Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 22
Found at i:2373220 original size:14 final size:16
Alignment explanation
Indices: 2373191--2373222 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2373181 CGTTCGTGAA
2373191 CGTTCGATTATATGTT
1 CGTTCGATTATATGTT
2373207 CGTTC-ATT-TATGTT
1 CGTTCGATTATATGTT
2373221 CG
1 CG
2373223 AACATAGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
CGTTCGATTATATGTT
Found at i:2373506 original size:23 final size:23
Alignment explanation
Indices: 2373480--2373523 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2373470 GTGTTTGTGT
*
2373480 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTACGTTCATTTATTA
*
2373503 TGTTCGTTTACGTTCGTTTAT
1 TGTTCGTTTACGTTCATTTAT
2373524 CATTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTACGTTCATTTATTA
Found at i:2391057 original size:12 final size:12
Alignment explanation
Indices: 2391040--2391064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2391030 TATTAAAAAA
2391040 TAATAATATTTT
1 TAATAATATTTT
2391052 TAATAATATTTT
1 TAATAATATTTT
2391064 T
1 T
2391065 TTAATCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATAATATTTT
Found at i:2391067 original size:14 final size:14
Alignment explanation
Indices: 2391038--2391077 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2391028 AATATTAAAA
2391038 AATAATAATATTTTT
1 AATAAT-ATATTTTT
*
2391053 AATAATATTTTTTT
1 AATAATATATTTTT
*
2391067 AATCATATATT
1 AATAATATATT
2391078 ATATTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATAATATATTTTT
Found at i:2392257 original size:9 final size:9
Alignment explanation
Indices: 2392245--2392417 Score: 77
Period size: 9 Copynumber: 20.4 Consensus size: 9
2392235 ATATAATATG
2392245 TATAAACTA
1 TATAAACTA
***
2392254 TATAGTTTA
1 TATAAACTA
2392263 TATAAACTA
1 TATAAACTA
2392272 TAT-AA-TA
1 TATAAACTA
2392279 TATAAACTA
1 TATAAACTA
*
2392288 TAT--AGTA
1 TATAAACTA
2392295 TATAAACTA
1 TATAAACTA
2392304 TAT--A-T-
1 TATAAACTA
*
2392309 TATAAAATA
1 TATAAACTA
*
2392318 TATATAACAA
1 TATA-AACTA
*
2392328 CATAAACTCTA
1 TATAAA--CTA
*
2392339 TATAAACTC
1 TATAAACTA
*
2392348 TAT--AGTA
1 TATAAACTA
2392355 TATAAACTA
1 TATAAACTA
*
2392364 TAT--ATTA
1 TATAAACTA
* * *
2392371 AATATACAA
1 TATAAACTA
2392380 TAT-AA-TA
1 TATAAACTA
2392387 TATAAACTA
1 TATAAACTA
* *
2392396 TATATAGTA
1 TATAAACTA
*
2392405 TATAAAGTA
1 TATAAACTA
2392414 TATA
1 TATA
2392418 TGTAGTTTAT
Statistics
Matches: 120, Mismatches: 27, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 27 0.22
8 8 0.07
9 68 0.57
10 6 0.05
11 7 0.06
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (9 bp):
TATAAACTA
Found at i:2392264 original size:16 final size:16
Alignment explanation
Indices: 2392245--2392417 Score: 144
Period size: 16 Copynumber: 10.8 Consensus size: 16
2392235 ATATAATATG
2392245 TATAAACTATATAGTTTA
1 TATAAACTATATAG--TA
*
2392263 TATAAACTATATAATA
1 TATAAACTATATAGTA
2392279 TATAAACTATATAGTA
1 TATAAACTATATAGTA
2392295 TATAAACTATATA-T-
1 TATAAACTATATAGTA
2392309 TATAAA--ATATA-TA
1 TATAAACTATATAGTA
* *
2392322 TA-ACAAC-ATAAACTCTA
1 TATA-AACTATATA--GTA
*
2392339 TATAAACTCTATAGTA
1 TATAAACTATATAGTA
*
2392355 TATAAACTATATATTA
1 TATAAACTATATAGTA
* * * *
2392371 AATATACAATATAATA
1 TATAAACTATATAGTA
2392387 TATAAACTATATATAGTA
1 TATAAAC--TATATAGTA
*
2392405 TATAAAGTATATA
1 TATAAACTATATA
2392418 TGTAGTTTAT
Statistics
Matches: 128, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
12 7 0.05
13 4 0.03
14 10 0.08
15 1 0.01
16 69 0.54
17 7 0.05
18 30 0.23
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (16 bp):
TATAAACTATATAGTA
Found at i:2392383 original size:60 final size:59
Alignment explanation
Indices: 2392276--2392401 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 59
2392266 AAACTATATA
*
2392276 ATATATAAACTATATAGTATATAAACTATATATTATAAAATATATATAACAACATAAACT
1 ATATATAAACTATATAGTATATAAACTATATATTATAAAATAAATATAA-AACATAAACT
* * * * *
2392336 CTATATAAACTCTATAGTATATAAACTATATATTA-AATATACAATATAATATATAAACT
1 ATATATAAACTATATAGTATATAAACTATATATTATAAAATA-AATATAAAACATAAACT
2392395 ATATATA
1 ATATATA
2392402 GTATATAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
59 19 0.33
60 39 0.67
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (59 bp):
ATATATAAACTATATAGTATATAAACTATATATTATAAAATAAATATAAAACATAAACT
Found at i:2392418 original size:18 final size:18
Alignment explanation
Indices: 2392235--2392418 Score: 93
Period size: 18 Copynumber: 10.2 Consensus size: 18
2392225 TTATATAATA
2392235 ATATAATATGTATAAACTAT
1 ATATAATA--TATAAACTAT
*
2392255 ATAGT-TTATATAAAC--T
1 ATA-TAATATATAAACTAT
2392271 ATATAATATATAAAC--T
1 ATATAATATATAAACTAT
*
2392287 ATATAGTATATAAACTAT
1 ATATAATATATAAACTAT
2392305 ATAT--TATA-AAA-TAT
1 ATATAATATATAAACTAT
* * *
2392319 ATATAACAACATAAACTCT
1 ATATAA-TATATAAACTAT
* * *
2392338 ATATAA-ACTCTATAGTAT
1 ATATAATA-TATAAACTAT
*
2392356 ATA-AACTATATATTAAATAT
1 ATATAA-TATATA--AACTAT
2392376 ACAATATAATATATAAACTAT
1 ---ATATAATATATAAACTAT
* *
2392397 ATATAGTATATAAAGTAT
1 ATATAATATATAAACTAT
2392415 ATAT
1 ATAT
2392419 GTAGTTTATA
Statistics
Matches: 129, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
14 7 0.05
15 4 0.03
16 32 0.25
17 5 0.04
18 46 0.36
19 9 0.07
20 9 0.07
21 6 0.05
23 9 0.07
24 2 0.02
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATAATATATAAACTAT
Found at i:2403533 original size:32 final size:31
Alignment explanation
Indices: 2403492--2403723 Score: 261
Period size: 32 Copynumber: 7.3 Consensus size: 31
2403482 TGGACAGATT
2403492 TTACCTATGTCTTTCGGGACATATAGACAAAA
1 TTACCTATGTCTTTCGGGACATAT-GACAAAA
* **
2403524 TTACCTATGTCTTTTGGGACATATGTACAGTA
1 TTACCTATGTCTTTCGGGACATATG-ACAAAA
* *
2403556 TTACCTATGTCTTTTGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATAT-GACAAAA
**
2403588 TTACCTATGTCTTTCGGGACATATGTACAGTA
1 TTACCTATGTCTTTCGGGACATATG-ACAAAA
** * *
2403620 TTATATATGTCTTTCGGGATATATGGACAATA
1 TTACCTATGTCTTTCGGGACATAT-GACAAAA
*
2403652 TTACCTATATCTTTCGGGACATATGGA-AAGAA
1 TTACCTATGTCTTTCGGGACATAT-GACAA-AA
* *
2403684 TTACCTATGTCTTTCGGGACATATGA-ACAG
1 TTACCTATGTCTTTCGGGACATATGACAAAA
2403714 TTACCTATGT
1 TTACCTATGT
2403724 TCTTAGGAAC
Statistics
Matches: 177, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
30 11 0.06
31 7 0.04
32 157 0.89
33 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGACAAAA
Found at i:2403575 original size:64 final size:64
Alignment explanation
Indices: 2403459--2403708 Score: 331
Period size: 64 Copynumber: 3.9 Consensus size: 64
2403449 TAGTCGATGG
* * * *
2403459 TTACCGATGTCCTTT-GAGACATATGGACAGATTTTACCTATGTCTTTCGGGACATATAGACAAA
1 TTACCTATGT-CTTTCGGGACATATGGACAG-TATTACCTATGTCTTTCGGGACATATGGACAAA
2403523 A
64 A
* * * *
2403524 TTACCTATGTCTTTTGGGACATATGTACAGTATTACCTATGTCTTTTGGGACATATGGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGTATTACCTATGTCTTTCGGGACATATGGACAAAA
* ** * *
2403588 TTACCTATGTCTTTCGGGACATATGTACAGTATTATATATGTCTTTCGGGATATATGGACAATA
1 TTACCTATGTCTTTCGGGACATATGGACAGTATTACCTATGTCTTTCGGGACATATGGACAAAA
* * *
2403652 TTACCTATATCTTTCGGGACATATGGAAAGAATTACCTATGTCTTTCGGGACATATG
1 TTACCTATGTCTTTCGGGACATATGGACAGTATTACCTATGTCTTTCGGGACATATG
2403709 AACAGTTACC
Statistics
Matches: 163, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
64 141 0.87
65 22 0.13
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (64 bp):
TTACCTATGTCTTTCGGGACATATGGACAGTATTACCTATGTCTTTCGGGACATATGGACAAAA
Found at i:2403629 original size:96 final size:95
Alignment explanation
Indices: 2403459--2403714 Score: 341
Period size: 96 Copynumber: 2.7 Consensus size: 95
2403449 TAGTCGATGG
* * * * **
2403459 TTACCGATGTCCTTTGAGACATATGGACAGATTTTACCTATGTCTTTCGGGACATATAGACAAAA
1 TTACCTATGTCTTTTGGGACATATGGACAGA-ATTACCTATGTCTTTCGGGACATAT-GACAGTA
* * * *
2403524 TTACCTATGTCTTTTGGGACATATGTACAGTA
64 TTACATATGTCTTTCGGGACATATGGACAATA
2403556 TTACCTATGTCTTTTGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATGTACAGTAT
1 TTACCTATGTCTTTTGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATG-ACAGTAT
* *
2403621 TATATATGTCTTTCGGGATATATGGACAATA
65 TACATATGTCTTTCGGGACATATGGACAATA
* * *
2403652 TTACCTATATCTTTCGGGACATATGGAAAGAATTACCTATGTCTTTCGGGACATATGAACAGT
1 TTACCTATGTCTTTTGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATG-ACAGT
2403715 TACCTATGTT
Statistics
Matches: 142, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
95 1 0.01
96 113 0.80
97 28 0.20
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (95 bp):
TTACCTATGTCTTTTGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATGACAGTATT
ACATATGTCTTTCGGGACATATGGACAATA
Found at i:2404690 original size:22 final size:23
Alignment explanation
Indices: 2404663--2404713 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2404653 GGGGTGTTAC
*
2404663 ATATATAG-TTTATATATAAACT
1 ATATATAGAATTATATATAAACT
*
2404685 ATATAT-GAATTATATATAAATT
1 ATATATAGAATTATATATAAACT
2404707 ATATATA
1 ATATATA
2404714 CTATGAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATATAGAATTATATATAAACT
Found at i:2404700 original size:13 final size:11
Alignment explanation
Indices: 2404672--2404713 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
2404662 CATATATAGT
2404672 TTATATATAAA
1 TTATATATAAA
* *
2404683 CTATATATGAA
1 TTATATATAAA
2404694 TTATATATAAA
1 TTATATATAAA
2404705 TTATATATA
1 TTATATATA
2404714 CTATGAGCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:2404865 original size:22 final size:21
Alignment explanation
Indices: 2404818--2404931 Score: 78
Period size: 22 Copynumber: 5.4 Consensus size: 21
2404808 TATATATATA
*
2404818 TATATATATATATATATATATA-
1 TATATATATAT-TATA-ATAAAC
*
2404840 TATATATATATTATAGTTAAAC
1 TATATATATATTATA-ATAAAC
*
2404862 TATATATGA-ACTAT-ATAAAC
1 TATATAT-ATATTATAATAAAC
* *
2404882 TATATAGTTTATTA-ACATAAAT
1 TATATA-TATATTATA-ATAAAC
2404904 TATATA-AT-TTATACATAAAC
1 TATATATATATTATA-ATAAAC
2404924 TATATATA
1 TATATATA
2404932 AACTATATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.04
20 25 0.34
21 12 0.16
22 33 0.45
23 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (21 bp):
TATATATATATTATAATAAAC
Found at i:2404868 original size:2 final size:2
Alignment explanation
Indices: 2404807--2404854 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2404797 TTTGTACCAA
2404807 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
2404849 AT -T AT A
1 AT AT AT A
2404855 GTTAAACTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2404915 original size:9 final size:9
Alignment explanation
Indices: 2404898--2404964 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
2404888 GTTTATTAAC
2404898 ATAAATTAT
1 ATAAATTAT
*
2404907 ATAATTTAT
1 ATAAATTAT
2404916 ACATAAACTATAT
1 --ATAAA-T-TAT
*
2404929 ATAAACTAT
1 ATAAATTAT
2404938 AT-AATTAT
1 ATAAATTAT
*
2404946 AT--AGTAT
1 ATAAATTAT
2404953 ATAAATTAT
1 ATAAATTAT
2404962 ATA
1 ATA
2404965 GTTTATACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
7 6 0.13
8 7 0.15
9 20 0.43
11 9 0.20
12 1 0.02
13 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAAATTAT
Found at i:2404941 original size:20 final size:20
Alignment explanation
Indices: 2404820--2404964 Score: 71
Period size: 20 Copynumber: 6.8 Consensus size: 20
2404810 TATATATATA
* *
2404820 TATATATATATATATATATA-
1 TATATATAAAT-TATATAAAC
*
2404840 TATATATATATTATAGTTAAAC
1 TATATATAAATTATA--TAAAC
* *
2404862 TATATATGAACTATATAAAC
1 TATATATAAATTATATAAAC
** *
2404882 TATATAGTTTATTAACATAAA-
1 TATATA-TAAATT-ATATAAAC
*
2404903 T-TATATAATTTATACATAAAC
1 TATATATAAATTAT--ATAAAC
* *
2404924 TATATATAAACTATATAATTATA
1 TATATATAAATTATATAA--A-C
2404947 TAGTATATAAATTATATA
1 TA-TATATAAATTATATA
2404965 GTTTATACTA
Statistics
Matches: 96, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.01
19 7 0.07
20 35 0.36
21 8 0.08
22 29 0.30
23 2 0.02
24 14 0.15
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (20 bp):
TATATATAAATTATATAAAC
Found at i:2404961 original size:16 final size:16
Alignment explanation
Indices: 2404935--2404971 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2404925 ATATATAAAC
2404935 TATAT-AATTATATAG
1 TATATAAATTATATAG
2404950 TATATAAATTATATAG
1 TATATAAATTATATAG
*
2404966 TTTATA
1 TATATA
2404972 CTATAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TATATAAATTATATAG
Found at i:2405639 original size:102 final size:100
Alignment explanation
Indices: 2405429--2405788 Score: 372
Period size: 102 Copynumber: 3.6 Consensus size: 100
2405419 TGTTCTTCCC
** * * * *
2405429 AACCCTCATTTGATCTTTACAAATACCAAAACCCAAGATCAAACCTTTTTTTTTATCAAACACCC
1 AACCCTCATTCAATCCTTACAAACACCAAAACCCAAGACCAAACCTTTTTTTTGATCAAACACCC
* * *
2405494 AAAACTCAACTCGT-GTTCATCTATATTTATCCCCAA
66 AAAACTCAA-TCATAGTTCATCTATATTCAT-CCTAA
* * *
2405530 AACCCTCATTCAATCCTCACAAACACCAAAACCCAAGATCAAACCTATTTTTTTTATCAAACACC
1 AACCCTCATTCAATCCTTACAAACACCAAAACCCAAGACCAAACCT-TTTTTTTGATCAAACACC
* * ** *
2405595 CAAAACTCAATCCTAATTCATCGGTGTTCATCCTTAA
65 CAAAACTCAATCATAGTTCATCTATATTCATCC-TAA
* * * *
2405632 AACCCTCATTCGATCCTTACAAACACCAAAACCCAATACCCAA-C-TTTTTTAGATCAAA-ACCC
1 AACCCTCATTCAATCCTTACAAACACCAAAACCCAAGACCAAACCTTTTTTTTGATCAAACACCC
* * *
2405694 AAACCTCAA-CATATGTTCATCTTTTTTCATCCT-A
66 AAAACTCAATCATA-GTTCATCTATATTCATCCTAA
* * * *
2405728 AACCCTCATTTAATCCTTACAAACACCCAAACCCAAGACCCAATCTATTTTTTTGATCAAA
1 AACCCTCATTCAATCCTTACAAACACCAAAACCCAAGACCAAACCT-TTTTTTTGATCAAA
2405789 ACCTAACCAC
Statistics
Matches: 222, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
96 40 0.18
97 5 0.02
98 26 0.12
99 25 0.11
101 47 0.21
102 79 0.36
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (100 bp):
AACCCTCATTCAATCCTTACAAACACCAAAACCCAAGACCAAACCTTTTTTTTGATCAAACACCC
AAAACTCAATCATAGTTCATCTATATTCATCCTAA
Found at i:2405778 original size:198 final size:195
Alignment explanation
Indices: 2405429--2405864 Score: 485
Period size: 198 Copynumber: 2.2 Consensus size: 195
2405419 TGTTCTTCCC
* * * * **
2405429 AACCCTCATTTGATCTTTACAAATACCAAAACCCAAGATCAAACCTTTTTTTTTATCAAACACCC
1 AACCCTCATTTGATCCTTACAAACACCAAAACCCAAGACCCAACCTTTTTTTAGATCAAACACCC
*
2405494 AAAACTCAACTCGTGTTCATCTATATTTATCCCCAAAACCCTCATTCAATCCTCACAAACACCAA
66 AAAACTCAACTCATGTTCATCTATATTTATCCCCAAAACCCTCATTCAATCCTCACAAACACCAA
* * *
2405559 AACCCAAGATCAAACCTATTTTTTTTATCAAACACCCAAAACTCAATCCTAATTCATCGGTGTTC
131 AACCCAAGACCAAACCTATTTTTTTGATCAAA-A-CC-AAAC-C-A--CT-ATTCATCGGAGTTC
2405624 ATCCTT-AA
188 AT-CTTCAA
* *
2405632 AACCCTCATTCGATCCTTACAAACACCAAAACCCAATACCCAA-C-TTTTTTAGATCAAA-ACCC
1 AACCCTCATTTGATCCTTACAAACACCAAAACCCAAGACCCAACCTTTTTTTAGATCAAACACCC
* * * * *
2405694 AAACCTCAACAT-ATGTTCATCT-T-TTT-TCATCCTAAACCCTCATTTAATCCTTACAAACACC
66 AAAACTCAAC-TCATGTTCATCTATATTTATC-CCCAAAACCCTCATTCAATCCTCACAAACACC
* * * * * *
2405755 CAAACCCAAGACCCAATCTATTTTTTTGATCAAAACCTAACCACTATTCATCTGAGTTTATCTTC
129 AAAACCCAAGACCAAACCTATTTTTTTGATCAAAACCAAACCACTATTCATCGGAGTTCATCTTC
2405820 AA
194 AA
*
2405822 AACCCTCATTTGATCCTTTCAAACAACC-AAACCCAAGACCCAA
1 AACCCTCATTTGATCCTTACAAAC-ACCAAAACCCAAGACCCAA
2405865 GATGTTTTTA
Statistics
Matches: 203, Mismatches: 26, Indels: 21
0.81 0.10 0.08
Matches are distributed among these distances:
189 3 0.01
190 51 0.25
191 5 0.02
193 1 0.00
194 1 0.00
195 3 0.01
196 2 0.01
197 3 0.01
198 60 0.30
199 1 0.00
200 22 0.11
201 13 0.06
202 1 0.00
203 37 0.18
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (195 bp):
AACCCTCATTTGATCCTTACAAACACCAAAACCCAAGACCCAACCTTTTTTTAGATCAAACACCC
AAAACTCAACTCATGTTCATCTATATTTATCCCCAAAACCCTCATTCAATCCTCACAAACACCAA
AACCCAAGACCAAACCTATTTTTTTGATCAAAACCAAACCACTATTCATCGGAGTTCATCTTCAA
Found at i:2405972 original size:49 final size:48
Alignment explanation
Indices: 2405910--2406075 Score: 174
Period size: 49 Copynumber: 3.4 Consensus size: 48
2405900 CTCTAACCTG
*
2405910 AAATCTAACCAAGACTCTTCTTCTTCTTCTGTTCATCTTTTTTAACCCT
1 AAATCTAA-CAAGACTCTTCTTCTTCTTCTGTTTATCTTTTTTAACCCT
* * * **
2405959 AAA-CTTAATCAAGACTCTTTTTCTTCTTTTGTTTATCTTCTCCAACCCT
1 AAATC-TAA-CAAGACTCTTCTTCTTCTTCTGTTTATCTTTTTTAACCCT
* *
2406008 AAATCTAACTGAGACTCTTCTTCTTCTTCTGTTTAT-TTTCTTTAACCTT
1 AAATCTAAC-AAGACTCTTCTTCTTCTTCTGTTTATCTTT-TTTAACCCT
* *
2406057 AAATATAACTGAGACTCTT
1 AAATCTAAC-AAGACTCTT
2406076 TATCTTATGT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
48 4 0.04
49 93 0.95
50 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.05, T:0.46
Consensus pattern (48 bp):
AAATCTAACAAGACTCTTCTTCTTCTTCTGTTTATCTTTTTTAACCCT
Found at i:2406030 original size:46 final size:46
Alignment explanation
Indices: 2405979--2406121 Score: 146
Period size: 46 Copynumber: 3.0 Consensus size: 46
2405969 AAGACTCTTT
* * *
2405979 TTCTTCTTTTGTTTATCTTCTCCAACCCTAAATCTAACTGAGACTC
1 TTCTTCTTTTGTTTATATTCTCTAACCATAAATCTAACTGAGACTC
* * * *
2406025 TTCTTCTTCTTCTGTTTATTTTCTTTAACCTTAAATATAACTGAGACTC
1 TTCTTC-T-TT-TGTTTATATTCTCTAACCATAAATCTAACTGAGACTC
* *
2406074 TT-TATCTTATGTTCATATTCTCTAACCATAAATCTAA-TAGAGACTC
1 TTCT-TCTTTTGTTTATATTCTCTAACCATAAATCTAACT-GAGACTC
2406120 TT
1 TT
2406122 TATATTCTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
45 1 0.01
46 38 0.47
47 2 0.02
48 4 0.05
49 36 0.44
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.46
Consensus pattern (46 bp):
TTCTTCTTTTGTTTATATTCTCTAACCATAAATCTAACTGAGACTC
Found at i:2406269 original size:17 final size:16
Alignment explanation
Indices: 2406241--2406279 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2406231 ACTTTTCATG
2406241 TTATTTTTTTTAT-TT
1 TTATTTTTTTTATATT
2406256 TTCATTTATTTTTATATT
1 TT-ATTT-TTTTTATATT
2406274 TTATTT
1 TTATTT
2406280 GAATTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 4 0.19
17 11 0.52
18 4 0.19
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTTTTTATATT
Found at i:2406273 original size:19 final size:21
Alignment explanation
Indices: 2406233--2406275 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
2406223 CGAGTTGAAC
*
2406233 TTTTCATGTTATTTTTTTTAT
1 TTTTCATGTTATTTTTTATAT
2406254 TTTTCAT-TTA-TTTTTATAT
1 TTTTCATGTTATTTTTTATAT
2406273 TTT
1 TTT
2406276 ATTTGAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCATGTTATTTTTTATAT
Found at i:2407985 original size:22 final size:23
Alignment explanation
Indices: 2407934--2407985 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2407924 GATATTCAAT
*
2407934 TTTATTTATTTTATTATGTTTTC
1 TTTATTTATATTATTATGTTTTC
* * *
2407957 ATAATTTA-ATTATTTTGTTTTC
1 TTTATTTATATTATTATGTTTTC
2407979 TTTATTT
1 TTTATTT
2407986 TTTTCCAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTATTTATATTATTATGTTTTC
Found at i:2409575 original size:16 final size:16
Alignment explanation
Indices: 2409554--2409584 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2409544 GATAATTTAT
2409554 AAGTCAAGTAAATATA
1 AAGTCAAGTAAATATA
2409570 AAGTCAAGTAAATAT
1 AAGTCAAGTAAATAT
2409585 CATATCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (16 bp):
AAGTCAAGTAAATATA
Found at i:2412357 original size:29 final size:29
Alignment explanation
Indices: 2412324--2412390 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
2412314 ACCTTCATAG
2412324 AAAGAATTCAAAGATCATTTTCATTTGCC
1 AAAGAATTCAAAGATCATTTTCATTTGCC
2412353 AAAGAATTCAAAGATCATTTTCATTTGCC
1 AAAGAATTCAAAGATCATTTTCATTTGCC
2412382 AAAGAATTC
1 AAAGAATTC
2412391 CCTAGAAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAGAATTCAAAGATCATTTTCATTTGCC
Found at i:2416504 original size:24 final size:24
Alignment explanation
Indices: 2416476--2416584 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
2416466 AAATATTTTA
*
2416476 TCTGATTTCTGA-CTTGAATTTTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
2416500 TCTGA-TACATTATCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
* *
2416524 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* **
2416548 TATGATACCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2416572 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2416585 ATCTCCGTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.03
24 62 0.93
25 3 0.04
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2416532 original size:48 final size:48
Alignment explanation
Indices: 2416476--2416586 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 48
2416466 AAATATTTTA
* * *
2416476 TCTGATTTCTGACT-TGAATTTTGTTCTGATACATTATCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTATGATACATGATCTGAATTCTGT
* *
2416524 TCTGATTTCTGATATGGATTCTGTTATGATACCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTATGATACATGATCTGAATTCTGT
*
2416572 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
2416587 CTCCGTTTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTATGATACATGATCTGAATTCTGT
Found at i:2417676 original size:20 final size:20
Alignment explanation
Indices: 2417651--2417730 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
2417641 GCGATATTTG
2417651 CGTTGCGATTTTAATTTTCA
1 CGTTGCGATTTTAATTTTCA
* * *
2417671 CGTTGCAATTTTCATTTTCG
1 CGTTGCGATTTTAATTTTCA
* *
2417691 CGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTAATTTTCA
* * *
2417711 TGTTGCGAATTTAAGTTTCA
1 CGTTGCGATTTTAATTTTCA
2417731 GAAACTACTC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.49
Consensus pattern (20 bp):
CGTTGCGATTTTAATTTTCA
Found at i:2419919 original size:21 final size:21
Alignment explanation
Indices: 2419895--2419963 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
2419885 CCTATCGTTC
2419895 AAGAGGCCCATCTCATCATTG
1 AAGAGGCCCATCTCATCATTG
* * * *
2419916 AAGAGGCCCATCCCACCGTTC
1 AAGAGGCCCATCTCATCATTG
2419937 AAGAGGCCCATCTCATCATTG
1 AAGAGGCCCATCTCATCATTG
2419958 AAGAGG
1 AAGAGG
2419964 ACACTCCCAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (21 bp):
AAGAGGCCCATCTCATCATTG
Found at i:2419928 original size:42 final size:42
Alignment explanation
Indices: 2419877--2420005 Score: 188
Period size: 42 Copynumber: 3.1 Consensus size: 42
2419867 ATCGTTCAAA
* *
2419877 AGGCACATCCTATCGTTCAAGAGGCCCATCTCATCATTGAAG
1 AGGCACATCCCACCGTTCAAGAGGCCCATCTCATCATTGAAG
*
2419919 AGGCCCATCCCACCGTTCAAGAGGCCCATCTCATCATTGAAG
1 AGGCACATCCCACCGTTCAAGAGGCCCATCTCATCATTGAAG
* * *
2419961 AGG-ACACTCCCACCGTTCAAGAGGCCCATGTCATCGTTCAAG
1 AGGCACA-TCCCACCGTTCAAGAGGCCCATCTCATCATTGAAG
2420003 AGG
1 AGG
2420006 TCCCGCCCGC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 2 0.03
42 77 0.97
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (42 bp):
AGGCACATCCCACCGTTCAAGAGGCCCATCTCATCATTGAAG
Found at i:2419982 original size:21 final size:21
Alignment explanation
Indices: 2419869--2420005 Score: 96
Period size: 21 Copynumber: 6.5 Consensus size: 21
2419859 CACCTATCAT
* * *
2419869 CGTTCAAAAGGCACATCCTAT
1 CGTTCAAGAGGCACATCCCAC
* * *
2419890 CGTTCAAGAGGCCCATCTCAT
1 CGTTCAAGAGGCACATCCCAC
* * *
2419911 CATTGAAGAGGCCCATCCCAC
1 CGTTCAAGAGGCACATCCCAC
* * *
2419932 CGTTCAAGAGGCCCATCTCAT
1 CGTTCAAGAGGCACATCCCAC
* *
2419953 CATTGAAGAGG-ACACTCCCAC
1 CGTTCAAGAGGCACA-TCCCAC
* ** *
2419974 CGTTCAAGAGGCCCATGTCAT
1 CGTTCAAGAGGCACATCCCAC
2419995 CGTTCAAGAGG
1 CGTTCAAGAGG
2420006 TCCCGCCCGC
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
20 2 0.02
21 87 0.96
22 2 0.02
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (21 bp):
CGTTCAAGAGGCACATCCCAC
Found at i:2420019 original size:42 final size:41
Alignment explanation
Indices: 2419890--2420025 Score: 191
Period size: 42 Copynumber: 3.2 Consensus size: 41
2419880 CACATCCTAT
2419890 CGTTCAAGAGGCCCATCTCATCATTGAAGAGGCCCATCCCAC
1 CGTTCAAGAGGCCCATCTCATCATTGAAGAGGCCC-TCCCAC
*
2419932 CGTTCAAGAGGCCCATCTCATCATTGAAGAGGACACTCCCAC
1 CGTTCAAGAGGCCCATCTCATCATTGAAGAGG-CCCTCCCAC
* * * * *
2419974 CGTTCAAGAGGCCCATGTCATCGTTCAAGAGGTCCCGCCCGC
1 CGTTCAAGAGGCCCATCTCATCATTGAAGAGG-CCCTCCCAC
2420016 CGTTCAAGAG
1 CGTTCAAGAG
2420026 CCCGATTCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (41 bp):
CGTTCAAGAGGCCCATCTCATCATTGAAGAGGCCCTCCCAC
Found at i:2421461 original size:14 final size:14
Alignment explanation
Indices: 2421442--2421468 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2421432 TTTTTGCTTG
2421442 TTGATTTGTAAAAA
1 TTGATTTGTAAAAA
2421456 TTGATTTGTAAAA
1 TTGATTTGTAAAA
2421469 GTTAAATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAA
Found at i:2421527 original size:20 final size:20
Alignment explanation
Indices: 2421502--2421540 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2421492 TTGTTGAGAT
2421502 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
2421522 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
2421541 TTTTCGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:2421588 original size:20 final size:20
Alignment explanation
Indices: 2421563--2421626 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
2421553 GATTTTGATT
2421563 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
2421583 TTTCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
2421603 TATCGCGTTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
2421623 TTTC
1 TTTC
2421627 ACAACAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:2421892 original size:18 final size:18
Alignment explanation
Indices: 2421869--2421904 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2421859 AAGCCGGTTG
*
2421869 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2421887 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2421905 ACTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2425185 original size:20 final size:20
Alignment explanation
Indices: 2425157--2425210 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2425147 ACTAAAACCT
* *
2425157 GTTGTGAATTCGAAAATACA
1 GTTGCGAATTTGAAAATACA
*
2425177 GTTGCGAATTTG-AAATTCA
1 GTTGCGAATTTGAAAATACA
2425196 GTTGCGAATTTGAAA
1 GTTGCGAATTTGAAA
2425211 TTCAGCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATACA
Found at i:2425197 original size:19 final size:19
Alignment explanation
Indices: 2425170--2425245 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
2425160 GTGAATTCGA
*
2425170 AAATACAGTTGCGAATTTG
1 AAATTCAGTTGCGAATTTG
2425189 AAATTCAGTTGCGAATTTG
1 AAATTCAGTTGCGAATTTG
* *
2425208 AAATTCA---GCTAATTTA
1 AAATTCAGTTGCGAATTTG
2425224 AAATTCAGTGTTGCGAATTTG
1 AAATTCA--GTTGCGAATTTG
2425245 A
1 A
2425246 CTTTTGTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
16 14 0.30
19 25 0.53
21 8 0.17
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (19 bp):
AAATTCAGTTGCGAATTTG
Found at i:2425256 original size:20 final size:20
Alignment explanation
Indices: 2425231--2425315 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
2425221 TTAAAATTCA
2425231 GTGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGACTTTT
* *
2425251 GTGTTGTGAATTTGACTTAT
1 GTGTTGCGAATTTGACTTTT
* *
2425271 GTATTGCAAATTTGACTTTT
1 GTGTTGCGAATTTGACTTTT
*
2425291 GTGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTTTT
2425311 GTGTT
1 GTGTT
2425316 ACGATTTACA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTTT
Found at i:2430275 original size:20 final size:22
Alignment explanation
Indices: 2430238--2430281 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 22
2430228 AACAAAATTG
2430238 TATAATAAAATTTAAATTTATTT
1 TATAATAAAA-TTAAATTTATTT
2430261 TATAATAAAA-T-AATTTATTT
1 TATAATAAAATTAAATTTATTT
2430281 T
1 T
2430282 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
23 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATAAAATTAAATTTATTT
Found at i:2434372 original size:34 final size:34
Alignment explanation
Indices: 2434329--2434453 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
2434319 TTCGTCCTAC
2434329 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
2434363 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
2434398 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2434427 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
2434454 CCACAAACAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2434740 original size:22 final size:21
Alignment explanation
Indices: 2434702--2434770 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
2434692 ATTGTTTTGT
*
2434702 TATTTTTTT--TTTCATGTAA
1 TATTTTTTTACTTTTATGTAA
*
2434721 TATTTTTTTACATTTTATGTAT
1 TATTTTTTTAC-TTTTATGTAA
*
2434743 TTTCTTTTTTAC-TTTA-GTATA
1 TAT-TTTTTTACTTTTATGTA-A
2434764 TATTTTT
1 TATTTTT
2434771 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 9 0.22
20 7 0.17
21 6 0.15
22 10 0.25
23 8 0.20
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (21 bp):
TATTTTTTTACTTTTATGTAA
Found at i:2434767 original size:24 final size:23
Alignment explanation
Indices: 2434724--2434769 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2434714 CATGTAATAT
*
2434724 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
2434747 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
2434770 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:2434855 original size:14 final size:14
Alignment explanation
Indices: 2434838--2434971 Score: 58
Period size: 13 Copynumber: 9.9 Consensus size: 14
2434828 TATATATATA
2434838 TATTTACTT-TTTTT
1 TATTT-CTTATTTTT
*
2434852 TATTTTTTATTTTT
1 TATTTCTTATTTTT
2434866 TATTT-TATATATATATAT
1 TATTTCT-TAT-T-T-T-T
2434884 TATTT-TTACTTTTT
1 TATTTCTTA-TTTTT
*
2434898 TA-TTATTA--TTT
1 TATTTCTTATTTTT
* *
2434909 TATTTATT-TGTTT
1 TATTTCTTATTTTT
*
2434922 TATTTC-TATATTT
1 TATTTCTTATTTTT
2434935 TATTTC-T-TTTTT
1 TATTTCTTATTTTT
*
2434947 T-TTTCTTTTTTTT
1 TATTTCTTATTTTT
*
2434960 TATAT-TTATTTT
1 TATTTCTTATTTT
2434972 ACTTACTATT
Statistics
Matches: 99, Mismatches: 6, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
11 9 0.09
12 12 0.12
13 36 0.36
14 26 0.26
15 2 0.02
16 2 0.02
17 4 0.04
18 8 0.08
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (14 bp):
TATTTCTTATTTTT
Found at i:2434873 original size:51 final size:49
Alignment explanation
Indices: 2434800--2434969 Score: 158
Period size: 51 Copynumber: 3.5 Consensus size: 49
2434790 TATAAAAATA
* * *
2434800 TTATTTTTTA-TTATCAGTTTTATTAATTTATATATATATATTTACTTTTTT
1 TTATTTTTTATTTTTTA-TTTTATT-ATATATATAT-TATATTTACTTTTTT
*
2434851 TTATTTTTTATTTTTTATTTTA-TATATATATATTATTTTTACTTTTTT
1 TTATTTTTTATTTTTTATTTTATTATATATATATTATATTTACTTTTTT
* *
2434899 ATTATTATTTTATTTATTTGTTTTATT-TCTATAT-TT-TATTT-CTTTTTT
1 -TTATT-TTTTATTT-TTTATTTTATTATATATATATTATATTTACTTTTTT
*
2434947 TT-TTCTTT-TTTTTTATATTTATT
1 TTATTTTTTATTTTTTAT-TTTATT
2434970 TTACTTACTA
Statistics
Matches: 104, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
43 4 0.04
44 9 0.09
45 3 0.03
46 2 0.02
47 2 0.02
48 21 0.20
49 18 0.17
50 11 0.11
51 29 0.28
52 5 0.05
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.74
Consensus pattern (49 bp):
TTATTTTTTATTTTTTATTTTATTATATATATATTATATTTACTTTTTT
Found at i:2434890 original size:38 final size:38
Alignment explanation
Indices: 2434832--2434948 Score: 110
Period size: 38 Copynumber: 3.0 Consensus size: 38
2434822 TTAATTTATA
* *
2434832 TATATATATTTACTTTTTTTTATTTTTTATTTTTTATTT
1 TATATATATATA-TTATTTTTATTTTTTATTTTTTATTT
*
2434871 TATATATATATATTATTTTTACTTTTTTA-TTATTATTT
1 TATATATATATATTATTTTTA-TTTTTTATTTTTTATTT
* * * * * * *
2434909 TATTTATTTGTTTTATTTCTATATTTTATTTCTTTTTTT
1 TATATATATATATTATTTTTATTTTTTATTT-TTTATTT
2434948 T
1 T
2434949 TTCTTTTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
37 6 0.09
38 34 0.53
39 24 0.38
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (38 bp):
TATATATATATATTATTTTTATTTTTTATTTTTTATTT
Found at i:2434923 original size:32 final size:28
Alignment explanation
Indices: 2434850--2434970 Score: 104
Period size: 32 Copynumber: 4.1 Consensus size: 28
2434840 TTTACTTTTT
2434850 TTTA-TTTTTTATTTTTTATTTTATATATA
1 TTTATTTTTTTATTTTTTATTTTAT-T-TA
*
2434879 TATATTATTTTTACTTTTTTATTATTATTTTA
1 TTTATT-TTTTTA-TTTTTTATT-TTA-TTTA
* *
2434911 TTTATTTGTTTTATTTCTATATTTTATTTC
1 TTTATTT-TTTTATTT-TTTATTTTATTTA
*
2434941 TTT-TTTTTTTCTTTTTT-TTTATATTTA
1 TTTATTTTTTTATTTTTTATTT-TATTTA
2434968 TTT
1 TTT
2434971 TACTTACTAT
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
26 3 0.04
27 10 0.13
28 7 0.09
29 6 0.08
30 7 0.09
31 13 0.17
32 26 0.34
33 4 0.05
34 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (28 bp):
TTTATTTTTTTATTTTTTATTTTATTTA
Found at i:2437497 original size:8 final size:8
Alignment explanation
Indices: 2437484--2437522 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2437474 GAACATTTCG
*
2437484 TGCATTCT
1 TGCATTTT
2437492 TGCA-TTT
1 TGCATTTT
2437499 TGCATTTT
1 TGCATTTT
*
2437507 TGCCTTTT
1 TGCATTTT
2437515 TGCATTTT
1 TGCATTTT
2437523 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:2438672 original size:22 final size:22
Alignment explanation
Indices: 2438649--2438710 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
2438639 CAAAAAGGGC
2438649 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
2438672 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
2438693 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
2438711 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:2438701 original size:20 final size:20
Alignment explanation
Indices: 2438649--2438718 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
2438639 CAAAAAGGGC
*
2438649 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
2438672 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
2438693 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
2438713 AAAAAG
1 AAAAAG
2438719 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:2439355 original size:22 final size:22
Alignment explanation
Indices: 2439327--2439377 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2439317 CCCCATCAAT
*
2439327 CCTTTGAGCATCAAATACTAAA
1 CCTTTGAGCATCAAATACCAAA
*
2439349 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
2439371 CCTTTGA
1 CCTTTGA
2439378 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:2440388 original size:37 final size:37
Alignment explanation
Indices: 2440321--2440407 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
2440311 ATTGAAAACA
** * *
2440321 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
2440357 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2440394 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2440408 TAAACATTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2440413 original size:102 final size:102
Alignment explanation
Indices: 2440237--2440777 Score: 1021
Period size: 102 Copynumber: 5.3 Consensus size: 102
2440227 GTGCTCACTA
*
2440237 TTGTCTCTCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440302 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
2440339 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
2440404 AACATAAACATTGGAAACA-TTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
2440440 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440505 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
2440542 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440607 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
*
2440644 TTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
2440709 AACATAAATATTGAAAACATTTCCCTTGAAATGAATT
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
* *
2440746 TCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
2440778 TAAACATTGA
Statistics
Matches: 430, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
101 100 0.23
102 330 0.77
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
AACATAAACATTGAAAACATTTCCCTTGAAATGAATT
Found at i:2440483 original size:37 final size:37
Alignment explanation
Indices: 2440423--2440508 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 37
2440413 ATTGGAAACA
** * *
2440423 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
2440459 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
*
2440496 TTCTCTTGAAACA
1 TTCCCTTGAAACA
2440509 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 11 0.25
37 33 0.75
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
Found at i:2440586 original size:203 final size:204
Alignment explanation
Indices: 2440237--2440777 Score: 1021
Period size: 203 Copynumber: 2.7 Consensus size: 204
2440227 GTGCTCACTA
*
2440237 TTGTCTCTCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440302 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
*
2440367 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA-TTCCCTTG
131 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
2440431 AAATGAATT
196 AAATGAATT
2440440 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440505 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
2440570 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
131 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
2440635 AAATGAATT
196 AAATGAATT
*
2440644 TTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
* * *
2440709 AACATAAATATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGA
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
2440774 AACA
131 AACA
2440778 TAAACATTGA
Statistics
Matches: 331, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
203 184 0.56
204 147 0.44
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (204 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
AAATGAATT
Found at i:2440591 original size:37 final size:37
Alignment explanation
Indices: 2440524--2440610 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
2440514 ATTGAAAACA
** * *
2440524 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
2440560 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
2440597 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2440611 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:2440683 original size:37 final size:38
Alignment explanation
Indices: 2440640--2440717 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
2440630 CCTTGAAATG
* *
2440640 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACA-A
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
* *
2440677 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
2440715 AAT
1 AAT
2440718 ATTGAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
Found at i:2440767 original size:65 final size:65
Alignment explanation
Indices: 2440677--2440846 Score: 297
Period size: 65 Copynumber: 2.6 Consensus size: 65
2440667 CTCGAAACAA
* *
2440677 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAATG
* *
2440742 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAATG
2440807 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAT
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAT
2440847 TTTGTCTCCC
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 3 0.03
65 96 0.97
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAATG
Found at i:2440840 original size:305 final size:301
Alignment explanation
Indices: 2440237--2440786 Score: 922
Period size: 305 Copynumber: 1.8 Consensus size: 301
2440227 GTGCTCACTA
*
2440237 TTGTCTCTCTTGAGATAGTTTCCCTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
*
2440302 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGA
*
2440367 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGGAAACATTCCCTTGA
131 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCCTTGA
* ** * *
2440432 AATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
196 AATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAACATTGTCTCCCTTGAAACAATT
**
2440497 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA-TGAATT
261 TCTCTT---ACAT--ACATTGAAAACATTTCCCTTGAAACAAAATT
2440542 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
2440607 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGA
66 AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGA
*
2440672 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTG
131 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA-TTCCCTTG
*
2440737 AAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTG
195 AAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAACATTG
2440787 AAAACATTTC
Statistics
Matches: 235, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
305 182 0.77
306 47 0.20
307 6 0.03
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (301 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGA
AACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGA
AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTCCCTTGA
AATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAACATTGTCTCCCTTGAAACAATT
TCTCTTACATACATTGAAAACATTTCCCTTGAAACAAAATT
Found at i:2440866 original size:167 final size:169
Alignment explanation
Indices: 2440560--2440877 Score: 541
Period size: 167 Copynumber: 1.9 Consensus size: 169
2440550 CTTGAGATAG
*
2440560 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
2440625 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
2440690 TTGAGACAG-TTTCTCTTGAAACATAAATATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAATATTGAAAACA
** * *
2440728 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
2440792 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
2440857 TTGAGACAGTTTTCTCTTGAA
131 TTGAGACAGTTTTCTCTTGAA
2440878 GCATCATCTT
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
167 117 0.84
168 23 0.16
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAATATTGAAAACA
Found at i:2441625 original size:105 final size:103
Alignment explanation
Indices: 2441485--2441851 Score: 439
Period size: 105 Copynumber: 3.6 Consensus size: 103
2441475 GCCAAACTTC
* *
2441485 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAA
* * *
2441550 CTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTT
66 CTTCACAACGAAGGGACGGCTGACTGTCAACAACAA-TT
* *
2441589 CTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGGCAACACAAGTTCA
1 -TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCA
* *
2441654 ACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GATT
65 ACTTCACAACGAAGGGACGGCTGACTGTCAACAACAATT
* * * *
2441692 TC--GTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACAGCACAAGCTT-
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACACAAG-TTC
* * *
2441753 AACTTCACAACGACGGGGCGGCTGACTGT---CGACAA--
64 AACTTCACAACGAAGGGACGGCTGACTGTCAACAACAATT
* * * * *
2441788 GCAATTTCGGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCA
1 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCA
2441852 CAAACAATTT
Statistics
Matches: 228, Mismatches: 27, Indels: 21
0.83 0.10 0.08
Matches are distributed among these distances:
96 1 0.00
97 4 0.02
98 50 0.22
99 3 0.01
100 73 0.32
101 2 0.01
102 2 0.01
103 2 0.01
104 1 0.00
105 90 0.39
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (103 bp):
TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAA
CTTCACAACGAAGGGACGGCTGACTGTCAACAACAATT
Found at i:2442045 original size:109 final size:109
Alignment explanation
Indices: 2441873--2442178 Score: 394
Period size: 109 Copynumber: 2.8 Consensus size: 109
2441863 CCAATTCCAT
* * *
2441873 AGCCGATTTCAACTCCACGACAGAGGATATCGTGCTAC-CTTAGACAACACAAGTTCAACTTCAC
1 AGCCGATTTCAACTCCACGACGGAGGATATCGTGCCACTC-GAGACAACACAAGTTCAACTTCAC
* *
2441937 AACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTC-AGTTTCATC
65 AACGAAGGGACGGCTGGTTGTCAACAAAC-ACTTTTCAAATTTCA-C
* *
2441983 CG-CGATTTTAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACA
1 AGCCGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACA
* *
2442047 ACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAG
66 ACGAAGGGACGGCTGGTTGTCAACAAACACTTTTCAAATTTCAC
* * *
2442091 AGCCAATTTCAACTTCGCA-G-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCA
1 AGCCGATTTCAAC-TC-CACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCA
*
2442151 CAACGAAGGGACGGCTGATTGTCAACAA
64 CAACGAAGGGACGGCTGGTTGTCAACAA
2442179 GATTTCGTTC
Statistics
Matches: 176, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
106 54 0.31
107 2 0.01
108 7 0.04
109 106 0.60
110 5 0.03
111 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (109 bp):
AGCCGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACA
ACGAAGGGACGGCTGGTTGTCAACAAACACTTTTCAAATTTCAC
Found at i:2442252 original size:100 final size:103
Alignment explanation
Indices: 2441914--2442340 Score: 423
Period size: 106 Copynumber: 4.1 Consensus size: 103
2441904 GTGCTACCTT
* *
2441914 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAC-A-TTTTCAG-TT
** * * * * *
2441979 CA-TCCGCGATTTTAACTCCACGACGGAGGATATCGT-GCCACTCG
63 CAGAGC-CAATTTCAACTTCACAACGAAGGATAT--TAG--ACTCG
* *
2442023 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACA-TTTTC--AGTT
* * *
2442088 CAGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCG
63 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCG
*
2442129 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGA-TTTC-GTTCAG
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAGTTCAG
* *
2442191 AGTCAATTTCATCTTCACAACGAAGGATATTAGACTCG
66 AGCCAATTTCAACTTCACAACGAAGGATATTAGACTCG
* * * * * * * *
2442229 AGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAATAAATAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-CATTT-TCAGTT-
* * * *
2442294 CAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
63 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCG
*
2442335 AAACAA
1 AGACAA
2442341 TATTTGGATT
Statistics
Matches: 272, Mismatches: 36, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
100 80 0.29
101 2 0.01
102 1 0.00
103 6 0.02
104 1 0.00
105 6 0.02
106 91 0.33
107 1 0.00
108 7 0.03
109 75 0.28
110 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (103 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACATTTTCAGTTCAG
AGCCAATTTCAACTTCACAACGAAGGATATTAGACTCG
Found at i:2442326 original size:206 final size:212
Alignment explanation
Indices: 2441914--2442340 Score: 510
Period size: 206 Copynumber: 2.0 Consensus size: 212
2441904 GTGCTACCTT
*
2441914 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAAC-TTTCAGTTT
* * * * * *
2441979 CATCCGCGATTTTAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTC
65 CATCAGCAATTTCAACTCCACAACGAAGGATATC-TG-CACTCGAGACAACACAAGCTCAACTTC
** * * * * *
2442044 ACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGC
128 ACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCAC
2442109 AGCGAAGGATATTGGACTCG
193 AGCGAAGGATATTGGACTCG
*
2442129 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC-G-TTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAACTTTCAGTTTC
* * * *
2442189 A-GAGTCAATTTCATCTTCACAACGAAGGATAT-TAG-ACTCGAGACAGCACAAGCTCAACTTCA
66 ATCAG-CAATTTCAACTCCACAACGAAGGATATCT-GCACTCGAGACAACACAAGCTCAACTTCA
* * * * * *
2442251 CAGCGAAGGGGCGGCTGACTGTCAATAAATAATTTCCCAGTTCCAGAACCAATTTCAACTTCACA
129 CAACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACA
*
2442316 GCGGAGGATATTGGACTCG
194 GCGAAGGATATTGGACTCG
*
2442335 AAACAA
1 AGACAA
2442341 TATTTGGATT
Statistics
Matches: 183, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
206 100 0.55
207 1 0.01
208 2 0.01
209 25 0.14
210 1 0.01
211 4 0.02
213 1 0.01
214 2 0.01
215 47 0.26
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (212 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACGAACAACTTTCAGTTTC
ATCAGCAATTTCAACTCCACAACGAAGGATATCTGCACTCGAGACAACACAAGCTCAACTTCACA
ACGAAGGGACGGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACAGC
GAAGGATATTGGACTCG
Found at i:2442839 original size:34 final size:34
Alignment explanation
Indices: 2442796--2442920 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
2442786 TTCGTCCTAC
2442796 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
2442830 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
2442865 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
2442894 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
2442921 CCACAAACAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:2443326 original size:8 final size:8
Alignment explanation
Indices: 2443310--2443430 Score: 54
Period size: 7 Copynumber: 14.5 Consensus size: 8
2443300 TATATATATA
2443310 TTTACTTTT
1 TTTA-TTTT
2443319 TTTA-TTT
1 TTTATTTT
2443326 TTTATTTAT
1 TTTATTT-T
2443335 ATATATATTATT
1 -T-T-TATT-TT
2443347 TTTACTTTT
1 TTTA-TTTT
*
2443356 TTTATTAT
1 TTTATTTT
*
2443364 TTTATTTA
1 TTTATTTT
*
2443372 TTTGTTTAT
1 TTTATTT-T
*
2443381 TTCTATATT
1 TT-TATTTT
*
2443390 TTT-TTCT
1 TTTATTTT
2443397 TTT-TTTT
1 TTTATTTT
* *
2443404 TCT-TTTC
1 TTTATTTT
2443411 TTTA-TTT
1 TTTATTTT
2443418 TTTATTTAT
1 TTTATTT-T
2443427 TTTA
1 TTTA
2443431 CTTACTATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 24
0.69 0.11 0.19
Matches are distributed among these distances:
7 28 0.33
8 20 0.23
9 23 0.27
10 7 0.08
11 2 0.02
12 5 0.06
13 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:2443336 original size:30 final size:28
Alignment explanation
Indices: 2443320--2443382 Score: 58
Period size: 30 Copynumber: 2.2 Consensus size: 28
2443310 TTTACTTTTT
*
2443320 TTATTTTTTATT-TATATATATATTATTT
1 TTATTTTTTATTATATATATTTATT-TTT
* *
2443348 TTACTTTTTTTATTAT-TTTATTTATTTGT
1 TTA--TTTTTTATTATATATATTTATTTTT
2443377 TTATTT
1 TTATTT
2443383 CTATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
27 3 0.10
28 3 0.10
29 5 0.17
30 17 0.59
31 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (28 bp):
TTATTTTTTATTATATATATTTATTTTT
Found at i:2443341 original size:32 final size:37
Alignment explanation
Indices: 2443283--2443372 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 37
2443273 TTATTATCAG
* *
2443283 TTTTATTAATTTATATATATATATA-TA-TTTACTTT
1 TTTTATTATTTTATTTATATATATATTATTTTACTTT
2443318 TTTTATT-TTTTATTTATATATATATTATTTTTACTTT
1 TTTTATTATTTTATTTATATATATATTA-TTTTACTTT
2443355 TTTTATTATTTTATTTAT
1 TTTTATTATTTTATTTAT
2443373 TTGTTTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
34 15 0.31
35 9 0.18
37 15 0.31
38 10 0.20
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (37 bp):
TTTTATTATTTTATTTATATATATATTATTTTACTTT
Found at i:2443342 original size:38 final size:38
Alignment explanation
Indices: 2443291--2443372 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
2443281 AGTTTTATTA
2443291 ATTTATATATATATATATATTTACTTTTTTTATT-TTTT
1 ATTTATATATATAT-TATATTTACTTTTTTTATTATTTT
*
2443329 ATTTATATATATATTATTTTTACTTTTTTTATTATTTT
1 ATTTATATATATATTATATTTACTTTTTTTATTATTTT
2443367 ATTTAT
1 ATTTAT
2443373 TTGTTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 18 0.43
38 24 0.57
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (38 bp):
ATTTATATATATATTATATTTACTTTTTTTATTATTTT
Found at i:2443373 original size:4 final size:4
Alignment explanation
Indices: 2443284--2443428 Score: 57
Period size: 4 Copynumber: 35.8 Consensus size: 4
2443274 TATTATCAGT
* * * *
2443284 TTTA TTAA TTTA TATATA TATA TATA TTTA CTTTT TTTA TTT- TTTA TTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
* * * * * *
2443334 TATA TATA TTATT TTTA CTTTT TTTA -TTA TTTTA TTTA TTTG TTTA TTTC
1 TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
* * * * *
2443384 TATA TTTT TTTC TTT- TTT- TTTCT TTTC TTTA TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTT
2443429 TACTTACTAT
Statistics
Matches: 108, Mismatches: 22, Indels: 22
0.71 0.14 0.14
Matches are distributed among these distances:
3 15 0.14
4 74 0.69
5 16 0.15
6 3 0.03
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:2443411 original size:15 final size:16
Alignment explanation
Indices: 2443391--2443420 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2443381 TTCTATATTT
2443391 TTTTCTTT-TTTTTTC
1 TTTTCTTTATTTTTTC
2443406 TTTTCTTTATTTTTT
1 TTTTCTTTATTTTTT
2443421 ATTTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTCTTTATTTTTTC
Found at i:2443420 original size:11 final size:11
Alignment explanation
Indices: 2443315--2443429 Score: 60
Period size: 11 Copynumber: 10.2 Consensus size: 11
2443305 ATATATTTAC
2443315 TTTT-TTTATT
1 TTTTATTTATT
2443325 TTTTATTTA-T
1 TTTTATTTATT
* *
2443335 ATATATATTA-T
1 TTTTAT-TTATT
2443346 TTTTACTTT-TT
1 TTTTA-TTTATT
2443357 TTATTATTTTATT
1 TT-TTA-TTTATT
*
2443370 TATTTGTTTATT
1 T-TTTATTTATT
*
2443382 TCTATATTT-TT
1 T-TTTATTTATT
* *
2443393 TTCTTTTTTTTT
1 TT-TTATTTATT
*
2443405 CTTTTCTTTATT
1 -TTTTATTTATT
2443417 TTTTATTTATT
1 TTTTATTTATT
2443428 TT
1 TT
2443430 ACTTACTATT
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
10 10 0.12
11 35 0.43
12 28 0.35
13 7 0.09
14 1 0.01
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:2443427 original size:46 final size:45
Alignment explanation
Indices: 2443314--2443472 Score: 137
Period size: 46 Copynumber: 3.4 Consensus size: 45
2443304 TATATATTTA
*
2443314 CTTTTTTTATTTTTTATTTATATATATATTATTTTTACTTTTTTT
1 CTTTTTTTATTTTTTATTTATTTATATATTATTTTTACTTTTTTT
* * * *
2443359 ATTATTTTATTTATTTGTTTATTTCTATATT-TTTTT-CTTTTTTTTT
1 CTTTTTTTATTT-TTTATTTATTTATATATTATTTTTAC--TTTTTTT
* *
2443405 CTTTTCTTTATTTTTTATTTATTT-TA-CTTACTATTTATCTTTGTTTT
1 CTTTT-TTTATTTTTTATTTATTTATATATTA-TTTTTA-CTTT-TTTT
* *
2443452 CTTTATCTTATCTTTTATTTA
1 CTTT-TTTTATTTTTTATTTA
2443473 ATTTGTTTTC
Statistics
Matches: 92, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
44 3 0.03
45 17 0.18
46 42 0.46
47 28 0.30
48 2 0.02
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (45 bp):
CTTTTTTTATTTTTTATTTATTTATATATTATTTTTACTTTTTTT
Found at i:2443534 original size:15 final size:15
Alignment explanation
Indices: 2443516--2443545 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2443506 TATTTATTTC
2443516 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2443531 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
2443546 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:2447911 original size:154 final size:155
Alignment explanation
Indices: 2447619--2447929 Score: 615
Period size: 154 Copynumber: 2.0 Consensus size: 155
2447609 AAATTGTCCG
2447619 TGACGTGAAGGAAAAGCTTGCTTATGTTGCCCTGGACTATGAGTAGGAACTGGAGACTGCCAAGA
1 TGACGTGAAGGAAAAGCTTGCTTATGTTGCCCTGGACTATGAGTAGGAACTGGAGACTGCCAAGA
2447684 GCAGCTCTTCTATTGAGAAGAACTATGAGATGCCTGTGAGCCCGACTTTAGTGGCGTCCAGTGGG
66 GCAGCTCTTCTATTGAGAAGAACTATGAGATGCCTGTGAGCCCGACTTTAGTGGCGTCCAGTGGG
2447749 AATTTTCCCTTAAGTGCATAAGACA
131 AATTTTCCCTTAAGTGCATAAGACA
2447774 TGACGTGAAGG-AAAGCTTGCTTATGTTGCCCTGGACTATGAGTAGGAACTGGAGACTGCCAAGA
1 TGACGTGAAGGAAAAGCTTGCTTATGTTGCCCTGGACTATGAGTAGGAACTGGAGACTGCCAAGA
2447838 GCAGCTCTTCTATTGAGAAGAACTATGAGATGCCTGTGAGCCCGACTTTAGTGGCGTCCAGTGGG
66 GCAGCTCTTCTATTGAGAAGAACTATGAGATGCCTGTGAGCCCGACTTTAGTGGCGTCCAGTGGG
2447903 AATTTTCCCTTAAGTGCATAAGACA
131 AATTTTCCCTTAAGTGCATAAGACA
2447928 TG
1 TG
2447930 CCAGGGATGG
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
154 145 0.93
155 11 0.07
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (155 bp):
TGACGTGAAGGAAAAGCTTGCTTATGTTGCCCTGGACTATGAGTAGGAACTGGAGACTGCCAAGA
GCAGCTCTTCTATTGAGAAGAACTATGAGATGCCTGTGAGCCCGACTTTAGTGGCGTCCAGTGGG
AATTTTCCCTTAAGTGCATAAGACA
Found at i:2448588 original size:35 final size:34
Alignment explanation
Indices: 2448542--2448674 Score: 176
Period size: 35 Copynumber: 3.8 Consensus size: 34
2448532 AGAAGAAAGA
*
2448542 AAGGAAGCATCGGCACTTTCGATTCAAGTGAACTG
1 AAGGAAGCATCGGCACTTTCGATTCAAGAGAAC-G
*
2448577 AAGGAAGCATCGGCACTTTCGATACAAGAAGAACG
1 AAGGAAGCATCGGCACTTTCGATTCAAG-AGAACG
* *
2448612 AAAGGAAGCTTCGGCACTTTCGATTTAAGAGAACAG
1 -AAGGAAGCATCGGCACTTTCGATTCAAGAGAAC-G
**
2448648 AAGGAAGCATAAGCACTTTCGATTCAA
1 AAGGAAGCATCGGCACTTTCGATTCAA
2448675 TTGTTCATCT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
35 56 0.65
36 30 0.35
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (34 bp):
AAGGAAGCATCGGCACTTTCGATTCAAGAGAACG
Found at i:2448651 original size:71 final size:71
Alignment explanation
Indices: 2448531--2448670 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 71
2448521 GAAGGTGAAT
* * **
2448531 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACTGAAGGAAGCATCGGCACTTT
1 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGAGAACAGAAGGAAGCATAAGCACTTT
2448596 CGATAC
66 CGATAC
* * *
2448602 AAGAAGAACGAAAGGAAGCTTCGGCACTTTCGATTTAAGAGAACAGAAGGAAGCATAAGCACTTT
1 AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGAGAACAGAAGGAAGCATAAGCACTTT
2448667 CGAT
66 CGAT
2448671 TCAATTGTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (71 bp):
AAGAAGAAAGAAAGGAAGCATCGGCACTTTCGATTCAAGAGAACAGAAGGAAGCATAAGCACTTT
CGATAC
Found at i:2449348 original size:32 final size:32
Alignment explanation
Indices: 2449312--2449375 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2449302 TTTGGGTGGG
2449312 ATGGAAAAAATTTGCCCTCTTTATGCTGATGT
1 ATGGAAAAAATTTGCCCTCTTTATGCTGATGT
2449344 ATGGAAAAAATTTGCCCTCTTTATGCTGATGT
1 ATGGAAAAAATTTGCCCTCTTTATGCTGATGT
2449376 GGAAAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (32 bp):
ATGGAAAAAATTTGCCCTCTTTATGCTGATGT
Found at i:2449381 original size:30 final size:31
Alignment explanation
Indices: 2449311--2449386 Score: 127
Period size: 32 Copynumber: 2.5 Consensus size: 31
2449301 ATTTGGGTGG
2449311 GATGGAAAAAATTTGCCCTCTTTATGCTGAT
1 GATGGAAAAAATTTGCCCTCTTTATGCTGAT
2449342 GTATGGAAAAAATTTGCCCTCTTTATGCTGAT
1 G-ATGGAAAAAATTTGCCCTCTTTATGCTGAT
*
2449374 G-TGGAAAACATTT
1 GATGGAAAAAATTT
2449387 ACCAATCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
30 11 0.26
31 1 0.02
32 31 0.72
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
GATGGAAAAAATTTGCCCTCTTTATGCTGAT
Found at i:2451564 original size:10 final size:10
Alignment explanation
Indices: 2451549--2451629 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 10
2451539 GTGTTTGTGT
2451549 TGTTCGTTTA
1 TGTTCGTTTA
2451559 TGTTCGTTTA
1 TGTTCGTTTA
2451569 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
2451582 TGTTCATTTA
1 TGTTCGTTTA
2451592 T-TAT-G-TT-
1 TGT-TCGTTTA
* *
2451599 CGTTCGTTTG
1 TGTTCGTTTA
*
2451609 TGTTTGTTTA
1 TGTTCGTTTA
2451619 TGTTCGTTTA
1 TGTTCGTTTA
2451629 T
1 T
2451630 CATTTAAATG
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
9 3 0.05
10 38 0.68
13 10 0.18
ACGTcount: A:0.10, C:0.09, G:0.20, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:2451575 original size:23 final size:23
Alignment explanation
Indices: 2451549--2451602 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
2451539 GTGTTTGTGT
* *
2451549 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCATTTATTA
2451572 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCATTTATTA
2451595 TGTTCGTT
1 TGTTCGTT
2451603 CGTTTGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTA
Found at i:2451618 original size:37 final size:36
Alignment explanation
Indices: 2451556--2451629 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
2451546 TGTTGTTCGT
2451556 TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
1 TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
* *
2451592 TTATGTTCGTTCGT-TTGTGTTTGTTTATGTTCGTTTA
1 TTATGTTCGTT--TATTGTGTTCGTTTATGTTCATTTA
2451629 T
1 T
2451630 CATTTAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 11 0.32
37 22 0.65
38 1 0.03
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (36 bp):
TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
Found at i:2457260 original size:35 final size:34
Alignment explanation
Indices: 2457212--2457277 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2457202 ACAAGATCAG
*
2457212 TCAACATCAGAAATTTTCAAAAATAAAAGAAGAAA
1 TCAACATCAGAAA-TGTCAAAAATAAAAGAAGAAA
* *
2457247 TCAA-ATCACGAAATGTCAAAATTAAATGAAG
1 TCAACATCA-GAAATGTCAAAAATAAAAGAAG
2457278 CGCATTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.70
35 8 0.30
ACGTcount: A:0.56, C:0.12, G:0.11, T:0.21
Consensus pattern (34 bp):
TCAACATCAGAAATGTCAAAAATAAAAGAAGAAA
Found at i:2457672 original size:16 final size:16
Alignment explanation
Indices: 2457651--2457688 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
2457641 CACAATGCAC
2457651 GGATTCAAACGGGCAT
1 GGATTCAAACGGGCAT
2457667 GGATTCAAACGGGCAT
1 GGATTCAAACGGGCAT
2457683 GGATTC
1 GGATTC
2457689 GACGCTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (16 bp):
GGATTCAAACGGGCAT
Found at i:2458099 original size:24 final size:24
Alignment explanation
Indices: 2458072--2458132 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
2458062 GTTCGTGAAT
2458072 GTTCAGTTATGTTCGTTTATGTTC
1 GTTCAGTTATGTTCGTTTATGTTC
* *
2458096 GTTCGGTTATATTCGTTTATGTTC
1 GTTCAGTTATGTTCGTTTATGTTC
* *
2458120 ATTCATTTATGTT
1 GTTCAGTTATGTT
2458133 TAACTCAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (24 bp):
GTTCAGTTATGTTCGTTTATGTTC
Found at i:2459000 original size:23 final size:23
Alignment explanation
Indices: 2458974--2459062 Score: 124
Period size: 23 Copynumber: 3.8 Consensus size: 23
2458964 TGGGGCAATG
*
2458974 TCGAGTTTGAATCGAGCTTAGAA
1 TCGAGTTTGAATCGAGCTCAGAA
2458997 TCGAGTTTGAATCGAGCTCAGAA
1 TCGAGTTTGAATCGAGCTCAGAA
* **
2459020 TCGAGTTTCAATCGAGCTCGAGTC
1 TCGAGTTTGAATCGAGCTC-AGAA
*
2459044 TCGAGTTTTAATCGAGCTC
1 TCGAGTTTGAATCGAGCTC
2459063 TTAGATTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 40 0.67
24 20 0.33
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (23 bp):
TCGAGTTTGAATCGAGCTCAGAA
Found at i:2459008 original size:11 final size:11
Alignment explanation
Indices: 2458974--2459035 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
2458964 TGGGGCAATG
2458974 TCGAGTTTGAA
1 TCGAGTTTGAA
*
2458985 TCGAGCTTAGAA
1 TCGAG-TTTGAA
2458997 TCGAGTTTGAA
1 TCGAGTTTGAA
**
2459008 TCGAGCTCAGAA
1 TCGAG-TTTGAA
*
2459020 TCGAGTTTCAA
1 TCGAGTTTGAA
2459031 TCGAG
1 TCGAG
2459036 CTCGAGTCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 23 0.55
12 19 0.45
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (11 bp):
TCGAGTTTGAA
Found at i:2459061 original size:47 final size:46
Alignment explanation
Indices: 2458974--2459062 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 46
2458964 TGGGGCAATG
* *
2458974 TCGAGTTTGAATCGAGCTTAGAATCGAGTTTGAATCGAGCTCAGAA
1 TCGAGTTTCAATCGAGCTGAGAATCGAGTTTGAATCGAGCTCAGAA
** *
2459020 TCGAGTTTCAATCGAGCTCGAGTCTCGAGTTTTAATCGAGCTC
1 TCGAGTTTCAATCGAGCT-GAGAATCGAGTTTGAATCGAGCTC
2459063 TTAGATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 17 0.46
47 20 0.54
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (46 bp):
TCGAGTTTCAATCGAGCTGAGAATCGAGTTTGAATCGAGCTCAGAA
Found at i:2460364 original size:17 final size:18
Alignment explanation
Indices: 2460327--2460364 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2460317 TCTTCTATCT
*
2460327 TTTGACATGTTTTCATCG
1 TTTGACATGTTGTCATCG
*
2460345 TTTGACA-GTTGTCTTCG
1 TTTGACATGTTGTCATCG
2460362 TTT
1 TTT
2460365 ATCTTTTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.13, C:0.16, G:0.18, T:0.53
Consensus pattern (18 bp):
TTTGACATGTTGTCATCG
Found at i:2464384 original size:22 final size:22
Alignment explanation
Indices: 2464343--2464385 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2464333 TCATTGCATA
2464343 AAAATTAAACAGTTATAACTCCT
1 AAAATTAAACAG-TATAACTCCT
2464366 AAAATTAAATCA-TATAACTC
1 AAAATTAAA-CAGTATAACTC
2464386 TTGTAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTAAACAGTATAACTCCT
Found at i:2472176 original size:16 final size:17
Alignment explanation
Indices: 2472141--2472177 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2472131 TTATGAGATG
2472141 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
2472158 AAAAAT-ATAATTATT-T
1 AAAAATAAT-ATTATTGT
2472174 AAAA
1 AAAA
2472178 TGATATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:2472271 original size:17 final size:16
Alignment explanation
Indices: 2472249--2472285 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2472239 CGAGATCATA
*
2472249 ATATTATTTTTTATATT
1 ATATTATATTTTATA-T
2472266 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2472282 ATAT
1 ATAT
2472286 AAATAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTATATTTTATAT
Found at i:2472694 original size:55 final size:55
Alignment explanation
Indices: 2472581--2472694 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
2472571 GTTACATTAC
* **
2472581 AGTAATGTTATTCTCAAATATAATCTTACATTCCGTGAACCAAACAACATATTCT
1 AGTAATGTTAGTCTCAAATATAATCTTACATTCCGTGAACCAAACAACATATAAT
* *
2472636 AGTAATGTTAGTCTCAAATATAATCTTACATTCCGTGAACCAAACATCCTATAAT
1 AGTAATGTTAGTCTCAAATATAATCTTACATTCCGTGAACCAAACAACATATAAT
2472691 AGTA
1 AGTA
2472695 CCCGAATTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (55 bp):
AGTAATGTTAGTCTCAAATATAATCTTACATTCCGTGAACCAAACAACATATAAT
Found at i:2473094 original size:27 final size:27
Alignment explanation
Indices: 2473064--2473120 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
2473054 AAGTTAAAAA
2473064 TCACTCTATAATAGATTTTTATAATAT
1 TCACTCTATAATAGATTTTTATAATAT
2473091 TCACTCTATAATAGATTTTTATAATAT
1 TCACTCTATAATAGATTTTTATAATAT
2473118 TCA
1 TCA
2473121 TTATAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (27 bp):
TCACTCTATAATAGATTTTTATAATAT
Found at i:2477893 original size:2 final size:2
Alignment explanation
Indices: 2477886--2477958 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
2477876 AATTCGGAAA
2477886 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
2477928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2477959 GGACTAAAAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2479254 original size:36 final size:34
Alignment explanation
Indices: 2479178--2479547 Score: 233
Period size: 35 Copynumber: 10.6 Consensus size: 34
2479168 AATATTTTCC
* *
2479178 CAAAACTTATATAATATATACTTTTAAAAATATTTT
1 CAAAAC-TATATATTATATA-TTTTAAAAATGTTTT
*
2479214 -AAAATTATATATTATATACTTTCTAAAAATGTTTT
1 CAAAACTATATATTATATA-TTT-TAAAAATGTTTT
*
2479249 CAAAA-T-TATA-TAGT-T-TTTAAAAAATGTTTTT
1 CAAAACTATATATTA-TATATTTTAAAAATG-TTTT
* * * *
2479280 TAAAACTATATATTATATGTTTTCAAAATGATTT
1 CAAAACTATATATTATATATTTTAAAAATGTTTT
* *
2479314 CAAAAACTATATAATATATTTATGTTTTCAAAATGTTTTT
1 C-AAAACTATAT-AT-TA--TATATTTTAAAAATGTT-TT
*
2479354 TAAAA--ACTATA-TATAT-TTTT-AAAATGTTTT
1 CAAAACTA-TATATTATATATTTTAAAAATGTTTT
* ** * *
2479384 AAAAACTATATAACATGTATTTTCAAAAATATTTT
1 CAAAACTATATATTATATATTTT-AAAAATGTTTT
* *
2479419 AAAAACTATATATTATATTAATTTTTAAAATGTTTTT
1 CAAAACTATATATTATA-T-ATTTTAAAAATG-TTTT
*
2479456 AAAAACTATATAATATATATATTTTCAAAAATGTTTT
1 CAAAACTATAT-AT-TATATATTTT-AAAAATGTTTT
* * * *
2479493 GAAAACCATATATTATATTAATTTTCAAAATGTCTT
1 CAAAACTATATATTATA-T-ATTTTAAAAATGTTTT
*
2479529 -AAGAACTATATAATATATA
1 CAA-AACTATATATTATATA
2479548 AATGTTTTCA
Statistics
Matches: 276, Mismatches: 27, Indels: 64
0.75 0.07 0.17
Matches are distributed among these distances:
30 13 0.05
31 23 0.08
32 9 0.03
33 15 0.05
34 28 0.10
35 67 0.24
36 36 0.13
37 47 0.17
38 12 0.04
39 24 0.09
40 2 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (34 bp):
CAAAACTATATATTATATATTTTAAAAATGTTTT
Found at i:2479320 original size:35 final size:34
Alignment explanation
Indices: 2479269--2479625 Score: 267
Period size: 37 Copynumber: 9.9 Consensus size: 34
2479259 TAGTTTTTAA
* *
2479269 AAAATGTTTTTTAAAACTATATATTATATGTTTTC
1 AAAATG-TTTTAAAAACTATATATTATATATTTTC
* *
2479304 AAAATGATTTCAAAAACTATATAATATATTTATGTTTTC
1 AAAATG-TTTTAAAAACTATAT-AT-TA--TATATTTTC
2479343 AAAATGTTTTTTAAAAAC--TATA-TATAT-TTTT-
1 AAAATG--TTTTAAAAACTATATATTATATATTTTC
** *
2479374 AAAATGTTTTAAAAACTATATAACATGTATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATTTTC
* *
2479408 AAAAATATTTTAAAAACTATATATTATATTAATTTTT
1 -AAAATGTTTTAAAAACTATATATTATA-T-ATTTTC
2479445 AAAATGTTTTTAAAAACTATATAATATATATATTTTC
1 AAAATG-TTTTAAAAACTATAT-AT-TATATATTTTC
* *
2479482 AAAAATGTTTTGAAAACCATATATTATATTAATTTTC
1 -AAAATGTTTTAAAAACTATATATTATA-T-ATTTTC
* * *
2479519 AAAATGTCTTAAGAACTATATAATATATAAATGTTTTC
1 AAAATGTTTTAAAAACTATAT-AT-TAT--ATATTTTC
* * *
2479557 AAACATGCTTTTCAAAATTATATATTATATATATATTA
1 AAA-ATG-TTTTAAAAACTATATATTATATAT-T-TTC
*
2479595 AAAATGTTTT-CAAACTATATACTGTATATAT
1 AAAATGTTTTAAAAACTATATA-T-TATATAT
2479626 ATATATATAG
Statistics
Matches: 264, Mismatches: 29, Indels: 56
0.76 0.08 0.16
Matches are distributed among these distances:
29 10 0.04
31 10 0.04
32 7 0.03
33 7 0.03
35 57 0.22
36 36 0.14
37 60 0.23
38 31 0.12
39 25 0.09
40 21 0.08
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
AAAATGTTTTAAAAACTATATATTATATATTTTC
Found at i:2479333 original size:40 final size:40
Alignment explanation
Indices: 2479287--2479374 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
2479277 TTTTAAAACT
2479287 ATATATTATATGTTTTCAAAATG-ATTTCAAAAACTATATA
1 ATATATT-TATGTTTTCAAAATGTATTTCAAAAACTATATA
* *
2479327 ATATATTTATGTTTTCAAAATGTTTTTTAAAAACTATAT-
1 ATATATTTATGTTTTCAAAATGTATTTCAAAAACTATATA
*
2479366 ATATTTTTA
1 ATATATTTA
2479375 AAATGTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 23 0.52
40 21 0.48
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (40 bp):
ATATATTTATGTTTTCAAAATGTATTTCAAAAACTATATA
Found at i:2479347 original size:74 final size:74
Alignment explanation
Indices: 2479263--2479615 Score: 340
Period size: 74 Copynumber: 4.9 Consensus size: 74
2479253 ATTATATAGT
* * *
2479263 TTTTAAAAAATGTTTTTTAAAACTATATATTATAT-GTTTTCAAAATGATTTCAAAAACTATATA
1 TTTTCAAAAATGTTTTTTAAAACTATATATTATATAATTTTCAAAATG-TTTTAAAAACTATATA
2479327 ATATATTTATG
65 ATATA-TTATG
2479338 TTTTC-AAAATGTTTTTTAAAA--ACTATA-TATAT--TTTT-AAAATGTTTTAAAAACTATATA
1 TTTTCAAAAATGTTTTTTAAAACTA-TATATTATATAATTTTCAAAATGTTTTAAAAACTATATA
* *
2479396 ACAT-GTA--
65 ATATATTATG
* * *
2479403 TTTTCAAAAAT-ATTTTAAAAACTATATATTATATTAATTTTTAAAATGTTTTTAAAAACTATAT
1 TTTTCAAAAATGTTTTTTAAAACTATATATTATA-TAATTTTCAAAATG-TTTTAAAAACTATAT
*
2479467 AATATA-TATA
64 AATATATTATG
* * * *
2479477 TTTTCAAAAATG-TTTTGAAAACCATATATTATATTAATTTTCAAAATGTCTTAAGAACTATATA
1 TTTTCAAAAATGTTTTTTAAAACTATATATTATA-TAATTTTCAAAATGTTTTAAAAACTATATA
*
2479541 ATATATAAATG
65 ATATAT-TATG
* * * * * * *
2479552 TTTTCAAACATGCTTTTCAAAATTATATATTATATATATATTAAAAATGTTTT-CAAACTATATA
1 TTTTCAAAAATGTTTTTTAAAACTATATATTATATA-ATTTTCAAAATGTTTTAAAAACTATATA
2479616 CTGTATATAT
Statistics
Matches: 237, Mismatches: 23, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
65 13 0.05
66 9 0.04
67 7 0.03
68 1 0.00
69 18 0.08
70 10 0.04
71 10 0.04
72 27 0.11
73 23 0.10
74 60 0.25
75 28 0.12
76 31 0.13
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (74 bp):
TTTTCAAAAATGTTTTTTAAAACTATATATTATATAATTTTCAAAATGTTTTAAAAACTATATAA
TATATTATG
Found at i:2481105 original size:2 final size:2
Alignment explanation
Indices: 2481098--2481140 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2481088 ATCTTAACGC
2481098 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
2481140 A
1 A
2481141 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2481145 original size:2 final size:2
Alignment explanation
Indices: 2481140--2481178 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2481130 ATATATATAT
2481140 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2481179 TATTATCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2483667 original size:32 final size:35
Alignment explanation
Indices: 2483595--2483675 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
2483585 ATCCTTTTAA
* *
2483595 ATTAATGCTCTAGC-AACTCTCTATATTATGTTAAT
1 ATTAATGCT-TAACAAACTCTCTATATTATGCTAAT
2483630 ATTAATGCTTAACAAACTCTCTATA-T-T-CTAAT
1 ATTAATGCTTAACAAACTCTCTATATTATGCTAAT
2483662 ATTAATGCTTAACA
1 ATTAATGCTTAACA
2483676 CTTTGCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 18 0.42
33 1 0.02
34 4 0.09
35 20 0.47
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (35 bp):
ATTAATGCTTAACAAACTCTCTATATTATGCTAAT
Found at i:2487932 original size:8 final size:8
Alignment explanation
Indices: 2487913--2488415 Score: 639
Period size: 8 Copynumber: 62.8 Consensus size: 8
2487903 CATGTAACAA
2487913 ATACACTAC
1 ATACA-TAC
2487922 ATACATAC
1 ATACATAC
*
2487930 ATATATAC
1 ATACATAC
2487938 ATACATAC
1 ATACATAC
2487946 ATACATAC
1 ATACATAC
*
2487954 ATATATAC
1 ATACATAC
2487962 ATACATAC
1 ATACATAC
*
2487970 ATGCATAC
1 ATACATAC
**
2487978 ATGTATAC
1 ATACATAC
*
2487986 ATGCATAC
1 ATACATAC
*
2487994 ATGCATAC
1 ATACATAC
*
2488002 ATGCATAC
1 ATACATAC
*
2488010 ATGCATAC
1 ATACATAC
*
2488018 ATGCATAC
1 ATACATAC
*
2488026 ATGCATAC
1 ATACATAC
*
2488034 ATGCATAC
1 ATACATAC
*
2488042 ATGCATAC
1 ATACATAC
*
2488050 ATGCATAC
1 ATACATAC
* *
2488058 AATGCA-GC
1 -ATACATAC
*
2488066 ATACATGC
1 ATACATAC
* *
2488074 ATGCATGC
1 ATACATAC
*
2488082 ATACATGC
1 ATACATAC
*
2488090 ATACATGC
1 ATACATAC
* *
2488098 ATGCATGC
1 ATACATAC
* *
2488106 ATGCATGC
1 ATACATAC
*
2488114 ATACATGC
1 ATACATAC
2488122 ATACATAC
1 ATACATAC
*
2488130 ATACATAT
1 ATACATAC
2488138 ATACATAC
1 ATACATAC
* *
2488146 ATGCATGC
1 ATACATAC
*
2488154 ATATATAC
1 ATACATAC
*
2488162 ATACATGC
1 ATACATAC
*
2488170 ATACATGC
1 ATACATAC
*
2488178 ATACATGC
1 ATACATAC
*
2488186 ATACATGC
1 ATACATAC
*
2488194 ATACATGC
1 ATACATAC
2488202 ATACATAC
1 ATACATAC
*
2488210 ATACATGC
1 ATACATAC
* *
2488218 ATGCATGC
1 ATACATAC
2488226 ATACATAC
1 ATACATAC
2488234 ATACATAC
1 ATACATAC
2488242 ATACATAC
1 ATACATAC
2488250 ATACATAC
1 ATACATAC
2488258 ATACATAC
1 ATACATAC
2488266 ATACATAC
1 ATACATAC
2488274 ATACATAC
1 ATACATAC
2488282 ATACATAC
1 ATACATAC
2488290 ATACATAC
1 ATACATAC
2488298 ATACATAC
1 ATACATAC
2488306 ATACATAC
1 ATACATAC
2488314 ATACATAC
1 ATACATAC
2488322 ATACATAC
1 ATACATAC
2488330 ATACATAC
1 ATACATAC
2488338 ATACATAC
1 ATACATAC
2488346 ATACATAC
1 ATACATAC
2488354 ATACATAC
1 ATACATAC
2488362 ATACATAC
1 ATACATAC
2488370 ATACATAC
1 ATACATAC
2488378 ATACATAC
1 ATACATAC
2488386 ATACATAC
1 ATACATAC
2488394 ATACATAC
1 ATACATAC
2488402 ATACATAC
1 ATACATAC
2488410 ATACAT
1 ATACAT
2488416 GTCATTATCA
Statistics
Matches: 464, Mismatches: 28, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
7 4 0.01
8 450 0.97
9 10 0.02
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.26
Consensus pattern (8 bp):
ATACATAC
Found at i:2488815 original size:20 final size:19
Alignment explanation
Indices: 2488791--2488858 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
2488781 TGTCCCATAG
*
2488791 GACCACTGATTGTTCCGAA
1 GACCACTGATTGTCCCGAA
2488810 GAACCACT-A-TGTCCCGAA
1 G-ACCACTGATTGTCCCGAA
* *
2488828 GGACCATTGTTTGTCCCGAA
1 -GACCACTGATTGTCCCGAA
2488848 TGACCACTGAT
1 -GACCACTGAT
2488859 AATCCCTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
18 13 0.33
19 3 0.08
20 23 0.59
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (19 bp):
GACCACTGATTGTCCCGAA
Found at i:2488832 original size:38 final size:38
Alignment explanation
Indices: 2488781--2488855 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
2488771 TCTGAATATT
*
2488781 TGTCCCATAGGACCACTGATTGTTCCGAA-GAACCACTA
1 TGTCCCATAGGACCACTGATTGTCCCGAATG-ACCACTA
* *
2488819 TGTCCCGA-AGGACCATTGTTTGTCCCGAATGACCACT
1 TGTCCC-ATAGGACCACTGATTGTCCCGAATGACCACT
2488856 GATAATCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 30 0.94
39 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (38 bp):
TGTCCCATAGGACCACTGATTGTCCCGAATGACCACTA
Found at i:2490239 original size:19 final size:19
Alignment explanation
Indices: 2490215--2490261 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
2490205 TTCCTTAACG
2490215 TGTGCATCGATGCACTACC
1 TGTGCATCGATGCACTACC
2490234 TGTGCATCGATGCACTACC
1 TGTGCATCGATGCACTACC
2490253 TGTGCATCG
1 TGTGCATCG
2490262 GTACACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (19 bp):
TGTGCATCGATGCACTACC
Found at i:2494128 original size:18 final size:18
Alignment explanation
Indices: 2494105--2494197 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
2494095 ACTGAATATT
2494105 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
2494123 TGTCCCAAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
2494142 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* * * *
2494161 TGTCCCGAAAGAACAATGTT
1 TGTCCCG-AAGGACCA-CTA
2494181 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2494198 GATAATCCCT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
18 23 0.38
19 15 0.25
20 22 0.37
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2494152 original size:38 final size:38
Alignment explanation
Indices: 2494104--2494197 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
2494094 CACTGAATAT
* *
2494104 TTGTCCCGAAGGACCACTATGTCCC-AAAGGACCACTGA
1 TTGTCCCGAAGGACCACTATGTCCCGAAA-GAACAATGA
* * *
2494142 TTGTTCCGAAGAACCACTATGTCCCGAAAGAACAATGT
1 TTGTCCCGAAGGACCACTATGTCCCGAAAGAACAATGA
2494180 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
2494198 GATAATCCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 45 0.94
39 3 0.06
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCGAAAGAACAATGA
Found at i:2494159 original size:20 final size:20
Alignment explanation
Indices: 2494104--2494200 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
2494094 CACTGAATAT
2494104 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
2494123 -TGTCCCAAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
2494142 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* * * *
2494161 -TGTCCCGAAAGAACAATGT
1 TTGTCCCGAAGGACCACTGA
2494180 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
2494200 T
1 T
2494201 AATCCCTCAA
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
18 28 0.47
19 2 0.03
20 30 0.50
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:2495182 original size:2 final size:2
Alignment explanation
Indices: 2495166--2495206 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2495156 CATGAATTAG
*
2495166 AT AT AT TT AT A- 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
2495207 TCATATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2514757 original size:17 final size:17
Alignment explanation
Indices: 2514735--2514771 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2514725 ATGAATATCT
2514735 AATTTGAAATAAAGCCC
1 AATTTGAAATAAAGCCC
2514752 AATTTGAAATAAAGCCC
1 AATTTGAAATAAAGCCC
2514769 AAT
1 AAT
2514772 GTATGTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (17 bp):
AATTTGAAATAAAGCCC
Found at i:2515417 original size:2 final size:2
Alignment explanation
Indices: 2515380--2515407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2515370 TTGCTCTGAA
2515380 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
2515408 GAATTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2516971 original size:22 final size:22
Alignment explanation
Indices: 2516941--2516989 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2516931 GCACTATTGC
2516941 AAGTATAATGGTTAATTTTAGA
1 AAGTATAATGGTTAATTTTAGA
* **
2516963 AAGTGTAATGGTTTTTTTTAGA
1 AAGTATAATGGTTAATTTTAGA
2516985 AAGTA
1 AAGTA
2516990 AATTACGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (22 bp):
AAGTATAATGGTTAATTTTAGA
Found at i:2519542 original size:15 final size:15
Alignment explanation
Indices: 2519524--2519553 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2519514 TAAGTTGTAA
2519524 AATTTAAAATATATT
1 AATTTAAAATATATT
*
2519539 AATTTAAACTATATT
1 AATTTAAAATATATT
2519554 TAAATTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAAATATATT
Found at i:2522530 original size:21 final size:20
Alignment explanation
Indices: 2522506--2522549 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2522496 TAAATGTTTT
2522506 TTAATTCAAAAAAAATTATAA
1 TTAATTCAAAAAAAA-TATAA
* * *
2522527 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAAAATATAA
2522547 TTA
1 TTA
2522550 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTCAAAAAAAATATAA
Found at i:2522714 original size:184 final size:182
Alignment explanation
Indices: 2522486--2522869 Score: 594
Period size: 184 Copynumber: 2.1 Consensus size: 182
2522476 TTTTCTAATT
* * *
2522486 TATATAA-AAATAAATGTTTTTTAATTCAAAAAAAATTATAATTAATTTAAATAATATATAATTA
1 TATATAATATATAAATATTTTTTAATTCAAAAAAAATTATAATTAATTTAAATAAAATATAATTA
*
2522550 TAAAATAAAAATGTCAGATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGG
66 TAAAATAAAAATGTCAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGG
* * * *
2522615 ATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTAGTTTATATGTTA
131 ATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGTCTATATGTTA
*
2522667 TATATAATATATATAATATTTTTTAATT-AAAAAATAGTTTATAATTAATTTAAATAAAATATAA
1 TATATAATATATA-AATATTTTTTAATTCAAAAAA-A-ATTATAATTAATTTAAATAAAATATAA
* * * *
2522731 TTATAAAATAAAAATTTTATATAATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
63 TTATAAAATAAAAATGTCAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
2522796 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGTCTATATGTTA
128 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGTCTATATGTTA
*
2522851 TATATAATATTTAAA-ATTT
1 TATATAATATATAAATATTT
2522870 AATTTCGGTT
Statistics
Matches: 185, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
181 7 0.04
182 14 0.08
183 16 0.09
184 148 0.80
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (182 bp):
TATATAATATATAAATATTTTTTAATTCAAAAAAAATTATAATTAATTTAAATAAAATATAATTA
TAAAATAAAAATGTCAGATAATTTTTTAAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGG
ATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGTCTATATGTTA
Found at i:2538681 original size:252 final size:239
Alignment explanation
Indices: 2538212--2538703 Score: 842
Period size: 252 Copynumber: 2.0 Consensus size: 239
2538202 ATACATTAAC
*
2538212 ATAAGGATGTAAATATGATAACTTACGACACATAACATTAAATAACATCATTAATAGCAGAATTG
1 ATAAGGATGTAAATATGATAACTTACGACACATAACATTAAATAAAATCATTAATAGCAGAATTG
2538277 ATTAAGAAGTTTTATCTTCGTAATCAGTAAACTCGTCAGAAATAAGATTAAATTTCAATTCCCCA
66 ATTAAGAAGTTTTATCTTCGTAATCAGTAAACTCGTCAGAAATAAGATTAAATTTCAATTCCCCA
2538342 TTCTTTTGTTATTGGAATTAGCTTTTGGGTCTCCATCATCTGTTTTGTCTTGGTCATTTGTCTGA
131 TTCTTTTGTTATTGGAATTAGCTTTTGGGTCTCCATCATCTGTTTTGTCTTGGTCATTTGTCTGA
2538407 GTTGGTGGGATATTCGAGCTAGAAGCGACATCGTCAATGCTACA
196 GTTGGTGGGATATTCGAGCTAGAAGCGACATCGTCAATGCTACA
2538451 ATAAGGATGTAAATATGATAACTTTACGAACACCATAAACATTAAATAAAATCATTAACATAGCA
1 ATAAGGATGTAAATATGATAAC-TTACG-ACA-CAT-AACATTAAATAAAATCATT-A-ATAGCA
2538516 -ATATTGATTAAGAAGTTTTAATCTTCGTAATCAGTAAACTCGTCAGAAATAAGATTAAATTCTT
60 GA-ATTGATTAAGAAGTTTT-ATCTTCGTAATCAGTAAACTCGTCAGAAATAAGATTAAA-T-TT
2538580 CAATTCCCCATTCTTTTTGTTATTGGAATTATGCTTTTGGGTCTCCATCATCTATGTTTTGTCTT
121 CAATTCCCCATTC-TTTTGTTATTGGAATTA-GCTTTTGGGTCTCCATCATC--TGTTTTGTCTT
2538645 GGTCATTTGTCTGAGTTGGTGGGATATTCGAGCTAGAAGCGACATCGTCAATGCTACA
182 GGTCATTTGTCTGAGTTGGTGGGATATTCGAGCTAGAAGCGACATCGTCAATGCTACA
2538703 A
1 A
2538704 GCAAGGTGGA
Statistics
Matches: 238, Mismatches: 1, Indels: 15
0.94 0.00 0.06
Matches are distributed among these distances:
239 22 0.09
240 5 0.02
241 3 0.01
242 3 0.01
243 18 0.08
244 2 0.01
245 23 0.10
246 39 0.16
247 1 0.00
248 15 0.06
249 17 0.07
250 20 0.08
252 70 0.29
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (239 bp):
ATAAGGATGTAAATATGATAACTTACGACACATAACATTAAATAAAATCATTAATAGCAGAATTG
ATTAAGAAGTTTTATCTTCGTAATCAGTAAACTCGTCAGAAATAAGATTAAATTTCAATTCCCCA
TTCTTTTGTTATTGGAATTAGCTTTTGGGTCTCCATCATCTGTTTTGTCTTGGTCATTTGTCTGA
GTTGGTGGGATATTCGAGCTAGAAGCGACATCGTCAATGCTACA
Found at i:2542610 original size:125 final size:126
Alignment explanation
Indices: 2542388--2542639 Score: 472
Period size: 125 Copynumber: 2.0 Consensus size: 126
2542378 AATTTTTAAG
2542388 ATATAGTAACCCAACATCACGTGATCCAAAGTTAGATTATTATTGGTAAACAGGGACGGAGCTCC
1 ATATAGTAACCCAACATCACGTGATCCAAAGTTAGATTATTATTGGTAAACAGGGACGGAGCTCC
*
2542453 CTTACGGCCCAAAGGGACCCCGACCCTGTTAAGATTTG-ATATTCGATATGATTTTAGTTT
66 CTTACGACCCAAAGGGACCCCGACCCTGTTAAGATTTGTATATTCGATATGATTTTAGTTT
2542513 ATATAGTAACCCAACATCACGTGATCCAAAGTTAGATTATTATTGGTAAACAGGGACGGAGCTCC
1 ATATAGTAACCCAACATCACGTGATCCAAAGTTAGATTATTATTGGTAAACAGGGACGGAGCTCC
2542578 CTTACGACCCAAAGGGA-CCCGACCCCTGTTAAGATTTGTATATTCGATATGATTTTAGTTT
66 CTTACGACCCAAAGGGACCCCGA-CCCTGTTAAGATTTGTATATTCGATATGATTTTAGTTT
2542639 A
1 A
2542640 ATAATATTTT
Statistics
Matches: 124, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
124 5 0.04
125 96 0.77
126 23 0.19
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (126 bp):
ATATAGTAACCCAACATCACGTGATCCAAAGTTAGATTATTATTGGTAAACAGGGACGGAGCTCC
CTTACGACCCAAAGGGACCCCGACCCTGTTAAGATTTGTATATTCGATATGATTTTAGTTT
Done.