Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003675.1 Hibiscus syriacus cultivar Beakdansim tig00007850_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: 106702
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:592 original size:84 final size:83
Alignment explanation
Indices: 441--1405 Score: 771
Period size: 84 Copynumber: 11.9 Consensus size: 83
431 TTTAAGACAA
* * * * *
441 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATC--TACCAACAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCCCAA-AAGACCTTCGAGTTCGACTAC
*
504 GCTCATCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
523 CATTTGCAACA-AAGCTCAAGGCAAAAAGGGTTATTTGTCTCCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAA-CTTAAGTCGAGAAGGGTTATCTGTC-CCAAAAGACCTTCGAGTTCGACTA
* * *
587 CGCTCAGCTCTAAGTCATAT
64 CGCTCAGCTCCAAGGCACAT
* *
607 CATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTG-CCAACCAAAGACCTTCGAGTTCGACT-
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCC--CAAAAGACCTTCGAGTTCGACTA
*
670 --TTCAGCTCCAAGG--CA-
64 CGCTCAGCTCCAAGGCACAT
* * * * * *
685 CATTTGTAGCATAGA-TTAAGTTGAGAAGGGCTATCTG--CC-AAAGACCCTCAAGTTCGATTAC
1 CATTTGCAGCATA-ACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTAC
* *
746 AC-CAGCT-CGAGGACACAT
65 GCTCAGCTCCAAGG-CACAT
* * * * * * * * *
764 CATTTACAACATAACTTAAGGCTAGAAAGGTTATCTATCACAAAAGACCTTTGAGTTCGACTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTACG
*
829 TTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * * * * * * * *
847 CA-TTGCAGCATAGCTTAAGTCAAGAAGGGCTAT-T-TTCC-AAAGGCCCTCAAGTTTGATTA--
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTACG
* * * *
906 CACAGTTCGAGGGCACAT
66 CTCAGCTCCAAGGCACAT
** * * *
924 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCTCCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-CCAAAAGACCTTCGAGTTCGACTAC
* *
989 GCTCAGCTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* *
1008 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGA-CTTTGAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCC--CAAAAGACCTTCGAGTTCGACTA
*
1071 CGCTCAGCTCCAAGTCACAT
64 CGCTCAGCTCCAAGGCACAT
* ** * * * * * *
1091 AATTTTTAGTATAGCTTAAGTCGAGAAGGGCTATCTG--CC-AAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTACG
* *
1153 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * *
1172 CA-TTACAACATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-CCAAAAGACCTTCGAGTTCGACTAC
* *
1236 GCTCAGCTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * *
1255 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTA-CTG-CCAAATAAAAGACCTTCGAGTTTGACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCC---CAAAAGACCTTCGAGTTCGACT
* *
1318 ACGCTCAACT---AGGAACAT
63 ACGCTCAGCTCCAAGGCACAT
* * *
1336 CATTTGCAGCATAGA-TTAAGTTGAGAAGGGCTATCTG--CC-AAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATA-ACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTAC
*
1397 ACTCAGCTC
65 GCTCAGCTC
1406 AGAGGCAAGT
Statistics
Matches: 702, Mismatches: 137, Indels: 92
0.75 0.15 0.10
Matches are distributed among these distances:
74 17 0.02
75 5 0.01
76 5 0.01
77 42 0.06
78 60 0.09
79 49 0.07
80 51 0.07
81 62 0.09
82 95 0.14
83 92 0.13
84 218 0.31
85 6 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCCCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:907 original size:161 final size:163
Alignment explanation
Indices: 441--1453 Score: 665
Period size: 161 Copynumber: 6.2 Consensus size: 163
431 TTTAAGACAA
* * *
441 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAAC--AAGACCTTCGAGTTTGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTAC
* * * * * * * *
504 GCTCATCTCCAAGGCACATCATTTGCAACAAAGCTCAAGGCAAAAAGGGTTATTTGTCTCCAAAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTA--TCT-TCC-AAA
* * * * * * * *
569 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGTCATAT
127 GACCCTCAAGTTCGATTACAC-CAGCTCGAGGACACAT
* * * ** *
607 CATTTGCAGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT-
1 CATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTA
* * * ** *
670 --TTCAGCTCCAAGG--CA-CATTTGTAGCATAGATTAAGTTGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTTCCAAAGAC
730 CCTCAAGTTCGATTACACCAGCTCGAGGACACAT
130 CCTCAAGTTCGATTACACCAGCTCGAGGACACAT
* * * *
764 CATTTACAACATAACTTAAGGCTAGAAAGGTTATCTATC-ACAAAAGACCTTTGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTAC
** * *
828 ATTCAGCTCCAAGGCACATCA-TTGCAGCATAGCTTAAGTCAAGAAGGGCTATTTTCCAAAGGCC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTTCCAAAGACC
* * *
892 CTCAAGTTTGATTACA-CAGTTCGAGGGCACAT
131 CTCAAGTTCGATTACACCAGCTCGAGGACACAT
* * **
924 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCTCCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTAC
* * * * *
989 GCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTT----CCAAA
* ** * * * * *
1054 GA-CTTTGAGTTCGACTACGCTCAGCTCCAAGTCACAT
127 GACCCTCAAGTTCGATTACAC-CAGCTCGAGGACACAT
* ** * * * * * * * * *
1091 AATTTTTAGTATAGCTTAAGTCGAGAAGGGCTATCT-GC--C-AAAGACCCTCGAGTTCGATTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTAC
* * * * * * * *
1152 ACTCAGCTTCGAGGGCACATCA-TTACAACATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAA
66 GCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCT-T--CC-AA
* * * ** * *
1216 AGACCTTCGAGTTCGACTATGCTCAGCTCTAAGG-CATAT
126 AGACCCTCAAGTTCGATTACAC-CAGCTC-GAGGACACAT
** * * * ** * *
1255 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTA-CTGCCAAATAAAAGACCTTCGAGTTTGACTA
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATC-AACAAAAGACCTTCGAGTTCGACTA
* * * ** *
1319 CGCTCAACT---AGGAACATCATTTGCAGCATAGATTAAGTTGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTTCCAAAGAC
* *
1381 CTTCGAGTTCGATTACACTCAGCTCAGAGG-CA-AGT
130 CCTCAAGTTCGATTACAC-CAGCTC-GAGGACACA-T
* * *
1416 CAAATTTACAGCATAGCTCAAAG-TAGAAAAGGTTATCT
1 C--ATTTACAGCATAACTCAAGGCTAG-AAGGGTTATCT
1454 GGTCAATAAA
Statistics
Matches: 686, Mismatches: 127, Indels: 70
0.78 0.14 0.08
Matches are distributed among these distances:
156 21 0.03
157 42 0.06
158 22 0.03
159 15 0.02
160 51 0.07
161 128 0.19
162 62 0.09
163 87 0.13
164 79 0.12
165 53 0.08
166 43 0.06
167 41 0.06
168 42 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (163 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCAACAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTTCCAAAGACC
CTCAAGTTCGATTACACCAGCTCGAGGACACAT
Found at i:1452 original size:247 final size:245
Alignment explanation
Indices: 441--1454 Score: 841
Period size: 245 Copynumber: 4.2 Consensus size: 245
431 TTTAAGACAA
* * *
441 CATTTGCAGCATAACTCAAGGCTAG-AAGGGTTATC--T-ACCAACAAGACCTTCGAGTTTGACT
1 CATTTACAGCATAACTCAAAG-TAGAAAGGGTTATCTGTCACCAA-AAGACCTTCGAGTTCGACT
* * * * * * * * * * **
502 ACGCTCATCTCCAAGGCACATCATTTGCAACA-AAGCTCAAGGCAAAAAGGGTTATTTGTCTCCA
64 ACGCTCAGCTCTAAGGCATATCATTTGCAGCATAA-CTTAAGTCGAGAAGGGTTATCTGCCAACA
* ** * * *
566 AAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGTCATATCATTTGCAGCATAACTTAAGTTGA
128 AAAGA-CTTCGAGTTCGACTACGCTCAACTC--AGGAACATCATTTGCAGCATAGCTTAAGTCGA
* * * *
631 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTT----TCAGCTCCAAGGCACAT
190 GAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA-TTACACTCAGCTCGAGGGCACAT
* * * * * *
688 --TTGT--AGCATAGA-T-TAAGTTGAGAAGGGCTATCTG---CC-AAAGACCCTCAAGTTCGAT
1 CATT-TACAGCATA-ACTCAAAGTAGA-AAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGAC
* * * * * * * * **
743 TACAC-CAGCTC-GAGGACACATCATTTACAACATAACTTAAGGCTAGAAAGGTTATCTATC-AC
63 TACGCTCAGCTCTAAGG-CATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
* ** * * *
805 AAAAGACCTTTGAGTTCGACTACATTCAGCTCCAAGGCACATCA-TTGCAGCATAGCTTAAGTCA
127 AAAAGA-CTTCGAGTTCGACTACGCTCAACT-C-AGGAACATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
869 AGAAGGGCTATTTTCCAAAGGCCCTCAAGTTTGATTACA--CAGTTCGAGGGCACAT
189 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCGAGGGCACAT
* * *
924 CATTTATAGCATAACTCAAGGCTAG-AAGGGTTATCTGTCTCCAAAAGACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTCAAAG-TAGAAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTA
* *
988 CGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAA
65 CGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAA
* * ** * ** *
1053 AGACTTTGAGTTCGACTACGCTCAGCTCCAAGTCACATAATTTTTAGTATAGCTTAAGTCGAGAA
130 AGACTTCGAGTTCGACTACGCTCAACT-C-AGGAACATCATTTGCAGCATAGCTTAAGTCGAGAA
1118 GGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
193 GGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGC-TCGAGGGCACAT
* * *
1172 CA-TTACAACATAACT-TAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTCAAAGTAGA-AAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTA
* * *
1235 TGCTCAGCTCTAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTA-CTGCCAAATAA
65 CGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-AACAA
* * *
1299 AAGACCTTCGAGTTTGACTACGCTCAACT-AGGAACATCATTTGCAGCATAGATTAAGTTGAGAA
129 AAGA-CTTCGAGTTCGACTACGCTCAACTCAGGAACATCATTTGCAGCATAGCTTAAGTCGAGAA
*
1363 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTC-AGAGGCA-AGT
193 GGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCGAG-GGCACA-T
* *
1416 CAAATTTACAGCATAGCTCAAAGTAGAAAAGGTTATCTG
1 C--ATTTACAGCATAACTCAAAGTAGAAAGGGTTATCTG
1455 GTCAATAAAA
Statistics
Matches: 630, Mismatches: 97, Indels: 80
0.78 0.12 0.10
Matches are distributed among these distances:
234 2 0.00
235 16 0.03
236 13 0.02
237 1 0.00
238 3 0.00
239 46 0.07
240 43 0.07
241 42 0.07
242 24 0.04
243 26 0.04
244 101 0.16
245 132 0.21
246 8 0.01
247 132 0.21
248 41 0.07
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (245 bp):
CATTTACAGCATAACTCAAAGTAGAAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAA
GACTTCGAGTTCGACTACGCTCAACTCAGGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
CTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCGAGGGCACAT
Found at i:2160 original size:38 final size:37
Alignment explanation
Indices: 2073--2414 Score: 195
Period size: 36 Copynumber: 9.6 Consensus size: 37
2063 GAAAAATACA
2073 TATATAATATAT-GATTTTTAAAAATACATTTTGAAAA-
1 TATATAATATATAG-TTTTTAAAAAT-CATTTTGAAAAC
* *
2110 TGTAT-ATAATATAGTTTTTAAAAAAT-ACCTTTGAAAAC
1 TATATAAT-ATATAGTTTTT-AAAAATCA-TTTTGAAAAC
2148 TATATAATATATAGTTTTT-AAAA-CATTTTTAGAAAAC
1 TATATAATATATAGTTTTTAAAAATCA-TTTT-GAAAAC
*
2185 ATAAATAATATATA-TAGTTTT-AAAATCATTTTGAAAAC
1 -TATATAATATATAGT--TTTTAAAAATCATTTTGAAAAC
*
2223 T-TAT-ATAATATAG-TTTT-AAAATCATTTTGAAATC
1 TATATAAT-ATATAGTTTTTAAAAATCATTTTGAAAAC
* *
2257 TATATAATATATAG-TTTAAAGAAAACATTTTTGAAAA-
1 TATATAATATATAGTTTTTAA-AAATCA-TTTTGAAAAC
* *
2294 -ATAT-A-ACATAG-TTTT-AAAA-CGTTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAAATC-ATTTTGAAAAC
* * *
2326 --TAT-ATATATAG--TTTGAAAA-CATTTTTAAAAT
1 TATATAATATATAGTTTTTAAAAATCATTTTGAAAAC
** *
2357 TATATAATATAT-GGCTTTGAAAAT-ATCTTTGAAATA-
1 TATATAATATATAGTTTTTAAAAATCAT-TTTGAAA-AC
*
2393 TATATTATATATAG-TTTTAAAA
1 TATATAATATATAGTTTTTAAAA
2415 CAATTTTTTA
Statistics
Matches: 251, Mismatches: 22, Indels: 65
0.74 0.07 0.19
Matches are distributed among these distances:
31 25 0.10
32 13 0.05
33 5 0.02
34 35 0.14
35 25 0.10
36 48 0.19
37 36 0.14
38 48 0.19
39 14 0.06
40 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAAATCATTTTGAAAAC
Found at i:2215 original size:40 final size:36
Alignment explanation
Indices: 2139--2422 Score: 196
Period size: 34 Copynumber: 8.1 Consensus size: 36
2129 AAAAAATACC
2139 TTTGAAAACT-ATATAATATATAGTTTTTAAAA-CATT
1 TTTGAAAACTAATAT-ATATATAG-TTTTAAAATCATT
2175 TTTAGAAAACATAAATAATATATATAGTTTTAAAATCA-T
1 TTT-GAAAAC-T-AAT-ATATATATAGTTTTAAAATCATT
*
2214 TTTGAAAACTTATATA-ATATAGTTTTAAAATCA-T
1 TTTGAAAACTAATATATATATAGTTTTAAAATCATT
* * *
2248 TTTGAAATCT-ATATAATATATAGTTTAAAGAAAACATT
1 TTTGAAAACTAATAT-ATATATAGTTT-TA-AAATCATT
* *
2286 TTTG-AAA--AATATA-ACATAGTTTTAAAA-CGTT
1 TTTGAAAACTAATATATATATAGTTTTAAAATCATT
*
2317 TTTGAAAAC---TATATATATAGTTTGAAAA-CATT
1 TTTGAAAACTAATATATATATAGTTTTAAAATCATT
* * * *
2349 TTT-AAAA-TTATATAATATATGGCTTTGAAAAT-ATC
1 TTTGAAAACTAATAT-ATATATAG-TTTTAAAATCATT
2384 TTTG-AAA-TATATATTATATATAGTTTTAAAA-CAATT
1 TTTGAAAACTA-ATA-TATATATAGTTTTAAAATC-ATT
2420 TTT
1 TTT
2423 TATATATAGT
Statistics
Matches: 205, Mismatches: 17, Indels: 52
0.75 0.06 0.19
Matches are distributed among these distances:
31 15 0.07
32 24 0.12
33 8 0.04
34 43 0.21
35 37 0.18
36 25 0.12
37 15 0.07
38 12 0.06
39 12 0.06
40 12 0.06
41 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (36 bp):
TTTGAAAACTAATATATATATAGTTTTAAAATCATT
Found at i:2239 original size:34 final size:34
Alignment explanation
Indices: 2073--2414 Score: 194
Period size: 38 Copynumber: 9.6 Consensus size: 34
2063 GAAAAATACA
2073 TATATAATATATGATTTTTAAAAATACATTTTGAAAA-T
1 TATATAATATA-G--TTTT-AAAAT-CATTTTGAAAACT
*
2111 GTATATAATATAGTTTTTAAAAAAT-ACCTTTGAAAAC-
1 -TATATAATATAG-TTTT--AAAATCA-TTTTGAAAACT
2148 TATATAATATATAGTTTTTAAAA-CATTTTTAGAAAACAT
1 TATAT-A-ATATAG-TTTTAAAATCA-TTTT-GAAAAC-T
*
2187 AAATAATATATATAGTTTTAAAATCATTTTGAAAACT
1 -TAT-ATA-ATATAGTTTTAAAATCATTTTGAAAACT
*
2224 TATATAATATAGTTTTAAAATCATTTTGAAATC-
1 TATATAATATAGTTTTAAAATCATTTTGAAAACT
* *
2257 TATATAATATATAGTTTAAAGAAAACATTTTTGAAAA--
1 TATAT-A-ATATAGTTT-TA-AAATCA-TTTTGAAAACT
* *
2294 -ATATAACATAGTTTTAAAA-CGTTTTTGAAAAC-
1 TATATAATATAGTTTTAAAATC-ATTTTGAAAACT
* *
2326 TATAT-ATATAGTTTGAAAA-CATTTTTAAAA-T
1 TATATAATATAGTTTTAAAATCATTTTGAAAACT
*
2357 TATATAATATATGGCTTTGAAAAT-ATCTTTG-AAA-T
1 TATATAATATA--G-TTTTAAAATCAT-TTTGAAAACT
2392 ATATATTATATATAGTTTTAAAA
1 -TATA-TA-ATATAGTTTTAAAA
2415 CAATTTTTTA
Statistics
Matches: 255, Mismatches: 18, Indels: 64
0.76 0.05 0.19
Matches are distributed among these distances:
31 23 0.09
32 21 0.08
33 10 0.04
34 36 0.14
35 34 0.13
36 29 0.11
37 28 0.11
38 37 0.15
39 23 0.09
40 12 0.05
41 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (34 bp):
TATATAATATAGTTTTAAAATCATTTTGAAAACT
Found at i:2430 original size:36 final size:35
Alignment explanation
Indices: 2148--2422 Score: 151
Period size: 35 Copynumber: 7.8 Consensus size: 35
2138 CTTTGAAAAC
* *
2148 TATATAATATATAGTTTTTAAAACATTTTTAGAAAACATA
1 TATATTATATATAG-TTTGAAAACATTTTT---AAA-ATA
* * * *
2188 AATAATATATATAGTTTTAAAATCATTTTGAAAACT-
1 TATATTATATATAGTTTGAAAA-CATTTTTAAAA-TA
* * *
2224 TATA-TA-ATATAGTTTTAAAATCA-TTTTGAAATC
1 TATATTATATATAGTTTGAAAA-CATTTTTAAAATA
* *
2257 TATATAATATATAGTTTAAAGAAAACATTTTTGAAA-A
1 TATATTATATATAGTTT---GAAAACATTTTTAAAATA
* * * *
2294 -ATA-TA-ACATAGTTTTAAAACGTTTTTGAAA-A
1 TATATTATATATAGTTTGAAAACATTTTTAAAATA
*
2325 -CTA-TATATATAGTTTGAAAACATTTTTAAAAT-
1 TATATTATATATAGTTTGAAAACATTTTTAAAATA
* * * * *
2357 TATATAATATATGGCTTTGAAAATATCTTTGAAATA
1 TATATTATATATAG-TTTGAAAACATTTTTAAAATA
*
2393 TATATTATATATAGTTTTAAAACAATTTTT
1 TATATTATATATAGTTTGAAAAC-ATTTTT
2423 TATATATAGT
Statistics
Matches: 189, Mismatches: 30, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
31 19 0.10
32 22 0.12
33 12 0.06
34 33 0.17
35 36 0.19
36 24 0.13
37 6 0.03
38 12 0.06
39 8 0.04
40 17 0.09
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (35 bp):
TATATTATATATAGTTTGAAAACATTTTTAAAATA
Found at i:2487 original size:25 final size:26
Alignment explanation
Indices: 2440--2515 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 26
2430 AGTATATTAT
2440 TTTATTTTATTCTTTTTTATTTACTA
1 TTTATTTTATTCTTTTTTATTTACTA
* *
2466 TTTATTTTGTT-TTTTGTT-TTTATTA
1 TTTATTTTATTCTTTT-TTATTTACTA
2491 TTTATTTAATCATT-TTTTTTATTTA
1 TTTATTT--T-ATTCTTTTTTATTTA
2516 TTTTTCTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 17 0.40
26 12 0.29
27 3 0.07
28 10 0.24
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTATTTTATTCTTTTTTATTTACTA
Found at i:4771 original size:29 final size:31
Alignment explanation
Indices: 4734--4794 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
4724 AATTTAGATA
*
4734 ATGGCCAAAAT-GAAAATTTTG-AAAGTTTG
1 ATGGCCAAAATAGAAAATTTGGAAAAGTTTG
* *
4763 ATGGTCAAAGTAGAAAATTTGGAAAAGTTTG
1 ATGGCCAAAATAGAAAATTTGGAAAAGTTTG
4794 A
1 A
4795 AGAATTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 9 0.33
31 9 0.33
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (31 bp):
ATGGCCAAAATAGAAAATTTGGAAAAGTTTG
Found at i:6938 original size:45 final size:45
Alignment explanation
Indices: 6874--6965 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
6864 GGTAACCATG
* *
6874 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGAAAATATATTGGT
6919 AAAATAAGCTTACGAGCTTATGGGATAAATGGAAAATATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGAAAATATATTGGT
6964 AA
1 AA
6966 GAAATTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGAAAATATATTGGT
Found at i:6948 original size:25 final size:25
Alignment explanation
Indices: 6875--6948 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
6865 GTAACCATGA
6875 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATGGGAT
* *
6900 AAAT--G-GTA--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TATGGGAT
6919 AAAATAAGCTTACGAGCTTATGGGAT
1 -AAATAAGCTTACGAGCTTATGGGAT
6945 AAAT
1 AAAT
6949 GGAAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
22 3 0.08
23 3 0.08
25 15 0.42
26 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATGGGAT
Found at i:10516 original size:20 final size:19
Alignment explanation
Indices: 10491--10543 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
10481 CTAGCCCCAG
10491 CAACCCAGCACCCCATTCTC
1 CAACCCA-CACCCCATTCTC
*
10511 CAACCCAACACCCCATTCTT
1 CAACCC-ACACCCCATTCTC
10531 CAACCCACACCCC
1 CAACCCACACCCC
10544 TAACCCTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 7 0.23
20 23 0.74
21 1 0.03
ACGTcount: A:0.28, C:0.57, G:0.02, T:0.13
Consensus pattern (19 bp):
CAACCCACACCCCATTCTC
Found at i:16069 original size:113 final size:113
Alignment explanation
Indices: 15828--16301 Score: 375
Period size: 113 Copynumber: 4.2 Consensus size: 113
15818 AATCAACATA
* * * * * * * * *
15828 TGATATGAGGTGATGTTTCACTACAAATAAAAGGACA-TAAATAGTTAAAATTCTATGTCATTTG
1 TGATTTGAGGTGATGTTTCACCACAAAGAAAA--AAAGTGAATAGTTAAGATCCTCTATCATTTG
* * * * * * *
15892 AAATTATTTTTATCTCAAATCATTATTTTCTTACAATATAAAGAAATTCC
64 AAATTATTATTATCTCGAATCATCATTTTCTTGCAGTATGAAGAAATTTC
* ** * *
15942 TTATACGAGATGATGTTTCACCATAAAGAAAAAAAGTGAATAGTTAAGATCCTCTATCATTTGAA
1 TGATTTGAGGTGATGTTTCACCACAAAGAAAAAAAGTGAATAGTTAAGATCCTCTATCATTTGAA
* *
16007 ATTATTATTATCTCGAATCATCATTTTCTTGTAGTATGAAGAAATTTT
66 ATTATTATTATCTCGAATCATCATTTTCTTGCAGTATGAAGAAATTTC
* * * * * * * * *
16055 TGATTTGAGGTGATGTTTCACTACACATAAGAATA-TGAATAGTTATGGTTCGT-TGTCATTTGA
1 TGATTTGAGGTGATGTTTCACCACAAAGAAAAAAAGTGAATAGTTA-AGATCCTCTATCATTTGA
* * * *
16118 AATCATTATTGTAC-C-AGATCATCATTTTCTTGCAGTTTGAAGAAAGTTC
65 AATTATTATTAT-CTCGA-ATCATCATTTTCTTGCAGTATGAAGAAATTTC
* * * * ** * * *
16167 TGATTTAATGTGATGTTTCCCCGCAAAGAATAAAGTGTGAATAATTAAGATTCTCTATCATTTAA
1 TGATTTGAGGTGATGTTTCACCACAAAGAA-AAAAAGTGAATAGTTAAGATCCTCTATCATTTGA
* * * * * *
16232 AATTATTATTGTCCCGGATTACCATTTTCTTGTAGTATGAAGGAAA-TTC
65 AATTATTATTATCTCGAATCATCATTTTCTTGCAGTATGAA-GAAATTTC
*
16281 TGATTTGAGGTGATATTTCAC
1 TGATTTGAGGTGATGTTTCAC
16302 TACGTATAAA
Statistics
Matches: 282, Mismatches: 68, Indels: 20
0.76 0.18 0.05
Matches are distributed among these distances:
111 1 0.00
112 83 0.29
113 99 0.35
114 95 0.34
115 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (113 bp):
TGATTTGAGGTGATGTTTCACCACAAAGAAAAAAAGTGAATAGTTAAGATCCTCTATCATTTGAA
ATTATTATTATCTCGAATCATCATTTTCTTGCAGTATGAAGAAATTTC
Found at i:16261 original size:114 final size:111
Alignment explanation
Indices: 15835--16301 Score: 360
Period size: 114 Copynumber: 4.1 Consensus size: 111
15825 ATATGATATG
* * ** * * * *
15835 AGGTGATGTTTCACTACAAATAAAAGGACATAAATAGTTAAAATTCTATGTCATTTGAAATTATT
1 AGGTGATGTTTCACCACAAAGAAAA--ATGTGAATAGTTAAGATTCTCTATCATTTGAAATTATT
* * * ** * ** * * * ***
15900 TTTATCTCAAATCATTATTTTCTTACAATATAAAGAAATTCCTTATACG
64 ATTGTCCCGGATCATCATTTTCTTGTAGTATGAAGAAATT-CTGATTTA
* * * *
15949 AGATGATGTTTCACCATAAAGAAAAAAAGTGAATAGTTAAGATCCTCTATCATTTGAAATTATTA
1 AGGTGATGTTTCACCACAAAG-AAAAATGTGAATAGTTAAGATTCTCTATCATTTGAAATTATTA
* * * * *
16014 TTATCTCGAATCATCATTTTCTTGTAGTATGAAGAAATTTTTGATTTG
65 TTGTCCCGGATCATCATTTTCTTGTAGTATGAAGAAA-TTCTGATTTA
* * * * * * * * *
16062 AGGTGATGTTTCACTACACATAAGAATATGAATAGTTATGGTTCGT-TGTCATTTGAAATCATTA
1 AGGTGATGTTTCACCACAAAGAAAAATGTGAATAGTTAAGATTC-TCTATCATTTGAAATTATTA
* * * *
16126 TTGTACCAGATCATCATTTTCTTGCAGTTTGAAGAAAGTTCTGATTTA
65 TTGTCCCGGATCATCATTTTCTTGTAGTATGAAGAAA-TTCTGATTTA
* * * * *
16174 ATGTGATGTTTCCCCGCAAAGAATAAAGTGTGAATAATTAAGATTCTCTATCATTTAAAATTATT
1 AGGTGATGTTTCACCACAAAGAA-AAA-TGTGAATAGTTAAGATTCTCTATCATTTGAAATTATT
* * *
16239 ATTGTCCCGGATTACCATTTTCTTGTAGTATGAAGGAAATTCTGATTTG
64 ATTGTCCCGGATCATCATTTTCTTGTAGTATGAA-GAAATTCTGATTTA
*
16288 AGGTGATATTTCAC
1 AGGTGATGTTTCAC
16302 TACGTATAAA
Statistics
Matches: 277, Mismatches: 69, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
112 88 0.32
113 86 0.31
114 95 0.34
115 8 0.03
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (111 bp):
AGGTGATGTTTCACCACAAAGAAAAATGTGAATAGTTAAGATTCTCTATCATTTGAAATTATTAT
TGTCCCGGATCATCATTTTCTTGTAGTATGAAGAAATTCTGATTTA
Found at i:16322 original size:114 final size:113
Alignment explanation
Indices: 15978--16355 Score: 378
Period size: 112 Copynumber: 3.4 Consensus size: 113
15968 AGAAAAAAAG
* * * *
15978 TGAATAGTTAAGATCCTCTATCATTTGAAATTATTATTATCTCGAATCATCATTTTCTTGTAGTA
1 TGAATAGTTAAGATTCTCTATCATTTGAAATTATTATTGTCCCGGATCATCATTTTCTTGTAGTA
* * *
16043 TGAAGAAATTTTTGATTTGAGGTGATGTTTCACTACACATAAGAAT-A
66 TGAAGAAAGTTCTGATTTGAGGTGATGTTTCACTACGCATAAGAATAA
* * * * * * *
16090 TGAATAGTTATGGTTCGT-TGTCATTTGAAATCATTATTGTACCAGATCATCATTTTCTTGCAGT
1 TGAATAGTTAAGATTC-TCTATCATTTGAAATTATTATTGTCCCGGATCATCATTTTCTTGTAGT
* * * *
16154 TTGAAGAAAGTTCTGATTTAATGTGATGTTTC-C-CCGCA-AAGAATAAA
65 ATGAAGAAAGTTCTGATTTGAGGTGATGTTTCACTACGCATAAGAAT-AA
* * * *
16201 GTGTGAATAATTAAGATTCTCTATCATTTAAAATTATTATTGTCCCGGATTACCATTTTCTTGTA
1 ---TGAATAGTTAAGATTCTCTATCATTTGAAATTATTATTGTCCCGGATCATCATTTTCTTGTA
* *
16266 GTATGAAGGAAA-TTCTGATTTGAGGTGATATTTCACTACGTATAA-AATGACA
63 GTATGAA-GAAAGTTCTGATTTGAGGTGATGTTTCACTACGCATAAGAAT-A-A
* * *
16318 TGAATAGTTAAGA--CTATGTCACTTGAAATTATTATTGT
1 TGAATAGTTAAGATTCTCTATCATTTGAAATTATTATTGT
16356 ACTGGATTGA
Statistics
Matches: 213, Mismatches: 41, Indels: 24
0.77 0.15 0.09
Matches are distributed among these distances:
109 6 0.03
110 3 0.01
111 2 0.01
112 99 0.46
113 2 0.01
114 86 0.40
115 5 0.02
116 7 0.03
117 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (113 bp):
TGAATAGTTAAGATTCTCTATCATTTGAAATTATTATTGTCCCGGATCATCATTTTCTTGTAGTA
TGAAGAAAGTTCTGATTTGAGGTGATGTTTCACTACGCATAAGAATAA
Found at i:17902 original size:19 final size:19
Alignment explanation
Indices: 17878--17916 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17868 TACTGATTAC
*
17878 ATACATATAACTTCCGAAA
1 ATACATATAAATTCCGAAA
*
17897 ATACATATAAATTCCTAAA
1 ATACATATAAATTCCGAAA
17916 A
1 A
17917 ATTCCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (19 bp):
ATACATATAAATTCCGAAA
Found at i:21596 original size:47 final size:48
Alignment explanation
Indices: 21509--21605 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
21499 GGTGCAAAAC
*
21509 ATATTGTGTTTAAACTTACCCGTAAAACAAATAATATAAAAGTTCAAA
1 ATATTGTGTTTAAACTTACCAGTAAAACAAATAATATAAAAGTTCAAA
* * * *
21557 ATATTGTGTTTGAACTT-CGAGTAAAACAAATAATCTAAAAGTTTAAA
1 ATATTGTGTTTAAACTTACCAGTAAAACAAATAATATAAAAGTTCAAA
21604 AT
1 AT
21606 TTTAACTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 28 0.64
48 16 0.36
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (48 bp):
ATATTGTGTTTAAACTTACCAGTAAAACAAATAATATAAAAGTTCAAA
Found at i:26663 original size:2 final size:2
Alignment explanation
Indices: 26656--26698 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
26646 AGATAAATTA
26656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26698 A
1 A
26699 AACCATCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30418 original size:21 final size:18
Alignment explanation
Indices: 30395--30433 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30385 CTTATTTATT
30395 ATTATATATT-TTTTAATA
1 ATTAT-TATTATTTTAATA
*
30413 ATTATTGTTATTTTAATA
1 ATTATTATTATTTTAATA
30431 ATT
1 ATT
30434 TTACTGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTATTATTATTTTAATA
Found at i:32140 original size:2 final size:2
Alignment explanation
Indices: 32133--32179 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
32123 AAATAAATAA
32133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32175 AT AT A
1 AT AT A
32180 CTAGCTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39694 original size:20 final size:20
Alignment explanation
Indices: 39662--39733 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
39652 ACTTATATAA
*
39662 AGTATCGAAACTCTTGTGGC-
1 AGTATCGATACTCTTG-GGCT
*
39682 AGAATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
39702 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
39722 AGTATCGATACT
1 AGTATCGATACT
39734 TTTAGTATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 3 0.06
20 45 0.94
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCT
Found at i:42132 original size:16 final size:16
Alignment explanation
Indices: 42108--42153 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
42098 TGGGGTCATT
*
42108 TTTAATTTTTTTAATC
1 TTTATTTTTTTTAATC
42124 TTTATTTTTTTT-A-C
1 TTTATTTTTTTTAATC
42138 TTT-TTTTATTTTAATC
1 TTTATTTT-TTTTAATC
42154 CTAAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 4 0.15
14 8 0.31
15 2 0.08
16 12 0.46
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTTTAATC
Found at i:42667 original size:31 final size:32
Alignment explanation
Indices: 42632--42696 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
42622 TTAATTTCTT
*
42632 AACCTTTTTGGCTCAACC-AAATATATTATGA
1 AACCTTTTCGGCTCAACCAAAATATATTATGA
42663 AACCTTTTCGGCTCAACCAAAATATATTATGA
1 AACCTTTTCGGCTCAACCAAAATATATTATGA
42695 AA
1 AA
42697 AAGGTAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (32 bp):
AACCTTTTCGGCTCAACCAAAATATATTATGA
Found at i:55508 original size:34 final size:34
Alignment explanation
Indices: 55460--55525 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
55450 CTTTGGCGTA
*
55460 ATCCTCATGAAGTTGATCTCCGGCCGTAAGGCAC
1 ATCCTCATGAAGTTGATCTCCGGCCGAAAGGCAC
*
55494 ATCCTCATGGAGTTGATCTCCGGCCGAAAGGC
1 ATCCTCATGAAGTTGATCTCCGGCCGAAAGGC
55526 GCTCGACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23
Consensus pattern (34 bp):
ATCCTCATGAAGTTGATCTCCGGCCGAAAGGCAC
Found at i:59477 original size:2 final size:2
Alignment explanation
Indices: 59404--59460 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
59394 AAAAAAAAGA
*
59404 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
59446 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
59461 CTTGATGGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66905 original size:13 final size:13
Alignment explanation
Indices: 66887--66938 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
66877 TTTTTTTCTA
66887 ATTTCAAAACTTG
1 ATTTCAAAACTTG
* *
66900 ATTTCAAAATTTTTCTA
1 ATTTCAAAA---CT-TG
66917 ATTTCAAAACTTG
1 ATTTCAAAACTTG
66930 ATTTCAAAA
1 ATTTCAAAA
66939 ATCTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 1 0.03
16 1 0.03
17 10 0.32
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:66913 original size:30 final size:30
Alignment explanation
Indices: 66879--66938 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
66869 AATTTCATTT
66879 TTTTTCTAATTTCAAAACTTGATTTCAAAA
1 TTTTTCTAATTTCAAAACTTGATTTCAAAA
66909 TTTTTCTAATTTCAAAACTTGATTTCAAAA
1 TTTTTCTAATTTCAAAACTTGATTTCAAAA
66939 ATCTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTTCTAATTTCAAAACTTGATTTCAAAA
Found at i:73965 original size:189 final size:189
Alignment explanation
Indices: 73645--74024 Score: 724
Period size: 189 Copynumber: 2.0 Consensus size: 189
73635 CAACTGACAT
73645 TAGAGACATTTGGCTGGTTGCTGATACCATTAATGACATTAAAAAAAAACTTGTATGTGAATAAT
1 TAGAGACATTTGGCTGGTTGCTGATACCATTAATGACATTAAAAAAAAACTTGTATGTGAATAAT
* *
73710 TTACTTGATAGTTGATACAGGACCGTAACAATATACAAAAGAAGGTAAATATTGGATGAACCAAT
66 TTACTTGATAGTTAATACAGGACAGTAACAATATACAAAAGAAGGTAAATATTGGATGAACCAAT
73775 AATTTATACCCTCCAATTGGGAAAACTTAAAAAAATGAACATATCTCAACACGTTTTCG
131 AATTTATACCCTCCAATTGGGAAAACTTAAAAAAATGAACATATCTCAACACGTTTTCG
* *
73834 TAGAGACATTTGGCTGGTTGCTGATACCATTAATGACATTAAAAAAAAACTTTTATGTGAATAGT
1 TAGAGACATTTGGCTGGTTGCTGATACCATTAATGACATTAAAAAAAAACTTGTATGTGAATAAT
73899 TTACTTGATAGTTAATACAGGACAGTAACAATATACAAAAGAAGGTAAATATTGGATGAACCAAT
66 TTACTTGATAGTTAATACAGGACAGTAACAATATACAAAAGAAGGTAAATATTGGATGAACCAAT
73964 AATTTATACCCTCCAATTGGGAAAACTTAAAAAAATGAACATATCTCAACACGTTTTCG
131 AATTTATACCCTCCAATTGGGAAAACTTAAAAAAATGAACATATCTCAACACGTTTTCG
74023 TA
1 TA
74025 CCCCTAAAAT
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 187 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (189 bp):
TAGAGACATTTGGCTGGTTGCTGATACCATTAATGACATTAAAAAAAAACTTGTATGTGAATAAT
TTACTTGATAGTTAATACAGGACAGTAACAATATACAAAAGAAGGTAAATATTGGATGAACCAAT
AATTTATACCCTCCAATTGGGAAAACTTAAAAAAATGAACATATCTCAACACGTTTTCG
Found at i:78411 original size:29 final size:29
Alignment explanation
Indices: 78368--78450 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
78358 CTCACCTAAC
78368 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
78398 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
78427 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
78451 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:83400 original size:29 final size:29
Alignment explanation
Indices: 83357--83437 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
83347 CTCACCTAAC
83357 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
83387 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
83416 TAAATGATGTAAGCAATGACAT
1 TAAATGATGTAAGCAATGACAT
83438 TAATTTAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:88390 original size:29 final size:29
Alignment explanation
Indices: 88347--88429 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
88337 CTCACCTAAC
88347 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
88377 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
88406 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
88430 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:91452 original size:24 final size:22
Alignment explanation
Indices: 91425--91468 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
91415 TATTCAACTA
91425 AATTGTATGTTAATGAAAAATTGG
1 AATTGTAT-TT-ATGAAAAATTGG
* *
91449 AATTTTATTTATTAAAAATT
1 AATTGTATTTATGAAAAATT
91469 TAACTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 2 0.11
24 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (22 bp):
AATTGTATTTATGAAAAATTGG
Found at i:96612 original size:13 final size:14
Alignment explanation
Indices: 96594--96626 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
96584 GTGATGCGAT
96594 GAATGAT-ATGTTA
1 GAATGATAATGTTA
96607 GAATGATAATGTTA
1 GAATGATAATGTTA
*
96621 AAATGA
1 GAATGA
96627 ACATTGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (14 bp):
GAATGATAATGTTA
Found at i:97879 original size:17 final size:18
Alignment explanation
Indices: 97846--97886 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
97836 TTATGAGGGA
97846 GGAATCTGTGAAGGAATT
1 GGAATCTGTGAAGGAATT
*
97864 GGAATCTGT-CAGGAATT
1 GGAATCTGTGAAGGAATT
97881 GGAATC
1 GGAATC
97887 CATTCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (18 bp):
GGAATCTGTGAAGGAATT
Found at i:98781 original size:248 final size:242
Alignment explanation
Indices: 98268--98828 Score: 743
Period size: 248 Copynumber: 2.3 Consensus size: 242
98258 GTTTCACCCA
* *
98268 ACCCGACCCGACCCGAATATATGAATTAGAAACTCGACCCG-AATAATAAAAAATTATTTTTATT
1 ACCCGA-CCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATT
*
98332 CAAT-AAAAATAGTGACTTAATTGGAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCC
65 CAATAAAAAACAGTGACTTAATTGG-AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCC
* *
98396 TAAATATAAGGTAAAATTATATTTTTAGGTCGGGTTAGGTATTTTCACCCTAAACCCGAACCGAC
129 TAAATATAAGGTAAAATTATATATTT--GTCGGGTCAGGTATTTTCACCCTAAACCCGAACCGAC
98461 CCGAATATCACACTTAAACAAAAACCGACCCGCCCAACCAAAATAAAGTTTC
192 CCGAATATCACACTT-AACAAAAACCGACCCGCCCAACCAAAATAAAGTTTC
98513 ACCCGACCGACCCGAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAAATATTTT
1 ACCCGACCGACCCGAATATATGAATTAG-AA---ACCCGACCCGAAATAAT-AAAAAAATATTTT
98578 TATTCAATAAAAAAACAGTGACTTAATT-G-AAAAATTATATATAGA-GGGT-TTATTGTAATTA
61 TATTCAAT-AAAAAACAGTGACTTAATTGGAAAAAATTATATATAGAGGGGTATTATTGTAATTA
98639 -TCCTAAATATATATGGT-AAATTATATATTT-TCGGGTCAGGTATTTTTCACCCTAAACCGAAC
125 TTCCTAAATATA-A-GGTAAAATTATATATTTGTCGGGTCAGGTA-TTTTCACCCTAAA-C---C
* ** * * *
98701 TCGACCCGACCCGAATATCACACTT-A-AAAGTCCGATCGGACCCGACCAAAATAAAGTTTC
183 -CGAACCGACCCGAATATCACACTTAACAAAAACCGACCCG-CCCAACCAAAATAAAGTTTC
98761 A-CCGACGCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATA-TTTTATT
1 ACCCGAC-CGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATT
98824 CAATA
65 CAATA
98829 TGAATAAGTT
Statistics
Matches: 287, Mismatches: 11, Indels: 40
0.85 0.03 0.12
Matches are distributed among these distances:
241 1 0.00
242 11 0.04
243 9 0.03
244 50 0.17
245 21 0.07
246 12 0.04
247 41 0.14
248 58 0.20
249 23 0.08
250 43 0.15
251 1 0.00
252 17 0.06
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (242 bp):
ACCCGACCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAAAAATATTTTTATTC
AATAAAAAACAGTGACTTAATTGGAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTA
AATATAAGGTAAAATTATATATTTGTCGGGTCAGGTATTTTCACCCTAAACCCGAACCGACCCGA
ATATCACACTTAACAAAAACCGACCCGCCCAACCAAAATAAAGTTTC
Found at i:101369 original size:15 final size:16
Alignment explanation
Indices: 101337--101377 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
101327 ATATGTGTAC
101337 TGTGTGAATACATATA
1 TGTGTGAATACATATA
101353 TGTGTGAATAC-TATA
1 TGTGTGAATACATATA
101368 TGTGTGAATA
1 TGTGTGAATA
101378 TGCCTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (16 bp):
TGTGTGAATACATATA
Found at i:101575 original size:15 final size:15
Alignment explanation
Indices: 101537--101576 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
101527 TGATATAAAT
101537 ATAAGAA-AT-TGTG
1 ATAAGAAGATATGTG
*
101550 ATATG-AGATATGTG
1 ATAAGAAGATATGTG
101564 ATAAGAAGATATG
1 ATAAGAAGATATG
101577 AGACTTCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 1 0.05
13 6 0.27
14 8 0.36
15 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (15 bp):
ATAAGAAGATATGTG
Found at i:104928 original size:3 final size:3
Alignment explanation
Indices: 104922--104952 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
104912 AATGTCCATA
104922 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
104953 ATAAAGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:104942 original size:17 final size:17
Alignment explanation
Indices: 104920--104952 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
104910 ATAATGTCCA
104920 TATATTATTATTATTAT
1 TATATTATTATTATTAT
104937 TATATTATTATTATTA
1 TATATTATTATTATTA
104953 ATAAAGATCC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTATTATTATTAT
Found at i:104944 original size:14 final size:14
Alignment explanation
Indices: 104925--104952 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
104915 GTCCATATAT
104925 TATTATTATTATTA
1 TATTATTATTATTA
104939 TATTATTATTATTA
1 TATTATTATTATTA
104953 ATAAAGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Done.