Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_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: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:845417 original size:6 final size:6
Alignment explanation
Indices: 845406--845448 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
845396 TTGGATTTAG
845406 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT G
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT G
845449 CAATTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (6 bp):
GGTTTT
Found at i:845565 original size:20 final size:20
Alignment explanation
Indices: 845540--845577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
845530 GGTTTGAATT
845540 AGGGTTGCATTTAGGGATTG
1 AGGGTTGCATTTAGGGATTG
**
845560 AGGGTTGGTTTTAGGGAT
1 AGGGTTGCATTTAGGGAT
845578 AAAACTGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.42, T:0.37
Consensus pattern (20 bp):
AGGGTTGCATTTAGGGATTG
Found at i:847980 original size:34 final size:30
Alignment explanation
Indices: 847942--848010 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
847932 TTGATATAAC
847942 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
847976 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
848005 AATTTA
1 AATTTA
848011 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:848021 original size:29 final size:30
Alignment explanation
Indices: 847951--848010 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
847941 CAATTTAAGG
847951 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
847982 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
848011 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:848233 original size:21 final size:21
Alignment explanation
Indices: 848207--848290 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
848197 TGCATCCTTT
*
848207 TGTGCATTGATGCATCAAGGC
1 TGTGCATCGATGCATCAAGGC
*
848228 TGTGCATCGATGCATCAAGGT
1 TGTGCATCGATGCATCAAGGC
* * *
848249 TGTGCATCAATGCATC-ATGT
1 TGTGCATCGATGCATCAAGGC
*
848269 TGTGCATCTATGCA-CGAAGGC
1 TGTGCATCGATGCATC-AAGGC
848290 T
1 T
848291 ACAACAGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 16 0.30
21 37 0.69
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
TGTGCATCGATGCATCAAGGC
Found at i:848273 original size:41 final size:41
Alignment explanation
Indices: 848188--848282 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
848178 AATGCAATTA
*** **
848188 GTGCATCGATGCATCCTTTTGTGCATTGATGCATCAAGGCT
1 GTGCATCGATGCATCAGGTTGTGCATCAATGCATCAAGGCT
* *
848229 GTGCATCGATGCATCAAGGTTGTGCATCAATGCATC-ATGTT
1 GTGCATCGATGCATC-AGGTTGTGCATCAATGCATCAAGGCT
*
848270 GTGCATCTATGCA
1 GTGCATCGATGCA
848283 CGAAGGCTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 30 0.67
42 15 0.33
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (41 bp):
GTGCATCGATGCATCAGGTTGTGCATCAATGCATCAAGGCT
Found at i:849979 original size:24 final size:24
Alignment explanation
Indices: 849931--850003 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
849921 GAACTCAAAA
*
849931 TAAAATTTAGAAGTTCGATTGAAGCC
1 TAAAATTT-G-AGTTCAATTGAAGCC
849957 TAAAATTTGAGCTT-AATTGAAGCC
1 TAAAATTTGAG-TTCAATTGAAGCC
849981 TAAAATTTGAGTTCAATTGAAGC
1 TAAAATTTGAGTTCAATTGAAGC
850004 GAAAGAATAG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 2 0.05
24 31 0.70
25 3 0.07
26 8 0.18
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (24 bp):
TAAAATTTGAGTTCAATTGAAGCC
Found at i:856676 original size:40 final size:40
Alignment explanation
Indices: 856621--856700 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
856611 TACAGGTGTA
856621 GGTTTAGCTGAGTGATTCATACGTGGACTTAGCAACTGGG
1 GGTTTAGCTGAGTGATTCATACGTGGACTTAGCAACTGGG
856661 GGTTTAGCTGAGTGATTCATACGTGGACTTAGCAACTGGG
1 GGTTTAGCTGAGTGATTCATACGTGGACTTAGCAACTGGG
856701 ATGTCCCAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (40 bp):
GGTTTAGCTGAGTGATTCATACGTGGACTTAGCAACTGGG
Found at i:858193 original size:2 final size:2
Alignment explanation
Indices: 858182--858274 Score: 57
Period size: 2 Copynumber: 52.5 Consensus size: 2
858172 TAACCCAAAA
* *
858182 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
858218 AT AT A- AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
858254 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
858275 ACCGGGGCGG
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
1 12 0.16
2 62 0.84
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:858263 original size:18 final size:17
Alignment explanation
Indices: 858179--858275 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 17
858169 CCCTAACCCA
*
858179 AAAATAT-TATATATAT
1 AAAATATATAAATATAT
858195 AATTAATATA-AAATATAT
1 AA--AATATATAAATATAT
858213 AAAATATAT-AATATAT
1 AAAATATATAAATATAT
858229 AATTAATATA-AAA-ATAT
1 AA--AATATATAAATATAT
*
858246 AAAATATTATATATATAT
1 AAAATA-TATAAATATAT
*
858264 ATATATATATAA
1 A-AAATATATAA
858276 CCGGGGCGGG
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
15 4 0.06
16 19 0.29
17 8 0.12
18 31 0.47
19 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATATAAATATAT
Found at i:858272 original size:34 final size:36
Alignment explanation
Indices: 858179--858275 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 36
858169 CCCTAACCCA
858179 AAAATATTATATATATA-AT-TAATATAAAATATAT
1 AAAATATTATATATATATATATAATATAAAATATAT
858213 AAAATA-TATA-ATATATA-ATTAATATAAAA-ATAT
1 AAAATATTATATATATATATA-TAATATAAAATATAT
858246 AAAATATTATATATATATATATATATATAA
1 AAAATATTATATATATATATATA-ATATAA
858276 CCGGGGCGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
32 5 0.09
33 15 0.27
34 20 0.36
35 9 0.16
36 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAATATTATATATATATATATAATATAAAATATAT
Found at i:860463 original size:20 final size:21
Alignment explanation
Indices: 860440--860480 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
860430 TAAATTAGTA
*
860440 AAAAATAAAA-TATTAAAAAT
1 AAAAATAAAATTACTAAAAAT
*
860460 AAAACTAAAATTACTAAAAAT
1 AAAAATAAAATTACTAAAAAT
860481 TAAAGATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATAAAATTACTAAAAAT
Found at i:860478 original size:36 final size:36
Alignment explanation
Indices: 860394--860489 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 36
860384 TGAAATATAC
* * *
860394 AAATATAC-AAAAATTAAATATAATTAAAAATTAAATT
1 AAAT-TACTAAAAATTAAAGAT-ATTAAAAATAAAATA
* *
860431 AAATTAGTAAAAAATAAA-ATATTAAAAATAAAACTA
1 AAATTACTAAAAATTAAAGATATTAAAAATAAAA-TA
860467 AAATTACTAAAAATTAAAGATAT
1 AAATTACTAAAAATTAAAGATAT
860490 ACGATTTTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
35 12 0.24
36 21 0.42
37 17 0.34
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (36 bp):
AAATTACTAAAAATTAAAGATATTAAAAATAAAATA
Found at i:860635 original size:14 final size:14
Alignment explanation
Indices: 860616--860645 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
860606 GACTTTACAA
860616 AATTTTAATTTTAT
1 AATTTTAATTTTAT
860630 AATTTTAATTTTAT
1 AATTTTAATTTTAT
860644 AA
1 AA
860646 GACTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTAATTTTAT
Found at i:861990 original size:28 final size:28
Alignment explanation
Indices: 861948--862004 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
861938 AATTTTGTCC
861948 CGTAGAACCACTATGTCCCGTAGGACCA
1 CGTAGAACCACTATGTCCCGTAGGACCA
861976 CGTAGAA-CACATATGTCCCGTAGGACCA
1 CGTAGAACCAC-TATGTCCCGTAGGACCA
862004 C
1 C
862005 TATGTCCCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.18
Consensus pattern (28 bp):
CGTAGAACCACTATGTCCCGTAGGACCA
Found at i:862008 original size:18 final size:18
Alignment explanation
Indices: 861987--862022 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
861977 GTAGAACACA
861987 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
862005 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
862023 GTAGAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:863438 original size:24 final size:24
Alignment explanation
Indices: 863411--863517 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
863401 AAACGGAGAT
*
863411 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
863435 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
863459 GTTAGGAATCAGAATAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
863483 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
863507 ATCAGAAATCA
1 ATCAGAAATCA
863518 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:863517 original size:48 final size:48
Alignment explanation
Indices: 863411--863519 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
863401 AAACGGAGAT
* * * *
863411 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
863459 GTTAGGAATCAGAATAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
863507 ATCAGAAATCAGA
1 ATCAGAAATCAGA
863520 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:864344 original size:2 final size:2
Alignment explanation
Indices: 864319--864400 Score: 51
Period size: 2 Copynumber: 46.5 Consensus size: 2
864309 TAACCCAAAA
* *
864319 AT AT -T AT AT AT -T A- AT AT A- AA AT AT AT A- AA AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
864355 AT AT A- AT -T A- AT AT A- AA AT AT A- AA 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
864392 AT AT AT AT A
1 AT AT AT AT A
864401 ACCGGGGCGG
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
1 11 0.17
2 54 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:864346 original size:9 final size:9
Alignment explanation
Indices: 864332--864394 Score: 56
Period size: 9 Copynumber: 6.6 Consensus size: 9
864322 TTATATATTA
864332 ATATAAAAT
1 ATATAAAAT
864341 ATATAAAAT
1 ATATAAAAT
*
864350 ATATAATAT
1 ATATAAAAT
864359 AATTAATATAAA-
1 -A-T-ATA-AAAT
864371 ATATAAAAT
1 ATATAAAAT
*
864380 ATATATATAT
1 ATATA-AAAT
864390 ATATA
1 ATATA
864395 TATATAACCG
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 3 0.07
9 25 0.56
10 10 0.22
11 2 0.04
12 3 0.07
13 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:864360 original size:14 final size:14
Alignment explanation
Indices: 864341--864401 Score: 68
Period size: 16 Copynumber: 4.1 Consensus size: 14
864331 AATATAAAAT
864341 ATATAAAATATATA
1 ATATAAAATATATA
*
864355 ATATAATTAATATAAA
1 ATATAA--AATATATA
864371 ATATAAAATATATA
1 ATATAAAATATATA
*
864385 TATATATATATATATA
1 -ATATA-AAATATATA
864401 A
1 A
864402 CCGGGGCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 13 0.32
15 6 0.15
16 21 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAAAATATATA
Found at i:864360 original size:23 final size:22
Alignment explanation
Indices: 864324--864401 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
864314 CAAAAATATT
864324 ATATATTAATATAAAATATATAAA
1 ATATA-TAATAT-AAATATATAAA
*
864348 ATATATAATATAATTAATATAAA
1 ATATATAATATAAAT-ATATAAA
* * *
864371 ATATAAAATATATATATATATAT
1 ATATATAATATAAATATATA-AA
864394 ATATATAA
1 ATATATAA
864402 CCGGGGCGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
22 8 0.17
23 33 0.72
24 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATATAATATAAATATATAAA
Found at i:864400 original size:32 final size:33
Alignment explanation
Indices: 864316--864401 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 33
864306 CCCTAACCCA
864316 AAAATAT-TATATAT-TA-ATATA-AAATATAT
1 AAAATATATATATATATATATATATAAATATAT
864345 AAAATATATA-ATATA-AT-TAATATAAA-ATAT
1 AAAATATATATATATATATAT-ATATAAATATAT
864375 AAAATATATATATATATATATATATAA
1 AAAATATATATATATATATATATATAA
864402 CCGGGGCGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
29 13 0.27
30 19 0.39
31 8 0.16
32 8 0.16
33 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAATATATATATATATATATATATAAATATAT
Found at i:866685 original size:20 final size:21
Alignment explanation
Indices: 866662--866703 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
866652 ATTAAATTAG
*
866662 TAAAAATAAAA-TATTAAAAA
1 TAAAAATAAAATTACTAAAAA
*
866682 TAAAACTAAAATTACTAAAAA
1 TAAAAATAAAATTACTAAAAA
866703 T
1 T
866704 TAAAGATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAATAAAATTACTAAAAA
Found at i:866701 original size:35 final size:36
Alignment explanation
Indices: 866617--866703 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 36
866607 TGAAATATAC
* * *
866617 AAATATACAAAAAAGTAAATATAATTAAAAATTAAATT
1 AAAT-TACTAAAAA-TAAATATAATTAAAAATAAAATA
*
866655 AAATTAGTAAAAATAAA-AT-ATTAAAAATAAAACTA
1 AAATTACTAAAAATAAATATAATTAAAAATAAAA-TA
866690 AAATTACTAAAAAT
1 AAATTACTAAAAAT
866704 TAAAGATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 12 0.28
35 16 0.37
36 4 0.09
37 7 0.16
38 4 0.09
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (36 bp):
AAATTACTAAAAATAAATATAATTAAAAATAAAATA
Found at i:866856 original size:14 final size:14
Alignment explanation
Indices: 866839--866868 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
866829 GACTTTACAA
866839 AATTTTAATTTTAT
1 AATTTTAATTTTAT
866853 AATTTTAATTTTAT
1 AATTTTAATTTTAT
866867 AA
1 AA
866869 GAATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTAATTTTAT
Found at i:876716 original size:35 final size:37
Alignment explanation
Indices: 876645--876717 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
876635 GTTAGAAAAT
* *
876645 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
876682 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
876717 A
1 A
876718 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:876720 original size:37 final size:37
Alignment explanation
Indices: 876640--876720 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
876630 AACAAGTTAG
* *
876640 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
* *
876677 ATAAAATTTATATATTTT-TTTACAAAATTGAAAATAT-
1 AAAAAATTTATATATTTTCTTTAAAAAATT-AAAAT-TC
876714 AAAAAAT
1 AAAAAAT
876721 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 10 0.27
37 26 0.70
38 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
Found at i:888991 original size:20 final size:20
Alignment explanation
Indices: 888947--889254 Score: 251
Period size: 20 Copynumber: 15.2 Consensus size: 20
888937 AATGACCAAC
*
888947 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
888966 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
888986 AAAATCGCAACGTGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
889006 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
889026 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
889046 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
889067 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
889088 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
889109 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
889130 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
889152 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
889170 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
889192 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
889210 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
889232 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
889250 AAAAT
1 AAAAT
889255 GAGTAAATTC
Statistics
Matches: 240, Mismatches: 26, Indels: 45
0.77 0.08 0.14
Matches are distributed among these distances:
18 9 0.04
19 15 0.06
20 166 0.69
21 15 0.06
22 35 0.15
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:889017 original size:40 final size:39
Alignment explanation
Indices: 888947--889254 Score: 284
Period size: 40 Copynumber: 7.6 Consensus size: 39
888937 AATGACCAAC
* *
888947 AAAATCGCAACGCGA--AATAAAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGATTAA-GAAAATCGCAACGCGATTCA
* * * **
888985 GAAAATCGCAACGTGATTTAGAAAATCGCAACGTTGA-AAA
1 -AAAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCA
*
889025 GAAAATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATATTCCA
1 -AAAATCGCAACGCGAT--TAAGAAAATCGCAACGCG--ATT-CA
* * *
889068 AGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TT-CA
* * *
889110 AGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
*
889150 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
*
889190 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
* *
889230 AGAATCGCAACGCGATTCAGAAAAT
1 AAAATCGCAACGCGATTAAGAAAAT
889255 GAGTAAATTC
Statistics
Matches: 236, Mismatches: 20, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
38 1 0.00
39 16 0.07
40 148 0.63
41 4 0.02
42 64 0.27
43 2 0.01
44 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (39 bp):
AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCA
Found at i:889371 original size:6 final size:6
Alignment explanation
Indices: 889362--889418 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
889352 CATTACCATT
889362 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
889410 ACCACG ACC
1 ACCACG ACC
889419 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:889936 original size:6 final size:6
Alignment explanation
Indices: 889925--890018 Score: 188
Period size: 6 Copynumber: 15.7 Consensus size: 6
889915 TCTCGTCTCG
889925 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
889973 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
890019 ATACGTGTCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 88 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:890138 original size:20 final size:20
Alignment explanation
Indices: 890113--890300 Score: 134
Period size: 20 Copynumber: 9.2 Consensus size: 20
890103 AAATTTACTC
890113 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* *
890133 ATTTTCTGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
890153 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
890175 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
890195 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
890217 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
890237 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
*
890257 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
890277 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
890296 ATTTT
1 ATTTT
890301 GTTGGTCATT
Statistics
Matches: 130, Mismatches: 27, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
18 4 0.03
19 14 0.11
20 74 0.57
21 12 0.09
22 26 0.20
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:890171 original size:42 final size:42
Alignment explanation
Indices: 890122--890223 Score: 177
Period size: 42 Copynumber: 2.4 Consensus size: 42
890112 CATTTTCTTA
890122 ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
* * *
890164 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAT
1 ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
890206 ATCGCGTTGCGATTTTCT
1 ATCGCGTTGCGATTTTCT
890224 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
Found at i:892132 original size:45 final size:46
Alignment explanation
Indices: 892081--892204 Score: 141
Period size: 42 Copynumber: 2.7 Consensus size: 46
892071 GTGGGCATTT
892081 AAAAAAA-TGCATGATTTATCATATTAATGGACTCAGTAGGAAATTC
1 AAAAAAATTGCATGATTTAT-ATATTAATGGACTCAGTAGGAAATTC
* *
892127 AAAAAAATTGCATGA--T-T-TATTAATGGACTCAGTAGGCATTTC
1 AAAAAAATTGCATGATTTATATATTAATGGACTCAGTAGGAAATTC
*
892169 AAAATAAAAATTGCATGCTTTATTATATTAATGGAC
1 --AA-AAAAATTGCATGATTTA-TATATTAATGGAC
892205 AAAGCATATA
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
42 23 0.35
44 3 0.05
45 13 0.20
46 7 0.11
47 8 0.12
49 1 0.02
50 11 0.17
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (46 bp):
AAAAAAATTGCATGATTTATATATTAATGGACTCAGTAGGAAATTC
Found at i:893504 original size:2 final size:2
Alignment explanation
Indices: 893499--893523 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
893489 CTGGATGTAT
893499 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
893524 ATTTAAAATC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:896798 original size:2 final size:2
Alignment explanation
Indices: 896791--896831 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
896781 TGAGTTTCTT
896791 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
896832 TCCTATATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:898872 original size:33 final size:33
Alignment explanation
Indices: 898826--898889 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
898816 GATTTCATAG
* * **
898826 TTTTCGAGTAAAATCCCAAGTCAATGATAATAA
1 TTTTCCAGGAAAATCCCAAACCAATGATAATAA
898859 TTTTCCAGGAAAATCCCAAACCAATGATAAT
1 TTTTCCAGGAAAATCCCAAACCAATGATAAT
898890 TTACAAAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (33 bp):
TTTTCCAGGAAAATCCCAAACCAATGATAATAA
Found at i:899107 original size:21 final size:21
Alignment explanation
Indices: 899082--899121 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
899072 TTGGATTTTG
899082 TATAAATATAA-AATTTTAATA
1 TATAAA-ATAATAATTTTAATA
*
899103 TATAAAATAATTATTTTAA
1 TATAAAATAATAATTTTAA
899122 AAAATTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAAATAATAATTTTAATA
Found at i:901520 original size:2 final size:2
Alignment explanation
Indices: 901513--901541 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
901503 AATAATTATC
901513 TA TA 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 TA TA T
901542 TAACGCGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:912136 original size:19 final size:21
Alignment explanation
Indices: 912094--912136 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
912084 TTTATTATTT
*
912094 TAAATTTTGAAAACAAGTTTC
1 TAAATTTTGAAAACAAGATTC
912115 TAAATTTTGAAAA-AA-ATTC
1 TAAATTTTGAAAACAAGATTC
912134 TAA
1 TAA
912137 GAAAACACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAATTTTGAAAACAAGATTC
Found at i:912533 original size:13 final size:13
Alignment explanation
Indices: 912514--912547 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
912504 CCAAAATTGG
912514 AATATTTT-AAAT
1 AATATTTTAAAAT
912526 ATATATTTTAAAAT
1 A-ATATTTTAAAAT
912540 AATATTTT
1 AATATTTT
912548 TTTTACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 14 0.70
14 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTTAAAAT
Found at i:920027 original size:57 final size:57
Alignment explanation
Indices: 919963--920079 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
919953 CCATCAACTC
919963 TACTTTATTCACAATATTTAACTATTATAATATTAATTTTACAAATATAAAAAAAAT
1 TACTTTATTCACAATATTTAACTATTATAATATTAATTTTACAAATATAAAAAAAAT
920020 TACTTTATTCACAATATTTAACTATTATAATATTAATTTTACAAATATAAAAAAAAT
1 TACTTTATTCACAATATTTAACTATTATAATATTAATTTTACAAATATAAAAAAAAT
920077 TAC
1 TAC
920080 AAAAAATCTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (57 bp):
TACTTTATTCACAATATTTAACTATTATAATATTAATTTTACAAATATAAAAAAAAT
Found at i:924437 original size:22 final size:22
Alignment explanation
Indices: 924411--924479 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
924401 AGTTTACATT
*
924411 TTTATTGGTACGCATTCATTCA
1 TTTATTGGTACCCATTCATTCA
924433 TTTATTGGTACCCATTCATTCA
1 TTTATTGGTACCCATTCATTCA
924455 TTTATTGGTACCCATTCATTCA
1 TTTATTGGTACCCATTCATTCA
924477 TTT
1 TTT
924480 TATGTGTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTATTGGTACCCATTCATTCA
Found at i:931481 original size:15 final size:16
Alignment explanation
Indices: 931444--931475 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
931434 TATTCAATAA
931444 TAAATAAACTTTTTTT
1 TAAATAAACTTTTTTT
931460 TAAATAAACTTTTTTT
1 TAAATAAACTTTTTTT
931476 GGATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATAAACTTTTTTT
Found at i:936101 original size:19 final size:19
Alignment explanation
Indices: 936077--936117 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
936067 AGCAAGCAAG
936077 GAACGCATTTGAGGTTGAT
1 GAACGCATTTGAGGTTGAT
936096 GAACGCATTTGAGGTTGAT
1 GAACGCATTTGAGGTTGAT
936115 GAA
1 GAA
936118 GCAAGCAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (19 bp):
GAACGCATTTGAGGTTGAT
Found at i:937228 original size:49 final size:49
Alignment explanation
Indices: 937171--937298 Score: 204
Period size: 49 Copynumber: 2.6 Consensus size: 49
937161 GCTCTTAGTG
* *
937171 CAGTCGTTAGTATTCTAACGATGTTCCATTACGCTCGACATGTTTTTAC
1 CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
* *
937220 CAGTCGTTAGTATTCTAACGATGTCCCATTACGATCGAAATGTTTTTGC
1 CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
*
937269 CAGTCGTTAATATTCTAAC-ATGTTCCATTA
1 CAGTCGTTAGTATTCTAACGATGTTCCATTA
937299 TGTTTGGCAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 10 0.14
49 63 0.86
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (49 bp):
CAGTCGTTAGTATTCTAACGATGTTCCATTACGATCGAAATGTTTTTAC
Found at i:939480 original size:18 final size:16
Alignment explanation
Indices: 939443--939486 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
939433 ATGTCTAAAT
939443 ATATTATATATTTTTAG
1 ATATTA-ATATTTTTAG
939460 ATATTAATATTTTATATG
1 ATATTAATATTTT-TA-G
*
939478 ATATAAATA
1 ATATTAATA
939487 AAATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 8 0.33
18 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
ATATTAATATTTTTAG
Found at i:956345 original size:27 final size:26
Alignment explanation
Indices: 956315--956365 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
956305 TAAATATGAA
* * *
956315 TGATTAAATTTATTGAATATCAAATCC
1 TGATAAAATTGATAGAATAT-AAATCC
956342 TGATAAAATTGATAGAATATAAAT
1 TGATAAAATTGATAGAATATAAAT
956366 TTTGGAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (26 bp):
TGATAAAATTGATAGAATATAAATCC
Found at i:956993 original size:31 final size:31
Alignment explanation
Indices: 956926--956985 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
956916 CAATTTAAGG
*
956926 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
956957 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
956986 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:957209 original size:21 final size:21
Alignment explanation
Indices: 957183--957223 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
957173 ATTTGAATAT
*
957183 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTAGCGATTCCC
957204 TATGAAGGGGTAGCGATTCC
1 TATGAAGGGGTAGCGATTCC
957224 TCCCATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTAGCGATTCCC
Found at i:957286 original size:21 final size:21
Alignment explanation
Indices: 957253--957292 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
957243 TTTTTGCAGA
*
957253 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
957275 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
957293 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:957546 original size:34 final size:32
Alignment explanation
Indices: 957507--957576 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
957497 TTTTGTAAAG
*
957507 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
957541 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
957573 GGGA
1 GGGA
957577 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:963617 original size:13 final size:13
Alignment explanation
Indices: 963599--963634 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
963589 TTAAAAACAC
963599 TTAAAATTATTAT
1 TTAAAATTATTAT
*
963612 TTAAAATTATTGT
1 TTAAAATTATTAT
*
963625 TTGAAATTAT
1 TTAAAATTAT
963635 AAGAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
TTAAAATTATTAT
Found at i:979370 original size:32 final size:35
Alignment explanation
Indices: 979329--979408 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 35
979319 TCTTATAACC
979329 TATAATATTTTT-TTATTTAA-AATTTTA-AAA-AA
1 TATAATATTTTTATT-TTTAATAATTTTATAAATAA
* * *
979361 TATATTATTTTTATTTTTAATGATTTTATAAATAT
1 TATAATATTTTTATTTTTAATAATTTTATAAATAA
979396 TATAATATTTTTA
1 TATAATATTTTTA
979409 AAATTCTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 16 0.40
33 8 0.20
34 3 0.08
35 13 0.32
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
TATAATATTTTTATTTTTAATAATTTTATAAATAA
Found at i:979423 original size:18 final size:18
Alignment explanation
Indices: 979378--979441 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
979368 TTTTTATTTT
* *
979378 TAATGATTTTATAAATATTA
1 TAATAATTTT-TAAA-ATTC
979398 TAAT-ATTTTTAAAATTC
1 TAATAATTTTTAAAATTC
979415 TAATAATTTCTT-AAATTC
1 TAATAATTT-TTAAAATTC
979433 T--TAATTTTT
1 TAATAATTTTT
979442 TCTTAAAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 2 0.05
16 6 0.15
17 7 0.17
18 15 0.37
19 7 0.17
20 4 0.10
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (18 bp):
TAATAATTTTTAAAATTC
Found at i:979428 original size:19 final size:19
Alignment explanation
Indices: 979398--979448 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
979388 ATAAATATTA
979398 TAATATTT-TTAAAATTC-
1 TAATATTTCTTAAAATTCT
979415 TAATAATTTCTT-AAATTCT
1 TAAT-ATTTCTTAAAATTCT
*
979434 TAATTTTTTCTTAAA
1 TAA-TATTTCTTAAA
979449 GATTAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 10 0.36
19 11 0.39
20 3 0.11
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTTCTTAAAATTCT
Found at i:987435 original size:31 final size:31
Alignment explanation
Indices: 987400--987461 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
987390 AATTAATAAA
*
987400 ACTTTGTTTCTTCGGGTAACCTTTTGCTTTT
1 ACTTTGTTTCTTCCGGTAACCTTTTGCTTTT
*
987431 ACTTTGTTTCTTCCTGTAACCTTTTGCTTTT
1 ACTTTGTTTCTTCCGGTAACCTTTTGCTTTT
987462 GTTTCGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.13, T:0.56
Consensus pattern (31 bp):
ACTTTGTTTCTTCCGGTAACCTTTTGCTTTT
Found at i:988315 original size:15 final size:17
Alignment explanation
Indices: 988284--988315 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
988274 ATGTATTTTT
988284 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
988301 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
988316 TTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:988470 original size:19 final size:19
Alignment explanation
Indices: 988438--988477 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
988428 AAGAAAGTAA
* *
988438 AAAAAAAACCAAAAATCAT
1 AAAAAAAACAAAAAATAAT
*
988457 AAAAATAACAAAAAATAAT
1 AAAAAAAACAAAAAATAAT
988476 AA
1 AA
988478 TATGTAGCGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (19 bp):
AAAAAAAACAAAAAATAAT
Found at i:988615 original size:13 final size:13
Alignment explanation
Indices: 988597--988623 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
988587 AGAGATTTTC
988597 TCTACTCTGGTGA
1 TCTACTCTGGTGA
988610 TCTACTCTGGTGA
1 TCTACTCTGGTGA
988623 T
1 T
988624 GCGCTGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TCTACTCTGGTGA
Found at i:993571 original size:30 final size:30
Alignment explanation
Indices: 993507--993592 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
993497 TTCAGAGCTC
* *
993507 AAATTGATATTTTATCTCAAATTCATGAGTT
1 AAATTGATATTTTAT-TTAAATTTATGAGTT
*
993538 AAATTGATATTTTATTTAAAGTTTA-GGGTT
1 AAATTGATATTTTATTTAAA-TTTATGAGTT
* * *
993568 AAATTAATATTCTATCTAAAATTTA
1 AAATTGATATTTTAT-TTAAATTTA
993593 AGTATCATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (30 bp):
AAATTGATATTTTATTTAAATTTATGAGTT
Found at i:997253 original size:36 final size:36
Alignment explanation
Indices: 997206--997276 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
997196 GTGTATTTTA
997206 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
1 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
997242 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAA
1 TACGAAAATTGAAAAGAAAATTAATAAAGAATAAA
997277 CTAAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (36 bp):
TACGAAAATTGAAAAGAAAATTAATAAAGAATAAAT
Found at i:997734 original size:11 final size:12
Alignment explanation
Indices: 997709--997747 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
997699 TTACTTTAGT
997709 TTTTTTATTAAA
1 TTTTTTATTAAA
*
997721 TTTTTTATT-TA
1 TTTTTTATTAAA
*
997732 TTTATTATTAAA
1 TTTTTTATTAAA
997744 TTTT
1 TTTT
997748 AAGTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTATTAAA
Found at i:1001047 original size:19 final size:19
Alignment explanation
Indices: 1001023--1001061 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1001013 ATAGTTATGG
*
1001023 ACTATATGTTGACTCTTAT
1 ACTATATGTCGACTCTTAT
1001042 ACTATATGTCGACTCTTAT
1 ACTATATGTCGACTCTTAT
1001061 A
1 A
1001062 GTGTCGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (19 bp):
ACTATATGTCGACTCTTAT
Found at i:1001950 original size:21 final size:21
Alignment explanation
Indices: 1001924--1002001 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
1001914 TTATTAAAAA
1001924 TATTATTTTTATCAATTTTAT
1 TATTATTTTTATCAATTTTAT
1001945 TATTATTTAAGGTTTTATCAATTTTAT
1 TATTA--T----TTTTATCAATTTTAT
* ** *
1001972 TATTATTTTAATGTATTTTGT
1 TATTATTTTTATCAATTTTAT
1001993 TATTATTTT
1 TATTATTTT
1002002 ATACTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
21 25 0.53
23 1 0.02
25 1 0.02
27 20 0.43
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (21 bp):
TATTATTTTTATCAATTTTAT
Found at i:1002038 original size:18 final size:20
Alignment explanation
Indices: 1002015--1002060 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1002005 CTTTATTAAA
*
1002015 AATATTT-AA-AAAAATATT
1 AATATTTAAATAAAAATAAT
1002033 AATATTTTAAATAAAAATAAT
1 AATA-TTTAAATAAAAATAAT
1002054 AATATTT
1 AATATTT
1002061 TATATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.17
19 3 0.12
20 5 0.21
21 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTTAAATAAAAATAAT
Found at i:1004904 original size:20 final size:21
Alignment explanation
Indices: 1004879--1004920 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1004869 AGTATCTTAA
*
1004879 TTATTAATT-CTATTTTATTT
1 TTATTAATTAATATTTTATTT
*
1004899 TTATTATTTAATATTTTATTT
1 TTATTAATTAATATTTTATTT
1004920 T
1 T
1004921 AAAATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTAATTAATATTTTATTT
Found at i:1005677 original size:37 final size:35
Alignment explanation
Indices: 1005593--1005830 Score: 160
Period size: 37 Copynumber: 6.6 Consensus size: 35
1005583 ATAGTTTAAA
* * * **
1005593 AAAATAGTTTTGGAAATATATAATATATAGTTTTGG
1 AAAATATTTTTGAAAACATATAATATATA-TTTTTT
* *
1005629 AAAACGATTTTTGAAAACATATAGTATATATTTTTT
1 AAAA-TATTTTTGAAAACATATAATATATATTTTTT
* * *
1005665 AAAAATATTTTTTG-AAGCGTATAACATATAGTTTTTT
1 -AAAATA-TTTTTGAAAACATATAATATATA-TTTTTT
* *
1005702 AAAA-ACGGTTTTGAAAACATATGATATATATTTTTT
1 AAAATA--TTTTTGAAAACATATAATATATATTTTTT
* *** * *
1005738 AAAATAATTAAAAAAACGTATAATATATAGTTTTT
1 AAAATATTTTTGAAAACATATAATATATATTTTTT
*
1005773 -AAATATTTTTGAAAACGTATACA-ATATAATTTTTT
1 AAAATATTTTTGAAAACATATA-ATATAT-ATTTTTT
*
1005808 GAAAACGTGTTTTTGAAAACATA
1 -AAAA--TATTTTTGAAAACATA
1005831 GCATATGATT
Statistics
Matches: 157, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
34 21 0.13
35 30 0.19
36 40 0.25
37 52 0.33
39 14 0.09
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (35 bp):
AAAATATTTTTGAAAACATATAATATATATTTTTT
Found at i:1005807 original size:35 final size:35
Alignment explanation
Indices: 1005549--1005827 Score: 120
Period size: 37 Copynumber: 7.6 Consensus size: 35
1005539 AAACATACAG
* *
1005549 TTTTTAAAATAATTTTTTAAAAACGTATAAATACATAGT
1 TTTTTAAAAT-A-TTTTTGAAAACGTATAAAT--ATAAT
*** * * ** *
1005588 TTAAAAAAATAGTTTTGGAAATATATAATATATAGT
1 TTTTTAAAATATTTTTGAAAACGTATAA-ATATAAT
** * * *
1005624 TTTGGAAAACGATTTTTGAAAACATAT-AGTATATAT
1 TTTTTAAAA-TATTTTTGAAAACGTATAAATATA-AT
* *
1005660 TTTTTAAAAATATTTTTTG-AAGCGTATAACATATAGT
1 TTTTT-AAAATA-TTTTTGAAAACGTATAA-ATATAAT
* * *
1005697 TTTTTAAAA-ACGGTTTTGAAAACATAT-GATATATAT
1 TTTTTAAAATA--TTTTTGAAAACGTATAAATATA-AT
* *** *
1005733 TTTTTAAAATAATTAAAAAAACGTAT-AATATATAG
1 TTTTTAAAATATTTTTGAAAACGTATAAATATA-AT
1005768 TTTTT-AAATATTTTTGAAAACGTATACAATATAAT
1 TTTTTAAAATATTTTTGAAAACGTATA-AATATAAT
*
1005803 TTTTTGAAAACGTGTTTTTGAAAAC
1 TTTTT-AAAA--TATTTTTGAAAAC
1005828 ATAGCATATG
Statistics
Matches: 180, Mismatches: 43, Indels: 34
0.70 0.17 0.13
Matches are distributed among these distances:
34 16 0.09
35 38 0.21
36 48 0.27
37 52 0.29
38 7 0.04
39 19 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTTTAAAATATTTTTGAAAACGTATAAATATAAT
Found at i:1005848 original size:106 final size:107
Alignment explanation
Indices: 1005642--1005849 Score: 248
Period size: 106 Copynumber: 1.9 Consensus size: 107
1005632 ACGATTTTTG
* * * *
1005642 AAAACATATAGTATATATTTTTTAAAAATATTTTTTGAAGCGTATAACATATAGTTTTTTAAAAA
1 AAAACATATAATATATAGTTTTT-AAAATATTTTTTGAAACGTATAACATATAATTTTTTAAAAA
* *
1005707 CGGTTTTGAAAACATATGATATATATTTTTTAAAATAATTAAA
65 CGGTTTTGAAAACATATGATATAGATTTTTGAAAATAATTAAA
* *
1005750 AAAACGTATAATATATAGTTTTT-AAATA-TTTTTGAAAACGTAT-ACAATATAATTTTTTGAAA
1 AAAACATATAATATATAGTTTTTAAAATATTTTTTG-AAACGTATAAC-ATATAATTTTTTAAAA
1005812 ACGTGTTTTTGAAAACATA-GCATAT-GA-TTTTGAAAATA
64 ACG-G-TTTTGAAAACATATG-ATATAGATTTTTGAAAATA
1005850 TAATATATTA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
105 8 0.09
106 39 0.45
107 3 0.03
108 37 0.43
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (107 bp):
AAAACATATAATATATAGTTTTTAAAATATTTTTTGAAACGTATAACATATAATTTTTTAAAAAC
GGTTTTGAAAACATATGATATAGATTTTTGAAAATAATTAAA
Found at i:1005857 original size:21 final size:21
Alignment explanation
Indices: 1005818--1005857 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1005808 GAAAACGTGT
*
1005818 TTTTGAAAACATAGCATATGA
1 TTTTGAAAACATAACATATGA
* *
1005839 TTTTGAAAATATAATATAT
1 TTTTGAAAACATAACATAT
1005858 TATATAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
TTTTGAAAACATAACATATGA
Found at i:1007155 original size:22 final size:22
Alignment explanation
Indices: 1007130--1007225 Score: 62
Period size: 21 Copynumber: 4.6 Consensus size: 22
1007120 AGCCTTTTAT
1007130 TTTTTTTTATTTTCTTCTATAA
1 TTTTTTTTATTTTCTTCTATAA
****
1007152 TTTTATTTTATTTAGACCT-TAA
1 TTTT-TTTTATTTTCTTCTATAA
*
1007174 -TTTTATT-TTTT-TT-TA-AA
1 TTTTTTTTATTTTCTTCTATAA
* *
1007191 TTCTTTTTTATTTACTTTTAT-A
1 TT-TTTTTTATTTTCTTCTATAA
1007213 TTTTTTTTATTTT
1 TTTTTTTTATTTT
1007226 AGTTTATTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 17
0.66 0.13 0.20
Matches are distributed among these distances:
17 3 0.05
18 1 0.02
19 8 0.15
20 6 0.11
21 15 0.27
22 12 0.22
23 10 0.18
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (22 bp):
TTTTTTTTATTTTCTTCTATAA
Found at i:1007218 original size:21 final size:22
Alignment explanation
Indices: 1007174--1007224 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1007164 TAGACCTTAA
**
1007174 TTTTATTTTTTTTTAAATTCTT
1 TTTTATTTACTTTTAAATTCTT
*
1007196 TTTTATTTACTTTTATATT-TT
1 TTTTATTTACTTTTAAATTCTT
1007217 TTTTATTT
1 TTTTATTT
1007225 TAGTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTATTTACTTTTAAATTCTT
Found at i:1007231 original size:21 final size:21
Alignment explanation
Indices: 1007174--1007237 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
1007164 TAGACCTTAA
* *
1007174 TTTTATTTTTTTTTAAATTCTT
1 TTTTATTTTATTTTATATT-TT
1007196 TTTTA-TTTACTTTTATATTTT
1 TTTTATTTTA-TTTTATATTTT
*
1007217 TTTTATTTTAGTTTATTATTT
1 TTTTATTTTATTTTA-TATTT
1007238 AATATTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 14 0.39
22 22 0.61
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTATTTTATTTTATATTTT
Found at i:1010755 original size:2 final size:2
Alignment explanation
Indices: 1010748--1010777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1010738 ACATATCATT
1010748 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
1010778 AATGATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1012239 original size:33 final size:33
Alignment explanation
Indices: 1012197--1012263 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1012187 GTAACACCTC
*
1012197 GACCCATACTCAACCCGGATACGAATCTGAGGT
1 GACCCATACTCAACCCGAATACGAATCTGAGGT
1012230 GACCCATACTCAACCCGAATACGAATCTGAGGT
1 GACCCATACTCAACCCGAATACGAATCTGAGGT
1012263 G
1 G
1012264 TCACATTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (33 bp):
GACCCATACTCAACCCGAATACGAATCTGAGGT
Found at i:1012982 original size:23 final size:23
Alignment explanation
Indices: 1012898--1012974 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
1012888 AAGTGCCACG
* *
1012898 TAGATTTGTTC-CGAAGGACTGCG
1 TAGATTTG-TCACGAAGGACTACA
* *
1012921 TAGAATTTGTCACGAAGGACCATA
1 TAG-ATTTGTCACGAAGGACTACA
*
1012945 TAGAATTGTCACGAAGGACTACA
1 TAGATTTGTCACGAAGGACTACA
1012968 TAGATTT
1 TAGATTT
1012975 ATCCCGAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 28 0.64
24 16 0.36
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (23 bp):
TAGATTTGTCACGAAGGACTACA
Found at i:1013168 original size:15 final size:15
Alignment explanation
Indices: 1013148--1013183 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1013138 CCTTTTCACT
*
1013148 CATTTTCATATATAA
1 CATTTTCAGATATAA
1013163 CATTTTCAGATATAA
1 CATTTTCAGATATAA
1013178 CATTTT
1 CATTTT
1013184 TCACGTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTTTCAGATATAA
Found at i:1014628 original size:27 final size:27
Alignment explanation
Indices: 1014593--1014646 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1014583 TAATATAAAG
1014593 TCTTAAACAAAATTTTCACAATTTGTC
1 TCTTAAACAAAATTTTCACAATTTGTC
1014620 TCTTAAACAAAATTTTCACAATTTGTC
1 TCTTAAACAAAATTTTCACAATTTGTC
1014647 CTTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (27 bp):
TCTTAAACAAAATTTTCACAATTTGTC
Found at i:1016933 original size:23 final size:23
Alignment explanation
Indices: 1016892--1016943 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1016882 TTTGTTTAGA
*
1016892 GTTTGTGAACATGCCCGTTTAAC
1 GTTTGTGAACATACCCGTTTAAC
**
1016915 GTTTGTGAACATATTCGTTTAAC
1 GTTTGTGAACATACCCGTTTAAC
*
1016938 GATTGT
1 GTTTGT
1016944 CAAACAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (23 bp):
GTTTGTGAACATACCCGTTTAAC
Found at i:1018087 original size:20 final size:21
Alignment explanation
Indices: 1018052--1018091 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1018042 TTTTTTTTAC
1018052 TTTTTAATCAACATTAATTTT
1 TTTTTAATCAACATTAATTTT
1018073 TTTTTAATCAA-ATTAATTT
1 TTTTTAATCAACATTAATTT
1018092 CCATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAATCAACATTAATTTT
Found at i:1042744 original size:2 final size:2
Alignment explanation
Indices: 1042737--1042835 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
1042727 TGTGTTAAAC
1042737 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
1042779 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
1042821 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1042836 GGATATGATC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1044500 original size:40 final size:41
Alignment explanation
Indices: 1044431--1044508 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
1044421 GTTATATCTA
*
1044431 TAAAGTGTGTGAGCATTTTCAATGATTAAAA-AAAAGCCTG
1 TAAAGTGTGTGAGCATTATCAATGATTAAAAGAAAAGCCTG
** *
1044471 TAAAGTGTGTGAGCATTATGGATGGTTAAAAGAAAAGC
1 TAAAGTGTGTGAGCATTATCAATGATTAAAAGAAAAGC
1044509 TTCCATTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (41 bp):
TAAAGTGTGTGAGCATTATCAATGATTAAAAGAAAAGCCTG
Found at i:1055088 original size:43 final size:43
Alignment explanation
Indices: 1055040--1055221 Score: 135
Period size: 43 Copynumber: 4.2 Consensus size: 43
1055030 TTTATTTTTG
* *
1055040 TAATTGATGCTCTTAATCTTTT-TAATTTAATTTTTT-CTCTTTA
1 TAATTGAGGCTCTTAAT-TTTTATAATCTAATTTTTTAC-CTTTA
* *
1055083 TAATTGAGGTTTTTAATTTTTATAATCTAATTTTTTACCTTTA
1 TAATTGAGGCTCTTAATTTTTATAATCTAATTTTTTACCTTTA
* * * *
1055126 TAACTGA-GATCCCTAATTTTT-TCAATACT-ATTTTTTACATTTA
1 TAATTGAGGCT-CTTAATTTTTAT-AAT-CTAATTTTTTACCTTTA
* * * * *
1055169 TAATTGAGAC-CTCTAATTTTTTTAA-CCACACTTTCTACCTTTA
1 TAATTGAGGCTCT-TAATTTTTATAATCTA-ATTTTTTACCTTTA
1055212 TAATTGAGGC
1 TAATTGAGGC
1055222 CCCTCATTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 20
0.74 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 8 0.07
43 98 0.88
44 4 0.04
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (43 bp):
TAATTGAGGCTCTTAATTTTTATAATCTAATTTTTTACCTTTA
Found at i:1055186 original size:86 final size:87
Alignment explanation
Indices: 1055096--1055260 Score: 192
Period size: 86 Copynumber: 1.9 Consensus size: 87
1055086 TTGAGGTTTT
* * * * *
1055096 TAATTTTTATAATCTA-ATTTTTTACCTTTATAACTGAGATCCCT-AATTTTTTCAATACT-ATT
1 TAATTTTTATAA-CCACACTTTCTACCTTTATAACTGAGACCCCTCAATTTTTTCAAT-CTCACT
*
1055158 TTTTACATTTATAATTGAGACCTC
64 GTTTACATTTATAATTGAGACCTC
* * * *
1055182 TAATTTTTTTAACCACACTTTCTACCTTTATAATTGAGGCCCCTCATTTTTTTCAATCTCACTGT
1 TAATTTTTATAACCACACTTTCTACCTTTATAACTGAGACCCCTCAATTTTTTCAATCTCACTGT
*
1055247 TTACTTTTATAATT
66 TTACATTTATAATT
1055261 TAGGCCCATA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
85 2 0.03
86 36 0.55
87 27 0.42
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (87 bp):
TAATTTTTATAACCACACTTTCTACCTTTATAACTGAGACCCCTCAATTTTTTCAATCTCACTGT
TTACATTTATAATTGAGACCTC
Found at i:1055231 original size:43 final size:44
Alignment explanation
Indices: 1055116--1055274 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 44
1055106 AATCTAATTT
* ** * * *
1055116 TTTACCTTTATAACTGAGATCCCTAA-TTTTTTCAA-TACTATTT
1 TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCAC-ACTG
* * *
1055159 TTTACATTTATAATTGAGACCTCTAATTTTTTT-AACCACACT-
1 TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
* * *
1055201 TTCTACCTTTATAATTGAGGCCCCTCATTTTTTTCAATCTCACTG
1 TT-TACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
* * *
1055246 TTTACTTTTATAATTTAGGCCCATAATTT
1 TTTACCTTTATAATTGAGGCCCCTAATTT
1055275 AATTTTTTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.02
43 53 0.56
44 38 0.40
45 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (44 bp):
TTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAACCACACTG
Found at i:1055848 original size:23 final size:23
Alignment explanation
Indices: 1055804--1055865 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
1055794 TTTATTATCA
1055804 TAATCGAATAAAGA-TTTTTTAT
1 TAATCGAATAAAGATTTTTTTAT
*
1055826 TAATCGAATAAATATTTTTTTAT
1 TAATCGAATAAAGATTTTTTTAT
1055849 TAATCGAATAAAGATTT
1 TAATCGAATAAAGATTT
1055866 CAAATGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 13 0.35
23 24 0.65
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (23 bp):
TAATCGAATAAAGATTTTTTTAT
Found at i:1056086 original size:20 final size:19
Alignment explanation
Indices: 1056057--1056095 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1056047 ATAACTTTCC
* *
1056057 TTTTTTATATTTTGTAATTA
1 TTTTTAATATGTTG-AATTA
1056077 TTTTTAATATGTTGAATTA
1 TTTTTAATATGTTGAATTA
1056096 AAAATAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTTTAATATGTTGAATTA
Found at i:1056176 original size:21 final size:21
Alignment explanation
Indices: 1056150--1056192 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1056140 AAGCATTCAC
*
1056150 ATGTGGTCATCGATGATGATG
1 ATGTGGTCATCGATGATAATG
1056171 ATGTGGTCATCGATGATAATG
1 ATGTGGTCATCGATGATAATG
1056192 A
1 A
1056193 GGCGTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (21 bp):
ATGTGGTCATCGATGATAATG
Found at i:1058263 original size:18 final size:18
Alignment explanation
Indices: 1058237--1058275 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1058227 ACCGGTCAAC
1058237 ACCCCACCCGACCCGTTG
1 ACCCCACCCGACCCGTTG
* *
1058255 ACCCGACCCGACCTGTTG
1 ACCCCACCCGACCCGTTG
1058273 ACC
1 ACC
1058276 GTTGACTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCCACCCGACCCGTTG
Found at i:1064570 original size:23 final size:24
Alignment explanation
Indices: 1064522--1064571 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
1064512 AAATAAAAAT
*
1064522 TTATCAAAAGATAAAAAAAACGTA
1 TTATCAAAAGATAAAAAAAACCTA
*
1064546 TTAT-AAAA-ATAGAAAAAATCCTA
1 TTATCAAAAGATA-AAAAAAACCTA
1064569 TTA
1 TTA
1064572 AGGCAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (24 bp):
TTATCAAAAGATAAAAAAAACCTA
Found at i:1066235 original size:25 final size:25
Alignment explanation
Indices: 1066207--1066257 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1066197 AATAAAAATA
1066207 TGGTGATTACACTTTACCACCGAGG
1 TGGTGATTACACTTTACCACCGAGG
1066232 TGGTGATTACACTTTACCACCGAGG
1 TGGTGATTACACTTTACCACCGAGG
1066257 T
1 T
1066258 CACTGGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (25 bp):
TGGTGATTACACTTTACCACCGAGG
Found at i:1071918 original size:21 final size:21
Alignment explanation
Indices: 1071892--1071942 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1071882 TGCTGGTTTT
1071892 CAAGCTCAGTTTCAGTTATCA
1 CAAGCTCAGTTTCAGTTATCA
1071913 CAAGCTCAGTTTCAGTTATCA
1 CAAGCTCAGTTTCAGTTATCA
1071934 CAAGCTCAG
1 CAAGCTCAG
1071943 GCCCTTGCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (21 bp):
CAAGCTCAGTTTCAGTTATCA
Found at i:1083415 original size:71 final size:71
Alignment explanation
Indices: 1083269--1083485 Score: 236
Period size: 71 Copynumber: 3.1 Consensus size: 71
1083259 GGTTAATATT
* * * *
1083269 AATATTTTTT-ATAAATAT-AGATAATTTCGAATTT-AAAAAA-ATGAAAAATGTGAATATTGCA
1 AATATTTTTTCATAAATATCA-ATAATTTCGAATTTAAAAAAATATGGAAAATGAGAAGACTGCA
1083330 AAGTATT-
65 AAGT-TTC
* * *
1083337 AATATTTTTTCATAAATATCAATACTTTCAAATTTAAAAAAATATGGAAAATGAGAAGACTGAAA
1 AATATTTTTTCATAAATATCAATAATTTCGAATTTAAAAAAATATGGAAAATGAGAAGACTGCAA
1083402 AGTTTC
66 AGTTTC
* * * *
1083408 AATATTTTTTCATAAATATCAATATTTTTGAA-TTAAAAAAATA--GAAAACGAGAAGGCTGCAA
1 AATATTTTTTCATAAATATCAATAATTTCGAATTTAAAAAAATATGGAAAATGAGAAGACTGCAA
*
1083470 AGTATC
66 AGTTTC
1083476 AA-ACTTTTTT
1 AATA-TTTTTT
1083486 TAAAATAAAT
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
67 1 0.01
68 39 0.30
69 20 0.16
70 20 0.16
71 49 0.38
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (71 bp):
AATATTTTTTCATAAATATCAATAATTTCGAATTTAAAAAAATATGGAAAATGAGAAGACTGCAA
AGTTTC
Found at i:1083995 original size:76 final size:76
Alignment explanation
Indices: 1083837--1083995 Score: 205
Period size: 76 Copynumber: 2.1 Consensus size: 76
1083827 TTTAACCGAT
* * * *
1083837 TAAAATAAAATAAGCGCAACATATTACGTTAAACTATCTACTAGTTTGTTTAAATGTATAATAAT
1 TAAAATAAAATAAGCGCAACATATTACGCTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
*
1083902 AATGTAACTGG
66 AATATAACTGG
* * * *
1083913 TTAAATAAAAT-AGACGCTACATATTATGCTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAT
1 TAAAATAAAATAAG-CGCAACATATTACGCTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAA
1083977 TAATATAAAC-GG
65 TAATAT-AACTGG
1083989 TAAAATA
1 TAAAATA
1083996 TTTACAACTT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
75 2 0.03
76 66 0.93
77 3 0.04
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (76 bp):
TAAAATAAAATAAGCGCAACATATTACGCTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
AATATAACTGG
Found at i:1084139 original size:101 final size:100
Alignment explanation
Indices: 1083910--1084209 Score: 419
Period size: 100 Copynumber: 3.0 Consensus size: 100
1083900 ATAATGTAAC
* * * * **
1083910 TGGTT-AAATAAAATAGACGCTACATATTATGCTAAACTAGCTACCAGTTTGTTTAAAGGTATAA
1 TGGTTAAAATAAAATAGGCACTACATATTAAGTTAAACTAGCTACTGGTTTGTTTAAAGGTATAA
1083974 TATTAATATAAACGGTAAAATATTTACAACTTAAT
66 TATTAATATAAACGGTAAAATATTTACAACTTAAT
*
1084009 TAGTTAAAATAAAATAGGCACTATC-TATTAAGTTAAACTAGCTACTGGTTTGTTTAAAGGTATA
1 TGGTTAAAATAAAATAGGCACTA-CATATTAAGTTAAACTAGCTACTGGTTTGTTTAAAGGTATA
1084073 ATATTAATATAAAACGGTAAAATATTTACAACTTAAT
65 ATATTAATAT-AAACGGTAAAATATTTACAACTTAAT
** * * *
1084110 TGGTTAAAATAAAATAGGCTTTACATATTACA-TTAAACTACCTA-TCGATTTGTTTAAAAGTAT
1 TGGTTAAAATAAAATAGGCACTACATATTA-AGTTAAACTAGCTACT-GGTTTGTTTAAAGGTAT
*
1084173 AATATTAATGTAAACGGTAAAATATTTACAACTTAAT
64 AATATTAATATAAACGGTAAAATATTTACAACTTAAT
1084210 CGTTTGAAAT
Statistics
Matches: 181, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
99 4 0.02
100 88 0.49
101 88 0.49
102 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (100 bp):
TGGTTAAAATAAAATAGGCACTACATATTAAGTTAAACTAGCTACTGGTTTGTTTAAAGGTATAA
TATTAATATAAACGGTAAAATATTTACAACTTAAT
Found at i:1085237 original size:21 final size:20
Alignment explanation
Indices: 1085152--1085308 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1085142 AATGACCAAT
** *
1085152 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
1085171 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
1085191 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
1085211 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
1085232 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
1085253 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
*
1085274 AAAATCGCAACGCGAATATT-
1 AAAATCGCAACGCG-ATTTTC
1085294 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1085309 ACACATAAAT
Statistics
Matches: 105, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:1085299 original size:20 final size:20
Alignment explanation
Indices: 1085211--1085327 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
1085201 ATCAGTTTCC
* *
1085211 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
1085231 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
1085251 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
1085272 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
1085294 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
1085313 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
1085328 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:1085337 original size:20 final size:20
Alignment explanation
Indices: 1085295--1085468 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
1085285 GCGAATATTA
* *
1085295 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1085315 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1085335 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1085355 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1085375 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1085395 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1085415 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1085435 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1085456 AAATCGCAACGCG
1 AAATCGCAACGCG
1085469 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1085359 original size:60 final size:60
Alignment explanation
Indices: 1085295--1085468 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
1085285 GCGAATATTA
* *
1085295 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
1085355 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
1085415 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
1085469 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:1085998 original size:21 final size:20
Alignment explanation
Indices: 1085968--1086042 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
1085958 TGCAGAAGAG
1085968 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* * ***
1085989 TCGTAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1086009 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
1086030 TCGCAACGCGAAA
1 TCGCAACGAGAAA
1086043 CCAAAATCGC
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1086071 original size:19 final size:19
Alignment explanation
Indices: 1086049--1086146 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1086039 GAAACCAAAA
*
1086049 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1086068 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1086082 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1086101 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1086115 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1086134 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1086147 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1086090 original size:14 final size:14
Alignment explanation
Indices: 1086071--1086160 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1086061 TTTCATTTCG
1086071 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1086085 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1086104 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1086118 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1086137 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1086151 CGTTGCGATT
1 CGTTGCGATT
1086161 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1086096 original size:33 final size:33
Alignment explanation
Indices: 1086054--1086168 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
1086044 CAAAATCGCA
1086054 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1086087 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1086120 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1086153 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1086169 AACCCAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1088025 original size:93 final size:93
Alignment explanation
Indices: 1087866--1088427 Score: 1099
Period size: 93 Copynumber: 6.1 Consensus size: 93
1087856 TAGATTGCTT
*
1087866 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1087931 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1087959 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1088024 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1088052 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1088117 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1088145 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1088210 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1088238 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAGCTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1088303 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1088331 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1088396 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1088423 AGTAA
1 AGTAA
1088428 TGCAATCCAT
Statistics
Matches: 466, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.01
93 460 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1088515 original size:19 final size:19
Alignment explanation
Indices: 1088475--1088603 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1088465 TAGTTTACTT
* *
1088475 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1088495 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1088514 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1088533 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1088547 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1088566 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1088580 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1088599 TCGCA
1 TCGCA
1088604 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1088554 original size:33 final size:32
Alignment explanation
Indices: 1088511--1088603 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1088501 CGCGAAACCA
**
1088511 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1088543 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1088576 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1088604 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1088601 original size:52 final size:52
Alignment explanation
Indices: 1088475--1088603 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1088465 TAGTTTACTT
**
1088475 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1088527 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1088580 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1088604 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1088621 original size:19 final size:18
Alignment explanation
Indices: 1088599--1088717 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
1088589 GAAACCAAAA
*
1088599 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
1088618 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
1088634 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
1088651 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
1088667 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
1088684 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
1088703 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1088718 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:1088640 original size:14 final size:14
Alignment explanation
Indices: 1088621--1088677 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1088611 TTTCATTTCG
1088621 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
1088635 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
1088652 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1088668 CGTTGCGATT
1 CGTTGCGATT
1088678 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1088646 original size:33 final size:33
Alignment explanation
Indices: 1088604--1088696 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1088594 CAAAATCGCA
*
1088604 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
1088637 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1088670 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1088697 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1088725 original size:20 final size:19
Alignment explanation
Indices: 1088599--1088733 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
1088589 GAAACCAAAA
*
1088599 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1088618 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
1088634 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
1088651 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
1088667 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1088684 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
1088703 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
1088723 TCGTGTTGCGA
1 TCGCGTTGCGA
1088734 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:1090678 original size:14 final size:14
Alignment explanation
Indices: 1090659--1090694 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1090649 ATTGTTTAAT
1090659 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1090673 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1090687 TGATTTGT
1 TGATTTGT
1090695 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1090869 original size:20 final size:19
Alignment explanation
Indices: 1090801--1090879 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
1090791 AAAAATGACT
1090801 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1090820 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1090834 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1090853 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1090873 ATCGCAA
1 ATCGCAA
1090880 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1090916 original size:19 final size:19
Alignment explanation
Indices: 1090888--1091109 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
1090878 AACGAGAGAA
*
1090888 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1090907 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1090926 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
1090942 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1090959 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1090978 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1090994 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1091011 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1091030 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
1091046 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1091063 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1091081 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1091097 TCGCATTGCGATT
1 TCGCATTGCGATT
1091110 CTCTCGTTGC
Statistics
Matches: 171, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.17
16 22 0.13
17 20 0.12
18 3 0.02
19 86 0.50
20 11 0.06
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1090951 original size:52 final size:52
Alignment explanation
Indices: 1090894--1091081 Score: 349
Period size: 52 Copynumber: 3.6 Consensus size: 52
1090884 AGAATCGCAA
*
1090894 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1090946 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1090998 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1091050 TGCGATTTTTATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
1091082 GTTGGGATTT
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 116 0.87
53 17 0.13
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1091131 original size:33 final size:33
Alignment explanation
Indices: 1090912--1091123 Score: 216
Period size: 33 Copynumber: 6.2 Consensus size: 33
1090902 TCATTTCGCA
*
1090912 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1090945 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1090981 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1091016 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
1091049 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1091083 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1091116 TTGCGATT
1 TTGCGATT
1091124 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 19, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 72 0.49
34 28 0.19
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1093663 original size:24 final size:24
Alignment explanation
Indices: 1093629--1093675 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1093619 CTGAAACATC
1093629 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1093653 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1093676 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1094384 original size:20 final size:20
Alignment explanation
Indices: 1094356--1094605 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1094346 AAATTTCAGT
* * *
1094356 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
1094376 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1094396 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1094416 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1094436 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1094456 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1094476 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1094496 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1094516 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1094536 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1094556 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1094576 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1094596 GTTGCGATTT
1 GTTGCGATTT
1094606 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Done.