Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019704.1 Corchorus olitorius cultivar O-4 contig19737, 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: 44998
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:12927 original size:5 final size:6
Alignment explanation
Indices: 12901--12930 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12891 CATATATGGC
12901 TTTCCT TTTCCT TTTCCT TTTCC- TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
12931 CTATTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTCCT
Found at i:25884 original size:2 final size:2
Alignment explanation
Indices: 25877--25908 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25867 GAAGCTTATG
25877 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
25909 GGAACTGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27132 original size:30 final size:30
Alignment explanation
Indices: 27096--27154 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
27086 TTACGTCCCA
*
27096 AAATTGAAGTTCATGGGGGCAAAATGTCCG
1 AAATTGAAGTTCATGGGGGCAAAACGTCCG
*
27126 AAATTGAAGTTTATGGGGGCAAAACGTCC
1 AAATTGAAGTTCATGGGGGCAAAACGTCC
27155 AAACGCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
AAATTGAAGTTCATGGGGGCAAAACGTCCG
Found at i:27993 original size:25 final size:25
Alignment explanation
Indices: 27959--28008 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27949 CCAGCAATCC
27959 CCTTCCATTTGACTATAGACATTGG
1 CCTTCCATTTGACTATAGACATTGG
27984 CCTTCCATTTGACTATAGACATTGG
1 CCTTCCATTTGACTATAGACATTGG
28009 TGGTGTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (25 bp):
CCTTCCATTTGACTATAGACATTGG
Found at i:35652 original size:42 final size:42
Alignment explanation
Indices: 35571--35784 Score: 329
Period size: 42 Copynumber: 5.0 Consensus size: 42
35561 AGATTGAGCT
* * *
35571 AGAAGTGTCGTAAAATACATAATTTCTAACGTAAAATTGGTG
1 AGAAATGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
* * * *
35613 AGAAATGTCATAAAATACACCATTTGTAACATAAGATTGGTG
1 AGAAATGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
35655 AGAAAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
1 AGAAA-TGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
* *
35698 AGAAATGTCATAAAATACATCATTTGTAACATAAAATTGGTG
1 AGAAATGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
35740 AGAAAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
1 AGAAA-TGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
35783 AG
1 AG
35785 TCCCGTAAGA
Statistics
Matches: 155, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
42 80 0.52
43 75 0.48
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (42 bp):
AGAAATGTCATAAAATACATCATTTCTAACGTAAAATTGGTG
Found at i:35673 original size:43 final size:43
Alignment explanation
Indices: 35573--35784 Score: 338
Period size: 43 Copynumber: 5.0 Consensus size: 43
35563 ATTGAGCTAG
* *
35573 AAGTGTCGTAAAATACATAATTTCTAACGTAAAATTGGTGAGA
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
* * * *
35616 AA-TGTCATAAAATACACCATTTGTAACATAAGATTGGTGAGA
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
35658 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
* *
35701 AA-TGTCATAAAATACATCATTTGTAACATAAAATTGGTGAGA
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
35743 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAG
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAG
35785 TCCCGTAAGA
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
42 76 0.50
43 77 0.50
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (43 bp):
AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGA
Found at i:35704 original size:85 final size:85
Alignment explanation
Indices: 35573--35784 Score: 388
Period size: 85 Copynumber: 2.5 Consensus size: 85
35563 ATTGAGCTAG
* *
35573 AAGTGTCGTAAAATACATAATTTCTAACGTAAAATTGGTGAGAAATGTCATAAAATACACCATTT
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGAAATGTCATAAAATACACCATTT
*
35638 GTAACATAAGATTGGTGAGA
66 GTAACATAAAATTGGTGAGA
*
35658 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGAAATGTCATAAAATACATCATTT
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGAAATGTCATAAAATACACCATTT
35723 GTAACATAAAATTGGTGAGA
66 GTAACATAAAATTGGTGAGA
35743 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAG
1 AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAG
35785 TCCCGTAAGA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 123 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (85 bp):
AAGTGTCATAAAATACATCATTTCTAACGTAAAATTGGTGAGAAATGTCATAAAATACACCATTT
GTAACATAAAATTGGTGAGA
Found at i:38884 original size:3 final size:3
Alignment explanation
Indices: 38871--38901 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
38861 ACGGTGTCAA
*
38871 AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
38902 GTGAATCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40833 original size:2 final size:2
Alignment explanation
Indices: 40826--40851 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40816 TTGAGTTCAA
40826 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
40852 TATTTTTTTT
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):
AT
Found at i:41582 original size:76 final size:76
Alignment explanation
Indices: 41494--41641 Score: 262
Period size: 76 Copynumber: 1.9 Consensus size: 76
41484 GTTTGTTTAT
* *
41494 TTGGTAGGTAGATAGTTTATTTATGATATAGTTTCGAGTTTGGGTTGAATTCAT-ATTTAGAAGT
1 TTGGTAGATAGATAGTTTATTTATGATATAGTTTCAAGTTTGGGTTGAATTC-TCATTTAGAAGT
41558 TTGGACATAGAG
65 TTGGACATAGAG
41570 TTGGTAGATAGATAGTTTATTTATGATATAGTTTCAAGTTTGGGTTGAATTCTCATTTAGAAGTT
1 TTGGTAGATAGATAGTTTATTTATGATATAGTTTCAAGTTTGGGTTGAATTCTCATTTAGAAGTT
41635 TGGACAT
66 TGGACAT
41642 TGAAATTTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
75 1 0.01
76 68 0.99
ACGTcount: A:0.28, C:0.05, G:0.24, T:0.43
Consensus pattern (76 bp):
TTGGTAGATAGATAGTTTATTTATGATATAGTTTCAAGTTTGGGTTGAATTCTCATTTAGAAGTT
TGGACATAGAG
Found at i:42790 original size:333 final size:331
Alignment explanation
Indices: 41962--42884 Score: 1272
Period size: 333 Copynumber: 2.8 Consensus size: 331
41952 AAAAAACCCT
* * *
41962 AAACTTTTCGGGTTAGTTTTTGCAAAATTTTAGCCGAAATTGTGTA-T-ACCATCAC-GGTTTTT
1 AAACTTTTCGGGTAAGTTTTTGCAAAA-TTTAGCCAAAATTGTGTATTAACCATCACAGTTTTTT
* * * * * * *
42024 GGCTAAAAACGTGTTCCGGAGTCCCAGCTCAATTTTGCTTGATTTTTGGTGCAAAGTCTACTTCA
65 AGCTAAAAACGCGTTCCGGAGTCCCCGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTAA
* **
42089 AATATCTATATTT-ATCTAACCAAATCTTAACCACAATGGATTTAAGGATTTGTTTTTACGAGTG
130 AATATCTAT-TTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCA
* * * * *
42153 TTTGAATATTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGGAAAACGATAATGAAAG
194 TTTAAATCTTGTTTCGATTTAATTAAAAATAAATT-AGAAAAAAAT-GGAAAACGATATTGGAAG
* * * *
42218 CGTGAAAAACCCTTTTAATTTTTTTGGGGTTGAATAATATACTTTTTCTGAGTATTGTGGTAAAA
257 CGTGAAAAACCCTTTTAATTTTTTCGGGGTTGAATAATATACTTTTTATAAGTATTGTGGCAAAA
42283 AATTGAGGAA
322 AATTGAGGAA
*
42293 AAAATTTTCGGGTAAGTTTTTGCAAAATCTTAGCCAAAATTGTGTATTAACCATCACAGTTTTTT
1 AAACTTTTCGGGTAAGTTTTTGCAAAAT-TTAGCCAAAATTGTGTATTAACCATCACAGTTTTTT
* *
42358 AGCTAAAAACGCGTTCAGGAGT-CCCGCCTCAATTTTGCTTGATTTTTGGCACAAAGACTCCTTA
65 AGCTAAAAACGCGTTCCGGAGTCCCCG-CTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTA
*
42422 AAATATCTATATTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCA
129 AAATATCTATTTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCA
* * *
42487 TCTAAATCTTGTTTCGATTTAATTAAAAATAAATTTGAAAAAAA-AGAATAACGATATTGGAAGC
194 TTTAAATCTTGTTTCGATTTAATTAAAAATAAATTAGAAAAAAATGGAA-AACGATATTGGAAGC
*
42551 GTG-AAAACCCATTTTAA-TTTTTCGGGGTTGAATAATATAGTTTTTTATAAGTATTGTGGCAAA
258 GTGAAAAACCC-TTTTAATTTTTTCGGGGTTGAATAATATA-CTTTTTATAAGTATTGTGGCAAA
*
42614 AAATTGAGGGA
321 AAATTGAGGAA
* *
42625 AAACTTTT-GGGTCAGTTTTTGCAAAATTTAAGCCAAAATCGTGTATTAACCATCACAGTTTTTT
1 AAACTTTTCGGGTAAGTTTTTGCAAAATTT-AGCCAAAATTGTGTATTAACCATCACAG--TTTT
* * * *
42689 TTTGCTAAAAATGCATTCCGGA-TCCCCGACTCAATTTTGCTTGATTGTTGGCGCAAAGACTCCT
63 TTAGCTAAAAACGCGTTCCGGAGTCCCCG-CTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCT
* *
42753 TGAAATATATATTTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAG
127 TAAAATATCTATTTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAG
* * *
42818 CATTTTAATCTTGTTTTGATTTAATTAAAAATAAATTCGAAAAAAATGGAAAAACGATATTGGAA
192 CATTTAAATCTTGTTTCGATTTAATTAAAAATAAATTAGAAAAAAATGG-AAAACGATATTGGAA
42883 GC
256 GC
42885 CGAAATCATG
Statistics
Matches: 528, Mismatches: 49, Indels: 27
0.87 0.08 0.04
Matches are distributed among these distances:
330 3 0.01
331 117 0.22
332 60 0.11
333 184 0.35
334 162 0.31
335 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (331 bp):
AAACTTTTCGGGTAAGTTTTTGCAAAATTTAGCCAAAATTGTGTATTAACCATCACAGTTTTTTA
GCTAAAAACGCGTTCCGGAGTCCCCGCTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTAAA
ATATCTATTTTCATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATT
TAAATCTTGTTTCGATTTAATTAAAAATAAATTAGAAAAAAATGGAAAACGATATTGGAAGCGTG
AAAAACCCTTTTAATTTTTTCGGGGTTGAATAATATACTTTTTATAAGTATTGTGGCAAAAAATT
GAGGAA
Found at i:43089 original size:225 final size:228
Alignment explanation
Indices: 42654--43104 Score: 554
Period size: 225 Copynumber: 2.0 Consensus size: 228
42644 TGCAAAATTT
* * * * *
42654 AAGCCAAAATCGTGTATTAACCATCACAGTTTTTTTTTGCTAAAAATGCATTCCGGATCCCCGAC
1 AAGCCAAAATCATGTACTAACCATCACAGTTTTTTTTGGCTAAAAACGCATTCAGGATCCCCGAC
* * *
42719 TCAATTTTGCTTGATTGTTGGCGCAAAGACTCCTTGAAATATATATTTTCATCTAACCAAATCTT
66 TCAATTTTGCATGATTGTTGGCGCAAAGACTCCCTGAAATATATATATTCATCTAACCAAATCTT
* * * * * *
42784 AGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAA
131 AGCCACAATGGATCTAAGGATTTGTTTTTACGAACAATTGAATATTGTTTCGATTTAATTAAAAA
* *
42849 TAAATTCGAAAAAAAT-GGAAAAACGATATTGG
196 TAAATTAGAAAAAAATAGAAAAAACGATATTGG
* * * * *
42881 AAGCCGAAATCATGTACTAACCATCACTG-TTTTTTTGGCTAACAACGCGTTCAAGG-T-CCCGG
1 AAGCCAAAATCATGTACTAACCATCACAGTTTTTTTTGGCTAAAAACGCATTC-AGGATCCCCGA
* * ** * *
42943 CTCAGTTTTGCATGATTTTTGGCGTC-AAGACTCCCTGTGATATCTATATTCATCTAACCAAATG
65 CTCAATTTTGCATGATTGTTGGCG-CAAAGACTCCCTGAAATATATATATTCATCTAACCAAATC
* *
43007 TTGGCCACATTGGATCTAAGGATTTGTTTTTACGAACAATTGAATATTGTTTCGATTTAATTAGA
129 TTAGCCACAATGGATCTAAGGATTTGTTTTTACGAACAATTGAATATTGTTTCGATTTAATTA-A
* *
43072 AATTAATTTAG-AAAAAATAGAAAAAACGATATT
193 AAATAAATTAGAAAAAAATAGAAAAAACGATATT
43105 AAAAATGTGA
Statistics
Matches: 189, Mismatches: 31, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
225 119 0.63
226 43 0.23
227 27 0.14
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (228 bp):
AAGCCAAAATCATGTACTAACCATCACAGTTTTTTTTGGCTAAAAACGCATTCAGGATCCCCGAC
TCAATTTTGCATGATTGTTGGCGCAAAGACTCCCTGAAATATATATATTCATCTAACCAAATCTT
AGCCACAATGGATCTAAGGATTTGTTTTTACGAACAATTGAATATTGTTTCGATTTAATTAAAAA
TAAATTAGAAAAAAATAGAAAAAACGATATTGG
Found at i:43404 original size:557 final size:555
Alignment explanation
Indices: 42335--43442 Score: 1410
Period size: 558 Copynumber: 2.0 Consensus size: 555
42325 GCCAAAATTG
* * *
42335 TGTATTAACCATCACAGTTTTTTAGCTAAAAACGCGTTCAGGAGTCCCGCCTCAATTTTGCTTGA
1 TGTACTAACCATCACAGTTTTTTAGCTAAAAACGCGTTCAAGAGTCCCGCCTCAATTTTGCATGA
* *
42400 TTTTTGGCACAAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTTAGCCACAATGGATT
66 TTTTTGGCACAAAGACTCCCTAAAATATCTATATTCATCTAACCAAATCTTAGCCACAATGGATC
* *
42465 TAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAAATAAATTTGAAAAAA
131 TAAGGATTTGTTTTTACGAACATCTAAATATTGTTTCGATTTAATTAAAAATAAATTTGAAAAAA
* ** * **
42530 AAGAATAACGATATTGGAAGCGTGAAAACCCATTTTAATTTTTCGGGGTTGAATAATATAGTTTT
196 AAGAAAAACGATATTAAAAACGTGAAAACCCA-TTTAATTTTTCGACGTTGAAT-ATATAGTTTT
* * * *** *
42595 TTATAAGTATTGTGGCAAAAAATTGAGGGAAAACTTTTGGGTCAGTTTTTGCAAAATTTAAGCCA
259 TTATAAGAATTGTGCCAAAAAATTGAGGAAAAACTTTAACGTCAATTTTTGCAAAATTTAAGCCA
* * * *
42660 AAATCGTGTATTAACCATCACAGTTTTTTTTTGCTAAAAATGCATTCCGGATCCCCGACTCAATT
324 AAATCGTGTAATAACCATCACAG-TGTTTTTGGCTAAAAACGCATTCCGGATCCCCGACTCAATT
* *
42725 TTGCTTGATTGTTGGCGCAAAGACTCCTTGAAATATATATTTTCATCTAACCAAATCTTAGCCAC
388 TTGCTTGATTGTTGGCGCAAAGACTACTTCAAATATATATTTT-ATCTAACCAAATCTTAGCCAC
* *
42790 AATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAAATT
452 AATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAAATT
*
42855 CG-AAAAAAATGGAAAAACGATATTGGAAGCCGAAATCA
517 CGAAAAAAAATGGAAAAACGATATTGAAAGCCGAAATCA
* * * * *
42893 TGTACTAACCATCACTGTTTTTTTGGCTAACAACGCGTTCAAG-GTCCCGGCTCAGTTTTGCATG
1 TGTACTAACCATCACAG-TTTTTTAGCTAAAAACGCGTTCAAGAGTCCCGCCTCAATTTTGCATG
* *** * * *
42957 ATTTTTGGCGTC-AAGACTCCCTGTGATATCTATATTCATCTAACCAAATGTTGGCCACATTGGA
65 ATTTTTGGC-ACAAAGACTCCCTAAAATATCTATATTCATCTAACCAAATCTTAGCCACAATGGA
* * *
43021 TCTAAGGATTTGTTTTTACGAACAAT-TGAATATTGTTTCGATTTAATTAGAAATTAATTTAGAA
129 TCTAAGGATTTGTTTTTACGAAC-ATCTAAATATTGTTTCGATTTAATTAAAAATAAATTT-GAA
* * *
43085 AAAATAGAAAAAACGATATTAAAAATGTGAAAAGCCC-TTTAATCTTTTTTGACGTTGAAT-TAT
192 AAAAAAG-AAAAACGATATTAAAAACGTGAAAA-CCCATTTAA--TTTTTCGACGTTGAATATAT
* * * * *
43148 ATTTTTTTGTTAA-AATTTTGCCCAAAAATTGAGGAAAAATCTTTAACGTCAATTTTTGTAAAAT
253 AGTTTTTT-ATAAGAATTGTGCCAAAAAATTGAGGAAAAA-CTTTAACGTCAATTTTTGCAAAAT
* ** * *
43212 TTTAGCTGAAATCGTGTAATAACCATCAC-G-GTTTTTGGCTAAAAACGCGTTTCGGAGT-CCCG
316 TTAAGCCAAAATCGTGTAATAACCATCACAGTGTTTTTGGCTAAAAACGCATTCCGGA-TCCCCG
* * * *
43274 GCTCAATTTTGCTTGATTTTTGGTGCAAAGTCTACTTCAAATATCTATATTTT-TCTAACCAAAT
380 ACTCAATTTTGCTTGATTGTTGGCGCAAAGACTACTTCAAATA--TATATTTTATCTAACCAAAT
* *
43338 CTTAGGCACAATGGATTTAAGGATTTGTTTTTACGAGCGTTTGAATCTTGTTTCGATTTAATTAA
443 CTTAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAA
*
43403 AAATAAATTCGAAAAAAAATGGGAAAACGATATTGAAAGC
508 AAATAAATTCGAAAAAAAATGGAAAAACGATATTGAAAGC
43443 GTGAAAAACC
Statistics
Matches: 472, Mismatches: 64, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
557 145 0.31
558 165 0.35
559 79 0.17
560 67 0.14
561 16 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (555 bp):
TGTACTAACCATCACAGTTTTTTAGCTAAAAACGCGTTCAAGAGTCCCGCCTCAATTTTGCATGA
TTTTTGGCACAAAGACTCCCTAAAATATCTATATTCATCTAACCAAATCTTAGCCACAATGGATC
TAAGGATTTGTTTTTACGAACATCTAAATATTGTTTCGATTTAATTAAAAATAAATTTGAAAAAA
AAGAAAAACGATATTAAAAACGTGAAAACCCATTTAATTTTTCGACGTTGAATATATAGTTTTTT
ATAAGAATTGTGCCAAAAAATTGAGGAAAAACTTTAACGTCAATTTTTGCAAAATTTAAGCCAAA
ATCGTGTAATAACCATCACAGTGTTTTTGGCTAAAAACGCATTCCGGATCCCCGACTCAATTTTG
CTTGATTGTTGGCGCAAAGACTACTTCAAATATATATTTTATCTAACCAAATCTTAGCCACAATG
GATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAA
AAAAAATGGAAAAACGATATTGAAAGCCGAAATCA
Found at i:43517 original size:332 final size:329
Alignment explanation
Indices: 42882--44104 Score: 1449
Period size: 332 Copynumber: 3.7 Consensus size: 329
42872 CGATATTGGA
* * ** * * *
42882 AGCCGAAATCATGTACTAACCATCACTGTTTTTTTGGCTAACAACGCGTTC-AAGGTCCCGGCTC
1 AGCCGAAATCGTGTATTAACCATCAC-GAGTTTTTGGCTAAAAACGCGTTCGGA-GCCCCGGCTC
* * * * *** * *
42946 AGTTTTGCATGATTTTTGGCGTC-AAGACTCCCTGTGATATCTATATTCATCTAACCAAATGTTG
64 AATTTTGCTTGATTTTTGGCG-CAAAGACTACTTCAAATATCTATATTCATCTAACCAAATCTTA
* * * * * *
43010 GCCACATTGGATCTAAGGATTTGTTTTTACGAACAATTGAATATTGTTTCGATTTAATTAGAAAT
128 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAAT
* * * * ** * **
43075 TAATT-TAGAAAAAATAGAAAAAACGATATTAAAAATGTGAAAAGCCC-TTTAATCTTTTTTGAC
193 AAATTCGA-AAAAAAT-GGAAAAACGATATTGAAAGCGTGAAAAACCCTTTTAA--TTTTTTGGG
* * * * * * *
43138 GTTGAATTATATTTTTTTGTTAA-AATTTTGCCCAAAAATTGAGGAAAAATCTTTAACGTCAATT
254 GTTGAATAATATCTTTTT-ATAAGTATTATG-GCAAAAATTGAGGAAAAATCTTTAAGGTCAATT
*
43202 TTTGTAAAATTTT
317 TTTGCAAAATTTT
* * *
43215 AGCTGAAATCGTGTAATAACCATCACG-GTTTTTGGCTAAAAACGCGTTTCGGAGTCCCGGCTCA
1 AGCCGAAATCGTGTATTAACCATCACGAGTTTTTGGCTAAAAACGCG-TTCGGAGCCCCGGCTCA
* * ** *
43279 ATTTTGCTTGATTTTTGGTGCAAAGTCTACTTCAAATATCTATATTTTTCTAACCAAATCTTAGG
65 ATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTCATCTAACCAAATCTTAGC
*
43344 CACAATGGATTTAAGGATTTGTTTTTACGAGCGTTTGAATCTTGTTTCGATTTAATTAAAAATAA
130 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAA
*
43409 ATTCGAAAAAAAATGGGAAAACGATATTGAAAGCGTGAAAAACCCTTTTAATTTTTTGGGGTTGA
195 ATTCG-AAAAAAATGGAAAAACGATATTGAAAGCGTGAAAAACCCTTTTAATTTTTTGGGGTTGA
* * * * *
43474 ATAATATACTTTTTCTGAGTATTATGGTAAATAATTGAGGAAAAAAT-TCTCAGGT-AAGTTTTT
259 ATAATAT-CTTTTTATAAGTATTATGGCAAA-AATTGAGG-AAAAATCTTTAAGGTCAA-TTTTT
*
43537 GCAAAATCTT
320 GCAAAATTTT
* * *
43547 AGCCAAAATCGTGTATTAACCATCACGATTTTTTAGCTAAAAACGCGTTCAGGAGCCCCGGCTCA
1 AGCCGAAATCGTGTATTAACCATCACGAGTTTTTGGCTAAAAACGCGTTC-GGAGCCCCGGCTCA
* * * * *
43612 ATTTCGCTTGATTTTTGGCACAAAGAGTCCTTAAAATATCTATATTCATCTAACCAAATCTTAGC
65 ATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTCATCTAACCAAATCTTAGC
* * * *
43677 CACAATGGATTTAAGGATTTATTTTTACGATCATCTAAATCTTGTTTCGATTTAATTAAAAATAA
130 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAA
* * * * *
43742 ATTTGAAAAAAATAGAAAAAAGATATTGGAAGCGTGAAAAACCATTTTAATTTTTTGGGGTTGAA
195 ATTCGAAAAAAATGGAAAAACGATATTGAAAGCGTGAAAAACCCTTTTAATTTTTTGGGGTTGAA
* * * ** *
43807 TAATATGGTTTTTATAAGTATTGTGGCAAAAAATTGAGGGAAAA-CTTTTGGGTCAGTTTTTGCA
260 TAATAT-CTTTTTATAAGTATTATGGC-AAAAATTGAGGAAAAATCTTTAAGGTCAATTTTTGCA
*
43871 AAATTTA
323 AAATTTT
43878 AGCCGAAATCGTGTATTAACCATCAC-AGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCA
1 AGCCGAAATCGTGTATTAACCATCACGAGTTTTTGGCTAAAAACGCGTT-CGGAGCCCCGGCTCA
* *
43942 ATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATATATTTTCATCTAACCAAATCTTAGC
65 ATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTCATCTAACCAAATCTTAGC
* *
44007 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAA
130 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAA
*
44072 ATTCGAAAAAAATGGAAAAACGATATTGGAAGC
195 ATTCGAAAAAAATGGAAAAACGATATTGAAAGC
44105 CGAAATCATC
Statistics
Matches: 765, Mismatches: 108, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
330 182 0.24
331 91 0.12
332 297 0.39
333 194 0.25
334 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (329 bp):
AGCCGAAATCGTGTATTAACCATCACGAGTTTTTGGCTAAAAACGCGTTCGGAGCCCCGGCTCAA
TTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATCTATATTCATCTAACCAAATCTTAGCC
ACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAAAAATAAA
TTCGAAAAAAATGGAAAAACGATATTGAAAGCGTGAAAAACCCTTTTAATTTTTTGGGGTTGAAT
AATATCTTTTTATAAGTATTATGGCAAAAATTGAGGAAAAATCTTTAAGGTCAATTTTTGCAAAA
TTTT
Found at i:44308 original size:226 final size:224
Alignment explanation
Indices: 43877--44330 Score: 520
Period size: 226 Copynumber: 2.0 Consensus size: 224
43867 TGCAAAATTT
* * * * *
43877 AAGCCGAAATCGTGTATTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCA
1 AAGCCGAAATCATCTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGACTCA
* * * ** **
43942 ATTTTGCTTGATTTTTGGCGCAAAGACTACTTCAAATATATATTTTCATCTAACCAAATCTTAGC
66 ATTTTACATGATTTTTGGCGCAAAGACTACTTCAAATATATATATTCATCTAAAAAAATCCCAGC
* * * *
44007 CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTTAATCTTGTTTTGATTTAATTAAAAATAA
131 CACAATAGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAAAAATAA
*
44072 ATTCGAAAAAA-ATGGAAAAACGATATTGG
196 ATTCGAAAAAATA-GGAAAAACGATATTAG
* * * *
44101 AAGCCGAAATCATCTACTAACCATCACTATTTTTTTGGCTAACAACGCGTTCTAGTG-CCCGACA
1 AAGCCGAAATCATCTACTAACCATCAC-A-GTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGAC-
* * * * * *
44165 TCAGTTTTACATGATTTTTGGGGCCAAGACTCCTTGAAATATCTATATTCATCTAAAAAAATCCC
63 TCAATTTTACATGATTTTTGGCGCAAAGACTACTTCAAATATATATATTCATCTAAAAAAATCCC
* * * *
44230 AGCCACATTAGATTTAAAGATTTGTTTTTATGAGCATCTGACTCTT-TTTTCGATTTAATT-CAA
128 AGCCACAATAGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTT-GATTTAATTAAAA
** *
44293 ATTTATTCAGAAAAAATAGGAAATACGATATTAG
192 ATAAATTC-GAAAAAATAGGAAAAACGATATTAG
44327 AAGC
1 AAGC
44331 GTGAAAAGCC
Statistics
Matches: 190, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
224 24 0.13
225 18 0.09
226 147 0.77
227 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (224 bp):
AAGCCGAAATCATCTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCAGAGCCCCGACTCA
ATTTTACATGATTTTTGGCGCAAAGACTACTTCAAATATATATATTCATCTAAAAAAATCCCAGC
CACAATAGATTTAAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAAAAATAA
ATTCGAAAAAATAGGAAAAACGATATTAG
Done.