Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007780.1 Hibiscus syriacus cultivar Beakdansim tig00110063_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: 764298
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:550198 original size:3 final size:3
Alignment explanation
Indices: 550184--550217 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
550174 TTACAATTTC
*
550184 TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
550218 AAACACTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:550383 original size:27 final size:28
Alignment explanation
Indices: 550329--550397 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 28
550319 TTTTGAAAAC
*
550329 GTTTTGAAAATATATATATATAATATATA
1 GTTTTGAAAACATATATATAT-ATATATA
* *
550358 GTTTTGAAAACATGTATATAT-TATATG
1 GTTTTGAAAACATATATATATATATATA
*
550385 GTTTTTAAAACAT
1 GTTTTGAAAACAT
550398 TTTTGAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 17 0.47
29 19 0.53
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (28 bp):
GTTTTGAAAACATATATATATATATATA
Found at i:550413 original size:68 final size:71
Alignment explanation
Indices: 550304--550438 Score: 197
Period size: 68 Copynumber: 1.9 Consensus size: 71
550294 TAAATATATA
*
550304 TATATAATATATAGTTTTTGAAAACGTTTTGAAAATATATATATATA-AT-ATATAG-TTTTGAA
1 TATATAATATATAGTTTTTGAAAACGTTTTGAAAACATATATATATATATAATATAGCTTTTGAA
550366 AACATG
66 AACATG
* * *
550372 TATATATTATATGGTTTTT-AAAACATTTTTGAAAACATATATATATATATAATATAGCTTTTGA
1 TATATAATATATAGTTTTTGAAAAC-GTTTTGAAAACATATATATATATATAATATAGCTTTTGA
550436 AAA
65 AAA
550439 TATTTTTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 5 0.08
68 37 0.63
69 2 0.03
70 6 0.10
71 9 0.15
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (71 bp):
TATATAATATATAGTTTTTGAAAACGTTTTGAAAACATATATATATATATAATATAGCTTTTGAA
AACATG
Found at i:550446 original size:44 final size:43
Alignment explanation
Indices: 550372--550462 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 43
550362 TGAAAACATG
* * *
550372 TATATATTATATGGTTTTTAAAACATTTTTGAAAACATATATA
1 TATATATAATATGCTTTTGAAAACATTTTTGAAAACATATATA
* *
550415 TATATATAATATAGCTTTTGAAAATATTTTTGAAAATATATATA
1 TATATATAATAT-GCTTTTGAAAACATTTTTGAAAACATATATA
550459 TATA
1 TATA
550463 CCCATGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 11 0.26
44 31 0.74
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (43 bp):
TATATATAATATGCTTTTGAAAACATTTTTGAAAACATATATA
Found at i:550826 original size:14 final size:14
Alignment explanation
Indices: 550791--550829 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
550781 TTCTTTATTT
550791 TTTTTA-TTTTTTA
1 TTTTTATTTTTTTA
*
550804 TTTCATATTTTTTTA
1 TTT-TTATTTTTTTA
550819 TTTTTATTTTT
1 TTTTTATTTTT
550830 GCATTCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 10 0.45
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:551634 original size:16 final size:16
Alignment explanation
Indices: 551613--551647 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
551603 TTTGTATACC
551613 AATTAAAATATATTTA
1 AATTAAAATATATTTA
* *
551629 AATTAAATTATGTTTA
1 AATTAAAATATATTTA
551645 AAT
1 AAT
551648 AGTTTTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTAAAATATATTTA
Found at i:554507 original size:18 final size:18
Alignment explanation
Indices: 554475--554516 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
554465 AACATAGAAT
*
554475 ATAAATAAACCAACA-AA
1 ATAAATAAACAAACATAA
*
554492 GATAAATAAAGAAACATAA
1 -ATAAATAAACAAACATAA
554511 ATAAAT
1 ATAAAT
554517 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.17
Consensus pattern (18 bp):
ATAAATAAACAAACATAA
Found at i:555936 original size:2 final size:2
Alignment explanation
Indices: 555929--555973 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
555919 ACGGTCAATT
555929 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
555971 TA T
1 TA T
555974 TTACAACCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:556535 original size:22 final size:21
Alignment explanation
Indices: 556492--556544 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
556482 TATCATTATC
* **
556492 GAATTTGAAGGATTGAGTATTT
1 GAATTT-AGGGATTGAAAATTT
556514 GGAATTTAGGGATTGAAAATTT
1 -GAATTTAGGGATTGAAAATTT
*
556536 AAATTTAGG
1 GAATTTAGG
556545 TATTTGAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
22 12 0.46
23 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
GAATTTAGGGATTGAAAATTT
Found at i:556691 original size:2 final size:2
Alignment explanation
Indices: 556684--556714 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
556674 GATTGAAGTT
556684 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 T
556715 TAAAAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558694 original size:21 final size:21
Alignment explanation
Indices: 558651--558694 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
558641 CAATTATAAA
* *
558651 AAATACATTATTATTTAAGTT
1 AAATACATTATTATTAAAATT
558672 AAATA-ATTAATTATTAAAATT
1 AAATACATT-ATTATTAAAATT
558693 AA
1 AA
558695 TATATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATACATTATTATTAAAATT
Found at i:571299 original size:14 final size:15
Alignment explanation
Indices: 571280--571317 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
571270 AAGTCAACGG
*
571280 GTTGACTCGGA-TGA
1 GTTGACTCGGACCGA
*
571294 GTTGACTCAGACCGA
1 GTTGACTCGGACCGA
571309 GTTGACTCG
1 GTTGACTCG
571318 AAAGGGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (15 bp):
GTTGACTCGGACCGA
Found at i:575853 original size:34 final size:36
Alignment explanation
Indices: 575814--575903 Score: 148
Period size: 34 Copynumber: 2.5 Consensus size: 36
575804 GTCCTACTAT
*
575814 ATTCAAACTCCTAAAAATAGGATAGAA-TTT-TAGG
1 ATTCAAACTCCTAAAAATAGGATAAAATTTTCTAGG
575848 ATTCAAACTCCTAAAAATAGGATAAAATTTTGCTAGG
1 ATTCAAACTCCTAAAAATAGGATAAAATTTT-CTAGG
575885 ATTCAAACTCCTAAAAATA
1 ATTCAAACTCCTAAAAATA
575904 TGATGATAGA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 26 0.50
35 3 0.06
37 23 0.44
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (36 bp):
ATTCAAACTCCTAAAAATAGGATAAAATTTTCTAGG
Found at i:576342 original size:18 final size:17
Alignment explanation
Indices: 576303--576345 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
576293 ATTATATGGA
576303 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
576319 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
576337 TATTATTAT
1 TATTATTAT
576346 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:576832 original size:2 final size:2
Alignment explanation
Indices: 576827--576893 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
576817 TTATATAGCT
*
576827 TA TA TA TT 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
576869 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
576894 CCTTTTTACA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:578082 original size:5 final size:5
Alignment explanation
Indices: 578072--578109 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
578062 TCTTTTCATC
578072 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
578110 CATCACTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:580610 original size:17 final size:16
Alignment explanation
Indices: 580582--580684 Score: 77
Period size: 17 Copynumber: 6.4 Consensus size: 16
580572 AGATCCAATC
580582 AAGAAGAAAAAAGAAAA
1 AAGAA-AAAAAAGAAAA
*
580599 GAAG-AAAAAAA-AACA
1 -AAGAAAAAAAAGAAAA
580614 AAGAAAAACAAAGAAAA
1 AAGAAAAA-AAAGAAAA
* * *
580631 AAGAGAAACACGAACAA
1 AAGAAAAAAAAGAA-AA
*
580648 AAGGAAAAAAAGAAAA
1 AAGAAAAAAAAGAAAA
* * *
580664 AA-AACAAGAATAAAA
1 AAGAAAAAAAAGAAAA
580679 AAGAAA
1 AAGAAA
580685 GAGGAACAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 3 0.05
15 18 0.27
16 19 0.29
17 23 0.35
18 3 0.05
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.01
Consensus pattern (16 bp):
AAGAAAAAAAAGAAAA
Found at i:580668 original size:46 final size:47
Alignment explanation
Indices: 580605--580695 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 47
580595 AAAAGAAGAA
*
580605 AAAAAAACAAAGAAAAACAAAGAA-AAAAGAGAAACACGAACAAAAGG
1 AAAAAAACAAAGAAAAAC-AAGAATAAAAAAGAAACACGAACAAAAGG
* * *
580652 AAAAAAAGAAA-AAAAACAAGAATAAAAAAGAAAGAGGAACAAAA
1 AAAAAAACAAAGAAAAACAAGAATAAAAAAGAAACACGAACAAAA
580696 AGCACATGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 5 0.13
46 24 0.62
47 10 0.26
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (47 bp):
AAAAAAACAAAGAAAAACAAGAATAAAAAAGAAACACGAACAAAAGG
Found at i:581345 original size:22 final size:22
Alignment explanation
Indices: 581317--581371 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
581307 GCTATCCCAT
581317 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
581339 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
581361 CAAACCTTTGA
1 CAAACCTTTGA
581372 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:581809 original size:18 final size:18
Alignment explanation
Indices: 581786--581821 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
581776 TCAACATCAA
* *
581786 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
581804 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
581822 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:582333 original size:71 final size:73
Alignment explanation
Indices: 582258--582581 Score: 248
Period size: 72 Copynumber: 4.6 Consensus size: 73
582248 TGTTTTTCTT
* * * * * *
582258 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
582320 TTTCCCTTG
65 TTTCCCTTG
* *
582329 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
582393 TTCCCTTG
66 TTCCCTTG
* * * * *
582401 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
582457 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
582466 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
582530 TTTCTCTTG
65 TTTCCCTTG
* * *
582539 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
582582 ATCTTTGAAT
Statistics
Matches: 205, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.22
66 5 0.02
70 8 0.04
71 25 0.12
72 78 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:582343 original size:36 final size:36
Alignment explanation
Indices: 582300--582581 Score: 321
Period size: 36 Copynumber: 8.0 Consensus size: 36
582290 ACTAGAAGAG
582300 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
582336 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
582372 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
582408 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
582444 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
582473 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
582510 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
582545 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
582582 ATCTTTGAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 142 0.69
37 35 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:582541 original size:102 final size:102
Alignment explanation
Indices: 582356--582544 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
582346 CTTGAGACAG
*
582356 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
582421 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
582458 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
582522 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
582545 TTTTCGTCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 34 0.43
102 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:582573 original size:138 final size:137
Alignment explanation
Indices: 582320--582644 Score: 454
Period size: 138 Copynumber: 2.4 Consensus size: 137
582310 CTTGAGACAG
*
582320 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
582385 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
582450 GAATATG
131 GAATATA
* * * * * * * *
582457 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
582522 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
582586 TTGAATTTA
129 TTGAATATA
* * * *
582595 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
582645 CAAAATCTTC
Statistics
Matches: 162, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
137 50 0.31
138 112 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:582643 original size:65 final size:66
Alignment explanation
Indices: 582539--582694 Score: 190
Period size: 66 Copynumber: 2.4 Consensus size: 66
582529 GTTTCTCTTG
** * * **
582539 AAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
582602 TA
65 TA
* *
582604 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAAC-AATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
582669 TA
65 TA
* *
582671 AAATAATTTTGTTTCCCTTGAGAC
1 AAACAATTTTGTCTCCCTTGAGAC
582695 CGTTTCTCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 24 0.31
66 27 0.35
67 27 0.35
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (66 bp):
AAACAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCCT
A
Found at i:582673 original size:67 final size:64
Alignment explanation
Indices: 582530--582694 Score: 186
Period size: 65 Copynumber: 2.5 Consensus size: 64
582520 CTTGAGACAG
* * ** * * **
582530 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTA
1 TTTCCCTTAAAACAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
* *
582595 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAAC-AATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
582660 TA
63 TA
* *
582662 TTTCCCTTAAAATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACAATTTTGTCTCCCTTGAGAC
582695 CGTTTCTCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 30 0.36
66 27 0.32
67 27 0.32
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (64 bp):
TTTCCCTTAAAACAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:583542 original size:105 final size:105
Alignment explanation
Indices: 583315--584080 Score: 1094
Period size: 105 Copynumber: 7.3 Consensus size: 105
583305 GCCATCTGCG
* * * * * *
583315 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
583380 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
583424 ATTTCAACTTCACAACGAAGAATATTGGACTCCAAACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
583489 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
583529 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
583594 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
583634 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
583699 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
583739 ATTTCAACTTCACAACGAAGGATATCGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
583804 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
583844 ATTTCAATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
583909 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * *
583944 ATTTCAACTTCATAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
584009 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
584050 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
584081 TGGAACAATG
Statistics
Matches: 600, Mismatches: 50, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.13
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 404 0.67
106 77 0.13
107 5 0.01
109 21 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:584672 original size:34 final size:36
Alignment explanation
Indices: 584628--584729 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
584618 TTTCGTCCTA
584628 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
* *
584663 -TAGGATTCAATCTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
584698 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
584730 GTTATACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 28 0.47
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:585156 original size:17 final size:17
Alignment explanation
Indices: 585121--585158 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
585111 TATGGATATT
*
585121 TTATTCATTTATTTTTA
1 TTATTCATTTATTTATA
585138 TTATTCATGTTA-TTATA
1 TTATTCAT-TTATTTATA
585155 TTAT
1 TTAT
585159 ATGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTCATTTATTTATA
Found at i:592953 original size:21 final size:23
Alignment explanation
Indices: 592917--592989 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
592907 CACCAAAGTG
*
592917 CCACGTAGAATT-TCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
* *
592939 CCATATAG-A-TGTCCCAAAGGA
1 CCACATAGAATTGTCCCGAAGGA
592960 CCACATAGAATTGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
592983 CCACATA
1 CCACATA
592990 AACCTTCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 17 0.40
22 7 0.16
23 18 0.42
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (23 bp):
CCACATAGAATTGTCCCGAAGGA
Found at i:592974 original size:23 final size:23
Alignment explanation
Indices: 592909--592989 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 23
592899 TAGAAATGCA
*
592909 CCAAAGTG-CCACGTAGAATT-TC
1 CCAAAG-GACCACATAGAATTGTC
* *
592931 CCGAAGGACCATATAG-A-TGTC
1 CCAAAGGACCACATAGAATTGTC
592952 CCAAAGGACCACATAGAATTGTC
1 CCAAAGGACCACATAGAATTGTC
*
592975 CCGAAGGACCACATA
1 CCAAAGGACCACATA
592990 AACCTTCTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 1 0.02
21 18 0.37
22 12 0.24
23 18 0.37
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (23 bp):
CCAAAGGACCACATAGAATTGTC
Found at i:593414 original size:139 final size:139
Alignment explanation
Indices: 593164--593588 Score: 519
Period size: 139 Copynumber: 3.1 Consensus size: 139
593154 TATTGTATCT
** * * * *
593164 AAATTATCCCTAAAGACGACTAGATATCCTCATCACGTAGGAATAATGTCGTCCACCAACAAGAT
1 AAATTATCCCTAAAGACGACTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
* * * * * * *
593229 CTCCTCATCACGTAAGAGCAGCGCCATCATCAGATAACCAAACTTCCTCATCACGTAAGAACCGT
66 CTCCTCATCGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAAGAACCGT
*
593294 GTTATCTCC
131 GTTGTCTCC
* * * * *
593303 AAATTTTCCCTAAAGACGGCTAGACGTCATCGTCACGTTGGAACAATGTCATCCACCGACCAGAT
1 AAATTATCCCTAAAGACGACTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
* * *
593368 CTCCTCATCGCGTAGGAGCAACGTCATCCTCAGACAATCAGACTTCCTCATCACGTAAAAACCAT
66 CTCCTCATCGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAAGAACCGT
*
593433 ATTGTCTCC
131 GTTGTCTCC
*
593442 AAATTATCCCTAAAGACGACCAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
1 AAATTATCCCTAAAGACGACTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
* ** * * * * * * *
593507 ATCCTCAAT-GCAAAGGAGCAGCGTCACCCTCAGTCAATAAGACTTCCTCATTATGTAGGAATCG
66 CTCCTC-ATCGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAAGAACCG
*
593571 TGTTGTCACC
130 TGTTGTCTCC
593581 AAATTATC
1 AAATTATC
593589 TCCAAATTGA
Statistics
Matches: 241, Mismatches: 44, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
139 239 0.99
140 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (139 bp):
AAATTATCCCTAAAGACGACTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
CTCCTCATCGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTAAGAACCGT
GTTGTCTCC
Found at i:594571 original size:40 final size:40
Alignment explanation
Indices: 594523--594672 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
594513 ACTGTAGTGC
*
594523 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGCAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGCAT
* *
594563 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGCAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGCAT
* *
594603 TACATATAAGGTCATTCCCACCATATACACCGAAGTGCAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGCAT
* *
594643 TACACATAAAGACATGCCCACCATATACAC
1 TACACATAAGGTCATGCCCACCATATACAC
594673 TTAATGTTTT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGCAT
Found at i:595584 original size:15 final size:15
Alignment explanation
Indices: 595564--595594 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
595554 TAAAAAGTAT
*
595564 TTTAATATCTATATA
1 TTTAATATATATATA
595579 TTTAATATATATATA
1 TTTAATATATATATA
595594 T
1 T
595595 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATATATATATA
Found at i:596059 original size:15 final size:13
Alignment explanation
Indices: 596023--596121 Score: 57
Period size: 14 Copynumber: 7.5 Consensus size: 13
596013 TAAAATAATA
596023 ATAATAATTAAAAT
1 ATAA-AATTAAAAT
* *
596037 ATTGAATTTAAACAT
1 A-TAAAATTAAA-AT
596052 ATAAAATTAAAAT
1 ATAAAATTAAAAT
596065 AT-AAA-TAAATAGT
1 ATAAAATTAAA-A-T
596078 GACTAAAA-T--AA-
1 -A-TAAAATTAAAAT
596089 ATAAAATTAAAACT
1 ATAAAATTAAAA-T
*
596103 ATAATATTAAAAT
1 ATAAAATTAAAAT
596116 ATAAAA
1 ATAAAA
596122 AAGTAATAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 4 0.06
12 6 0.09
13 12 0.18
14 28 0.42
15 6 0.09
16 4 0.06
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:596103 original size:21 final size:21
Alignment explanation
Indices: 596079--596121 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
596069 ATAAATAGTG
596079 ACTAAAATAAATAAAAT-TAAA
1 ACTAAAAT-AATAAAATATAAA
* *
596100 ACTATAATATTAAAATATAAA
1 ACTAAAATAATAAAATATAAA
596121 A
1 A
596122 AAGTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ACTAAAATAATAAAATATAAA
Found at i:597424 original size:3 final size:3
Alignment explanation
Indices: 597416--597474 Score: 66
Period size: 3 Copynumber: 18.7 Consensus size: 3
597406 CCTGAAATGA
*
597416 AAT AAT AAT AAT AAT AAT AAAT AAAT AAAT AAAT AAA AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT AAT AAT AAT AAT AAT
597464 AAT AAT AAT AA
1 AAT AAT AAT AA
597475 AAAAAATGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 35 0.67
4 15 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:597978 original size:122 final size:122
Alignment explanation
Indices: 597839--598165 Score: 523
Period size: 123 Copynumber: 2.7 Consensus size: 122
597829 GAATTAAGGC
*
597839 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
597904 GAACACTTCTGGAAATGCTTATGCTGATCTATCTCCTTCTGTGATAGCGTC-ATGCAA
66 GAACTCTTCTGGAAATGCTTATGCTAATCTATCTCCTTCTGTGATAGCGTCGA-GCAA
* * *
597961 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATAAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
598026 GAACTTTCTCTGGAAAAGTTTATGCTAATCTATCTCCTTCTGTGATAGCGTCGAGCAA
66 GAACTCT-TCTGGAAATGCTTATGCTAATCTATCTCCTTCTGTGATAGCGTCGAGCAA
*
598084 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATTA
598148 TGAACTCTTCTGGAAATG
65 TGAACTCTTCTGGAAATG
598166 TTGATCCATC
Statistics
Matches: 187, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
122 77 0.41
123 109 0.58
124 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCTGGAAATGCTTATGCTAATCTATCTCCTTCTGTGATAGCGTCGAGCAA
Found at i:598613 original size:22 final size:22
Alignment explanation
Indices: 598552--598614 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
598542 AAATCCAATA
* * *
598552 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
*
598574 AATCTATCATCTTTGAAGAGAT
1 AATCTATCATCTTTGAAGAGAG
598596 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
598615 ATGTAGATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:599320 original size:18 final size:18
Alignment explanation
Indices: 599283--599320 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
599273 TATATAAAAG
*
599283 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
599301 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
599319 AA
1 AA
599321 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:606805 original size:15 final size:15
Alignment explanation
Indices: 606785--606816 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
606775 TGCAATGAAT
606785 AATGAATGTATGCAA
1 AATGAATGTATGCAA
606800 AATGAATGTATGCAA
1 AATGAATGTATGCAA
606815 AA
1 AA
606817 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:610544 original size:2 final size:2
Alignment explanation
Indices: 610537--610581 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
610527 AATTTTTAAA
* *
610537 AT AT AT AT -T A- AT AT CT AT AT AT TT A- 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
610576 AT AT AT
1 AT AT AT
610582 TTAAAAGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:610564 original size:15 final size:16
Alignment explanation
Indices: 610537--610575 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
610527 AATTTTTAAA
*
610537 ATATATATTAATATCT
1 ATATATATTAATATAT
610553 ATATAT-TTAATATAT
1 ATATATATTAATATAT
610568 ATATATAT
1 ATATATAT
610576 ATATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATATTAATATAT
Found at i:610566 original size:23 final size:23
Alignment explanation
Indices: 610536--610585 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
610526 TAATTTTTAA
*
610536 AATATATATTAATATCTATATATTT
1 AATATATA-T-ATATATATATATTT
610561 AATATATATATATATATATATTT
1 AATATATATATATATATATATTT
610584 AA
1 AA
610586 AAGTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
24 1 0.04
25 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATATATATATATATATATTT
Found at i:611064 original size:50 final size:51
Alignment explanation
Indices: 610988--611108 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 51
610978 TATTAATATG
* ** *
610988 ATTAAAATA-AAAT-AATAATAATTAAAAT--ATTGAATTTAAACATATAAA
1 ATTAAAATATAAATAAATAATAACTAAAATAAATAAAATTAAAAC-TATAAA
* **
611036 ATTAAAATATAAATAAATAATGACTAAAATAAATAAAATTAAAACTATAGT
1 ATTAAAATATAAATAAATAATAACTAAAATAAATAAAATTAAAACTATAAA
611087 ATTAAAATATAAA-AAATAATAA
1 ATTAAAATATAAATAAATAATAA
611109 AACTTATAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
48 9 0.15
49 4 0.07
50 21 0.34
51 17 0.28
52 10 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (51 bp):
ATTAAAATATAAATAAATAATAACTAAAATAAATAAAATTAAAACTATAAA
Found at i:612334 original size:3 final size:3
Alignment explanation
Indices: 612326--612373 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
612316 CCTCAAATGA
612326 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
612372 AA
1 AA
612374 CCAAATGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:613620 original size:30 final size:29
Alignment explanation
Indices: 613586--613658 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
613576 GACCAATTGT
*
613586 AACTTTTCAAAATTACCATTTTGGTCCCTA
1 AACTTTTCAAAATTA-CATTTTGGTCACTA
* *
613616 AACTTTTCAAAGTTTATATTTTGGTCACTA
1 AACTTTTCAAA-ATTACATTTTGGTCACTA
*
613646 AACTTTACAAAAT
1 AACTTTTCAAAAT
613659 CTTATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (29 bp):
AACTTTTCAAAATTACATTTTGGTCACTA
Found at i:613670 original size:31 final size:30
Alignment explanation
Indices: 613605--613670 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
613595 AAATTACCAT
* * * *
613605 TTTGGTCCCTAAACTTTTCAAAGTTTATAT
1 TTTGGTCACTAAACTTTACAAAATTTATAA
613635 TTTGGTCACTAAACTTTACAAAATCTTATAA
1 TTTGGTCACTAAACTTTACAAAAT-TTATAA
613666 TTTGG
1 TTTGG
613671 CCTCTCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTGGTCACTAAACTTTACAAAATTTATAA
Found at i:615244 original size:9 final size:9
Alignment explanation
Indices: 615228--615324 Score: 78
Period size: 9 Copynumber: 11.1 Consensus size: 9
615218 TCATCTCTCA
615228 TCTTTTT-T
1 TCTTTTTCT
615236 TCTTTTT-T
1 TCTTTTTCT
**
615244 T-TCCTTCT
1 TCTTTTTCT
615252 TCTTTTTCT
1 TCTTTTTCT
*
615261 TCTTCTTCT
1 TCTTTTTCT
*
615270 TCTTCTTCT
1 TCTTTTTCT
*
615279 TCTTTATTTT
1 TCTTT-TTCT
*
615289 TCTTTTCTTT
1 TCTTTT-TCT
*
615299 TCTTCTTC-
1 TCTTTTTCT
615307 TCTTTTTCT
1 TCTTTTTCT
615316 T-TTTTTCT
1 TCTTTTTCT
615324 T
1 T
615325 ATTCTTTAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
7 3 0.04
8 26 0.35
9 29 0.39
10 16 0.22
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:615253 original size:3 final size:3
Alignment explanation
Indices: 615247--615330 Score: 77
Period size: 3 Copynumber: 29.0 Consensus size: 3
615237 CTTTTTTTTC
* * *
615247 CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTTT ATT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
* * *
615293 -TT CTT -TT CTT CTT C-T CTT TTT CTT -TT TTT CTT ATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
615331 TAATCTGTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
2 8 0.12
3 56 0.85
4 2 0.03
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (3 bp):
CTT
Found at i:615257 original size:12 final size:11
Alignment explanation
Indices: 615228--615331 Score: 80
Period size: 11 Copynumber: 9.7 Consensus size: 11
615218 TCATCTCTCA
*
615228 TCTTTTTTTCT
1 TCTTCTTTTCT
615239 T-TT-TTTTCCT
1 TCTTCTTTT-CT
615249 TCTTC-TTT-T
1 TCTTCTTTTCT
615258 TCTTCTTCTTCT
1 TCTTCTT-TTCT
615270 TCTTCTTCTTCT
1 TCTTCTT-TTCT
615282 T-TAT-TTTTCT
1 TCT-TCTTTTCT
615292 T-TTCTTTTCT
1 TCTTCTTTTCT
615302 TCTTCTCTTT-T
1 TCTTCT-TTTCT
*
615313 TCTTTTTTTCT
1 TCTTCTTTTCT
*
615324 TATTCTTT
1 TCTTCTTT
615332 AATCTGTAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 22
0.76 0.03 0.21
Matches are distributed among these distances:
9 11 0.14
10 22 0.28
11 28 0.35
12 18 0.23
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTCTTTTCT
Found at i:615260 original size:6 final size:6
Alignment explanation
Indices: 615232--615319 Score: 67
Period size: 6 Copynumber: 14.8 Consensus size: 6
615222 CTCTCATCTT
* * * * *
615232 TTTTTC -TTTT- TTTTCC TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
615278 TTCTTTA TTTTTC -TTTTC -TTTTC TTCTTCTC TTTTTC TTTTT
1 TT-TTTC TTTTTC TTTTTC TTTTTC TT-TT-TC TTTTTC TTTTT
615320 TTCTTATTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
5 17 0.25
6 39 0.57
7 8 0.12
8 4 0.06
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:618233 original size:24 final size:24
Alignment explanation
Indices: 618201--618249 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
618191 AGTCTTCCTG
618201 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
618225 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
618249 A
1 A
618250 ATTTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:620560 original size:21 final size:21
Alignment explanation
Indices: 620534--620594 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
620524 GGCACATAGA
620534 ATTTGTCCCGAAGGACCACAT
1 ATTTGTCCCGAAGGACCACAT
* *
620555 ATTTGTCCAGAATGACCACAT
1 ATTTGTCCCGAAGGACCACAT
**
620576 AGATGTCCCGAAGGACCAC
1 ATTTGTCCCGAAGGACCAC
620595 TCCTTAAGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (21 bp):
ATTTGTCCCGAAGGACCACAT
Found at i:621637 original size:65 final size:65
Alignment explanation
Indices: 621504--621663 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
621494 GTGCACAAGA
* * * *
621504 GTGCATCGATGCATCCAGTGCATTCAATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGATG
* *
621568 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-GAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGAT
*
621631 AT
65 -G
* *
621633 GTGCATCGATGCATGAAATACATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
621664 CAATTTATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 29 0.35
65 52 0.62
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGATG
Found at i:621702 original size:65 final size:64
Alignment explanation
Indices: 621504--621713 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 64
621494 GTGCACAAGA
* * * * * **
621504 GTGCATCGATGCATCCAGTGCATTCAATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGA-T
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCAT-GATT
621567 G
64 G
*
621568 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGATAT
1 GTGCATCGATGCATCAAATACATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGAT-T
621633 -
64 G
* ** *
621633 GTGCATCGATGCATGAAATACATTCGATG-TTCA-ATTTAT-TTCATGGTGCATCGATGCATGAA
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATA-AAATCCTCA--GTGCATCGATGCATG-A
621695 TTG
62 TTG
*
621698 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
621714 CTATGAAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
62 4 0.03
63 6 0.05
64 44 0.35
65 66 0.53
66 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGATTG
Found at i:623995 original size:12 final size:13
Alignment explanation
Indices: 623927--624005 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 13
623917 TTAGAGGGAA
*
623927 AAATGAATAAATG
1 AAATAAATAAATG
*
623940 AAA-AAATGAA-G
1 AAATAAATAAATG
* *
623951 AATAAAAATAAGT-
1 AA-ATAAATAAATG
* *
623964 AAAAAAATAAAAG
1 AAATAAATAAATG
*
623977 GAA-AAATAAAT-
1 AAATAAATAAATG
623988 AAATAAATAAATG
1 AAATAAATAAATG
624001 AAATA
1 AAATA
624006 TTAAAAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
11 5 0.10
12 29 0.57
13 17 0.33
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (13 bp):
AAATAAATAAATG
Found at i:624282 original size:19 final size:19
Alignment explanation
Indices: 624260--624297 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
624250 AAAAGTATAT
624260 ATATA-TATAAAAATAATAA
1 ATATAGTATAAAAA-AATAA
*
624279 ATATAGTATTAAAAAATAA
1 ATATAGTATAAAAAAATAA
624298 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATATAGTATAAAAAAATAA
Found at i:624293 original size:22 final size:22
Alignment explanation
Indices: 624230--624297 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
624220 TAATACACTT
*
624230 ATAAGTAAA-ATATTTTAAAAA
1 ATAAGTAAATATATATTAAAAA
*
624251 A-AAGTATATATATA-TATAAAA
1 ATAAGTAAATATATATTA-AAAA
624272 ATAA-TAAATATAGTATTAAAAA
1 ATAAGTAAATATA-TATTAAAAA
624294 ATAA
1 ATAA
624298 CCAAATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.21
21 17 0.44
22 12 0.31
23 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (22 bp):
ATAAGTAAATATATATTAAAAA
Found at i:624870 original size:37 final size:37
Alignment explanation
Indices: 624829--624925 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
624819 GGATCATATC
* *
624829 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
* * *
624866 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
624903 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
624926 GACGAAAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
Found at i:625833 original size:106 final size:106
Alignment explanation
Indices: 625649--626704 Score: 1608
Period size: 106 Copynumber: 10.0 Consensus size: 106
625639 GCATTGTTCT
* * * *
625649 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATTGGGAAGTTGCTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
*
625713 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
625755 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTAATGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
625820 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
625861 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
625926 CCAGCGGTCCCTTCATCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
625967 GAGTCCAATATCCTTCGTTGTGAAGTTGGAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
626032 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
626073 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
626138 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
626179 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
626244 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
626285 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
626350 CCAGCGGTCCC-T--TC-----GTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
626383 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
626448 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * * * *
626489 GAGTCCAATATCCTTCATTGTTAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
** *
626554 CCAGCGGTCCCTTAATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
626595 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
626660 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
626701 GAGT
1 GAGT
626705 GGCACGATAT
Statistics
Matches: 864, Mismatches: 77, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
98 89 0.10
99 1 0.00
101 2 0.00
103 2 0.00
105 1 0.00
106 768 0.89
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:627469 original size:14 final size:13
Alignment explanation
Indices: 627430--627470 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
627420 AAGAGTTTCG
627430 AAAGATGTTTATT
1 AAAGATGTTTATT
*
627443 CAAGA-GTTT-TT
1 AAAGATGTTTATT
627454 AAAGATGTTTAATT
1 AAAGATGTTT-ATT
627468 AAA
1 AAA
627471 AGTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 6 0.26
12 8 0.35
13 4 0.17
14 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.41
Consensus pattern (13 bp):
AAAGATGTTTATT
Found at i:627474 original size:24 final size:24
Alignment explanation
Indices: 627430--627476 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
627420 AAGAGTTTCG
*
627430 AAAGATGTTTATTCAAGAGTTTTT
1 AAAGATGTTTATTCAAAAGTTTTT
627454 AAAGATGTTTAATT-AAAAGTTTT
1 AAAGATGTTT-ATTCAAAAGTTTT
627477 GAAAATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (24 bp):
AAAGATGTTTATTCAAAAGTTTTT
Found at i:627696 original size:22 final size:22
Alignment explanation
Indices: 627670--627746 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
627660 TTGTGTTTGG
627670 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
627692 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
627714 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
627736 TCAACGGTTTG
1 TCAAAGGTTTG
627747 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:628376 original size:20 final size:19
Alignment explanation
Indices: 628351--628437 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
628341 TTTTTTTCCC
628351 TTTTTCTTTTTGAT-TTTTG
1 TTTTTCTTTTT-ATCTTTTG
*
628370 TTCTTTCTTTTTTTCTTTTG
1 TT-TTTCTTTTTATCTTTTG
628390 TTTTTCTTTTT-TC-TTTG
1 TTTTTCTTTTTATCTTTTG
*
628407 TTTTT-TTTCT-TCTTTTG
1 TTTTTCTTTTTATCTTTTG
628424 CATCTTTTCTTTTT
1 --T-TTTTCTTTTT
628438 TTTTCTTGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
16 6 0.10
17 13 0.22
18 2 0.03
19 13 0.22
20 20 0.34
21 4 0.07
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTATCTTTTG
Found at i:628380 original size:26 final size:25
Alignment explanation
Indices: 628350--628441 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 25
628340 CTTTTTTTCC
* *
628350 CTTTTTCTTTTTGATTTTTGTTCTTT
1 CTTTTTTTTTTTG-TTTTTCTTCTTT
*
628376 CTTTTTTTCTTTTGTTTTTCTTTTTT
1 CTTTTTTT-TTTTGTTTTTCTTCTTT
* *
628402 CTTTGTTTTTTTTCTTCTTTTGCATCTTTT
1 CTTT-TTTTTTTT-GT-TTTT-CTTC-TTT
628432 CTTTTTTTTT
1 CTTTTTTTTT
628442 CTTGATTGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 25 0.46
27 10 0.19
28 4 0.07
29 8 0.15
30 7 0.13
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.79
Consensus pattern (25 bp):
CTTTTTTTTTTTGTTTTTCTTCTTT
Found at i:628383 original size:23 final size:22
Alignment explanation
Indices: 628357--628422 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
628347 TCCCTTTTTC
628357 TTTTTGATTTTTGTTCTTTC-TT
1 TTTTTG-TTTTTGTTCTTTCTTT
*
628379 TTTTT-CTTTTGTT-TTTCTTTT
1 TTTTTGTTTTTGTTCTTTC-TTT
*
628400 TTCTTTGTTTTTTTTC-TTCTTT
1 TT-TTTGTTTTTGTTCTTTCTTT
628422 T
1 T
628423 GCATCTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 4 0.11
22 12 0.33
23 9 0.25
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (22 bp):
TTTTTGTTTTTGTTCTTTCTTT
Found at i:628423 original size:17 final size:16
Alignment explanation
Indices: 628377--628423 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
628367 TTGTTCTTTC
628377 TTTTTTTCTTTTGTTT
1 TTTTTTTCTTTTGTTT
628393 TTCTTTTT-TCTTTGTTT
1 TT-TTTTTCT-TTTGTTT
628410 TTTTTCTTCTTTTG
1 TTTTT-TTCTTTTG
628424 CATCTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.22
17 20 0.74
18 1 0.04
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTTTGTTT
Found at i:632882 original size:12 final size:12
Alignment explanation
Indices: 632853--632927 Score: 80
Period size: 12 Copynumber: 6.2 Consensus size: 12
632843 TGTTAGAAGG
*
632853 AAAAAATGAATA
1 AAAAAATAAATA
*
632865 ATAAAAATAAGTA
1 A-AAAAATAAATA
632878 AAAAAATAAA-A
1 AAAAAATAAATA
*
632889 GGAAAAATAAATA
1 -AAAAAATAAATA
*
632902 AATAAATAAATA
1 AAAAAATAAATA
*
632914 AATAAATAAATA
1 AAAAAATAAATA
632926 AA
1 AA
632928 TGAAATATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
11 1 0.02
12 42 0.78
13 11 0.20
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:632902 original size:4 final size:4
Alignment explanation
Indices: 632893--632934 Score: 75
Period size: 4 Copynumber: 10.2 Consensus size: 4
632883 ATAAAAGGAA
632893 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
632935 TTAAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:632946 original size:2 final size:2
Alignment explanation
Indices: 632939--632964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
632929 GAAATATTAA
632939 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
632965 GAGTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:633028 original size:18 final size:18
Alignment explanation
Indices: 632979--633032 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
632969 AAAATAGAAA
*
632979 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
633000 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
633019 AATA-TAATATAAAA
1 AATAGTAATATAAAA
633033 AAACAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:633033 original size:18 final size:19
Alignment explanation
Indices: 632983--633033 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
632973 TAGAAAAATA
*
632983 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
633003 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
633022 ATAATATAAAAA
1 ATAATATAAAAA
633034 AACAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:633180 original size:2 final size:2
Alignment explanation
Indices: 633173--633222 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
633163 GATAATTACA
633173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
633215 AT -T AT AT A
1 AT AT AT AT A
633223 GTAAAATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:633248 original size:38 final size:38
Alignment explanation
Indices: 633206--633278 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
633196 TATATATATA
* *
633206 TATATATATATTATATAGTAAAATA-TTTTAAAAAAAAG
1 TATATATATA-TATATAATAAAATAGTATTAAAAAAAAG
*
633244 TATATATATATATATAATAATATAGTATTAAAAAA
1 TATATATATATATATAATAAAATAGTATTAAAAAA
633279 TAACCAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (38 bp):
TATATATATATATATAATAAAATAGTATTAAAAAAAAG
Found at i:633838 original size:37 final size:37
Alignment explanation
Indices: 633797--633901 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
633787 GTGCTTATGG
* * *
633797 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* ** * *
633834 ATCCTATTTTTAAGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
633871 ATCCTATTTTTTGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
633902 GACGAAAATG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:634284 original size:2 final size:2
Alignment explanation
Indices: 634277--634319 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
634267 CTGATTTTCG
634277 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
634319 A
1 A
634320 ATTTAAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:634757 original size:23 final size:21
Alignment explanation
Indices: 634726--634820 Score: 79
Period size: 23 Copynumber: 4.4 Consensus size: 21
634716 GACCTTGTGC
634726 ATCGATGCACATTCAAGGTGTT
1 ATCGATGCACATTCAAGGTG-T
* *
634748 CATC-AGTGCACCTTCATGGTGT
1 -ATCGA-TGCACATTCAAGGTGT
*
634770 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
* *
634792 ATAGATGCACTATT--AGGTGA
1 ATCGATGCAC-ATTCAAGGTGT
634812 ATCGATGCA
1 ATCGATGCA
634821 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
20 10 0.17
21 17 0.28
22 14 0.23
23 19 0.32
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:640734 original size:65 final size:65
Alignment explanation
Indices: 640601--640760 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
640591 TGCACTAAGA
* * * *
640601 GTGCATCGATGCATCCAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCACTGATGCATGTCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCACTGATGCATGTATG
* *
640665 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCA-TCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCACT-GATGCAT-GT
640728 AT-
63 ATG
*
640730 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
640761 CAATTTATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 28 0.33
65 51 0.60
66 6 0.07
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCACTGATGCATGTATG
Found at i:641707 original size:19 final size:22
Alignment explanation
Indices: 641654--641709 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
641644 GATACTCTTA
* *
641654 CTATAGTACCGACACTACCCGC
1 CTATGGTACCGATACTACCCGC
*
641676 CTATGGTATCGATACT-CCC-C
1 CTATGGTACCGATACTACCCGC
641696 CTA-GGTACCGATAC
1 CTATGGTACCGATAC
641710 CATTTTTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 10 0.33
20 4 0.13
21 3 0.10
22 13 0.43
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (22 bp):
CTATGGTACCGATACTACCCGC
Found at i:647863 original size:9 final size:10
Alignment explanation
Indices: 647850--647889 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
647840 TAAAATAACA
647850 AAATAAAAA-
1 AAATAAAAAC
647859 AAATAAAAAC
1 AAATAAAAAC
647869 AACATAAATAAC
1 AA-ATAAA-AAC
647881 AAATAAAAA
1 AAATAAAAA
647890 TAAAATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
10 4 0.14
11 10 0.36
12 5 0.18
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (10 bp):
AAATAAAAAC
Found at i:648931 original size:15 final size:15
Alignment explanation
Indices: 648911--648945 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
648901 AACCAAAAGG
648911 AAAAAAGGAAAGAAA
1 AAAAAAGGAAAGAAA
*
648926 AAAAAAGGAGAGAAA
1 AAAAAAGGAAAGAAA
648941 AAAAA
1 AAAAA
648946 TGTCAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAGAAA
Found at i:650444 original size:19 final size:19
Alignment explanation
Indices: 650420--650470 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
650410 ACCAACTAAA
650420 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
650439 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
*
650458 TCGCAACGCGATC
1 TCGCAATGCGATC
650471 TCCCGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:650601 original size:42 final size:42
Alignment explanation
Indices: 650552--650740 Score: 342
Period size: 42 Copynumber: 4.5 Consensus size: 42
650542 GTTGCGATAG
* *
650552 TCCAAGTTCGTTGCGATAGTCAAAGTTCGAGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
650594 TCCAAGTTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
650636 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
650678 TCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
650720 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
650741 CAAAATCGCA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:651527 original size:6 final size:6
Alignment explanation
Indices: 651516--651572 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
651506 GTCGGGTTGA
* * *
651516 GGTCGT GGTCGT GGTCGT GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
651564 GGTCGT GGT
1 GGTCGT GGT
651573 AATACGTGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:651712 original size:42 final size:40
Alignment explanation
Indices: 651662--652337 Score: 457
Period size: 42 Copynumber: 16.4 Consensus size: 40
651652 CGTTGCGATT
*
651662 TTGGACTATCGCAACAAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* * ** *
651704 TTCGACTATCACAACGCGAACTTGG-A-CCATCGCAACGAAT
1 TTGGACTATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* * *
651744 TTGGAATAAATCGCAACGTGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAAC--GAACTTGGAATAAATCGCAACGAAC
*
651786 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* * * *
651828 TTCGACTATCGCAATGAACATGGAATAAATCGCAATGTAAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACG--AAC
* * *
651870 TTCGACTATCGCAACGAACTTGGACT--ATCGCAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * *
651908 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* * * *
651950 TTGGACTATCACAACGAATTTGAAATAAATCGCTACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGC-A-ACGAAC
* * *
651992 TTCGACTATCGCAATGAACTTGGAATAAATCGCAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * * *
652032 TTGGAATAAATCGCAACGCGAACTTTGACT--ATCGCAACGAAT
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* * *
652074 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
*
652116 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* * * *
652158 TTCGACTATCGCAACGAACTTAGAATAAATCACAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * * *
652198 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAT
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* * *
652240 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* *
652282 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
*
652324 TTCGACTATCGCAA
1 TTGGACTATCGCAA
652338 ATCAGTTTCC
Statistics
Matches: 524, Mismatches: 72, Indels: 76
0.78 0.11 0.11
Matches are distributed among these distances:
38 40 0.08
40 98 0.19
41 2 0.00
42 356 0.68
43 1 0.00
44 27 0.05
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
Found at i:651815 original size:61 final size:59
Alignment explanation
Indices: 651662--652337 Score: 472
Period size: 61 Copynumber: 10.9 Consensus size: 59
651652 CGTTGCGATT
* * *
651662 TTGGACTATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTGGACTATCGCAA--CGAAC
* * *
651725 TTGGACCATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAAC--GAACTTGGACTATCGCAACGAAC
* * *
651786 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTGGACTATCGCAACGAAC
* * * * * *
651847 ATGGAATAAATCGCAATGTAAACTTCGACT--ATCGCAACGAACTTGGACTATCGCAACGAAT
1 TTGGACT--ATCGCAACG--AACTTGGAATAAATCGCAACGAACTTGGACTATCGCAACGAAC
* * * * *
651908 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAACTTGGACTATCACAACGAAT
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAACTTGGACTATCGCAACGAAC
* * * * * * * *
651969 TTGAAATAAATCGCTACGCGAACTTCGACT--ATCGCAATGAACTTGGAATAAATCGCAACGAAT
1 TTGGACT--ATCGC-A-ACGAACTTGGAATAAATCGCAACGAACTTGGACT--ATCGCAACGAAC
* * * * *
652032 TTGGAATAAATCGCAACGCGAACTTTGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGA
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAACTTGGACT--ATCGCAA--CGA
652095 AC
58 AC
* * * *
652097 TTCGACTATCGCAACGAACTTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACT--ATCGCAA--CGAAC
* * * * *
652158 TTCGACTATCGCAACGAACTTAGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACT--ATCGCAA--CGAAC
* * *
652221 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTGGACTATCGCAACGAAC
* * *
652282 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTGGACTATCGCAA
652338 ATCAGTTTCC
Statistics
Matches: 548, Mismatches: 43, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
61 314 0.57
62 2 0.00
63 207 0.38
65 25 0.05
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (59 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTGGACTATCGCAACGAAC
Found at i:651852 original size:103 final size:103
Alignment explanation
Indices: 651715--651954 Score: 417
Period size: 103 Copynumber: 2.3 Consensus size: 103
651705 TCGACTATCA
* * * *
651715 CAACGCGAACTTGGACCATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCA
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGTAAACTTCGACTATCGCA
651780 ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
66 ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
* * *
651818 CAACGCGAACTTCGACTATCGCAATGAACATGGAATAAATCGCAATGTAAACTTCGACTATCGCA
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGTAAACTTCGACTATCGCA
651883 ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
66 ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
651921 CAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGA
651955 CTATCACAAC
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 128 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (103 bp):
CAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGTAAACTTCGACTATCGCA
ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
Found at i:651991 original size:103 final size:101
Alignment explanation
Indices: 651715--652188 Score: 387
Period size: 103 Copynumber: 4.6 Consensus size: 101
651705 TCGACTATCA
* * * * * *
651715 CAACGCGAACTTGGACCATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACT--ATCG
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGACT--ATCGCAAC--GAA-TTTGAATAAATCG
* * *
651778 CA-ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
61 CACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
* * * * * *
651818 CAACGCGAACTTCGACTATCGCAATGAACATGGAATAAATCGCAATGTAAACTTCGACT--ATCG
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGACT--ATCGCAACG--AA-TTTGAATAAATCG
* * *
651881 CA-ACGAACTTGGACTATCGCAACGAATTTGGAATAAATCG
61 CACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
*
651921 CAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCACAACGAATTTGAAATAAATCGCTAC
1 CAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTG-AATAAATCGC-AC
*
651986 GCGAACTTCGACTATCGCAATGAACTTGGAATAAATCG
64 GCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
* * * *
652024 CAA--CGAATTTGGAATAAATCGCAACGCGAACTTTGACTATCGCAACGAATTTGGAATAAATCG
1 CAACGCGAACTTCGACT--ATCGCAA--CGAACTTGGACTATCGCAACGAATTT-GAATAAATCG
*
652087 CAACGCGAACTTCGACTATCGCAACGAACTTGGACT--ATCG
61 C-ACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
* * * * *
652127 CAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAATAAATC
1 CAACGCGAACTTCGACT--ATCGCAA--CGAACTTGGACTATCGCAACGAA-TTTGAATAAATC
652189 ACAACGAATT
Statistics
Matches: 331, Mismatches: 27, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
98 3 0.01
99 4 0.01
101 22 0.07
102 1 0.00
103 232 0.70
104 2 0.01
105 66 0.20
106 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (101 bp):
CAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGAATAAATCGCACGC
GAACTTCGACTATCGCAACGAACTTGGAATAAATCG
Found at i:652123 original size:166 final size:164
Alignment explanation
Indices: 651665--652399 Score: 1062
Period size: 166 Copynumber: 4.4 Consensus size: 164
651655 TGCGATTTTG
* * *
651665 GACTATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGCGAACTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTCGAATATCGCAACGCGAACTTGGA
* *
651730 CCATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTGGACTAT
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
651795 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
129 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
651831 GACTATCGCAATGAACATGGAATAAATCGCAATGTAAACTTCGACTATCGCAA--CGAACTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACG--AACTTCGAATATCGCAACGCGAACTTGGA
651894 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
* * *
651959 CACAACGAATTTGAAATAAATCGCTACGCGAACTTC
129 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * *
651995 GACTATCGCAATGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTTGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGAAT--ATCGCAACGCGAACTTGGA
652060 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
652125 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
129 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * * * *
652161 GACTATCGCAACGAACTTAGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGAAT--ATCGCAACGCGAACTTGGA
652226 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTAT
*
652291 CGCAACGAATTTGTAATAAATCGCAACGCGAACTTC
129 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*** * *** * * * *
652327 GACTATCGCAAATCAGTTTCCA-GATTCGCAACGCGAACTTCGACTATCGCAACGCGAACTTAGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTCGAATATCGCAACGCGAACTTGGA
652391 CTATCGCAA
64 CTATCGCAA
652400 TGCTAATATG
Statistics
Matches: 523, Mismatches: 38, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
162 7 0.01
164 146 0.28
165 33 0.06
166 328 0.63
167 9 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (164 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGAACTTCGAATATCGCAACGCGAACTTGGACT
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCG
CAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:663810 original size:2 final size:2
Alignment explanation
Indices: 663803--663834 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
663793 TTTGTTTTTC
663803 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
663835 TAAGGGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:664347 original size:2 final size:2
Alignment explanation
Indices: 664340--664378 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
664330 AAGAAAATGA
664340 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 A
664379 ATTAGAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:664753 original size:2 final size:2
Alignment explanation
Indices: 664746--664775 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
664736 TATTAATCTA
664746 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
664776 GTAAAAATGA
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):
AT
Found at i:667111 original size:23 final size:23
Alignment explanation
Indices: 667033--667114 Score: 128
Period size: 23 Copynumber: 3.6 Consensus size: 23
667023 GTCGAGGGTT
*
667033 CTATGTGGTTCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
667056 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* *
667079 CTATGTGGTCCTTCGGGATAAAC
1 CTATGTGGTCCTTCGGGACAAAA
667102 CTATGTGGTCCTT
1 CTATGTGGTCCTT
667115 TAGGACAGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:668892 original size:18 final size:18
Alignment explanation
Indices: 668869--668905 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
668859 TTGTAGAATA
668869 CCCAAAGTTAAGAATGTG
1 CCCAAAGTTAAGAATGTG
668887 CCCAAAGTTAAGAATGTG
1 CCCAAAGTTAAGAATGTG
668905 C
1 C
668906 AATAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (18 bp):
CCCAAAGTTAAGAATGTG
Found at i:671273 original size:44 final size:44
Alignment explanation
Indices: 671162--671323 Score: 243
Period size: 44 Copynumber: 3.6 Consensus size: 44
671152 TTTTCATCAT
* * * *
671162 TTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATACTTACCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
* *
671206 TTTAATTCCATAAGCTCTTAAGCTTATTTGACCAATATACTTGCCA
1 -TT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
671252 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
*
671296 TTATTCCATAAGCTCATAAGCTTATTTT
1 TTATTCCATAAGCTCGTAAGCTTATTTT
671324 CCAGTTTATC
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
44 67 0.63
45 4 0.04
46 36 0.34
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:671553 original size:61 final size:61
Alignment explanation
Indices: 671437--671553 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
671427 GCTAAATCTG
* * *
671437 CACTAAGCTTACGTCATAGTGCTAATCCGGATATGACACATAAGGTCGTGCCCACCACCTA
1 CACTAAGCTTACGTCATAGTGCTAATCCAGACATGACACATAAGGTCGTACCCACCACCTA
* *
671498 CACTAAGCTTACG-CTATAGTGCTAATCCAGACATGATACATAAGGTCGTATCCACC
1 CACTAAGCTTACGTC-ATAGTGCTAATCCAGACATGACACATAAGGTCGTACCCACC
671554 TTCCCGCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (61 bp):
CACTAAGCTTACGTCATAGTGCTAATCCAGACATGACACATAAGGTCGTACCCACCACCTA
Found at i:678085 original size:46 final size:45
Alignment explanation
Indices: 678017--678227 Score: 318
Period size: 46 Copynumber: 4.7 Consensus size: 45
678007 AATTTCTCAT
* *
678017 CATTTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATACTTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
678062 CATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
1 CATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
* *
678108 CATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTTC
1 CATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
* * * *
678154 CA-TTATTCTATAAGCTTGTAAGCTTATTTTACCAATATACTTGC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
678198 CA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CATTTATTCCATAAGCTCGTAAGCTTATTTT
678228 CCAGTTTATC
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 65 0.42
45 7 0.04
46 84 0.54
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTAC
Found at i:678456 original size:61 final size:61
Alignment explanation
Indices: 678336--678457 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
678326 GTAGTGCTAA
* ** * *
678336 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGATGTGACATATAAGGTCGTGTCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTATCCACC
* * * *
678397 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGACATGATACATTAGGTTGTATCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTATCCACC
678458 TTCTCGCACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCGGACATGACACATAAGGTCGTATCCACC
Found at i:680230 original size:30 final size:30
Alignment explanation
Indices: 680194--680266 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
680184 TAAATTACAT
*
680194 TTTGGTCACTGAACTTTTCCAAGTTTATAA
1 TTTGGTCACTAAACTTTTCCAAGTTTATAA
*
680224 TTTGGTCACCAAACTTTTCCAAGTTTATAA
1 TTTGGTCACTAAACTTTTCCAAGTTTATAA
*
680254 TTGGGTCACTAAA
1 TTTGGTCACTAAA
680267 TAAATCCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (30 bp):
TTTGGTCACTAAACTTTTCCAAGTTTATAA
Found at i:681930 original size:18 final size:18
Alignment explanation
Indices: 681907--681949 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
681897 GTAATAAGTG
681907 TAAATGAGTTTAAAGGTA
1 TAAATGAGTTTAAAGGTA
681925 TAAATGAGTTTAAAGGTA
1 TAAATGAGTTTAAAGGTA
681943 TAAATGA
1 TAAATGA
681950 AGTCTAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.33
Consensus pattern (18 bp):
TAAATGAGTTTAAAGGTA
Found at i:687029 original size:21 final size:21
Alignment explanation
Indices: 686990--687052 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
686980 AATAATATGA
* *
686990 ACTGGATGAACAA-TATCGAT
1 ACTGGTTGAAGAAGTATCGAT
687010 ACTGGTTGAAGAAGTATCGAT
1 ACTGGTTGAAGAAGTATCGAT
*
687031 ACTGTTTTGAAG--GTATCGAT
1 ACTG-GTTGAAGAAGTATCGAT
687051 AC
1 AC
687053 CAAGGATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 21 0.55
21 11 0.29
22 6 0.16
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (21 bp):
ACTGGTTGAAGAAGTATCGAT
Found at i:687048 original size:20 final size:20
Alignment explanation
Indices: 687003--687052 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
686993 GGATGAACAA
687003 TATCGATACTGGTTGAAGAAG
1 TATCGATACTGGTTGAAG-AG
*
687024 TATCGATACTGTTTTGAAG-G
1 TATCGATACTG-GTTGAAGAG
687044 TATCGATAC
1 TATCGATAC
687053 CAAGGATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGATACTGGTTGAAGAG
Found at i:692796 original size:20 final size:20
Alignment explanation
Indices: 692771--692822 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
692761 GGTTGAAGAA
*
692771 GTATCGATACTGATG-TGAAG
1 GTATCGATACTGAGGAT-AAG
**
692791 GTATCGATACCAAGGATAAG
1 GTATCGATACTGAGGATAAG
692811 GTATCGATACTG
1 GTATCGATACTG
692823 TAAGTAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACTGAGGATAAG
Found at i:693665 original size:23 final size:23
Alignment explanation
Indices: 693628--693714 Score: 129
Period size: 23 Copynumber: 3.8 Consensus size: 23
693618 GTCGAGGGTT
*
693628 CTATGTGGTTCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* *
693651 CTACGTGGTCATTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* *
693674 CTATATGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
693697 CTATGTGGTCCTTCGGGA
1 CTATGTGGTCCTTCGGGA
693715 TAGATATGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:699492 original size:23 final size:23
Alignment explanation
Indices: 699452--699556 Score: 135
Period size: 23 Copynumber: 4.7 Consensus size: 23
699442 TTGAGGGTTT
* *
699452 TATGTGGTTCTTCAGGACAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
* *
699475 TATGTTGTCCTTTGGGACAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
*
699498 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAC
699521 TATGTGGTCCTTCGGGAC-AAA-
1 TATGTGGTCCTTCGGGACAAAAC
699542 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
699557 TGCAAATTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
20 1 0.01
21 13 0.18
22 2 0.03
23 57 0.78
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAC
Found at i:710468 original size:124 final size:124
Alignment explanation
Indices: 710248--710480 Score: 333
Period size: 124 Copynumber: 1.9 Consensus size: 124
710238 TGTCAGATTT
* *
710248 GAGTGTCGGATATAAGAATATACTCAATGTACGATTATCAAATACATGTTCAATACAAATATTTC
1 GAGTGTCGGATATAAGAATATACCCAATGTACGAGTATCAAATACATGTTCAATACAAATATTTC
* *
710313 TGATGAATCCCCAATCTCAAGGGAAGTTTCGAAGTTCCAAATGTATTGTTATTCTATGC
66 TAATGAATCCCCAATCTCAAAGGAAGTTTCGAAGTTCCAAATGTATTGTTATTCTATGC
* ** * ** *
710372 GAGTGTCGGATATAAGGATATACCCTTTGTACGAGTATCAAATACGTGTTTGATATAAATATTT-
1 GAGTGTCGGATATAAGAATATACCCAATGTACGAGTATCAAATACATGTTCAATACAAATATTTC
* *
710436 TCAATGAATTCCTAATCTCAAAGGAAGTTTCGAAGTTCCAAATGT
66 T-AATGAATCCCCAATCTCAAAGGAAGTTTCGAAGTTCCAAATGT
710481 CTACATTATT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 1 0.01
124 94 0.99
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (124 bp):
GAGTGTCGGATATAAGAATATACCCAATGTACGAGTATCAAATACATGTTCAATACAAATATTTC
TAATGAATCCCCAATCTCAAAGGAAGTTTCGAAGTTCCAAATGTATTGTTATTCTATGC
Found at i:711502 original size:20 final size:20
Alignment explanation
Indices: 711477--711521 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
711467 TAAATGAATG
711477 AACAATTGTGGCGTTTCCTA
1 AACAATTGTGGCGTTTCCTA
711497 AACAATTGTGGCGTTTCCTA
1 AACAATTGTGGCGTTTCCTA
711517 AACAA
1 AACAA
711522 ACGCCACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (20 bp):
AACAATTGTGGCGTTTCCTA
Found at i:715885 original size:18 final size:18
Alignment explanation
Indices: 715862--715905 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
715852 GTTATTAAAT
715862 TATATATAATAATA-ATAA
1 TATATATAATAATATAT-A
**
715880 TATATATGTTAATATATA
1 TATATATAATAATATATA
715898 TATATATA
1 TATATATA
715906 TGTATATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATATAATAATATATA
Found at i:715902 original size:20 final size:18
Alignment explanation
Indices: 715871--715908 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
715861 TTATATATAA
715871 TAATAATAATATATATGT
1 TAATAATAATATATATGT
715889 TAATATATATATATATATGT
1 TAATA-ATA-ATATATATGT
715909 ATATGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TAATAATAATATATATGT
Found at i:731184 original size:15 final size:15
Alignment explanation
Indices: 731164--731196 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
731154 TTTTTCGAAC
731164 TTTTACGAGCTTCAA
1 TTTTACGAGCTTCAA
731179 TTTTACGAGCTTCAA
1 TTTTACGAGCTTCAA
731194 TTT
1 TTT
731197 ATGATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (15 bp):
TTTTACGAGCTTCAA
Found at i:732075 original size:2 final size:2
Alignment explanation
Indices: 732068--732105 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
732058 AAACATGTAT
732068 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
732106 ATTCCCCCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:732215 original size:18 final size:18
Alignment explanation
Indices: 732194--732228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
732184 TTATTAAACC
732194 TTATTTCCAGATTAAGGT
1 TTATTTCCAGATTAAGGT
**
732212 TTATTTTTAGATTAAGG
1 TTATTTCCAGATTAAGG
732229 GCTACTAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (18 bp):
TTATTTCCAGATTAAGGT
Found at i:732606 original size:16 final size:17
Alignment explanation
Indices: 732577--732610 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
732567 AACACTTAAA
*
732577 ATTATAACATTAAAAAT
1 ATTATAACACTAAAAAT
732594 ATTA-AACACTAAAAAT
1 ATTATAACACTAAAAAT
732610 A
1 A
732611 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTATAACACTAAAAAT
Found at i:736870 original size:29 final size:29
Alignment explanation
Indices: 736831--736911 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
736821 TATATGATAT
736831 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
736861 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
736890 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
736912 ACATATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:737318 original size:22 final size:22
Alignment explanation
Indices: 737293--737348 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
737283 ATGGTAAGAA
737293 TGCATATTCATTAAAATATTGT
1 TGCATATTCATTAAAATATTGT
*
737315 TGCATATTCATGAAAATATTGT
1 TGCATATTCATTAAAATATTGT
*
737337 TACATATTCATT
1 TGCATATTCATT
737349 TATTGCCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (22 bp):
TGCATATTCATTAAAATATTGT
Found at i:745099 original size:18 final size:19
Alignment explanation
Indices: 745064--745100 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
745054 CACGGAATGT
745064 AAGATTACTAGTGGGAATAA
1 AAGATTACTAG-GGGAATAA
745084 AAGATTACTA-GGGAATA
1 AAGATTACTAGGGGAATA
745101 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTACTAGGGGAATAA
Found at i:745289 original size:36 final size:38
Alignment explanation
Indices: 745240--745316 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
745230 ATAATATTAC
745240 AAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
* * * *
745277 AAATT-TATAATATTTATGTAATTTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
745314 AAA
1 AAA
745317 AATATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 12 0.34
37 23 0.66
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:745884 original size:2 final size:2
Alignment explanation
Indices: 745877--745910 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
745867 ATCTTCCATG
745877 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
745911 GGTTCATTTT
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:747135 original size:13 final size:13
Alignment explanation
Indices: 747111--747145 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
747101 TATTTATTAT
747111 ATATTT-ATAAAA
1 ATATTTAATAAAA
747123 ATATTTAAT-AAA
1 ATATTTAATAAAA
747135 ATATTTAATAA
1 ATATTTAATAA
747146 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Done.