Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008143.1 Hibiscus syriacus cultivar Beakdansim tig00110705_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: 1142845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:647021 original size:20 final size:20
Alignment explanation
Indices: 646996--647047 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
646986 AAGAATCGCG
*
646996 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
647016 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
647036 TTGCGATTCTGG
1 TTGCGATTCTGG
647048 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:649815 original size:20 final size:20
Alignment explanation
Indices: 649790--649827 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
649780 TTCCCATTGA
649790 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
649810 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
649828 TTAATAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:651487 original size:17 final size:17
Alignment explanation
Indices: 651465--651498 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
651455 GATTTTTACA
651465 TAGGGATTTATTTGCAG
1 TAGGGATTTATTTGCAG
651482 TAGGGATTTATTTGCAG
1 TAGGGATTTATTTGCAG
651499 GAATTACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (17 bp):
TAGGGATTTATTTGCAG
Found at i:655901 original size:12 final size:12
Alignment explanation
Indices: 655884--655910 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
655874 AGATTATTAA
655884 TATTTAATATAT
1 TATTTAATATAT
655896 TATTTAATATAT
1 TATTTAATATAT
655908 TAT
1 TAT
655911 AAAATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:658054 original size:24 final size:24
Alignment explanation
Indices: 658027--658089 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
658017 CAGAAGGGCG
*
658027 TTGAATGTTG-AAGCCCCTAGAA-TT
1 TTGAATGTTGCAAGCCCC-A-AAGCT
658051 TTGAATGTTGCAAGCCCCAAAGCT
1 TTGAATGTTGCAAGCCCCAAAGCT
*
658075 TTGAATGTTGTAAGC
1 TTGAATGTTGCAAGC
658090 ACTAAACCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 26 0.74
25 7 0.20
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (24 bp):
TTGAATGTTGCAAGCCCCAAAGCT
Found at i:658100 original size:24 final size:24
Alignment explanation
Indices: 658050--658101 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
658040 CCCCTAGAAT
* *
658050 TTTGAATGTTGCAAGCCCCAAAGC
1 TTTGAATGTTGCAAGCACCAAACC
* *
658074 TTTGAATGTTGTAAGCACTAAACC
1 TTTGAATGTTGCAAGCACCAAACC
658098 TTTG
1 TTTG
658102 TGTTTCACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (24 bp):
TTTGAATGTTGCAAGCACCAAACC
Found at i:667970 original size:2 final size:2
Alignment explanation
Indices: 667952--667994 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
667942 TGAATTAAAA
*
667952 AT AT A- AT AT AA 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
667993 AT
1 AT
667995 TAATTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:668970 original size:15 final size:15
Alignment explanation
Indices: 668946--669018 Score: 103
Period size: 15 Copynumber: 4.9 Consensus size: 15
668936 TTGGTTTTCC
668946 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
668961 GGAATTTGAATTACT
1 GGAAAATGAATTACT
668976 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
668991 GGAATTTGAATTA-T
1 GGAAAATGAATTACT
669005 GGAAAATGAATTAC
1 GGAAAATGAATTAC
669019 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:669017 original size:29 final size:30
Alignment explanation
Indices: 668946--669018 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
668936 TTGGTTTTCC
668946 GGAAAATGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATTACT
668976 GGAAAATGAATTACTGGAATTTGAATTA-T
1 GGAAAATGAATTACTGGAATTTGAATTACT
669005 GGAAAATGAATTAC
1 GGAAAATGAATTAC
669019 ATTTCTGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.35
30 28 0.65
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (30 bp):
GGAAAATGAATTACTGGAATTTGAATTACT
Found at i:669256 original size:29 final size:28
Alignment explanation
Indices: 669193--669293 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 28
669183 TCTTACTAAA
* *
669193 ATATTATTGAAATAT-ATAAATATATTAT
1 ATATTATT-AAATATAAAAAAAATATTAT
669221 -TCATTATTAAATATAAAAAAAATTATTAT
1 AT-ATTATTAAATATAAAAAAAA-TATTAT
669250 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATAAAAA-A-AATAT-TAT
669279 ATATTA-TAAATATAA
1 ATATTATTAAATATAA
669294 TTGATTATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
27 7 0.11
28 22 0.35
29 30 0.48
30 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATTATTAAATATAAAAAAAATATTAT
Found at i:669261 original size:19 final size:19
Alignment explanation
Indices: 669239--669342 Score: 52
Period size: 19 Copynumber: 5.5 Consensus size: 19
669229 AAATATAAAA
669239 AAAATTATTATATATTATT
1 AAAATTATTATATATTATT
* ** *
669258 AAAATAAAAATATAATATCT
1 AAAATTATTATATATTAT-T
* * * *
669278 TATATTA-TAAATATAATT
1 AAAATTATTATATATTATT
** *
669296 GATTATT-TTATATAATATT
1 -AAAATTATTATATATTATT
* *
669315 AAAAATATAATATATTATT
1 AAAATTATTATATATTATT
669334 AAAA-TATTA
1 AAAATTATTA
669343 ATAAATATAT
Statistics
Matches: 59, Mismatches: 22, Indels: 9
0.66 0.24 0.10
Matches are distributed among these distances:
18 8 0.14
19 46 0.78
20 5 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (19 bp):
AAAATTATTATATATTATT
Found at i:669344 original size:19 final size:19
Alignment explanation
Indices: 669305--669350 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
669295 TGATTATTTT
669305 ATATAATATTAAAAATATA
1 ATATAATATTAAAAATATA
*
669324 ATATATTATT-AAAATATTA
1 ATATAATATTAAAAATA-TA
669343 ATA-AATAT
1 ATATAATAT
669351 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATATTAAAAATATA
Found at i:669350 original size:23 final size:23
Alignment explanation
Indices: 669318--669379 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
669308 TAATATTAAA
669318 AATATAATATATTATTAAA-ATATT
1 AATA-AATATATT-TTAAATATATT
*
669342 AATAAATATATTTTAAATATTTT
1 AATAAATATATTTTAAATATATT
*
669365 AATAATTAATATTTT
1 AATAAAT-ATATTTT
669380 GATGAAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 5 0.15
23 18 0.53
24 11 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATAAATATATTTTAAATATATT
Found at i:669359 original size:21 final size:24
Alignment explanation
Indices: 669248--669368 Score: 74
Period size: 23 Copynumber: 4.9 Consensus size: 24
669238 AAAAATTATT
**
669248 ATATATTATTAAAATAAAAATATA
1 ATATATTATTAAAATATTAATATA
* *
669272 ATATCTTATATTATAAATA-TAAT-TG
1 ATAT-AT-TATTA-AAATATTAATATA
669297 AT-TATT-TTATATAATATTAAAAATATA
1 ATATATTATTA-A-AATATT---AATATA
669324 ATATATTATTAAAATATTAATA-A
1 ATATATTATTAAAATATTAATATA
*
669347 ATATATT-TTAAATATTTTAATA
1 ATATATTATTAAA-ATATTAATA
669369 ATTAATATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
21 5 0.06
22 10 0.13
23 18 0.23
24 9 0.11
25 4 0.05
26 11 0.14
27 14 0.18
28 5 0.06
29 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
ATATATTATTAAAATATTAATATA
Found at i:669659 original size:43 final size:43
Alignment explanation
Indices: 669552--669672 Score: 201
Period size: 42 Copynumber: 2.9 Consensus size: 43
669542 ATGAATTACA
*
669552 TTCCGG-AAAACGAATTACGTGAAACAAACACAGGAAAACGTT
1 TTCCGGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
*
669594 TTCC-GAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
*
669636 TTCCGGAAAAACAAATTACGTGAAACAAACACAGGAA
1 TTCCGGAAAAACGAATTACGTGAAACAAACACAGGAA
669673 TTCGGGGAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.01
42 42 0.58
43 30 0.41
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (43 bp):
TTCCGGAAAAACGAATTACGTGAAACAAACACAGGAAAACATT
Found at i:671064 original size:14 final size:14
Alignment explanation
Indices: 671047--671084 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
671037 AGTTACGCTG
671047 GAAATGAAAAGAGA
1 GAAATGAAAAGAGA
671061 GAAATGAAAAGAGA
1 GAAATGAAAAGAGA
671075 GAAATGAAAA
1 GAAATGAAAA
671085 ATGAAATTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.08
Consensus pattern (14 bp):
GAAATGAAAAGAGA
Found at i:671278 original size:31 final size:30
Alignment explanation
Indices: 671238--671318 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
671228 GCGTCAAACG
*
671238 GTTGGGGACCATTTTGCAAACAGACAAAAT
1 GTTGGGGACCATATTGCAAACAGACAAAAT
* *
671268 GTTGGTGGACCATATTGCAAACGGACTAAAT
1 GTTGG-GGACCATATTGCAAACAGACAAAAT
**
671299 GTTAGGGGACTGTATTGCAA
1 GTT-GGGGACCATATTGCAA
671319 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 5 0.11
31 37 0.84
32 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (30 bp):
GTTGGGGACCATATTGCAAACAGACAAAAT
Found at i:671692 original size:19 final size:19
Alignment explanation
Indices: 671647--671694 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
671637 GAATTTTTTA
*
671647 ATATTTTTAATTAAATCTT
1 ATATTTTTAATTAAACCTT
671666 ATAATTTTTAATTAAACCTT
1 AT-ATTTTTAATTAAACCTT
671686 CAT-TTTTTA
1 -ATATTTTTA
671695 TTATTCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 16 0.62
21 2 0.08
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTTTAATTAAACCTT
Found at i:676068 original size:21 final size:22
Alignment explanation
Indices: 676044--676102 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 22
676034 ATCATACCCC
676044 ATAACATAATATAAAAATA-TT
1 ATAACATAATATAAAAATATTT
* **
676065 ATAATCCT-ATAT-ATTATATTT
1 ATAA-CATAATATAAAAATATTT
*
676086 AAAACATAATATAAAAA
1 ATAACATAATATAAAAA
676103 ATGTTTTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 7
0.66 0.17 0.17
Matches are distributed among these distances:
20 6 0.22
21 17 0.63
22 4 0.15
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAACATAATATAAAAATATTT
Found at i:677643 original size:30 final size:31
Alignment explanation
Indices: 677584--677653 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
677574 ATCCATTCAT
677584 GGTGACAATATCGATCGACACCCTAACTTCC
1 GGTGACAATATCGATCGACACCCTAACTTCC
*
677615 GGTGACAATATCGATCGACA-CGTAACTTCC
1 GGTGACAATATCGATCGACACCCTAACTTCC
**
677645 CATGACAAT
1 GGTGACAAT
677654 TTGAAGATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (31 bp):
GGTGACAATATCGATCGACACCCTAACTTCC
Found at i:680051 original size:20 final size:20
Alignment explanation
Indices: 680008--680053 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
679998 CGGTTCTCCC
*
680008 CGGTTCTACCGATTTCCAGC
1 CGGTTCTACCGATTTCCAGA
* * *
680028 CGGTTCTACTGGTTTTCAGA
1 CGGTTCTACCGATTTCCAGA
680048 CGGTTC
1 CGGTTC
680054 GTTGCCAGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.28, G:0.24, T:0.35
Consensus pattern (20 bp):
CGGTTCTACCGATTTCCAGA
Found at i:681353 original size:32 final size:32
Alignment explanation
Indices: 681309--681393 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 32
681299 TAGCACACTT
*
681309 AAAAAAGCCTGACCCGACCCCAAAAATTTAAA
1 AAAAAAACCTGACCCGACCCCAAAAATTTAAA
* * * *
681341 AAAAAAATCTGACTCGATCCC--GAATTTAAA
1 AAAAAAACCTGACCCGACCCCAAAAATTTAAA
* *
681371 AAAAAAACCCGACCGGACCCCAA
1 AAAAAAACCTGACCCGACCCCAA
681394 CCCGAATATC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
30 24 0.59
32 17 0.41
ACGTcount: A:0.48, C:0.28, G:0.11, T:0.13
Consensus pattern (32 bp):
AAAAAAACCTGACCCGACCCCAAAAATTTAAA
Found at i:683421 original size:2 final size:2
Alignment explanation
Indices: 683414--683458 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
683404 TCCCTCCCAA
* * *
683414 CT CT CT CT CT CT CT CC CT CT CC CT CT CT CC CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
683456 CT C
1 CT C
683459 CCCCACCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
CT
Found at i:688505 original size:44 final size:44
Alignment explanation
Indices: 688432--688524 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
688422 GTATTGAATC
* *
688432 AGAGGAAATATGCTTTGGAGTTAGCTGACGATACACGGATAAGG
1 AGAGCAAATATGCTTTGGAGTTAGCTGACGATACACGGACAAGG
* *
688476 AGAGCAAATATGCTTTGGAGTTAGTTGACGATACATGGACAAGG
1 AGAGCAAATATGCTTTGGAGTTAGCTGACGATACACGGACAAGG
688520 AGAGC
1 AGAGC
688525 CAAAACTACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.23
Consensus pattern (44 bp):
AGAGCAAATATGCTTTGGAGTTAGCTGACGATACACGGACAAGG
Found at i:692066 original size:60 final size:61
Alignment explanation
Indices: 691936--692072 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 61
691926 AACTTTTGAG
* * * *
691936 TATTCCAATTTCAT-CCTCAAACTATGACTCTCATTCTAAATTAATCTTCAAAATTTTGAA
1 TATTCAAATTTCATCCCTCAAACTATGACCCTCATTCTAAATTAATCTCCAAAATTTTAAA
* * * * * *
691996 CAGTCTAATTTCATCCCT-AAATTATGACCCTCTTTCTAAATTAATC-CCAAACCTTTTAAA
1 TATTCAAATTTCATCCCTCAAACTATGACCCTCATTCTAAATTAATCTCCAAA-ATTTTAAA
692056 TATTCAAATTTCATCCC
1 TATTCAAATTTCATCCC
692073 CAAGTTCATC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 4 0.06
60 56 0.89
61 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.39
Consensus pattern (61 bp):
TATTCAAATTTCATCCCTCAAACTATGACCCTCATTCTAAATTAATCTCCAAAATTTTAAA
Found at i:692310 original size:60 final size:60
Alignment explanation
Indices: 692199--692321 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
692189 GTATATAATT
* ** *
692199 ATAGTTTGGGATGAAATTGGAATATTCAAAAAGATTGGGGATCAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGAAATATTCAAAAAGATTAAGAATCAATTTAGAATGATA-GTC
* * *
692259 ATAGTTTGGAGATGAAATTGAAATGTTCAAAAA-TTTAAGAATTAATTTAGAATGATAGTC
1 ATAGTTTGG-GATGAAATTGAAATATTCAAAAAGATTAAGAATCAATTTAGAATGATAGTC
692319 ATA
1 ATA
692322 ATTTAAGGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 32 0.59
61 22 0.41
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATATTCAAAAAGATTAAGAATCAATTTAGAATGATAGTC
Found at i:697651 original size:32 final size:32
Alignment explanation
Indices: 697593--697657 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
697583 TCCTTTAGAG
* *
697593 TTCATCATTCTCCTCCCTTCCGGATATGATTA
1 TTCATCATTCTCCTCCCTTCCAGATATAATTA
*
697625 TTCATCATTCTCCTCCCTTCTAGATATAATTA
1 TTCATCATTCTCCTCCCTTCCAGATATAATTA
697657 T
1 T
697658 GATTAGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (32 bp):
TTCATCATTCTCCTCCCTTCCAGATATAATTA
Found at i:702413 original size:31 final size:31
Alignment explanation
Indices: 702378--702451 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
702368 TTAATCATTT
*
702378 AAATTTATTTTTATATAATTATTTAACTTTC
1 AAATTTATTTTTATATAATCATTTAACTTTC
* * *
702409 AAA-TTATTCCTAATTTAATCATTTAACTTTC
1 AAATTTATT-TTTATATAATCATTTAACTTTC
702440 AAATTTATTTTT
1 AAATTTATTTTT
702452 TTATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 5 0.14
31 25 0.71
32 5 0.14
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.55
Consensus pattern (31 bp):
AAATTTATTTTTATATAATCATTTAACTTTC
Found at i:702415 original size:16 final size:16
Alignment explanation
Indices: 702394--702449 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
702384 ATTTTTATAT
702394 AATTATTTAACTTTCA
1 AATTATTTAACTTTCA
702410 AATTATTCCTAA-TTT--
1 AATTATT--TAACTTTCA
*
702425 AATCATTTAACTTTCA
1 AATTATTTAACTTTCA
702441 AATTTATTT
1 AA-TTATTT
702450 TTTTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
13 3 0.09
14 3 0.09
15 6 0.19
16 9 0.28
17 8 0.25
18 3 0.09
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTTAACTTTCA
Found at i:703819 original size:23 final size:23
Alignment explanation
Indices: 703793--703883 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
703783 CACCACAACT
*
703793 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
703816 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
* *
703839 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
703862 TGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
703884 ATATAATGTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:705518 original size:40 final size:42
Alignment explanation
Indices: 705469--705566 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 42
705459 TGCACTACTT
*
705469 GTGCATCGATGCA-TAAAATACATTCGATGTTTG-TATTT-TA
1 GTGCATCGATGCACT-AAATACATTCGATGTTTGTTATTTAGA
** *
705509 GTGCATCGATGCACTACTTGCATTCGATGTTTGTTTATTTGAGA
1 GTGCATCGATGCACTAAATACATTCGATGTTTG-TTATTT-AGA
705553 GTGCATCGATGCAC
1 GTGCATCGATGCAC
705567 ACAACCTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 28 0.57
41 1 0.02
42 5 0.10
44 15 0.31
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.38
Consensus pattern (42 bp):
GTGCATCGATGCACTAAATACATTCGATGTTTGTTATTTAGA
Found at i:708501 original size:25 final size:24
Alignment explanation
Indices: 708473--708541 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
708463 GGAGAAAACG
708473 ACAAAT-TTCATATATTTTGAACTGA
1 ACAAATCTT-ATA-ATTTTGAACTGA
708498 AC-AATGCTTATAATTTTGAACTGA
1 ACAAAT-CTTATAATTTTGAACTGA
708522 AC-AATGCTTATAATTTTGAA
1 ACAAAT-CTTATAATTTTGAA
708542 TTATGAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
24 35 0.83
25 5 0.12
26 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (24 bp):
ACAAATCTTATAATTTTGAACTGA
Found at i:708513 original size:24 final size:24
Alignment explanation
Indices: 708486--708541 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
708476 AATTTCATAT
708486 ATTTTGAACTGAACAATGCTTATA
1 ATTTTGAACTGAACAATGCTTATA
708510 ATTTTGAACTGAACAATGCTTATA
1 ATTTTGAACTGAACAATGCTTATA
708534 ATTTTGAA
1 ATTTTGAA
708542 TTATGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (24 bp):
ATTTTGAACTGAACAATGCTTATA
Found at i:712300 original size:27 final size:27
Alignment explanation
Indices: 712262--712316 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
712252 AGATTACGAT
712262 TGGTTTATTAGTGCATACCAAAACAAA
1 TGGTTTATTAGTGCATACCAAAACAAA
*
712289 TGGTTTATTAGTGCATACCACAACAAA
1 TGGTTTATTAGTGCATACCAAAACAAA
712316 T
1 T
712317 ACTCATAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (27 bp):
TGGTTTATTAGTGCATACCAAAACAAA
Found at i:714444 original size:31 final size:32
Alignment explanation
Indices: 714409--714513 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 32
714399 ATGACGGTAG
* * **
714409 AGTGACCATTTTGTTTA-AAATCGATAATGTT
1 AGTGACCAATTTGTTTACAAATAGATAACATT
*
714440 AGTGACTAATTTG-TTACAAATAGATAACATT
1 AGTGACCAATTTGTTTACAAATAGATAACATT
* *
714471 AGTGACCAATTTG-TTACAAATCA-ATAAAACT
1 AGTGACCAATTTGTTTACAAAT-AGATAACATT
*
714502 AATGACCAATTT
1 AGTGACCAATTT
714514 ATTATTTATG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.05
31 59 0.94
32 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (32 bp):
AGTGACCAATTTGTTTACAAATAGATAACATT
Found at i:717380 original size:110 final size:104
Alignment explanation
Indices: 717144--717607 Score: 564
Period size: 110 Copynumber: 4.4 Consensus size: 104
717134 TGTTTCAATT
* * * * *
717144 GATCATA-TCAGTCTTGTTTCTGGATTTACTATTTGTTGCAAAATTATTAGTTGGTTGTTCTTTT
1 GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGC-AAA--ATTA-TTGGTTG---GTTA
* *
717208 TTCTTTTCTTTTCTTTTTAAATTTAGTTTATTTGATTGTCTGTTTCTCTA
59 TT-TTTT-TTTTC--TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
* *
717258 GATCATATTCAGTCTTGCTTCTGGTTTTAATGTTTGTTGCAAAATTATTGGTTCGTTATTCTTTT
1 GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGCAAAATTATTGGTTGGTTA----TTT
*
717323 TTTCTTCTTCTTTAAATTTAGTTTATTTGATTATCTGCTTCTCTC
62 TTT-TT-TTCTTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
717368 GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGCAAAATTATTGGTTGGTTA--TTTTT
1 GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTT
*
717431 TTTATTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
66 TTTCTTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
* *
717470 GATCATATTCAGTTTTGCTTCTGGTTTTACTGTTTTTTGCAAAATTATTGGTT-G--ATTTTTTT
1 GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTT
* * *
717532 TTGCTTTAAATCTAGTTTATTTGATTGTTTGCTTCTCTC
66 TTTCTTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
*
717571 GATCATATTCGGTCTTGCTTCTGGTTTTA-TGGTTTGT
1 GATCATATTCAGTCTTGCTTCTGGTTTTACT-GTTTGT
717608 CGAAAATGAA
Statistics
Matches: 318, Mismatches: 23, Indels: 31
0.85 0.06 0.08
Matches are distributed among these distances:
99 1 0.00
100 1 0.00
101 73 0.23
102 87 0.27
103 2 0.01
104 4 0.01
108 2 0.01
110 88 0.28
111 13 0.04
112 9 0.03
114 10 0.03
115 28 0.09
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (104 bp):
GATCATATTCAGTCTTGCTTCTGGTTTTACTGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTT
TTTCTTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTC
Found at i:717510 original size:102 final size:102
Alignment explanation
Indices: 717223--717607 Score: 558
Period size: 102 Copynumber: 3.7 Consensus size: 102
717213 TTCTTTTCTT
* * *
717223 TTTAAATTTAGTTTATTTGATTGTCTGTTTCTCTAGATCATATTCAGTCTTGCTTCTGGTTTTAA
1 TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
*
717288 TGTTTGTTGCAAAATTATTGGTTCGTTATTCTTTTTTTCTTCTTC
66 TGTTTGTTGCAAAATTATTGGTTGGTTA------TTTT-TT-TTC
*
717333 TTTAAATTTAGTTTATTTGATTATCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
1 TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
*
717398 TGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTTTA
66 TGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTTTC
*
717435 TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTTTTGCTTCTGGTTTTAC
1 TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
* * *
717500 TGTTTTTTGCAAAATTATTGGTTGATT-TTTTTTTGC
66 TGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTTTC
* * *
717536 TTTAAATCTAGTTTATTTGATTGTTTGCTTCTCTCGATCATATTCGGTCTTGCTTCTGGTTTTA-
1 TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
717600 TGGTTTGT
66 T-GTTTGT
717608 CGAAAATGAA
Statistics
Matches: 257, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
100 1 0.00
101 72 0.28
102 90 0.35
103 2 0.01
104 4 0.02
110 88 0.34
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (102 bp):
TTTAAATTTAGTTTATTTGATTGTCTGCTTCTCTCGATCATATTCAGTCTTGCTTCTGGTTTTAC
TGTTTGTTGCAAAATTATTGGTTGGTTATTTTTTTTC
Found at i:726748 original size:20 final size:20
Alignment explanation
Indices: 726723--726762 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
726713 AGCAACAGAA
*
726723 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
726743 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
726763 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:726804 original size:20 final size:20
Alignment explanation
Indices: 726776--726814 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
726766 TAATAGAATA
* *
726776 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
726796 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
726815 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:729056 original size:20 final size:20
Alignment explanation
Indices: 729031--729070 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
729021 AGCAACAGAA
729031 TAAAAATGATTCTATCTAAT
1 TAAAAATGATTCTATCTAAT
729051 TAAAAATGATTCTATCTAAT
1 TAAAAATGATTCTATCTAAT
729071 AACTAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATTCTATCTAAT
Found at i:729112 original size:20 final size:20
Alignment explanation
Indices: 729084--729122 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
729074 TAATAGAATA
* *
729084 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
729104 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
729123 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:730568 original size:26 final size:25
Alignment explanation
Indices: 730539--730591 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
730529 CGAGCGCAGG
730539 ATTTTATGAAGGG-GCGAACTTATAAA
1 ATTTTA-G-AGGGAGCGAACTTATAAA
*
730565 ATTTTAGGGGGAAGCGAACTTATAAA
1 ATTTTAGAGGG-AGCGAACTTATAAA
730591 A
1 A
730592 AAAGCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 1 0.04
26 20 0.83
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.28
Consensus pattern (25 bp):
ATTTTAGAGGGAGCGAACTTATAAA
Found at i:735287 original size:27 final size:27
Alignment explanation
Indices: 735253--735306 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
735243 TATAAATTCT
735253 TTTTTACTTATTTCGTTATTATTTTAA
1 TTTTTACTTATTTCGTTATTATTTTAA
*
735280 TTTTTACTTATTTTGTTATTATTTTAA
1 TTTTTACTTATTTCGTTATTATTTTAA
735307 GGTTGAACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTTACTTATTTCGTTATTATTTTAA
Found at i:741384 original size:64 final size:64
Alignment explanation
Indices: 741283--741413 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 64
741273 AGTAGTAACC
* * *
741283 TTATGAATGAGTAAATGACGAATATGTCCCTTTTATGGCCAAATTATTAAACTATCCTTGAGTG
1 TTATGAATGAGTAAATGACAAATATATCCCTTTTATGGCCAAATTATTAAACTATCCTTAAGTG
741347 TTATGAATGAGTAAATGACAAATATATCCCTTTTATGGCCAAATTATTAAACTATCCTTAAGTG
1 TTATGAATGAGTAAATGACAAATATATCCCTTTTATGGCCAAATTATTAAACTATCCTTAAGTG
741411 TTA
1 TTA
741414 AAGAGATTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (64 bp):
TTATGAATGAGTAAATGACAAATATATCCCTTTTATGGCCAAATTATTAAACTATCCTTAAGTG
Found at i:742128 original size:22 final size:22
Alignment explanation
Indices: 742077--742129 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
742067 TCGGGATGAT
742077 TGAACTTCTCCTATTGTCAAAC
1 TGAACTTCTCCTATTGTCAAAC
** *
742099 TGGCCTTCTTCTATTGTCAAAC
1 TGAACTTCTCCTATTGTCAAAC
742121 TGAACTTCT
1 TGAACTTCT
742130 GTTTCAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (22 bp):
TGAACTTCTCCTATTGTCAAAC
Found at i:743988 original size:40 final size:41
Alignment explanation
Indices: 743943--744023 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
743933 ACATAGTGAT
*
743943 TATTCTGTTAAATGTC-CTATCCTTTTTGCCTTAAAATGAA
1 TATTCTGTCAAATGTCACTATCCTTTTTGCCTTAAAATGAA
* * *
743983 TATTCTGTCAAATGTCATTGTCTTTTTTGCCTTAAAATGAA
1 TATTCTGTCAAATGTCACTATCCTTTTTGCCTTAAAATGAA
744024 ATGTTGGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 15 0.42
41 21 0.58
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (41 bp):
TATTCTGTCAAATGTCACTATCCTTTTTGCCTTAAAATGAA
Found at i:748144 original size:2 final size:2
Alignment explanation
Indices: 748139--748202 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
748129 TATTTTCAAT
748139 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
748181 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
748203 GGTTAAGGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:762301 original size:18 final size:18
Alignment explanation
Indices: 762242--762305 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
762232 ATTTTTAATA
* *
762242 TAATGATATTT-TTATTT
1 TAATAATATTTATTATAT
* *
762259 TAATAAATAATTAATATAAT
1 TAAT-AATATTTATTAT-AT
*
762279 TAATAATATTTATTATCT
1 TAATAATATTTATTATAT
762297 TAATAATAT
1 TAATAATAT
762306 AATATAGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 4 0.11
18 15 0.41
19 13 0.35
20 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATAATATTTATTATAT
Found at i:762339 original size:35 final size:33
Alignment explanation
Indices: 762236--762340 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 33
762226 ATTACAATTT
*
762236 TTAATATAATGATAT-TTTTATTTTAATAAATAA
1 TTAATATAAT-ATATATTTTATTTTCATAAATAA
*
762269 TTAATATAAT-TAATAATATTTATTATC-T---TAA
1 TTAATATAATAT-AT-AT-TTTATTTTCATAAATAA
762300 -TAATATAATATAGTATTCTTATTTTCATAAATAA
1 TTAATATAATATA-TATT-TTATTTTCATAAATAA
762334 TTAATAT
1 TTAATAT
762341 GATTTATAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 22
0.70 0.04 0.27
Matches are distributed among these distances:
29 1 0.02
30 19 0.33
31 7 0.12
32 2 0.04
33 10 0.18
34 5 0.09
35 13 0.23
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (33 bp):
TTAATATAATATATATTTTATTTTCATAAATAA
Found at i:762853 original size:18 final size:18
Alignment explanation
Indices: 762827--762900 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 18
762817 ACTATTTATT
*
762827 ATATTATTAAAATAATAT
1 ATATTATTAAAATAATAA
*
762845 ATTTTATTAAAATAATAA
1 ATATTATTAAAATAATAA
* * *
762863 ATATTATTAATTATATTAG
1 ATATTATTAA-AATAATAA
*
762882 TTATGTATTAAAATAATAA
1 ATAT-TATTAAAATAATAA
762901 TAATATATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
18 25 0.57
19 13 0.30
20 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTATTAAAATAATAA
Found at i:766691 original size:31 final size:31
Alignment explanation
Indices: 766632--766689 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
766622 GTACGATTTT
766632 GATAAAAATAAAAGTTTAAATACTAAAATGA
1 GATAAAAATAAAAGTTTAAATACTAAAATGA
* * *
766663 GATAAAGATAATAGTTTAAGTA-TAAAA
1 GATAAAAATAAAAGTTTAAATACTAAAA
766690 ATCTGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.28
Consensus pattern (31 bp):
GATAAAAATAAAAGTTTAAATACTAAAATGA
Found at i:767554 original size:197 final size:197
Alignment explanation
Indices: 767217--767604 Score: 566
Period size: 197 Copynumber: 2.0 Consensus size: 197
767207 TGGTTTAATC
* * *
767217 GACAGGAAAGTTTCACGTGCGGTCACTTAATATACGATTAAGAAAAAGTGTTATAAAAAATATTA
1 GACAGGAAAGTCTCACGTGCGGCCACCTAATATACGATTAAGAAAAAGTGTTATAAAAAATATTA
* * *
767282 TTATTTTTTTAATATTTCTGATAAAAAATTATCGAAAATATTATTATTTCTACCGGAAATATTAT
66 TTATTTTTTTAACATTTCTGATAAAAAATTATCGAAAACATTATTATTTCTACCGAAAATATTAT
* *
767347 TGGATGTTTTATCGGGTTTGTTAACATATCT-AGTAAAAATCTACATAAAACATTATTTTTTCTA
131 TGGATGTTTTATCGGGTTTGTTAACATATATGA-TAAAAAGCTACATAAAACATTATTTTTTCTA
767411 CCG
195 CCG
* * ** *
767414 GACAGGAAAGTCTCACGTGCGGCCACCTAATATACGGTTAAGAAAAGGTGTTATCGAAAATGTTA
1 GACAGGAAAGTCTCACGTGCGGCCACCTAATATACGATTAAGAAAAAGTGTTATAAAAAATATTA
* * *
767479 TTATTTTTTTAACATTTCTGGTAAAAAATTA-CTGAAAGCATTATTATTTCTACCGAAAATATTT
66 TTATTTTTTTAACATTTCTGATAAAAAATTATC-GAAAACATTATTATTTCTACCGAAAATATTA
* *
767543 TTAGG-TGTTTTATCGGGTTTGTTAACATATATGATAAAACGCTACCTAAAACATTATTTTTT
130 TT-GGATGTTTTATCGGGTTTGTTAACATATATGATAAAAAGCTACATAAAACATTATTTTTT
767605 TTCTACCGAA
Statistics
Matches: 170, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
196 1 0.01
197 166 0.98
198 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (197 bp):
GACAGGAAAGTCTCACGTGCGGCCACCTAATATACGATTAAGAAAAAGTGTTATAAAAAATATTA
TTATTTTTTTAACATTTCTGATAAAAAATTATCGAAAACATTATTATTTCTACCGAAAATATTAT
TGGATGTTTTATCGGGTTTGTTAACATATATGATAAAAAGCTACATAAAACATTATTTTTTCTAC
CG
Found at i:767672 original size:22 final size:22
Alignment explanation
Indices: 767647--767688 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
767637 CTGGAAATGT
*
767647 TAAAAAACATTAATGTTTTAGA
1 TAAAAAACAATAATGTTTTAGA
*
767669 TAAAAAATAATAATGTTTTA
1 TAAAAAACAATAATGTTTTA
767689 CGTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
TAAAAAACAATAATGTTTTAGA
Found at i:771280 original size:39 final size:38
Alignment explanation
Indices: 771192--771283 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 38
771182 TGTTTGATCC
* *
771192 TAACATTCTAAATTCTTATTTTCTTAAATTGTTTCACAA
1 TAACATT-TAAATTATTAATTTCTTAAATTGTTTCACAA
* * **
771231 TAATATTTTAAATTATTAATTTCTTATATTGTTTCACGT
1 TAACA-TTTAAATTATTAATTTCTTAAATTGTTTCACAA
771270 TAACGATTTAAATT
1 TAAC-ATTTAAATT
771284 GTTTCTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 41 0.93
40 3 0.07
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (38 bp):
TAACATTTAAATTATTAATTTCTTAAATTGTTTCACAA
Found at i:771366 original size:94 final size:95
Alignment explanation
Indices: 771268--771456 Score: 344
Period size: 95 Copynumber: 2.0 Consensus size: 95
771258 ATTGTTTCAC
*
771268 GTTAACGATTTAAATTGTTTCTCAAATTA-TTTTTTATTTTAAATTTAAGTGTATTTATTTAATT
1 GTTAACGATTTAAATTATTTCTCAAATTATTTTTTTATTTTAAATTTAAGTGTATTTATTTAATT
*
771332 GTATTTCTAATAAGTTTTATCTTTGAATAT
66 GTATTTCTAATAAGTTTAATCTTTGAATAT
*
771362 GTTAACGATTTAAATTATTTCTCTAATTATTTTTTTATTTTAAATTTAAGTGTATTTATTTAATT
1 GTTAACGATTTAAATTATTTCTCAAATTATTTTTTTATTTTAAATTTAAGTGTATTTATTTAATT
771427 GTATTTCTAATAAGTTTAATCTTTGAATAT
66 GTATTTCTAATAAGTTTAATCTTTGAATAT
771457 ATACTTTAAA
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
94 27 0.30
95 64 0.70
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (95 bp):
GTTAACGATTTAAATTATTTCTCAAATTATTTTTTTATTTTAAATTTAAGTGTATTTATTTAATT
GTATTTCTAATAAGTTTAATCTTTGAATAT
Found at i:771373 original size:49 final size:50
Alignment explanation
Indices: 771299--771456 Score: 147
Period size: 49 Copynumber: 3.3 Consensus size: 50
771289 TCAAATTATT
*
771299 TTTTAT-TTT-AA-ATTTAAGTGTATTTATTTAATTGTATTTCTAATAAG
1 TTTTATCTTTGAATATTTAAGCGTATTTATTTAATTGTATTTCTAATAAG
* * *
771346 TTTTATCTTTGAATATGTTAA-CG-ATTTA---AATTAT-TTCTCTAATTAT
1 TTTTATCTTTGAATAT-TTAAGCGTATTTATTTAATTGTATT-TCTAATAAG
* * * *
771392 TTTTTTATTTTAA-ATTTAAGTGTATTTATTTAATTGTATTTCTAATAAG
1 TTTTATCTTTGAATATTTAAGCGTATTTATTTAATTGTATTTCTAATAAG
*
771441 TTTAATCTTTGAATAT
1 TTTTATCTTTGAATAT
771457 ATACTTTAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
44 4 0.05
45 5 0.06
46 27 0.32
47 6 0.07
48 3 0.04
49 28 0.33
50 7 0.08
51 4 0.05
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (50 bp):
TTTTATCTTTGAATATTTAAGCGTATTTATTTAATTGTATTTCTAATAAG
Found at i:772689 original size:31 final size:31
Alignment explanation
Indices: 772651--772742 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
772641 CCCGAAGGAC
* * *
772651 CAGTCCATA-GATTCCGAAGATCCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
772682 CAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
772713 CAGTCCATATGTCCCGAATAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
772743 CCCTCAACCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:773017 original size:15 final size:16
Alignment explanation
Indices: 772989--773020 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
772979 TATAACATGT
772989 ATCACATGAGCATATA
1 ATCACATGAGCATATA
773005 ATCACAT-AGCATATA
1 ATCACATGAGCATATA
773020 A
1 A
773021 ACTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (16 bp):
ATCACATGAGCATATA
Found at i:780354 original size:20 final size:19
Alignment explanation
Indices: 780329--780414 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
780319 TTTTGATGCA
*
780329 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
780349 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
*
780370 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATACCCCCT
*
780391 -AGGGGAATCGATACCCCCT
1 GA-GGGAACCGATACCCCCT
780410 GAGGG
1 GAGGG
780415 TTCTGGTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.35
20 17 0.30
21 3 0.05
22 1 0.02
23 16 0.28
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:780396 original size:19 final size:20
Alignment explanation
Indices: 780331--780414 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
780321 TTGATGCAGA
* *
780331 GGGAATCGATACCCCCATGA-
1 GGGAACCGATTCCCCC-TGAG
780351 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TG-AG
780374 GGGAACCGATTCCCCCT-AG
1 GGGAACCGATTCCCCCTGAG
* *
780393 GGGAATCGATACCCCCTGAG
1 GGGAACCGATTCCCCCTGAG
780413 GG
1 GG
780415 TTCTGGTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
19 17 0.31
20 18 0.33
21 3 0.05
22 1 0.02
23 16 0.29
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCTGAG
Found at i:784615 original size:24 final size:25
Alignment explanation
Indices: 784587--784646 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
784577 ATAGATGGAC
784587 AAAAAAATAA-TGTAGACACCAATTT
1 AAAAAAA-AATTGTAGACACCAATTT
784612 AAAAAAAAATTGTAGACACCAATTT
1 AAAAAAAAATTGTAGACACCAATTT
784637 AGAAAAAAAA
1 A-AAAAAAAA
784647 AATATAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.06
25 23 0.70
26 8 0.24
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (25 bp):
AAAAAAAAATTGTAGACACCAATTT
Found at i:785131 original size:16 final size:16
Alignment explanation
Indices: 785106--785148 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
785096 AACAAATTGT
*
785106 AAATAGAAAATACAAA
1 AAATATAAAATACAAA
*
785122 AAATATAAAATATAAA
1 AAATATAAAATACAAA
*
785138 ATATATAAAAT
1 AAATATAAAAT
785149 TTTAAAGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AAATATAAAATACAAA
Found at i:785458 original size:2 final size:2
Alignment explanation
Indices: 785451--785477 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
785441 ATATGAAGAT
785451 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
785478 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:788392 original size:22 final size:22
Alignment explanation
Indices: 788364--788406 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
788354 GTTCAACCGT
*
788364 GGTTGAATCCGATTGAACCAGC
1 GGTTGAACCCGATTGAACCAGC
788386 GGTTGAACCCGATTGAACCAG
1 GGTTGAACCCGATTGAACCAG
788407 TACTTTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (22 bp):
GGTTGAACCCGATTGAACCAGC
Found at i:790359 original size:23 final size:23
Alignment explanation
Indices: 790333--790401 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
790323 CACCACAGCT
* *
790333 CGTATAATTGCACCGAAGTGCTA
1 CGTAGAATTGCACCGAAGTGCCA
* *
790356 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
790379 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
790402 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:790580 original size:103 final size:103
Alignment explanation
Indices: 790417--790629 Score: 354
Period size: 103 Copynumber: 2.1 Consensus size: 103
790407 TAATGTCCAT
* * * * * *
790417 AAGGACTACATATCATTCCTTAAGAATTATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
*
790482 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
790520 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
790585 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
790623 AAGGACC
1 AAGGACC
790630 GCGTAGACCC
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:792338 original size:21 final size:21
Alignment explanation
Indices: 792314--792358 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
792304 TTTTGTTCGT
* *
792314 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
792335 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
792356 TTG
1 TTG
792359 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:795251 original size:32 final size:32
Alignment explanation
Indices: 795215--795276 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
795205 CAATACAAAC
*
795215 ATATAATTGTATAAATAAAATTTTAAAATTAG
1 ATATAATTGTATAAAGAAAATTTTAAAATTAG
*
795247 ATATATTTGTATAAAGAAAATTTTAAAATT
1 ATATAATTGTATAAAGAAAATTTTAAAATT
795277 TATAGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (32 bp):
ATATAATTGTATAAAGAAAATTTTAAAATTAG
Found at i:802965 original size:48 final size:51
Alignment explanation
Indices: 802886--803077 Score: 236
Period size: 48 Copynumber: 3.9 Consensus size: 51
802876 TGTAAATATG
*
802886 TGTTAAATACTATATTTTTTTATTTTA-TCACTTATACCGATATAAGTATA
1 TGTTAAATACTATATTTTTTTATTTTATTCACTTACACCGATATAAGTATA
* *
802936 TGTTAAATA-T-TA-TTTTTTATTTTATTCACTTACACCGGTATAAATATA
1 TGTTAAATACTATATTTTTTTATTTTATTCACTTACACCGATATAAGTATA
* ** * *
802984 TGTTAAATACTATATTTTTTTATTTTATTCACCTACACTAATGTAAGTATG
1 TGTTAAATACTATATTTTTTTATTTTATTCACTTACACCGATATAAGTATA
* *
803035 CGTT-AATAC-AT-TTTTTTTAATTTTATTCACTTACACCGGTATA
1 TGTTAAATACTATATTTTTTT-ATTTTATTCACTTACACCGATATA
803078 TATATATATA
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
47 12 0.10
48 38 0.31
49 23 0.19
50 16 0.13
51 32 0.26
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (51 bp):
TGTTAAATACTATATTTTTTTATTTTATTCACTTACACCGATATAAGTATA
Found at i:802992 original size:98 final size:100
Alignment explanation
Indices: 802878--803084 Score: 294
Period size: 98 Copynumber: 2.1 Consensus size: 100
802868 TTATATTGTG
* * * * *
802878 TAAATATGTGTTAAATACTATATTTTTTTATTTTA-TCACTTATACCGATATAAGTATATGTTAA
1 TAAATATATGTTAAATACTATATTTTTTTATTTTATTCACCTACACCAATATAAGTATACGTTAA
*
802942 -ATATTATTTTTT-ATTTTATTCACTTACACCGGTA
66 TACATT-TTTTTTAATTTTATTCACTTACACCGGTA
* * *
802976 TAAATATATGTTAAATACTATATTTTTTTATTTTATTCACCTACACTAATGTAAGTATGCGTTAA
1 TAAATATATGTTAAATACTATATTTTTTTATTTTATTCACCTACACCAATATAAGTATACGTTAA
803041 TACATTTTTTTTAATTTTATTCACTTACACCGGTA
66 TACATTTTTTTTAATTTTATTCACTTACACCGGTA
*
803076 TATATATAT
1 TAAATATAT
803085 ATATATATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 34 0.35
99 28 0.29
100 34 0.35
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (100 bp):
TAAATATATGTTAAATACTATATTTTTTTATTTTATTCACCTACACCAATATAAGTATACGTTAA
TACATTTTTTTTAATTTTATTCACTTACACCGGTA
Found at i:807384 original size:39 final size:39
Alignment explanation
Indices: 807330--807406 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
807320 GGTTTTCAGG
807330 TACGTCAATTGTTCTTCTCCTGTAAGTTTGCCATTTTTT
1 TACGTCAATTGTTCTTCTCCTGTAAGTTTGCCATTTTTT
*
807369 TACGTCAATTGTTCTTCTCCTGTGAGTTTGCCATTTTT
1 TACGTCAATTGTTCTTCTCCTGTAAGTTTGCCATTTTT
807407 CTCCTACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (39 bp):
TACGTCAATTGTTCTTCTCCTGTAAGTTTGCCATTTTTT
Found at i:809350 original size:17 final size:18
Alignment explanation
Indices: 809327--809363 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
809317 TAAATATATT
809327 GAGAGAAACTTAGAAATAA
1 GAGA-AAACTTAGAAATAA
*
809346 GAGAAAATTTAGAAATAA
1 GAGAAAACTTAGAAATAA
809364 AAATTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (18 bp):
GAGAAAACTTAGAAATAA
Found at i:809595 original size:15 final size:15
Alignment explanation
Indices: 809577--809607 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
809567 ATTATTATTA
809577 TTGTTTTATAAATTT
1 TTGTTTTATAAATTT
809592 TTGTTTTATAAATTT
1 TTGTTTTATAAATTT
809607 T
1 T
809608 AAAATTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTGTTTTATAAATTT
Found at i:809612 original size:23 final size:24
Alignment explanation
Indices: 809580--809628 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
809570 ATTATTATTG
* * *
809580 TTTTATAAATTTTTGTTTTATAAA
1 TTTTATAAATTTATGATTTAAAAA
809604 TTTTA-AAATTTATGATTTAAAAA
1 TTTTATAAATTTATGATTTAAAAA
809627 TT
1 TT
809629 AGTTTAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTATAAATTTATGATTTAAAAA
Found at i:811499 original size:29 final size:29
Alignment explanation
Indices: 811439--811507 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
811429 AATACTGTGA
* * *
811439 TTTATTTTATTTTATGTGAAGTATGATTT
1 TTTATTTTATTTTATGTAAAATATGATCT
811468 TTTATTTTATTTTATGTAAAATAATGA-CT
1 TTTATTTTATTTTATGTAAAAT-ATGATCT
*
811497 TTT-TGTTATTT
1 TTTATTTTATTT
811508 GCTGCCACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.20
29 24 0.69
30 4 0.11
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (29 bp):
TTTATTTTATTTTATGTAAAATATGATCT
Found at i:815512 original size:30 final size:30
Alignment explanation
Indices: 815438--815532 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 30
815428 ATTTTAGTCG
*
815438 AATTTAGAGATTAAATTAATATTTTATTTAA
1 AATTTA-AGATTAAAATAATATTTTATTTAA
* *
815469 AGTATAAGATTAAAATAATATTTTATTTAA
1 AATTTAAGATTAAAATAATATTTTATTTAA
* * *
815499 AATTTATAG-TTAAACTAGTATTTTATCTAA
1 AATTTA-AGATTAAAATAATATTTTATTTAA
815529 AATT
1 AATT
815533 AAAAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 49 0.89
31 6 0.11
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (30 bp):
AATTTAAGATTAAAATAATATTTTATTTAA
Found at i:815624 original size:23 final size:24
Alignment explanation
Indices: 815598--815643 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
815588 CTTGGTAATC
815598 AAAATGTATCAATC-ATAATATAT
1 AAAATGTATCAATCGATAATATAT
*
815621 AAAATGTATTAATCGATAATATA
1 AAAATGTATCAATCGATAATATA
815644 AATGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (24 bp):
AAAATGTATCAATCGATAATATAT
Found at i:816999 original size:17 final size:19
Alignment explanation
Indices: 816959--816998 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
816949 ATTTTTAATA
*
816959 AAAATATATTAATCTTTTT
1 AAAATATATTAATCATTTT
816978 AAAATATA-TAATCATTTT
1 AAAATATATTAATCATTTT
816996 AAA
1 AAA
816999 TTTTCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATATTAATCATTTT
Found at i:831339 original size:5 final size:5
Alignment explanation
Indices: 831329--831363 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
831319 CCCTGGGATT
831329 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
831364 AATTTATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:834247 original size:2 final size:2
Alignment explanation
Indices: 834240--834273 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
834230 GGGTACGAGG
834240 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
834274 CTGTTTCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:838968 original size:12 final size:12
Alignment explanation
Indices: 838951--838983 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
838941 ATGAAGAGAT
838951 TAGGGGAATGCA
1 TAGGGGAATGCA
838963 TAGGGGAATGCA
1 TAGGGGAATGCA
838975 TAGGGGAAT
1 TAGGGGAAT
838984 TAACCAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.42, T:0.18
Consensus pattern (12 bp):
TAGGGGAATGCA
Found at i:840781 original size:41 final size:41
Alignment explanation
Indices: 840735--840817 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
840725 ATTTAGTAAA
840735 TGTGTGATATGCTGTGAAGGGAATATTACGGGCAGTTTCAT
1 TGTGTGATATGCTGTGAAGGGAATATTACGGGCAGTTTCAT
*
840776 TGTGTGATATGCTGTGAAGGGAATATTATGGGCAGTTTCAT
1 TGTGTGATATGCTGTGAAGGGAATATTACGGGCAGTTTCAT
840817 T
1 T
840818 CTTGCTTCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.08, G:0.31, T:0.36
Consensus pattern (41 bp):
TGTGTGATATGCTGTGAAGGGAATATTACGGGCAGTTTCAT
Found at i:843838 original size:24 final size:23
Alignment explanation
Indices: 843811--843860 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
843801 TCAATTCACT
*
843811 CTAAATTTGATATATCAGCATGAA
1 CTAAA-TTGATATATCAGCACGAA
*
843835 CT-AATTGATATATCAGTACGAA
1 CTAAATTGATATATCAGCACGAA
843857 CTAA
1 CTAA
843861 GTGATCTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 18 0.78
23 3 0.13
24 2 0.09
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (23 bp):
CTAAATTGATATATCAGCACGAA
Found at i:843845 original size:22 final size:22
Alignment explanation
Indices: 843817--843865 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
843807 CACTCTAAAT
*
843817 TTGATATATCAGCATGAACTAA
1 TTGATATATCAGCACGAACTAA
*
843839 TTGATATATCAGTACGAACTAA
1 TTGATATATCAGCACGAACTAA
*
843861 GTGAT
1 TTGAT
843866 CTCGGTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
TTGATATATCAGCACGAACTAA
Found at i:846032 original size:14 final size:15
Alignment explanation
Indices: 846013--846041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
846003 TATGCTCAAA
846013 GAAATG-TATTATTT
1 GAAATGTTATTATTT
846027 GAAATGTTATTATTT
1 GAAATGTTATTATTT
846042 TTTAAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
GAAATGTTATTATTT
Found at i:855404 original size:67 final size:67
Alignment explanation
Indices: 855317--855450 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
855307 TTATACATAA
855317 AGAGCATCAAACCCAAAAAATGTGTATGCAAAGATGTCTATATAAGCATATCAAAAGATCAAAAA
1 AGAGCATCAAACCCAAAAAATGTGTATGCAAAGATGTCTATATAAGCATATCAAAAGATCAAAAA
855382 GC
66 GC
855384 AGAGCATCAAACCCAAAAAATGTGTATGCAAAGATGTCTATATAAGCATATCAAAAGATCAAAAA
1 AGAGCATCAAACCCAAAAAATGTGTATGCAAAGATGTCTATATAAGCATATCAAAAGATCAAAAA
855449 GC
66 GC
855451 TAAATTCGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (67 bp):
AGAGCATCAAACCCAAAAAATGTGTATGCAAAGATGTCTATATAAGCATATCAAAAGATCAAAAA
GC
Found at i:857802 original size:144 final size:140
Alignment explanation
Indices: 857644--857902 Score: 340
Period size: 144 Copynumber: 1.8 Consensus size: 140
857634 AAAAGAAAAT
* *
857644 TCAAAATAAATCAAACCCA-TCAAAACCAAATGTATCCTAACACTAAATCCAGTGTTTATAATCA
1 TCAAAATAAATCAAACCCACT-AAAACCAAAGGTATCCAAACACTAAATCCAGTGTTTATAATCA
** * **
857708 CTCATTAACATATATGAATGGAAAATTAAGCAAAATTAATTAAAGATCCAATGAAACAGGAGAAG
65 CTCAAAAACA-A-AT--ATGAAAAATTAAGCAAAATTAACAAAAGATCCAATGAAACAGGAGAAG
857773 AAAAAAAGGGAACAG
126 AAAAAAAGGGAACAG
* * * * * *
857788 TCAAAATAAATCAAACCCACTAAAATCGAAGGTATCCAAATACTAAATTCGGTGTTTATCATCAC
1 TCAAAATAAATCAAACCCACTAAAACCAAAGGTATCCAAACACTAAATCCAGTGTTTATAATCAC
*
857853 TCAAAAACAAATATGAAAAATTAAGCAAAATTAACAAAAGATTCAATGAA
66 TCAAAAACAAATATGAAAAATTAAGCAAAATTAACAAAAGATCCAATGAA
857903 CGGAAGGGCA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
140 34 0.34
142 2 0.02
143 1 0.01
144 62 0.62
145 1 0.01
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (140 bp):
TCAAAATAAATCAAACCCACTAAAACCAAAGGTATCCAAACACTAAATCCAGTGTTTATAATCAC
TCAAAAACAAATATGAAAAATTAAGCAAAATTAACAAAAGATCCAATGAAACAGGAGAAGAAAAA
AAGGGAACAG
Found at i:869852 original size:2 final size:2
Alignment explanation
Indices: 869847--869887 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
869837 ACACACACAC
869847 AT AT AT AT AT 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 AT AT AT AT AT A
869888 AATTTTAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:871941 original size:3 final size:3
Alignment explanation
Indices: 871935--871994 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
871925 ATTTATTATT
* * *
871935 TAA TAA TAA TAA TTA TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
871983 TAA TAA TAA TAA
1 TAA TAA TAA TAA
871995 ATAAAAATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:871947 original size:21 final size:22
Alignment explanation
Indices: 871923--871989 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 22
871913 ATTGGGCTTG
871923 TAATTTATTATT-TAATAATAA
1 TAATTTATTATTATAATAATAA
871944 TAA-TTATTATTATAATAATAA
1 TAATTTATTATTATAATAATAA
* * *
871965 TAA-TAATAATAATAATAATAA
1 TAATTTATTATTATAATAATAA
871986 TAAT
1 TAAT
871990 AATAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.20
21 33 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTATTATTATAATAATAA
Found at i:872378 original size:124 final size:120
Alignment explanation
Indices: 872156--872766 Score: 394
Period size: 113 Copynumber: 5.1 Consensus size: 120
872146 TGGGATTAGC
* * * * * * * *
872156 TCTTCTCATTATGAACTTTTCTGCTGG---GGATGATGTTGACCTATTTCCTTCTGTGATAGAGT
1 TCTTCTCATTATGAAC-TTTCT-CTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAAT
* * * * *
872218 CATTCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTTTCCCCTTCATATGAGT
64 CATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-TT---CTTCAGATGAGT
* *
872279 TTTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAATTA
1 TCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAATCA
*
872344 TGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
66 TGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
* * *** * * *
872399 TCTTCTCATTATGAACTTTCTCTGGAAA-----A-GCTGATCCA--TC-AGATG--ATGGATTTG
1 TCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGA-ATC
**
872453 A-GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
65 ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGT
* * * *** * * *
872512 TCTTCTCATTATGAACTTTTTCTGGAAA-----A-GCTGATCCA--TC-AGATG--ATGGATTTG
1 TCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGA-ATC
**
872566 A-GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCTTCAGATGAGT
65 ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA------CTTC-TTCTTCTTCAGATGAGT
* * * * * * * * *
872628 TCTTCTCATTATGAGCTGTCTCTGGAAATGTTGATACTGATCTATCTCCTTCCGTTATAGAGTCA
1 TCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAATCA
* **
872693 TGCAAAAGGCTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGT
66 TGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT--TCTTCAGATGAGT
*
872750 TCTTCTTATTATGAACT
1 TCTTCTCATTATGAACT
872767 CTTTCTAGCA
Statistics
Matches: 417, Mismatches: 45, Indels: 53
0.81 0.09 0.10
Matches are distributed among these distances:
109 34 0.08
110 2 0.00
111 2 0.00
112 8 0.02
113 102 0.24
114 7 0.02
115 1 0.00
116 46 0.11
117 2 0.00
120 42 0.10
121 9 0.02
122 40 0.10
123 17 0.04
124 66 0.16
125 1 0.00
126 2 0.00
127 36 0.09
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (120 bp):
TCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAATCA
TGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:872536 original size:113 final size:113
Alignment explanation
Indices: 872345--872884 Score: 614
Period size: 113 Copynumber: 4.7 Consensus size: 113
872335 ATAGAATTAT
** *
872345 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
872406 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
872454 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
872519 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
872567 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCTTCAGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC---CTTCTTCAGATGAGTTCTT
* * * * *** * * *
872632 CTCATTATGAGCTGTCTCTGGAAATGTTGATACTGATCTATCTCCTTCCGTTATAGA-GTCA
63 CTCATTATGAACTTTCTCTGGAAA-----A-GCTGATCCATC-AGAT--G--ATGGATTTGA
* *
872693 TGCAAAAGGCTGAACAAATTCTTCTCATTATGAACTTCTTC-TCC-TCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
872756 TATTATGAACTCTT-TCTAGCAATA-CTGATCCATC-GAATGATGAAATCGA
65 CATTATGAACT-TTCTCT-GGAAAAGCTGATCCATCAG-ATGATGGATTTGA
* * *
872805 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTCCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
872870 ATTATGAACTCTTCT
66 ATTATGAACT-TTCT
872885 TTCTTCTTCA
Statistics
Matches: 369, Mismatches: 36, Indels: 47
0.82 0.08 0.10
Matches are distributed among these distances:
109 30 0.08
111 39 0.11
112 9 0.02
113 145 0.39
114 1 0.00
115 1 0.00
116 49 0.13
118 1 0.00
121 1 0.00
122 40 0.11
123 6 0.02
125 1 0.00
126 4 0.01
127 42 0.11
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
Found at i:872860 original size:351 final size:346
Alignment explanation
Indices: 872222--872879 Score: 953
Period size: 351 Copynumber: 1.9 Consensus size: 346
872212 TAGAGTCATT
* * * * *
872222 CAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTTTTCTTTCCCCTTCATATGAGTTTTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCCCCTTCAGATGAGTTCTTCTCA
* * * * *
872287 TTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTCTTTCTGTAATAGAATTATGCAAAAG
66 TTATGAACTGTCTCTGGAAAGGTTGATACTAATCTATCTCCTTCCGTAATAGAATCATGCAAAAG
* * *
872352 GTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
131 GCTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * *
872417 TCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATT
196 TCTCTGCAAAAGCTGATCCATCAGATGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATT
*
872482 ATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGAT
261 ATGAATTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGAT
872547 CCATCAGATGATGGATTTGAG
326 CCATCAGATGATGGATTTGAG
**
872568 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCTTCAGATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA---CTTCTTCTTTCCCCTTCAGATGAGTTCTTC
* * * * *
872633 TCATTATGAGCTGTCTCTGGAAATGTTGATACTGATCTATCTCCTTCCGTTATAGAGTCATGCAA
63 TCATTATGAACTGTCTCTGGAAAGGTTGATACTAATCTATCTCCTTCCGTAATAGAATCATGCAA
* *
872698 AAGGCTGAACAAATTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGTTCTTCTTATTATG
128 AAGGCTGAACAAACTCTTCTCATTATGAACTTCTTCT--TCTTCAGATGAGTTCTTCTCATTATG
*
872763 AACTCTT-TCTAGCAATA-CTGATCCATC-GAATGATGAAATCGAGCAAAAAGTTGAACAAATTC
191 AACT-TTCTCT-GCAAAAGCTGATCCATCAG-ATGATGAAATCGAGCAAAAAGTTGAACAAATTC
*
872825 TTCTCATTATGAATTCCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT
253 TTCTCATTATGAATTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
872880 CTTCTTTCTT
Statistics
Matches: 274, Mismatches: 30, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
346 30 0.11
349 113 0.41
350 1 0.00
351 124 0.45
352 6 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (346 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCCCCTTCAGATGAGTTCTTCTCA
TTATGAACTGTCTCTGGAAAGGTTGATACTAATCTATCTCCTTCCGTAATAGAATCATGCAAAAG
GCTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
TCTCTGCAAAAGCTGATCCATCAGATGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATT
ATGAATTCCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGAT
CCATCAGATGATGGATTTGAG
Found at i:872895 original size:39 final size:39
Alignment explanation
Indices: 872822--872961 Score: 255
Period size: 39 Copynumber: 3.6 Consensus size: 39
872812 GTTGAACAAA
*
872822 TTCTTCTCATTATGAATTCCTTCTTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACT-CTTCTTTCTTCTTCAGATGAG
872862 TTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
872901 TTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
872940 TTCTTCTCATTATGAACT-TTCT
1 TTCTTCTCATTATGAACTCTTCT
872962 CTGGAAAAGC
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
38 4 0.04
39 78 0.79
40 17 0.17
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
Found at i:872899 original size:23 final size:23
Alignment explanation
Indices: 872873--872938 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 23
872863 TCTTCTCATT
872873 ATGAACTCTTCTTTCTTCTTCAG
1 ATGAACTCTTCTTTCTTCTTCAG
*
872896 ATG-A--GTTC-TTC-TCATT---
1 ATGAACTCTTCTTTCTTC-TTCAG
872912 ATGAACTCTTCTTTCTTCTTCAG
1 ATGAACTCTTCTTTCTTCTTCAG
872935 ATGA
1 ATGA
872939 GTTCTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 18
0.62 0.04 0.35
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 2 0.06
19 8 0.25
20 8 0.25
21 2 0.06
22 1 0.03
23 7 0.22
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.47
Consensus pattern (23 bp):
ATGAACTCTTCTTTCTTCTTCAG
Found at i:872955 original size:191 final size:189
Alignment explanation
Indices: 872711--873074 Score: 540
Period size: 191 Copynumber: 1.9 Consensus size: 189
872701 GCTGAACAAA
*
872711 TTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGTTCTTCTTATTATGAACTCTT-TCTAG
1 TTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT-G
*
872775 CAATA-CTGATCCATCGAA-TGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA
64 CAAAAGCTGATCCATC-AAGTGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA
*
872838 -TTCCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAG
128 CTT-CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTTTCTTCTTCAGATGAG
*
872901 TTCTTCTCATTATGAAC-TCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTC--TCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
872965 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
64 CAAAAGCTGATCCATCAAGTGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
873030 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
129 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
873075 CTGGAAAAGT
Statistics
Matches: 158, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
189 5 0.03
190 29 0.18
191 122 0.77
192 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (189 bp):
TTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGCA
AAAGCTGATCCATCAAGTGATGAAATCGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTCTTCTTCAGATGAG
Found at i:873057 original size:113 final size:113
Alignment explanation
Indices: 872899--873332 Score: 630
Period size: 113 Copynumber: 3.9 Consensus size: 113
872889 TCTTCAGATG
*
872899 AGTTCTTCTCATTATGAAC-TCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-
* * *
872962 CTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACA
65 CTGGAAAAGTTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
873011 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-
* *
873075 CTGGAAAAGTTGATCCAT--TGTTATGGATTTGAACAAAAAGTTGAACA
65 CTGGAAAAGTTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
* * *
873122 AGTTATTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
* * * * **
873187 TGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
66 TGGAAAAGTTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
*
873235 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
* *
873300 -GGAAATGTTGATCCATTGAA-TGATGGATTTGAA
66 TGGAAAAGTTGATCCA-TCAAGTGATGGATTTGAA
873333 TCTTTGCTAA
Statistics
Matches: 292, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
111 99 0.34
112 45 0.15
113 148 0.51
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC
TGGAAAAGTTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
Found at i:873162 original size:224 final size:223
Alignment explanation
Indices: 872899--873332 Score: 660
Period size: 224 Copynumber: 1.9 Consensus size: 223
872889 TCTTCAGATG
* *
872899 AGTTCTTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTC
1 AGTTATTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-C
* * ** * *
872963 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
65 TGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
873028 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATCCA
130 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTC-C-GGAAAAGTTGATCCA
*
873092 TTG-TTATGGATTTGAACAAAAAGTTGAACA
193 TTGATGATGGATTTGAACAAAAAGTTGAACA
873122 AGTTATTCTCATTATGAACTTCTTC-TTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 AGTTATTCTCATTATGAAC-TCTTCTTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * *
873186 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
64 CTGGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
* *
873251 AACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGAAATGTTGATCCAT
129 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGAAAAGTTGATCCAT
873316 TGAATGATGGATTTGAA
194 TG-ATGATGGATTTGAA
873333 TCTTTGCTAA
Statistics
Matches: 191, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
223 38 0.20
224 136 0.71
225 17 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (223 bp):
AGTTATTCTCATTATGAACTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
GGAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGAAAAGTTGATCCATTG
ATGATGGATTTGAACAAAAAGTTGAACA
Found at i:873757 original size:22 final size:22
Alignment explanation
Indices: 873732--873808 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
873722 GATAAAGCTT
*
873732 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
873754 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
873776 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
873798 TCATCTTTGAA
1 TCATCTTTGAA
873809 GAGTGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:874260 original size:40 final size:40
Alignment explanation
Indices: 874195--874270 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
874185 TTTCAGCTTA
*
874195 GATGTAAAACACTTGACAACACATTCATCCTTTTCTATGG
1 GATGTAAAACACTTAACAACACATTCATCCTTTTCTATGG
* * *
874235 GATGTAAAACATTTAACACCGCATTCATCCTTTTCT
1 GATGTAAAACACTTAACAACACATTCATCCTTTTCT
874271 GTGGACTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (40 bp):
GATGTAAAACACTTAACAACACATTCATCCTTTTCTATGG
Found at i:876553 original size:114 final size:114
Alignment explanation
Indices: 876353--876665 Score: 520
Period size: 114 Copynumber: 2.7 Consensus size: 114
876343 GATCATGCAG
* * * * * *
876353 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
876418 ACACTTCCAGAAGATGCTATTGGGTC-TCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTACTATGAGCAAA
*
876467 TTCATCTCTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
876532 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* * *
876581 TTTATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
876646 ACACTTCCAGAAGATGCTAT
66 ACACTTCCAGAAGATGCTAT
876666 GAGCACATGA
Statistics
Matches: 187, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 185 0.99
115 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:882223 original size:14 final size:14
Alignment explanation
Indices: 882189--882242 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
882179 TTGTGCAATA
* *
882189 CAAATGCAAAGATG
1 CAAATGTAAATATG
882203 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
882218 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
882232 TAAATGTAAAT
1 CAAATGTAAAT
882243 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:884624 original size:22 final size:21
Alignment explanation
Indices: 884599--884648 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
884589 GATACACAAT
* *
884599 AATAATATTTAAATATATAAAA
1 AATAATATTAAAACA-ATAAAA
*
884621 AATAAAATTAAAACAATAAAA
1 AATAATATTAAAACAATAAAA
884642 ATATAAT
1 A-ATAAT
884649 TAGAACTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAATATTAAAACAATAAAA
Found at i:885954 original size:3 final size:3
Alignment explanation
Indices: 885948--886001 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
885938 ATTTATTATT
* * * *
885948 TAA TAA TAA TAA TTA TTA TTA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
885996 TAA TAA
1 TAA TAA
886002 ATAAAAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:885971 original size:18 final size:18
Alignment explanation
Indices: 885940--885996 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
885930 GGCTTGTAAT
885940 TTATTATTTAATAATAATAA
1 TTATTA-TT-ATAATAATAA
885960 TTATTATTATAATAATAA
1 TTATTATTATAATAATAA
* *
885978 TTATAATAATAATAATAA
1 TTATTATTATAATAATAA
885996 T
1 T
885997 AATAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 27 0.77
19 2 0.06
20 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTATTATAATAATAA
Found at i:887388 original size:19 final size:19
Alignment explanation
Indices: 887349--887387 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
887339 TATAAAAAGT
887349 AATCAAATAAATATTTTAA
1 AATCAAATAAATATTTTAA
*
887368 AATCTAATAAA-ATTTTAA
1 AATCAAATAAATATTTTAA
887386 AA
1 AA
887388 AATCCTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AATCAAATAAATATTTTAA
Found at i:887429 original size:52 final size:51
Alignment explanation
Indices: 887357--887456 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 51
887347 GTAATCAAAT
* *
887357 AAATATTTTAAAATCTAAT-AAAATTTTAAAAAATCCTAACCAAAATATATA
1 AAATATTATAAAATCCAATAAAAATTTT-AAAAATCCTAACCAAAATATATA
*
887408 AAATAATTATAAAATCCAATAAAAATTTTAAAAATCTTAACCAAAATAT
1 AAAT-ATTATAAAATCCAATAAAAATTTTAAAAATCCTAACCAAAATAT
887457 TCCAAGACAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 4 0.09
52 32 0.73
53 8 0.18
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (51 bp):
AAATATTATAAAATCCAATAAAAATTTTAAAAATCCTAACCAAAATATATA
Found at i:892211 original size:21 final size:21
Alignment explanation
Indices: 892186--892339 Score: 143
Period size: 21 Copynumber: 7.5 Consensus size: 21
892176 TCGCAAATTT
892186 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** ** *
892207 GCGTTGCGAT-TTTCCATTTT
1 GCGTTGCGATAGTTGAAAATC
892227 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** **
892248 GCGTTGCGAT-TTTCCATTTC
1 GCGTTGCGATAGTTGAAAATC
892268 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
* ** **
892289 GCGTTGCGAT-TTTCCATTTC
1 GCGTTGCGATAGTTGAAAATC
892309 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAGTTGAAAATC
892330 GCGTTGCGAT
1 GCGTTGCGAT
892340 TTTCCATTTC
Statistics
Matches: 98, Mismatches: 32, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 44 0.45
21 54 0.55
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (21 bp):
GCGTTGCGATAGTTGAAAATC
Found at i:892232 original size:20 final size:20
Alignment explanation
Indices: 892205--892420 Score: 171
Period size: 20 Copynumber: 10.6 Consensus size: 20
892195 TAGTTGAAAA
892205 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
892225 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
892246 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
892266 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
892287 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
892307 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
892328 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
892348 TCGTGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
892368 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
892389 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
892409 TCACGTTGCGAT
1 TCGCGTTGCGAT
892421 AGTCTACAAT
Statistics
Matches: 145, Mismatches: 47, Indels: 8
0.73 0.23 0.04
Matches are distributed among these distances:
20 87 0.60
21 58 0.40
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:892240 original size:41 final size:41
Alignment explanation
Indices: 892182--892356 Score: 325
Period size: 41 Copynumber: 4.3 Consensus size: 41
892172 ACTATCGCAA
892182 ATTT-GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
*
892222 ATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
892263 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
892304 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
*
892345 ATTTCGTGTTGC
1 ATTTCGCGTTGC
892357 AATTTTCCAT
Statistics
Matches: 132, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
40 4 0.03
41 128 0.97
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
Found at i:892362 original size:61 final size:61
Alignment explanation
Indices: 892182--892420 Score: 266
Period size: 61 Copynumber: 3.9 Consensus size: 61
892172 ACTATCGCAA
* * **
892182 ATTT-GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTTGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCC
** * ** ** * ** **
892243 AAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTCC
* *
892304 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGTGTTGCAATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCC
* *
892365 ATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCACGTTGCGAT
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
892421 AGTCTACAAT
Statistics
Matches: 141, Mismatches: 34, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
61 102 0.72
62 39 0.28
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (61 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCC
Found at i:892363 original size:102 final size:102
Alignment explanation
Indices: 892250--892447 Score: 328
Period size: 102 Copynumber: 1.9 Consensus size: 102
892240 TGAAAATCGC
* * *
892250 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
1 GTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCACGTTG
892315 CGATAGT-TGAAAATCG-CGTTGCGATTTTCCATTTCGT
66 CGATAGTCT-AAAAT-GTCGTTGCGATTTTCCATTTCGT
892352 GTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCACGTTG
1 GTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCACGTTG
*
892417 CGATAGTCTACAATGTCGTTGCGATTTTCCA
66 CGATAGTCTAAAATGTCGTTGCGATTTTCCA
892448 AATTCGTTGC
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
101 1 0.01
102 88 0.98
103 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (102 bp):
GTTGCAATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCACGTTG
CGATAGTCTAAAATGTCGTTGCGATTTTCCATTTCGT
Found at i:892396 original size:82 final size:82
Alignment explanation
Indices: 892182--892400 Score: 226
Period size: 82 Copynumber: 2.7 Consensus size: 82
892172 ACTATCGCAA
* * * * ** **
892182 ATTT-GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTTGCGTTGCGATAGTTGAAAA
1 ATTTCGCGTTGCAATAGTTCAAAATCGCGTTGCGATGTTCAAAATCACGTTGCGATAGTTGAAAA
892246 TCGCGTTGCGATTTTCC
66 TCGCGTTGCGATTTTCC
* * * * ** *
892263 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 ATTTCGCGTTGCAATAGTTCAAAATCGCGTTGCGATGTTCAAAATCACGTTGCGATAGTTGAAAA
892328 TCGCGTTGCGATTTTCC
66 TCGCGTTGCGATTTTCC
* * * ** *
892345 ATTTCGTGTTGCAAT-TTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGAT
1 ATTTCGCGTTGCAATAGTTCAAAATCGCGTTGCGAT-GTTCAAAATCACGTTGCGAT
892401 TTTCCATTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
81 19 0.16
82 103 0.84
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (82 bp):
ATTTCGCGTTGCAATAGTTCAAAATCGCGTTGCGATGTTCAAAATCACGTTGCGATAGTTGAAAA
TCGCGTTGCGATTTTCC
Found at i:892405 original size:41 final size:40
Alignment explanation
Indices: 892352--892466 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 40
892342 TCCATTTCGT
*
892352 GTTGCAATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCAC
1 GTTGCGATTTTCCATTTC-CGTTGCGATAGTCT-AAAATCAC
* **
892393 GTTGCGATTTTCCATTTCACGTTGCGATAGTCTACAATGTC
1 GTTGCGATTTTCCATTTC-CGTTGCGATAGTCTAAAATCAC
*
892434 GTTGCGATTTTCCAAATT-CGTTGCGATAGTCTA
1 GTTGCGATTTTCC-ATTTCCGTTGCGATAGTCTA
892467 CAGTTGTTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
40 15 0.23
41 47 0.71
42 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTTCCATTTCCGTTGCGATAGTCTAAAATCAC
Found at i:892475 original size:19 final size:20
Alignment explanation
Indices: 892413--892495 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
892403 TCCATTTCAC
*
892413 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
892434 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
892453 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
892475 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
892494 GT
1 GT
892496 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:892480 original size:22 final size:22
Alignment explanation
Indices: 892412--892504 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
892402 TTCCATTTCA
*
892412 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
892433 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
892452 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
892474 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
892496 CGTTGCGAT
1 CGTTGCGAT
892505 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:893134 original size:12 final size:12
Alignment explanation
Indices: 893117--893155 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
893107 TCTCGTCTCG
893117 GGTCGGGGTCGT
1 GGTCGGGGTCGT
893129 GGTCGGGGTCGT
1 GGTCGGGGTCGT
*
893141 GGTCGTGGTCGT
1 GGTCGGGGTCGT
893153 GGT
1 GGT
893156 TAACTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.28
Consensus pattern (12 bp):
GGTCGGGGTCGT
Found at i:893152 original size:6 final size:6
Alignment explanation
Indices: 893117--893155 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
893107 TCTCGTCTCG
* *
893117 GGTCGG GGTCGT GGTCGG GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
893156 TAACTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:896755 original size:2 final size:2
Alignment explanation
Indices: 896710--896740 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
896700 TCAGTCTTTC
896710 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
896741 AGATAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:906044 original size:55 final size:56
Alignment explanation
Indices: 905985--906184 Score: 135
Period size: 55 Copynumber: 3.6 Consensus size: 56
905975 ATGACGAGCC
* *
905985 TGCTCCCTATACCTTTAG-GAAGTATAAGACTCAAACAATCTTC-ATAAAATGTTTA
1 TGCTCCCTATACATTCAGAG-AGTATAAGACTCAAACAATCTTCAATAAAATGTTTA
* * ** * * *
906040 TGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACAG-GTC
1 TGCTCCCTATACATTCAGAGAGTATAAGACTCAAACAATCTTCAATAAAA-TGTTTA
* * * * * *
906096 CGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAA-AATCTTCAATAAACA-G-GTC
1 TGCTCCCTATACATTCAGAGAGTATAAG-ACTC-AAACAATCTTCAATAAA-ATGTTTA
* * * *
906151 CGCTCCCTATTCTTTCAGAGAGTATAGGACTCAA
1 TGCTCCCTATACATTCAGAGAGTATAAGACTCAA
906185 TCTTTAACAA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
54 2 0.02
55 68 0.56
56 48 0.39
57 4 0.03
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (56 bp):
TGCTCCCTATACATTCAGAGAGTATAAGACTCAAACAATCTTCAATAAAATGTTTA
Done.