Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005748.1 Corchorus capsularis cultivar CVL-1 contig05766, 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: 3824
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:120 original size:16 final size:16
Alignment explanation
Indices: 70--121 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
60 TCAGTAGGGC
70 TCATATAGTTGCATAT
1 TCATATAGTTGCATAT
* * *
86 TCA-GTAG-GGTCATAA
1 TCATATAGTTG-CATAT
101 TCATATAGTTGCATAT
1 TCATATAGTTGCATAT
117 TCATA
1 TCATA
122 GGGGCCATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.37
16 15 0.56
17 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (16 bp):
TCATATAGTTGCATAT
Found at i:351 original size:62 final size:57
Alignment explanation
Indices: 1--1462 Score: 963
Period size: 57 Copynumber: 25.6 Consensus size: 57
*
1 TAGGGCCATAGTCATATAGTTGCATATTCAGTAGGGGCCGTAATCATATAGTTGCATATTCAG
1 TAGGG-CATAATCATATAGTTGCATATTCAGTA-GGGCC---AT-ATATAGTTGCATATTCAG
*
64 TAGGGC----TCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCA-
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGG-C--CAT-ATATAGTTGCATATTCAG
120 TAGGGGC-----CATATAGTTGCATATTCAGTAGGGGCC--ATATAGTTGCATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTA-GGGCCATATATAGTTGCATATTCAG
172 TAGGGGC-----C--ATAGTTGCATATTCAGTAGGG-C-TCATATAGTTGCATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTAGGGCCAT-ATATAGTTGCATATTCAG
222 TAGGGGC-----CATATAGTTGCATATTCAGTAGGAG-C--ATATAGTTGCATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTAGG-GCCATATATAGTTGCATATTCAG
273 TATGGGC-----CATATAGTTGCATATTCAGTAGGGGCCATATAGT-GTTGCATATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTA-GGGCCATATA-TAGTTGC--ATATTCAG
*
329 TAGAGGCAGTAATAATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAG
1 TAG-GGCA-TAATCATATAGTTGCATATTCAGTAGGGCC---AT-ATATAGTTGCATATTCAG
* *
392 TAGTGGTCATAATCATATAGTTGCATATTCAGTATGG-C-TCATATAGTTGCATATTTAG
1 TAG-GG-CATAATCATATAGTTGCATATTCAGTAGGGCCAT-ATATAGTTGCATATTCAG
*
450 TAGGAGC----TCATATAGTTGCATATT-AGAGAGCGGCC--ATATAGTTGCATATTCAG
1 TAGG-GCATAATCATATAGTTGCATATTCAG-TAG-GGCCATATATAGTTGCATATTCAG
*
503 TAGGGC----TCATATAGTTGCATATTCAGTAGGGCCATGATCATATAGTAGCATATTCAG
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGGCC---AT-ATATAGTTGCATATTCAG
* * * *
560 TAGGGCCATAATCATATAGTTGCATATTCAATACGG-CTTATATAGTTGCATATTTAG
1 TAGGG-CATAATCATATAGTTGCATATTCAGTAGGGCCATATATAGTTGCATATTCAG
* *
617 TATGGCCATAATCATGTAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTAGGGCC---AT-ATATAGTTGCATATTCAG
* *
679 TAGGGCCGTAATCATATAGTTGCATATTCAGTAAGGCCATAATCATATAGTTGCATATTCAG
1 TAGGG-CATAATCATATAGTTGCATATTCAGTAGGGCC---AT-ATATAGTTGCATATTCAG
741 TAGGGC----TCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAG
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGGCC---AT-ATATAGTTGCATATTCAG
* * * *
798 TAGGGC----TCATATAGTTGCATATTCAGTAGGGTACACTCGTATAGTTGCATGTTCAA
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGG-CCA-T-ATATAGTTGCATATTCAG
* *
854 TAGGGC-TCACTCATATAGTTGCATGTTCAGTAGGGCTCACTCATATAGTTGCATATTCAG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGTAGGGC-CA-T-ATATAGTTGCATATTCAG
* *
914 TAGGGC-TCACTCATATAGTTGCATATTCAGTA-GGCC-TCATATAGTTGTATATTCAG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGTAGGGCCAT-ATATAGTTGCATATTCAG
* *
970 TAGGGC-TCACTCATATAGTTGCATATTCAGTAGGGCTCACTCATATAGTTGTATATTCAG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGTAGGGC-CA-T-ATATAGTTGCATATTCAG
* * *
1030 TAGGGC-TCACTCATATAGTTGCATATTCAGTAAGGG----ACATA--TGCAT-CTCAG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGT-AGGGCCATATATAGTTGCATATTCAG
* * **
1081 TAGAGC-TCACTCATATATAGTTGCATATTCAGTAGGG-C-TCACGTAGTTGCATATTCAG
1 TAGGGCAT-AATC--ATATAGTTGCATATTCAGTAGGGCCAT-ATATAGTTGCATATTCAG
1139 TATGGG----A-CATATAGTTGCATATTCAGTAGGGGCTCACTCATATAGTTGCATATTCAG
1 TA-GGGCATAATCATATAGTTGCATATTCAGTA-GGGC-CA-T-ATATAGTTGCATATTCAG
* * * * * *
1196 TAGGGC-TCACTCATATAGTTGCATATTCTGTA-GGCGACATATAGTTGCATGTTTAG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGTAGGGCCATATATAGTTGCATATTCAG
* * * *
1252 TAGGGC----TCATGTAGTTGCATGTTCTGTAGGG--ATCATATAGGTACTG-A-ACTCATG
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGGCCAT-ATATA-GT--TGCATATTCA-G
*
1306 TAGTTGCATGTTCAGTAGGGATCATATAGTTGCTTATTCAGTAGGGCTCACTCATATAGTTGCAT
1 TAG--G---G--CA-TA---ATCATATAGTTGCATATTCAGTAGGGC-CA-T-ATATAGTTGCAT
*
1371 GTTCAG
52 ATTCAG
*
1377 TAGGGC----TCATATAGTTGCATATTCAGTA-GGAC-TCATATAGTTGCATATTCAG
1 TAGGGCATAATCATATAGTTGCATATTCAGTAGGGCCAT-ATATAGTTGCATATTCAG
*
1429 TAGGGC-TCACTCATATAGTTGCATATTCAGTAGG
1 TAGGGCAT-AATCATATAGTTGCATATTCAGTAGG
1463 ACATATAGTA
Statistics
Matches: 1211, Mismatches: 71, Indels: 240
0.80 0.05 0.16
Matches are distributed among these distances:
48 1 0.00
49 3 0.00
50 44 0.04
51 83 0.07
52 132 0.11
53 71 0.06
54 21 0.02
55 13 0.01
56 180 0.15
57 209 0.17
58 61 0.05
59 9 0.01
60 126 0.10
61 35 0.03
62 122 0.10
63 44 0.04
64 6 0.00
65 8 0.01
66 1 0.00
69 22 0.02
70 2 0.00
71 5 0.00
72 6 0.00
73 7 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (57 bp):
TAGGGCATAATCATATAGTTGCATATTCAGTAGGGCCATATATAGTTGCATATTCAG
Found at i:352 original size:88 final size:85
Alignment explanation
Indices: 12--1478 Score: 1007
Period size: 88 Copynumber: 17.5 Consensus size: 85
2 AGGGCCATAG
12 TCATATAGTTGCATATTCAGTAGGGGCCGTAATCATATAGTTGCATATTCAGTA-GGG-C----T
1 TCATATAGTTGCATATTCAGTA-GGG-C---A-CATATAGTTGCATATTCAGTAGGGGCCATAAT
71 CATATAGTTGCATATTCAGTAGGGTCAT
60 CATATAGTTGCATATTCAGTAGGG-C-T
99 AATCATATAGTTGCATATTCA-TAGGGGC-CATATAGTTGCATATTCAGTAGGGG-C-----CAT
1 --TCATATAGTTGCATATTCAGTA-GGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCAT
156 ATAGTTGCATATTCAGTAGGGGC-
63 ATAGTTGCATATTCAGTA-GGGCT
*
179 -C--ATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGG-C-----CATATA
1 TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCATATA
235 GTTGCATATTCAGTAGGAG--
66 GTTGCATATTCAGTAGG-GCT
*
254 -CATATAGTTGCATATTCAGTATGGGC-CATATAGTTGCATATTCAGTAGGGGCCAT-AT-A-GT
1 TCATATAGTTGCATATTCAGTA-GGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCATAT
314 -GTTGCATATATTCAGTAGAGGCAGT
65 AGTTGC--ATATTCAGTAG-GGC--T
* * *
339 AATAATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGTGGTCATAA
1 --TCATATAGTTGCATATTCAGTAGGG-C---A-CATATAGTTGCATATTCAGTAGGGGCCATAA
*
404 TCATATAGTTGCATATTCAGTATGGC-
59 TCATATAGTTGCATATTCAGTAGGGCT
* *
430 TCATATAGTTGCATATTTAGTAGGAGCTCATATAGTTGCATATT-AG-AGAGCGG-C-----CAT
1 TCATATAGTTGCATATTCAGTAGG-GCACATATAGTTGCATATTCAGTAG-G-GGCCATAATCAT
487 ATAGTTGCATATTCAGTAGGGC-
63 ATAGTTGCATATTCAGTAGGGCT
*
509 TCATATAGTTGCATATTCAGTAGGGCCATGATCATATAGTAGCATATTCAGTA-GGGCCATAATC
1 TCATATAGTTGCATATTCAGTAGGG-C---A-CATATAGTTGCATATTCAGTAGGGGCCATAATC
* *
573 ATATAGTTGCATATTCAATACGGCT
61 ATATAGTTGCATATTCAGTAGGGCT
* * *
598 T-ATATAGTTGCATATTTAGTATGGCCATAATCATGTAGTTGCATATTCAGTA-GGGCCATAATC
1 TCATATAGTTGCATATTCAGTA-GGGC---A-CATATAGTTGCATATTCAGTAGGGGCCATAATC
661 ATATAGTTGCATATTCAGTAGGGCCGT
61 ATATAGTTGCATATTCAGTAGGG-C-T
*
688 AATCATATAGTTGCATATTCAGTAAGGCCATAATCATATAGTTGCATATTCAGTA-GGG-C----
1 --TCATATAGTTGCATATTCAGT-AGGGC---A-CATATAGTTGCATATTCAGTAGGGGCCATAA
747 TCATATAGTTGCATATTCAGTAGGGCCAT
59 TCATATAGTTGCATATTCAGTAGGG-C-T
* * * * *
776 AATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTA-GGG-TACACTCGTA
1 --TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCATA
* *
839 TAGTTGCATGTTCAATAGGGCT
64 TAGTTGCATATTCAGTAGGGCT
*
861 CACTCATATAGTTGCATGTTCAGTAGGGCTCACTCATATAGTTGCATATTCAGTA-GGG-C-TCA
1 ---TCATATAGTTGCATATTCAGTAGGG--CA--CATATAGTTGCATATTCAGTAGGGGCCAT-A
* *
923 CTCATATAGTTGCATATTCAGTA-GGCC
58 ATCATATAGTTGCATATTCAGTAGGGCT
* *
950 TCATATAGTTGTATATTCAGTAGGGCTCACTCATATAGTTGCATATTCAGTA-GGG-C-TCACTC
1 TCATATAGTTGCATATTCAGTAGGG--CA--CATATAGTTGCATATTCAGTAGGGGCCAT-AATC
*
1012 ATATAGTTGTATATTCAGTAGGGCT
61 ATATAGTTGCATATTCAGTAGGGCT
* * *
1037 CACTCATATAGTTGCATATTCAGTAAGGG-AC--ATA--TGCAT-CTCAGTA-GAGCTCACTCAT
1 ---TCATATAGTTGCATATTCAGT-AGGGCACATATAGTTGCATATTCAGTAGGGGC-CA-TAAT
1095 -ATATAGTTGCATATTCAGTAGGGC-
60 CATATAGTTGCATATTCAGTAGGGCT
** *
1119 TCACGTAGTTGCATATTCAGTATGGG-ACATATAGTTGCATATTCAGTAGGGG-C-TCACTCATA
1 TCATATAGTTGCATATTCAGTA-GGGCACATATAGTTGCATATTCAGTAGGGGCCAT-AATCATA
1181 TAGTTGCATATTCAGTAGGGCT
64 TAGTTGCATATTCAGTAGGGCT
* * *
1203 CACTCATATAGTTGCATATTCTGTA-GGCGACATATAGTTGCATGTTTAGTA-GGG-C----TCA
1 ---TCATATAGTTGCATATTCAGTAGGGC-ACATATAGTTGCATATTCAGTAGGGGCCATAATCA
* * * *
1261 TGTAGTTGCATGTTCTGTAGGG-A
62 TATAGTTGCATATTCAGTAGGGCT
** * * *
1284 TCATATAG--G--TA--C--T-GAACTCATGTAGTTGCATGTTCAGTA-GGG-----ATCATATA
1 TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCATATA
*
1334 GTTGCTTATTCAGTAGGGCT
66 GTTGCATATTCAGTAGGGCT
* * *
1354 CACTCATATAGTTGCATGTTCAGTAGGGCTCATATAGTTGCATATTCAGTA--GG----ACTCAT
1 ---TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCAT
1413 ATAGTTGCATATTCAGTAGGGCT
63 ATAGTTGCATATTCAGTAGGGCT
*
1436 CACTCATATAGTTGCATATTCAGTA-GG-ACATATAGTAGCATAT
1 ---TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATAT
1479 ATTGGTGGTG
Statistics
Matches: 1185, Mismatches: 86, Indels: 223
0.79 0.06 0.15
Matches are distributed among these distances:
69 43 0.04
70 2 0.00
72 1 0.00
73 8 0.01
74 2 0.00
75 23 0.02
76 51 0.04
77 45 0.04
78 15 0.01
79 78 0.07
80 15 0.01
81 30 0.03
82 146 0.12
83 104 0.09
84 15 0.01
85 25 0.02
86 110 0.09
87 72 0.06
88 178 0.15
89 49 0.04
90 67 0.06
91 4 0.00
92 2 0.00
93 77 0.06
94 6 0.01
95 11 0.01
96 1 0.00
97 5 0.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (85 bp):
TCATATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGGGCCATAATCATATA
GTTGCATATTCAGTAGGGCT
Found at i:402 original size:16 final size:15
Alignment explanation
Indices: 346--429 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 15
336 AGTAATAATA
*
346 TAGTTGCATATTCAG
1 TAGTGGCATATTCAG
* *
361 TAG-GGCCATAATCATA
1 TAGTGG-CATATTCA-G
*
377 TAGTTGCATATTCAG
1 TAGTGGCATATTCAG
* *
392 TAGTGGTCATAATCATA
1 TAGTGG-CATATTCA-G
*
409 TAGTTGCATATTCAG
1 TAGTGGCATATTCAG
424 TA-TGGC
1 TAGTGGC
430 TCATATAGTT
Statistics
Matches: 51, Mismatches: 13, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.08
15 17 0.33
16 24 0.47
17 6 0.12
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (15 bp):
TAGTGGCATATTCAG
Found at i:488 original size:53 final size:52
Alignment explanation
Indices: 44--1478 Score: 772
Period size: 56 Copynumber: 25.8 Consensus size: 52
34 GGGGCCGTAA
* *
44 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGTC
1 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGG-C
* *
97 ATAATCATATAGTTGCATATTCA-TAGGGGC-CATATAGTTGCATATTCAGTAGGGGC
1 ----TCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGGA-CGGC
* *
153 -CATATAGTTGCATATTCAGTAGGGGC-C--ATAGTTGCATATTCAGTAGGGC
1 TCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGGACGGC
* *
202 TCATATAGTTGCATATTCAGTAGGGGC-CATATAGTTGCATATTCAGTA-GGA
1 TCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGGACGGC
* * *
253 GCATATAGTTGCATATTCAGTATGGGC-CATATAGTTGCATATTCAGTAGGGGC
1 TCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGGA-CGGC
* * *
306 -CATATAGTGTTGCATATATTCAGTAGAGGCAGTAATAATATAGTTGCATATTCAGTAGGGCC
1 TCATATA--GTTGC--ATATTCAGTAG-GGC-----TCATATAGTTGCATATTCAGGACGG-C
* *
368 ATAATCATATAGTTGCATATTCAGTAGTGGTCATAATCATATAGTTGCATATTCAGTATGGC
1 ----TCATATAGTTGCATATTCAGTAG-GG-C----TCATATAGTTGCATATTCAGGACGGC
*
430 TCATATAGTTGCATATTTAGTAGGAGCTCATATAGTTGCATATT-AGAGAGCGGC
1 TCATATAGTTGCATATTCAGTAGG-GCTCATATAGTTGCATATTCAG-GA-CGGC
* *
484 -CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGCC
1 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGG-C
* **
536 ATGATCATATAGTAGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAATACGGC
1 ----TCATATAGTTGCATATTCAGTAGGG-C----TCATATAGTTGCATATTCAGGACGGC
* * * * * *
597 TTATATAGTTGCATATTTAGTATGGCCATAATCATGTAGTTGCATATTCAGTAGGGCC
1 TCATATAGTTGCATATTCAGTA-GGGC----TCATATAGTTGCATATTCAGGACGG-C
* *
655 ATAATCATATAGTTGCATATTCAGTAGGGCCGTAATCATATAGTTGCATATTCAGTAAGGCC
1 ----TCATATAGTTGCATATTCAGTAGGG-C----TCATATAGTTGCATATTCAGGACGG-C
* *
717 ATAATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGCC
1 ----TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGG-C
* *
774 ATAATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGTACAC
1 ----TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGG----C
* * * * * *
834 TCGTATAGTTGCATGTTCAATAGGGCTCACTCATATAGTTGCATGTTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGG----C
*
894 TCATATAGTTGCATATTCAGTAGGGCTCACTCATATAGTTGCATATTCAGTA-GGCC
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGG-C
* * *
950 TCATATAGTTGTATATTCAGTAGGGCTCACTCATATAGTTGCATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGG----C
* * *
1010 TCATATAGTTGTATATTCAGTAGGGCTCACTCATATAGTTGCATATTCAGTAAGG-
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGGC
* * * * * *
1065 -GACATA--TGCAT-CTCAGTAGAGCTCACTCATATATAGTTGCATATTCAGTAGGGC
1 TCATATAGTTGCATATTCAGTAG-G---GCTC--ATATAGTTGCATATTCAGGACGGC
** * * *
1119 TCACGTAGTTGCATATTCAGTATGGG-ACATATAGTTGCATATTCAGTAGGGGCTCAC
1 TCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGGA-CGG----C
* *
1176 TCATATAGTTGCATATTCAGTAGGGCTCACTCATATAGTTGCATATTCTGTA-GGC
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGGC
* * * * * * * * *
1231 GACATATAGTTGCATGTTTAGTAGGGCTCATGTAGTTGCATGTTCTGTAGGGA
1 -TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGGC
** * * * * *
1284 TCATATAG--G--TA--C--T-GAACTCATGTAGTTGCATGTTCAGTAGGGA
1 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGGC
* * * *
1327 TCATATAGTTGCTTATTCAGTAGGGCTCACTCATATAGTTGCATGTTCAGTAGGGC
1 TCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGCATATTCAGGACGGC
* * *
1383 TCATATAGTTGCATATTCAGTAGGACTCATATAGTTGCATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGG----C
* *
1439 TCATATAGTTGCATATTCAGTA-GG-ACATATAGTAGCATAT
1 TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATAT
1479 ATTGGTGGTG
Statistics
Matches: 1194, Mismatches: 84, Indels: 203
0.81 0.06 0.14
Matches are distributed among these distances:
43 35 0.03
44 1 0.00
45 1 0.00
47 2 0.00
48 1 0.00
49 5 0.00
50 46 0.04
51 79 0.07
52 134 0.11
53 71 0.06
54 27 0.02
55 7 0.01
56 207 0.17
57 206 0.17
58 34 0.03
59 5 0.00
60 132 0.11
61 27 0.02
62 123 0.10
63 39 0.03
64 1 0.00
65 5 0.00
67 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (52 bp):
TCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGGACGGC
Found at i:843 original size:30 final size:28
Alignment explanation
Indices: 12--1291 Score: 1069
Period size: 26 Copynumber: 45.3 Consensus size: 28
2 AGGGCCATAG
*
12 TCATATAGTTGCATATTCAGTAGGGGCCGTAA
1 TCATATAGTTGCATATTCAGTA-GGG-C--AC
44 TCATATAGTTGCATATTCAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
70 TCATATAGTTGCATATTCAGTAGGGTCATAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
*
101 TCATATAGTTGCATATTCA-TAGGG-GC
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
127 -CATATAGTTGCATATTCAGTAGGG-GC
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
153 -CATATAGTTGCATATTCAGTAGGG-GC
1 TCATATAGTTGCATATTCAGTAGGGCAC
179 -C--ATAGTTGCATATTCAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
202 TCATATAGTTGCATATTCAGTAGGG-GC
1 TCATATAGTTGCATATTCAGTAGGGCAC
229 -CATATAGTTGCATATTCAGTA-GG-A-
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
253 GCATATAGTTGCATATTCAGTATGGG--C
1 TCATATAGTTGCATATTCAGTA-GGGCAC
*
280 -CATATAGTTGCATATTCAGTAGGG-GC
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
306 -CATATAGTGTTGCATATATTCAGTAGAGGCAGTAA
1 TCATATA--GTTGC--ATATTCAGTAG-GGC---AC
* *
341 TAATATAGTTGCATATTCAGTAGGGCCATAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
*
372 TCATATAGTTGCATATTCAGTAGTGGTCATAA
1 TCATATAGTTGCATATTCAGTAG-GG-C--AC
*
404 TCATATAGTTGCATATTCAGTATGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
430 TCATATAGTTGCATATTTAGTA-GG-AGC
1 TCATATAGTTGCATATTCAGTAGGGCA-C
* *
457 TCATATAGTTGCATATT-AG-AGAGCGGC
1 TCATATAGTTGCATATTCAGTAGGGC-AC
484 -CATATAGTTGCATATTCAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
509 TCATATAGTTGCATATTCAGTAGGGCCATGA
1 TCATATAGTTGCATATTCAGTAGGG-CA--C
* *
540 TCATATAGTAGCATATTCAGTAGGGCCATAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
* *
571 TCATATAGTTGCATATTCAATACGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
* * * *
597 TTATATAGTTGCATATTTAGTATGGCCATAA
1 TCATATAGTTGCATATTCAGTA-GGGC--AC
* *
628 TCATGTAGTTGCATATTCAGTAGGGCCATAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
*
659 TCATATAGTTGCATATTCAGTAGGGCCGTAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
* *
690 TCATATAGTTGCATATTCAGTAAGGCCATAA
1 TCATATAGTTGCATATTCAGT-AGGGC--AC
721 TCATATAGTTGCATATTCAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
747 TCATATAGTTGCATATTCAGTAGGGCCATAA
1 TCATATAGTTGCATATTCAGTAGGG-C--AC
778 TCATATAGTTGCATATTCAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
804 TCATATAGTTGCATATTCAGTAGGGTACAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
* * *
834 TCGTATAGTTGCATGTTCAATAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
*
864 TCATATAGTTGCATGTTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
894 TCATATAGTTGCATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
924 TCATATAGTTGCATATTCAGTA-GGC-C
1 TCATATAGTTGCATATTCAGTAGGGCAC
*
950 TCATATAGTTGTATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
980 TCATATAGTTGCATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
*
1010 TCATATAGTTGTATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
1040 TCATATAGTTGCATATTCAGTAAGGG-A-
1 TCATATAGTTGCATATTCAGT-AGGGCAC
* *
1067 -C--ATA--TGCAT-CTCAGTAGAGCTCAC
1 TCATATAGTTGCATATTCAGTAG-G-GCAC
1091 TCATATATAGTTGCATATTCAGTAGGG--C
1 TC--ATATAGTTGCATATTCAGTAGGGCAC
**
1119 TCACGTAGTTGCATATTCAGTATGGG-A-
1 TCATATAGTTGCATATTCAGTA-GGGCAC
1146 -CATATAGTTGCATATTCAGTAGGGGCTCAC
1 TCATATAGTTGCATATTCAGTA-GGG--CAC
1176 TCATATAGTTGCATATTCAGTAGGGCTCAC
1 TCATATAGTTGCATATTCAGTAGGG--CAC
*
1206 TCATATAGTTGCATATTCTGTA-GGCGA-
1 TCATATAGTTGCATATTCAGTAGGGC-AC
* *
1233 -CATATAGTTGCATGTTTAGTAGGG--C
1 TCATATAGTTGCATATTCAGTAGGGCAC
* * *
1258 TCATGTAGTTGCATGTTCTGTAGGG-A-
1 TCATATAGTTGCATATTCAGTAGGGCAC
1284 TCATATAG
1 TCATATAG
1292 GTACTGAACT
Statistics
Matches: 1091, Mismatches: 70, Indels: 180
0.81 0.05 0.13
Matches are distributed among these distances:
20 2 0.00
21 6 0.01
22 5 0.00
23 2 0.00
24 25 0.02
25 49 0.04
26 371 0.34
27 34 0.03
28 13 0.01
29 9 0.01
30 234 0.21
31 257 0.24
32 73 0.07
33 1 0.00
34 5 0.00
36 5 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (28 bp):
TCATATAGTTGCATATTCAGTAGGGCAC
Found at i:1335 original size:26 final size:27
Alignment explanation
Indices: 1299--1478 Score: 219
Period size: 26 Copynumber: 6.7 Consensus size: 27
1289 TAGGTACTGA
* *
1299 ACTCATGTAGTTGCATGTTCAGTAGGG
1 ACTCATATAGTTGCATATTCAGTAGGG
*
1326 A-TCATATAGTTGCTTATTCAGTAGGG
1 ACTCATATAGTTGCATATTCAGTAGGG
*
1352 CTCACTCATATAGTTGCATGTTCAGTAGGG
1 ---ACTCATATAGTTGCATATTCAGTAGGG
1382 -CTCATATAGTTGCATATTCAGTA-GG
1 ACTCATATAGTTGCATATTCAGTAGGG
1407 ACTCATATAGTTGCATATTCAGTAGGG
1 ACTCATATAGTTGCATATTCAGTAGGG
1434 CTCACTCATATAGTTGCATATTCAGTA-GG
1 ---ACTCATATAGTTGCATATTCAGTAGGG
*
1463 A--CATATAGTAGCATAT
1 ACTCATATAGTTGCATAT
1479 ATTGGTGGTG
Statistics
Matches: 137, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
24 14 0.10
25 2 0.01
26 68 0.50
27 3 0.02
29 3 0.02
30 47 0.34
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (27 bp):
ACTCATATAGTTGCATATTCAGTAGGG
Found at i:1362 original size:125 final size:123
Alignment explanation
Indices: 1174--1416 Score: 321
Period size: 125 Copynumber: 1.9 Consensus size: 123
1164 GTAGGGGCTC
* *
1174 ACTCATATAGTTGCATATTCAGTAGGGCTCACTCATATAGTTGCATATTCTGTAGGCGACATATA
1 ACTCATATAGTTGCATATTCAGTAGGG--CACTCATATAGTTGCATATTCAGTAGGCCACATATA
* * * *
1239 GTTGCATGTTTAGTAGGGCTCATGTAGTTGCATGTTCTGTAGGGA-TCATATAGGTACTGA
64 GTTGCATGTTCAGTAGGGCTCATATAGTTGCATATTCAGTA-GGACTCATATAGGTACTGA
* * *
1299 ACTCATGTAGTTGCATGTTCAGTAGGG-A-TCATATAGTTGCTTATTCAGTAGGGCTCACTCATA
1 ACTCATATAGTTGCATATTCAGTAGGGCACTCATATAGTTGCATATTCAGTA-GGC-CA--CATA
1362 TAGTTGCATGTTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGACTCATATAG
62 TAGTTGCATGTTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGACTCATATAG
1417 TTGCATATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
121 20 0.19
122 4 0.04
123 1 0.01
124 3 0.03
125 76 0.73
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (123 bp):
ACTCATATAGTTGCATATTCAGTAGGGCACTCATATAGTTGCATATTCAGTAGGCCACATATAGT
TGCATGTTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGACTCATATAGGTACTGA
Found at i:1363 original size:636 final size:610
Alignment explanation
Indices: 12--1478 Score: 1597
Period size: 636 Copynumber: 2.3 Consensus size: 610
2 AGGGCCATAG
* * *
12 TCATATAGTTGCATATTCAGTAGGGGCCGTAATCAT-A-TAGTTGCATATTCAGTAGGGCTCATA
1 TCATGTAGTTGCATATTCAGTA-GGGCCATAATCATCATTAGTTGCATATTCAGTAGGGATCATA
75 TAGTTGCATATTCAGTAGGG-TCATAATCATATAGTTGCATATTCA-TAGGGGC-CATATAGTTG
65 TAGTTGCATATTCAGTAGGGCTCA-AATCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTG
137 CATATTCAGTAGGGGC--CATATAGTTGCATATTCAGTAGGGGC-C--ATAGTTGCATATTCAGT
128 CATATTCAGTA-GGGCATCATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGT
* *
197 AGGGCTCATATAGTTGCATATTCAGTAGGGGCCATATAGTTGCATATTCAGTAGGAGCATATAGT
191 AGGGCTCATATAGTTGCATATTCAATAGGGACCATATAGTTGCATATTCAGTAGGAGCATATAGT
*
262 TGCATATTCAGTATGGGCCATATAGTTGCATATTCAGTAGGGGCCATATAGTGTTGCATATATTC
256 TGCATATTCAGTATGGGCCATATAGTTGCATATTCAGTAGGGCCCATATAG-GTTG-ATATATTC
327 AGTAGAGGCAGTAATAATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAG
319 AGTAGAGGCA-TAATAATATAGTTGCATATTCAGTAGGGCCA-AATCATATAGTTGCATATTCAG
* * * *
392 TAGTGGTCATAATCATATAGTTGCATATTCAGTATGGCTCATATAGTTGCATATTTAGTAGGAGC
382 TAGTGGTCA-AATCATATAGTTGCATATTCAGTAAGGC-CACATAG-TGCATACTCAGTAGGAGC
* *
457 TCATATAGTTGCATATTAGAGAGCGGCCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCA
444 TCATATAGTTGCATATTAGAGAGCGGCCACATAGTTGCATATTCAGTAGGGCACATATAGTTGCA
*
522 TATTCAGTAGGGCCATGATCATATAGTAGCATATTCAGTAGGGCCATAATCATATAGTTGCATAT
509 TATTCAGTAGGGCCATCATCATATAGTAGCATATTCAGTAGGGCCA-AATCATATAGTTGCATAT
**
587 TCAATACGGCTTATATAGTTGCATATTTAGTATGGCCATAA
573 TCAATACGGCACATATAGTTGCATATTTAGTATGGCC---A
628 TCATGTAGTTGCATATTCAGTAGGGCCATAATCAT-A-TAGTTGCATATTCAGTAGGGCCGTAAT
1 TCATGTAGTTGCATATTCAGTAGGGCCATAATCATCATTAGTTGCATATTCAGTA-GG--G--AT
*
691 CATATAGTTGCATATTCAGTAAGGC-CATAATCATATAGTTGCATATTCAGTAGGGCTCATATAG
61 CATATAGTTGCATATTCAGTAGGGCTCA-AATCATATAGTTGCATATTCAGTAGGGCTCATATAG
755 TTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATAT
125 TTGCATATTCAGTAGGG-C---ATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATAT
* * *
820 TCAGTAGGGTACACTCGTATAGTTGCATGTTCAATAGGGCTCACTCATATAGTTGCATGTTCAGT
186 TCAGTAGGG----CTCATATAGTTGCATATTCAATAGGG---AC-CATATAGTTGCATATTCAGT
*
885 AGGGCTCACTCATATAGTTGCATATTCAGTA-GGGCTCACTCATATAGTTGCATATTCAGTA-GG
243 A-GG---A-GCATATAGTTGCATATTCAGTATGGG----C-CATATAGTTGCATATTCAGTAGGG
* *
948 CCTCATATA-GTTG-TATATTCAGTAG-GGC-TCACTCATATAGTTGCATATTCAGTAGGGCTC-
298 CC-CATATAGGTTGATATATTCAGTAGAGGCAT-AATAATATAGTTGCATATTCAGTAGGGC-CA
* * * *
1008 ACTCATATAGTTGTATATTCAGTAG-GGCTC-ACTCATATAGTTGCATATTCAGTAAGG-GACAT
360 AATCATATAGTTGCATATTCAGTAGTGG-TCAAATCATATAGTTGCATATTCAGTAAGGCCACAT
* *
1070 A-TGCAT-CTCAGTA-GAGCTCACTCATATATAGTTGCATATTCAG-TAG-GGCTCACGTAGTTG
424 AGTGCATACTCAGTAGGAG----CTC--ATATAGTTGCATATT-AGAGAGCGGC-CACATAGTTG
* *
1130 CATATTCAGTATGGG-ACATATAGTTGCATATTCAGTAGGGGC-TCACTCATATAGTTGCATATT
481 CATATTCAGTA-GGGCACATATAGTTGCATATTCAGTAGGGCCATCA-TCATATAGTAGCATATT
* ** *
1193 CAGTAGGGCTC-ACTCATATAGTTGCATATTCTGTA-GGCGACATATAGTTGCATGTTTAGTA-G
544 CAGTAGGGC-CAAATCATATAGTTGCATATTCAATACGGC-ACATATAGTTGCATATTTAGTATG
*
1255 GGC-
607 GCCA
* * * *
1258 TCATGTAGTTGCATGTTCTGTAGGGATCATATAGGTACTGAACTCATGTAGTTGCATGTTCAGTA
1 TCATGTAGTTGCATATTCAGTAGGG-CCATA-A--T-C---A-TCAT-TAGTTGCATATTCAGTA
* * *
1323 GGGATCATATAGTTGCTTATTCAGTAGGGCTC-ACTCATATAGTTGCATGTTCAGTAGGGCTCAT
56 GGGATCATATAGTTGCATATTCAGTAGGGCTCAAATCATATAGTTGCATATTCAGTAGGGCTCAT
*
1387 ATAGTTGCATATTCAGTAGGAC-TCATATAGTTGCATATTCAGTAGGGCTCACTCATATAGTTGC
121 ATAGTTGCATATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGG----CTCATATAGTTGC
* *
1451 ATATTCAGTA-GG-ACATATAGTAGCATAT
182 ATATTCAGTAGGGCTCATATAGTTGCATAT
1479 ATTGGTGGTG
Statistics
Matches: 735, Mismatches: 48, Indels: 123
0.81 0.05 0.14
Matches are distributed among these distances:
615 30 0.04
616 23 0.03
618 1 0.00
620 55 0.07
621 24 0.03
625 4 0.01
626 22 0.03
628 21 0.03
629 12 0.02
630 26 0.04
631 34 0.05
632 29 0.04
634 16 0.02
635 71 0.10
636 181 0.25
637 35 0.05
638 28 0.04
639 28 0.04
640 9 0.01
641 35 0.05
642 16 0.02
643 4 0.01
644 4 0.01
645 27 0.04
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (610 bp):
TCATGTAGTTGCATATTCAGTAGGGCCATAATCATCATTAGTTGCATATTCAGTAGGGATCATAT
AGTTGCATATTCAGTAGGGCTCAAATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCAT
ATTCAGTAGGGCATCATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGC
TCATATAGTTGCATATTCAATAGGGACCATATAGTTGCATATTCAGTAGGAGCATATAGTTGCAT
ATTCAGTATGGGCCATATAGTTGCATATTCAGTAGGGCCCATATAGGTTGATATATTCAGTAGAG
GCATAATAATATAGTTGCATATTCAGTAGGGCCAAATCATATAGTTGCATATTCAGTAGTGGTCA
AATCATATAGTTGCATATTCAGTAAGGCCACATAGTGCATACTCAGTAGGAGCTCATATAGTTGC
ATATTAGAGAGCGGCCACATAGTTGCATATTCAGTAGGGCACATATAGTTGCATATTCAGTAGGG
CCATCATCATATAGTAGCATATTCAGTAGGGCCAAATCATATAGTTGCATATTCAATACGGCACA
TATAGTTGCATATTTAGTATGGCCA
Found at i:1437 original size:82 final size:81
Alignment explanation
Indices: 1300--1478 Score: 272
Period size: 82 Copynumber: 2.2 Consensus size: 81
1290 AGGTACTGAA
* * *
1300 CTCATGTAGTTGCATGTTCAGTAGGGATCATATAGTTGCTTATTCAGTAGGGCTCACTCATATAG
1 CTCATATAGTTGCATATTCAGTAGGGATCATATAGTTGCATATTCAGTAGGGCTCACTCATATAG
*
1365 TTGCATGTTCAGTAGGG
66 TTGCATATTCAGTA-GG
1382 CTCATATAGTTGCATATTCAGTA-GGACTCATATAGTTGCATATTCAGTAGGGCTCACTCATATA
1 CTCATATAGTTGCATATTCAGTAGGGA-TCATATAGTTGCATATTCAGTAGGGCTCACTCATATA
1446 GTTGCATATTCAGTAGG
65 GTTGCATATTCAGTAGG
* *
1463 -ACATATAGTAGCATAT
1 CTCATATAGTTGCATAT
1479 ATTGGTGGTG
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
80 14 0.16
81 5 0.06
82 71 0.79
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (81 bp):
CTCATATAGTTGCATATTCAGTAGGGATCATATAGTTGCATATTCAGTAGGGCTCACTCATATAG
TTGCATATTCAGTAGG
Found at i:3502 original size:643 final size:646
Alignment explanation
Indices: 2152--3824 Score: 2082
Period size: 643 Copynumber: 2.6 Consensus size: 646
2142 TTACAAATTT
* * * * * * * *
2152 ATTTCTTATTAAATCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAACTAATGTGGT
1 ATTTCTAATTAAATCGAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGC
* * * * * ** * * * *
2217 TGAGATTTGGTTAGATGTATATATTTATTTCAAGGTGTCTTT-TCGCCAAAAATCTTGCGAAA-T
66 TGACATTTGGCTCGATGAATAAAGATATTTCAAGGAGTCTTTGT-GTCAAAAATCATGCAAAATT
* * * * * * * *
2280 CAAGCCGAGGCCCCAGAAACGCGTTTTTAGCCAAAAAAAACCGTGATGGTTAGCACATGATTTTG
130 C-ATCCGGGGCTCC-GGAACGCGTTTTTA-CC--CAAAAACC--GATGGATAGTACATGATTTCG
* * * * ** * * *
2345 TCTAAAAACTGA-CC-AAAATGTTTTTTTTCCCTGAA-TTTTTCCCGTAATATTTAGAAAAAATA
188 GCTAAAAACTGACCCGAAAAAG---TTTTT--CTAAATTTTTTGCCACAACACTCAGAAAAAATA
* * * * * *
2407 TATAACTT-AACGTCAAAAAGATTGACGAGCTTTTCACGCTTCTAATATCGTTTTTCCTC-TTTT
248 T-TAAATTCAACGCCAAAAAGATTGACGGGCTTTACACACTTCTAATATCGTTTTT-TTCATTTT
** * * *
2470 TTTTCCGTATTAATTTCTAATTAAATCGAAACAAGATT-TGCATGCTAGTAAAAAC-AATTCATT
311 TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAG-ATACTTGTAAAAACAAATTC-TT
** * * *
2533 A-AATCGAATGTGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAACAGTTTTTGCGCCAAA
374 ATAATCGAATGTGGCTGACATTTGGCTCGATGAATATAGATATTTAAAACAGTCTTTGCGCCAAA
* *
2597 AATCATGCAAAATTAAGCCGGGGCTCCCGAACGAGTTTTTAACCAAAAACCGTGATGGTTACTAC
439 AATAATGCAAAATTAAGCCGGGGCTCCAGAACGAGTTTTTAACCAAAAACCGTGATGGTTACTAC
* * *
2662 ACGATTTCGGCTAAAAAAATGACCCGAACAAGTTTTCTTAATTTTTTGCCACAATACTCAGAAAA
504 ACGATTTCGGCTAAAAAAATGACCCGAAAAAGTTTTCTAAATTTTTTCCCACAATACTCAGAAAA
* * * * *
2727 AAATATTTAATTTATGGTCAAAAAGATTGACGGGTTTTACACGGTTCTAATATCGTTTTTTCATT
569 AAATATTTAATTCAAGGCCAAAAAGATTGACGGGCTTTACACGCTTCTAATATCGTTTTTTCATT
*
2792 TTTTTCCGAACTA
634 TTTTTCCGAAATA
* *
2805 ATTTCTAATTGAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGC
* *
2870 TGACATTTGGTTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTG
66 TGACATTTGGCTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTC
* *
2935 ATTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG-T-GAT-GTACATGATTTCGGCTAAAAA
131 ATCCGGGGCTCCGGAACGCGTTTTTACCCAAAAACCGATGGATAGTACATGATTTCGGCTAAAAA
* * *
2997 CTGACCTGAAAAAGTTTTTCTTAATTTTTTGCCACAACACTCAGAAAAAATATTAAATTCAAGGC
196 CTGACCCGAAAAAGTTTTTCTAAATTTTTTGCCACAACACTCAGAAAAAATATTAAATTCAACGC
3062 CAAAAAGATTGACGGGCTTTACACACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAATT
261 CAAAAAGATTGACGGGCTTTACACACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAATT
*
3127 TCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAACAAATTCTTATATTC-AATGTGGCTG
326 TCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAACAAATTCTTATAATCGAATGTGGCTG
* * * * *
3191 ACATTTGGCTCGATGAATATTTATATATTTAAAAGAGTCTTTGTGTCAAAAATAATGCAAAGTTA
391 ACATTTGGCTCGATGAATA--TAGATATTTAAAACAGTCTTTGCGCCAAAAATAATGCAAAATTA
* * * * * *
3256 ATCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTTGGCT-AA
454 AGCCGGGGCTCCAGAACGAGTTTTTAACCAAAAACCGTGATGGTTACTACACGATTTCGGCTAAA
* *
3320 AAACTGACCCGAAAAAGTTTTTCTAAATTTTTTCCCACAGTACTCAGAAAAAAAT-TTTAATTCA
519 AAAATGACCCGAAAAAG-TTTTCTAAATTTTTTCCCACAATACTCAGAAAAAAATATTTAATTCA
* * *
3384 AGGCCAAAAATATTGACGGGCTTTACACTCTTCTGATATCGTTTTTTCATTTTTTTCCGAAATA
583 AGGCCAAAAAGATTGACGGGCTTTACACGCTTCTAATATCGTTTTTTCATTTTTTTCCGAAATA
* * *
3448 ATTTCTAATTAAATCGATACAAGATTAAGATACTCGTAAAAACAAATTCTTATATTCAATGTGGC
1 ATTTCTAATTAAATCGAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGC
* *
3513 TGACATTTGGCTCGATGAATATAGATATTTGAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTC
66 TGACATTTGGCTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTC
* * *
3578 ATCCGGGTCTTCGGAACGCGTTTTTACCCAAAAACCGTAATGGTTAGTACATGATTTCGGCTAAA
131 ATCCGGGGCTCCGGAACGCGTTTTTACCCAAAAACCG--ATGGATAGTACATGATTTCGGCTAAA
** * * * *
3643 AACTGACCCGAAAAAGTTTTTCTAAATTTTTTGCCACAGTAGTCAGAATAAATGTTTAATTCAAC
194 AACTGACCCGAAAAAGTTTTTCTAAATTTTTTGCCACAACACTCAGAAAAAATATTAAATTCAAC
* *
3708 ACCAAAAAGATTGACGGGTTTTACACACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAA
259 GCCAAAAAGATTGACGGGCTTTACACACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAA
*
3773 TTTCTAATTAAATCGAAACAAGATTCAGATACTTGTCAAAACAAATTCTTAT
324 TTTCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAACAAATTCTTAT
Statistics
Matches: 892, Mismatches: 110, Indels: 41
0.86 0.11 0.04
Matches are distributed among these distances:
641 11 0.01
642 145 0.16
643 249 0.28
644 147 0.16
645 3 0.00
646 7 0.01
647 3 0.00
648 189 0.21
649 7 0.01
651 1 0.00
652 13 0.01
653 115 0.13
654 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (646 bp):
ATTTCTAATTAAATCGAAACAAGATTAAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGC
TGACATTTGGCTCGATGAATAAAGATATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTC
ATCCGGGGCTCCGGAACGCGTTTTTACCCAAAAACCGATGGATAGTACATGATTTCGGCTAAAAA
CTGACCCGAAAAAGTTTTTCTAAATTTTTTGCCACAACACTCAGAAAAAATATTAAATTCAACGC
CAAAAAGATTGACGGGCTTTACACACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAATT
TCTAATTAAATCGAAACAAGATTCAGATACTTGTAAAAACAAATTCTTATAATCGAATGTGGCTG
ACATTTGGCTCGATGAATATAGATATTTAAAACAGTCTTTGCGCCAAAAATAATGCAAAATTAAG
CCGGGGCTCCAGAACGAGTTTTTAACCAAAAACCGTGATGGTTACTACACGATTTCGGCTAAAAA
AATGACCCGAAAAAGTTTTCTAAATTTTTTCCCACAATACTCAGAAAAAAATATTTAATTCAAGG
CCAAAAAGATTGACGGGCTTTACACGCTTCTAATATCGTTTTTTCATTTTTTTCCGAAATA
Found at i:3780 original size:324 final size:322
Alignment explanation
Indices: 2050--3824 Score: 2008
Period size: 322 Copynumber: 5.5 Consensus size: 322
2040 TCCTCAATTT
* ** * * *
2050 TTTTTTGCCACAATAGTCAGAAAAAAT-TTATAATTCAACGGAAAAAAAACATTGAAGGGTTTTT
1 TTTTTTGCCACAATACTCAGAAAAAATATT-TAATTCAAC-G-CCAAAAAGATTGACGGGTTTTA
* * * * * * *
2114 CACACTAC-AACTATAGTTTTTCCA-TTTTTTACAAATTTATTTCTTATTAAATCGAAAAAAGAT
63 CACACTTCTAA-TATCGTTTTTTCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
* * ** * * * * *
2177 TCAGATGCTCGTAAAAACAAATCCTTA-AAACTAATGTGGTTGAGATTTGGTTAGATGTATATAT
127 TCAGATACTCGTAAAAACAAATTCTTATATTC-AATGTGGCTGACATTTGGTTCGATGAATATAG
* * * * * * * * * *
2241 TTATTTCAAGGTGTCTTT-TCGCCAAAAATCTTGCGAAATCAAGCCGAGGCCCCAGAAACGCGTT
191 ATATTTCAAGGAGTCTTTGT-GTCAAAAATCATGCAAAATTAATCCGGGGCTCC-GGAACGCGTT
* * * * *
2305 TTTAGCCAAAAAAAACCGTGATGGTTAGCACATGATTTTGTCTAAAAACTGA-CC-AAAATGTTT
254 TTTA-CC--CAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAG---
*
2368 TTTTTCCCTGAA
313 TTTTT--CTAAA
* ** * * * * *
2380 -TTTTTCCCGTAATATTTAGAAAAAATATATAACTT-AACGTCAAAAAGATTGACGAGCTTTT-C
1 TTTTTTGCCACAATACTCAGAAAAAATATTTAA-TTCAACGCCAAAAAGATTGACG-GGTTTTAC
* * **
2442 ACGCTTCTAATATCGTTTTTCCTCTTTTTTTTCCGTATTAATTTCTAATTAAATCGAAACAAGAT
64 ACACTTCTAATATCGTTTTT--TCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * **
2507 T-TGCATGCTAGTAAAAAC-AATTCATTA-AATCGAATGTGGCTGGGATTTGGTTCGATGAATAT
127 TCAG-ATACTCGTAAAAACAAATTC-TTATATTC-AATGTGGCTGACATTTGGTTCGATGAATAT
** * * * * * *
2569 AGATATTTCAAACAGTTTTTGCGCCAAAAATCATGCAAAATTAAGCCGGGGCTCCCGAACGAGTT
189 AGATATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTAATCCGGGGCTCCGGAACGCGTT
* * * * *
2634 TTTAACCAAAAACCGTGATGGTTACTACACGATTTCGGCTAAAAAAATGACCCGAACAAG-TTTT
254 TTTACCCAAAAACCGTGATGGTTAGTACATGATTTCGGCT-AAAAACTGACCCGAAAAAGTTTTT
*
2698 CTTAA
318 CTAAA
* ** *
2703 TTTTTTGCCACAATACTCAGAAAAAAATATTTAATTTATGGTCAAAAAGATTGACGGGTTTTACA
1 TTTTTTGCCACAATACTCAG-AAAAAATATTTAATTCAACGCCAAAAAGATTGACGGGTTTTACA
** * * *
2768 CGGTTCTAATATCGTTTTTTCATTTTTTTCCGAACTAATTTCTAATTGAATCGAAACAAGATTCA
65 CACTTCTAATATCGTTTTTTCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * *
2833 GATACTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATAAAGATAT
130 GATACTCGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGTTCGATGAATATAGATAT
* * *
2898 TTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTGATTCGGGGCTCCGGAACGCGTTTTTAGC
195 TTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTAATCCGGGGCTCCGGAACGCGTTTTTACC
* *
2963 CAAAAACCGTGA----T-GTACATGATTTCGGCTAAAAACTGACCTGAAAAAGTTTTTCTTAA
260 CAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAGTTTTTCTAAA
* * * *
3021 TTTTTTGCCACAACACTCAGAAAAAATATTAAATTCAAGGCCAAAAAGATTGACGGGCTTTACAC
1 TTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACGCCAAAAAGATTGACGGGTTTTACAC
3086 ACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
66 ACTTCTAATATCG-TTTTTTCA-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
* * *
3151 AGATACTTGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGCTCGATGAATATTTATA
129 AGATACTCGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGTTCGATGAATA--TAGA
* * * * *
3216 TATTTAAAAGAGTCTTTGTGTCAAAAATAATGCAAAGTTAATCCGGGGCTCCAGAACGCGTTTTT
192 TATTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTAATCCGGGGCTCCGGAACGCGTTTTT
* *
3281 AGCCAAAAACCGTGATGGTTAGTACATGATTTTGGCTAAAAACTGACCCGAAAAAGTTTTTCTAA
257 ACCCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAGTTTTTCTAA
3346 A
322 A
* * * * *
3347 TTTTTTCCCACAGTACTCAGAAAAAA-ATTTTAATTCAAGGCCAAAAATATTGACGGGCTTTACA
1 TTTTTTGCCACAATACTCAGAAAAAATA-TTTAATTCAACGCCAAAAAGATTGACGGGTTTTACA
* * * *
3411 CTCTTCTGATATCGTTTTTTCATTTTTTTCCGAAA-TAATTTCTAATTAAATCGATACAAGATTA
65 CACTTCTAATATCGTTTTTTCATTTTTTTCC-AAATTAATTTCTAATTAAATCGAAACAAGATTC
*
3475 AGATACTCGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGCTCGATGAATATAGATA
129 AGATACTCGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGTTCGATGAATATAGATA
* * * *
3540 TTTGAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTCATCCGGGTCTTCGGAACGCGTTTTTAC
194 TTTCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTAATCCGGGGCTCCGGAACGCGTTTTTAC
*
3605 CCAAAAACCGTAATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAGTTTTTCTAAA
259 CCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAGTTTTTCTAAA
* * * * *
3669 TTTTTTGCCACAGTAGTCAGAATAAATGTTTAATTCAACACCAAAAAGATTGACGGGTTTTACAC
1 TTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACGCCAAAAAGATTGACGGGTTTTACAC
3734 ACTTCTAATATCGTTTTTTTCATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
66 ACTTCTAATATCG-TTTTTTCA-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTC
* *
3799 AGATACTTGTCAAAACAAATTCTTAT
129 AGATACTCGTAAAAACAAATTCTTAT
Statistics
Matches: 1250, Mismatches: 159, Indels: 78
0.84 0.11 0.05
Matches are distributed among these distances:
317 67 0.05
318 50 0.04
319 95 0.08
321 75 0.06
322 190 0.15
323 169 0.14
324 182 0.15
325 66 0.05
326 139 0.11
327 34 0.03
328 11 0.01
329 48 0.04
330 124 0.10
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (322 bp):
TTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACGCCAAAAAGATTGACGGGTTTTACAC
ACTTCTAATATCGTTTTTTCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAG
ATACTCGTAAAAACAAATTCTTATATTCAATGTGGCTGACATTTGGTTCGATGAATATAGATATT
TCAAGGAGTCTTTGTGTCAAAAATCATGCAAAATTAATCCGGGGCTCCGGAACGCGTTTTTACCC
AAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAAGTTTTTCTAAA
Done.