Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 89 of 335
Found at i:29097470 original size:220 final size:220
Alignment explanation
Indices: 29097054--29097471 Score: 553
Period size: 220 Copynumber: 1.9 Consensus size: 220
29097044 TATTATACGT
* *
29097054 GTCTATCCCAATCTTTTTTTACAGGTTGTTTTAAATAATATCTATCCCAACCTTTTTAAGGTTGC
1 GTCTATCCCAATCTTTTTTTACAGGTTGTTTTAAAGAATATCGATCCCAACCTTTTTAAGGTTGC
* * *
29097119 TTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTTAAACATGGTCTATCCCAACCTTTTT
66 TTTAAACAGGTCTATCCCAACCGTTTTTAAAAGTTACCTTAAACATGGACTATACCAACCTTTTT
* *
29097184 AAGATTGCCTTAAACGAGTCTATTCCAACCTTTTTTAAAGGTTGCCTTAGACATGGTCTCTCCTA
131 AAGATTGCCTTAAACGAGTCTATTCCAACCTTTTTCAAAGGTTGCCTTAGACATGGTCTATCCTA
29097249 ACCTGCTTAAGGTTGCCTTAGACAG
196 ACCTGCTTAAGGTTGCCTTAGACAG
* * *
29097274 GTCTATCCCAA-CATTTTTTTATAGGTTGTTTTAGAGAATGTCGATCCCAACCTTTTTAAGGTTG
1 GTCTATCCCAATC-TTTTTTTACAGGTTGTTTTAAAGAATATCGATCCCAACCTTTTTAAGGTTG
* * * *
29097338 CTTTAGAC-GGCTCTATCCCAACCGTTTTTAAAAGTTGCCTTAAACA-GGAACTATATCGACCTT
65 CTTTAAACAGG-TCTATCCCAACCGTTTTTAAAAGTTACCTTAAACATGG-ACTATACCAACCTT
* * * * *
29097401 TTTAAGGTTGTCTTAGAC-AGGTTTA-TCACAACCTTTTTCAAAGGTTGGTCTTA-AC-TAGGTC
128 TTTAAGATTGCCTTAAACGA-GTCTATTC-CAACCTTTTTCAAAGGTT-GCCTTAGACAT-GGTC
29097462 TATCCTAACC
189 TATCCTAACC
29097472 CTTTTTAAAG
Statistics
Matches: 172, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
219 9 0.05
220 158 0.92
221 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (220 bp):
GTCTATCCCAATCTTTTTTTACAGGTTGTTTTAAAGAATATCGATCCCAACCTTTTTAAGGTTGC
TTTAAACAGGTCTATCCCAACCGTTTTTAAAAGTTACCTTAAACATGGACTATACCAACCTTTTT
AAGATTGCCTTAAACGAGTCTATTCCAACCTTTTTCAAAGGTTGCCTTAGACATGGTCTATCCTA
ACCTGCTTAAGGTTGCCTTAGACAG
Found at i:29097475 original size:147 final size:143
Alignment explanation
Indices: 29097095--29097479 Score: 371
Period size: 147 Copynumber: 2.6 Consensus size: 143
29097085 TAAATAATAT
* * * **
29097095 CTATCCCAACCTTTTTAAGGTTGCTTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCTTA
1 CTATCCTAACCTTTTTAAGGTTGC-TTAGACAGGTCTATCCCAACCTTTTTTAAAGGTTGTCTT-
* * *
29097160 AACATGGTCTATCCCAACCTTTTTAAGATTGCCTTAAACGAGTCTATTCCAACCTTTTTTAAAGG
64 AACA-GGTCTATCCCAACCTTTTTAAGATTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAAAG
* *
29097225 TTGCCTTAGACATGGT
128 TTGCCTTAAACATGGA
* ** * * *
29097241 CTCTCCTAACCTGCTTAAGGTTGCCTTAGACAGGTCTATCCCAACATTTTTTTATAGGTTGTTTT
1 CTATCCTAACCTTTTTAAGGTTG-CTTAGACAGGTCTATCCCAAC-CTTTTTTAAAGGTTGTCTT
* * * * * *
29097306 AGAGAATGTCGATCCCAACCTTTTTAAGGTTGCTTTAGACG-GCTCTATCCCAACCGTTTTTAAA
64 A-A-CAGGTCTATCCCAACCTTTTTAAGATTGCCTTAAACGAG-TCTATCCCAACCGTTTTTAAA
29097370 AGTTGCCTTAAACA-GGAA
126 AGTTGCCTTAAACATGG-A
* * * * *
29097388 CTAT-ATCGACCTTTTTAAGGTTGTCTTAGACAGGTTTATCACAACCTTTTTCAAAGGTTGGTCT
1 CTATCCT-AACCTTTTTAAGGTTG-CTTAGACAGGTCTATCCCAACCTTTTTTAAAGGTT-GTCT
*
29097452 TAACTAGGTCTATCCTAACCCTTTTTAA
63 TAAC-AGGTCTATCCCAA-CCTTTTTAA
29097480 AGGTCGGCAT
Statistics
Matches: 191, Mismatches: 38, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
146 65 0.34
147 125 0.65
148 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (143 bp):
CTATCCTAACCTTTTTAAGGTTGCTTAGACAGGTCTATCCCAACCTTTTTTAAAGGTTGTCTTAA
CAGGTCTATCCCAACCTTTTTAAGATTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAAAGTTG
CCTTAAACATGGA
Found at i:29101939 original size:32 final size:32
Alignment explanation
Indices: 29101903--29101964 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
29101893 TCAATGACAT
* * * *
29101903 AAATAAAAACTTTTGTATAGTTTAGTGACTTA
1 AAATAAAAAATTTCGAATAGTTCAGTGACTTA
29101935 AAATAAAAAATTTCGAATAGTTCAGTGACT
1 AAATAAAAAATTTCGAATAGTTCAGTGACT
29101965 ATTTTGTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (32 bp):
AAATAAAAAATTTCGAATAGTTCAGTGACTTA
Found at i:29102348 original size:15 final size:16
Alignment explanation
Indices: 29102319--29102363 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
29102309 TTTTATAATT
29102319 ATTTTTTTGAATTTT-A
1 ATTTTTTT-AATTTTAA
*
29102335 ATTTTTTTATTTTTAA
1 ATTTTTTTAATTTTAA
29102351 ATATTTTTTAATT
1 AT-TTTTTTAATT
29102364 ATTTTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 11 0.44
17 9 0.36
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
ATTTTTTTAATTTTAA
Found at i:29107565 original size:126 final size:127
Alignment explanation
Indices: 29107412--29107646 Score: 323
Period size: 126 Copynumber: 1.9 Consensus size: 127
29107402 CATTATCTCA
* * * *
29107412 TTTTAATTTAAGAAAACATGGATGAAATTTTAAAAGGATATTCTGTATTTTAGTCGAATGGA-AA
1 TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCG-ATGGAGAA
* * * *
29107476 ATC-AAAGCCCAGCATGATTGGGCACGATCTCCCAAATC-CCCAAAACACAAAATATTGCCTCG
65 ATCGAAA-CCCAACACGATTAGGCACGATCTCCCAAACCTCCCAAAACACAAAATATTGCCTCG
* * *
29107538 TTTTAATTTAAGAAAACATAGACGAAATTTCACAAGGATATTTTGTATTCTAGTCGATTGAGAAA
1 TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCGATGGAGAAA
*
29107603 TCGAAACCCAACACGATTAGGCACGATCTCTCAAACCTCCCAAA
66 TCGAAACCCAACACGATTAGGCACGATCTCCCAAACCTCCCAAA
29107647 CACGGAAGAT
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
125 4 0.04
126 81 0.86
127 9 0.10
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (127 bp):
TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCGATGGAGAAA
TCGAAACCCAACACGATTAGGCACGATCTCCCAAACCTCCCAAAACACAAAATATTGCCTCG
Found at i:29114267 original size:4 final size:4
Alignment explanation
Indices: 29114260--29114287 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29114250 ATAAATATTG
29114260 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
29114288 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:29114764 original size:5 final size:5
Alignment explanation
Indices: 29114754--29114778 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29114744 ATTTAATGCC
29114754 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
29114779 CTATGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:29115639 original size:27 final size:27
Alignment explanation
Indices: 29115601--29115653 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
29115591 TCTTAATGAA
29115601 AAATTAAATATATATAT-ATATATATAT
1 AAATTAAATATATAT-TCATATATATAT
*
29115628 AAATTCAATATATATTCATATATATA
1 AAATTAAATATATATTCATATATATA
29115654 ATTAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATTAAATATATATTCATATATATAT
Found at i:29116078 original size:19 final size:18
Alignment explanation
Indices: 29116035--29116078 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
29116025 AAAATATAAA
29116035 TTCAAAAAATTTTAAAAT
1 TTCAAAAAATTTTAAAAT
* *
29116053 TTCCAAAACATTTTGAAAGT
1 TT-CAAAAAATTTT-AAAAT
29116073 TTCAAA
1 TTCAAA
29116079 TTAAAAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (18 bp):
TTCAAAAAATTTTAAAAT
Found at i:29116361 original size:2 final size:2
Alignment explanation
Indices: 29116312--29116346 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29116302 ATAAACCTTT
29116312 TA TA 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 TA TA T
29116347 GTGTGTGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29118365 original size:88 final size:88
Alignment explanation
Indices: 29118266--29118474 Score: 330
Period size: 88 Copynumber: 2.4 Consensus size: 88
29118256 AAAAAGATCT
* *
29118266 CTCAAACTTTTTCAAAAAAAGCAATTAAGGTCCTATTTTTTTTTCACTCATTTGAATACTTGAAC
1 CTCAAACTTTTTCAAAAAAAGCAATTAAGGTCCTATTTTTTTTGCACTCAATTGAATACTTGAAC
29118331 TTTCAAAATGCATCAAAAAAACC
66 TTTCAAAATGCATCAAAAAAACC
** * **
29118354 CTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTGCGCTCAATTGGGTACTTGAAC
1 CTCAAACTTTTTCAAAAAAAGCAATTAAGGTCCTATTTTTTTTGCACTCAATTGAATACTTGAAC
* *
29118419 TTTCAAAATGCATCAAAAAGACT
66 TTTCAAAATGCATCAAAAAAACC
29118442 CTCAAACTTTTTCAAAAAAAGCAATTAA-GTCCT
1 CTCAAACTTTTTCAAAAAAAGCAATTAAGGTCCT
29118475 TGCTTTTAGT
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 3 0.03
88 107 0.97
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (88 bp):
CTCAAACTTTTTCAAAAAAAGCAATTAAGGTCCTATTTTTTTTGCACTCAATTGAATACTTGAAC
TTTCAAAATGCATCAAAAAAACC
Found at i:29118512 original size:9 final size:9
Alignment explanation
Indices: 29118498--29118675 Score: 73
Period size: 10 Copynumber: 19.4 Consensus size: 9
29118488 AATTAGACAA
29118498 AAAAATTAT
1 AAAAATTAT
29118507 AAAAA-T-T
1 AAAAATTAT
*
29118514 -AAAATCAAT
1 AAAAAT-TAT
**
29118523 AAAAGCTAT
1 AAAAATTAT
*
29118532 AAATATTATT
1 AAAAATTA-T
**
29118542 AAATTTTAAT
1 AAAAATT-AT
*
29118552 AAAAAAT-T
1 AAAAATTAT
*
29118560 AAATATTA-
1 AAAAATTAT
29118568 AAAAATTATT
1 AAAAATTA-T
29118578 AAAAA-TAT
1 AAAAATTAT
**
29118586 AAAAATCGT
1 AAAAATTAT
*
29118595 AAAAATATAA
1 AAAAAT-TAT
*
29118605 AAAAATTGT
1 AAAAATTAT
*
29118614 AAAATTTTAT
1 AAAA-ATTAT
*
29118624 AAAAATTGT
1 AAAAATTAT
29118633 AAAAAATTAT
1 -AAAAATTAT
29118643 -AAAATATAT
1 AAAAAT-TAT
* *
29118652 AGATATATAT
1 AAAAAT-TAT
29118662 AAAAAATTAT
1 -AAAAATTAT
29118672 AAAA
1 AAAA
29118676 TTTTATAAAG
Statistics
Matches: 123, Mismatches: 30, Indels: 32
0.66 0.16 0.17
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
8 25 0.20
9 37 0.30
10 51 0.41
11 5 0.04
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29118578 original size:18 final size:18
Alignment explanation
Indices: 29118536--29118590 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
29118526 AGCTATAAAT
*
29118536 ATTATTAAATTTTAATAAA
1 ATTATTAAATATTAA-AAA
*
29118555 A-AATTAAATATTAAAAA
1 ATTATTAAATATTAAAAA
*
29118572 ATTATTAAAAATATAAAAA
1 ATTATTAAATAT-TAAAAA
29118591 TCGTAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.13
18 19 0.63
19 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTATTAAATATTAAAAA
Found at i:29118627 original size:29 final size:29
Alignment explanation
Indices: 29118594--29118684 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
29118584 ATAAAAATCG
*
29118594 TAAAAATATAAAAAAATTGTAAAATTTTA
1 TAAAAATATAAAAAAATTATAAAATTTTA
* *
29118623 TAAAAAT-TGTAAAAAATTATAAAA-TATA
1 TAAAAATAT-AAAAAAATTATAAAATTTTA
* *
29118651 TAGATATATATAAAAAATTATAAAATTTTA
1 TAAAAATATA-AAAAAATTATAAAATTTTA
29118681 TAAA
1 TAAA
29118685 GTTGTAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 9 0.18
29 35 0.70
30 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAAATATAAAAAAATTATAAAATTTTA
Found at i:29118642 original size:19 final size:19
Alignment explanation
Indices: 29118564--29118734 Score: 86
Period size: 19 Copynumber: 9.1 Consensus size: 19
29118554 AAAATTAAAT
* *
29118564 ATTA-AAAAATTATTAAAA
1 ATTATAAAAATTGTAAAAA
*
29118582 A-TATAAAAATCGT-AAAA
1 ATTATAAAAATTGTAAAAA
* *
29118599 ATATAAAAAAATTGTAAAAT
1 AT-TATAAAAATTGTAAAAA
*
29118619 TTTATAAAAATTGTAAAAA
1 ATTATAAAAATTGTAAAAA
* * *
29118638 ATTAT-AAAA-TATATAGAT
1 ATTATAAAAATTGTA-AAAA
* *
29118656 ATATATAAAAAAT-TATAAA
1 AT-TATAAAAATTGTAAAAA
* *
29118675 ATTTTATAAAGTTGTAAGAAA
1 ATTATA-AAAATTGTAA-AAA
*
29118696 ATTATACAAAA-AGTAAAAA
1 ATTATA-AAAATTGTAAAAA
* **
29118715 AATATAAATTTTGTAAAAA
1 ATTATAAAAATTGTAAAAA
29118734 A
1 A
29118735 GAAAAAGAAA
Statistics
Matches: 114, Mismatches: 27, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
17 10 0.09
18 21 0.18
19 55 0.48
20 16 0.14
21 12 0.11
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATAAAAATTGTAAAAA
Found at i:29118672 original size:10 final size:10
Alignment explanation
Indices: 29118566--29118722 Score: 66
Period size: 10 Copynumber: 16.4 Consensus size: 10
29118556 AATTAAATAT
29118566 TAAAAAATTA
1 TAAAAAATTA
*
29118576 TTAAAAA-TA
1 TAAAAAATTA
**
29118585 T-AAAAATCG
1 TAAAAAATTA
29118594 T-AAAAA-TA
1 TAAAAAATTA
*
29118602 TAAAAAAATTG
1 T-AAAAAATTA
**
29118613 TAAAATTTTA
1 TAAAAAATTA
*
29118623 T-AAAAATTG
1 TAAAAAATTA
29118632 TAAAAAATTA
1 TAAAAAATTA
*
29118642 TAAAATA-TA
1 TAAAAAATTA
* *
29118651 T-AGATATATA
1 TAAAAAAT-TA
29118661 TAAAAAATTA
1 TAAAAAATTA
*
29118671 T--AAAATTT
1 TAAAAAATTA
* * *
29118679 TATAAAGTTG
1 TAAAAAATTA
29118689 TAAGAAAATTA
1 TAA-AAAATTA
*
29118700 TACAAAAAGTA
1 TA-AAAAATTA
29118711 -AAAAAA-TA
1 TAAAAAATTA
29118719 TAAA
1 TAAA
29118723 TTTTGTAAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 27
0.68 0.15 0.17
Matches are distributed among these distances:
8 19 0.17
9 26 0.24
10 45 0.41
11 19 0.17
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:29118696 original size:29 final size:27
Alignment explanation
Indices: 29118604--29118701 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 27
29118594 TAAAAATATA
*
29118604 AAAAAATTGTAAAATTTTATAAAAATTGT
1 AAAAAATTATAAAATTTTAT--AAATTGT
* *
29118633 AAAAAATTATAAAA-TATATAGATATATAT
1 AAAAAATTATAAAATTTTATA-A-AT-TGT
29118662 AAAAAATTATAAAATTTTATAAAGTTGT
1 AAAAAATTATAAAATTTTATAAA-TTGT
29118690 AAGAAAATTATA
1 AA-AAAATTATA
29118702 CAAAAAGTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 11 0.19
29 40 0.69
30 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (27 bp):
AAAAAATTATAAAATTTTATAAATTGT
Found at i:29118925 original size:29 final size:29
Alignment explanation
Indices: 29118878--29118933 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29118868 TTAGAGGTCA
* **
29118878 TTAATTTTTTTTATGATTTTTATAAAATT
1 TTAAATTTTTTTACAATTTTTATAAAATT
29118907 TTAAATTTTTTTACAATTTTTATAAAA
1 TTAAATTTTTTTACAATTTTTATAAAA
29118934 AAATTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTAAATTTTTTTACAATTTTTATAAAATT
Found at i:29118946 original size:19 final size:19
Alignment explanation
Indices: 29118924--29118967 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
29118914 TTTTTACAAT
29118924 TTTTATAAAAAAATTAT-AA
1 TTTT-TAAAAAAATTATAAA
* *
29118943 TTTTTAATAAATTTATAAA
1 TTTTTAAAAAAATTATAAA
29118962 TTTTTA
1 TTTTTA
29118968 TATTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAAAATTATAAA
Found at i:29118960 original size:18 final size:18
Alignment explanation
Indices: 29118937--29118993 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
29118927 TATAAAAAAA
29118937 TTATAATTTTTAATAAAT
1 TTATAATTTTTAATAAAT
*
29118955 TTATAAATTTTT-AT-ATT
1 TTAT-AATTTTTAATAAAT
**
29118972 TTATTAAAATTTAATAAAT
1 TTA-TAATTTTTAATAAAT
29118991 TTA
1 TTA
29118994 CTAAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 10 0.32
18 9 0.29
19 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATAATTTTTAATAAAT
Found at i:29118993 original size:19 final size:18
Alignment explanation
Indices: 29118945--29119003 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
29118935 AATTATAATT
*
29118945 TTTAATAAATTTATAAAT
1 TTTAATAAATTTATAAAA
* *
29118963 TTTTAT-ATTTTATTAAAA
1 TTTAATAAATTTA-TAAAA
29118981 TTTAATAAATTTACTAAAA
1 TTTAATAAATTTA-TAAAA
29119000 TTTA
1 TTTA
29119004 TTATTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 5 0.15
18 14 0.42
19 14 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATAAATTTATAAAA
Found at i:29120304 original size:264 final size:264
Alignment explanation
Indices: 29119834--29120362 Score: 959
Period size: 264 Copynumber: 2.0 Consensus size: 264
29119824 ATTTTGATGA
29119834 TCAGATTAGTCGTCAATGGGATCGCTGTAATGCTTTAGTCTTGTCTTGGATCATCAATACCGTGA
1 TCAGATTAGTCGTCAATGGGATCGCTGTAATGCTTTAGTCTTGTCTTGGATCATCAATACCGTGA
* * *
29119899 ACCGCGATTTGTCCGCCGGTATTGTGTTTGCTTCCAGTGTTGCATTGGTTTGGGGAGATTTGAAA
66 ACCCCGATTTGTCCGCCGGTATTGTGTTTGCTTCCAGCGTTGCATTGGTTTGGGGAGACTTGAAA
*
29119964 GAGAGATTCAATAAGATCGATGGGGCGAGGATTTTTTACTTGCTTAGAGAGATTGCCACGGCAAG
131 GAGAGATTCAATAAGATCGATGGGGCGAGGATTTTTTACTTGCATAGAGAGATTGCCACGGCAAG
29120029 TCAGGGTGATTCTTCGATTGCTGCATACTTTAATCGATTGAAGTTGTTGTGGGATAAGCATAGTG
196 TCAGGGTGATTCTTCGATTGCTGCATACTTTAATCGATTGAAGTTGTTGTGGGATAAGCATAGTG
29120094 CTCT
261 CTCT
*
29120098 TCAGATTAGTCGTCAATGGGATCGTTGTAATGCTTTAGTCTTGTCTTGGATCATCAATACCGTGA
1 TCAGATTAGTCGTCAATGGGATCGCTGTAATGCTTTAGTCTTGTCTTGGATCATCAATACCGTGA
* * * * *
29120163 TCCCCGATTTGTCCGTCGGTGTTGTGTTTGCTTCTAGCGTTGCATTGGTTTGGGGAGACTTGAAG
66 ACCCCGATTTGTCCGCCGGTATTGTGTTTGCTTCCAGCGTTGCATTGGTTTGGGGAGACTTGAAA
29120228 GAGAGATTCAATAAGATCGATGGGGCGAGGATTTTTTACTTGCATAGAGAGATTGCCACGGCAAG
131 GAGAGATTCAATAAGATCGATGGGGCGAGGATTTTTTACTTGCATAGAGAGATTGCCACGGCAAG
*
29120293 TCAGGGTGATTCTTCGATTGCTGCATACTTTAATCGATTGAAGTTGTTGTGGGATGAGCATAGTG
196 TCAGGGTGATTCTTCGATTGCTGCATACTTTAATCGATTGAAGTTGTTGTGGGATAAGCATAGTG
29120358 CTCT
261 CTCT
29120362 T
1 T
29120363 GTACCCTATA
Statistics
Matches: 254, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
264 254 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (264 bp):
TCAGATTAGTCGTCAATGGGATCGCTGTAATGCTTTAGTCTTGTCTTGGATCATCAATACCGTGA
ACCCCGATTTGTCCGCCGGTATTGTGTTTGCTTCCAGCGTTGCATTGGTTTGGGGAGACTTGAAA
GAGAGATTCAATAAGATCGATGGGGCGAGGATTTTTTACTTGCATAGAGAGATTGCCACGGCAAG
TCAGGGTGATTCTTCGATTGCTGCATACTTTAATCGATTGAAGTTGTTGTGGGATAAGCATAGTG
CTCT
Found at i:29122435 original size:46 final size:44
Alignment explanation
Indices: 29122376--29122490 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
29122366 ACAGGACAGA
* *
29122376 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
29122422 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
29122466 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
29122491 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:29122471 original size:44 final size:45
Alignment explanation
Indices: 29122376--29122509 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
29122366 ACAGGACAGA
* *
29122376 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
29122422 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
29122466 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29122510 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:29124994 original size:47 final size:47
Alignment explanation
Indices: 29124886--29124996 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
29124876 CCGGGATAAG
* *
29124886 CACATAGTGCTTCATCGGAACAAATTCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
29124933 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
*
29124980 CACATAGTGTTTCATCG
1 CACATAGTGCTTCATCG
29124997 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 53 0.96
48 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:29125774 original size:12 final size:12
Alignment explanation
Indices: 29125757--29125787 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29125747 TTCCCTTTTC
29125757 TATTTCTTTCTT
1 TATTTCTTTCTT
29125769 TATTTCTTTCTT
1 TATTTCTTTCTT
*
29125781 TCTTTCT
1 TATTTCT
29125788 CACGTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTCTTTCTT
Found at i:29128226 original size:3 final size:3
Alignment explanation
Indices: 29128220--29128248 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29128210 TAAAAGTATG
29128220 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29128249 TCTACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29128475 original size:25 final size:25
Alignment explanation
Indices: 29128420--29128475 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
29128410 AATAGTAATA
*
29128420 ATAATATATACACAATATGGTATTT
1 ATAATATATACACAATATGGTATAT
* * *
29128445 AAAATATATATATATATAT-GTATAT
1 ATAATATATACACA-ATATGGTATAT
29128470 ATAATA
1 ATAATA
29128476 GTATTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (25 bp):
ATAATATATACACAATATGGTATAT
Found at i:29128544 original size:39 final size:38
Alignment explanation
Indices: 29128445--29128544 Score: 94
Period size: 39 Copynumber: 2.6 Consensus size: 38
29128435 TATGGTATTT
* * * *
29128445 AAAATATATATATATATATGTATATATAATAGTATTTA
1 AAAATATATACATATATATATATATATAATAGCATTAA
* * * *
29128483 AGAATATATACATA-AGAAATATATAACTAATGGCATTAA
1 AAAATATATACATATATATATATAT-A-TAATAGCATTAA
29128522 AAAATATATACATGATATATATA
1 AAAATATATACAT-ATATATATA
29128545 AAATACCTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 7 0.15
38 13 0.28
39 21 0.45
40 1 0.02
41 5 0.11
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (38 bp):
AAAATATATACATATATATATATATATAATAGCATTAA
Found at i:29129090 original size:27 final size:27
Alignment explanation
Indices: 29129053--29129108 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
29129043 TTTCTTTTTC
29129053 TTCTTCTTTTTTTGGGGGGTTAGGTTT
1 TTCTTCTTTTTTTGGGGGGTTAGGTTT
* ***
29129080 TTCTTTTTTTTTTTTTGGGTTAGGTTT
1 TTCTTCTTTTTTTGGGGGGTTAGGTTT
29129107 TT
1 TT
29129109 TGGGGGGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.04, C:0.05, G:0.23, T:0.68
Consensus pattern (27 bp):
TTCTTCTTTTTTTGGGGGGTTAGGTTT
Found at i:29129906 original size:73 final size:73
Alignment explanation
Indices: 29129767--29129985 Score: 260
Period size: 72 Copynumber: 3.0 Consensus size: 73
29129757 ACAGACATTA
* * * ** * * *
29129767 AAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAAATCACCTCTCGCAATATAAGT
1 AAAACAAAAATTGAAAATACCTCA--ACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
29129832 TGATTTTTTG
64 TGATTTTTTG
** ** *
29129842 AAAACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTG
1 AAAACAAAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
29129907 A-ATTTTG
66 ATTTTTTG
* * *
29129914 AAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAAAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
29129979 ATTTTTT
66 ATTTTTT
29129986 TTGAAAGGCA
Statistics
Matches: 120, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
72 63 0.52
73 35 0.29
75 22 0.18
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (73 bp):
AAAACAAAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTG
Found at i:29130025 original size:90 final size:89
Alignment explanation
Indices: 29129920--29130095 Score: 248
Period size: 92 Copynumber: 2.0 Consensus size: 89
29129910 TTTGAAAACA
* * *
29129920 GAAATTGAAATTACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGA-CTT
29129984 TTTTGA-AAGGCAGAAATTGAAAAATG
65 TTTTGACAA--CAGAAATTGAAAAATG
* * *
29130010 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
29130075 TTTTGACAACAGAAATTGAAA
65 TTTTGACAACAGAAATTGAAA
29130096 TTACCTCAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
90 34 0.44
91 8 0.10
92 35 0.45
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (89 bp):
GAAATTGAAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACAGAAATTGAAAAATG
Found at i:29130133 original size:74 final size:75
Alignment explanation
Indices: 29130010--29130171 Score: 238
Period size: 74 Copynumber: 2.1 Consensus size: 75
29130000 TTGAAAAATG
* *
29130010 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
29130075 TTTTGACAA-CA
65 TTTTGA-AAGCA
* * *
29130086 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
29130150 TTTGAAAGGCA
66 TTTGAAA-GCA
29130161 GAAATTGAAAA
1 GAAATTGAAAA
29130172 ACGGAAATTG
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
73 2 0.03
74 42 0.54
75 12 0.15
76 22 0.28
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGAAAGCA
Found at i:29130220 original size:165 final size:165
Alignment explanation
Indices: 29129849--29130663 Score: 1179
Period size: 165 Copynumber: 4.8 Consensus size: 165
29129839 TTGAAAACAA
** * ** * * *
29129849 AAATTGAAAATACCTCAACGTGT--CTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGA--AT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
* *
29129910 TTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
66 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
29129975 GTTGATTTTTTTTGAAAGGCAGAAATTGAAAAATGG
131 GTTGA-TTTTTTTGAAAGGCAGAAATTGAAAAACGG
*
29130011 AAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
29130076 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
66 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
29130141 GTTGATTTTTTTGAAAGGCAGAAATTGAAAAACGG
131 GTTGATTTTTTTGAAAGGCAGAAATTGAAAAACGG
*
29130176 AAATTGAAAATACCTCGGCGTGCGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
* *
29130241 TTTGACAATAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTAAACTCACCTCTCGCAATATGA
66 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
29130306 GTTGATTTTTTTGAAAGGCAGAAATTGAAAAACGG
131 GTTGATTTTTTTGAAAGGCAGAAATTGAAAAACGG
* * *
29130341 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
*
29130406 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTTTCGCAATATGA
66 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
29130471 GTTGATTTTTTTTTTTTGAAAGACAGAAATTGAAAAACGA
131 GTTGA-----TTTTTTTGAAAGGCAGAAATTGAAAAACGG
*
29130511 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACAAGTTGATTCT
1 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGA--CT
* * * *
29130576 TTCAAAAACATAATAATGAAAATAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCAC
64 TT--------T--T--TGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
*
29130641 CTCTCGCAATATGAGCTGATTTT
117 CTCTCGCAATATGAGTTGATTTT
29130664 GAAAAAGTAG
Statistics
Matches: 595, Mismatches: 35, Indels: 29
0.90 0.05 0.04
Matches are distributed among these distances:
162 21 0.04
164 30 0.05
165 318 0.53
166 69 0.12
170 86 0.14
172 3 0.01
179 4 0.01
180 1 0.00
182 1 0.00
184 62 0.10
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (165 bp):
AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTGAAAGGCAGAAATTGAAAAACGG
Found at i:29130298 original size:74 final size:75
Alignment explanation
Indices: 29130175--29130336 Score: 220
Period size: 74 Copynumber: 2.1 Consensus size: 75
29130165 TTGAAAAACG
* *
29130175 GAAATTGAAAATACCTCGGCGTGCGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCAGCGT-CGACCTGAGGCTAAACTCACCTCTCGCAATACGAGTTGACTT
29130240 TTTTGACAATA
65 TTTTGACAATA
* * * *
29130251 GAAATTGAAATTACCTCAGCGT-GTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTCGACCTGAGGCTAAACTCACCTCTCGCAATACGAGTTGACTTT
*
29130315 TTTGA-AAGGCA
66 TTTGACAA--TA
29130326 GAAATTGAAAA
1 GAAATTGAAAA
29130337 ACGGAAATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 2 0.03
74 43 0.57
75 11 0.14
76 20 0.26
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTCGACCTGAGGCTAAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAATA
Found at i:29130404 original size:91 final size:88
Alignment explanation
Indices: 29130251--29130425 Score: 253
Period size: 91 Copynumber: 2.0 Consensus size: 88
29130241 TTTGACAATA
* * *
29130251 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTAAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTAAACTCACCACTCGCAATACGAGTTGATTTTT
29130316 TTGA-AAGGCAGAAATTGAAAAACG
66 TTGACAA--CAGAAATTGAAAAACG
* * *
29130340 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTAAACTCACCACTCGCAATACGAGTTGATTT
29130405 TTTTGACAACAGAAATTGAAA
64 TTTTGACAACAGAAATTGAAA
29130426 TTACCTCAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
89 22 0.29
90 12 0.16
91 41 0.53
92 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (88 bp):
GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTAAACTCACCACTCGCAATACGAGTTGATTTTT
TTGACAACAGAAATTGAAAAACG
Found at i:29130484 original size:76 final size:75
Alignment explanation
Indices: 29130340--29130482 Score: 216
Period size: 74 Copynumber: 1.9 Consensus size: 75
29130330 TTGAAAAACG
* *
29130340 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
29130405 TTTTGACAACA
65 TTTTGACAACA
* ** *
29130416 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
29130480 TTT
66 TTT
29130483 TTTTTGAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 39 0.64
76 22 0.36
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:29134862 original size:46 final size:46
Alignment explanation
Indices: 29134809--29134984 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
29134799 TATTTGGGCA
29134809 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
29134855 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
29134902 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
29134948 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29134985 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:29134964 original size:93 final size:93
Alignment explanation
Indices: 29134805--29134976 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
29134795 GGGATATTTG
* *
29134805 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29134870 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
29134898 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29134963 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29134977 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29142070 original size:3 final size:3
Alignment explanation
Indices: 29142064--29142095 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29142054 TAAAAGTATG
29142064 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29142096 TCTACAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29142231 original size:29 final size:29
Alignment explanation
Indices: 29142177--29142232 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
29142167 AAAATAATGA
*
29142177 TATGTACAAAATATATATATATATATACG
1 TATGTACAAAATATATACATATATATACG
29142206 TATGTACATAAA-ATATACACTA-ATATA
1 TATGTACA-AAATATATACA-TATATATA
29142233 ATAATAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (29 bp):
TATGTACAAAATATATACATATATATACG
Found at i:29142402 original size:39 final size:39
Alignment explanation
Indices: 29142301--29142407 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
29142291 TATGGTATTT
* * * * *
29142301 AAAATATATATATATATATATGTATATATAATAGTATTTA
1 AAAATATATACATA-ATATATATATAAATAATAGCATTAA
* * * * *
29142341 AGAATATATACATAAGAAATATATAACTAATGGCATTAA
1 AAAATATATACATAATATATATATAAATAATAGCATTAA
29142380 AAAATATATACATAATATATATA-AAATA
1 AAAATATATACATAATATATATATAAATA
29142408 CCTAAAAAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
38 4 0.08
39 37 0.70
40 12 0.23
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATAAATAATAGCATTAA
Found at i:29146722 original size:35 final size:36
Alignment explanation
Indices: 29146683--29146752 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
29146673 GAATTTAAGA
* *
29146683 TTTAGGGCTTAGAGTTTAAGATTTT-AATTTTAGGG
1 TTTAGGGCTTAAAATTTAAGATTTTGAATTTTAGGG
* * *
29146718 TTTAGGGTTTAAAATTTAATATTTTGAGTTTTAGG
1 TTTAGGGCTTAAAATTTAAGATTTTGAATTTTAGG
29146753 TTAGAGAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.49
Consensus pattern (36 bp):
TTTAGGGCTTAAAATTTAAGATTTTGAATTTTAGGG
Found at i:29146748 original size:28 final size:28
Alignment explanation
Indices: 29146668--29146741 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
29146658 AAGATTCAAT
* * *
29146668 GTTTAGAATTTAAGATTTAGGGCTTAGA
1 GTTTAAAATTTAATATTTAGGGTTTAGA
* *
29146696 GTTTAAGATTTTAAT-TTTAGGGTTTAGG
1 GTTTAA-AATTTAATATTTAGGGTTTAGA
29146724 GTTTAAAATTTAATATTT
1 GTTTAAAATTTAATATTT
29146742 TGAGTTTTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 7 0.18
28 25 0.66
29 6 0.16
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.47
Consensus pattern (28 bp):
GTTTAAAATTTAATATTTAGGGTTTAGA
Found at i:29147450 original size:25 final size:26
Alignment explanation
Indices: 29147421--29147471 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
29147411 CTTATTTCAT
*
29147421 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
29147446 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
29147472 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:29147463 original size:26 final size:24
Alignment explanation
Indices: 29147433--29147481 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
29147423 AATAAAAAAT
*
29147433 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
29147459 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
29147482 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:29147501 original size:21 final size:21
Alignment explanation
Indices: 29147444--29147507 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
29147434 TTAAAAATAT
*
29147444 AATAAAT-CAAAT-ATATTTAA
1 AATAAATAAAAATAATA-TTAA
* *
29147464 AA-ACATAAAAACAAATATTAA
1 AATAAATAAAAA-TAATATTAA
*
29147485 AATAAATAAAAATAATACTAA
1 AATAAATAAAAATAATATTAA
29147506 AA
1 AA
29147508 CAATTCTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 15 0.44
22 11 0.32
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAATAATATTAA
Found at i:29148412 original size:17 final size:18
Alignment explanation
Indices: 29148390--29148423 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29148380 TATAATTATG
29148390 ATTAATATA-ATAAATTT
1 ATTAATATATATAAATTT
29148407 ATTAATATATATAAATT
1 ATTAATATATATAAATT
29148424 GTAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATATATAAATTT
Found at i:29153053 original size:14 final size:15
Alignment explanation
Indices: 29153034--29153076 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
29153024 TCATTAATTG
29153034 ATATATTTTTATA-A
1 ATATATTTTTATATA
29153048 ATATATTTTTTAATATA
1 ATATA-TTTTT-ATATA
*
29153065 AAATATTTTTAT
1 ATATATTTTTAT
29153077 TCACTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.20
15 7 0.28
16 8 0.32
17 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATTTTTATATA
Found at i:29153649 original size:29 final size:30
Alignment explanation
Indices: 29153599--29153664 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
29153589 TTTTATAAAA
* * *
29153599 TAATTAAGTTTTTAAACGAAAATT-ACACT
1 TAATTAAATTTTTAAACAAAAATTAACAAT
**
29153628 TAATTAAATTTTTAATTAAAAATTAACAAT
1 TAATTAAATTTTTAAACAAAAATTAACAAT
29153658 TAATTAA
1 TAATTAA
29153665 GGCCTTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATTAAATTTTTAAACAAAAATTAACAAT
Found at i:29153891 original size:30 final size:28
Alignment explanation
Indices: 29153843--29153900 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
29153833 TAAATATTCT
* *
29153843 AAATATTATTACATTATTATGAATAAATGA
1 AAATATTATTAAAATATTAT-AA-AAATGA
*
29153873 AAATGTTATTAAAATATTATAAAAATGA
1 AAATATTATTAAAATATTATAAAAATGA
29153901 GAAACTATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 2 0.08
30 17 0.68
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
AAATATTATTAAAATATTATAAAAATGA
Found at i:29154039 original size:20 final size:20
Alignment explanation
Indices: 29154001--29154039 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29153991 ATATATTTTT
* *
29154001 TTATAATTTTCTAAAAATTG
1 TTATAATATTATAAAAATTG
*
29154021 TTATAATATTATAATAATT
1 TTATAATATTATAAAAATT
29154040 TCTAATCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTATAATATTATAAAAATTG
Found at i:29154465 original size:18 final size:18
Alignment explanation
Indices: 29154442--29154479 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29154432 ATCCAACATA
29154442 AACCCAAATACCCAACCC
1 AACCCAAATACCCAACCC
*
29154460 AACCCAATTACCCAACCC
1 AACCCAAATACCCAACCC
29154478 AA
1 AA
29154480 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.47, G:0.00, T:0.08
Consensus pattern (18 bp):
AACCCAAATACCCAACCC
Found at i:29154472 original size:13 final size:13
Alignment explanation
Indices: 29154456--29154480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29154446 CAAATACCCA
29154456 ACCCAACCCAATT
1 ACCCAACCCAATT
29154469 ACCCAACCCAAT
1 ACCCAACCCAAT
29154481 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:29154523 original size:6 final size:6
Alignment explanation
Indices: 29154502--29154597 Score: 104
Period size: 6 Copynumber: 15.3 Consensus size: 6
29154492 CAAATAATTT
* * *
29154502 AATAAA TAAAAAA AATAAA AATAAA AATCTAAA ACTAAA ACTAAA AAT-AA
1 AATAAA -AATAAA AATAAA AATAAA AA--TAAA AATAAA AATAAA AATAAA
*
29154552 AATAAA AATCTAAA ACTAAA AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AA--TAAA AATAAA AATAAA AATAAA AATAAA AATAAA AA
29154598 ACATATAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.06
6 58 0.74
7 5 0.06
8 10 0.13
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:29154547 original size:25 final size:26
Alignment explanation
Indices: 29154513--29154597 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 26
29154503 ATAAATAAAA
29154513 AAAATAAAAATAAAAATCTAAAACTA
1 AAAATAAAAATAAAAATCTAAAACTA
* *
29154539 AAACTAAAAAT-AAAAT-AAAAATCTA
1 AAAATAAAAATAAAAATCTAAAA-CTA
* *
29154564 AAACTAAAAATAAAAA--TAAAAATA
1 AAAATAAAAATAAAAATCTAAAACTA
29154588 AAAATAAAAA
1 AAAATAAAAA
29154598 ACATATAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
24 15 0.29
25 23 0.44
26 14 0.27
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (26 bp):
AAAATAAAAATAAAAATCTAAAACTA
Found at i:29154557 original size:31 final size:32
Alignment explanation
Indices: 29154512--29154592 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 32
29154502 AATAAATAAA
*
29154512 AAAAATAAAAATAAAAATCTAAAACTAAAACT
1 AAAAATAAAAATAAAAATCTAAAACTAAAAAT
29154544 AAAAAT-AAAATAAAAATCTAAAACTAAAAAT
1 AAAAATAAAAATAAAAATCTAAAACTAAAAAT
29154575 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAT
29154593 AAAAAACATA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 30 0.64
32 17 0.36
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (32 bp):
AAAAATAAAAATAAAAATCTAAAACTAAAAAT
Found at i:29154646 original size:18 final size:17
Alignment explanation
Indices: 29154625--29154685 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
29154615 AATAATTTGG
29154625 TTAATTTGGTTAATTCGA
1 TTAATTTGGTTAATTC-A
*
29154643 TTAATTTGGGTAATTCA
1 TTAATTTGGTTAATTCA
* *
29154660 GGTAATTCGGTTAATTCAA
1 -TTAATTTGGTTAATTC-A
29154679 TTAATTT
1 TTAATTT
29154686 TATACTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.94
19 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (17 bp):
TTAATTTGGTTAATTCA
Found at i:29154656 original size:27 final size:27
Alignment explanation
Indices: 29154617--29154675 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
29154607 TTTATACAAA
* *
29154617 TAATTTGGTTAATT-TGGTTAATTCGAT
1 TAATTTGGGTAATTCAGG-TAATTCGAT
*
29154644 TAATTTGGGTAATTCAGGTAATTCGGT
1 TAATTTGGGTAATTCAGGTAATTCGAT
29154671 TAATT
1 TAATT
29154676 CAATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.47
Consensus pattern (27 bp):
TAATTTGGGTAATTCAGGTAATTCGAT
Found at i:29154676 original size:9 final size:9
Alignment explanation
Indices: 29154617--29154676 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
29154607 TTTATACAAA
*
29154617 TAATTTGGT
1 TAATTCGGT
*
29154626 TAATTTGGT
1 TAATTCGGT
*
29154635 TAATTCGAT
1 TAATTCGGT
* *
29154644 TAATTTGGG
1 TAATTCGGT
29154653 TAATTCAGG-
1 TAATTC-GGT
29154662 TAATTCGGT
1 TAATTCGGT
29154671 TAATTC
1 TAATTC
29154677 AATTAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.05
9 39 0.91
10 2 0.05
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (9 bp):
TAATTCGGT
Found at i:29155080 original size:20 final size:19
Alignment explanation
Indices: 29155055--29155110 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
29155045 TCAAAATAAC
29155055 AATTTTTTATATTTTAAAT
1 AATTTTTTATATTTTAAAT
* *
29155074 AA-ATTTTATAACTTTTTAAT
1 AATTTTTTAT-A-TTTTAAAT
29155094 AATTTTTGTATTATTTT
1 AATTTTT-TA-TATTTT
29155111 CTATAACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 6 0.21
19 3 0.10
20 9 0.31
21 7 0.24
22 3 0.10
23 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTTATATTTTAAAT
Found at i:29156705 original size:26 final size:26
Alignment explanation
Indices: 29156676--29156727 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29156666 ATTCATAATG
29156676 TCTAAGTTTCAAATTCATAATTTTAT
1 TCTAAGTTTCAAATTCATAATTTTAT
29156702 TCTAAGTTTCAAATTCATAATTTTAT
1 TCTAAGTTTCAAATTCATAATTTTAT
29156728 AGAGTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50
Consensus pattern (26 bp):
TCTAAGTTTCAAATTCATAATTTTAT
Found at i:29160803 original size:2 final size:2
Alignment explanation
Indices: 29160796--29160824 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29160786 GTTCATATGC
29160796 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 T
29160825 GCAAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29163885 original size:106 final size:107
Alignment explanation
Indices: 29163714--29164001 Score: 420
Period size: 106 Copynumber: 2.7 Consensus size: 107
29163704 TCAATGCATT
**
29163714 AATAAAATAAGGGGAAGGTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACGATAATCT
1 AATAAAATAAGGGGAAATTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACGATAATCT
* * * *
29163779 TGTGACAAAATAAAA-TTCAAATGTCAAATTAATTAATGTATA
66 TGTTACAAAATAAAACTT-AAATGTAAAATTAATCAATATATA
*
29163821 AATAAAATAAGGGGAAATTTTTCTAAAA-TTTATATAAATATAAGTATCTTAAATACGATGATCT
1 AATAAAATAAGGGGAAATTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACGATAATCT
* *
29163885 TGTTACAAAATAAAACTTAAATGTAAAATTTATCGATATATA
66 TGTTACAAAATAAAACTTAAATGTAAAATTAATCAATATATA
* * * * *
29163927 AATAAAATAAAGGG-AATTTTTTTAAAATTTTATATAAATATAAATATTTTAAATACAATAATCT
1 AATAAAATAAGGGGAAATTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACGATAATCT
29163991 TGTTACAAAAT
66 TGTTACAAAAT
29164002 GTCTGTGATG
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
105 12 0.07
106 124 0.76
107 28 0.17
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (107 bp):
AATAAAATAAGGGGAAATTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACGATAATCT
TGTTACAAAATAAAACTTAAATGTAAAATTAATCAATATATA
Found at i:29182222 original size:22 final size:22
Alignment explanation
Indices: 29182197--29182241 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29182187 TTTAATAAAA
29182197 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
29182219 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
29182241 A
1 A
29182242 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:29186821 original size:22 final size:22
Alignment explanation
Indices: 29186796--29186840 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29186786 TTTAATAAAA
29186796 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
29186818 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
29186840 A
1 A
29186841 CATAAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:29189999 original size:39 final size:39
Alignment explanation
Indices: 29189945--29190023 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
29189935 TAAAAAAAGT
29189945 ATGAAATTTCTGGTAGCAATGATACAAAATAAGATCTTA
1 ATGAAATTTCTGGTAGCAATGATACAAAATAAGATCTTA
*
29189984 ATGAAATTTCTGGTAGCAGTGATACAAAATAAGATCTTA
1 ATGAAATTTCTGGTAGCAATGATACAAAATAAGATCTTA
29190023 A
1 A
29190024 ACTATAAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (39 bp):
ATGAAATTTCTGGTAGCAATGATACAAAATAAGATCTTA
Found at i:29193042 original size:2 final size:2
Alignment explanation
Indices: 29193037--29193062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29193027 TCACACACAC
29193037 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
29193063 TTATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29193206 original size:8 final size:8
Alignment explanation
Indices: 29193193--29193233 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
29193183 ATTATTTGAT
29193193 AATTTTAA
1 AATTTTAA
*
29193201 ATTTTTAA
1 AATTTTAA
29193209 AATTTTAA
1 AATTTTAA
29193217 AA--TTAA
1 AATTTTAA
29193223 AATATTTAA
1 AAT-TTTAA
29193232 AA
1 AA
29193234 GATAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 6 0.21
8 16 0.57
9 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTTAA
Found at i:29193224 original size:14 final size:15
Alignment explanation
Indices: 29193205--29193233 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29193195 TTTTAAATTT
29193205 TTAAAAT-TTTAAAA
1 TTAAAATATTTAAAA
29193219 TTAAAATATTTAAAA
1 TTAAAATATTTAAAA
29193234 GATAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATATTTAAAA
Found at i:29194316 original size:16 final size:16
Alignment explanation
Indices: 29194295--29194325 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29194285 TTAAAATTTT
29194295 TTTAAAAAAAATTATA
1 TTTAAAAAAAATTATA
*
29194311 TTTAAATAAAATTAT
1 TTTAAAAAAAATTAT
29194326 CAACAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAAAAATTATA
Found at i:29196186 original size:14 final size:14
Alignment explanation
Indices: 29196169--29196195 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29196159 TATTTAAAAG
29196169 TATTAAATATTTAC
1 TATTAAATATTTAC
29196183 TATTAAATATTTA
1 TATTAAATATTTA
29196196 TTTATTTATA
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:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTAAATATTTAC
Found at i:29207619 original size:47 final size:47
Alignment explanation
Indices: 29207565--29207758 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
29207555 TTAGGATTTT
** * *
29207565 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
29207612 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
29207659 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
29207706 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
29207753 ATGTGA
1 ATGTGA
29207759 AATATGTATG
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:29207665 original size:22 final size:22
Alignment explanation
Indices: 29207594--29207665 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
29207584 GTATATATGA
29207594 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
29207616 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
29207641 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
29207663 GAT
1 GAT
29207666 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:29207714 original size:25 final size:25
Alignment explanation
Indices: 29207639--29207714 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
29207629 ATGCATATAT
29207639 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
29207664 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
29207686 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
29207711 GTGA
1 GTGA
29207715 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:29208132 original size:37 final size:37
Alignment explanation
Indices: 29208024--29208132 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
29208014 GGAAATATAT
*
29208024 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
29208061 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
29208098 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
29208133 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:29216893 original size:38 final size:38
Alignment explanation
Indices: 29216842--29216918 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
29216832 CTTAAATGTT
29216842 TCCTAATTATTAGTTCGGTTTTAGATTAATTTTTAGAC
1 TCCTAATTATTAGTTCGGTTTTAGATTAATTTTTAGAC
29216880 TCCTAATTATTAGTTCGGTTTTAGATTAATTTTTAGAC
1 TCCTAATTATTAGTTCGGTTTTAGATTAATTTTTAGAC
29216918 T
1 T
29216919 AAGATTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (38 bp):
TCCTAATTATTAGTTCGGTTTTAGATTAATTTTTAGAC
Found at i:29217471 original size:51 final size:51
Alignment explanation
Indices: 29217407--29217522 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
29217397 ATGGAAACAT
** * * *
29217407 GATATGATATTATAATCTTAGAGATCTTAGATATGATATGGAATCTTATAA
1 GATATGATATTATAAGATTACAGATCTTAGATAAGATATGGAATCTTAGAA
* * * ** *
29217458 GATATTATTTTATAAGATTACATATCTTATCTAAGATATGTAATCTTAGAA
1 GATATGATATTATAAGATTACAGATCTTAGATAAGATATGGAATCTTAGAA
29217509 GATATGATATTATA
1 GATATGATATTATA
29217523 TTTGGTAGTA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (51 bp):
GATATGATATTATAAGATTACAGATCTTAGATAAGATATGGAATCTTAGAA
Found at i:29218103 original size:11 final size:11
Alignment explanation
Indices: 29218074--29218105 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29218064 CGACAGAATG
*
29218074 ATTTTATCAAT
1 ATTTTATTAAT
29218085 ATTTTATTAAT
1 ATTTTATTAAT
29218096 ATTTTATTAA
1 ATTTTATTAA
29218106 CTCAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAT
Found at i:29220809 original size:19 final size:19
Alignment explanation
Indices: 29220770--29220809 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29220760 TATTGAATTC
*
29220770 AAATATAAAATATACATAT
1 AAATATAAAATATACAAAT
29220789 AAATATAAAATGA-ACAAAT
1 AAATATAAAAT-ATACAAAT
29220808 AA
1 AA
29220810 GAGCAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATATAAAATATACAAAT
Found at i:29224508 original size:25 final size:25
Alignment explanation
Indices: 29224421--29224632 Score: 124
Period size: 25 Copynumber: 8.7 Consensus size: 25
29224411 AACGATATAT
29224421 AAATATATACAT-ATAT-GTATT-A
1 AAATATATACATAATATAGTATTAA
* * * * *
29224443 AAATATGTACGTAACAATAGGAATAA
1 AAATATATACATAA-TATAGTATTAA
*
29224469 AAA-GTAT--ATAA-ATAGTATTAA
1 AAATATATACATAATATAGTATTAA
* * *
29224490 AAATATGTACATAATATAGTGTTCA
1 AAATATATACATAATATAGTATTAA
*
29224515 AAATACATACATAATATAGTTATTAAA
1 AAATATATACATAATATAG-TATT-AA
* * **
29224542 AAATATATACATGAGATAACA-TAA
1 AAATATATACATAATATAGTATTAA
*
29224566 AAAGTATATGA-ATAGTAT-GATATTAA
1 AAA-TATAT-ACATAATATAG-TATTAA
29224592 AAATATATACATAATATA-TA-TAA
1 AAATATATACATAATATAGTATTAA
* * *
29224615 AAACAGATACATTATATA
1 AAATATATACATAATATA
29224633 TATATATATT
Statistics
Matches: 142, Mismatches: 32, Indels: 31
0.69 0.16 0.15
Matches are distributed among these distances:
21 11 0.08
22 12 0.08
23 22 0.15
24 14 0.10
25 52 0.37
26 15 0.11
27 16 0.11
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (25 bp):
AAATATATACATAATATAGTATTAA
Found at i:29224755 original size:3 final size:3
Alignment explanation
Indices: 29224747--29224805 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
29224737 ATACTAGTAC
29224747 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29224795 TAA TAA TAA TA
1 TAA TAA TAA TA
29224806 TATGCATATG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29224927 original size:21 final size:23
Alignment explanation
Indices: 29224903--29224949 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
29224893 AAAATATAAA
29224903 TATAATA-ATAGTATTAAAAA-G
1 TATAATACATAGTATTAAAAATG
29224924 TAT-ATACATAGTATTAAAAATG
1 TATAATACATAGTATTAAAAATG
29224946 TATA
1 TATA
29224950 CATATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 16 0.70
22 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (23 bp):
TATAATACATAGTATTAAAAATG
Found at i:29225165 original size:23 final size:21
Alignment explanation
Indices: 29225110--29225182 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 21
29225100 TATAGTTATT
*
29225110 AAAAAA-ATATATACATAAGATA
1 AAAAAATATATATA-AT-ATATA
* *
29225132 ATAAGATATATGAATAATATGATA
1 AAAAAATATAT--ATAATAT-ATA
29225156 TAAAAAATATATATAATATATA
1 -AAAAAATATATATAATATATA
29225178 AAAAA
1 AAAAA
29225183 TATTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
21 5 0.12
22 7 0.17
23 12 0.29
24 5 0.12
25 12 0.29
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAATATATATAATATATA
Found at i:29225167 original size:11 final size:11
Alignment explanation
Indices: 29225153--29225199 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
29225143 GAATAATATG
29225153 ATATAAAAAAT
1 ATATAAAAAAT
*
29225164 ATAT--ATAAT
1 ATATAAAAAAT
29225173 ATATAAAAAAT
1 ATATAAAAAAT
29225184 AT-TAAAAAAT
1 ATATAAAAAAT
29225194 AATATA
1 -ATATA
29225200 CGTAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 8 0.27
10 8 0.27
11 12 0.40
12 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAAAAAAT
Found at i:29225176 original size:25 final size:25
Alignment explanation
Indices: 29225011--29225176 Score: 66
Period size: 25 Copynumber: 6.7 Consensus size: 25
29225001 AATACTACAT
*
29225011 AAATATACACATATATAT-ATATAAA
1 AAATATACATA-ATATATGATATAAA
29225036 AATATATACATAATA-ATGATATTAAA
1 AA-ATATACATAATATATGATA-TAAA
* * *
29225062 AGCATGTACGTAATATAGTG-T-TAAA
1 A-AATATACATAATATA-TGATATAAA
* *
29225087 AATACATACATAATATA-GTTATTAAA
1 AA-ATATACATAATATATGATA-TAAA
* *
29225113 AAA-ATATATACATA-A-GATAATAAG
1 AAATATACATA-ATATATGAT-ATAAA
* *
29225137 ATATATGA-ATAATAT-G-ATATAAA
1 AAATAT-ACATAATATATGATATAAA
*
29225160 AAATATATATAATATAT
1 AAATATACATAATATAT
29225177 AAAAAATATT
Statistics
Matches: 108, Mismatches: 15, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
22 1 0.01
23 17 0.16
24 22 0.20
25 34 0.31
26 30 0.28
27 2 0.02
28 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (25 bp):
AAATATACATAATATATGATATAAA
Found at i:29225327 original size:10 final size:9
Alignment explanation
Indices: 29225314--29225356 Score: 59
Period size: 10 Copynumber: 4.4 Consensus size: 9
29225304 AAAACTATTA
29225314 ATAATACTAT
1 ATAATA-TAT
29225324 ATAATATAT
1 ATAATATAT
29225333 ATATATATAT
1 ATA-ATATAT
29225343 ATATATATAT
1 ATA-ATATAT
29225353 ATAA
1 ATAA
29225357 AAGTATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATATAT
Found at i:29225332 original size:2 final size:2
Alignment explanation
Indices: 29225321--29225355 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
29225311 TTAATAATAC
29225321 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29225356 AAAGTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29227031 original size:25 final size:27
Alignment explanation
Indices: 29226994--29227046 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
29226984 TCAAACATGC
29226994 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
29227020 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
29227046 A
1 A
29227047 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:29228581 original size:25 final size:26
Alignment explanation
Indices: 29228524--29228631 Score: 166
Period size: 25 Copynumber: 4.2 Consensus size: 26
29228514 ACATGAATTC
29228524 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29228550 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
29228575 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
29228601 TTGTCATG-AACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29228626 TTATCA
1 TTATCA
29228632 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
25 43 0.57
26 32 0.43
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29228602 original size:51 final size:51
Alignment explanation
Indices: 29228524--29228631 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
29228514 ACATGAATTC
29228524 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCATTATCATG-AACATTTACCTAACCCA
* * * *
29228575 TTATCATGGAATATTTACCTAATCCATTGTCATGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
29228626 TTATCA
1 TTATCA
29228632 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 13 0.25
51 39 0.75
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (51 bp):
TTATCATGAAACATTTACCTAACCCATTATCATGAACATTTACCTAACCCA
Found at i:29233448 original size:11 final size:11
Alignment explanation
Indices: 29233432--29233469 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
29233422 AGTACTACCT
29233432 CGGCTCGACCA
1 CGGCTCGACCA
29233443 CGGCTCGACCA
1 CGGCTCGACCA
29233454 CGGCCTCGACCA
1 CGG-CTCGACCA
29233466 CGGC
1 CGGC
29233470 CTCTTCCCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.16, C:0.47, G:0.29, T:0.08
Consensus pattern (11 bp):
CGGCTCGACCA
Found at i:29233463 original size:12 final size:12
Alignment explanation
Indices: 29233435--29233472 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
29233425 ACTACCTCGG
29233435 CTCGACCACGG-
1 CTCGACCACGGC
29233446 CTCGACCACGGC
1 CTCGACCACGGC
29233458 CTCGACCACGGC
1 CTCGACCACGGC
29233470 CTC
1 CTC
29233473 TTCCCCGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.16, C:0.50, G:0.24, T:0.11
Consensus pattern (12 bp):
CTCGACCACGGC
Found at i:29235105 original size:24 final size:26
Alignment explanation
Indices: 29235069--29235117 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
29235059 TCAAACATGC
29235069 ATTTAGGTCAATTTAAC-CCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
* *
29235094 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
29235118 GTAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCCTAGGGT
Found at i:29236637 original size:26 final size:26
Alignment explanation
Indices: 29236601--29236710 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
29236591 CATGTAATTC
29236601 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29236627 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
29236653 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29236679 TTGTCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29236705 TTATCA
1 TTATCA
29236711 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29237670 original size:9 final size:10
Alignment explanation
Indices: 29237654--29237680 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29237644 AATGATAAAA
29237654 AATAAAAATC
1 AATAAAAATC
29237664 AATAAAAATC
1 AATAAAAATC
29237674 AATAAAA
1 AATAAAA
29237681 GTTATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (10 bp):
AATAAAAATC
Found at i:29237736 original size:10 final size:10
Alignment explanation
Indices: 29237721--29237814 Score: 70
Period size: 10 Copynumber: 9.5 Consensus size: 10
29237711 ATAAAAATTT
29237721 AAAATTATAA
1 AAAATTATAA
29237731 AAAATT-TAA
1 AAAATTATAA
*
29237740 AAAATCTTTAA
1 AAAAT-TATAA
29237751 AAAATTATAA
1 AAAATTATAA
*
29237761 AAGA-TAT--
1 AAAATTATAA
* *
29237768 AGAAGTATAGA
1 AAAATTATA-A
* *
29237779 AAAATTTTAT
1 AAAATTATAA
*
29237789 AAAATCATAA
1 AAAATTATAA
29237799 GAAAATTATAA
1 -AAAATTATAA
29237810 AAAAT
1 AAAAT
29237815 GTAAAGAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
7 2 0.03
8 3 0.05
9 11 0.17
10 26 0.40
11 23 0.35
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAATTATAA
Found at i:29237739 original size:28 final size:29
Alignment explanation
Indices: 29237707--29237762 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
29237697 ATTTTTAATT
29237707 TTTAATAAAA-ATTT-AAAATTATAAAAAA
1 TTTAA-AAAATATTTAAAAATTATAAAAAA
*
29237735 TTTAAAAAATCTTTAAAAAATTATAAAA
1 TTTAAAAAATATTT-AAAAATTATAAAA
29237763 GATATAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
28 8 0.33
30 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTAAAAAATATTTAAAAATTATAAAAAA
Found at i:29237740 original size:9 final size:9
Alignment explanation
Indices: 29237713--29237762 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
29237703 AATTTTTAAT
29237713 AAAAATTT-
1 AAAAATTTA
29237721 -AAAATTATA
1 AAAAATT-TA
29237730 AAAAATTTA
1 AAAAATTTA
29237739 AAAAATCTTTA
1 AAAAA--TTTA
29237750 AAAAATTATA
1 AAAAATT-TA
29237760 AAA
1 AAA
29237763 GATATAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 6 0.17
8 1 0.03
9 9 0.25
10 11 0.31
11 9 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTTA
Found at i:29237824 original size:10 final size:9
Alignment explanation
Indices: 29237721--29237830 Score: 51
Period size: 10 Copynumber: 11.3 Consensus size: 9
29237711 ATAAAAATTT
*
29237721 AAAATTATA
1 AAAAATATA
*
29237730 AAAAATTTA
1 AAAAATATA
*
29237739 AAAAATCTTTA
1 AAAAA--TATA
29237750 AAAAATTATA
1 AAAAA-TATA
*
29237760 AAAGATAT-
1 AAAAATATA
* *
29237768 AGAAGTATA
1 AAAAATATA
*
29237777 GAAAAATTTTA
1 -AAAAA-TATA
*
29237788 TAAAATCATA
1 AAAAAT-ATA
29237798 AGAAAATTATA
1 A-AAAA-TATA
*
29237809 AAAAATGTA
1 AAAAATATA
29237818 AAGAAATATA
1 AA-AAATATA
29237828 AAA
1 AAA
29237831 TTTGTAAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
8 5 0.07
9 22 0.29
10 28 0.37
11 20 0.26
12 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (9 bp):
AAAAATATA
Found at i:29238092 original size:20 final size:20
Alignment explanation
Indices: 29238069--29238138 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
29238059 TTTTATAAAA
29238069 TTTTACAATTTTTTATATTT
1 TTTTACAATTTTTTATATTT
*
29238089 TTTTACTA-TTTTTATATTT
1 TTTTACAATTTTTTATATTT
*
29238108 TTTT-CAAATTTTTAATATTT
1 TTTTAC-AATTTTTTATATTT
* *
29238128 TATTAAAATTT
1 TTTTACAATTT
29238139 AATAATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 1 0.02
19 16 0.38
20 25 0.60
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACAATTTTTTATATTT
Found at i:29238111 original size:19 final size:19
Alignment explanation
Indices: 29238037--29238104 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
29238027 TTTTCGATGC
*
29238037 ATTTTTATAAATTTTTAAT
1 ATTTTTATAAATTTTTACT
* *
29238056 GATTTTTATAAAATTTTACA
1 -ATTTTTATAAATTTTTACT
**
29238076 ATTTTTTATATTTTTTTACT
1 A-TTTTTATAAATTTTTACT
29238096 ATTTTTATA
1 ATTTTTATA
29238105 TTTTTTTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 9 0.22
20 31 0.77
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (19 bp):
ATTTTTATAAATTTTTACT
Found at i:29238118 original size:19 final size:18
Alignment explanation
Indices: 29238037--29238134 Score: 70
Period size: 20 Copynumber: 5.1 Consensus size: 18
29238027 TTTTCGATGC
**
29238037 ATTTTTATAAATTTTTAA
1 ATTTTTATATTTTTTTAA
***
29238055 TGATTTTTATAAAATTTTACA
1 --ATTTTTATATTTTTTTA-A
*
29238076 ATTTTTTATATTTTTTTACT
1 A-TTTTTATATTTTTTTA-A
29238096 ATTTTTATATTTTTTTCAA
1 ATTTTTATATTTTTTT-AA
*
29238115 ATTTTTAATATTTTATTAA
1 ATTTTT-ATATTTTTTTAA
29238134 A
1 A
29238135 ATTTAATAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
19 25 0.37
20 41 0.61
21 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
ATTTTTATATTTTTTTAA
Found at i:29243819 original size:20 final size:20
Alignment explanation
Indices: 29243794--29243839 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29243784 TCTGGGCCTT
29243794 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
29243814 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
29243833 GCCCATA
1 GCCCATA
29243840 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:29243848 original size:19 final size:20
Alignment explanation
Indices: 29243806--29243849 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
29243796 CCATATTAAC
** *
29243806 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
29243826 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
29243845 ACAGT
1 ACAGT
29243850 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:29244984 original size:19 final size:20
Alignment explanation
Indices: 29244960--29244999 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29244950 TCTTTAATCG
*
29244960 AGAGAAAAGATGAGTA-AAA
1 AGAGAAAAGAAGAGTAGAAA
*
29244979 AGAGAAGAGAAGAGTAGAAA
1 AGAGAAAAGAAGAGTAGAAA
29244999 A
1 A
29245000 AGATAGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (20 bp):
AGAGAAAAGAAGAGTAGAAA
Found at i:29249395 original size:18 final size:18
Alignment explanation
Indices: 29249355--29249397 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29249345 GTTCAAGGTA
29249355 TAATTAATCTAAAATTTT
1 TAATTAATCTAAAATTTT
* *
29249373 CAATTAAT-TAAATTTATT
1 TAATTAATCTAAAATT-TT
29249391 TAATTAA
1 TAATTAA
29249398 AAATCTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATTAATCTAAAATTTT
Found at i:29249944 original size:6 final size:7
Alignment explanation
Indices: 29249926--29249953 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29249916 AAAGGGTCAT
29249926 ATTTTTA
1 ATTTTTA
29249933 ATTTTTA
1 ATTTTTA
29249940 ATTTTTA
1 ATTTTTA
29249947 ATTTTTA
1 ATTTTTA
29249954 CAGTTTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:29254309 original size:3 final size:3
Alignment explanation
Indices: 29254303--29254506 Score: 195
Period size: 3 Copynumber: 68.7 Consensus size: 3
29254293 AAAAAGAAAT
* * *
29254303 ATA ATA ATA ATA GTA ATA ATA TTA A-A TTA ATTA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
* * * * * *
29254347 ATA AGTA A-A CAAA CACA AAA AGA A-A AT- ATA ATT ATA ATA GTA ATA
1 ATA A-TA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * *
29254392 ATA ATA AAA ATA ATA GCA ATA ATA ATA GTG ATA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29254439 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
29254487 ATA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
29254507 GTTAAATTAA
Statistics
Matches: 167, Mismatches: 25, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
2 10 0.06
3 147 0.88
4 10 0.06
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:29256194 original size:143 final size:144
Alignment explanation
Indices: 29255997--29256710 Score: 907
Period size: 143 Copynumber: 5.0 Consensus size: 144
29255987 GATTTGTAAC
* * * * * * * * * *
29255997 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTCTATCTTCAGTTTGCTCT
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* *
29256062 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATATGCTCCACTGCAACTTCAAGAAGATA
66 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
29256127 AGATTCGCCAT-AT
131 AGATTCGCCATAAT
* * *
29256140 TTGTAGTTTTAATTTGTTCCACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * *
29256205 -ACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGTTCCACTTCAACTTCAAGAAGATA
66 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
29256269 AGATTCGCCATAAT
131 AGATTCGCCATAAT
* **
29256283 TTGTAGCTTTAATCTGTTCCACTATAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * * ** * *
29256348 GTA--ACAACTTTAGAGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGTGACTTTAGGAAGAT
66 -TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGAT
* *
29256411 AAGATCCTCCATAAT
130 AAGATTCGCCATAAT
* * * * *
29256426 TTGTAGTTTTAATCTGTTCTACTACGACGTCAGGGAAATAAGATTCGTTGTCTTCAGTCTACTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
29256491 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
66 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
* * *
29256556 ATA-TCATCTATAAT
131 AGATTC-GCCATAAT
* ** * *
29256570 TTGTAGCTTTAATCTGTTCCACTACAATGTCAGCTAAATAAGATTCGCTGTCTTCAGTTTACTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * * *
29256635 TACTGCAACTTCAGGGAGATAAGGTTGATGGCTTCAATCTGTTCTACTGCAACTTTAGGAAGATA
66 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
29256700 AGATTCGCCAT
131 AGATTCGCCAT
29256711 TTTCGATCTA
Statistics
Matches: 489, Mismatches: 75, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
142 71 0.15
143 233 0.48
144 182 0.37
145 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (144 bp):
TTGTAGCTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATA
AGATTCGCCATAAT
Found at i:29256226 original size:45 final size:45
Alignment explanation
Indices: 29256157--29256276 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 45
29256147 TTTAATTTGT
* * * * *
29256157 TCCACTGCAACGTCAGGGAAATAAGATTCGCTGTCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCTGGCATCAATCTGC
* * *
29256202 TCCACTGCAACTTCAGGGAGATAAGACT-GGTGGCATCAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTCGCTGGCATCAATCTGC
* * *
29256246 TCCACTTCAACTTCAAGAAGATAAGATTCGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGC
29256277 CATAATTTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 35 0.57
45 26 0.43
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCGCTGGCATCAATCTGC
Found at i:29256577 original size:287 final size:285
Alignment explanation
Indices: 29255997--29256710 Score: 928
Period size: 287 Copynumber: 2.5 Consensus size: 285
29255987 GATTTGTAAC
* * * * ** * * * * * * *
29255997 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCCTCTATCTTCAGTTTGCTCT
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTACTCC
* * * * *
29256062 TACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTTAATATGCTCCACTGCAACTTCAAGAAGATA
66 TAC-ACAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGCAACTTTAGGAAGATA
* * *
29256127 AGATTCGCCATATTTGTAGTTTTAATTTGTTCCACTGCAACGTCAGGGAAATAAGATTCGCTGTC
130 AGATCCGCCATATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTC
* * *
29256192 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGTTCCACTTCAAC
195 TTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCAAC
29256257 TTCAAGAAGATAAGATTCGCCATAAT
260 TTCAAGAAGATAAGATTCGCCATAAT
* *
29256283 TTGTAGCTTTAATCTGTTCCACTATAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTACTCC
* * **
29256348 GTA-ACAACTTTAGAGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGTGACTTTAGGAAGATA
66 -TACACAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGCAACTTTAGGAAGATA
* * * *
29256412 AGATCCTCCATAATTTGTAGTTTTAATCTGTTCTACTACGACGTCAGGGAAATAAGATTCGTTGT
130 AGATCCGCCAT-ATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGT
* *
29256477 CTTCAGTCTACTCCTACTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCA
194 CTTCAGTCTACTCC-ACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCA
* * *
29256542 ACTTCAAGAAGATAATA-TCATCTATAAT
258 ACTTCAAGAAGATAAGATTC-GCCATAAT
* * *
29256570 TTGTAGCTTTAATCTGTTCCACTACAATGTCAGCTAAATAAGATTCGCTGTCTTCAGTTTACTCC
1 TTGTAGCTTTAATCTGTTCCACTACAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTACTCC
* * * * *
29256635 TACTGCAACTTCAGGGAGATAAGGTTGATGGCTTCAATCTGTTCTACTGCAACTTTAGGAAGATA
66 TAC-ACAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGCAACTTTAGGAAGATA
*
29256700 AGATTCGCCAT
130 AGATCCGCCAT
29256711 TTTCGATCTA
Statistics
Matches: 369, Mismatches: 53, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
285 61 0.17
286 117 0.32
287 130 0.35
288 61 0.17
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (285 bp):
TTGTAGCTTTAATCTGTTCCACTACAACGTCAGCAAAATAAGATTCGCTGTCTTCAGTCTACTCC
TACACAACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTCTACTGCAACTTTAGGAAGATAA
GATCCGCCATATTTGTAGTTTTAATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGTCT
TCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCATCAATCTGCTCCACTGCAACT
TCAAGAAGATAAGATTCGCCATAAT
Found at i:29256759 original size:89 final size:90
Alignment explanation
Indices: 29256580--29256793 Score: 222
Period size: 89 Copynumber: 2.4 Consensus size: 90
29256570 TTGTAGCTTT
* ** * *
29256580 AATCTGTTCCACTACAA-TGTCAGCTAA-ATAAGATTCGCTGTCTTC-AGTTTACTCCTACTGCA
1 AATCTGTTCCACTACAACT-TCAG-GAAGATAAGATTCGCCATTTTCGA-TCTACTCCTACTGCA
* * ***
29256642 ACTTCAGGGAGATAAGGTTGATGGCTTC
63 ACTTCAAGGAGATAAGATTGACAACTTC
* * *
29256670 AATCTGTTCTACTGCAACTTTAGGAAGATAAGATTCGCCATTTTCGATCTACTCC-ACTGCAACT
1 AATCTGTTCCACTACAACTTCAGGAAGATAAGATTCGCCATTTTCGATCTACTCCTACTGCAACT
29256734 TCAAGGAGATAAGATCT-ACAACTTC
66 TCAAGGAGATAAGAT-TGACAACTTC
* *
29256759 AATCTGTTCCACTACTACTTCAGGGAGATAAGATT
1 AATCTGTTCCACTACAACTTCAGGAAGATAAGATT
29256794 TGTGGATTTA
Statistics
Matches: 102, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
89 59 0.58
90 41 0.40
91 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (90 bp):
AATCTGTTCCACTACAACTTCAGGAAGATAAGATTCGCCATTTTCGATCTACTCCTACTGCAACT
TCAAGGAGATAAGATTGACAACTTC
Found at i:29260690 original size:15 final size:15
Alignment explanation
Indices: 29260667--29260697 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29260657 CGCAAATAGG
*
29260667 AGAAGAAAAAGGGGA
1 AGAAAAAAAAGGGGA
29260682 AGAAAAAAAAGGGGA
1 AGAAAAAAAAGGGGA
29260697 A
1 A
29260698 AAATTGGGAT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAGGGGA
Found at i:29267191 original size:3 final size:3
Alignment explanation
Indices: 29267183--29267397 Score: 145
Period size: 3 Copynumber: 72.0 Consensus size: 3
29267173 AAAGGAAGAC
* *
29267183 AAT AAT AAT AGT AAT AAT AATT AA- ATT AATT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT
* * * * *
29267228 AAGT AAAT AA- ACAC AAA AAG AA- AAT -AT AAT TAT AAT AGT AAT AAT
1 AA-T -AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
29267273 AAT AAA AAC AAT AAC AAT AAT AAT AGT GAT AA- AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
29267320 AGT AAT AAT AAT AAT AAT GAT AGT AAT AAT AAT AGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * **
29267368 AAT GAT AGT AAT AAT AGC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29267398 GTTAAATTAA
Statistics
Matches: 166, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
2 10 0.06
3 145 0.87
4 9 0.05
5 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29274140 original size:24 final size:24
Alignment explanation
Indices: 29274074--29274147 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
29274064 TAAGTCATAT
* *
29274074 ATTAGATATTAGTAATATAATAACA
1 ATTA-ATATTAATAAGATAATAACA
* **
29274099 ATTACTATTAATTTGATAATAACA
1 ATTAATATTAATAAGATAATAACA
29274123 ATTAATATTACA-AAGATAAT-ACA
1 ATTAATATTA-ATAAGATAATAACA
29274146 AT
1 AT
29274148 ATAGTGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 5 0.12
24 30 0.75
25 5 0.12
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (24 bp):
ATTAATATTAATAAGATAATAACA
Found at i:29275690 original size:32 final size:32
Alignment explanation
Indices: 29275648--29275715 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
29275638 AAACAAAAGT
29275648 GAAC-AAAGTAAGCAAACATACAACCATTGTC
1 GAACAAAAGTAAGCAAACATACAACCATTGTC
29275679 GAACAAAAGTAAGCAAACATACAACCATTGTC
1 GAACAAAAGTAAGCAAACATACAACCATTGTC
*
29275711 AAACA
1 GAACA
29275716 TCATGAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (32 bp):
GAACAAAAGTAAGCAAACATACAACCATTGTC
Found at i:29276032 original size:17 final size:16
Alignment explanation
Indices: 29275998--29276029 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29275988 TATCAAGCAC
*
29275998 TTTGATAGTTTTTGAA
1 TTTGATACTTTTTGAA
29276014 TTTGATACTTTTTGAA
1 TTTGATACTTTTTGAA
29276030 ATTCCATGTG
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:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (16 bp):
TTTGATACTTTTTGAA
Found at i:29277355 original size:20 final size:20
Alignment explanation
Indices: 29277302--29277357 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
29277292 TGGTGAGCTC
29277302 CAAGCTCACACCAAAA-TTT
1 CAAGCTCACACCAAAATTTT
* ** *
29277321 CTAAGAT-TTAGCAAAATTTT
1 C-AAGCTCACACCAAAATTTT
29277341 CAAGCTCACACCAAAAT
1 CAAGCTCACACCAAAAT
29277358 ATCTAACTTC
Statistics
Matches: 26, Mismatches: 8, Indels: 5
0.67 0.21 0.13
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (20 bp):
CAAGCTCACACCAAAATTTT
Found at i:29278129 original size:13 final size:13
Alignment explanation
Indices: 29278111--29278137 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29278101 ATTAAACTTT
29278111 TATCACAATTTCC
1 TATCACAATTTCC
29278124 TATCACAATTTCC
1 TATCACAATTTCC
29278137 T
1 T
29278138 TATTCAGATA
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:0.30, G:0.00, T:0.41
Consensus pattern (13 bp):
TATCACAATTTCC
Done.