289 GTATTTAAGAAATATGTTTGAATAATAAGGGTACAAT
66 ACATTTAAGAAATATGTTTGAATAATAAGGGTACAAT
29326 GGTCGATTCA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 99 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (108 bp):
ATATTAGATTTAATTGATTAAAAATAAAGTTTTTAGTAGAATAAAACTATAATAGTTAAGTAATG
ACATTTAAGAAATATGTTTGAATAATAAGGGTACAATCGAAAG
Found at i:30862 original size:27 final size:27
Alignment explanation
Indices: 30832--30893 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
30822 ACCATTAACT
* * *
30832 GCCACCACAACCACCGCCACCGCCACC
1 GCCACAACAACCACCGCAACCACCACC
*
30859 GCCACAACCACCACCGCAACCACCACC
1 GCCACAACAACCACCGCAACCACCACC
30886 GCCACAAC
1 GCCACAAC
30894 TGCAACCTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.60, G:0.10, T:0.00
Consensus pattern (27 bp):
GCCACAACAACCACCGCAACCACCACC
Found at i:30869 original size:12 final size:12
Alignment explanation
Indices: 30836--30882 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
30826 TTAACTGCCA
30836 CCACAACCACCG
1 CCACAACCACCG
**
30848 CCACCGCCACCG
1 CCACAACCACCG
*
30860 CCACAACCACCA
1 CCACAACCACCG
*
30872 CCGCAACCACC
1 CCACAACCACC
30883 ACCGCCACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.30, C:0.62, G:0.09, T:0.00
Consensus pattern (12 bp):
CCACAACCACCG
Found at i:30893 original size:15 final size:15
Alignment explanation
Indices: 30854--30893 Score: 59
Period size: 12 Copynumber: 2.9 Consensus size: 15
30844 ACCGCCACCG
30854 CCACCGCCACAACCA
1 CCACCGCCACAACCA
30869 CCACCG---CAACCA
1 CCACCGCCACAACCA
30881 CCACCGCCACAAC
1 CCACCGCCACAAC
30894 TGCAACCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.55
15 10 0.45
ACGTcount: A:0.33, C:0.60, G:0.07, T:0.00
Consensus pattern (15 bp):
CCACCGCCACAACCA
Found at i:32564 original size:16 final size:16
Alignment explanation
Indices: 32543--32593 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
32533 ACAATTCAGA
32543 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
32559 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
*
32575 AAGCAGAAAAGCTCCG
1 AAGCAGAAAAGCTCTG
32591 AAG
1 AAG
32594 TATTTCAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:32942 original size:44 final size:44
Alignment explanation
Indices: 32859--32942 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 44
32849 TGTTTGTTCA
* * * * *
32859 AGATCAAGTCACCAAGACCCTTGAGTCAAATTATCATCAATTTG
1 AGATCAAGTCACAAAGACCCTCGAATCAAATCATAATCAATTTG
*
32903 AGATCAAGTCATCAAAGACCCTCGAATCGAATCA-AATCAA
1 AGATCAAGTCA-CAAAGACCCTCGAATCAAATCATAATCAA
32943 ATTCCCAAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
44 16 0.48
45 17 0.52
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (44 bp):
AGATCAAGTCACAAAGACCCTCGAATCAAATCATAATCAATTTG
Found at i:34943 original size:71 final size:68
Alignment explanation
Indices: 34843--34994 Score: 205
Period size: 71 Copynumber: 2.2 Consensus size: 68
34833 CAGTCAAACC
* * * *
34843 AAAAAAAAAAAAAAGCTCGTTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
1 AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACTTAGAGC
34908 AAA
66 AAA
* *
34911 AAAAAAAAAAAAAGGAGGCTCGCTAAGTTGAAAATCCTGAAAAGGATGACTTTGGCAAAACTTAG
1 AAAAAAAAAAAAA--A-GCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACTTAG
**
34976 AGCACC
63 AGCAAA
34982 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
34995 TGAACTACGT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
68 13 0.18
70 1 0.01
71 59 0.81
ACGTcount: A:0.53, C:0.13, G:0.19, T:0.15
Consensus pattern (68 bp):
AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGAAAAGGACGACTTAGGCAAAACTTAGAGC
AAA
Found at i:38319 original size:199 final size:198
Alignment explanation
Indices: 37651--39703 Score: 2553
Period size: 199 Copynumber: 10.3 Consensus size: 198
37641 TTAAAATAAG
* * * *
37651 GATTATTATACAATATATTGTCAGTGTAAATCTTAGACTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
***
37716 ATA-CCTCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACATGT
66 ATACCCT-ATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGT
** * *
37780 CAACCCTTAAACCCCGTGCGTGTAGTCTGCTAAACTCCACTAACGGTGTATTGTATAATTTTTTT
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTT
37845 ATAT
195 ATAT
* * *
37849 GATTATTATACAATACACTGTAAGTGTAAATCTTAGACTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * * * *
37914 ATGCTCTAATTCATAATTAATTAAATATAAAATATTAATACATATTCCTTAAGGGGACACATGTT
66 ATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTC
** * * * *
37979 AACCCTTAAACCACGTGCGTGCGTGTAGTTTGCTAAACTCCATTGACGGTGTATTGCATAATTTT
131 AACCCTTAAACC-C---CGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
38044 TTTATAT
192 TTTATAT
*
38051 GAATATTATACAATACACTGTCAGTGTAAATTTTGGACAT-CATAAGCGGGTTAAGAAGTTGACA
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGAC-TCCATAAGCGGGTTAAGAAGTTGACA
*
38115 CATACCCTATTTCATAATTAATTAAATACAAAATATTAATACATATTCCCTAAGGGGACACATGT
65 CATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGT
* *
38180 CAACCCTTAAACCCCGCGCGTGCAGTCTGCTAAACTCCACTGACCGTGTATTGTATAATTCTTTT
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT-TTTT
*
38245 AATAT
194 TATAT
*
38250 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTTCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * *
38315 ATACCCTAATTCATAATTAATTAAATATAAAATATTAATACATACTCCCTAAGGGGGCACATGTC
66 ATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTC
* ** * *
38380 AACTCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACTGATGGTGTATCGTATAATTATTTTT
131 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATT-TTTTT
38445 ATAT
195 ATAT
* * * * * *
38449 GATTATTATACAATATACTATCAATGTAAATTTTAGACTCCATATGTGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* ** *
38514 ATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAAGGGGACACATGTC
66 ATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTC
* ** * * * * *
38579 AACGCTTAAACCATGCACGTCCAGTCAGCTAAAATCAACTGATGGTGTATTGTATAATTTTTTTA
131 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTA
38644 T-T
196 TAT
* * * *
38646 GGATTATTATACAATACACTGTCAATGTAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTGACA
1 -GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACA
* * **
38711 CATACCCTATTTCGTAATTAATTAAATATGAATTAATAATAATACATATTCCCTAACGGAAACAC
65 CATACCCTATTTCATAATTAATTAAATAT-AA--AATATTAATACATATTCCCTAA-GGGGACAC
* * *
38776 ATGTCAACCCTTAAACCTCGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGTATAATTT
126 ATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTT
38841 TTTT-TAT
191 TTTTATAT
* * * * *
38848 -A-T-GT-TAC-ATACACCGTTAGTATAAATTTTGCACAT-CATAAGCGGGTTAAGAAGTTGACA
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGAC-TCCATAAGCGGGTTAAGAAGTTGACA
* * * *
38907 GATACCCTATTCCACAATTAATTAAAATATAAAATATTAATACATATATTCCCTAAGGGAACACA
65 CATACCCTATTTCATAATTAATT-AAATATAAAATATTAATAC--ATATTCCCTAAGGGGACACA
* * * *
38972 TATCAACCCTTAAAGCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAA-TAT
127 TGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
39036 TTTATAT
192 TTTATAT
*
39043 GATTATTATACAATACACTGTCAGTGTAAATTTTGGATTCCATAAGCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
**
39108 ATA-CCTCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT
66 ATACCCT-ATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGT
* * * *
39172 CAACCCCTGAACCCCGCATGTGCAGTCTGCT--ACTCCACTGACAGTGTATTGCT-TAATTTTTC
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTG-TATAATTTTT-
*
39234 TTATAA
193 TTATAT
* * * *
39240 GATTATTATACAATACACTGTTAGTATAAATTTTGGACTCCATAGGTGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* ***
39305 ACACCGC-ATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACATGT
66 ATACC-CTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGT
* ** * * * * * * * *
39369 CAACCTTTAAATACTGTACATGCAGTCTGCTAAAATTCACTAACGG-GAACTGTATAATTTTTCT
130 CAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT-T
*
39433 TATAA
194 TATAT
* *
39438 GATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAATCGGGTTAAGAAGTTGACAC
1 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
* * ** * * *
39503 ATACCCCATTTCATAATTAA--ATAT-TTTAATATTAATATATATTCCCTAAGGGTACACATGTT
66 ATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTC
* * *
39565 AACCCTTAAAGTTAAACTCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTATTGTATAAAT
131 AACCC------TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTAT-AAT
39630 TTTCTTATATAT
189 TTT-TT-TATAT
* * *
39642 AGAATTATTATACAATACACTGTCAGTGTAAAATTTGGACACTATAAGCGGGTTAAGAAGTT
1 -G-ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTT
39704 TTTGTACCAA
Statistics
Matches: 1623, Mismatches: 185, Indels: 86
0.86 0.10 0.05
Matches are distributed among these distances:
194 15 0.01
195 125 0.08
196 83 0.05
197 207 0.13
198 359 0.22
199 396 0.24
200 62 0.04
201 54 0.03
202 254 0.16
203 8 0.00
204 5 0.00
205 1 0.00
206 54 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (198 bp):
GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
ATACCCTATTTCATAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGGACACATGTC
AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTA
TAT
Found at i:38736 original size:798 final size:789
Alignment explanation
Indices: 37646--39703 Score: 2738
Period size: 798 Copynumber: 2.6 Consensus size: 789
37636 AAGCTTTAAA
* * *
37646 ATAAGGATTATTATACAATATATTGTCAGTGTAAATCTTAGACTCCATAAGCGGGTTAAGAAGTT
1 ATAA-GATTATTATACAATATACTGTCAGTGTAAATTTTAGACTCCATAAGTGGGTTAAGAAGTT
*
37711 GACACATACCTCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACAC
65 GACACATACCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACAC
** * * *
37776 ATGTCAACCCTTAAACCCCGTGCGTGTAGTCTGCTAAACTCCACTAACGGTGTATTGTATAATTT
130 ATGTCAA-CCTTAAACCATGTACGTGCAGTCTGCTAAAAT-CACTAACGGTGTATTGTATAATTT
*
37841 TTTTATATGATTATTATACAATACACTGT-AAGTGTAAATCTT-AGACTCCATAAGCGGGTTAAG
193 TTTTAT-TGATTATTATACAATACACTGTCAA-TGTAAATCTTGA-ACTCCATAAGTGGGTTAAG
* * * *
37904 AAGTTGACACATGCTCTAATTCATAATTAATTAAATATAAAATATTAATACATATTCCTTAAGGG
255 AAGTTGACACATACCCTATTTC-TAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGG
* * * * *
37969 GACACATGTTAACCCTTAAACCACGTGCGTGCGTGTAGTTTGCTAAACTCCATTGACGGTGTATT
319 AACACATGTTAACCCTTAAA-CAC-T-CGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGTATT
*
38034 GCATAATTTTTTTATATGAATATTATACAATACACTGTCAGTGTAAATTTTGGACATCATAAGCG
381 GTATAATTTTTTTATATGAATATTATACAATACACTGTCAGTGTAAATTTTGGACATCATAAGCG
* *
38099 GGTTAAGAAGTTGACACATACCCTATTTCATAATTAATT-AAATACAAAATATTAATAC-ATATT
446 GGTTAAGAAGTTGACACATACCCTATTCCACAATTAATTAAAATACAAAATATTAATACAATATT
* * *
38162 CCCTAAGGGGACACATGTCAACCCTTAAACCCCGCGCGTGCAGTCTGCTAAACTCCACTGACCGT
511 CCCTAAGGGAACACATATCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACCGT
* *
38227 GTATTGTATAATTCTTTTAATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTT-C
576 GTATTATATAA-TATTTT-ATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGA-TTCC
38291 ATAAGCGGGTTAAGAAGTTGACACATACC-CTAATTCATAATTAATTAAATATAAAATATTAATA
638 ATAAGCGGGTTAAGAAGTTGACACATACCTC-AATTCATAATTAATTAAATATAAAATATTAATA
* * * **
38355 CATACTCCCTAAGGGGGCACATGTCAACTCTTAAACCCCGTGCGTGCAGTCTGCTAAACTCCACT
702 CATACTCCCTAAGGGGACACATGTCAACCCCTAAACCCCGCACGTGCAGTCTGCT--ACTCCACT
**
38420 GATGGTGTATCG-TATAATTATTT-TT
765 GACAGTGTATCGCT-TAATT-TTTCTT
* * * *
38445 ATATGATTATTATACAATATACTATCAATGTAAATTTTAGACTCCATATGTGGGTTAAGAAGTTG
1 ATAAGATTATTATACAATATACTGTCAGTGTAAATTTTAGACTCCATAAGTGGGTTAAGAAGTTG
* *
38510 ACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCTTAAGGGGACACA
66 ACACATACCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACA
* * * * *
38575 TGTCAACGCTTAAACCATGCACGTCCAGTCAGCTAAAATCAACTGATGGTGTATTGTATAATTTT
131 TGTCAAC-CTTAAACCATGTACGTGCAGTCTGCTAAAATC-ACTAACGGTGTATTGTATAATTTT
38640 TTTATTGGATTATTATACAATACACTGTCAATGTAAATCTTGAACTCCATAAGTGGGTTAAGAAG
194 TTTATT-GATTATTATACAATACACTGTCAATGTAAATCTTGAACTCCATAAGTGGGTTAAGAAG
*
38705 TTGACACATACCCTATTTCGTAATTAATTAAATATGAATTAATAATAATACATATTCCCTAACGG
258 TTGACACATACCCTATTTC-TAATTAATTAAATAT-AA--AATATTAATACATATTCCCTAA-GG
* * *
38770 AAACACATGTCAACCCTTAAAC-CTCGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGCATTGT
318 GAACACATGTTAACCCTTAAACACTCGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGT
* * * * *
38834 ATAATTTTTTT-TAT--AT-GT-TAC-ATACACCGTTAGTATAAATTTTGCACATCATAAGCGGG
383 ATAATTTTTTTATATGAATATTATACAATACACTGTCAGTGTAAATTTTGGACATCATAAGCGGG
* *
38893 TTAAGAAGTTGACAGATACCCTATTCCACAATTAATTAAAATATAAAATATTAATACATATATTC
448 TTAAGAAGTTGACACATACCCTATTCCACAATTAATTAAAATACAAAATATTAATACA-ATATTC
* *
38958 CCTAAGGGAACACATATCAACCCTTAAAGCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTG
512 CCTAAGGGAACACATATCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACCGTG
39023 TATTATATAATATTTTATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGATTCCATAA
577 TATTATATAATATTTTATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGATTCCATAA
* ** *
39088 GCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATATTAATACATAT
642 GCGGGTTAAGAAGTTGACACATACCTCAATTCATAATTAATTAAATATAAAATATTAATACATAC
* *
39153 TCCCTAAGGGGACACATGTCAACCCCTGAACCCCGCATGTGCAGTCTGCTACTCCACTGACAGTG
707 TCCCTAAGGGGACACATGTCAACCCCTAAACCCCGCACGTGCAGTCTGCTACTCCACTGACAGTG
*
39218 TATTGCTTAATTTTTCTT
772 TATCGCTTAATTTTTCTT
* * * * *
39236 ATAAGATTATTATACAATACACTGTTAGTATAAATTTTGGACTCCATAGGTGGGTTAAGAAGTTG
1 ATAAGATTATTATACAATATACTGTCAGTGTAAATTTTAGACTCCATAAGTGGGTTAAGAAGTTG
* *
39301 ACACACACCGCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACA
66 ACACATACCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACA
* * * *
39366 TGTCAACCTTTAAA-TACTGTACATGCAGTCTGCTAAAATTCACTAACGG-GAACTGTATAATTT
131 TGTCAACC-TTAAACCA-TGTACGTGCAGTCTGCTAAAA-TCACTAACGGTGTATTGTATAATTT
* * * * *
39429 TTCTTATAAGATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCATAA-TCGGGTTAAG
193 TT-TTAT-TGATTATTATACAATACACTGTCAATGTAAATCTTGAACTCCATAAGT-GGGTTAAG
* ** *
39493 AAGTTGACACATACCCCATTTC--A-TAATTAAATATTTTAATATTAATATATATTCCCTAAGGG
255 AAGTTGACACATACCCTATTTCTAATTAATTAAATA-TAAAATATTAATACATATTCCCTAAGGG
* * * * *
39555 TACACATGTTAACCCTTAAAGTTAAACTCCGCACGTGCAGTCTACTAAACTCCACTAACGGTGTA
319 AACACATGTTAACCCTT-AA---ACACT-CGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGTA
*
39620 TTGTATAAATTTTCTTATATATAGAATTATTATACAATACACTGTCAGTGTAAAATTTGGACA-C
379 TTGTAT-AATTTT-TT-TATAT-GAA-TATTATACAATACACTGTCAGTGTAAATTTTGGACATC
39684 TATAAGCGGGTTAAGAAGTT
439 -ATAAGCGGGTTAAGAAGTT
39704 TTTGTACCAA
Statistics
Matches: 1107, Mismatches: 111, Indels: 80
0.85 0.09 0.06
Matches are distributed among these distances:
784 17 0.02
785 22 0.02
787 10 0.01
788 3 0.00
789 2 0.00
790 58 0.05
791 257 0.23
792 75 0.07
793 170 0.15
794 10 0.01
795 77 0.07
797 7 0.01
798 302 0.27
799 10 0.01
800 5 0.00
801 62 0.06
802 20 0.02
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (789 bp):
ATAAGATTATTATACAATATACTGTCAGTGTAAATTTTAGACTCCATAAGTGGGTTAAGAAGTTG
ACACATACCCCATTTCATAATTAATTAAATATTTGATATTAATACATATTCCCTAAGGGGACACA
TGTCAACCTTAAACCATGTACGTGCAGTCTGCTAAAATCACTAACGGTGTATTGTATAATTTTTT
TATTGATTATTATACAATACACTGTCAATGTAAATCTTGAACTCCATAAGTGGGTTAAGAAGTTG
ACACATACCCTATTTCTAATTAATTAAATATAAAATATTAATACATATTCCCTAAGGGAACACAT
GTTAACCCTTAAACACTCGCGCGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
TTTATATGAATATTATACAATACACTGTCAGTGTAAATTTTGGACATCATAAGCGGGTTAAGAAG
TTGACACATACCCTATTCCACAATTAATTAAAATACAAAATATTAATACAATATTCCCTAAGGGA
ACACATATCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACCGTGTATTATATA
ATATTTTATATGATTATTATACAATACACTGTCAGTGTAAATTTTGGATTCCATAAGCGGGTTAA
GAAGTTGACACATACCTCAATTCATAATTAATTAAATATAAAATATTAATACATACTCCCTAAGG
GGACACATGTCAACCCCTAAACCCCGCACGTGCAGTCTGCTACTCCACTGACAGTGTATCGCTTA
ATTTTTCTT
Done.