Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019098.1 Corchorus olitorius cultivar O-4 contig19131, 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: 71560
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:548 original size:15 final size:15
Alignment explanation
Indices: 528--556 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
518 TTACTGGTAA
528 TTAATGCATGCATGG
1 TTAATGCATGCATGG
543 TTAATGCATGCATG
1 TTAATGCATGCATG
557 CACATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (15 bp):
TTAATGCATGCATGG
Found at i:5356 original size:13 final size:13
Alignment explanation
Indices: 5338--5362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5328 ATAGCTATGT
5338 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
5351 TTTTTTTTTCTT
1 TTTTTTTTTCTT
5363 TTTACATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:5803 original size:17 final size:18
Alignment explanation
Indices: 5783--5816 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5773 ATTCACCCTG
5783 CAACAATGTCA-AAAAAA
1 CAACAATGTCATAAAAAA
5800 CAACAATGTCATAAAAA
1 CAACAATGTCATAAAAA
5817 TGATTCGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.18, G:0.06, T:0.15
Consensus pattern (18 bp):
CAACAATGTCATAAAAAA
Found at i:9598 original size:15 final size:16
Alignment explanation
Indices: 9558--9598 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
9548 TCAAAACATA
9558 ATTTTT-TAA-AATTT
1 ATTTTTATAATAATTT
9572 ATTTTTAT-ATAATTT
1 ATTTTTATAATAATTT
9587 -TTTTTATAATAA
1 ATTTTTATAATAA
9599 AAGATCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTTATAATAATTT
Found at i:10337 original size:2 final size:2
Alignment explanation
Indices: 10330--10363 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10320 GCTAAATAAT
10330 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
10364 CTTTCCATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14227 original size:31 final size:31
Alignment explanation
Indices: 14163--14230 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
14153 ATGAGAATTT
* * *
14163 AATTGACCCAATCTTGTGAGTATATGGATTA
1 AATTGACCCAATCTTGCGAGTAAATGGACTA
*
14194 AATTGACTCAATCTTGCGAGTACAAT-GACTA
1 AATTGACCCAATCTTGCGAGTA-AATGGACTA
14225 AATTGA
1 AATTGA
14231 TCGCTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (31 bp):
AATTGACCCAATCTTGCGAGTAAATGGACTA
Found at i:14370 original size:24 final size:25
Alignment explanation
Indices: 14342--14388 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
14332 CAAATTAATC
14342 GAGATTGT-AAAAAATCATATTAAA
1 GAGATTGTAAAAAAATCATATTAAA
*
14366 GAGATTGTAAAAAAATCTTATTA
1 GAGATTGTAAAAAAATCATATTA
14389 TATTAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (25 bp):
GAGATTGTAAAAAAATCATATTAAA
Found at i:22991 original size:14 final size:14
Alignment explanation
Indices: 22968--22998 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22958 GGCCTAGCTT
*
22968 AAAGTTCTTCTGAA
1 AAAGTGCTTCTGAA
22982 AAAGTGCTTCTGAA
1 AAAGTGCTTCTGAA
22996 AAA
1 AAA
22999 AACTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (14 bp):
AAAGTGCTTCTGAA
Found at i:31472 original size:21 final size:21
Alignment explanation
Indices: 31380--31526 Score: 104
Period size: 22 Copynumber: 6.8 Consensus size: 21
31370 TCATAAGAAG
*
31380 GTTAT-AAAA-TTCATAGGAAA
1 GTTATCAAAATTTCATAGG-TA
* * *
31400 GTTTATTAAAATTTAATAGTTA
1 G-TTATCAAAATTTCATAGGTA
* **
31422 GGTTATCAAAGTTTTTTATGG-A
1 -GTTATCAAAATTTCATA-GGTA
*
31444 GTTTATCACAATTTCATAGGTA
1 G-TTATCAAAATTTCATAGGTA
*
31466 ATTATCAAAATTTCATA-GTA
1 GTTATCAAAATTTCATAGGTA
*
31486 TGGTTATCAAAATTTAATAGGATA
1 --GTTATCAAAATTTCATAGG-TA
31510 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
31527 AAAACATTTA
Statistics
Matches: 99, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.04
21 22 0.22
22 62 0.63
23 9 0.09
24 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTA
Found at i:36052 original size:10 final size:10
Alignment explanation
Indices: 36022--36052 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
36012 TCATGTAACG
*
36022 TGTTTTGTTT
1 TGTTTTTTTT
36032 TGTTTTTTTT
1 TGTTTTTTTT
36042 TGTTTTTTTT
1 TGTTTTTTTT
36052 T
1 T
36053 CCAAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TGTTTTTTTT
Found at i:42641 original size:29 final size:30
Alignment explanation
Indices: 42585--42664 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
42575 GCTAAATACC
*
42585 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTTGGGA
42616 CAAAATAATCCCTTATGTTTT-TTTTGGGA
1 CAAAATAATCCCTTATGTTTTCTTTTGGGA
* * *
42645 CAAATTAATCCATTACGTTT
1 CAAAATAATCCCTTATGTTT
42665 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTTGGGA
Found at i:42832 original size:31 final size:31
Alignment explanation
Indices: 42797--42861 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
42787 AAGGGACTGA
42797 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
42828 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
42859 TTT
1 TTT
42862 TAGTATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:43912 original size:30 final size:31
Alignment explanation
Indices: 43851--43911 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
43841 AAATTATAGA
43851 CTAAATACTAAAAAAAATCCCTTATGTTTTT
1 CTAAATACTAAAAAAAATCCCTTATGTTTTT
43882 CTAAATACTAAAAAAAATCCCTTATGTTTT
1 CTAAATACTAAAAAAAATCCCTTATGTTTT
43912 CATTTTGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (31 bp):
CTAAATACTAAAAAAAATCCCTTATGTTTTT
Found at i:43927 original size:31 final size:31
Alignment explanation
Indices: 43861--43956 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
43851 CTAAATACTA
** ***
43861 AAAAAAATCCCTTATGTTTTTCTAAATACTA-
1 AAAAAAATCCCTTATGTTTTTCT-TTTGGGAC
43892 AAAAAAATCCCTTATG-TTTTCATTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTC-TTTTGGGAC
*
43923 AAAAAAATCTCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
43954 AAA
1 AAA
43957 TCAGTCCCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 7 0.12
31 44 0.79
32 5 0.09
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:44142 original size:29 final size:30
Alignment explanation
Indices: 44100--44173 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
44090 CTCATTTTTG
* *
44100 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
44129 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
*
44160 AAACATAAGAGATT
1 AAACATAAGGGATT
44174 TTTTTTGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.64
31 14 0.36
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:45970 original size:106 final size:106
Alignment explanation
Indices: 45783--46031 Score: 392
Period size: 106 Copynumber: 2.3 Consensus size: 106
45773 GTTTGAGGAT
* *
45783 AACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACTCTATAATAATAAATTATTAATTTTAA
1 AACTTAGTGACATTAGTTTTATATTTTAATTCT-AAACCCTATAACAATAAATTATTAATTTTAA
45848 AATTTACCCTTAAAATTAAACTAAAATTTTAATTTGGGGCTA
65 AATTTACCCTTAAAATTAAACTAAAATTTTAATTTGGGGCTA
* **
45890 AACTTAGTGACATTAGTTTTATATTTTAATTCTAAACCCTATAACAATTAATTATTAATTTTGGA
1 AACTTAGTGACATTAGTTTTATATTTTAATTCTAAACCCTATAACAATAAATTATTAATTTTAAA
* *
45955 ATTTACCCTTAAAATTAAATTATAATTTTAATTTGGGGCTA
66 ATTTACCCTTAAAATTAAACTAAAATTTTAATTTGGGGCTA
* *
45996 AGCTCAGTGACATTAGTTTTATA-TTTAATTTCTAAA
1 AACTTAGTGACATTAGTTTTATATTTTAA-TTCTAAA
46032 AAGAATAAAA
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
105 5 0.04
106 94 0.71
107 33 0.25
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (106 bp):
AACTTAGTGACATTAGTTTTATATTTTAATTCTAAACCCTATAACAATAAATTATTAATTTTAAA
ATTTACCCTTAAAATTAAACTAAAATTTTAATTTGGGGCTA
Found at i:52965 original size:107 final size:106
Alignment explanation
Indices: 52778--53106 Score: 343
Period size: 107 Copynumber: 3.1 Consensus size: 106
52768 AAATTTTGAT
*** * ** *
52778 TTTTAAGAGTAAATTATGAAATTAA-AGTTT-TT-TTATTATAAAGTTTTAGAAATAAAAAATAA
1 TTTTAAGAGTAAATTCCAAAATTAATAATTTATTGTTA-TATAGGGTTTTAGAAAT--AAAACAA
*
52840 AATTAATTTCACTAAGTTTAGCTCTAAATTAAAATTTTATTTTTA
63 AACTAATTTCACTAAGTTTAGCTC-AAATTAAAATTTTATTTTTA
*
52885 TTTTAAGAGTAAATTTCAAAATTAATAATTTATTG-T-TATAGGGTTTTAGAAATATAATACAAA
1 TTTTAAGAGTAAATTCCAAAATTAATAATTTATTGTTATATAGGGTTTTAGAAATA-AA-ACAAA
* *
52948 ACTAATTTCACTGAGTTTAGTCCCAAATT-AAATTTT-TTTTTA
64 ACTAATTTCACTAAGTTTAG-CTCAAATTAAAATTTTATTTTTA
* *
52990 TTTTAA-AGGTAAATTCCATAATTAATAATTTATTGTTATATAGGGTTTTACAAATAAAACATAT
1 TTTTAAGA-GTAAATTCCAAAATTAATAATTTATTGTTATATAGGGTTTTAGAAATAAAACA-A-
* * ** *
53054 AACTAA-TTCACTAAGTTTAGCACAAATTAAAAATAAATTTTCA
63 AACTAATTTCACTAAGTTTAGCTCAAATTAAAATTTTATTTTTA
53097 TTTTAAGAGT
1 TTTTAAGAGT
53107 TAGAAAAATT
Statistics
Matches: 189, Mismatches: 19, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
104 1 0.01
105 48 0.25
106 30 0.16
107 100 0.53
108 7 0.04
109 3 0.02
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (106 bp):
TTTTAAGAGTAAATTCCAAAATTAATAATTTATTGTTATATAGGGTTTTAGAAATAAAACAAAAC
TAATTTCACTAAGTTTAGCTCAAATTAAAATTTTATTTTTA
Found at i:64075 original size:284 final size:283
Alignment explanation
Indices: 63513--64081 Score: 637
Period size: 284 Copynumber: 2.0 Consensus size: 283
63503 TAAAAATGAC
* *
63513 CCGAAAGATTTTTCCTCAATTTTTGACAAAAATACTCATAAAATATATATAATTAAACGCCAAAA
1 CCGAAAGATATTTCCTCAATTTTTGACAAAAATACTCATAAAATATATATAATTAAACACCAAAA
** * * * * **
63578 TTATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATTTTTTTCTGAATTAATTTCTACTTA
66 AGATTGAAGGACTTTTAACGCTTCTAATATCGTTTTTCATTTCTTTCCAAATTAATTTCTACTTA
* * * * ** *
63643 AATCAATACAAGATTCGGATACACATAAAAACAAATCTTTAAATCCAATGTGGCTGTGATTTTAT
131 AATCAATACAACACTCAGATACACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGAT
* * *
63708 TAGATGAATAAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAGTCGTGGCC
196 TAGATGAATAAAAGATATTTAAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAG-CCTGGCC
*
63773 TTGGAACGCGTTTTTAGCCAAAAA
260 TCGGAACGCGTTTTTAGCCAAAAA
* * * ** * *
63797 CCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATGAAAA-ATATATGATTCGATATCAAA
1 CCGAAAGATATTTCCTCAATTTTTGACAAAAATACTCAT-AAAATATATATAATTAAACACCAAA
* *
63861 AAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTCTTTCCAAATTAATTTCTTA
65 AAGATTGAAGGACTTTTAACGCTTCTAATATCGTTTTT-C-ATTTCTTTCCAAATTAATTTC-TA
* * * * * *
63926 -TTAAATCGAA-CCAACACTCAGATGCTCGTAAAAATAAATCCTTAAATCTAATGTGGCTAAGAT
127 CTTAAATC-AATACAACACTCAGATACACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGAT
* * * *
63989 TTGGTTAGATGAAT-ATAGATATTTAAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGA-CCT
191 TTGATTAGATGAATAAAAGATATTTAAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAGCCT
* * *
64052 AGATCC-CGGAATGCGTTTTTAGCCGAAAA
256 -G-GCCTCGGAACGCGTTTTTAGCCAAAAA
64081 C
1 C
64082 TGTGATGGTT
Statistics
Matches: 235, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
283 2 0.01
284 103 0.44
285 48 0.20
286 78 0.33
287 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (283 bp):
CCGAAAGATATTTCCTCAATTTTTGACAAAAATACTCATAAAATATATATAATTAAACACCAAAA
AGATTGAAGGACTTTTAACGCTTCTAATATCGTTTTTCATTTCTTTCCAAATTAATTTCTACTTA
AATCAATACAACACTCAGATACACATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGAT
TAGATGAATAAAAGATATTTAAAGGAGTCTCGGCACCAAAAATCATGCAAAACAGAGCCTGGCCT
CGGAACGCGTTTTTAGCCAAAAA
Found at i:64445 original size:333 final size:330
Alignment explanation
Indices: 63797--68132 Score: 1881
Period size: 332 Copynumber: 13.3 Consensus size: 330
63787 TAGCCAAAAA
* * * * * * * *
63797 CCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATGAAAAATATATGATTCGA-TATCAAA
1 CCGAAATAT-TTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAA
* ** *
63861 AAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTCTTTCCAAATTAATTTCTTA
65 AAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTT-TTTCCAAATTAATTTCTAA
* * * ** *
63926 TTAAATCGAACCAACACTCAGATGCTCGTAAAAATAAATCCTTAAATCTAATGTGGCTAAGATTT
129 TTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAATC-AATGTGGCTAAGATTT
* *
63991 GGTTAGATGAATAT--AGATATTTAAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGACCTA-
193 GGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGACCCAG
* * * ** * *
64053 GATCCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACAATATTTCAGCTAAAATTTTC
258 GA-CCCGAAACGCGTTTTTAGCCAAAAACTGTGATGG-T-GTACACGATTTCGGCTAAAATTTTG
64118 CAAAAATTGAC
320 CAAAAATTGAC
* * *
64129 CCGAAATATTTTTCCTCGATTTGTAGCGAAAATACTCATGAAAAATATATAATTCAACGA-CAAA
1 CCGAAATATTTTT-CTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAA
* * * * *
64193 AA-AATGAAAGCCTTTTTCACGCTTTTAATAACGTTTTCCCTATTTTATTTCCAAATTAATTTCT
65 AAGATTGAAGGGC-TTTTCACGCTTCTAATAACGTTTTTCCTA-TTT-TTTCCAAATTAATTTCT
* * * * * * * *
64257 GATTAGATCAAAACAAGATTTAGAAATTCATAAAAACAAATCCTTAAATACAATTTGGCTGAGAT
127 AATTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAAGAT
* * * *
64322 TTGGTTAGATAAATATAAATATATTTTAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGACCC
191 TTGGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGACCC
* * **
64387 AGGACACAGGAACGCGTTTTTAGCCAAATAACAATGAT-G-GTACACGATTTCGGCTAAAATTTT
256 AGGAC-CCGAAACGCGTTTTTAGCCAAA-AACTGTGATGGTGTACACGATTTCGGCTAAAATTTT
*
64450 GCAAAAATTAAC
319 GCAAAAATTGAC
* * *
64462 CCGAAATATTTTTCTCAATTTTTACCCACAATACTCATTAAAAATATATAATTCAACG-CCAAAA
1 CCGAAATATTTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAAA
** * * **
64526 AGATT---GGGCTTCACACGCTTCTAATATA-ATTATTCCTATTTTTT-CAAATTAAAATCTAAT
66 AGATTGAAGGGCTTTTCACGCTTCTAATA-ACGTTTTTCCTATTTTTTCCAAATTAATTTCTAAT
* * * * *
64586 TAAATTGAAACATGATTCA-AATGCTCGCAAAAACAAATCCTTAAATCAAGTGTGGCTAAAATTT
130 TAAATCGAAACAAGATTCAGAA-ACTCGTAAAAACAAATCCTTAAATCAA-TGTGGCTAAGATTT
* * **
64650 GGTTAGATG---A-AAAGATATTTGAAGGA-TTTTTCCACCAAAAATCATGCAAAACTGACCCAG
193 GGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGACCCAG
*
64710 GACCCCGAAACGC-TTTTTAGCCAAAAAACTGTGAT-G-GTACACGATTTTGGCTAAAATTTTGC
258 GA-CCCGAAACGCGTTTTTAGCC-AAAAACTGTGATGGTGTACACGATTTCGGCTAAAATTTTGC
*
64772 AACAATTGAC
321 AAAAATTGAC
* *
64782 CCGAAATATTTTGTCTCAA-TTTTAGGCCACAACACTCAT-AAAATATATATAATTCAAC-ACCA
1 CCGAAATATTTT-TCTCAATTTTTA-GCCAAAATACTCATGAAAA-ATATATAATTCAACGACCA
* * * * * * * * **
64844 AAAAGACTGGAGGACTTTTCACGTTTTTAGTATCGTTTTTCATATATTTTTCTGAATTAATTTCT
63 AAAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTAT-TTTTTCCAAATTAATTTCT
* * * *
64909 AATTAAATTGAAACAAGATTCAGAGACTCGTAAAAACAAATCCTTAGATTCAATGTGGCTGAGAT
127 AATTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTA-AATCAATGTGGCTAAGAT
* * * * ** ** * * *
64974 TTGATTAGATGAATAT--AGATTTTTCAAGAAGTCTCAATGCAAAACAATCATGCAAAACTAAGC
191 TTGGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAA-AATCATGCAAAACTGACC
** *
65037 TGGGGCCTCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATT
255 CAGGACC-CGAAACGCGTTTTTAGCCAAAAACTGTGATGG-T-GTACACGATTTCGGCTAAAATT
65102 TTGCAAAAATTGAC
317 TTGCAAAAATTGAC
* * * * *
65116 CCGAAA-ATTTTTTTCGAAAATTTTTGGCTAAAATACTCATAATATATATATATATATATAATTT
1 CCGAAATATTTTTCTC---AATTTTTAGCCAAAATACTC---AT-GA-A-A-A-ATATATAATTC
* * ** * * * ** **
65180 AATG-CCAAAAAGATTGGAGAACTTTTCATGCTTTTAATATCGTTTTTATTA-TTTTTCTGAATT
55 AACGACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATT
* ** * * *
65243 AATTTCTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAACAAATTCTT-AATCCAATGTTG
120 AATTTCTAATTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAAT-CAATGTGG
* * * * * **
65307 CTGATATTTGATTAGATGAATAT--GGATATCTCAAA-GAGTCTTGACGGCAAAAATCATGCAAA
184 CTAAGATTTGGTTAGATGAATATAAAGATAT-TTAAAGGAGTCTTGACACCAAAAATCATGCAAA
** * ** * * *
65369 ACTGAGCCGGGGTCCCGAAACGCGAGTTTAGCCAAAAACCGTGATGAT-TATCA--A--AC-G--
248 ACTGA-CCCAGGACCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTGTA-CACGATTTCGGCT
*
65426 ---ATTTTAGC--TAA---A-
311 AAAATTTT-GCAAAAATTGAC
* * * * * * *
65438 --G--TTA-TTTCCTCAATTTTTAGGCACAATACTCATTAAAATTATATAATTCAAC-ACCAATA
1 CCGAAATATTTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAAA
* * * * * * *
65497 AGATTGAAGGGCTTTTCATGGTTCTAATATCGTTTTTCCTATTATTTTTCGAGTTAATTTCTGAT
66 AGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATT-TTTTCCAAATTAATTTCTAAT
* ** * *** * ** **
65562 TAAATCGAAACATGATTCAGATGCTTGT-TTTAGAAATCCTTAAATCCAATGTAACCGAGATTTG
130 TAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAAGATTTG
* * * * ** *
65626 GTTAGATGAATAT--AGATATTTCAAGGAGTC-TCAGCGCCAAAAATCATGCAACACT-ATATCG
194 GTTAGATGAATATAAAGATATTTAAAGGAGTCTTGA-CACCAAAAATCATGCAAAACTGA-CCCA
** * * *
65687 GGACCCCGAAACGCGTTTTTAGGAAAAAAAAAC-GTAAAT-TTCGACTAACGAACAGGATTTTGG
257 GGA-CCCGAAACGCGTTTTTA-G--CCAAAAACTGT-GATGGT-G--T-AC--AC--GATTTCGG
* *
65750 CTAATATTTTGCAAAAACTGAC
309 CTAAAATTTTGCAAAAATTGAC
* * ** * * * **
65772 CAGAATTATTTTTCCTCAA----T-G-CAAAA-A-AGATTGCAGAA-CT-T--TTCAACG--CTT
1 CCGAAATATTTTT-CTCAATTTTTAGCCAAAATACTCA-TGAAAAATATATAATTCAACGACCAA
** ** * ** * ** ** *** ** *
65823 TTA-A-T--ATCGTTTTTCA-TTTTTTTTTGAA--TTAATTTCAAATTAAAT-CAAAACAAGATT
64 AAAGATTGAAGGGCTTTTCACGCTTCTAAT-AACGTT--TTTCCTATTTTTTCCAAATTAA-TTT
* ** * * ** * * * ** * * *
65880 C-AGATGCT-CATAAAAAC-ACATCCTTAAA-T-GCAATGTAGCTAAGATTTGATTAGATAAATA
125 CTA-AT--TAAATCGAAACAAGATTCAGAAACTCGTAA--AAAC-AA-A--TCCTTAAATCAATG
* * * * * ** * ** * *
65940 TAG---ATATTTCAAGGAGTCTCGACG-ACA-AAA-ATCATGCAAAACTGAGTCGGGGC-CCCAA
181 TGGCTAAGATTT----G-GT-TAGATGAATATAAAGAT-AT-TTAAA-GGAGTCTTGACACCAAA
**** * * *
65998 AA-C--GC-GTTTTTA---A-GA----AAA---------A--AAAAAACTATGATGGTTAGTACA
237 AATCATGCAAAACTGACCCAGGACCCGAAACGCGTTTTTAGCCAAAAACTGTGATGG-T-GTACA
* * *
66040 CAATTTCGGCTAAAATTTTGAAAAAAAATGAC
300 CGATTTCGGCTAAAATTTTG-CAAAAATTGAC
* * * * * *
66072 CAGAAAAATTTTTCCTTAATTTTT-GTCTAAAATACTCATGAAATATATATAATTTAACG-CCAA
1 CCGAAATATTTTT-CTCAATTTTTAG-CCAAAATACTCATGAAAAATATATAATTCAACGACCAA
* * * * * ** *
66135 AAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCAC-ATTATTTT-TGAATTAATTTGT
64 AAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTC-CTATT-TTTTCCAAATTAATTTCT
* * ** * * * *
66198 AATTAAATCAAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATGCAACGTGGATGAGAT
127 AATTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAAGAT
* * * * * * * * *
66263 TTGATTAGATTAATAT--GGATATATCAAGGATTCTTAACACCAAAAATCATACAAAACTGACTT
191 TTGGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGAC-C
* * * * * * * * * *
66326 GAGG-CCCTAGAATGTGTTTTTAGTCAAAAACCGTGATGATTTATTACACGATTTCAGCTAACAT
255 CAGGACCCGA-AACGCGTTTTTAGCCAAAAACTGTGATG--GT-GTACACGATTTCGGCTAAAAT
66390 TTTGCAAAAATTGA-
316 TTTGCAAAAATTGAC
* * * * ** * * *
66404 CCGAAAAAAAATATTTCCTCGATTTTTGGTTAAAATACTCATAAAAAATATATATACTTTATCG-
1 CCG---AAATAT-TTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATA-A-TTCAACGA
* * * * * * * *
66468 CCAAAAATACTGAAGGGTTTTTTACGCTTCTAATATCTTTTTTCCTACTTTTTCCGAATTAATTT
60 CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTT
* * * * *
66533 CTAATTAAATCGAAACAAGATTTA-AATGCTCGT-AAAA-AAATCCATAATTCCAATGTGGCTGA
125 CTAATTAAATCGAAACAAGATTCAGAA-ACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAA
** ** * * * *
66595 GATTTAATTAGATGAATAT--AGATATTTGCATGATTTTTTG-CGCCAAAAATCATGCAAAACTG
188 GATTTGGTTAGATGAATATAAAGATATTTAAAGGA-GTCTTGACACCAAAAATCATGCAAAACTG
* * * * * *
66657 ATCCGGTGCCCCGGAA--C-ATTTTGGCCAAAAAAAAACTGTGAT-GT-TACACGATTTCGGCTA
252 ACCCAG-GACCCGAAACGCGTTTTTAGCC----AAAAACTGTGATGGTGTACACGATTTCGGCTA
*
66717 ATATTTTGCAAAAATTGAC
312 AAATTTTGCAAAAATTGAC
* * * * *
66736 CCAAAATATTTTTCCTCAATTTTTAGGCACAATACTTAT-AAAAAGTATATAATTCAACG-CTAA
1 CCGAAATATTTTT-CTCAATTTTTAGCCAAAATACTCATGAAAAA-TATATAATTCAACGACCAA
* * * * * *
66799 AACA-ATTAAAGGGCTTTTCATGCTTCTAATACCGTTTTTCTTATTTTTTCCGAATTAATTTTTA
64 AA-AGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTTCTA
* ** * **
66863 ATTAAAAT-GAAACATGATTCAGATGCTTGT-------AA-----AAA-CAA-G-GGCTGGGATT
128 ATT-AAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAATCAATGTGGCTAAGATT
* * * * *
66912 TAGTTAGATGAATAT--AGATATTTCAAGGAGTCTATG-CGCCAAAAATCATTCAAAACTGAACT
192 TGGTTAGATGAATATAAAGATATTTAAAGGAGTCT-TGACACCAAAAATCATGCAAAACTG-ACC
* * * * *
66974 C-GG-CTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACAATTTCGGCTAAAATT
255 CAGGAC-CCGAAACGCGTTTTTAGCCAAAAACTGTGATG-GT-GTACACGATTTCGGCTAAAATT
67037 TTGCAAAAATTGAC
317 TTGCAAAAATTGAC
* * * * * ***
67051 CTGAAAGATATTTCCTCAATTTTTAGCCATAATACTCA--ACAAAATATATGATTCGGTG-CCAA
1 CCGAAATAT-TTTTCTCAATTTTTAGCCAAAATACTCATGA-AAAATATATAATTCAACGACCAA
* * * * * ** *
67113 AAAGATTGAAGGGCTTTTCGCGCTTTTAATACCCTTTTTCATA-TTTTTCTGAATTAATTTCTAC
64 AAAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTTCTAA
** * *
67177 TTAAATCGAAACAAGATTCAGATGCTCAT-AAAACAAATCCTTAAATGTAATGTGGCTAAGATTT
129 TTAAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAAGATTT
** * * * * * * * *
67241 TATTAGACGAATAT--AGATATTTCATGGAGTGTCTG-CGCCAAAAAACTTGCAAAACTGAGCCG
193 GGTTAGATGAATATAAAGATATTTAAAGGAGTCT-TGACACCAAAAATCATGCAAAACTGA-CCC
* * * * *
67303 AGGCCCCGAAACGCTTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTTGGCTAAAGTTCT
256 AGGACCCGAAACGCGTTTTTAGCCAAAAACTGTGATGG-T-GTACACGATTTCGGCTAAAATTTT
* * *
67368 GAAAAAAATGTC
319 GCAAAAATTGAC
* * ** *
67380 CCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAA-TCTAACG-CCAA
1 CCGAAATATTTTT-CTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTC-AACGACCAA
* * * * * * *
67443 AACA-ATTGGAGGACTTTTCATGCTTTTAATATCATTTTTCATA-TTTTTCTC-AATTAATTTCT
64 AA-AGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTC-CAAATTAATTTCT
* * * *
67505 AATTAAATCGAAACAAAATTCA-AATACTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGA
127 AATTAAATCGAAACAAGATTCAGAA-ACTCGTAAAAACAAATCCTTAAAT-CAATGTGGCTAAGA
* * * * * * * * *
67569 TTTGATTAGATGAATAT-GA-ATATCTCAAGGAGTCTTGGCGCCAAAAATCAGGCATAACTGAGC
190 TTTGGTTAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGACC
* ** * *
67632 CGGGATCCTAAAACGCAGTTTTTAGCCAAAAACTGTGATGATTAATACACGATTTCGGCTAAAAT
255 CAGGA-CCCGAAACGC-GTTTTTAGCCAAAAACTGTGATG-GT-GTACACGATTTCGGCTAAAAT
*
67697 TTTGTAAAAATTGAC
316 TTTGCAAAAATTGAC
* * * * * * *
67712 CCAAAATATATTTCCTCATTTTTTGGCTAAAATACTCATAAAAAACATATAATTCAACG-CCAAA
1 CCGAAATAT-TTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAA
* * * *
67776 AAGATTGAAGGGCTTTTGATGTTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAAT
65 AAGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTTCTAAT
** * *
67841 TAAATCGAAACAAGATTTC-GATGCTCGTAAAAACAAACCCTTAAATCTAATGTGGCTGAGATTT
130 TAAATCGAAACAAGA-TTCAGAAACTCGTAAAAACAAATCCTTAAATC-AATGTGGCTAAGATTT
* * * * * * *
67905 GATTTGATGAATAT-AA-ATATTTCAAGTAGTCTTGGA-GCCAAAAATCATGCAAAATTGAGCCA
193 GGTTAGATGAATATAAAGATATTTAAAGGAGTCTT-GACACCAAAAATCATGCAAAACTGACCCA
* * * * * * * *
67967 GTA-CCTAGAACGTGGTTTTAGCCAAAAAACCGCGATTGTTTGTTAGTACACAATTTCGACTAAA
257 GGACCCGA-AACGCGTTTTTAGCC-AAAAACTGTGA-TG---G-T-GTACACGATTTCGGCTAAA
68031 ATTTTGCAAAAATTGAC
314 ATTTTGCAAAAATTGAC
* * * * *
68048 ACGAAAGATTTCTTCTCAATTTTT-GACTAAAATACTCAT-AAAAATATAAAATTCAATG-CCAA
1 CCGAAATATTT-TTCTCAATTTTTAG-CCAAAATACTCATGAAAAATATATAATTCAACGACCAA
* *
68110 AAAGATTGGAGGGCTTTTTACGC
64 AAAGATTGAAGGGCTTTTCACGC
68133 ATTTCTTATT
Statistics
Matches: 3072, Mismatches: 649, Indels: 563
0.72 0.15 0.13
Matches are distributed among these distances:
299 16 0.01
300 25 0.01
301 2 0.00
303 2 0.00
304 12 0.00
305 1 0.00
306 6 0.00
307 55 0.02
308 26 0.01
309 126 0.04
310 8 0.00
311 28 0.01
312 34 0.01
313 106 0.03
314 56 0.02
315 101 0.03
316 35 0.01
317 16 0.01
318 14 0.00
319 3 0.00
320 72 0.02
321 87 0.03
322 26 0.01
323 18 0.01
324 55 0.02
325 13 0.00
326 141 0.05
327 102 0.03
328 107 0.03
329 168 0.05
330 147 0.05
331 159 0.05
332 295 0.10
333 292 0.10
334 74 0.02
335 204 0.07
336 126 0.04
337 88 0.03
338 6 0.00
339 48 0.02
340 55 0.02
341 62 0.02
342 1 0.00
343 54 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
CCGAAATATTTTTCTCAATTTTTAGCCAAAATACTCATGAAAAATATATAATTCAACGACCAAAA
AGATTGAAGGGCTTTTCACGCTTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTTCTAATT
AAATCGAAACAAGATTCAGAAACTCGTAAAAACAAATCCTTAAATCAATGTGGCTAAGATTTGGT
TAGATGAATATAAAGATATTTAAAGGAGTCTTGACACCAAAAATCATGCAAAACTGACCCAGGAC
CCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTGTACACGATTTCGGCTAAAATTTTGCAAAAA
TTGAC
Found at i:67662 original size:976 final size:978
Alignment explanation
Indices: 65929--67876 Score: 2230
Period size: 976 Copynumber: 2.0 Consensus size: 978
65919 TAAGATTTGA
*
65929 TTAGATAAATATAGATATTTCAAGGAGTCTCGACGACAAAAATCATGCAAAACTGAGTCGGGGCC
1 TTAGATAAATATAGATATTTCAAGGAGTCTCGACGACAAAAATCATGCAAAACTGACTC-GGGCC
* *
65994 CCAAAACGCGTTTTTAAGAAAAAAAAAAACTATGATGGTTAGTACACAATTTCGGCTAAAATTTT
65 CCAAAACGCGTTTTTAAG---AAAAAAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTT
* * * **
66059 GAAAAAAAATGACCAGAAAAATTTTTCCTTAATTTTTGTCTAAAATACTCATGAAATATATATAA
127 GAAAAAAAATGACCAGAAAAATATTTCCTCAATTTTTGTCCAAAATACTCAACAAATATATATAA
* * * * * *
66124 TTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCACATTATTTTTGAA
192 TTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATACCCTTTTTCACATTATTTCTGAA
* *
66189 TTAATTTGTAATTAAATCAAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATGCAACGT
257 TTAATTTCTAATTAAATCAAAACAAGATACAGATGCTCATAAAAACAAATCATTAAATGCAACGT
* ** * *
66254 GGATGAGATTTGATTAGATTAATATGGATATATCAAGGATTCTTAACACCAAAAATCATACAAAA
322 GGATAAGATTTGATTAGACGAATATAGATATATCAAGGATTCTTAACACCAAAAAACATACAAAA
* * * * * *
66319 CTGACTTGAGGCCCTAGAATGTGTTTTTAGTCAAAAACCGTGATGATTTATTACACGATTTCAGC
387 CTGACTCGAGGCCCGAGAACGTGTTTTTAGCCAAAAACCGTGATGAGTTAGTACACGATTTCAGC
* * * * *
66384 TAACATTTTGCAAAAATTGACCGAAAAAAAATATTTCCTCGATTTTTGGTTAAAATACTCATAAA
452 TAACATTCTGAAAAAAATGACCG--AAAAAATATTTCCTCAATTTTTGGATAAAATACTCATAAA
* * ** * * *
66449 AAATATATATACTTTATCGCCAAAAATACTGAAGGGTTTTTTACGCTTCTAATATCTTTTTTCCT
515 AAATATATATACTCTAACGCCAAAAATACTGAAGGACTTTTCACGCTTCTAATATCATTTTTCAT
* * *
66514 ACTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAAAATCCATA
580 ACTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAAATACTCGTAAAAAAATCCATA
* * * * * *
66579 ATTCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTGCATGATTTTTTGCGCCAAAAA
645 AATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATCTGCAGGAGTCTTGGCGCCAAAAA
* * ** *
66644 TCATGCAAAACTGATCCGGTGCCCCGGAACATTTTGGCCAAAAAAAAACTGTGATG-T-TACACG
710 TCAGGCAAAACTGAGCCGGTGCCCCAAAACATTTTAGCC----AAAAACTGTGATGATATACACG
* * *
66707 ATTTCGGCTAATATTTTGCAAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGGC-ACAATAC
771 ATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATATTTCCTC-ATTTTTAGGCTAAAATAC
* ** *
66771 TTATAAAAAGTATATAATTCAACGCTAAAACA-ATTAAAGGGCTTTTCATGCTTCTAATACCGTT
835 TCATAAAAAACATATAATTCAACGCCAAAA-AGATTAAAGGGCTTTTCATGCTTCTAATACCGTT
* * * * *
66835 TTTCTTATTTTTTCCGAATTAATTTTTAATTAAAAT-GAAACATGA-TTCAGATGCTTGTAAAAA
899 TTTCCTATTTTTTCCAAATTAATTTCTAATT-AAATCGAAACAAGATTTC-GATGCTCGTAAAAA
66898 CAAGGGCTGGGATTTAG
962 CAAGGGCTGGGATTTAG
* * * *
66915 TTAGATGAATATAGATATTTCAAGGAGTCTATG-CGCCAAAAATCATTCAAAACTGAACTC-GGC
1 TTAGATAAATATAGATATTTCAAGGAGTCT-CGACGACAAAAATCATGCAAAACTG-ACTCGGGC
* ** ** * *
66978 TCCGGAACGCGTTTTT-AG-CCAAAAACCGTGATGATTATTACACAATTTCGGCTAAAATTTTG-
64 CCCAAAACGCGTTTTTAAGAAAAAAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTTGA
* * * * * *
67040 CAAAAATTGACCTGAAAGATATTTCCTCAATTTTTAG-CCATAATACTCAACAAA-ATATATGAT
129 AAAAAAATGACCAGAAAAATATTTCCTCAATTTTT-GTCCAAAATACTCAACAAATATATATAAT
*** * * *
67103 TCGGTGCCAAAAAGATTGAAGGGCTTTTCGCGCTTTTAATACCCTTTTTCATATT-TTTCTGAAT
193 TCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATACCCTTTTTCACATTATTTCTGAAT
* * * * * *
67167 TAATTTCTACTTAAATCGAAACAAGATTCAGATGCTCAT-AAAACAAATCCTTAAATGTAATGTG
258 TAATTTCTAATTAAATCAAAACAAGATACAGATGCTCATAAAAACAAATCATTAAATGCAACGTG
* * * * * * * *
67231 GCTAAGATTTTATTAGACGAATATAGATATTTCATGGAGTGTC-T-GCGCCAAAAAACTTGCAAA
323 GATAAGATTTGATTAGACGAATATAGATATATCAAGGA-T-TCTTAACACCAAAAAACATACAAA
*
67294 ACTGAGC-CGAGGCCCCGA-AACGCT-TTTTTAGCCAAAAACTGTGATG-GTTAGTACACGATTT
386 ACTGA-CTCGAGG-CCCGAGAACG-TGTTTTTAGCCAAAAACCGTGATGAGTTAGTACACGATTT
** * *
67355 TGGCTAA-AGTTCTGAAAAAAATGTCCCG-AAAAATTTTTCCTCAATTTTTGGATAAAATACTCA
448 CAGCTAACA-TTCTGAAAAAAATG-ACCGAAAAAATATTTCCTCAATTTTTGGATAAAATACTCA
* * * *
67418 TAAAAAATATATA-A-TCTAACGCCAAAACA-ATTGGAGGACTTTTCATGCTTTTAATATCATTT
511 TAAAAAATATATATACTCTAACGCCAAAA-ATACTGAAGGACTTTTCACGCTTCTAATATCATTT
*
67480 TTCATA-TTTTTCTC-AATTAATTTCTAATTAAATCGAAACAAAATTCAAATACTTGTAAAAACA
575 TTCATACTTTTTC-CGAATTAATTTCTAATTAAATCGAAACAAAATTCAAATACTCGT-AAAA-A
* * *
67543 AATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT-GAATATCT-CAAGGAGTCTTG
637 AATCCATAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAG-ATATCTGC-AGGAGTCTTG
* * *
67606 GCGCCAAAAATCAGGCATAACTGAGCCGG-GATCCTAAAACGCAGTTTTTAGCCAAAAACTGTGA
700 GCGCCAAAAATCAGGCAAAACTGAGCCGGTG-CCCCAAAA--CA--TTTTAGCCAAAAACTGTGA
*
67670 TGATTAATACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAATATATTTCCTCATTTTT
760 TGA-T-ATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATATTTCCTCATTTTT
* * * *
67735 TGGCTAAAATACTCATAAAAAACATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGATGTTT
823 AGGCTAAAATACTCATAAAAAACATATAATTCAACGCCAAAAAGATTAAAGGGCTTTTCATGCTT
*
67800 CTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTCGATGC
888 CTAATACCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTCGATGC
67865 TCGTAAAAACAA
953 TCGTAAAAACAA
67877 ACCCTTAAAT
Statistics
Matches: 809, Mismatches: 124, Indels: 68
0.81 0.12 0.07
Matches are distributed among these distances:
970 44 0.05
971 49 0.06
972 96 0.12
973 45 0.06
974 4 0.00
975 43 0.05
976 269 0.33
977 53 0.07
978 54 0.07
979 42 0.05
980 39 0.05
984 2 0.00
985 16 0.02
986 49 0.06
987 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (978 bp):
TTAGATAAATATAGATATTTCAAGGAGTCTCGACGACAAAAATCATGCAAAACTGACTCGGGCCC
CAAAACGCGTTTTTAAGAAAAAAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTTGAAA
AAAAATGACCAGAAAAATATTTCCTCAATTTTTGTCCAAAATACTCAACAAATATATATAATTCA
ACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATACCCTTTTTCACATTATTTCTGAATTAA
TTTCTAATTAAATCAAAACAAGATACAGATGCTCATAAAAACAAATCATTAAATGCAACGTGGAT
AAGATTTGATTAGACGAATATAGATATATCAAGGATTCTTAACACCAAAAAACATACAAAACTGA
CTCGAGGCCCGAGAACGTGTTTTTAGCCAAAAACCGTGATGAGTTAGTACACGATTTCAGCTAAC
ATTCTGAAAAAAATGACCGAAAAAATATTTCCTCAATTTTTGGATAAAATACTCATAAAAAATAT
ATATACTCTAACGCCAAAAATACTGAAGGACTTTTCACGCTTCTAATATCATTTTTCATACTTTT
TCCGAATTAATTTCTAATTAAATCGAAACAAAATTCAAATACTCGTAAAAAAATCCATAAATCCA
ATGTGGCTGAGATTTAATTAGATGAATATAGATATCTGCAGGAGTCTTGGCGCCAAAAATCAGGC
AAAACTGAGCCGGTGCCCCAAAACATTTTAGCCAAAAACTGTGATGATATACACGATTTCGGCTA
AAATTTTGCAAAAATTGACCCAAAATATATTTCCTCATTTTTAGGCTAAAATACTCATAAAAAAC
ATATAATTCAACGCCAAAAAGATTAAAGGGCTTTTCATGCTTCTAATACCGTTTTTCCTATTTTT
TCCAAATTAATTTCTAATTAAATCGAAACAAGATTTCGATGCTCGTAAAAACAAGGGCTGGGATT
TAG
Found at i:67752 original size:332 final size:331
Alignment explanation
Indices: 65795--68127 Score: 1909
Period size: 332 Copynumber: 7.1 Consensus size: 331
65785 CCTCAATGCA
* ** * * * * * *
65795 AAAAAGATTGCAGAACTTTTCAACGCTTTTAATATCGTTTTTCATTTTTTTTTGAATTAATTTCA
1 AAAAAGATTGAAGGGCTTTTC-ATGCTTTTAATATCATTTTTCATATTTTTCTCAATTAATTTCT
* * * * * *
65860 AATTAAATCAAAACAAGATTCAGATGCTCATAAAAACACATCCTTAAATGC-AATGTAGCTAAGA
65 AATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CTAATGTGGCTGAGA
* * * *
65924 TTTGATTAGATAAATATAGATATTTCAAGGAGTCT-CGACGACAAAAATCATGCAAAACTGAGTC
129 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTATG-CGCCAAAAATCATGCAAAACTGAGCC
** * ** ** *
65988 GGGGCCCCAAAACGCGTTTTTAAGAAAAAAAAAAACTATGATGGTTAGTACACAATTTCGGCTAA
193 GGGATCCTAAAACGCGTTTTT-AG----CCAAAAACCGTGATGATTAGTACACAATTTCGGCTAA
* * * * * * * *
66053 AATTTTGAAAAAAAATGA-CCAGAAAAATTTTTCCTTAATTTTTGTCTAAAATACTCATGAAATA
253 AATTTTG-CAAAAATTGACCCA-AAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAA
*
66117 TATATAATTTAACGCC
316 TATATAATTCAACGCC
* * * * * * * * *
66133 AAAAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCACATTATTTTTGAATTAATTTGT
1 AAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATATT-TTTCTCAATTAATTTCT
* * * * * *
66198 AATTAAATCAAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATGC-AACGTGGATGAGA
65 AATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CTAATGTGGCTGAGA
* * * * * * *
66262 TTTGATTAGATTAATATGGATATATCAAGGATTCT-TAACACCAAAAATCATACAAAACTGA-CT
129 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTAT-GCGCCAAAAATCATGCAAAACTGAGC-
* * * * * * * * * *
66325 TGAGG-CCCTAGAATGTGTTTTTAGTCAAAAACCGTGATGATTTATTACACGATTTCAGCTAACA
192 CG-GGATCCTAAAACGCGTTTTTAGCCAAAAACCGTGATGA-TTAGTACACAATTTCGGCTAAAA
* * * *
66389 TTTTGCAAAAATTGACCGAAAAAAAATATTTCCTCGATTTTTGGTTAAAATACTCATAAAAAATA
255 TTTTGCAAAAATTGACC--CAAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATA
* *
66454 TATATACTTTATCGCC
318 TATA-A-TTCAACGCC
* * * * * * * *
66470 AAAAATACTGAAGGGTTTTTTACGCTTCTAATATCTTTTTTCCTACTTTTTC-CGAATTAATTTC
1 AAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATA-TTTTTCTC-AATTAATTTC
* * * * * *
66534 TAATTAAATCGAAACAAGATTTAAATGCTCGT-AAAA-AAATCCATAATTCCAATGTGGCTGAGA
64 TAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGA
* * * * * *
66597 TTTAATTAGATGAATATAGATATTTGC-ATGATTTTTTGCGCCAAAAATCATGCAAAACTGATCC
129 TTTGATTAGATGAATATAGATATTT-CAAGGAGTCTATGCGCCAAAAATCATGCAAAACTGAGCC
* *** * * * *
66661 GGTG-CCCCGGAA--C-ATTTTGGCCAAAAAAAAAC-TG-TGA-T-GTTACACGATTTCGGCTAA
193 GG-GATCCTAAAACGCGTTTTTAGCC---AAAAACCGTGATGATTAG-TACACAATTTCGGCTAA
* * * * * *
66718 TATTTTGCAAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGGC-ACAATACTTATAAAAAGT
253 AATTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTT-GGCTAAAATACTCATAAAAAAT
*
66782 ATATAATTCAACGCT
317 ATATAATTCAACGCC
* * * * *
66797 AAAACA-ATTAAAGGGCTTTTCATGCTTCTAATACCGTTTTTCTTATTTTT-TCCGAATTAATTT
1 AAAA-AGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATATTTTTCT-C-AATTAATTT
* ** * *
66860 TTAATTAAAAT-GAAACATGATTCAGATGCTTGT-------AA-----AAA-C-AA-G-GGCTGG
63 CTAATT-AAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGA
* *
66908 GATTT-AGTTAGATGAATATAGATATTTCAAGGAGTCTATGCGCCAAAAATCATTCAAAACTGAA
127 GATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACTGAG
* ** *
66972 CTC-GGCTCC-GGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACAATTTCGGCTAAAA
191 C-CGGGATCCTAAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACAATTTCGGCTAAAA
** * * * *
67035 TTTTGCAAAAATTGACCTGAAAGATATTTCCTCAATTTTTAGCCATAATACTCA-ACAAAATATA
255 TTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATA
* ***
67099 TGATTCGGTGCC
320 TAATTCAACGCC
** * * *
67111 AAAAAGATTGAAGGGCTTTTCGCGCTTTTAATACCCTTTTTCATATTTTTCTGAATTAATTTCTA
1 AAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATATTTTTCTCAATTAATTTCTA
* * * * *
67176 CTTAAATCGAAACAAGATTCAGATGCTCAT-AAAACAAATCCTTAAATGTAATGTGGCTAAGATT
66 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATT
* * * * * * *
67240 TTATTAGACGAATATAGATATTTCATGGAGTGTCTGCGCCAAAAAACTTGCAAAACTGAGCCGAG
131 TGATTAGATGAATATAGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACTGAGCCG-G
* ** * * * * * * *
67305 G-CCCCGAAACGCTTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTTGGCTAAAGTTCTG
195 GATCCTAAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACAATTTCGGCTAAAATTTTG
* * * * *
67369 AAAAAAATGTCCCGAAAA-ATTTTTCCTCAATTTTTGGATAAAATACTCATAAAAAATATATAA-
260 CAAAAATTGACCC-AAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
67432 TCTAACGCC
324 TC-AACGCC
* *
67441 AAAACA-ATTGGAGGACTTTTCATGCTTTTAATATCATTTTTCATATTTTTCTCAATTAATTTCT
1 AAAA-AGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATATTTTTCTCAATTAATTTCT
* * * * *
67505 AATTAAATCGAAACAAAATTCAAATACTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGAT
65 AATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAT
* * *
67570 TTGATTAGATGAATAT-GAATATCTCAAGGAGTCT-TGGCGCCAAAAATCAGGCATAACTGAGCC
130 TTGATTAGATGAATATAG-ATATTTCAAGGAGTCTAT-GCGCCAAAAATCATGCAAAACTGAGCC
* * *
67633 GGGATCCTAAAACGCAGTTTTTAGCCAAAAACTGTGATGATTAATACACGATTTCGGCTAAAATT
193 GGGATCCTAAAACGC-GTTTTTAGCCAAAAACCGTGATGATTAGTACACAATTTCGGCTAAAATT
* * * *
67698 TTGTAAAAATTGACCCAAAATATATTTCCTCATTTTTTGGCTAAAATACTCATAAAAAACATATA
257 TTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATA
67763 ATTCAACGCC
322 ATTCAACGCC
* * *
67773 AAAAAGATTGAAGGGCTTTTGATG-TTTCTAATATCGTTTTTCCTATTTTT-TCCAAATTAATTT
1 AAAAAGATTGAAGGGCTTTTCATGCTTT-TAATATCATTTTTCATATTTTTCT-C-AATTAATTT
* *
67836 CTAATTAAATCGAAACAAGATTTC-GATGCTCGTAAAAACAAACCCTTAAATCTAATGTGGCTGA
63 CTAATTAAATCGAAACAA-AATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGA
* * * * *
67900 GATTTGATTTGATGAATATAAATATTTCAAGTAGTCT-TGGAGCCAAAAATCATGCAAAATTGAG
127 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTAT-GCGCCAAAAATCATGCAAAACTGAG
* * * * * * * *
67964 CCAGTA-CCTAGAACGTGGTTTTAGCCAAAAAACCGCGATTGTTTGTTAGTACACAATTTCGACT
191 CCGGGATCCTAAAACGCGTTTTTAGCC-AAAAACCGTGA-TG---ATTAGTACACAATTTCGGCT
* * * *
68028 AAAATTTTGCAAAAATTGACACGAAAGAT-TTCTTCTCAATTTTTGACTAAAATACTCAT-AAAA
251 AAAATTTTGCAAAAATTGACCCAAAAGATATT-TCCTCAATTTTTGGCTAAAATACTCATAAAAA
* *
68091 ATATAAAATTCAATGCC
315 ATATATAATTCAACGCC
*
68108 AAAAAGATTGGAGGGCTTTT
1 AAAAAGATTGAAGGGCTTTT
68128 TACGCATTTC
Statistics
Matches: 1634, Mismatches: 278, Indels: 169
0.79 0.13 0.08
Matches are distributed among these distances:
312 17 0.01
313 98 0.06
314 65 0.04
315 72 0.04
316 1 0.00
317 2 0.00
319 2 0.00
322 2 0.00
324 3 0.00
326 7 0.00
327 77 0.05
328 67 0.04
329 129 0.08
330 103 0.06
331 142 0.09
332 166 0.10
333 146 0.09
334 33 0.02
335 162 0.10
336 74 0.05
337 107 0.07
338 157 0.10
339 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
AAAAAGATTGAAGGGCTTTTCATGCTTTTAATATCATTTTTCATATTTTTCTCAATTAATTTCTA
ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGATT
TGATTAGATGAATATAGATATTTCAAGGAGTCTATGCGCCAAAAATCATGCAAAACTGAGCCGGG
ATCCTAAAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACAATTTCGGCTAAAATTTTGC
AAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTC
AACGCC
Found at i:71364 original size:29 final size:29
Alignment explanation
Indices: 71322--71384 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
71312 TTGAACTTCA
*
71322 TCCAATAGACAATAGACAATACTCAATTC
1 TCCATTAGACAATAGACAATACTCAATTC
71351 TCCATTAGACAATAGACAATACTCAATTC
1 TCCATTAGACAATAGACAATACTCAATTC
71380 TCCAT
1 TCCAT
71385 GATAACATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (29 bp):
TCCATTAGACAATAGACAATACTCAATTC
Done.