Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012422.1 Corchorus capsularis cultivar CVL-1 contig12443, 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: 80847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:222 original size:33 final size:32
Alignment explanation
Indices: 107--218 Score: 179
Period size: 32 Copynumber: 3.5 Consensus size: 32
97 GCCTTGTCGC
* *
107 CCTAGTGGGGCGGCTAGCCGTGGGAGAGCCGT
1 CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGT
*
139 CCTAGTGGGGCGGCTAGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGT
*
171 CCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGT
1 CCTAGTGGGGAGGCT-AGCCGTGGCAGAGCCGT
204 CCTAGTGGGGAGGCT
1 CCTAGTGGGGAGGCT
219 CCGCGTGGCT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 45 0.59
33 31 0.41
ACGTcount: A:0.12, C:0.27, G:0.45, T:0.16
Consensus pattern (32 bp):
CCTAGTGGGGAGGCTAGCCGTGGCAGAGCCGT
Found at i:4378 original size:12 final size:11
Alignment explanation
Indices: 4355--4385 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
4345 ACTATAAAAT
4355 AAATAAATAAA
1 AAATAAATAAA
4366 AAATAATATAAA
1 AAATAA-ATAAA
4378 AAATAAAT
1 AAATAAAT
4386 TATAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:7951 original size:2 final size:2
Alignment explanation
Indices: 7944--7978 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7934 AACAAATTAT
* *
7944 TA TA TA TA CA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7979 TGAGATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8733 original size:29 final size:29
Alignment explanation
Indices: 8675--8739 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
8665 TTTCCTGCAT
*
8675 AAAACAATCTGTTTTTTTTTTGCACCAAA
1 AAAAAAATCTGTTTTTTTTTTGCACCAAA
* *
8704 AACAAAATCTGTTTTTTTTTTGGCA-GAAA
1 AAAAAAATCTGTTTTTTTTTT-GCACCAAA
8733 AAAAAAA
1 AAAAAAA
8740 CCATGGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (29 bp):
AAAAAAATCTGTTTTTTTTTTGCACCAAA
Found at i:8737 original size:27 final size:26
Alignment explanation
Indices: 8645--8737 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 26
8635 CCACTGGTAA
* *
8645 AGAAGAAAAATCTGTTTTTCTTTCCTGC
1 AGAAAAAAAATCTGTTTTT-TTT-TTGC
* *
8673 A-TAAAACAATCTGTTTTTTTTTTGC
1 AGAAAAAAAATCTGTTTTTTTTTTGC
*
8698 ACCAAAAACAAAATCTGTTTTTTTTTTGGC
1 A--GAAAA-AAAATCTGTTTTTTTTTT-GC
8728 AGAAAAAAAA
1 AGAAAAAAAA
8738 AACCATGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
25 4 0.08
26 3 0.06
27 18 0.34
28 8 0.15
29 17 0.32
30 3 0.06
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (26 bp):
AGAAAAAAAATCTGTTTTTTTTTTGC
Found at i:14662 original size:2 final size:2
Alignment explanation
Indices: 14655--14697 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
14645 AGATTGTAAT
14655 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14697 A
1 A
14698 AACTTATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25300 original size:2 final size:2
Alignment explanation
Indices: 25293--25334 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25283 TTTTGCAGCA
25293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25335 TCACAGCACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28179 original size:3 final size:3
Alignment explanation
Indices: 28171--28219 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
28161 TACCGATATA
*
28171 TAT TAT TAT GTGT -AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28216 TAT T
1 TAT T
28220 TGCAATATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.93
4 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28393 original size:174 final size:175
Alignment explanation
Indices: 28097--28420 Score: 385
Period size: 174 Copynumber: 1.8 Consensus size: 175
28087 CACAAAATCA
* * * *
28097 ATTTTGTTTGAAAACGTGAAATACCATCTCACCTATGTAAATTTTTAATGATTTTATGTACTTAT
1 ATTTTATTTGAAAACGTGAAATACCATCTCACCTATATAAATGTTTAATGATGTTATGTACTTAT
* * ** *
28162 ACCGATATATATTATTATGTGTATTATTATTATTATTATTATTATTA-TTATTATTATTTGC-AA
66 A-CGATAGATATTATCATGTGTATTATTATTACCATGATTATTATTAGTTATTATTATTTGCAAA
*
28225 TATAGATCGATATTTGAGATTATGCATATATATTTGAATCATAGCT
130 TATAGATCAATATTTGAGATTATGCATATATATTTGAATCATAGCT
28271 ATTTTATTTGAAAACGTGAAATACCATCTCACCTATATAGATCGATGTTTAATGATGTTATGTAC
1 ATTTTATTTGAAAACGTGAAATACCATCTCACCTATATA-A---ATGTTTAATGATGTTATGTAC
* *
28336 TTATA-TA-ACGATA-TATCATGTGTATTATTA-TGCCATGGA-TATTATGT-GTATTATTATTA
62 TTATACGATA-GATATTATCATGTGTATTATTATTACCAT-GATTATTAT-TAG--TTATTATTA
28395 TTTGCAAAATATAGATCAATATTTGA
122 TTTGC-AAATATAGATCAATATTTGA
28421 AACTATATAT
Statistics
Matches: 126, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
174 46 0.37
175 20 0.16
176 4 0.03
177 14 0.11
178 24 0.19
179 18 0.14
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (175 bp):
ATTTTATTTGAAAACGTGAAATACCATCTCACCTATATAAATGTTTAATGATGTTATGTACTTAT
ACGATAGATATTATCATGTGTATTATTATTACCATGATTATTATTAGTTATTATTATTTGCAAAT
ATAGATCAATATTTGAGATTATGCATATATATTTGAATCATAGCT
Found at i:34602 original size:2 final size:2
Alignment explanation
Indices: 34595--34624 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34585 ATGCACGTTA
*
34595 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34625 TTGTAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:36337 original size:19 final size:19
Alignment explanation
Indices: 36315--36379 Score: 52
Period size: 21 Copynumber: 3.6 Consensus size: 19
36305 TGGGTTTCTT
36315 TTCTTTTCTTTTTCCTTTG
1 TTCTTTTCTTTTTCCTTTG
36334 TTC--TTC--TTTCC-TT-
1 TTCTTTTCTTTTTCCTTTG
*
36347 TCCTTCTTCTTTTTCCTTTTG
1 TTCTT-TTCTTTTTCC-TTTG
36368 TTCTTTCTCTTT
1 TTCTTT-TCTTT
36380 CTTTCCAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 5 0.14
16 3 0.09
17 3 0.09
18 5 0.14
19 3 0.09
20 3 0.09
21 9 0.26
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (19 bp):
TTCTTTTCTTTTTCCTTTG
Found at i:36347 original size:22 final size:21
Alignment explanation
Indices: 36310--36366 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
36300 TTTCCTGGGT
*
36310 TTCTT-TTCTTTTCTTTTTCC
1 TTCTTCTTCTTTCCTTTTTCC
*
36330 TTTGTTCTTCTTTCC--TTTCC
1 -TTCTTCTTCTTTCCTTTTTCC
36350 TTCTTCTT-TTTCCTTTT
1 TTCTTCTTCTTTCCTTTT
36367 GTTCTTTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 7 0.23
21 4 0.13
22 7 0.23
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (21 bp):
TTCTTCTTCTTTCCTTTTTCC
Found at i:36355 original size:16 final size:15
Alignment explanation
Indices: 36320--36358 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
36310 TTCTTTTCTT
*
36320 TTCTT-TTTCCTTTG
1 TTCTTCTTTCCTTTC
36334 TTCTTCTTTCCTTTCC
1 TTCTTCTTTCCTTT-C
36350 TTCTTCTTT
1 TTCTTCTTT
36359 TTCCTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TTCTTCTTTCCTTTC
Found at i:37608 original size:23 final size:24
Alignment explanation
Indices: 37582--37626 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
37572 AAATCATAAA
37582 AAATGAAAAAGA-AAAAAGAAATT
1 AAATGAAAAAGATAAAAAGAAATT
* * *
37605 AAATTAAAGAGATAAAGAGAAA
1 AAATGAAAAAGATAAAAAGAAA
37627 AAGAAAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (24 bp):
AAATGAAAAAGATAAAAAGAAATT
Found at i:37980 original size:12 final size:12
Alignment explanation
Indices: 37933--37982 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
37923 CAGTTTATGA
*
37933 TGTTGCTGCTGC
1 TGTTGTTGCTGC
* *
37945 TGCTGTTGCTGT
1 TGTTGTTGCTGC
37957 TGTTGTTGCTGC
1 TGTTGTTGCTGC
*
37969 TGTTGATGCTGC
1 TGTTGTTGCTGC
37981 TG
1 TG
37983 CTGCATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.02, C:0.18, G:0.34, T:0.46
Consensus pattern (12 bp):
TGTTGTTGCTGC
Found at i:43921 original size:2 final size:2
Alignment explanation
Indices: 43914--43943 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43904 TTTGATGATC
43914 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
43944 ATGTAATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46668 original size:21 final size:21
Alignment explanation
Indices: 46644--46684 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46634 TGCTTGAGAA
* *
46644 TATTAATTTCTCTACCATCAT
1 TATTAAATTCTCTACAATCAT
*
46665 TATTAAATTGTCTACAATCA
1 TATTAAATTCTCTACAATCA
46685 AGAAACTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAAATTCTCTACAATCAT
Found at i:49274 original size:2 final size:2
Alignment explanation
Indices: 49267--49302 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49257 AATATTCGTA
49267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49303 GAATACGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50410 original size:18 final size:18
Alignment explanation
Indices: 50387--50428 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
50377 GCGGTCTCCG
50387 AGAAGCCCTAGATTGTAA
1 AGAAGCCCTAGATTGTAA
**
50405 AGAAGCTTTAGATTGTAA
1 AGAAGCCCTAGATTGTAA
50423 AGAAGC
1 AGAAGC
50429 TTAGACGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (18 bp):
AGAAGCCCTAGATTGTAA
Found at i:50429 original size:18 final size:18
Alignment explanation
Indices: 50395--50430 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
50385 CGAGAAGCCC
50395 TAGATTGTAAAGAAGCTT
1 TAGATTGTAAAGAAGCTT
50413 TAGATTGTAAAGAAGCTT
1 TAGATTGTAAAGAAGCTT
50431 AGACGCTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (18 bp):
TAGATTGTAAAGAAGCTT
Found at i:56492 original size:2 final size:2
Alignment explanation
Indices: 56485--56535 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
56475 TTAGTTAGAG
56485 AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
56524 AT AT AG AT AT AT
1 AT AT AT AT AT AT
56536 CGAGAAACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:64099 original size:11 final size:11
Alignment explanation
Indices: 64056--64093 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64046 TTCCTATATA
*
64056 AAATAAATTAT
1 AAATTAATTAT
64067 CAAA-TAATTAT
1 -AAATTAATTAT
64078 AAATTAATTAT
1 AAATTAATTAT
64089 AAATT
1 AAATT
64094 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:64688 original size:2 final size:2
Alignment explanation
Indices: 64681--64707 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64671 TGATTGGTTA
64681 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
64708 GTAATGCAGT
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:75943 original size:483 final size:482
Alignment explanation
Indices: 75037--76005 Score: 1807
Period size: 483 Copynumber: 2.0 Consensus size: 482
75027 CTCACTTGCC
75037 AAAAGGATAAAAAAATTCAAATGGAGCCTCCTCATCGATCTTCAAAGGGACTTTTGGTAAATCCC
1 AAAAGGATAAAAAAATTCAAATGGAGCCTCCTCATCGATCTTCAAAGGGACTTTTGGTAAATCCC
*
75102 GTGGGTGTTTCAATTAATATTTAGTATATATATTTTCGACTTTGATAAAGACAAGTATTATTGAA
66 GTGGGTGTTTCAATTAACATTTAGTATATATATTTTCGACTTTGATAAAGACAAGTATTATTGAA
* *
75167 ATAGGAGAGTTTTTTTTCCTTACGCCTTTTTTTGTAATTCGGCCTAAAATAGACTCGTCTAAGGA
131 ATAGGAGAGTTTTTTTTCCTTACGCCTTTTTTTGTAATTCAGCCTAAAATAGACTCATCTAAGGA
* * *
75232 TTTTAGCTCGTTGGTCCAATTAGTGAAAAAGCTTAAAAAATTGAATCCAATAATTCTTCGATAAA
196 TTTTAGCTCGTTGGCCCAATTAGTGAAAAAGCTTAAAAAATTAAATCAAATAATTCTTCGATAAA
*
75297 TAACATGTTCCTCGACAATCTACATCTTTCTCCTTCAATTTCCTGCACCTGTGAAAGTCCACATA
261 TAACATGTTCCTCGACAATCTACATCTTTCTCCTTCAATTTCCTGCACCTGTCAAAGTCCACATA
*
75362 AATTTCTAAAATCAAATAAAAGATCACTTCCTTTTTGCGTGTTTTTTTTTCTTTTCAAATTCTCC
326 AATTTCTAAAATAAAATAAAAGATCACTTCCTTTTTGCGTGTTTTTTTTTCTTTTCAAATTCTCC
75427 TTTTCATTTAACCACCAAACCAAATCGTTTTCTGAATTATATTTTCCAAATTGTTTCTTTTTATT
391 TTTTCATTTAACCACCAAACCAAATCGTTTTCTGAATTATATTTTCCAAATTGTTT-TTTTTATT
75492 AAATTAAGATTTTATATCAATGTTTTTT
455 AAATTAAGATTTTATATCAATGTTTTTT
*
75520 AAAAGGAT-AAAAAATTCAAATGGAGCCTTCTCATCGATCTTCAAAAGGGACTTTTGGTAAATCC
1 AAAAGGATAAAAAAATTCAAATGGAGCCTCCTCATCGATCTTC-AAAGGGACTTTTGGTAAATCC
75584 CGTGGGTGTTTCAATTAACATTTAGTATATATATTTTCGACTTTGATAAAGACAAGTATTATTGA
65 CGTGGGTGTTTCAATTAACATTTAGTATATATATTTTCGACTTTGATAAAGACAAGTATTATTGA
75649 AATAGGAGAGTTTTTTTTTCCTTACGCC-TTTTTTGTAATTCAGCCTAAAATAGACTCATCTAAG
130 AATAGGAGAG-TTTTTTTTCCTTACGCCTTTTTTTGTAATTCAGCCTAAAATAGACTCATCTAAG
75713 GATTTTAGCTCGTTGGCCCAATTAGTGAAAAAGCTTAAAAAATTAAATCAAATAATTCTTCGATA
194 GATTTTAGCTCGTTGGCCCAATTAGTGAAAAAGCTTAAAAAATTAAATCAAATAATTCTTCGATA
75778 AATAACATGTTCCTCGACAATCTACATCTTTCTCCTTCAATTTCCTGCACCTGTCAAAGTCCACA
259 AATAACATGTTCCTCGACAATCTACATCTTTCTCCTTCAATTTCCTGCACCTGTCAAAGTCCACA
75843 TAAATTTCTAAAATAAAATAAAAGATCACTTCCTTTTTGCGTGTTTTTTTTTCTTTTCAAATTCT
324 TAAATTTCTAAAATAAAATAAAAGATCACTTCCTTTTTGCGTGTTTTTTTTTCTTTTCAAATTCT
*
75908 CCTTTTCATTTAACCACCAAACCAAATTGTTTTCTGAATTATATTTTCCAAATTGTTTTTTTTAT
389 CCTTTTCATTTAACCACCAAACCAAATCGTTTTCTGAATTATATTTTCCAAATTGTTTTTTTTAT
75973 TAAATTAAGATTTTATATCAATGTTTTTT
454 TAAATTAAGATTTTATATCAATGTTTTTT
76002 AAAA
1 AAAA
76006 TGAGTTTTGT
Statistics
Matches: 474, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
482 73 0.15
483 384 0.81
484 17 0.04
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (482 bp):
AAAAGGATAAAAAAATTCAAATGGAGCCTCCTCATCGATCTTCAAAGGGACTTTTGGTAAATCCC
GTGGGTGTTTCAATTAACATTTAGTATATATATTTTCGACTTTGATAAAGACAAGTATTATTGAA
ATAGGAGAGTTTTTTTTCCTTACGCCTTTTTTTGTAATTCAGCCTAAAATAGACTCATCTAAGGA
TTTTAGCTCGTTGGCCCAATTAGTGAAAAAGCTTAAAAAATTAAATCAAATAATTCTTCGATAAA
TAACATGTTCCTCGACAATCTACATCTTTCTCCTTCAATTTCCTGCACCTGTCAAAGTCCACATA
AATTTCTAAAATAAAATAAAAGATCACTTCCTTTTTGCGTGTTTTTTTTTCTTTTCAAATTCTCC
TTTTCATTTAACCACCAAACCAAATCGTTTTCTGAATTATATTTTCCAAATTGTTTTTTTTATTA
AATTAAGATTTTATATCAATGTTTTTT
Found at i:80648 original size:2 final size:2
Alignment explanation
Indices: 80641--80678 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
80631 TCAGTACCGA
80641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80679 TACTAATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.