Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011096.1 Corchorus capsularis cultivar CVL-1 contig11117, 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: 52905
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4781 original size:109 final size:109
Alignment explanation
Indices: 4585--4880 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
4575 ACTATTATAG
* * *
4585 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTA-AAA-ACT-TTATT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
4650 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
4699 TTTTATTCTACTAAAAACTTTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTTTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
4764 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* * **
4808 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTTTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
4872 TTTTTACCA
63 TTTTTACCA
4881 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 125 0.73
110 8 0.05
111 19 0.11
112 2 0.01
113 3 0.02
114 13 0.08
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTTTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:7718 original size:27 final size:27
Alignment explanation
Indices: 7676--7728 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
7666 GGATGCAAAG
7676 TGAAGAGGAACGGGCTGAGCGATTGCA
1 TGAAGAGGAACGGGCTGAGCGATTGCA
* *
7703 TGAAGAGGAGCTGGCTGAGCGATTGC
1 TGAAGAGGAACGGGCTGAGCGATTGC
7729 GTGGATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.42, T:0.17
Consensus pattern (27 bp):
TGAAGAGGAACGGGCTGAGCGATTGCA
Found at i:8104 original size:72 final size:72
Alignment explanation
Indices: 7971--8106 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 72
7961 CAATGAAAAA
* * * * * * * *
7971 GAATTTGAAGAAGAGCGCTCCAGATGGGATGAGGAAAGGGAAGATCTCTATTTGAAGCTGGATGA
1 GAATTTGAAGAAGAGCGCTCAAGATGGAATGAGGAAAAGGAAAATCTCAACTCGAAACTGGATGA
8036 ATTGGAT
66 ATTGGAT
8043 GAATTTGAAGAAGAGCGCCTCAAG-TGGAATGAGGAAAAGGAAAATCTCAACTCGAAACTGGATG
1 GAATTTGAAGAAGAGCG-CTCAAGATGGAATGAGGAAAAGGAAAATCTCAACTCGAAACTGGATG
8107 CTGCCACTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 50 0.91
73 5 0.09
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.21
Consensus pattern (72 bp):
GAATTTGAAGAAGAGCGCTCAAGATGGAATGAGGAAAAGGAAAATCTCAACTCGAAACTGGATGA
ATTGGAT
Found at i:8333 original size:168 final size:171
Alignment explanation
Indices: 7920--8363 Score: 481
Period size: 168 Copynumber: 2.6 Consensus size: 171
7910 ACTCCAAGCA
* *
7920 AAACTTGATGCTGCCAATAAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTTGAAGAAGA
1 AAACTGGATGCTGCCACTAAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTTGAAGAAGA
* * * *
7985 GCGCTCCAGATGGGATGAGGAAAGGGAAGATCTCTATTTGAAGCTGGATGAATTGGATGAATTTG
66 GCGCTCCAGATGGAACGAGGAAAGGGAAGATCTCTATTTGAA----GATG-ACTGGATGAATTCG
*
8050 AAGAAGAGCGCCTCAAGTGGAATGAGGAAAAGGAAAATCTCAACTCG
126 AACAAGAGCG-CTCAAGTGGAATGAGGAAAAGGAAAATCTCAACTCG
*
8097 AAACTGGATGCTGCCACTAAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTCGAAGAAGA
1 AAACTGGATGCTGCCACTAAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTTGAAGAAGA
* * *
8162 GCGCTGCAGTTGGAACGAGGAAAGGGAAGATTTCTATTT-AA-A-G-CTGGATGAATTCGAACAA
66 GCGCTCCAGATGGAACGAGGAAAGGGAAGATCTCTATTTGAAGATGACTGGATGAATTCGAACAA
* * * * * *
8223 GAGTG-TCACAGTTGGGATGAGGAAAGGGAAGATCTCCATTAC-
131 GAGCGCTCA-AG-TGGAATGAGGAAAAGGAAAATCTCAACT-CG
* * * * * * *
8265 AAGCTGGATGCTGCCACTAAAG-AGTTGGAGAATTACCAAGTCATTGAAAATGATTTTGCAGTAG
1 AAACTGGATGCTGCCACT-AAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTTGAAGAAG
* * * *
8329 AGCGCCTCAAG-TGGAATGAGGAAAAGGAAAATCTC
65 AGCG-CTCCAGATGGAACGAGGAAAGGGAAGATCTC
8364 CATTACAAGC
Statistics
Matches: 231, Mismatches: 31, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
166 3 0.01
167 2 0.01
168 118 0.51
169 8 0.03
170 1 0.00
171 1 0.00
176 2 0.01
177 96 0.42
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (171 bp):
AAACTGGATGCTGCCACTAAGCAGTTGGAGATTTACCAAGTCAATGAAAAAGAATTTGAAGAAGA
GCGCTCCAGATGGAACGAGGAAAGGGAAGATCTCTATTTGAAGATGACTGGATGAATTCGAACAA
GAGCGCTCAAGTGGAATGAGGAAAAGGAAAATCTCAACTCG
Found at i:8421 original size:105 final size:105
Alignment explanation
Indices: 8239--8596 Score: 646
Period size: 105 Copynumber: 3.4 Consensus size: 105
8229 CACAGTTGGG
* *
8239 ATGAGGAAAGGGAAGATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
1 ATGAGGAAAAGGAAAATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
8304 GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
66 GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
8344 ATGAGGAAAAGGAAAATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
1 ATGAGGAAAAGGAAAATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
8409 GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
66 GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
*
8449 ATGAGGAAAAGGAAAATCTCCATTCCAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
1 ATGAGGAAAAGGAAAATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
* *
8514 GTCATTGAAAATGATTTTGCAGCAGAGCGCCTAAAGTGGA
66 GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
*
8554 ATGAGGAAAAGGAAAATCTCCATT-CTAAACTGGATGCTGCCAC
1 ATGAGGAAAAGGAAAATCTCCATTAC-AAGCTGGATGCTGCCAC
8597 CGCTCTTTTG
Statistics
Matches: 246, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
104 1 0.00
105 245 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (105 bp):
ATGAGGAAAAGGAAAATCTCCATTACAAGCTGGATGCTGCCACTAAAGAGTTGGAGAATTACCAA
GTCATTGAAAATGATTTTGCAGTAGAGCGCCTCAAGTGGA
Found at i:22946 original size:11 final size:11
Alignment explanation
Indices: 22932--22969 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22922 ATTCATAACA
22932 AATTTATAATT
1 AATTTATAATT
22943 AATTTATAATT
1 AATTTATAATT
22954 -ATTTGATAATT
1 AATTT-ATAATT
*
22965 TATTT
1 AATTT
22970 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:23268 original size:17 final size:17
Alignment explanation
Indices: 23246--23278 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
23236 TGAATAGTTT
23246 TTGGTAGTTTTTTTAAA
1 TTGGTAGTTTTTTTAAA
23263 TTGGTAGTTTTTTTAA
1 TTGGTAGTTTTTTTAA
23279 TGATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (17 bp):
TTGGTAGTTTTTTTAAA
Found at i:29396 original size:14 final size:15
Alignment explanation
Indices: 29377--29406 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29367 ATACCTTCAC
29377 TTGCAGC-TTTGCTT
1 TTGCAGCGTTTGCTT
29391 TTGCAGCGTTTGCTT
1 TTGCAGCGTTTGCTT
29406 T
1 T
29407 GCCGAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.07, C:0.20, G:0.23, T:0.50
Consensus pattern (15 bp):
TTGCAGCGTTTGCTT
Found at i:29856 original size:21 final size:20
Alignment explanation
Indices: 29823--29863 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29813 TTAATCCGTC
* *
29823 AATCTCTCAATTTTACCCTT
1 AATCTATCAATTTGACCCTT
29843 AATCTATCTAATTTGACCCTT
1 AATCTATC-AATTTGACCCTT
29864 CTTCTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (20 bp):
AATCTATCAATTTGACCCTT
Found at i:32883 original size:10 final size:10
Alignment explanation
Indices: 32870--32898 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
32860 TAGGGAAAGA
32870 AAGGGGAGGG
1 AAGGGGAGGG
32880 AAGGGGAGGG
1 AAGGGGAGGG
32890 AAGGGGAGG
1 AAGGGGAGG
32899 CGGCTAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (10 bp):
AAGGGGAGGG
Found at i:34933 original size:31 final size:31
Alignment explanation
Indices: 34884--34948 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
34874 AAGCATTTTT
**
34884 TTTGTTTGTTGGTGCATCAAATCGGTAAACA
1 TTTGTTTGTTGGCACATCAAATCGGTAAACA
* * *
34915 TTTGTTTTTTGGCACATCAAATTGGTAAGCA
1 TTTGTTTGTTGGCACATCAAATCGGTAAACA
34946 TTT
1 TTT
34949 TTCTAGCAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (31 bp):
TTTGTTTGTTGGCACATCAAATCGGTAAACA
Found at i:35347 original size:13 final size:13
Alignment explanation
Indices: 35309--35352 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
35299 TAATAAATTT
35309 AAAAAGATTAAAA
1 AAAAAGATTAAAA
*** *
35322 AAAATCCTCAAAA
1 AAAAAGATTAAAA
35335 AAAAAGATTAAAA
1 AAAAAGATTAAAA
35348 AAAAA
1 AAAAA
35353 AGCCCAAATG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAGATTAAAA
Found at i:46479 original size:17 final size:17
Alignment explanation
Indices: 46459--46492 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46449 AATCTATATA
46459 TATATATATATACACAC
1 TATATATATATACACAC
46476 TATATATATATACACAC
1 TATATATATATACACAC
46493 ACACTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
TATATATATATACACAC
Found at i:46481 original size:15 final size:15
Alignment explanation
Indices: 46461--46490 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46451 TCTATATATA
46461 TATATATATACACAC
1 TATATATATACACAC
*
46476 TATATATATATACAC
1 TATATATATACACAC
46491 ACACACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (15 bp):
TATATATATACACAC
Found at i:46494 original size:21 final size:21
Alignment explanation
Indices: 46455--46502 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
46445 TATCAATCTA
* *
46455 TATATATATATATATACACAC
1 TATATATATATACACACACAC
46476 TATATATATATACACACACAC
1 TATATATATATACACACACAC
46497 TATATA
1 TATATA
46503 CTACTGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (21 bp):
TATATATATATACACACACAC
Found at i:46500 original size:17 final size:17
Alignment explanation
Indices: 46462--46502 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
46452 CTATATATAT
*
46462 ATATATATACACACTAT
1 ATATATATACACACTAC
46479 ATATATATACACAC-AC
1 ATATATATACACACTAC
46495 ACTATATA
1 A-TATATA
46503 CTACTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATACACACTAC
Found at i:46502 original size:19 final size:19
Alignment explanation
Indices: 46457--46494 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
46447 TCAATCTATA
*
46457 TATATATATATATACACAC
1 TATATATATATACACACAC
46476 TATATATATATACACACAC
1 TATATATATATACACACAC
46495 ACTATATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (19 bp):
TATATATATATACACACAC
Found at i:46646 original size:27 final size:26
Alignment explanation
Indices: 46590--46643 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
46580 TTATAATAAG
*
46590 TATTTTTTTAATCATTTAACTTTTTT
1 TATTTTTTTAATCATTCAACTTTTTT
*
46616 TATTTTTTTGAGATGATTCAACTTTTTT
1 TATTTTTTT-A-ATCATTCAACTTTTTT
46644 ATTAATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 1 0.04
28 14 0.58
ACGTcount: A:0.22, C:0.07, G:0.06, T:0.65
Consensus pattern (26 bp):
TATTTTTTTAATCATTCAACTTTTTT
Found at i:48492 original size:330 final size:331
Alignment explanation
Indices: 47166--49071 Score: 1812
Period size: 331 Copynumber: 5.7 Consensus size: 331
47156 AAATCTCAAA
* * * ** *
47166 CACATTGGATTTAAGAATTTGTTTTTACTAGCATCTGAATCTGGTTTCGATTTAATTAGAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
* * * * * * * * ** * * *
47231 ATTTAGGAAAAATAAGAAATACGATATAAAAAGCATGAAAAGCCCTATAA-TATTTTTGGAGTTG
66 ATTCAGAAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTA-CTTTGGCGTTA
* * *
47295 AATTATATAT-TTTTATGAGTAATTTTAGCCAAAAATTGAGGAGAAATATTTT-GTGTCATTTTT
130 AATTATATATATTTCATGAGT-ATTTTAGCCAAAAATGGAGGAAAAAT-TTTTCG-GTCATTTTT
* * * * * *
47358 TGCAAAATTTTAGCCGAAATCGTGTACTAACAAACCATCACGATTTTTAGC---CAA-G-G--AC
192 TGCAAAATTTTAGCCGAAATCATGTA-T---TAACCATCACGGTTTTTGGCTAAAAACGCGTTTC
* * * ** * * * *
47416 ----CCAC--CTCAATTATGCATGATTTTTTACTCCGAAACTACTTGAAATATCTATATTCAACT
253 GGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCT
* *
47475 AATCAAATCTCAGC
318 AATAAAATCTCTGC
* *
47489 CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
* * * * ** * * *
47554 ATT-TGGAAAAATAGGAAAAATGATATTGGAAA-CGT-AAAAACCCTTCAA-TATTTTTGGCATT
66 ATTCAGAAAAAATATGAAAAATGATA-TGAAAAGCGTGAAAAGTCCTCCAACTA-CTTTGGCGTT
* * * * * * * * *
47615 GAAA-CATATATTTTTTTATGATTATATTAGCCAAAAATTGA-GAAAATATCTTTTGGGTAACTT
129 -AAATTATATA-TATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAA-AT-TTTTCGGTCATTT
* * * * * * * *
47678 TTTACAAAATTTTAGCCAAAAT-AGTGTAATAATCATCACAGTTTGTGACTAAAAAAGCG-TTCT
190 TTTGCAAAATTTTAGCCGAAATCA-TGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-
* * * * * *
47741 GAGGCCCCGGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCCTTGAAATATCCATATTCACCT
253 GGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCT
* **
47806 AATCAAATCTCAAC
318 AATAAAATCTCTGC
* * * * * * * *
47820 TACATTGGATTTAAGAATTTGTTTTTATGAGCATCTGAATC-AATTTTGATTTAATTAAAAATTA
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
* * * *
47884 ATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAATCCTCCAA-TATTTTTGGTGTTA
66 ATTCAGAAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTA-CTTTGGCGTTA
* ** * ** *
47948 AATTATATATATGTT-ATGAGTATTTTATCCAAAAATTTATGAAAAAATTTTGGGGTCATCTTTT
130 AATTATATATAT-TTCATGAGTATTTTAGCCAAAAATGGA-GGAAAAATTTTTCGGTCATTTTTT
** * * * *
48012 GCAAAATTTTAGCTAAAATCGTGTACTACTACTAACCATTACGGTTTTTGGCTGAAAACACGTTT
193 GCAAAATTTTAGCCGAAATCATG---TA-T--TAACCATCACGGTTTTTGGCTAAAAACGCGTTT
* * **
48077 CGGGGCCTCGACTCAGTTTTGCATGATTTTTGGTGCCGAGTTTCCTTGAAATATCTATATTCATC
252 CGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
* *
48142 TAATAAAATAT-TATC
317 TAATAAAATCTCT-GC
** *
48157 CACATTCCATTTAAGGATTTGTTTTTACGAGCAT-TCGAATCTTATTTCGATTTAATTAGAAATT
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-AAATCTTATTTCGATTTAATTAGAAATT
* *
48221 GATTCAGAAAAAAATATCAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTT
65 GATTCAG-AAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTT
* * *
48286 AAATTATATATATTTCATGAGTATTTTAGCC-AAAATGGGGGAAATATTTTTCGGTCAGTTTTTG
129 AAATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAAATTTTTCGGTCATTTTTTG
*
48350 CAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTT-GCTAAAAACGTGTTTCGGGGCC
194 CAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCC
* * * * *
48414 TCGGTTTAGTTTTACATGATTTTTGGCCCCGAGACTCCTTGAAATATCCATATTCATCTAATAAA
259 TCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAA
*
48479 ATCGCTGC
324 ATCTCTGC
* *
48487 CACATTGGATTTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTG
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
* * *
48552 ATTCAGAAAAAATATGAAAAATGATATGAAAAGCGTCAAAAGTCCTCCAACCACTTTGGCATTAA
66 ATTCAGAAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTTAA
* * *
48617 CTTATATATATTTCAAGAGTATTTTAGCCAAAAATGGAGGAAAAATTTTTCCGGTCTTTTTTTTT
131 ATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAAATTTTT-CGGTC--ATTTTTT
* *
48682 GCAAAATTTTAGCCGAAATCGA-GTATTAACCATTACGGTTTTTGGCTAAATACGTC-TTTCGGG
193 GCAAAATTTTAGCCGAAATC-ATGTATTAACCATCACGGTTTTTGGCTAAAAACG-CGTTTCGGG
* * * *
48745 GCCTCGGTTCAGTTTTGCATGATTTTTGGCGTCAAGGCTCCTTGAAATATCTATATTCATCTAAT
256 GCCTCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAT
48810 AAAATCT-TAGC
321 AAAATCTCT-GC
* ** * * * *
48821 CACATTGCATTTCTGGATTTGTCTTAACGAGCATTTAAATCTTGTTTCGATTTAATTAGAAATTG
1 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
* *
48886 ATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACAACTTTTGGCGTT
66 ATTCAGAAAAAATATG-AAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTAC-TTTGGCGTT
* *
48951 AAATTATATATATATATATTTCATGAGTATATTAGCC-AAAATGGAGGAAAAATTTTTTGGTCAT
129 --A--A-AT-TATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAAATTTTTCGGTCAT
* * * ** *
49015 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCTTCACGAATTTTGGTTAAAAA
188 TTTTTGCAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAAA
49072 ATATAAAAAA
Statistics
Matches: 1323, Mismatches: 200, Indels: 105
0.81 0.12 0.06
Matches are distributed among these distances:
318 13 0.01
321 32 0.02
322 76 0.06
323 77 0.06
324 1 0.00
329 84 0.06
330 187 0.14
331 195 0.15
332 31 0.02
333 51 0.04
334 161 0.12
335 35 0.03
336 9 0.01
337 158 0.12
338 85 0.06
339 75 0.06
340 7 0.01
341 21 0.02
342 25 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (331 bp):
CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTG
ATTCAGAAAAAATATGAAAAATGATATGAAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTTAA
ATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAAATTTTTCGGTCATTTTTTGCA
AAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTC
GGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAAT
CTCTGC
Found at i:48541 original size:668 final size:662
Alignment explanation
Indices: 47453--49056 Score: 1899
Period size: 668 Copynumber: 2.4 Consensus size: 662
47443 TCCGAAACTA
* * * *
47453 CTTGAAATATCTATATTCAACTAATCAAATCTCAGCCACATTCGATTTAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTCCATTTAAGGATTTGTTTTTACG
* * * ** *
47518 AGCA-TCTAAATCTTATTTCGATTTAATTAGAAATTAATT-TGGAAAAATAGGAAAAATGATATT
66 AGCATTC-AAATCTTATTTCGATTTAATTAGAAATTGATTCAGAAAAAATATAAAAAACGATA-T
* ** * * * * * *
47581 GGAAA-CGT-AAAAACCCTTCAA-TATTTTTGGCATTGAAACA-TATAT-TTTTTTATGATTATA
129 GAAAAGCGTGAAAAGTCCTCCAACTA-CTTTGGCGTT-AAA-ATTATATATATTTCATGAGTATA
* * * * * *
47641 TTAGCCAAAAATTGAGAAAATATCTTTTGGGTAACTTTTTACAAAATTTTAGCCAAAAT-AGTGT
191 TTAGCC-AAAATGGAGGAAATAT-TTTTCGGTCACTTTTTGCAAAATTTTAGCCGAAATCA-TGT
* * *
47705 AATAATCATCACAGTTTGTGACTAAAAAAGCGTTCTGAGGCCCCGGCTCAGTTTTGCATGATTTT
253 AATAACCATCACGGTTTGTGACTAAAAAAGCGTTCTGAGGCCCCGGCTCAGTTTTACATGATTTT
* * * *
47770 TAGCGCCAAGACTCCTTGAAATATCCATATTCACCTAATCAAATCTCAACTACATTGGATTTAAG
318 TAGCCCCAAGACTCCTTGAAATATCCATATTCACCTAATAAAATCGCAACCACATTGGATTTAAG
* * *
47835 AATTTGTTTTTATGAGCATCTGAATCAATTTTGATTTAATTAAAAATTAATTCAGAAAAAATATG
383 AATTTGGTTTTACGAGCATCTAAATCAATTTTGATTTAATTAAAAATTAATTCAGAAAAAATATG
* * * * **
47900 AAAAATGATATTAAAAGCGTGAAAAATCCTCCAA-TATTTTTGGTGTTAAATTATATATATGTT-
448 AAAAATGATATGAAAAGCGTCAAAAATCCTCCAACCA-CTTTGGCATTAAATTATATATAT-TTC
* * ** * ** *
47963 ATGAGTATTTTATCCAAAAATTTATGAAAAAATTTTGGGGTC-ATCTTTTGCAAAATTTTAGCTA
511 AAGAGTATTTTAGCCAAAAATGGAGGAAAAAATTTTCCGGTCTATCTTTTGCAAAATTTTAGCCA
48027 AAATCGTGTACTACTACTAACCATTACGGTTTTTGGCTGAAAACACG-TTTCGGGGCCTCGACTC
576 AAATC--G-ACTA-T--TAACCATTACGGTTTTTGGCT--AAACACGCTTTCGGGGCCTCGACTC
* * **
48091 AGTTTTGCATGATTTTTGGTGCCGAGTTTC
633 AGTTTTGCATGATTTTTGGCGCCAAGGCTC
* *
48121 CTTGAAATATCTATATTCATCTAATAAAATATTATCCACATTCCATTTAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTCCATTTAAGGATTTGTTTTTACG
* *
48186 AGCATTCGAATCTTATTTCGATTTAATTAGAAATTGATTCAGAAAAAAATATCAAAAACGATATG
66 AGCATTCAAATCTTATTTCGATTTAATTAGAAATTGATTCAG-AAAAAATATAAAAAACGATATG
*
48251 AAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTT-AAATTATATATATTTCATGAGTATTTTAG
130 AAAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTTAAAATTATATATATTTCATGAGTATATTAG
* * *
48315 CCAAAATGGGGGAAATATTTTTCGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTATTAACC
195 CCAAAATGGAGGAAATATTTTTCGGTCACTTTTTGCAAAATTTTAGCCGAAATCATGTAATAACC
* * * * * * * *
48380 ATCACGGTTTTTG-CTAAAAACGTGTT-TCGGGGCCTCGGTTTAGTTTTACATGATTTTTGGCCC
260 ATCACGGTTTGTGACTAAAAAAGCGTTCT-GAGGCCCCGGCTCAGTTTTACATGATTTTTAGCCC
* * ** *
48443 CGAGACTCCTTGAAATATCCATATTCATCTAATAAAATCGCTGCCACATTGGATTTAAGGATTTG
324 CAAGACTCCTTGAAATATCCATATTCACCTAATAAAATCGCAACCACATTGGATTTAAGAATTTG
* * *
48508 GTTTTACGAGCATCTAAATC-TTGTTTCGATTTAATTAGAAATTGATTCAGAAAAAATATGAAAA
389 GTTTTACGAGCATCTAAATCAAT-TTT-GATTTAATTAAAAATTAATTCAGAAAAAATATGAAAA
* *
48572 ATGATATGAAAAGCGTCAAAAGTCCTCCAACCACTTTGGCATTAACTTATATATATTTCAAGAGT
452 ATGATATGAAAAGCGTCAAAAATCCTCCAACCACTTTGGCATTAAATTATATATATTTCAAGAGT
* * * *
48637 ATTTTAGCCAAAAATGGAGGAAAAATTTTTCCGGTCTTTTTTTTTGCAAAATTTTAGCCGAAATC
517 ATTTTAGCCAAAAATGGAGGAAAAAATTTTCCGGTC-TATCTTTTGCAAAATTTTAGCCAAAATC
* * **
48702 GAGTATTAACCATTACGGTTTTTGGCTAAATACGTCTTTCGGGGCCTCGGTTCAGTTTTGCATGA
581 GACTATTAACCATTACGGTTTTTGGCTAAACACG-CTTTCGGGGCCTCGACTCAGTTTTGCATGA
*
48767 TTTTTGGCGTCAAGGCTC
645 TTTTTGGCGCCAAGGCTC
* ** * *
48785 CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTCTGGATTTGTCTTAACG
1 CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTCCATTTAAGGATTTGTTTTTACG
* *
48850 AGCATTTAAATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAAATATGAAAAAACGATATG
66 AGCATTCAAATCTTATTTCGATTTAATTAGAAATTGATTCAGAAAAAATAT-AAAAAACGATATG
*
48915 AAAAGCGTGAAAAGTCCTCCAACAACTTTTGGCGTTAAATTATATATATATATATTTCATGAGTA
130 AAAAGCGTGAAAAGTCCTCCAACTAC-TTTGGCGTT-AA--A-AT-TATATATATTTCATGAGTA
* * * *
48980 TATTAGCCAAAATGGAGGAAAAATTTTTTGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTA
189 TATTAGCCAAAATGGAGGAAATATTTTTCGGTCACTTTTTGCAAAATTTTAGCCGAAATCATGTA
* *
49045 CTAACCTTCACG
254 ATAACCATCACG
49057 AATTTTGGTT
Statistics
Matches: 803, Mismatches: 107, Indels: 49
0.84 0.11 0.05
Matches are distributed among these distances:
662 6 0.01
663 9 0.01
664 195 0.24
665 9 0.01
666 3 0.00
667 122 0.15
668 259 0.32
669 31 0.04
670 61 0.08
671 106 0.13
672 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (662 bp):
CTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTCCATTTAAGGATTTGTTTTTACG
AGCATTCAAATCTTATTTCGATTTAATTAGAAATTGATTCAGAAAAAATATAAAAAACGATATGA
AAAGCGTGAAAAGTCCTCCAACTACTTTGGCGTTAAAATTATATATATTTCATGAGTATATTAGC
CAAAATGGAGGAAATATTTTTCGGTCACTTTTTGCAAAATTTTAGCCGAAATCATGTAATAACCA
TCACGGTTTGTGACTAAAAAAGCGTTCTGAGGCCCCGGCTCAGTTTTACATGATTTTTAGCCCCA
AGACTCCTTGAAATATCCATATTCACCTAATAAAATCGCAACCACATTGGATTTAAGAATTTGGT
TTTACGAGCATCTAAATCAATTTTGATTTAATTAAAAATTAATTCAGAAAAAATATGAAAAATGA
TATGAAAAGCGTCAAAAATCCTCCAACCACTTTGGCATTAAATTATATATATTTCAAGAGTATTT
TAGCCAAAAATGGAGGAAAAAATTTTCCGGTCTATCTTTTGCAAAATTTTAGCCAAAATCGACTA
TTAACCATTACGGTTTTTGGCTAAACACGCTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTG
GCGCCAAGGCTC
Found at i:50064 original size:333 final size:333
Alignment explanation
Indices: 49300--50194 Score: 855
Period size: 337 Copynumber: 2.7 Consensus size: 333
49290 ACTTCTTGGA
* *
49300 ATATCTATATTCATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
1 ATATCTATATTCATCTAACCAAATCTAAT-CACATTGCATTTAAGGATTTGTTTTTACGAGCATC
* * * * * *
49365 TAAATCTTGATTCGATTTAATTAGAAATTAATTCAGAAAAAT-ATGAAAAACGATATCAAAAGCG
65 TAAATCTTGTTTCGATTTAATTAGAAATTATTTGAAAAAAATAAT-AAAAACGATATTAGAAGCG
* * * * * * *
49429 TGAAAAGTCCTCCAATCTTATCGGAGTTGAATTAATATATATTTTCTGAGTATTTTAGG-TGAAA
129 TGAAAAGCCCTTCAATCTTTTTGGAGTTGAATT-ATATATTTTTTATGAGTA-TTTAGGCTAAAA
* * *
49493 ATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCGA
192 ATTGA-GAAAAATATTTCGGGTCAATTTTCGCAAAATATTAGCCGAAATCGTGTAC-TCAGTCGA
* * * *
49558 AATCGCGGTTTTTGACTAAAAATGCGTTCCAGGGCCCCGATTCAGTGTTCATTGATTTTTTGAGG
255 AATCGCGGTTTTTGACTAAAAACGCGTTCCAGGGACCCGATCCAGTGTTCATTGATTTTTTGACG
*
49623 CAGAACTCATTCAT
320 CAGAACTCATTAAT
* * ** * * *
49637 ATATTTATATTCATCTTACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATT
1 ATATCTATATTCATCTAACCAAATC-TAATCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
* * * *
49702 TGAATCATGTTACGATTTAATTAGAAATTACTTTGAAAAAAATAATAAAAACAATATTAGAAGCG
65 TAAATCTTGTTTCGATTTAATTAGAAATTA-TTTGAAAAAAATAATAAAAACGATATTAGAAGCG
* * * **
49767 CGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT-TCTTTTTATGAGTATTGGGGCTAAAAA
129 TGAAAAGCCCTTCAATCTTTTTGGAGTTGAATTATATAT-TTTTTATGAGTATTTAGGCTAAAAA
*
49831 TTGA-AAAAATATTTCGGGTCAATTTTCGCAAAAT-TTCAGCCGAAATCGTGTA-TCA-TC-ACG
193 TTGAGAAAAATATTTCGGGTCAATTTTCGCAAAATATT-AGCCGAAATCGTGTACTCAGTCGA-A
* ** * * *
49891 GTTTC-TTTTTTGGCTAAAAACGCGTTCCAGGGACCC-ATGCCAGT-TTTATTTGA-TTTTTGAC
256 ATCGCGGTTTTTGACTAAAAACGCGTTCCAGGGACCCGAT-CCAGTGTTCA-TTGATTTTTTGAC
* *
49952 TCTA-AGACTCCTTAAAAT
319 GC-AGA-ACTCATT--AAT
* * * * *
49970 ATATCTATATTCATCTAACCAAATCTAAATGACATTGTATTTAAGCATTT-TGATTTACGAGTAT
1 ATATCTATATTCATCTAACCAAATCT-AATCACATTGCATTTAAGGATTTGT-TTTTACGAGCAT
** ** * *
50034 CTAAATCTTGTTTCGATTTAATCCGAAATTAATTTGTAAATAAAATAGGAAAAATGATATTCGAA
64 CTAAATCTTGTTTCGATTTAATTAGAAATT-ATTTG-AAA-AAAATAATAAAAACGATATTAGAA
* * * * * **
50099 GTGTGAAAAAGGCTTTCAATTTTTTTGGAGTTGAATTATATATTTTTAATGAGTATTTTCGCTAA
126 GCGTG-AAAAGCCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTTATGAGTATTTAGGCTAA
* * *
50164 TAATTGACGAAAAATCTCTCGGGTCAATTTT
190 AAATTGA-GAAAAATATTTCGGGTCAATTTT
50195 TGAGTATTTT
Statistics
Matches: 453, Mismatches: 83, Indels: 43
0.78 0.14 0.07
Matches are distributed among these distances:
330 14 0.03
331 43 0.09
332 6 0.01
333 82 0.18
334 6 0.01
335 65 0.14
336 59 0.13
337 104 0.23
338 72 0.16
339 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (333 bp):
ATATCTATATTCATCTAACCAAATCTAATCACATTGCATTTAAGGATTTGTTTTTACGAGCATCT
AAATCTTGTTTCGATTTAATTAGAAATTATTTGAAAAAAATAATAAAAACGATATTAGAAGCGTG
AAAAGCCCTTCAATCTTTTTGGAGTTGAATTATATATTTTTTATGAGTATTTAGGCTAAAAATTG
AGAAAAATATTTCGGGTCAATTTTCGCAAAATATTAGCCGAAATCGTGTACTCAGTCGAAATCGC
GGTTTTTGACTAAAAACGCGTTCCAGGGACCCGATCCAGTGTTCATTGATTTTTTGACGCAGAAC
TCATTAAT
Found at i:51403 original size:335 final size:330
Alignment explanation
Indices: 50242--51808 Score: 1787
Period size: 328 Copynumber: 4.7 Consensus size: 330
50232 TCATGTCAGT
* ** * *
50242 TTTTAGCCGAAACCGTGTAATAACCATCACTATTTCTT-GCTAAAAACGTGTTTCGAGGCCTCGA
1 TTTTAGCCGAAATCGTGTAA-AACCATCACGGTTT-TTGGCTAAAAACGTGTTTCGGGGCCTCGG
* * * * *
50306 CTCTA-TTTTGCATGATTTCTGGCATA-C-AAACTCCTTGAAATATATATATTCATGTAACAAAA
64 CTC-AGTTTTGCATGATTTTTGG--TACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAA
*
50368 TCTCT-GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
126 TCT-TAGCCACATTGCATTTAAGGATTTG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * *
50432 AGAAATTGATTCAG-AAAAATATG-AAAAATGATATGAAAAGCGTCAAAAGTCCTCCAACCACTT
189 AGAAATTAATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTT
*
50495 TGGCATTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAAT-TTTTTCGGGT
254 TGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAATATTTTT--GGT
50559 CATTTTTTTGGCAAAA
317 CA-TTTTTT-GCAAAA
* * * *
50575 TTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAATACGTGTTTCAGGGCCTCGGT
1 TTTTAGCCGAAATCGTGTA-AAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGGC
* ** *
50640 TCAGTTTTGAATGATTTTTGACACCGAGACTCCTTGAAATATCTATATTCATATAATAAAATCTT
65 TCAGTTTTGCATGATTTTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTT
** * * *
50705 AGCCACATTGCATTTCTGGATTTGTCTTAACGAGCATTTAAATCTTGTTTCGATTTAATTAGAAA
130 AGCCACATTGCATTTAAGGATTTGT-TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* *
50770 TTGATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGTG
194 TTAATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGCG
* * **
50835 TTAAATCATATATATATTTCTTGAGTATTTTAGCC-AAAGTGGAGGAAAA-AAATTTGGTCATTT
259 TTAAAT--TATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAATATTTTTGGTCATTT
50898 TTTGCAAAA
322 TTTGCAAAA
*
50907 TTTTAGCCGAAATCGTGT---ACCATCACGGTTTTTCGCTAAAAACGTG-TTCTGGGGCCTCGGC
1 TTTTAGCCGAAATCGTGTAAAACCATCACGGTTTTTGGCTAAAAACGTGTTTC-GGGGCCTCGGC
* * * *
50968 TCAGTTTTGCATGATTTTCGGTACCCAGACTCCTTGAAAAATCTATATTCATCTAATGAAATCTT
65 TCAGTTTTGCATGATTTTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTT
** * * * *
51033 AGCCACATTGCATTTCTGGATTTGTCTTAACGAGCATTTAAAGCTTGTTTCGATTTAATTAGAAA
130 AGCCACATTGCATTTAAGGATTTGT-TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* *
51098 TTTATTCAGAAAAAATATGAAAAAACGATGTGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGCG
194 TTAATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGCG
* * *
51163 TTAAATTATTTATATATTTCATGAGTATTTTAGTCAAAAATGGACGAACAATTTTTTTGGTCATT
259 TTAAATTA--TATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAA-AATATTTTTGGTCATT
51228 TTTTGCAAAA
321 TTTTGCAAAA
51238 TTTTAGCCGAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGGC
1 TTTTAGCCGAAATCGTGTA-AAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGGC
* * *
51303 TCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATATTTATCTAATGAAATCTT
65 TCAGTTTTGCATGATTTTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTT
* * *
51368 AGCCGA-ATTGCATTTAAGGATTTGTTTCTACGAGCATCTGAATATTGTTTCAAATTAATTAGAA
130 AGCC-ACATTGCATTTAAGGATTTGTTT-TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * * ** *
51432 ATTAATTCAGAAAAAATATAAAAAAATGATATTAAAAGCATGAAAAGTCCT-CAAATATTTTTGG
193 ATTAATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCA-CTTTGG
* * * * * * * *
51496 CTTTAAATTATATATA-TT-ATGAGTATTGTGGCCAAAAATTGAGGAAAAAACTTTAGGTTCAAT
257 CGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAATATTTTTGG-TCATT
* *
51559 TTCTACAAAA
321 TTTTGCAAAA
* * * * ** * ** * ** *
51569 TTTTAGACGGAATCATGTACTAGTCTTCACGAATTTTGGTTAAAAACGCATTTCGGGGCAC-CGA
1 TTTTAGCCGAAATCGTGTA-AAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGC-CTCGG
* * * * * * * * *
51633 CTTACTTTCGCACGGATTTTATTGT--CGAGACTTCTTGAAATATCTATACTAATCTAATCAAAT
64 CTCAGTTTTGCA-TGATTTT-TGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAAT
* * *
51696 CTCATCCACATTGCATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAG
127 CTTAGCCACATTGCATTTAAGGATTTG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* **
51761 AAATTAATTCAG--AAAATATG-AAAAACGATATCAAATCCGTGAAAAGTC
191 AAATTAATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTC
51809 GAAATCAAAA
Statistics
Matches: 1077, Mismatches: 125, Indels: 69
0.85 0.10 0.05
Matches are distributed among these distances:
326 2 0.00
327 3 0.00
328 270 0.25
329 17 0.02
330 10 0.01
331 231 0.21
332 42 0.04
333 182 0.17
334 20 0.02
335 254 0.24
336 20 0.02
337 26 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
TTTTAGCCGAAATCGTGTAAAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGGCT
CAGTTTTGCATGATTTTTGGTACCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTA
GCCACATTGCATTTAAGGATTTGTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
AATTCAGAAAAAATATGAAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGCGTT
AAATTATATATATTTCATGAGTATTTTAGCCAAAAATGGAGGAAAATATTTTTGGTCATTTTTTG
CAAAA
Found at i:51804 original size:663 final size:659
Alignment explanation
Indices: 50280--51808 Score: 1858
Period size: 663 Copynumber: 2.3 Consensus size: 659
50270 ACTATTTCTT
* * * *
50280 GCTAAAAACGTGTT-TCGAGGCCTCGACTCTA-TTTTGCATGA-TTTCTGGCATA-CAAACTCCT
1 GCTAAAAACGTGTTCT-GGGGCCTCGACTC-ACTTTCGCAGGATTTTC-GG--TACCAGACTCCT
* * *
50341 TGAAATATATATATTCATGTAA-CAAAATCTC-TGCCACATTGGATTTAAGGATTTGTTTTTACG
61 TGAAATATCTATATTCATCTAATC-AAATCTCAT-CCACATTGCATTTAAGGATTTGTTTTTACG
* *
50404 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAATATGAAAAATGATATGAA
124 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATGAA
*
50469 AAGCGTCAAAAGTCCTCCAACCACTTTGGCATTAAATTATATATATTTCATGAGTATTTTAGCCA
189 AAGCGTGAAAAGTCCTCCAACCACTTTGGCATTAAATTATATATATTTCATGAGTATTTTAGCCA
* **
50534 AAAATGGAGGAAAATTTTTTCGGGTCATTTTTTTGGCAAAATTTTAGCCGAAATCGTGTATTAAC
254 AAAATGGACGAAAATTTTTTCGGGTCATTTTTTTGGCAAAATTTTAGCCGAAATCGTGTACAAAC
* *
50599 CATCACGGTTTTTGGCTAAATACGTGTTTCAGGGCCTCGGTTCAGTTTTGAATGATTTTTGACAC
319 CATCACGGTTTTTGGCTAAAAACGTGTTTCAGGGCCTCGGCTCAGTTTTGAATGATTTTTGACAC
**
50664 CGAGACTCCTTGAAATATCTATATTCATATAATAAAATCTTAGCCACATTGCATTTCTGGATTTG
384 CGAGACTCCTTGAAATATCTATATTCATATAATAAAATCTTAGCCACATTGCATTTAAGGATTTG
* * * * * *
50729 TCTTAACGAGCATTTAAATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAAATATGAAAAA
449 TCTTAACGAGCATCTAAATATTGTTTCAAATTAATTAGAAATTAATTCAGAAAAAATATAAAAAA
* * *
50794 ACGATATGAAAAGCGTGAAAAGTCCTCCAACCACTTTGGTGTTAAATCATATATATATTTCTTGA
514 ACGATATGAAAAGCATGAAAAGTCCTCCAAACACTTTGGTGTTAAAT-ATATATATATTTCATGA
* * * * * * *
50859 GTATTTTAGCCAAAGTGGAGGAAAAAAATTTGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG
578 GTATTGTAGCCAAAATGGAGGAAAAAAATTTGGTCAATTTCTACAAAATTTTAGACGAAATCATG
**
50924 TACCATCACGGTTTTTC
643 TACCATCACGAATTTTC
* * * *
50941 GCTAAAAACGTGTTCTGGGGCCTCGGCTCAGTTTTGCATGATTTTCGGTACCCAGACTCCTTGAA
1 GCTAAAAACGTGTTCTGGGGCCTCGACTCACTTTCGCAGGATTTTCGGTA-CCAGACTCCTTGAA
* * * * ** * * *
51006 AAATCTATATTCATCTAATGAAATCTTAGCCACATTGCATTTCTGGATTTGTCTTAACGAGCATT
65 ATATCTATATTCATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTACGAGCATC
* * * *
51071 TAAAGCTTGTTTCGATTTAATTAGAAATTTATTCAGAAAAAATATGAAAAAACGATGTGAAAAGC
130 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATG-AAAAACGATATGAAAAGC
* *
51136 GTGAAAAGTCCTCCAACCACTTTGGCGTTAAATTATTTATATATTTCATGAGTATTTTAGTCAAA
193 GTGAAAAGTCCTCCAACCACTTTGGCATTAAATTA--TATATATTTCATGAGTATTTTAGCCAAA
*
51201 AATGGACGAACAATTTTTT-TGGTCA-TTTTTT-GCAAAATTTTAGCCGAAATCGTGTACAAACC
256 AATGGACGAA-AATTTTTTCGGGTCATTTTTTTGGCAAAATTTTAGCCGAAATCGTGTACAAACC
* * ***
51263 ATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGGCTCAGTTTTGCATGATTTTTGGTGCC
320 ATCACGGTTTTTGGCTAAAAACGTGTTTCAGGGCCTCGGCTCAGTTTTGAATGATTTTTGACACC
* * *
51328 GAGACTCCTTGAAATATCTATATTTATCTAATGAAATCTTAGCCGA-ATTGCATTTAAGGATTTG
385 GAGACTCCTTGAAATATCTATATTCATATAATAAAATCTTAGCC-ACATTGCATTTAAGGATTTG
* *
51392 T-TTCTACGAGCATCTGAATATTGTTTCAAATTAATTAGAAATTAATTCAGAAAAAATATAAAAA
449 TCTT-AACGAGCATCTAAATATTGTTTCAAATTAATTAGAAATTAATTCAGAAAAAATATAAAAA
* * * *
51456 AATGATATTAAAAGCATGAAAAGTCCT-CAAATATTTTTGGCT-TTAAAT-TATATATA-TT-AT
513 AACGATATGAAAAGCATGAAAAGTCCTCCAAACA-CTTTGG-TGTTAAATATATATATATTTCAT
* * * *
51516 GAGTATTGTGGCCAAAAATTGAGGAAAAAACTTTAGGTTCAATTTCTACAAAATTTTAGACGGAA
576 GAGTATTGTAGCC-AAAATGGAGGAAAAAAATTT-GG-TCAATTTCTACAAAATTTTAGACGAAA
* *
51581 TCATGTACTAGTCTTCACGAATTTTG
638 TCATGTAC----CATCACGAATTTTC
* * ** * *
51607 GTTAAAAACGCAT-TTC-GGGGCAC-CGACTTACTTTCGCACGGATTTTATTGT-CGAGACTTCT
1 GCTAAAAACG--TGTTCTGGGGC-CTCGACTCACTTTCGCA-GGATTTT-CGGTACCAGACTCCT
* * *
51668 TGAAATATCTATACTAATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTATGAG
61 TGAAATATCTATATTCATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTACGAG
* *
51733 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAATATGAAAAACGATATCAAAT
126 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATGAAAA
*
51797 CCGTGAAAAGTC
191 GCGTGAAAAGTC
51809 GAAATCAAAA
Statistics
Matches: 742, Mismatches: 98, Indels: 54
0.83 0.11 0.06
Matches are distributed among these distances:
659 14 0.02
660 20 0.03
661 143 0.19
662 49 0.07
663 305 0.41
664 16 0.02
665 41 0.06
666 141 0.19
667 10 0.01
668 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (659 bp):
GCTAAAAACGTGTTCTGGGGCCTCGACTCACTTTCGCAGGATTTTCGGTACCAGACTCCTTGAAA
TATCTATATTCATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCT
GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATGAAAAGCGTG
AAAAGTCCTCCAACCACTTTGGCATTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATGG
ACGAAAATTTTTTCGGGTCATTTTTTTGGCAAAATTTTAGCCGAAATCGTGTACAAACCATCACG
GTTTTTGGCTAAAAACGTGTTTCAGGGCCTCGGCTCAGTTTTGAATGATTTTTGACACCGAGACT
CCTTGAAATATCTATATTCATATAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTCTTAAC
GAGCATCTAAATATTGTTTCAAATTAATTAGAAATTAATTCAGAAAAAATATAAAAAAACGATAT
GAAAAGCATGAAAAGTCCTCCAAACACTTTGGTGTTAAATATATATATATTTCATGAGTATTGTA
GCCAAAATGGAGGAAAAAAATTTGGTCAATTTCTACAAAATTTTAGACGAAATCATGTACCATCA
CGAATTTTC
Done.