Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012470.1 Corchorus capsularis cultivar CVL-1 contig12491, 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: 98227
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--29 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30 CAGAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6180 original size:1 final size:1
Alignment explanation
Indices: 6174--6199 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6164 TTTTACTACT
6174 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
6200 CCCCACAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11184 original size:3 final size:3
Alignment explanation
Indices: 11176--11218 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
11166 ATATATTATA
11176 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11219 TATGAGCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37961 original size:36 final size:37
Alignment explanation
Indices: 37914--38052 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 37
37904 AATAGGCGGA
37914 TTGTGTAGCATTACTCTTCCAACACA-ATGAGACGGG
1 TTGTGTAGCATTACTCTTCCAACACAGATGAGACGGG
***
37950 TTGTGTAGCATTACTCTTCCAACACAGATGA-AAAAG
1 TTGTGTAGCATTACTCTTCCAACACAGATGAGACGGG
* * * *
37986 --ATG-AGC-TCACTCGGCATCCAACATAGATGAGACGGG
1 TTGTGTAGCATTACT---CTTCCAACACAGATGAGACGGG
38022 TTGTGTAGCATTACTCTTCCAACACAGATGA
1 TTGTGTAGCATTACTCTTCCAACACAGATGA
38053 AAAAGATGAG
Statistics
Matches: 80, Mismatches: 14, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
32 4 0.05
33 3 0.04
34 2 0.03
35 14 0.17
36 30 0.38
37 18 0.22
38 2 0.03
39 3 0.04
40 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (37 bp):
TTGTGTAGCATTACTCTTCCAACACAGATGAGACGGG
Found at i:38057 original size:72 final size:71
Alignment explanation
Indices: 37931--38075 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 71
37921 GCATTACTCT
37931 TCCAACACAATGAGACGGGTTGTGTAGCATTACTCTTCCAACACAGATGAAAAAGATGAGCTCAC
1 TCCAACACAATGAGACGGGTTGTGTAGCATTACTCTTCCAACACAGATGAAAAAGATGAGCTCAC
37996 TCGGCA
66 TCGGCA
*
38002 TCCAACATAGATGAGACGGGTTGTGTAGCATTACTCTTCCAACACAGATGAAAAAGATGAGCTCA
1 TCCAACACA-ATGAGACGGGTTGTGTAGCATTACTCTTCCAACACAGATGAAAAAGATGAGCTCA
38067 CTCGGCA
65 CTCGGCA
38074 TC
1 TC
38076 TTGTAGTGAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 8 0.11
72 64 0.89
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (71 bp):
TCCAACACAATGAGACGGGTTGTGTAGCATTACTCTTCCAACACAGATGAAAAAGATGAGCTCAC
TCGGCA
Found at i:40222 original size:6 final size:6
Alignment explanation
Indices: 40211--40236 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40201 AACAGTTAAT
40211 ACATGG ACATGG ACATGG ACATGG AC
1 ACATGG ACATGG ACATGG ACATGG AC
40237 GTGGTATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (6 bp):
ACATGG
Found at i:45333 original size:2 final size:2
Alignment explanation
Indices: 45328--45353 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45318 AGCTATATAC
45328 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
45354 TATGTATGTA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:51766 original size:27 final size:27
Alignment explanation
Indices: 51735--51789 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
51725 GTTTGCTTCC
*
51735 ATTCCCCTTCTAAAACTATTTTTGAGT
1 ATTCCCCTTCTAAAACTAATTTTGAGT
51762 ATTCCCCTTCTAAAACTAATTTTGAGT
1 ATTCCCCTTCTAAAACTAATTTTGAGT
51789 A
1 A
51790 GCAATTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
ATTCCCCTTCTAAAACTAATTTTGAGT
Found at i:72960 original size:17 final size:17
Alignment explanation
Indices: 72938--72992 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
72928 GATCACCTCT
*
72938 AGATCACTGGTGATCTA
1 AGATCACTGGTGATCAA
72955 AGATCACTGGTGATCAA
1 AGATCACTGGTGATCAA
72972 AGATCACTGGTGATCAA
1 AGATCACTGGTGATCAA
72989 AGAT
1 AGAT
72993 TACATGGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (17 bp):
AGATCACTGGTGATCAA
Found at i:73321 original size:22 final size:25
Alignment explanation
Indices: 73278--73326 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
73268 CTTCAATACT
* *
73278 TAAGTAAGGTTTATGGTAATTTTAA
1 TAAGTAAGGTTTATGATAATTTGAA
73303 TAAGTAAGGTTT-T-AT-ATTTGAA
1 TAAGTAAGGTTTATGATAATTTGAA
73325 TA
1 TA
73327 TTGTGAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
24 1 0.05
25 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAAGTAAGGTTTATGATAATTTGAA
Found at i:74467 original size:29 final size:29
Alignment explanation
Indices: 74412--74467 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
74402 ACAATTAAAT
** **
74412 AGAAACAAGTGAGTGTTTTTTTTAAAGGA
1 AGAAACAAGTGAGTGTTAATTAAAAAGGA
74441 AGAAACAAGTGAGTGTTAATTAAAAAG
1 AGAAACAAGTGAGTGTTAATTAAAAAG
74468 AACAAGGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.29
Consensus pattern (29 bp):
AGAAACAAGTGAGTGTTAATTAAAAAGGA
Found at i:75173 original size:20 final size:20
Alignment explanation
Indices: 75148--75185 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75138 TTTAAGTGAA
75148 TTACTAAATACCGCCCCTTT
1 TTACTAAATACCGCCCCTTT
**
75168 TTACTAGCTACCGCCCCT
1 TTACTAAATACCGCCCCT
75186 CTCTTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.39, G:0.08, T:0.32
Consensus pattern (20 bp):
TTACTAAATACCGCCCCTTT
Found at i:82734 original size:2 final size:2
Alignment explanation
Indices: 82722--82773 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
82712 TAGTTAATGC
* * * *
82722 CT CT AT CT CT CT CT GT CT CT GT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
82764 CT CT CT CT CT
1 CT CT CT CT CT
82774 GCGTGCACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.02, C:0.42, G:0.06, T:0.50
Consensus pattern (2 bp):
CT
Found at i:88244 original size:2 final size:2
Alignment explanation
Indices: 88231--88285 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
88221 GCTTGCCGTC
*
88231 TA TA TC TA TA TA 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 TA TA
* *
88273 GA TA CA TA TA TA T
1 TA TA TA TA TA TA T
88286 GAGTATTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:88323 original size:2 final size:2
Alignment explanation
Indices: 88316--88341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88306 GGAATACGTG
88316 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
88342 ACCAGCAATT
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:90121 original size:7 final size:7
Alignment explanation
Indices: 90109--90141 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
90099 ATTGCCATTG
90109 GCATGTA
1 GCATGTA
90116 GCATGTA
1 GCATGTA
90123 GCATGTA
1 GCATGTA
90130 GCATGTA
1 GCATGTA
90137 GCATG
1 GCATG
90142 ATGATGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (7 bp):
GCATGTA
Found at i:92045 original size:24 final size:25
Alignment explanation
Indices: 92018--92081 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
92008 ATATTTAATT
92018 TTTAAATAAAAATAATAA-CTAAAA
1 TTTAAATAAAAATAATAATCTAAAA
** *
92042 TTTATTTAAAAATAA-AATTTAAAA
1 TTTAAATAAAAATAATAATCTAAAA
* *
92066 TTAAAACAAAAATAAT
1 TTTAAATAAAAATAAT
92082 CTAATCTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (25 bp):
TTTAAATAAAAATAATAATCTAAAA
Found at i:92202 original size:23 final size:25
Alignment explanation
Indices: 92173--92221 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
92163 CAAATATATT
92173 TTTTAA-T-TGCTATAATTAAAATA
1 TTTTAATTATGCTATAATTAAAATA
* *
92196 TTTTAATTATGTTATTATTAAAATA
1 TTTTAATTATGCTATAATTAAAATA
92221 T
1 T
92222 GATTTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTAATTATGCTATAATTAAAATA
Found at i:92326 original size:93 final size:93
Alignment explanation
Indices: 92157--92326 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 93
92147 GATTATACAT
* * * * *
92157 TTTTTTCAAATATATTTTTTAATTGCTATAATTAAAATATTTTAATTATGTTATTATTAAAATAT
1 TTTTTTCAAATATATTTCTAAATTGCTATAATTAAAATATTTTAACTATGTCACTATTAAAATAT
*
92222 GATTTTATGTATTTTTCCCATTGTACCA
66 GAATTTATGTATTTTTCCCATTGTACCA
*
92250 TTTTTTCAAATATATTTCTAAATTGAC-ATCATTAAAATATATTTTAACTATGTCACTATTAAAA
1 TTTTTTCAAATATATTTCTAAATTG-CTATAATT-AAA-ATATTTTAACTATGTCACTATTAAAA
92314 TAT-AATTT-TGTAT
63 TATGAATTTATGTAT
92327 ATATATCTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
93 33 0.49
94 8 0.12
95 26 0.39
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (93 bp):
TTTTTTCAAATATATTTCTAAATTGCTATAATTAAAATATTTTAACTATGTCACTATTAAAATAT
GAATTTATGTATTTTTCCCATTGTACCA
Found at i:92344 original size:29 final size:28
Alignment explanation
Indices: 92306--92378 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
92296 ACTATGTCAC
* * *
92306 TATTAAAATATAATTTTGTATATAT-ATCT
1 TATTCAAATATAATTTTG-AAAT-TCATAT
*
92335 TTTTCAAATAT-ATTTTGAAATTCATAT
1 TATTCAAATATAATTTTGAAATTCATAT
92362 TATTCAAATATAATTTT
1 TATTCAAATATAATTTT
92379 TTAATTAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 16 0.43
28 11 0.30
29 9 0.24
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTCAAATATAATTTTGAAATTCATAT
Found at i:93943 original size:629 final size:620
Alignment explanation
Indices: 92599--94136 Score: 1566
Period size: 629 Copynumber: 2.4 Consensus size: 620
92589 GCCTCGACTC
* * *
92599 CATTTTGCGTGATTTTTGGCACCAAGTCTCAATGAAATATCTATATCCATCTAACCAAATCTCAC
1 CATTTTGCATGATTTTTGGC-GCAAGTCTC-ATGAAATATCTATATACATCTAACCAAATCTCAC
* * *
92664 CCACATTGGATTTAAGGATTTGTTTTCACGAGCATTTGAATCATGTTTCGATTCAATTAGAAACT
64 CCACATTGGATTTAAGGATTTGTTTT-ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATT
* * *
92729 AATTCGG-AGAAAATAGGAAACACGATATTAGAAGCGTGAAAAGCCTTTCAATCA-TTTTGGCGT
128 AATTCGGAAAAAAATAGGAAAAACGATAATAGAAGCGTGAAAAGCCTTTCAAT-ATTTTTGGCGT
* *
92792 TGAATTATATACTTTTATGAGTATCATGACCAAAAATTGAAGAAAACTCTTTCATGTAAAATTTT
192 TGAATTATATACTCTTATGAGTATCATGACCAAAAATTGAAGAAAAATCTTTCATGTAAAATTTT
* * * * * *
92857 GCAAAATTTTAGCCGAAATCGTCACGATTTTTGACAAAAAATGAGTTATGGGGCCCAGGCTCGGT
257 GCAAAAATTTAGCCGAAATCATCACGATTTTTGACAAAAAACGAGTTACGGGGCCCAGACTCAGT
* * * *
92922 TTTGCATGATTTTTGGTGTCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCATCCA
322 TTTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATCCATCTAAACAAATCTCAGCCA
** * * * * *
92987 CATTTTATTTAAGGATTTTTTCTTGCAAGTATCTGAATCATGTTTCGATTTAATTAGAAATTAGT
387 CATTGAATTTAAGGATTGTTTCTTACAAGTATCTCAATCAGGTTTCGATTTAATTAGAAATTAAT
* * *
93052 TCAGAAAAAATAGAAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGACGTTGAAT
452 ACAGAAAAAATAGAAAAACCAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGACGTTGAAT
* * ** ** * *
93117 TATATATTTTTTATGAGTTCCGTGGCCGAAATTTTTTGCAAAAGTTTTAGCTGATATCGTGTACA
517 TATATATTTTTTACGAGTT-CGTAGCCGAAAAGTTGAGCAAAAGTTTCAGCTGAAATC-TGT--A
** * ***
93182 TCGTCACGATTTTTGGCTGGAAACACGTTCCGGGGAACAGGCT
578 TCGTCAAAATTTTTGACCAAAAACACGTTCCGGGGAACAGGCT
* * * *
93225 CAGTTTGACATGTTTTTTGGTGTCAAGACTCCATGAAATATCTATATACATCTAACCAAATCTCA
1 CATTTTG-CATGATTTTTGGCG-CAAGTCT-CATGAAATATCTATATACATCTAACCAAATCTCA
*** *
93290 TGGACATTGGATTTAAGGATTTGTTTCTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
63 CCCACATTGGATTTAAGGATTTGTTT-TACGAGCATCTGAATCATGTTTCGATTTAATTAGAAAT
* *
93355 TAATTCGGAAAAAAACTAGGAAAAACGATAATAGAAGCGTGAAAAGCCCTTCAATATTTTTGGCA
127 TAATTCGGAAAAAAA-TAGGAAAAACGATAATAGAAGCGTGAAAAGCCTTTCAATATTTTTGGCG
* * ** * * *
93420 TTGAATTATATGTA-TCTTATTAGTGTTGTGGCTAAAAATTGAGTGAAAAAT-TTTCAAT-TAAA
191 TTGAATTATA--TACTCTTATGAGTATCATGACCAAAAATTGA-AGAAAAATCTTTC-ATGTAAA
* * * * * *
93482 TTTTTGCAAAAATTTAGTCGAAATCAACCATCACGGTTTTTGGCTAAAAACGTA-TTCCGGGGCC
252 ATTTTGCAAAAATTTAGCCGAAAT----CATCACGATTTTTGACAAAAAACG-AGTTACGGGGCC
* * * *
93546 CCGACTCAGTTTTGCGTGATTTTTGGCGTCAAGACTCATTGAAATATCTATATTCATCTAAAGAA
312 CAGACTCAGTTTTGCATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATCCATCTAAACAA
* *
93611 ATCTCAGCCACATTGAATTTAAGGAGTTGTTT-TTACGAGTATCTCAATCCGGTTTCGATTTAAT
377 ATCTCAGCCACATTGAATTTAAGGA-TTGTTTCTTACAAGTATCTCAATCAGGTTTCGATTTAAT
*
93675 TAGAAATTAATACGGAAAAAAATAGGAAAAA-CAATATTAGAAGCATGAGAAA--CTCTTCAATC
441 TAGAAATTAATACAG-AAAAAATA-GAAAAACCAATATTAGAAGCATGA-AAAGCCT-TTCAATC
* ** *
93737 TTTTTGGCGTTGTGTTATATATTTTTTACGAGAATT-GTAGCC-AAAAGTTGAGGAGAAATGTTT
502 TTTTTGACGTTGAATTATATATTTTTTACGAG--TTCGTAGCCGAAAAGTTGAGCA-AAA-GTTT
* * ** ** ***
93800 CAGGT-AAAT-T-T-TTG-CAAAATTTTATGACCAAAAATGCGTTCCGGGGCCCTTTCT
563 CAGCTGAAATCTGTATCGTCAAAATTTT-TGACCAAAAACACGTTCCGGGGAACAGGCT
* *
93854 CTATTTTGCATGATTTTTGGCGCAAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTAA
1 C-ATTTTGCATGATTTTTGGCGC-AAGTCTCA-TGAAATATCTATATACATCTAACCAAATCTCA
* * * *
93919 CCCACATTAGATTTAAGTATTTGTTTTTATGAGCATCTGAAACATGTTTTC-ATTTAATTAGAAA
63 CCCACATTGGATTTAAGGATTTG-TTTTACGAGCATCTGAATCATG-TTTCGATTTAATTAGAAA
* * * * *
93983 TTAATTCAGAAAAAAAAATAAGAAAAACGATAATAGAAGCGTGAGAAGTCTTTCAATCTTTTTGG
126 TTAATTC-G-GAAAAAAATAGGAAAAACGATAATAGAAGCGTGAAAAGCCTTTCAATATTTTTGG
* * * * * * * * * * *
94048 CGTTGAGTCATATATTTTTTATGAGTAACGTGGCCAAAAATTGAGGAAAATTCTTT-TTGGTCAA
189 CGTTGAATTATATA-CTCTTATGAGTATCATGACCAAAAATTGAAGAAAAATCTTTCAT-GTAAA
* *
94112 TTTTTGCAAAAATTTAACCGAAATC
252 ATTTTGCAAAAATTTAGCCGAAATC
94137 GTGTACTAAC
Statistics
Matches: 751, Mismatches: 123, Indels: 76
0.79 0.13 0.08
Matches are distributed among these distances:
626 7 0.01
627 112 0.15
628 21 0.03
629 182 0.24
630 164 0.22
631 17 0.02
632 1 0.00
633 1 0.00
634 153 0.20
635 75 0.10
636 16 0.02
637 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (620 bp):
CATTTTGCATGATTTTTGGCGCAAGTCTCATGAAATATCTATATACATCTAACCAAATCTCACCC
ACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAAT
TCGGAAAAAAATAGGAAAAACGATAATAGAAGCGTGAAAAGCCTTTCAATATTTTTGGCGTTGAA
TTATATACTCTTATGAGTATCATGACCAAAAATTGAAGAAAAATCTTTCATGTAAAATTTTGCAA
AAATTTAGCCGAAATCATCACGATTTTTGACAAAAAACGAGTTACGGGGCCCAGACTCAGTTTTG
CATGATTTTTGGCGTCAAGACTCATTGAAATATCTATATCCATCTAAACAAATCTCAGCCACATT
GAATTTAAGGATTGTTTCTTACAAGTATCTCAATCAGGTTTCGATTTAATTAGAAATTAATACAG
AAAAAATAGAAAAACCAATATTAGAAGCATGAAAAGCCTTTCAATCTTTTTGACGTTGAATTATA
TATTTTTTACGAGTTCGTAGCCGAAAAGTTGAGCAAAAGTTTCAGCTGAAATCTGTATCGTCAAA
ATTTTTGACCAAAAACACGTTCCGGGGAACAGGCT
Found at i:95690 original size:333 final size:334
Alignment explanation
Indices: 94859--98227 Score: 4383
Period size: 333 Copynumber: 10.1 Consensus size: 334
94849 TTTACGAGCA
* * *
94859 TCTCACGTTTCTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACTG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
* * * * *
94924 GATTTGAGATACTCGTAAAAACAAATCCTTAAATCC-AAG-GGATCTAAGCTTTCATTAGATGAA
66 GA-TTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGG--GTGATCTTTCATTATATGAA
* ** * * **
94987 TATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGTAAAACTTAGCTAGGGCCCCGGAACGC
128 TATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
* * ** * * *
95052 GTTTTTAGTCAAAAATCATGAAAGTTAGTACGA-GATTTTGGATAAAATTTTGCAAAAATTG-CC
193 GTTTTTAGTCAAAAACCGTGATGGTTAGTAC-ATGATTTCGGCTAAAATTTTGCAAAATTTGACC
* **
95115 CTGAAA-AATTCTCCTCAAATTTT-GG-CA-ACAATACTCAT-AAAAATTATTTAACTCAACGTC
257 C-GAAACATTTCTCCTC-AATTTTCGGCCATA-AATACTCATGAAAAA-TATAAAACTCAACG-C
95175 AAAAAA-ATTGAAGGGCT
317 AAAAAAGATTGAAGGGCT
* * * * * * * * *
95192 TCTAACGCTTCTAATATCATTTTTTTTCATTTTTATTTTTTCCGAATGAATTTATAAATAAATCG
1 TCTCACGCTTGTAATATCA---TTTTTC--CTAT-TTTTTTCCGAATTAGTTTCTGATTAAATCG
* * * * * *
95257 AAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTCAACTTTCGTTAGAT
60 AAACCGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATAT
* * * * *
95322 GAATATAGATATTTCAATGAGTCTTGACT-CCAAAAATTATGCAAAACTTAGTCGGGGCCCCGGA
125 GAATATAGATATTGCAATGAGTCTTG-TTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGA
* * * * *
95386 ACGCGTTTTTAGTCAAAAACCATGATGGTTATTACATGATATCGACTAAATTTTTGCAAAATTTG
189 ACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTG
** * *
95451 ACTGGAAACATTTCTCCTCAATTTT-GGCCATAAATACTCA-AAAAGAATATACAACTCAACGCA
254 ACCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAA-AATATAAAACTCAACGCA
* *
95514 AAAAAGATTGAACGCCT
318 AAAAAGATTGAAGGGCT
* * * * *
95531 TCACACGCTTCTAATATAATTTTTCATGTTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
* * * * * *
95596 GATTGAGATACTCGTAAAAACAAATCCTTAATTCCAATGTGGTTGATCTTTCGTTAGATGAATAT
66 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATAT
** * * * * * *
95661 AGATATTTTAATGAGTCATGTCGCCAAAAATCATGCAAAACTGAGTCGGGGCCCTGGAATGTGTT
131 AGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTT
* * * * *
95726 TATAGTAAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTTACCCAAA
196 TTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAA
* * * ** * * *
95791 ACATTTCACCTCAATTTTTGGCCATAAATACGCATGAAAAATATACGACTTAACGCCAAAAATAT
261 ACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAAGAT
95856 TGAAGGGCT
326 TGAAGGGCT
* * * * * *
95865 TCTCAGGCTTCTGATATCATTTTTCCTAATTTTTTTCCGAATTAGTTTATAATTAAATCGAAATC
1 TCTCACGCTTGTAATATCATTTTTCCT-ATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACC
* * *
95930 GGATTGAGATGCTCGTAAAAAAAAATCCTTAAATCC-AA-TGGGTCTGAGCTTTCATTAGATGAA
65 GGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGG--TGATCTTTCATTATATGAA
* ** *
95993 TATAGATATTCCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCGGAACGC
128 TATAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
**
96058 GTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGGTCC
193 GTTTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACCC
* * * *
96123 GAAACATTTCTCCTCAATTTTCGACCATAAATGCTCATGAAAAATATAAAACTCAATGCTAAAAA
258 GAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAA
96188 GATTGAAGGGCT
323 GATTGAAGGGCT
* * *
96200 TCTCACTCCTGTAATATCA---TTCC-A-TTTTTTGCGAATTAGTTTCTGATTAAATCGAAACCG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
* *
96260 GATTGAGATACTCGTAAAAACAAATCCTTAATTCCAAAGTGGGTGATCTTTCATTATATGAATAT
66 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATAT
* * *
96325 AGATATTTCAATGAGTCTTGTTGCCAAAACTCATGCAAAACTAAGCC-GGGCCCTCGGAACGCGT
131 AGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCC-CGGAACGCGT
* * * **
96389 TTTTAGTCAAAAACTGTGATGGTTAATACATGATTTCGCCTAAAATTTTG-ATAAATTTGGTCCG
195 TTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCA-AAATTTGACCCG
* * * *
96453 AAATATTTCTCCTAAATTTTTGGCCATAAATACTCATGAAAAATATAAAACTCAACGCTAAAAAG
259 AAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAAG
96518 ATTGAAGGGCT
324 ATTGAAGGGCT
* *
96529 TCTCACG-TATGTAATATCATTTTTCCTATTTTTTT-CGAAGTAGTTTCTGATTAAACCGAAACC
1 TCTCACGCT-TGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACC
*
96592 GGATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAAAGTGGGTGATCTTTCATTATATGAATA
65 GGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATA
* *
96657 TAGATATTGCAATGAGTATTGTTGCCAAAAATTATGCAAAACTGAGCC-GGGCCTCCGGAACGCG
130 TAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCC-CCGGAACGCG
*
96721 TTTTTAGTCAAAAACCGTGATGGTTAGTACATTAATTT-GGCTAAAATTTTGCAAAATTTGACCC
194 TTTTTAGTCAAAAACCGTGATGGTTAGTACA-TGATTTCGGCTAAAATTTTGCAAAATTTGACCC
* * **
96785 GAAACATTTCTCCTCAATTTTCGACCATAAATAGTCATGAAAAATATAAAACTCAACAAAAAAAA
258 GAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAA
96850 GATTGAAGGGCT
323 GATTGAAGGGCT
* * * * * *
96862 TCTCACTCATGTAATATCATTTTTCCTA-TTTTTTGCGAAGTAGTTTTTGATTAAACCGAAACCG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
*
96926 GATTGAGATGCTCGTAAAAACAAATCCTTAATTCCAAAGTGGGTGATCTTTCATTATATGAATAT
66 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATAT
* * * * *
96991 AGATATTGCAATGAGTATTGTTGCCAAAAATCATGCGAAACTGAGCCGGGCCCCCGGAATGCCTT
131 AGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTT
* * *
97056 TTTAGTCAAAAAACCGTGATGGTTAGAACATGGTTTCGGCTAAAATTTTGCAAAATTTGACCCGG
196 TTTAGTC-AAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACCCGA
* *
97121 AACATTTCTCCTCAATTTCCGGCCATAAATGCTCATGAAAAATATAAAACTCAACGCAAAAAAGA
260 AACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAAGA
*
97186 TTGAAGGGTT
325 TTGAAGGGCT
* * * * * *
97196 TCTCACTCATGTAATATCGTTTTTCCTATTTTTTT-CGTAAGTAATTT-TGATTAAACCGAAACC
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCG-AATTAGTTTCTGATTAAATCGAAACC
* *
97259 GGATTGAGATGCTCGTAAAATCAAATCCTTAAATCCAAAGTGGGTGATC-TTCGTTATATGAATA
65 GGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATA
* *
97323 TAGATATTGCAAGGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGTCCCCGGAACGCGT
130 TAGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGT
* * *
97388 TTATAGTTAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTACAAAATTTGACCCGA
195 TTTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACCCGA
** * * *
97453 AACATTTCTATTCAATTTTCAGCCATAAATACTCATGAAAAATATACAACTCAACGCAAAAAAGT
260 AACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAAGA
97518 TTGAAGGGCT
325 TTGAAGGGCT
* * *
97528 TCTCACGCATGTAATATCATTTTTCCTA-TTTTTTGCGAATTAGTTTCTGACTAAATCGAAACCG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
* *
97592 GATTGAGATACTACGTAAAAACAAATTCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATA
66 GATTGAGATGCT-CGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATA
* *
97657 TAGATACTGCAATGAGTCTTGTTGACCAAAAATCATGCAAAACTGAGCCGGGCCCCCGGAAACGC
130 TAGATATTGCAATGAGTCTTGTTG-CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGG-AACGC
* *
97722 GTTTTTAGTCAAAAAACTGTGATGGATAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACC
193 GTTTTTAGTC-AAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACC
* * *
97787 CGAAACATTTCTCCTCAATTTTCGGCCATAACTACTCATGAAAAATATACAACTCAATGCAAAAA
257 CGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAA
97852 AGATTGAAGGGCT
322 AGATTGAAGGGCT
* * *
97865 TCTCACGCATGTAATATCATTTTTCCAATTTTTTT-CGAAGTAGTTTCTGATTAAATCGAAACCG
1 TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
* **
97929 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAGAGTGGGTGAGATTTCATTATATGAATAT
66 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATAT
* * *
97994 AGATATTGCAATGAGTCATGTTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCCGGAAAGCGTT
131 AGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTT
* *
98059 TTTAGTCGAAAACCGTGATGGTTAGTACTTAGTACATGATTTCGGCTAATATTTT-CAAAATTTG
196 TTTAGTCAAAAACCGTGAT-G---G---TTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTG
* *
98123 ACCCGAAACATTTCTCCTCAATTTTCGGCAATAAATGCTCATGAAAAATATAAAACTCAACGCAA
254 ACCCGAAACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAA
*
98188 AAAAGATTGAAGGGTT
319 AAAAGATTGAAGGGCT
* *
98204 TCTCACTCATGTAATATCATTTTT
1 TCTCACGCTTGTAATATCATTTTT
Statistics
Matches: 2708, Mismatches: 270, Indels: 110
0.88 0.09 0.04
Matches are distributed among these distances:
328 6 0.00
329 281 0.10
330 3 0.00
331 17 0.01
332 188 0.07
333 810 0.30
334 344 0.13
335 361 0.13
336 95 0.04
337 190 0.07
338 182 0.07
339 201 0.07
340 30 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (334 bp):
TCTCACGCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTAGTTTCTGATTAAATCGAAACCG
GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAAAGTGGGTGATCTTTCATTATATGAATAT
AGATATTGCAATGAGTCTTGTTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTT
TTTAGTCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAA
ACATTTCTCCTCAATTTTCGGCCATAAATACTCATGAAAAATATAAAACTCAACGCAAAAAAGAT
TGAAGGGCT
Done.