Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold414
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: 2018024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:775775 original size:22 final size:19
Alignment explanation
Indices: 775748--775796 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
775738 GGCTGATGGG
775748 AAAGAAAAAAGAAAAGAAAA
1 AAAGAAAAAAG-AAAGAAAA
*
775768 GAGAAGAAAAAAGAGAGAAAA
1 -A-AAGAAAAAAGAAAGAAAA
775789 AAAGAAAA
1 AAAGAAAA
775797 TCCAAAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 8 0.31
22 10 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAGAAAGAAAA
Found at i:779646 original size:13 final size:13
Alignment explanation
Indices: 779628--779654 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
779618 ACAACATTCC
779628 TTGTATCGATACA
1 TTGTATCGATACA
779641 TTGTATCGATACA
1 TTGTATCGATACA
779654 T
1 T
779655 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:780121 original size:20 final size:21
Alignment explanation
Indices: 780096--780137 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
780086 AATCACCTCT
* *
780096 AGGTCGTGATCGGCA-CTCCC
1 AGGTCGTAACCGGCAGCTCCC
780116 AGGTCGTAACCGGCAGCTCCC
1 AGGTCGTAACCGGCAGCTCCC
780137 A
1 A
780138 CACCCACTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.17
Consensus pattern (21 bp):
AGGTCGTAACCGGCAGCTCCC
Found at i:782220 original size:19 final size:19
Alignment explanation
Indices: 782178--782248 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
782168 ACACACAGAA
* *
782178 GTATCGATACATTATGCTTT
1 GTATCGATACATGAT-CATT
782198 GTATCGATACATGATCATT
1 GTATCGATACATGATCATT
782217 GTATCGATACATGGA-CAATT
1 GTATCGATACAT-GATC-ATT
*
782237 GTATTGATACAT
1 GTATCGATACAT
782249 AAAACTGGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (19 bp):
GTATCGATACATGATCATT
Found at i:782313 original size:13 final size:13
Alignment explanation
Indices: 782295--782323 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
782285 GATACATAGG
782295 ACATTGTATCGAT
1 ACATTGTATCGAT
782308 ACATTGTATCGAT
1 ACATTGTATCGAT
782321 ACA
1 ACA
782324 GGATGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:782320 original size:33 final size:33
Alignment explanation
Indices: 782278--782346 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
782268 CTACCACTTT
*
782278 TTGTATCGATACA-TAGGACATTGTATCGATACA
1 TTGTATCGATACAGGAGGA-ATTGTATCGATACA
*
782311 TTGTATCGATACAGGATGAATTGTATCGATACA
1 TTGTATCGATACAGGAGGAATTGTATCGATACA
782344 TTG
1 TTG
782347 CTTGTAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACAGGAGGAATTGTATCGATACA
Found at i:783209 original size:67 final size:67
Alignment explanation
Indices: 783094--783299 Score: 218
Period size: 67 Copynumber: 3.1 Consensus size: 67
783084 CAATTAGAAA
* * * **
783094 AGACCAAGGTAGAACCTAAGTCGAAAAAGGTATTAACCAAGGCAAAATCGATAAAGTCAACTAAA
1 AGACAAAGGTAGAACCTAAGTCGAAAAAGGTATTGACCAGGGTGAAATCGATAAAGTCAACTAAA
783159 AG
66 AG
* * * * *
783161 AGACAAAGGTAAAACCTAAGTTGAAAAGGGTATTGACTAGGGTGAAATCGATAAAGTTAACTAAA
1 AGACAAAGGTAGAACCTAAGTCGAAAAAGGTATTGACCAGGGTGAAATCGATAAAGTCAACTAAA
783226 AG
66 AG
* * * * * * * *
783228 AGACAAGGGCAGAACCTAGGCCGAAAATGGTGTTGACCAGCGTGAAA-CTGAT-AAGACTAACTA
1 AGACAAAGGTAGAACCTAAGTCGAAAAAGGTATTGACCAGGGTGAAATC-GATAAAGTC-AACTA
783291 AAAG
64 AAAG
783295 AGACA
1 AGACA
783300 GGGATGAAAC
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
66 4 0.03
67 111 0.97
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.17
Consensus pattern (67 bp):
AGACAAAGGTAGAACCTAAGTCGAAAAAGGTATTGACCAGGGTGAAATCGATAAAGTCAACTAAA
AG
Found at i:783419 original size:80 final size:81
Alignment explanation
Indices: 783312--783524 Score: 254
Period size: 80 Copynumber: 2.6 Consensus size: 81
783302 GATGAAACCT
* *
783312 ATAAAGTCAATAAGTTAG-AGGGATTGGCCAGAGTGAAACCGATAAAGCCAACGAGGTAAGGGAT
1 ATAAAGTCAACAAGTTAGAAGGG-TTGGCCAGAGCGAAACCGATAAAGCCAACGAGGTAAGGGAT
*
783376 TGACTAGAGA-AAAACTG
65 TGACCAG-GACAAAACTG
* * * * * *
783393 ATAAA-TCAACAAGTTAGAAGGGTTGGCCA-AGACGAAACCGATAAAACAAACTAGTTAGGGGGT
1 ATAAAGTCAACAAGTTAGAAGGGTTGGCCAGAG-CGAAACCGATAAAGCCAACGAGGTAAGGGAT
783456 TGACCAGGACAAAACTG
65 TGACCAGGACAAAACTG
* * * *
783473 ATAAAGTCAACAAGTTAGAAGGGTTGGCTAGGGCAAAACTGATAAAGCCAAC
1 ATAAAGTCAACAAGTTAGAAGGGTTGGCCAGAGCGAAACCGATAAAGCCAAC
783525 ATGTTAGAAG
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
79 4 0.04
80 60 0.54
81 47 0.42
82 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (81 bp):
ATAAAGTCAACAAGTTAGAAGGGTTGGCCAGAGCGAAACCGATAAAGCCAACGAGGTAAGGGATT
GACCAGGACAAAACTG
Found at i:783436 original size:40 final size:41
Alignment explanation
Indices: 783369--783625 Score: 200
Period size: 41 Copynumber: 6.2 Consensus size: 41
783359 CCAACGAGGT
*
783369 AAGGGATTGACTAGAGA-AAAACTGATAAA-TCAACAAGTTAG
1 AAGGG-TTGACCA-AGACAAAACTGATAAAGTCAACAAGTTAG
* * * * *
783410 AAGGGTTGGCCAAGACGAAACCGATAAA-ACAAACTAGTTAG
1 AAGGGTTGACCAAGACAAAACTGATAAAGTC-AACAAGTTAG
* *
783451 -GGGGTTGACCAGGACAAAACTGATAAAGTCAACAAGTTAG
1 AAGGGTTGACCAAGACAAAACTGATAAAGTCAACAAGTTAG
* * * * * *
783491 AAGGGTTGGCTAGGGCAAAACTGATAAAGCCAACATGTTAG
1 AAGGGTTGACCAAGACAAAACTGATAAAGTCAACAAGTTAG
* * * * * * *
783532 AAGGGGTGATCAAGGCGAAACTGATAAAGCCAATAAGTTTAA
1 AAGGGTTGACCAAGACAAAACTGATAAAGTCAACAAG-TTAG
* * *
783574 AAGGGGTTGACTAAGGCAAAACAGATAAAGTCAACTAA-TTAG
1 AA-GGGTTGACCAAGACAAAACTGATAAAGTCAAC-AAGTTAG
*
783616 AGGGGTTGAC
1 AAGGGTTGAC
783626 ACCTACAAGT
Statistics
Matches: 172, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
39 3 0.02
40 47 0.27
41 86 0.50
42 9 0.05
43 25 0.15
44 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.18
Consensus pattern (41 bp):
AAGGGTTGACCAAGACAAAACTGATAAAGTCAACAAGTTAG
Found at i:783517 original size:81 final size:80
Alignment explanation
Indices: 783386--783626 Score: 238
Period size: 81 Copynumber: 3.0 Consensus size: 80
783376 TGACTAGAGA
* * * *
783386 AAAACTGATAAA-TCAACAAGTTAGAAGGGTTGGCCAAGACGAAACCGATAAAACAAACTAGTTA
1 AAAACTGATAAAGTCAACAAGTTAGAAGGGTTGGCTAAGGCAAAACAGATAAAAC-AACTAGTTA
*
783450 G-GGGGTTGACCAGGAC
65 GAGGGGTTGACAAGG-C
* * *
783466 AAAACTGATAAAGTCAACAAGTTAGAAGGGTTGGCTAGGGCAAAACTGATAAAGCCAAC-ATGTT
1 AAAACTGATAAAGTCAACAAGTTAGAAGGGTTGGCTAAGGCAAAACAGATAAA-ACAACTA-GTT
783530 AGAAGGGG-TGATCAAGGC
64 AG-AGGGGTTGA-CAAGGC
* * * * * * *
783548 GAAACTGATAAAGCCAATAAGTTTAAAAGGGGTTGACTAAGGCAAAACAGATAAAGTCAACTAAT
1 AAAACTGATAAAGTCAACAAG-TTAGAA-GGGTTGGCTAAGGCAAAACAGATAAA-ACAACTAGT
783613 TAGAGGGGTTGACA
63 TAGAGGGGTTGACA
783627 CCTACAAGTT
Statistics
Matches: 135, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
80 13 0.10
81 43 0.32
82 23 0.17
83 20 0.15
84 35 0.26
85 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (80 bp):
AAAACTGATAAAGTCAACAAGTTAGAAGGGTTGGCTAAGGCAAAACAGATAAAACAACTAGTTAG
AGGGGTTGACAAGGC
Found at i:783778 original size:40 final size:40
Alignment explanation
Indices: 783701--783788 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
783691 GTTAACCGGG
*
783701 ATGAAACCAATCAACCTAACAATTGAGAAGGTGGATCGAA
1 ATGAAACCAATCAACCTAACAATTGAGAAAGTGGATCGAA
* * *
783741 ATGAAACCAA-CAA-GTCAACAATTGAGAAAAGTTGATCGAG
1 ATGAAACCAATCAACCT-AACAATTGAG-AAAGTGGATCGAA
*
783781 ACGAAACC
1 ATGAAACC
783789 GATGAATCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.02
39 13 0.32
40 27 0.66
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (40 bp):
ATGAAACCAATCAACCTAACAATTGAGAAAGTGGATCGAA
Found at i:786181 original size:155 final size:153
Alignment explanation
Indices: 785985--786555 Score: 549
Period size: 155 Copynumber: 3.7 Consensus size: 153
785975 AATTCACACC
* * * * * **
785985 TTCGGCGTAAAAGTGGACCCAGTGACAACCTA-AAGCTCGATTTTAAAAAATTACAAAAATGTCC
1 TTCGGCATAAAAGTGAACTCGGTGACAACCTAGGA-CTCGATTTTAAAAAATTACAAAAATACCC
* * *
786049 CTAAAGGATACCTTTGACTTAAAGGTGCTCGATGCCTCTAAAAGACTTAAAAAGGATTATAAATG
65 CTAAAGGATACCTTCGACTTAAA-GTGCTCGATACC-CTAAAAGACTTAAAAAGGATTATAGATG
786114 GGATGAAACTATCCCAAATACCCACA
128 GGATGAAACTATCCCAAATACCCACA
* *
786140 TTGGGCATAAAAGTGAACTCGGTGACAACCTAGGACTCGATTTTAGAAAATTACAAAAATACCCC
1 TTCGGCATAAAAGTGAACTCGGTGACAACCTAGGACTCGATTTTAAAAAATTACAAAAATACCCC
* * * *
786205 TGAAGGATATCTTCGACTTAAAAGTGCTTGATATCCCTAAAGGACTTTAAAAA-GATTATAGATG
66 TAAAGGATACCTTCGACTT-AAAGTGCTCGATA-CCCTAAAAGAC-TTAAAAAGGATTATAGATG
* ** *
786269 GGATGAACCTATCCCAAATACTTACT
128 GGATGAAACTATCCCAAATACCCACA
* * * * * * * **
786295 TTTGGCATAAAAGTGGAC-CATGTGACAATCTAGGACTCGACTCTGAAAAATTATGAAAATACCC
1 TTCGGCATAAAAGTGAACTC-GGTGACAACCTAGGACTCGATTTTAAAAAATTACAAAAATACCC
** * * * *
786359 CTAGGGGATACCTTCAACTTAGAAGTG-TCTAATACCCCTAAAAGACTTTAAAAGGATCATAGAT
65 CTAAAGGATACCTTCGACTTA-AAGTGCTC-GATA-CCCTAAAAGACTTAAAAAGGATTATAGAT
** *
786423 GGGATG-AACATATCATAAATACCCACC
127 GGGATGAAAC-TATCCCAAATACCCACA
* ** * * * * * *
786450 TTCGGCATAAAAGTAAACTCGGTGACAACCTAGGACTTAACTCTGAAAAATTACGAAAATACTCG
1 TTCGGCATAAAAGTGAACTCGGTGACAACCTAGGACTCGATTTTAAAAAATTACAAAAATACCCC
* * *
786515 TAAAGGATACCTTCAACTTAGAAGTGCCCGATACCCCAAAA
66 TAAAGGATACCTTCGACTTA-AAGTGCTCGATACCCTAAAA
786556 AAGCTCAAAA
Statistics
Matches: 343, Mismatches: 62, Indels: 23
0.80 0.14 0.05
Matches are distributed among these distances:
154 18 0.05
155 310 0.90
156 15 0.04
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (153 bp):
TTCGGCATAAAAGTGAACTCGGTGACAACCTAGGACTCGATTTTAAAAAATTACAAAAATACCCC
TAAAGGATACCTTCGACTTAAAGTGCTCGATACCCTAAAAGACTTAAAAAGGATTATAGATGGGA
TGAAACTATCCCAAATACCCACA
Found at i:786803 original size:28 final size:30
Alignment explanation
Indices: 786772--786828 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
786762 TAAAATTAAG
786772 ATAATAATTTTTA-TTTAT-TTTT-TATTTA
1 ATAAT-ATTTTTATTTTATATTTTCTATTTA
*
786800 ATAATTTTTTTATTTTATATTTTCTATTT
1 ATAATATTTTTATTTTATATTTTCTATTT
786829 TCAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 10 0.40
29 4 0.16
30 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (30 bp):
ATAATATTTTTATTTTATATTTTCTATTTA
Found at i:786815 original size:23 final size:25
Alignment explanation
Indices: 786773--786821 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
786763 AAAATTAAGA
*
786773 TAATAATTTTTATTTATTTTTTATT
1 TAATAATTTTTATTTATTTTATATT
786798 TAATAA-TTTT-TTTATTTTATATT
1 TAATAATTTTTATTTATTTTATATT
786821 T
1 T
786822 TCTATTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
24 4 0.17
25 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TAATAATTTTTATTTATTTTATATT
Found at i:795106 original size:31 final size:30
Alignment explanation
Indices: 795066--795158 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
795056 GTCAAAAGGA
* *
795066 TGCAAAAAAATAAATTGCATAAATTAAAAT
1 TGCAAAAAAATAAAATGCATAAATTTAAAT
* *
795096 TGCAACAAAAATAAAATACACAAATTTAAAT
1 TGCAA-AAAAATAAAATGCATAAATTTAAAT
* * * *
795127 TACAATAAAAGTAAAGTGCATCAATTTAAAT
1 TGCAA-AAAAATAAAATGCATAAATTTAAAT
795158 T
1 T
795159 ACTTTTAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (30 bp):
TGCAAAAAAATAAAATGCATAAATTTAAAT
Found at i:797607 original size:28 final size:29
Alignment explanation
Indices: 797566--797624 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
797556 TTTCAAATAA
797566 TTTAAAGAAAAATACTACA-TTGAAAAAAT
1 TTTAAAGAAAAATACTA-AGTTGAAAAAAT
* *
797595 TTTAAA-AAGAATACTAAGTTGAAAATAT
1 TTTAAAGAAAAATACTAAGTTGAAAAAAT
797623 TT
1 TT
797625 ATACTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 20 0.74
29 6 0.22
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (29 bp):
TTTAAAGAAAAATACTAAGTTGAAAAAAT
Found at i:798774 original size:3 final size:3
Alignment explanation
Indices: 798766--798816 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
798756 TTACTATCTA
*
798766 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
798814 TAT
1 TAT
798817 ATAAAAGGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:799024 original size:19 final size:19
Alignment explanation
Indices: 798983--799025 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
798973 ATTCCTTATT
* * *
798983 AATATAATTTTTCTTAATT
1 AATATAATTTTTATAAATA
*
799002 AATATACTTTTTATAAATA
1 AATATAATTTTTATAAATA
799021 AATAT
1 AATAT
799026 TTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATAATTTTTATAAATA
Found at i:799858 original size:28 final size:31
Alignment explanation
Indices: 799808--799865 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 31
799798 AAATTTTAAA
*
799808 TTATTTAATTATATCATAATTATTAAAAATT
1 TTATTTAATTATATCATAATTATAAAAAATT
*
799839 TTATTTTATTAT-T-AT-ATTATAAAAAAT
1 TTATTTAATTATATCATAATTATAAAAAAT
799866 ATGAACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 2 0.08
30 1 0.04
31 11 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
TTATTTAATTATATCATAATTATAAAAAATT
Found at i:803026 original size:13 final size:13
Alignment explanation
Indices: 803008--803033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
802998 CAATTTTTTG
803008 TGTATCGATACAT
1 TGTATCGATACAT
803021 TGTATCGATACAT
1 TGTATCGATACAT
803034 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:807708 original size:15 final size:15
Alignment explanation
Indices: 807688--807718 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
807678 ATTTCGTTTG
*
807688 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
807703 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
807718 G
1 G
807719 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:809551 original size:21 final size:21
Alignment explanation
Indices: 809522--809566 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
809512 AAGTTTTCAT
*
809522 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
809542 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
809564 TTT
1 TTT
809567 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:811774 original size:13 final size:13
Alignment explanation
Indices: 811756--811781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
811746 TACAAGCTAA
811756 TGTATCGATACAT
1 TGTATCGATACAT
811769 TGTATCGATACAT
1 TGTATCGATACAT
811782 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:812708 original size:27 final size:27
Alignment explanation
Indices: 812678--812732 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
812668 ATCATCTTGC
812678 AGTTAACTTTGAATTGGTGATTATATT
1 AGTTAACTTTGAATTGGTGATTATATT
*
812705 AGTTAAGTTTGAATTGGTGATTATATT
1 AGTTAACTTTGAATTGGTGATTATATT
812732 A
1 A
812733 AATTGTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (27 bp):
AGTTAACTTTGAATTGGTGATTATATT
Found at i:817955 original size:21 final size:21
Alignment explanation
Indices: 817891--817955 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
817881 TTTTGAATTA
* *
817891 AATTTGAAATAAGATTTTAAT
1 AATTTGAAATAATATTTAAAT
* * **
817912 AATTTGTATTAAT-TTTACTT
1 AATTTGAAATAATATTTAAAT
*
817932 AATTTGAAATATTATTTAAAT
1 AATTTGAAATAATATTTAAAT
817953 AAT
1 AAT
817956 AAAATATAAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
AATTTGAAATAATATTTAAAT
Found at i:818040 original size:40 final size:39
Alignment explanation
Indices: 817962--818040 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 39
817952 TAATAAAATA
* *
817962 TAATTTTTAATTTAAATTTAATTATAAAAATAATTTTTT
1 TAATTTTTAATTTAAATTTAATAATAAAAATAACTTTTT
*
818001 TAATATTTTAATTT-ATTTTAAATAAT-AAAATAGACTTTTT
1 TAAT-TTTTAATTTAAATTT-AATAATAAAAATA-ACTTTTT
818041 AAAATTGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 14 0.41
40 20 0.59
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (39 bp):
TAATTTTTAATTTAAATTTAATAATAAAAATAACTTTTT
Found at i:820492 original size:22 final size:22
Alignment explanation
Indices: 820467--820513 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
820457 GTAATGTATA
*
820467 ATATGTGTATATATATGCATAT
1 ATATGTATATATATATGCATAT
*
820489 ATATGTATATATATATGCATGT
1 ATATGTATATATATATGCATAT
820511 ATA
1 ATA
820514 CACACACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (22 bp):
ATATGTATATATATATGCATAT
Found at i:822996 original size:23 final size:23
Alignment explanation
Indices: 822966--823014 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
822956 TTCTCTTTCG
822966 TTTTAGTTTTTTATGTGTCCAGA
1 TTTTAGTTTTTTATGTGTCCAGA
822989 TTTTAGTTTTTTATGTGTCCAGA
1 TTTTAGTTTTTTATGTGTCCAGA
823012 TTT
1 TTT
823015 CTGCAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTTAGTTTTTTATGTGTCCAGA
Found at i:825573 original size:50 final size:50
Alignment explanation
Indices: 825535--825726 Score: 280
Period size: 50 Copynumber: 3.8 Consensus size: 50
825525 ATTATTTTTT
* * *
825535 ACCAACTTTTGATAATAGAAAGAGGTGATCATAATTGTTGACGATTCTTC
1 ACCAACCTTTGACAATAGAAGGAGGTGATCATAATTGTTGACGATTCTTC
* *
825585 ACCAACCTTTGACAATAGAGGGAGGTGGTCATAATTGTTGACGATTCTTC
1 ACCAACCTTTGACAATAGAAGGAGGTGATCATAATTGTTGACGATTCTTC
* *
825635 ATCAACCTTTGACAATAGAAGGAGGTTG-TCATAATTGTTGACGATCCTTC
1 ACCAACCTTTGACAATAGAAGGAGG-TGATCATAATTGTTGACGATTCTTC
*
825685 ACCAACCTTTGACAATAGAGGGAGGTGA-CTATAATTGTTGAC
1 ACCAACCTTTGACAATAGAAGGAGGTGATC-ATAATTGTTGAC
825727 TCTAAGTATA
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
49 3 0.02
50 124 0.96
51 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (50 bp):
ACCAACCTTTGACAATAGAAGGAGGTGATCATAATTGTTGACGATTCTTC
Found at i:826806 original size:21 final size:20
Alignment explanation
Indices: 826782--826820 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
826772 GGTAAAAAAG
*
826782 GGCACAATAAGAAAGAGTGTT
1 GGCAAAATAA-AAAGAGTGTT
*
826803 GGCAAAATAAAAGGAGTG
1 GGCAAAATAAAAAGAGTG
826821 GAGAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (20 bp):
GGCAAAATAAAAAGAGTGTT
Found at i:830199 original size:50 final size:50
Alignment explanation
Indices: 830119--830278 Score: 230
Period size: 50 Copynumber: 3.2 Consensus size: 50
830109 AAGTTGTTAC
* * *
830119 AATTATTGACTATCTTTCACCAACCTTTGACAATAGAAGGAGGTGGTCAT
1 AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCAT
* * * **
830169 AATTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCAT
1 AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCAT
* *
830219 AATTATTGACGATCCTTCACCAACCTTTGACAATAGAGGGAGGTGGTCAT
1 AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCAT
830269 AATTGTTGAC
1 AATTGTTGAC
830279 TCTAAGTATA
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (50 bp):
AATTGTTGACGATCCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCAT
Found at i:832329 original size:10 final size:11
Alignment explanation
Indices: 832303--832340 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
832293 TTTTACAAAA
*
832303 AAATTAATAAT
1 AAATAAATAAT
832314 AAATAAATAA-
1 AAATAAATAAT
832324 AAATAAA-AAT
1 AAATAAATAAT
832334 AAATAAA
1 AAATAAA
832341 GGGTAAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 2 0.08
10 14 0.56
11 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:832334 original size:20 final size:21
Alignment explanation
Indices: 832301--832340 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
832291 GATTTTACAA
*
832301 AAAAATTAATAATAAATAAAT
1 AAAAATTAAAAATAAATAAAT
832322 AAAAA-TAAAAATAAATAAA
1 AAAAATTAAAAATAAATAAA
832341 GGGTAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATTAAAAATAAATAAAT
Found at i:832335 original size:16 final size:17
Alignment explanation
Indices: 832308--832340 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
832298 CAAAAAAATT
832308 AATAATAAATAAATAAA
1 AATAATAAATAAATAAA
832325 AATAA-AAATAAATAAA
1 AATAATAAATAAATAAA
832341 GGGTAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAATAAATAAATAAA
Found at i:835434 original size:154 final size:156
Alignment explanation
Indices: 835215--835502 Score: 411
Period size: 154 Copynumber: 1.9 Consensus size: 156
835205 GCAGATTTAA
* * * *
835215 CTTTAAATTAAATAAAAATTAAAAATAAATTCAATTTTTGGCTAATAAAATTTTAAGAATTAATT
1 CTTTAAATTAAATAAAAATTAAAAATAAATTCAAATTTTGGCCAATAAAATTTCAAGAATGAATT
* * * * * *
835280 GGTCATCTAATTAAAGTTATTTTAGAATTTCTTTGCAAAAAGTT-TAATCCATTTAAAACTCTAT
66 GATCATCCAATTAAAGTTATTTTAGAACTTCTTTACAAAAACTTCAAATCCATTTAAAACTCTAT
835344 CTCACCAAGCACACTAGCAAATCTAT
131 CTCACCAAGCACACTAGCAAATCTAT
835370 CTTTAAATTAAATAAAAA-TAAAAGAT-AATTCAAATTTTGGCCAATAAAATTTCAAGAATGAAT
1 CTTTAAATTAAATAAAAATTAAAA-ATAAATTCAAATTTTGGCCAATAAAATTTCAAGAATGAAT
* * * **
835433 TGATCGTCCAATTAAGGTTATTTTAGAACTTCTTTACAAAGACTTCAAATCTTTTTAAAACTCTA
65 TGATCATCCAATTAAAGTTATTTTAGAACTTCTTTACAAAAACTTCAAATCCATTTAAAACTCTA
835498 TCTCA
130 TCTCA
835503 ACAAACAGGC
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
154 75 0.65
155 41 0.35
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (156 bp):
CTTTAAATTAAATAAAAATTAAAAATAAATTCAAATTTTGGCCAATAAAATTTCAAGAATGAATT
GATCATCCAATTAAAGTTATTTTAGAACTTCTTTACAAAAACTTCAAATCCATTTAAAACTCTAT
CTCACCAAGCACACTAGCAAATCTAT
Found at i:836769 original size:34 final size:34
Alignment explanation
Indices: 836713--836930 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
836703 TATCTTGTTT
*
836713 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * * *
836746 TTATTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
836780 TTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
836814 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
836848 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* * *
836882 TTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
836916 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
836931 TGGTTTTTAC
Statistics
Matches: 159, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 15 0.09
34 143 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:836888 original size:102 final size:101
Alignment explanation
Indices: 836713--836930 Score: 355
Period size: 102 Copynumber: 2.1 Consensus size: 101
836703 TATCTTGTTT
** * * *
836713 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
836778 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
66 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
836814 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
836879 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCA
65 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
836916 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
836931 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 15 0.14
102 93 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCA
Found at i:837291 original size:19 final size:19
Alignment explanation
Indices: 837235--837297 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
837225 TGGTTGTCGA
**
837235 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
837254 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
837273 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
837292 GTTACT
1 GGTACT
837298 GTACCGTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:841419 original size:34 final size:34
Alignment explanation
Indices: 841362--841580 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
841352 AAGTGGGAGA
*
841362 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
841395 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
841429 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
841463 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
841497 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
841531 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
841565 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
841581 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:841502 original size:102 final size:101
Alignment explanation
Indices: 841362--841580 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
841352 AAGTGGGAGA
** * * *
841362 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
841427 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
841463 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
841528 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
841565 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
841581 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:844981 original size:40 final size:40
Alignment explanation
Indices: 844925--845005 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
844915 AATGTTTACG
844925 GGTCTAAACTCAAGTCATGGACATCTGAACATCTGTGACA
1 GGTCTAAACTCAAGTCATGGACATCTGAACATCTGTGACA
*
844965 GGTCTAAACTCGAGTCATGGACATCTGAACATCTGTGACA
1 GGTCTAAACTCAAGTCATGGACATCTGAACATCTGTGACA
845005 G
1 G
845006 AAGGGAAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (40 bp):
GGTCTAAACTCAAGTCATGGACATCTGAACATCTGTGACA
Found at i:845425 original size:19 final size:19
Alignment explanation
Indices: 845399--845437 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
845389 ATTCAATGAG
*
845399 ATGCTGG-ACATATTAAAA
1 ATGCTGGAACATAGTAAAA
845417 ATGCATGGAACATAGTAAAA
1 ATGC-TGGAACATAGTAAAA
845437 A
1 A
845438 AATGCATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (19 bp):
ATGCTGGAACATAGTAAAA
Found at i:846521 original size:28 final size:28
Alignment explanation
Indices: 846487--846973 Score: 596
Period size: 28 Copynumber: 17.4 Consensus size: 28
846477 CACCAACTTG
*
846487 TGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
846515 TGTGGGCTTCGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
846543 TGTGGGCTTT-CAAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
846571 TGTGGGCTTTGAAAGGATGCCGCTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
846599 CGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
846627 TGTGGGCTTTGAAAAGG-TGCCACT-ATCT
1 TGTGGGCTTTG-AAAGGATGCCACTGA-CT
* *
846655 TATGGGCTTCG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
846683 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
846711 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
846739 TATGGGCTTTAGAAA-GATGCCACTGACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
*
846767 TGTGGGCTTTG-AAGAGATGCCATTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
846795 TGTGGGCTTAGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
846823 GGTGGGCTTTGGAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
846851 CGTGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
846879 TGTGGGCTTT-AGAAGGATGCTACTGGCT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
* * *
846907 TGTGGGCTTTAAAATGATGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
846935 TGCGAGCTTTGAAAGAGGTGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
846964 TGTGGGCTTT
1 TGTGGGCTTT
846974 AAAAAGGGTC
Statistics
Matches: 398, Mismatches: 42, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.02
27 8 0.02
28 337 0.85
29 42 0.11
30 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:847272 original size:26 final size:26
Alignment explanation
Indices: 847234--847290 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
847224 TATAAAAATA
** * *
847234 ATGATGTTTAATGTTATTATGAATGC
1 ATGATGTGGAATGCTATCATGAATGC
**
847260 ATGATGTGGAATGCTATCATGGTTGC
1 ATGATGTGGAATGCTATCATGAATGC
847286 ATGAT
1 ATGAT
847291 ACAAAGTCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (26 bp):
ATGATGTGGAATGCTATCATGAATGC
Found at i:858379 original size:28 final size:27
Alignment explanation
Indices: 858298--858379 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
858288 TTTTGGAGAT
*
858298 AATAACGGGGTTGGAGTGTTCCCTCGA-A
1 AATAACGGGGTTGGAGT-AT-CCTCGATA
*
858326 AGTAACGGGGTTGGAGTA-CCTCCGATGA
1 AATAACGGGGTTGGAGTATCCT-CGAT-A
*
858354 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCTCGAT
858380 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
28 37 0.80
29 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCTCGATA
Found at i:858424 original size:52 final size:51
Alignment explanation
Indices: 858364--858531 Score: 183
Period size: 52 Copynumber: 3.3 Consensus size: 51
858354 AATAACGAGG
* * *
858364 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTA
1 TTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGGGA
* * * * * *
858416 TTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGGGA
*** * *
858468 TTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGG
1 TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGGGA
*
858519 TTTGAGTATCCCC
1 TTGGAGTATCCCC
858532 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 37 0.39
52 49 0.51
53 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGGGA
Found at i:858518 original size:51 final size:51
Alignment explanation
Indices: 858362--858695 Score: 212
Period size: 51 Copynumber: 6.4 Consensus size: 51
858352 GAAATAACGA
* *
858362 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
** * * * * *
858414 TATTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
858466 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
* * **** * *
858517 GGTTTGAGTATCCCC--TCA-GAAATAACGGGGTTAGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-G-GTATTTTGGA-AATAAAATCGG
* * *
858572 GGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTGGAAATAAAATCGG
* * * * *
858626 AGTTGGAATATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTGGAAATAAAATCGG
* *
858677 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
858696 GTGGAGAATT
Statistics
Matches: 213, Mismatches: 52, Indels: 35
0.71 0.17 0.12
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
51 75 0.35
52 51 0.24
53 26 0.12
54 22 0.10
55 16 0.08
56 6 0.03
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:858654 original size:211 final size:211
Alignment explanation
Indices: 858303--858695 Score: 571
Period size: 211 Copynumber: 1.9 Consensus size: 211
858293 GAGATAATAA
* * *
858303 CGGGGTTGGAGTGTTCCCTCGAAAGTAACGGGGTTGGAGTACCTCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTAGAGTACCTCCGATGAAATAACGAGGTTGG
* *
858368 AGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTATTGGAGTATCCCCGATT
66 AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTATTGGAATATCCCCGATT
* * *
858433 AAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
858498 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* * *
858514 CGGGGTTTGAGTATCCCCTCAGAAA-TAACGGGGTTAGAGTATCC-CCGATG-ATTAACGGGGTT
1 CGGGGTTGGAGTATCCCCTC-GAAAGTAACGGGGTTAGAGTA-CCTCCGATGAAATAACGAGGTT
* *
858576 GGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG-AGTTGGAATATCCC
64 GGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGTA-TTGGAATATCCC
* *
858640 CGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATT
126 CGATTAAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
858696 GTGGAGAATT
Statistics
Matches: 162, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
210 28 0.17
211 91 0.56
212 43 0.27
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCGAAAGTAACGGGGTTAGAGTACCTCCGATGAAATAACGAGGTTGG
AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTATTGGAATATCCCCGATT
AAAGGAAAATTAGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:861164 original size:13 final size:13
Alignment explanation
Indices: 861146--861170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
861136 AATACTTATG
861146 TATCGATACATTA
1 TATCGATACATTA
861159 TATCGATACATT
1 TATCGATACATT
861171 TGGATTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:861999 original size:55 final size:54
Alignment explanation
Indices: 861915--862749 Score: 974
Period size: 55 Copynumber: 15.0 Consensus size: 54
861905 ATAAAGTGTA
* * *
861915 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
861970 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
862025 TCCTGCTCTTTGA-G---G--A-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
862072 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
862127 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
862182 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGT------G
* * *
862243 TCCTGCTCTCTGAGGACTGGAACGTGCCACCAACTTGTGTGGGATTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
862298 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
862353 TCCTGCTCTTTAAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
862408 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
862467 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
862525 T-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCG
1 TCCT-GCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTG
*
862582 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * * *
862640 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTG
* * *
862697 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
862750 AAAAGGCATC
Statistics
Matches: 706, Mismatches: 40, Indels: 68
0.87 0.05 0.08
Matches are distributed among these distances:
47 41 0.06
48 3 0.00
49 1 0.00
51 1 0.00
52 1 0.00
54 37 0.05
55 303 0.43
56 16 0.02
57 68 0.10
58 119 0.17
59 66 0.09
60 2 0.00
61 48 0.07
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:862328 original size:171 final size:169
Alignment explanation
Indices: 861915--862775 Score: 1015
Period size: 171 Copynumber: 5.1 Consensus size: 169
861905 ATAAAGTGTA
* * *
861915 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
861979 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTT---GA--
65 TTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT
862038 GG---ATGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
128 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTAAGGCG
* *
862072 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTCGAAAG-GG-GTCCTGCTC
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTT-TAAAGAGGCGTCCTGCTC
* *
862135 TTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACT
64 TTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT
862200 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGCG
128 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT-AAGGCG
* * * *
862243 TCCTGCTCTCTGAGGACTGGAACGTGCCACCAACTTGTGTGGGATTT-AAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
* *
862307 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTAAGGACTG
65 TTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
*
862372 AAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
129 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTAAGGCG
* *
862408 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGC
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGCGTCCTGC
862473 TCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-GT-CTCGCTCTTT
62 TCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT-GCTCTTT
** **
862536 GAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-AAAAGGCG
121 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTAAGGCG
* *
862582 TCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-GTCCCGC
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGCGTCCTGC
* * *
862646 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCGTCCTGCTCTTTGAG
62 TCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT---GAAAGGTGTCCTGCTCTTTGAG
* * * *
862711 GACTGGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAGGCA
124 GACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG-TAAGGCG
862758 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
862776 AAAAAGCGGA
Statistics
Matches: 622, Mismatches: 40, Indels: 65
0.86 0.06 0.09
Matches are distributed among these distances:
157 105 0.17
158 5 0.01
160 2 0.00
162 2 0.00
164 26 0.04
165 49 0.08
166 3 0.00
168 27 0.04
169 24 0.04
170 5 0.01
171 175 0.28
172 39 0.06
173 78 0.13
174 59 0.09
176 23 0.04
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (169 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTT
TGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGA
AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTAAGGCG
Found at i:862554 original size:226 final size:226
Alignment explanation
Indices: 861915--862775 Score: 1106
Period size: 226 Copynumber: 3.8 Consensus size: 226
861905 ATAAAGTGTA
* * *
861915 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
861980 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTGCTCTTT---G
66 TGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGG
862037 A--GG--A-TGCCACCAACTTGTGTGGGCTTT--GAAAGGTGTCCTGCTCTTTGAGGACTGGAAA
130 ACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA
* *
862095 ATGCCACCAACTTGTGTGGGCTTCGAAAGGGG
195 ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
862127 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
** * ** *
862192 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGCGTCCTGCTCTCTGAG
66 TGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCTGCTCTTTGAG
* *
862257 GACTGGAACGTGCCACCAACTTGTGTGGGATTTAAG--AGGTGTCCTGCTCTTTGAGGACTGGAA
129 GACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGTGTCCTGCTCTTTGAGGACTGGAA
*
862320 AATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
194 AATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
862353 TCCTGCTCTTTAAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
862418 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGA
862483 CT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-GT-CTCGCTCTTTGAGGACT-G
131 CTGGAAAGTGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGTGTCCT-GCTCTTTGAGGACTGG
** *
862544 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGGCG
192 AAAATGCCACCAACTTGTGTGGGCTTT---GAAAGGCG
* *
862582 TCCCGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-GTCCCG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTG
862645 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-AAAAGGCGTCCTGCTCTTT
61 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTT
* * **
862708 GAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGG
126 GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT--AA-G-AAAGGTGTCCTGCTCTTTGAGG
862773 ACT
187 ACT
862776 AAAAAGCGGA
Statistics
Matches: 573, Mismatches: 41, Indels: 49
0.86 0.06 0.07
Matches are distributed among these distances:
212 92 0.16
213 1 0.00
215 2 0.00
218 14 0.02
221 2 0.00
223 28 0.05
224 26 0.05
225 29 0.05
226 176 0.31
227 16 0.03
228 30 0.05
229 23 0.04
230 25 0.04
231 33 0.06
232 54 0.09
233 20 0.03
234 2 0.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (226 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGA
CTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:863784 original size:20 final size:20
Alignment explanation
Indices: 863761--863799 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
863751 TTTTCTCTCC
* *
863761 TTTTCTTTTTTTGTTTTTTG
1 TTTTATTTTTTTCTTTTTTG
863781 TTTTATTTTTTTCTTTTTT
1 TTTTATTTTTTTCTTTTTT
863800 TTGGCGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (20 bp):
TTTTATTTTTTTCTTTTTTG
Found at i:876271 original size:28 final size:28
Alignment explanation
Indices: 876190--876271 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
876180 TTTTGGAGAT
*
876190 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-AT-CCTCGATGA
* * *
876218 AGTAACGGGGTTGGAGTACCCCCGATGA
1 AATAACGGGGTTGGAGTATCCTCGATGA
*
876246 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCTCGAT
876272 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.09
28 40 0.91
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCTCGATGA
Found at i:876410 original size:51 final size:51
Alignment explanation
Indices: 876254--876587 Score: 185
Period size: 51 Copynumber: 6.4 Consensus size: 51
876244 GAAATAACGA
* * * *
876254 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAATCGG
** * * * ** *
876306 TATTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAATCGG
*** *
876358 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
* **** * *
876409 GGTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-G-GTATTTTGGA-AATAAAATCGG
* * *
876464 GGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATT-G-GTATTTTGGAAATAAAATCGG
* * * * * *
876518 AGTTGGAATATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTGGTATTTTGGAAATAAAATCGG
* *
876569 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
876588 GTGGAGAATT
Statistics
Matches: 211, Mismatches: 54, Indels: 35
0.70 0.18 0.12
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
51 74 0.35
52 49 0.23
53 26 0.12
54 22 0.10
55 17 0.08
56 6 0.03
57 3 0.01
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAATCGG
Found at i:876469 original size:27 final size:28
Alignment explanation
Indices: 876406--876481 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
876396 GAAATAAAGT
*
876406 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
876434 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
876461 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
876482 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:876546 original size:211 final size:211
Alignment explanation
Indices: 876195--876587 Score: 558
Period size: 211 Copynumber: 1.9 Consensus size: 211
876185 GAGATAATAA
* * * *
876195 CGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTACCCCCGATGAAATAACGAGGTTGG
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTACCCCCGATGAAATAACGAGGTTGG
* * * *
876260 AGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCAGTATTGGAGTATCCCCGATT
66 AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAGGATTGGAATATCCCCGATT
* * * *
876325 AAAGGAAAATTGGTGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
131 AAAGGAAAATTAGTGTTTTAAAAATAAAACCAGAGTTGGAATATCCCCGATTATGAAAAATCAAT
876390 ATTTTGGAAATAAAGT
196 ATTTTGGAAATAAAGT
* * *
876406 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGG
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTACCCCCGATGAAATAACGAGGTTGG
* *
876470 AGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATC-GGAGTTGGAATATCCCCG
66 AGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCAGGA-TTGGAATATCCCCG
* * *
876534 ATTATA-GAAAATTAGTGTTTTGAAAATAAAATCAGAGTTGGAATATCCCCGATT
128 ATTAAAGGAAAATTAGTGTTTTAAAAATAAAACCAGAGTTGGAATATCCCCGATT
876588 GTGGAGAATT
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
210 28 0.18
211 96 0.60
212 35 0.22
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (211 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTACCCCCGATGAAATAACGAGGTTGG
AGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAGGATTGGAATATCCCCGATT
AAAGGAAAATTAGTGTTTTAAAAATAAAACCAGAGTTGGAATATCCCCGATTATGAAAAATCAAT
ATTTTGGAAATAAAGT
Found at i:878978 original size:13 final size:13
Alignment explanation
Indices: 878960--878985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
878950 ACAAAGATCC
878960 ATGTATCGATACA
1 ATGTATCGATACA
878973 ATGTATCGATACA
1 ATGTATCGATACA
878986 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:878981 original size:33 final size:33
Alignment explanation
Indices: 878939--879005 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
878929 AAAATTTCCA
***
878939 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
878972 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
879005 A
1 A
879006 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:879049 original size:19 final size:18
Alignment explanation
Indices: 879025--879092 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
879015 CAGTAGCTAA
879025 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
879044 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
879059 -T-TGTATCAATACAAAAC
1 TTATGTATCGATAC-AAAC
879076 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
879093 TTTTTAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:879071 original size:32 final size:32
Alignment explanation
Indices: 879028--879090 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
879018 TAGCTAATTA
* *
879028 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCAATACAAAACTTATGTATCGATACAT
879060 TGTATCAATACAAAACTTATGTATCGATACA
1 TGTATCAATACAAAACTTATGTATCGATACA
879091 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCAATACAAAACTTATGTATCGATACAT
Found at i:887249 original size:20 final size:20
Alignment explanation
Indices: 887224--887347 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
887214 TTTTAACTAG
887224 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
887244 ATGTATCGATACATTTGGGTAAAAAGACAGA
1 ATGTATCGATACA-TT--G-----A-A-A-A
* * *
887275 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
887295 ATGTATTGAT--ATTGTAAAA
1 ATGTATCGATACATTG-AAAA
*
887314 TTGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
887334 ATGTATCGATACAT
1 ATGTATCGATACAT
887348 CTAAGTAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
18 3 0.04
19 10 0.12
20 39 0.49
21 7 0.09
23 2 0.03
28 1 0.01
29 1 0.01
30 3 0.04
31 14 0.17
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:891396 original size:19 final size:19
Alignment explanation
Indices: 891372--891428 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
891362 CTTTGATTTT
891372 ATGAAAAAAAAAAGAAAAA
1 ATGAAAAAAAAAAGAAAAA
* *
891391 ATGAAAAAAATATA-TAAAA
1 ATGAAAAAAA-AAAGAAAAA
891410 ATGTAGAAAAAAAAAGAAA
1 ATG-A-AAAAAAAAAGAAA
891429 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 17 0.57
20 5 0.17
21 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (19 bp):
ATGAAAAAAAAAAGAAAAA
Found at i:891440 original size:30 final size:32
Alignment explanation
Indices: 891386--891453 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
891376 AAAAAAAAAG
*
891386 AAAAAATGAAAAAAATATATAAAAATGTAGAA
1 AAAAAAAGAAAAAAATATATAAAAATGTAGAA
* * *
891418 AAAAAAAGAAATAAA-ATA-AAAAATTTTGAA
1 AAAAAAAGAAAAAAATATATAAAAATGTAGAA
891448 AAAAAA
1 AAAAAA
891454 TTATTGCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 16 0.50
31 3 0.09
32 13 0.41
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (32 bp):
AAAAAAAGAAAAAAATATATAAAAATGTAGAA
Found at i:899768 original size:13 final size:13
Alignment explanation
Indices: 899750--899776 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
899740 ATTTTAGGCA
899750 TGTATCGATACAT
1 TGTATCGATACAT
899763 TGTATCGATACAT
1 TGTATCGATACAT
899776 T
1 T
899777 TACTATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:901428 original size:19 final size:19
Alignment explanation
Indices: 901404--901440 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
901394 TCAAAAACCT
* *
901404 AGAATGTATCGATACAATG
1 AGAATGTAACAATACAATG
901423 AGAATGTAACAATACAAT
1 AGAATGTAACAATACAAT
901441 TGTAAGCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (19 bp):
AGAATGTAACAATACAATG
Found at i:902285 original size:239 final size:237
Alignment explanation
Indices: 901858--902294 Score: 558
Period size: 239 Copynumber: 1.8 Consensus size: 237
901848 TAACACTAAC
* * * *
901858 AATTAATGTGACAATATATAATTTTTTATGAATATTTAATTTTTTTATATTATTATGACACGTCT
1 AATTAACGTGACAATATATAAATTTTTATGAATATATAATTTTTTTATATGATTATGACACGTCT
* * * * *
901923 TAAATTTACAATTTCTCCCTTTCAATTAATGCTCCAAGTTTGTCATTGACTACAAATAAAGCTAG
66 TAAATTTACAATTTCT-CATTTCAATAAATACTCCAAGTTTGTAATTGACTACAAATAAAACTAG
** * * * *
901988 AAGTCATTTGTTAACTTTTTTGGCTAGCAAGGAAACTAGAGAATGCTTAAAACACCTATTGTAGA
130 AAGTCATTTGTTAACTTTTTCAGCCAGCAAGGAAACCAAAAAATGCTTAAAACACCTATTGTAGA
902053 CACGTCTTAGGTTGTTAACCATTTTATAATTAAAGCATTTGGT
195 CACGTCTTAGGTTGTTAACCATTTTATAATTAAAGCATTTGGT
*
902096 AATTAACGTGACAATTTATAAATTTTTATGAATATATAATTCTTTTGT-TATGATTATGACACGT
1 AATTAACGTGACAATATATAAATTTTTATGAATATATAATT-TTTT-TATATGATTATGACACGT
* * * *
902160 CTTAAGTTTACCATTTACT-ATTTCAATAAATACTCCAAGTTT-TAATTGATTGCAAATAAAACT
64 CTTAAATTTACAATTT-CTCATTTCAATAAATACTCCAAGTTTGTAATTGACTACAAATAAAACT
** * **
902223 AGAAGAGTCATTTGTTAACTTTTTCAGCCAGTGAGGAAGCCAAAAAATGC-TATAGGCACCTATT
128 AG-A-AGTCATTTGTTAACTTTTTCAGCCAGCAAGGAAACCAAAAAATGCTTA-AAACACCTATT
902287 GTAGACAC
190 GTAGACAC
902295 AAGGTCGCTC
Statistics
Matches: 168, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
237 19 0.11
238 60 0.36
239 86 0.51
240 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (237 bp):
AATTAACGTGACAATATATAAATTTTTATGAATATATAATTTTTTTATATGATTATGACACGTCT
TAAATTTACAATTTCTCATTTCAATAAATACTCCAAGTTTGTAATTGACTACAAATAAAACTAGA
AGTCATTTGTTAACTTTTTCAGCCAGCAAGGAAACCAAAAAATGCTTAAAACACCTATTGTAGAC
ACGTCTTAGGTTGTTAACCATTTTATAATTAAAGCATTTGGT
Found at i:904546 original size:28 final size:27
Alignment explanation
Indices: 904460--904548 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 27
904450 GTAAACTTAT
* *
904460 AATTTTAAATTAAA-TTTTTTACATATA
1 AATTTTTAATTAAACTTTTGTACATA-A
* *
904487 GAATTTTTAATTGAACTTTTG--CATTCCA
1 -AATTTTTAATTAAACTTTTGTACA-T-AA
904515 AATTTTTAATTAAACTTTATGTACATAA
1 AATTTTTAATTAAACTTT-TGTACATAA
904543 AATTTT
1 AATTTT
904549 ACTTAAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
27 19 0.39
28 23 0.47
29 5 0.10
30 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.49
Consensus pattern (27 bp):
AATTTTTAATTAAACTTTTGTACATAA
Found at i:904912 original size:12 final size:11
Alignment explanation
Indices: 904897--904936 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
904887 ATAAAAAATG
*
904897 AAAACAAAAGA
1 AAAAAAAAAGA
904908 AAAAAAAAAGA
1 AAAAAAAAAGA
904919 AAAGAAAAAAGA
1 AAA-AAAAAAGA
*
904931 CAAAAA
1 AAAAAA
904937 GCTTTGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:904916 original size:16 final size:16
Alignment explanation
Indices: 904897--904928 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
904887 ATAAAAAATG
904897 AAAACAAAAGAAAAAA
1 AAAACAAAAGAAAAAA
*
904913 AAAAGAAAAGAAAAAA
1 AAAACAAAAGAAAAAA
904929 GACAAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAACAAAAGAAAAAA
Found at i:905278 original size:14 final size:14
Alignment explanation
Indices: 905261--905299 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
905251 TTATTTTATT
905261 TTAATTTATGTTAC
1 TTAATTTATGTTAC
* *
905275 TTAATTTTTGTTAT
1 TTAATTTATGTTAC
905289 TTAAATTTATG
1 TT-AATTTATG
905300 CCATGTACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (14 bp):
TTAATTTATGTTAC
Found at i:905752 original size:78 final size:75
Alignment explanation
Indices: 905567--905803 Score: 197
Period size: 78 Copynumber: 3.0 Consensus size: 75
905557 CCATCCGAAA
* * * * *
905567 TTAATTCTTTAGGATCATGTTAGTACTTTTATGTTAAAACTATCCTTTAGGACTATTTTGGAATA
1 TTAA-TCTTTAAGATCATGTTAG-AATTTCATGTTAAAACTAACCTTTAGG-CTATTTTGGAACA
905632 TTTATACCATTTC
63 TTTATACCATTTC
* * ** *
905645 TTAACCCTTAAGATCACATTAGAACTTTCATGTTAAAACTAAACCTTTAGGCTCATGTTGGAACA
1 TTAATCTTTAAGATCATGTTAGAA-TTTCATGTTAAAACT-AACCTTTAGGCT-ATTTTGGAACA
*
905710 TTTATACGATTT-
63 TTTATACCATTTC
* * * * * * *
905722 TCTAATCTTTACGATTATGTTAGCAATTTCATGTGAGAACTGAACTTTTAGGATAATTTTGAAAC
1 T-TAATCTTTAAGATCATGTTAG-AATTTCATGTTAAAACT-AACCTTTAGGCT-ATTTTGGAAC
* *
905787 ATTTATGCTATTTC
62 ATTTATACCATTTC
905801 TTA
1 TTA
905804 GCCTTTAGGG
Statistics
Matches: 126, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
76 1 0.01
77 30 0.24
78 92 0.73
79 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (75 bp):
TTAATCTTTAAGATCATGTTAGAATTTCATGTTAAAACTAACCTTTAGGCTATTTTGGAACATTT
ATACCATTTC
Found at i:911212 original size:26 final size:26
Alignment explanation
Indices: 911165--911235 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
911155 AAGAAGCTCA
* *
911165 TAAT-TTTTAAAAATATTATTAAAAT
1 TAATATTTAAAAAATATTTTTAAAAT
911190 TAATATTTAAAAAATATTTTTAAAAT
1 TAATATTTAAAAAATATTTTTAAAAT
* *
911216 TAAAATTAAATAAAATATTT
1 TAATATTTAA-AAAATATTT
911236 ATTATTCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 4 0.10
26 27 0.68
27 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATATTTAAAAAATATTTTTAAAAT
Found at i:912752 original size:28 final size:28
Alignment explanation
Indices: 912719--912772 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
912709 TATTTTAAGG
912719 TTTTATAAAATAAA-ATTATAATAAATTA
1 TTTTATAAAATAAATATT-TAATAAATTA
912747 TTTTATAAAATAAATATTTAATAAAT
1 TTTTATAAAATAAATATTTAATAAAT
912773 AATTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTTATAAAATAAATATTTAATAAATTA
Found at i:912770 original size:16 final size:17
Alignment explanation
Indices: 912738--912771 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
912728 ATAAAATTAT
*
912738 AATAAATTATTTTATAA
1 AATAAATTATTTAATAA
912755 AATAAA-TATTTAATAA
1 AATAAATTATTTAATAA
912771 A
1 A
912772 TAATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATTATTTAATAA
Found at i:913272 original size:26 final size:24
Alignment explanation
Indices: 913227--913274 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
913217 GAGGATTTAT
**
913227 TTTTTTAATTTTTTTTAATTATAA
1 TTTTTTAATTTTTTGAAATTATAA
913251 TTTTTTAACTTATTTTGAAATTAT
1 TTTTTTAA-TT-TTTTGAAATTAT
913275 GTATTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 2 0.10
26 10 0.50
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTTAATTTTTTGAAATTATAA
Found at i:913361 original size:21 final size:20
Alignment explanation
Indices: 913324--913362 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
913314 TTTATTAAAT
* *
913324 TTTTTTAATTTTTTATTTTA
1 TTTTTTAATTATGTATTTTA
913344 TTTTTTATATTATGTATTT
1 TTTTTTA-ATTATGTATTT
913363 AAAATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTTTAATTATGTATTTTA
Found at i:913594 original size:13 final size:13
Alignment explanation
Indices: 913576--913626 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
913566 ATTTTTAGTT
913576 TTTTATATTTAAA
1 TTTTATATTTAAA
*
913589 TTTTATATTT-TA
1 TTTTATATTTAAA
*
913601 TTTTATTTTTAAA
1 TTTTATATTTAAA
**
913614 TAATATATTTAAA
1 TTTTATATTTAAA
913627 ATAATTGTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTATATTTAAA
Found at i:913604 original size:25 final size:25
Alignment explanation
Indices: 913576--913623 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
913566 ATTTTTAGTT
**
913576 TTTTATATTTAAATTTTATATTTTA
1 TTTTATATTTAAATAATATATTTTA
*
913601 TTTTATTTTTAAATAATATATTT
1 TTTTATATTTAAATAATATATTT
913624 AAAATAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATATTTAAATAATATATTTTA
Found at i:914216 original size:38 final size:36
Alignment explanation
Indices: 914148--914229 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 36
914138 GTCATTTTAA
*
914148 GTTTGAATCAATCAGATTTAACATTCAATTTAAATTAG
1 GTTTGAATCAATCAGATTTAACACTCAATTT--ATTAG
*
914186 GTTTGAATCAATCA-AGTTTAATAC-CTAATTTATTAG
1 GTTTGAATCAATCAGA-TTTAACACTC-AATTTATTAG
*
914222 GTTCGAAT
1 GTTTGAAT
914230 TACTTCAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
36 12 0.31
37 2 0.05
38 25 0.64
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (36 bp):
GTTTGAATCAATCAGATTTAACACTCAATTTATTAG
Found at i:916646 original size:2 final size:2
Alignment explanation
Indices: 916613--916638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
916603 TATAGAAATT
916613 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
916639 CAATATATTG
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):
TA
Found at i:917318 original size:16 final size:16
Alignment explanation
Indices: 917269--917318 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
917259 GTCCGAACAT
917269 GATCTAATTCTTGTTA
1 GATCTAATTCTTGTTA
* ** **
917285 GATATAATTAGTCATA
1 GATCTAATTCTTGTTA
917301 GATCTAATTCTTGTTA
1 GATCTAATTCTTGTTA
917317 GA
1 GA
917319 CATAATTAGG
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (16 bp):
GATCTAATTCTTGTTA
Found at i:917971 original size:4 final size:4
Alignment explanation
Indices: 917962--917991 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
917952 ATGTGAAGGC
917962 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
917992 AATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:919165 original size:24 final size:24
Alignment explanation
Indices: 919125--919172 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
919115 TGAATTCAAT
* *
919125 AAAAATAATATATTAAATATATAA
1 AAAAATAAAATATTAAATAAATAA
919149 AAAAATAAAATGA-TAAATAAATAA
1 AAAAATAAAAT-ATTAAATAAATAA
919173 GCTTTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAATAAAATATTAAATAAATAA
Found at i:920025 original size:2 final size:2
Alignment explanation
Indices: 920018--920061 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
920008 GTTTTAGAGA
920018 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
920060 AT
1 AT
920062 TATGGTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:920554 original size:2 final size:2
Alignment explanation
Indices: 920547--920581 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
920537 GGTATACTTC
* *
920547 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
920582 TGTGAACATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:921008 original size:129 final size:129
Alignment explanation
Indices: 920773--921021 Score: 390
Period size: 129 Copynumber: 1.9 Consensus size: 129
920763 CCGGAAGTGA
* * *
920773 TATATTTATATAATGTATTGTGCCTTATTATAATCTATTTAAGGTATTTTATTTTTATATAAATT
1 TATATTTAAATAATGTATTGTGCCTTATTATAATCAATTTAAGATATTTTATTTTTATATAAATT
* * * * *
920838 TTAATATTTTAATAATTTGTATTATATAAATTTTAATATATTTATGTCTATTTATAACAAATCG
66 TTAATACTCTAATAATTTATATTATATAAATTTTAAAATATTTATATCTATTTATAACAAATCG
*
920902 TATATTTAAATTATGTATTGTGCCTTATTATAATCAATTTAAGATATTTTATTTTTATATAAATT
1 TATATTTAAATAATGTATTGTGCCTTATTATAATCAATTTAAGATATTTTATTTTTATATAAATT
* * *
920967 TTGATACTCTAATAATTTATATTATATGAATTTTAAAATATTTATATCTGTTTAT
66 TTAATACTCTAATAATTTATATTATATAAATTTTAAAATATTTATATCTATTTAT
921022 GTTATTTTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 108 1.00
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (129 bp):
TATATTTAAATAATGTATTGTGCCTTATTATAATCAATTTAAGATATTTTATTTTTATATAAATT
TTAATACTCTAATAATTTATATTATATAAATTTTAAAATATTTATATCTATTTATAACAAATCG
Found at i:922382 original size:13 final size:14
Alignment explanation
Indices: 922360--922396 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
922350 TTTAAAAAAA
922360 ATTATTTTTAATTT
1 ATTATTTTTAATTT
*
922374 -TTATATTTAATTT
1 ATTATTTTTAATTT
922387 ATTATTTTTA
1 ATTATTTTTA
922397 TTGAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTATTTTTAATTT
Found at i:922387 original size:18 final size:19
Alignment explanation
Indices: 922366--922406 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
922356 AAAAATTATT
*
922366 TTTAATT-TTTATATTTAA
1 TTTAATTATTTATATTGAA
*
922384 TTT-ATTATTTTTATTGAA
1 TTTAATTATTTATATTGAA
922402 TTTAA
1 TTTAA
922407 AAAATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 3 0.16
18 15 0.79
19 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTAATTATTTATATTGAA
Found at i:923006 original size:14 final size:14
Alignment explanation
Indices: 922987--923014 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
922977 TTTTTTGATT
922987 TTAAATATATTTTA
1 TTAAATATATTTTA
923001 TTAAATATATTTTA
1 TTAAATATATTTTA
923015 AATATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:923268 original size:16 final size:16
Alignment explanation
Indices: 923249--923301 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
923239 AAATTATAAA
923249 AATATTTTTTAAATTT
1 AATATTTTTTAAATTT
* * * *
923265 AATAATTTTAAAAATA
1 AATATTTTTTAAATTT
*
923281 AATATTATTTTTAATTT
1 AATATT-TTTTAAATTT
923298 AATA
1 AATA
923302 ATATTAAAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTTTTTAAATTT
Found at i:923302 original size:33 final size:33
Alignment explanation
Indices: 923248--923327 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
923238 AAAATTATAA
*
923248 AAATATT-TTTTAAATTTAATAATTTTAAAAAT
1 AAATATTATTTTAAATTTAATAATATTAAAAAT
*
923280 AAATATTATTTTTAATTTAATAATATTAAAAAT
1 AAATATTATTTTAAATTTAATAATATTAAAAAT
* *
923313 AAATGTTATCTTAAA
1 AAATATTATTTTAAA
923328 ATTTTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 7 0.17
33 35 0.83
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
AAATATTATTTTAAATTTAATAATATTAAAAAT
Found at i:923429 original size:27 final size:27
Alignment explanation
Indices: 923367--923447 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
923357 ATTATTAGAG
**
923367 ATAATT-TTTTTATTTTAAAAATTTTA
1 ATAATTATTTTTATTTTAAAAAAATTA
* *
923393 AAAATAATTTTTATTTTAAAAAAATTA
1 ATAATTATTTTTATTTTAAAAAAATTA
* **
923420 TTAATTATTTATTAATTTTTTAAAAATT
1 ATAATTATTT-TT-ATTTTAAAAAAATT
923448 TTGTAACGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
26 4 0.09
27 25 0.58
28 2 0.05
29 12 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATAATTATTTTTATTTTAAAAAAATTA
Found at i:924142 original size:14 final size:14
Alignment explanation
Indices: 924123--924158 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
924113 CATCTAAATT
924123 TATTTTTTATTTAA
1 TATTTTTTATTTAA
924137 TA-TTTTTATTTAA
1 TATTTTTTATTTAA
*
924150 AATTTTTTA
1 TATTTTTTA
924159 AATATTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTTTATTTAA
Found at i:927087 original size:37 final size:36
Alignment explanation
Indices: 927046--927122 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
927036 ATGAAAAAAT
*
927046 AAATCAAACCGAATATATATCATTAATATCTAAATCA
1 AAATCAAACCAAATATAT-TCATTAATATCTAAATCA
** * * *
927083 AAATCAAATTAAATATATTTATTAATATTTAAATTA
1 AAATCAAACCAAATATATTCATTAATATCTAAATCA
927119 AAAT
1 AAAT
927123 AAATTTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 19 0.56
37 15 0.44
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.36
Consensus pattern (36 bp):
AAATCAAACCAAATATATTCATTAATATCTAAATCA
Found at i:927116 original size:36 final size:36
Alignment explanation
Indices: 927057--927127 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
927047 AATCAAACCG
927057 AATATATATCATTAATATCTAAATCAAAATCAAATTA
1 AATATATATCATTAATATCTAAATCAAAAT-AAATTA
* * *
927094 AATATAT-TTATTAATATTTAAATTAAAATAAATT
1 AATATATATCATTAATATCTAAATCAAAATAAATT
927128 TAATTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 5 0.16
36 19 0.61
37 7 0.23
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (36 bp):
AATATATATCATTAATATCTAAATCAAAATAAATTA
Found at i:928736 original size:35 final size:34
Alignment explanation
Indices: 928658--928753 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 34
928648 TTAAATTTTA
* **
928658 TTTTATTATTATAATAATATTAAAATATCATTTATAT
1 TTTTATTATTATAATAA-ATTTAAATAT-A-AAATAT
*
928695 ATTTA-T-TTATAATAAATTTAAATATAAAATAT
1 TTTTATTATTATAATAAATTTAAATATAAAATAT
928727 TTTTATTATTA-AATAAGAATTTAAATA
1 TTTTATTATTATAAT-A-AATTTAAATA
928754 AAATTAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
32 8 0.16
33 5 0.10
34 13 0.26
35 19 0.38
36 1 0.02
37 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
TTTTATTATTATAATAAATTTAAATATAAAATAT
Found at i:930645 original size:2 final size:2
Alignment explanation
Indices: 930640--930666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
930630 TGATTTTTTC
930640 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 T
930667 TGGTCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:931637 original size:2 final size:2
Alignment explanation
Indices: 931630--931661 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
931620 GACAAGATCG
931630 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
931662 TTGATTGAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:932799 original size:2 final size:2
Alignment explanation
Indices: 932792--932834 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
932782 CCAACAACAA
932792 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
932834 A
1 A
932835 TCGGTTCCTC
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:933207 original size:5 final size:5
Alignment explanation
Indices: 933197--933225 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
933187 TTTTTGGGTT
933197 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
933226 AAACTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:934564 original size:20 final size:20
Alignment explanation
Indices: 934524--934582 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
934514 AAATATTAAT
* *
934524 ACATATGTTATTTACTTTTTA
1 ACATATATTTTTTA-TTTTTA
934545 ACATATATTTTTTATTTTTA
1 ACATATATTTTTTATTTTTA
* *
934565 AAATTTATTTTTTATTTT
1 ACATATATTTTTTATTTT
934583 ATATATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
ACATATATTTTTTATTTTTA
Found at i:934743 original size:4 final size:4
Alignment explanation
Indices: 934734--934760 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
934724 TGTTTATCTT
934734 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
934761 TGGATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:937173 original size:21 final size:21
Alignment explanation
Indices: 937149--937192 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
937139 AAAGAATAAA
937149 ATATATATAGAAAAA-TATATT
1 ATATATATAGAAAAAGTA-ATT
* *
937170 ATATATCTTGAAAAAGTAATT
1 ATATATATAGAAAAAGTAATT
937191 AT
1 AT
937193 GTAGTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
ATATATATAGAAAAAGTAATT
Found at i:937332 original size:25 final size:27
Alignment explanation
Indices: 937290--937343 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
937280 TTCATTAAAC
** *
937290 TTTTTAAAATAATGATAAT-TAATTTA
1 TTTTTAAAATAAAAATAATATAATATA
937316 TTTTT-AAATAAAAATAATATAATATA
1 TTTTTAAAATAAAAATAATATAATATA
937342 TT
1 TT
937344 AATATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTTAAAATAAAAATAATATAATATA
Found at i:937348 original size:13 final size:13
Alignment explanation
Indices: 937330--937370 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
937320 TAAATAAAAA
937330 TAATATAATATAT
1 TAATATAATATAT
*
937343 TAATATAA-AAAT
1 TAATATAATATAT
937355 TAATAT-ATATAAT
1 TAATATAATAT-AT
937368 TAA
1 TAA
937371 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.04
12 10 0.42
13 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATAATATAT
Found at i:937364 original size:24 final size:23
Alignment explanation
Indices: 937306--937379 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 23
937296 AAATAATGAT
* *
937306 AATTAATTTAT-TTTTAAATAAA
1 AATTAATATATATATTAAATAAA
937328 AA-TAATATAATATATTAATATAAA
1 AATTAATAT-ATATATTAA-ATAAA
937352 AATTAATATATATAATTAAATTAAA
1 AATTAATATATAT-ATTAAA-TAAA
937377 AAT
1 AAT
937380 AAATTTAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.11
22 4 0.09
23 5 0.11
24 12 0.27
25 18 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTAATATATATATTAAATAAA
Found at i:940178 original size:37 final size:39
Alignment explanation
Indices: 940089--940190 Score: 120
Period size: 39 Copynumber: 2.7 Consensus size: 39
940079 AATTTATACA
* * * * *
940089 TTAAAAAAT-TGATTTTTCTTAAAGAGGGATTGATTTCTC
1 TTAAAAAATATAATTTTT-TTAAAAAAGAATTGATCTCTC
940128 TTAAAAAATATAATTTTTTTAAAAAAGAATTGATCTCTC
1 TTAAAAAATATAATTTTTTTAAAAAAGAATTGATCTCTC
*
940167 -TAATAAA-ATAATTTTTTTAAAAAA
1 TTAAAAAATATAATTTTTTTAAAAAA
940191 TATTAAATGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
37 17 0.30
38 6 0.11
39 26 0.46
40 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (39 bp):
TTAAAAAATATAATTTTTTTAAAAAAGAATTGATCTCTC
Found at i:940661 original size:2 final size:2
Alignment explanation
Indices: 940615--940645 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
940605 TTCTCACGTT
940615 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
940646 GCATATTAGA
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:941573 original size:16 final size:16
Alignment explanation
Indices: 941552--941589 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
941542 AAAAAAATAT
941552 TATTTTAAAGAATTTAA
1 TATTTT-AAGAATTTAA
*
941569 T-TTTTAATAATTTAA
1 TATTTTAAGAATTTAA
941584 TATTTT
1 TATTTT
941590 TATTAGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 8 0.42
17 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTTTAAGAATTTAA
Found at i:944468 original size:22 final size:22
Alignment explanation
Indices: 944442--944490 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
944432 GATTAAATAG
*
944442 TGATTTGGTAGTTTATTATTAT
1 TGATTTGGTAGTTTATCATTAT
*
944464 TGATTTGGTAGTTTGTCATTAT
1 TGATTTGGTAGTTTATCATTAT
944486 TGATT
1 TGATT
944491 AAATGAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.57
Consensus pattern (22 bp):
TGATTTGGTAGTTTATCATTAT
Found at i:944510 original size:34 final size:33
Alignment explanation
Indices: 944465--944611 Score: 152
Period size: 33 Copynumber: 4.4 Consensus size: 33
944455 TATTATTATT
* *
944465 GATTTGGTAGTTTGTCATTATTGATTAAATGAGA
1 GATTTGGTAGTTTGCCATTGTTGATTAAATG-GA
* * *
944499 GATTTGATAGTTTACCACTGTTGATTAAATGG-
1 GATTTGGTAGTTTGCCATTGTTGATTAAATGGA
* * *
944531 GTAATTGGTGGTTTGCCATTGTTGACTAAATGGA
1 G-ATTTGGTAGTTTGCCATTGTTGATTAAATGGA
* * *
944565 GATTTGGTAGTTTACCATTGTTAATTAAATAGGT
1 GATTTGGTAGTTTGCCATTGTTGATTAAAT-GGA
*
944599 GATTTGGTGGTTT
1 GATTTGGTAGTTT
944612 TTACCAAACC
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
32 1 0.01
33 50 0.54
34 41 0.45
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (33 bp):
GATTTGGTAGTTTGCCATTGTTGATTAAATGGA
Found at i:944561 original size:67 final size:67
Alignment explanation
Indices: 944468--944611 Score: 191
Period size: 67 Copynumber: 2.1 Consensus size: 67
944458 TATTATTGAT
* * * * *
944468 TTGGTAGTTTGTCATTATTGATTAAATGAGAGATTTGATAGTTTACCACTGTTGATTAAATGGGT
1 TTGGTGGTTTGCCATTATTGACTAAATG-GAGATTTGATAGTTTACCACTGTTAATTAAATAGGT
944533 -AA
65 GAA
* * *
944535 TTGGTGGTTTGCCATTGTTGACTAAATGGAGATTTGGTAGTTTACCATTGTTAATTAAATAGGTG
1 TTGGTGGTTTGCCATTATTGACTAAATGGAGATTTGATAGTTTACCACTGTTAATTAAATAGGTG
*
944600 AT
66 AA
944602 TTGGTGGTTT
1 TTGGTGGTTT
944612 TTACCAAACC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
66 32 0.48
67 35 0.52
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (67 bp):
TTGGTGGTTTGCCATTATTGACTAAATGGAGATTTGATAGTTTACCACTGTTAATTAAATAGGTG
AA
Found at i:951443 original size:20 final size:20
Alignment explanation
Indices: 951418--951484 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
951408 ATTTGCCTGC
951418 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
951438 ATGTATCGAT------A-CA
1 ATGTATCGATACAAAGATCA
951451 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
951471 ATGTATCGATACAA
1 ATGTATCGATACAA
951485 TGTATCGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.30
14 1 0.03
19 1 0.03
20 26 0.65
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGATCA
Found at i:951454 original size:13 final size:13
Alignment explanation
Indices: 951436--951496 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
951426 ATACAAAGAT
951436 CAATGTATCGATA
1 CAATGTATCGATA
951449 CAATGTATCGATA
1 CAATGTATCGATA
951462 CAA---A--GAT-
1 CAATGTATCGATA
951469 CAATGTATCGATA
1 CAATGTATCGATA
951482 CAATGTATCGATA
1 CAATGTATCGATA
951495 CA
1 CA
951497 TTTAAGTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.07
8 3 0.07
10 2 0.05
12 3 0.07
13 31 0.74
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:951460 original size:33 final size:33
Alignment explanation
Indices: 951418--951496 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
951408 ATTTGCCTGC
951418 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
951451 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
951484 ATGTATCGATACA
1 ATGTATCGATACA
951497 TTTAAGTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCGATACA
Found at i:951577 original size:13 final size:13
Alignment explanation
Indices: 951559--951583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
951549 CCAAAAAATA
951559 TGTATCGATACAT
1 TGTATCGATACAT
951572 TGTATCGATACA
1 TGTATCGATACA
951584 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:952673 original size:49 final size:49
Alignment explanation
Indices: 952464--952973 Score: 680
Period size: 49 Copynumber: 10.7 Consensus size: 49
952454 AAAAGGATGT
*
952464 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
952516 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
952559 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
952607 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
952656 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
952705 TAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
952754 CAATATGCTGATTCAAAGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
952797 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
952846 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
952889 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
952938 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
952974 GAAGGGTTGC
Statistics
Matches: 407, Mismatches: 32, Indels: 41
0.85 0.07 0.09
Matches are distributed among these distances:
43 117 0.29
45 2 0.00
47 2 0.00
48 48 0.12
49 206 0.51
52 32 0.08
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:952839 original size:92 final size:92
Alignment explanation
Indices: 952508--952978 Score: 657
Period size: 92 Copynumber: 5.1 Consensus size: 92
952498 TAAAGATGGA
* * *
952508 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
952567 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
952594 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* * * *
952659 TGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
61 TATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * *
952697 AAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
952762 TGATTCAAAGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
952789 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
952854 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
952881 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
952946 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
952973 AGAAGG
1 A-AAGG
952979 GTTGCCACCG
Statistics
Matches: 348, Mismatches: 19, Indels: 28
0.88 0.05 0.07
Matches are distributed among these distances:
87 2 0.01
91 39 0.11
92 180 0.52
93 4 0.01
95 1 0.00
97 39 0.11
98 80 0.23
102 2 0.01
103 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:953017 original size:33 final size:33
Alignment explanation
Indices: 952973--953092 Score: 183
Period size: 32 Copynumber: 3.7 Consensus size: 33
952963 TATTGGGCTT
952973 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
953006 AGAATGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
953038 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
953071 AAGAA-GG-TGCCACGGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
953093 GACTTAAAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 44 0.55
33 33 0.41
34 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Done.