Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold266
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: 653600
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 22668 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:329454 original size:21 final size:21
Alignment explanation
Indices: 329412--329471 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
329402 TTCGAGGATC
*
329412 TGCAACCTTAGATATG--ATA
1 TGCAATCTTAGATATGATATA
329431 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGATATA
329452 TGCAATCTTAGATATGATAT
1 TGCAATCTTAGATATGATAT
329472 GTAATCTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 15 0.39
21 23 0.61
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGCAATCTTAGATATGATATA
Found at i:329501 original size:23 final size:22
Alignment explanation
Indices: 329421--329505 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
329411 CTGCAACCTT
*
329421 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
329442 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
329461 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
329483 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
329506 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:329515 original size:22 final size:23
Alignment explanation
Indices: 329471--329515 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
329461 AGATATGATA
*
329471 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
329494 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
329516 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:329950 original size:3 final size:3
Alignment explanation
Indices: 329942--329981 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
329932 ATTAATTTTG
*
329942 TTA TTA TTA TTT TTA TTA TTA -TA TTA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
329982 ACCTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:329950 original size:15 final size:15
Alignment explanation
Indices: 329926--329980 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
329916 GTTTTTAGTC
329926 TATT-TTATTAATTT
1 TATTATTATTAATTT
* *
329940 TGTTATTATTATTTT
1 TATTATTATTAATTT
329955 TATTATTA-T-ATTAT
1 TATTATTATTAATT-T
329969 ATATTATTATTA
1 -TATTATTATTA
329981 TACCTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 5 0.16
15 24 0.75
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:329957 original size:12 final size:12
Alignment explanation
Indices: 329928--329979 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
329918 TTTTAGTCTA
329928 TTTTATTAATT-T
1 TTTTATT-ATTAT
*
329940 TGTTATTATTAT
1 TTTTATTATTAT
329952 TTTTATTATTAT
1 TTTTATTATTAT
329964 ATTATATATTATTAT
1 -TT-T-TATTATTAT
329979 T
1 T
329980 ATACCTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 2 0.06
14 2 0.06
15 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:330330 original size:52 final size:51
Alignment explanation
Indices: 330249--330348 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
330239 GTTTTTATAT
330249 TATACTTATATATTTCATTTTTTAGTAAATGCATGAATATATTTTATATGTG
1 TATACTTATATATTTCATTTTTTAGTAAATGCAT-AATATATTTTATATGTG
* * * *
330301 TATATTTATAT-TTTCCTTGTTTTCA-TAAATGCATTATGTATTTTATAT
1 TATACTTATATATTTCATT-TTTT-AGTAAATGCATAATATATTTTATAT
330349 ATATATAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 18 0.43
52 23 0.55
53 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (51 bp):
TATACTTATATATTTCATTTTTTAGTAAATGCATAATATATTTTATATGTG
Found at i:336805 original size:6 final size:6
Alignment explanation
Indices: 336794--336826 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
336784 CATTCTCAAA
336794 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
336827 TAAATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:337027 original size:44 final size:44
Alignment explanation
Indices: 336979--337205 Score: 111
Period size: 44 Copynumber: 5.2 Consensus size: 44
336969 GATAACAGAT
*
336979 CTTGCCTTCCTGTACTGGCAGCGAAACAGATCAAAGACACCAGC
1 CTTGCCTTCCTGCACTGGCAGCGAAACAGATCAAAGACACCAGC
* ** * ** * * * * * *
337023 CTTGCCTCCCTGGGCT-GCAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCACTGGCAGCGAAACAGATCAAAGACACCAG-C
* * * *
337067 CTTGCCTTCCTGCACCGACAGCGAACCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGGCAGCGAAACAGATCAAAGACACCAGC
** * * * * * * * *
337111 CTTGCC-TCCTTG-GGTTGCAGCGGAGCAG-GCTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCACTGGCAGCGAAACAGATC-AAAGACACCAG-C
* * * *
337155 CTTGCCTTCCTGCACCGACAGCGAACCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGGCAGCGAAACAGATCAAAGACACCAGC
337199 CTTGCCT
1 CTTGCCT
337206 CCTTGGGTTG
Statistics
Matches: 122, Mismatches: 53, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
42 1 0.01
43 37 0.30
44 48 0.39
45 35 0.29
46 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTGCACTGGCAGCGAAACAGATCAAAGACACCAGC
Found at i:337130 original size:88 final size:88
Alignment explanation
Indices: 336965--337523 Score: 839
Period size: 88 Copynumber: 6.4 Consensus size: 88
336955 AGCAGATTAG
* * * * * * *
336965 TAAAGATAACAGATCTTGCCTTCCTGTACTGGCAGCGAAACAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
337030 CCCTGGGCTGCAGCGGAGTAGGT
66 CCCTGGGTTGCAGCGGAGCAGGC
*
337053 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAACCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
337118 CCTTGGGTTGCAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
*
337141 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAACCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
337206 CCTTGGGTTGCAGCGGAGTAGGT
66 CCCTGGGTTGCAGCGGAGCAGGC
* ** * *
337229 TAAAAATAGCAGATCTTGCCTTCTTGCACCGACAATGAAGCAGATCGAAGTCACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
337294 CCTTGGGTTGCAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* *
337317 TAAAAATAGCAGATATTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
337382 CCCTGTGTTGCAGCAGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGC
* *
337405 TGAAAATAGCAGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
337470 CCCTGGGTTACAGCGGAGCAAGT
66 CCCTGGGTTGCAGCGGAGCAGGC
337493 TAAAAATAGCAGATCTTGCCTTCCTGCACCG
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCG
337524 GGAATAGGTT
Statistics
Matches: 429, Mismatches: 42, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 429 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGC
Found at i:337247 original size:44 final size:44
Alignment explanation
Indices: 337023--337254 Score: 121
Period size: 44 Copynumber: 5.3 Consensus size: 44
337013 AGACACCAGC
* *
337023 CTTGCCTCCCTGGGCTGCAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCTTGGGCTGCAGCGGAGCAGGTTAAAAATAGCAGAT
** * * * * ** * * * *
337067 CTTGCCTTCC-TGCACCGACAGCGAACCAGATCGAAGACACCAG-C
1 CTTGCC-TCCTTGGGCTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
337111 CTTGCCTCCTTGGGTTGCAGCGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCTTGGGCTGCAGCGGAGCAGGTTAAAAATAGCAGAT
** * * * * ** * * * *
337155 CTTGCCTTCC-TGCACCGACAGCGAACCAGATCGAAGACACCAG-C
1 CTTGCC-TCCTTGGGCTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
* *
337199 CTTGCCTCCTTGGGTTGCAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCTTGGGCTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
337243 CTTGCCTTCTTG
1 CTTGCCTCCTTG
337255 CACCGACAAT
Statistics
Matches: 124, Mismatches: 56, Indels: 16
0.63 0.29 0.08
Matches are distributed among these distances:
43 38 0.31
44 48 0.39
45 38 0.31
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCTTGGGCTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:337380 original size:44 final size:44
Alignment explanation
Indices: 337332--337474 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 44
337322 ATAGCAGATA
*
337332 TTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCC
1 TTGCCTCCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCC
***** * * * * *
337376 TTGCCTCCCTG-TGTTGCAGC-AGAGCAG-GCTGAAAATAGCAGATC
1 TTGCCTCCCTGCACCAACAGCGA-AGCAGATC-GAAGACACCAG-CC
** *
337420 TTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
1 TTGCCTCCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCC
337464 TTGCCTCCCTG
1 TTGCCTCCCTG
337475 GGTTACAGCG
Statistics
Matches: 68, Mismatches: 25, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
42 2 0.03
43 17 0.25
44 30 0.44
45 17 0.25
46 2 0.03
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (44 bp):
TTGCCTCCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCC
Found at i:337590 original size:44 final size:44
Alignment explanation
Indices: 337524--337883 Score: 483
Period size: 44 Copynumber: 8.2 Consensus size: 44
337514 TCCTGCACCG
* *
337524 GGAATAGGTT-AAGATTGTGAATCCTATCTCCCTAGTCAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
* *
337567 GGAATAGGTTGAAGATTGAGAATCCTATCTCCTTGGACAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
* *
337611 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
* *
337655 GGAATAGGTTGAAGATTGAGAATCCTATCTCCTTGGACAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
* *
337699 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
* * *
337743 GGAATAGGTTGAAGATTGAGAATTCTATTTCCCTGGGCAGCAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
** *
337787 GGAATAAATTGAAGATTGTAG-GTCCTATCTCCCTGGTCAGCAGT
1 GGAATAGGTTGAAGATTG-AGAATCCTATCTCCCTGGTCAGCAGT
* * * * *
337831 GGAATAGGTTGAAGATGGTGAAACTTATCTCCCTGAG-CAGTAGT
1 GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTG-GTCAGCAGT
*
337875 GGAGTAGGT
1 GGAATAGGT
337884 GGAAAATAGC
Statistics
Matches: 277, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
43 11 0.04
44 263 0.95
45 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (44 bp):
GGAATAGGTTGAAGATTGAGAATCCTATCTCCCTGGTCAGCAGT
Found at i:337636 original size:88 final size:88
Alignment explanation
Indices: 337524--337846 Score: 542
Period size: 88 Copynumber: 3.7 Consensus size: 88
337514 TCCTGCACCG
*
337524 GGAATAGGTT-AAGATTGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGA
1 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
337588 ATCCTATCTCCTTGGACAGCAGT
66 ATCCTATCTCCTTGGACAGCAGT
337611 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
1 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
337676 ATCCTATCTCCTTGGACAGCAGT
66 ATCCTATCTCCTTGGACAGCAGT
337699 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
1 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
* * * *
337764 ATTCTATTTCCCTGGGCAGCAGT
66 ATCCTATCTCCTTGGACAGCAGT
** * *
337787 GGAATAAATTGAAGATTGT-AGGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGAT
1 GGAATAGGTTAAAGATTGTGA-ATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGAT
337847 GGTGAAACTT
Statistics
Matches: 225, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
87 11 0.05
88 214 0.95
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (88 bp):
GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
ATCCTATCTCCTTGGACAGCAGT
Found at i:338283 original size:44 final size:44
Alignment explanation
Indices: 338190--338297 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
338180 ATGACAAATT
* *
338190 TTATCTCCCTAAAGTTGCAATGAAACAGATTAAAGCCGATAATC
1 TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGATAATC
* * * * * *
338234 CTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC-TTGGATC
1 TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGAT-AATC
*
338278 TTATCTCTCTAAAGTTGCAG
1 TTATCTCCCTAAAGTTGCAG
338298 AGAGCAGAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGATAATC
Found at i:338760 original size:20 final size:21
Alignment explanation
Indices: 338728--338779 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
338718 CTTCGAGGAT
338728 ATGCAATCTTAGATATGATAA
1 ATGCAATCTTAGATATGATAA
338749 ATGCAA-CTTAGATATGAT--
1 ATGCAATCTTAGATATGATAA
*
338767 ATGTAATCTTAGA
1 ATGCAATCTTAGA
338780 AGATATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 6 0.21
20 12 0.41
21 6 0.21
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGCAATCTTAGATATGATAA
Found at i:338786 original size:22 final size:23
Alignment explanation
Indices: 338758--338802 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
338748 AATGCAACTT
338758 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
338780 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
338803 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:338812 original size:22 final size:23
Alignment explanation
Indices: 338768--338812 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
338758 AGATATGATA
*
338768 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
338791 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
338813 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:339017 original size:21 final size:19
Alignment explanation
Indices: 338980--339018 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
338970 ACTGTTTTCT
*
338980 TTTTTTCCTTTTTCGATTA
1 TTTTTTACTTTTTCGATTA
338999 TTTTTTACTTATTTACGATT
1 TTTTTTACTT-TTT-CGATT
339019 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTACTTTTTCGATTA
Found at i:339251 original size:15 final size:15
Alignment explanation
Indices: 339222--339277 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
339212 GTTTTTAGTC
*
339222 TATT-TTATTAATTT
1 TATTATTATTATTTT
*
339236 TGTTATTATTATTTT
1 TATTATTATTATTTT
*
339251 TATTGTTA-TATTTT
1 TATTATTATTATTTT
339265 ATATTATTATTAT
1 -TATTATTATTAT
339278 ACCTACATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.26
15 22 0.65
16 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TATTATTATTATTTT
Found at i:341067 original size:21 final size:21
Alignment explanation
Indices: 341026--341110 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
341016 CCAAGAACAA
*
341026 AGCAAAAAAGAGAGGAGAAACC
1 AGCAAAAACGAG-GGAGAAACC
*
341048 AGCAAAAACGAGGGACAAACC
1 AGCAAAAACGAGGGAGAAACC
* * *
341069 AGTAAGAACAAGGGAGAAACC
1 AGCAAAAACGAGGGAGAAACC
* *
341090 AGCAAGAACTAGGGGAGAAAC
1 AGCAAAAACGA-GGGAGAAAC
341111 TGTTATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 34 0.63
22 20 0.37
ACGTcount: A:0.53, C:0.16, G:0.28, T:0.02
Consensus pattern (21 bp):
AGCAAAAACGAGGGAGAAACC
Found at i:345362 original size:26 final size:26
Alignment explanation
Indices: 345333--345385 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
345323 ATCGGTTTTA
345333 TCTGTAAGTTGAATCCACCATAATAG
1 TCTGTAAGTTGAATCCACCATAATAG
*
345359 TCTGTAAGTTGAATTCACCATAATAG
1 TCTGTAAGTTGAATCCACCATAATAG
345385 T
1 T
345386 AATTTGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (26 bp):
TCTGTAAGTTGAATCCACCATAATAG
Found at i:348890 original size:18 final size:19
Alignment explanation
Indices: 348855--348914 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
348845 GTGACCCTTA
348855 TTTTC-AAAATTTTCCTAT
1 TTTTCTAAAATTTTCCTAT
348873 TTTTCTAAAATTTT-CTAT
1 TTTTCTAAAATTTTCCTAT
*
348891 TTTGTTTAAAATTTGTCCCTAT
1 TTT-TCTAAAATTT-T-CCTAT
348913 TT
1 TT
348915 GTTCCCGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 12 0.33
19 17 0.47
20 1 0.03
22 6 0.17
ACGTcount: A:0.25, C:0.13, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTCTAAAATTTTCCTAT
Found at i:352470 original size:2 final size:2
Alignment explanation
Indices: 352463--352490 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
352453 GTATAATAAC
352463 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
352491 CGATTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354698 original size:13 final size:13
Alignment explanation
Indices: 354680--354709 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
354670 TGACGAGATG
354680 CAAAAGTGCAAGC
1 CAAAAGTGCAAGC
*
354693 CAAAAGTTCAAGC
1 CAAAAGTGCAAGC
354706 CAAA
1 CAAA
354710 TGGGGGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (13 bp):
CAAAAGTGCAAGC
Found at i:361055 original size:23 final size:23
Alignment explanation
Indices: 361025--361134 Score: 118
Period size: 23 Copynumber: 4.9 Consensus size: 23
361015 NNNGTATCTT
* *
361025 AGGCACTTTATGTGTCGTACATC
1 AGGCACCTTATGTGTCGTATATC
* *
361048 AGGCACTTTATGTGTCGTATTTC
1 AGGCACCTTATGTGTCGTATATC
** *
361071 AGGCACCTCGTGTGTCGTATTTC
1 AGGCACCTTATGTGTCGTATATC
*
361094 AGGCACCTTGTGTGTC--ATATC
1 AGGCACCTTATGTGTCGTATATC
*
361115 AGGCA-CTTATGTGTCATATA
1 AGGCACCTTATGTGTCGTATA
361135 CTGATCAGGT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
20 9 0.12
21 9 0.12
22 3 0.04
23 56 0.73
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
AGGCACCTTATGTGTCGTATATC
Found at i:363832 original size:28 final size:27
Alignment explanation
Indices: 363795--363849 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
363785 GGTTAAATAG
* *
363795 TTTAGGTACCAGTTCTAACAAAAA-AAAA
1 TTTAGATACCAATT-TAA-AAAAACAAAA
363823 TTTAGATACCAATTTAAAAAAACAAAA
1 TTTAGATACCAATTTAAAAAAACAAAA
363850 CTAGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 12 0.50
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (27 bp):
TTTAGATACCAATTTAAAAAAACAAAA
Found at i:365140 original size:19 final size:17
Alignment explanation
Indices: 365118--365158 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
365108 TACTTTAGAC
365118 TTTTTTCATTTTCTATATA
1 TTTTTTCATTTTCT-TA-A
*
365137 TTTTTTTATTTTCTTAA
1 TTTTTTCATTTTCTTAA
365154 TTTTT
1 TTTTT
365159 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCATTTTCTTAA
Found at i:374036 original size:28 final size:27
Alignment explanation
Indices: 374005--374058 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
373995 ACAATTTGGA
374005 ATTTGTAAT-AATTTTATAATTATTTTAC
1 ATTTGTAATAAATTTTA-AATT-TTTTAC
*
374033 ATTTTTAATAAATTTTAAATTTTTTA
1 ATTTGTAATAAATTTTAAATTTTTTA
374059 TTTTAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 12 0.50
29 7 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTGTAATAAATTTTAAATTTTTTAC
Found at i:377210 original size:3 final size:3
Alignment explanation
Indices: 377202--377244 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
377192 TAAATTTGAC
*
377202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
377245 TTTTTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:377365 original size:7 final size:7
Alignment explanation
Indices: 377353--377378 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
377343 ATTATATCAT
377353 TTTATTA
1 TTTATTA
377360 TTTATTA
1 TTTATTA
377367 TTTATTA
1 TTTATTA
377374 TTTAT
1 TTTAT
377379 GTCCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:377434 original size:14 final size:14
Alignment explanation
Indices: 377417--377457 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
377407 TTACTATATT
377417 TTATTTATATTTAC
1 TTATTTATATTTAC
*
377431 TTATTTATATTTTTC
1 TTATTTATA-TTTAC
377446 TTATTATATATT
1 TTATT-TATATT
377458 ATTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 11 0.46
16 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTATATTTAC
Found at i:377457 original size:16 final size:15
Alignment explanation
Indices: 377417--377457 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
377407 TTACTATATT
377417 TTATTTATA-TTTAC
1 TTATTTATATTTTAC
*
377431 TTATTTATATTTTTC
1 TTATTTATATTTTAC
377446 TTATTATATATT
1 TTATT-TATATT
377458 ATTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTATATTTTAC
Found at i:377461 original size:10 final size:10
Alignment explanation
Indices: 377446--377479 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
377436 TATATTTTTC
377446 TTATTATATA
1 TTATTATATA
377456 TTATTATATAA
1 TTATTATAT-A
377467 TTATTTATATA
1 TTA-TTATATA
377478 TT
1 TT
377480 TTTTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 7 0.32
12 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATATA
Found at i:385541 original size:14 final size:14
Alignment explanation
Indices: 385519--385552 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
385509 ACTACACAAT
385519 TAATAACATGATTA
1 TAATAACATGATTA
*
385533 TAATGACATGATTA
1 TAATAACATGATTA
*
385547 AAATAA
1 TAATAA
385553 TATAACTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (14 bp):
TAATAACATGATTA
Found at i:385922 original size:27 final size:27
Alignment explanation
Indices: 385883--385942 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
385873 TATTATGCTT
385883 TGTTGCCCAACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
*
385910 TGTTGCCCGACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
385937 TGTTGC
1 TGTTGC
385943 TAATACTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (27 bp):
TGTTGCCCAACAAAGCTCACAGTACAA
Found at i:387489 original size:21 final size:22
Alignment explanation
Indices: 387463--387507 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
387453 ATGATTCGAC
387463 TTATTTTT-AATTAAGTGCTAT
1 TTATTTTTAAATTAAGTGCTAT
387484 TTATTTTTAAATTAAGTGCTAT
1 TTATTTTTAAATTAAGTGCTAT
387506 TT
1 TT
387508 TTCTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (22 bp):
TTATTTTTAAATTAAGTGCTAT
Found at i:388052 original size:111 final size:109
Alignment explanation
Indices: 387851--388983 Score: 1115
Period size: 111 Copynumber: 10.2 Consensus size: 109
387841 TATACAGGGG
* * * *
387851 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA-TTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * *
387914 CATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *******
387957 AAAAAACGAAAATTTTGGTGGTGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAAAAAAT
1 AAAAAA--AAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AAATTTTTTTT
* *
388022 TTACATTTTGGGTTGTCATTGGTCGGCACCAGTATAC-AAAAAATTC
63 TTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *
388068 AAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATG-CAATTTTTTT
1 --AAAAAAAAA--TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTT
* *
388132 TTTACATTTTGGGCTGTCATTAGCCGGCACCAGTATACAAAAAAATT-
62 TTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *
388179 AAAAAAAAA-TTTTGGTGGTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--------TTT
**
388243 TTTTTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTC
58 TTTTTTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAA-AATTC
***** *
388296 AAAATTTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * ** *
388361 CATTTTGGGCTATAATTGGTTGGCACCAGTATACAAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
*** * * * *
388405 --AAAATTTTTTTTTGAGGTGGCCTGGCAATGGCCTGCACCACCTTTAAGT-AATTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * *
388467 CATTTTGGACTGTCATTGGCTGACACTAGTATACGAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
***** * * * **
388511 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAATTTTTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--TTTTTTTTT
* * *
388576 TACATTTTGGGCTATCATTGGCAGGCACCAGTATACGAAAAAGTT-
64 TACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
388621 AAAAAAAAAATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT----AAATTTTTTT
* * *
388686 TTTACATTTTGGGCTGTCATTGGCCTGCACTAGTATATGAAAAAAATT-
62 TTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACG-AAAAAATTC
** * ******
388734 AAAAAAAAATTTTTCATGGTGGCCTGGCAATGGCCGGCACCACTTTTATGTAAA-AAAAAATTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * *
388798 CATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
388842 AAAAAAAATTTTTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTT
1 AAAAAAAA--ATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA----TTTTT
* *
388906 CTTTTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGA
60 -TTTTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATT-C
*
388958 AAAAAAAAACTTTTAGGTGGTGGCCT
1 AAAAAAAAA-TTTTTGGTGGTGGCCT
388984 AAAAATTGCC
Statistics
Matches: 846, Mismatches: 138, Indels: 77
0.80 0.13 0.07
Matches are distributed among these distances:
106 90 0.11
107 53 0.06
108 120 0.14
109 22 0.03
110 122 0.14
111 132 0.16
112 48 0.06
113 97 0.11
114 3 0.00
115 103 0.12
116 12 0.01
117 4 0.00
118 40 0.05
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
Found at i:388508 original size:331 final size:327
Alignment explanation
Indices: 387852--388983 Score: 1175
Period size: 331 Copynumber: 3.4 Consensus size: 327
387842 ATACAGGGGA
* * * * *
387852 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA------TTTTTT
1 AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTT
* * **
387910 TTTACATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTCAAAAAACGAAAATTTTG
66 TTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATT-AAAAAA--AAAATTTTG
* ** **** *
387974 GTGGTGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAAAAAATTTACATTTTGGGTTGTC
128 GTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTGTC
* * * *
388039 ATTGGTCGGCACCAGTATAC-AAAAAATTCAAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAAT
193 ATTGGTTGGCACCAGTATACAAAAAAATTC------AAAAATTTTTTTTGAGGTGGCCTGGCAAT
* * *
388103 GGCCGACACCACCTTTATGCAATTTTTTTTTTACATTTTGGGCTGTCATTAGCCGGCACCAGTAT
252 GGCCG-CACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTAT
*
388168 ACAAAAAAATT-
316 ACGAAAAAATTC
* * *
388179 AAAAAAAAATTTTGGTGGTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTTT
1 AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAA-T--TTTTTTTT
* ******
388244 TTTTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTCAAAATTTTTTTTT
63 TTTTTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAA-AATT-AAAAAAAAAATTT
* * *
388309 TGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AATTTTTTTTTTTACATTTTGGGCTA
126 TGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTG
* *
388373 TAATTGGTTGGCACCAGTATACAAAAAAATTCAAAATTTTTTTTTGAGGTGGCCTGGCAATGGCC
191 TCATTGGTTGGCACCAGTATACAAAAAAATTCAAAAATTTTTTTTGAGGTGGCCTGGCAATGGCC
* * * *
388438 TGCACCACCTTTAAGTAATTTTTTTTTTACATTTTGGACTGTCATTGGCTGACACTAGTATACGA
256 -GCACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTATACGA
388503 AAAAATTC
320 AAAAATTC
**** * * **
388511 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAA---TTTTTTTT
1 AAAA-AAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTT
* *
388573 TTTTACATTTTGGGCTATCATTGG-CAGGCACCAGTATACGAAAAAGTTAAAAAAAAAATTTTGG
65 TTTTACATTTTGGGCTGTCATTGGCCA-GCACCAGTATACGAAAAAATTAAAAAAAAAATTTTGG
388637 TGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTACATTTTGGGCTG
129 TGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT---AAAATTATTTTTTTACATTTTGGGCTG
* * * * *** *
388702 TCATTGGCCT-GCACTAGTATATGAAAAAAATTAAAAAAAAATTTTTCATGGTGGCCTGGCAATG
191 TCATTGG-TTGGCACCAGTATA-CAAAAAAATTCAAAAATTTTTTTTGA-GGTGGCCTGGCAATG
* ******* * *
388766 GCCGGCACCACTTTTATGTAAAAAAAAATTTACATTTTGGGCTATCATTGGCCGGCA-TCAATAT
253 GCC-GCACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACT-AGTAT
388830 ACGAAAAAATTC
316 ACGAAAAAATTC
388842 AAAAAAAATTTTTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTT
1 AAAAAAAA---TTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTT
* * *
388906 CTTTTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGAAAAAAAAAACTTT
63 TTTTTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATT-AAAAAAAAAA-TTT
388971 TAGGTGGTGGCCT
126 T-GGTGGTGGCCT
388984 AAAAATTGCC
Statistics
Matches: 665, Mismatches: 105, Indels: 59
0.80 0.13 0.07
Matches are distributed among these distances:
325 45 0.07
326 5 0.01
327 89 0.13
328 2 0.00
329 39 0.06
330 21 0.03
331 169 0.25
332 8 0.01
333 75 0.11
335 49 0.07
336 47 0.07
337 92 0.14
338 15 0.02
339 9 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (327 bp):
AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTT
TTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATTAAAAAAAAAATTTTGGTG
GTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTGTCATT
GGTTGGCACCAGTATACAAAAAAATTCAAAAATTTTTTTTGAGGTGGCCTGGCAATGGCCGCACC
ACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTATACGAAAAAAT
TC
Found at i:388756 original size:223 final size:221
Alignment explanation
Indices: 387851--388983 Score: 1141
Period size: 223 Copynumber: 5.1 Consensus size: 221
387841 TATACAGGGG
* * * *
387851 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA-TTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * *
387914 CATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTCAAAAAACGAAAATTTTGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATT-AAAAAA--AAAATTTTGGTGG
* **** *
387978 TGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAA---AAAATTTACATTTTGGGTTGTCA
128 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCA
*
388040 TTGGTCGGCACCAGTATAC-AAAAAATTC
193 TTGGCCGGCACCAGTATACGAAAAAATTC
* * *
388068 AAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATG-CAATTTTTTT
1 --AAAAAAAAA--TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTT
* *
388132 TTTACATTTTGGGCTGTCATTAGCCGGCACCAGTATACAAAAAAATT-AAAAAAAAATTTTGGTG
62 TTTACATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTG
* * * ****
388196 GTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTTTTTTTTTACATTTTGGGC
127 GTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA----AAAATTTTTTTTTTACATTTTGGGC
**
388261 TGTCATTGGCCAACACCAGTATACGAAAACAATTC
188 TGTCATTGGCCGGCACCAGTATACGAAAA-AATTC
***** *
388296 AAAATTTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* ** * **** * *
388361 CATTTTGGGCTATAATTGGTTGGCACCAGTATACAAAAAAATT-CAAAATTTTTTTTTGAGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGTGG
* * *
388425 CCTGGCAATGGCCTGCACCACCTTTAAGT-----AATTTTTTTTTTACATTTTGGACTGTCATTG
131 CCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCATTG
* * *
388485 GCTGACACTAGTATACGAAAAAATTC
196 GCCGGCACCAGTATACGAAAAAATTC
***** * * * **
388511 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAATTTTTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--TTTTTTTTT
* * *
388576 TACATTTTGGGCTATCATTGGCAGGCACCAGTATACGAAAAAGTTAAAAAAAAAATTTTGGTGGT
64 TACATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGT
*
388641 GGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTACATTTTGGGCTGTCAT
129 GGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCAT
* * *
388706 TGGCCTGCACTAGTATATGAAAAAAATT-
194 TGGCCGGCACCAGTATACG-AAAAAATTC
** * ******
388734 AAAAAAAAATTTTTCATGGTGGCCTGGCAATGGCCGGCACCACTTTTATGTAAA-AAAAAATTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * **
388798 CATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTCAAAAAAAATTTTTTTTGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATT-AAAAAAAA--AATTTTGGTGG
* ****
388863 TGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTTCTTTTTACATTTTGGGCTGTC
128 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTT-TTTTTACATTTTGGGCTGTC
* *
388927 ATTGGCCGGTACCAGTATACGAAAAAATTGA
192 ATTGGCCGGCACCAGTATACGAAAAAATT-C
*
388958 AAAAAAAAACTTTTAGGTGGTGGCCT
1 AAAAAAAAA-TTTTTGGTGGTGGCCT
388984 AAAAATTGCC
Statistics
Matches: 764, Mismatches: 119, Indels: 56
0.81 0.13 0.06
Matches are distributed among these distances:
215 53 0.07
216 46 0.06
217 49 0.06
218 41 0.05
219 53 0.07
220 43 0.06
221 53 0.07
222 55 0.07
223 167 0.22
224 56 0.07
225 101 0.13
226 38 0.05
227 4 0.01
228 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (221 bp):
AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGTGG
CCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCATTG
GCCGGCACCAGTATACGAAAAAATTC
Found at i:389000 original size:115 final size:115
Alignment explanation
Indices: 388794--389000 Score: 279
Period size: 115 Copynumber: 1.8 Consensus size: 115
388784 TAAAAAAAAA
* *** *
388794 TTTACATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTCAAAAAAAATTTTTTTTG
1 TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
* *** *
388859 GTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGAAATTTTTTTTTCTT
66 GTGGTGGCCTAAAAATGGCCGACACCACCTTTATGAAATTTTTTTTTCTT
* * * *
388909 TTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGAAAAAAAAAACTTTTAG
1 TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
*
388974 GTGGTGGCCTAAAAATTGCCGACACCA
66 GTGGTGGCCTAAAAATGGCCGACACCA
389001 AATTTATCAA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (115 bp):
TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
GTGGTGGCCTAAAAATGGCCGACACCACCTTTATGAAATTTTTTTTTCTT
Found at i:391953 original size:54 final size:55
Alignment explanation
Indices: 391874--391992 Score: 152
Period size: 56 Copynumber: 2.2 Consensus size: 55
391864 ATATTCTTGT
* *
391874 AAAAATAAATTTGCATTGAAAATAG-AAAT-TTTAAATATAAAATGAAATGAGAA
1 AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
* * * **
391927 AAAAATTAAATTTCCTTTGGAAATAGAAAATATGTAGATATAAAATGAAATGAGGT
1 AAAAA-TAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
391983 AAAAATAAAT
1 AAAAATAAAT
391993 GTTATCAGGC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.09
54 17 0.30
55 9 0.16
56 25 0.45
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.29
Consensus pattern (55 bp):
AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
Found at i:396183 original size:33 final size:33
Alignment explanation
Indices: 396136--396203 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
396126 AAGCTGCACA
* *
396136 TAAGGTATCTGGGCACCAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
396169 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
396202 TA
1 TA
396204 TTCGGAGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (33 bp):
TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
Found at i:399622 original size:28 final size:28
Alignment explanation
Indices: 399582--399636 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
399572 TTTTTTTTAC
399582 TTTTTTTTTATAATTGG-ATATAAGTAGA
1 TTTTTTTTTATAA-TGGAATATAAGTAGA
399610 TTTTTTTTTATAATGGAATATAAGTAG
1 TTTTTTTTTATAATGGAATATAAGTAG
399637 TGAGATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (28 bp):
TTTTTTTTTATAATGGAATATAAGTAGA
Found at i:400208 original size:28 final size:28
Alignment explanation
Indices: 400168--400222 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
400158 GTGTAGAGGC
*
400168 GGCATTGCTTTATATGAGTAAAAAATAT
1 GGCACTGCTTTATATGAGTAAAAAATAT
400196 GGCACTGCTTTATATGAGTAAAAAATA
1 GGCACTGCTTTATATGAGTAAAAAATA
400223 CGGGATACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (28 bp):
GGCACTGCTTTATATGAGTAAAAAATAT
Found at i:409361 original size:15 final size:15
Alignment explanation
Indices: 409341--409371 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
409331 TTTTATTTTT
409341 TATTTTAAGTCATGA
1 TATTTTAAGTCATGA
409356 TATTTTAAGTCATGA
1 TATTTTAAGTCATGA
409371 T
1 T
409372 TTAGCCAATG
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:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TATTTTAAGTCATGA
Found at i:411168 original size:32 final size:32
Alignment explanation
Indices: 411132--411196 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
411122 TTTGTTAGAT
*
411132 ATTTATTATGTTTTAAGCTTGTTAGATTTTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
*
411164 ATTTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
411196 A
1 A
411197 ATGATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (32 bp):
ATTTATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:426679 original size:18 final size:18
Alignment explanation
Indices: 426658--426697 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
426648 AAAATATTTA
*
426658 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
426676 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
426694 TTTT
1 TTTT
426698 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:430735 original size:22 final size:20
Alignment explanation
Indices: 430699--430757 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
430689 AGCCCGGCCC
430699 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
430721 ATTTATTTTAAAAATGAAAAA
1 ATTTATTTTAAAAAT-AAAAA
**
430742 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
430758 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 8 0.24
23 7 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:430814 original size:42 final size:39
Alignment explanation
Indices: 430737--430864 Score: 166
Period size: 40 Copynumber: 3.2 Consensus size: 39
430727 TTTAAAAATG
430737 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
1 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
* * * *
430776 TTAAAGAAGTTTTTTAAAAAAATTTTAAAATTTAAAAAATTAA
1 -AAAAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAA--AA
* *
430819 AAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAAT
1 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
430858 AAAAAAA
1 AAAAAAA
430865 TAAAAATATT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
39 8 0.11
40 25 0.33
41 16 0.21
42 24 0.32
43 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (39 bp):
AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAA
Found at i:430836 original size:11 final size:11
Alignment explanation
Indices: 430822--430847 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
430812 AAATTAAAAA
430822 AAAAGTATTTT
1 AAAAGTATTTT
430833 AAAAGTATTTT
1 AAAAGTATTTT
430844 AAAA
1 AAAA
430848 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:432238 original size:20 final size:20
Alignment explanation
Indices: 432213--432255 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
432203 AGGAGCACAT
432213 CGTAGGATGCAACCTTTACC
1 CGTAGGATGCAACCTTTACC
*
432233 CGTAGGATGTAACCTTTACC
1 CGTAGGATGCAACCTTTACC
432253 CGT
1 CGT
432256 TTGTGTGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (20 bp):
CGTAGGATGCAACCTTTACC
Found at i:448144 original size:14 final size:14
Alignment explanation
Indices: 448118--448176 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
448108 ACTGTTGAAC
448118 TTAAAATATAAAATT
1 TTAAAA-ATAAAATT
448133 TTAAAAATAAAATT
1 TTAAAAATAAAATT
448147 TATAAAAATAAGAA-T
1 T-TAAAAATAA-AATT
* *
448162 ATAAAAATTAAATT
1 TTAAAAATAAAATT
448176 T
1 T
448177 CAAATATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 18 0.47
15 16 0.42
16 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TTAAAAATAAAATT
Found at i:448479 original size:26 final size:27
Alignment explanation
Indices: 448444--448495 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
448434 ATAAAAAATA
448444 ATCAAAATATTATAATT-TTTTTATTT
1 ATCAAAATATTATAATTATTTTTATTT
448470 ATCAAAATATTATAATTATTTTTATT
1 ATCAAAATATTATAATTATTTTTATT
448496 ATTTACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
ATCAAAATATTATAATTATTTTTATTT
Found at i:448512 original size:29 final size:29
Alignment explanation
Indices: 448444--448513 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 29
448434 ATAAAAAATA
448444 ATCAAAATATTAT-A--ATTTTTTTATTT
1 ATCAAAATATTATAATTATTTTTTTATTT
448470 ATCAAAATATTATAATTATTTTTATTATTT
1 ATCAAAATATTATAATTATTTTT-TTATTT
448500 A-CTAAAATA-TATAA
1 ATC-AAAATATTATAA
448514 AAAACAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
29 12 0.31
30 13 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
ATCAAAATATTATAATTATTTTTTTATTT
Found at i:448604 original size:27 final size:27
Alignment explanation
Indices: 448574--448644 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
448564 AGGCCAATGG
*
448574 CATTGGCGGCACCAGA-GGTGCCAAAGC
1 CATTGGCGGCACCA-ATGGTGCCAAAAC
*
448601 CATTGGCGGCACCAATGGTGCCAAAAT
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
448628 CATTGGTGGCACCAATG
1 CATTGGCGGCACCAATG
448645 CCATAATAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:448786 original size:65 final size:65
Alignment explanation
Indices: 448689--448998 Score: 538
Period size: 65 Copynumber: 4.8 Consensus size: 65
448679 GGAGAGGGAA
448689 AGAAG-GAAAGAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
1 AGAAGAGAAA-AAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAG
448753 G
65 G
448754 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
448819 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
448884 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
* *
448949 AGAAGAGAAAAAA-AAAGAAGAGGGAAGGA-AGAAAAAAAAAGAAAAA-AAGG
1 AGAAGAGAAAAAAGAAAGAA-A-GGAAGGAGAG-GAAAGAAAGAAAAAGAAGG
448999 TAATTTTTTT
Statistics
Matches: 239, Mismatches: 2, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
64 6 0.03
65 210 0.88
66 23 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (65 bp):
AGAAGAGAAAAAAGAAAGAAAGGAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGG
Found at i:448788 original size:47 final size:47
Alignment explanation
Indices: 448721--448922 Score: 202
Period size: 43 Copynumber: 4.6 Consensus size: 47
448711 GAAGGAGAGG
448721 AAAGAAAGAAA--AA-GA-AGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAGGAAGGAGAGGAAAGAAAAGGAAAGGAGAAGAGAAA
*
448764 AAAGAAAGAAAGGAAGGAGAGGAAAG-AAA-GAAA-AAGAAG-GAAA
1 AAAGAAAGAAAGGAAGGAGAGGAAAGAAAAGGAAAGGAGAAGAGAAA
* * * * * * **
448807 GAA-AAGGAAAGG-AGAAGA-GAAAAAAGAAAGAAAGGA-AGGAGAGG
1 AAAGAAAGAAAGGAAGGAGAGGAAAGAA-AAGGAAAGGAGAAGAGAAA
448851 AAAGAAAGAAA--AA-GA-AGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAAGAAAGAAAGGAAGGAGAGGAAAGAAAAGGAAAGGAGAAGAGAAA
448894 AAAGAAAGAAAGGAAGGAGAGGAAAGAAA
1 AAAGAAAGAAAGGAAGGAGAGGAAAGAAA
448923 GAAAAAGAAG
Statistics
Matches: 125, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
40 4 0.03
41 6 0.05
42 20 0.16
43 46 0.37
44 11 0.09
45 14 0.11
46 7 0.06
47 17 0.14
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (47 bp):
AAAGAAAGAAAGGAAGGAGAGGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:448947 original size:18 final size:18
Alignment explanation
Indices: 448685--448947 Score: 129
Period size: 18 Copynumber: 14.3 Consensus size: 18
448675 AGAAGGAGAG
448685 GGAAAGAAGGAAAG-AAA
1 GGAAAGAAGGAAAGAAAA
* *
448702 -GAAAGAAAGG-AAGGAGA
1 GGAAAG-AAGGAAAGAAAA
*
448719 GGAAAGAAAGAAA-AAGAA
1 GGAAAGAAGGAAAGAA-AA
*
448737 GGAAAGAAAAGGAAAGGAGAA
1 GGAAAG--AAGGAAA-GAAAA
*
448758 GAGAAA-AAAGAAAG-AAA
1 G-GAAAGAAGGAAAGAAAA
*
448775 GGAAGGAGAGGAAAG-AAA
1 GGAAAGA-AGGAAAGAAAA
*
448793 GAAAAAGAAGGAAAGAAAA
1 G-GAAAGAAGGAAAGAAAA
*
448812 GGAAAGGA-GAAGAGAAAAA
1 GGAAAGAAGGAA-AG-AAAA
* * *
448831 AGAAAGAAAGG-AAGGAGA
1 GGAAAG-AAGGAAAGAAAA
*
448849 GGAAAGAAAGAAA-AAGAA
1 GGAAAGAAGGAAAGAA-AA
*
448867 GGAAAGAAAAGGAAAGGAGAA
1 GGAAAG--AAGGAAA-GAAAA
*
448888 GAGAAA-AAAGAAAG-AAA
1 G-GAAAGAAGGAAAGAAAA
*
448905 GGAAGGAGAGGAAAG-AAA
1 GGAAAGA-AGGAAAGAAAA
*
448923 GAAAAAGAAGGAAAGAAAA
1 G-GAAAGAAGGAAAGAAAA
448942 GGAAAG
1 GGAAAG
448948 GAGAAGAGAA
Statistics
Matches: 186, Mismatches: 31, Indels: 57
0.68 0.11 0.21
Matches are distributed among these distances:
16 14 0.08
17 25 0.13
18 77 0.41
19 39 0.21
20 14 0.08
21 7 0.04
22 10 0.05
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GGAAAGAAGGAAAGAAAA
Found at i:449716 original size:27 final size:27
Alignment explanation
Indices: 449686--449741 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
449676 AAAGAGGGTG
* *
449686 ATGGAGGGGAATAAAAAAGCGGCATCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
*
449713 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
449740 AT
1 AT
449742 ATGTGGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.32, T:0.11
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAAGCGGCACCA
Found at i:456466 original size:3 final size:3
Alignment explanation
Indices: 456458--456563 Score: 94
Period size: 3 Copynumber: 35.7 Consensus size: 3
456448 TATTAATACT
* * *
456458 AAC AAC AAC AAC AAC AAC AAC AAC AAC TAA- AAC TAT AAC AAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC AAC AAC
* * * *
456503 ATA- ATC AAC AAT ATA- AAC AA- TAT AAC AAC AAC AAC AAC AAC AAC
1 A-AC AAC AAC AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
456547 AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AA
456564 TAATAATAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.05
3 77 0.91
4 4 0.05
ACGTcount: A:0.65, C:0.25, G:0.00, T:0.09
Consensus pattern (3 bp):
AAC
Found at i:456715 original size:10 final size:11
Alignment explanation
Indices: 456698--456726 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
456688 TAAAAATTAC
456698 CTTCTTTTTCT
1 CTTCTTTTTCT
456709 C-TCTTTTTCT
1 CTTCTTTTTCT
456719 CTTCTTTT
1 CTTCTTTT
456727 CCGCAGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:456856 original size:27 final size:27
Alignment explanation
Indices: 456826--456911 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
456816 CCAATCTGTA
*
456826 TGGCCCCATTGGTGTCGCCAATGGCTT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
*
456853 TGGCACCATTGGTGCCGCCAATGGCTT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
* * * * *
456880 TGGCGCCTTTGGTGCCGGCAATGCCAT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
456907 TGGCC
1 TGGCC
456912 TGATCAGACT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.12, C:0.30, G:0.31, T:0.27
Consensus pattern (27 bp):
TGGCCCCATTGGTGCCGCCAATGGCTT
Found at i:456996 original size:30 final size:27
Alignment explanation
Indices: 456958--457028 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
456948 CAGGTTTTTT
456958 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAAT-A-AAAAA-AA
*
456987 TTATAATATTTTGGTAAATAAAAAAAG
1 TTATAATATTTTGGTAAATAAAAAAAA
457014 TTATAATATTTTGGT
1 TTATAATATTTTGGT
457029 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 16 0.40
28 5 0.12
29 5 0.12
30 14 0.35
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
TTATAATATTTTGGTAAATAAAAAAAA
Found at i:459714 original size:20 final size:19
Alignment explanation
Indices: 459682--459735 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
459672 TCTCTCAACA
459682 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
* *
459702 CAAAAATTTAAAATCATTTT
1 -AAAAATTCAAAATAATTTT
*
459722 TAAAATTCAAAATA
1 AAAAATTCAAAATA
459736 TTTATGTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.39
20 10 0.36
21 7 0.25
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:463074 original size:30 final size:30
Alignment explanation
Indices: 463012--463100 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
463002 ATAGGTTGGC
* * * *
463012 ACATGGGCGTGTGTCCAGCCCGTGTGGCTT
1 ACATAGGCATGTGCCCAACCCGTGTGGCTT
* *
463042 ACATAGGCATGTGCCCAACCCTTGTGGGTT
1 ACATAGGCATGTGCCCAACCCGTGTGGCTT
* *
463072 ACATGGGCATGTGCCCAGCCCGTGTGGCT
1 ACATAGGCATGTGCCCAACCCGTGTGGCT
463101 CTTGAAATCT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (30 bp):
ACATAGGCATGTGCCCAACCCGTGTGGCTT
Found at i:463923 original size:11 final size:11
Alignment explanation
Indices: 463907--463932 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
463897 ATAATCAATA
463907 TTTTTTTATTT
1 TTTTTTTATTT
463918 TTTTTTTATTT
1 TTTTTTTATTT
463929 TTTT
1 TTTT
463933 AAGAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:464846 original size:6 final size:6
Alignment explanation
Indices: 464835--464941 Score: 144
Period size: 6 Copynumber: 17.8 Consensus size: 6
464825 AGAAACAACC
464835 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
* * * * *
464883 TAAAAA TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAAA -AAAGAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA-AA
*
464931 AAAAAA TAAAA
1 TAAAAA TAAAA
464942 TCAATGATCC
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
5 3 0.03
6 90 0.94
7 3 0.03
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.15
Consensus pattern (6 bp):
TAAAAA
Found at i:466597 original size:15 final size:15
Alignment explanation
Indices: 466556--466683 Score: 64
Period size: 15 Copynumber: 8.9 Consensus size: 15
466546 ATAGTTAAAT
*
466556 AACATAACAATAATAA
1 AACATAATAATAAT-A
466572 GAACA-AA-AATAATA
1 -AACATAATAATAATA
466586 AACATAATAATAA-A
1 AACATAATAATAATA
*
466600 AACA-AAT-AGAA-A
1 AACATAATAATAATA
*
466612 GA-ATAATAATAA-A
1 AACATAATAATAATA
* *
466625 ACAAATGATAATAAATA
1 A-ACATAATAAT-AATA
466642 AA-ATAATAAATAATAA
1 AACATAAT-AATAAT-A
466658 AACA-AATAATAATTA
1 AACATAATAATAA-TA
466673 AA-ATAA-AATAA
1 AACATAATAATAA
466684 AAATAAAGAG
Statistics
Matches: 92, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.01
12 8 0.09
13 11 0.12
14 15 0.16
15 35 0.38
16 15 0.16
17 7 0.08
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.20
Consensus pattern (15 bp):
AACATAATAATAATA
Found at i:466641 original size:34 final size:34
Alignment explanation
Indices: 466594--466689 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 34
466584 TAAACATAAT
* *
466594 AATAAAAACAAATAGAAAGAAT-AATAATAAAACA
1 AATAATAATAAATA-AAAGAATAAATAATAAAACA
* *
466628 AATGATAATAAATAAAATAATAAATAATAAAACA
1 AATAATAATAAATAAAAGAATAAATAATAAAACA
*
466662 AATAATAATTAAAATAAAATAA-AAATAA
1 AATAATAA-T-AAATAAAAGAATAAATAA
466690 AGAGCACGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.11
34 30 0.56
35 7 0.13
36 11 0.20
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (34 bp):
AATAATAATAAATAAAAGAATAAATAATAAAACA
Found at i:466643 original size:19 final size:17
Alignment explanation
Indices: 466614--466690 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 17
466604 AATAGAAAGA
466614 ATAATAATAAAACAAAT
1 ATAATAATAAAACAAAT
*
466631 GATAATAAATAAAA-TAAT
1 -ATAAT-AATAAAACAAAT
466649 A-AATAATAAAAC-AA-
1 ATAATAATAAAACAAAT
*
466663 ATAATAATTAAAATAAA-
1 ATAATAA-TAAAACAAAT
*
466680 ATAAAAATAAA
1 ATAATAATAAA
466691 GAGCACGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
14 1 0.02
15 14 0.27
16 12 0.24
17 9 0.18
18 8 0.16
19 7 0.14
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (17 bp):
ATAATAATAAAACAAAT
Found at i:466647 original size:12 final size:12
Alignment explanation
Indices: 466577--466690 Score: 65
Period size: 12 Copynumber: 9.2 Consensus size: 12
466567 AATAAGAACA
*
466577 AAAATAATAAAC
1 AAAATAATAAAT
* *
466589 ATAATAATAAAA
1 AAAATAATAAAT
* *
466601 ACAAAT-AGAAAG
1 A-AAATAATAAAT
*
466613 AATAATAATAAAAC
1 AA-AATAAT-AAAT
466627 AAATGATAATAAAT
1 AAA--ATAATAAAT
466641 AAAATAATAAAT
1 AAAATAATAAAT
*
466653 AATAA-AACAAAT
1 AA-AATAATAAAT
*
466665 AATAATTA-AAAT
1 AA-AATAATAAAT
466677 AAAATAA-AAAT
1 AAAATAATAAAT
466688 AAA
1 AAA
466691 GAGCACGGGT
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
11 12 0.14
12 47 0.57
13 8 0.10
14 11 0.13
15 5 0.06
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:470492 original size:5 final size:5
Alignment explanation
Indices: 470484--470525 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
470474 AACTAAAAAC
470484 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
470526 ATGGCTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:475756 original size:12 final size:13
Alignment explanation
Indices: 475741--475773 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
475731 TTTGAAATAT
475741 TTTTATTTTTC-A
1 TTTTATTTTTCTA
475753 TTTTATTTTTCTA
1 TTTTATTTTTCTA
*
475766 TTTAATTT
1 TTTTATTT
475774 CTAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:485541 original size:18 final size:21
Alignment explanation
Indices: 485518--485555 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
485508 TGGGAGTAAA
485518 TTTAGG-TTT-TA-TTAAATT
1 TTTAGGATTTGTAGTTAAATT
485536 TTTAGGATTTGTAGTTAAAT
1 TTTAGGATTTGTAGTTAAAT
485556 CATGGGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 2 0.12
21 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTAGGATTTGTAGTTAAATT
Found at i:494308 original size:27 final size:27
Alignment explanation
Indices: 494266--494518 Score: 321
Period size: 27 Copynumber: 9.4 Consensus size: 27
494256 CCCTAAAATA
*
494266 GGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
*
494293 GGTAAAATAACCGAAATATCCCC-ATAG
1 GGTAAAATGACCGAAATA-CCCCTATAG
** * *
494320 GGTAAAATGACTAAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
494347 GGTAAAATGAACAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* * *
494374 GGTAAAATGATCGAAGTACCCCTATAT
1 GGTAAAATGACCGAAATACCCCTATAG
*
494401 GGTAAAATGACCTAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
494428 GATAAAATGACCGAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
494455 GGTAAAATGACCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCTATAG
*
494482 GGTAAAATGATCGAAATACCCC-ATAG
1 GGTAAAATGACCGAAATACCCCTATAG
*
494508 GGTAAGATGAC
1 GGTAAAATGAC
494519 TATTATACCC
Statistics
Matches: 195, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
26 16 0.08
27 175 0.90
28 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCTATAG
Found at i:501597 original size:59 final size:59
Alignment explanation
Indices: 501534--501683 Score: 194
Period size: 59 Copynumber: 2.5 Consensus size: 59
501524 GCCAGAAACA
* * *
501534 CATCCTTTTCTTTCAATACTCGCCATAAAGGCTTTCCATTAAAAAATTTTCTATAAAGG
1 CATCCTTTTCTTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
* * * *
501593 CATCCTTTTCATTT-AGTACTCGCCACAAAGGCTTTCCTTTTAGAGATTTTCAATAAAGG
1 CATCCTTTTC-TTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
* * *
501652 AATCATTTTCTTTCAGTACTCGACACAAAGGC
1 CATCCTTTTCTTTCAGTACTCGCCACAAAGGC
501684 ATCCTTCGTC
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 3 0.04
59 73 0.92
60 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (59 bp):
CATCCTTTTCTTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
Found at i:505532 original size:19 final size:21
Alignment explanation
Indices: 505508--505550 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
505498 GCACCTAGGA
505508 TGATTGT-TTTGA-CATGTTT
1 TGATTGTATTTGATCATGTTT
*
505527 TGATTGTATTTGATCGTGTTT
1 TGATTGTATTTGATCATGTTT
505548 TGA
1 TGA
505551 ACTGGTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (21 bp):
TGATTGTATTTGATCATGTTT
Found at i:527860 original size:24 final size:25
Alignment explanation
Indices: 527824--527871 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
527814 TTTCTTTCCA
527824 TTTTCTTTCTATT-TCTTTATTATG
1 TTTTCTTTCTATTATCTTTATTATG
527848 TTTTCATTT-TATTATCTTTATTAT
1 TTTTC-TTTCTATTATCTTTATTAT
527872 TATCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTCTTTCTATTATCTTTATTATG
Found at i:527873 original size:12 final size:12
Alignment explanation
Indices: 527851--527885 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
527841 TATTATGTTT
527851 TCATT-TTATTA
1 TCATTATTATTA
*
527862 TCTTTATTATTA
1 TCATTATTATTA
527874 TCATTATTATTA
1 TCATTATTATTA
527886 AAGTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (12 bp):
TCATTATTATTA
Found at i:544173 original size:20 final size:20
Alignment explanation
Indices: 544144--544187 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
544134 ATTAGAATTT
*
544144 AAAA-ATTAAATTAAAAACA
1 AAAATATTAAAATAAAAACA
*
544163 AAAATATTAAAATAAAAAGA
1 AAAATATTAAAATAAAAACA
544183 AAAAT
1 AAAAT
544188 GGCTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:549636 original size:50 final size:49
Alignment explanation
Indices: 549526--549640 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 49
549516 GCAAACACAC
* * *
549526 CATAGCTCGTATGAGCTTACCAATTTTAGCTTGTGAGAGCTTACCAATT
1 CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
* * *
549575 C-TCAACTCGTATGAGCTTACCGATTTCCAGCTCGTGAGAGCATACCGATT
1 CAT-AGCTCGTATGAGCTTACCAATTT-CAGCTCGTGAGAGCATACCAATT
549625 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
549641 ATACATGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
48 1 0.02
49 22 0.39
50 32 0.57
51 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (49 bp):
CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
Found at i:549644 original size:25 final size:24
Alignment explanation
Indices: 549528--549640 Score: 104
Period size: 25 Copynumber: 4.6 Consensus size: 24
549518 AAACACACCA
*
549528 TAGCTCGTATGAGCTTACCAATTT
1 TAGCTCGTATGAGCTTACCAATTC
*
549552 TAGCTTGTGA-GAGCTTACCAATTC
1 TAGCTCGT-ATGAGCTTACCAATTC
* *
549576 TCAACTCGTATGAGCTTACCGATTTC
1 T-AGCTCGTATGAGCTTACC-AATTC
* * *
549602 CAGCTCGTGA-GAGCATACCGATTC
1 TAGCTCGT-ATGAGCTTACCAATTC
549626 ATAGCTCGTATGAGC
1 -TAGCTCGTATGAGC
549641 ATACATGTAC
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
24 26 0.37
25 40 0.56
26 5 0.07
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (24 bp):
TAGCTCGTATGAGCTTACCAATTC
Found at i:552364 original size:18 final size:18
Alignment explanation
Indices: 552336--552370 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
552326 ATATATTAAT
552336 AAATAAATTATT-TAGTA
1 AAATAAATTATTATAGTA
552353 AAATATAATTATTATAGT
1 AAATA-AATTATTATAGT
552371 TGCAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATAAATTATTATAGTA
Found at i:558065 original size:25 final size:25
Alignment explanation
Indices: 557998--558067 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
557988 GAGGATACTC
*
557998 CACAGCTTGTGTGAGCACACCGATT
1 CACAGCTTGTGTGAGCATACCGATT
* *
558023 CACAGCTCGTGTGAGCATATCGATT
1 CACAGCTTGTGTGAGCATACCGATT
*
558048 CATAGCTTGTGTGAGCATAC
1 CACAGCTTGTGTGAGCATAC
558068 ATGTACAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
CACAGCTTGTGTGAGCATACCGATT
Found at i:566694 original size:41 final size:41
Alignment explanation
Indices: 566572--566702 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
566562 TACCTAATAA
* *
566572 AATACACC-GACACGAAGCTTGCTAGGCTCAAAGCTTGATAT
1 AATACACCAG-CACGAAGCTTGCTAGGCACAAAGCCTGATAT
* * * *
566613 AACACACCAGCACGAAGCCTGCTTGG-ATAAAGCCTGATAT
1 AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
***
566653 AATACATTGGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
1 AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
566694 AATACACCA
1 AATACACCA
566703 CAACATCACG
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
40 31 0.43
41 40 0.56
42 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (41 bp):
AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
Found at i:568177 original size:29 final size:29
Alignment explanation
Indices: 568144--568342 Score: 220
Period size: 29 Copynumber: 6.8 Consensus size: 29
568134 ATCAAATAAA
*
568144 GAAAAGGGAAGGTTTCGACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
*
568173 GAAAAGGGATGGCTTCGACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
** ** *
568202 GAGTAGGGATGACTTCGACCAACGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
** *
568231 GAAAAGGGATGACTTCAACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
*
568260 GAAAAGGGATGACTTT-GACCATCGAATAT
1 GAAAAGGGATG-GTTTCGACCATCGAATAT
* * * *
568289 GAAAATGGATGGTTTCAACCATCGATTAAA
1 GAAAAGGGATGGTTTCGACCATCGAAT-AT
* *
568319 GAGAAGGGATGGTTTCGACTATCG
1 GAAAAGGGATGGTTTCGACCATCG
568343 TTTAGCACAC
Statistics
Matches: 145, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
28 3 0.02
29 119 0.82
30 23 0.16
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (29 bp):
GAAAAGGGATGGTTTCGACCATCGAATAT
Found at i:571725 original size:40 final size:40
Alignment explanation
Indices: 571681--571816 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
571671 TTATTTATAA
* * ** * *
571681 TAGATTCAGTTGGTATGGCTTGAGGGCACATACGTTTTAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
571721 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
* ** *
571761 TAGATTCAGTAGGTATGGATCGAAAGTGCATACGTTTCAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
*
571801 TAGATTCGGTAGGTAT
1 TAGATTCAGTAGGTAT
571817 CACTCGATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (40 bp):
TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
Found at i:573861 original size:45 final size:44
Alignment explanation
Indices: 573766--573973 Score: 141
Period size: 45 Copynumber: 4.6 Consensus size: 44
573756 ATGTCATGGT
* * ** **
573766 GTCTTTCAACCATTGTCTTATTCATTTCCTGTCATGTTGCCATAGC
1 GTCTTTCAACTATGGTCTTATTCATTTGAT-TCATG-ACCCATAGC
*
573812 GTCTTTCAACTATGGTCTTATTCATTTGATTCATGACGTCATAGC
1 GTCTTTCAACTATGGTCTTATTCATTTGATTCATGAC-CCATAGC
* * * * * *
573857 GTCTTTCAGCTATGGTCTTACTCGA-TAGAATCGTGATCCCATAAC
1 GTCTTTCAACTATGGTCTTATTC-ATTTGATTCATGA-CCCATAGC
* * * * * * * *
573902 GTCTTTCAACTATGGTCTCACTCGTTTCTAGTC-TGGTCTCATAGT
1 GTCTTTCAACTATGGTCTTATTCATTT-GATTCAT-GACCCATAGC
*
573947 GTCTTTCAACTATGGTCTTATTTATTT
1 GTCTTTCAACTATGGTCTTATTCATTT
573974 TCGATATAGT
Statistics
Matches: 128, Mismatches: 28, Indels: 13
0.76 0.17 0.08
Matches are distributed among these distances:
45 96 0.75
46 32 0.25
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (44 bp):
GTCTTTCAACTATGGTCTTATTCATTTGATTCATGACCCATAGC
Found at i:573962 original size:24 final size:24
Alignment explanation
Indices: 573935--574007 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
573925 GTTTCTAGTC
*
573935 TGGTCTCATAGTGTCTTTCAACTA
1 TGGTCTCATAATGTCTTTCAACTA
* * * *
573959 TGGTCTTAT-TTAT-TTTCGA-TA
1 TGGTCTCATAATGTCTTTCAACTA
* *
573980 TAGTGTCATAATGTCTTTCAACTA
1 TGGTCTCATAATGTCTTTCAACTA
574004 TGGT
1 TGGT
574008 TTTAATCATT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 8 0.23
22 7 0.20
23 7 0.20
24 13 0.37
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (24 bp):
TGGTCTCATAATGTCTTTCAACTA
Found at i:579468 original size:41 final size:41
Alignment explanation
Indices: 579407--579533 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 41
579397 TTACAACTTA
* * *
579407 CCTGATACAACACACTGGCACGAAGCCTGATAAGCTCAAAG
1 CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
* * *
579448 CTTGATATAACACACAGGCACGAAGCCTGCTAGGCACAAAG
1 CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
* ** * * *
579489 CCTGATATAATAGTTCA-GCATGAAGCCTGCTAGGCACAAAG
1 CCTGATATAACA-CACAGGCACGAAGCCTGATAAGCACAAAG
579530 CCTG
1 CCTG
579534 CTATGCACAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 72 0.97
42 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (41 bp):
CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
Found at i:579532 original size:16 final size:16
Alignment explanation
Indices: 579511--579548 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
579501 GTTCAGCATG
579511 AAGCCTGCTAGGCACA
1 AAGCCTGCTAGGCACA
*
579527 AAGCCTGCTATGCACA
1 AAGCCTGCTAGGCACA
579543 AAGCCT
1 AAGCCT
579549 AATATACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (16 bp):
AAGCCTGCTAGGCACA
Found at i:579842 original size:45 final size:45
Alignment explanation
Indices: 579782--579943 Score: 161
Period size: 45 Copynumber: 3.6 Consensus size: 45
579772 TTGTCACAGT
* * * * *
579782 GTCTTTCAACTATGGTCTTATTC-ATTTGATTTGTTATGCTATAGC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCATA-C
* *
579827 GTCTTTCAGCTATGGTCTTACTCGA-TAGAATCGTAATGCCATTAC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCA-TAC
* * * *
579872 ATCTTTCAGCTATAGTCTTACTCGATAT-AATTGTGATGCCATAAC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCAT-AC
*
579917 GTCTTTCAGCTATGGTTTTACTC-ATTT
1 GTCTTTCAGCTATGGTCTTACTCGATTT
579944 CTGGTATGGT
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
44 4 0.04
45 89 0.93
46 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (45 bp):
GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCATAC
Found at i:579957 original size:45 final size:44
Alignment explanation
Indices: 579908--580033 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 44
579898 ATAATTGTGA
* * * * *
579908 TGCCATAACGTCTTTCAGCTATGGTTTTACTCATTTCTGGTATGG
1 TGCCATAA-GTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
* * *
579953 TGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTCCGGTATAG
1 TGCCATA-AGTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
*
579998 TGCCATAGATTCTTTCAACTATGGTCTTAATCATTT
1 TGCCATA-AGTCTTTCAACTATGGTCTTAATCATTT
580034 TCTTCAAGCC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (44 bp):
TGCCATAAGTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
Found at i:589299 original size:74 final size:74
Alignment explanation
Indices: 589154--589301 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
589144 CCATATAAGC
* * *
589154 ACTAATTAAATAGAAGTTTGAACCCCTTTAGACATAATAAATATTTTGTAATTTTTCATACCTAA
1 ACTAATCAAATAGAAGTTTAAACCCCTTTAGACATAATAAATATTTTCTAATTTTTCATACCTAA
589219 GTTAAAAAG
66 GTTAAAAAG
* *
589228 ACTAATCAAATAGAAGTTTAAACCCCTTTAGAC-TAAATAACTATTTTTCTAGTTTTTCATACCT
1 ACTAATCAAATAGAAGTTTAAACCCCTTTAGACAT-AATAAATA-TTTTCTAATTTTTCATACCT
*
589292 AAGTAAAAAA
64 AAGTTAAAAA
589302 AGGGTATCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 1 0.02
74 38 0.58
75 27 0.41
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (74 bp):
ACTAATCAAATAGAAGTTTAAACCCCTTTAGACATAATAAATATTTTCTAATTTTTCATACCTAA
GTTAAAAAG
Found at i:591772 original size:6 final size:6
Alignment explanation
Indices: 591758--591791 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
591748 AGGATTGCAA
*
591758 ATTTCC ATTTTC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
591792 TTAGAAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTCC
Found at i:599555 original size:13 final size:13
Alignment explanation
Indices: 599537--599576 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
599527 CATGAAAATT
*
599537 AAAAGAAAGGAAG
1 AAAAGAAAGAAAG
599550 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
* *
599563 CAAAGAGAGAAAG
1 AAAAGAAAGAAAG
599576 A
1 A
599577 GACGCACGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:600730 original size:43 final size:43
Alignment explanation
Indices: 600669--600754 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
600659 TATATGATTG
* *
600669 ATATTGGAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
*
600712 ATATTGAAATGGCAAAGATGAGAAACGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
600755 TGAAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (43 bp):
ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
Found at i:600763 original size:19 final size:19
Alignment explanation
Indices: 600727--600777 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
600717 GAAATGGCAA
*
600727 AGATGAGAAACG-AATATG
1 AGATGAGAAATGAAATATG
600745 AGATGAGAAATGAAATATG
1 AGATGAGAAATGAAATATG
*
600764 AAATGATGAAATGA
1 AGATGA-GAAATGA
600778 GATGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 7 0.24
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.20
Consensus pattern (19 bp):
AGATGAGAAATGAAATATG
Found at i:600772 original size:27 final size:27
Alignment explanation
Indices: 600742--600796 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
600732 AGAAACGAAT
*
600742 ATGAGATGAGAAATGAAA-TATGAAATG
1 ATGAAATGAGAAATGAAACT-TGAAATG
**
600769 ATGAAATGAGATGTGAAACTTGAAATG
1 ATGAAATGAGAAATGAAACTTGAAATG
600796 A
1 A
600797 ATTCAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (27 bp):
ATGAAATGAGAAATGAAACTTGAAATG
Found at i:600786 original size:20 final size:19
Alignment explanation
Indices: 600729--600777 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
600719 AATGGCAAAG
* *
600729 ATGAGAAACG-AATATGAG
1 ATGAGAAATGAAATATGAA
600747 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
600766 ATGATGAAATGA
1 ATGA-GAAATGA
600778 GATGTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 9 0.33
19 11 0.41
20 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.20
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:601292 original size:25 final size:22
Alignment explanation
Indices: 601260--601304 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 22
601250 TAGTTGAGGC
601260 AATGTTGGTATGGTAGCTTAGCAT
1 AATGTTGGTAT-GT-GCTTAGCAT
601284 AATGCTTGGTATGTGCTTAGC
1 AATG-TTGGTATGTGCTTAGC
601305 TTCAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
AATGTTGGTATGTGCTTAGCAT
Found at i:601694 original size:54 final size:54
Alignment explanation
Indices: 601619--601738 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 54
601609 CACACGCGGG
* * ***
601619 CGTGTGACCCAAGTCAGTGAGTTACACGA-GCTGAGACACGGGCTGGGACACGGC
1 CGTGTGTCCCAAGTCAGTGAGTTACA-GAGGCTGAGACACAGGCAAAGACACGGC
* * *
601673 CGTGTGTCTCAAGTCAGTGAGTTACATAGGCTGAGACATAGGCAAAGACACGGC
1 CGTGTGTCCCAAGTCAGTGAGTTACAGAGGCTGAGACACAGGCAAAGACACGGC
601727 CGTGTGTCCCAA
1 CGTGTGTCCCAA
601739 CTTCGAGAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (54 bp):
CGTGTGTCCCAAGTCAGTGAGTTACAGAGGCTGAGACACAGGCAAAGACACGGC
Found at i:611226 original size:34 final size:34
Alignment explanation
Indices: 611188--611252 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
611178 TTTAAGTCGT
611188 TTTCTACACCGCCAATAAAGAAATCAATAGATGA
1 TTTCTACACCGCCAATAAAGAAATCAATAGATGA
* *
611222 TTTCTGCACCGCCGATAAAGAAATCAATAGA
1 TTTCTACACCGCCAATAAAGAAATCAATAGA
611253 CCGGTGTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (34 bp):
TTTCTACACCGCCAATAAAGAAATCAATAGATGA
Found at i:613279 original size:42 final size:42
Alignment explanation
Indices: 613226--613316 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
613216 ATAGTTGAAA
* *
613226 GATAGAACGTTGTTTCTACAACAAATCCGAGAGTTGCAAAAT
1 GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
*
613268 GATAGACCGTTGTTTCTACAACAAATGCAAGAGTTGCAAAAT
1 GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
613310 GAT-GACC
1 GATAGACC
613317 CGAAGCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (42 bp):
GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
Found at i:616539 original size:28 final size:28
Alignment explanation
Indices: 616504--616634 Score: 127
Period size: 28 Copynumber: 4.7 Consensus size: 28
616494 CAGTAATAGT
616504 ACAGTGTGGGCCTTAGCCCAATACAGCA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
** * *
616532 ATGGTGTGGGCCTTATCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * **
616560 ACAATGTGGGCCTTAGCCCAAAACAATA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * * *
616588 ACAATGTGAGCCTTAGCCCAATAGAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * *
616616 ACAATATAGGCCTTAGCCC
1 ACAGTGTGGGCCTTAGCCC
616635 TAAACAATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGCA
Found at i:616576 original size:56 final size:56
Alignment explanation
Indices: 616508--616641 Score: 160
Period size: 56 Copynumber: 2.4 Consensus size: 56
616498 AATAGTACAG
* * *** * *
616508 TGTGGGCCTTAGCCCAATACAGCAATGGTGTGGGCCTTATCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
* *
616564 TGTGGGCCTTAGCCCAAAACAATAACAATGTGAGCCTTAGCCCAATAGAGTAACAA
1 TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
* * *
616620 TATAGGCCTTAGCCCTAAACAA
1 TGTGGGCCTTAGCCCAAAACAA
616642 TATCAGTACA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (56 bp):
TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
Found at i:616642 original size:56 final size:56
Alignment explanation
Indices: 616536--616643 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
616526 ACAGCAATGG
* * * *
616536 TGTGGGCCTTATCCCAATACAGTAACAATGTGGGCCTTAGCCCAAAACAATAACAA
1 TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATAACAA
* *
616592 TGTGAGCCTTAGCCCAATAGAGTAACAATATAGGCCTTAGCCCTAAACAATA
1 TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATA
616644 TCAGTACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (56 bp):
TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATAACAA
Found at i:616785 original size:26 final size:26
Alignment explanation
Indices: 616751--616830 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
616741 AACACACCAA
616751 TATCGCAGCAAAGCTGCCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAATAG
* *
616777 TATCACAGCAAAGCTGCCAATAACA-
1 TATCGCAGCAAAGCTGCCAATAATAG
* *
616802 TATCGCAGCAAAACTACCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAATAG
616828 TAT
1 TAT
616831 ACTGCCTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 21 0.45
26 26 0.55
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAATAATAG
Found at i:617220 original size:28 final size:27
Alignment explanation
Indices: 616976--617387 Score: 286
Period size: 27 Copynumber: 15.3 Consensus size: 27
616966 GGGTTATAAT
*
616976 AGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * *
617003 -GATCATTTTACCCTATGGTGGTAATTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
* * *
617030 GGTCATTTTACCCTATGAGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * * *
617057 -GATCATTTCACGCTTCGAGGGTATTTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
* * **
617084 GGTCATTTCA-CC-TTCAGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
*
617109 AGTCATTTTA-CCTTATGGGGGTAATTC
1 AGTCATTTTACCCTT-TGGGGGTATTTC
* * *
617136 GGTGATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
**
617163 -GATCATTTCT-CCCTTCAGGGGTATTTC
1 AG-TCATTT-TACCCTTTGGGGGTATTTC
* *
617190 AGTTATTTCACCCTTTGGGGGGTATTTC
1 AGTCATTTTACCCTTT-GGGGGTATTTC
* *** *
617218 AGTCATTTTACCCATCAAGGGTATTTT
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * * * *
617245 GGTCATTTTACCCTTCGAGGGAATTTT
1 AGTCATTTTACCCTTTGGGGGTATTTC
* ** *
617272 GGTCATTTTA-CCTTGTATGGGTATTTT
1 AGTCATTTTACCCTT-TGGGGGTATTTC
* * * *
617299 GGTTATTTTACCCTGTAGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
*
617326 AGTCATTTTATCCTTT-GGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* *
617352 -GATCATTTTACCCTTCGGGGGCATTTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
617379 AGTCATTTT
1 AGTCATTTT
617388 CCCACAAATC
Statistics
Matches: 313, Mismatches: 55, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
25 22 0.07
26 31 0.10
27 227 0.73
28 33 0.11
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (27 bp):
AGTCATTTTACCCTTTGGGGGTATTTC
Found at i:623868 original size:18 final size:18
Alignment explanation
Indices: 623828--623861 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
623818 CCATGAGGTC
623828 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGGGCCCACA
623846 TGCCCGTGT-GGCCCAC
1 TGCCCGTGTGGGCCCAC
623862 TTAGCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.41, G:0.32, T:0.18
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:625750 original size:43 final size:43
Alignment explanation
Indices: 625672--625821 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
625662 TGTCTCAAAC
* * *
625672 ATGGTCTTACATGGAAATCTCATATCAATGGCAATATTCCAACT
1 ATGGTCTTACA-CGAAATCTCATATCAATGCCAATATCCCAACT
* * * * *
625716 ATGGTCTTACACGAAGTCTCATATCGATGCCAATAGCCTAGCT
1 ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCAACT
* * *
625759 ATGGTCTTACAAGAAGTCTTATATCAATGCC-ATATCCCAGA-T
1 ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCA-ACT
*
625801 ATGGTCTTATACGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
625822 AATGCCAATG
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
42 24 0.28
43 52 0.60
44 11 0.13
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCAACT
Found at i:625837 original size:44 final size:44
Alignment explanation
Indices: 625783--625916 Score: 169
Period size: 48 Copynumber: 3.0 Consensus size: 44
625773 AGTCTTATAT
**
625783 CAATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATGC
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATGC
* * *
625827 CAATGGCATATCCCAGATATGGCCTTATACGGGATTTCAAATCGATGC
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTC-AA---ATGC
* *
625875 CGATGCCATATCCCAAATATGGTCTTATACGGGATCTCAAAT
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAAT
625917 CAATTCGGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
44 35 0.46
45 2 0.03
47 2 0.03
48 37 0.49
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (44 bp):
CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATGC
Found at i:632161 original size:42 final size:43
Alignment explanation
Indices: 632018--632165 Score: 199
Period size: 43 Copynumber: 3.4 Consensus size: 43
632008 TGTCCCAAAC
*
632018 ATGGTCTTACATGGAAATCTCATATCGATGCCAATATCCCAGCT
1 ATGGTCTTACA-CGAAATCTCATATCGATGCCAATATCCCAGCT
* *
632062 ATGGTCTTACACGAAGTCTCATATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
* * * *
632105 ATGGTCTTACACGAAATTTCATATCAATGAC-ATATCCCAGAT
1 ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
* *
632147 ATTGTCTTATACGAAATCT
1 ATGGTCTTACACGAAATCT
632166 TAAATCAATG
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 25 0.27
43 56 0.61
44 11 0.12
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
Found at i:632177 original size:85 final size:87
Alignment explanation
Indices: 632018--632177 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 87
632008 TGTCCCAAAC
* * * * *
632018 ATGGTCTTACATGGAAATCTCATATCGATGCCAATATCCCAGCTATGGTCTTACACGAAGTCTCA
1 ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
* *
632083 TATCGATGCCAATAGCCCAGCT
66 AATCAATGCCAATAGCCCAGCT
* * * *
632105 ATGGTCTTACA-CGAAATTTCATATCAATGAC-ATATCCCAGATATTGTCTTATACGAAATCTTA
1 ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
632168 AATCAATGCC
66 AATCAATGCC
632178 GATGCCATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
85 35 0.56
86 16 0.26
87 11 0.18
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (87 bp):
ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
AATCAATGCCAATAGCCCAGCT
Found at i:632206 original size:48 final size:48
Alignment explanation
Indices: 632135--632315 Score: 202
Period size: 48 Copynumber: 3.8 Consensus size: 48
632125 ATATCAATGA
* * * *
632135 CATATCCCAGATATTGTCTTATACGAAATCTTAAATCAATGCCGATGC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
* * * * **
632183 CATATCCTATATCTGGTCTTATAC-AGGATCTCAAATGGATGTTGATGC
1 CATATCCCAGATATGGTCTTATACGA-GATCTCAAATCGATGCCGATGC
* *
632231 CATATCCCAGATATGGTCTTATACGGGATCTCAAAACGATGCCGATGC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
** * *
632279 CATATTTCAGATATGGTCTTATATGGGATCTCAAATC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATC
632316 AATCCGGCAA
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 108 0.99
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (48 bp):
CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
Found at i:632250 original size:96 final size:96
Alignment explanation
Indices: 632135--632314 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
632125 ATATCAATGA
* * * * *
632135 CATATCCCAGATATTGTCTTATACGAAATCTTAAATCAATGCCGATGCCATATC-CTATATCTGG
1 CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTC-AGATATGG
632199 TCTTATACAGGATCTCAAATGGATGTTGATGC
65 TCTTATACAGGATCTCAAATGGATGTTGATGC
** * *
632231 CATATCCCAGATATGGTCTTATACGGGATCTCAAAACGATGCCGATGCCATATTTCAGATATGGT
1 CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTCAGATATGGT
**
632296 CTTATATGGGATCTCAAAT
66 CTTATACAGGATCTCAAAT
632315 CAATCCGGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 71 0.99
97 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (96 bp):
CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTCAGATATGGT
CTTATACAGGATCTCAAATGGATGTTGATGC
Found at i:632344 original size:30 final size:30
Alignment explanation
Indices: 632310--632404 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 30
632300 TATGGGATCT
*
632310 CAAATCAATCCGGCAATATATATACATATA
1 CAAATCAATTCGGCAATATATATACATATA
** * *
632340 CAAATCAATTCGAAAATGTATATATCTACATA
1 CAAATCAATTCGGCAATATATATA-C-ATATA
*
632372 TAAATCAATTCGGCAATATATAATACATATA
1 CAAATCAATTCGGCAATATAT-ATACATATA
632403 CA
1 CA
632405 TTTGAATTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
30 20 0.39
31 6 0.12
32 22 0.43
33 3 0.06
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATATATATACATATA
Found at i:641837 original size:9 final size:10
Alignment explanation
Indices: 641817--641845 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
641807 ATTGCGTGTT
641817 TGAATAGAAA
1 TGAATAGAAA
641827 TGAAT-GAAA
1 TGAATAGAAA
641836 TGAATAGAAA
1 TGAATAGAAA
641846 ATGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:642579 original size:24 final size:24
Alignment explanation
Indices: 642552--642600 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
642542 TGTTTCTATT
*
642552 AAAGAAGAGAAAACTTTCATTTTC
1 AAAGAAAAGAAAACTTTCATTTTC
* *
642576 AAAGAAAAGAGAATTTTCATTTTC
1 AAAGAAAAGAAAACTTTCATTTTC
642600 A
1 A
642601 CCCCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AAAGAAAAGAAAACTTTCATTTTC
Done.