Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 62 of 78
Found at i:12402530 original size:31 final size:30
Alignment explanation
Indices: 12402359--12402543 Score: 110
Period size: 31 Copynumber: 5.8 Consensus size: 30
12402349 TAATGTATTA
* *
12402359 TATAGTTTATATTAATGTTAATTATCT-TAAC
1 TATATTTTATATTAATATTAATT-T-TATAAC
12402390 TATGA-TTTATATTAATATAATATATAGTTTATAAAC
1 TAT-ATTTTATATTAATAT--TA-AT--TTTAT-AAC
* * *
12402426 TATA--ATGTATTAATATTAATTATATTAAC
1 TATATTTTATATTAATATTAATTTTA-TAAC
* *
12402455 TATAGTTTATAAACTATACTATATAA-TTTATAAC
1 TATA-TTT-TATA-T-TAATAT-TAATTTTATAAC
*
12402489 ATATAGTTTATATTAATATTAATTTTATAGAC
1 -TATATTTTATATTAATATTAATTTTATA-AC
12402521 TATATTTTATATTAATATTAATT
1 TATATTTTATATTAATATTAATT
12402544 ATAAATTATA
Statistics
Matches: 122, Mismatches: 13, Indels: 38
0.71 0.08 0.22
Matches are distributed among these distances:
29 10 0.08
30 4 0.03
31 50 0.41
32 6 0.05
33 7 0.06
34 20 0.16
35 15 0.12
36 10 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (30 bp):
TATATTTTATATTAATATTAATTTTATAAC
Found at i:12402581 original size:44 final size:40
Alignment explanation
Indices: 12402532--12402614 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 40
12402522 ATATTTTATA
12402532 TTAATATTAATTATAAATTATAAACTAGATTATATTAATATAAG
1 TTAATATTAA-TATAAATTATAAA-TAG-TT-TATTAATATAAG
*
12402576 TTAATATTAATATTAATTATAAATAGTTTATTAATATAA
1 TTAATATTAATATAAATTATAAATAGTTTATTAATATAA
12402615 ATTTTATAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
40 11 0.29
41 2 0.05
42 3 0.08
43 12 0.32
44 10 0.26
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (40 bp):
TTAATATTAATATAAATTATAAATAGTTTATTAATATAAG
Found at i:12402596 original size:131 final size:131
Alignment explanation
Indices: 12402358--12402598 Score: 307
Period size: 131 Copynumber: 1.8 Consensus size: 131
12402348 TTAATGTATT
* **
12402358 ATATAGTTTATATTAATGTTAATTATCTTAACTATGATTTATATTAATATAATATATAGTTTATA
1 ATATAGTTTATATTAATATTAATTATCTTAACTATGATTTATATTAATATAATATATAAATTATA
* * *
12402423 AACTATAATGTATTAATATTAATTATATTAACTATAGTTTATAAACTATACTATATAATTTATAA
66 AACTAGAATATATTAATATTAATTATATTAACTATAGATTATAAACTATACTATATAATTTATAA
12402488 C
131 C
12402489 ATATAGTTTATATTAATATTAATT-T-TATAGACTAT-ATTTTATATTAATATTAAT-TATAAAT
1 ATATAGTTTATATTAATATTAATTATCT-TA-ACTATGA-TTTATATTAATA-TAATATATAAAT
*
12402550 TATAAACTAGATTATATTAATA-TAAGTTAATATTAA-TATTA-ATTATAAA
62 TATAAACTAGAATATATTAATATTAA-TT-ATATTAACTA-TAGATTATAAA
12402599 TAGTTTATTA
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
129 1 0.01
130 7 0.07
131 75 0.78
132 13 0.14
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (131 bp):
ATATAGTTTATATTAATATTAATTATCTTAACTATGATTTATATTAATATAATATATAAATTATA
AACTAGAATATATTAATATTAATTATATTAACTATAGATTATAAACTATACTATATAATTTATAA
C
Found at i:12402944 original size:15 final size:15
Alignment explanation
Indices: 12402882--12402963 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
12402872 TTTATATATA
12402882 TATATATATATAATAT
1 TATATATATATAAT-T
* *
12402898 TA-ATAAATTTAATT
1 TATATATATATAATT
* * * *
12402912 TAAAT-TAAAAAATA
1 TATATATATATAATT
12402926 TATATATA-AT-ATT
1 TATATATATATAATT
12402939 TATATAT-T-TAATT
1 TATATATATATAATT
*
12402952 TAAATATATATA
1 TATATATATATA
12402964 CCCGGCCCGA
Statistics
Matches: 49, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
12 1 0.02
13 18 0.37
14 13 0.27
15 15 0.31
16 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:12403246 original size:8 final size:8
Alignment explanation
Indices: 12403233--12403257 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12403223 CATTTACTCT
12403233 CGTTTTCC
1 CGTTTTCC
12403241 CGTTTTCC
1 CGTTTTCC
12403249 CGTTTTCC
1 CGTTTTCC
12403257 C
1 C
12403258 TGCCTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.12, T:0.48
Consensus pattern (8 bp):
CGTTTTCC
Found at i:12406317 original size:13 final size:13
Alignment explanation
Indices: 12406298--12406335 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
12406288 TAATTTAGTG
12406298 ATTATAAATAA-A
1 ATTATAAATAAGA
12406310 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
12406325 ATTATAAATAA
1 ATTATAAATAA
12406336 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:12406335 original size:18 final size:18
Alignment explanation
Indices: 12406314--12406383 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
12406304 AATAAAATTT
12406314 ATAATATAAGAATTATAA
1 ATAATATAAGAATTATAA
**
12406332 ATAATATAAAGAATTGGAA
1 ATAATAT-AAGAATTATAA
*
12406351 TTAATATACA-AATTATAA
1 ATAATATA-AGAATTATAA
* *
12406369 TTAATATAAAAATTA
1 ATAATATAAGAATTA
12406384 AATTTCAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.02
18 27 0.61
19 16 0.36
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAATATAAGAATTATAA
Found at i:12407197 original size:13 final size:14
Alignment explanation
Indices: 12407179--12407211 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12407169 TCTTCCTTTA
12407179 TCTTTCTCT-TTTT
1 TCTTTCTCTATTTT
*
12407192 TCTTTCTGTATTTT
1 TCTTTCTCTATTTT
12407206 TCTTTC
1 TCTTTC
12407212 GATGTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (14 bp):
TCTTTCTCTATTTT
Found at i:12407219 original size:13 final size:14
Alignment explanation
Indices: 12407179--12407223 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
12407169 TCTTCCTTTA
*
12407179 TCTTTCTCT-TTTT
1 TCTTTCTGTATTTT
12407192 TCTTTCTGTATTTT
1 TCTTTCTGTATTTT
12407206 TCTTTC-G-ATGTTT
1 TCTTTCTGTAT-TTT
12407219 TCTTT
1 TCTTT
12407224 TTTAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 17 0.59
14 10 0.34
ACGTcount: A:0.04, C:0.18, G:0.07, T:0.71
Consensus pattern (14 bp):
TCTTTCTGTATTTT
Found at i:12409975 original size:21 final size:21
Alignment explanation
Indices: 12409931--12409969 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12409921 GGTTAGTGAA
12409931 AAAAACAAAAATAAAAAAAAT
1 AAAAACAAAAATAAAAAAAAT
*
12409952 AAAAA-AAAAATGAAAAAA
1 AAAAACAAAAATAAAAAAA
12409970 TTTAAAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.87, C:0.03, G:0.03, T:0.08
Consensus pattern (21 bp):
AAAAACAAAAATAAAAAAAAT
Found at i:12411173 original size:15 final size:16
Alignment explanation
Indices: 12411131--12411173 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12411121 GCATGGAAGA
12411131 AAAAGAGTGGAAAAATG
1 AAAAGAGT-GAAAAATG
*
12411148 AAAAGAATGAAAAATG
1 AAAAGAGTGAAAAATG
*
12411164 -AGAGAGTGAA
1 AAAAGAGTGAA
12411174 TGAAAGAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 8 0.35
17 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (16 bp):
AAAAGAGTGAAAAATG
Found at i:12412494 original size:21 final size:21
Alignment explanation
Indices: 12412468--12412508 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12412458 AGATATGCGG
12412468 TATCGATACTAATGTAATTAA
1 TATCGATACTAATGTAATTAA
* *
12412489 TATCGATACTGATGTGATTA
1 TATCGATACTAATGTAATTA
12412509 TCGATACTAA
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:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TATCGATACTAATGTAATTAA
Found at i:12412788 original size:165 final size:165
Alignment explanation
Indices: 12412592--12412922 Score: 662
Period size: 165 Copynumber: 2.0 Consensus size: 165
12412582 TCGATACCAT
12412592 AATATAGAAGTATCGATAATAGGAGAAAGATATTGATACAATGGATTCCAGAATGCCGAAATGGT
1 AATATAGAAGTATCGATAATAGGAGAAAGATATTGATACAATGGATTCCAGAATGCCGAAATGGT
12412657 ATCGATACTGAAAGAGAGTATCGGTACCATAGTATAGAAGTATCGATACCATGGTGAGGGTACCG
66 ATCGATACTGAAAGAGAGTATCGGTACCATAGTATAGAAGTATCGATACCATGGTGAGGGTACCG
12412722 ATACTATTAAGCCATAAATTATAAGATATGCTGAA
131 ATACTATTAAGCCATAAATTATAAGATATGCTGAA
12412757 AATATAGAAGTATCGATAATAGGAGAAAGATATTGATACAATGGATTCCAGAATGCCGAAATGGT
1 AATATAGAAGTATCGATAATAGGAGAAAGATATTGATACAATGGATTCCAGAATGCCGAAATGGT
12412822 ATCGATACTGAAAGAGAGTATCGGTACCATAGTATAGAAGTATCGATACCATGGTGAGGGTACCG
66 ATCGATACTGAAAGAGAGTATCGGTACCATAGTATAGAAGTATCGATACCATGGTGAGGGTACCG
12412887 ATACTATTAAGCCATAAATTATAAGATATGCTGAA
131 ATACTATTAAGCCATAAATTATAAGATATGCTGAA
12412922 A
1 A
12412923 TTGTTATATA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 166 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.25
Consensus pattern (165 bp):
AATATAGAAGTATCGATAATAGGAGAAAGATATTGATACAATGGATTCCAGAATGCCGAAATGGT
ATCGATACTGAAAGAGAGTATCGGTACCATAGTATAGAAGTATCGATACCATGGTGAGGGTACCG
ATACTATTAAGCCATAAATTATAAGATATGCTGAA
Found at i:12413285 original size:81 final size:81
Alignment explanation
Indices: 12413138--12413403 Score: 354
Period size: 81 Copynumber: 3.3 Consensus size: 81
12413128 GTGAGTGTTG
** * * * *
12413138 AATGCCTTTGAGTAAAAGATTAATTATCTAGCTGTGTATTTGGCAGTAAGGTTCCAAGATTGCAA
1 AATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAA
12413203 GTTAGATGAAA-AACTA
66 GTTAGATGAAAGAA-TA
* * * * *
12413219 AATTCTTTTGAGTAAAATATTAATTGCCTAGATGTGCATTTGGCAGAAAGGTGCCAATATTCCAA
1 AATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAA
12413284 GTTAGATGAAAGAATA
66 GTTAGATGAAAGAATA
* **
12413300 AATGCCTTTGAGTAAAAGATTATTTGCCTAGCTGTGCATTTGGCAGAAAGGTGTTAATATTGCAA
1 AATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAA
**
12413365 GTTAGATGAAAGGCTA
66 GTTAGATGAAAGAATA
* *
12413381 AATGCCATTGAGAAAAAGATTAA
1 AATGCCTTTGAGTAAAAGATTAA
12413404 ATGATTAACA
Statistics
Matches: 160, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
81 158 0.99
82 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
AATGCCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAA
GTTAGATGAAAGAATA
Found at i:12413785 original size:26 final size:26
Alignment explanation
Indices: 12413730--12413787 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
12413720 AAGTTAAGAA
*
12413730 AATATTTTTGTAATGTATTTAAAGTG
1 AATATTTTTGTAATATATTTAAAGTG
* *
12413756 -ATATTTTTAGTAATATGTTTCAA-TG
1 AATATTTTT-GTAATATATTTAAAGTG
12413781 AATATTT
1 AATATTT
12413788 AATCATTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (26 bp):
AATATTTTTGTAATATATTTAAAGTG
Found at i:12420122 original size:81 final size:81
Alignment explanation
Indices: 12419987--12420557 Score: 856
Period size: 81 Copynumber: 7.1 Consensus size: 81
12419977 AAAATTAAAT
* * *
12419987 ATTAATTGCCTAGCTATACATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAATGCTAAC
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
*
12420052 TACCTTTGAGTAAAAG
66 TGCCTTTGAGTAAAAG
* * * * *
12420068 ATTAATTGCCTAGTTGTGCATTTGGTAGAAATGTTCCAATATTGCAAGTTAGATGAAAGGCTAAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
*
12420133 TGCTTTTGAGTAAAAG
66 TGCCTTTGAGTAAAAG
* * * *
12420149 ATTAATTGCCTAGTTCTGCATTTGACAGAAAGGTTCCAATATTGCAAGTTAGATGAAAGGCTAAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
12420214 TGCCTTTGAGTAAAAG
66 TGCCTTTGAGTAAAAG
* *
12420230 ATTAATTGCCTAGCCATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTATATGAAAGGCTAAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
12420295 TGCCTTTGAGTAAAAG
66 TGCCTTTGAGTAAAAG
* *
12420311 ATTAATTGCCTAGCTGTGCATTTGGCAAAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
*
12420376 TGCCTTTGTGTAAAAG
66 TGCCTTTGAGTAAAAG
* * * * * **
12420392 ATTAATTGCATAGTTGTGCATTTGGAAGAAAGGTGCCAATATTTCAAGTTAGATGAAAGAATAAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
*
12420457 TGCCTTTGTGTAAAAG
66 TGCCTTTGAGTAAAAG
* * *
12420473 ATTAATTGTCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAA-ATAGATGAAAGGCTGAA
1 ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
*
12420537 TGCCTTTGAGTAAAAT
66 TGCCTTTGAGTAAAAG
12420553 ATTAA
1 ATTAA
12420558 ATGATTAACA
Statistics
Matches: 445, Mismatches: 45, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
80 32 0.07
81 413 0.93
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
ATTAATTGCCTAGCTATGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGGCTAAA
TGCCTTTGAGTAAAAG
Found at i:12421825 original size:17 final size:18
Alignment explanation
Indices: 12421784--12421828 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12421774 ATTCATGCAT
12421784 CTAGTTCATTGAATAAAG
1 CTAGTTCATTGAATAAAG
*
12421802 TTAGTTCATT-AATTAAA-
1 CTAGTTCATTGAA-TAAAG
12421819 CTAGTTCATT
1 CTAGTTCATT
12421829 CATCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
CTAGTTCATTGAATAAAG
Found at i:12432490 original size:13 final size:13
Alignment explanation
Indices: 12432472--12432496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12432462 AAAGGCACAT
12432472 ACAATAAATATAA
1 ACAATAAATATAA
12432485 ACAATAAATATA
1 ACAATAAATATA
12432497 GTGATTTGAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
ACAATAAATATAA
Found at i:12433240 original size:13 final size:13
Alignment explanation
Indices: 12433222--12433246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12433212 TAGGTAAACG
12433222 CGGTAAAAAAATC
1 CGGTAAAAAAATC
12433235 CGGTAAAAAAAT
1 CGGTAAAAAAAT
12433247 GATGATTTCG
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:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
CGGTAAAAAAATC
Found at i:12434305 original size:51 final size:50
Alignment explanation
Indices: 12434214--12434349 Score: 140
Period size: 51 Copynumber: 2.7 Consensus size: 50
12434204 AATCACATTT
* * *
12434214 TTCAATTTATTAAAA--AATTAACTTTTCGTC-TCAAATATCAATCTATTC
1 TTCAATTTATTAAAATTATTTAACTTTTCTTCTTC-AACATCAATCTATTC
*
12434262 TTCAATTTATTTAAAATTATTTAACTTTTCTTCTTCAACATCAATTTATTC
1 TTCAATTTA-TTAAAATTATTTAACTTTTCTTCTTCAACATCAATCTATTC
*
12434313 TT-AAGTTTATTAAATATT-TTTAA-TTATTCTTTTTCAA
1 TTCAA-TTTATTAAA-ATTATTTAACTT-TTCTTCTTCAA
12434350 ACCATACCCA
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
48 9 0.12
49 8 0.11
50 22 0.29
51 35 0.46
52 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.51
Consensus pattern (50 bp):
TTCAATTTATTAAAATTATTTAACTTTTCTTCTTCAACATCAATCTATTC
Found at i:12435805 original size:18 final size:18
Alignment explanation
Indices: 12435778--12435817 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12435768 TTAACATAAT
12435778 GAAAAGAAAACA-ATGAAA
1 GAAAAGAAAA-AGATGAAA
*
12435796 GAAAATAAAAAGATGAAA
1 GAAAAGAAAAAGATGAAA
12435814 GAAA
1 GAAA
12435818 GTATAACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAAGATGAAA
Found at i:12439012 original size:84 final size:84
Alignment explanation
Indices: 12438916--12439144 Score: 253
Period size: 84 Copynumber: 2.7 Consensus size: 84
12438906 AATCAATAAT
* * *
12438916 CTCAACAGAACGTGGTGACGCCTTATTTGAATCAGTAATATGTCCAAAAATAAAATTTGTGAGAG
1 CTCAACAGAACGTGGTCACGCCTTATTAGAATCAGTAATATGTCCAAAAATAAAATTTGTGAGAA
*
12438981 TCAAGATCAATATAATATC
66 TCAAGATCAATACAATATC
* * * * *
12439000 CTCAACAGAACGTTGTCACGCCTTGTAAGAATCAGTAATATGT-CAAAGAATAAAATTTATGGGA
1 CTCAACAGAACGTGGTCACGCCTTATTAGAATCAGTAATATGTCCAAA-AATAAAATTTGTGAGA
** * * *
12439064 ATCAATCTTAGTACACTATC
65 ATCAAGATCAATACAATATC
* * * * * * *
12439084 CTCAACAGAAAGTGGTCACACCTTATTCGAATCAGTAATATATCCAAGAATGAAACTTGTG
1 CTCAACAGAACGTGGTCACGCCTTATTAGAATCAGTAATATGTCCAAAAATAAAATTTGTG
12439145 GTAATGGTTT
Statistics
Matches: 118, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
83 4 0.03
84 111 0.94
85 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (84 bp):
CTCAACAGAACGTGGTCACGCCTTATTAGAATCAGTAATATGTCCAAAAATAAAATTTGTGAGAA
TCAAGATCAATACAATATC
Found at i:12444421 original size:24 final size:24
Alignment explanation
Indices: 12444389--12444441 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12444379 CACTAGTCAT
*
12444389 TCTAGATTCCAAAAAT-TAATAGTC
1 TCTAAATT-CAAAAATCTAATAGTC
*
12444413 TCTAAATTCAAAAATCTAATATTC
1 TCTAAATTCAAAAATCTAATAGTC
12444437 TCTAA
1 TCTAA
12444442 TTCTAACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (24 bp):
TCTAAATTCAAAAATCTAATAGTC
Found at i:12444776 original size:105 final size:105
Alignment explanation
Indices: 12444651--12444883 Score: 369
Period size: 105 Copynumber: 2.2 Consensus size: 105
12444641 GAAAAATTCG
* ** *
12444651 GTTTGCCTAACCTCCGAGACAAACTGAATCCCCTTTAAATAATCTTTTTATGAAAAATAATAATT
1 GTTTGCCTAACATCTAAGACAAACCGAATCCCCTTTAAATAAT-TTTTTATGAAAAATAATAATT
* ***
12444716 AGTAATTGATGTGAAAC-AAAAATGAAATCTTGAGAATTTA
65 AGTAATTGATGTGAAACGAAAAATAAAATCAAAAGAATTTA
*
12444756 TTTTGCCTAACATCTAAGACAAACCGAATCCCCTTTAAATAATTTTTTATGAAAAATAATAATTA
1 GTTTGCCTAACATCTAAGACAAACCGAATCCCCTTTAAATAATTTTTTATGAAAAATAATAATTA
12444821 GTAATTGATGTGAAACGAAAAATAAAATCAAAAGAATTTA
66 GTAATTGATGTGAAACGAAAAATAAAATCAAAAGAATTTA
12444861 GTTTGCCTAACATCTAAGACAAA
1 GTTTGCCTAACATCTAAGACAAA
12444884 AGAGGTTCCC
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
104 38 0.32
105 79 0.68
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (105 bp):
GTTTGCCTAACATCTAAGACAAACCGAATCCCCTTTAAATAATTTTTTATGAAAAATAATAATTA
GTAATTGATGTGAAACGAAAAATAAAATCAAAAGAATTTA
Found at i:12447282 original size:44 final size:44
Alignment explanation
Indices: 12447224--12447340 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 44
12447214 TGTTAACCCG
* * *
12447224 CCTCTTTCTGTGATAGAATCGAACAAAATGTCGATGTTTATCTA
1 CCTCATTCTGTGATAGAATCGAGCAAAATGTCGATGTTGATCTA
* * * * *
12447268 TCTCATTCTATGATAGAATTGAGTAAAATGTTGATGTTGATCTA
1 CCTCATTCTGTGATAGAATCGAGCAAAATGTCGATGTTGATCTA
* *
12447312 CCTCTTTCTGTGATAAAATCGAGCAAAAT
1 CCTCATTCTGTGATAGAATCGAGCAAAAT
12447341 AAGGTTATGT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (44 bp):
CCTCATTCTGTGATAGAATCGAGCAAAATGTCGATGTTGATCTA
Found at i:12464955 original size:8 final size:9
Alignment explanation
Indices: 12464926--12464956 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12464916 GAAGTAAGTC
12464926 TAAAGGAGT
1 TAAAGGAGT
12464935 TAAAGGAGT
1 TAAAGGAGT
12464944 TAAAGG-GT
1 TAAAGGAGT
12464952 TAAAG
1 TAAAG
12464957 TCGTACACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (9 bp):
TAAAGGAGT
Found at i:12467312 original size:9 final size:9
Alignment explanation
Indices: 12467300--12467330 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12467290 GAGTATTGTT
*
12467300 TTCTTTGTA
1 TTCTTTGCA
12467309 TTCTTTGCA
1 TTCTTTGCA
12467318 TTCTTTGCA
1 TTCTTTGCA
12467327 TTCT
1 TTCT
12467331 CCCATTGTTA
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:0.10, C:0.19, G:0.10, T:0.61
Consensus pattern (9 bp):
TTCTTTGCA
Found at i:12470670 original size:13 final size:13
Alignment explanation
Indices: 12470652--12470676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12470642 TTTTGTTCCC
12470652 TTGATGTGATTCT
1 TTGATGTGATTCT
12470665 TTGATGTGATTC
1 TTGATGTGATTC
12470677 AAAATCAATT
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:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (13 bp):
TTGATGTGATTCT
Found at i:12472038 original size:14 final size:14
Alignment explanation
Indices: 12472019--12472064 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
12472009 TCTAAAATAA
*
12472019 TAAAAATAGATAAT
1 TAAAAATAGAAAAT
12472033 TAAAAACTA-AAACAT
1 TAAAAA-TAGAAA-AT
12472048 TAAAAATAGAAAAT
1 TAAAAATAGAAAAT
12472062 TAA
1 TAA
12472065 GGGTCTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (14 bp):
TAAAAATAGAAAAT
Found at i:12472968 original size:20 final size:22
Alignment explanation
Indices: 12472927--12472971 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12472917 CAAAACGGAA
12472927 ACGTTTTGAGTCTAATATATAT
1 ACGTTTTGAGTCTAATATATAT
12472949 ACGTTTTGAGTCTAATATATAT
1 ACGTTTTGAGTCTAATATATAT
12472971 A
1 A
12472972 TGTTATTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (22 bp):
ACGTTTTGAGTCTAATATATAT
Found at i:12474498 original size:117 final size:116
Alignment explanation
Indices: 12474292--12474710 Score: 512
Period size: 117 Copynumber: 3.7 Consensus size: 116
12474282 AAGCGTTGGA
* * * * *
12474292 TTGAAAAATTTCTTCTCATTATGAACTTC-TCCTCTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTTATTGGACGAGTTCTTCTCATTATGAA
*
12474356 CTCTTCACTGAAAATGTTGAGTCACCTCCTTCTGCGGTGGAATCGAACCAAGG
65 CTCTCCACTGAAAATGTTGAGTCACCTCCTTCTGCGGTGGAAT-GAACCAAGG
*
12474409 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGACGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTGGACGAGTTCTTCTCATTATGAAC
* *
12474474 TCTCCACTGAAAATGTTGAGTCACCTCCTTCTGCAGTGGACTTG-A--AA-G
66 TCTCCACTGAAAATGTTGAGTCACCTCCTTCTGCGGTGGA-ATGAACCAAGG
* * *
12474522 --GAATAAGTTCTTCTCATTATGAAC-T-TTC-TCCTT-TAGGACGAGTTCTTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTGGACGAGTTCTTCTCATTATGAAC
** * * *
12474581 TCT--TTTGGAAATGTTG-GTTCACCTCTTTCTACGGTGG-A--AACCAAGG
66 TCTCCACTGAAAATGTTGAG-TCACCTCCTTCTGCGGTGGAATGAACCAAGG
*
12474627 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTGGACGAGTTCTTCTCATTATGAAC
*
12474692 TCTCCACTGGAAATGTTGA
66 TCTCCACTGAAAATGTTGA
12474711 TCCTTCAAGC
Statistics
Matches: 260, Mismatches: 26, Indels: 35
0.81 0.08 0.11
Matches are distributed among these distances:
102 1 0.00
104 3 0.01
105 27 0.10
107 50 0.19
108 5 0.02
109 6 0.02
110 6 0.02
111 49 0.19
113 12 0.05
114 2 0.01
116 1 0.00
117 93 0.36
118 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (116 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTATTGGACGAGTTCTTCTCATTATGAAC
TCTCCACTGAAAATGTTGAGTCACCTCCTTCTGCGGTGGAATGAACCAAGG
Found at i:12475755 original size:10 final size:8
Alignment explanation
Indices: 12475726--12475790 Score: 69
Period size: 8 Copynumber: 7.9 Consensus size: 8
12475716 CCTTTTTCTC
*
12475726 TCTTTATT
1 TCTTTTTT
*
12475734 T-TTTATT
1 TCTTTTTT
12475741 TCTTTCTTCT
1 TCTTT-TT-T
12475751 TCTTTTTT
1 TCTTTTTT
12475759 TCTTTTTT
1 TCTTTTTT
12475767 TCTTTTTT
1 TCTTTTTT
*
12475775 TTTCTTTTT
1 TCT-TTTTT
12475784 TCTTTTT
1 TCTTTTT
12475791 ATTTGTTCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
7 7 0.14
8 27 0.54
9 10 0.20
10 6 0.12
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TCTTTTTT
Found at i:12475762 original size:18 final size:17
Alignment explanation
Indices: 12475718--12475790 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 17
12475708 CAAACCCTCC
* *
12475718 TTTTTCTCTCTTTATTTT
1 TTTTTCT-TTTTTCTTTT
*
12475736 TTATTTCTTTCTTCTTCTT
1 TT-TTTCTTTTTTCTT-TT
12475755 TTTTTCTTTTTTTCTTTT
1 TTTTTC-TTTTTTCTTTT
12475773 TTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
12475790 T
1 T
12475791 ATTTGTTCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
17 12 0.25
18 19 0.40
19 17 0.35
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTT
Found at i:12475768 original size:26 final size:25
Alignment explanation
Indices: 12475717--12475790 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
12475707 TCAAACCCTC
* *
12475717 CTTTTTCTCTCTTTATTT-TTTATTT
1 CTTTTTCT-TCTTTTTTTCTTTTTTT
12475742 CTTTCTTCTTCTTTTTTTCTTTTTTT
1 CTTT-TTCTTCTTTTTTTCTTTTTTT
*
12475768 CTTTTT-TTTTCTTTTTTCTTTTT
1 CTTTTTCTTCT-TTTTTTCTTTTT
12475791 ATTTGTTCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 3 0.07
25 26 0.60
26 14 0.33
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (25 bp):
CTTTTTCTTCTTTTTTTCTTTTTTT
Found at i:12475803 original size:26 final size:25
Alignment explanation
Indices: 12475733--12475807 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 25
12475723 CTCTCTTTAT
12475733 TTTTTATTTCTTTCTTCTTCTTTTTTTC
1 TTTTTATTT-TTTCTT-TTC-TTTTTTC
*
12475761 TTTTT-TTCTTTTTTTTTCTTTTTTC
1 TTTTTATT-TTTTCTTTTCTTTTTTC
* *
12475786 TTTTTATTTGTTCCTTT-TTTTT
1 TTTTTATTTTTTCTTTTCTTTTT
12475808 CAAGCATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.12
25 18 0.44
26 5 0.12
27 7 0.17
28 6 0.15
ACGTcount: A:0.03, C:0.13, G:0.01, T:0.83
Consensus pattern (25 bp):
TTTTTATTTTTTCTTTTCTTTTTTC
Found at i:12487167 original size:14 final size:14
Alignment explanation
Indices: 12487148--12487193 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
12487138 TCTAAAATAA
*
12487148 TAAAAATAGATAAT
1 TAAAAATAGAAAAT
12487162 TAAAAACTA-AAACAT
1 TAAAAA-TAGAAA-AT
12487177 TAAAAATAGAAAAT
1 TAAAAATAGAAAAT
12487191 TAA
1 TAA
12487194 GGGTCTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (14 bp):
TAAAAATAGAAAAT
Found at i:12496699 original size:104 final size:103
Alignment explanation
Indices: 12496578--12496808 Score: 365
Period size: 104 Copynumber: 2.2 Consensus size: 103
12496568 AAAAAAAATC
* * *
12496578 AGTTTGCCTAACCTCTAAGGCAAA-CTGAATCCCCTTTAAATAATCTTTATGGAAAATAATAATT
1 AGTTTGCCTAACATCTAAGACAAATC-AAATCCCCTTTAAATAATCTTTATGGAAAATAATAATT
* *
12496642 AGTAATTTATGTGAAACGAAAATGAAATTGAGAGAATTT
65 AGTAATTGATGTGAAACGAAAATGAAATCGAGAGAATTT
* *
12496681 AGTTTTGCCTAACATCTAAGACAAATCAAATCCCCTTTAAATACTTTTTATGGAAAATAATAATT
1 AG-TTTGCCTAACATCTAAGACAAATCAAATCCCCTTTAAATAATCTTTATGGAAAATAATAATT
12496746 AGTAATTGATGTGAAACGAAAATGAAATCGAGAGAATTT
65 AGTAATTGATGTGAAACGAAAATGAAATCGAGAGAATTT
*
12496785 AGTTTGCCTAAAATCTAAGACAAA
1 AGTTTGCCTAACATCTAAGACAAA
12496809 AGAAATTTCC
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 23 0.19
104 94 0.80
105 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (103 bp):
AGTTTGCCTAACATCTAAGACAAATCAAATCCCCTTTAAATAATCTTTATGGAAAATAATAATTA
GTAATTGATGTGAAACGAAAATGAAATCGAGAGAATTT
Found at i:12498582 original size:6 final size:6
Alignment explanation
Indices: 12498492--12498580 Score: 97
Period size: 6 Copynumber: 14.8 Consensus size: 6
12498482 CAAACAGTGA
* * * *
12498492 TGATGG TGTTGG TGTTGG TGATGG TGATGG TGATGA TGATGG TGATGT
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
* * * * *
12498540 TGATGG TTATAG TGATGG TGATGG TGGTGA TGATGA TGATG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATG
12498581 ATAAGATAGA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (6 bp):
TGATGG
Found at i:12498662 original size:3 final size:3
Alignment explanation
Indices: 12498647--12498698 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
12498637 GTCGAGTGCT
* * * * *
12498647 TGA TGA TGG TGA TGA TGA TGA TGA TGG TGA TGA TGA TTA TGG TGA TGG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
12498695 TGA T
1 TGA T
12498699 CATCATAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:12498667 original size:15 final size:15
Alignment explanation
Indices: 12498647--12498698 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
12498637 GTCGAGTGCT
* *
12498647 TGATGATGGTGATGA
1 TGATGATGATGGTGA
12498662 TGATGATGATGGTGA
1 TGATGATGATGGTGA
*
12498677 TGATGATTATGGTGA
1 TGATGATGATGGTGA
*
12498692 TGGTGAT
1 TGATGAT
12498699 CATCATAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (15 bp):
TGATGATGATGGTGA
Found at i:12498779 original size:3 final size:3
Alignment explanation
Indices: 12498771--12498897 Score: 56
Period size: 3 Copynumber: 42.3 Consensus size: 3
12498761 AGGTCTTGAA
* * * * * **
12498771 GGT GGT GGT GGT GGT GGT GAT GAT GGT GTT GGT GTT GGT GAT GGT CAT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * ** * * * * * * * * * *
12498819 AGT GAT GGT CAT AGT GAT GGT GAT GGT GAT GAT GAT GAT GAT GAT GAT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
*
12498867 GGT GGT GGT GGT GGT GGT GGT GAT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
12498898 ATGATGATGA
Statistics
Matches: 96, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.14, C:0.02, G:0.50, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:12498782 original size:6 final size:6
Alignment explanation
Indices: 12498771--12499143 Score: 242
Period size: 6 Copynumber: 62.2 Consensus size: 6
12498761 AGGTCTTGAA
* * * * * * *
12498771 GGTGGT GGTGGT GGTGGT GATGAT GGTGTT GGTGTT GGTGAT GGTCAT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * * *
12498819 AGTGAT GGTCAT AGTGAT GGTGAT GGTGAT GATGAT GATGAT GATGAT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * * * *
12498867 GGTGGT GGTGGT GGTGGT GGTGAT GGTGGT GATGAT GATGAT GATGAT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * *
12498915 GATGAT GGTGTT GGTGTT GGTGAT GGTCAT AGTGAT GGTGAT GGTGAT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * ** * * *
12498963 GGTGAT GATGAT GATGAT GATGAT GACGAT GATGAT GGTGGT GGTGGT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * * * * *
12499011 GGTGGT GGTGGT GGTGGT GCTGAT GATGAT GATGAT GGTGTT GGTGTT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * * * **
12499059 GTTGAT GGTCAT AGTGAT GGTGAT GGTAAT GATGAT GATGAT GACGAT
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT
* * * * * * *
12499107 GATGGT GGTGGT AGTGGT GGTGAT GATGAT GATGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT G
12499144 ATAATGATGA
Statistics
Matches: 312, Mismatches: 55, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 312 1.00
ACGTcount: A:0.18, C:0.02, G:0.45, T:0.35
Consensus pattern (6 bp):
GGTGAT
Found at i:12498902 original size:3 final size:3
Alignment explanation
Indices: 12498896--12499163 Score: 137
Period size: 3 Copynumber: 89.3 Consensus size: 3
12498886 GTGATGGTGG
* * * * * * *
12498896 TGA TGA TGA TGA TGA TGA TGA TGA TGG TGT TGG TGT TGG TGA TGG TCA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* * *
12498944 T-A GTGA TGG TGA TGG TGA TGG TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* * * * * * * * * * * *
12498989 CGA TGA TGA TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGC TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* * * * * * * *
12499037 TGA TGA TGA TGG TGT TGG TGT TGT TGA TGG TCA T-A GTGA TGG TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA TGA
* * * * * * * *
12499082 TGG TAA TGA TGA TGA TGA TGA CGA TGA TGG TGG TGG T-A GTGG TGG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA
*
12499127 TGA TGA TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
12499164 AAGGCGGAAA
Statistics
Matches: 217, Mismatches: 42, Indels: 12
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.01
3 213 0.98
4 2 0.01
ACGTcount: A:0.22, C:0.02, G:0.42, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:12499406 original size:127 final size:126
Alignment explanation
Indices: 12499180--12499429 Score: 367
Period size: 127 Copynumber: 2.0 Consensus size: 126
12499170 GAAAAAATGG
* * *
12499180 TGGTTACACCACTGTATGAGCCAGCTGGTTCATTTGTTGTCGAGCTCTTAAAGGTTAGATTTGGT
1 TGGTTACACCACTGTATGAGCCACCTCGTTCATTTGTTATCGAGCTCTTAAAGGTTAGATTTGGT
* * * *
12499245 CTTATTCTGAAACTTCTCCTGGATATGCATAAGCCTCT-CTACTATTAACTCCAAAGATGAT
66 CTTATTCTGAAACTTCTACTGGATAAGAACAAGCCTCTAC-ACTATTAACTCCAAAGATGAT
* * *
12499306 TGGTTACACCACTGTTTGAGCCACCTCGTTCATTTCTTTATCGAGCTCTTAAAGGTTAGCTTTGG
1 TGGTTACACCACTGTATGAGCCACCTCGTTCATTT-GTTATCGAGCTCTTAAAGGTTAGATTTGG
* *
12499371 TCTTATTCTGAAACTTCTACTGGCTAAGAACAAGCCTCTACACTATTGACTCCAAAGAT
65 TCTTATTCTGAAACTTCTACTGGATAAGAACAAGCCTCTACACTATTAACTCCAAAGAT
12499430 AATTTCTTCG
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
126 32 0.29
127 77 0.70
128 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (126 bp):
TGGTTACACCACTGTATGAGCCACCTCGTTCATTTGTTATCGAGCTCTTAAAGGTTAGATTTGGT
CTTATTCTGAAACTTCTACTGGATAAGAACAAGCCTCTACACTATTAACTCCAAAGATGAT
Found at i:12501323 original size:28 final size:28
Alignment explanation
Indices: 12501283--12501344 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
12501273 TGATTCCCTA
12501283 CACGTGAGGTATATTTATCTTCTAAGTT
1 CACGTGAGGTATATTTATCTTCTAAGTT
*
12501311 CACGTGAGGTATATTTGTCTTCTAAGTT
1 CACGTGAGGTATATTTATCTTCTAAGTT
12501339 CACGTG
1 CACGTG
12501345 TGGGGCTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (28 bp):
CACGTGAGGTATATTTATCTTCTAAGTT
Found at i:12501756 original size:2 final size:2
Alignment explanation
Indices: 12501749--12501800 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
12501739 AGTCCTTAGA
* * *
12501749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
12501791 GT AT GT AT AT
1 AT AT AT AT AT
12501801 TGCAACATGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12518964 original size:20 final size:21
Alignment explanation
Indices: 12518939--12518981 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12518929 CCTCCTTTAT
12518939 TTCCAAATA-CTTCATTTTTC
1 TTCCAAATATCTTCATTTTTC
*
12518959 TTCCAAGTATCTTCATTTTTC
1 TTCCAAATATCTTCATTTTTC
12518980 TT
1 TT
12518982 ACCTTCTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.53
Consensus pattern (21 bp):
TTCCAAATATCTTCATTTTTC
Found at i:12524602 original size:24 final size:24
Alignment explanation
Indices: 12524574--12524621 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12524564 AACACTTATA
*
12524574 AATGTTGATATTGATAAGGCTAAT
1 AATGTTGATATTAATAAGGCTAAT
* *
12524598 AATGTTGATGTTAATAATGCTAAT
1 AATGTTGATATTAATAAGGCTAAT
12524622 GCTTTTGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (24 bp):
AATGTTGATATTAATAAGGCTAAT
Found at i:12528124 original size:13 final size:13
Alignment explanation
Indices: 12528108--12528132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12528098 TTAATTTAAA
12528108 AAATAAAAACAAT
1 AAATAAAAACAAT
12528121 AAATAAAAACAA
1 AAATAAAAACAA
12528133 ACAAACAAAC
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:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAATAAAAACAAT
Found at i:12535693 original size:40 final size:39
Alignment explanation
Indices: 12535639--12535726 Score: 160
Period size: 40 Copynumber: 2.3 Consensus size: 39
12535629 GATTTTCTTT
12535639 CCTTTT-TTTCTTTTAATTCACTTGATGCAACTACTTAA
1 CCTTTTCTTTCTTTTAATTCACTTGATGCAACTACTTAA
12535677 CCTTTTCTTTACTTTTAATTCACTTGATGCAACTACTTAA
1 CCTTTTCTTT-CTTTTAATTCACTTGATGCAACTACTTAA
12535717 CCTTTTCTTT
1 CCTTTTCTTT
12535727 TGACTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 6 0.12
39 3 0.06
40 39 0.81
ACGTcount: A:0.22, C:0.23, G:0.05, T:0.51
Consensus pattern (39 bp):
CCTTTTCTTTCTTTTAATTCACTTGATGCAACTACTTAA
Found at i:12541627 original size:106 final size:105
Alignment explanation
Indices: 12541442--12541642 Score: 257
Period size: 106 Copynumber: 1.9 Consensus size: 105
12541432 CAAGATCGAC
12541442 TCAACTTCACAACAAATGAGTCAACCACAATTTAGCTTAACCAAAGACCAAGCAACAATTTTTTA
1 TCAACTTCACAACAAATGAGTCAACCACAATTTAGCTTAACCAAAGACCAAGCAAC-ATTTTTTA
*
12541507 TCCTAGATTTCGAGTCAA-ATTTCAACTTCATCAACCTTGAT
65 GCCTAGATTTCGAGT-AATATTTCAACTTCATCAACCTTGAT
* * ** * *
12541548 TCAACTTCACGACAAATGAGTCATCCACAATTTAGCTTAACTCAACA-A-TGAGGAGC-TTTTTT
1 TCAACTTCACAACAAATGAGTCAACCACAATTTAGCTTAAC-CAA-AGACCAAGCAACATTTTTT
12541610 CCAGCCTAGATTTCGAGTAATATTTCAACTTCA
64 --AGCCTAGATTTCGAGTAATATTTCAACTTCA
12541643 CGACGAAGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
104 6 0.07
105 2 0.02
106 70 0.84
107 4 0.05
108 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.30
Consensus pattern (105 bp):
TCAACTTCACAACAAATGAGTCAACCACAATTTAGCTTAACCAAAGACCAAGCAACATTTTTTAG
CCTAGATTTCGAGTAATATTTCAACTTCATCAACCTTGAT
Found at i:12541940 original size:34 final size:30
Alignment explanation
Indices: 12541902--12541970 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
12541892 TTGATATAAC
12541902 AATTTAAGGCAAAATGGTTTTTGGAATTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAATT-AATTG
*
12541936 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGAATTAATTG
12541965 AATTTA
1 AATTTA
12541971 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGAATTAATTG
Found at i:12541981 original size:29 final size:30
Alignment explanation
Indices: 12541911--12541970 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
12541901 CAATTTAAGG
12541911 CAAAATGGTTTTTGGAATTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
*
12541942 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
12541971 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:12542076 original size:21 final size:21
Alignment explanation
Indices: 12542050--12542127 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
12542040 AGGGTGTCAA
*
12542050 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCATAC
**
12542071 AGTGCATCCATGCACCTGTAC
1 AGTGCATCCATGCACCCATAC
*
12542092 TAGTGCATCGATGCA-CCATAC
1 -AGTGCATCCATGCACCCATAC
*
12542113 AGTGCATCTATGCAC
1 AGTGCATCCATGCAC
12542128 TTAAACACCG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.27
21 23 0.47
22 13 0.27
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATAC
Found at i:12542362 original size:20 final size:22
Alignment explanation
Indices: 12542324--12542363 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
12542314 TTTGAGTAGA
12542324 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
12542346 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
12542364 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:12542617 original size:34 final size:31
Alignment explanation
Indices: 12542578--12542646 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 31
12542568 TTTTGTAAAG
*
12542578 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAA-CTA
*
12542612 GGGAAAGGTTCTAGTTTAGCCCGGAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAACTA
12542643 GGGA
1 GGGA
12542647 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 7 0.21
32 4 0.12
33 1 0.03
34 21 0.64
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (31 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAACTA
Found at i:12544696 original size:21 final size:21
Alignment explanation
Indices: 12544657--12544696 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12544647 AAACAATTGG
*
12544657 TAACAATTGATATCATTTTGT
1 TAACAATTGACATCATTTTGT
* *
12544678 TAACAATTGGCATCTTTTT
1 TAACAATTGACATCATTTT
12544697 CATTAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (21 bp):
TAACAATTGACATCATTTTGT
Found at i:12544836 original size:34 final size:30
Alignment explanation
Indices: 12544798--12544866 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 30
12544788 TTGATATAAC
12544798 AATTTAAGGCAAAATGGTTTTTGGACATGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAC-TGAATTG
*
12544832 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTGAATTG
12544861 AATTTA
1 AATTTA
12544867 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.33
30 10 0.30
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTGAATTG
Found at i:12544877 original size:29 final size:30
Alignment explanation
Indices: 12544807--12544866 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
12544797 CAATTTAAGG
12544807 CAAAATGGTTTTTGGACATGAATTGAATTTA
1 CAAAAT-GTTTTTGGACATGAATTGAATTTA
*
12544838 CAAAATGTTTTTGGAC-TTAATTGAATTTA
1 CAAAATGTTTTTGGACATGAATTGAATTTA
12544867 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 10 0.36
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACATGAATTGAATTTA
Found at i:12544972 original size:21 final size:20
Alignment explanation
Indices: 12544946--12545044 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
12544936 AGGGTGTCAA
12544946 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
12544967 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
12544988 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
12545009 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
12545030 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12545045 TCAAACACCG
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 36 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:12544980 original size:13 final size:14
Alignment explanation
Indices: 12544977--12545044 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
12544967 AGTGCATCCA
*
12544977 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
12544990 TGCATCCATGCACC
1 TGCATCCATGCACG
*
12545004 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
12545019 ATGCA-CCATGCA-G
1 -TGCATCCATGCACG
12545032 TGCATCCATGCAC
1 TGCATCCATGCAC
12545045 TCAAACACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 5 0.11
16 6 0.14
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:12545093 original size:20 final size:20
Alignment explanation
Indices: 12545068--12545119 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
12545058 GCAATTAGTA
12545068 CATCGATGCATCCTTCTGTG
1 CATCGATGCATCCTTCTGTG
12545088 CATCGATGCATCCTTCTGTG
1 CATCGATGCATCCTTCTGTG
12545108 CATCGATGCATC
1 CATCGATGCATC
12545120 AAGGTTGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (20 bp):
CATCGATGCATCCTTCTGTG
Found at i:12545134 original size:21 final size:21
Alignment explanation
Indices: 12545104--12545174 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
12545094 TGCATCCTTC
12545104 TGTGCATCGATGCATCAAGGT
1 TGTGCATCGATGCATCAAGGT
*
12545125 TGTACATCGATGCATCAAGGT
1 TGTGCATCGATGCATCAAGGT
*
12545146 TGTGCATCGATGCATCAAGGC
1 TGTGCATCGATGCATCAAGGT
12545167 TGTGCATC
1 TGTGCATC
12545175 CATACACGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (21 bp):
TGTGCATCGATGCATCAAGGT
Found at i:12546094 original size:132 final size:132
Alignment explanation
Indices: 12545855--12546102 Score: 318
Period size: 132 Copynumber: 1.9 Consensus size: 132
12545845 ATCCCAACAG
* * *
12545855 ATTTCAACTTCATGACAAAGGATATCATGCTTAAATCATCCAAGATTGACTCAACTTCACAACGA
1 ATTTCAACTTCATAACAAAGGATATCAAGCTTAAATCATCCAAGATCGACTCAACTTCACAACGA
** *
12545920 ATGAGTCAACCACAATTTAGTTTAACCAAACAACGAGCAGCTATTTTTATCGTAGATTTCGAGTC
66 ATGAGTCAACCACAACATAGCTTAACCAAACAACGAGCAGCTATTTTTATCGTAGATTTCGAGTC
12545985 AA
131 AA
* * * * * **
12545987 ATTTCAACTTCATAACGAAGGATATCAAGGTTGAGTCATCCGAGATCGACTCAACTTCATGACGA
1 ATTTCAACTTCATAACAAAGGATATCAAGCTTAAATCATCCAAGATCGACTCAACTTCACAACGA
* * * * *
12546052 ATGAGTTATCCATAACATAGCTTAACTC-AACAGCGAGGAGCTATTTTTATC
66 ATGAGTCAACCACAACATAGCTTAAC-CAAACAACGAGCAGCTATTTTTATC
12546103 CAACTTAACT
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
132 96 0.99
133 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (132 bp):
ATTTCAACTTCATAACAAAGGATATCAAGCTTAAATCATCCAAGATCGACTCAACTTCACAACGA
ATGAGTCAACCACAACATAGCTTAACCAAACAACGAGCAGCTATTTTTATCGTAGATTTCGAGTC
AA
Found at i:12547585 original size:21 final size:20
Alignment explanation
Indices: 12547539--12547586 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
12547529 GATTCTGACT
12547539 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
12547559 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
12547581 ATCGCA
1 ATCGCA
12547587 ACGCGATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:12547655 original size:20 final size:20
Alignment explanation
Indices: 12547578--12547655 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
12547568 GCGATTTTCC
* *
12547578 TAAATCGCAACGCGATTACG
1 TAAATCGCAATGCGAATACG
*
12547598 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAA-TACG
*
12547619 AAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
*
12547639 TAAATCGCAATGTGAAT
1 TAAATCGCAATGCGAAT
12547656 CTGACTATCG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 32 0.64
21 18 0.36
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:12548232 original size:20 final size:20
Alignment explanation
Indices: 12548207--12548257 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
12548197 TTCTAAACTT
*
12548207 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
12548227 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
12548247 ACTATCGCAAC
1 AAAATCGCAAC
12548258 GAGAGAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:12548287 original size:33 final size:33
Alignment explanation
Indices: 12548229--12548321 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
12548219 TGAAAATGAA
* **
12548229 AATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AATCGCAACGCG-AAATGAAAATCGCAACGAGAG
*
12548263 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* **
12548296 AATCGCAACGCAAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
12548322 TTACGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.79
34 11 0.21
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:12548387 original size:20 final size:21
Alignment explanation
Indices: 12548364--12548410 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
12548354 GTTGAGATAG
12548364 TCATTTC-CGCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
*
12548384 TCA-TTCTCTCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
12548404 TCATTTC
1 TCATTTC
12548411 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.49
Consensus pattern (21 bp):
TCATTTCTCGCGTTGCGATTT
Found at i:12550262 original size:94 final size:94
Alignment explanation
Indices: 12550101--12550480 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
12550091 TAGATTGCTT
* * *
12550101 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12550166 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
12550195 AGTAAATTTATTCGGGTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12550260 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
12550289 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12550354 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
12550383 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
12550448 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
12550476 AGTAA
1 AGTAA
12550481 TGCAATCCAT
Statistics
Matches: 273, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 26 0.10
94 247 0.90
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:12550593 original size:19 final size:19
Alignment explanation
Indices: 12550571--12550628 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
12550561 AAAAATGACT
12550571 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATAAAA
* *
12550590 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATAAAA
12550604 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATAAAA
12550623 ATCGCA
1 ATCGCA
12550629 TTGCGATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 15 0.50
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATAAAA
Found at i:12550671 original size:33 final size:33
Alignment explanation
Indices: 12550624--12550701 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
12550614 GAAATAAAAA
**
12550624 TCGCATTGCGATTCTCTCGTCGCGGTTTTCATT
1 TCGCATTGCGATTCTCTCGTCGCAATTTTCATT
* *
12550657 TCGCGTTGCGATTCTCTCGTTGCAATTTTCATT
1 TCGCATTGCGATTCTCTCGTCGCAATTTTCATT
12550690 TCGCATTGCGAT
1 TCGCATTGCGAT
12550702 AGTCATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTCGCAATTTTCATT
Found at i:12551232 original size:24 final size:24
Alignment explanation
Indices: 12551198--12551251 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12551188 CTGAAAAATC
12551198 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
12551222 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
12551246 ATCAAA
1 ATCAAA
12551252 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:12552178 original size:25 final size:20
Alignment explanation
Indices: 12552114--12552178 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
12552104 AGAATCTCGT
12552114 TGCGATTTAC-TAAATCGCGA
1 TGCGA-TTACGTAAATCGCGA
12552134 TGCGATTACGTAAATCGCGA
1 TGCGATTACGTAAATCGCGA
*
12552154 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCGA
12552174 TGCGA
1 TGCGA
12552179 ATTTGGGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 4 0.09
20 39 0.91
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCGA
Found at i:12554839 original size:25 final size:26
Alignment explanation
Indices: 12554803--12554864 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
12554793 TATCGGTGTT
* *
12554803 GTTGGTCG-TTTAAGGTCACGACTAC
1 GTTGGCCGATTTAAGGTCACGACAAC
*
12554828 GTTGGCC-ATTTAAGGTCACGGCAAC
1 GTTGGCCGATTTAAGGTCACGACAAC
12554853 GTTGGCCGATTT
1 GTTGGCCGATTT
12554865 TGAGGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 28 0.88
26 4 0.12
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (26 bp):
GTTGGCCGATTTAAGGTCACGACAAC
Found at i:12557869 original size:2 final size:2
Alignment explanation
Indices: 12557862--12557933 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
12557852 AATGAAATGC
12557862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12557904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12557934 TTCTCACAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12558134 original size:18 final size:17
Alignment explanation
Indices: 12558102--12558138 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
12558092 AGTGGTATAG
12558102 TTTGTTTGTTATCTTAT
1 TTTGTTTGTTATCTTAT
*
12558119 TTTGTATTGTTGTCTTAT
1 TTTGT-TTGTTATCTTAT
12558137 TT
1 TT
12558139 CATTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTATCTTAT
Found at i:12564496 original size:44 final size:44
Alignment explanation
Indices: 12564428--12564635 Score: 264
Period size: 44 Copynumber: 4.7 Consensus size: 44
12564418 TTACAAATGT
*
12564428 CGCTATATACC-AACCTTTCGCGGCGTTTGTATCCTAAAAACGC
1 CGCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAACGC
*
12564471 CGCTATATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAACGC
1 CGCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAACGC
*
12564515 CGCTATATACCAAACCTTTAGC-G-GTATTGTTTTCCTAAAAACGC
1 CGCTATATACCAAACCTTTAGCGGCGT-TTG-TATCCTAAAAACGC
** * *
12564559 CGCTATATACCAAAGTTTTAGCGGTGTTTGTTTCCTAAAAACGC
1 CGCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAACGC
*
12564603 CGCTAAAT-CTCAAAACCTATT-GCGGCGTTTGTA
1 CGCTATATAC-C-AAACCT-TTAGCGGCGTTTGTA
12564636 AGAAAAATAC
Statistics
Matches: 146, Mismatches: 11, Indels: 14
0.85 0.06 0.08
Matches are distributed among these distances:
42 2 0.01
43 16 0.11
44 106 0.73
45 18 0.12
46 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CGCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAACGC
Found at i:12564693 original size:43 final size:44
Alignment explanation
Indices: 12564597--12564736 Score: 135
Period size: 43 Copynumber: 3.2 Consensus size: 44
12564587 TGTTTCCTAA
* * * * * *
12564597 AAACGCCGCTAAATCTCAAAACCTATTGCGGCGTTTGTAAGAAA
1 AAACGTCGCTAAATATCAGAACCTATTGCAGCGTTTGTATGAAC
12564641 AATAC--CGCTAAATATCAGAACCTATTGCAGCGTTTGT-TGAAC
1 AA-ACGTCGCTAAATATCAGAACCTATTGCAGCGTTTGTATGAAC
* * * *
12564683 AAACGTCGCTATATATC-GTTACCTATTGCAGCGTTTTTCATTAAC
1 AAACGTCGCTAAATATCAG-AACCTATTGCAGCGTTTGT-ATGAAC
12564728 AAACGTCGC
1 AAACGTCGC
12564737 AAACTTTAGC
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
41 2 0.02
42 6 0.07
43 56 0.69
44 2 0.02
45 15 0.19
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (44 bp):
AAACGTCGCTAAATATCAGAACCTATTGCAGCGTTTGTATGAAC
Found at i:12566424 original size:20 final size:20
Alignment explanation
Indices: 12566399--12566442 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
12566389 TTAATCTATC
12566399 CTCACTAATGTTGGTTTCAG
1 CTCACTAATGTTGGTTTCAG
12566419 CTCACTAATGTTGGTTTCAG
1 CTCACTAATGTTGGTTTCAG
12566439 CTCA
1 CTCA
12566443 TCTCCCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
CTCACTAATGTTGGTTTCAG
Found at i:12568542 original size:23 final size:23
Alignment explanation
Indices: 12568512--12568558 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
12568502 CGAGGGAGCT
12568512 TTCTCTTCGACCAGTCCATAGGG
1 TTCTCTTCGACCAGTCCATAGGG
12568535 TTCTCTTCGACCAGTCCATAGGG
1 TTCTCTTCGACCAGTCCATAGGG
12568558 T
1 T
12568559 AGATCGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (23 bp):
TTCTCTTCGACCAGTCCATAGGG
Found at i:12570341 original size:19 final size:20
Alignment explanation
Indices: 12570319--12570360 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12570309 TGATTCTATC
*
12570319 AAAATTTTAATT-AGGATTA
1 AAAATTTTAATTAAGGAATA
*
12570338 AAAATTTTTATTAAGGAATA
1 AAAATTTTAATTAAGGAATA
12570358 AAA
1 AAA
12570361 TGATCATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
AAAATTTTAATTAAGGAATA
Found at i:12583394 original size:18 final size:18
Alignment explanation
Indices: 12583367--12583426 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
12583357 TTTTCAAATT
*
12583367 GCATTATACATTTGCATA
1 GCATTCTACATTTGCATA
12583385 GCATTCTACATTTGCATA
1 GCATTCTACATTTGCATA
*
12583403 GCATTCTACATTTCCATA
1 GCATTCTACATTTGCATA
*
12583421 ACATTC
1 GCATTC
12583427 ATTAGTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (18 bp):
GCATTCTACATTTGCATA
Found at i:12589709 original size:8 final size:8
Alignment explanation
Indices: 12589691--12589776 Score: 51
Period size: 8 Copynumber: 11.4 Consensus size: 8
12589681 AAGAGATATG
12589691 AAAAT-GA
1 AAAATGGA
12589698 AAAATGGA
1 AAAATGGA
12589706 AAAATGG-
1 AAAATGGA
*
12589713 -AAATGAA
1 AAAATGGA
*
12589720 AAAATGAA
1 AAAATGGA
**
12589728 AAAATAAA
1 AAAATGGA
12589736 AAAAT--A
1 AAAATGGA
*
12589742 AAAATTGAA
1 AAAA-TGGA
12589751 AAAAT-GA
1 AAAATGGA
*
12589758 ACAAT-GA
1 AAAATGGA
12589765 ATAAATGGA
1 A-AAATGGA
12589774 AAA
1 AAA
12589777 TGAAGAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
6 10 0.15
7 14 0.21
8 34 0.52
9 8 0.12
ACGTcount: A:0.70, C:0.01, G:0.14, T:0.15
Consensus pattern (8 bp):
AAAATGGA
Found at i:12589709 original size:15 final size:15
Alignment explanation
Indices: 12589691--12589796 Score: 101
Period size: 15 Copynumber: 7.1 Consensus size: 15
12589681 AAGAGATATG
*
12589691 AAAATGAAAAATGGA
1 AAAATGAAAAATGAA
*
12589706 AAAATG-GAAATGAA
1 AAAATGAAAAATGAA
*
12589720 AAAATGAAAAAATAAA
1 AAAATG-AAAAATGAA
12589736 AAAAT-AAAAATTGAA
1 AAAATGAAAAA-TGAA
*
12589751 AAAATGAACAATGAA
1 AAAATGAAAAATGAA
* *
12589766 TAAATGGAAAATGAA
1 AAAATGAAAAATGAA
*
12589781 GAAAAAGAAAAA-GAA
1 -AAAATGAAAAATGAA
12589796 A
1 A
12589797 TGGGAGGGCC
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
14 18 0.24
15 33 0.45
16 23 0.31
ACGTcount: A:0.71, C:0.01, G:0.15, T:0.13
Consensus pattern (15 bp):
AAAATGAAAAATGAA
Found at i:12589715 original size:22 final size:21
Alignment explanation
Indices: 12589688--12589780 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 21
12589678 AAGAAGAGAT
*
12589688 ATGAAAATGAAAAATGGAAAA
1 ATGAAAATGAAAAATGAAAAA
*
12589709 ATGGAAATGAAAAAATGAAAAA
1 ATGAAAATG-AAAAATGAAAAA
*
12589731 ATAAAAAAAT-AAAAATTGAAAAA
1 AT--GAAAATGAAAAA-TGAAAAA
*
12589754 ATGAACAATGAATAAATG-GAAA
1 ATGAA-AATGAA-AAATGAAAAA
12589776 ATGAA
1 ATGAA
12589781 GAAAAAGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
21 10 0.17
22 29 0.49
23 13 0.22
24 7 0.12
ACGTcount: A:0.68, C:0.01, G:0.15, T:0.16
Consensus pattern (21 bp):
ATGAAAATGAAAAATGAAAAA
Found at i:12590154 original size:3 final size:3
Alignment explanation
Indices: 12590148--12590193 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
12590138 CCCTTTTGTA
* **
12590148 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA AAC ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12590194 CAAAATACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12591698 original size:10 final size:10
Alignment explanation
Indices: 12591683--12591713 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
12591673 TAGACTTTAA
12591683 ATTTTAATTT
1 ATTTTAATTT
12591693 ATTTTAATTT
1 ATTTTAATTT
12591703 ATTTTAATTT
1 ATTTTAATTT
12591713 A
1 A
12591714 GCCCTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:12599705 original size:47 final size:45
Alignment explanation
Indices: 12599654--12599742 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 45
12599644 TCATACTTAC
* *
12599654 AATGCA-CCATTATGCATTTTTCATATATGACATTCTTTCATGCCAAT
1 AATGCACCCA-TATACA-TTTT-ATATATGACATCCTTTCATGCCAAT
*
12599701 AATGCACCCATATACATTTTATTTATGACATCCTTTCATGCC
1 AATGCACCCATATACATTTTATATATGACATCCTTTCATGCC
12599743 CTTTTATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 20 0.53
46 4 0.11
47 11 0.29
48 3 0.08
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (45 bp):
AATGCACCCATATACATTTTATATATGACATCCTTTCATGCCAAT
Found at i:12599783 original size:91 final size:92
Alignment explanation
Indices: 12599672--12599842 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 92
12599662 ATTATGCATT
* *
12599672 TTTCATATATGACATTCTTTCATGCCAAT-AATGCACCCA-TATACATTTTATTTATGACATCCT
1 TTTCATATATGACATTCTTTCATGCCAATCAATACA-CCATTATACATTTCATTTATGACATCCT
12599735 TTCATGCCCTTT-TATAAGCTATTATACA
65 TTCATG-CCTTTCTATAAGCTATTATACA
* * ** * * *
12599763 TTTCATTTATGGCATTCTTTCATGCCCTTCTATACACTATTATACCTTTCATTTATGACATCCTT
1 TTTCATATATGACATTCTTTCATGCCAATCAATACACCATTATACATTTCATTTATGACATCCTT
12599828 TCATGCCTTTCTATA
66 TCATGCCTTTCTATA
12599843 CAACGTTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
91 32 0.47
92 36 0.53
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (92 bp):
TTTCATATATGACATTCTTTCATGCCAATCAATACACCATTATACATTTCATTTATGACATCCTT
TCATGCCTTTCTATAAGCTATTATACA
Found at i:12599852 original size:46 final size:47
Alignment explanation
Indices: 12599711--12599856 Score: 192
Period size: 46 Copynumber: 3.2 Consensus size: 47
12599701 AATGCACCCA
* *
12599711 TATACATTTTATTTATGACATCCTTTCATGCCCTTT-TATA-AGCTAT
1 TATACATTTCATTTATGACATCCTTTCATG-CCTTTCTATACAACTAT
* * *
12599757 TATACATTTCATTTATGGCATTCTTTCATGCCCTTCTATAC-ACTAT
1 TATACATTTCATTTATGACATCCTTTCATGCCTTTCTATACAACTAT
* *
12599803 TATACCTTTCATTTATGACATCCTTTCATGCCTTTCTATACAAC-GT
1 TATACATTTCATTTATGACATCCTTTCATGCCTTTCTATACAACTAT
12599849 TATACATT
1 TATACATT
12599857 GTCACACATC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
45 4 0.05
46 80 0.93
47 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (47 bp):
TATACATTTCATTTATGACATCCTTTCATGCCTTTCTATACAACTAT
Found at i:12600257 original size:56 final size:55
Alignment explanation
Indices: 12600095--12600684 Score: 833
Period size: 55 Copynumber: 10.7 Consensus size: 55
12600085 TTTATTAAGA
* * * *
12600095 TGCACACGTAGTGCCTCTACGG-TAGTTCATCAACTCATGATGAATTCTGTGG-GT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* ** * *
12600149 TGCACACATCGTGTATGTACGGTTATTTATCAACTCATGATGAATTACGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
12600204 TCCACACATAGTGCTTGTACGGTTATTCAATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCGTGGATT
*
12600260 TGCACACATAGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCGTGGATT
* * *
12600316 TGCATACATAGTACCTGTACGATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
12600371 TGCACACATAGTGTCTGTACGGTTATTCCATAAACTCATGATGAATTCCGTGAATT
1 TGCACACATAGTGCCTGTACGGTTATT-CATCAACTCATGATGAATTCCGTGGATT
* * *
12600427 TTCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
12600482 TGTACACATAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
12600537 TGTACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
12600592 TGCACACATAGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCGTGGATT
* * *
12600648 TGCACACATAGTGTCTATACGGTTATTCTTCAACTCA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCA
12600685 AGAATCATAC
Statistics
Matches: 486, Mismatches: 45, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
54 41 0.08
55 238 0.49
56 207 0.43
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:12600368 original size:111 final size:111
Alignment explanation
Indices: 12600095--12600684 Score: 839
Period size: 111 Copynumber: 5.3 Consensus size: 111
12600085 TTTATTAAGA
* * * *
12600095 TGCACACGTAGTGCCTCTACGG-TAGTTCATCAACTCATGATGAATTCTGTGG-GTTGCACACAT
1 TGCACACATAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGGATTTGCACACAT
* ** * *
12600158 CGTGTATGTACGGTTATT-TATCAACTCATGATGAATTACGTGGATT
65 AGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
* *
12600204 TCCACACATAGTGCTTGTACGGTTATTCAATCAACTCATGATGAATTCTGTGGATTTGCACACAT
1 TGCACACATAGTGCATGTACGGTTATTC-ATCAACTCATGATGAATTCTGTGGATTTGCACACAT
*
12600269 AGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCTGTGGATT
65 AGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
* * * * *
12600316 TGCATACATAGTACCTGTACGATTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATA
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACATA
* * * *
12600381 GTGTCTGTACGGTTATTCCATAAACTCATGATGAATTCCGTGAATT
66 GTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
* *
12600427 TTCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGTACACATA
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACATA
* *
12600492 GTGCATGTACGATTATTC-ATCAACTCATGATGAATTCCGTGGATT
66 GTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
* **
12600537 TGTACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATA
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACATA
*
12600602 GTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATT
66 GTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
* *
12600648 TGCACACATAGTGTC-TATACGGTTATTCTTCAACTCA
1 TGCACACATAGTG-CATGTACGGTTATTCATCAACTCA
12600685 AGAATCATAC
Statistics
Matches: 430, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
109 21 0.05
110 127 0.30
111 233 0.54
112 49 0.11
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (111 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACATA
GTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
Found at i:12604822 original size:46 final size:45
Alignment explanation
Indices: 12604772--12604913 Score: 178
Period size: 46 Copynumber: 3.1 Consensus size: 45
12604762 CACCCATATG
* * *
12604772 CATTTTATTTATGACATCATTTCATGCCCTTTTATAAGTTATTATA
1 CATTTCATTTATGGCATC-TTTCATGCCCTTTTATAAGCTATTATA
* *
12604818 CATTTCATTTATGGCATTCTTTCATGCCCTTCTATACGCTATTATA
1 CATTTCATTTATGGCA-TCTTTCATGCCCTTTTATAAGCTATTATA
* *
12604864 CCTTTCATTTATGGCATCCTTTCATGCCCTTTTATACAAC-ATTATA
1 CATTTCATTTATGGCAT-CTTTCATGCCCTTTTATA-AGCTATTATA
12604910 CATT
1 CATT
12604914 GTCACACATC
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 1 0.01
46 79 0.95
47 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (45 bp):
CATTTCATTTATGGCATCTTTCATGCCCTTTTATAAGCTATTATA
Found at i:12605323 original size:56 final size:55
Alignment explanation
Indices: 12605152--12605686 Score: 646
Period size: 56 Copynumber: 9.7 Consensus size: 55
12605142 TTTATTAAGA
* * * **
12605152 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATT--ATGTGGGT
1 TGCACACATAGTGCTTGTACGGTTA-TTCATCAACTCATGATGAATTCCATG-GATT
** * * *
12605206 TGCACACATCTTGTTTGTACGGTTATTCATCAACTCATGATGAATTACGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
12605261 TTCACACATAGTGCTTGTACGGTTATTCAATCAACTTATGATGAATTCCATGTATT
1 TGCACACATAGTGCTTGTACGGTTATTC-ATCAACTCATGATGAATTCCATGGATT
* * *
12605317 TACACACATAGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCTTGTACGGTTATTC-ATCAACTCATGATGAATTCCATGGATT
* *
12605373 TGCACACATAGTGCATGTATGGTTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * * * * *
12605428 TGTACATATAGTGCCTGTACGGTTATTCAATGAACTCATGATGAATTCCGTGTATT
1 TGCACACATAGTGCTTGTACGGTTATTC-ATCAACTCATGATGAATTCCATGGATT
* *
12605484 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATAATGAATTCCATGGATT
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
12605539 TGCACACATAGTG-TCTATAGGGTTATTCATCAACTCAAGATGAATTCCATGGATT
1 TGCACACATAGTGCT-TGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * * * * **
12605594 TGCACACATAGTGCCTCTACGATTATTCAATCAACTCATTATGAATTCCGTAAATT
1 TGCACACATAGTGCTTGTACGGTTATTC-ATCAACTCATGATGAATTCCATGGATT
*
12605650 TGCACACATAATGCTTGTACGGTTATTCATCAACTCA
1 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCA
12605687 AGAATCATAC
Statistics
Matches: 415, Mismatches: 58, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
54 37 0.09
55 182 0.44
56 196 0.47
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
Found at i:12605442 original size:111 final size:111
Alignment explanation
Indices: 12605152--12605686 Score: 677
Period size: 111 Copynumber: 4.8 Consensus size: 111
12605142 TTTATTAAGA
* * * **
12605152 TGCACACGTAGTGCCTATACGG-TAGTTC-ATCAACTCATGATGAATT--ATGTGGGTTGCACAC
1 TGCACACATAGTGCATGTACGGTTA-TTCAATCAACTCATGATGAATTCCATG-GATTTGCACAC
** ** *
12605213 ATCTTGTTTGTACGGTTATTCATCAACTCATGATGAATTACGTGGATT
64 ATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
12605261 TTCACACATAGTGCTTGTACGGTTATTCAATCAACTTATGATGAATTCCATGTATTTACACACAT
1 TGCACACATAGTGCATGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATTTGCACACAT
12605326 AGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATT
66 AGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCGTGGATT
* * *
12605373 TGCACACATAGTGCATGTATGGTTATTC-ATCAACTCATGATGAATTCCATGGATTTGTACATAT
1 TGCACACATAGTGCATGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATTTGCACACAT
* *
12605437 AGTGCCTGTACGGTTATTCAATGAACTCATGATGAATTCCGTGTATT
66 AGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCGTGGATT
*
12605484 TGCACACATAGTGCATGTACGGTTATTC-ATCAACTCATAATGAATTCCATGGATTTGCACACAT
1 TGCACACATAGTGCATGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATTTGCACACAT
* * * * *
12605548 AGTGTCTATAGGGTTATTCATCAACTCAAGATGAATTCCATGGATT
66 AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * * **
12605594 TGCACACATAGTGCCTCTACGATTATTCAATCAACTCATTATGAATTCCGTAAATTTGCACACAT
1 TGCACACATAGTGCATGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATTTGCACACAT
* *
12605659 AATGCTTGTACGGTTATTCATCAACTCA
66 AGTGCCTGTACGGTTATTCATCAACTCA
12605687 AGAATCATAC
Statistics
Matches: 373, Mismatches: 47, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
109 21 0.06
110 67 0.18
111 231 0.62
112 54 0.14
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (111 bp):
TGCACACATAGTGCATGTACGGTTATTCAATCAACTCATGATGAATTCCATGGATTTGCACACAT
AGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:12605595 original size:166 final size:166
Alignment explanation
Indices: 12605152--12605686 Score: 720
Period size: 166 Copynumber: 3.2 Consensus size: 166
12605142 TTTATTAAGA
* * **
12605152 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATT--ATGTGGGTTGCACACA
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCATG-GATTTGCACACA
** * * * *
12605214 TCTTGTTTGTACGGTTATTCATCAACTCATGATGAATTACGTGGATTT-TCACACATAGTGCTTG
64 TAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGT-ACACATAGTGCCTG
* *
12605278 TACGGTTATTCAATCAACTTATGATGAATTCCATGTATT
128 TACGGTTATTCAATCAACTCATGATGAATTCCGTGTATT
* *
12605317 TACACACATAGTGCCTGTACGGTTATTCAATCAACTCATGATGAATTCCGTGGATTTGCACACAT
1 TGCACACATAGTGCCTGTACGGTTATTC-ATCAACTCATGATGAATTCCATGGATTTGCACACAT
* *
12605382 AGTG-CATGTATGGTTATTCATCAACTCATGATGAATTCCATGGATTTGTACATATAGTGCCTGT
65 AGTGTC-TGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGTACACATAGTGCCTGT
*
12605446 ACGGTTATTCAATGAACTCATGATGAATTCCGTGTATT
129 ACGGTTATTCAATCAACTCATGATGAATTCCGTGTATT
* *
12605484 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATAATGAATTCCATGGATTTGCACACATA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATA
* * * * *
12605549 GTGTCTATAGGGTTATTCATCAACTCAAGATGAATTCCATGGATTTGCACACATAGTGCCTCTAC
66 GTGTCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGTACACATAGTGCCTGTAC
* * **
12605614 GATTATTCAATCAACTCATTATGAATTCCGTAAATT
131 GGTTATTCAATCAACTCATGATGAATTCCGTGTATT
* *
12605650 TGCACACATAATGCTTGTACGGTTATTCATCAACTCA
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCA
12605687 AGAATCATAC
Statistics
Matches: 329, Mismatches: 34, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
165 22 0.07
166 178 0.54
167 126 0.38
168 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (166 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATA
GTGTCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTGTACACATAGTGCCTGTAC
GGTTATTCAATCAACTCATGATGAATTCCGTGTATT
Found at i:12607049 original size:2 final size:2
Alignment explanation
Indices: 12607023--12607187 Score: 71
Period size: 2 Copynumber: 84.0 Consensus size: 2
12607013 CTATATAGTT
* *
12607023 TA TA TT TA TA T- TA T- TA TA TA T- TA TA TA TA AA CTA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
12607062 TA TG TA TA AA CTA TA TA GTG TA TA TA TA TA GTA TA TA TA T- TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
12607104 TA CA TA TA -A AA TA TA TA -A TT TA TA TT TA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
12607142 TA CTA CA TA TA AA CTA TA TA TA TT TA T- TA TG TA TA AA CTA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12607184 TA TA
1 TA TA
12607188 CCATGTATAA
Statistics
Matches: 119, Mismatches: 27, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
1 10 0.08
2 100 0.84
3 9 0.08
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12607051 original size:11 final size:11
Alignment explanation
Indices: 12607022--12607168 Score: 81
Period size: 11 Copynumber: 13.4 Consensus size: 11
12607012 ACTATATAGT
*
12607022 TTATATTTATA
1 TTATATATATA
12607033 TTAT-TATATA
1 TTATATATATA
*
12607043 TTATATATAAA
1 TTATATATATA
*
12607054 CTATATAT-TA
1 TTATATATATA
*
12607064 TGTATAAACTATA
1 T-TATATA-TATA
*
12607077 -TAGTGTATATA
1 TTA-TATATATA
12607088 TATAGTATATATA
1 T-TA-TATATATA
*
12607101 TTATACATATA
1 TTATATATATA
**
12607112 AAATATATA-A
1 TTATATATATA
*
12607122 TTTATATTTATA
1 -TTATATATATA
12607134 TTAT-TATATA
1 TTATATATATA
* * *
12607144 CTACATATAAA
1 TTATATATATA
*
12607155 CTATATATAT-
1 TTATATATATA
12607165 TTAT
1 TTAT
12607169 TATGTATAAA
Statistics
Matches: 103, Mismatches: 23, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
10 21 0.20
11 63 0.61
12 6 0.06
13 13 0.13
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (11 bp):
TTATATATATA
Found at i:12607060 original size:18 final size:18
Alignment explanation
Indices: 12607037--12607162 Score: 83
Period size: 18 Copynumber: 6.4 Consensus size: 18
12607027 TTTATATTAT
12607037 TATATATTATATATAAAC
1 TATATATTATATATAAAC
*
12607055 TATATATTATGTATAAAC
1 TATATATTATATATAAAC
12607073 TATATAGTGTATATATATAGTA-
1 TATATA-T-TATATATA-A--AC
*
12607095 TATATATTATACATATAAAA
1 TATATATTAT--ATATAAAC
* *
12607115 TATATAATTTATATTTATATTAT
1 TATAT-A-TTATA--TATA-AAC
* *
12607138 TATATACTACATATAAAC
1 TATATATTATATATAAAC
12607156 TATATAT
1 TATATAT
12607163 ATTTATTATG
Statistics
Matches: 86, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
18 30 0.35
19 6 0.07
20 16 0.19
21 7 0.08
22 20 0.23
23 7 0.08
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATATTATATATAAAC
Found at i:12607091 original size:13 final size:13
Alignment explanation
Indices: 12607014--12607101 Score: 64
Period size: 13 Copynumber: 7.2 Consensus size: 13
12607004 TCTAATAAAC
*
12607014 TATATAGTTTATA
1 TATATAGTATATA
*
12607027 TTTATA-T-TAT-
1 TATATAGTATATA
12607037 TATATA-T-TATA
1 TATATAGTATATA
* *
12607048 TATAAACTATATA
1 TATATAGTATATA
*
12607061 T-TAT-GTATAAA
1 TATATAGTATATA
*
12607072 CTATATAGTGTATA
1 -TATATAGTATATA
12607086 TATATAGTATATA
1 TATATAGTATATA
12607099 TAT
1 TAT
12607102 TATACATATA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
10 9 0.15
11 13 0.22
12 5 0.08
13 28 0.47
14 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATAGTATATA
Found at i:12607558 original size:24 final size:24
Alignment explanation
Indices: 12607526--12607572 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12607516 TTGTGTTACA
12607526 AAACTAAAAGTAGTCGATCTCCCT
1 AAACTAAAAGTAGTCGATCTCCCT
12607550 AAACTAAAAGTAGTCGATCTCCC
1 AAACTAAAAGTAGTCGATCTCCC
12607573 CTGATGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (24 bp):
AAACTAAAAGTAGTCGATCTCCCT
Found at i:12607911 original size:44 final size:44
Alignment explanation
Indices: 12607836--12607979 Score: 198
Period size: 44 Copynumber: 3.2 Consensus size: 44
12607826 GAGCCTGCGA
* * * * * *
12607836 TAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCCTACAGTAACAG
1 TAAGGTCTTACCCT-TGCACATAGCAAAGGAGCCTGCGGTAACGG
*
12607881 TAAGGTCTTACCCTTGCACATAGCAAAGGAGTCTGCGGTAACGG
1 TAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTGCGGTAACGG
*
12607925 TAAGGTCTTACCCTTGCATATAGCAAAGGAGCCTGCGGTAACGG
1 TAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTGCGGTAACGG
*
12607969 TTAGGTCTTAC
1 TAAGGTCTTAC
12607980 TAGTCATAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 76 0.85
45 13 0.15
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (44 bp):
TAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTGCGGTAACGG
Found at i:12614714 original size:39 final size:39
Alignment explanation
Indices: 12614671--12614751 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
12614661 GTACACCTGC
* * *
12614671 TAAGGGCTTAACCTATGCACAAAGTAGAGGAGCCTGCGG
1 TAAGGGCTTAACATATGCACAAAGCAGAGGAGCATGCGG
* *
12614710 TAAGGTCTTATCATATGCACAAAGCAGAGGAGCATGCGG
1 TAAGGGCTTAACATATGCACAAAGCAGAGGAGCATGCGG
12614749 TAA
1 TAA
12614752 CGGTAAGGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (39 bp):
TAAGGGCTTAACATATGCACAAAGCAGAGGAGCATGCGG
Found at i:12614804 original size:44 final size:44
Alignment explanation
Indices: 12614707--12614853 Score: 161
Period size: 44 Copynumber: 3.3 Consensus size: 44
12614697 GAGGAGCCTG
* * * * * * **
12614707 CGGTAAGGTCTTATCATATGCACAAAGCAGAGGAGCATGCGGTAA
1 CGGTAAGGTCTTACCCT-TGAACATAGCAAATGAGCATGTAGTAA
* *
12614752 CGGTAAGGTCTTACCCTTGAACATAGTAAA-GTAGCCTGTAGTAA
1 CGGTAAGGTCTTACCCTTGAACATAGCAAATG-AGCATGTAGTAA
* *
12614796 CGGTAAGGTCTTACCCTTGCACATAGCAAATGAGCATGTGGTAA
1 CGGTAAGGTCTTACCCTTGAACATAGCAAATGAGCATGTAGTAA
12614840 CGGTAAGGTCTTAC
1 CGGTAAGGTCTTAC
12614854 AAGTCATATA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 70 0.80
45 16 0.18
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (44 bp):
CGGTAAGGTCTTACCCTTGAACATAGCAAATGAGCATGTAGTAA
Found at i:12616352 original size:22 final size:22
Alignment explanation
Indices: 12616327--12616368 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12616317 AGGGTGTGAC
12616327 ATATAAACTATATAGTTTATTA
1 ATATAAACTATATAGTTTATTA
*
12616349 ATATAAAGTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
12616369 ACATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (22 bp):
ATATAAACTATATAGTTTATTA
Found at i:12616374 original size:20 final size:22
Alignment explanation
Indices: 12616329--12616382 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
12616319 GGTGTGACAT
*
12616329 ATAAACTATATAGTTTATTAAT
1 ATAAACTATATAGTTTATTAAC
*
12616351 ATAAAGTATATAGTTTA-T-AC
1 ATAAACTATATAGTTTATTAAC
*
12616371 ATAAATTATATA
1 ATAAACTATATA
12616383 TGAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 12 0.41
21 1 0.03
22 16 0.55
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
ATAAACTATATAGTTTATTAAC
Found at i:12616573 original size:3 final size:3
Alignment explanation
Indices: 12616525--12616554 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12616515 ATAATAATAA
12616525 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12616555 AAAGTATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12616705 original size:15 final size:14
Alignment explanation
Indices: 12616661--12616712 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
12616651 ATATATAAAC
12616661 TATAAAGTATAT-A
1 TATAAAGTATATAA
* *
12616674 TATAAAGT-TTTAG
1 TATAAAGTATATAA
12616687 TATAAAGTATAATAA
1 TATAAAGTAT-ATAA
*
12616702 TATAAAATATA
1 TATAAAGTATA
12616713 AGTTTTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 2 0.06
13 16 0.52
14 2 0.06
15 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (14 bp):
TATAAAGTATATAA
Found at i:12616753 original size:27 final size:22
Alignment explanation
Indices: 12616723--12616840 Score: 74
Period size: 17 Copynumber: 5.5 Consensus size: 22
12616713 AGTTTTAAAC
12616723 ATAAAGTATATATACATGTATAATAAT
1 ATAAAGTATATA-A-ATGTAT--T-AT
*
12616750 ATAAAGTATATAAGTGTATTAT
1 ATAAAGTATATAAATGTATTAT
12616772 ATAAAGTATAT-AA-G---TAT
1 ATAAAGTATATAAATGTATTAT
*
12616789 ATAAAGTATAT--ATATA-TAT
1 ATAAAGTATATAAATGTATTAT
*
12616808 ATAAAGTATA-AGTATGTATATAT
1 ATAAAGTATATA-AATGTAT-TAT
*
12616831 ATAAACTATA
1 ATAAAGTATA
12616841 AAGTAAAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.01
17 14 0.18
19 13 0.17
20 1 0.01
21 5 0.06
22 13 0.17
23 13 0.17
25 5 0.06
26 1 0.01
27 12 0.15
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
ATAAAGTATATAAATGTATTAT
Found at i:12616782 original size:47 final size:45
Alignment explanation
Indices: 12616644--12617441 Score: 196
Period size: 47 Copynumber: 17.6 Consensus size: 45
12616634 CATACATACA
*
12616644 TATATATATATATAAACTATA-AAGTATA-TATATAAAGTTTTAGTATAAAG
1 TATA-ATA-ATATAAA-TATATAAGTATATTATATAAAG---TA-TATAATG
*
12616694 TATAATAATATAAA-ATATAAGT-T-TTAAACATAAAGTATATATACATG
1 TATAATAATATAAATATATAAGTATATT--ATATAAAG--TATATA-ATG
*
12616741 TATAATAATATAAAGTATATAAGTGTATTATATAAAGTATATAA-G
1 TATAATAATATAAA-TATATAAGTATATTATATAAAGTATATAATG
* * * *
12616786 TAT-ATAA-AGTATATATAT-A-TATA-TAAAGTATAAGTATGTATATA
1 TATAATAATA-TAAATATATAAGTATATTATA-TA-AAGTATATA-ATG
* * *
12616830 TATAA-ACTATAAAGTA-A-AAGTATATCTATAAAAACTATA-AAT-
1 TATAATAATATAAA-TATATAAGTATAT-TATATAAAGTATATAATG
* * * * *
12616872 TA-AGT-GTGTATATATAT-AGT-T-TTAGTATAAAGTATATATACATA
1 TATAATAATATAAATATATAAGTATATTA-TATAAAG--TATATA-ATG
* * *
12616916 TATAATAATATAAA-CTATAAGTATATTATATATA-TAATCTAAT-
1 TATAATAATATAAATATATAAGTATATTATATAAAGT-ATATAATG
*
12616959 TATAA-AGACTA-AAGTATATATACA-TATA-CATATAAAGTATA-AGTATG
1 TATAATA-A-TATAA--ATATATA-AGTATATTATATAAAGTATATA--ATG
* *
12617006 TATATATATATATATATAAACTATAAAGTATA-TATATAAAGTTTTAGTATAAAG
1 TATA-ATA-ATATA-A-ATA-TAT-AAGTATATTATATAAAG---TA-TATAATG
* *
12617060 TATAATAATATAAA-ATATAAGTAT-TAAACATAAAGTATATATACATG
1 TATAATAATATAAATATATAAGTATAT-TATATAAAG--TATATA-ATG
* *
12617107 TATAATAATATAAAGTATATAAGTGTATTATATAAAGTATATAAGTA
1 TATAATAATATAAA-TATATAAGTATATTATATAAAGTATATAA-TG
** * * * **
12617154 TATAAAGTATATATATGTATATAAAGTATAAGTATGTATA-TATATAAAC
1 TAT-AA-TA-ATATAAATATAT-AAGTAT-ATTATATAAAGTATATAATG
* * ** *
12617203 TATAA-AGTGTGTATATATATAGT-T-TTAGTATAAAGTATATATACATA
1 TATAATAATATAAATATATA-AGTATATTA-TATAAAG--TATATA-ATG
* * *
12617250 TATAATAATATAAA-GTATAAGTATATTATATATA-TAATCTAAT-
1 TATAATAATATAAATATATAAGTATATTATATAAAGT-ATATAATG
* * *
12617293 TATAA-AGA-ATAAATTATATAAGCATATAATATAAAGTATATATACG
1 TATAATA-ATATAAA-TATATAAGTATATTATATAAAGTATATA-ATG
*
12617339 TAT-ATAATAT--ATATATATGTATA-TA-AT-AA-TATA-AA-G
1 TATAATAATATAAATATATAAGTATATTATATAAAGTATATAATG
* * *
12617375 TAT-ATAAGTGTTAAATGTATAAGTATA-TATATAAACTATA-AA-G
1 TATAATAA-T-ATAAATATATAAGTATATTATATAAAGTATATAATG
*
12617418 TAT-ATATATATAAA-GTATAAGTAT
1 TATAATA-ATATAAATATATAAGTAT
12617442 TTGTATATGT
Statistics
Matches: 571, Mismatches: 81, Indels: 201
0.67 0.09 0.24
Matches are distributed among these distances:
36 8 0.01
37 2 0.00
38 4 0.01
39 10 0.02
40 21 0.04
41 32 0.06
42 28 0.05
43 53 0.09
44 52 0.09
45 54 0.09
46 50 0.09
47 94 0.16
48 41 0.07
49 51 0.09
50 29 0.05
51 23 0.04
52 5 0.01
53 3 0.01
54 8 0.01
55 2 0.00
56 1 0.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (45 bp):
TATAATAATATAAATATATAAGTATATTATATAAAGTATATAATG
Found at i:12616800 original size:19 final size:19
Alignment explanation
Indices: 12616748--12617469 Score: 117
Period size: 19 Copynumber: 38.2 Consensus size: 19
12616738 ATGTATAATA
*
12616748 ATATAAAGTATATAAGTGTATT
1 ATATAAAGTATAT-A-TATA-T
*
12616770 ATATAAAGTATATA-A-GT
1 ATATAAAGTATATATATAT
12616787 ATATAAAGTATATATATAT
1 ATATAAAGTATATATATAT
12616806 ATATAAAGTATAAGTATGTATAT
1 ATATAAAGTAT-A-TA--TATAT
* * *
12616829 ATATAAACTATAAAGTA-AA
1 ATATAAAGTATATA-TATAT
** * *
12616848 AGTAT-ATCTATAAAAACTAT
1 A-TATAAAGTATATATA-TAT
* * * *
12616868 AAATTAAGTGTGTATATAT
1 ATATAAAGTATATATATAT
**
12616887 ATAGTTTTAGTATA-A-AGTAT
1 ATA--TAAAGTATATATA-TAT
*
12616907 ATATACA-TATATAATAATAT
1 ATATAAAGTATAT-AT-ATAT
*
12616927 AAACTATAAGTATAT-TATAT
1 ATA-TA-AAGTATATATATAT
** *
12616947 ATATAATCTA-AT-TATAA
1 ATATAAAGTATATATATAT
*
12616964 AGACTAAAGTATATATACATAT
1 ATA-TAAAGTATATAT--ATAT
*
12616986 ACATATAAAGTATA-AGTATGT
1 --ATATAAAGTATATA-TATAT
* *
12617007 ATATATA-TATATATATAA
1 ATATAAAGTATATATATAT
*
12617025 ACTATAAAGTATATATATAA
1 A-TATAAAGTATATATATAT
** *
12617045 AGT-TTTAGTATAAAGTATAAT
1 A-TATAAAGTATATA-TAT-AT
*
12617066 AATATAAA--ATATA-A-GT
1 -ATATAAAGTATATATATAT
*
12617082 AT-TAAA-CATA-A-AGTAT
1 ATATAAAGTATATATA-TAT
* *
12617098 ATATACA-TGTATA-ATA-
1 ATATAAAGTATATATATAT
*
12617114 ATATAAAGTATATAAGTGTATT
1 ATATAAAGTATAT-A-TATA-T
*
12617136 ATATAAAGTATATA-A-GT
1 ATATAAAGTATATATATAT
*
12617153 ATATAAAGTATATATATGT
1 ATATAAAGTATATATATAT
12617172 ATATAAAGTATAAGTATGTATAT
1 ATATAAAGTAT-A-TA--TATAT
* *
12617195 ATATAAACTATA-A-AGTGT
1 ATATAAAGTATATATA-TAT
* *
12617213 GTAT--A-TATATAGT-TTT
1 ATATAAAGTATATA-TATAT
*
12617229 AGTATAAAGTATATATACAT
1 A-TATAAAGTATATATATAT
12617249 ATAT-AA-TA-ATATA-A-
1 ATATAAAGTATATATATAT
12617263 AGTAT-AAGTATAT-TATAT
1 A-TATAAAGTATATATATAT
** *
12617281 ATATAATCTA-AT-TATAA
1 ATATAAAGTATATATATAT
* * *
12617298 AGAATAAATTATATAAGCATAT
1 A-TATAAAGTATAT-A-TATAT
**
12617320 AATATAAAGTATATATACGT
1 -ATATAAAGTATATATATAT
12617340 ATAT-AA-TATATATATAT
1 ATATAAAGTATATATATAT
* *
12617357 GTATATAA-TA-ATATAAAGT
1 ATATA-AAGTATATATATA-T
*
12617376 ATAT-AAGTGT-TA-A-AT
1 ATATAAAGTATATATATAT
* *
12617391 GTAT-AAGTATATATATAA
1 ATATAAAGTATATATATAT
12617409 ACTATAAAGTATATATATAT
1 A-TATAAAGTATATATATAT
* *
12617429 AAAGTATAAGTAT-T-TGTAT
1 ATA-TA-AAGTATATATATAT
* * *
12617448 ATGTATAGTTTATATATAT
1 ATATAAAGTATATATATAT
12617467 ATA
1 ATA
12617470 CTTTATATTT
Statistics
Matches: 517, Mismatches: 96, Indels: 177
0.65 0.12 0.22
Matches are distributed among these distances:
14 7 0.01
15 24 0.05
16 26 0.05
17 92 0.18
18 57 0.11
19 102 0.20
20 84 0.16
21 29 0.06
22 49 0.09
23 45 0.09
24 2 0.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATAAAGTATATATATAT
Found at i:12617037 original size:22 final size:22
Alignment explanation
Indices: 12617012--12617383 Score: 103
Period size: 22 Copynumber: 17.0 Consensus size: 22
12617002 TATGTATATA
*
12617012 TATATATATATAAACTATAAAG
1 TATATATATATAAAGTATAAAG
12617034 TATATATATA-AAGTTTTAGTATAAAG
1 TATATATATATAA-----AGTATAAAG
*
12617060 TATA-ATAATATAAAATAT-AAG
1 TATATAT-ATATAAAGTATAAAG
* *
12617081 TAT-TAAACATAAAGTAT--A-
1 TATATATATATAAAGTATAAAG
* * *
12617099 TATACATGTATAATAATATAAAG
1 TATATATATATAA-AGTATAAAG
* *
12617122 TATATA-AGTGTATTA-TATAAAG
1 TATATATA-TATA-AAGTATAAAG
12617144 TATATAAGTATATAAAGTAT--A-
1 TATAT-A-TATATAAAGTATAAAG
*
12617165 TATATGTATATAAAGTAT-AAG
1 TATATATATATAAAGTATAAAG
*
12617186 TATGTATATATATAAACTATAAAG
1 TA--TATATATATAAAGTATAAAG
* * * **
12617210 TGTGTATATATATAGT-TTTAG
1 TATATATATATAAAGTATAAAG
* * * *
12617231 TATAAAGTATATATA-CATATA-
1 TATATA-TATATAAAGTATAAAG
12617252 TA-ATA-ATATAAAGTAT-AAG
1 TATATATATATAAAGTATAAAG
* *
12617271 TATATTATATATATAA-TCT-AAT
1 TATA-TATATATA-AAGTATAAAG
* * *
12617293 TATAAAGA-ATAAATTATATAAG
1 TATATATATATAAAGTATA-AAG
*
12617315 CATATA-ATATAAAGTATATATACG
1 TATATATATATAAAGTATA-A-A-G
* *
12617339 TATATA-ATATATA-TAT-ATG
1 TATATATATATAAAGTATAAAG
12617358 TATATAATAATATAAAGTATATAAG
1 TATAT-AT-ATATAAAGTATA-AAG
12617383 T
1 T
12617384 GTTAAATGTA
Statistics
Matches: 258, Mismatches: 48, Indels: 85
0.66 0.12 0.22
Matches are distributed among these distances:
18 10 0.04
19 30 0.12
20 23 0.09
21 30 0.12
22 86 0.33
23 34 0.13
24 22 0.09
25 6 0.02
26 15 0.06
27 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.39
Consensus pattern (22 bp):
TATATATATATAAAGTATAAAG
Found at i:12617099 original size:79 final size:82
Alignment explanation
Indices: 12616880--12617256 Score: 228
Period size: 79 Copynumber: 4.5 Consensus size: 82
12616870 ATTAAGTGTG
* *
12616880 TATATATATAGTTTTAGTATAAAGTATATATACATAT-ATA-AT-A--ATATAAAC-TATAAGTA
1 TATATATAAAGTTTTAGTATAAAGTATATATACATATAAAATATAAGTATATAAACATA-AAGTA
* **
12616939 TATTATATA-TATAATCTA
65 TA-TATAAACTATAAAGTA
* ** * * * * * * *
12616957 -AT-TATAAAGACTAAAGTATATA-TACATATACATATAAAGTATAAGTATGTATATATATA-TA
1 TATATATAAAG-TTTTAGTATAAAGTATATATACATATAAAATATAAGTATATAAACATAAAGTA
12617018 TATATAAACTATAAAGTA
65 TATATAAACTATAAAGTA
12617036 TATATATAAAGTTTTAGTATAAAGTATA-ATA-ATATAAAATATAAGTAT-TAAACATAAAGTAT
1 TATATATAAAGTTTTAGTATAAAGTATATATACATATAAAATATAAGTATATAAACATAAAGTAT
** *
12617098 ATATACATGTATAATAATA
66 ATATA-AACTATAA-AGTA
* *
12617117 TAAAGTATATAAGTGTATTA-TATAAAGTATATA-AGTATATAAAGTATATATATGTATATAAAG
1 TATA-TATA-AAGT-T-TTAGTATAAAGTATATATA-CATATAAA--ATATA-A-GTATATAAA-
* *
12617180 TATAAGTATGTATATATATAAACTATAAAGTGTG
56 CATAA--A-G--TATATATAAACTATAAA--GTA
* *
12617214 TATATATATAGTTTTAGTATAAAGTATATATACATATATAATA
1 TATATATAAAGTTTTAGTATAAAGTATATATACATATAAAATA
12617257 ATATAAAGTA
Statistics
Matches: 227, Mismatches: 37, Indels: 57
0.71 0.12 0.18
Matches are distributed among these distances:
75 18 0.08
76 11 0.05
77 2 0.01
78 13 0.06
79 35 0.15
80 25 0.11
81 18 0.08
82 4 0.02
83 4 0.02
84 13 0.06
85 4 0.02
86 7 0.03
88 5 0.02
89 1 0.00
90 4 0.02
91 4 0.02
92 7 0.03
93 3 0.01
94 21 0.09
95 6 0.03
96 10 0.04
97 12 0.05
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (82 bp):
TATATATAAAGTTTTAGTATAAAGTATATATACATATAAAATATAAGTATATAAACATAAAGTAT
ATATAAACTATAAAGTA
Found at i:12617128 original size:9 final size:9
Alignment explanation
Indices: 12617114--12617183 Score: 70
Period size: 9 Copynumber: 7.3 Consensus size: 9
12617104 ATGTATAATA
12617114 ATATAAAGT
1 ATATAAAGT
*
12617123 ATATAAGTGT
1 ATATAA-AGT
12617133 ATTATATAAAGT
1 A---TATAAAGT
12617145 ATAT-AAGT
1 ATATAAAGT
12617153 ATATAAAGT
1 ATATAAAGT
*
12617162 ATATATATGT
1 ATATA-AAGT
12617172 ATATAAAGT
1 ATATAAAGT
12617181 ATA
1 ATA
12617184 AGTATGTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 8 0.16
9 24 0.47
10 11 0.22
12 3 0.06
13 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (9 bp):
ATATAAAGT
Found at i:12617253 original size:366 final size:369
Alignment explanation
Indices: 12616552--12617287 Score: 1096
Period size: 366 Copynumber: 2.0 Consensus size: 369
12616542 TTATTATTAT
* *
12616552 TATAAAGTATAAGTATATTATTTATATAAAAAGTTTAATTATAAAGACTAAAGTATATATACATA
1 TATAAACTATAAGTATATTA-TTATATAAAAAGTCTAATTATAAAGACTAAAGTATATATACATA
12616617 TAAAGTATAAGTATGTACATACATACATATATATATATATAAACTATAAAGTATATATATAAAGT
65 TAAAGTATAAGTA-GTACATACATACATATATATATATATAAACTATAAAGTATATATATAAAGT
*
12616682 TTTAGTATAAAGTATAATAATATAAAATATAAGTTTTAAACATAAAGTATATATACATGTATAAT
129 TTTAGTATAAAGTATAATAATATAAAATATAAGTATTAAACATAAAGTATATATACATGTATAAT
12616747 AATATAAAGTATATAAGTGTATTATATAAAGTATATAAGTATATAAAGTATATATATATATATAA
194 AATATAAAGTATATAAGTGTATTATATAAAGTATATAAGTATATAAAGTATATATATATATATAA
* *
12616812 AGTATAAGTATGTATATATATAAACTATAAAGTAAAAGTATATCTATAAAAACTATAAATTAAGT
259 AGTATAAGTATGTATATATATAAACTATAAAGT-AAAGTATATATATAAAAACTATAAAGTAAGT
* ** * **
12616877 GTGTATATAT-ATAGT-TTTAGTATAAAGTATATATACATATATAATAA
323 ATACATATATAATAATATAAAGTAT-AAGTATAT-TACATATATAATAA
*
12616924 TATAAACTATAAGTATATTA-TATAT-ATAA-TCTAATTATAAAGACTAAAGTATATATACATAT
1 TATAAACTATAAGTATATTATTATATAAAAAGTCTAATTATAAAGACTAAAGTATATATACATAT
* ** *
12616986 ACA-TATAAAGTA-TA-AGTATGTATATATATATATATATAAACTATAAAGTATATATATAAAGT
66 AAAGTAT-AAGTAGTACA-TACATACATATATATATATATAAACTATAAAGTATATATATAAAGT
12617048 TTTAGTATAAAGTATAATAATATAAAATATAAGTATTAAACATAAAGTATATATACATGTATAAT
129 TTTAGTATAAAGTATAATAATATAAAATATAAGTATTAAACATAAAGTATATATACATGTATAAT
*
12617113 AATATAAAGTATATAAGTGTATTATATAAAGTATATAAGTATATAAAGTATATATATGTATATAA
194 AATATAAAGTATATAAGTGTATTATATAAAGTATATAAGTATATAAAGTATATATATATATATAA
** *** *
12617178 AGTATAAGTATGTATATATATAAACTATAAAGT-GTGTATATATATAGTTTTAGTATAAAGTATA
259 AGTATAAGTATGTATATATATAAACTATAAAGTAAAGTATATATATA--AAAACTATAAAGTA-A
*
12617242 -TATACATATATAATAATATAAAGTATAAGTATATTATATATATAAT
321 GTATACATATATAATAATATAAAGTATAAGTATATTACATATATAAT
12617288 CTAATTATAA
Statistics
Matches: 333, Mismatches: 24, Indels: 20
0.88 0.06 0.05
Matches are distributed among these distances:
364 10 0.03
365 1 0.00
366 234 0.70
367 16 0.05
368 45 0.14
369 3 0.01
370 5 0.02
372 19 0.06
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (369 bp):
TATAAACTATAAGTATATTATTATATAAAAAGTCTAATTATAAAGACTAAAGTATATATACATAT
AAAGTATAAGTAGTACATACATACATATATATATATATAAACTATAAAGTATATATATAAAGTTT
TAGTATAAAGTATAATAATATAAAATATAAGTATTAAACATAAAGTATATATACATGTATAATAA
TATAAAGTATATAAGTGTATTATATAAAGTATATAAGTATATAAAGTATATATATATATATAAAG
TATAAGTATGTATATATATAAACTATAAAGTAAAGTATATATATAAAAACTATAAAGTAAGTATA
CATATATAATAATATAAAGTATAAGTATATTACATATATAATAA
Found at i:12617309 original size:14 final size:15
Alignment explanation
Indices: 12617289--12617334 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
12617279 ATATATAATC
12617289 TAATTATAAAGAATA
1 TAATTATAAAGAATA
*
12617304 -AATTATATAAGCATA
1 TAATTATA-AAGAATA
*
12617319 TAA-TATAAAGTATA
1 TAATTATAAAGAATA
12617333 TA
1 TA
12617335 TACGTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 15 0.56
15 10 0.37
16 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (15 bp):
TAATTATAAAGAATA
Found at i:12617373 original size:68 final size:64
Alignment explanation
Indices: 12617254--12617382 Score: 147
Period size: 68 Copynumber: 2.0 Consensus size: 64
12617244 TACATATATA
* *
12617254 ATAATATAAAGTATAAGTATATTATATATATAATCTAATTATAAAGAATAAATTATATAAGCAT
1 ATAATATAAAGTATAAGTATATAATATATATAATCTAATTATAAAGAATAAAGTATATAAGCAT
*
12617318 ATAATATAAAGTATATATACGTATATAATATATATATATGT-A-TATAATA-ATATAAAGTATAT
1 ATAATATAAAG--TATA-A-GTATATAATATATATA-ATCTAATTATAA-AGA-ATAAAGTATAT
12617380 AAG
59 AAG
12617383 TGTTAAATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
64 11 0.20
66 4 0.07
67 7 0.13
68 30 0.55
69 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (64 bp):
ATAATATAAAGTATAAGTATATAATATATATAATCTAATTATAAAGAATAAAGTATATAAGCAT
Found at i:12617469 original size:15 final size:15
Alignment explanation
Indices: 12617445--12617932 Score: 184
Period size: 14 Copynumber: 33.7 Consensus size: 15
12617435 TAAGTATTTG
* *
12617445 TATATGTATAGTTTA
1 TATATATATACTTTA
12617460 TATATATATACTTTA
1 TATATATATACTTTA
*
12617475 TATTTA-ATACTTATA
1 TATATATATACTT-TA
*
12617490 TACTTTATATTA-TTGTA
1 TA-TATATA-TACTT-TA
12617507 TACCTATATATACTTTA
1 TA--TATATATACTTTA
*
12617524 TATTTATATAC-TTA
1 TATATATATACTTTA
*
12617538 TATACTTTAGT-CTTTA
1 TATA-TATA-TACTTTA
12617554 TA-AT-TATACTTTA
1 TATATATATACTTTA
*
12617567 TATATATATA-TATA
1 TATATATATACTTTA
* * * ***
12617581 TATACACACACACAA
1 TATATATATACTTTA
12617596 TATACT-TATACTTTA
1 TATA-TATATACTTTA
*
12617611 TAT-TAT-TA-TATA
1 TATATATATACTTTA
* *
12617623 TGTATATATTCTTTA
1 TATATATATACTTTA
12617638 TACTA-A-A-AC-TT-
1 TA-TATATATACTTTA
12617649 TATATATATACTTTA
1 TATATATATACTTTA
12617664 TAGT-T-TATA---TA
1 TA-TATATATACTTTA
12617675 TATATATATACTTTA
1 TATATATATACTTTA
12617690 TAT-T-TCATAC-TTA
1 TATATAT-ATACTTTA
12617703 TATACT-TATA-TTTA
1 TATA-TATATACTTTA
12617717 -ATACTTATATACTTTA
1 TATA--TATATACTTTA
12617733 TAT-TATATACTTATA
1 TATATATATACTT-TA
*
12617748 TACTTTATATTA-TTATA
1 TA-TATATA-TACTT-TA
* *
12617765 TACAAATATACACTTTA
1 T--ATATATATACTTTA
12617782 TACTA-A-A-ACTTTA
1 TA-TATATATACTTTA
12617795 TATATATACTA-TTTA
1 TATATATA-TACTTTA
*
12617810 GT-T-TTTATA-TTTA
1 -TATATATATACTTTA
12617823 TATATATATA---TA
1 TATATATATACTTTA
12617835 TATATATATACTTTA
1 TATATATATACTTTA
*
12617850 TATGTCTATATACTTTA
1 TA--TATATATACTTTA
*
12617867 TA-ATA-AAACTTTA
1 TATATATATACTTTA
*
12617880 TATAT-TATTATTATTA
1 TATATATA-TACT-TTA
*
12617896 T-TATATATA-TATA
1 TATATATATACTTTA
*
12617909 TATATATATA-TATA
1 TATATATATACTTTA
12617923 TATATATATA
1 TATATATATA
12617933 TTATAACATC
Statistics
Matches: 369, Mismatches: 40, Indels: 129
0.69 0.07 0.24
Matches are distributed among these distances:
10 3 0.01
11 8 0.02
12 28 0.08
13 56 0.15
14 93 0.25
15 92 0.25
16 27 0.07
17 43 0.12
18 18 0.05
19 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATATATACTTTA
Found at i:12617494 original size:8 final size:8
Alignment explanation
Indices: 12617464--12617767 Score: 108
Period size: 8 Copynumber: 40.9 Consensus size: 8
12617454 AGTTTATATA
12617464 TATATACT
1 TATATACT
*
12617472 T-TATATT
1 TATATACT
12617479 TA-ATACT
1 TATATACT
12617486 TATATACTT
1 TATATAC-T
12617495 TATATTA-T
1 TATA-TACT
*
12617503 TGTATACCT
1 TATATA-CT
12617512 ATATATACT
1 -TATATACT
*
12617521 T-TATATT
1 TATATACT
12617528 TATATACT
1 TATATACT
12617536 TATATACT
1 TATATACT
12617544 T-TAGT-CT
1 TATA-TACT
*
12617551 T-TATA-A
1 TATATACT
12617557 T-TATACT
1 TATATACT
12617564 T-TATA-T
1 TATATACT
12617570 ATATATA-T
1 -TATATACT
*
12617578 ATATATACA
1 -TATATACT
* * *
12617587 CACACAC-
1 TATATACT
*
12617594 AATATAC-
1 TATATACT
12617601 T-TATACTT
1 TATATAC-T
12617609 TATATTA-T
1 TATA-TACT
12617617 TATATA-T
1 TATATACT
12617624 GTATATATTCT
1 -TATATA--CT
12617635 T-TATAC-
1 TATATACT
*
12617641 TA-AAACT
1 TATATACT
12617648 T-TATA--
1 TATATACT
12617653 TATATACT
1 TATATACT
*
12617661 T-TATAGT
1 TATATACT
12617668 T-TATA--
1 TATATACT
12617673 TATATA--
1 TATATACT
12617679 TATATACT
1 TATATACT
12617687 T-TATA-T
1 TATATACT
12617693 T-TCATACT
1 TAT-ATACT
12617701 TATATACT
1 TATATACT
12617709 TATAT--T
1 TATATACT
12617715 TA-ATACT
1 TATATACT
12617722 TATATACT
1 TATATACT
12617730 T-TATA-T
1 TATATACT
12617736 TATATACT
1 TATATACT
12617744 TATATACTT
1 TATATAC-T
12617753 TATATTA-T
1 TATA-TACT
12617761 TATATAC
1 TATATAC
12617768 AAATATACAC
Statistics
Matches: 235, Mismatches: 19, Indels: 84
0.70 0.06 0.25
Matches are distributed among these distances:
5 4 0.02
6 38 0.16
7 74 0.31
8 86 0.37
9 20 0.09
10 12 0.05
11 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (8 bp):
TATATACT
Done.