Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 128 of 320
Found at i:41898694 original size:44 final size:45
Alignment explanation
Indices: 41898631--41898725 Score: 156
Period size: 44 Copynumber: 2.1 Consensus size: 45
41898621 ACTTCAACCT
* *
41898631 GCTCCACTGCAACTTCAGGGAGGCAGAATCT-GTATCTTCGATCA
1 GCTCCACTGCAACTTCAGGGAGGAAAAATCTGGTATCTTCGATCA
*
41898675 GCTCCACTGCAACTTCAGGGAGGAAAAATCTGGTGTCTTCGATCA
1 GCTCCACTGCAACTTCAGGGAGGAAAAATCTGGTATCTTCGATCA
41898720 GCTCCA
1 GCTCCA
41898726 GCCTTTATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 29 0.62
45 18 0.38
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGGAAAAATCTGGTATCTTCGATCA
Found at i:41899021 original size:73 final size:74
Alignment explanation
Indices: 41898833--41899217 Score: 418
Period size: 75 Copynumber: 5.1 Consensus size: 74
41898823 AGTAAAAAAC
* * *
41898833 TAAAAATACCTCAGTGTGTGACTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTT
1 TAAAAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTT
* *
41898898 TATAAAAAGCGGAAA-
61 T-GAAAAA-CAGAAAT
* ** * *
41898913 TAGAAAATACATCA-CGTGTGATTCGAGGCTCAACTCACCTCTCACAGTATGAGTTGATTTTTGA
1 TA-AAAATACCTCAGCGTGTGCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
41898977 AAAACAGAAAT
64 AAAACAGAAAT
* * *
41898988 TAAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTAAAA
1 TAAAAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
*
41899052 AACAGGAAT
66 AACAGAAAT
* * * *
41899061 TGAAAATACCTCAGCGTGTGAACTGAGGCTCAACTCATCTATCGCAATATGAGTTGATATTTTTG
1 TAAAAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTTG
41899126 AAAAACAGAAAT
63 AAAAACAGAAAT
** *
41899138 TGTAAATACCTCAGCGTGTGAGCC-GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGA
1 TAAAAATACCTCAGCGTGT--GCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
41899202 AAGACAGAAAT
64 AAAACAGAAAT
41899213 TAAAA
1 TAAAA
41899218 CATCAGAGCA
Statistics
Matches: 263, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
73 63 0.24
74 16 0.06
75 64 0.24
76 5 0.02
77 64 0.24
78 1 0.00
79 3 0.01
80 37 0.14
81 10 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (74 bp):
TAAAAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
AACAGAAAT
Found at i:41899157 original size:77 final size:74
Alignment explanation
Indices: 41898835--41899217 Score: 448
Period size: 77 Copynumber: 5.1 Consensus size: 74
41898825 TAAAAAACTA
* *
41898835 AAAATACCTCAGTGTGTGACTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTA
1 AAAATACCTCAGCGTGTGAC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTT-
* * *
41898900 TAAAAAGCGGAAATAG
60 GAAAAA-CAGAAATTG
* * * *
41898916 AAAATACATCA-CGTGTGATTCGAGGCTCAACTCACCTCTCACAGTATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGTGACT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
*
41898980 ACAGAAATTA
65 ACAGAAATTG
* * * *
41898990 AAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAA
1 AAAATACCTCAGCGTGTGACTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
*
41899054 CAGGAATTG
66 CAGAAATTG
* *
41899063 AAAATACCTCAGCGTGTGAACTGAGGCTCAACTCATCTATCGCAATATGAGTTGATATTTTTGAA
1 AAAATACCTCAGCGTGTG-ACTGAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTTGAA
41899128 AAACAGAAATTG
63 AAACAGAAATTG
* * * *
41899140 TAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAG
1 AAAATACCTCAGCGTGTGA-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
41899205 ACAGAAATT-
65 ACAGAAATTG
41899214 AAAA
1 AAAA
41899218 CATCAGAGCA
Statistics
Matches: 262, Mismatches: 33, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
73 63 0.24
74 20 0.08
75 60 0.23
76 6 0.02
77 66 0.25
79 1 0.00
80 36 0.14
81 10 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (74 bp):
AAAATACCTCAGCGTGTGACTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
CAGAAATTG
Found at i:41909159 original size:20 final size:20
Alignment explanation
Indices: 41909134--41909200 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
41909124 TTGCTGGTCA
41909134 TTAATACAACTTATCTTAGT
1 TTAATACAACTTATCTTAGT
* *
41909154 TTAATAGATGAGTTA-C-TAGT
1 TTAATACA--ACTTATCTTAGT
*
41909174 CATTAATACAACTCATCTTAGT
1 --TTAATACAACTTATCTTAGT
41909196 TTAAT
1 TTAAT
41909201 TAAATGAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 19 0.53
21 2 0.06
22 15 0.42
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (20 bp):
TTAATACAACTTATCTTAGT
Found at i:41909165 original size:42 final size:42
Alignment explanation
Indices: 41909105--41909210 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
41909095 CATTTAAGCC
* * *
41909105 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTTA
1 TCTTAGTTTAATAAATGAGTTACTAGTCATTAATACAACTCA
*
41909147 TCTTAGTTTAATAGATGAGTTACTAGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTACTAGTCATTAATACAACTCA
41909189 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
41909211 TATTTAATGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 49 0.84
43 9 0.16
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTACTAGTCATTAATACAACTCA
Found at i:41909212 original size:14 final size:14
Alignment explanation
Indices: 41909193--41909237 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
41909183 AACTCATCTT
*
41909193 AGTTTAATTAAATG
1 AGTTTAATTTAATG
41909207 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
41909220 AATTTAATTTAATG
1 AGTTTAATTTAATG
41909234 AGTT
1 AGTT
41909238 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:41912943 original size:21 final size:20
Alignment explanation
Indices: 41912919--41912962 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41912909 ATACGTAATA
41912919 ATAGGAATAAAAAGTATATAC
1 ATAGGAATAAAAA-TATATAC
* * *
41912940 ATAGTATTAAAAATATGTAC
1 ATAGGAATAAAAATATATAC
41912960 ATA
1 ATA
41912963 ATATAGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (20 bp):
ATAGGAATAAAAATATATAC
Found at i:41912955 original size:47 final size:44
Alignment explanation
Indices: 41912887--41912987 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 44
41912877 ATATAAATAT
* * *
41912887 ATACATATAT-GTATTAAAATATATACGTAATAATAGGAATAAAA
1 ATACATACATAGTATTAAAATATATACATAAT-ATAGCAATAAAA
* * *
41912931 AGTATATACATAGTATTAAAAATATGTACATAATATAGCATTAAAA
1 A-TACATACATAGTATT-AAAATATATACATAATATAGCAATAAAA
41912977 ATACATACATA
1 ATACATACATA
41912988 ATATAGTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 1 0.02
45 16 0.34
46 16 0.34
47 14 0.30
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (44 bp):
ATACATACATAGTATTAAAATATATACATAATATAGCAATAAAA
Found at i:41913011 original size:27 final size:25
Alignment explanation
Indices: 41912881--41913163 Score: 169
Period size: 25 Copynumber: 11.7 Consensus size: 25
41912871 AACGATATAT
41912881 AAATATATACAT-ATAT-GTATT-A
1 AAATATATACATAATATAGTATTAA
* * *
41912903 AAATATATACGTAATAATAGGAATAA
1 AAATATATACATAAT-ATAGTATTAA
41912929 AAAGTATATAC-----ATAGTATTAA
1 AAA-TATATACATAATATAGTATTAA
* *
41912950 AAATATGTACATAATATAGCATTAA
1 AAATATATACATAATATAGTATTAA
*
41912975 AAATACATACATAATATAGTTATTAAA
1 AAATATATACATAATATAG-TATT-AA
*
41913002 AAATATATACATACGATAATATGTA-AAA
1 AAATATATACATA--AT-ATA-GTATTAA
*
41913030 TATATATATATAAATAATATAGTATTAA
1 -A-A-ATATATACATAATATAGTATTAA
*
41913058 AAATATATACATGATATA-TA-T-A
1 AAATATATACATAATATAGTATTAA
*
41913080 AAA-ATATA-AT-AT-T--TA-AAA
1 AAATATATACATAATATAGTATTAA
* * *
41913098 GATATATATACGTAATATA-TA-TAT
1 -AAATATATACATAATATAGTATTAA
*
41913122 AAATGTATACATAATATAGTATT-A
1 AAATATATACATAATATAGTATTAA
*
41913146 AAATATTTACATAATATA
1 AAATATATACATAATATA
41913164 TGCATATTAG
Statistics
Matches: 205, Mismatches: 27, Indels: 56
0.71 0.09 0.19
Matches are distributed among these distances:
17 2 0.01
18 2 0.01
19 4 0.02
20 13 0.06
21 17 0.08
22 17 0.08
23 19 0.09
24 25 0.12
25 44 0.21
26 8 0.04
27 25 0.12
28 7 0.03
29 5 0.02
30 6 0.03
31 11 0.05
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (25 bp):
AAATATATACATAATATAGTATTAA
Found at i:41913015 original size:31 final size:30
Alignment explanation
Indices: 41912977--41913069 Score: 106
Period size: 27 Copynumber: 3.2 Consensus size: 30
41912967 AGCATTAAAA
41912977 ATACATACATAATATAGTTATTAAAAAATAT
1 ATACATACATAATATAG-TATTAAAAAATAT
*
41913008 ATACATACGATAATAT-G---TAAAATATAT
1 ATACATAC-ATAATATAGTATTAAAAAATAT
* *
41913035 ATATATAAATAATATAGTATT-AAAAATAT
1 ATACATACATAATATAGTATTAAAAAATAT
41913064 ATACAT
1 ATACAT
41913070 GATATATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
26 7 0.13
27 16 0.31
29 12 0.23
30 1 0.02
31 9 0.17
32 7 0.13
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
ATACATACATAATATAGTATTAAAAAATAT
Found at i:41913043 original size:15 final size:15
Alignment explanation
Indices: 41913020--41913122 Score: 53
Period size: 14 Copynumber: 7.2 Consensus size: 15
41913010 ACATACGATA
*
41913020 ATATGTAAAATATAT
1 ATATATAAAATATAT
41913035 ATATAT-AAATA-AT
1 ATATATAAAATATAT
41913048 ATAGTATTAAAA-ATAT
1 ATA-TA-TAAAATATAT
* *
41913064 ATACAT----GATAT
1 ATATATAAAATATAT
41913075 ATATA-AAAATATA-
1 ATATATAAAATATAT
* *
41913088 ATATTTAAAAGATAT
1 ATATATAAAATATAT
*
41913103 ATATACGTAATATATAT
1 ATATA--TAAAATATAT
41913120 ATA
1 ATA
41913123 AATGTATACA
Statistics
Matches: 66, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
11 8 0.12
13 9 0.14
14 18 0.27
15 12 0.18
16 8 0.12
17 11 0.17
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATATAAAATATAT
Found at i:41913048 original size:17 final size:17
Alignment explanation
Indices: 41913028--41913139 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
41913018 TAATATGTAA
41913028 AATATATATATATAAAT
1 AATATATATATATAAAT
*
41913045 AATATAGTAT-TAAAAAT
1 AATATA-TATATATAAAT
41913062 ATATACATGATATATATAAA-
1 A-AT--AT-ATATATATAAAT
*
41913082 AATATA-ATATTTAAA-
1 AATATATATATATAAAT
**
41913097 AGATATATATACGTAATAT
1 A-ATATATATATATAA-AT
* * *
41913116 ATATATAAATGTATACAT
1 A-ATATATATATATAAAT
41913134 AATATA
1 AATATA
41913140 GTATTAAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
15 9 0.12
16 6 0.08
17 26 0.35
18 9 0.12
19 12 0.16
20 6 0.08
21 6 0.08
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (17 bp):
AATATATATATATAAAT
Found at i:41913049 original size:13 final size:13
Alignment explanation
Indices: 41913017--41913164 Score: 66
Period size: 13 Copynumber: 11.7 Consensus size: 13
41913007 TATACATACG
*
41913017 ATAATATGTA-AA
1 ATAATATATATAA
41913029 ATATATATATATAA
1 ATA-ATATATATAA
*
41913043 ATAATATAGTATTA
1 ATAATATA-TATAA
*
41913057 A-AA-ATATATAC
1 ATAATATATATAA
*
41913068 ATGATATATATAA
1 ATAATATATATAA
41913081 A-AATATAATATTTAA
1 ATAATAT-ATA--TAA
*
41913096 A-AGATATATATAC
1 ATA-ATATATATAA
*
41913109 GTAATATATAT--
1 ATAATATATATAA
* *
41913120 ATAA-ATGTATAC
1 ATAATATATATAA
*
41913132 ATAATATAGTATTA
1 ATAATATA-TATAA
*
41913146 A-AATAT-T-TAC
1 ATAATATATATAA
41913156 ATAATATAT
1 ATAATATAT
41913165 GCATATTAGA
Statistics
Matches: 104, Mismatches: 16, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
10 7 0.07
11 13 0.12
12 16 0.15
13 41 0.39
14 15 0.14
15 8 0.08
16 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.39
Consensus pattern (13 bp):
ATAATATATATAA
Found at i:41913062 original size:14 final size:14
Alignment explanation
Indices: 41913020--41913107 Score: 53
Period size: 15 Copynumber: 6.4 Consensus size: 14
41913010 ACATACGATA
*
41913020 ATATGTAAAATATAT
1 ATATATAAAA-ATAT
41913035 ATATATAAATAATAT
1 ATATATAAA-AATAT
41913050 AGTAT-TAAAAATAT
1 A-TATATAAAAATAT
* *
41913064 ATACAT-----GAT
1 ATATATAAAAATAT
41913073 ATATATAAAAATAT
1 ATATATAAAAATAT
*
41913087 AATATTTAAAAGATAT
1 -ATATATAAAA-ATAT
41913103 ATATA
1 ATATA
41913108 CGTAATATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
9 7 0.12
13 2 0.04
14 9 0.16
15 30 0.54
16 8 0.14
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.38
Consensus pattern (14 bp):
ATATATAAAAATAT
Found at i:41913063 original size:23 final size:22
Alignment explanation
Indices: 41913037--41913164 Score: 72
Period size: 23 Copynumber: 5.7 Consensus size: 22
41913027 AAATATATAT
41913037 ATATAA-ATAATATAGTATTAAAA
1 ATATAACATAATATA-TA-TAAAA
*
41913060 ATATATACATGATATATATAAAA
1 ATATA-ACATAATATATATAAAA
41913083 ATAT-A-AT-AT-T-TA-AAAGA
1 ATATAACATAATATATATAAA-A
* *
41913100 TATATATACGTAATATATATATAA
1 -ATATA-ACATAATATATATAAAA
* *
41913124 ATGTATACATAATATAGTATTAAA
1 ATATA-ACATAATATA-TATAAAA
*
41913148 ATATTTACATAATATAT
1 ATA-TAACATAATATAT
41913165 GCATATTAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
16 3 0.04
17 3 0.04
18 5 0.06
19 2 0.02
20 3 0.04
21 2 0.02
22 2 0.02
23 30 0.36
24 23 0.28
25 10 0.12
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (22 bp):
ATATAACATAATATATATAAAA
Found at i:41913116 original size:37 final size:38
Alignment explanation
Indices: 41913033--41913120 Score: 106
Period size: 38 Copynumber: 2.2 Consensus size: 38
41913023 TGTAAAATAT
* *
41913033 ATATATATAAATAATATAGTATTAAAAATATATACATG
1 ATATATATAAATAATATAATATTAAAAATATATACACG
*
41913071 ATATATATAAA-AATATAATATTTAAAAGATATATATACG
1 ATATATATAAATAATATAATA-TTAAAA-ATATATACACG
41913110 TAATATATATA
1 --ATATATATA
41913121 TAAATGTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 8 0.19
38 17 0.40
39 9 0.21
41 9 0.21
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (38 bp):
ATATATATAAATAATATAATATTAAAAATATATACACG
Found at i:41913234 original size:21 final size:20
Alignment explanation
Indices: 41913205--41913258 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
41913195 TAATACTACA
*
41913205 TAAATATATACATATATATAT
1 TAAACATATACATATATA-AT
*
41913226 TAAAGATATATACATATATAAT
1 T-AA-ACATATACATATATAAT
*
41913248 AAAACATATAC
1 TAAACATATAC
41913259 TAATATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 4 0.14
23 15 0.52
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAACATATACATATATAAT
Found at i:41913321 original size:18 final size:17
Alignment explanation
Indices: 41913253--41913336 Score: 59
Period size: 15 Copynumber: 4.9 Consensus size: 17
41913243 ATAATAAAAC
*
41913253 ATATACTAATATTAATA
1 ATATAATAATATTAATA
* *
41913270 ATGATAATAAGAATAAT-
1 AT-ATAATAATATTAATA
*
41913287 ATA-AATAATAGT-A-A
1 ATATAATAATATTAATA
41913301 ATATAATAATATTAAATA
1 ATATAATAATATT-AATA
*
41913319 ATATTAAAAATAATTAAT
1 ATA-TAATAAT-ATTAAT
41913337 TTAATAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.08
15 15 0.29
16 1 0.02
17 5 0.10
18 15 0.29
19 9 0.17
20 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.36
Consensus pattern (17 bp):
ATATAATAATATTAATA
Found at i:41913342 original size:34 final size:34
Alignment explanation
Indices: 41913281--41913345 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
41913271 TGATAATAAG
*
41913281 AATAATATAAATAATAGTAAATATAATAATATTA
1 AATAATATAAATAATAATAAATATAATAATATTA
* *
41913315 AATAATATTAAA-AATAATTAATTTAATAATA
1 AATAATA-TAAATAATAATAAATATAATAATA
41913346 AAGAAATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 23 0.85
35 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (34 bp):
AATAATATAAATAATAATAAATATAATAATATTA
Found at i:41915694 original size:20 final size:20
Alignment explanation
Indices: 41915669--41915709 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41915659 TTATACTTAG
* *
41915669 TTGATAGAGAATGCAATTAC
1 TTGATAAAGAATGCAACTAC
41915689 TTGATAAAGAATGCAACTAC
1 TTGATAAAGAATGCAACTAC
41915709 T
1 T
41915710 CACTAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
TTGATAAAGAATGCAACTAC
Found at i:41916129 original size:63 final size:62
Alignment explanation
Indices: 41916027--41916167 Score: 187
Period size: 63 Copynumber: 2.3 Consensus size: 62
41916017 ACCCAAGCCC
* * * *
41916027 GTCCCTAGCCCGTGTGGCCTAAAATACAAATAGTGAGTTACACGGCCTGGACACA-CACTCAT
1 GTCCCTAGCCCGTGTGACCTAAAATACAAATAGTAAGTTACACGGCCTAGACACACCCCT-AT
* *
41916089 GTCCCTAGCCCATGTGACC-AAACAGTACAAATAGTAAGTTACACGGCCTAGACACACCCCTGT
1 GTCCCTAGCCCGTGTGACCTAAA-A-TACAAATAGTAAGTTACACGGCCTAGACACACCCCTAT
41916152 GTCCCTAGCCCGTGTG
1 GTCCCTAGCCCGTGTG
41916168 CCTCCAATTC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 3 0.04
62 18 0.26
63 45 0.65
64 3 0.04
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (62 bp):
GTCCCTAGCCCGTGTGACCTAAAATACAAATAGTAAGTTACACGGCCTAGACACACCCCTAT
Found at i:41916514 original size:20 final size:20
Alignment explanation
Indices: 41916481--41916519 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41916471 AAGTCATTAT
*
41916481 TTATTTTAAGTTTTATTTTA
1 TTATTTTAACTTTTATTTTA
* *
41916501 TTATTTTTACTTTTGTTTT
1 TTATTTTAACTTTTATTTT
41916520 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TTATTTTAACTTTTATTTTA
Found at i:41929303 original size:20 final size:19
Alignment explanation
Indices: 41929270--41929317 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
41929260 TTGCACCAGG
*
41929270 TTTTTAATTTTTTAAATATTT
1 TTTTTAA-TTTTT-AATAATT
41929291 TTTTTAATTTTTAATAATT
1 TTTTTAATTTTTAATAATT
*
41929310 TATTTAAT
1 TTTTTAAT
41929318 CAAATTAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 5 0.20
21 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATTTTTAATAATT
Found at i:41930132 original size:25 final size:25
Alignment explanation
Indices: 41930104--41930151 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
41930094 ACTATAAAAA
*
41930104 TAAAATAATTTATATACATAATTTT
1 TAAAATAAATTATATACATAATTTT
* * *
41930129 TAAATTAAATTATTTTCATAATT
1 TAAAATAAATTATATACATAATT
41930152 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAATAAATTATATACATAATTTT
Found at i:41939328 original size:49 final size:49
Alignment explanation
Indices: 41939261--41939506 Score: 303
Period size: 49 Copynumber: 5.0 Consensus size: 49
41939251 GTAGCCAAAG
* * * * *
41939261 CTATCTGGTACGCATAGTAGCCTACACATAGTACTACACATGTGACCAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
*
41939310 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
* *
41939359 CTATCCGGTACACGTAGTAGCCTGCACTTAGTATTACACACGTGACCTAA
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC-AA
* * * * *
41939409 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAG
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAA
* * * * *
41939460 TTTTCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
41939507 TCACAATATA
Statistics
Matches: 172, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
49 88 0.51
50 44 0.26
51 39 0.23
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
CTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
Found at i:41939507 original size:101 final size:99
Alignment explanation
Indices: 41939261--41939507 Score: 316
Period size: 101 Copynumber: 2.5 Consensus size: 99
41939251 GTAGCCAAAG
* * * * ** *
41939261 CTATCTGGTACGCATAGTAGCCTACACATAGTACTACACATGTGACC-AATTATCCGGTACACGT
1 CTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCCGATACACGT
*
41939325 AGTAGCCTGCACTTAGTACTACACATGTGACCAA
66 AGTAGCCTGCACTTAGTACTACACACGTGACCAA
* * * * *
41939359 CTATCCGGTACACGTAGTAGCCTGCACTTAGTATTACACACGTGACCTAACCATCTGATACACGT
1 CTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCCGATACACGT
*
41939424 AGTAGCCTGCACTTAGTACTACACACGTGATCACAG
66 AGTAGCCTGCACTTAGTACTACACACGTGA-C-CAA
* * *
41939460 TTTTCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 CTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT
41939508 CACAATATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 40 0.32
99 42 0.33
100 1 0.01
101 43 0.34
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (99 bp):
CTATCAGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCCGATACACGT
AGTAGCCTGCACTTAGTACTACACACGTGACCAA
Found at i:41940110 original size:8 final size:8
Alignment explanation
Indices: 41940097--41940122 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
41940087 CTTCATAATC
41940097 AAGCTTGG
1 AAGCTTGG
41940105 AAGCTTGG
1 AAGCTTGG
41940113 AAGCTTGG
1 AAGCTTGG
41940121 AA
1 AA
41940123 ACCTTAGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.23
Consensus pattern (8 bp):
AAGCTTGG
Found at i:41941692 original size:52 final size:53
Alignment explanation
Indices: 41941610--41941739 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 53
41941600 TCTCTGACTT
**
41941610 GGGTCACACGGCCAA-CCACACACCTGTGTGCTAAGCCGTGTGAAAGGTTC-A
1 GGGTCACACGGCCAAGCCACACACCCATGTGCTAAGCCGTGTGAAAGGTTCAA
* *
41941661 GGGTCACACGGCTAAGCCACACACCCATGTGCTAGGCCGTGTGAAAGGTTCAA
1 GGGTCACACGGCCAAGCCACACACCCATGTGCTAAGCCGTGTGAAAGGTTCAA
*
41941714 GGGTCACTCGGCCAAGCCACACACCC
1 GGGTCACACGGCCAAGCCACACACCC
41941740 GCGTGCTAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
51 14 0.20
52 32 0.45
53 25 0.35
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (53 bp):
GGGTCACACGGCCAAGCCACACACCCATGTGCTAAGCCGTGTGAAAGGTTCAA
Found at i:41941746 original size:53 final size:52
Alignment explanation
Indices: 41941610--41941756 Score: 215
Period size: 53 Copynumber: 2.8 Consensus size: 52
41941600 TCTCTGACTT
* *
41941610 GGGTCACACGGCCAA-CCACACACCTGTGTGCTAAGCCGTGTGAAAGGTTCA
1 GGGTCACACGGCCAAGCCACACACCCGTGTGCTAGGCCGTGTGAAAGGTTCA
* *
41941661 GGGTCACACGGCTAAGCCACACACCCATGTGCTAGGCCGTGTGAAAGGTTCAA
1 GGGTCACACGGCCAAGCCACACACCCGTGTGCTAGGCCGTGTGAAAGGTTC-A
* * *
41941714 GGGTCACTCGGCCAAGCCACACACCCGCGTGCTAGGCCATGTG
1 GGGTCACACGGCCAAGCCACACACCCGTGTGCTAGGCCGTGTG
41941757 CAAAAACCTG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 14 0.16
52 32 0.38
53 39 0.46
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (52 bp):
GGGTCACACGGCCAAGCCACACACCCGTGTGCTAGGCCGTGTGAAAGGTTCA
Found at i:41942639 original size:21 final size:21
Alignment explanation
Indices: 41942613--41942677 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
41942603 AATAGAAACC
41942613 CATAAGGGTTGAATGGAAGCT
1 CATAAGGGTTGAATGGAAGCT
* * *
41942634 CATAAGAGTTGAACGGAAAC-
1 CATAAGGGTTGAATGGAAGCT
*
41942654 CTATAAGGGTT-AAGTTGAAGCT
1 C-ATAAGGGTTGAA-TGGAAGCT
41942676 CA
1 CA
41942678 GAAGAGCTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 3 0.09
21 30 0.88
22 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (21 bp):
CATAAGGGTTGAATGGAAGCT
Found at i:41942654 original size:42 final size:43
Alignment explanation
Indices: 41942606--41942709 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 43
41942596 GGTGCTAAAT
* *
41942606 AGAAACCCATAAGGGTTGAA-TGGAAGCTCATAAGAGTTGAAC
1 AGAAACCCATAAGGGTTGAAGTGGAAGCTCAGAAGAGCTGAAC
* * *
41942648 GGAAACCTATAAGGGTT-AAGTTGAAGCTCAGAAGAGCTGAAC
1 AGAAACCCATAAGGGTTGAAGTGGAAGCTCAGAAGAGCTGAAC
41942690 AGAAACCCA-ATAGGGTTGAA
1 AGAAACCCATA-AGGGTTGAA
41942710 CTAAAACTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 3 0.06
42 47 0.90
43 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.18
Consensus pattern (43 bp):
AGAAACCCATAAGGGTTGAAGTGGAAGCTCAGAAGAGCTGAAC
Found at i:41946894 original size:22 final size:21
Alignment explanation
Indices: 41946853--41946895 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
41946843 TTTTTCATTT
*
41946853 ATTTCACATTTCTACCATAAA
1 ATTTCACATTTCTACAATAAA
41946874 ATTTCCACATTTC-ACAAATAAA
1 ATTT-CACATTTCTAC-AATAAA
41946896 TCCCTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTTCACATTTCTACAATAAA
Found at i:41952186 original size:17 final size:18
Alignment explanation
Indices: 41952164--41952197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41952154 TTCTTCTACA
41952164 TTTCTTC-ATTTTTTTTC
1 TTTCTTCTATTTTTTTTC
41952181 TTTCTTCTATTTTTTTT
1 TTTCTTCTATTTTTTTT
41952198 TCTTAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTCTATTTTTTTTC
Found at i:41954239 original size:77 final size:77
Alignment explanation
Indices: 41954144--41954299 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
41954134 AATATCATAC
41954144 CTCATTATTAGTCAATTTGATACATCATAACCAAGGCTTGTTAAGCTTCAATATTTCTCAACAAT
1 CTCATTATTAGTCAATTTGATACATCATAACCAAGGCTTGTTAAGCTTCAATATTTCTCAACAAT
41954209 TTTTCTAACACA
66 TTTTCTAACACA
41954221 CTCATTATTAGTCAATTTGATACATCATAACCAAGGCTTGTTAAGCTTCAATATTTCTCAACAAT
1 CTCATTATTAGTCAATTTGATACATCATAACCAAGGCTTGTTAAGCTTCAATATTTCTCAACAAT
41954286 TTTTCTAACACA
66 TTTTCTAACACA
41954298 CT
1 CT
41954300 AACTTGTGGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (77 bp):
CTCATTATTAGTCAATTTGATACATCATAACCAAGGCTTGTTAAGCTTCAATATTTCTCAACAAT
TTTTCTAACACA
Found at i:41958131 original size:15 final size:17
Alignment explanation
Indices: 41958105--41958136 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41958095 GAATTATTGA
41958105 ATAAATTTATG-TGTTT
1 ATAAATTTATGTTGTTT
41958121 ATAAA-TTATGTTGTTT
1 ATAAATTTATGTTGTTT
41958137 TCTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
ATAAATTTATGTTGTTT
Found at i:41968550 original size:14 final size:14
Alignment explanation
Indices: 41968531--41968564 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41968521 GTTTCATTGG
41968531 AAATGATTTTAAGA
1 AAATGATTTTAAGA
**
41968545 AAATGATTTTTGGA
1 AAATGATTTTAAGA
41968559 AAATGA
1 AAATGA
41968565 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (14 bp):
AAATGATTTTAAGA
Found at i:41971611 original size:27 final size:28
Alignment explanation
Indices: 41971569--41971708 Score: 143
Period size: 27 Copynumber: 5.2 Consensus size: 28
41971559 GTGATGAAGT
*
41971569 CACCAGATACAG--ATATTGTAGCAGAGC
1 CACCAGA-ACAGATATATTGTGGCAGAGC
*
41971596 CA-CAGAACAGATATA-TGTGGTAGAGC
1 CACCAGAACAGATATATTGTGGCAGAGC
*
41971622 CACCA-AATCAGATA-ATTGTGGCATAGC
1 CACCAGAA-CAGATATATTGTGGCAGAGC
* *
41971649 CACCAGGACAAATATA-TGTGGCAGAGC
1 CACCAGAACAGATATATTGTGGCAGAGC
* *
41971676 CACCAGATCAGATA-ATTGTGGCATAGC
1 CACCAGAACAGATATATTGTGGCAGAGC
41971703 CACCAG
1 CACCAG
41971709 GACGCTTCCT
Statistics
Matches: 94, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.04
26 19 0.20
27 69 0.73
28 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (28 bp):
CACCAGAACAGATATATTGTGGCAGAGC
Found at i:41971676 original size:54 final size:54
Alignment explanation
Indices: 41971569--41971711 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
41971559 GTGATGAAGT
* * * * *
41971569 CACCAGATACAGAT-ATTGTAGCAGAGCCA-CAGAACAGATATATGTGGTAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAAATATATGTGGCAGAGC
*
41971622 CACCAAATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTGGCAGAGC
41971676 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
41971712 GCTTCCTCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
52 5 0.06
53 20 0.25
54 56 0.69
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAAATATATGTGGCAGAGC
Found at i:41973335 original size:26 final size:26
Alignment explanation
Indices: 41973305--41973360 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
41973295 TGAAATGCCC
41973305 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
41973331 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41973357 ATCA
1 ATCA
41973361 CTTTTTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41984190 original size:28 final size:28
Alignment explanation
Indices: 41984133--41984313 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
41984123 TAAATTGTGC
*
41984133 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41984160 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
41984188 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
41984216 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
41984244 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
41984272 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
41984299 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41984314 GACTTAATAT
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 39 0.27
28 108 0.73
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41992910 original size:104 final size:104
Alignment explanation
Indices: 41992714--41992903 Score: 229
Period size: 104 Copynumber: 1.8 Consensus size: 104
41992704 ATCTTTTCTC
* * * * * * **
41992714 TCTAAAGGTGAACCATCCTCGAGCGTAATTCTAAATGGTTGCCTACGAGCGTAATCCTAAAAGGT
1 TCTAAAGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
* *
41992779 GGCTCATTACTTATTGCTTAATCTTACATCTCTCCGCCT
66 GGCTCATTACTTATTACTCAATCTTACATCTCTCCGCCT
* * * *
41992818 TCTAAGGGTGAACCATTCTCAAACGTAATTCCAAATGGATGCCCATGAGCATAATCCTAAATGAC
1 TCTAAAGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
*
41992883 GGCTTATTA-TGTATTACTCAA
66 GGCTCATTACT-TATTACTCAA
41992904 CTTTACAACT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
103 1 0.01
104 69 0.99
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (104 bp):
TCTAAAGGTGAACCATCCTCAAACGTAATTCCAAATGGATGCCCACGAGCATAATCCTAAAAGAC
GGCTCATTACTTATTACTCAATCTTACATCTCTCCGCCT
Found at i:41998620 original size:47 final size:47
Alignment explanation
Indices: 41998567--41998908 Score: 540
Period size: 47 Copynumber: 7.3 Consensus size: 47
41998557 ACAAGATATG
41998567 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
41998614 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41998661 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * *
41998708 TATATGTGACAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
41998755 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * *
41998802 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
41998849 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
41998896 TAAATGTGATAAG
1 TATATGTGATAAG
41998909 TCCCGAAGGG
Statistics
Matches: 268, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 268 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:41998908 original size:94 final size:94
Alignment explanation
Indices: 41998567--41998904 Score: 595
Period size: 94 Copynumber: 3.6 Consensus size: 94
41998557 ACAAGATATG
41998567 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
41998632 ATGGCCGATGTGATGAATGTGAAAGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
41998661 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
*
41998726 ATGGCCGATGTGGTGAATGTGAAAGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
* * *
41998755 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGAGATAAGACCTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
* *
41998820 ATGGCCGATGTGATGGATGTGAAGGTGTA
66 ATGGCCGATGTGATGAATGTGAAAGTGTA
* * *
41998849 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTATATAAATGTGA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGA
41998905 TAAGTCCCGA
Statistics
Matches: 233, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 233 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (94 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCTA
ATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:42002781 original size:46 final size:46
Alignment explanation
Indices: 42002731--42002904 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
42002721 GTTGAGCATG
42002731 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * * *
42002777 CGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
*
42002824 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-C
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
42002869 CCAAGCTCGTTGAGTTGAGTCCGAGTTCCCTTATGG
1 CGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42002905 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 7 0.07
46 56 0.52
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:42002895 original size:93 final size:93
Alignment explanation
Indices: 42002726--42002896 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
42002716 GGATGGTTGA
* * *
42002726 GCATGCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
*
42002791 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
42002819 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG
42002883 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
42002897 CCTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42010356 original size:46 final size:46
Alignment explanation
Indices: 42010306--42010481 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42010296 TGGTTGAGCA
42010306 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42010352 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42010397 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
42010445 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42010482 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42010462 original size:93 final size:93
Alignment explanation
Indices: 42010303--42010474 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42010293 GGATGGTTGA
* *
42010303 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42010368 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42010396 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
42010461 TGAGTCTGAGTTCG
66 TGAGTCCGAGTTCG
42010475 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42013095 original size:42 final size:42
Alignment explanation
Indices: 42013032--42013158 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
42013022 CTTTGTTTTC
** * *
42013032 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
42013075 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
*
42013116 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
42013157 TC
1 TC
42013159 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:42013185 original size:46 final size:47
Alignment explanation
Indices: 42013117--42013236 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
42013107 ATTCATATAT
* * * * *
42013117 CGATGCCATAGCCTAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
* * * *
42013163 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
*
42013210 CAATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
42013237 TACGGAAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 25 0.40
47 37 0.60
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC
Found at i:42013300 original size:31 final size:31
Alignment explanation
Indices: 42013265--42013413 Score: 192
Period size: 31 Copynumber: 4.8 Consensus size: 31
42013255 CTTGTCACTT
* *
42013265 GTAGCCGAAGCTACCACTATTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42013296 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42013327 GTAGCCGGAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
42013358 GTAGCTGGAA-CTACCACTTTTCACTGATTAG
1 GTAGC-CGAAGCTACCACTTTTCACTGATCAG
* *
42013389 GTAACTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
42013414 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 3 0.03
31 99 0.95
32 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:42013488 original size:50 final size:51
Alignment explanation
Indices: 42013395--42013517 Score: 187
Period size: 50 Copynumber: 2.4 Consensus size: 51
42013385 TTAGGTAACT
* *
42013395 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
* *
42013446 GAAGCTATAACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGTGTAGCC
42013496 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
42013518 TGCCATGGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 44 0.68
51 21 0.32
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
Found at i:42013652 original size:14 final size:15
Alignment explanation
Indices: 42013633--42013661 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42013623 TTTTATCATC
42013633 AATACAT-ATGAAAT
1 AATACATCATGAAAT
42013647 AATACATCATGAAAT
1 AATACATCATGAAAT
42013662 TCATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (15 bp):
AATACATCATGAAAT
Found at i:42018636 original size:15 final size:15
Alignment explanation
Indices: 42018584--42018636 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
42018574 ATTTAGAAAT
*
42018584 TAAATTAAAGTATTA
1 TAAATTAAATTATTA
42018599 TAAATTACAATATTTATTA
1 TAAATT--AA-A-TTATTA
*
42018618 TAAATTAAATTAATA
1 TAAATTAAATTATTA
42018633 TAAA
1 TAAA
42018637 GTAGCATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.47
16 1 0.03
17 4 0.12
18 1 0.03
19 11 0.34
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
TAAATTAAATTATTA
Found at i:42026323 original size:15 final size:15
Alignment explanation
Indices: 42026303--42026334 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42026293 TTCTTGTCCA
42026303 TTTCCTTTATTTCTT
1 TTTCCTTTATTTCTT
*
42026318 TTTCCTTTCTTTCTT
1 TTTCCTTTATTTCTT
42026333 TT
1 TT
42026335 CGGTTTGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCCTTTATTTCTT
Found at i:42027477 original size:18 final size:18
Alignment explanation
Indices: 42027456--42027495 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42027446 TTTCTGGACT
*
42027456 TTTTGGGATTGCTTTTGG
1 TTTTGGGATTGATTTTGG
* *
42027474 TTTTGGGTTTTATTTTGG
1 TTTTGGGATTGATTTTGG
42027492 TTTT
1 TTTT
42027496 CTAGGCGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.03, G:0.28, T:0.65
Consensus pattern (18 bp):
TTTTGGGATTGATTTTGG
Found at i:42034926 original size:52 final size:52
Alignment explanation
Indices: 42034868--42034977 Score: 195
Period size: 52 Copynumber: 2.1 Consensus size: 52
42034858 CTTGGATAGT
*
42034868 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCGAGTGAGCTTGGA
1 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
*
42034920 TTGATTCAATACTGGGAATGGACTGGCTGGTTAAACACCAAGTGAGCTTGGA
1 TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
42034972 TT-ATTC
1 TTGATTC
42034978 TACTAAACAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 4 0.07
52 52 0.93
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (52 bp):
TTGATTCAATACTGGGAATGAACTGGCTGGTTAAACACCAAGTGAGCTTGGA
Found at i:42044035 original size:30 final size:30
Alignment explanation
Indices: 42043994--42044050 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
42043984 AAAATCATAT
***
42043994 TTTGACAAAATTATGTTTTTGCCCCTAAAC
1 TTTGACAAAATTACACTTTTGCCCCTAAAC
*
42044024 TTTGTCAAAATTACACTTTTGCCCCTA
1 TTTGACAAAATTACACTTTTGCCCCTA
42044051 GGCTCGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (30 bp):
TTTGACAAAATTACACTTTTGCCCCTAAAC
Found at i:42049382 original size:11 final size:11
Alignment explanation
Indices: 42049363--42049399 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
42049353 TGGGATAGTG
*
42049363 TTTTTATTTTA
1 TTTTAATTTTA
42049374 TTTTAATTTTA
1 TTTTAATTTTA
*
42049385 TTTTAATTTTG
1 TTTTAATTTTA
42049396 TTTT
1 TTTT
42049400 TTTCCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:42049973 original size:30 final size:30
Alignment explanation
Indices: 42049937--42049996 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42049927 GCATGATATG
*
42049937 TTAATTTTGATATTTGTTAATCTGTTTTAT
1 TTAATTTTGAAATTTGTTAATCTGTTTTAT
42049967 TTAATTTTGAAATTTGTTAATCTGTTTTAT
1 TTAATTTTGAAATTTGTTAATCTGTTTTAT
42049997 CTGAGATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (30 bp):
TTAATTTTGAAATTTGTTAATCTGTTTTAT
Found at i:42053366 original size:32 final size:32
Alignment explanation
Indices: 42053330--42053394 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
42053320 ACAAAAGATA
42053330 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
1 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
* *
42053362 TAAATGTTAAGGGCAAAATTTATCATTTTTCT
1 TAAATGTTAAGGGAAAAATTTATCACTTTTCT
42053394 T
1 T
42053395 TTTCCCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (32 bp):
TAAATGTTAAGGGAAAAATTTATCACTTTTCT
Found at i:42072618 original size:19 final size:20
Alignment explanation
Indices: 42072594--42072633 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
42072584 CTTAAATTAT
42072594 TCAT-AAAAAAAGTGGAAAA
1 TCATAAAAAAAAGTGGAAAA
42072613 TCATAAAAAAAAAGTGGAAAA
1 TCAT-AAAAAAAAGTGGAAAA
42072634 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.65, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
TCATAAAAAAAAGTGGAAAA
Found at i:42075427 original size:26 final size:23
Alignment explanation
Indices: 42075368--42075428 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
42075358 CTCATCGTTG
*
42075368 CCCTCTGCTGGTTCTTTGTTCTG
1 CCCTCTGCTGGTTCTTTGTTCTA
* *
42075391 CCCTTTGCTGGTTCTTTATTCCTCTA
1 CCCTCTGCTGGTTCTTT-GT--TCTA
42075417 CCCTCTGCTGGT
1 CCCTCTGCTGGT
42075429 GAGTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 16 0.52
24 1 0.03
26 14 0.45
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.46
Consensus pattern (23 bp):
CCCTCTGCTGGTTCTTTGTTCTA
Found at i:42077467 original size:8 final size:8
Alignment explanation
Indices: 42077456--42077483 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42077446 TTTAATTTTT
42077456 ATATTTAA
1 ATATTTAA
42077464 ATATTTAA
1 ATATTTAA
42077472 ATATTTAA
1 ATATTTAA
42077480 ATAT
1 ATAT
42077484 AGTTTATATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTTAA
Found at i:42077761 original size:13 final size:13
Alignment explanation
Indices: 42077741--42077775 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
42077731 CTCAAATTTA
42077741 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
42077754 TGAAAAGCACTTC
1 TCAAAAGCACTTC
42077767 TCAAAAGCA
1 TCAAAAGCA
42077776 ATGAAGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:42080763 original size:16 final size:17
Alignment explanation
Indices: 42080742--42080775 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42080732 AAAATTTAAT
42080742 TATTTT-ATTGAAATAA
1 TATTTTAATTGAAATAA
*
42080758 TATTTTAATTGAGATAA
1 TATTTTAATTGAAATAA
42080775 T
1 T
42080776 TTTCATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
TATTTTAATTGAAATAA
Found at i:42082294 original size:12 final size:12
Alignment explanation
Indices: 42082277--42082301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42082267 ATAGGTAAAA
42082277 TGGTTTAATTTT
1 TGGTTTAATTTT
42082289 TGGTTTAATTTT
1 TGGTTTAATTTT
42082301 T
1 T
42082302 TTATACATGT
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TGGTTTAATTTT
Found at i:42085639 original size:13 final size:13
Alignment explanation
Indices: 42085621--42085645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42085611 TTGATTTGAT
42085621 TTGATTATGTAAA
1 TTGATTATGTAAA
42085634 TTGATTATGTAA
1 TTGATTATGTAA
42085646 TCTTGTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:42106884 original size:48 final size:49
Alignment explanation
Indices: 42106797--42106898 Score: 163
Period size: 48 Copynumber: 2.1 Consensus size: 49
42106787 ACTTTAAATG
*
42106797 TTTA-GGCCATTATGTTAAAAAAATCAATAGTAACTAACTTTTCCATCT
1 TTTATGGCCATTATGTTAAAAAAATCAATAGTAAATAACTTTTCCATCT
* *
42106845 TTTATGGCCATTATGTT-AAGAAATTAATAGTAAATAACTTTTCCATCT
1 TTTATGGCCATTATGTTAAAAAAATCAATAGTAAATAACTTTTCCATCT
42106893 TTTATG
1 TTTATG
42106899 ATTTAGTCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 38 0.76
49 12 0.24
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (49 bp):
TTTATGGCCATTATGTTAAAAAAATCAATAGTAAATAACTTTTCCATCT
Found at i:42110120 original size:46 final size:46
Alignment explanation
Indices: 42110070--42110245 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42110060 TGGTTGAGCA
42110070 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42110116 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42110161 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
42110209 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42110246 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42110226 original size:93 final size:93
Alignment explanation
Indices: 42110067--42110238 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42110057 GGATGGTTGA
* * *
42110067 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
42110132 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42110160 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
42110225 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42110239 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42113562 original size:2 final size:2
Alignment explanation
Indices: 42113555--42113583 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42113545 TGTTTCCAGT
42113555 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
42113584 GGTCTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42117682 original size:14 final size:14
Alignment explanation
Indices: 42117663--42117692 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42117653 GATTCCCTCT
42117663 TTTATAGTATATGA
1 TTTATAGTATATGA
*
42117677 TTTATAGTTTATGA
1 TTTATAGTATATGA
42117691 TT
1 TT
42117693 CAAGGGTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (14 bp):
TTTATAGTATATGA
Found at i:42120707 original size:66 final size:66
Alignment explanation
Indices: 42120601--42120779 Score: 195
Period size: 66 Copynumber: 2.7 Consensus size: 66
42120591 GTTCAAGAAC
* * * ** *
42120601 TTGAGAAGACCCGATATCTTGTTT-AGGAGCTTGAGAAGACTCGATATCTTGTTCAAGATCTTGG
1 TTGAGAAGACCTGATAT-TTCTTTCAGGAGCTTGGGAAGACTCGATATCGAGTTCAAGAGCTTGG
42120665 GA
65 GA
** *
42120667 TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTTAATATCGAGTTCAGGAGCTTGGG
1 TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTCGATATCGAGTTCAAGAGCTTGGG
42120732 A
66 A
* *
42120733 TTGAGAAGA-CTGA-ATATCTAGTCCAGGAGCTTGGGAAGA-TCTGATAT
1 TTGAGAAGACCTGATATTTCT--TTCAGGAGCTTGGGAAGACTC-GATAT
42120780 TTAATTTTTC
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 5 0.05
65 10 0.10
66 81 0.84
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.30
Consensus pattern (66 bp):
TTGAGAAGACCTGATATTTCTTTCAGGAGCTTGGGAAGACTCGATATCGAGTTCAAGAGCTTGGG
A
Found at i:42121138 original size:21 final size:21
Alignment explanation
Indices: 42121111--42121157 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
42121101 AGTGTTGCCA
42121111 CCTTACGAGAGGAAGATAATT
1 CCTTACGAGAGGAAGATAATT
*
42121132 TCTTACGAGAGGAAGATAATT
1 CCTTACGAGAGGAAGATAATT
42121153 CCTTA
1 CCTTA
42121158 GCAAGACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (21 bp):
CCTTACGAGAGGAAGATAATT
Found at i:42122943 original size:30 final size:31
Alignment explanation
Indices: 42122909--42122970 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
42122899 GATTCATCCA
*
42122909 TGGAAAAT-AAAATAAAGAAAATGATGA-AAT
1 TGGAAAATGAAAAAAAAGAAAA-GATGATAAT
* *
42122939 TGGAAAGTGAAAAAAAATAAAAGATGATAAT
1 TGGAAAATGAAAAAAAAGAAAAGATGATAAT
42122970 T
1 T
42122971 AATTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (31 bp):
TGGAAAATGAAAAAAAAGAAAAGATGATAAT
Found at i:42128497 original size:46 final size:46
Alignment explanation
Indices: 42128430--42128595 Score: 174
Period size: 46 Copynumber: 3.6 Consensus size: 46
42128420 TTTGTGTGCT
42128430 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGCC
* * *
42128476 AGTGTAAGACATGTCTGGGACATGCTTCGGCCTCGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATA-TGAGAGCC
* * * * * * * * *
42128524 GGCGTAATACATGTTTGGGACATGCATCGG-TATTAAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAATATGAGAGCC
42128570 AGTGTAAGACATGTCTGGGACATGCA
1 AGTGTAAGACATGTCTGGGACATGCA
42128596 CCACCCTCGT
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 59 0.61
47 2 0.02
48 32 0.33
49 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGCC
Found at i:42128604 original size:94 final size:94
Alignment explanation
Indices: 42128433--42128616 Score: 235
Period size: 94 Copynumber: 2.0 Consensus size: 94
42128423 GTGTGCTAGT
* *
42128433 GTAAGACATGTCTGGGACATGCATCGGCCACAATATGAGAGCCAGTGTAAGACATGTCTGGGACA
1 GTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCCAGTGTAAGACATGTCTGGGACA
** ** *
42128498 TGCTTCGGCCTCGAGATATTTAAGCCGGC
66 TGCACCACCCTCGAGATATTCAAGCCGGC
* * * * *
42128527 GTAATACATGTTTGGGACATGCATCGG-TATTAAGACGAGAGCTAGTGTAAGACATGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCA-CAAGACGAGAGCCAGTGTAAGACATGTCTGGGAC
*
42128591 ATGCACCACCCTCGTGATATTCAAGC
65 ATGCACCACCCTCGAGATATTCAAGC
42128617 TAGTGTATGA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 75 0.99
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (94 bp):
GTAAGACATGTCTGGGACATGCATCGGCCACAAGACGAGAGCCAGTGTAAGACATGTCTGGGACA
TGCACCACCCTCGAGATATTCAAGCCGGC
Found at i:42128718 original size:49 final size:48
Alignment explanation
Indices: 42128661--42128784 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 48
42128651 TGTTGCGTGT
42128661 CAGTGTAAGACCTGTCTAGGACATGGAATCGACAC-CAATAGATGAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGAATCGAC-CTCAATAGATGA-AGC
* * * ** * ** *
42128710 CAGTGTAAGACCTATCTGGGATATGTCATCGGCCTCGCTATATGAAGC
1 CAGTGTAAGACCTGTCTAGGACATGGAATCGACCTCAATAGATGAAGC
42128758 CAGTGTAAGACCATGTCTAGGACATGG
1 CAGTGTAAGACC-TGTCTAGGACATGG
42128785 CGTTGGCATC
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
48 16 0.27
49 44 0.73
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTAGGACATGGAATCGACCTCAATAGATGAAGC
Found at i:42132727 original size:32 final size:32
Alignment explanation
Indices: 42132663--42132736 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
42132653 ATTACCATAG
* *
42132663 CTGATGGCTATGTGCCGAACTTATTACAGCTA
1 CTGATGGCTTTGTGCCGAACTTAATACAGCTA
* *
42132695 CTGATGGCTTTGTGCC-AATTGTAATACCGCTA
1 CTGATGGCTTTGTGCCGAACT-TAATACAGCTA
*
42132727 CTGAAGGCTT
1 CTGATGGCTT
42132737 AAAGCTGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (32 bp):
CTGATGGCTTTGTGCCGAACTTAATACAGCTA
Found at i:42137168 original size:24 final size:24
Alignment explanation
Indices: 42137132--42137181 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
42137122 GTATAATAAT
42137132 TTTTTAGAATTTTAAATATT-TTTA
1 TTTTTAGAATTTTAAA-ATTATTTA
* *
42137156 TTTTTATATTTTTAAAATTATTTA
1 TTTTTAGAATTTTAAAATTATTTA
42137180 TT
1 TT
42137182 GATATGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTAGAATTTTAAAATTATTTA
Found at i:42141934 original size:40 final size:40
Alignment explanation
Indices: 42141651--42141923 Score: 426
Period size: 40 Copynumber: 6.8 Consensus size: 40
42141641 CGGATGATAA
*
42141651 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
42141691 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
42141731 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
42141771 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
*
42141811 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-T
* *
42141851 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTGACTAAT-T
*
42141891 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTG
42141924 GCTATATCCG
Statistics
Matches: 223, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
39 4 0.02
40 217 0.97
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATT
Found at i:42148119 original size:30 final size:30
Alignment explanation
Indices: 42148061--42148119 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
42148051 ATTTTCGAGC
**
42148061 ATAGGGGAAAAATGGTCATTTTGTCAAAGT
1 ATAGGGGAAAAATGGTCATTTTACCAAAGT
* *
42148091 ATAGGGGCAAAATGGTCGTTTTACCAAAG
1 ATAGGGGAAAAATGGTCATTTTACCAAAG
42148120 ATATGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (30 bp):
ATAGGGGAAAAATGGTCATTTTACCAAAGT
Found at i:42152093 original size:39 final size:40
Alignment explanation
Indices: 42151990--42152212 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
42151980 TTGGATGATG
*
42151990 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
42152028 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
42152069 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42152108 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
42152147 TCGGGGATAAGTCCCGAAGGCATTTGTGC-AAATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
42152186 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
42152213 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 91 0.57
40 56 0.35
41 11 0.07
42 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42168337 original size:15 final size:15
Alignment explanation
Indices: 42168317--42168347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42168307 AAATATTAAA
42168317 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
42168332 GATATGTTTTGTATT
1 GATATGTTTTGGATT
42168347 G
1 G
42168348 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:42169019 original size:56 final size:55
Alignment explanation
Indices: 42168957--42169067 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 55
42168947 GACCATGGCA
*
42168957 TCGATATATGTATGCGAGGAAGACCACGTTTA-ATACGTTGGCATCGATATGTGATT
1 TCGATATATGTATGCGAGGAAGACCACGTTTAGATAC--TGACATCGATATGTGATT
* * **
42169013 TCGATATATGTGTGCGAGTAAGACCTTGTTTAGGATACTGACATCGATATGTGAT
1 TCGATATATGTATGCGAGGAAGACCACGTTTA-GATACTGACATCGATATGTGAT
42169068 AACATGTAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 44 0.92
58 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (55 bp):
TCGATATATGTATGCGAGGAAGACCACGTTTAGATACTGACATCGATATGTGATT
Found at i:42169293 original size:19 final size:18
Alignment explanation
Indices: 42169269--42169312 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
42169259 GATACAAATT
42169269 ATATATGATGCAAATGAAA
1 ATATATG-TGCAAATGAAA
* *
42169288 ATATATGTGTATATGAAA
1 ATATATGTGCAAATGAAA
42169306 AGTATAT
1 A-TATAT
42169313 TCGGCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (18 bp):
ATATATGTGCAAATGAAA
Found at i:42176516 original size:27 final size:27
Alignment explanation
Indices: 42176486--42176662 Score: 176
Period size: 27 Copynumber: 6.5 Consensus size: 27
42176476 TATTGAGTTT
* *
42176486 GCACACTCAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTACATAATCAACTC
* *
42176513 GCACACTTAGTGCTACGTAATCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
*
42176540 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAATC-AACTC
** ** *
42176568 GCACACTTAGTGCCGCATGGTCAATTC
1 GCACACTTAGTGCTACATAATCAACTC
* **
42176595 GCACACTTAGTGC-ATCATATTCATTTC
1 GCACACTTAGTGCTA-CATAATCAACTC
* * *
42176622 GCACACTTAGTGCAACATAGTCAAATC
1 GCACACTTAGTGCTACATAATCAACTC
*
42176649 ACACACTTAGTGCT
1 GCACACTTAGTGCT
42176663 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAATCAACTC
Found at i:42176624 original size:82 final size:81
Alignment explanation
Indices: 42176506--42176661 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
42176496 TGCTATATAA
* * *
42176506 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCACA
42176571 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42176588 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCACA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACA
42176652 CACTTAGTGC
65 CACTTAGTGC
42176662 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 51 0.77
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCACAC
ACTTAGTGCCGCATGG
Found at i:42184699 original size:27 final size:27
Alignment explanation
Indices: 42184669--42184846 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42184659 ATATTGAGTC
* * * *
42184669 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42184696 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42184723 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42184751 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42184778 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42184805 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42184832 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42184847 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42184808 original size:82 final size:81
Alignment explanation
Indices: 42184690--42184845 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42184680 TGCTATATAA
* *
42184690 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42184755 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42184772 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42184836 CACTTAGTGC
65 CACTTAGTGC
42184846 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42194829 original size:28 final size:28
Alignment explanation
Indices: 42194797--42194852 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42194787 CACGGGTGAG
42194797 CACGGACGTGTCTAGACCGTGTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
42194825 CACGGACGTGTCTAGACCGTGTAAATGA
1 CACGGACGTGTCTAGACCGTGTAAATGA
42194853 TTACGGGCCA
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:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (28 bp):
CACGGACGTGTCTAGACCGTGTAAATGA
Found at i:42204412 original size:11 final size:11
Alignment explanation
Indices: 42204396--42204437 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
42204386 TAAATAATCA
42204396 TATGATTAATG
1 TATGATTAATG
42204407 TATGATTAATG
1 TATGATTAATG
*
42204418 T-TGCTT-AT-
1 TATGATTAATG
42204426 TATGATTAATG
1 TATGATTAATG
42204437 T
1 T
42204438 TGCTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.04
9 6 0.23
10 6 0.23
11 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (11 bp):
TATGATTAATG
Found at i:42204431 original size:19 final size:19
Alignment explanation
Indices: 42204407--42204447 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
42204397 ATGATTAATG
42204407 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
42204426 TATGATTAATGTTGCTTAT
1 TATGATTAATGTTGCTTAT
42204445 TAT
1 TAT
42204448 TTGCATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGATTAATGTTGCTTAT
Found at i:42206374 original size:27 final size:27
Alignment explanation
Indices: 42206344--42206521 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42206334 ATATTGAGTC
* * * *
42206344 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42206371 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42206398 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42206426 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42206453 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42206480 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42206507 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42206522 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42206483 original size:82 final size:81
Alignment explanation
Indices: 42206365--42206520 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42206355 TGCTATATAA
* *
42206365 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42206430 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42206447 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42206511 CACTTAGTGC
65 CACTTAGTGC
42206521 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42220889 original size:3 final size:3
Alignment explanation
Indices: 42220877--42220950 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
42220867 TTATTTTTGC
* * * *
42220877 TAT T-T TAT TAT TAA AAT TAAT TAAT TAC TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT T-AT TAT TAT TAT TAT TAT TAT TAT
* ** *
42220923 TAT TAT CAT TAT CGT TAT AAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42220951 CTTAAAACTA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
2 2 0.04
3 44 0.83
4 7 0.13
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:42221047 original size:22 final size:22
Alignment explanation
Indices: 42221004--42221059 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
42220994 TATTAGATTC
*
42221004 TATTATTTTATTTCTTTCTTTA
1 TATTATTTTATTCCTTTCTTTA
*
42221026 TATATATTTT-TTCCTTTTTTTA
1 TAT-TATTTTATTCCTTTCTTTA
*
42221048 TATTATTATATT
1 TATTATTTTATT
42221060 GTTATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 18 0.62
23 6 0.21
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTATTTTATTCCTTTCTTTA
Found at i:42221451 original size:13 final size:13
Alignment explanation
Indices: 42221429--42221465 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
42221419 TTATTATTCC
42221429 TTTA-TTATTTTA
1 TTTATTTATTTTA
*
42221441 TTTATTTATTTCA
1 TTTATTTATTTTA
42221454 TTTATTTATTTT
1 TTTATTTATTTT
42221466 GTTTTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:42224404 original size:39 final size:39
Alignment explanation
Indices: 42224265--42224385 Score: 188
Period size: 39 Copynumber: 3.1 Consensus size: 39
42224255 GCTCTGATGA
* * *
42224265 GCTTCAGTTCGTCTTCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
42224304 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTACGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
42224343 GCTTCAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
42224382 GCTT
1 GCTT
42224386 TGGCTAGATT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:42226766 original size:27 final size:27
Alignment explanation
Indices: 42226736--42226792 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
42226726 AACATAGGTA
*
42226736 AGTCCACT-GGGACATTAAAAACGGGGT
1 AGTCC-CTCGGGACATTAAAAACAGGGT
* *
42226763 AGTCCGTCGGGACATTAAAAATAGGGT
1 AGTCCCTCGGGACATTAAAAACAGGGT
42226790 AGT
1 AGT
42226793 TCGCCAGGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (27 bp):
AGTCCCTCGGGACATTAAAAACAGGGT
Found at i:42226802 original size:27 final size:27
Alignment explanation
Indices: 42226745--42226802 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
42226735 AAGTCCACTG
* * *
42226745 GGACATTAAAAACGGGGTAGTCCGTCG
1 GGACATTAAAAACAGGGTAGTCCGCCA
* *
42226772 GGACATTAAAAATAGGGTAGTTCGCCA
1 GGACATTAAAAACAGGGTAGTCCGCCA
42226799 GGAC
1 GGAC
42226803 GTGAAACATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (27 bp):
GGACATTAAAAACAGGGTAGTCCGCCA
Found at i:42231708 original size:90 final size:90
Alignment explanation
Indices: 42231614--42231926 Score: 268
Period size: 90 Copynumber: 3.6 Consensus size: 90
42231604 TTTGTATCTG
42231614 TAAATTTAATTTAGT-TCGTATTATATGTAGTTTGAATTTAAAATTTTTGCGTATTAATTTTACC
1 TAAATTTAATTTAGTCT-GTATTATATGTAGTTTGAATTTAAAATTTTTGCGTATTAATTTTACC
42231678 CATCTGTTTGTAGTTTGTTGGGTGTT
65 CATCTGTTTGTAGTTTGTTGGGTGTT
* * ** *
42231704 TAAATTTAATTTAGTCTGTATTATATATAGTTTGAATTTAAAA--TTTACCCATCT-GTTTGT--
1 TAAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTTGCGTAT-TAATTT-TAC
* ** *
42231764 --A---GTTTGTTGGGTGTT---T-A-
64 CCATCTGTTTGTAGTTTGTTGGGTGTT
* * * * * **
42231781 --AATTTAATTTAGTCCGTAATATATGCAATTTGAATTTAAAATTTTCGTATATTAATTTTACCC
1 TAAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTTGCGTATTAATTTTACCC
*
42231844 ATCTATTTGTAGTTTGTTGGGTGTT
66 ATCTGTTTGTAGTTTGTTGGGTGTT
* * * *
42231869 TAAATTTAATTTAGTCTGTATTATTTGTTA-TTTGAATTTTATATTTTTGTGTATTAAT
1 TAAATTTAATTTAGTCTGTATTATATG-TAGTTTGAATTTAAAATTTTTGCGTATTAAT
42231927 ATTCTAGAAT
Statistics
Matches: 169, Mismatches: 33, Indels: 42
0.69 0.14 0.17
Matches are distributed among these distances:
75 36 0.21
76 2 0.01
77 7 0.04
79 1 0.01
80 1 0.01
82 11 0.07
83 10 0.06
85 1 0.01
86 1 0.01
88 9 0.05
89 2 0.01
90 86 0.51
91 2 0.01
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.52
Consensus pattern (90 bp):
TAAATTTAATTTAGTCTGTATTATATGTAGTTTGAATTTAAAATTTTTGCGTATTAATTTTACCC
ATCTGTTTGTAGTTTGTTGGGTGTT
Found at i:42231761 original size:75 final size:75
Alignment explanation
Indices: 42231672--42231824 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
42231662 GCGTATTAAT
* * * *
42231672 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCTGTATTATATATAGTTT
1 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
42231737 GAATTTAAAA
66 GAATTTAAAA
*
42231747 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATGCAATTT
1 TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
42231812 GAATTTAAAA
66 GAATTTAAAA
42231822 TTT
1 TTT
42231825 TCGTATATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.50
Consensus pattern (75 bp):
TTTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTAATATATACAATTT
GAATTTAAAA
Found at i:42234606 original size:17 final size:17
Alignment explanation
Indices: 42234549--42234607 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
42234539 TTTTATTTTC
* **
42234549 ATTTCATTTCCATTTCC
1 ATTTAATTTCCATTTAA
42234566 ATTTAATTT-CATTTAA
1 ATTTAATTTCCATTTAA
***
42234582 AAAAAATTTCCATTTAA
1 ATTTAATTTCCATTTAA
42234599 ATTTAATTT
1 ATTTAATTT
42234608 TTTCTCATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATTTCCATTTAA
Found at i:42234624 original size:16 final size:15
Alignment explanation
Indices: 42234599--42234637 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
42234589 TTCCATTTAA
42234599 ATTTAATTTTTTCTC
1 ATTTAATTTTTTCTC
*
42234614 ATTTCAATTTTTTTTC
1 ATTT-AATTTTTTCTC
42234630 ATATTAAT
1 AT-TTAAT
42234638 AACAATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATTTTTTCTC
Found at i:42234755 original size:5 final size:5
Alignment explanation
Indices: 42234745--42234812 Score: 55
Period size: 5 Copynumber: 12.2 Consensus size: 5
42234735 CATTACAAAA
* *
42234745 TTCAT TTCAT TTGCATT TTCAT TACAAAT TACAT TTCAT TTCAT ATTCAT
1 TTCAT TTCAT TT-CA-T TTCAT TTC--AT TTCAT TTCAT TTCAT -TTCAT
42234795 TTAACAT TTCAT TTCAT T
1 TT--CAT TTCAT TTCAT T
42234813 ATTTTTTTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
5 32 0.59
6 9 0.17
7 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (5 bp):
TTCAT
Found at i:42234765 original size:17 final size:16
Alignment explanation
Indices: 42234745--42234812 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 16
42234735 CATTACAAAA
42234745 TTCATTTCATTTGCATT
1 TTCATTTCATTT-CATT
* *
42234762 TTCATTACAAATTACA-T
1 TTCATTTC--ATTTCATT
42234779 TTCATTTCATATTCATT
1 TTCATTTCAT-TTCATT
*
42234796 TAACATTTCATTTCATT
1 T-TCATTTCATTTCATT
42234813 ATTTTTTTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.05
16 3 0.07
17 23 0.56
18 10 0.24
19 3 0.07
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (16 bp):
TTCATTTCATTTCATT
Found at i:42234769 original size:29 final size:28
Alignment explanation
Indices: 42234721--42234812 Score: 98
Period size: 28 Copynumber: 3.2 Consensus size: 28
42234711 TAAACTGTCG
* *
42234721 TTTCATTCCATAATCATTACAAAATTCA
1 TTTCATTTCATATTCATTACAAAATTCA
*
42234749 TTTCATTTGCATTTTCATTAC-AAATTACA
1 TTTCATTT-CATATTCATTACAAAATT-CA
* *
42234778 TTTCATTTCATATTCATTTA-ACATTTCA
1 TTTCATTTCATATTCA-TTACAAAATTCA
42234806 TTTCATT
1 TTTCATT
42234813 ATTTTTTTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
28 28 0.52
29 26 0.48
ACGTcount: A:0.32, C:0.18, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTCATTTCATATTCATTACAAAATTCA
Found at i:42234795 original size:11 final size:10
Alignment explanation
Indices: 42234745--42234812 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 10
42234735 CATTACAAAA
42234745 TTCATTTCAT
1 TTCATTTCAT
42234755 TTGCATTTTCAT
1 TT-CA-TTTCAT
* *
42234767 TACAAATTACAT
1 TTC--ATTTCAT
42234779 TTCATTTCAT
1 TTCATTTCAT
42234789 ATTCATTTAACAT
1 -TTCATTT--CAT
42234802 TTCATTTCAT
1 TTCATTTCAT
42234812 T
1 T
42234813 ATTTTTTTCC
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 12 0.26
11 10 0.21
12 21 0.45
13 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.01, T:0.53
Consensus pattern (10 bp):
TTCATTTCAT
Found at i:42234946 original size:55 final size:55
Alignment explanation
Indices: 42234861--42234977 Score: 134
Period size: 55 Copynumber: 2.1 Consensus size: 55
42234851 TTTTTTTTCA
* * *
42234861 TATTAATCACAAGTAGTCTCATTTCAATTTT-TTT-CATTTCATTTCATATTTTTAT
1 TATTAATTACAAGTAGTCTCATTACAATTTTATTTAAATTT-ATTTCATA-TTTTAT
* *
42234916 TATTAATTATAAGTAGTCTCAATTAC-ATTTTATTTAAATTTTTTTCATATTTTAT
1 TATTAATTACAAGTAGTCTC-ATTACAATTTTATTTAAATTTATTTCATATTTTAT
42234971 T-TTAATT
1 TATTAATT
42234978 TTTTCTCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
54 6 0.11
55 30 0.56
56 14 0.26
57 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.56
Consensus pattern (55 bp):
TATTAATTACAAGTAGTCTCATTACAATTTTATTTAAATTTATTTCATATTTTAT
Found at i:42234967 original size:22 final size:22
Alignment explanation
Indices: 42234942--42234989 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
42234932 TCTCAATTAC
42234942 ATTTTATTTAAATTTTTT-TCA
1 ATTTTATTTAAATTTTTTCTCA
*
42234963 TATTTTATTTTAATTTTTTCTCA
1 -ATTTTATTTAAATTTTTTCTCA
42234986 ATTT
1 ATTT
42234990 AAATATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTATTTAAATTTTTTCTCA
Found at i:42234980 original size:23 final size:21
Alignment explanation
Indices: 42234942--42234989 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
42234932 TCTCAATTAC
*
42234942 ATTTTATTTAAATTTTTTTCA
1 ATTTTATTTAAATTTTTCTCA
*
42234963 TATTTTATTTTAATTTTTTCTCA
1 -ATTTTA-TTTAAATTTTTCTCA
42234986 ATTT
1 ATTT
42234990 AAATATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTATTTAAATTTTTCTCA
Found at i:42235375 original size:15 final size:15
Alignment explanation
Indices: 42235286--42235376 Score: 64
Period size: 15 Copynumber: 6.1 Consensus size: 15
42235276 ATTTGTTTTT
*
42235286 TTTCATTTAAATTTA
1 TTTCATTTTAATTTA
*
42235301 TTTCATTTTCCA--T-
1 TTTCATTTT-AATTTA
*
42235314 TTT-ATTTTAAGTTTT
1 TTTCATTTTAA-TTTA
* *
42235329 TTTCATATTAATTTT
1 TTTCATTTTAATTTA
*
42235344 TGTCTCATTGTAATTTA
1 T-T-TCATTTTAATTTA
42235361 TTTCATTTTAATTTA
1 TTTCATTTTAATTTA
42235376 T
1 T
42235377 ACTTTATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
11 1 0.02
12 5 0.08
13 3 0.05
14 2 0.03
15 29 0.48
16 9 0.15
17 11 0.18
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTCATTTTAATTTA
Found at i:42235429 original size:29 final size:30
Alignment explanation
Indices: 42235371--42235454 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 30
42235361 TTTCATTTTA
* * *
42235371 ATTT-ATACTTTATTTTCATTGCATATTTC
1 ATTTCATATTTTATTTTCATTTCATAATTC
*
42235400 ATTTCATATTTTAGTTTCATTTCA-AATTC
1 ATTTCATATTTTATTTTCATTTCATAATTC
* *
42235429 ACTTCATATTTTATTTTCGTTTCATA
1 ATTTCATATTTTATTTTCATTTCATA
42235455 TTTTCACTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 29 0.63
30 17 0.37
ACGTcount: A:0.25, C:0.14, G:0.04, T:0.57
Consensus pattern (30 bp):
ATTTCATATTTTATTTTCATTTCATAATTC
Found at i:42235467 original size:29 final size:29
Alignment explanation
Indices: 42235360--42235467 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 29
42235350 ATTGTAATTT
* * *
42235360 ATTTCAT-TTTAATTTATACTTTATTTTC
1 ATTTCATATTTCACTTATATTTTATTTTC
* * *
42235388 ATTGCATATTTCATTTCATATTTTAGTTTC
1 ATTTCATATTTCACTT-ATATTTTATTTTC
*
42235418 ATTTCA-AATTCACTTCATATTTTATTTTC
1 ATTTCATATTTCACTT-ATATTTTATTTTC
*
42235447 GTTTCATATTTTCACTT-TATT
1 ATTTCATA-TTTCACTTATATT
42235468 CACTTATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.09
29 36 0.55
30 17 0.26
31 7 0.11
ACGTcount: A:0.24, C:0.14, G:0.03, T:0.59
Consensus pattern (29 bp):
ATTTCATATTTCACTTATATTTTATTTTC
Found at i:42237166 original size:25 final size:24
Alignment explanation
Indices: 42237133--42237238 Score: 74
Period size: 25 Copynumber: 4.4 Consensus size: 24
42237123 AAATGAATTA
* *
42237133 AAATAATATAAAAATATTTAAAAGT
1 AAATGATATAAAAAGATTTAAAA-T
* *
42237158 AAATGATATAACAAGGTTTAAAAT
1 AAATGATATAAAAAGATTTAAAAT
** *
42237182 AAATGATAAATAAAACCATTTAAAGT
1 AAATGAT--ATAAAAAGATTTAAAAT
* *
42237208 AAA--AAACAAAAAG-TTTAAAAT
1 AAATGATATAAAAAGATTTAAAAT
*
42237229 AAATAATATA
1 AAATGATATA
42237239 TGAAATGGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
21 10 0.16
22 5 0.08
23 3 0.05
24 9 0.15
25 19 0.31
26 15 0.25
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATGATATAAAAAGATTTAAAAT
Found at i:42237351 original size:11 final size:12
Alignment explanation
Indices: 42237326--42237387 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
42237316 AATTTAAAGT
42237326 AAATAATATATA
1 AAATAATATATA
*
42237338 AAATAATTTA-A
1 AAATAATATATA
*
42237349 AAATAATAATACA
1 AAATAAT-ATATA
*
42237362 AAACAA-AT-TA
1 AAATAATATATA
42237372 AAATAATATGATA
1 AAATAATAT-ATA
42237385 AAA
1 AAA
42237388 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 6 0.15
11 12 0.30
12 11 0.28
13 11 0.28
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (12 bp):
AAATAATATATA
Found at i:42237356 original size:23 final size:23
Alignment explanation
Indices: 42237326--42237397 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
42237316 AATTTAAAGT
42237326 AAATAATATATAAAATAATTTAA
1 AAATAATATATAAAATAATTTAA
* * *
42237349 AAATAATAATACAAAACAAATT-A
1 AAATAAT-ATATAAAATAATTTAA
42237372 AAATAATATGATAAAACT-ATTTAA
1 AAATAATAT-ATAAAA-TAATTTAA
42237396 AA
1 AA
42237398 CAAATACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
22 2 0.05
23 23 0.59
24 14 0.36
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (23 bp):
AAATAATATATAAAATAATTTAA
Found at i:42237402 original size:27 final size:26
Alignment explanation
Indices: 42237326--42237441 Score: 77
Period size: 27 Copynumber: 4.7 Consensus size: 26
42237316 AATTTAAAGT
*
42237326 AAATAATATATAAAA-TAATT-TAA-
1 AAATAATATATAAAACTAATTAAAAC
* *
42237349 AAATAATAATACAAAACAAATT---A-
1 AAATAAT-ATATAAAACTAATTAAAAC
*
42237372 AAATAATATGATAAAACTATTTAAAAC
1 AAATAATAT-ATAAAACTAATTAAAAC
* ** *
42237399 AAATACTATATCAAAAAAAATTAAAAT
1 AAATAATATAT-AAAACTAATTAAAAC
42237426 AAATAATA-ATAAAACT
1 AAATAATATATAAAACT
42237442 GTTCAAAATA
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
22 2 0.03
23 24 0.33
24 7 0.10
25 8 0.11
26 5 0.07
27 26 0.36
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.28
Consensus pattern (26 bp):
AAATAATATATAAAACTAATTAAAAC
Found at i:42237439 original size:23 final size:25
Alignment explanation
Indices: 42237319--42237439 Score: 69
Period size: 26 Copynumber: 4.9 Consensus size: 25
42237309 ATAGAGCAAT
* *
42237319 TTAAAGTAAATAATATATAAAATAA
1 TTAAAATAAATAATACATAAAATAA
42237344 TTTAAAA-ATAATAATACA-AAACA-AA
1 -TTAAAATA-AATAATACATAAA-ATAA
* *
42237369 TTAAAAT-AAT-AT-GATAAAACTAT
1 TTAAAATAAATAATACATAAAA-TAA
* *
42237392 TTAAAACAAATACTATATCA-AAAAAAA
1 TTAAAATAAATA--ATA-CATAAAATAA
42237419 TTAAAATAAATAATA-ATAAAA
1 TTAAAATAAATAATACATAAAA
42237440 CTGTTCAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 28
0.66 0.08 0.25
Matches are distributed among these distances:
21 2 0.03
22 5 0.07
23 11 0.15
24 13 0.18
25 9 0.12
26 14 0.19
27 14 0.19
28 4 0.05
29 1 0.01
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (25 bp):
TTAAAATAAATAATACATAAAATAA
Done.