Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001605.1 Hibiscus syriacus cultivar Beakdansim tig00003189_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: 98105
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:860 original size:2 final size:2
Alignment explanation
Indices: 848--895 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
838 AGATACAGAA
848 AT AT A- AT AT AT AT AT AT AT -T 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
888 AT AT AT AT
1 AT AT AT AT
896 GGTTAATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12688 original size:2 final size:2
Alignment explanation
Indices: 12681--12708 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12671 ATAGGATTAG
12681 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
12709 TTTTAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15257 original size:23 final size:23
Alignment explanation
Indices: 15227--15279 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
15217 TACTTTACCC
*
15227 TTATTATTGTTATATTAT-TATTA
1 TTATTATTATTAT-TTATCTATTA
*
15250 TTATTATTATTATTTTTCTATTA
1 TTATTATTATTATTTATCTATTA
*
15273 TTTTTAT
1 TTATTAT
15280 AGGGTTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTATTATTATTTATCTATTA
Found at i:15274 original size:3 final size:3
Alignment explanation
Indices: 15227--15263 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
15217 TACTTTACCC
*
15227 TTA TTA TTG TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
15264 TTTCTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15691 original size:11 final size:10
Alignment explanation
Indices: 15651--15701 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
15641 AAGAAATCAG
*
15651 AGAAAAAAAA
1 AGAAAGAAAA
15661 AGAAA-AAAA
1 AGAAAGAAAA
*
15670 CATAAAG-AAA
1 -AGAAAGAAAA
15680 AGAAACGAAAA
1 AGAAA-GAAAA
15691 AGAAAGAAAA
1 AGAAAGAAAA
15701 A
1 A
15702 AGAGACCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 8 0.23
10 19 0.54
11 8 0.23
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:15696 original size:15 final size:14
Alignment explanation
Indices: 15651--15699 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
15641 AAGAAATCAG
*
15651 AGAAAAAAAAAGAA
1 AGAAACAAAAAGAA
* *
15665 AAAAACATAAAGAAA
1 AGAAACAAAAAG-AA
15680 AGAAACGAAAAAGAA
1 AGAAAC-AAAAAGAA
15695 AGAAA
1 AGAAA
15700 AAAGAGACCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (14 bp):
AGAAACAAAAAGAA
Found at i:16637 original size:2 final size:2
Alignment explanation
Indices: 16630--16654 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16620 TAACCTAAGT
16630 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16655 GTAACATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17924 original size:46 final size:46
Alignment explanation
Indices: 17873--17977 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
17863 CTATATGACT
* * *
17873 ATATGAAATTATATATGAATATGCAATATGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
*
17919 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
17965 ATATGAAAT-ACAT
1 ATATGAAATGACAT
17978 GGTTACACAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 51 0.93
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
Found at i:18182 original size:38 final size:38
Alignment explanation
Indices: 18126--18221 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
18116 TATAGGACAT
* *
18126 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
18164 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
18202 ATGATAGGTCCTTGGGGACA
1 ATGATAGGTCCTTCGGGACA
18222 TTTATACGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:18198 original size:21 final size:21
Alignment explanation
Indices: 18134--18202 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
18124 ATATGATAGG
* *
18134 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
18155 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
18172 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
18193 TCCTTCGGGA
1 TCCTTCGGGA
18203 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:18827 original size:2 final size:2
Alignment explanation
Indices: 18820--18864 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18810 GGGTGTTACA
18820 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
18862 AT A
1 AT A
18865 AATAGATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25226 original size:12 final size:13
Alignment explanation
Indices: 25197--25226 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25187 TTTGTAAGTA
25197 AAAAAATGTTAAG
1 AAAAAATGTTAAG
*
25210 AAAAAATGTTAAT
1 AAAAAATGTTAAG
25223 AAAA
1 AAAA
25227 TAAAAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
AAAAAATGTTAAG
Found at i:26508 original size:25 final size:23
Alignment explanation
Indices: 26480--26537 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
26470 TTTTCAAAAT
26480 ATTTTCAAAACTATATATTATATAC
1 ATTTTCAAAACTATATA--ATATAC
* * *
26505 ATTTTTACAACTATATAATATAT
1 ATTTTCAAAACTATATAATATAC
26528 ATTTTCAAAA
1 ATTTTCAAAA
26538 TATTTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 13 0.46
25 15 0.54
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTTCAAAACTATATAATATAC
Found at i:26509 original size:36 final size:36
Alignment explanation
Indices: 26365--26867 Score: 393
Period size: 36 Copynumber: 14.1 Consensus size: 36
26355 TATTAAATAA
* * *
26365 AAAATCATTTTTAAAACTATATATTATATATGTTTTTA
1 AAAAT-ATTTTCAAAACTATATATTATATAT-ATTTTC
* * *
26403 AAAATTGTTTTCAAAAC-ATATAATATATGTATTTTC
1 AAAA-TATTTTCAAAACTATATATTATATATATTTTC
* *
26439 AAAAATTATTTTTACAACTATATA--ATATATATTTTC
1 -AAAA-TATTTTCAAAACTATATATTATATATATTTTC
26475 AAAATATTTTCAAAACTATATA-T-TATATA----C
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
* *
26505 ---AT-TTTT-ACAACTATATAATATATAT-T-TTC
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
26534 AAAATATTTTCAAAACTATATA-T-TATATA----C
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
26564 -----ATTTTCAAAACTATATATTATATATATTTTC
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
*
26595 AAAATATTTTTAAAAAACTATAAATTATATATATATATATTT-
1 AAAATA-TTTT-CAAAACTAT--A-TAT-TATATATAT-TTTC
*
26637 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAATATTTTC-AAAACTATATATTATATATA--TTTTC
*
26676 AAAATATTTTTAAAAACTATATATTATATATATGTTTTC
1 AAAATA-TTTTCAAAACTATATATTATATATA--TTTTC
*
26715 AAAATATTTTTAAAAACTATATATTATATATATATGTTTTC
1 AAAATA-TTTTCAAAACTATATA-T-TATATATA--TTTTC
*
26756 AAAATATTTTCAAAACTATATAATATATATA-TTTC
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
*
26791 AAAAATGTTTTCAAAACTATATATTATATATATTTTC
1 -AAAATATTTTCAAAACTATATATTATATATATTTTC
** *
26828 AAAATGCTTTCAAAACTATATA--ATATATTTTTTC
1 AAAATATTTTCAAAACTATATATTATATATATTTTC
26862 GAAAAT
1 -AAAAT
26868 CAATTTTTTT
Statistics
Matches: 397, Mismatches: 25, Indels: 89
0.78 0.05 0.17
Matches are distributed among these distances:
25 27 0.07
26 6 0.02
27 13 0.03
29 1 0.00
30 2 0.01
31 1 0.00
32 7 0.02
33 5 0.01
34 43 0.11
35 13 0.03
36 66 0.17
37 41 0.10
38 40 0.10
39 58 0.15
40 21 0.05
41 36 0.09
42 14 0.04
43 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (36 bp):
AAAATATTTTCAAAACTATATATTATATATATTTTC
Found at i:26514 original size:59 final size:59
Alignment explanation
Indices: 26446--26625 Score: 288
Period size: 59 Copynumber: 3.0 Consensus size: 59
26436 TTCAAAAATT
26446 ATTTTTACAACTATATAATATATATTTTCAAAATATTTTCAAAACTATATATTATATAC
1 ATTTTTACAACTATATAATATATATTTTCAAAATATTTTCAAAACTATATATTATATAC
26505 ATTTTTACAACTATATAATATATATTTTCAAAATATTTTCAAAACTATATATTATATAC
1 ATTTTTACAACTATATAATATATATTTTCAAAATATTTTCAAAACTATATATTATATAC
* * * *
26564 ATTTTCAAAACTATATATTATATATATTTTCAAAATATTTTTAAAAAACTATAAATTATATA
1 ATTTTTACAACTATATA--ATATATATTTTCAAAATA-TTTT-CAAAACTATATATTATATA
26626 TATATATATT
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
59 74 0.65
61 18 0.16
62 4 0.04
63 17 0.15
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (59 bp):
ATTTTTACAACTATATAATATATATTTTCAAAATATTTTCAAAACTATATATTATATAC
Found at i:26585 original size:23 final size:25
Alignment explanation
Indices: 26539--26598 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
26529 TTTTCAAAAT
26539 ATTTTCAAAACTATATATTATATAC
1 ATTTTCAAAACTATATATTATATAC
*
26564 ATTTTCAAAACTATATATTATATAT
1 ATTTTCAAAACTATATATTATATAC
26589 ATTTTCAAAA
1 ATTTTCAAAA
26599 TATTTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTTCAAAACTATATATTATATAC
Found at i:26660 original size:28 final size:28
Alignment explanation
Indices: 26628--26679 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
26618 ATTATATATA
26628 TATATATT-TA-AAATGTTTTCAAAAAC
1 TATATATTATATAAATGTTTTCAAAAAC
*
26654 TATATATTATATATATGTTTTCAAAA
1 TATATATTATATAAATGTTTTCAAAA
26680 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 2 0.09
28 13 0.57
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
TATATATTATATAAATGTTTTCAAAAAC
Found at i:26680 original size:39 final size:37
Alignment explanation
Indices: 26564--26867 Score: 334
Period size: 39 Copynumber: 8.0 Consensus size: 37
26554 TATTATATAC
26564 ATTTTCAAAACTATATATTATATATA-TTTTCAAAAT
1 ATTTTCAAAACTATATATTATATATATTTTTCAAAAT
* * *
26600 ATTTTTAAAAAACTATAAATTATATATATATATATTTAAAAT
1 A-TTTT-CAAAACTATATATTATATATAT-T-T-TTCAAAAT
*
26642 GTTTTCAAAAACTATATATTATATATATGTTTTCAAAAT
1 ATTTTC-AAAACTATATATTATATATAT-TTTTCAAAAT
*
26681 ATTTTTAAAAACTATATATTATATATATGTTTTCAAAAT
1 A-TTTTCAAAACTATATATTATATATAT-TTTTCAAAAT
*
26720 ATTTTTAAAAACTATATATTATATATATATGTTTTCAAAAT
1 A-TTTTCAAAACTATATA-T-TATATATAT-TTTTCAAAAT
*
26761 ATTTTCAAAACTATATA--ATATATATATTTCAAAAAT
1 ATTTTCAAAACTATATATTATATATATTTTTC-AAAAT
*
26797 GTTTTCAAAACTATATATTATATATA-TTTTCAAAAT
1 ATTTTCAAAACTATATATTATATATATTTTTCAAAAT
**
26833 GCTTTCAAAACTATATA--ATATAT-TTTTTCGAAAAT
1 ATTTTCAAAACTATATATTATATATATTTTTC-AAAAT
26868 CAATTTTTTT
Statistics
Matches: 238, Mismatches: 15, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
34 11 0.05
35 9 0.04
36 51 0.21
37 8 0.03
38 26 0.11
39 57 0.24
40 22 0.09
41 47 0.20
42 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
ATTTTCAAAACTATATATTATATATATTTTTCAAAAT
Found at i:28203 original size:15 final size:14
Alignment explanation
Indices: 28140--28207 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 14
28130 TTCATATTCA
28140 AGAAAA-AAAAAAG
1 AGAAAAGAAAAAAG
28153 AGAAAAGATAGAAAAAG
1 AGAAAAG--A-AAAAAG
*
28170 AGAAGAAGGAGAAGAAG
1 AGAA-AA-GA-AAAAAG
*
28187 A-AGAAGAAAAAAG
1 AGAAAAGAAAAAAG
28200 AGAAAAGA
1 AGAAAAGA
28208 TAGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
13 12 0.27
14 7 0.16
15 2 0.05
16 2 0.05
17 18 0.41
18 2 0.05
19 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (14 bp):
AGAAAAGAAAAAAG
Found at i:28223 original size:19 final size:18
Alignment explanation
Indices: 28146--28260 Score: 79
Period size: 18 Copynumber: 6.7 Consensus size: 18
28136 TTCAAGAAAA
28146 AAAAAAGAGAAAAGATAG
1 AAAAAAGAGAAAAGATAG
28164 -AAAAAGAG--AAGA-AG
1 AAAAAAGAGAAAAGATAG
* * *
28178 -GAGAAGA-AGAAGA-AG
1 AAAAAAGAGAAAAGATAG
28193 AAAAAAGAGAAAAGATAG
1 AAAAAAGAGAAAAGATAG
* *
28211 AAAAATAGGGAAAATATAGG
1 AAAAA-AGAGAAAAGATA-G
28231 AAAAAAGA-AGAAA-ATAGG
1 AAAAAAGAGA-AAAGATA-G
28249 AAAAAAGA-AAAA
1 AAAAAAGAGAAAA
28261 AAAATAAAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.09
15 10 0.12
16 5 0.06
17 16 0.20
18 22 0.27
19 15 0.19
20 6 0.07
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (18 bp):
AAAAAAGAGAAAAGATAG
Found at i:31078 original size:216 final size:218
Alignment explanation
Indices: 30644--31095 Score: 667
Period size: 216 Copynumber: 2.1 Consensus size: 218
30634 TCATCTGTTG
* **
30644 GTCTTTCGAGCAAGATGATAAGTCATTCAGGCCACCTATAAGACCTTTGGGCAAGTTACTTTCAT
1 GTCTTTCGAGCAAGATGACAAGTCATTCAGGCCACCTATAAGACCTTTGGGCAAAATACTTTCAT
* * * **
30709 ATGATGATTTGAAAAATGAAAAAAATGATTTTCAAAGTTTCTCATTCAATATTTTTAGAAAATTA
66 ATGATAATTTGAAAAATGAAAAAAATGATTTTCAAAGTTCCTCATTCAATATTTTCAGAAAAACA
30774 AAATTATGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAAATTGG
131 AAATTATGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAAATTGG
*
30839 TAAGTCATTCGGGTCAACAGTAA
196 TAAGTCATTCGGGCCAACAGTAA
* * * *
30862 GTTTTTCGAGCAAGATGACAAGTCATTCAGGTCATCTATAAGACCTTTGGGCAAAATGCTTTCAT
1 GTCTTTCGAGCAAGATGACAAGTCATTCAGGCCACCTATAAGACCTTTGGGCAAAATACTTTCAT
* * * *
30927 ATGATAATTTGAAAAATGACAAAGA-GA-TTTCAAAGTTCCTCATTTAGTATTTTCA-AAAAACA
66 ATGATAATTTGAAAAATGAAAAAAATGATTTTCAAAGTTCCTCATTCAATATTTTCAGAAAAACA
* *
30989 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAATTTG
131 AAA-TTATGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAAATTG
* * *
31054 GTAAGTCCTTTGGGCCATCAGTAA
195 GTAAGTCATTCGGGCCAACAGTAA
*
31078 GTCTTTCGAGCATGATGA
1 GTCTTTCGAGCAAGATGA
31096 TTAAATCCTT
Statistics
Matches: 209, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
215 8 0.04
216 119 0.57
217 2 0.01
218 80 0.38
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (218 bp):
GTCTTTCGAGCAAGATGACAAGTCATTCAGGCCACCTATAAGACCTTTGGGCAAAATACTTTCAT
ATGATAATTTGAAAAATGAAAAAAATGATTTTCAAAGTTCCTCATTCAATATTTTCAGAAAAACA
AAATTATGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAAATTGG
TAAGTCATTCGGGCCAACAGTAA
Found at i:31321 original size:258 final size:258
Alignment explanation
Indices: 30865--31381 Score: 777
Period size: 258 Copynumber: 2.0 Consensus size: 258
30855 ACAGTAAGTT
* * * *
30865 TTTCGAGCAAGATGACAAGTCATTCAGGTCATCTATAAGACCTTTGGGCAAAATGCTTTCATATG
1 TTTCGAGCAAGATGACAAGTCATTCAGGCCATCTATAAGACATTTAGGCAAAATGCTTTCATAAG
30930 ATAATTTGAAAAATGACAAAGAGATTTCAAAGTTCCTCATTTAGTATTTTCAAAAAACAAAATTT
66 ATAATTTGAAAAATGACAAAGAGATTTCAAAGTTCCTCATTTAGTATTTTCAAAAAACAAAATTT
* * *
30995 TTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACTTAGTAAACTATTTCCAAATTTGGTAAGT
131 TTGAAAAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAATTTAGTAAGT
*** *
31060 CCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAATC
196 CCTTCAAGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAATC
* * *
31123 TTTCGAGCAAGATGACAAGTCTTTCGGGCCATCTATAAGACATTTAGGCAAGATGCTTTCATAAG
1 TTTCGAGCAAGATGACAAGTCATTCAGGCCATCTATAAGACATTTAGGCAAAATGCTTTCATAAG
* * * ***
31188 ATAATTTGAAAAATGAGAAAGCA-ATTTTAAAGGTTTCTCATTTAGTATTTTCAAAAAGTGAAAT
66 ATAATTTGAAAAATGACAAAG-AGATTTCAAA-GTTCCTCATTTAGTATTTTCAAAAAACAAAAT
*
31252 TTTTTAAAAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAA-TTAGTAA
129 TTTTGAAAAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAATTTAGTAA
* * * *
31316 GTCCTTCAAGCCATCGGCAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATTTTTCAATC
194 GTCCTTCAAGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAATC
31381 T
1 T
31382 CACTTAAGAC
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
258 149 0.64
259 83 0.36
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (258 bp):
TTTCGAGCAAGATGACAAGTCATTCAGGCCATCTATAAGACATTTAGGCAAAATGCTTTCATAAG
ATAATTTGAAAAATGACAAAGAGATTTCAAAGTTCCTCATTTAGTATTTTCAAAAAACAAAATTT
TTGAAAAGTAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAATTTAGTAAGT
CCTTCAAGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAATC
Found at i:31518 original size:3 final size:3
Alignment explanation
Indices: 31512--31542 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31502 GGTTTTTTTA
31512 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31543 TATTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35376 original size:45 final size:45
Alignment explanation
Indices: 35315--35447 Score: 221
Period size: 45 Copynumber: 3.0 Consensus size: 45
35305 AAATTTCTTG
* *
35315 CCAATATATTTTCCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
* *
35360 CCAATATGCTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
*
35405 TCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
35448 GCATGGTTAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (45 bp):
CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
Found at i:38599 original size:35 final size:35
Alignment explanation
Indices: 38560--38639 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
38550 GGAGTTGGGC
* *
38560 ATGTAATTGAAGTGTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
*
38595 ATGTAATTGAAGTATTTTGGATTTTGAGGTTTAAA
1 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
38630 ATGTAATTGA
1 ATGTAATTGA
38640 TGATTGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAAA
Found at i:39014 original size:18 final size:17
Alignment explanation
Indices: 38991--39033 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
38981 ATAATATTTT
*
38991 AATAATAATTTTGACATA
1 AATAATAATATTGAC-TA
39009 AATAATAATATTGACTA
1 AATAATAATATTGACTA
39026 AATTAATA
1 AA-TAATA
39034 TAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
AATAATAATATTGACTA
Found at i:39749 original size:2 final size:2
Alignment explanation
Indices: 39742--39767 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39732 AATTTGAATA
39742 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
39768 TTGTAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49428 original size:90 final size:90
Alignment explanation
Indices: 49275--49589 Score: 497
Period size: 90 Copynumber: 3.5 Consensus size: 90
49265 AGCATTTTGC
* * * * *
49275 CTGAAGGTCTTATGG-TTGCCTGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAATTTCT
1 CTGAAGGTCTTACGGATGGCCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCT
*
49339 TAAATCTCATTTGAAAACATCCTGCA
65 TAGATCTCATTTGAAAACATCCTGCA
* * *
49365 CTGAAGGTCTTACGGATGGCCTGAAGGACTTAAAAATCAGGAAACCCTCGAAGGCTCAGTTTCTT
1 CTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTT
49430 AGATCTCATTTGAAAACATCCTGCA
66 AGATCTCATTTGAAAACATCCTGCA
* *
49455 CTGAAGGTCTTACAGATGGCCCGAAGGACTTAAAAATCATGAAACCCCCGAAGGCTCAGTTTCTT
1 CTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTT
*
49520 AGATCTCATTTGAAAACATCCTACA
66 AGATCTCATTTGAAAACATCCTGCA
*
49545 CTGAAGGTCTTATGGATGGCCCGAAGGACTTAAAAATCAAGAAAC
1 CTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAAC
49590 TCTTGAAAAT
Statistics
Matches: 209, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
90 195 0.93
91 14 0.07
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (90 bp):
CTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTT
AGATCTCATTTGAAAACATCCTGCA
Found at i:49738 original size:43 final size:43
Alignment explanation
Indices: 49677--49873 Score: 171
Period size: 43 Copynumber: 4.3 Consensus size: 43
49667 AAATTTGTCT
* *
49677 TCAAGGAACTCCTACATATCACGATGGTCCCTCAAGTTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGTTTTTCA
* *
49720 TCAAGAAACCCCTACATATCACGATGGTTTCTCAACCTTGTCATCAAATTTGTCA
1 TCAAGAAACCCCTACATATCACGATGG----T---CC----C-TCAAGTTTTTCA
*
49775 TCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTT-A
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAG-TTTTTCA
* * ** * *
49818 TCAAGAATCCCCTACATGTCACGATGGTTTCTCAAGCTTTTCT
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGTTTTTCA
49861 TCAAGAAACCCCT
1 TCAAGAAACCCCT
49874 GAAAATCAGG
Statistics
Matches: 125, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
42 4 0.03
43 73 0.58
44 5 0.04
47 1 0.01
48 2 0.02
50 2 0.02
51 1 0.01
54 1 0.01
55 36 0.29
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (43 bp):
TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGTTTTTCA
Found at i:49797 original size:98 final size:98
Alignment explanation
Indices: 49662--49852 Score: 330
Period size: 98 Copynumber: 1.9 Consensus size: 98
49652 CCTCAAGTGT
* *
49662 TCATCAAATTTGTCTTCAAGGAACTCCTACATATCACGATGGTCCCTCAAG-TTTTTCATCAAGA
1 TCATCAAATTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTT-ATCAAGA
49726 AACCCCTACATATCACGATGGTTTCTCAACCTTG
65 AACCCCTACATATCACGATGGTTTCTCAACCTTG
49760 TCATCAAATTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAA
1 TCATCAAATTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAA
* *
49825 TCCCCTACATGTCACGATGGTTTCTCAA
66 ACCCCTACATATCACGATGGTTTCTCAA
49853 GCTTTTCTTC
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 83 0.94
99 5 0.06
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (98 bp):
TCATCAAATTTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAA
ACCCCTACATATCACGATGGTTTCTCAACCTTG
Found at i:49948 original size:39 final size:39
Alignment explanation
Indices: 49895--49971 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
49885 TTAGTTTCTA
*
49895 AAAATATTGTGTTTCGAGCGAAACTATCTCAAGCGAGAT
1 AAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGAT
* * * * * *
49934 AAAATCTTTTGTTTCAAGTGAAATTGTCTCAAGGGAGA
1 AAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGA
49972 CTGTCTCAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (39 bp):
AAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGAT
Found at i:49986 original size:15 final size:15
Alignment explanation
Indices: 49958--49987 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49948 CAAGTGAAAT
*
49958 TGTCTCAAGGGAGAC
1 TGTCTCAAGAGAGAC
49973 TGTCTCAAGAGAGAC
1 TGTCTCAAGAGAGAC
49988 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (15 bp):
TGTCTCAAGAGAGAC
Found at i:50004 original size:36 final size:36
Alignment explanation
Indices: 49957--50239 Score: 431
Period size: 36 Copynumber: 7.9 Consensus size: 36
49947 TCAAGTGAAA
* * *
49957 TTGTCTCAAGGGAGACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
49993 TTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
50029 TTGTTTCAATGGAAACTGTCTCATGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
50065 TTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* *
50101 GTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
* * *
50137 TGGTTTCGAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
50173 TTGTTTCAAGGGAAACCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
*
50209 TTGTTTCAAGGGAAAGTGTCTCAAGGGAGAC
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAGAC
50240 TGTCTCAAGG
Statistics
Matches: 223, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 223 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
Found at i:50181 original size:21 final size:21
Alignment explanation
Indices: 50157--50221 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
50147 AGAAACTGTC
50157 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
** *
50178 TCAA-GG-G---AAA-CCGTC
1 TCAAGGGAGACAAAATTTGTT
50193 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
50214 TCAAGGGA
1 TCAAGGGA
50222 AAGTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 1 0.03
19 1 0.03
20 5 0.16
21 14 0.44
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:50252 original size:15 final size:15
Alignment explanation
Indices: 50214--50253 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
50204 AAAATTTGTT
* *
50214 TCAAGGGAAAGTGTC
1 TCAAGGGAGACTGTC
50229 TCAAGGGAGACTGTC
1 TCAAGGGAGACTGTC
50244 TCAAGGGAGA
1 TCAAGGGAGA
50254 TAAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.35, T:0.17
Consensus pattern (15 bp):
TCAAGGGAGACTGTC
Found at i:50623 original size:34 final size:33
Alignment explanation
Indices: 50584--50681 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 33
50574 ATCTCAGAGA
* *
50584 AAATTGTCTCAAGCGAGACGGAATTTTTTTTGAG
1 AAATTGTCTCAAGTGAGAC-AAATTTTTTTTGAG
*
50618 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGAC-AAATTTTTTTTGAG
*
50652 AAATTATCTCAAGTGAGACAAATTTTTTTT
1 AAATTGTCTCAAGTGAGACAAATTTTTTTT
50682 TTAAAGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 10 0.17
34 48 0.83
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (33 bp):
AAATTGTCTCAAGTGAGACAAATTTTTTTTGAG
Found at i:50863 original size:32 final size:32
Alignment explanation
Indices: 50782--51004 Score: 356
Period size: 32 Copynumber: 6.9 Consensus size: 32
50772 TATTGAATGT
* * *
50782 CCCAATATTCGATATTGAATCTCCAAAGATGC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
50814 CCCAACATTTTGATGTTGAATCTCCAAAGATGC
1 CCCAACA-TTTGATGTTGAATCTCCAAAGATGC
50847 CCCAACATTTGATGTTGAATCTCCAAAGATGC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
50879 CCCAACATTTGATGTTGAATCTCCAAAGATGC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
* *
50911 CCCAACATTTGATTTTGAATCTCCAAAGATAC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
* *
50943 CCTAACATTTGATGTTGAATCTCCAAAGATAC
1 CCCAACATTTGATGTTGAATCTCCAAAGATGC
* *
50975 CCCAACATGTGATGTTGAATCTTCAAAGAT
1 CCCAACATTTGATGTTGAATCTCCAAAGAT
51005 TCCCTCTATT
Statistics
Matches: 180, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
32 150 0.83
33 30 0.17
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (32 bp):
CCCAACATTTGATGTTGAATCTCCAAAGATGC
Found at i:51413 original size:32 final size:32
Alignment explanation
Indices: 51376--51455 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
51366 GGTTATTGTG
*
51376 TTTGGTCAATGATTTGAATGTCTCAGGCTATT
1 TTTGGTCAATGGTTTGAATGTCTCAGGCTATT
* *
51408 TTTGGTCAATGGTTTGAATGTCTCAGGTTGTT
1 TTTGGTCAATGGTTTGAATGTCTCAGGCTATT
*
51440 TTTGGTTAATGGTTTG
1 TTTGGTCAATGGTTTG
51456 GCCTTCTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.47
Consensus pattern (32 bp):
TTTGGTCAATGGTTTGAATGTCTCAGGCTATT
Found at i:53354 original size:6 final size:6
Alignment explanation
Indices: 53337--53375 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
53327 AATGAATGTT
*
53337 ATGCATA ATGCAA ATGCAG ATGCCAA ATGCAA ATGCAA A
1 ATGCA-A ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
53376 AGGTGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:57626 original size:2 final size:2
Alignment explanation
Indices: 57619--57649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57609 AAGACAAACA
57619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57650 ACAGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71734 original size:60 final size:60
Alignment explanation
Indices: 71658--71817 Score: 200
Period size: 60 Copynumber: 2.7 Consensus size: 60
71648 TAAATTGGTT
* *
71658 CCTAAA-TTTTTAAATATTTTAATTTCATCCTTAAACTAT-GATTATCATTCTAGATTAATC
1 CCTAAACTTTTTAAATATTTTAATTTCATCC-TAAACTATAAATT-TCATTCTAAATTAATC
* * *
71718 CTTAAACTTTTT-AATATTTCATTTTCATCCCTAAACTATAAATTTCATTCTAAATTAATC
1 CCTAAACTTTTTAAATATTTTAATTTCAT-CCTAAACTATAAATTTCATTCTAAATTAATC
* * *
71778 CCTAATCTTTTTGAATATTTTAATTTCATCCCAAACTATA
1 CCTAAACTTTTTAAATATTTTAATTTCATCCTAAACTATA
71818 TGCATATAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
60 62 0.72
61 24 0.28
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.46
Consensus pattern (60 bp):
CCTAAACTTTTTAAATATTTTAATTTCATCCTAAACTATAAATTTCATTCTAAATTAATC
Found at i:72068 original size:60 final size:60
Alignment explanation
Indices: 71911--72085 Score: 185
Period size: 60 Copynumber: 2.9 Consensus size: 60
71901 AAACTATGGT
** * * * *
71911 TTAGAATATTCAAAAGTTTGGGGACTAATATAGAATGAAATTCATAGTTTATGGATGAAA
1 TTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAA
*
71971 TTAGAAATGTTCAAAAGTTTAAGGACTAA-TTAGAATGAGAGTCATAGTTTAGGGAT-AAGA
1 TTAG-AATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAA-A
* * * * * *
72031 TTAGAATATTCCAAAGTCTAAGGACCAATTTAAAATGATG-GTTATAGTTTGGGGA
1 TTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGA-GAGTCATAGTTTAGGGA
72086 CATATGATGC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
59 22 0.23
60 53 0.55
61 22 0.23
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (60 bp):
TTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAA
Found at i:81915 original size:2 final size:2
Alignment explanation
Indices: 81908--81962 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
81898 TAATTTAAGT
81908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81950 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
81963 TTTTCAAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82111 original size:2 final size:2
Alignment explanation
Indices: 82104--82135 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
82094 AAGTATTTAA
82104 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
82136 CTATGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82233 original size:25 final size:24
Alignment explanation
Indices: 82202--82250 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
82192 ATTATTTAAA
**
82202 AAATTAAAATGTTATAAATTAAAAT
1 AAATTAAAAAATTA-AAATTAAAAT
82227 AAATTAAAAAATTAAAATTAAAAT
1 AAATTAAAAAATTAAAATTAAAAT
82251 GACTTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATTAAAAAATTAAAATTAAAAT
Found at i:89525 original size:116 final size:115
Alignment explanation
Indices: 89275--89862 Score: 640
Period size: 116 Copynumber: 5.1 Consensus size: 115
89265 CAATTCTTTA
* * *
89275 TGTGATGGAAAT-GAGCTAAGGTTGAACAAGTTATTCTCATTATGAA--T-TTCTCCCTCATAGG
1 TGTGATGG-AATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGG
* * * * *
89336 ATGAGTTATTCTTATTATGAAC-CCTGTACTGGAAATGTTGATTCATCTCCTTC
65 ATGAGTTCTTCTCATTATGAACTCC--TCCT-GAAATGTTGATCCACCTCCTTC
* * * * *
89389 TGTGATGGAATCAAAC-AAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCCCTCGTCGGA
1 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGA
* * *
89453 TGAGTTCTTCTCATTATGAACTCCTACTAGAAATGTTGA-CTCACCTCATTT
66 TGAGTTCTTCTCATTATGAACTCCTCCT-GAAATGTTGATC-CACCTCCTTC
* * * *
89504 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTATTCTCTTTATGAACTTCTTCTCCTTCATCAGA
1 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGA
89569 TGAGTTCTTCTCATTATGAACT-CTCCCTTGAAATGTTGATCCACCTCCTTC
66 TGAGTTCTTCTCATTATGAACTCCT-CC-TGAAATGTTGATCCACCTCCTTC
* * * * * * *
89620 TGTGATTGAAT--ATCCAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCACTCATCAGA
1 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGA
* *
89683 TGAGTTCTTCTCATTATGAACTCTCCCCTGAAATGTTGATCCACCTACTTC
66 TGAGTTCTTCTCATTATGAACTC-CTCCTGAAATGTTGATCCACCTCCTTC
** * * * * *
89734 CATGATGTAATCGAGCTAAGGTTGAAA-AAGTTCTTCTCATTATGAACTTATTATCCTTCATCGA
1 TGTGATGGAATCGAGCTAAGGTT-AAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGG
* * * *
89798 AAGAGTTCTTTTCATTATTAACTCTCCCCTGAAATGTTGATCCACCTCCTTC
65 ATGAGTTCTTCTCATTATGAACTC-CTCCTGAAATGTTGATCCACCTCCTTC
89850 TGTGATGGAATCG
1 TGTGATGGAATCG
89863 TCAAGTCTTC
Statistics
Matches: 400, Mismatches: 59, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
113 28 0.07
114 105 0.26
115 40 0.10
116 221 0.55
117 6 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (115 bp):
TGTGATGGAATCGAGCTAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGA
TGAGTTCTTCTCATTATGAACTCCTCCTGAAATGTTGATCCACCTCCTTC
Found at i:89698 original size:230 final size:230
Alignment explanation
Indices: 89275--89861 Score: 717
Period size: 230 Copynumber: 2.6 Consensus size: 230
89265 CAATTCTTTA
* *
89275 TGTGATGGAAAT-GAGCTAAGGTTGAACAAGTTATTCTCATTATGAA--TTTCTCCCTCAT-AGG
1 TGTGATGG-AATCGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTTTCTCCTTCATCA-G
* * * ** * * *
89336 ATGAGTTATTCTTATTATGAACCCTGTACTGGAAATGTTGATTCATCTCCTTCTGTGATGGAATC
64 ATGAGTTCTTCTCATTATGAACTCT-CCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATC
* * *
89401 AAACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCA
128 AAACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCA
* *
89466 TTATGAACTC-CTACTAGAAATGTTGA-CTCACCT-CATTT
193 TTATGAACTCTCCACT-GAAATGTTGATC-CACCTAC-TTC
*
89504 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTATTCTCTTTATGAACTTCTTCTCCTTCATCAGA
1 TGTGATGGAATCGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTT-TTCTCCTTCATCAGA
* *
89569 TGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATTGAAT-AT
65 TGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAA
* * * * *
89633 CCAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATT
130 ACAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATT
*
89698 ATGAACTCTCCCCTGAAATGTTGATCCACCTACTTC
195 ATGAACTCTCCACTGAAATGTTGATCCACCTACTTC
** * * *
89734 CATGATGTAATCGAGCTAAGGTTGAAA-AAGTTCTTCTCATTATGAACTTATTATCCTTCATC-G
1 TGTGATGGAATCGAGCTAAGGTT-AAACAAGTTATTCTCATTATGAACTT-TTCTCCTTCATCAG
* * * *
89797 AAAGAGTTCTTTTCATTATTAACTCTCCCCTGAAATGTTGATCCACCTCCTTCTGTGATGGAATC
64 -ATGAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATC
89862 GTCAAGTCTT
Statistics
Matches: 311, Mismatches: 36, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
228 3 0.01
229 41 0.13
230 192 0.62
231 41 0.13
232 33 0.11
233 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (230 bp):
TGTGATGGAATCGAGCTAAGGTTAAACAAGTTATTCTCATTATGAACTTTTCTCCTTCATCAGAT
GAGTTCTTCTCATTATGAACTCTCCCTTGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAA
CAAGGTTAAACAAGTTCTTATAATTATGAACTTCTTCTCACTCATCAGATGAGTTCTTCTCATTA
TGAACTCTCCACTGAAATGTTGATCCACCTACTTC
Found at i:90186 original size:26 final size:25
Alignment explanation
Indices: 90152--90212 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
90142 ATTTTTTGCA
90152 TCTCATTTTTTAGCATATTTTATT-TTT
1 TCTC-TTTTTTA--ATATTTTATTATTT
*
90179 TCTCTTTTTTATTATTTTATTATTT
1 TCTCTTTTTTAATATTTTATTATTT
90204 T-TCTTTTTT
1 TCTCTTTTTT
90213 TAAACACCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 17 0.53
25 4 0.12
26 7 0.22
27 4 0.12
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.74
Consensus pattern (25 bp):
TCTCTTTTTTAATATTTTATTATTT
Found at i:90194 original size:24 final size:24
Alignment explanation
Indices: 90167--90212 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
90157 TTTTTTAGCA
90167 TATTTTATT-TTTTCTCTTTTTTAT
1 TATTTTATTATTTT-TCTTTTTTAT
90191 TATTTTATTATTTTTCTTTTTT
1 TATTTTATTATTTTTCTTTTTT
90213 TAAACACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (24 bp):
TATTTTATTATTTTTCTTTTTTAT
Found at i:90856 original size:239 final size:237
Alignment explanation
Indices: 90267--91060 Score: 1042
Period size: 239 Copynumber: 3.3 Consensus size: 237
90257 CTCGAAGAAA
* * * *
90267 TTATCATCTTGCTCGAAAGGCTTATAGATGACTTGAAGGATTTAAGCATCATACTCGAAAGACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
* * *
90332 ACTGATGGCTCGAAGGACTTACTAAGTAAAAAACTTTGGAAATCGTTTTCTTACTTTTTAAAAAA
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTAC---TT-AAAAA
* * **
90397 AATTAATTTT-AAAAAATTATTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTGTTTTGAAA
127 AATCAATTTTCAAAAAA-TATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTT-TTTTGAAA
* * *
90461 ATCATGTGAAAAATCC-AGCCTAACGATCTTATGGATGGTCC-AAAGAAC
190 ATCATGTGAAAAATCCTACCCTAA-GGTCTTATGGATGGCCCGAAAG-AC
* * * * *
90509 TTATCATCTTGCTCAAAAGGCTTTTAGATGACC-GAAGGATTTAGGCATAATGTTTGAAAGGCTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
90573 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
* *
90638 AATTTTCATAAAATATTTAAATGAGAAACTTTGGAAACCATTTTCTCATTTTTTTCGAAAATCAT
131 AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTTTT-GAAAATCAT
90703 GTGAAAACATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
195 GTGAAAA-ATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
* * *
90747 TTATCATCTTGCTCAAAAGTCTTATAGATGACCTGAAAGATTTAGGCATCATGCTCGAAATACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
* *
90812 ATTGATGGCCCAAAAGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
66 ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
* * *
90877 AATTTTCAGAAAAGATTTAAATGAGAAACTTTGG-AATCTTTTTCTCATTTTTTTTTGAAAATCA
131 AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCA--TTTTTTTGAAAATCA
* * * * * *
90941 TGTGAAAATATCATGCCCGAAGGTCTTATGGATGTACCGGATA-AC
194 TGTGAAAA-ATCCTACCCTAAGGTCTTATGGATG-GCCCGAAAGAC
** * * * *
90986 TTATCATCTTGCTGGAAAGGCTTATAGATGACCCGAAGGATTCAGGCATCATTCTCAAAAGACTT
1 TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
*
91051 ACTCATGGCC
66 ACTGATGGCC
91061 TGAGGGACTT
Statistics
Matches: 490, Mismatches: 53, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
236 4 0.01
237 64 0.13
238 70 0.14
239 234 0.48
240 12 0.02
241 76 0.16
242 30 0.06
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (237 bp):
TTATCATCTTGCTCAAAAGGCTTATAGATGACCTGAAGGATTTAGGCATCATGCTCGAAAGACTT
ACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTAAAAAAATC
AATTTTCAAAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTTTTGAAAATCATG
TGAAAAATCCTACCCTAAGGTCTTATGGATGGCCCGAAAGAC
Found at i:91237 original size:53 final size:54
Alignment explanation
Indices: 91074--91600 Score: 530
Period size: 54 Copynumber: 9.8 Consensus size: 54
91064 GGGACTTACT
* * ** * ** * *
91074 CATCAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAAAAAAATCATTGGAAGA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * * * *
91128 CATAAAGAAACCCTTGAAAATAAGGCTTAGCTCCTTT-AAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
*
91181 CATCAA-AAACCCCTAAAAATCAGGCTCAGCTTCTTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * *
91234 CATCAAGAAACCCCTAAAAATTAGGCTTATCTTATTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * *
91288 CATCAACAAACCCCTAAAAATCATGCTTAGCTTCTTTCAAAAATCA-TTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * * *
91341 CATCAAGAAACCCCTGAAAATCAAGCTTAGCTTCTTTCAAAAATCATTTGAATA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
* * *
91395 CATCAAGAAACCCTTAAAAATTATGCTTAGCTT-TCTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCT-TTCAAAATTCATTTGAAGA
* * ** *
91449 CATCAAGAAACCCCTAAAAATTATGCTTAAATTCTTTCAAAAATCATTTGAAGAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAG--A
* * * * * * *
91505 TCATCAAGAAACTTCC-GAAAATC-GGACTCAGATTTTTTAAAAATT-ATTTGAAAA
1 -CATCAAGAAAC-CCCTAAAAATCAGG-CTTAGCTTCTTTCAAAATTCATTTGAAGA
** * *
91559 CATCAAGAAACCCCT-AAAATCAAACTTAGTTTCTTTAAAAAT
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAAT
91601 ATGATATCGA
Statistics
Matches: 403, Mismatches: 58, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
52 48 0.12
53 100 0.25
54 213 0.53
55 1 0.00
56 9 0.02
57 30 0.07
58 2 0.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (54 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
Found at i:91348 original size:107 final size:108
Alignment explanation
Indices: 91074--91577 Score: 536
Period size: 107 Copynumber: 4.7 Consensus size: 108
91064 GGGACTTACT
* * ** * ** * *
91074 CATCAAGAAACCCTTGAAAATCAAACTTAGTTTCTTAAAAAAATCATTGGAAGACATAAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAAATCATTTGAAGACATCAAGAAAC
* * * * * *
91139 CCTTGAAAATAAGGCTTAGCTCCTTT-AAAATTCATTTGAAAA
66 CCCTAAAAATTAGGCTTAGCTTCTTTCAAAAATCATTTGAAGA
* *
91181 CATCAA-AAACCCCTAAAAATCAGGCTCAGCTTCTTTCAAAATTCATTTGAAGACATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAAATCATTTGAAGACATCAAGAAAC
* * *
91245 CCCTAAAAATTAGGCTTATCTTATTTCAAAATTCATTTGAAGA
66 CCCTAAAAATTAGGCTTAGCTTCTTTCAAAAATCATTTGAAGA
* * *
91288 CATCAACAAACCCCTAAAAATCATGCTTAGCTTCTTTCAAAAATCA-TTGAAAACATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAAATCATTTGAAGACATCAAGAAAC
* * * *
91352 CCCTGAAAATCAAGCTTAGCTTCTTTCAAAAATCATTTGAATA
66 CCCTAAAAATTAGGCTTAGCTTCTTTCAAAAATCATTTGAAGA
* * * *
91395 CATCAAGAAACCCTTAAAAATTATGCTTAGCTT-TCTTCAAAATTCATTTGAAGACATCAAGAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCT-TTCAAAAATCATTTGAAGACATCAAGAAA
* **
91459 CCCCTAAAAATTATGCTTAAATTCTTTCAAAAATCATTTGAAGAAA
65 CCCCTAAAAATTAGGCTTAGCTTCTTTCAAAAATCATTTGAAG--A
* * * * * * *
91505 TCATCAAGAAACTTCC-GAAAATC-GGACTCAGATT-TTTTAAAAATTATTTGAAAACATCAAGA
1 -CATCAAGAAAC-CCCTAAAAATCAGG-CTTAGCTTCTTTCAAAAATCATTTGAAGACATCAAGA
91567 AACCCCTAAAA
63 AACCCCTAAAA
91578 TCAAACTTAG
Statistics
Matches: 337, Mismatches: 51, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
106 68 0.20
107 120 0.36
108 89 0.26
110 36 0.11
111 23 0.07
112 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (108 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAAAATCATTTGAAGACATCAAGAAAC
CCCTAAAAATTAGGCTTAGCTTCTTTCAAAAATCATTTGAAGA
Found at i:91400 original size:161 final size:162
Alignment explanation
Indices: 91074--91577 Score: 601
Period size: 161 Copynumber: 3.1 Consensus size: 162
91064 GGGACTTACT
* * * ** * * * *
91074 CATCAAGAAACCCTTGAAAATCAAACTTAG-TTTCTTAAAAAAATCATTGGAAGACATAAAGAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTTCTT-CAAAATTCATTTGAAGACATCAAGAAA
* * * * * *
91138 CCCTTGAAAATAAGGCTTAGCTCCTTT-AAAATTCATTTGAAAACATCAA-AAACCCCTAAAAAT
65 CCCCTAAAAATAATGCTTAGCTTCTTTCAAAAATCATTTGAAAACATCAAGAAACCCCTGAAAAT
* *
91201 CAGGCTCAGCTTCTTTCAAAATTCATTTGAAGA
130 CAGGCTCAGCTTCTTTCAAAAATCATTTGAAAA
* *
91234 CATCAAGAAACCCCTAAAAATTAGGCTTATCTTAT-TTCAAAATTCATTTGAAGACATCAACAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTT-TCTTCAAAATTCATTTGAAGACATCAAGAAA
*
91298 CCCCTAAAAATCATGCTTAGCTTCTTTCAAAAATCA-TTGAAAACATCAAGAAACCCCTGAAAAT
65 CCCCTAAAAATAATGCTTAGCTTCTTTCAAAAATCATTTGAAAACATCAAGAAACCCCTGAAAAT
* * *
91362 CAAGCTTAGCTTCTTTCAAAAATCATTTGAATA
130 CAGGCTCAGCTTCTTTCAAAAATCATTTGAAAA
* *
91395 CATCAAGAAACCCTTAAAAATTATGCTTAGCTTTCTTCAAAATTCATTTGAAGACATCAAGAAAC
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTTCTTCAAAATTCATTTGAAGACATCAAGAAAC
* ** *
91460 CCCTAAAAATTATGCTTAAATTCTTTCAAAAATCATTTGAAGAAATCATCAAGAAACTTCC-GAA
66 CCCTAAAAATAATGCTTAGCTTCTTTCAAAAATCATTTG-A-AAA-CATCAAGAAAC-CCCTGAA
* * *
91524 AATC-GGACTCAGATT-TTTTAAAAATTATTTGAAAA
127 AATCAGG-CTCAGCTTCTTTCAAAAATCATTTGAAAA
91559 CATCAAGAAACCCCTAAAA
1 CATCAAGAAACCCCTAAAA
91578 TCAAACTTAG
Statistics
Matches: 296, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
160 82 0.28
161 144 0.49
162 4 0.01
163 1 0.00
164 39 0.13
165 24 0.08
166 2 0.01
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (162 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTTCTTCAAAATTCATTTGAAGACATCAAGAAAC
CCCTAAAAATAATGCTTAGCTTCTTTCAAAAATCATTTGAAAACATCAAGAAACCCCTGAAAATC
AGGCTCAGCTTCTTTCAAAAATCATTTGAAAA
Found at i:92380 original size:15 final size:17
Alignment explanation
Indices: 92358--92406 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
92348 ATACCCATGC
92358 AGGGGTATCGGTACCC-
1 AGGGGTATCGGTACCCA
* *
92374 A-GGGTATTGATACCCA
1 AGGGGTATCGGTACCCA
92390 TAGGGGTATCGGTACCC
1 -AGGGGTATCGGTACCC
92407 TTTTTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.46
16 1 0.04
17 1 0.04
18 12 0.46
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (17 bp):
AGGGGTATCGGTACCCA
Found at i:92400 original size:33 final size:34
Alignment explanation
Indices: 92340--92406 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
92330 TGGAGCTAGG
92340 GGGTATTGATACCCATGCAGGGGTATCGGTACCCA
1 GGGTATTGATACCCAT-CAGGGGTATCGGTACCCA
92375 GGGTATTGATACCCAT-AGGGGTATCGGTACCC
1 GGGTATTGATACCCATCAGGGGTATCGGTACCC
92407 TTTTTGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 16 0.50
35 16 0.50
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.24
Consensus pattern (34 bp):
GGGTATTGATACCCATCAGGGGTATCGGTACCCA
Found at i:92545 original size:22 final size:23
Alignment explanation
Indices: 92484--92545 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
92474 TCGGAACCTA
92484 GGGTATCGATACCCATTCATAGG
1 GGGTATCGATACCCATTCATAGG
* *
92507 GGGTATTGATACTCATTCATA-G
1 GGGTATCGATACCCATTCATAGG
92529 GGGTATC-AGTACCCATT
1 GGGTATCGA-TACCCATT
92546 TGCATTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 14 0.41
23 19 0.56
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (23 bp):
GGGTATCGATACCCATTCATAGG
Found at i:93982 original size:28 final size:28
Alignment explanation
Indices: 93915--93988 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
93905 TTAGGCTGAC
*
93915 TTGGGAAAGTAGA-GTGTTTCAGATTAAT
1 TTGGGGAAGTA-ATGTGTTTCAGATTAAT
*
93943 TTGGGGAAGTAATGTGTTTCAGGTTAAT
1 TTGGGGAAGTAATGTGTTTCAGATTAAT
* * *
93971 TTTGGGAGGTAATATGTT
1 TTGGGGAAGTAATGTGTT
93989 ACATGTTGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.39
Consensus pattern (28 bp):
TTGGGGAAGTAATGTGTTTCAGATTAAT
Found at i:94799 original size:25 final size:24
Alignment explanation
Indices: 94767--94855 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 24
94757 ATTTTTTTTG
94767 TTTTTTTTTCTCTTTTTCTTAT-T
1 TTTTTTTTTCTCTTTTTCTTATAT
* *
94790 TATTTATTTTCTCTATTTT-TTATGT
1 T-TTTTTTTTCTCT-TTTTCTTATAT
*
94815 TTTTTTTCTTCT-TTTTACTATATAT
1 TTTTTTT-TTCTCTTTTTCT-TATAT
94840 TCTTTTTTTTCTCTTT
1 T-TTTTTTTTCTCTTT
94856 ATGTTGTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.07
24 22 0.41
25 19 0.35
26 9 0.17
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTCTCTTTTTCTTATAT
Found at i:94801 original size:16 final size:16
Alignment explanation
Indices: 94780--94812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
94770 TTTTTTCTCT
94780 TTTTCT-TATTTATTTA
1 TTTTCTCTATTT-TTTA
94796 TTTTCTCTATTTTTTA
1 TTTTCTCTATTTTTTA
94812 T
1 T
94813 GTTTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTCTATTTTTTA
Found at i:94828 original size:47 final size:50
Alignment explanation
Indices: 94757--94853 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 50
94747 TTTTTTTTTG
*
94757 ATTTTTTTTGTTTTTTTTTCTCTTTTT-CT-TAT-TTATTTATTTTCTCT
1 ATTTTTTATGTTTTTTTTTCTCTTTTTACTATATATTATTTATTTTCTCT
* *
94804 ATTTTTTATG-TTTTTTTTCTTCTTTTTACTATATATTCTTTTTTTTCTCT
1 ATTTTTTATGTTTTTTTTTC-TCTTTTTACTATATATTATTTATTTTCTCT
94854 TTATGTTGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 9 0.21
47 16 0.37
48 2 0.05
49 3 0.07
50 13 0.30
ACGTcount: A:0.10, C:0.11, G:0.02, T:0.76
Consensus pattern (50 bp):
ATTTTTTATGTTTTTTTTTCTCTTTTTACTATATATTATTTATTTTCTCT
Found at i:96191 original size:20 final size:20
Alignment explanation
Indices: 96166--96219 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
96156 TATAGATGCT
96166 AATGCAAAGATGCACATGTA
1 AATGCAAAGATGCACATGTA
96186 AATGCAAAGATGCACATGTA
1 AATGCAAAGATGCACATGTA
*
96206 AATGCAAATATGCA
1 AATGCAAAGATGCA
96220 AAAAATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
AATGCAAAGATGCACATGTA
Found at i:97471 original size:17 final size:17
Alignment explanation
Indices: 97449--97481 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
97439 ACACCGTTTC
97449 ATTTTAATGTGTGATCG
1 ATTTTAATGTGTGATCG
97466 ATTTTAATGTGTGATC
1 ATTTTAATGTGTGATC
97482 TAGACACCAT
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:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (17 bp):
ATTTTAATGTGTGATCG
Done.