Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 138 of 167
Found at i:46245630 original size:19 final size:20
Alignment explanation
Indices: 46245606--46245644 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
46245596 ATAAAATATA
*
46245606 TTTAATATATTTA-ACATTT
1 TTTAATATATATATACATTT
*
46245625 TTTAATTTATATATACATTT
1 TTTAATATATATATACATTT
46245645 CAAATCCGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATATATATACATTT
Found at i:46268459 original size:22 final size:22
Alignment explanation
Indices: 46268433--46268480 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
46268423 CCTGAGTTGT
46268433 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
46268455 ATGTTTCTTTGATAAGTTGATC
1 ATGTTTCTTTGATAAGTTGATC
46268477 -TGTT
1 ATGTT
46268481 GTGGTTCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (22 bp):
ATGTTTCTTTGATAAGTTGATC
Found at i:46270977 original size:15 final size:15
Alignment explanation
Indices: 46270935--46270980 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
46270925 AAAGAAACTT
* *
46270935 GAAAAATGAAAAAAAA
1 GAAAAA-GAAAAGAAG
*
46270951 GAAAAAAAAAAGAAG
1 GAAAAAGAAAAGAAG
46270966 GAAAAAGAAAAGAAG
1 GAAAAAGAAAAGAAG
46270981 AGGAGCAGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAAAGAAG
Found at i:46272821 original size:21 final size:21
Alignment explanation
Indices: 46272782--46272822 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46272772 CAGCGGTGGC
* *
46272782 GGTGAGATTAGTTACTGTAGT
1 GGTGAGATTAGATAATGTAGT
*
46272803 GGTGAGATTGGATAATGTAG
1 GGTGAGATTAGATAATGTAG
46272823 CGGTANAGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
GGTGAGATTAGATAATGTAGT
Found at i:46272834 original size:56 final size:55
Alignment explanation
Indices: 46272773--46272885 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 55
46272763 GATTAAAAAC
46272773 AGCGGTGGCGGTGAGATTAGTTACTGTAGTGGTGAGATTGGATAATGTAGCGGTA
1 AGCGGTGGCGGTGAGATTAGTTACTGTAGTGGTGAGATTGGATAATGTAGCGGTA
46272828 NAGCGGTGGCGGTGAGATTAGTTACTGTAGTGGTGAGATTGGATAATGTAGCGGTA
1 -AGCGGTGGCGGTGAGATTAGTTACTGTAGTGGTGAGATTGGATAATGTAGCGGTA
46272884 AG
1 AG
46272886 ATTAGAAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 2 0.04
56 55 0.96
ACGTcount: A:0.24, C:0.07, G:0.40, T:0.28
Consensus pattern (55 bp):
AGCGGTGGCGGTGAGATTAGTTACTGTAGTGGTGAGATTGGATAATGTAGCGGTA
Found at i:46272862 original size:21 final size:21
Alignment explanation
Indices: 46272836--46272891 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
46272826 TANAGCGGTG
* *
46272836 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATAATGTA
* *
46272857 GTGGTGAGATTGGATAATGTA
1 GCGGTGAGATTAGATAATGTA
*
46272878 GCGGTAAGATTAGA
1 GCGGTGAGATTAGA
46272892 AACAATGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATAATGTA
Found at i:46274951 original size:30 final size:29
Alignment explanation
Indices: 46274914--46274990 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
46274904 TAGCAATTAA
46274914 TTAATTCTTTAAAAATTAAAAATATTTTT
1 TTAATTCTTTAAAAATTAAAAATATTTTT
* **
46274943 TATAATTC-TT-AAATTTTTAAATATTTTT
1 T-TAATTCTTTAAAAATTAAAAATATTTTT
46274971 TTATATT-TTTAAAAATTAAA
1 TTA-ATTCTTTAAAAATTAAA
46274991 TAATTGCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.05
28 21 0.55
29 9 0.24
30 6 0.16
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTAATTCTTTAAAAATTAAAAATATTTTT
Found at i:46286810 original size:46 final size:46
Alignment explanation
Indices: 46286740--46286894 Score: 256
Period size: 46 Copynumber: 3.4 Consensus size: 46
46286730 CGCGGGAGTG
* **
46286740 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
46286786 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
* * *
46286832 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGT
1 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
46286878 TGAAAGATACCATGGCA
1 TGAAAGATACCATGGCA
46286895 GCATGACAGA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 103 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
Found at i:46286902 original size:46 final size:46
Alignment explanation
Indices: 46286740--46286949 Score: 233
Period size: 46 Copynumber: 4.5 Consensus size: 46
46286730 CGCGGGAGTG
* * * ** *
46286740 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATAGT
* * * *
46286786 TGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATAGT
*
46286832 TGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATAGT
1 TGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATAGT
*
46286878 TGAAAGATACCATGGCAGCATGACA-GAAAATGAATGAGTAAGACCATAGT
1 TGAAAGATACCATGGCAACATGACATGAAAA-G-A--A-TAAGACCATAGT
* * *
46286928 TGAAAGACACTATGGCATCATG
1 TGAAAGATACCATGGCAACATG
46286950 TCAAAGATAA
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
45 5 0.03
46 110 0.74
47 1 0.01
49 1 0.01
50 31 0.21
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
TGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATAGT
Found at i:46289500 original size:196 final size:196
Alignment explanation
Indices: 46289160--46290142 Score: 1930
Period size: 196 Copynumber: 5.0 Consensus size: 196
46289150 TAATGTGAGC
* *
46289160 TTTGTAAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTACTAAGTTTTATCTTTGAATT
1 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
46289225 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
46289290 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
46289355 T
196 T
46289356 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
1 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
46289421 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
46289486 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
46289551 T
196 T
46289552 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
1 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
46289617 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
46289682 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
46289747 T
196 T
46289748 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
1 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
46289813 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
46289878 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
46289943 T
196 T
46289944 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
1 TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
46290009 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
66 GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
* *
46290074 ATAAATGAAATATTTGGACTTGTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
131 ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
46290139 T
196 T
46290140 TTT
1 TTT
46290143 ATGTATTTTG
Statistics
Matches: 783, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 783 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (196 bp):
TTTGTTAAGTTTGATGATAGTAAATGAAAGATATGTGTTAGATTTCTAAGTTTTATCTTTGAATT
GTTTATGAATTTGAGTAATTTGGGCTAAATTGTGAAATTTGAAAATTGAGGGACTAAAATGTGAA
ATAAATGAAATATGTGGACTTTTATGAGTGCTATGAATATTCGTCTAGGCATGTGTACAAAGAAA
T
Found at i:46290643 original size:44 final size:42
Alignment explanation
Indices: 46290577--46290731 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 42
46290567 TGTTATCGTA
*
46290577 TAAGACCATGTTTGGGATGTTGGCATCGACTTATGATTTACGTG
1 TAAGACCATGTTTGGGACGTTGGCATCGA-TT-TGATTTACGTG
*
46290621 TAAGACCATGTTTGAGACGTTGGCATCGTATTTGATTT-CGTG
1 TAAGACCATGTTTGGGACGTTGGCATCG-ATTTGATTTACGTG
* * * * *
46290663 TAAAACCCTGTCTGGGATAG-TGGCATCGATATTTGA-TTACATG
1 TAAGACCATGTTTGGGA-CGTTGGCATCG--ATTTGATTTACGTG
* *
46290706 TAAGACCACGTTCGGGACGTTGGCAT
1 TAAGACCATGTTTGGGACGTTGGCAT
46290732 TGTACGACAT
Statistics
Matches: 92, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
42 28 0.30
43 35 0.38
44 28 0.30
45 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
TAAGACCATGTTTGGGACGTTGGCATCGATTTGATTTACGTG
Found at i:46294093 original size:26 final size:26
Alignment explanation
Indices: 46294057--46294114 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
46294047 TGCCTATGTG
46294057 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
46294083 ATTGATTCGAAAATGTCAGAAAAGAA
1 ATTGATTCGAAAATGTCAGAAAAGAA
46294109 AGTTGA
1 A-TTGA
46294115 ATCAGTGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (26 bp):
ATTGATTCGAAAATGTCAGAAAAGAA
Found at i:46296405 original size:39 final size:37
Alignment explanation
Indices: 46296338--46296430 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
46296328 ACCAGAATGG
* *
46296338 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
46296377 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
46296414 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
46296431 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:46297557 original size:17 final size:16
Alignment explanation
Indices: 46297525--46297558 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
46297515 TTGGCTATTC
*
46297525 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
46297541 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
46297558 T
1 T
46297559 AAATTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:46297607 original size:16 final size:17
Alignment explanation
Indices: 46297579--46297610 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
46297569 TTGTTTATTA
46297579 TTTAATAAATATAATAC
1 TTTAATAAATATAATAC
46297596 TTTAAT-AATATAATA
1 TTTAATAAATATAATA
46297611 TAATATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATAAATATAATAC
Found at i:46300531 original size:43 final size:42
Alignment explanation
Indices: 46300413--46300534 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 42
46300403 AACTTATGAT
* * *
46300413 TTACGTGTAAGACAACGTTTGGGATGTTGGCATCGTATTTGA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTATTTGA
* ** * ** *
46300455 TTTCGTGTAAGACCTTGTCTGGGACAATAGCATTGATATTTGA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTG-TATTTGA
* *
46300498 TTACATGTAAGACCACATTTGGGACGTTGGCATTGTA
1 TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTA
46300535 CGAGATTTTT
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
42 27 0.45
43 33 0.55
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (42 bp):
TTACGTGTAAGACCACGTTTGGGACGTTGGCATTGTATTTGA
Found at i:46303198 original size:21 final size:21
Alignment explanation
Indices: 46303148--46303200 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
46303138 TAGAAACTCG
46303148 AAAGCTGAACAGAACCTCATA
1 AAAGCTGAACAGAACCTCATA
* *
46303169 AGAGCTGAACAGGAA-CTCGTA
1 AAAGCTGAACA-GAACCTCATA
*
46303190 AAAGTTGAACA
1 AAAGCTGAACA
46303201 AAAGCTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAGCTGAACAGAACCTCATA
Found at i:46303221 original size:21 final size:21
Alignment explanation
Indices: 46303197--46303240 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
46303187 GTAAAAGTTG
46303197 AACAAAAGCTCGAAAGAACTA
1 AACAAAAGCTCGAAAGAACTA
* * *
46303218 AACAGAGGCTCGAAAGAGCTA
1 AACAAAAGCTCGAAAGAACTA
46303239 AA
1 AA
46303241 TAGAAAGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.09
Consensus pattern (21 bp):
AACAAAAGCTCGAAAGAACTA
Found at i:46306545 original size:39 final size:40
Alignment explanation
Indices: 46306488--46306575 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
46306478 ATACTTTTAA
* * *
46306488 AATC-AGTGAAAATGATTTTAAC-CAAGCCAAATGA-TTTC
1 AATCAAGTTAAAATCATTTTAACAC-AGCAAAATGATTTTC
*
46306526 AATCAAGTTAAAATCATTTTAACACATCAAAATGATTTTC
1 AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
*
46306566 AAACAAGTTA
1 AATCAAGTTA
46306576 GAATTGCTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.10
39 24 0.57
40 14 0.33
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (40 bp):
AATCAAGTTAAAATCATTTTAACACAGCAAAATGATTTTC
Found at i:46306563 original size:19 final size:19
Alignment explanation
Indices: 46306496--46306564 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
46306486 AAAATCAGTG
*
46306496 AAAATGATTTTAAC-CAAGC
1 AAAATGATTTTAACAC-ATC
* * *
46306515 CAAATGATTTCAATCA-AGTT
1 AAAATGATTTTAA-CACA-TC
*
46306535 AAAATCATTTTAACACATC
1 AAAATGATTTTAACACATC
46306554 AAAATGATTTT
1 AAAATGATTTT
46306565 CAAACAAGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
19 25 0.68
20 12 0.32
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATGATTTTAACACATC
Found at i:46314342 original size:23 final size:22
Alignment explanation
Indices: 46314291--46314342 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
46314281 CCTCGTCTTT
*
46314291 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
46314313 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
46314336 TTCTTTT
1 TTCTTTT
46314343 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:46316556 original size:32 final size:32
Alignment explanation
Indices: 46316520--46316620 Score: 141
Period size: 32 Copynumber: 3.2 Consensus size: 32
46316510 GAAAGAATTG
* **
46316520 ATCAGTAAC-GATAATATAATTAGTACAAAGCC
1 ATCAGTAACAG-TAATATGATCGGTACAAAGCC
*
46316552 ATCAGTAACAGTAATATGATCGGCACAAAGCC
1 ATCAGTAACAGTAATATGATCGGTACAAAGCC
*
46316584 ATCAGTAACAGTGATATGATCGGTACAAAGCC
1 ATCAGTAACAGTAATATGATCGGTACAAAGCC
46316616 ATCAG
1 ATCAG
46316621 GGGTACTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
32 61 0.98
33 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (32 bp):
ATCAGTAACAGTAATATGATCGGTACAAAGCC
Found at i:46317081 original size:27 final size:27
Alignment explanation
Indices: 46316788--46317088 Score: 306
Period size: 27 Copynumber: 11.2 Consensus size: 27
46316778 TATTTTGGTT
* *
46316788 ATTTTACCCTTTAGGGGTAATT-TAGTC
1 ATTTTACCCTTCAGGGGTAATTCGA-TC
* * *
46316815 ATTTTACCCTTTAAGGGTAATTCGGTC
1 ATTTTACCCTTCAGGGGTAATTCGATC
*
46316842 ATTTTACCCTTCAGGGGTAATTCGGTC
1 ATTTTACCCTTCAGGGGTAATTCGATC
* * *
46316869 ATTTTACCCTTCAAGGGTACTTCGGTC
1 ATTTTACCCTTCAGGGGTAATTCGATC
* * *
46316896 TTTTTACCCTTCAAGGGTAATTTTG-TC
1 ATTTTACCCTTCAGGGGTAA-TTCGATC
** *
46316923 ATTTTACCCTTTGGGGGTAATT-TAGTC
1 ATTTTACCCTTCAGGGGTAATTCGA-TC
*
46316950 A-TTTACCCTTCGGGGGTAATTC-AGTC
1 ATTTTACCCTTCAGGGGTAATTCGA-TC
* *
46316976 ATTTTACCTTTCGGGGGTAATTCGATC
1 ATTTTACCCTTCAGGGGTAATTCGATC
**
46317003 ATTTTACCCTTTGGGGGTAATTCGATC
1 ATTTTACCCTTCAGGGGTAATTCGATC
* * *
46317030 ATTTTAACTTTCGGGGGTAATTCGATC
1 ATTTTACCCTTCAGGGGTAATTCGATC
* *
46317057 ATTTTACCCTTCAGCGGTAATTCGACC
1 ATTTTACCCTTCAGGGGTAATTCGATC
46317084 ATTTT
1 ATTTT
46317089 TTGACCTCTC
Statistics
Matches: 240, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
26 26 0.11
27 210 0.88
28 4 0.02
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTCAGGGGTAATTCGATC
Found at i:46317087 original size:134 final size:134
Alignment explanation
Indices: 46316788--46317087 Score: 316
Period size: 134 Copynumber: 2.2 Consensus size: 134
46316778 TATTTTGGTT
* * * * *** *
46316788 ATTTTACCCTTTAGGGGTAATTTAGTCATTTTACCCTTTAAGGGTAATTCGGTCATTTTACCCTT
1 ATTTTACCCTTCAGCGGTAATTGAGCCA-TTTACCCTTCGGGGGTAATTCAGTCATTTTACCCTT
* * * * *
46316853 CAGGGGTAATTCGGTCATTTTACCCTTCAAGGGTACTTCGGTCTTTTTACCCTTCAAGGGTAATT
65 CAGGGGTAATTCGATCATTTTACCCTTCAAGGGTAATTCGATCATTTTAACCTTCAAGGGTAATT
*
46316918 TTGTC
130 TCGTC
** * * * *
46316923 ATTTTACCCTTTGGGGGTAATTTAGTCATTTACCCTTCGGGGGTAATTCAGTCATTTTACCTTTC
1 ATTTTACCCTTCAGCGGTAATTGAGCCATTTACCCTTCGGGGGTAATTCAGTCATTTTACCCTTC
* *** * **
46316988 GGGGGTAATTCGATCATTTTACCCTTTGGGGGTAATTCGATCATTTTAACTTTCGGGGGTAA-TT
66 AGGGGTAATTCGATCATTTTACCCTTCAAGGGTAATTCGATCATTTTAACCTTCAAGGGTAATTT
46317052 CGATC
131 CG-TC
46317057 ATTTTACCCTTCAGCGGTAATTCGA-CCATTT
1 ATTTTACCCTTCAGCGGTAATT-GAGCCATTT
46317088 TTTGACCTCT
Statistics
Matches: 139, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
133 3 0.02
134 108 0.78
135 28 0.20
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (134 bp):
ATTTTACCCTTCAGCGGTAATTGAGCCATTTACCCTTCGGGGGTAATTCAGTCATTTTACCCTTC
AGGGGTAATTCGATCATTTTACCCTTCAAGGGTAATTCGATCATTTTAACCTTCAAGGGTAATTT
CGTC
Found at i:46319690 original size:32 final size:32
Alignment explanation
Indices: 46319522--46319692 Score: 211
Period size: 32 Copynumber: 5.4 Consensus size: 32
46319512 GAATGGATAC
* * *
46319522 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
46319553 AAGCCATCAATAATGGTAATATGATCAGCAGA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
46319585 AAGCCATCAATAACGGTAATATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
46319617 AAGCCATCAGTAACGGTAATATGATCGGCAGA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
46319649 AAGCCATCAGTAATGGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
46319681 AA-CCGATCAGTA
1 AAGCC-ATCAGTA
46319693 GCATTACAGT
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
31 11 0.09
32 110 0.91
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:46319690 original size:64 final size:64
Alignment explanation
Indices: 46319536--46319692 Score: 235
Period size: 64 Copynumber: 2.5 Consensus size: 64
46319526 CATAAGTACA
* *
46319536 GTAATATGATTGGCACAAAGCCATCAATAATGGTAATATGATCAGCAGAAAGCCATCAATAACG
1 GTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCAGCAGAAAGCCATCAATAACG
* * *
46319600 GTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCGGCAGAAAGCCATCAGTAATG
1 GTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCAGCAGAAAGCCATCAATAACG
* *
46319664 GTGATATGATCGGCACAAA-CCGATCAGTA
1 GTAATATGATTGGCACAAAGCC-ATCAGTA
46319693 GCATTACAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
63 2 0.02
64 83 0.98
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (64 bp):
GTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCAGCAGAAAGCCATCAATAACG
Found at i:46319921 original size:24 final size:24
Alignment explanation
Indices: 46319894--46319997 Score: 131
Period size: 24 Copynumber: 4.3 Consensus size: 24
46319884 AAGCAAAATG
*
46319894 GTCATTTGA-ATCACAGTCAAATCA
1 GTCATTT-ACATCACAGACAAATCA
*
46319918 GTCATTTA-AGTCATAGACAAATCA
1 GTCATTTACA-TCACAGACAAATCA
* *
46319942 GTCATTTACATCATAAACAAATCA
1 GTCATTTACATCACAGACAAATCA
46319966 GTCATTTACATCACAGACAAATCA
1 GTCATTTACATCACAGACAAATCA
*
46319990 ATCATTTA
1 GTCATTTA
46319998 ACCTCGAGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.03
24 69 0.96
25 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (24 bp):
GTCATTTACATCACAGACAAATCA
Found at i:46320086 original size:27 final size:27
Alignment explanation
Indices: 46320056--46320480 Score: 183
Period size: 27 Copynumber: 15.8 Consensus size: 27
46320046 TTTTACTTTA
* * *
46320056 TAGGGGGATTTTGGTAATTTTACCCTT
1 TAGGGGGAATTCGGTCATTTTACCCTT
* *
46320083 TAGGGGTAATTCGGTCATTTTACCGTT
1 TAGGGGGAATTCGGTCATTTTACCCTT
* * * *
46320110 TCGGGGTAATTCAGTTATTTTACCCTT
1 TAGGGGGAATTCGGTCATTTTACCCTT
*
46320137 TAGGGGGTAATTCGATCATTTTACCCTT
1 TAGGGGG-AATTCGGTCATTTTACCCTT
*
46320165 T-GGGGGTAATTCGGTCATGTTACCC-T
1 TAGGGGG-AATTCGGTCATTTTACCCTT
* * ** *
46320191 TCGAGGGTAATTCAATCATTTTA-CCAT
1 TAG-GGGGAATTCGGTCATTTTACCCTT
* * * * *
46320218 TCGAGGGTAATTTGATCATTTTAACC-T
1 TAG-GGGGAATTCGGTCATTTTACCCTT
* * ** *
46320245 TCGGGGGTAATTCAGTCAACTTACCATT
1 TAGGGGG-AATTCGGTCATTTTACCCTT
* * * *
46320273 CAGGGGTAATTTGATCA-TTTA-CCTT
1 TAGGGGGAATTCGGTCATTTTACCCTT
* * * *
46320298 TTGGGTGTAATTCGGTCAGTCTA-CCTT
1 TAGGG-GGAATTCGGTCATTTTACCCTT
* *
46320325 TTGGGGGTAATTCAGTCATTTTACCC-T
1 TAGGGGG-AATTCGGTCATTTTACCCTT
* **
46320352 TCGGGGGTAATTCAATCATTTTACCC-T
1 TAGGGGG-AATTCGGTCATTTTACCCTT
* ** *
46320379 TCGGGACTAATTCAGTCA-TTTACCC--
1 TAGGG-GGAATTCGGTCATTTTACCCTT
**
46320404 TACGGGGGTAATTCTATCATTTTACCC-T
1 TA-GGGGG-AATTCGGTCATTTTACCCTT
* * *
46320432 TCGGGGGTAAGTCAGTCATTTTACCCTT
1 TAGGGGG-AATTCGGTCATTTTACCCTT
* * * *
46320460 CAAGGGTAATTCAGTCATTTT
1 TAGGGGGAATTCGGTCATTTT
46320481 TTAACCTCTC
Statistics
Matches: 315, Mismatches: 66, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
25 7 0.02
26 39 0.12
27 234 0.74
28 35 0.11
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (27 bp):
TAGGGGGAATTCGGTCATTTTACCCTT
Found at i:46320134 original size:54 final size:53
Alignment explanation
Indices: 46320072--46320480 Score: 353
Period size: 54 Copynumber: 7.6 Consensus size: 53
46320062 GATTTTGGTA
* ** *
46320072 ATTTTACCCTTTAGGGGTAATTCGGTCATTTTACCGTTTCGGGGTAATTCAGTT
1 ATTTTACCCTTCAGGGGTAATTCAATCATTTTACC-TTTCGGGGTAATTCAGTC
* * * *
46320126 ATTTTACCCTTTAGGGGGTAATTCGATCATTTTACCCTTTGGGGGTAATTCGGTC
1 ATTTTACCCTTCA-GGGGTAATTCAATCATTTTA-CCTTTCGGGGTAATTCAGTC
* * *
46320181 ATGTTACCCTTC-GAGGGTAATTCAATCATTTTACCATTCGAGGGTAATT-TGATC
1 ATTTTACCCTTCAG-GGGTAATTCAATCATTTTACCTTTCG-GGGTAATTCAG-TC
* * * ** * *
46320235 ATTTTAACCTTCGGGGGTAATTCAGTCAACTTACCATTCAGGGGTAATT-TGATC
1 ATTTTACCCTTCAGGGGTAATTCAATCATTTTACCTTTC-GGGGTAATTCAG-TC
** ** * * *
46320289 A-TTTA-CCTTTTGGGTGTAATTCGGTCAGTCTACCTTTTGGGGGTAATTCAGTC
1 ATTTTACCCTTCAGGG-GTAATTCAATCATTTTACC-TTTCGGGGTAATTCAGTC
* * *
46320342 ATTTTACCCTTCGGGGGTAATTCAATCATTTTACCCTTCGGGACTAATTCAGTC
1 ATTTTACCCTTCAGGGGTAATTCAATCATTTTACCTTTCGGG-GTAATTCAGTC
* * * * *
46320396 A-TTTACCCTACGGGGGTAATTCTATCATTTTACCCTTCGGGGGTAAGTCAGTC
1 ATTTTACCCTTCAGGGGTAATTCAATCATTTTACCTTTC-GGGGTAATTCAGTC
* *
46320449 ATTTTACCCTTCAAGGGTAATTCAGTCATTTT
1 ATTTTACCCTTCAGGGGTAATTCAATCATTTT
46320481 TTAACCTCTC
Statistics
Matches: 298, Mismatches: 42, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
52 7 0.02
53 88 0.30
54 148 0.50
55 53 0.18
56 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (53 bp):
ATTTTACCCTTCAGGGGTAATTCAATCATTTTACCTTTCGGGGTAATTCAGTC
Found at i:46320344 original size:107 final size:105
Alignment explanation
Indices: 46320074--46320480 Score: 390
Period size: 107 Copynumber: 3.8 Consensus size: 105
46320064 TTTTGGTAAT
* * * *
46320074 TTTACCCTTTAGGGGTAATTCGGTCATTTTACCGTTTC-GGGGTAATTCAGTTATTTTACCCTTT
1 TTTACCC-TTCGGGGTAATTCGATCATTTTACC-ATTCGGGGGTAATTCAGTCATTTTACCC-TT
* * * *
46320138 AGGGGGTAATTC-GATCATTTTACCCTTTGGGGGTAATTCGGTCA
63 CGGGGGTAATTCAG-TCATTTTACCC-TTCGGGGTAATTTGATCA
* * * *
46320182 TGTTACCCTTCGAGGGTAATTCAATCATTTTACCATTCGAGGGTAATT-TGATCATTTTAACCTT
1 T-TTACCCTTCG-GGGTAATTCGATCATTTTACCATTCGGGGGTAATTCAG-TCATTTTACCCTT
** *
46320246 CGGGGGTAATTCAGTCAACTTACCATTCAGGGGTAATTTGATCA
63 CGGGGGTAATTCAGTCATTTTACCCTTC-GGGGTAATTTGATCA
* * * * * * *
46320290 TTTACCTTTTGGGTGTAATTCGGTCAGTCTACCTTTTGGGGGTAATTCAGTCATTTTACCCTTCG
1 TTTACCCTTCGGG-GTAATTCGATCATTTTACCATTCGGGGGTAATTCAGTCATTTTACCCTTCG
* * *
46320355 GGGGTAATTCAATCATTTTACCCTTCGGGACTAA-TTCAGTCA
65 GGGGTAATTCAGTCATTTTACCCTTCGGG-GTAATTTGA-TCA
* * * * *
46320397 TTTACCCTACGGGGGTAATTCTATCATTTTACCCTTCGGGGGTAAGTCAGTCATTTTACCCTTCA
1 TTTACCCTTC-GGGGTAATTCGATCATTTTACCATTCGGGGGTAATTCAGTCATTTTACCCTTCG
*
46320462 AGGGTAATTCAGTCATTTT
65 GGGGTAATTCAGTCATTTT
46320481 TTAACCTCTC
Statistics
Matches: 243, Mismatches: 45, Indels: 23
0.78 0.14 0.07
Matches are distributed among these distances:
106 8 0.03
107 145 0.60
108 47 0.19
109 43 0.18
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (105 bp):
TTTACCCTTCGGGGTAATTCGATCATTTTACCATTCGGGGGTAATTCAGTCATTTTACCCTTCGG
GGGTAATTCAGTCATTTTACCCTTCGGGGTAATTTGATCA
Found at i:46325598 original size:58 final size:58
Alignment explanation
Indices: 46325477--46325595 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 58
46325467 AGAAATGGTT
* * * *
46325477 AAAATGGAGAAATGGAATACATTTGGAAATGATTATGGTTTTCTCCAAATCAAAAATG
1 AAAATGGAAAAATGGAATACATTTGGAAATGAATATGGTTATCTCAAAATCAAAAATG
* * *
46325535 AAAATGGAAAAATGGAA-CCGTTTGGAAATGAATGTGGTTATCTTCAAAAT-AAAAATG
1 AAAATGGAAAAATGGAATACATTTGGAAATGAATATGGTTATC-TCAAAATCAAAAATG
46325592 AAAA
1 AAAA
46325596 ATGAAAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 31 0.58
58 22 0.42
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (58 bp):
AAAATGGAAAAATGGAATACATTTGGAAATGAATATGGTTATCTCAAAATCAAAAATG
Found at i:46325817 original size:23 final size:23
Alignment explanation
Indices: 46325790--46325835 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
46325780 TTAATAAAAG
46325790 TAATCAAACTTAAATTTAAAACA
1 TAATCAAACTTAAATTTAAAACA
*
46325813 TAATCAAACTTAAATTTCAAACA
1 TAATCAAACTTAAATTTAAAACA
46325836 AACATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.30
Consensus pattern (23 bp):
TAATCAAACTTAAATTTAAAACA
Found at i:46331568 original size:30 final size:30
Alignment explanation
Indices: 46331527--46331603 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
46331517 AGAAATACCT
*
46331527 TCGTGTGCCTCACACGGCCGTGTGGCCAGG
1 TCGTGTGCCTCACACGGCCATGTGGCCAGG
* *
46331557 TCGTATGCCTCACACGGCCATGTGGCTAGG
1 TCGTGTGCCTCACACGGCCATGTGGCCAGG
46331587 TCGTGTGCCTCACACGG
1 TCGTGTGCCTCACACGG
46331604 ATGAGACACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.22
Consensus pattern (30 bp):
TCGTGTGCCTCACACGGCCATGTGGCCAGG
Found at i:46335465 original size:22 final size:22
Alignment explanation
Indices: 46335439--46335485 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
46335429 TAACCTTGGA
*
46335439 AACAAAAAGCTGATGCTTACAC
1 AACAAAAAGCTGACGCTTACAC
46335461 AACAAAAAGCTGACGCTTACAC
1 AACAAAAAGCTGACGCTTACAC
46335483 AAC
1 AAC
46335486 CACCACCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.26, G:0.13, T:0.15
Consensus pattern (22 bp):
AACAAAAAGCTGACGCTTACAC
Found at i:46335956 original size:9 final size:9
Alignment explanation
Indices: 46335944--46335974 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46335934 GTCAAGATGA
*
46335944 ATATATTTT
1 ATATATGTT
46335953 ATATATGTT
1 ATATATGTT
46335962 ATATATGTT
1 ATATATGTT
46335971 ATAT
1 ATAT
46335975 TAACATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (9 bp):
ATATATGTT
Found at i:46342669 original size:21 final size:22
Alignment explanation
Indices: 46342643--46342703 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
46342633 GGTATTTGGG
46342643 AATTGGTACGAAATGGTAT-GC
1 AATTGGTACGAAATGGTATGGC
* *
46342664 AATTGGTATGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGC
* *
46342686 ATTTGGTACGAATTGGTA
1 AATTGGTACGAAATGGTA
46342704 ATGGTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGC
Found at i:46343624 original size:50 final size:50
Alignment explanation
Indices: 46343562--46343664 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
46343552 AAATTAACAC
*
46343562 TAAAATTCTGCACATTAAATTCGGCAGCCTTAGGACATAATTAAAACAAG
1 TAAAATGCTGCACATTAAATTCGGCAGCCTTAGGACATAATTAAAACAAG
46343612 TAAAATGCTGCACATTAAATTCGGCAGCCTTAGGACATAATTAAAACAAG
1 TAAAATGCTGCACATTAAATTCGGCAGCCTTAGGACATAATTAAAACAAG
46343662 TAA
1 TAA
46343665 TAAAGTTAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (50 bp):
TAAAATGCTGCACATTAAATTCGGCAGCCTTAGGACATAATTAAAACAAG
Found at i:46355340 original size:18 final size:19
Alignment explanation
Indices: 46355319--46355377 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
46355309 TGAAGGCAAA
46355319 GGAACAAAAAGAAAAGA-T
1 GGAACAAAAAGAAAAGAGT
*
46355337 GGAA-AAAGAAAAAAAGAGT
1 GGAACAAA-AAGAAAAGAGT
46355356 GAGAAAACAAAAAGAAAA-AGT
1 G-G--AACAAAAAGAAAAGAGT
46355377 G
1 G
46355378 AGTTGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 2 0.06
20 1 0.03
21 4 0.12
22 8 0.24
23 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (19 bp):
GGAACAAAAAGAAAAGAGT
Found at i:46355379 original size:21 final size:21
Alignment explanation
Indices: 46355321--46355379 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
46355311 AAGGCAAAGG
46355321 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
*
46355341 AA-AGAAAA-AAAGAGTGAGAA
1 AACA-AAAAGAAAAAGTGAGAA
46355361 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
46355380 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.09
20 19 0.59
21 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:46359799 original size:20 final size:20
Alignment explanation
Indices: 46359773--46359819 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
46359763 AGCTCGTTTC
46359773 CAGCTCACTT-GAGCTCAAGTT
1 CAGCTCA-TTCGAGCTCAA-TT
46359794 -AGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
46359813 CAGCTCA
1 CAGCTCA
46359820 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:46361397 original size:9 final size:9
Alignment explanation
Indices: 46361385--46361410 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
46361375 AAAAAAATCA
46361385 AAAAAAAAG
1 AAAAAAAAG
46361394 AAAAAAAAG
1 AAAAAAAAG
46361403 AAAAAAAA
1 AAAAAAAA
46361411 AGAAGTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:46361397 original size:19 final size:19
Alignment explanation
Indices: 46361374--46361414 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
46361364 ATCAAAATTC
46361374 AAAAAAAATCAAAAAAAAAG
1 AAAAAAAA-CAAAAAAAAAG
*
46361394 AAAAAAAAGAAAAAAAAAG
1 AAAAAAAACAAAAAAAAAG
46361413 AA
1 AA
46361415 GTGTGATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.02
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAAAG
Found at i:46361411 original size:10 final size:10
Alignment explanation
Indices: 46361374--46361414 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
46361364 ATCAAAATTC
**
46361374 AAAAAAAATC
1 AAAAAAAAAG
46361384 AAAAAAAAAG
1 AAAAAAAAAG
46361394 -AAAAAAAAG
1 AAAAAAAAAG
46361403 AAAAAAAAAG
1 AAAAAAAAAG
46361413 AA
1 AA
46361415 GTGTGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:46362743 original size:21 final size:21
Alignment explanation
Indices: 46362698--46362760 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
46362688 TTTGAACCAT
* *
46362698 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
46362720 TACCATTTTGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
46362741 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
46362761 CAAATACTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:46372103 original size:20 final size:20
Alignment explanation
Indices: 46372080--46372117 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46372070 TTGAGTTGAA
46372080 TTGAGCTCGAA-TGAGCTGAC
1 TTGAGCTC-AAGTGAGCTGAC
46372100 TTGAGCTCAAGTGAGCTG
1 TTGAGCTCAAGTGAGCTG
46372118 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (20 bp):
TTGAGCTCAAGTGAGCTGAC
Found at i:46376312 original size:45 final size:45
Alignment explanation
Indices: 46376248--46376390 Score: 223
Period size: 45 Copynumber: 3.2 Consensus size: 45
46376238 CATGAAATTA
*
46376248 AGGAAGCATTTGACCAACATCATGCATAATTCCTGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* *
46376293 AGGAAGCATTTGACCAACATCATTCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
46376338 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
46376383 AGGAAGCA
1 AGGAAGCA
46376391 CCATGGCCGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:46385776 original size:6 final size:6
Alignment explanation
Indices: 46385765--46385797 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
46385755 TACGGCAAAC
46385765 CATATA CATATA CATATA CATATA CATATA CAT
1 CATATA CATATA CATATA CATATA CATATA CAT
46385798 TGAACAGTTA
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:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:46393283 original size:15 final size:15
Alignment explanation
Indices: 46393263--46393316 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
46393253 GTCCGTATGT
46393263 AATTAATTTTTAAAA
1 AATTAATTTTTAAAA
* * *
46393278 AATTAAAAAATATAAAAA
1 AATT---AATTTTTAAAA
46393296 AATTAATTTTTAAAA
1 AATTAATTTTTAAAA
46393311 AATTAA
1 AATTAA
46393317 AAAATATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAATTTTTAAAA
Found at i:46393295 original size:10 final size:8
Alignment explanation
Indices: 46393272--46393329 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
46393262 TAATTAATTT
46393272 TTAAAAAA
1 TTAAAAAA
46393280 TTAAAAAA
1 TTAAAAAA
46393288 TATAAAAAAA
1 T-T-AAAAAA
***
46393298 TT-AATTT
1 TTAAAAAA
46393305 TTAAAAAA
1 TTAAAAAA
46393313 TTAAAAAA
1 TTAAAAAA
46393321 TATAAAAAA
1 T-TAAAAAA
46393330 CATTTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
7 4 0.10
8 20 0.50
9 9 0.22
10 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:46393305 original size:33 final size:33
Alignment explanation
Indices: 46393263--46393329 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
46393253 GTCCGTATGT
46393263 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
1 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
46393296 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
1 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
46393329 A
1 A
46393330 CATTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (33 bp):
AATTAATTTTTAAAAAATTAAAAAATATAAAAA
Found at i:46393337 original size:31 final size:32
Alignment explanation
Indices: 46393263--46393341 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 32
46393253 GTCCGTATGT
46393263 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
1 AATT-ATTTTTAAAAAATTAAAAAATATAAAAA
46393296 AATTAATTTTTAAAAAATTAAAAAATATAAAAA
1 AATT-ATTTTTAAAAAATTAAAAAATATAAAAA
46393329 ACA-T-TTTTTAAAA
1 A-ATTATTTTTAAAA
46393342 TTAAAATCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 9 0.20
33 35 0.78
34 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AATTATTTTTAAAAAATTAAAAAATATAAAAA
Found at i:46396688 original size:21 final size:21
Alignment explanation
Indices: 46396649--46396690 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46396639 TTTTCCTAGG
*
46396649 ATGTGAATTGGATGGAATTGA
1 ATGTGAATTGGATGAAATTGA
* *
46396670 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATGAAATTGA
46396691 GTTAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
ATGTGAATTGGATGAAATTGA
Found at i:46397190 original size:27 final size:26
Alignment explanation
Indices: 46397126--46397199 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 26
46397116 ATTCTGTTAT
* *
46397126 ATGGCTCTTCGTGAGCTTCCTGATTAA
1 ATGGCTCTTTGTGAGCTTCC-CATTAA
46397153 A-GGCTCTTTGTGAGCTTCCCATTAA
1 ATGGCTCTTTGTGAGCTTCCCATTAA
46397178 ATTGGCTCTTTGTGAGCTTCCC
1 A-TGGCTCTTTGTGAGCTTCCC
46397200 GATATGACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.14
26 17 0.40
27 20 0.47
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
ATGGCTCTTTGTGAGCTTCCCATTAA
Found at i:46400926 original size:19 final size:18
Alignment explanation
Indices: 46400898--46400934 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
46400888 CATGAATAAC
*
46400898 AAGAATTATAAAATCATTA
1 AAGAAATATAAAAT-ATTA
46400917 AAGAAATATAAAATATTA
1 AAGAAATATAAAATATTA
46400935 TTATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
AAGAAATATAAAATATTA
Found at i:46401663 original size:12 final size:12
Alignment explanation
Indices: 46401646--46401673 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
46401636 AATATTGCAG
46401646 TATTATACTCAT
1 TATTATACTCAT
46401658 TATTATACTCAT
1 TATTATACTCAT
46401670 TATT
1 TATT
46401674 TTATCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATACTCAT
Found at i:46410022 original size:66 final size:66
Alignment explanation
Indices: 46409916--46410045 Score: 242
Period size: 66 Copynumber: 2.0 Consensus size: 66
46409906 ATCAAATCTT
46409916 GATAATAATTGCATTATAACAGAAGCCAGTAAAATATCCAACCTTCCATTTCTGATTTGTGGTTC
1 GATAATAATTGCATTATAACAGAAGCCAGTAAAATATCCAACCTTCCATTTCTGATTTGTGGTTC
46409981 A
66 A
* *
46409982 GATAATAATTGCATTATTACAGAAGCCAGTAAAATATCCAACCTTCCATTTCTGCTTTGTGGTT
1 GATAATAATTGCATTATAACAGAAGCCAGTAAAATATCCAACCTTCCATTTCTGATTTGTGGTT
46410046 TAGCAGGTAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (66 bp):
GATAATAATTGCATTATAACAGAAGCCAGTAAAATATCCAACCTTCCATTTCTGATTTGTGGTTC
A
Found at i:46410993 original size:61 final size:61
Alignment explanation
Indices: 46410919--46411050 Score: 246
Period size: 61 Copynumber: 2.2 Consensus size: 61
46410909 CCTAGAGCTC
46410919 AAGCATGAAATGTTATTCTTTCATGCACAATAAAATTGTTTATAAGGCTGAGTGTTATGTG
1 AAGCATGAAATGTTATTCTTTCATGCACAATAAAATTGTTTATAAGGCTGAGTGTTATGTG
* *
46410980 AAGCATGAAATGTTTTTCTTTCATGCACAGTAAAATTGTTTATAAGGCTGAGTGTTATGTG
1 AAGCATGAAATGTTATTCTTTCATGCACAATAAAATTGTTTATAAGGCTGAGTGTTATGTG
46411041 AAGCATGAAA
1 AAGCATGAAA
46411051 AGCCAGAGAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (61 bp):
AAGCATGAAATGTTATTCTTTCATGCACAATAAAATTGTTTATAAGGCTGAGTGTTATGTG
Found at i:46412971 original size:13 final size:13
Alignment explanation
Indices: 46412955--46412991 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
46412945 GTGTATATTT
*
46412955 AAAATTTATATAA
1 AAAATTAATATAA
*
46412968 AAAAATAATATAA
1 AAAATTAATATAA
46412981 AAAATTAATAT
1 AAAATTAATAT
46412992 GGGCGGGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTAATATAA
Found at i:46413357 original size:28 final size:29
Alignment explanation
Indices: 46413326--46413385 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
46413316 AAAAAATTTA
* *
46413326 TTTTTT-TATTTTTTTTGAAAGAT-TAAT
1 TTTTTTCTATTTTTATTAAAAGATATAAT
*
46413353 TTTTTTCTATTTTTATTAAAAGATATACT
1 TTTTTTCTATTTTTATTAAAAGATATAAT
46413382 TTTT
1 TTTT
46413386 AATATAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (29 bp):
TTTTTTCTATTTTTATTAAAAGATATAAT
Found at i:46413539 original size:22 final size:22
Alignment explanation
Indices: 46413484--46413539 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
46413474 TTTTTAACTA
46413484 TTTGA-ATTTTTAAATATATTT
1 TTTGAGATTTTTAAATATATTT
** **
46413505 TTTGATTTTTTTACTTATATTT
1 TTTGAGATTTTTAAATATATTT
*
46413527 TTTTAGATTTTTA
1 TTTGAGATTTTTA
46413540 TAACTTCTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTGAGATTTTTAAATATATTT
Found at i:46415971 original size:21 final size:21
Alignment explanation
Indices: 46415945--46416004 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
46415935 TTCTCTAACC
46415945 ATGGTCAAAATTATTTTGAAA
1 ATGGTCAAAATTATTTTGAAA
** *
46415966 ATGGTCAAAATTATAATGGAA
1 ATGGTCAAAATTATTTTGAAA
* *
46415987 GTGGTCAGAATTATTTTG
1 ATGGTCAAAATTATTTTG
46416005 CTGGTCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (21 bp):
ATGGTCAAAATTATTTTGAAA
Found at i:46416027 original size:18 final size:17
Alignment explanation
Indices: 46415987--46416032 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
46415977 TATAATGGAA
* *
46415987 GTGGTCAGAATTATTTT
1 GTGGTCAAAATTATATT
46416004 GCTGGTCAAAATTATGATT
1 G-TGGTCAAAATTAT-ATT
46416023 GTGGTCAAAA
1 GTGGTCAAAA
46416033 GTGGTATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 3 0.12
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (17 bp):
GTGGTCAAAATTATATT
Found at i:46427517 original size:15 final size:14
Alignment explanation
Indices: 46427499--46427529 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
46427489 TTAATTTATT
46427499 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
46427514 TAATAATAATCTAA
1 TAATAATAATCTAA
46427528 TA
1 TA
46427530 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:46427540 original size:21 final size:20
Alignment explanation
Indices: 46427516--46427584 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
46427506 AATGCTAATA
46427516 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
46427537 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
46427556 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
46427577 ATAATAAT
1 ATAATAAT
46427585 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:46437035 original size:23 final size:23
Alignment explanation
Indices: 46437007--46437060 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
46436997 ACAATTTATA
46437007 AATATTTTATAATATA-AAATATG
1 AATATTTTA-AATATATAAATATG
* *
46437030 ATTATTTTAATTATATAAATATG
1 AATATTTTAAATATATAAATATG
46437053 AATATTTT
1 AATATTTT
46437061 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
AATATTTTAAATATATAAATATG
Found at i:46438284 original size:76 final size:75
Alignment explanation
Indices: 46438153--46438297 Score: 263
Period size: 76 Copynumber: 1.9 Consensus size: 75
46438143 TTCTAATGAT
*
46438153 AACAAATCTTTTGAGATTTTGTTTGTATTGCTTTCAATATCTAACCATATATTTCGTCCCCCCCC
1 AACAAATATTTTGAGATTTTGTTTGTATTGCTTTCAATATCTAACCATATATTTCGTCCCCCCCC
46438218 CCCCCACAAA
66 CCCCCACAAA
*
46438228 ANACAAATATTTTGAGATTTTGTTTGTATTGCTTTCAATATCTAACCATATCTTTCGTCCCCCCC
1 A-ACAAATATTTTGAGATTTTGTTTGTATTGCTTTCAATATCTAACCATATATTTCGTCCCCCCC
46438293 CCCCC
65 CCCCC
46438298 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 1 0.01
76 66 0.99
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.37
Consensus pattern (75 bp):
AACAAATATTTTGAGATTTTGTTTGTATTGCTTTCAATATCTAACCATATATTTCGTCCCCCCCC
CCCCCACAAA
Found at i:46440366 original size:26 final size:24
Alignment explanation
Indices: 46440337--46440384 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
46440327 ATATTGTGGG
*
46440337 GAGA-AGAAAAAATCAGAGAGTTAA
1 GAGAGAGAAAAAATAAG-GAGTTAA
46440361 GAGAGAGAAAAAATAAGGAGTTAA
1 GAGAGAGAAAAAATAAGGAGTTAA
46440385 TAAAGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.12
Consensus pattern (24 bp):
GAGAGAGAAAAAATAAGGAGTTAA
Found at i:46447293 original size:24 final size:24
Alignment explanation
Indices: 46447266--46447317 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
46447256 TACACACATG
46447266 TACACATGTAATAATTCATCACCA
1 TACACATGTAATAATTCATCACCA
46447290 TACACATGTAATAATTCATCACCA
1 TACACATGTAATAATTCATCACCA
46447314 TACA
1 TACA
46447318 TTTGTCACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (24 bp):
TACACATGTAATAATTCATCACCA
Found at i:46447801 original size:44 final size:42
Alignment explanation
Indices: 46447726--46447810 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 42
46447716 TTGTTGTTTA
* *
46447726 AATCTACTCCATTACAACTTCAAGGAGATAAGACTTGTAGCTTC
1 AATCTACTCCACTACAACTTCAAGGAAATAAGA-TT-TAGCTTC
*
46447770 AATCTACTCCACTGCAACTTC-AGTGAAATAAGATTTAGCTT
1 AATCTACTCCACTACAACTTCAAG-GAAATAAGATTTAGCTT
46447811 GTAGCTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 6 0.16
43 4 0.11
44 27 0.73
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (42 bp):
AATCTACTCCACTACAACTTCAAGGAAATAAGATTTAGCTTC
Found at i:46447955 original size:50 final size:49
Alignment explanation
Indices: 46447856--46448084 Score: 140
Period size: 44 Copynumber: 4.8 Consensus size: 49
46447846 GATTCACTAT
** * * *
46447856 CTTCAATCTGCTCTACTGCAACTTCAGAGAGATGAGA-TT-T---GTGA
1 CTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGATTTGTCACGTGA
*
46447900 CTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTGTCACGGTGA
1 CTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGATTTGTCAC-GTGA
* * * * * *
46447950 CTTCAATCCA-TCCTAGTGCAACTTCAGGG-GTTTAGGATTTGTGACTTGTA
1 CTTCAATCTATTCC-ACTGCAACTTCAGGGAG-ATAAGATTTGTCACGTG-A
* * * *
46448000 GCTTTAATCTATTCCACTGAAACTTCAGGGAAATAAGATTCG-CA--T--
1 -CTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGATTTGTCACGTGA
* * * * *
46448045 CCTCAATCTACTCCATTGCAAATTTAGGGAGATAAGATTT
1 CTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGATTT
46448085 ATAACTCGTA
Statistics
Matches: 143, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
44 63 0.44
45 2 0.01
46 1 0.01
48 1 0.01
49 6 0.04
50 39 0.27
51 28 0.20
52 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (49 bp):
CTTCAATCTATTCCACTGCAACTTCAGGGAGATAAGATTTGTCACGTGA
Found at i:46450320 original size:15 final size:15
Alignment explanation
Indices: 46450300--46450335 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46450290 TGTTCATTTA
46450300 TTTATTAATATATAT
1 TTTATTAATATATAT
* *
46450315 TTTATTCATTTATAT
1 TTTATTAATATATAT
46450330 TTTATT
1 TTTATT
46450336 TTAATTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTAATATATAT
Found at i:46450320 original size:19 final size:20
Alignment explanation
Indices: 46450296--46450344 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
46450286 CGTTTGTTCA
46450296 TTTATTTATTAATA-TATAT
1 TTTATTTATTAATATTATAT
* * *
46450315 TTTATTCATTTATATTTTAT
1 TTTATTTATTAATATTATAT
*
46450335 TTTAATTATT
1 TTTATTTATT
46450345 GTATCCATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTATTAATATTATAT
Found at i:46450404 original size:17 final size:17
Alignment explanation
Indices: 46450366--46450407 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
46450356 CCTATCGTTC
46450366 TTTTATTTCTTTTCAAT
1 TTTTATTTCTTTTCAAT
46450383 TTTTACTTTC-TTTC-AT
1 TTTTA-TTTCTTTTCAAT
46450399 TATTTATTT
1 T-TTTATTT
46450408 TATTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
17 13 0.57
18 4 0.17
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTTCTTTTCAAT
Found at i:46450449 original size:21 final size:21
Alignment explanation
Indices: 46450419--46450473 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
46450409 ATTTATATTT
46450419 TTAT-TATTATTACCATTTTA
1 TTATCTATTATTACCATTTTA
**
46450439 TTATCTATTATTATTATTTTA
1 TTATCTATTATTACCATTTTA
46450460 TTCATCTATCTATT
1 TT-ATCTAT-TATT
46450474 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 4 0.13
21 16 0.53
22 6 0.20
23 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATCTATTATTACCATTTTA
Found at i:46450476 original size:21 final size:21
Alignment explanation
Indices: 46450433--46450480 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
46450423 TATTATTACC
46450433 ATTTTATTATCTATTATTATT
1 ATTTTATTATCTATTATTATT
46450454 ATTTTATTCATCTATCTA-T-TT
1 ATTTTATT-ATCTAT-TATTATT
46450475 ATTTTA
1 ATTTTA
46450481 AAAATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 16 0.64
22 7 0.28
23 2 0.08
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTATTATCTATTATTATT
Found at i:46450560 original size:3 final size:3
Alignment explanation
Indices: 46450554--46450586 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
46450544 AATAATAATA
*
46450554 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46450587 GTTGTTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:46452120 original size:18 final size:18
Alignment explanation
Indices: 46452099--46452134 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46452089 AGAAAATGAG
46452099 CCAAAGTACGAAATCAAC
1 CCAAAGTACGAAATCAAC
46452117 CCAAAGTACGAAATCAAC
1 CCAAAGTACGAAATCAAC
46452135 ACGGCCTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.11, T:0.11
Consensus pattern (18 bp):
CCAAAGTACGAAATCAAC
Found at i:46467777 original size:46 final size:46
Alignment explanation
Indices: 46467725--46467906 Score: 222
Period size: 46 Copynumber: 4.0 Consensus size: 46
46467715 AGTGTGCTCT
* * *
46467725 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
46467771 CTGATATGAGATGTGTAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
46467817 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
46467863 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
46467907 TCACGTCAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.01
46 118 0.99
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:46468212 original size:23 final size:25
Alignment explanation
Indices: 46468168--46468213 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
46468158 ATAAATATAT
*
46468168 ATAAAATATATGGAAATGATGAAGC
1 ATAAAATATATGGAAATAATGAAGC
*
46468193 ATAAAATAT-T-GATATAATGAA
1 ATAAAATATATGGAAATAATGAA
46468214 ATGAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 1 0.05
25 9 0.47
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (25 bp):
ATAAAATATATGGAAATAATGAAGC
Found at i:46470025 original size:47 final size:48
Alignment explanation
Indices: 46469958--46470080 Score: 140
Period size: 47 Copynumber: 2.6 Consensus size: 48
46469948 GGGCTATCGA
** *
46469958 CATCGATATGTGATCCCATGTAAGACCGTGTCTGAGACATAGCATTCG
1 CATCGATATGACATCCCATGTAAGACCATGTCTGAGACATAGCATTCG
* * * * * *
46470006 CATCGATCT-ACATCCCATGTAAGACTATGTTTGGGACATGGCATTGG
1 CATCGATATGACATCCCATGTAAGACCATGTCTGAGACATAGCATTCG
**
46470053 CATCGATATGTGATCCCATGTAAGACCA
1 CATCGATATGACATCCCATGTAAGACCA
46470081 GATCGGGGAT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 38 0.62
48 23 0.38
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (48 bp):
CATCGATATGACATCCCATGTAAGACCATGTCTGAGACATAGCATTCG
Found at i:46470095 original size:48 final size:47
Alignment explanation
Indices: 46469879--46470104 Score: 171
Period size: 48 Copynumber: 4.9 Consensus size: 47
46469869 GGTTATGTAC
* *
46469879 GATCCCATGTAAGA-CATGTCTGGGACATTGCTTTGGCATCGATATGT
1 GATCCCATGTAAGACCA-GTCTGGGACATGGCATTGGCATCGATATGT
* ** * * *
46469926 AATTTCGTGTAAGACCA-TAGCTGGG-C-T---ATCGACATCGATATGT
1 GATCCCATGTAAGACCAGT--CTGGGACATGGCATTGGCATCGATATGT
* * * * * *
46469969 GATCCCATGTAAGACCGTGTCTGAGACATAGCATTCGCATCGATCT-A
1 GATCCCATGTAAGACC-AGTCTGGGACATGGCATTGGCATCGATATGT
* * *
46470016 CATCCCATGTAAGACTATGTTTGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCA-GTCTGGGACATGGCATTGGCATCGATATGT
* *
46470064 GATCCCATGTAAGACCAGATCGGGGATATGGCATTGGCATC
1 GATCCCATGTAAGACCAG-TCTGGGACATGGCATTGGCATC
46470105 CTACCATGTG
Statistics
Matches: 134, Mismatches: 32, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
43 29 0.22
44 1 0.01
45 2 0.01
46 2 0.01
47 49 0.37
48 51 0.38
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (47 bp):
GATCCCATGTAAGACCAGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:46470623 original size:14 final size:14
Alignment explanation
Indices: 46470601--46470634 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
46470591 CTTCGTCTTT
*
46470601 GCATATGAGCATGA
1 GCATGTGAGCATGA
46470615 GCATGTGAGCATGA
1 GCATGTGAGCATGA
46470629 GCATGT
1 GCATGT
46470635 ATAGGGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (14 bp):
GCATGTGAGCATGA
Found at i:46471850 original size:19 final size:19
Alignment explanation
Indices: 46471826--46471880 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
46471816 GGTCTTTTTT
*
46471826 ATGAAACTTAATGCATATG-
1 ATGAAA-TTAATGCAAATGA
46471845 ATGAAATGTAATGCAAATGA
1 ATGAAAT-TAATGCAAATGA
46471865 ATGAAATTAATGCAAA
1 ATGAAATTAATGCAAA
46471881 AAAAGGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.76
20 7 0.21
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.27
Consensus pattern (19 bp):
ATGAAATTAATGCAAATGA
Found at i:46479090 original size:23 final size:23
Alignment explanation
Indices: 46479063--46479160 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
46479053 AGTGTTATTG
46479063 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
46479086 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
46479109 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46479131 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
46479154 ATCAGTG
1 ATCAGTG
46479161 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:46479129 original size:45 final size:45
Alignment explanation
Indices: 46479065--46479153 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
46479055 TGTTATTGAT
* *
46479065 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
46479110 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
46479154 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:46482003 original size:9 final size:9
Alignment explanation
Indices: 46481989--46482021 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
46481979 AATGAAGGAA
46481989 TTGAGAGAG
1 TTGAGAGAG
46481998 TTGAGAGAG
1 TTGAGAGAG
*
46482007 TTGAGAGAA
1 TTGAGAGAG
46482016 TTGAGA
1 TTGAGA
46482022 ATTTAGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.24
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:46482030 original size:9 final size:9
Alignment explanation
Indices: 46481986--46482034 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
46481976 TAAAATGAAG
46481986 GAATTGAGA
1 GAATTGAGA
*
46481995 GAGTTGAGA
1 GAATTGAGA
*
46482004 GAGTTGAGA
1 GAATTGAGA
46482013 GAATTGAGA
1 GAATTGAGA
*
46482022 -ATTTAGAGA
1 GAATT-GAGA
46482031 GAAT
1 GAAT
46482035 AAAAAAAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 3 0.09
9 29 0.85
10 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (9 bp):
GAATTGAGA
Found at i:46482171 original size:2 final size:2
Alignment explanation
Indices: 46482158--46482194 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
46482148 TTCAACTCAA
*
46482158 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
46482195 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:46487794 original size:14 final size:15
Alignment explanation
Indices: 46487775--46487804 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46487765 GAAGGGATAC
46487775 TTTGTTT-TTTCTTT
1 TTTGTTTGTTTCTTT
46487789 TTTGTTTGTTTCTTT
1 TTTGTTTGTTTCTTT
46487804 T
1 T
46487805 ATTAGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTGTTTGTTTCTTT
Found at i:46495024 original size:16 final size:16
Alignment explanation
Indices: 46494991--46495024 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46494981 TGTTAGTGTT
* *
46494991 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
46495007 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
46495023 AA
1 AA
46495025 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:46497852 original size:21 final size:21
Alignment explanation
Indices: 46497826--46497866 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46497816 AGACGAGCAA
* *
46497826 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
46497847 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
46497867 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:46502854 original size:3 final size:3
Alignment explanation
Indices: 46502846--46502878 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
46502836 GCTTATGTTA
46502846 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46502879 TTAAGAGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46506938 original size:8 final size:8
Alignment explanation
Indices: 46506925--46506954 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
46506915 ACAAGCAAGC
46506925 AAACAAAG
1 AAACAAAG
46506933 AAACAAAG
1 AAACAAAG
*
46506941 AAACAAAC
1 AAACAAAG
46506949 AAACAA
1 AAACAA
46506955 GCACTGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.77, C:0.17, G:0.07, T:0.00
Consensus pattern (8 bp):
AAACAAAG
Found at i:46509893 original size:19 final size:19
Alignment explanation
Indices: 46509866--46509903 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
46509856 GTCATTACTT
46509866 AATAAGGCTACCATACATA
1 AATAAGGCTACCATACATA
*
46509885 AATAGGGCTACCATACATA
1 AATAAGGCTACCATACATA
46509904 GGATAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (19 bp):
AATAAGGCTACCATACATA
Found at i:46510810 original size:3 final size:3
Alignment explanation
Indices: 46510802--46510832 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
46510792 TAGTGTGCTG
46510802 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46510833 GTAGTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46517299 original size:5 final size:6
Alignment explanation
Indices: 46517284--46517309 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
46517274 TCTCTGTATG
46517284 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
46517310 GCACTAGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:46521171 original size:14 final size:13
Alignment explanation
Indices: 46521154--46521196 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
46521144 TAAAAATCTC
46521154 AACTTAAACTCTAA
1 AACTTAAA-TCTAA
*
46521168 AACTTAAATCTTA
1 AACTTAAATCTAA
46521181 AACTATAAATCCTAA
1 AACT-TAAAT-CTAA
46521196 A
1 A
46521197 CTCTAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.32
14 13 0.52
15 4 0.16
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (13 bp):
AACTTAAATCTAA
Found at i:46521180 original size:21 final size:20
Alignment explanation
Indices: 46521154--46521238 Score: 82
Period size: 21 Copynumber: 4.2 Consensus size: 20
46521144 TAAAAATCTC
*
46521154 AACTTAAACTCTAAAACTTA
1 AACTTAAACTCTAAAACCTA
* *
46521174 AATCTTAAACTATAAATCCTA
1 AA-CTTAAACTCTAAAACCTA
**
46521195 AACTCTAATGT-TAAAAACCTA
1 AACT-TAAACTCT-AAAACCTA
*
46521216 AACTTAAACTCTAAAACTTA
1 AACTTAAACTCTAAAACCTA
46521236 AAC
1 AAC
46521239 CCTAAACTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 19 0.37
21 33 0.63
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.29
Consensus pattern (20 bp):
AACTTAAACTCTAAAACCTA
Found at i:46521244 original size:21 final size:21
Alignment explanation
Indices: 46521158--46521251 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
46521148 AATCTCAACT
* * *
46521158 TAAACTCTAAAACTTAAATCT
1 TAAACTCTAAAACCTAAACCC
* * *
46521179 TAAACTATAAATCCTAAACTC
1 TAAACTCTAAAACCTAAACCC
** *
46521200 TAATGT-TAAAAACCTAAA-CT
1 TAAACTCT-AAAACCTAAACCC
*
46521220 TAAACTCTAAAACTTAAACCC
1 TAAACTCTAAAACCTAAACCC
*
46521241 TAAACTTTAAA
1 TAAACTCTAAA
46521252 TGATAAATTT
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 14 0.26
21 40 0.74
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.30
Consensus pattern (21 bp):
TAAACTCTAAAACCTAAACCC
Found at i:46521251 original size:14 final size:13
Alignment explanation
Indices: 46521212--46521247 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
46521202 ATGTTAAAAA
46521212 CCTAAACTTAAAC
1 CCTAAACTTAAAC
*
46521225 TCTAAAACTTAAAC
1 CCT-AAACTTAAAC
46521239 CCTAAACTT
1 CCTAAACTT
46521248 TAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (13 bp):
CCTAAACTTAAAC
Found at i:46524237 original size:43 final size:43
Alignment explanation
Indices: 46524103--46524242 Score: 172
Period size: 43 Copynumber: 3.3 Consensus size: 43
46524093 GTTCTCCAAC
* *
46524103 AAACGCCGCTATAGATCATGACTTTTAGCGGCACTTCTCCCAT
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAT
*** *
46524146 AAACATAGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAT
* * * ***
46524189 GAACGCCGCTATAGATCATGACTTCTAGCGGTGCTTTTTTTAT
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAT
46524232 AAACGCCGCTA
1 AAACGCCGCTA
46524243 AAAAACACGA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAT
Found at i:46524500 original size:9 final size:9
Alignment explanation
Indices: 46524486--46524537 Score: 86
Period size: 9 Copynumber: 5.8 Consensus size: 9
46524476 TTTGGTTAAA
46524486 AATTACCCG
1 AATTACCCG
46524495 AATTACCCG
1 AATTACCCG
46524504 AATTACCCG
1 AATTACCCG
*
46524513 AATTAACCG
1 AATTACCCG
*
46524522 AATTAACCG
1 AATTACCCG
46524531 AATTACC
1 AATTACC
46524538 GAAAAATACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:46525363 original size:40 final size:40
Alignment explanation
Indices: 46525282--46525363 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
46525272 AAACGCCGTA
* * * *
46525282 AATGCGCGACCTATAGCGGCGTTTTTAAAAAAGCGCTGCT
1 AATGCGCGAACTATAGCAGCGTTTTTAAAAAAGCACCGCT
*
46525322 AATGCTCGAACTATAGCAGCGTTTTTAAAAAAGCACCGCT
1 AATGCGCGAACTATAGCAGCGTTTTTAAAAAAGCACCGCT
46525362 AA
1 AA
46525364 CGCCACCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCGCGAACTATAGCAGCGTTTTTAAAAAAGCACCGCT
Found at i:46526668 original size:9 final size:9
Alignment explanation
Indices: 46526654--46526803 Score: 63
Period size: 9 Copynumber: 15.9 Consensus size: 9
46526644 AATATATTAT
46526654 AATTTTTAA
1 AATTTTTAA
46526663 AA-TTTTAA
1 AATTTTTAA
*
46526671 AATTCTTATA
1 AATTTTTA-A
**
46526681 AATTTCAAA
1 AATTTTTAA
*
46526690 TAATTTTTTAC
1 -AA-TTTTTAA
*
46526701 ATTTTTTAA
1 AATTTTTAA
*
46526710 TCATTTTT-A
1 -AATTTTTAA
*
46526719 ATTTTTTAA
1 AATTTTTAA
*
46526728 ATGATTTTCTCA
1 A--ATTTT-TAA
*
46526740 ATTTTTTAA
1 AATTTTTAA
46526749 AATTTTTAA
1 AATTTTTAA
46526758 TAA-TTTTATA
1 -AATTTTTA-A
*
46526768 AATCTTTAA
1 AATTTTTAA
* * *
46526777 TATGTTCAA
1 AATTTTTAA
*
46526786 ATATTTTTAT
1 A-ATTTTTAA
46526796 AATTTTTA
1 AATTTTTA
46526804 TTAAGTCTTA
Statistics
Matches: 102, Mismatches: 26, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
8 13 0.13
9 47 0.46
10 31 0.30
11 8 0.08
12 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (9 bp):
AATTTTTAA
Found at i:46526734 original size:19 final size:18
Alignment explanation
Indices: 46526694--46526794 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 18
46526684 TTCAAATAAT
46526694 TTTTTACATTTTTT-AATCA
1 TTTTTA-ATTTTTTAAAT-A
46526713 TTTTTAATTTTTTAAATGA
1 TTTTTAATTTTTTAAAT-A
46526732 TTTTCTCAATTTTTTAAA-A
1 TTTT-T-AATTTTTTAAATA
*
46526751 TTTTTAATAATTTTATAA-A
1 TTTTTAAT-TTTTTA-AATA
* * *
46526770 TCTTTAATATGTTCAAATA
1 TTTTTAAT-TTTTTAAATA
46526789 TTTTTA
1 TTTTTA
46526795 TAATTTTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.04
18 15 0.22
19 39 0.57
20 1 0.01
21 11 0.16
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTTAATTTTTTAAATA
Found at i:46526765 original size:39 final size:39
Alignment explanation
Indices: 46526665--46526765 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 39
46526655 ATTTTTAAAA
* * *
46526665 TTTTAAAATTCTT-ATAAATTTCAAATAATTTTTTACATT
1 TTTTAAAATTTTTAAT-AATTTTAAATAATTTTTCACATT
* * *
46526704 TTTTAATCATTTTTAAT-TTTTTAAATGATTTTCTCA-ATT
1 TTTTAA-AATTTTTAATAATTTTAAATAATTTT-TCACATT
46526743 TTTTAAAATTTTTAATAATTTTA
1 TTTTAAAATTTTTAATAATTTTA
46526766 TAAATCTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
38 9 0.18
39 32 0.64
40 7 0.14
41 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (39 bp):
TTTTAAAATTTTTAATAATTTTAAATAATTTTTCACATT
Found at i:46527224 original size:64 final size:64
Alignment explanation
Indices: 46527020--46527350 Score: 368
Period size: 64 Copynumber: 5.2 Consensus size: 64
46527010 AGAAATCACA
* *
46527020 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTG
1 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
* ** * * * * *
46527084 TTTGTAATGCTTTTGAGTGTTCGGGGTTT-ACT-CTTTTTTATTTGCATACAACAGTGG-CTTTC
1 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCA-TTGAAGACAACAGTGGTCTTT-
46527146 G
64 G
* ** *
46527147 TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAGTACTGGTCTTTG
1 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
* * * * * * *
46527211 TTTGTAATGCTTTTGAGTGTTTGGGGTTT-ACT-CTTTTTTACTTGCACACAACAGTGG-CTTTC
1 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCA-TTGAAGACAACAGTGGTCTTT-
46527273 G
64 G
* *
46527274 TTTGTTATGCTTTTGGGTGTTTAGAGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
1 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
*
46527338 TTTGTATTGCTTT
1 TTTGTAATGCTTT
46527351 CGGTGTAGCC
Statistics
Matches: 213, Mismatches: 44, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
62 20 0.09
63 79 0.37
64 94 0.44
65 20 0.09
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.48
Consensus pattern (64 bp):
TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTG
Found at i:46527246 original size:127 final size:127
Alignment explanation
Indices: 46527020--46527350 Score: 581
Period size: 127 Copynumber: 2.6 Consensus size: 127
46527010 AGAAATCACA
*
46527020 TTTGTAATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTGT
1 TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTGT
* *
46527085 TTGTAATGCTTTTGAGTGTTCGGGGTTTACTCTTTTTTATTTGCATACAACAGTGGCTTTCG
66 TTGTAATGCTTTTGAGTGTTCGGGGTTTACTCTTTTTTACTTGCACACAACAGTGGCTTTCG
*
46527147 TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAGTACTGGTCTTTGT
1 TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTGT
*
46527212 TTGTAATGCTTTTGAGTGTTTGGGGTTTACTCTTTTTTACTTGCACACAACAGTGGCTTTCG
66 TTGTAATGCTTTTGAGTGTTCGGGGTTTACTCTTTTTTACTTGCACACAACAGTGGCTTTCG
* * *
46527274 TTTGTTATGCTTTTGGGTGTTTAGAGTTTCATTGCTTTCTCATTGAAGACAACAGTGGTCTTTGT
1 TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTGT
*
46527339 TTGTATTGCTTT
66 TTGTAATGCTTT
46527351 CGGTGTAGCC
Statistics
Matches: 194, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 194 1.00
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.48
Consensus pattern (127 bp):
TTTGTTATGCTTTTGGGTGTTTAGGGTTTCATTGCTTTCTCATTGAAGACAATACTGGTCTTTGT
TTGTAATGCTTTTGAGTGTTCGGGGTTTACTCTTTTTTACTTGCACACAACAGTGGCTTTCG
Found at i:46530390 original size:16 final size:16
Alignment explanation
Indices: 46530369--46530412 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
46530359 ATTTTGTTAC
*
46530369 AACAATTATTACAATT
1 AACAATTAATACAATT
46530385 AACAATTAATACAATT
1 AACAATTAATACAATT
*
46530401 AATAATTTAATA
1 AACAA-TTAATA
46530413 ATTTTACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:46530498 original size:16 final size:16
Alignment explanation
Indices: 46530477--46530518 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
46530467 AATAATTTGA
* *
46530477 TAATTTTACTAATAAT
1 TAATTTTAATAACAAT
46530493 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
46530509 TAATTTTAAT
1 TAATTTTAAT
46530519 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:46532516 original size:48 final size:48
Alignment explanation
Indices: 46532460--46532555 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
46532450 ATCAATTGGG
46532460 TGGTCAGTTGGTGCCACTCTTGGATATGCACAGGCTGTTCCAGAGAAA
1 TGGTCAGTTGGTGCCACTCTTGGATATGCACAGGCTGTTCCAGAGAAA
*
46532508 TGGTCAGTTGGTGCCACTCTTGGATATGCACAGGCTGTTCCGGAGAAA
1 TGGTCAGTTGGTGCCACTCTTGGATATGCACAGGCTGTTCCAGAGAAA
46532556 CGTGTCATCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (48 bp):
TGGTCAGTTGGTGCCACTCTTGGATATGCACAGGCTGTTCCAGAGAAA
Found at i:46534053 original size:14 final size:14
Alignment explanation
Indices: 46534034--46534060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46534024 TTGAATCGAA
46534034 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
46534048 TCGAGTTAAATTA
1 TCGAGTTAAATTA
46534061 AAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:46535211 original size:15 final size:15
Alignment explanation
Indices: 46535191--46535220 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46535181 GATGTGTATT
*
46535191 TTATAAATTCGGATA
1 TTATAAATTCAGATA
46535206 TTATAAATTCAGATA
1 TTATAAATTCAGATA
46535221 ACATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (15 bp):
TTATAAATTCAGATA
Found at i:46538738 original size:44 final size:44
Alignment explanation
Indices: 46538675--46538760 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
46538665 TGATTGAATT
* *
46538675 GAATTGACTCGAATAAAAAATATTTGAGTTAGTCAAGTTGACAA
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
46538719 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
46538761 GAGTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (44 bp):
GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
Found at i:46539140 original size:20 final size:20
Alignment explanation
Indices: 46539108--46539160 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
46539098 AACCTTTATT
46539108 TTTTA-AAATTTTTATAAAAA
1 TTTTAGAAA-TTTTATAAAAA
*
46539128 TTTTAGAAATTTTATAAATA
1 TTTTAGAAATTTTATAAAAA
*
46539148 TTTT-GAAAATTTA
1 TTTTAGAAATTTTA
46539161 AGGTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTAGAAATTTTATAAAAA
Found at i:46539144 original size:45 final size:45
Alignment explanation
Indices: 46539057--46539144 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 45
46539047 TTTATCATTT
* * *
46539057 TTTATTTTTTTAATTTTTTAAAGATTTTTAGAATTTTATATAACC
1 TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
46539102 TTTATTTTTTAAAATTTTTATAAA-AATTTTAGAAATTT-TATAA
1 TTTATTTTTT-AAATTTTT-TAAAGAATTTTAGAAATTTATATAA
46539145 ATATTTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 15 0.39
46 19 0.50
47 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (45 bp):
TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
Found at i:46541491 original size:104 final size:104
Alignment explanation
Indices: 46541208--46541668 Score: 477
Period size: 104 Copynumber: 4.4 Consensus size: 104
46541198 ATCAGTATAC
* * *
46541208 TCAGAATCAAATATCAGTATACGAAAAAAGT--AAAAAAAAATTATGGGTGCTGGCCTGTCAATG
1 TCAGAATCAGATATAAATATACGAAAAAA-TAAAAAAAAAAATT-TGGGTGCTGGCCTGTCAATG
46541271 GCCGGCACCCAGTACAAATTTAAAAGAAAATTTCTTTTTTTTTTCGTG
64 GCCGGCACCCAGTACAAATTTAAAA-AAAA------TTTTTTTTCGTG
* *
46541319 TCAAAATCAGATATAAATATACG-AAAAA-AATAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC
1 TCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC
***
46541382 CGGCACCCAGTACAAA-TTAAAAAAAAAAATTTTT-GTG
66 CGGCACCCAGTACAAATTTAAAAAAAATTTTTTTTCGTG
*
46541419 TCAGAATCAGATATAAATATACGCAAAAAATAAAAATAAAAAATTTGGGTGCTAGCCTGTCAATG
1 TCAGAATCAGATATAAATATACG-AAAAAATAAAAA-AAAAAATTTGGGTGCTGGCCTGTCAATG
*
46541484 GCCGGCACCCAGTACAAATTTAAAAAAATTCTTTTTTTTTTCGTG
64 GCCGGCACCCAGTACAAATTTAAAAAAA----ATTTTTTTTCGTG
*
46541529 TCAGAATCAGATATAAATATACG----------AAAAAAATTTTGGGTGCTGGCCTGTCAATGGC
1 TCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC
* * *
46541584 TGGCACCCAGTACAAATTTTTTAAAAAAATTCTTTTTTTTTGTGTG
66 CGGCACCCAGTACAAA---TTTAAAAAAA---ATTTTTTTT-CGTG
46541630 TCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAA
1 TCAGAATCAGATATAAATATACG-AAAAAATAAAAAAAA
46541669 TTATATATAA
Statistics
Matches: 302, Mismatches: 21, Indels: 53
0.80 0.06 0.14
Matches are distributed among these distances:
98 43 0.14
99 2 0.01
100 35 0.12
101 41 0.14
102 5 0.02
103 4 0.01
104 45 0.15
105 9 0.03
107 4 0.01
108 6 0.02
109 43 0.14
110 41 0.14
111 19 0.06
112 5 0.02
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (104 bp):
TCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGC
CGGCACCCAGTACAAATTTAAAAAAAATTTTTTTTCGTG
Found at i:46541620 original size:98 final size:97
Alignment explanation
Indices: 46541241--46541660 Score: 427
Period size: 101 Copynumber: 4.1 Consensus size: 97
46541231 AAAAAAGTAA
* *
46541241 AAAAAAATTATGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAGAAAATTTCT
1 AAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTT-AAA-AAAA-TTC-
* *
46541306 TTTTTTTTTCGTGTCAAAATCAGATATAAATATACG
62 TTTTTTTTGCGTGTCAGAATCAGATATAAATATACG
*
46541342 AAAAAAATAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTAAAAAA
1 AAAAAAAT--------TTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAA
****
46541406 A--AAAATTTTT--GTGTCAGAATCAGATATAAATATACG
58 ATTCTTTTTTTTGCGTGTCAGAATCAGATATAAATATACG
46541442 CAAAAAATAAAAATAAAAAATTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTAA
1 -----AA-AAAAAT------TTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTAA
*
46541507 AAAAATTCTTTTTTTTTTCGTGTCAGAATCAGATATAAATATACG
54 AAAAATTC-TTTTTTTTGCGTGTCAGAATCAGATATAAATATACG
* *
46541552 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTACAAATTTTTTAAAAAAATTCT
1 AAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAA---TTTAAAAAAATTC-
*
46541617 TTTTTTTTGTGTGTCAGAATCAGATATAAATATACG
62 TTTTTTTTGCGTGTCAGAATCAGATATAAATATACG
46541653 AAAAAAAT
1 AAAAAAAT
46541661 AAAAAAAATT
Statistics
Matches: 281, Mismatches: 15, Indels: 46
0.82 0.04 0.13
Matches are distributed among these distances:
98 38 0.14
100 25 0.09
101 64 0.23
102 5 0.02
104 51 0.18
105 13 0.05
106 10 0.04
107 3 0.01
108 7 0.02
109 39 0.14
110 26 0.09
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (97 bp):
AAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAATTCTTTT
TTTTGCGTGTCAGAATCAGATATAAATATACG
Found at i:46542381 original size:29 final size:28
Alignment explanation
Indices: 46542348--46542402 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
46542338 TCGTAATATT
*
46542348 TAAAAATATA-AGGACTAAATTCTTAAAAA
1 TAAAAATATACA-AACTAAATT-TTAAAAA
46542377 TAAAAATATACAAACTAAATTTTAAA
1 TAAAAATATACAAACTAAATTTTAAA
46542403 TTTACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 18 0.75
30 1 0.04
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (28 bp):
TAAAAATATACAAACTAAATTTTAAAAA
Found at i:46542411 original size:29 final size:29
Alignment explanation
Indices: 46542345--46542411 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
46542335 ACTTCGTAAT
*
46542345 ATTTAAAAATATAAGGACTAAATTCTTAA
1 ATTTAAAAATATAAGAACTAAATTCTTAA
**
46542374 AAATAAAAATATACA-AACTAAATT-TTAA
1 ATTTAAAAATATA-AGAACTAAATTCTTAA
46542402 ATTTACAAAA
1 ATTTA-AAAA
46542412 AATATATAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.31
Consensus pattern (29 bp):
ATTTAAAAATATAAGAACTAAATTCTTAA
Done.