Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 190 of 214
Found at i:55762988 original size:9 final size:9
Alignment explanation
Indices: 55762974--55763013 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
55762964 GTAGTGATTC
55762974 AATTCGGTT
1 AATTCGGTT
55762983 AATTCGGTT
1 AATTCGGTT
55762992 AATTCTGG-T
1 AATTC-GGTT
*
55763001 AATTCAGTT
1 AATTCGGTT
55763010 AATT
1 AATT
55763014 TTTAACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.89
10 2 0.07
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55766193 original size:16 final size:16
Alignment explanation
Indices: 55766172--55766205 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55766162 GTCAGTGTTT
*
55766172 TTTAGCATTTTTATTA
1 TTTAGCATTATTATTA
*
55766188 TTTAGCCTTATTATTA
1 TTTAGCATTATTATTA
55766204 TT
1 TT
55766206 GTTGTTGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAGCATTATTATTA
Found at i:55766402 original size:17 final size:18
Alignment explanation
Indices: 55766373--55766409 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55766363 TTTTTTTATT
55766373 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
55766391 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
55766408 TT
1 TT
55766410 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:55772972 original size:100 final size:100
Alignment explanation
Indices: 55772799--55774225 Score: 1911
Period size: 100 Copynumber: 14.3 Consensus size: 100
55772789 AAACCATAGT
* **
55772799 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTTCAGGCAATGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * * **
55772864 TTGAAGCTACGACGGTGAACCTCACTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * *
55772899 TTGCAATTTAAAAGATTGAAGCCACAGCGGCAAATCTTACATTCCAGGCGGTGCAGCGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
*
55772964 TTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * *
55772999 TTACAATTAAAAATATTGAAGCTACAACGGTGAATCATACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * * ** * *
55773064 TTGAAACTACGACGGTGAATCTCACTTCCTCAACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * * * *
55773099 ATGCAATTTAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCAGGCGGTGCAGCGAAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* *
55773164 TTGAAGCTACAACGGTGAATCTTGCTTCCCCAACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * *
55773199 TTGCAATTAAAAAGATTGAAGCTACAATGGCGAATCTTACTTTCCAGGTGGTCCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
*
55773264 TTGAAGCTACAACAGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * **
55773299 TTGCAATTAAAAAGATTGAAGTTACAATGGCGAATCTTACATTCCAGGCGGTGCAGCAAAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * *
55773364 TTAAAACTACAACGGTGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
55773399 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGAAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * * *
55773464 TTGAAGCTACGACGGCGTATCTTACTTCCCCGATA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * * * *
55773499 TTGCAATTAAAAAGATTAAAGCTACAATGACGAATCTTACTTTTCAAGCGGTGCAGTGAAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
55773564 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * *
55773599 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTTCAGGCGGTGTAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * * *
55773664 TTAAAGTTACAACGGCGAATTTTGTTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * *
55773699 TTGCAATTAAAAAGATTGAAGCTACAATGGCTAATCTTACTTTCCAGGCGGTGCAGCGGAACAAA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* * *
55773764 TTGAAGCTACAACGGCGAATCTTGTTTCACTGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* *
55773799 TTGCAATTAAAAAGATTGAAGCTACAATGGCGAATCTTACTTTCTAGGCGGTGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
55773864 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * **
55773899 TTGCAATTAAAAAGATTGAAGTTACAATGGCGAATCTTACATTCCAGGCGGTGCAGCAAAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* *
55773964 TTAAAACTACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * *
55773999 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGAAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* ** *
55774064 TTGAAGCTACGACGGCGAATCTCACTTCCTCGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
* * * * *
55774099 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCAGTGCAGCAGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
* *
55774164 TTGAAGCTACAACGGTGAATCTTGCTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
*
55774199 TTACAATTAAAAAGATT-AATGCTACAA
1 TTGCAATTAAAAAGATTGAA-GCTACAA
55774226 GTCAGAACTC
Statistics
Matches: 1166, Mismatches: 160, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
99 2 0.00
100 1164 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACGGCGAATCTTACTTTCCAGGCGGTGCAGCGGAACAGA
TTGAAGCTACAACGGCGAATCTTGCTTCCCCGACA
Found at i:55775904 original size:17 final size:18
Alignment explanation
Indices: 55775875--55775911 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55775865 TTTTTTTATT
55775875 TTATATAGATATAAATAC
1 TTATATAGATATAAATAC
*
55775893 TTATAT-GATATATATAC
1 TTATATAGATATAAATAC
55775910 TT
1 TT
55775912 TACACTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TTATATAGATATAAATAC
Found at i:55778613 original size:24 final size:23
Alignment explanation
Indices: 55778582--55778731 Score: 106
Period size: 26 Copynumber: 6.2 Consensus size: 23
55778572 AAAACAAAAC
* **
55778582 AATATATAGAACAATTTGGAGTA
1 AATATATAAAACAATTTAAAGTA
55778605 AATAGTATAAAACAATTTAAAGTA
1 AATA-TATAAAACAATTTAAAGTA
* *
55778629 AATAATATGTAAAACAAATTAAAATA
1 AAT-ATA--TAAAACAATTTAAAGTA
*
55778655 AATAATATACAAAGCAATTTAAAATA
1 AAT-ATATA-AAA-CAATTTAAAGTA
* *
55778681 AATAACATATAAGACAATTTAAAAT-
1 AAT---ATATAAAACAATTTAAAGTA
* *
55778706 AATATATAAAA-ATTTTAAAATA
1 AATATATAAAACAATTTAAAGTA
55778728 AATA
1 AATA
55778732 ATATGTAAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.08
22 11 0.10
23 4 0.04
24 23 0.21
25 7 0.06
26 47 0.44
27 2 0.02
28 5 0.05
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (23 bp):
AATATATAAAACAATTTAAAGTA
Found at i:55778650 original size:26 final size:26
Alignment explanation
Indices: 55778605--55778976 Score: 292
Period size: 26 Copynumber: 14.1 Consensus size: 26
55778595 ATTTGGAGTA
*
55778605 AATAGTATAAAACAATTTAAAGTAAAT
1 AATA-TATAAAACAATTTAAAATAAAT
* *
55778632 AATATGTAAAACAAATTAAAATAAAT
1 AATATATAAAACAATTTAAAATAAAT
* *
55778658 AATATACAAAGCAATTTAAAATAAAT
1 AATATATAAAACAATTTAAAATAAAT
* *
55778684 AACATATAAGACAATTT---A-AAAT
1 AATATATAAAACAATTTAAAATAAAT
*
55778706 AATATATAAAA-ATTTTAAAATAAAT
1 AATATATAAAACAATTTAAAATAAAT
* *
55778731 AATATGTAAAAAGAAGTTTAAAATAAAT
1 AATATAT-AAAACAA-TTTAAAATAAAT
* * *
55778759 AATGTACAAAACAGTTTAAAAATAAAT
1 AATATATAAAACAATTT-AAAATAAAT
*
55778786 GATATATATAAAAAACAATTCAAAATAAAT
1 -A-ATATAT--AAAACAATTTAAAATAAAT
**
55778816 AATATATATGACAATTTAAAAATAAAT
1 AATATATAAAACAATTT-AAAATAAAT
* **
55778843 AATATATAAAAAAATTTAAAATGGAT
1 AATATATAAAACAATTTAAAATAAAT
* * * * *
55778869 AATAGTTTGAAATAGTTTAAAATACAT
1 AATA-TATAAAACAATTTAAAATAAAT
* * ** *
55778896 GATATGTGGAA-AACTTAAAATAAAT
1 AATATATAAAACAATTTAAAATAAAT
55778921 AATA-ATAAAACAATTTAAAATAAAT
1 AATATATAAAACAATTTAAAATAAAT
*
55778946 AATAAATGAGAAA-AAGGTTTAAAATAAAT
1 AATATAT-A-AAACAA--TTTAAAATAAAT
55778975 AA
1 AA
55778977 ATAACAAATT
Statistics
Matches: 275, Mismatches: 50, Indels: 38
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.01
22 13 0.05
23 1 0.00
24 4 0.01
25 41 0.15
26 86 0.31
27 64 0.23
28 26 0.09
29 19 0.07
30 9 0.03
31 8 0.03
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
AATATATAAAACAATTTAAAATAAAT
Found at i:55778719 original size:20 final size:23
Alignment explanation
Indices: 55778680--55778728 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
55778670 AATTTAAAAT
55778680 AAATAACATATAAGACAA-TTTA
1 AAATAACATATAAGACAATTTTA
*
55778702 AAATAATATATAA-A-AATTTTA
1 AAATAACATATAAGACAATTTTA
55778723 AAATAA
1 AAATAA
55778729 ATAATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATAACATATAAGACAATTTTA
Found at i:55778777 original size:75 final size:74
Alignment explanation
Indices: 55778628--55778864 Score: 192
Period size: 75 Copynumber: 3.1 Consensus size: 74
55778618 AATTTAAAGT
* * *
55778628 AAATAATATGTAAAACAAATTAAAATAAATAATATACAAAGCAATTTAAAATAAATAACATATAA
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAAGCAATTTAAAATAAATAACATACAA
*
55778693 GACAATTTA
66 AACAATTTA
** **
55778702 AAATAATATATAAAA-ATTTTAAAATAAATAATATGTAAAAAG-AAGTTTAAAATAAATAATGTA
1 AAATAATATATAAAACAAATTAAAATAAATAATA--TAAAAAGCAA-TTTAAAATAAATAACATA
*
55778765 CAAAACAGTTTAAAAA
63 CAAAACAATTT----A
* * *
55778781 TAAATGATATATATAAAAAACAATTCAAAATAAATAATAT-ATATGACAATTTAAAAATAAATAA
1 -AAAT-A-ATATATAAAACA-AATT-AAAATAAATAATATAAAAAG-CAATTT-AAAATAAATAA
* * *
55778845 TATATAAAAAAATTTA
59 CATACAAAACAATTTA
55778861 AAAT
1 AAAT
55778865 GGATAATAGT
Statistics
Matches: 130, Mismatches: 17, Indels: 27
0.75 0.10 0.16
Matches are distributed among these distances:
73 16 0.12
74 16 0.12
75 30 0.23
79 5 0.04
80 5 0.04
81 1 0.01
82 13 0.10
83 5 0.04
84 26 0.20
85 13 0.10
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (74 bp):
AAATAATATATAAAACAAATTAAAATAAATAATATAAAAAGCAATTTAAAATAAATAACATACAA
AACAATTTA
Found at i:55778811 original size:57 final size:56
Alignment explanation
Indices: 55778702--55778856 Score: 172
Period size: 57 Copynumber: 2.8 Consensus size: 56
55778692 AGACAATTTA
* * * * * *
55778702 AAATAATATA-TAAA-AATTTTAAAATAAATAATATGTAAAAAGA-AGTTTAAAAT
1 AAATAATATACAAAACAATTTAAAAATAAATAATATATAAAAAAACAATTCAAAAT
* * *
55778755 AAATAATGTACAAAACAGTTTAAAAATAAATGATATATATAAAAAACAATTCAAAAT
1 AAATAATATACAAAACAATTTAAAAATAAATAATATATA-AAAAAACAATTCAAAAT
* **
55778812 AAATAATATATATGACAATTTAAAAATAAATAATATATAAAAAAA
1 AAATAATATACAAAACAATTTAAAAATAAATAATATATAAAAAAA
55778857 TTTAAAATGG
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
53 9 0.11
54 3 0.04
55 19 0.23
56 11 0.13
57 41 0.49
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (56 bp):
AAATAATATACAAAACAATTTAAAAATAAATAATATATAAAAAAACAATTCAAAAT
Found at i:55778819 original size:110 final size:104
Alignment explanation
Indices: 55778605--55778976 Score: 307
Period size: 110 Copynumber: 3.5 Consensus size: 104
55778595 ATTTGGAGTA
* *
55778605 AATAGTATAAAACAATTTAAAGTAAATAATATGTAAAACAAA--TTAAAATAAATAATA-TACAA
1 AATA-TATAAAA-ATTTTAAAATAAATAATATGTAAAA-AAAGTTTAAAATAAATAATAGTACAA
* * * * * *
55778667 AGCAATTTAAAATAAATAACATATAAGACAA-TT--TA-AAAT
63 AACAGTTTAAAATAAATGATATATAA-AAAACTTAAAATAAAT
55778706 AATATATAAAAATTTTAAAATAAATAATATGTAAAAAGAAGTTTAAAATAAATAAT-GTACAAAA
1 AATATATAAAAATTTTAAAATAAATAATATGTAAAAA-AAGTTTAAAATAAATAATAGTACAAAA
55778770 CAGTTTAAAAATAAATGATATATATAAAAAACAATTCAAAATAAAT
65 CAGTTT-AAAATAAATG--ATATATAAAAAAC--TT-AAAATAAAT
* * * ** ***
55778816 AATATATATGACAATTTAAAAATAAATAATATATAAAAAAA-TTTAAAATGGATAATAGTTTGAA
1 AATATATA--AAAATTTTAAAATAAATAATATGTAAAAAAAGTTTAAAATAAATAATAGTACAAA
* * * **
55778880 ATAGTTTAAAATACATGATATGTGGAAAACTTAAAATAAAT
64 ACAGTTTAAAATAAATGATATATAAAAAACTTAAAATAAAT
* *
55778921 AATA-ATAAAACAATTTAAAATAAATAATAAATG-AGAAAAAGGTTTAAAATAAATAA
1 AATATATAAAA-ATTTTAAAATAAATAAT--ATGTA-AAAAAAGTTTAAAATAAATAA
55778977 ATAACAAATT
Statistics
Matches: 221, Mismatches: 28, Indels: 39
0.77 0.10 0.14
Matches are distributed among these distances:
98 1 0.00
99 25 0.11
100 7 0.03
101 29 0.13
102 11 0.05
103 18 0.08
104 11 0.05
105 20 0.09
106 16 0.07
108 10 0.05
109 1 0.00
110 34 0.15
111 12 0.05
112 26 0.12
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (104 bp):
AATATATAAAAATTTTAAAATAAATAATATGTAAAAAAAGTTTAAAATAAATAATAGTACAAAAC
AGTTTAAAATAAATGATATATAAAAAACTTAAAATAAAT
Found at i:55778945 original size:29 final size:29
Alignment explanation
Indices: 55778913--55778980 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
55778903 GGAAAACTTA
*
55778913 AAATAAATAATAATAAAACA-ATTTAAAAT
1 AAATAAATAATAAGAAAA-AGATTTAAAAT
* *
55778942 AAAT-AATAAATGAGAAAAAGGTTTAAAAT
1 AAATAAAT-AATAAGAAAAAGATTTAAAAT
55778971 AAATAAATAA
1 AAATAAATAA
55778981 CAAATTTGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 4 0.12
29 26 0.79
30 3 0.09
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (29 bp):
AAATAAATAATAAGAAAAAGATTTAAAAT
Found at i:55779797 original size:18 final size:17
Alignment explanation
Indices: 55779770--55779804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55779760 TAAAAAGGAT
55779770 AAACAGAAAACAAAAAA
1 AAACAGAAAACAAAAAA
*
55779787 AAACGAGAAAAGAAAAAA
1 AAAC-AGAAAACAAAAAA
55779805 GAGCAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (17 bp):
AAACAGAAAACAAAAAA
Found at i:55787038 original size:27 final size:27
Alignment explanation
Indices: 55786997--55787060 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
55786987 TTTAAATTAA
55786997 AAATTCTTAAAAATA-AAAACAAAAAAAT
1 AAATT-TTAAAAATATAAAA-AAAAAAAT
* * *
55787025 ATATTTTAAAAATATAAAATATAAAAT
1 AAATTTTAAAAATATAAAAAAAAAAAT
55787052 AAATTTTAA
1 AAATTTTAA
55787061 TCTCTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATTTTAAAAATATAAAAAAAAAAAT
Found at i:55787684 original size:30 final size:30
Alignment explanation
Indices: 55787643--55787731 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
55787633 AACTTTTAAG
*
55787643 ATTTTTAAAAATAAAAAAATTTATAAATTT
1 ATTTTTTAAAATAAAAAAATTTATAAATTT
* * *
55787673 ATTTTTTAAAATTAAAAAGTATA-AAATTT
1 ATTTTTTAAAATAAAAAAATTTATAAATTT
* * * *
55787702 ATTTTCTAAAA-AATAATATTTTTAAATTT
1 ATTTTTTAAAATAAAAAAATTTATAAATTT
55787731 A
1 A
55787732 AAAAATCAAT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 5 0.11
29 23 0.49
30 19 0.40
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTTTTTAAAATAAAAAAATTTATAAATTT
Found at i:55793712 original size:7 final size:8
Alignment explanation
Indices: 55793683--55793710 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
55793673 AAATGCGTAC
55793683 AAAAAGAA
1 AAAAAGAA
55793691 AAAAAGAA
1 AAAAAGAA
55793699 AAAAAGAA
1 AAAAAGAA
55793707 AAAA
1 AAAA
55793711 GAGAGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:55806445 original size:85 final size:84
Alignment explanation
Indices: 55806315--55806503 Score: 227
Period size: 85 Copynumber: 2.2 Consensus size: 84
55806305 TTTAAAAAAA
* * * *
55806315 AAAAAAAGCAATTAAGTCCCTCTTTTTTTGTATTCAATTAAGTACTTGAACTTTCAAAATATATC
1 AAAAAAAGCAATTAAG-CCCTATTTTTTTGCACTCAATTAAGTACTTAAACTTTCAAAATATAT-
* *
55806380 AAAAAAGCCCTCAAACTTCTTT
64 AAAAAAACCCTCAAAATT-TTT
** * *
55806402 AAAAAAAGCAATTAAGCCCTATTTTTTT-CACTCAATTGGGTACTTAAACTTTTAAAATGTATAA
1 AAAAAAAGCAATTAAGCCCTATTTTTTTGCACTCAATTAAGTACTTAAACTTTCAAAATATATAA
55806466 AAAAACCCTCAAAATTTTT
66 AAAAACCCTCAAAATTTTT
* * *
55806485 CAAATAAGAAATTAAGCCC
1 AAAAAAAGCAATTAAGCCC
55806504 CTGCTCTTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
83 19 0.21
84 16 0.18
85 27 0.30
86 11 0.12
87 16 0.18
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (84 bp):
AAAAAAAGCAATTAAGCCCTATTTTTTTGCACTCAATTAAGTACTTAAACTTTCAAAATATATAA
AAAAACCCTCAAAATTTTT
Found at i:55806794 original size:19 final size:19
Alignment explanation
Indices: 55806755--55806795 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
55806745 TTTTTTAATG
**
55806755 ATTTTTATAAAATTTTATA
1 ATTTTTATAAAAAATTATA
*
55806774 ATTTTTATAAAAAATTCTA
1 ATTTTTATAAAAAATTATA
55806793 ATT
1 ATT
55806796 CTTAATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTATAAAAAATTATA
Found at i:55806853 original size:10 final size:11
Alignment explanation
Indices: 55806838--55806863 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55806828 AAATTTATTG
55806838 TTTTTTGTAAT
1 TTTTTTGTAAT
55806849 TTTTTTGTAAT
1 TTTTTTGTAAT
55806860 TTTT
1 TTTT
55806864 AATAAGAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTGTAAT
Found at i:55810439 original size:17 final size:17
Alignment explanation
Indices: 55810417--55810480 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
55810407 CATCAAATGC
*
55810417 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
55810434 TACAATTAGAA-CTCTAA
1 TACAATTAGAAGCTGT-A
*
55810451 GACATAATTAGAAGCTGTA
1 TAC--AATTAGAAGCTGTA
55810470 TACAATTAGAA
1 TACAATTAGAA
55810481 CTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:55810461 original size:19 final size:17
Alignment explanation
Indices: 55810435--55810488 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
55810425 AAAGCTGTAT
55810435 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
55810452 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
55810471 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
55810488 A
1 A
55810489 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:55810467 original size:36 final size:36
Alignment explanation
Indices: 55810420--55810488 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
55810410 CAAATGCTAC
55810420 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
*
55810456 AATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
55810489 TTAAATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
Found at i:55813123 original size:17 final size:17
Alignment explanation
Indices: 55813101--55813164 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
55813091 CATCAAAGGC
*
55813101 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
55813118 TACAATTAGAA-CTCTAA
1 TACAATTAGAAGCTGT-A
*
55813135 GACATAATTAGAAGCTGTA
1 TAC--AATTAGAAGCTGTA
55813154 TACAATTAGAA
1 TACAATTAGAA
55813165 CTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 21 0.55
19 11 0.29
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:55813145 original size:19 final size:17
Alignment explanation
Indices: 55813119--55813172 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
55813109 AAAGCTGTAT
55813119 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
55813136 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
55813155 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
55813172 A
1 A
55813173 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:55813151 original size:36 final size:36
Alignment explanation
Indices: 55813104--55813172 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
55813094 CAAAGGCTAC
55813104 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
*
55813140 AATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
55813173 TTAAATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
Found at i:55813525 original size:3 final size:3
Alignment explanation
Indices: 55813512--55813549 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
55813502 TAGTTGTAAT
55813512 ACA ATCA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA A-CA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
55813550 AAACCAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.32, G:0.00, T:0.03
Consensus pattern (3 bp):
ACA
Found at i:55816290 original size:19 final size:20
Alignment explanation
Indices: 55816263--55816300 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
55816253 TTGTAAAGGT
*
55816263 TATATTTTA-ATATCTAAAA
1 TATAATTTATATATCTAAAA
*
55816282 TATAATTTATATATTTAAA
1 TATAATTTATATATCTAAA
55816301 TTAAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTTATATATCTAAAA
Found at i:55824911 original size:16 final size:16
Alignment explanation
Indices: 55824877--55824914 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
55824867 AATAAAAAAT
55824877 AAAAAATATTACCCAA
1 AAAAAATATTACCCAA
55824893 AAAAACATATTACCCAA
1 AAAAA-ATATTACCCAA
55824910 AAAAA
1 AAAAA
55824915 GAGGGGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATATTACCCAA
Found at i:55826324 original size:11 final size:11
Alignment explanation
Indices: 55826286--55826330 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
55826276 AATTTATTCT
55826286 AAAA-ATTTT-
1 AAAATATTTTA
55826295 AAAAT-TTTTA
1 AAAATATTTTA
55826305 AAAATTATTTTA
1 AAAA-TATTTTA
55826317 AAAATATTTTA
1 AAAATATTTTA
55826328 AAA
1 AAA
55826331 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.25
10 4 0.12
11 11 0.34
12 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:55826331 original size:32 final size:31
Alignment explanation
Indices: 55826273--55826332 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
55826263 ATAAAATACC
55826273 AAAAATTTATTCTAAAAATTTTAAAATTTTT
1 AAAAATTTATTCTAAAAATTTTAAAATTTTT
*
55826304 AAAAA-TTATTTTAAAAATATTTTAAAATT
1 AAAAATTTATTCT-AAAA-ATTTTAAAATT
55826333 AAAAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.23
31 9 0.35
32 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
AAAAATTTATTCTAAAAATTTTAAAATTTTT
Found at i:55826335 original size:29 final size:28
Alignment explanation
Indices: 55826302--55826379 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
55826292 TTTAAAATTT
55826302 TTAAAAATTATTTTAAAAATA-TTTTAAAA
1 TTAAAAA--ATTTTAAAAATATTTTTAAAA
*
55826331 TTAAAAAAATTTAAAAAAGTATTTTTAAAA
1 TT-AAAAAATTTTAAAAA-TATTTTTAAAA
*
55826361 TTAAAAAAATTTAAAAATA
1 TTAAAAAATTTTAAAAATA
55826380 AATATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 11 0.26
29 17 0.40
30 15 0.35
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
TTAAAAAATTTTAAAAATATTTTTAAAA
Found at i:55826338 original size:30 final size:28
Alignment explanation
Indices: 55826302--55826379 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 28
55826292 TTTAAAATTT
*
55826302 TTAAAAATTATTTTAAAAATATTTTAAAA
1 TTAAAAA-AATTTTAAAAATATTTTAAAA
*
55826331 TTAAAAAAATTTAAAAAAGTATTTTTAAAA
1 TTAAAAAAATTTTAAAAA-TA-TTTTAAAA
55826361 TTAAAAAAA-TTTAAAAATA
1 TTAAAAAAATTTTAAAAATA
55826380 AATATATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 11 0.25
29 16 0.36
30 17 0.39
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
TTAAAAAAATTTTAAAAATATTTTAAAA
Found at i:55826339 original size:31 final size:30
Alignment explanation
Indices: 55826273--55826379 Score: 93
Period size: 30 Copynumber: 3.7 Consensus size: 30
55826263 ATAAAATACC
* *
55826273 AAAAATTTATTCT-AAAA-ATTTTAAAATTTT
1 AAAAAATTATTTTAAAAATATTTTAAAA--TT
*
55826303 TAAAAATTATTTTAAAAATATTTTAAAATT
1 AAAAAATTATTTTAAAAATATTTTAAAATT
*
55826333 AAAAAA--ATTTAAAAAAGTATTTTTAAAATT
1 AAAAAATTATTTTAAAAA-TA-TTTTAAAATT
55826363 AAAAAA--A-TTTAAAAATA
1 AAAAAATTATTTTAAAAATA
55826380 AATATATTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
28 11 0.16
29 9 0.13
30 34 0.51
31 4 0.06
32 9 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAAAATTATTTTAAAAATATTTTAAAATT
Found at i:55826820 original size:19 final size:18
Alignment explanation
Indices: 55826792--55826862 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
55826782 ATCTAAACTA
*
55826792 ATTTTTAAAATTAAAAAT
1 ATTTTAAAAATTAAAAAT
55826810 ATTTATAAAAATTCAAAACTTAT
1 ATTT-TAAAAATT-AAAA---AT
55826833 ATTTTTAACAAATTATAAAA-
1 A-TTTTAA-AAATTA-AAAAT
55826853 ATTTTAAAAA
1 ATTTTAAAAA
55826863 ATTCTAAAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
18 7 0.16
19 13 0.30
20 5 0.11
21 1 0.02
23 7 0.16
24 11 0.25
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAAAATTAAAAAT
Found at i:55826965 original size:17 final size:17
Alignment explanation
Indices: 55826939--55826972 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55826929 TCTTATCATA
55826939 TTAAAGTATTTTATTTT
1 TTAAAGTATTTTATTTT
* *
55826956 TTAAATTATTTTGTTTT
1 TTAAAGTATTTTATTTT
55826973 GAACTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTAAAGTATTTTATTTT
Found at i:55827325 original size:7 final size:7
Alignment explanation
Indices: 55827302--55827346 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
55827292 CCGTAACAGG
55827302 ATTTT-A
1 ATTTTAA
* *
55827308 ATTTGAC
1 ATTTTAA
55827315 ATTTTAA
1 ATTTTAA
55827322 ATTTTAA
1 ATTTTAA
55827329 ATTTTAA
1 ATTTTAA
55827336 ATTTTAA
1 ATTTTAA
55827343 ATTT
1 ATTT
55827347 AACTTAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
6 4 0.12
7 30 0.88
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (7 bp):
ATTTTAA
Found at i:55829064 original size:16 final size:17
Alignment explanation
Indices: 55829033--55829067 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55829023 CAAATATTAC
55829033 TATTTATGTATTTTTTA
1 TATTTATGTATTTTTTA
*
55829050 TATTTAT-TCTTTTTTA
1 TATTTATGTATTTTTTA
55829066 TA
1 TA
55829068 GATTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TATTTATGTATTTTTTA
Found at i:55829517 original size:28 final size:28
Alignment explanation
Indices: 55829485--55829540 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
55829475 AGTAAAAAAT
55829485 TTAAAAATTTATGAAAATGACCTTAATA
1 TTAAAAATTTATGAAAATGACCTTAATA
55829513 TTAAAAATTTATGAAAATGACCTTAATA
1 TTAAAAATTTATGAAAATGACCTTAATA
55829541 CTAGATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (28 bp):
TTAAAAATTTATGAAAATGACCTTAATA
Found at i:55829930 original size:20 final size:20
Alignment explanation
Indices: 55829892--55829932 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55829882 TATGTTGAAA
* **
55829892 GAAAAAAAATGTGTTATATT
1 GAAAAAAAATGAGAGATATT
55829912 GAAAAAAAATGAGAGATATT
1 GAAAAAAAATGAGAGATATT
55829932 G
1 G
55829933 TTATTATGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (20 bp):
GAAAAAAAATGAGAGATATT
Found at i:55830821 original size:51 final size:52
Alignment explanation
Indices: 55830743--55830864 Score: 156
Period size: 52 Copynumber: 2.4 Consensus size: 52
55830733 TAAGTGATTA
* * **
55830743 AAATAATATGGCGGCATCAAAAGATAAA-TTTTATTCAATTTAGGTGCCTCC
1 AAATAATATGGCGGCACCAAAAAATAAATTTTTATTCAATTTAGGCACCTCC
* ** *
55830794 AAATAATGTGGCGGCACCAAAAAATAAATTTTTATTTTATTTTGGCACCTCC
1 AAATAATATGGCGGCACCAAAAAATAAATTTTTATTCAATTTAGGCACCTCC
*
55830846 AAATAACATGGCGGCACCA
1 AAATAATATGGCGGCACCA
55830865 CAAATATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 25 0.42
52 35 0.58
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (52 bp):
AAATAATATGGCGGCACCAAAAAATAAATTTTTATTCAATTTAGGCACCTCC
Found at i:55834617 original size:17 final size:17
Alignment explanation
Indices: 55834592--55834624 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55834582 CAAATACTCT
*
55834592 AAACCTTGAAAGATGAC
1 AAACATTGAAAGATGAC
55834609 AAACATTGAAAGATGA
1 AAACATTGAAAGATGA
55834625 AAATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAACATTGAAAGATGAC
Found at i:55840654 original size:15 final size:15
Alignment explanation
Indices: 55840634--55840685 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
55840624 ACTAGAAAAC
55840634 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
55840649 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
55840668 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
55840683 ATT
1 ATT
55840686 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:55840743 original size:15 final size:17
Alignment explanation
Indices: 55840718--55840753 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
55840708 AAGTGAATAA
55840718 TATTGTTTAAAA-TTAT
1 TATTGTTTAAAATTTAT
55840734 TATT-TTTAAAATTTAT
1 TATTGTTTAAAATTTAT
55840750 TATT
1 TATT
55840754 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTGTTTAAAATTTAT
Found at i:55840749 original size:13 final size:14
Alignment explanation
Indices: 55840713--55840759 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
55840703 ACAATAAGTG
*
55840713 AATAATATTGTTTAA
1 AATATTATT-TTTAA
55840728 AATTATTATTTTTAA
1 AA-TATTATTTTTAA
*
55840743 AAT-TTATTATTAA
1 AATATTATTTTTAA
55840756 AATA
1 AATA
55840760 AAATTGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
15 9 0.32
16 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
AATATTATTTTTAA
Found at i:55843359 original size:46 final size:44
Alignment explanation
Indices: 55843300--55843414 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
55843290 ACAGGACAGA
* *
55843300 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
55843346 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
55843390 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
55843415 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:55843395 original size:44 final size:45
Alignment explanation
Indices: 55843300--55843433 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
55843290 ACAGGACAGA
* *
55843300 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
55843346 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
55843390 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
55843434 CCGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:55850740 original size:46 final size:44
Alignment explanation
Indices: 55850681--55850795 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
55850671 ACAGGACAGA
* *
55850681 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
55850727 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
55850771 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
55850796 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:55850776 original size:44 final size:45
Alignment explanation
Indices: 55850681--55850814 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
55850671 ACAGGACAGA
* *
55850681 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
55850727 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
55850771 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
55850815 CAGGGTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:55853147 original size:31 final size:31
Alignment explanation
Indices: 55853112--55853170 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
55853102 TTATAACATA
* *
55853112 TTTCATATTCTGTTTTCAATTCACTATCGTT
1 TTTCACATTCTATTTTCAATTCACTATCGTT
55853143 TTTCACATTCTATTTTCAATTCACTATC
1 TTTCACATTCTATTTTCAATTCACTATC
55853171 TCATATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTCACATTCTATTTTCAATTCACTATCGTT
Found at i:55853336 original size:25 final size:25
Alignment explanation
Indices: 55853254--55853388 Score: 142
Period size: 25 Copynumber: 5.6 Consensus size: 25
55853244 CTGTTATGCA
*
55853254 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACTAACGTG
*
55853279 CT-AT-A-CAGAGAGCAC-AGATGTG
1 CTAATAATCAGAGAGCACTA-ACGTG
* *
55853301 CT-A-AA-CAGAGAGTACTGACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
55853323 CTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
55853348 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
55853373 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
55853389 GCGCTAAAGT
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 34 0.36
24 4 0.04
25 56 0.59
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAACGTG
Found at i:55855643 original size:21 final size:21
Alignment explanation
Indices: 55855619--55855658 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55855609 TCTTTTCATA
* *
55855619 TTAATTTCATGTATCATTTAC
1 TTAACTTCATATATCATTTAC
55855640 TTAACTTCATATATCATTT
1 TTAACTTCATATATCATTT
55855659 CATAAATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAACTTCATATATCATTTAC
Found at i:55857130 original size:23 final size:23
Alignment explanation
Indices: 55857104--55857199 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
55857094 ATAAATGCCA
55857104 CACTAATATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* * * *
55857127 CACTGATAAGTAGCTGTAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
*
55857150 CACTGAA-ATGTAGCTGAAGCTAC
1 CACT-AATATGTAGCCGAAGCTAC
* *
55857173 CACTAATGTGTAGCCGTAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
55857196 CACT
1 CACT
55857200 GATCAATAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
22 2 0.03
23 58 0.95
24 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTAATATGTAGCCGAAGCTAC
Found at i:55857186 original size:46 final size:46
Alignment explanation
Indices: 55857111--55857201 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
55857101 CCACACTAAT
* *
55857111 ATGTAGCCGAAGCTACCACTGATAAGTAGCTGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTAATAAGTAGCCGTAGCTACCACTGAA
* **
55857157 ATGTAGCTGAAGCTACCACTAATGTGTAGCCGTAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTAATAAGTAGCCGTAGCTACCACTGA
55857202 TCAATAACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTAATAAGTAGCCGTAGCTACCACTGAA
Found at i:55858412 original size:18 final size:18
Alignment explanation
Indices: 55858389--55858424 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55858379 CAAACGTCAA
55858389 AATTTTCAAACGAATTTT
1 AATTTTCAAACGAATTTT
55858407 AATTTTCAAACGAATTTT
1 AATTTTCAAACGAATTTT
55858425 TCACAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTTTCAAACGAATTTT
Found at i:55860194 original size:19 final size:18
Alignment explanation
Indices: 55860153--55860226 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
55860143 AACAAAAACT
*
55860153 TGGCACATGAAGTGCATAC
1 TGGCACAT-AAGCGCATAC
* *
55860172 TGGCGCATAAGCGCATATT
1 TGGCACATAAGCGCATA-C
*
55860191 TGGCACATGAAGTGCATAC
1 TGGCACAT-AAGCGCATAC
*
55860210 TGGCACATAAGCTCATA
1 TGGCACATAAGCGCATA
55860227 ATATTGTACT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
18 15 0.33
19 22 0.49
20 8 0.18
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (18 bp):
TGGCACATAAGCGCATAC
Found at i:55860196 original size:38 final size:38
Alignment explanation
Indices: 55860152--55860226 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
55860142 AAACAAAAAC
*
55860152 TTGGCACATGAAGTGCATACTGGCGCATAAGCGCATAT
1 TTGGCACATGAAGTGCATACTGGCACATAAGCGCATAT
*
55860190 TTGGCACATGAAGTGCATACTGGCACATAAGCTCATA
1 TTGGCACATGAAGTGCATACTGGCACATAAGCGCATA
55860227 ATATTGTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (38 bp):
TTGGCACATGAAGTGCATACTGGCACATAAGCGCATAT
Found at i:55860313 original size:6 final size:6
Alignment explanation
Indices: 55860302--55860332 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
55860292 GGTATCAAAA
*
55860302 TCCAAT TCCAAT TCCAAT TCAAAT TCCAAT T
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT T
55860333 TAGTACACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCAAT
Found at i:55860319 original size:12 final size:12
Alignment explanation
Indices: 55860296--55860332 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
55860286 TAATAGGGTA
*
55860296 TCAAAATCCAAT
1 TCAAATTCCAAT
*
55860308 TCCAATTCCAAT
1 TCAAATTCCAAT
55860320 TCAAATTCCAAT
1 TCAAATTCCAAT
55860332 T
1 T
55860333 TAGTACACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (12 bp):
TCAAATTCCAAT
Found at i:55861887 original size:23 final size:22
Alignment explanation
Indices: 55861844--55861901 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
55861834 AAAGGGTATC
* *
55861844 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
55861865 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
55861888 TGCATATCATATCT
1 TACAAATCATATCT
55861902 AACATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:55866926 original size:45 final size:45
Alignment explanation
Indices: 55866877--55867032 Score: 147
Period size: 46 Copynumber: 3.4 Consensus size: 45
55866867 TAATCATACG
*
55866877 TGATAAATTCAAAATATTAATATATAATAAATTTAAA-AATATTAA
1 TGATAAATTTAAAATA-TAATATATAATAAATTTAAATAATATTAA
* * *
55866922 TGATAAATTTGAAATA-AATATACATGATAAATTTAAATAATGTTAA
1 TGATAAATTTAAAATATAATAT--ATAATAAATTTAAATAATATTAA
* * * * *
55866968 TGATGAGTTTAAAATAATAACATATTAA-AAATTAAAATAATATTGA
1 TGATAAATTTAAAAT-ATAATATA-TAATAAATTTAAATAATATTAA
*
55867014 TAATAAATTTAAAAATATA
1 TGATAAATTT-AAAATATA
55867033 TTAAGCTTGA
Statistics
Matches: 89, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
43 5 0.06
45 27 0.30
46 45 0.51
47 8 0.09
48 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (45 bp):
TGATAAATTTAAAATATAATATATAATAAATTTAAATAATATTAA
Found at i:55866927 original size:24 final size:24
Alignment explanation
Indices: 55866879--55866927 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
55866869 ATCATACGTG
* *
55866879 ATAAATTCAAAATATTAATATATA
1 ATAAATTAAAAATATTAATAGATA
55866903 ATAAATTTAAAAATATTAAT-GATA
1 ATAAA-TTAAAAATATTAATAGATA
55866927 A
1 A
55866928 ATTTGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAAATTAAAAATATTAATAGATA
Found at i:55866940 original size:24 final size:23
Alignment explanation
Indices: 55866903--55867036 Score: 84
Period size: 22 Copynumber: 5.9 Consensus size: 23
55866893 TTAATATATA
55866903 ATAAATTT-AA-AAATATTAATG
1 ATAAATTTAAATAAATATTAATG
55866924 ATAAATTTGAAATAAATA-TACATG
1 ATAAATTT-AAATAAATATTA-ATG
*
55866948 ATAAATTTAAAT-AATGTTAATG
1 ATAAATTTAAATAAATATTAATG
* * ** *
55866970 ATGAGTTTAAA-ATAATAACATATT
1 ATAAATTTAAATA-AATATTA-ATG
* * * *
55866994 AAAAATTAAAAT-AATATTGATA
1 ATAAATTTAAATAAATATTAATG
55867016 ATAAATTTAAA-AATATATTAA
1 ATAAATTTAAATAA-ATATTAA
55867037 GCTTGAACAT
Statistics
Matches: 84, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
21 8 0.10
22 27 0.32
23 24 0.29
24 25 0.30
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (23 bp):
ATAAATTTAAATAAATATTAATG
Found at i:55867025 original size:23 final size:23
Alignment explanation
Indices: 55866879--55867036 Score: 96
Period size: 23 Copynumber: 6.9 Consensus size: 23
55866869 ATCATACGTG
* * *
55866879 ATAAATTCAAAATATTAATATATA
1 ATAAATTTAAAATAATATTA-ATA
*
55866903 ATAAATTT-AAA-AATATTAATG
1 ATAAATTTAAAATAATATTAATA
* *
55866924 ATAAATTTGAAATAA-ATATACATG
1 ATAAATTTAAAATAATAT-TA-ATA
* *
55866948 ATAAATTT-AAATAATGTTAATG
1 ATAAATTTAAAATAATATTAATA
* *
55866970 ATGAGTTTAAAATAATA--ACATA
1 ATAAATTTAAAATAATATTA-ATA
* * *
55866992 TTAAAAATTAAAATAATATTGATA
1 AT-AAATTTAAAATAATATTAATA
55867016 ATAAATTTAAAA-ATATATTAA
1 ATAAATTTAAAATA-ATATTAA
55867037 GCTTGAACAT
Statistics
Matches: 106, Mismatches: 17, Indels: 23
0.73 0.12 0.16
Matches are distributed among these distances:
21 11 0.10
22 23 0.22
23 49 0.46
24 23 0.22
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (23 bp):
ATAAATTTAAAATAATATTAATA
Found at i:55868661 original size:50 final size:50
Alignment explanation
Indices: 55868602--55868717 Score: 207
Period size: 50 Copynumber: 2.3 Consensus size: 50
55868592 ATAAAATATC
55868602 TATTAAGTACAAGATTCTAAATAAAAATATCAATTATTTCAAACAAGTTG
1 TATTAAGTACAAGATTCTAAATAAAAATATCAATTATTTCAAACAAGTTG
55868652 TATTAAGTACAAGATTCTAAATAAAAATATCAATTATTTCAAACAAGTTG
1 TATTAAGTACAAGATTCTAAATAAAAATATCAATTATTTCAAACAAGTTG
55868702 TGATTATA-TACAAGAT
1 T-ATTA-AGTACAAGAT
55868718 AGGGAATAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
50 51 0.80
51 12 0.19
52 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (50 bp):
TATTAAGTACAAGATTCTAAATAAAAATATCAATTATTTCAAACAAGTTG
Found at i:55869829 original size:22 final size:22
Alignment explanation
Indices: 55869802--55869844 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
55869792 CTAGTACCTA
55869802 GGAATTATACATGAAAACTAAG
1 GGAATTATACATGAAAACTAAG
55869824 GGAATTATACATGAAAACTAA
1 GGAATTATACATGAAAACTAA
55869845 CTAGACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (22 bp):
GGAATTATACATGAAAACTAAG
Found at i:55873742 original size:42 final size:42
Alignment explanation
Indices: 55873696--55873798 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
55873686 TGCTAAACAG
* * * **
55873696 AAACCCATAAAGGTTAGACAGAAG-TTCATAGGAGCTGAACGA
1 AAACCCATAAGGGTTAAACAGAAGCTCCA-AAAAGCTGAACGA
* * *
55873738 AAACCCATACGGGTTAAACTGAAGCTCCAAAAAGCTGAACGG
1 AAACCCATAAGGGTTAAACAGAAGCTCCAAAAAGCTGAACGA
55873780 AAACCCATAAGGGTTAAAC
1 AAACCCATAAGGGTTAAAC
55873799 TGAAACTCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACAGAAGCTCCAAAAAGCTGAACGA
Found at i:55873809 original size:21 final size:20
Alignment explanation
Indices: 55873779--55873843 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
55873769 AAGCTGAACG
* *
55873779 GAAACCCATAAGGGTTAAACT
1 GAAACTCATAAGAGTTAAA-T
*
55873800 GAAACTCATATGAGTTAAAT
1 GAAACTCATAAGAGTTAAAT
* * * *
55873820 GAAGCTCATGAGAGCTAAAC
1 GAAACTCATAAGAGTTAAAT
55873840 GAAA
1 GAAA
55873844 AGTAAACATG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAACTCATAAGAGTTAAAT
Found at i:55879554 original size:21 final size:21
Alignment explanation
Indices: 55879530--55879648 Score: 112
Period size: 21 Copynumber: 5.7 Consensus size: 21
55879520 AGTTAACTCA
* *
55879530 TATGAGTTTCCGTTTAACCCC
1 TATGAGTTTCCGTTCAACCCT
* **
55879551 TATGAGTTTCCATTCAACTTT
1 TATGAGTTTCCGTTCAACCCT
* * * *
55879572 TTTGAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* *
55879593 TATGGGTTTCCGTTCAACTCT
1 TATGAGTTTCCGTTCAACCCT
* *
55879614 TACGAGCTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
*
55879635 TATGGGTTTCCGTT
1 TATGAGTTTCCGTT
55879649 TAGCTCTCAT
Statistics
Matches: 73, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:55879588 original size:42 final size:42
Alignment explanation
Indices: 55879524--55879664 Score: 156
Period size: 42 Copynumber: 3.4 Consensus size: 42
55879514 AGCTTTAGTT
* * * *
55879524 AACTCATATGAGTTTCCGTTTAACCCCTATGAGTTTCCATTC
1 AACTCTTATGAGCTTCCGTTTAACCCTTATGGGTTTCCATTC
* * * *
55879566 AACTTTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTC
1 AACTCTTATGAGCTTCCGTTTAACCCTTATGGGTTTCCATTC
* * * *
55879608 AACTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTCCGTTT
1 AACTCTTATGAGCTTCCGTTTAACCCTTATGGGTTTCCATTC
* *
55879650 AGCTCTCATGAGCTT
1 AACTCTTATGAGCTT
55879665 TTGTTTAGCC
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (42 bp):
AACTCTTATGAGCTTCCGTTTAACCCTTATGGGTTTCCATTC
Found at i:55879630 original size:63 final size:62
Alignment explanation
Indices: 55879512--55879631 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 62
55879502 TTAGATCTTA
* * * * *
55879512 TGAGCTTTAGTTAACTCATATGAGTTTCCGTTTAACCCCTATGAGTTTCCATTCAACTTTTT
1 TGAGCTTCAGTTAACCCATATGAGTTTCCGTTCAACCCCTACGAGCTTCCATTCAACTTTTT
* * * * *
55879574 TGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAGCTTCCGTTCAAC
1 TGAGCTTCAG-TTAACCCATATGAGTTTCCGTTCAACCCCTACGAGCTTCCATTCAAC
55879632 CCTTATGGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
62 9 0.19
63 38 0.81
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (62 bp):
TGAGCTTCAGTTAACCCATATGAGTTTCCGTTCAACCCCTACGAGCTTCCATTCAACTTTTT
Found at i:55882457 original size:9 final size:9
Alignment explanation
Indices: 55882440--55882476 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55882430 TGAGTTTTCG
55882440 AATTCGAAT
1 AATTCGAAT
*
55882449 AACTCGAAT
1 AATTCGAAT
55882458 AATTCGAAT
1 AATTCGAAT
55882467 AATTCGAAT
1 AATTCGAAT
55882476 A
1 A
55882477 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55882724 original size:30 final size:31
Alignment explanation
Indices: 55882690--55882749 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
55882680 AAACCTTTTA
*
55882690 TTTTCCCCCAAAATTTTTACTTCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTTCCTTCCCAC
* *
55882720 TTTTCCCCTAAAACTTTTATTTCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTTCCTTCCCA
55882750 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTTCCTTCCCAC
Found at i:55882833 original size:19 final size:19
Alignment explanation
Indices: 55882801--55882837 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
55882791 TTTTTAATAT
55882801 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
55882821 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
55882838 TTCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:55883932 original size:34 final size:35
Alignment explanation
Indices: 55883873--55883941 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
55883863 AATATTTATG
*
55883873 GCTCGGTTTATAAAATCAAGGTCTCGATGCCTCTT
1 GCTCGGTTTATAAAATCAAGGTCTCGATACCTCTT
55883908 GCTCGGTTTATAAAA-CAAGGTCTCGATACCTCTT
1 GCTCGGTTTATAAAATCAAGGTCTCGATACCTCTT
55883942 TTTCTTAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (35 bp):
GCTCGGTTTATAAAATCAAGGTCTCGATACCTCTT
Found at i:55885497 original size:27 final size:26
Alignment explanation
Indices: 55885467--55885524 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
55885457 CACATAATCA
55885467 GGAAGCCCTC-TCTCGAGCCATATAACG
1 GGAAG-CCTCATCT-GAGCCATATAACG
*
55885494 GGAAG-CTCATGTGAGCCATATAACG
1 GGAAGCCTCATCTGAGCCATATAACG
55885519 GGAAGC
1 GGAAGC
55885525 TTATCCAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 21 0.75
26 2 0.07
27 5 0.18
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCCTCATCTGAGCCATATAACG
Found at i:55885511 original size:25 final size:25
Alignment explanation
Indices: 55885481--55885705 Score: 135
Period size: 24 Copynumber: 9.2 Consensus size: 25
55885471 GCCCTCTCTC
*
55885481 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* *
55885506 GAGCCATATAACGGGAAGCTTATCCA
1 GAGCCATATAACGGGAAGCTCAT-GA
** * *
55885532 G-GCTGTATAATGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGA
** *
55885556 GAGCCATA-ATTGGGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGA
* *
55885580 GAGCCA-ATAACGGGTAGCTC-CGAA
1 GAGCCATATAACGGGAAGCTCATG-A
*
55885604 GAGCCAT-TAATGGGAAGCTC-TGAA
1 GAGCCATATAACGGGAAGCTCATG-A
* * * * * *
55885628 TAGCCATATATCGAGAAGTTCAAGT
1 GAGCCATATAACGGGAAGCTCATGA
* **
55885653 GAGCCATAT--TGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCA-TGA
*
55885677 GAGCCATATAACGGGACA-CTCATAA
1 GAGCCATATAACGGGA-AGCTCATGA
55885702 GAGC
1 GAGC
55885706 TGTGGTGTGT
Statistics
Matches: 153, Mismatches: 36, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
23 10 0.07
24 66 0.43
25 66 0.43
26 10 0.07
27 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:55890206 original size:7 final size:7
Alignment explanation
Indices: 55890194--55890220 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55890184 TTATTTCTTT
55890194 ATTTCAA
1 ATTTCAA
55890201 ATTTCAA
1 ATTTCAA
55890208 ATTTCAA
1 ATTTCAA
55890215 ATTTCA
1 ATTTCA
55890221 CTTTTCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTCAA
Found at i:55890370 original size:6 final size:6
Alignment explanation
Indices: 55890333--55890375 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
55890323 CCAAACACAC
* *
55890333 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
55890376 TTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (6 bp):
CAGTAA
Found at i:55890423 original size:45 final size:44
Alignment explanation
Indices: 55890359--55890504 Score: 202
Period size: 45 Copynumber: 3.2 Consensus size: 44
55890349 GTAACGGTAG
* * *
55890359 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAACCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC-GTAA
* *
55890404 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAGTCGATAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG-TAA
* *
55890449 CAATAATAGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC-GTAA
55890494 CAGTAACAGTA
1 CAGTAACAGTA
55890505 GTCGGCACAT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.01
45 86 0.98
46 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (44 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGTAA
Found at i:55891490 original size:9 final size:9
Alignment explanation
Indices: 55891446--55891472 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55891436 CATTTGAATA
55891446 AATAATTAT
1 AATAATTAT
55891455 AATAATTAT
1 AATAATTAT
55891464 AATAATTAT
1 AATAATTAT
55891473 GTACATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:55894061 original size:19 final size:19
Alignment explanation
Indices: 55894037--55894075 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55894027 TTTCGTAAAT
55894037 TATATAATGTA-TGATGAAA
1 TATAT-ATGTATTGATGAAA
*
55894056 TATATATTTATTGATGAAA
1 TATATATGTATTGATGAAA
55894075 T
1 T
55894076 GAGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
TATATATGTATTGATGAAA
Found at i:55894294 original size:45 final size:46
Alignment explanation
Indices: 55894156--55894447 Score: 477
Period size: 46 Copynumber: 6.5 Consensus size: 46
55894146 TAATCAGTGA
* *
55894156 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
* *
55894202 CCAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
55894248 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
* * *
55894293 CAAGTGACAAAGTGATAAGTAGTAGCTTTAGCTACTCTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
55894339 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
55894384 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
*
55894429 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
55894448 ATCATACATA
Statistics
Matches: 234, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
43 12 0.05
44 5 0.02
45 106 0.45
46 111 0.47
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGAT
Found at i:55894312 original size:91 final size:91
Alignment explanation
Indices: 55894156--55894447 Score: 491
Period size: 91 Copynumber: 3.2 Consensus size: 91
55894146 TAATCAGTGA
* * *
55894156 CAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCCAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
55894221 TGGTAGCTTTAGCTACACTTATCTGAT
65 TGGTAGCTTTAGCTACACTTATCTGAT
55894248 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
* *
55894313 AGTAGCTTTAGCTACTCTTATCTGAT
66 GGTAGCTTTAGCTACACTTATCTGAT
55894339 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
55894404 GGTAGC-CTAGCTACACTTATCTGAT
66 GGTAGCTTTAGCTACACTTATCTGAT
*
55894429 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
55894448 ATCATACATA
Statistics
Matches: 191, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
88 12 0.06
89 5 0.03
90 18 0.09
91 131 0.69
92 25 0.13
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
GGTAGCTTTAGCTACACTTATCTGAT
Found at i:55903698 original size:18 final size:18
Alignment explanation
Indices: 55903675--55903739 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
55903665 CAATCCCAAC
* *
55903675 TACTGTATACGTGAACAG
1 TACTGTATACGTAAATAG
55903693 TACTGTATACGTAAATAG
1 TACTGTATACGTAAATAG
*
55903711 TGCTGTATACGTAAATAG
1 TACTGTATACGTAAATAG
55903729 TACTGTATACG
1 TACTGTATACG
55903740 GTCGTATTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (18 bp):
TACTGTATACGTAAATAG
Found at i:55904638 original size:12 final size:12
Alignment explanation
Indices: 55904621--55904645 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55904611 TATTCGTGGT
55904621 AGGAGATCCGGA
1 AGGAGATCCGGA
55904633 AGGAGATCCGGA
1 AGGAGATCCGGA
55904645 A
1 A
55904646 ATGGCAATAA
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:0.36, C:0.16, G:0.40, T:0.08
Consensus pattern (12 bp):
AGGAGATCCGGA
Found at i:55918707 original size:29 final size:30
Alignment explanation
Indices: 55918651--55918721 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
55918641 ACAAAAATAA
* *
55918651 AAAATTATATTTTGGCCCCTAAACTTTT-T
1 AAAAGTATATTTTGACCCCTAAACTTTTCT
* * *
55918680 GAAAGTATATTTTGACCCCTAGATTTTTCT
1 AAAAGTATATTTTGACCCCTAAACTTTTCT
*
55918710 AAAATTATATTT
1 AAAAGTATATTT
55918722 AAACCTCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (30 bp):
AAAAGTATATTTTGACCCCTAAACTTTTCT
Found at i:55918721 original size:30 final size:29
Alignment explanation
Indices: 55918651--55918817 Score: 88
Period size: 30 Copynumber: 5.7 Consensus size: 29
55918641 ACAAAAATAA
*
55918651 AAAATTATATTTTGGCCCCTAAACTTTTT
1 AAAATTATATTTTGACCCCTAAACTTTTT
* * * *
55918680 GAAAGTATATTTTGACCCCTAGATTTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTT-T
** * *
55918710 AAAATTATATTTAAACCTCTAAAATATTTTT
1 AAAATTATATTTTGACCCCT-AAA-CTTTTT
* * **
55918741 AAAA-TAGATTTTAACCTATAAA-TGTTTT
1 AAAATTATATTTTGACCCCTAAACT-TTTT
* * * *
55918769 GAAATTACATTATGACCCCT-AAGTTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTT-T
* *
55918798 CAAAATTATGTTTTGGCCCC
1 -AAAATTATATTTTGACCCC
55918818 AGAGGTTTTG
Statistics
Matches: 104, Mismatches: 26, Indels: 15
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.01
28 12 0.12
29 38 0.37
30 42 0.40
31 7 0.07
32 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCTAAACTTTTT
Found at i:55919077 original size:14 final size:16
Alignment explanation
Indices: 55919036--55919079 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
55919026 AGAAAATAGG
55919036 AGAGAAAAGAGAAAGA
1 AGAGAAAAGAGAAAGA
*
55919052 AGAGGAAGAA-AGGAAGA
1 AGA-GAA-AAGAGAAAGA
55919069 AGAGAAAAGAG
1 AGAGAAAAGAG
55919080 GGGAAGGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 2 0.08
16 8 0.33
17 12 0.50
18 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AGAGAAAAGAGAAAGA
Found at i:55919427 original size:28 final size:26
Alignment explanation
Indices: 55919388--55919487 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 26
55919378 CCCAGCAGAA
55919388 AAAAAAAG-AGAAAATGAAGAAAAAAGG
1 AAAAAAAGAAGAAAA-GAAGAAAAAA-G
*
55919415 AAAAAAAGAAGAAAA-AAG--AGAAG
1 AAAAAAAGAAGAAAAGAAGAAAAAAG
*
55919438 -AAAATAGAAGAAAA-AAG-AAAAAG
1 AAAAAAAGAAGAAAAGAAGAAAAAAG
55919461 AGAAAAAAG-AGAAAAAGAA-AAAAAAG
1 A-AAAAAAGAAG-AAAAGAAGAAAAAAG
55919487 A
1 A
55919488 GGTTCAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
22 16 0.26
23 5 0.08
24 5 0.08
25 10 0.16
26 12 0.19
27 8 0.13
28 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAAAAGAAGAAAAGAAGAAAAAAG
Found at i:55919440 original size:40 final size:38
Alignment explanation
Indices: 55919384--55919473 Score: 118
Period size: 37 Copynumber: 2.4 Consensus size: 38
55919374 GCAGCCCAGC
55919384 AGAA-AAAAAA-AG-AGAAAAT-GAAGAAAAAAGGAAAAAA
1 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAA-G--AAAA
55919421 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
1 AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
55919459 AG-AGAAAAAAGAGAA
1 AGAAGAAAAAAGAGAA
55919474 AAAGAAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
37 17 0.35
38 12 0.24
39 2 0.04
40 8 0.16
41 10 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (38 bp):
AGAAGAAAAAAGAGAAGAAAATAGAAGAAAAAAGAAAA
Found at i:55919479 original size:40 final size:41
Alignment explanation
Indices: 55919384--55919481 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 41
55919374 GCAGCCCAGC
*
55919384 AGAAAAAA-AAAGAGAAAATGAAGAAAAAAGGAAAAAAAGA
1 AGAAAAAAGAAAAAGAAAATGAAGAAAAAAGGAAAAAAAGA
* *
55919424 AGAAAAAAG-AGAAGAAAATAGAAGAAAAAA-GAAAAAGAGA
1 AGAAAAAAGAAAAAGAAAAT-GAAGAAAAAAGGAAAAAAAGA
*
55919464 A-AAAAGAGAAAAAGAAAA
1 AGAAAAAAGAAAAAGAAAA
55919482 AAAAGAGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 6 0.12
40 34 0.68
41 10 0.20
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (41 bp):
AGAAAAAAGAAAAAGAAAATGAAGAAAAAAGGAAAAAAAGA
Found at i:55919487 original size:9 final size:9
Alignment explanation
Indices: 55919387--55919485 Score: 69
Period size: 9 Copynumber: 10.6 Consensus size: 9
55919377 GCCCAGCAGA
55919387 AAAAAAAAG
1 AAAAAAAAG
* *
55919396 -AGAAAATG
1 AAAAAAAAG
55919404 AAGAAAAAAG
1 AA-AAAAAAG
*
55919414 GAAAAAAAG
1 AAAAAAAAG
55919423 AAGAAAAAAG
1 AA-AAAAAAG
55919433 AGAAGAAAATAG
1 A-AA-AAAA-AG
55919445 AAGAAAAAAG
1 AA-AAAAAAG
*
55919455 -AAAAAGAG
1 AAAAAAAAG
*
55919463 AAAAAAGAG
1 AAAAAAAAG
55919472 AAAAAGAAA-
1 AAAAA-AAAG
55919481 AAAAA
1 AAAAA
55919486 GAGGTTCAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
8 12 0.16
9 28 0.38
10 19 0.26
11 10 0.14
12 4 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:55919831 original size:18 final size:18
Alignment explanation
Indices: 55919810--55920310 Score: 192
Period size: 17 Copynumber: 28.1 Consensus size: 18
55919800 ATTGTAAATA
55919810 TTCAAAAAATTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
55919828 TTCACAAAAAATTTCCT-TGT
1 TT--CAAAAAATTTCGTGT-T
* * **
55919848 TTC-GAAATTTTCGTGGC
1 TTCAAAAAATTTCGTGTT
55919865 TTCAAAATAATTTTTC-TCGTGT
1 TTCAAAA-AA--TTTCGT-GT-T
55919887 TTC-AAAAATATTCGTGTT
1 TTCAAAAAAT-TTCGTGTT
* * *
55919905 TTCAAAAGATTCCAT-TT
1 TTCAAAAAATTTCGTGTT
*
55919922 TTC-AAAATTTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
* *
55919940 TTCTAAAAATTTCCATG-T
1 TTCAAAAAATTT-CGTGTT
*
55919958 TTC-TAAAATTT-GTG-T
1 TTCAAAAAATTTCGTGTT
* *
55919973 TTCAAAAATTTTCGTGTA
1 TTCAAAAAATTTCGTGTT
**
55919991 TTC-AAAAATTTTTTGTAT
1 TTCAAAAAATTTCGTGT-T
** *
55920009 TTTGAACAATTCTCGTG-T
1 TTCAAAAAATT-TCGTGTT
* *
55920027 TTCACAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
**** **
55920045 TT-AATTTTTTTTATGTT
1 TTCAAAAAATTTCGTGTT
*
55920062 TTAAAAAAAATTATCGTG-T
1 TT-CAAAAAATT-TCGTGTT
*
55920081 TTCAAAAAATTGTCGTCTT
1 TTCAAAAAATT-TCGTGTT
* *
55920100 TT-AAAAATTTTTGTG-T
1 TTCAAAAAATTTCGTGTT
* * *
55920116 TTCTAAAATTTTCGT-AT
1 TTCAAAAAATTTCGTGTT
*
55920133 TTCAAAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
55920151 TTC-AAAAATTCCG-GTGT
1 TTCAAAAAATTTCGTGT-T
*
55920168 TTCAAAAAATTCCCGTGTT
1 TTCAAAAAATT-TCGTGTT
55920187 TT--AAAAATTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
*
55920204 TTC-AAAAATTTCGTGGT
1 TTCAAAAAATTTCGTGTT
**
55920221 TTC--AAAATTTTTTGTAT
1 TTCAAAAAATTTCGTGT-T
* *
55920238 TTC-AAAAATCCTCATGTT
1 TTCAAAAAAT-TTCGTGTT
*
55920256 TTC-AAAAATTTCAGTGTG
1 TTCAAAAAATTTC-GTGTT
* *
55920274 TT-GAAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
55920291 TTCAAAAAAATCTCGTGTT
1 TTC-AAAAAATTTCGTGTT
55920310 T
1 T
55920311 CATAAATTTT
Statistics
Matches: 363, Mismatches: 77, Indels: 85
0.69 0.15 0.16
Matches are distributed among these distances:
15 6 0.02
16 25 0.07
17 129 0.36
18 103 0.28
19 62 0.17
20 27 0.07
21 8 0.02
22 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (18 bp):
TTCAAAAAATTTCGTGTT
Found at i:55919903 original size:17 final size:17
Alignment explanation
Indices: 55919881--55920321 Score: 250
Period size: 17 Copynumber: 25.1 Consensus size: 17
55919871 ATAATTTTTC
*
55919881 TCGTGTTTCAAAAATAT
1 TCGTGTTTCAAAAATTT
55919898 TCGTGTTTTCAAAAGA-TT
1 TCGTG-TTTCAAAA-ATTT
* * *
55919916 CCATTTTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
55919932 TCCGTGTTTTCTAAAAATTT
1 T-CGTG-TTTC-AAAAATTT
* * *
55919952 CCATGTTTCTAAAA-TT
1 TCGTGTTTCAAAAATTT
55919968 T-GTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
55919984 TCGTGTATTCAAAAATTTT
1 TCGTGT-TTCAAAAA-TTT
* * * * *
55920003 TTGTATTTTGAACAATTC
1 TCGT-GTTTCAAAAATTT
*
55920021 TCGTGTTTCACAAATTT
1 TCGTGTTTCAAAAATTT
* ***
55920038 TCGTGTTTTAATTTTTT
1 TCGTGTTTCAAAAATTT
** * *
55920055 TTATGTTTTAAAAAAAATTA
1 TCGTG-TTT--CAAAAATTT
*
55920075 TCGTGTTTCAAAAAATTG
1 TCGTGTTTC-AAAAATTT
* *
55920093 TCGTCTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
55920110 TTGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
*
55920127 TCGTATTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
55920144 TCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
* *
55920161 CCGGTGTTTCAAAAAATTC
1 TC-GTGTTTC-AAAAATTT
* *
55920180 CCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
*
55920197 CCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
*
55920214 TCGTGGTTTCAAAATTTT
1 TCGT-GTTTCAAAAATTT
* * **
55920232 TTGTATTTCAAAAATCC
1 TCGTGTTTCAAAAATTT
*
55920249 TCATGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
*
55920266 TCAGTGTGTT-GAAAATTT
1 TC-GTGT-TTCAAAAATTT
* *
55920284 TCGTGTTTTCAAAAAAATC
1 TCGTG-TTTC-AAAAATTT
*
55920303 TCGTGTTTCATAAATTT
1 TCGTGTTTCAAAAATTT
55920320 TC
1 TC
55920322 ATTTTTTTAA
Statistics
Matches: 318, Mismatches: 76, Indels: 60
0.70 0.17 0.13
Matches are distributed among these distances:
15 11 0.03
16 10 0.03
17 142 0.45
18 108 0.34
19 32 0.10
20 15 0.05
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:55919975 original size:15 final size:15
Alignment explanation
Indices: 55919955--55920001 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
55919945 AAAATTTCCA
*
55919955 TGTTTCTAAAATTTG
1 TGTTTCAAAAATTTG
55919970 TGTTTCAAAAATTTTCG
1 TGTTTCAAAAA-TTT-G
55919987 TGTATTCAAAAATTT
1 TGT-TTCAAAAATTT
55920002 TTTGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 3 0.11
17 7 0.25
18 8 0.29
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (15 bp):
TGTTTCAAAAATTTG
Found at i:55920036 original size:54 final size:51
Alignment explanation
Indices: 55919921--55920367 Score: 199
Period size: 52 Copynumber: 8.5 Consensus size: 51
55919911 AGATTCCATT
** *
55919921 TTTC-AAAATTTTCCGTGTTTTCTAAAAATTTCCATGTTTCTAAAATT-T-GTG
1 TTTCAAAAATTTT-CGTG-TTTC-AAAAATTTTTATGTTTTTAAAATTATCGTG
*
55919972 TTTCAAAAATTTTCGTGTATTCAAAAATTTTT-TGTATTTTGAACAATTCTCGTG
1 TTTCAAAAATTTTCGTGT-TTCAAAAATTTTTATGT-TTTT-AA-AATTATCGTG
* * *** *
55920026 TTTCACAAATTTTCGTGTTTTAATTTTTTTTATGTTTTAAAAAAAATTATCGTG
1 TTTCAAAAATTTTCGTGTTTCAAAAATTTTTATGTTTT---TAAAATTATCGTG
* * * * * * *
55920080 TTTCAAAAAATTGTCGTCTTTTAAAAATTTTTGTGTTTCTAAAATTTTCGTA
1 TTTC-AAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTTAAAATTATCGTG
**** ** **
55920132 TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGGTGTTTCAAAAAATTCCCGTG
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTATGTTT-TTAAAATTATCGTG
* * ** * * * * *
55920185 TTTTAAAAATTTCCGTGTTTTCAAAAA-TTTCGTGGTTTCAAAATTTTTTGTA
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTATGTTTTTAAAA-TTATCGTG
** * * * * *
55920237 TTTCAAAAATCCTCATGTTTTCAAAAA-TTTCAGTGTGTTGAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG-TTTCAAAAATTTTTA-TGTTTTTAAAATTATCGTG
* * * * * * *
55920289 TTTTCAAAAAAATCTCGTGTTTCATAAATTTTCATTTTTTTAAAAAATAAT--TA
1 -TTTC-AAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTT--AAAATTATCGTG
* *
55920342 TTTCAAAAATCTTCGTGTTTTAAAAA
1 TTTCAAAAATTTTCGTGTTTCAAAAA
55920368 AAATTCGTTT
Statistics
Matches: 305, Mismatches: 70, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
49 3 0.01
50 12 0.04
51 45 0.15
52 88 0.29
53 72 0.24
54 51 0.17
55 34 0.11
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (51 bp):
TTTCAAAAATTTTCGTGTTTCAAAAATTTTTATGTTTTTAAAATTATCGTG
Found at i:55920171 original size:35 final size:34
Alignment explanation
Indices: 55919810--55920368 Score: 240
Period size: 35 Copynumber: 15.8 Consensus size: 34
55919800 ATTGTAAATA
* *
55919810 TTCAAAAAATTTCGTGTTTTCACAAAAAATTTCCTTGT
1 TTCAAAAATTTTCGTGTTTT--C-AAAAA-TTCCGTGT
* **
55919848 TTC-GAAATTTTCGTGGCTTCAAAATAATTTTTCTCGTGT
1 TTCAAAAATTTTCGTGTTTTC-AAA-AA---TTC-CGTGT
* * *
55919887 TTCAAAAATATTCGTGTTTTCAAAAGATTCCATTT
1 TTCAAAAATTTTCGTGTTTTCAAAA-ATTCCGTGT
*
55919922 TTC-AAAATTTTCCGTGTTTTCTAAAAATTTCCATGT
1 TTCAAAAATTTT-CGTGTTTTC-AAAAA-TTCCGTGT
* *
55919958 TTCTAAAA-TTT-GTG-TTTCAAAAATTTTCGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAA-TTCCGTGT
* * * *
55919990 ATTCAAAAATTTTTTGTATTTTGAACAATTCTCGTGT
1 -TTCAAAAA-TTTTCGTGTTTTCAAAAATTC-CGTGT
* *** ***
55920027 TTCACAAATTTTCGTGTTTT-AATTTTTTTTATGTT
1 TTCAAAAATTTTCGTGTTTTCAA-AAATTCCGTG-T
* * * *
55920062 TTAAAAAAAATTATCGTG-TTTCAAAAAATTGTCGTCT
1 TT--CAAAAATTTTCGTGTTTTC-AAAAATT-CCGTGT
* * * * *
55920099 TTTAAAAATTTTTGTG-TTTCTAAAATTTTCGTAT
1 TTCAAAAATTTTCGTGTTTTC-AAAAATTCCGTGT
55920133 TTCAAAAATTTTCGTGTTTTCAAAAATTCCGGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAATTCC-GTGT
**
55920168 TTCAAAAAATTCCCGTGTTTT-AAAAATTTCCGTGTT
1 TTC-AAAAATTTTCGTGTTTTCAAAAA-TTCCGTG-T
* * ** *
55920204 TTCAAAAA-TTTCGTGGTTTCAAAATTTTTTGTAT
1 TTCAAAAATTTTCGTGTTTTCAAAA-ATTCCGTGT
** * *
55920238 TTCAAAAATCCTCATGTTTTCAAAAATTTCAGTGT
1 TTCAAAAATTTTCGTGTTTTCAAAAA-TTCCGTGT
* *
55920273 GTT-GAAAATTTTCGTGTTTTCAAAAAAATCTCGTGT
1 -TTCAAAAATTTTCGTGTTTTC-AAAAATTC-CGTGT
* * * * * *** *
55920309 TTCATAAATTTTCATTTTTTTAAAAAATAATTAT
1 TTCAAAAATTTTCGTGTTTTCAAAAATTCCGTGT
* *
55920343 TTCAAAAATCTTCGTGTTTTAAAAAA
1 TTCAAAAATTTTCGTGTTTTCAAAAA
55920369 AATTCGTTTT
Statistics
Matches: 399, Mismatches: 86, Indels: 76
0.71 0.15 0.14
Matches are distributed among these distances:
32 12 0.03
33 11 0.03
34 80 0.20
35 133 0.33
36 83 0.21
37 44 0.11
38 12 0.03
39 11 0.03
40 13 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (34 bp):
TTCAAAAATTTTCGTGTTTTCAAAAATTCCGTGT
Found at i:55920256 original size:87 final size:87
Alignment explanation
Indices: 55919904--55920321 Score: 246
Period size: 87 Copynumber: 4.8 Consensus size: 87
55919894 ATATTCGTGT
* * * * *
55919904 TTTCAAAAGATT-CCAT-TTTTCAAAATTTTCCGTGTTTTCTAAAAATTTCCATGTTTCTAAAA-
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTT-CGTGTTTTCAAAAAATTT-CGTGTTTC-AAAAT
** *
55919966 TTT-GTG-TTTCAAAAATTTTCGTG
63 TTTCGTGTTTTCAAAAATTCCCATG
* *** * * * * * * **
55919989 TATTCAAAAATTTTTTGTATTTTGAACAATTCTCGTG-TTTCACAAATTTTCGTGTTTTAATTTT
1 T-TTCAAAAAATTCCCGTGTTTT-AAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTCAA-AAT
** * ** *
55920053 TTTTATGTTTTAAAAAAAATTATCGTG
63 TTTCGTGTTTT--CAAAAATTCCCATG
** * * * * *
55920080 TTTCAAAAAATTGTCGTCTTTTAAAAATTTTTGTG-TTTCTAAAATTTTCGTATTTCAAAAATTT
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTC-AAAATTT
**
55920144 TCGTGTTTTCAAAAATTCCGGTG
65 TCGTGTTTTCAAAAATTCCCATG
*
55920167 TTTCAAAAAATTCCCGTGTTTTAAAAATTTCCGTGTTTTC-AAAAATTTCGTGGTTTCAAAATTT
1 TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGT-GTTTCAAAATTT
*
55920231 T-TTGTATTTCAAAAA-TCCTCATG
65 TCGTGT-TTTCAAAAATTCC-CATG
* * * * *
55920254 TTTTC-AAAAATTTCAGTGTGTTGAAAATTTTCGTGTTTTCAAAAAAATCTCGTGTTTCATAAAT
1 -TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTC-AAAAAATTTCGTGTTTCA-AAAT
55920318 TTTC
63 TTTC
55920322 ATTTTTTTAA
Statistics
Matches: 260, Mismatches: 53, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
85 3 0.01
86 21 0.08
87 113 0.43
88 28 0.11
89 63 0.24
90 19 0.07
91 13 0.05
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (87 bp):
TTTCAAAAAATTCCCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTCGTGTTTCAAAATTTT
CGTGTTTTCAAAAATTCCCATG
Found at i:55931241 original size:8 final size:8
Alignment explanation
Indices: 55931228--55931257 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
55931218 TATTATGCCT
55931228 AAAAAAAG
1 AAAAAAAG
55931236 AAAAAAAAG
1 -AAAAAAAG
55931245 AAAAAAAG
1 AAAAAAAG
55931253 AAAAA
1 AAAAA
55931258 GAAAAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:55931242 original size:9 final size:9
Alignment explanation
Indices: 55931228--55931257 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
55931218 TATTATGCCT
55931228 AAAAAAAGA
1 AAAAAAAGA
55931237 AAAAAAAG-
1 AAAAAAAGA
55931245 AAAAAAAGA
1 AAAAAAAGA
55931254 AAAA
1 AAAA
55931258 GAAAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:55932005 original size:76 final size:76
Alignment explanation
Indices: 55931785--55933394 Score: 1614
Period size: 76 Copynumber: 20.8 Consensus size: 76
55931775 CAAGAAATAT
* *
55931785 TTTTTTAAATTTCTGTTTTTTCCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTT-AATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55931850 CACGCTGAGGTA
65 CACGCTGAGGTA
* * *
55931862 -TTTTTATTTTTTATTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGAG
1 TTTTTTAATTTCTA--TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
55931926 TCACGCTGAGGTA
64 TCACGCTGAGGTA
*
55931939 -TTTTTAATTTCTATTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTTAATTTCTATT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932003 CACGCTGAGGTA
65 CACGCTGAGGTA
*
55932015 TTTTTTTAATTTCTA-TTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGA
1 -TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
*
55932079 CACACTGAGGTA
65 CACGCTGAGGTA
* * *
55932091 -TTTTTAATTTCTGTTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGCGCCTCGGGT
1 TTTTTTAATTTCTATT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932155 CACGCTGAGGTA
65 CACGCTGAGGTA
* * *
55932167 TTTTTTAATTT-T-TGTTTTTTCAAAACTCAACTCATAATATGAGAGGTAAGTTGAGCCTCGGGT
1 TTTTTTAATTTCTAT-TTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932230 ----CTGAGGTA
65 CACGCTGAGGTA
* * * *
55932238 -TTTTTAATTTCTGTTGTTTTACAAAAATCAACTCATAGTACGAGAGGTGAGTTGAACCTCGGGT
1 TTTTTTAATTTCTATT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932302 CACGCTGAGGTA
65 CACGCTGAGGTA
*
55932314 TTTTTTAATTTCT-GTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
*
55932378 ATGCTGAGGTA
66 ACGCTGAGGTA
*
55932389 -TTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTTAATTTCT-ATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932453 CACGCTGAGGTA
65 CACGCTGAGGTA
* *
55932465 TTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGG
1 --TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
55932530 TCACGCTGAGGTA
64 TCACGCTGAGGTA
* * *
55932543 TTTCTTTTGAATTTCTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 -TT-TTTT-AATTTC----TATT-TTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGA
** * *
55932608 GCCTCGGACCATGCCGAGGTA
56 GCCTCGGGTCACGCTGAGGTA
* * * *
55932629 TTTCTTTTAAATT-TATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 -TT-TTTTAATTTCTATTTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
** * *
55932693 ACCATGCCGAGGTA
63 GTCACGCTGAGGTA
* * * * * * *
55932707 TTTCTTTTTAATTTCTATTTTTTT--TAAATTAGCTCATATTGCGAGAGATGAGTTGAGCCTC-C
1 --T-TTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
* *
55932769 GACACATGCCGAGGTA
63 GTCAC--GCTGAGGTA
*
55932785 TTTCTTTTAAATTTC--TGTTTTTCAAAAATCAACTCAT--TACGAGAGGTGAGTTGAGCCTCGG
1 -TT-TTTT-AATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
55932846 GTCACGCTGAGGTA
63 GTCACGCTGAGGTA
*
55932860 TTTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGT
1 -TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGT
55932925 CACGCTGAGGTA
65 CACGCTGAGGTA
* * *
55932937 TTTCTTTTAAATTTCTTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
1 -TT-TTTT-AATTTC-----TATT-TTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTG
** * *
55933002 AGCCTCGGACCATGCCGAGGTA
55 AGCCTCGGGTCACGCTGAGGTA
* * * *
55933024 TTTCTTTTAAATT-TATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 -TT-TTTTAATTTCTATTTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
** * *
55933088 ACCATGCCGAGGTA
63 GTCACGCTGAGGTA
* * * * * *
55933102 TTTCTTTTTAATTTCT-GTTTTTTAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC-C
1 --T-TTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
*
55933165 GACACATGAC-GAGGTA
63 GTCAC--G-CTGAGGTA
* *
55933181 TTTCTTTTAAATTTC--TGTTTTTCAAAAATCAACTCAT--TACGAGAGATGAGTTGAGCCTCGG
1 -TT-TTTT-AATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
*
55933242 GTCGCATGCTGAGGTA
63 GT--CACGCTGAGGTA
* * * * * * *
55933258 -TTTTAAATATCTA-TTTTTGCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGAGTC
1 TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
55933321 -CAG-TCGAGGTA
66 AC-GCT-GAGGTA
* * **** * * *
55933332 TTTTTCAAATTT-TACTTCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCGG
1 TTTTT-TAATTTCTA-TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
55933395 ATCGCATGCC
Statistics
Matches: 1340, Mismatches: 116, Indels: 154
0.83 0.07 0.10
Matches are distributed among these distances:
70 10 0.01
71 10 0.01
72 43 0.03
73 12 0.01
74 58 0.04
75 147 0.11
76 324 0.24
77 230 0.17
78 278 0.21
79 76 0.06
80 16 0.01
83 3 0.00
84 9 0.01
85 10 0.01
86 59 0.04
87 55 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (76 bp):
TTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTA
Found at i:55932517 original size:78 final size:78
Alignment explanation
Indices: 55931782--55933316 Score: 1656
Period size: 78 Copynumber: 19.8 Consensus size: 78
55931772 TTTCAAGAAA
* *
55931782 TATTTTTTTAAATTTCTGTTTTTTCCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
55931847 GGTCACGCTGAGG
66 GGTCACGCTGAGG
* *
55931860 TATTTTTATTT--TTTATTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1 TATTTTT-TTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
*
55931923 GAGTCACGCTGAGG
65 GGGTCACGCTGAGG
* *
55931937 TA---TTTTTAATTTCTATTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGAGCCTC
1 TATTTTTTTTAATTTCTGTT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
55931999 GGGTCACGCTGAGG
65 GGGTCACGCTGAGG
*
55932013 TA-TTTTTTTAATTTCT-ATTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
* *
55932076 GGACACACTGAGG
66 GGTCACGCTGAGG
* *
55932089 TA---TTTTTAATTTCTGTTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGCGCCTC
1 TATTTTTTTTAATTTCTGTT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
55932151 GGGTCACGCTGAGG
65 GGGTCACGCTGAGG
* * * *
55932165 TA--TTTTTTAATTTTTG-TTTTTTCAAAACTCAACTCATAATATGAGAGGTAAGTTGAGCCTCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
55932227 GGT----CTGAGG
66 GGTCACGCTGAGG
* * *
55932236 TA---TTTTTAATTTCTGTTGTTTTACAAAAATCAACTCATAGTACGAGAGGTGAGTTGAACCTC
1 TATTTTTTTTAATTTCTGTT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
55932298 GGGTCACGCTGAGG
65 GGGTCACGCTGAGG
55932312 TA--TTTTTTAATTTCTG-TTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
*
55932374 GGTCATGCTGAGG
66 GGTCACGCTGAGG
55932387 TA---TTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1 TATTTTTTTTAATTTCTG-TTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
55932449 GGGTCACGCTGAGG
65 GGGTCACGCTGAGG
*
55932463 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
55932528 GGTCACGCTGAGG
66 GGTCACGCTGAGG
* * * *
55932541 TATTTCTTTTGAATTTCTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
1 TATTT-TTTTTAATTTC----TGTT-TTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTT
** * *
55932606 GAGCCTCGGACCATGCCGAGG
58 GAGCCTCGGGTCACGCTGAGG
* * * *
55932627 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TATTT-TTTTTAATTTCTGTTTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
** * *
55932690 CGGACCATGCCGAGG
64 CGGGTCACGCTGAGG
* * * * * * *
55932705 TATTTCTTTTTAATTTCTATTTTTTT--TAAATTAGCTCATATTGCGAGAGATGAGTTGAGCCTC
1 TATTT-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
* * *
55932768 -CGACACATGCCGAGG
65 GGGTCAC--GCTGAGG
*
55932783 TATTTCTTTTAAATTTCTG--TTTTTCAAAAATCAACTCAT--TACGAGAGGTGAGTTGAGCCTC
1 TATTT-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
55932844 GGGTCACGCTGAGG
65 GGGTCACGCTGAGG
* *
55932858 TA-TTTTTTTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
55932922 GGTCACGCTGAGG
66 GGTCACGCTGAGG
* * * *
55932935 TATTTCTTTTAAATTTCTTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 TATTT-TTTTTAATTTC-----TGTT-TTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGT
** * *
55933000 TGAGCCTCGGACCATGCCGAGG
57 TGAGCCTCGGGTCACGCTGAGG
* * * *
55933022 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TATTT-TTTTTAATTTCTGTTTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
** * *
55933085 CGGACCATGCCGAGG
64 CGGGTCACGCTGAGG
* * * *
55933100 TATTTCTTTTTAATTTCTG-TTTTTTAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TATTT-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
* *
55933164 -CGACACATGAC-GAGG
65 GGGTCAC--G-CTGAGG
* *
55933179 TATTTCTTTTAAATTTCTG--TTTTTCAAAAATCAACTCAT--TACGAGAGATGAGTTGAGCCTC
1 TATTT-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
*
55933240 GGGTCGCATGCTGAGG
65 GGGT--CACGCTGAGG
* * * * * * *
55933256 TA---TTTTAAATATCT-ATTTTTGCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCG
1 TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
55933317 AGTCCAGTCG
Statistics
Matches: 1290, Mismatches: 105, Indels: 126
0.85 0.07 0.08
Matches are distributed among these distances:
70 12 0.01
71 9 0.01
72 42 0.03
73 25 0.02
74 48 0.04
75 134 0.10
76 309 0.24
77 174 0.13
78 313 0.24
79 77 0.06
80 6 0.00
82 2 0.00
83 3 0.00
84 9 0.01
85 6 0.00
86 60 0.05
87 61 0.05
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (78 bp):
TATTTTTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCG
GGTCACGCTGAGG
Found at i:55932881 original size:317 final size:309
Alignment explanation
Indices: 55931782--55933447 Score: 1499
Period size: 317 Copynumber: 5.4 Consensus size: 309
55931772 TTTCAAGAAA
* ** * *
55931782 TATTT-TTTTAAATTTCTGTTTTTTCCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC
1 TATTTCTTTTTAATTTCTGTTTTTT--TTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * * *
55931846 GGGTCAC--GCTGAGGTATTT-TTATTT--TTTATTTTTTTTTCAAAAATCAACTCATAATACGA
64 -GGACACATGCCGAGGTATTTCTT-TTTAATTT-CTGTTTTTTCAAAAATCAACTCAT--TACGA
* * *
55931906 GAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTA--T-TTTTAATTTC-TATTGTTTTTCAAAAAT
124 GAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAATTTCATTTTTTTTTTCAAAAAT
* * *
55931967 CAACTCATAGTACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTCTAT-
189 CAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGCCACGCTGAGGTA-TTTTTTAAATT-TATG
* * *
55932031 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGACACA--CTGAGG
252 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGG
* * * *
55932089 TA----TTTTTAATTTCTGTTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGCGCCT
1 TATTTCTTTTTAATTTCTGTT-TTTTT--TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * * * *
55932150 CGGGTCAC--GCTGAGGTA--T-TTTTTAATTTTTGTTTTTTCAAAACTCAACTCATAATATGAG
63 C-GGACACATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTCAAAAATCAACTCAT--TACGAG
* * * *
55932210 AGGTAAGTTGAGCCTCGGGT----CTGAGGTA--T-TTTTAATTTC-TGTTGTTTTACAAAAATC
125 AGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAATTTCATTTTTTTTTTCAAAAATC
* * * *
55932267 AACTCATAGTACGAGAGGTGAGTTGAACCTCGGGTCACGCTGAGGTATTTTTT-AATTTCTGTTT
190 AACTCATATTACGAGAGGTGAGTTGAGCCTCGGGCCACGCTGAGGTATTTTTTAAATTTATG-TT
* * ** *
55932331 TTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGG
254 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
* *
55932387 TA----TTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCT
1 TATTTCTTTTTAATTTCTGTTTTTTTT---AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
55932448 CGGGTCAC--GCTGAGGTATTT-TTTTTAATTTCTGTTTTTTTCAAAAATCAACTCATAATACGA
63 C-GGACACATGCCGAGGTATTTCTTTTTAATTTCTG-TTTTTTCAAAAATCAACTCAT--TACGA
* *
55932510 GAGGTGAGTTGAGCATCGGGTCACGCTGAGGTATTTCTTTTGAATTTCTTTTTTTTCTTTTTCAA
124 GAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTT-AATTTC--ATTTTT-TTTTTC--
* * * *
55932575 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAA
183 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGCCACGCTGAGGTA-TT-TTTTAAA
55932640 TTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
246 TTTATGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
* * * * *
55932705 TATTTCTTTTTAATTTCTATTTTTTTTAAATTAGCTCATATTGCGAGAGATGAGTTGAGCCTCCG
1 TATTTCTTTTTAATTTCTGTTTTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
55932770 ACACATGCCGAGGTATTTCTTTTAAATTTCTG-TTTTTCAAAAATCAACTCATTACGAGAGGTGA
66 ACACATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATTACGAGAGGTGA
*
55932834 GTTGAGCCTCGGGTCACGCTGAGGTATTT-TTTTAATTTC--TATTTTTTTCAAAAATCAACTCA
131 GTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAATTTCATTTTTTTTTTCAAAAATCAACTCA
* * * *
55932896 TAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGTATTTCTTTTAAATTTCTTTTTTTTT
196 TATTACGAGAGGTGAGTTGAGCCTCGGGCCACGCTGAGGTA-TT-TTTTAAA--------TTTAT
*
55932961 CTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
251 GTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
* * ***
55933022 TATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TATTTCTTTTTAATTTCTGTTTTT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * *
55933087 GAC-CATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTAAAAAATCAGCTCATATTGCGAGAGG
65 GACACATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTCAAAAATCAACTC--ATTACGAGAGG
* * *
55933151 TGAGTTGAGCCTC-CGACACATGAC-GAGGTATTTCTTTTAA----ATTTCTGTTTTTCAAAAAT
128 TGAGTTGAGCCTCGGGTCAC--G-CTGAGGTATTTCTTTTAATTTCATTT-TTTTTTTCAAAAAT
* *
55933210 CAACTC--ATTACGAGAGATGAGTTGAGCCTCGGGTCGCATGCTGAGGTA--TTTTAAATATCTA
189 CAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG-C-CACGCTGAGGTATTTTTTAAAT-T-TA
* * * *
55933271 T-TTTTGCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGAGTCCA-GTCGAGG
250 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GACCATGCCGAGG
** ****** *
55933330 TA-TT-TTTCAAATTTTACT-TCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCT
1 TATTTCTTTTTAA-TTT-CTGT-TTTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * * * * *
55933392 CGGATCGCATGCCAATGTA-TTCTTTTCAGTTTCTG-TTTTCCAAAAAATCAACTCAT
63 CGGA-CACATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTC-AAAAATCAACTCAT
55933448 AATTCGAAAG
Statistics
Matches: 1186, Mismatches: 102, Indels: 143
0.83 0.07 0.10
Matches are distributed among these distances:
296 4 0.00
297 10 0.01
298 123 0.10
299 81 0.07
300 13 0.01
301 45 0.04
302 3 0.00
303 50 0.04
304 17 0.01
305 63 0.05
306 8 0.01
307 54 0.05
308 136 0.11
309 21 0.02
310 12 0.01
311 5 0.00
312 3 0.00
313 5 0.00
315 53 0.04
316 16 0.01
317 159 0.13
318 112 0.09
319 79 0.07
320 35 0.03
321 52 0.04
322 27 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (309 bp):
TATTTCTTTTTAATTTCTGTTTTTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
ACACATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATTACGAGAGGTGA
GTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAATTTCATTTTTTTTTTCAAAAATCAACTCA
TATTACGAGAGGTGAGTTGAGCCTCGGGCCACGCTGAGGTATTTTTTAAATTTATGTTTTTCAAA
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
Found at i:55932992 original size:395 final size:382
Alignment explanation
Indices: 55931785--55933468 Score: 1861
Period size: 395 Copynumber: 4.4 Consensus size: 382
55931775 CAAGAAATAT
* * * * *
55931785 TTTTTTAAATTTCTGT-TTTTTC-CAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGG
1 TTTTTTAAATTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
** * * * ** *
55931848 GTCACGCTGAGGTATTTTTATTTTTTATTT-T-TTTTTC-AAAAATCAACTCATAATACGAGAGG
66 ACCATGCCGAGGTA--TTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTACGAGAGG
* * *
55931910 TGAGTTGAGCCTC-GAGTCACGCTGAGGTA-TTTTTAATTTCTATTGTTTTTCAAAAATCAACTC
129 TGAGTTGAGCCTCGGA-CCACGCCGAGGTATTTTTTAATTTCTA-T-TTTTTAAAAAATCAACTC
* * * * *
55931973 ATAGTACGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTTTTTAATTTCTATTTTTT
191 ATATTACGAGAGGTGAGTTGAGCCTC-CGACACATGCCGAGGTATTTTTTTAATTTCT-GTTTTT
* *
55932036 CAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAATTT
254 CAAAAATCAACTCAT-ATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT
* * * *
55932101 CTGTTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGCGCCTCGGGTCACGCTGAGGT
318 CTATT-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGT
55932166 A
382 A
* * * ** *
55932167 TTTTTT-AATTTTTGT-TTTTTC--AAAACTCAACTCATAATATGAGAGGTAAGTTGAGCCTCGG
1 TTTTTTAAATTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* * * * *
55932228 ---GT-CTGAGGTA--T-TTTT-AATTTCTGTTGTTTTACAAAAATCAACTCATAGTACGAGAGG
66 ACCATGCCGAGGTATTTCTTTTAAATTTATGTT-TTTCA-AAAAATCAACTCATATTACGAGAGG
* ** * * *
55932285 TGAGTTGAACCTCGGGTCACGCTGAGGTATTTTTTAATTTCTGTTTTTTCAAAAATCAACTCATA
129 TGAGTTGAGCCTCGGACCACGCCGAGGTATTTTTTAATTTCTATTTTTTAAAAAATCAACTCATA
* *** *
55932350 ATACGAGAGGTGAGTTGAGCCT-CGGGTCATGCTGAGGTA--TTTTTAATTTCTGTTTTTTTTCA
194 TTACGAGAGGTGAGTTGAGCCTCCGACACATGCCGAGGTATTTTTTTAATTTCTG---TTTTTCA
55932412 AAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATT
256 AAAATCAACTCAT-ATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAATT
*
55932477 TCTGTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGT
317 TCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGT
55932542 A
382 A
*
55932543 TTTCTTTTGAATTTCTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 -TT-TTTT-AA----ATTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
*
55932608 GCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCG
59 GCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTACG
* ** *
55932673 AGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTTAATTTCTATTTTTT-TTAAATT
124 AGAGGTGAGTTGAGCCTCGGACCACGCCGAGGTA--T-TTTTTAATTTCTATTTTTTAAAAAATC
* * *
55932737 AGCTCATATTGCGAGAGATGAGTTGAGCCTCCGACACATGCCGAGGTATTTCTTTTAAATTTCTG
186 AACTCATATTACGAGAGGTGAGTTGAGCCTCCGACACATGCCGAGGTATTT-TTTT-AATTTCTG
55932802 TTTTTCAAAAATCAACTCAT-TACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTT
249 TTTTTCAAAAATCAACTCATATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--TTTT
55932866 TAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCT
312 TAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCT
55932931 GAGGTA
377 GAGGTA
55932937 TTTCTTTTAAATTTCTTTTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
1 -TT-TTTTAAA------TTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
55933002 AGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGC
58 AGCCTCGGACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTAC
* *
55933067 GAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTTAATTTCTGTTTTTTAAAAAAT
123 GAGAGGTGAGTTGAGCCTCGGACCACGCCGAGGTA--T-TTTTTAATTTCTATTTTTTAAAAAAT
* * *
55933132 CAGCTCATATTGCGAGAGGTGAGTTGAGCCTCCGACACATGACGAGGTATTTCTTTTAAATTTCT
185 CAACTCATATTACGAGAGGTGAGTTGAGCCTCCGACACATGCCGAGGTATTT-TTTT-AATTTCT
* *
55933197 GTTTTTCAAAAATCAACTCAT-TACGAGAGATGAGTTGAGCCTCGGGTCGCATGCTGAGGTATTT
248 GTTTTTCAAAAATCAACTCATATACGAGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTATTT
* * * * * * * *
55933261 TAAATATCTA-TTTTTGCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGAGTC-CAG
311 TTAATTTCTATTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCAC-G
55933324 -TCGAGGTA
375 CT-GAGGTA
* * * ** *
55933332 TTTTTCAAA--TTTTACTTCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCGG
1 TTTTTTAAATTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* * * * * * *
55933395 ATCGCATGCCAATGTA-TTCTTTTCAGTTTCTGTTTTCCAAAAAATCAACTCATAATT-CGAAAG
66 A-C-CATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCAT-ATTACGAGAG
*
55933458 GAGAGTTGAGC
128 GTGAGTTGAGC
55933469 TTTGGGTTGC
Statistics
Matches: 1161, Mismatches: 85, Indels: 108
0.86 0.06 0.08
Matches are distributed among these distances:
370 4 0.00
371 5 0.00
372 17 0.01
373 3 0.00
374 109 0.09
375 50 0.04
376 78 0.07
377 17 0.01
378 4 0.00
380 38 0.03
381 14 0.01
382 6 0.01
384 6 0.01
385 56 0.05
386 49 0.04
387 48 0.04
390 1 0.00
391 7 0.01
393 56 0.05
394 96 0.08
395 299 0.26
396 154 0.13
397 20 0.02
398 12 0.01
399 4 0.00
400 8 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (382 bp):
TTTTTTAAATTTTTTTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
ACCATGCCGAGGTATTTCTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTACGAGAGGTG
AGTTGAGCCTCGGACCACGCCGAGGTATTTTTTAATTTCTATTTTTTAAAAAATCAACTCATATT
ACGAGAGGTGAGTTGAGCCTCCGACACATGCCGAGGTATTTTTTTAATTTCTGTTTTTCAAAAAT
CAACTCATATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTATTTTT
TTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCATCGGGTCACGCTGAGGTA
Found at i:55933726 original size:29 final size:28
Alignment explanation
Indices: 55933675--55933829 Score: 130
Period size: 30 Copynumber: 5.2 Consensus size: 28
55933665 AAAAATAAAA
**
55933675 AAAATTACATTTTGGCCCTTAAACTTTTT
1 AAAATTACATTTTAACCCTTAAA-TTTTT
* *
55933704 AAAATTGCATTTTAACCCCTAAATTTTCCT
1 AAAATTACATTTTAACCCTTAAATTTT--T
*
55933734 AAAATTATATTTTAACCCTTAAAATTTTTT
1 AAAATTACATTTTAACCCTT-AAA-TTTTT
* * *
55933764 TAAACTACATTTTAACCCATAAAATTTTT
1 AAAATTACATTTTAACCC-TTAAATTTTT
* * * *
55933793 GAAATTACATTATGACCCTTAAGTTTTCT
1 AAAATTACATTTTAACCCTTAAATTTT-T
55933822 CAAAATTA
1 -AAAATTA
55933830 TGTTTTGGCC
Statistics
Matches: 101, Mismatches: 18, Indels: 13
0.77 0.14 0.10
Matches are distributed among these distances:
28 11 0.11
29 39 0.39
30 43 0.43
31 4 0.04
32 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.43
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTTAAATTTTT
Found at i:55933738 original size:59 final size:58
Alignment explanation
Indices: 55933675--55933814 Score: 156
Period size: 59 Copynumber: 2.4 Consensus size: 58
55933665 AAAAATAAAA
* * * *
55933675 AAAATTACATTTTGGCCCTTAAACTTTTTAAAATTGCATTTTAACCCCT-AAATTTTCCT
1 AAAATTACATTTTGACCCTTAAACTTTTTAAAACTACATTTTAACCCATAAAATTTT--T
* * * *
55933734 AAAATTATATTTTAACCCTTAAAATTTTTTTAAACTACATTTTAACCCATAAAATTTTT
1 AAAATTACATTTTGACCCTT-AAACTTTTTAAAACTACATTTTAACCCATAAAATTTTT
* *
55933793 GAAATTACATTATGACCCTTAA
1 AAAATTACATTTTGACCCTTAA
55933815 GTTTTCTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.03
59 34 0.51
60 24 0.36
61 7 0.10
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (58 bp):
AAAATTACATTTTGACCCTTAAACTTTTTAAAACTACATTTTAACCCATAAAATTTTT
Found at i:55934075 original size:16 final size:16
Alignment explanation
Indices: 55934056--55934089 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
55934046 AAAGGGAAAT
55934056 AGGAGAAAAAAGAGAA
1 AGGAGAAAAAAGAGAA
*
55934072 AGGAGAGAAAAGAGAA
1 AGGAGAAAAAAGAGAA
55934088 AG
1 AG
55934090 AAGAGGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AGGAGAAAAAAGAGAA
Found at i:55934116 original size:14 final size:16
Alignment explanation
Indices: 55934063--55934118 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
55934053 AATAGGAGAA
*
55934063 AAAAGAGAAAGGAGAG
1 AAAAGAGAAAGAAGAG
55934079 AAAAGAGAAAGAAGAGG
1 AAAAGAGAAAGAAGA-G
*
55934096 AAGAA-AGGAAGAAGAG
1 AA-AAGAGAAAGAAGAG
55934112 AAAAGAG
1 AAAAGAG
55934119 GGGAAGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 19 0.54
17 12 0.34
18 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AAAAGAGAAAGAAGAG
Found at i:55934186 original size:3 final size:3
Alignment explanation
Indices: 55934178--55934211 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
55934168 AGTTTCCAAG
* *
55934178 AGA AGA AGA AGA AGA AGG AGA AGG AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
55934212 AAACAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55934200 original size:18 final size:18
Alignment explanation
Indices: 55934177--55934211 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55934167 GAGTTTCCAA
55934177 GAGAAGAAGAAGAAGAAG
1 GAGAAGAAGAAGAAGAAG
*
55934195 GAGAAGGAGAAGAAGAA
1 GAGAAGAAGAAGAAGAA
55934212 AAACAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (18 bp):
GAGAAGAAGAAGAAGAAG
Found at i:55934266 original size:12 final size:12
Alignment explanation
Indices: 55934249--55934284 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
55934239 CAGGTCAGAC
55934249 CGACCCGACCCA
1 CGACCCGACCCA
*
55934261 CGACCCGACCCG
1 CGACCCGACCCA
*
55934273 TGACCCGACCCA
1 CGACCCGACCCA
55934285 ACACCAGCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.56, G:0.19, T:0.03
Consensus pattern (12 bp):
CGACCCGACCCA
Found at i:55934510 original size:10 final size:10
Alignment explanation
Indices: 55934495--55934590 Score: 73
Period size: 9 Copynumber: 10.0 Consensus size: 10
55934485 CCAGTAGAAA
55934495 AAAAAAAGAG
1 AAAAAAAGAG
55934505 -AAAAAAGAAG
1 AAAAAAAG-AG
*
55934515 AAAAAAGGA-
1 AAAAAAAGAG
*
55934524 AAAAAAAAAG
1 AAAAAAAGAG
55934534 AAGAAAAAAGAG
1 -A-AAAAAAGAG
55934546 AAGAAAAA-AG
1 AA-AAAAAGAG
*
55934556 AAGAAAAGAG
1 AAAAAAAGAG
55934566 --AAAAAGAG
1 AAAAAAAGAG
55934574 --AAAAAGA-
1 AAAAAAAGAG
55934581 AAAAAAAGAG
1 AAAAAAAGAG
55934591 GTTCAATTCG
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
8 14 0.20
9 25 0.36
10 10 0.14
11 13 0.19
12 8 0.11
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:55934530 original size:22 final size:22
Alignment explanation
Indices: 55934505--55934588 Score: 100
Period size: 22 Copynumber: 3.8 Consensus size: 22
55934495 AAAAAAAGAG
55934505 AAAAAAGAAGAAAAAAGGAAAA
1 AAAAAAGAAGAAAAAAGGAAAA
*
55934527 AAAAAAGAAGAAAAAA-GAGAAG
1 AAAAAAGAAGAAAAAAGGA-AAA
* *
55934549 AAAAAAGAAGAAAAGAGAAAAA
1 AAAAAAGAAGAAAAAAGGAAAA
55934571 GAGAAAAAGAA-AAAAAAG
1 -A-AAAAAGAAGAAAAAAG
55934589 AGGTTCAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
21 2 0.04
22 35 0.66
23 8 0.15
24 8 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAAAAAGGAAAA
Found at i:55934554 original size:44 final size:42
Alignment explanation
Indices: 55934494--55934590 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 42
55934484 CCCAGTAGAA
*
55934494 AAAAAAAAGAGAAAAAAGAAGAAAAAAGGAAAAA-AAAAAGAAG
1 AAAAAAAAGAGAAAAAAGAAGAAAAAA-GAAAAAGAGAAA-AAG
* *
55934537 AAAAAAGAGAAGAAAAAAGAAGAAAAGAGAAAAAGAGAAAAAG
1 AAAAAAAAG-AGAAAAAAGAAGAAAAAAGAAAAAGAGAAAAAG
55934580 AAAAAAAAGAG
1 AAAAAAAAGAG
55934591 GTTCAATTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.04
43 25 0.52
44 21 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (42 bp):
AAAAAAAAGAGAAAAAAGAAGAAAAAAGAAAAAGAGAAAAAG
Found at i:55934587 original size:34 final size:32
Alignment explanation
Indices: 55934490--55934587 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 32
55934480 GCAGCCCAGT
*
55934490 AGAAAAAAAAAAGAGAAAAAAGAAGAAAAAAG
1 AGAAAAAAAAAAGAGAAAAAAGAAAAAAAAAG
55934522 -GAAAAAAAAAAGAAGAAAAAAGAGAAGAAAAAAG
1 AGAAAAAAAAAAG-AGAAAAAAGA-AA-AAAAAAG
55934556 AAGAAAAGAGAAAAAGAG-AAAAAGAAAAAAAA
1 -AGAAAA-A-AAAAAGAGAAAAAAGAAAAAAAA
55934588 GAGGTTCAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
31 12 0.21
32 10 0.17
33 1 0.02
34 12 0.21
35 2 0.03
36 12 0.21
37 3 0.05
38 6 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (32 bp):
AGAAAAAAAAAAGAGAAAAAAGAAAAAAAAAG
Found at i:55934932 original size:18 final size:18
Alignment explanation
Indices: 55934911--55935294 Score: 124
Period size: 18 Copynumber: 21.5 Consensus size: 18
55934901 AATGTAAATA
55934911 TTCAAAAAATTTCGTGTT
1 TTCAAAAAATTTCGTGTT
*
55934929 TTCACAAAAAATTTCCATG-T
1 TT--CAAAAAATTT-CGTGTT
* * **
55934949 TTC-GAAATTTTCGTGGC
1 TTCAAAAAATTTCGTGTT
55934966 TTCAAAATAATTTTTC-TCGTGT
1 TTCAAAA-AA--TTTCGT-GT-T
*
55934988 TTCAAAAAATATTCCTGTT
1 TTCAAAAAAT-TTCGTGTT
* *
55935007 TTCAAAAGA-TTC-TATTT
1 TTCAAAAAATTTCGT-GTT
*
55935024 TTC-AAAATTTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
* *
55935042 TTCTAAAAATTTCCATG-T
1 TTCAAAAAATTT-CGTGTT
*
55935060 TTC-TAAAATTT-GTG-T
1 TTCAAAAAATTTCGTGTT
* *
55935075 TTCAAAAATTTTCGTGTA
1 TTCAAAAAATTTCGTGTT
* * *
55935093 TTCAAAAATTTTTTGTATT
1 TTCAAAAA-ATTTCGTGTT
*
55935112 TTC-AACAATTCTCGTG-T
1 TTCAAAAAATT-TCGTGTT
* * *
55935129 TTCACAAATTTTCATGTT
1 TTCAAAAAATTTCGTGTT
*** **
55935147 TT-AAATTTTTTTATG-T
1 TTCAAAAAATTTCGTGTT
* * *
55935163 TTCTAAAATTTTTGTG-T
1 TTCAAAAAATTTCGTGTT
*
55935180 TTC-TAAAATTTCCGTGTT
1 TTCAAAAAATTT-CGTGTT
* * *
55935198 TTCAAAAATTTTTGTGGT
1 TTCAAAAAATTTCGTGTT
** *
55935216 TTCAAAATTTTTCGT-AT
1 TTCAAAAAATTTCGTGTT
*
55935233 TTC-AAAAATCCTCGTGTT
1 TTCAAAAAAT-TTCGTGTT
55935251 TTC-AAAAATTTCGGTGTT
1 TTCAAAAAATTTC-GTGTT
* *
55935269 TT-GAAAATTTTCGTGTT
1 TTCAAAAAATTTCGTGTT
55935286 TTCAAAAAA
1 TTCAAAAAA
55935295 ATCGCATGTT
Statistics
Matches: 275, Mismatches: 58, Indels: 66
0.69 0.15 0.17
Matches are distributed among these distances:
15 6 0.02
16 26 0.09
17 81 0.29
18 86 0.31
19 39 0.14
20 19 0.07
21 11 0.04
22 7 0.03
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (18 bp):
TTCAAAAAATTTCGTGTT
Found at i:55935077 original size:15 final size:15
Alignment explanation
Indices: 55935057--55935103 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
55935047 AAAATTTCCA
*
55935057 TGTTTCTAAAATTTG
1 TGTTTCAAAAATTTG
55935072 TGTTTCAAAAATTTTCG
1 TGTTTCAAAAA-TTT-G
55935089 TGTATTCAAAAATTT
1 TGT-TTCAAAAATTT
55935104 TTTGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.36
16 3 0.11
17 7 0.25
18 8 0.29
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (15 bp):
TGTTTCAAAAATTTG
Found at i:55935099 original size:17 final size:17
Alignment explanation
Indices: 55934982--55935293 Score: 193
Period size: 17 Copynumber: 17.8 Consensus size: 17
55934972 ATAATTTTTC
*
55934982 TCGTGTTTCAAAAAATAT
1 TCGTGTTTC-AAAAATTT
* *
55935000 TCCTGTTTTCAAAAGATTC
1 TCGTG-TTTCAAAA-ATTT
* *
55935019 T-ATTTTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
55935034 TCCGTGTTTTCTAAAAATTT
1 T-CGTG-TTTC-AAAAATTT
* * *
55935054 CCATGTTTCTAAAA-TT
1 TCGTGTTTCAAAAATTT
55935070 T-GTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
55935086 TCGTGTATTCAAAAATTTT
1 TCGTGT-TTCAAAAA-TTT
* * * *
55935105 TTGTATTTTCAACAATTC
1 TCGT-GTTTCAAAAATTT
*
55935123 TCGTGTTTCACAAATTT
1 TCGTGTTTCAAAAATTT
* * **
55935140 TCATGTTTTAAATTTTT
1 TCGTGTTTCAAAAATTT
** *
55935157 TTATGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
* *
55935174 TTGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
*
55935191 CCGTGTTTTCAAAAATTT
1 TCGTG-TTTCAAAAATTT
* *
55935209 TTGTGGTTTCAAAATTTT
1 TCGT-GTTTCAAAAATTT
* **
55935227 TCGTATTTCAAAAATCC
1 TCGTGTTTCAAAAATTT
55935244 TCGTGTTTTCAAAAA-TT
1 TCGTG-TTTCAAAAATTT
**
55935261 TCGGTGTTTTGAAAATTT
1 TC-GTGTTTCAAAAATTT
55935279 TCGTGTTTTCAAAAA
1 TCGTG-TTTCAAAAA
55935294 AATCGCATGT
Statistics
Matches: 224, Mismatches: 52, Indels: 36
0.72 0.17 0.12
Matches are distributed among these distances:
15 14 0.06
16 8 0.04
17 90 0.40
18 80 0.36
19 24 0.11
20 8 0.04
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:55935287 original size:35 final size:34
Alignment explanation
Indices: 55934982--55935293 Score: 165
Period size: 35 Copynumber: 8.9 Consensus size: 34
55934972 ATAATTTTTC
* * *
55934982 TCGTGTTTCAAAAAATATTCCTGTTTTCAAAAGA-T
1 TCGTGTTT-TAAAAATTTTCGTGTTTTCAAAA-ATT
* *
55935017 TC-TATTTTTCAAAATTTTCCGTGTTTTCTAAAAATT
1 TCGT-GTTTTAAAAATTTT-CGTGTTTTC-AAAAATT
*
55935053 TCCATGTTTCT-AAAA-TTT-GTG-TTTCAAAAATTT
1 T-CGTGTTT-TAAAAATTTTCGTGTTTTCAAAAA-TT
* * * *
55935086 TCGTGTATTCAAAAATTTTTTGTATTTTCAACAATT
1 TCGTGT-TTTAAAAA-TTTTCGTGTTTTCAAAAATT
* * * **
55935122 CTCGTGTTTCACAAATTTTCATGTTTT-AAATTTTT
1 -TCGTGTTTTAAAAATTTTCGTGTTTTCAAA-AATT
** * *
55935157 TTATGTTTCT-AAAATTTTTGTG-TTTCTAAAATT
1 TCGTGTTT-TAAAAATTTTCGTGTTTTCAAAAATT
* * *
55935190 TCCGTGTTTTCAAAAATTTTTGTGGTTTCAAAATTTT
1 T-CGTGTTTT-AAAAATTTTCGTGTTTTCAAAA-ATT
* * **
55935227 TCGTATTTCAAAAATCCTCGTGTTTTCAAAAATT
1 TCGTGTTTTAAAAATTTTCGTGTTTTCAAAAATT
*
55935261 TCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 TC-GTGTTTTAAAAATTTTCGTGTTTTCAAAAA
55935294 AATCGCATGT
Statistics
Matches: 211, Mismatches: 42, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
32 9 0.04
33 20 0.09
34 39 0.18
35 83 0.39
36 33 0.16
37 25 0.12
38 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (34 bp):
TCGTGTTTTAAAAATTTTCGTGTTTTCAAAAATT
Found at i:55938175 original size:32 final size:32
Alignment explanation
Indices: 55938134--55938194 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
55938124 GGTAATGAAG
*
55938134 TTTATGCTTTAGCAATGTGCT-TAAGTATTCAA
1 TTTATGCTTTAGCAATATG-TGTAAGTATTCAA
55938166 TTTATGCTTTAGCAATATGTGTAAGTATT
1 TTTATGCTTTAGCAATATGTGTAAGTATT
55938195 TTCCTCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (32 bp):
TTTATGCTTTAGCAATATGTGTAAGTATTCAA
Done.