Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014552.1 Corchorus capsularis cultivar CVL-1 contig14573, 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: 230014
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:873 original size:328 final size:324
Alignment explanation
Indices: 3--1602 Score: 1065
Period size: 311 Copynumber: 4.9 Consensus size: 324
1 AT
* * * * *
3 TTTTTGCCACAATACTCAGAAAAAATATGTAACTCAACGCCAAAAAAATTGAAGGG-TTTTCATG
1 TTTTTGCCACAATACTCAG-AAAAATATATAATTCAACGGCAAAAAAGTTGAAGGGATTTTCACG
* * * * * *
67 CTCCTAATATTGTTTTCATATTTTTTCCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGA
65 CTTCTAATATTTTTTTC-CATTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGA
** * * * * * * *
132 TTCTCGTAAAATCAAATCCTTATATCCAATGTGTCTGATATTTGGTTAGATGAATATAGATATTT
128 TGATCATAAAA--AAATCCTTATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGATATTT
* * * * * * * *
197 CAAGGAAT-TTTTCTGCCAAAAATCATGCAAAACTT-AGTCGG-GAC-CCCGAAACACGTTTTTT
191 CAAAGAGTCTTTGC-GACAAAAATCATACAAAA-TTGAGT-GGAG-CTTCAG-AACGCG-TTTTT
* * * * * *
258 AGCCGTAAAACCCTGATGGTCAGTATACGATTT-A-C--------GCTAAAAACTAACCCGAAA-
250 AGCC-AAAAATCGTGATGGTTAGTACACGATTTCAGCTAAATTTTGC-AAAAACTGACCCGAAAG
*
312 TATTTT-TTCCGAAA
313 T-TTTTCTT-C-TAA
* * * ** * * * * *
326 TTTTTTACGACTACGCTCATAAAAAATATATAATTCAATGAC-AAGAAGATT-AATGGGCTTTTC
1 -TTTTTGCCACAATACTCA-GAAAAATATATAATTCAACGGCAAAAAAG-TTGAA-GGGATTTTC
* *
389 ACGCTTCTAATATCGTTTTTCCAAATTTTTTCCTAATTAATTTCTAATTAAATCGAAACAAGTTT
62 ACGCTTCTAATAT-TTTTTTCC--ATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTT
* * * * * *
454 CAGATGTTCTTGAAAGCAAATCCTTATCTTCAATGTGGTTGAGAATTGATTCGATGAATACAGAT
124 CAGATGATCAT-AAA-AAAATCCTTATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGAT
* * *
519 ACTTCAAAGTGTCTTTGCGACAAAAATCATGCAAAATTGAGTTGGAGCTTCAGAACGCGTTTTTA
187 ATTTCAAAGAGTCTTTGCGACAAAAATCATACAAAATTGAG-TGGAGCTTCAGAACGCGTTTTTA
* *
584 GTCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAGAAGT
251 GCCAAAAATCGTGATGGTTAGTACACGATTTCAGCT-AAATTTTGCAAAAACTGACCCGA-AAGT
649 TTTTCTTCTAA
314 TTTTCTTCTAA
* *
660 TTTTTGCCACAATACTCAGAAAAATATATAATTCTAC-GCAAAAGAAAAG-TGAATGGATTTTCA
1 TTTTTGCCACAATACTCAGAAAAATATATAATTCAACGGC--AA-AAAAGTTGAAGGGATTTTCA
* * * *
723 CGCTTCTAATATTTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAATCGAAACCAGATTAAGA
63 CGCTTCTAATATTTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGA
* * * * **
788 TGATCATAAAAAAATCCTTGA-ATGCACTGTGACTGAGATTTGATTCGATGAATATTGATATTT-
128 TGATCATAAAAAAATCCTT-ATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGATATTTC
* * * * *
851 ACAGGAGTCTTT-CTGTCAAAAATCATACAAAATTGAGCTGGGGAC--CCGAAACGCATTTTTAG
192 A-AAGAGTCTTTGC-GACAAAAATCATACAAAATTGAG-TGGAG-CTTCAG-AACGCGTTTTTAG
* *
913 CCCAAAAATCGTGATGGTTAGTACACGATTTCAGC-------T--AAAAACTGACCCGAAAATAT
252 -CCAAAAATCGTGATGGTTAGTACACGATTTCAGCTAAATTTTGCAAAAACTGACCCGAAAGTTT
969 TT-TTCTGAA
316 TTCTTCT-AA
* * * ** *
978 TTTATTACCACAATACTCATAAAAATATATAATTCAACGGCAAAAAGGTTGTCGGGCTTTTCACG
1 TTT-TTGCCACAATACTCAGAAAAATATATAATTCAACGGCAAAAAAGTTGAAGGGATTTTCACG
*
1043 CTTCTAATATTGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAG
65 CTTCTAATATT-TTTTTCCA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAG
* * *
1108 ATGCTCATAAAAGCAAATCCTTATCTCCAATGTGGCTGAGATTTGGTACGATGAATACAGATATT
127 ATGATCATAAAA--AAATCCTTATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGATATT
* * * * ** * * *
1173 TCAAACAGTCTTTGCGCCAAAAATCATATAAAGTTGAGTCAAGATTCTGGAACGCGCTTTTAGCC
190 TCAAAGAGTCTTTGCGACAAAAATCATACAAAATTGAGTGGAGCTTC-AGAACGCGTTTTTAGCC
* ** * * **
1238 AAAAATCTTGATAATTAGTATACGATTTCAGTTAAATTTTTGCAAAAACTGATTCGAAAAGTTTT
254 AAAAATCGTGATGGTTAGTACACGATTTCAGCTAAA-TTTTGCAAAAACTGACCCG-AAAGTTTT
* *
1303 TCCTCTATT
317 TCTTCTA-A
* * *** *
1312 TTTTTG-C-C---A--C---------------TCAACGCCAAAAAGATTTTTCGGGCTTTTCACG
1 TTTTTGCCACAATACTCAGAAAAATATATAATTCAACGGCAAAAA-AGTTGAAGGGATTTTCACG
* * * * *
1355 CTTCTAATATCATTTTTGCATTTTTTTCCGAATTAATTTCTTATTAAATCGTAACAAATTTCAGA
65 CTTCTAATAT-TTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGA
* * * *
1420 TGCTCATAAATGCAAATCCTTATCTCCAATGTAGCTGAGATTTGGTTCGATGAATACAGATATTT
128 TGATCATAAA--AAAATCCTTATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGATATTT
* * * *
1485 CAAAGAGTCTTTGCGCAATAAAAAACA-AGCAAAATTGAGCCGG-GAC-TCCGAAACGCGTTTTT
191 CAAAGAGTCTTTGCG--ACAAAAATCATA-CAAAATTGAG-TGGAG-CTTCAG-AACGCGTTTTT
* * *
1547 AACCAAAAA-CTGTGATGGTTAGTACACGATTTCAGATAAAATCTTGCAAAAACTGA
250 AGCCAAAAATC-GTGATGGTTAGTACACGATTTCAGCT-AAATTTTGCAAAAACTGA
1603 GCTGAAAAAT
Statistics
Matches: 1027, Mismatches: 170, Indels: 169
0.75 0.12 0.12
Matches are distributed among these distances:
311 128 0.12
312 36 0.04
313 71 0.07
314 3 0.00
317 8 0.01
318 36 0.04
319 52 0.05
320 2 0.00
321 51 0.05
322 32 0.03
323 88 0.09
324 61 0.06
325 26 0.03
326 120 0.12
327 22 0.02
328 87 0.08
329 37 0.04
330 46 0.04
331 2 0.00
332 35 0.03
333 44 0.04
334 24 0.02
335 13 0.01
336 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (324 bp):
TTTTTGCCACAATACTCAGAAAAATATATAATTCAACGGCAAAAAAGTTGAAGGGATTTTCACGC
TTCTAATATTTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGATGA
TCATAAAAAAATCCTTATCTCCAATGTGGCTGAGATTTGATTCGATGAATACAGATATTTCAAAG
AGTCTTTGCGACAAAAATCATACAAAATTGAGTGGAGCTTCAGAACGCGTTTTTAGCCAAAAATC
GTGATGGTTAGTACACGATTTCAGCTAAATTTTGCAAAAACTGACCCGAAAGTTTTTCTTCTAA
Found at i:2891 original size:16 final size:16
Alignment explanation
Indices: 2870--2900 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2860 TTCTTCTCCA
2870 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
2886 TATTCTCTTGTCTTT
1 TATTCTATTGTCTTT
2901 TCCATATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:8264 original size:19 final size:20
Alignment explanation
Indices: 8240--8277 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
8230 AGCCCTGTTT
8240 GGCCCATATCTACT-TTTTG
1 GGCCCATATCTACTATTTTG
*
8259 GGCCCATTTCTACTATTTT
1 GGCCCATATCTACTATTTT
8278 CAGTAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (20 bp):
GGCCCATATCTACTATTTTG
Found at i:31242 original size:183 final size:184
Alignment explanation
Indices: 30933--31286 Score: 629
Period size: 183 Copynumber: 1.9 Consensus size: 184
30923 ATTAAAAAAA
*
30933 TTTAAATTTACAGATTTATAAGGATCAATTAGCTACTACCAAAAAACAATGTATAACTTAAAAGC
1 TTTAAATTTACAGATTTATAAGGATCAATTAGCTACTACCAAAAAACAATGCATAACTTAAAAGC
30998 CACCAATAACTTTAGTTATCAGCAGCTAAATCACAATTAGTGCCTATAATTTGATCAGACCAAGA
66 CACCAATAACTTTAGTTATCAGCAGCTAAATCACAATTAGTGCCTATAATTTGATCAGACCAAGA
31063 AAGAACATAGCAGACATCAATTATCAAGAAAATAATCGGTTTAAAAAAATCCAT
131 AAGAACATAGCAGACATCAATTATCAAGAAAATAATCGGTTTAAAAAAATCCAT
** *
31117 TTTAAATTTACAGATTTATAAGGATCAATTAGCTACTACCAAGGATCAATGCATAACTT-AAAGC
1 TTTAAATTTACAGATTTATAAGGATCAATTAGCTACTACCAAAAAACAATGCATAACTTAAAAGC
*
31181 CACCAATAACTTTAGTTATCAGCAGCTAAATCACATTTAGTGCCTATAATTTGATCAGACCAAGA
66 CACCAATAACTTTAGTTATCAGCAGCTAAATCACAATTAGTGCCTATAATTTGATCAGACCAAGA
* * *
31246 CAGAACATAGCATACATCAATTATCAAGAAAATAATTGGTT
131 AAGAACATAGCAGACATCAATTATCAAGAAAATAATCGGTT
31287 GTTGATTAAC
Statistics
Matches: 162, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
183 107 0.66
184 55 0.34
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (184 bp):
TTTAAATTTACAGATTTATAAGGATCAATTAGCTACTACCAAAAAACAATGCATAACTTAAAAGC
CACCAATAACTTTAGTTATCAGCAGCTAAATCACAATTAGTGCCTATAATTTGATCAGACCAAGA
AAGAACATAGCAGACATCAATTATCAAGAAAATAATCGGTTTAAAAAAATCCAT
Found at i:38615 original size:28 final size:28
Alignment explanation
Indices: 38542--38615 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
38532 TAGTCTTAGG
*
38542 GAAGCAAAACATCCCAAAATTAAAGCTCA
1 GAAGCAAAATAT-CCAAAATTAAAGCTCA
* * * * * *
38571 TAGGTAAAATGTTCAAAATTAAAGTTCA
1 GAAGCAAAATATCCAAAATTAAAGCTCA
38599 GAAGCAAAATATCCAAA
1 GAAGCAAAATATCCAAA
38616 CGCGCTACAA
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (28 bp):
GAAGCAAAATATCCAAAATTAAAGCTCA
Found at i:42710 original size:9 final size:9
Alignment explanation
Indices: 42696--42725 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
42686 TTACTCATTG
42696 CCCTCTCAA
1 CCCTCTCAA
42705 CCCTCTCAA
1 CCCTCTCAA
42714 CCCTCTCAA
1 CCCTCTCAA
42723 CCC
1 CCC
42726 CAACCCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (9 bp):
CCCTCTCAA
Found at i:43633 original size:7 final size:7
Alignment explanation
Indices: 43621--43647 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
43611 ATTATATTAT
43621 AATGAAA
1 AATGAAA
43628 AATGAAA
1 AATGAAA
43635 AATGAAA
1 AATGAAA
43642 AATGAA
1 AATGAA
43648 TTAAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AATGAAA
Found at i:44791 original size:3 final size:3
Alignment explanation
Indices: 44783--44808 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44773 CAAAAGAGAA
44783 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
44809 AAGGTGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48873 original size:5 final size:5
Alignment explanation
Indices: 48865--48926 Score: 66
Period size: 4 Copynumber: 13.8 Consensus size: 5
48855 GAAAATGACT
*
48865 TTTTC TTTTC TTTTC TTTTC TTTTA TTTTC -TTTC -TTTC -TTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
48911 -TTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTT
48927 AAGAAAATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
4 28 0.52
5 26 0.48
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:57079 original size:11 final size:11
Alignment explanation
Indices: 57065--57094 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
57055 TACAAAAATG
57065 AGAAAAAAAAA
1 AGAAAAAAAAA
57076 AGAAAAAAAAA
1 AGAAAAAAAAA
57087 AGGAAAAA
1 A-GAAAAA
57095 GTCTAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:72905 original size:6 final size:6
Alignment explanation
Indices: 72884--72923 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
72874 GAAAAAAAAA
* * *
72884 TTCATT TTCTTC TTCATC TTCATC TTCATC ATCATC TTCA
1 TTCATC TTCATC TTCATC TTCATC TTCATC TTCATC TTCA
72924 AAGGTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCATC
Found at i:81435 original size:2 final size:2
Alignment explanation
Indices: 81428--81458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
81418 AAAGTGAGAT
81428 TA TA TA TA TA 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 T
81459 TGGCATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81786 original size:31 final size:31
Alignment explanation
Indices: 81751--81826 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 31
81741 TTTTTTGGCA
*
81751 CACGTAGCGTGCC-TCATGTCACTTTTTGATC
1 CACGTAGCCTGCCAT-ATGTCACTTTTTGATC
* * * *
81782 CACGTGGCCTGCCATGTGTTACTTTTTTATC
1 CACGTAGCCTGCCATATGTCACTTTTTGATC
* *
81813 CACGTGGCATGCCA
1 CACGTAGCCTGCCA
81827 CGTCGGACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (31 bp):
CACGTAGCCTGCCATATGTCACTTTTTGATC
Found at i:90008 original size:29 final size:28
Alignment explanation
Indices: 89937--90009 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
89927 GTAGCGTTTA
89937 GACGTTTTATCCCCCGAACTTCAATCTTG
1 GACGTTTTA-CCCCCGAACTTCAATCTTG
* * * *
89966 GACATTTTGTCCCCTGAACTTCAATTTTG
1 GACGTTTT-ACCCCCGAACTTCAATCTTG
89995 TGACGTTTTACCCCC
1 -GACGTTTTACCCCC
90010 TCAACCTAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (28 bp):
GACGTTTTACCCCCGAACTTCAATCTTG
Found at i:93002 original size:29 final size:29
Alignment explanation
Indices: 92960--93018 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
92950 ATATGCCAAC
92960 TAAATAAGATGAAACAGTGCAAATAGGTT
1 TAAATAAGATGAAACAGTGCAAATAGGTT
*
92989 TAAATAAGATGAAACAGTGCACATAGGTT
1 TAAATAAGATGAAACAGTGCAAATAGGTT
93018 T
1 T
93019 TAGAGATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.25
Consensus pattern (29 bp):
TAAATAAGATGAAACAGTGCAAATAGGTT
Found at i:121284 original size:29 final size:29
Alignment explanation
Indices: 121251--121309 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
121241 TTACAAACCA
121251 AGATCGAATTAAGCTGATTAAATATCAAT
1 AGATCGAATTAAGCTGATTAAATATCAAT
121280 AGATCGAATTAAGCTGATTAAATATCAAT
1 AGATCGAATTAAGCTGATTAAATATCAAT
121309 A
1 A
121310 CAGTGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.31
Consensus pattern (29 bp):
AGATCGAATTAAGCTGATTAAATATCAAT
Found at i:136118 original size:92 final size:92
Alignment explanation
Indices: 136013--136196 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
136003 TTACGTACAT
136013 TTTTTGTGTGTAAATGTCAATCCCGTTAGATATGAATGACGTGGCGTCTTGTGAATGGTTAATAG
1 TTTTTGTGTGTAAATGTCAATCCCGTTAGATATGAATGACGTGGCGTCTTGTGAATGGTTAATAG
136078 AGCGGTGAGTTTCCTTAAGGCTGACCC
66 AGCGGTGAGTTTCCTTAAGGCTGACCC
136105 TTTTTGTGTGTAAATGTCAATCCCGTTAGATATGAATGACGTGGCGTCTTGTGAATGGTTAATAG
1 TTTTTGTGTGTAAATGTCAATCCCGTTAGATATGAATGACGTGGCGTCTTGTGAATGGTTAATAG
136170 AGCGGTGAGTTTCCTTAAGGCTGACCC
66 AGCGGTGAGTTTCCTTAAGGCTGACCC
136197 AAGTCAAAGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (92 bp):
TTTTTGTGTGTAAATGTCAATCCCGTTAGATATGAATGACGTGGCGTCTTGTGAATGGTTAATAG
AGCGGTGAGTTTCCTTAAGGCTGACCC
Found at i:139497 original size:3 final size:3
Alignment explanation
Indices: 139489--139513 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
139479 TTTTATTACT
139489 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
139514 CTAGACCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:141508 original size:16 final size:16
Alignment explanation
Indices: 141487--141524 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
141477 GTAATTGGGC
141487 GGGTTCGGGTATTTTT
1 GGGTTCGGGTATTTTT
141503 GGGTTCGGGTATTTTT
1 GGGTTCGGGTATTTTT
141519 GGGTTC
1 GGGTTC
141525 TGTCAGGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.08, G:0.39, T:0.47
Consensus pattern (16 bp):
GGGTTCGGGTATTTTT
Found at i:142330 original size:16 final size:15
Alignment explanation
Indices: 142309--142353 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
142299 CGGGCTCGGG
142309 TCGGGTTTGGGTTGTC
1 TCGGGTTTGGGTT-TC
* *
142325 TCGGGTTCGGGTATTT
1 TCGGGTTTGGGT-TTC
142341 TCGGGTTTGGGTT
1 TCGGGTTTGGGTT
142354 CGGACGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.02, C:0.11, G:0.42, T:0.44
Consensus pattern (15 bp):
TCGGGTTTGGGTTTC
Found at i:154241 original size:39 final size:37
Alignment explanation
Indices: 154192--154338 Score: 122
Period size: 39 Copynumber: 3.9 Consensus size: 37
154182 AAGCAGTAGA
* *
154192 GAAAGGGAGAAGGAAAGGGACAGAGAAAGGAGAGATAGG
1 GAAA-GGAGAAAGAAAGGGAGAGAGAAAGGAGAGA-AGG
* * *
154231 GATAAGGAGAAAGAAAGGGATAGGGATAGG-GAG-A-G
1 GA-AAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAAGG
* ** * *
154266 GAGA-GAGAGGGAAAAGGAGAGAGAAAGGAGGGAGAGG
1 GAAAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGA-AGG
*
154303 GAGAAGGAGAAAGAAAGGGAGAGAGAAAGAAGAGAA
1 GA-AAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAA
154339 CGAAGCAGCA
Statistics
Matches: 83, Mismatches: 18, Indels: 15
0.72 0.16 0.13
Matches are distributed among these distances:
33 18 0.22
34 3 0.04
35 3 0.04
36 2 0.02
37 3 0.04
38 5 0.06
39 47 0.57
40 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.47, T:0.03
Consensus pattern (37 bp):
GAAAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAAGG
Found at i:154245 original size:27 final size:27
Alignment explanation
Indices: 154215--154328 Score: 102
Period size: 27 Copynumber: 4.5 Consensus size: 27
154205 AAAGGGACAG
*
154215 AGAAAGGAGAGATAGGGATAAGGAGAA
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
*
154242 AGAAA-G-G-GATAGGGAT-AGG-G--
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
* *
154262 AG--AGGAGAGAGAGGGAAAAGGAGAG
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
* *
154287 AGAAAGGAGGGAGAGGGAGAAGGAGAA
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
154314 AGAAAGGGAGAGAGA
1 AGAAA-GGAGAGAGA
154329 AAGAAGAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 3 0.04
21 7 0.10
22 4 0.06
23 4 0.06
24 9 0.13
25 3 0.04
26 1 0.01
27 30 0.42
28 8 0.11
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.04
Consensus pattern (27 bp):
AGAAAGGAGAGAGAGGGATAAGGAGAA
Found at i:154284 original size:21 final size:22
Alignment explanation
Indices: 154260--154315 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
154250 ATAGGGATAG
*
154260 GGAGAGGAGAGA-GAGGGAAAA
1 GGAGAGGAGAAAGGAGGGAAAA
* *
154281 GGAGA-GAGAAAGGAGGGAGAG
1 GGAGAGGAGAAAGGAGGGAAAA
154302 GGAGAAGGAGAAAG
1 GGAG-AGGAGAAAG
154316 AAAGGGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.17
21 16 0.55
22 1 0.03
23 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (22 bp):
GGAGAGGAGAAAGGAGGGAAAA
Found at i:166200 original size:2 final size:2
Alignment explanation
Indices: 166193--166222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
166183 AATTATGTTC
166193 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
166223 CATTTTAATA
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):
AT
Found at i:167946 original size:2 final size:2
Alignment explanation
Indices: 167941--167976 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
167931 TGTGTGTGTG
167941 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
167977 ACCAAACTAC
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):
TA
Found at i:176672 original size:17 final size:17
Alignment explanation
Indices: 176645--176680 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
176635 TATTTATGTG
176645 TATTATTATTTATATCTA
1 TATTATTATTTATAT-TA
176663 TATT-TTATTTATATTA
1 TATTATTATTTATATTA
176679 TA
1 TA
176681 GCGTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATTTATATTA
Found at i:185898 original size:30 final size:30
Alignment explanation
Indices: 185853--185993 Score: 201
Period size: 30 Copynumber: 4.7 Consensus size: 30
185843 CGGGGAAACG
* * * *
185853 CAAATCTCCGGTGGATTAGCGATTGCTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
*
185883 CAAATCGCCGATGGATTAGACATTGGTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
*
185913 CAAATCGCCGAGGGATTAGCCATTGGTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
*
185943 CAAATCGCCGAGGGATTAGCCATTGGTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
* *
185973 CAAATCGCAGGTGGATTAGCC
1 CAAATCGCCGATGGATTAGCC
185994 GGTGAAACGC
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 101 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (30 bp):
CAAATCGCCGATGGATTAGCCATTGGTGAC
Found at i:186071 original size:15 final size:15
Alignment explanation
Indices: 186051--186110 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
186041 GGCTAGCTCA
186051 GCAGAAGAACCACCG
1 GCAGAAGAACCACCG
* *
186066 GAAGAAGAACCAACG
1 GCAGAAGAACCACCG
*
186081 TCAGAAGAACCACCG
1 GCAGAAGAACCACCG
186096 GCAGAAGAACCACCG
1 GCAGAAGAACCACCG
186111 TGATCATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.43, C:0.30, G:0.25, T:0.02
Consensus pattern (15 bp):
GCAGAAGAACCACCG
Found at i:192864 original size:137 final size:137
Alignment explanation
Indices: 192618--192896 Score: 558
Period size: 137 Copynumber: 2.0 Consensus size: 137
192608 AAGTTTAAAC
192618 CATTTAAATTATGATTTACCTTTTTTCCCCTTGTTAGGAACTTTGTTTTCCCACCCTACATATTT
1 CATTTAAATTATGATTTACCTTTTTTCCCCTTGTTAGGAACTTTGTTTTCCCACCCTACATATTT
192683 CTTCGGATAATGTTGTATCGCTTTGTCAAAATTTTTTGTTTGTCATATTTTGGTGGTAGTGCAGA
66 CTTCGGATAATGTTGTATCGCTTTGTCAAAATTTTTTGTTTGTCATATTTTGGTGGTAGTGCAGA
192748 AGAGGTT
131 AGAGGTT
192755 CATTTAAATTATGATTTACCTTTTTTCCCCTTGTTAGGAACTTTGTTTTCCCACCCTACATATTT
1 CATTTAAATTATGATTTACCTTTTTTCCCCTTGTTAGGAACTTTGTTTTCCCACCCTACATATTT
192820 CTTCGGATAATGTTGTATCGCTTTGTCAAAATTTTTTGTTTGTCATATTTTGGTGGTAGTGCAGA
66 CTTCGGATAATGTTGTATCGCTTTGTCAAAATTTTTTGTTTGTCATATTTTGGTGGTAGTGCAGA
192885 AGAGGTT
131 AGAGGTT
192892 CATTT
1 CATTT
192897 CTTAAGATAT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 142 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (137 bp):
CATTTAAATTATGATTTACCTTTTTTCCCCTTGTTAGGAACTTTGTTTTCCCACCCTACATATTT
CTTCGGATAATGTTGTATCGCTTTGTCAAAATTTTTTGTTTGTCATATTTTGGTGGTAGTGCAGA
AGAGGTT
Found at i:203060 original size:19 final size:19
Alignment explanation
Indices: 203010--203061 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
203000 CCTAAGTTGC
203010 AAAAAAAAA--AAAAAAAA
1 AAAAAAAAAGGAAAAAAAA
**
203027 AAAAAAAAATTAAAAAAAA
1 AAAAAAAAAGGAAAAAAAA
*
203046 AAAAAAGAAGGAAAAA
1 AAAAAAAAAGGAAAAA
203062 TCAGAAGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 9 0.30
19 21 0.70
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAGGAAAAAAAA
Found at i:203061 original size:1 final size:1
Alignment explanation
Indices: 203010--203051 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
203000 CCTAAGTTGC
**
203010 AAAAAAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
203052 GAAGGAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:204933 original size:117 final size:117
Alignment explanation
Indices: 204727--204959 Score: 396
Period size: 117 Copynumber: 2.0 Consensus size: 117
204717 TGCCAAATCC
204727 CCGACGAGTAATCATATCCCTAATTAAAGATTAATAATAAAAAATGTTAATAAGGTATATGTTTG
1 CCGACGAGTAATCATATCCCTAATTAAAGATTAATAATAAAAAATGTTAATAAGGTATATGTTTG
* * *
204792 ATCATGTCTATAGGTACTTGTTAAGCTTATTCACGTGATTAATAAATGAAAT
66 ATCATGCCTATAGGTACCTGTTAAGCTTATTCACGCGATTAATAAATGAAAT
*
204844 CCGACGAGTAATCATATCTCTAATTAAAGATTAATAAT-AAAAATGTTAATAAGGTATATGTTTT
1 CCGACGAGTAATCATATCCCTAATTAAAGATTAATAATAAAAAATGTTAATAAGGTATATG-TTT
* *
204908 GATCGTGCCTATAGGTACCTGTTAAGCTTATTGACGCGATTAATAAATGAAA
65 GATCATGCCTATAGGTACCTGTTAAGCTTATTCACGCGATTAATAAATGAAA
204960 AATGGTAAGT
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 22 0.20
117 87 0.80
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (117 bp):
CCGACGAGTAATCATATCCCTAATTAAAGATTAATAATAAAAAATGTTAATAAGGTATATGTTTG
ATCATGCCTATAGGTACCTGTTAAGCTTATTCACGCGATTAATAAATGAAAT
Found at i:210101 original size:34 final size:36
Alignment explanation
Indices: 210040--210124 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 36
210030 TTGCCCCTAA
*
210040 TTTTTT-TGTTTTTTAATAAAAATAAAAAAATCAATT
1 TTTTTTCTGTTTTTT-ATAAAAATAAAAAAACCAATT
* *
210076 TTTTTTCTGTTTTTT-TCAAAA-AAAAAAACCCATT
1 TTTTTTCTGTTTTTTATAAAAATAAAAAAACCAATT
*
210110 TTGTTTCT-TTTTTTA
1 TTTTTTCTGTTTTTTA
210125 AAGAAGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 6 0.14
34 18 0.42
35 5 0.12
36 6 0.14
37 8 0.19
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (36 bp):
TTTTTTCTGTTTTTTATAAAAATAAAAAAACCAATT
Found at i:210712 original size:31 final size:31
Alignment explanation
Indices: 210670--210729 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
210660 ATGCAAATAG
*
210670 GTCCCTGAAGTGAACTTAAGTGAGCAATTGA
1 GTCCCTAAAGTGAACTTAAGTGAGCAATTGA
* * *
210701 GTCCCTAAAGTGGAGTTAATTGAGCAATT
1 GTCCCTAAAGTGAACTTAAGTGAGCAATT
210730 AGGCCCTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (31 bp):
GTCCCTAAAGTGAACTTAAGTGAGCAATTGA
Found at i:221032 original size:36 final size:36
Alignment explanation
Indices: 220985--221057 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
220975 TGCGAGTTAT
220985 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
1 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
221021 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
1 CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
221057 C
1 C
221058 ACTCCCACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
CTGAATTTGCATTTATCTGAAATCAGTCTACACTAG
Found at i:223185 original size:2 final size:2
Alignment explanation
Indices: 223180--223217 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
223170 ACACACACAG
223180 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
223218 TCCATCGAAT
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
Found at i:226893 original size:31 final size:30
Alignment explanation
Indices: 226822--226903 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
226812 TCTCGTTTTT
226822 AAAAGTTAAGGGGCTAATTTGTCCCGAAAA
1 AAAAGTTAAGGGGCTAATTTGTCCCGAAAA
226852 AAAAGTTAAGGGG-TCAATTTGTCCC-AAAA
1 AAAAGTTAAGGGGCT-AATTTGTCCCGAAAA
* *
226881 TGGATAGTTAAGGGGCTAATTTG
1 --AAAAGTTAAGGGGCTAATTTG
226904 GGTATTAAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 5 0.11
30 23 0.50
31 17 0.37
32 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.27
Consensus pattern (30 bp):
AAAAGTTAAGGGGCTAATTTGTCCCGAAAA
Found at i:227035 original size:27 final size:27
Alignment explanation
Indices: 227005--227155 Score: 167
Period size: 27 Copynumber: 5.5 Consensus size: 27
226995 TAGGTTCAAG
* *
227005 GTTATATCATATAGATTCAGGCCCAGC
1 GTTACATCATATAGATTTAGGCCCAGC
*
227032 GTTACATCATATAGATTTAGGACCAGC
1 GTTACATCATATAGATTTAGGCCCAGC
* * * *
227059 TTTACATCATCATATAGTCTTTGGTCCAGC
1 GTTACATCAT-ATAGA-T-TTAGGCCCAGC
* *
227089 GTTACATCATATAGACTTAGACCCAGC
1 GTTACATCATATAGATTTAGGCCCAGC
* *
227116 GTTACATCATATAAATTTAGGCCCAAC
1 GTTACATCATATAGATTTAGGCCCAGC
*
227143 ATTACATCATATA
1 GTTACATCATATA
227156 CATCATATAA
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
27 76 0.74
28 4 0.04
29 5 0.05
30 18 0.17
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (27 bp):
GTTACATCATATAGATTTAGGCCCAGC
Found at i:227165 original size:36 final size:36
Alignment explanation
Indices: 227118--227188 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
227108 GACCCAGCGT
*
227118 TACATCATATAAATTTAGGCCCAACATTACATCATA
1 TACATCATATAAATATAGGCCCAACATTACATCATA
*
227154 TACATCATATAAATATAGGCCCAACGTTACATCAT
1 TACATCATATAAATATAGGCCCAACATTACATCAT
227189 TAGTTGCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (36 bp):
TACATCATATAAATATAGGCCCAACATTACATCATA
Found at i:227340 original size:113 final size:110
Alignment explanation
Indices: 227185--227395 Score: 298
Period size: 113 Copynumber: 1.9 Consensus size: 110
227175 CAACGTTACA
* *
227185 TCATTAGTTGCATGTTCAGTAGGAGTCATCTGCATCATGTAGTTGCATATTCAATAAGGCATCAT
1 TCATTAGTTGCATATTCAGTAGGAGTCATCTGAATCATGTAGTTGCAT-TTCAATAAGGCATCAT
* * *
227250 GTAGCTCATATTCAGTAGG-GTCGTATAGTTGCATTTTCTCAGTAGGG
65 ATAGCTC--ATTCAGTAGGCATCATATAGTTGCATTTTCTCAGTAGGG
* * * *
227297 TCATATAGTTTCATATTCAGTAGGGGTCATCTGAATCATGTAGTTGCATTTCTATAGGGCATCAT
1 TCAT-TAGTTGCATATTCAGTAGGAGTCATCTGAATCATGTAGTTGCATTTCAATAAGGCATCAT
227362 ATAGCTCATTCAGTAGGCATCATATAGTTGCATT
65 ATAGCTCATTCAGTAGGCATCATATAGTTGCATT
227396 GAATTATATA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
110 10 0.11
111 14 0.16
112 24 0.27
113 40 0.45
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (110 bp):
TCATTAGTTGCATATTCAGTAGGAGTCATCTGAATCATGTAGTTGCATTTCAATAAGGCATCATA
TAGCTCATTCAGTAGGCATCATATAGTTGCATTTTCTCAGTAGGG
Found at i:228670 original size:655 final size:655
Alignment explanation
Indices: 227392--230001 Score: 3559
Period size: 655 Copynumber: 4.0 Consensus size: 655
227382 CATATAGTTG
*
227392 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGACAAT
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAAT
*
227457 TTTTGCAAAATTTTAGCCGAAATCATTTACTATCCATCACGATTTTTGGCTAAATTCGCGTTTC-
66 TTTTGCAAAATTTTAGCCGAAATC---TA-TA---A-CACGATTTTTGGCTAAATACGCGTTTCA
* * * * * *
227521 GGGGCCCGGCTCATTTTTTCATGA-TTTTTACGCCAAGACTTATTGAAATATCTACATTCATCTA
123 AGAGCCCGGCTCAGTTTTTCAAGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTA
* * * *
227585 ACCAAATTTCAGCCACATTGAATTTAAGAATTTATTTTTACGAGTATCTGAATCATATTTCGATT
188 ACCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATT
* *
227650 TTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATC
253 TTATTAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATA
*
227715 TTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGATATAATTTTTC
318 TTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGA-AAAATTTTTC
* * * * **
227780 AGGTCAATTTTTGCAAAATTTTAACCGAAATCA--TA-TA-CAATCA--A---AT--C-CGAAA-
382 GGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAAC
* * * *
227832 ---T-CA-TGCCCTGACTCATTTTTTCATGA-TTTTTACGCCAAGACTCATTGAAATATCTATAT
447 TGCTACAGGGCCCCGACTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATAT
* ** * * * ***** * *
227891 TCATTTAACCAAATCTCGGCCACGTTGGATTTCAGAATTTGTTTTTACGAGCATGTAAATCATAT
512 TCATCTAACCAAATCTCAACCACATTGGATTTAAAAAAAAAATTTTACCAGCATCTAAATCATAT
*
227956 TTCGATTTTAATAGAAATTAATTCAGTAAAAATA-GAAAAACGATATTGAAAGCGTGAAAAGCCT
577 TTCGATTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCT
228020 TTCAATCTTTTTGA
642 TTCAATCTTTTTGA
*
228034 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATTATTTTTCGGGTCAA
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTTCGGGTCAA
*
228098 TTTTTGCAAAATTTTAGCCGAAATC-ATAACACGATTTTTGGCTAAATACGCGTTTCAAGATCCC
65 TTTTTGCAAAATTTTAGCCGAAATCTATAACACGATTTTTGGCTAAATACGCGTTTCAAGAGCCC
* *
228162 GGCTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTGACCAAA
130 GGCTCAGTTTTTCAAGA-TTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAA
* * *
228227 TCTCAGTCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCTATTTTATTA
194 TCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATTTTATTA
* *
228292 GAAATTAATTCAGTAAAAATAGGAAAAACGGTATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTG
259 GAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTTTTG
* * * * *
228357 GCATTTAATTATATATTATTTACGAGTATTGGGTCCAAAAATTGATGAAAAACTTTTCGGGTCAA
324 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
228422 TTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGTGCTAC
389 TTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAAC-TGCTAC
*
228487 AGGGCCCCGACTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATCT
453 AGGGCCCCGACTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATCT
*
228552 AACCAAATCTCAACCACATTGGATTT-AAAAAAAAATTTTACCAGCATCTAAATCATATTTTGAT
518 AACCAAATCTCAACCACATTGGATTTAAAAAAAAAATTTTACCAGCATCTAAATCATATTTCGAT
228616 TTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAAT
583 TTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAAT
228681 CTTTTTGA
648 CTTTTTGA
*
228689 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATTATTTTTCGGGTCAA
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTTCGGGTCAA
* *
228753 TTTTTGCAAAATTTTAGCCGAAATC-ATAACACGATTTTTGGCTAAATACTCGTTTCAAGATCCC
65 TTTTTGCAAAATTTTAGCCGAAATCTATAACACGATTTTTGGCTAAATACGCGTTTCAAGAGCCC
* *
228817 GGCTCAGTTTTTCAAGATTTTTTTACGCCAACACTCATTGAAATATCTATATTCATCTGACCAAA
130 GGCTCAGTTTTTCAAGA-TTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAA
** * *
228882 TCTCAATCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCTATTTTATTA
194 TCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATTTTATTA
228947 GAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTTTTG
259 GAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTTTTG
*
229012 GCATTTAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
324 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
*
229077 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGCTAC
389 TTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAAC-TGCTAC
*
229142 -GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATC
453 AG-GGCCCCGACTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATC
* *
229206 TAACCAAATCTCAACCACATTGGATTTAAAAAAAAAAAATTTACCAGCATCTAAATCATATTTTG
517 TAACCAAATCTCAACCACATTGGATTT-AAAAAAAAAATTTTACCAGCATCTAAATCATATTTCG
229271 ATTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCA
581 ATTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCA
*
229336 ATCTTTTTGC
646 ATCTTTTTGA
*
229346 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAAT
*
229411 TTTTGCAAAATTTTAGCCGAAATAATGTACTATCCATCACGATTTTTGGCTAAA-ACCGCG-TTC
66 TTTTGCAAAATTTTAGCCG--A-AA--T-CTAT--AACACGATTTTTGGCTAAATA-CGCGTTTC
** * * * * * * *
229474 CGGGGCCCGGCTCAATTTTTTATGATTTTTTAGGGCAAGACTTC-TTGAAATATCTATATTTATC
122 AAGAGCCCGGCTCAGTTTTTCAAGATTTTTTACGCCAAGAC-TCATTGAAATATCTATATTCATC
* * * * *
229538 TAACCAAATTTCCGCCAGATTGAATATAA-AGATTTGTTTTTACGAGCATCTGAATCATATTTCG
186 TAACCAAATCTCAGCCACATTGAATTTAAGA-ATTTGTTTTTACGAGCATCTAAATCATATTTCG
* *
229602 ATTTTCA-TAGAATTTAATTCA-TAAAAAATAGGAAAAACAATATTGAAAGCGTGAAAAGCCTTT
250 ATTTT-ATTAGAAATTAATTCAGT-AAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTT
*
229665 CAATATTTTTGGCATTGGATTATATATTTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAT
313 CAATATTTTTGGCATTGAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAT
* *
229730 TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTTGCAA
377 TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTA
* * * ** * * * *
229795 AAAACTCGTTCCGGGGCCCCGGTTCAGTTTTTTCATAATTGTTTACGCGAAGGCTCCTTGAAATA
442 AAAACT-GCTACAGGGCCCCGACTCAG-TTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATA
* * * ** ** *** ** *
229860 TCTATATTTATCTAACCAAATTTCAGCCAGGTTGGATTT-AAGGATTTATTCTTACGGGCATCTG
505 TCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAAAAAAAAATT-TTACCAGCATCTA
** * * *
229924 AATCATATTTCGATTT-TCTCAGAATTTAATTCA-TAAAAA-ATGTAAAAACGATATTGGAAGCG
569 AATCATATTTCGATTTAAAT-AGAAATTAATTCAGTAAAAATA-GGAAAAACGATATTGAAAGCG
*
229986 TGAAAATCCTTTCAAT
632 TGAAAAGCCTTTCAAT
230002 AATTTTGGCA
Statistics
Matches: 1791, Mismatches: 127, Indels: 78
0.90 0.06 0.04
Matches are distributed among these distances:
633 26 0.01
634 19 0.01
635 39 0.02
636 208 0.12
637 4 0.00
638 3 0.00
639 5 0.00
641 5 0.00
642 82 0.05
644 1 0.00
646 1 0.00
647 3 0.00
652 1 0.00
653 2 0.00
654 76 0.04
655 633 0.35
657 186 0.10
658 4 0.00
659 1 0.00
660 2 0.00
662 1 0.00
663 4 0.00
664 214 0.12
665 182 0.10
666 89 0.05
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (655 bp):
CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAAT
TTTTGCAAAATTTTAGCCGAAATCTATAACACGATTTTTGGCTAAATACGCGTTTCAAGAGCCCG
GCTCAGTTTTTCAAGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
TCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATTTTATTAGA
AATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTTTTGGC
ATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAATT
TTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACTGCTACAGG
GCCCCGACTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATCTAAC
CAAATCTCAACCACATTGGATTTAAAAAAAAAATTTTACCAGCATCTAAATCATATTTCGATTTA
AATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCTT
TTTGA
Found at i:229328 original size:333 final size:332
Alignment explanation
Indices: 227391--230014 Score: 3410
Period size: 333 Copynumber: 8.0 Consensus size: 332
227381 TCATATAGTT
*
227391 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGACAA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
* ** *
227456 TTTTTGCAAAATTTTAGCCGAAATCATTTACTATCCATCACGATTTTTGGCTAAATTCGCGTTTC
66 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTTC
* * * *
227521 G-GGGCCCGGCTCATTTTTTCATGA-TTTTTACGCCAAGACTTATTGAAATATCTACATTCATCT
131 GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCT
* * * * * *
227584 AACCAAATTTCAGCCACATTGAATTTAAGAATTTATTTTTACGAGTATCTGAATCATATTTCGAT
196 AACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGAT
227649 TTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAAT
261 TTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAAT
227714 CTTTTTG
326 CTTTTTG
* *
227721 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGATATAATTTTTCAGGTCA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGA-AAAATTTTTCGGGTCA
* * * **
227786 ATTTTTGCAAAATTTTAACCGAAATCA--TA-TA-CAATCA--A---AT--C-CGAAA------T
65 ATTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTT
* * * * *
227833 C-ATGCCCTGACTCATTTTTTCATGA-TTTTTACGCCAAGACTCATTGAAATATCTATATTCATT
130 CGAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATC
* * * * *
227896 TAACCAAATCTCGGCCACGTTGGATTTCAGAATTTGTTTTTACGAGCATGTAAATCATATTTCGA
195 TAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGA
227961 TTTTAATAGAAATTAATTCAGTAAAAATA-GAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
260 TTTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
228025 TCTTTTTG
325 TCTTTTTG
* *
228033 ACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATTATTTTTCGGGTCA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTTCGGGTCA
* *
228097 ATTTTTGCAAAATTTTAGCCG-AA--ATC-A-TA---A-CACGATTTTTGGCTAAATACGCGTTT
65 ATTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTT
* ** * *
228153 CAAGATCCCGGCTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTATATTCAT
130 CGAGGCCCCGGCTCAGTTTTTCATGA-TTTTTTACGCCAAGACTCATTGAAATATCTATATTCAT
* * * *
228218 CTGACCAAATCTCAGTCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCT
194 CTAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCG
* *
228283 ATTTTATTAGAAATTAATTCAGTAAAAATAGGAAAAACGGTATTGAAAGCGTGAAAAGCCTTTCA
259 ATTTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCA
228348 ATCTTTTTG
324 ATCTTTTTG
* * * * *
228357 GCATTTAATTATATATTATTTACGAGTATTGGGTCCAAAAATTGATGAAAAACTTTTCGGGTCAA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
* * *
228422 TTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGTGCTAC
66 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTTC
* * *
228487 -AGGGCCCCGACTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATC
131 GA-GGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATC
* **** * *
228551 TAACCAAATCTCAACCACATTGGATTTAAAAA-AAAATTTTACCAGCATCTAAATCATATTTTGA
195 TAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGA
*
228615 TTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
260 TTTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
228680 TCTTTTTG
325 TCTTTTTG
* *
228688 ACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATTATTTTTCGGGTCA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTTCGGGTCA
*
228752 ATTTTTGCAAAATTTTAGCCG-AA--ATC-A-TA---A-CACGATTTTTGGCTAAATAC-TCGTT
65 ATTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGT-GTT
* ** * *
228807 TCAAGATCCCGGCTCAGTTTTTCAAGATTTTTTTACGCCAACACTCATTGAAATATCTATATTCA
129 TCGAGGCCCCGGCTCAGTTTTTCATGA-TTTTTTACGCCAAGACTCATTGAAATATCTATATTCA
* ** *
228872 TCTGACCAAATCTCAATCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTC
193 TCTAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTC
* *
228937 TATTTTATTAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTC
258 GATTTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTC
*
229002 AATATTTTTG
323 AATCTTTTTG
*
229012 GCATTTAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
* *
229077 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGCTAC
66 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTTC
*
229142 GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATCT
131 GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCT
* ****** * *
229207 AACCAAATCTCAACCACATTGGATTTAAAAAAAAAAAATTTACCAGCATCTAAATCATATTTTGA
196 AACCAAATCTCAGCCACATTGGATTT-AAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGA
*
229272 TTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
260 TTTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAA
229337 TCTTTTTG
325 TCTTTTTG
* *
229345 CCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAA
1 GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
* * * * *
229410 TTTTTGCAAAATTTTAGCCGAAATAATGTACTATCCATCACGATTTTTGGCTAAAACCGCGTTCC
66 TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTTC
* * * * * *
229475 G-GGGCCCGGCTCAATTTTTTATGATTTTTTAGGGCAAGACTTC-TTGAAATATCTATATTTATC
131 GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGAC-TCATTGAAATATCTATATTCATC
* * * * * * *
229538 TAACCAAATTTCCGCCAGATTGAATATAAAGATTTGTTTTTACGAGCATCTGAATCATATTTCGA
195 TAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGA
* * *
229603 TTTTCATAGAATTTAATTCA-TAAAAAATAGGAAAAACAATATTGAAAGCGTGAAAAGCCTTTCA
260 TTTTAATAGAAATTAATTCAGT-AAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCA
*
229667 ATATTTTTG
324 ATCTTTTTG
*
229676 GCATTGGATTATATATTTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCA
1 GCATTGAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCA
* * *
229741 ATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTTGCAAAAAAC-TCGTT
65 ATTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGT-GTT
* * * * * * * * *
229805 CCGGGGCCCCGGTTCAGTTTTTTCATAATTGTTTACGCGAAGGCTCCTTGAAATATCTATATTTA
129 TCGAGGCCCCGGCTCAG-TTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCA
* ** ** * * * *
229870 TCTAACCAAATTTCAGCCAGGTTGGATTTAAGGATTTATTCTTACGGGCATCTGAATCATATTTC
193 TCTAACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTC
* * * * *
229935 GATTTT-CTCAGAATTTAATTCA-TAAAAA-ATGTAAAAACGATATTGGAAGCGTGAAAATCCTT
258 GATTTTAAT-AGAAATTAATTCAGTAAAAATA-GGAAAAACGATATTGAAAGCGTGAAAAGCCTT
**
229997 TCAATAATTTTG
321 TCAATCTTTTTG
230009 GCATTG
1 GCATTG
Statistics
Matches: 2024, Mismatches: 210, Indels: 117
0.86 0.09 0.05
Matches are distributed among these distances:
306 2 0.00
307 1 0.00
308 2 0.00
309 3 0.00
310 3 0.00
311 35 0.02
312 87 0.04
313 142 0.07
314 2 0.00
319 1 0.00
320 3 0.00
321 17 0.01
322 41 0.02
323 191 0.09
324 288 0.14
325 13 0.01
326 2 0.00
327 11 0.01
328 6 0.00
329 6 0.00
330 55 0.03
331 315 0.16
332 315 0.16
333 368 0.18
334 115 0.06
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (332 bp):
GCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGTCAA
TTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAACGTGTTTC
GAGGCCCCGGCTCAGTTTTTCATGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCT
AACCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTAAATCATATTTCGAT
TTTAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAAT
CTTTTTG
Found at i:229369 original size:988 final size:974
Alignment explanation
Indices: 227392--230014 Score: 3607
Period size: 988 Copynumber: 2.7 Consensus size: 974
227382 CATATAGTTG
* *
227392 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAATTTTTCGGGACAAT
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
* **
227457 TTTTGCAAAATTTTAGCCGAAATCATTTACTATCCATCACGATTTTTGGCTAAATTCGCGTTTCG
66 TTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGCG-TTCG
* * *
227522 GGGCCCGGCTCATTTTTTCATGA-TTTTTACGCCAAGACTTATTGAAATATCTACATTCATCTAA
130 GGGCCCGGCTCAATTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATATCTATATTCATCTAA
*
227586 CCAAATTTCAGCCACATTGAATTTAAGAATTTATTTTTACGAGTATCTGAATCATATTTCGATTT
195 CCAAATTTCAGCCACATTGAATTTAA-AATTTATTTTTACGAGCATCTGAATCATATTTCGATTT
227651 TAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCT
259 TAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCT
* *
227716 TTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGATATAATTTTTCA
324 TTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAATAATTTTTCG
* * ** *
227781 GGTCAATTTTTGCAAAATTTTAACCGAAATCATATACA--A----T-CAAAT-C-CGAAATCATG
389 GGTCAATTTTTGCAAAATTTTAGCCGAAATCATACACACGATTTTTGCAAATACTCG-TTTCAAG
* * * *
227837 CCCTGACTCATTTTTTCATGA-TTTTTACGCCAAGACTCATTGAAATATCTATATTCATTTAACC
453 CCC-GGCTCAGTTTTTCAAGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACC
* * *
227901 AAATCTCGGCCACGTTGGATTTCAGAATTTGTTTTTACGAGCATGTAAATCATATTTCGATTTTA
517 AAATCTCAGCCACGTTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATTTTA
* *
227966 ATAGAAATTAATTCAGTAAAAATA-GAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTT
582 TTAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTT
* *
228030 TTGACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGAAATTATTTTTCGGGT
647 TTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGAAATAATTTTTCGGGT
* * * *
228095 CAATTTTTGCAAAATTTTAGCCGAAATCATAACACGATTTTTGGCTAAATACGCGTTTCAAGATC
712 CAATTTTTGCAAAATTTTAGCCGAAATCATAACACGATTTTTGGCTAAAAACGCGCTACAAGACC
*
228160 CCGGCTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTGACCA
777 CCGGCTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCA
** * ****** * * *
228225 AATCTCAGTCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCTATTTTAT
842 AATCTCAACCACATTGGATTTAAAAAAAAAAATTTACCAGCATCTAAATCATATTTCTATTTAAA
*
228290 TAGAAATTAATTCAGTAAAAATAGGAAAAACGGTATTGAAAGCGTGAAAAGCCTTTCAATCTTTT
907 TAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTT
*
228355 TGG
972 TGC
* * * * *
228358 CATTTAATTATATATTATTTACGAGTATTGGGTCCAAAAATTGATGAAAAACTTTTCGGGTCAAT
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
* *
228423 TTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGTGCTACA
66 TTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGCG-TTC-
* * * * *
228488 GGGCCCCGACTTAGTTTTTCATGATTTTTTACGCCAAGACTCCTTGAAATATCTATATTCATCTA
129 GGGGCCCGGCTCAATTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATATCTATATTCATCTA
* * * *** * * * *
228553 ACCAAATCTCAACCACATTGGATTTAAAAAAAAATTTTACCAGCATCTAAATCATATTTTGATTT
194 ACCAAATTTCAGCCACATTGAATTTAAAATTTATTTTTACGAGCATCTGAATCATATTTCGATTT
*
228618 AAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCT
259 TAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCT
* *
228683 TTTTGACATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATTATTTTTCG
324 TTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAATAATTTTTCG
228747 GGTCAATTTTTGCAAAATTTTAGCCGAAATCATA-ACACGATTTTTGGCTAAATACTCGTTTCAA
389 GGTCAATTTTTGCAAAATTTTAGCCGAAATCATACACACGATTTTT-GC-AAATACTCGTTTCAA
* *
228811 GATCCCGGCTCAGTTTTTCAAGATTTTTTTACGCCAACACTCATTGAAATATCTATATTCATCTG
452 G--CCCGGCTCAGTTTTTCAAGA-TTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTA
** * *
228876 ACCAAATCTCAATCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCTATT
514 ACCAAATCTCAGCCACGTTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATT
228941 TTATTAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATA
579 TTATTAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATA
*
229006 TTTTTGGCATTTAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTTC
644 TTTTTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGA-GAAATAATTTTTC
229070 GGGTCAATTTTTGCAAAATTTTAGCCGAAATCATCTACTATCCATCACGATTTTTGGCTAAAAAC
708 GGGTCAATTTTTGCAAAATTTTAGCCG-AA--ATC-A-TA---A-CACGATTTTTGGCTAAAAAC
* * * * * *
229135 GTGCTACGAGGCCCCGGCTCAGTTTTTCATGA-TTTTTTACGCCAAGACTCCTTGAAATATCTAT
764 GCGCTACAAGACCCCGGCTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTAT
229199 ATTCATCTAACCAAATCTCAACCACATTGGATTTAAAAAAAAAAAATTTACCAGCATCTAAATCA
829 ATTCATCTAACCAAATCTCAACCACATTGGATTT-AAAAAAAAAAATTTACCAGCATCTAAATCA
229264 TATTT-TGATTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
893 TATTTCT-ATTTAAATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
229328 GCCTTTCAATCTTTTTGC
957 GCCTTTCAATCTTTTTGC
229346 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
1 CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
* *
229411 TTTTGCAAAATTTTAGCCGAAATAATGTACTATCCATCACGATTTTTGGCTAAAACCGCGTTCCG
66 TTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGCGTT-CG
* * * *
229476 GGGCCCGGCTCAATTTTTTATGATTTTTTAGGGCAAGACTTCTTGAAATATCTATATTTATCTAA
130 GGGCCCGGCTCAATTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATATCTATATTCATCTAA
* * * *
229541 CCAAATTTCCGCCAGATTGAATATAAAGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTT
195 CCAAATTTCAGCCACATTGAATTTAAA-ATTTATTTTTACGAGCATCTGAATCATATTTCGATTT
* * * *
229606 TCATAGAATTTAATTCA-TAAAAAATAGGAAAAACAATATTGAAAGCGTGAAAAGCCTTTCAATA
259 TAATAGAAATTAATTCAGT-AAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATC
*
229670 TTTTTGGCATTGGATTATATATTTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAA-AATTTTT
323 TTTTTGGCATTGAATTATATA-TTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAATAATTTTT
*
229734 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTTGCAAAAAA
387 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATC----A-TA--CA-CACGA-TTTTTGC-AAATA
* ** * * * * *
229799 CTCGTTCCGGGGCCCCGGTTCAGTTTTTTCATA-ATTGTTTACGCGAAGGCTCCTTGAAATATCT
442 CTCGTTTC-AAG-CCCGGCTCAG-TTTTTCA-AGATTTTTTACGCCAAGACTCATTGAAATATCT
* * * * * * * *
229863 ATATTTATCTAACCAAATTTCAGCCAGGTTGGATTTAAGGATTTATTCTTACGGGCATCTGAATC
503 ATATTCATCTAACCAAATCTCAGCCACGTTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATC
* * * * *
229928 ATATTTCGATTTTCTCAGAATTTAATTCA-TAAAAA-ATGTAAAAACGATATTGGAAGCGTGAAA
568 ATATTTCGATTTTATTAGAAATTAATTCAGTAAAAATA-GGAAAAACGATATTGAAAGCGTGAAA
* *
229991 ATCCTTTCAATAATTTTGGCATTG
632 AGCCTTTCAATATTTTTGGCATTG
Statistics
Matches: 1453, Mismatches: 155, Indels: 67
0.87 0.09 0.04
Matches are distributed among these distances:
965 3 0.00
966 161 0.11
967 164 0.11
968 61 0.04
971 1 0.00
973 1 0.00
974 4 0.00
975 5 0.00
976 16 0.01
977 3 0.00
978 121 0.08
979 119 0.08
980 6 0.00
982 3 0.00
983 1 0.00
984 2 0.00
987 144 0.10
988 364 0.25
989 69 0.05
990 4 0.00
993 1 0.00
994 2 0.00
996 1 0.00
997 52 0.04
998 130 0.09
999 14 0.01
1000 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (974 bp):
CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAAAAATTTTCGGGTCAAT
TTTTGCAAAATTTTAGCCGAAATCATGTACTATCCATCACGATTTTTGGCTAAAAACGCGTTCGG
GGCCCGGCTCAATTTTTCATGATTTTTTACGCCAAGACTTCTTGAAATATCTATATTCATCTAAC
CAAATTTCAGCCACATTGAATTTAAAATTTATTTTTACGAGCATCTGAATCATATTTCGATTTTA
ATAGAAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTT
TTGGCATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGGAAATAATTTTTCGGG
TCAATTTTTGCAAAATTTTAGCCGAAATCATACACACGATTTTTGCAAATACTCGTTTCAAGCCC
GGCTCAGTTTTTCAAGATTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
CTCAGCCACGTTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCATATTTCGATTTTATTAG
AAATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATATTTTTGG
CATTGAATTATATATTTTTTACGAGTATTGTGTCCAAAAATTGAGAAATAATTTTTCGGGTCAAT
TTTTGCAAAATTTTAGCCGAAATCATAACACGATTTTTGGCTAAAAACGCGCTACAAGACCCCGG
CTCAGTTTCTCAAGATTTTTTTACGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATC
TCAACCACATTGGATTTAAAAAAAAAAATTTACCAGCATCTAAATCATATTTCTATTTAAATAGA
AATTAATTCAGTAAAAATAGGAAAAACGATATTGAAAGCGTGAAAAGCCTTTCAATCTTTTTGC
Done.