Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002337.1 Hibiscus syriacus cultivar Beakdansim tig00004774_pilon, 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: 86217
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5926 original size:20 final size:22
Alignment explanation
Indices: 5898--5937 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
5888 AGAAAATCAA
5898 AAATCAAAGTAAAA-AAGAAAG
1 AAATCAAAGTAAAATAAGAAAG
5919 AAAT-AAAGTAAAATAAGAA
1 AAATCAAAGTAAAATAAGAA
5938 TGTTAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (22 bp):
AAATCAAAGTAAAATAAGAAAG
Found at i:7047 original size:19 final size:19
Alignment explanation
Indices: 7023--7062 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
7013 AACTGAGCCT
7023 GCTTTGCTGGGTCAGGCTG
1 GCTTTGCTGGGTCAGGCTG
*
7042 GCTTTGTTGGGTCAGGCTG
1 GCTTTGCTGGGTCAGGCTG
7061 GC
1 GC
7063 ATAGCTCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.20, G:0.42, T:0.33
Consensus pattern (19 bp):
GCTTTGCTGGGTCAGGCTG
Found at i:7246 original size:22 final size:22
Alignment explanation
Indices: 7221--7264 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7211 AACTATATAA
*
7221 TATATATTATATTTTCAAAAAC
1 TATATAATATATTTTCAAAAAC
*
7243 TATATAATATGTTTTCAAAAAC
1 TATATAATATATTTTCAAAAAC
7265 CGTTTCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
TATATAATATATTTTCAAAAAC
Found at i:7247 original size:29 final size:26
Alignment explanation
Indices: 7195--7252 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
7185 TAATATGTAC
*
7195 TATATATTTATTTATAAACTATATAA
1 TATATATTTATTTAAAAACTATATAA
7221 TATATATTATATTTTCAAAAACTATATAA
1 TATATATT-TA-TTT-AAAAACTATATAA
7250 TAT
1 TAT
7253 GTTTTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.29
27 2 0.07
28 3 0.11
29 15 0.54
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (26 bp):
TATATATTTATTTAAAAACTATATAA
Found at i:7324 original size:36 final size:35
Alignment explanation
Indices: 7229--7324 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 35
7219 AATATATATT
7229 ATATTTTCAAAAACTATATA-ATATGTTTTCAAAA
1 ATATTTTCAAAAACTATATATATATGTTTTCAAAA
*** *
7263 ACCGTTTCTAAAACTATATACTATATGTTTTCAAAA
1 ATATTTTCAAAAACTATATA-TATATGTTTTCAAAA
7299 ATATTTTCAAAAACTATACTATATAT
1 ATATTTTCAAAAACTATA-TATATAT
7325 TGTTATATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 16 0.31
36 33 0.65
37 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (35 bp):
ATATTTTCAAAAACTATATATATATGTTTTCAAAA
Found at i:10003 original size:99 final size:97
Alignment explanation
Indices: 9801--9985 Score: 255
Period size: 101 Copynumber: 1.9 Consensus size: 97
9791 ACCGAGAATG
* * **
9801 TTAGAAAAAGATTAATATTTTAGATTGCGCTTTACCGAAATATTATGTTTTTTATAACATTTTCG
1 TTAGAAAAAGATTAATATTTTAGATTGCGCATAACAAAAATATTATGTTTTTTATAACATTTTCG
** *
9866 GTTATGCCAATTCTCTGTTAAGGAACCGAAAAAA
66 GTTACACCAATTCTCTATT-A-GAACCGAAAAAA
9900 TTAGAAAAAGATTAATATTTTCAG-TTGCGCATAACAAAAAATATTATGTTTTTTTATAACATTT
1 TTAGAAAAAGATTAATATTTT-AGATTGCGCATAAC-AAAAATATTATG-TTTTTTATAACATTT
9964 TCGGTTACACCAATTCTCTATT
63 TCGGTTACACCAATTCTCTATT
9986 GTTCCTTAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 30 0.39
100 12 0.16
101 34 0.45
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (97 bp):
TTAGAAAAAGATTAATATTTTAGATTGCGCATAACAAAAATATTATGTTTTTTATAACATTTTCG
GTTACACCAATTCTCTATTAGAACCGAAAAAA
Found at i:16637 original size:32 final size:32
Alignment explanation
Indices: 16553--16629 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
16543 ATGTAAAAAA
16553 AAGCCCTTAAACTATGTTTTTGTTTTTATTTT
1 AAGCCCTTAAACTATGTTTTTGTTTTTATTTT
*
16585 AAGCCCTTAAACTATGTTTTTGTTTTTGTTTT
1 AAGCCCTTAAACTATGTTTTTGTTTTTATTTT
*
16617 AAGTCCTTAAACT
1 AAGCCCTTAAACT
16630 GTTTTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.52
Consensus pattern (32 bp):
AAGCCCTTAAACTATGTTTTTGTTTTTATTTT
Found at i:23755 original size:3 final size:3
Alignment explanation
Indices: 23737--23811 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
23727 AATATGAATA
* * *
23737 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT TAT AAT AAT GAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
23783 TAT AAT AAT AAT AAT TAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23812 AATGAGTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:23772 original size:15 final size:15
Alignment explanation
Indices: 23738--23811 Score: 112
Period size: 15 Copynumber: 4.9 Consensus size: 15
23728 ATATGAATAA
* *
23738 ATAATATATATTAATA
1 ATAATA-ATAATAATT
23754 ATAATAATAATAATT
1 ATAATAATAATAATT
*
23769 ATAATAATGATAATT
1 ATAATAATAATAATT
23784 ATAATAATAATAATT
1 ATAATAATAATAATT
23799 ATAATAATAATAA
1 ATAATAATAATAA
23812 AATGAGTAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
15 48 0.89
16 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:24230 original size:36 final size:36
Alignment explanation
Indices: 24181--24267 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
24171 GAACAAGCTC
* *
24181 TTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTA
1 TTCTCATTATGAACTTCTTCTTCTTCAGATGAATTA
* *
24217 TTCTCATTATGAACTTCTTTTTCTTCAGATGAATTC
1 TTCTCATTATGAACTTCTTCTTCTTCAGATGAATTA
*
24253 CTCTCATTATGAACT
1 TTCTCATTATGAACT
24268 CTACCTGGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (36 bp):
TTCTCATTATGAACTTCTTCTTCTTCAGATGAATTA
Found at i:24388 original size:19 final size:19
Alignment explanation
Indices: 24366--24423 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
24356 AGATGACAAA
24366 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* **
24385 TTCTTCTTCA-GATG-ACGAG
1 TTCTTC-TCATTATGAAC-TC
24404 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
24423 T
1 T
24424 ATCTGACAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
18 5 0.17
19 19 0.66
20 5 0.17
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:24396 original size:38 final size:39
Alignment explanation
Indices: 24318--24423 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 39
24308 AAAAGGTTGA
24318 ACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATG
1 ACAAATTCTTCTCATTATGAAC----TCTTCCTTCTTCAGATG
24361 ACAAATTCTTCTCATTATGAACTCTT-CTTCTTCAGATG
1 ACAAATTCTTCTCATTATGAACTCTTCCTTCTTCAGATG
* *
24399 ACGAGTTCTTCTCATTATGAACTCT
1 ACAAATTCTTCTCATTATGAACTCT
24424 ATCTGACAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 35 0.57
39 4 0.07
43 22 0.36
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.42
Consensus pattern (39 bp):
ACAAATTCTTCTCATTATGAACTCTTCCTTCTTCAGATG
Found at i:24444 original size:154 final size:147
Alignment explanation
Indices: 24162--24534 Score: 536
Period size: 154 Copynumber: 2.5 Consensus size: 147
24152 TAGAATTATG
* ** * *
24162 CAAAGGGTTGAACAAGCTCTTCTCATTGTGAAC--TTCTT-CTTCTTCAGATGAGTTATTCTCAT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
24224 TATGAACTTCTTTTTCTTCAGATGAATTCCTCTCATTATGAACTCTACCTGGCAATGTTAATCCA
66 TATGAAC-TCTTCTTCTTCAGATGAATTCCTCTCATTATGAACTCTACCTGACAATGTTAATCCA
24289 TCAAATGATGAATTTAAA
130 TCAAATGATGAATTTAAA
*
24307 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACAAATTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTT-TTCTTCCTTCTTCAGATG---AGTTCTTC
* *
24372 TCATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTATCTGACAATGTT
62 TCATTATGAACTCTTCTTCTTCAGATGA--A-TTCCTCTCATTATGAACTCTACCTGACAATGTT
*
24437 AATCCATCAATTGATGAATTTAAA
124 AATCCATCAAATGATGAATTTAAA
*
24461 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAAC-TTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
24526 TTATGAACT
65 TTATGAACT
24535 TTTTCTGGAA
Statistics
Matches: 204, Mismatches: 13, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
145 29 0.14
148 5 0.02
149 12 0.06
151 35 0.17
152 17 0.08
153 1 0.00
154 103 0.50
155 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (147 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTTCTTCTTCAGATGAATTCCTCTCATTATGAACTCTACCTGACAATGTTAATCCAT
CAAATGATGAATTTAAA
Found at i:24555 original size:113 final size:113
Alignment explanation
Indices: 24361--24904 Score: 871
Period size: 113 Copynumber: 4.8 Consensus size: 113
24351 TCTTCAGATG
** * *
24361 ACAAATTCTTCTCATTATGAAC-TCTTCTT-CTTC-AGATGACGAGTTCTTCTCATTATGAACTC
1 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTT
* * * * * * **
24423 TATCT-GACAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGA
65 TCTCTGGA-AAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
* *
24472 ACAAATTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
*
24537 TTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
66 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
*
24585 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
24650 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
66 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
*
24698 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
24763 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
66 CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
* *
24811 ACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTT
1 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
24876 CTCTGGAAAAGCTGATCCATCAAGTGATG
66 CTCTGGAAAAGCTGATCCATCAAGTGATG
24905 GATTTAAATC
Statistics
Matches: 408, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
111 21 0.05
112 6 0.01
113 378 0.93
114 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT
CTCTGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGA
Found at i:25979 original size:83 final size:83
Alignment explanation
Indices: 25843--28095 Score: 2724
Period size: 83 Copynumber: 26.7 Consensus size: 83
25833 GGTTTCATAT
* * * *
25843 CAAACAAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
* *
25907 ATTCAATAACTGGTTTTAT
65 ATTCAATGACTGGTTTTAC
*
25926 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
25991 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* *
26009 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26074 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* * *
26092 CAAACCAGATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26157 TTCAATAACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
26175 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26240 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
26258 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26323 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
*
26341 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26406 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* * * * *
26424 CAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26489 TTCAATAACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
26507 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26572 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* *
26590 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
*
26654 ATTCAATAACTGGTTTTAC
65 ATTCAATGACTGGTTTTAC
*
26673 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26738 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
*
26756 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26821 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* * * * *
26839 CAAACCAGATCAGAGAACTCAAAGAACACTTTCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
26904 TTCAATAACTGGTTCTGTGGTTCATAC
66 TTCAATGACT-G----GT--TT--TAC
* * *
26931 CAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTC-TAC
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-C-AC--A-TTCAT-C
* *** ***
26995 TATGAGCAAATTC-ATCTTTCAAATTTA-
59 T-T--TCAAATTCAATGACT-GGTTTTAC
* *** * * *** ** * *
27022 -ATGATTGGTTCTG-TGGTTTCATATCAA-A---CCAGATCAGATAACTCA-AAG-A-A-T-A-C
1 CA-AACCAGATCAGAT-AACTCA-AAGAACACTTCCAGA--AGAT-GCT-ATGAGCACATTCATC
* * * ** *
27075 TTCCAGAAGATGTTATTGGCACATTCCTCTT-C
59 TTTC--AA-AT-TCAAT-G-AC--TGGTTTTAC
* * * * * *
27107 CAAATTCA-ATAACTGGTTTTATCAAAC-CAGATCAGATA-AC-TCAAAGAACACTTCCA-GAAG
1 CAAA-CCAGAT--C-AG----AT--AACTCA-A--AGA-ACACTTC-CAGAAGA-TGCTATG-AG
* * ** * * * **
27167 -ATGC-TATGATCACATTCATCTTTCAAATTCAATGATTGGTTTTA
49 CA--CAT-TCAT--CTTTCA-AATTC-AA-TGACTG---GTTTTAC
* * * ** * *
27211 CCAAAC-CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGATCACATTCATCTTTCA
1 CAAACCAGA-TC-AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCA
* *
27275 AATTCAATGATTGATTTTAC
64 AATTCAATGACTGGTTTTAC
* * * *
27295 CAAACCAGATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
27360 TTCAATAACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
27378 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
27443 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
27461 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
27526 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* *
27544 CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
27609 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* * * * *
27627 CAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
27692 TTCAATAACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
27710 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
27775 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
* *
27793 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
*
27857 ATTCAATAACTGGTTTTAC
65 ATTCAATGACTGGTTTTAC
27876 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
27941 TTCAATGACTGGTTTTAC
66 TTCAATGACTGGTTTTAC
*
27959 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
28024 TTCAATGATTGGTTTTAC
66 TTCAATGACTGGTTTTAC
*
28042 CAAACCAGATCAGATAACTCAAAGAACAATTCCAGAAGATGCTATGAGCACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
28096 GCATTTGTTC
Statistics
Matches: 1890, Mismatches: 194, Indels: 172
0.84 0.09 0.08
Matches are distributed among these distances:
77 1 0.00
79 3 0.00
80 4 0.00
81 1 0.00
82 8 0.00
83 1665 0.88
84 13 0.01
85 5 0.00
86 3 0.00
87 5 0.00
88 10 0.01
89 3 0.00
90 14 0.01
91 11 0.01
92 54 0.03
93 11 0.01
94 15 0.01
95 4 0.00
96 7 0.00
97 10 0.01
98 9 0.00
99 4 0.00
100 4 0.00
101 8 0.00
102 4 0.00
103 7 0.00
104 4 0.00
105 3 0.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATGACTGGTTTTAC
Found at i:26123 original size:166 final size:166
Alignment explanation
Indices: 25843--28095 Score: 3407
Period size: 166 Copynumber: 13.3 Consensus size: 166
25833 GGTTTCATAT
* * * *
25843 CAAACAAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
* *
25907 ATTCAATAACTGGTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
65 ATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
25972 ATCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
130 AGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
26009 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* * *
26074 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
26139 GCACATTCCTCTTTCAAATTCAATAACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
26175 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26240 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
26305 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
*
26341 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* * * *
26406 TTCAATGATTGGTTTTACCAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
26471 GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
26507 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26572 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG
* * *
26637 -GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
130 AGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
*
26673 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
26738 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
26803 TCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* * * * *
26839 CAAACCAGATCAGAGAACTCAAAGAACACTTTCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
26904 TTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAG
66 TTCAATGACT-G----GT--TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * * *
26969 ATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCT
122 ATGCTA-TGAG-C-AC--A--T-T-C-AT---C----T-----TTCAAATTCAATGA-----C--
*
27034 GTGGTTTCATAT
158 -TGGTTT--TAC
* * * *
27046 CAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGTTATTG-GCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAA
* *
27110 ATTCAATAACTGGTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
65 ATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
27175 ATCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
130 AGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
27212 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* * * *
27277 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
27342 GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
27378 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
27443 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
27508 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
27544 CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* * * *
27609 TTCAATGATTGGTTTTACCAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
27674 GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
27710 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
27775 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG
* * *
27840 -GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
130 AGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
27876 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
27941 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
28006 TCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
*
28042 CAAACCAGATCAGATAACTCAAAGAACAATTCCAGAAGATGCTATGAGCACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
28096 GCATTTGTTC
Statistics
Matches: 1929, Mismatches: 110, Indels: 96
0.90 0.05 0.04
Matches are distributed among these distances:
165 8 0.00
166 1683 0.87
167 3 0.00
168 6 0.00
171 3 0.00
173 2 0.00
175 46 0.02
176 15 0.01
177 1 0.00
178 1 0.00
180 1 0.00
181 1 0.00
182 1 0.00
183 1 0.00
184 1 0.00
185 3 0.00
188 3 0.00
189 1 0.00
190 1 0.00
191 1 0.00
192 1 0.00
193 1 0.00
195 1 0.00
196 1 0.00
197 15 0.01
198 45 0.02
200 2 0.00
202 3 0.00
205 6 0.00
206 1 0.00
207 70 0.04
208 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (166 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
Found at i:26255 original size:249 final size:249
Alignment explanation
Indices: 25843--28095 Score: 3448
Period size: 249 Copynumber: 8.9 Consensus size: 249
25833 GGTTTCATAT
* * * *
25843 CAAACAAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
*
25908 TTCAATAACTGGTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
25973 TCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* * *
26038 TTCCAGAAGATGATATGATCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
*
26092 CAAACCAGATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
26157 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
26222 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
26287 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* * *
26341 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
* * * * *
26406 TTCAATGATTGGTTTTACCAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
26471 GCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
26536 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
26590 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
26655 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
26720 GCATATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* *
26785 TTCCAGAAGATGCTATGATCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* * *
26839 CAAACCAGATCAGAGAACTCAAAGAACACTTTCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
*
26904 TTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAG
66 TTCAATAACT-G----GT--TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG-A-
* *
26969 ATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCT
120 A-G--A-T--G--------------CTATGAGCACATTCATCTTTCAAATTCAATGA------C-
* * *
27034 GTGGTTTCATATCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGTTATTG-GCACA
158 -TGGTTT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACA
* * * *
27098 TTCCTCTTCCAAATTCAATAACTGGTTTTAT
219 TTCATCTTTCAAATTCAATGACTGGTTTTAC
* * *
27129 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
* * *
27194 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * * *
27259 TCACATTCATCTTTCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCTAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* * * *
27324 TTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
27378 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
* *
27443 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
27508 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAAAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* *
27573 TTCCAGAAGATGCTATGATCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* * *
27627 CAAACCATATCAGATAACTCTAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
27692 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
27757 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* * *
27822 TTCCAGAAGATGCTATTG-GCACATTCCTCTTCCAAATTCAATAACTGGTTTTAC
196 TTCCAGAAGATGCTA-TGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
* *
27876 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
*
27941 TTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* * *
28006 TCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAA
131 GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
28071 TTCCAGAAGATGCTATGAGCACATT
196 TTCCAGAAGATGCTATGAGCACATT
28096 GCATTTGTTC
Statistics
Matches: 1849, Mismatches: 110, Indels: 90
0.90 0.05 0.04
Matches are distributed among these distances:
248 3 0.00
249 1535 0.83
250 3 0.00
251 5 0.00
254 2 0.00
256 2 0.00
258 37 0.02
259 29 0.02
260 1 0.00
261 1 0.00
263 1 0.00
264 1 0.00
266 1 0.00
273 1 0.00
275 1 0.00
276 1 0.00
278 1 0.00
279 1 0.00
280 31 0.02
281 37 0.02
283 2 0.00
285 2 0.00
286 1 0.00
288 6 0.00
289 1 0.00
290 141 0.08
291 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (249 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTTCAAA
TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTAC
Found at i:29247 original size:1 final size:1
Alignment explanation
Indices: 29243--29279 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
29233 TTGACCCCCC
* *
29243 TTTTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29280 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:29256 original size:10 final size:10
Alignment explanation
Indices: 29243--29280 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
29233 TTGACCCCCC
29243 TTTTTTTCTT
1 TTTTTTTCTT
*
29253 TTTTTTTTTT
1 TTTTTTTCTT
29263 TTTTTTTCTT
1 TTTTTTTCTT
29273 TTTTTTTC
1 TTTTTTTC
29281 AAGCATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:36604 original size:15 final size:15
Alignment explanation
Indices: 36581--36612 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36571 TGAAATGAAT
36581 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
36596 AATGCATGTATGCAA
1 AATGAATGTATGCAA
36611 AA
1 AA
36613 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:41557 original size:16 final size:15
Alignment explanation
Indices: 41532--41561 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41522 TGTGGTCCTT
41532 CTTTTTTTTTCTTTC
1 CTTTTTTTTTCTTTC
41547 CTTTTTCTTTTCTTT
1 CTTTTT-TTTTCTTT
41562 GCAGGTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTTTTTCTTTC
Found at i:42003 original size:3 final size:3
Alignment explanation
Indices: 41985--42044 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
41975 AATATGAATA
* *
41985 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
42031 TAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
42045 AATGAGTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:44793 original size:13 final size:13
Alignment explanation
Indices: 44749--44799 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
44739 TGAATTTTTG
*
44749 ATGACGAGCATTT
1 ATGACGCGCATTT
*
44762 ATGACACGCATTT
1 ATGACGCGCATTT
44775 ATGACGCGCATTT
1 ATGACGCGCATTT
*
44788 ATGACGTGCATT
1 ATGACGCGCATT
44800 GAGCGTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (13 bp):
ATGACGCGCATTT
Found at i:44870 original size:85 final size:84
Alignment explanation
Indices: 44771--44936 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 84
44761 TATGACACGC
* * * * * * *
44771 ATTTATGACGCGCATTTATGACGTGCATTGAGCGTCATTGAAGCCCTCGTCATAAATTAAGACAA
1 ATTTATGACACGCATATATGACGTACATTGAGCGTCATTGAAGCCCCCATCATAAATGAAAACAA
44836 CACACATTTGTGTGTCATAA
66 CACACA-TTGTGTGTCATAA
* * * **
44856 ATTTATGACACGCATATATGACTTACATTGTGTGTCATTGAAGCCCCCATCATAAATGAAAATGA
1 ATTTATGACACGCATATATGACGTACATTGAGCGTCATTGAAGCCCCCATCATAAATGAAAACAA
44921 CACACATTGTGTGTCA
66 CACACATTGTGTGTCA
44937 GAGAGTATAT
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 10 0.14
85 59 0.86
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATATATGACGTACATTGAGCGTCATTGAAGCCCCCATCATAAATGAAAACAA
CACACATTGTGTGTCATAA
Found at i:47330 original size:15 final size:17
Alignment explanation
Indices: 47300--47331 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
47290 TTGTATCCTG
47300 AGAATGAACTAAAAGCA
1 AGAATGAACTAAAAGCA
47317 AGAA-GAAC-AAAAGCA
1 AGAATGAACTAAAAGCA
47332 CTCATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.06
Consensus pattern (17 bp):
AGAATGAACTAAAAGCA
Found at i:61056 original size:20 final size:22
Alignment explanation
Indices: 61026--61067 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
61016 CTTCTATAGT
*
61026 AATTATATTTATTA-CATTAAA
1 AATTATATTTATAATCATTAAA
61047 AATT-TATTTATAATCATTAAA
1 AATTATATTTATAATCATTAAA
61068 TTAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTATATTTATAATCATTAAA
Found at i:61741 original size:284 final size:284
Alignment explanation
Indices: 61137--61788 Score: 797
Period size: 283 Copynumber: 2.3 Consensus size: 284
61127 GTTTAATTAA
** * *
61137 AACTTTTAAAATGAATG-AATTTAGTTTAATTTTATATTAATTTCAGTTTTACATTTTACAATTG
1 AACTTTTAAAATGAATGCAATTTAGTCCAATTTGATATTAA-TTCAGATTTACATTTTACAATTG
* *
61201 TTCCAATTTGAT-CACTATGTGTTCCTTAATTTATTTAAATTTTATTTATAATTTCATATTTATT
65 TTTCAATTTGATCCACTATGTGTTCCTTAATTTATTTAAATTTCATTTATAATTTCATATTTATT
* * * *
61265 TAATTTAATCCTTAAAAGTATATTTTTTTATCTAAAAATGTCCCATAATTATTTTTATTTTTATA
130 CAAGTTAATCCTTAAAAG-ATA-TTTTTTATCCAAAAATGTCCCATAATTATTTCTATTTTTAT-
*
61330 ATTTACTCCAAATCCTATAAATCACATCATAAATTTCATTTCAAACCCTATAAATTATATCATAA
192 ATTTACTCCAAATCCTATAAACCACATCATAAATTTCATTTCAAACCCTATAAATTATATCATAA
* *
61395 TCTTCAAACCTATAAACTTTTCTTTACT
257 CCTTCAAACCTATAAACTTTTCTTAACT
* * *
61423 ATA-TTTTTAAATGAATACAATTTAGTCCAATTTGATATTAATTCCAGCTTTACATTTTACAATT
1 A-ACTTTTAAAATGAATGCAATTTAGTCCAATTTGATATTAATT-CAGATTTACATTTTACAATT
* * ** *
61487 GTTTTAATTTGATCCA-TGTGTGTTGTTTAATTTATTTAAATTTCACTTTATAATTTCATGTTTA
64 GTTTCAATTTGATCCACTATGTGTTCCTTAATTTATTTAAATTTCA-TTTATAATTTCATATTTA
* * *
61551 TTCAAGTTAGTCCTTAAAA-ATA-TTTTTATCCAAAACTAG-CTCATAATTATTTCTATTTTGTA
128 TTCAAGTTAATCCTTAAAAGATATTTTTTATCCAAAAAT-GTCCCATAATTATTTCTATTTT-TA
* *
61613 T-TTTACTCTAAA-CCTTATAAACCACATTATAAATTTCATTTCAAACCCTATAAATTATATCAT
191 TATTTACTCCAAATCC-TATAAACCACATCATAAATTTCATTTCAAACCCTATAAATTATATCAT
* * *
61676 AACCTTCAAGCCTTGTAAACTTTTGTTCAAC-
255 AACCTTCAAACC-TATAAACTTTTCTT-AACT
* * * *
61707 AACTTTTCAAATGAATGCAATTTAGTCCAATTTGATATTTATTTAGATTTACGA-TTTAAAATTG
1 AACTTTTAAAATGAATGCAATTTAGTCCAATTTGATATTAATTCAGATTTAC-ATTTTACAATTG
*
61771 TTTCAATTTAATCC-CTAT
65 TTTCAATTTGATCCACTAT
61789 ATTTTATCCA
Statistics
Matches: 316, Mismatches: 37, Indels: 29
0.83 0.10 0.08
Matches are distributed among these distances:
282 2 0.01
283 97 0.31
284 82 0.26
285 6 0.02
286 18 0.06
287 76 0.24
288 35 0.11
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (284 bp):
AACTTTTAAAATGAATGCAATTTAGTCCAATTTGATATTAATTCAGATTTACATTTTACAATTGT
TTCAATTTGATCCACTATGTGTTCCTTAATTTATTTAAATTTCATTTATAATTTCATATTTATTC
AAGTTAATCCTTAAAAGATATTTTTTATCCAAAAATGTCCCATAATTATTTCTATTTTTATATTT
ACTCCAAATCCTATAAACCACATCATAAATTTCATTTCAAACCCTATAAATTATATCATAACCTT
CAAACCTATAAACTTTTCTTAACT
Found at i:61971 original size:217 final size:214
Alignment explanation
Indices: 61574--62000 Score: 527
Period size: 216 Copynumber: 2.0 Consensus size: 214
61564 TTAAAAATAT
* * * *
61574 TTTTATCCAAAACTAGCTCATAATTATTTCTATTTTGTATTTTACTCTAAACCTTATAAACCACA
1 TTTTATCCAAAACTAGCTCATAATTATTTATATTTTGTAATTTACTCCAAACCCTATAAACCACA
* * * * * * *
61639 TTATAAATTTCATTTCAAACCCTATAAATTATATCATAACCTTCAAGCCTTGTAAACTTTTGTTC
66 TCATAAAATTCATTTAAAACCCTATAAATTAAATCATAACCTCCAA-CATTGTAAAATTTTGTTC
* * *
61704 AACAACTTTTCAAATGAATGCAATTTAGTCCAATTTGATATTTATTTAGATTTACGATTTAAAAT
130 AACAACTTTTCAAATGAATGCAATTTAATCCAATTTGATATTAATTTAGATTCAC-ATTTAAAAT
*
61769 TGTTTCAATTTAATCCCTATA
194 TATTTCAATTTAATCCCTATA
* * *
61790 TTTTATCCAAAATTAGC-CAATAATTATTTATATTTTTGTAATTTACTCCAAACCCTCTAAATCA
1 TTTTATCCAAAACTAGCTC-ATAATTATTTATA-TTTTGTAATTTACTCCAAACCCTATAAACCA
* *
61854 CATCATAAAATTCATTTAAAACCCTGTAAATTAAATCATAATCTCCAA-ATTGTATAAATTTTGT
64 CATCATAAAATTCATTTAAAACCCTATAAATTAAATCATAACCTCCAACATTGTA-AAATTTTGT
* * * * *
61918 TCACCTACATTTT-AAATGAATGCAATTTAATCCATTTTTATATTAACTTTAGATTCACATTTAT
128 TCAACAAC-TTTTCAAATGAATGCAATTTAATCCAATTTGATATTAA-TTTAGATTCACATTTAA
* *
61982 AATTATTTTAATTTGATCC
191 AATTATTTCAATTTAATCC
62001 TTGTATGTTG
Statistics
Matches: 179, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
215 6 0.03
216 92 0.51
217 81 0.45
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (214 bp):
TTTTATCCAAAACTAGCTCATAATTATTTATATTTTGTAATTTACTCCAAACCCTATAAACCACA
TCATAAAATTCATTTAAAACCCTATAAATTAAATCATAACCTCCAACATTGTAAAATTTTGTTCA
ACAACTTTTCAAATGAATGCAATTTAATCCAATTTGATATTAATTTAGATTCACATTTAAAATTA
TTTCAATTTAATCCCTATA
Found at i:63587 original size:20 final size:21
Alignment explanation
Indices: 63562--63603 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
63552 AGGGTGAGTG
* *
63562 TCGATACTCAAATG-TTAGTA
1 TCGATACTAAAAGGCTTAGTA
63582 TCGATACTAAAAGGCTTAGTA
1 TCGATACTAAAAGGCTTAGTA
63603 T
1 T
63604 TGGTACCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (21 bp):
TCGATACTAAAAGGCTTAGTA
Found at i:64043 original size:26 final size:26
Alignment explanation
Indices: 64014--64070 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
64004 TACATCCCAA
64014 GATGCAGAACCCTCTGACTACACCAT
1 GATGCAGAACCCTCTGACTACACCAT
64040 GATGCAGAACCCTCTGACTACACCAT
1 GATGCAGAACCCTCTGACTACACCAT
64066 GATGC
1 GATGC
64071 TTACCTCAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (26 bp):
GATGCAGAACCCTCTGACTACACCAT
Found at i:68347 original size:94 final size:94
Alignment explanation
Indices: 68185--68372 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 94
68175 TAACAATTAG
68185 CACAACCTATTGAAGATGCCATAGTTGTTTCTTGCTACAAATGTTAGAAGTTTTCCCAATGCCCA
1 CACAACCTATTGAAGATGCCATAGTTGTTTCTTGCTACAAATGTTAGAAGTTTTCCCAATGCCCA
*
68250 AAACCATCTTTTCAGGTGGATAACTTTTA
66 AAACCATCTTTTCAAGTGGATAACTTTTA
* ** * *
68279 CACAACCTATTGAAGGTGCCATAGTTGTTTCTTGCTACAAATGTTAGTTGTTTTCTCAATGCCTA
1 CACAACCTATTGAAGATGCCATAGTTGTTTCTTGCTACAAATGTTAGAAGTTTTCCCAATGCCCA
*
68344 AAACCATCTTTTCAAGTGGATTACTTTTA
66 AAACCATCTTTTCAAGTGGATAACTTTTA
68373 AAATACCTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (94 bp):
CACAACCTATTGAAGATGCCATAGTTGTTTCTTGCTACAAATGTTAGAAGTTTTCCCAATGCCCA
AAACCATCTTTTCAAGTGGATAACTTTTA
Done.