Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 30 of 45
Found at i:5287524 original size:2 final size:2
Alignment explanation
Indices: 5287477--5287512 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5287467 AAGAAAAGAT
*
5287477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5287513 AGTTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5288059 original size:14 final size:13
Alignment explanation
Indices: 5288042--5288109 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 13
5288032 TATTTAAGTT
5288042 TTTATATTATTAAA
1 TTTATATT-TTAAA
*
5288056 TTTAATATTTTAATT
1 TTT-ATATTTTAA-A
5288071 TTTATATTATTAAA
1 TTTATATT-TTAAA
*
5288085 TTTAATATTTTAATT
1 TTT-ATATTTTAA-A
5288100 TTTATATTTT
1 TTTATATTTT
5288110 TAAAATTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 26 0.57
15 20 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATATTTTAAA
Found at i:5288062 original size:29 final size:29
Alignment explanation
Indices: 5288030--5288113 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
5288020 CAGTGAAGAA
5288030 AATA-TTTAAGTTTTTATATTATTAAATTT
1 AATATTTTAA-TTTTTATATTATTAAATTT
5288059 AATATTTTAATTTTTATATTATTAAATTT
1 AATATTTTAATTTTTATATTATTAAATTT
*
5288088 AATATTTTAATTTTTATATTTTTAAA
1 AATATTTTAATTTTTATATTATTAAA
5288114 ATTATGATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 48 0.91
30 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
AATATTTTAATTTTTATATTATTAAATTT
Found at i:5288069 original size:8 final size:8
Alignment explanation
Indices: 5288056--5288109 Score: 57
Period size: 7 Copynumber: 7.4 Consensus size: 8
5288046 TATTATTAAA
5288056 TTTAATAT
1 TTTAATAT
5288064 TTTAAT-T
1 TTTAATAT
5288071 TTT-ATAT
1 TTTAATAT
5288078 TATTAA-A-
1 T-TTAATAT
5288085 TTTAATAT
1 TTTAATAT
5288093 TTTAAT-T
1 TTTAATAT
5288100 TTT-ATAT
1 TTTAATAT
5288107 TTT
1 TTT
5288110 TAAAATTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 8 0.20
7 16 0.40
8 15 0.38
9 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATAT
Found at i:5288812 original size:15 final size:16
Alignment explanation
Indices: 5288794--5288823 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5288784 TTTATGAATT
5288794 TATTTATT-ATTATTC
1 TATTTATTAATTATTC
5288809 TATTTATTAATTATT
1 TATTTATTAATTATT
5288824 TTTATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTAATTATTC
Found at i:5289901 original size:53 final size:53
Alignment explanation
Indices: 5289817--5290420 Score: 482
Period size: 53 Copynumber: 11.7 Consensus size: 53
5289807 CCAAAAGTTC
*
5289817 TTTAAAAATTAATAAAAAAATT-TAAAATATTTTATATTAAATTTCTAATTACTA
1 TTTAAAAA-TAAT-AAAAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
* * * * *
5289871 TTTAAAAATAATAAAAAATTAAAAAGTATTTTAAATTAAATCTCTAACTAGTA
1 TTTAAAAATAATAAAAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
* * * **
5289924 TTTTAAAATAATATCAAAATT-AAAAATATTATATATTAAA-TTAGAATTACTA
1 TTTAAAAATAATA-AAAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
* * * * *
5289976 TTT-AAAA-AATAACAAAAATAAAAAATATCTTATATTAAATATCAAAGTACTA
1 TTTAAAAATAATAA-AAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
* ** *
5290028 TTTAAAAAATAAT-AACAATT-AAAAGGATTTTATATTAAA-TTCTTAATTATTA
1 TTT-AAAAATAATAAAAAATTAAAAAATATTTTATATTAAATTTC-TAATTACTA
* * *
5290080 CTTAAAAATAATAAAAAATATAAAGAACATATTTT-TATTAAATCTCGAATTACTA
1 TTTAAAAATAATAAAAAAT-TAAA-AA-ATATTTTATATTAAATTTCTAATTACTA
* * * *
5290135 TTT---AA-AATAAAATAGT-AAAAA-A--TTATTTTAAA-TTCTGAATTATTA
1 TTTAAAAATAATAAAAAATTAAAAAATATTTTATATTAAATTTCT-AATTACTA
* * * *
5290180 ATTAAAAATAATAAAAAAATTAAGAAAATATAATTTATTTTAAATCTT-GAATTAGTA
1 TTTAAAAATAAT-AAAAAATTAA-AAAATAT--TTTATATTAAAT-TTCTAATTACTA
* * *
5290237 ATTAAAAACTAAT-AAAAATTAAAAAATATTTTATATTAAATCTCAAATTACTA
1 TTTAAAAA-TAATAAAAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
* *
5290290 TTT-AAAA-AAT-AAAAATTAAAAAATATTTTTTATTAAATCTT-GAATTACT-
1 TTTAAAAATAATAAAAAATTAAAAAATATTTTATATTAAAT-TTCTAATTACTA
*
5290339 TTTTAAAA-AAT----AATTAAAAAATATTTTATATTAAATTT-TAAATTACTA
1 TTTAAAAATAATAAAAAATTAAAAAATATTTTATATTAAATTTCT-AATTACTA
5290387 TTTAAAAATAAT--AAAATTAAAAAATATTTTATAT
1 TTTAAAAATAATAAAAAATTAAAAAATATTTTATAT
5290421 ATGTATTGGG
Statistics
Matches: 447, Mismatches: 63, Indels: 83
0.75 0.11 0.14
Matches are distributed among these distances:
44 4 0.01
45 15 0.03
46 3 0.01
47 32 0.07
48 11 0.02
49 11 0.02
50 60 0.13
51 62 0.14
52 69 0.15
53 84 0.19
54 21 0.05
55 28 0.06
56 16 0.04
57 25 0.06
58 4 0.01
59 2 0.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (53 bp):
TTTAAAAATAATAAAAAATTAAAAAATATTTTATATTAAATTTCTAATTACTA
Found at i:5290142 original size:157 final size:153
Alignment explanation
Indices: 5289827--5290416 Score: 545
Period size: 157 Copynumber: 3.8 Consensus size: 153
5289817 TTTAAAAATT
** *
5289827 AATAAAAAAATTTAAAATATTTTATATTAAATTTCTAATTACTATTTAAAAATAATAAAAAATTA
1 AATAAAAAAATAAAAAATATTTTATATTAAA-TTCGAATTACTATTTAAAAATAATAAAAAATTA
* * * *
5289892 AAAAGTATTTTAAATTAAATCTCT-AACTAGTATTTTAAAATAATATCAAAATT-AAAAATATTA
65 AAAAGTATTTTATATTAAATCT-TAAATTAGTATTTAAAAATAATA-AAAAATTAAAAAATATT-
* *
5289955 TATATTAAAT-TAGAATTACTATTTAAAA
127 TTTATTAAATCTCGAATTACTATTT--AA
* * * *
5289983 AATAACAAAAATAAAAAATATCTTATATTAAATATCAAAGTACTATTTAAAAAATAAT-AACAAT
1 AATAA-AAAAATAAAAAATATTTTATATTAAAT-TCGAATTACTATTT-AAAAATAATAAAAAAT
* * *
5290047 T-AAAAGGATTTTATATTAAATTCTT-AATTATTACTTAAAAATAATAAAAAATATAAAGAACAT
63 TAAAAAGTATTTTATATTAAA-TCTTAAATTAGTATTTAAAAATAATAAAAAAT-TAAA-AA-AT
5290110 ATTTTTATTAAATCTCGAATTACTATTTAA
124 ATTTTTATTAAATCTCGAATTACTATTTAA
* * * * *
5290140 AATAAAATAGT-AAAAA-A--TTATTTTAAATTCTGAATTATTAATTAAAAATAATAAAAAAATT
1 AATAAAAAAATAAAAAATATTTTATATTAAATTC-GAATTACTATTTAAAAATAAT-AAAAAATT
* * * *
5290201 AAGAAAATATAATTTATTTTAAATCTTGAATTAGTAATTAAAAACTAAT-AAAAATTAAAAAATA
64 AA-AAAGTAT--TTTATATTAAATCTTAAATTAGTATTTAAAAA-TAATAAAAAATTAAAAAATA
*
5290265 TTTTATATTAAATCTCAAATTACTATTTAA
125 TTTT-TATTAAATCTCGAATTACTATTTAA
* * *
5290295 AA-AATAAAAATTAAAAAATATTTTTTATTAAATCTTGAATTACT-TTTTAAAA-AAT----AAT
1 AATAA-AAAAA-TAAAAAATATTTTATATTAAAT-TCGAATTACTATTTAAAAATAATAAAAAAT
* * *
5290353 TAAAAAATATTTTATATTAAATTTTAAATTACTATTTAAAAATAAT--AAAATTAAAAAATATTT
63 TAAAAAGTATTTTATATTAAATCTTAAATTAGTATTTAAAAATAATAAAAAATTAAAAAATATTT
5290416 T
128 T
5290417 ATATATGTAT
Statistics
Matches: 366, Mismatches: 42, Indels: 60
0.78 0.09 0.13
Matches are distributed among these distances:
148 18 0.05
149 4 0.01
150 27 0.07
151 11 0.03
152 25 0.07
153 12 0.03
154 11 0.03
155 46 0.13
156 55 0.15
157 88 0.24
158 28 0.08
159 24 0.07
160 16 0.04
161 1 0.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (153 bp):
AATAAAAAAATAAAAAATATTTTATATTAAATTCGAATTACTATTTAAAAATAATAAAAAATTAA
AAAGTATTTTATATTAAATCTTAAATTAGTATTTAAAAATAATAAAAAATTAAAAAATATTTTTA
TTAAATCTCGAATTACTATTTAA
Found at i:5290176 original size:45 final size:42
Alignment explanation
Indices: 5290117--5290201 Score: 100
Period size: 45 Copynumber: 2.0 Consensus size: 42
5290107 CATATTTTTA
*
5290117 TTAAATCTCGAATTACTATTTAAAATAAAATAGTAAAAAATTATT
1 TTAAATCTCGAATTACTAATTAAAA-AAAATA--AAAAAATTATT
* *
5290162 TTAAAT-TCTGAATTATTAATTAAAAATAATAAAAAAATTA
1 TTAAATCTC-GAATTACTAATTAAAAAAAATAAAAAAATTA
5290202 AGAAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 9 0.25
44 7 0.19
45 20 0.56
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (42 bp):
TTAAATCTCGAATTACTAATTAAAAAAAATAAAAAAATTATT
Found at i:5290190 original size:100 final size:101
Alignment explanation
Indices: 5290057--5290243 Score: 261
Period size: 100 Copynumber: 1.9 Consensus size: 101
5290047 TAAAAGGATT
* * *
5290057 TTATATTAAATTCTTAATTATTACTTAAAAATAATAAAAAATATAAAGAACATAT-TTT-TATTA
1 TTATATTAAATTCTGAATTATTAATTAAAAATAATAAAAAA-ATAAAGAAAATATATTTATATTA
*
5290120 AATCTCGAATTACTATTTAAAATAAAATAGTAAAAAA
65 AATCTCGAATTACTAATTAAAATAAAATAGTAAAAAA
* * *
5290157 TTATTTTAAATTCTGAATTATTAATTAAAAATAATAAAAAAATTAAGAAAATATAATTTATTTTA
1 TTATATTAAATTCTGAATTATTAATTAAAAATAATAAAAAAATAAAGAAAATAT-ATTTATATTA
* *
5290222 AATCTTGAATTAGTAATTAAAA
65 AATCTCGAATTACTAATTAAAA
5290244 ACTAATAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
99 11 0.15
100 38 0.51
101 3 0.04
102 23 0.31
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (101 bp):
TTATATTAAATTCTGAATTATTAATTAAAAATAATAAAAAAATAAAGAAAATATATTTATATTAA
ATCTCGAATTACTAATTAAAATAAAATAGTAAAAAA
Found at i:5290218 original size:57 final size:54
Alignment explanation
Indices: 5289818--5290418 Score: 282
Period size: 52 Copynumber: 11.6 Consensus size: 54
5289808 CAAAAGTTCT
* * * * *
5289818 TTAAAAATTAATAAAAAAATT-TAAAATATTTTATATTAAATT-TCT-AATTACTAT
1 TTAAAAACTAAT--AAAAATTAAAAAATATTTTATTTTAAATTCT-TGAATTAGTAA
* ** * *
5289872 TTAAAAA-TAATAAAAAATTAAAAAGTATTTTAAATTAAA-TCTCT-AACTAGTAT
1 TTAAAAACTAAT-AAAAATTAAAAAATATTTTATTTTAAATTCT-TGAATTAGTAA
* * * * * *
5289925 TTTAAAA-TAATATCAAAATT-AAAAATATTATATATTAAA-T-TAGAATTACTAT
1 TTAAAAACTAATA--AAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
* * * * * * * *
5289977 TTAAAAAATAACAAAAA-TAAAAAATATCTTATATTAAATATC--AAAGTACTAT
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAAT-TCTTGAATTAGTAA
* * ** * * *
5290029 TTAAAAAATAATAACAATT-AAAAGGATTTTATATTAAATTCTT-AATTATTAC
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
* * *
5290081 TTAAAAA-TAATAAAAAATATAAAGAACATATTTT-TATTAAA-TCTCGAATTACT-A
1 TTAAAAACTAAT-AAAAAT-TAAA-AA-ATATTTTATTTTAAATTCTTGAATTAGTAA
* * * *
5290135 TTTAAAA-T-A-AAATAGT-AAAAA-A--TTATTTTAAATTC-TGAATTATTAA
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
5290181 TTAAAAA-TAATAAAAAAATTAAGAAAATATAATTTATTTTAAA-TCTTGAATTAGTAA
1 TTAAAAACTAAT--AAAAATTAA-AAAATAT--TTTATTTTAAATTCTTGAATTAGTAA
* ** *
5290238 TTAAAAACTAATAAAAATTAAAAAATATTTTATATTAAA-TCTCAAATTACT-A
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
* * *
5290290 TTTAAAA--AATAAAAATTAAAAAATATTTT-TTATTAAA-TCTTGAATTACT-T
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATT-TTAAATTCTTGAATTAGTAA
* * * * *
5290340 TTTAAAA--AAT---AATTAAAAAATATTTTATATTAAATT-TTAAATTACTAT
1 TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
5290388 TTAAAAA-TAAT-AAAATTAAAAAATATTTTAT
1 TTAAAAACTAATAAAAATTAAAAAATATTTTAT
5290419 ATATGTATTG
Statistics
Matches: 451, Mismatches: 54, Indels: 87
0.76 0.09 0.15
Matches are distributed among these distances:
44 2 0.00
45 13 0.03
46 11 0.02
47 32 0.07
48 11 0.02
49 6 0.01
50 54 0.12
51 50 0.11
52 93 0.21
53 85 0.19
54 25 0.06
55 22 0.05
56 16 0.04
57 27 0.06
58 4 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (54 bp):
TTAAAAACTAATAAAAATTAAAAAATATTTTATTTTAAATTCTTGAATTAGTAA
Found at i:5290448 original size:97 final size:96
Alignment explanation
Indices: 5289840--5290420 Score: 331
Period size: 104 Copynumber: 5.7 Consensus size: 96
5289830 AAAAAAATTT
* * * *
5289840 AAAATATTTTATATTAAATTTCTAATTACTATTTAAAAATAATAAAAAATTAAAAAGTATTTTAA
1 AAAATATTTTATATTAAATCTCAAATTACTATTT-AAAA-AAT-AAAAATTAAAAAATATTTTAT
** * *
5289905 ATTAAATCTCTAACTAGTATTTTAAAATAATATCAAAATT-A
63 ATTAAATCTGGAATTA-CA-TTT-AAA-AA-AT---AATTAA
* * *
5289946 AAAATATTATATATTAAAT-T-AGAATTACTATTTAAAAAATAACAAAAATAAAAAATATCTTAT
1 AAAATATTTTATATTAAATCTCA-AATTACTATTTAAAAAAT-A-AAAATTAAAAAATATTTTAT
* ** * *
5290009 ATTAAATATCAAAGTACTATTTAAAAAATAATAACAA
63 ATTAAATCTGGAATTAC-ATTTAAAAAATAAT--TAA
* * * *
5290046 TTAAAAGGATTTTATATTAAAT-TCTTAATTATTACTTAAAAATAATAAAAAATATAAAGAACAT
1 --AAAA-TATTTTATATTAAATCTC-AAATTACTA-TTTAAAA-AAT-AAAAAT-TAAA-AA-AT
*
5290110 ATTTT-TATTAAATCTCGAATTACTATTTAAAATAA-AA-TAGTA
56 ATTTTATATTAAATCTGGAATTAC-ATTTAAAA-AATAATTA--A
* * * *
5290152 AAAA-A--TTATTTTAAAT-TCTGAATTATTAATTAAAAATAATAAAAAAATTAAGAAAATATAA
1 AAAATATTTTATATTAAATCTC-AAATTACT-ATTTAAAA-AAT--AAAAATTAA-AAAATAT--
* * * *
5290213 TTTATTTTAAATCTTGAATTAGTAATTAAAAACTAATAAAAATTAA
58 TTTATATTAAATCTGGAATTA--CATTTAAAA--AAT---AATTAA
*
5290259 AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAAATAAAAATTAAAAAATATTTTTTATT
1 AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAAATAAAAATTAAAAAATATTTTATATT
* *
5290324 AAATCTTGAATTACTTTTTAAAAAATAATTAA
66 AAATCTGGAATTAC-ATTTAAAAAATAATTAA
* *
5290356 AAAATATTTTATATTAAATTTTAAATTACTATTT-AAAAATAATAAAATTAAAAAATATTTTATA
1 AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAAAT-A-AAAATTAAAAAATATTTTATA
5290420 T
64 T
5290421 ATGTATTGGG
Statistics
Matches: 395, Mismatches: 40, Indels: 88
0.76 0.08 0.17
Matches are distributed among these distances:
96 6 0.02
97 42 0.11
98 21 0.05
99 4 0.01
100 42 0.11
101 14 0.04
102 29 0.07
103 48 0.12
104 49 0.12
105 29 0.07
106 37 0.09
107 33 0.08
108 14 0.04
109 9 0.02
110 16 0.04
111 2 0.01
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (96 bp):
AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAAATAAAAATTAAAAAATATTTTATATT
AAATCTGGAATTACATTTAAAAAATAATTAA
Found at i:5293053 original size:50 final size:49
Alignment explanation
Indices: 5292999--5293254 Score: 323
Period size: 50 Copynumber: 5.1 Consensus size: 49
5292989 GTTGTCATTA
* *
5292999 TTGACTATTCTTCACTAACCTTTGACAATCGAAAGAGGTGACAGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACA-TAATTG
* * *
5293049 TTGACTATTCTTCACCAACCTTTGATAATCGAGTGAGGTGGCTATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGAC-ATAATTG
* * *
5293099 TTGACGATTCTTCACCAACCTTTGACAATCGAGAAAGGTGGCCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGT-GACATAATTG
* * *
5293149 TTGACGATTCTTCACCAAACTTTGACAATTGAGAGAGGTGATCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGA-CATAATTG
* * * * *
5293199 TTGATTATTCTTCACCAACCTTTGACAATGGAGAGAGATGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGT-GACATAATTG
5293249 TTGACT
1 TTGACT
5293255 CTAAGCAACT
Statistics
Matches: 180, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 175 0.97
51 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (49 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACATAATTG
Found at i:5297756 original size:50 final size:50
Alignment explanation
Indices: 5297640--5297942 Score: 414
Period size: 50 Copynumber: 6.1 Consensus size: 50
5297630 AGGTGTTAAC
* * * *
5297640 ATTGTTGACTATTCTTCACCAACTTTTGACAATCAAGAAAGGT-G--GTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
*
5297687 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* *
5297737 ATTGTTGACGATTCTTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
*
5297787 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* * * * *
5297837 ATTGTTGACGATTCTTCACCGACCTTTGACAATTGAGAAAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
* * * * * *
5297887 ATTGTTGACTATTCTTTACCAACATTTGACAATAGATAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
5297937 ATTGTT
1 ATTGTT
5297943 AACTCTAAAT
Statistics
Matches: 230, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
47 40 0.17
48 1 0.00
50 189 0.82
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
Found at i:5300406 original size:20 final size:19
Alignment explanation
Indices: 5300381--5300450 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
5300371 AAATAGATAA
* *
5300381 TTTTAAATTTTAACTAATTT
1 TTTTAAATTATAAATAA-TT
**
5300401 TTTTAAAAAATAAATAATT
1 TTTTAAATTATAAATAATT
* *
5300420 TTTTAAA-TCTAAGTAATT
1 TTTTAAATTATAAATAATT
5300438 TTTTAAA-TATAAA
1 TTTTAAATTATAAA
5300451 ATACATAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 19 0.46
19 9 0.22
20 13 0.32
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (19 bp):
TTTTAAATTATAAATAATT
Found at i:5300421 original size:18 final size:18
Alignment explanation
Indices: 5300399--5300450 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
5300389 TTTAACTAAT
*
5300399 TTTTTTAAAAAATAAATAA
1 TTTTTT-AAATATAAATAA
* *
5300418 TTTTTTAAATCTAAGTAA
1 TTTTTTAAATATAAATAA
5300436 TTTTTTAAATATAAA
1 TTTTTTAAATATAAA
5300451 ATACATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTTTAAATATAAATAA
Found at i:5300444 original size:37 final size:37
Alignment explanation
Indices: 5300360--5300441 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
5300350 AGTGAGTAGT
* *
5300360 TTTTTGTTAAAAAATAGATAATTTTAAATTTTAACTAA
1 TTTTT-TTAAAAAATAAATAATTTTAAATTCTAACTAA
*
5300398 TTTTTTTAAAAAATAAATAATTTTTTAAA-TCTAAGTAA
1 TTTTTTTAAAAAATAAATAA--TTTTAAATTCTAACTAA
5300436 TTTTTT
1 TTTTTT
5300442 AAATATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 14 0.36
38 18 0.46
39 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (37 bp):
TTTTTTTAAAAAATAAATAATTTTAAATTCTAACTAA
Found at i:5303368 original size:2 final size:2
Alignment explanation
Indices: 5303361--5303387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5303351 AATCAAAACC
5303361 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5303388 CTTTTCCCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5303661 original size:2 final size:2
Alignment explanation
Indices: 5303654--5303691 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5303644 TGTTATATGC
* *
5303654 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5303692 GGCTCAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5304950 original size:24 final size:24
Alignment explanation
Indices: 5304901--5304954 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5304891 TTAAAAATGA
* * *
5304901 AATAAATTTTTATTTACTGTAGTT
1 AATAAATTTTTATATAATGTAATT
5304925 AATAAATTTATTATATAAT-TAATT
1 AATAAATTT-TTATATAATGTAATT
5304949 AATAAA
1 AATAAA
5304955 CATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AATAAATTTTTATATAATGTAATT
Found at i:5305152 original size:37 final size:38
Alignment explanation
Indices: 5305099--5305172 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
5305089 TCAATTTTAA
* *
5305099 TTATTATTTAACATAAAATATA-ATTTTAA-TATATATT
1 TTATTATTAAAAAT-AAATATAGATTTTAATTATATATT
*
5305136 TTATTATTAAAAATAAATATAGTTTTTAATTATATAT
1 TTATTATTAAAAATAAATATAGATTTTAATTATATAT
5305173 ATTCATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.22
37 18 0.56
38 7 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TTATTATTAAAAATAAATATAGATTTTAATTATATATT
Found at i:5305184 original size:38 final size:36
Alignment explanation
Indices: 5305114--5305184 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
5305104 ATTTAACATA
*
5305114 AAATATAATTTTAATATATATTTTATTATTAAAAAT
1 AAATATAATTTTAATATATATTTCATTATTAAAAAT
*
5305150 AAATATAGTTTTTAATTATATATATTCATT-TTAAA
1 AAATATA-ATTTTAA-TATATAT-TTCATTATTAAA
5305185 TTAATATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 6 0.20
38 12 0.40
39 5 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
AAATATAATTTTAATATATATTTCATTATTAAAAAT
Found at i:5306412 original size:19 final size:19
Alignment explanation
Indices: 5306366--5306412 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5306356 TTTTTATAAC
5306366 AATTATTTAATTATAATTT
1 AATTATTTAATTATAATTT
* *
5306385 GATTTTTTAATTA-AATTT
1 AATTATTTAATTATAATTT
5306403 AAATTATTTA
1 -AATTATTTA
5306413 GGTTTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
AATTATTTAATTATAATTT
Found at i:5310128 original size:2 final size:2
Alignment explanation
Indices: 5310121--5310154 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5310111 TATCATCTTC
5310121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5310155 TGCCAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5315532 original size:22 final size:22
Alignment explanation
Indices: 5315489--5315533 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5315479 AATAAAGAAA
** * *
5315489 GAATAAAATAGCTATTATATAG
1 GAATAAAATAGAGAGTAAATAG
5315511 GAATAAAATAGAGAGTAAATAG
1 GAATAAAATAGAGAGTAAATAG
5315533 G
1 G
5315534 TATTTCATAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.24
Consensus pattern (22 bp):
GAATAAAATAGAGAGTAAATAG
Found at i:5315739 original size:21 final size:21
Alignment explanation
Indices: 5315715--5315780 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
5315705 CAAATAAAAA
*
5315715 AATTAATTATATAATTAATAT
1 AATTAATTATAAAATTAATAT
*
5315736 AATTTAATTACAAAATT-ATCAT
1 AA-TTAATTATAAAATTAAT-AT
*
5315758 -ATTCATTATTAAAATTAATAT
1 AATTAATTA-TAAAATTAATAT
5315779 AA
1 AA
5315781 ATATATAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
20 6 0.17
21 13 0.36
22 17 0.47
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAATTATAAAATTAATAT
Found at i:5317610 original size:52 final size:52
Alignment explanation
Indices: 5317548--5317655 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
5317538 TATAAGTGTC
5317548 TATATGGAAGTGGAAGCAGAATACTCTCACCAAAAGAATTACAAATTTAGTG
1 TATATGGAAGTGGAAGCAGAATACTCTCACCAAAAGAATTACAAATTTAGTG
5317600 TATATGGAAGTGGAAGCAGAATACTCTCACCAAAAGAATTACAAATTTAGTG
1 TATATGGAAGTGGAAGCAGAATACTCTCACCAAAAGAATTACAAATTTAGTG
5317652 TATA
1 TATA
5317656 ATCCTTCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (52 bp):
TATATGGAAGTGGAAGCAGAATACTCTCACCAAAAGAATTACAAATTTAGTG
Found at i:5318026 original size:40 final size:40
Alignment explanation
Indices: 5317971--5318055 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
5317961 CATCAAATTT
5317971 TAAAATATCCAAAGGGAATGAATCTGTAAATTCAGCAACA
1 TAAAATATCCAAAGGGAATGAATCTGTAAATTCAGCAACA
* *
5318011 TAAAATATCCAAAGGGAATGAATCTGTACATTCGGCAACA
1 TAAAATATCCAAAGGGAATGAATCTGTAAATTCAGCAACA
*
5318051 AAAAA
1 TAAAA
5318056 GAAAGGCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.21
Consensus pattern (40 bp):
TAAAATATCCAAAGGGAATGAATCTGTAAATTCAGCAACA
Found at i:5321952 original size:19 final size:19
Alignment explanation
Indices: 5321930--5321969 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5321920 AAAATATTGA
*
5321930 AAATATTAAAAATTAATTT
1 AAATAATAAAAATTAATTT
* *
5321949 AAATAATAATATTTAATTT
1 AAATAATAAAAATTAATTT
5321968 AA
1 AA
5321970 TTTCAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAATAAAAATTAATTT
Found at i:5322179 original size:14 final size:14
Alignment explanation
Indices: 5322160--5322207 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
5322150 ATTTTTAAAA
5322160 TTTTTAAAATATAT
1 TTTTTAAAATATAT
5322174 TTTTTAGAAA-ATAT
1 TTTTTA-AAATATAT
*
5322188 TTTTTAAAATGTAT
1 TTTTTAAAATATAT
5322202 TTTTTA
1 TTTTTA
5322208 TATAAGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 3 0.10
14 25 0.81
15 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATATAT
Found at i:5322328 original size:67 final size:68
Alignment explanation
Indices: 5322257--5322425 Score: 186
Period size: 66 Copynumber: 2.4 Consensus size: 68
5322247 AAATAACAGT
* * ** *
5322257 TAAAAAATTAATTAAATTAAAAAATTTATGTT-A-AAATT-ACGTATTAATTATTATTTTTTTAA
1 TAAAAAATTAATTAAATTAAAAAAATTATATTAATAAATTAAAATATTAATTATTA-TATTTTAA
5322319 TAAAA
65 -AAAA
5322324 TAAAAATAATATTTAATTAAATTTAAAAAAATTATATTAATAAATTAAAATATTAATTATTATAT
1 T--AAA-AA-A-TTAATTAAA-TTAAAAAAATTATATTAATAAATTAAAATATTAATTATTATAT
5322389 TTTAAAAAA
60 TTTAAAAAA
5322398 TAAAAAATT--TTAAATTAAAAAAATTATA
1 TAAAAAATTAATTAAATTAAAAAAATTATA
5322426 GGTGAAACAC
Statistics
Matches: 88, Mismatches: 5, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
66 14 0.16
67 6 0.07
69 5 0.06
70 3 0.03
71 3 0.03
72 12 0.14
73 14 0.16
74 6 0.07
75 12 0.14
76 13 0.15
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (68 bp):
TAAAAAATTAATTAAATTAAAAAAATTATATTAATAAATTAAAATATTAATTATTATATTTTAAA
AAA
Found at i:5322364 original size:45 final size:43
Alignment explanation
Indices: 5322315--5322398 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
5322305 TATTATTTTT
*
5322315 TTAATAAAATAAAAATAATATTTAATTAAATTTAAAAAAATTATA
1 TTAAT-AAATAAAAATAATAATT-ATTAAATTTAAAAAAATTATA
* * * *
5322360 TTAATAAATTAAAATATTAATTATTATATTTTAAAAAAT
1 TTAATAAATAAAAATAATAATTATTAAATTTAAAAAAAT
5322399 AAAAAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 15 0.44
44 14 0.41
45 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (43 bp):
TTAATAAATAAAAATAATAATTATTAAATTTAAAAAAATTATA
Found at i:5322367 original size:23 final size:22
Alignment explanation
Indices: 5322325--5322398 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
5322315 TTAATAAAAT
*
5322325 AAAAATAATATTTAATTAAATTTAA
1 AAAAATTATA-TTAA-TAAATTT-A
5322350 AAAAATTATATTAATAAA-TTA
1 AAAAATTATATTAATAAATTTA
* * *
5322371 AAATATTA-ATTATTATATTTTA
1 AAAAATTATATTAATA-AATTTA
5322393 AAAAAT
1 AAAAAT
5322399 AAAAAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 6 0.14
21 9 0.21
22 10 0.24
23 4 0.10
24 4 0.10
25 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAAATTATATTAATAAATTTA
Found at i:5322381 original size:25 final size:22
Alignment explanation
Indices: 5322314--5322384 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
5322304 TTATTATTTT
*
5322314 TTTAATAAAATAAAAATAA-TA
1 TTTAATAAATTAAAAATAATTA
5322335 TTTAATTAAATTTAAAAA-AATTA
1 TTTAA-TAAA-TTAAAAATAATTA
5322358 TATTAATAAATTAAAATATTAATTA
1 T-TTAATAAATTAAAA-A-TAATTA
5322383 TT
1 TT
5322385 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
21 5 0.12
22 12 0.29
23 14 0.33
24 5 0.12
25 6 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAATAAATTAAAAATAATTA
Found at i:5322383 original size:76 final size:70
Alignment explanation
Indices: 5322264--5322403 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 70
5322254 AGTTAAAAAA
* * ** *
5322264 TTAATTAAATTAAAAAATTTATGTTAAAATTACGTATTAATTATTATTTTTTTAATAAAATAAAA
1 TTAATTAAATTAAAAAAATTATATTAAAATTAAATATTAATTATTA-TATTTTAA-AAAATAAAA
5322329 ATAATAT
64 ATAATAT
5322336 TTAATTAAATTTAAAAAAATTATATTAATAAATTAAAATATTAATTATTATATTTTAAAAAATAA
1 TTAATTAAA-TTAAAAAAATTATATT-A-AAATT-AAATATTAATTATTATATTTTAAAAAATAA
5322401 AAA
62 AAA
5322404 ATTTTAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
72 9 0.15
73 14 0.24
74 11 0.19
75 12 0.20
76 13 0.22
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (70 bp):
TTAATTAAATTAAAAAAATTATATTAAAATTAAATATTAATTATTATATTTTAAAAAATAAAAAT
AATAT
Found at i:5322395 original size:72 final size:67
Alignment explanation
Indices: 5322257--5322425 Score: 168
Period size: 76 Copynumber: 2.4 Consensus size: 67
5322247 AAATAACAGT
* * ** *
5322257 TAAAAAATTAATTAAATTAAAAAATTTATGTTAAAATTACGTATTAATTATTATT-TTTTTAATA
1 TAAAAAATTAATTAAATTAAAAAAATTATATTAAAATTAAATATTAATTATTATTATTTATAA-A
5322321 AAA
65 AAA
5322324 TAAAAATAATATTTAATTAAATTTAAAAAAATTATATTAATAAATTAAAATATTAATTATTA-TA
1 T--AAA-AA-A-TTAATTAAA-TTAAAAAAATTATATT-A-AAATT-AAATATTAATTATTATTA
5322388 TTT-TAAAAAA
57 TTTATAAAAAA
5322398 TAAAAAATT--TTAAATTAAAAAAATTATA
1 TAAAAAATTAATTAAATTAAAAAAATTATA
5322426 GGTGAAACAC
Statistics
Matches: 88, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
66 14 0.16
67 6 0.07
69 5 0.06
70 3 0.03
71 3 0.03
72 12 0.14
73 14 0.16
74 6 0.07
75 9 0.10
76 16 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (67 bp):
TAAAAAATTAATTAAATTAAAAAAATTATATTAAAATTAAATATTAATTATTATTATTTATAAAA
AA
Found at i:5322733 original size:23 final size:23
Alignment explanation
Indices: 5322690--5322733 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5322680 TTTAAAGTTA
* *
5322690 TTTTATTTTAAAGTATGATTTAT
1 TTTTATTTTAAAATATAATTTAT
5322713 TTTTATTTATAAAAT-TAATTT
1 TTTTATTT-TAAAATATAATTT
5322734 GATCAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAAAATATAATTTAT
Found at i:5322842 original size:69 final size:70
Alignment explanation
Indices: 5322750--5322933 Score: 221
Period size: 69 Copynumber: 2.6 Consensus size: 70
5322740 AAGTATTATT
* * * * *
5322750 TATTTTTATTTGTATAAGTTTAAATTTATTTTTATTGATTATATGAGTTTAAATTTTTTA-GGTA
1 TATTTTTATTTGTAAAAATTTAAATTTATTTTTATTGATTATATAAGTTAAAATTTTTAATGGTA
5322814 TAATC
66 TAATC
* *
5322819 TATTTTGATTCGTAAAAATTTAAATTTA-TTTT-TTGATATGATATAAGTTAAAATTTTTAATGG
1 TATTTTTATTTGTAAAAATTTAAATTTATTTTTATTGAT-T-ATATAAGTTAAAATTTTTAATGG
*
5322882 TATAATT
64 TATAATC
*
5322889 TATTTTTATTTATAAAAATTTAAAATTTATTTTTTATTTGATTAT
1 TATTTTTATTTGTAAAAATTT-AAATTTA-TTTTTA-TTGATTAT
5322934 GTACCACAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
67 5 0.05
68 5 0.05
69 41 0.43
70 26 0.27
71 7 0.07
73 6 0.06
74 1 0.01
75 5 0.05
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.57
Consensus pattern (70 bp):
TATTTTTATTTGTAAAAATTTAAATTTATTTTTATTGATTATATAAGTTAAAATTTTTAATGGTA
TAATC
Found at i:5328087 original size:52 final size:52
Alignment explanation
Indices: 5328006--5328126 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
5327996 TGAAAAGTTA
*
5328006 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
* *
5328058 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
5328110 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
5328127 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
Found at i:5328139 original size:52 final size:51
Alignment explanation
Indices: 5328006--5328146 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
5327996 TGAAAAGTTA
5328006 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
* * *
5328058 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
*
5328110 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
5328147 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAATTTGC
Found at i:5328153 original size:13 final size:13
Alignment explanation
Indices: 5328135--5328159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5328125 CAAAGATCAG
5328135 TGTATCGATACAA
1 TGTATCGATACAA
5328148 TGTATCGATACA
1 TGTATCGATACA
5328160 TGTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5328242 original size:33 final size:33
Alignment explanation
Indices: 5328200--5328269 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
5328190 GGCAGTAGCT
5328200 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
5328233 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
5328266 TACA
1 TACA
5328270 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:5328243 original size:13 final size:13
Alignment explanation
Indices: 5328225--5328249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5328215 CAAAAAAATA
5328225 TGTATCGATACAT
1 TGTATCGATACAT
5328238 TGTATCGATACA
1 TGTATCGATACA
5328250 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5331888 original size:166 final size:165
Alignment explanation
Indices: 5331442--5331892 Score: 492
Period size: 166 Copynumber: 2.7 Consensus size: 165
5331432 AATCCATGTA
* * * * ** * *
5331442 TCATGCATTAATCTTATTAACTTCTTTCATATCAGAATGAATCTGATTTCTATTAACAATCTATG
1 TCATGCATTAGTATTATCAATTTCTTTCATATCAGAAAAAATCTGATTCCTATTAAAAATCTATG
* * * * * * *
5331507 CATTAATCATATTTATTTC-AAAATAGAATTCATGTATTAGTCCTATCTTTCGTATTTCAATCAA
66 CATTTATCATATTTA-TTCAAAAACAGAATTCATGTATAATTCC-ATCTTTCGAACTCCAATCAA
** *
5331571 TGCATTAGTCTATTTGTTACAGTCTGACATTTACAAT
129 TGCATTAGTCTATTCCTTACAGTCTAACATTTACAAT
* * * * * * *
5331608 TTATGCATTAGTCTTATCAATTTTTTTTATAT-AAAAAAGAATCTGATTCCCATTAAAAATCCAT
1 TCATGCATTAGTATTATCAATTTCTTTCATATCAGAAAA-AATCTGATTCCTATTAAAAATCTAT
** * * * * *
5331672 AAATTTATTATATTTATTCAAAAACAGAATTCATGCATTAGTCCCATCTTTCGAACTCCAATCTA
65 GCATTTATCATATTTATTCAAAAACAGAATTCATGTA-TAATTCCATCTTTCGAACTCCAATCAA
*
5331737 TGCATTAGTCTATTCCTTACAGTCTAACATTTATAAT
129 TGCATTAGTCTATTCCTTACAGTCTAACATTTACAAT
* * *
5331774 TCATGTATTAGTATTATCAATTTCTTTCATATCAGAAAAAATCTAATTCCTATTAAGAATCTATG
1 TCATGCATTAGTATTATCAATTTCTTTCATATCAGAAAAAATCTGATTCCTATTAAAAATCTATG
* * *
5331839 CATTTATCATATTTATTCAAAAACAAAATCCATGTATCAATTTCATCTTTCGAA
66 CATTTATCATATTTATTCAAAAACAGAATTCATGTAT-AATTCCATCTTTCGAA
5331893 TTTTAATAAA
Statistics
Matches: 230, Mismatches: 50, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
165 7 0.03
166 215 0.93
167 8 0.03
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (165 bp):
TCATGCATTAGTATTATCAATTTCTTTCATATCAGAAAAAATCTGATTCCTATTAAAAATCTATG
CATTTATCATATTTATTCAAAAACAGAATTCATGTATAATTCCATCTTTCGAACTCCAATCAATG
CATTAGTCTATTCCTTACAGTCTAACATTTACAAT
Found at i:5331925 original size:39 final size:39
Alignment explanation
Indices: 5331882--5332012 Score: 118
Period size: 39 Copynumber: 3.4 Consensus size: 39
5331872 GTATCAATTT
**
5331882 CATCTTTCGAATTTTAATAAAAAATTTATATATTAGTCA
1 CATCTTTTAAATTTTAATAAAAAATTTATATATTAGTCA
* * * * * *
5331921 CATCTTTTAAATTTCAATAAATAATCTATACATTACTAA
1 CATCTTTTAAATTTTAATAAAAAATTTATATATTAGTCA
* * * * * *
5331960 TATCTTTTAAAATCTAACAAAAAATTCATGTATTAGTCA
1 CATCTTTTAAATTTTAATAAAAAATTTATATATTAGTCA
* *
5331999 TATCTTTTAGATTT
1 CATCTTTTAAATTT
5332013 CAGTTAACCG
Statistics
Matches: 69, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (39 bp):
CATCTTTTAAATTTTAATAAAAAATTTATATATTAGTCA
Found at i:5333587 original size:24 final size:24
Alignment explanation
Indices: 5333510--5333588 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
5333500 TATATAATGA
5333510 AAATTTATTATAATACGAATACAT
1 AAATTTATTATAATACGAATACAT
* * * *
5333534 AAATTTATCAAAAT-CTATATA-TT
1 AAATTTATTATAATACGA-ATACAT
5333557 AAATTTATTATAATACGAATACAT
1 AAATTTATTATAATACGAATACAT
5333581 AAATTTAT
1 AAATTTAT
5333589 CAAAATTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 18 0.41
24 26 0.59
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (24 bp):
AAATTTATTATAATACGAATACAT
Found at i:5333623 original size:38 final size:38
Alignment explanation
Indices: 5333581--5333717 Score: 105
Period size: 36 Copynumber: 3.7 Consensus size: 38
5333571 ACGAATACAT
*
5333581 AAATTTATCAAAATTTATATATTAAATCTATATAATGA
1 AAATTTATCAAAATTTATATATTAAATCAATATAATGA
* *
5333619 AAATTTAT-AAAATTTATA-ATAAAAT-AATTTTAATGA
1 AAATTTATCAAAATTTATATATTAAATCAA-TATAATGA
* *
5333655 AAATTT-TAATAAATTTAT-TA-T-AATACGAATA-CATG-
1 AAATTTATCA-AAATTTATATATTAAAT-C-AATATAATGA
5333690 -AATTTATCAAAATCTATATATATTAAAT
1 AAATTTATCAAAAT-T-TATATATTAAAT
5333718 TTTTATAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
34 9 0.11
35 8 0.10
36 26 0.33
37 22 0.28
38 11 0.14
39 3 0.04
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (38 bp):
AAATTTATCAAAATTTATATATTAAATCAATATAATGA
Found at i:5333635 original size:47 final size:47
Alignment explanation
Indices: 5333485--5333616 Score: 212
Period size: 47 Copynumber: 2.8 Consensus size: 47
5333475 ATTTATAATA
*
5333485 AAATTTATCAAAATCTATATAATGAAAATTTATTATAATACGAATACAT
1 AAATTTATCAAAATCTATAT-AT-TAAATTTATTATAATACGAATACAT
5333534 AAATTTATCAAAATCTATATATTAAATTTATTATAATACGAATACAT
1 AAATTTATCAAAATCTATATATTAAATTTATTATAATACGAATACAT
* *
5333581 AAATTTATCAAAATTTATATATTAAATCTA-TATAAT
1 AAATTTATCAAAATCTATATATTAAATTTATTATAAT
5333617 GAAAATTTAT
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
46 6 0.08
47 52 0.65
48 2 0.03
49 20 0.25
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (47 bp):
AAATTTATCAAAATCTATATATTAAATTTATTATAATACGAATACAT
Found at i:5333658 original size:36 final size:37
Alignment explanation
Indices: 5333581--5333677 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 37
5333571 ACGAATACAT
* * *
5333581 AAATTTATCAAAATTTATATATTAAATCTATATAATGA
1 AAATTTATAAAAATTTATA-ATAAAATATATATAATGA
*
5333619 AAATTTAT-AAAATTTATAATAAAATA-ATTTTAATGA
1 AAATTTATAAAAATTTATAATAAAATATA-TATAATGA
*
5333655 AAATTT-TAATAAATTTATTATAA
1 AAATTTATAA-AAATTTATAATAA
5333678 TACGAATACA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
35 2 0.04
36 20 0.38
37 22 0.42
38 8 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (37 bp):
AAATTTATAAAAATTTATAATAAAATATATATAATGA
Found at i:5333678 original size:26 final size:27
Alignment explanation
Indices: 5333627--5333678 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
5333617 GAAAATTTAT
*
5333627 AAAATTTATAATAAAATAATTTTAATG
1 AAAATTTATAATAAAATAATTATAATG
* *
5333654 AAAATTT-TAATAAATTTATTATAAT
1 AAAATTTATAATAAAATAATTATAAT
5333679 ACGAATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAATTTATAATAAAATAATTATAATG
Found at i:5333691 original size:36 final size:33
Alignment explanation
Indices: 5333556--5333691 Score: 73
Period size: 37 Copynumber: 3.8 Consensus size: 33
5333546 ATCTATATAT
5333556 TAAATTTATTATAATACGAATACAT--AAA-TTTA
1 TAAATTTATTATAA-ACGAATA-ATGAAAATTTTA
*
5333588 TCAAAATTTATATATTAAATCTATATAATGAAAA-TTTA
1 T--AAATTTAT-TA-TAAA-CGA-ATAATGAAAATTTTA
* **
5333626 TAAAATTTATAATAAAATAATTTTAATGAAAATTTTAA
1 T-AAATTTATTATAAACGAA---TAATGAAAATTTT-A
5333664 TAAATTTATTATAATACGAATACATGAA
1 TAAATTTATTATAA-ACGAATA-ATGAA
5333692 TTTATCAAAA
Statistics
Matches: 83, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
32 1 0.01
33 1 0.01
34 10 0.12
35 9 0.11
36 22 0.27
37 27 0.33
38 13 0.16
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (33 bp):
TAAATTTATTATAAACGAATAATGAAAATTTTA
Found at i:5338200 original size:17 final size:15
Alignment explanation
Indices: 5338182--5338227 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
5338172 ATTATTGTTA
5338182 ATAATATAT-TAAAT
1 ATAATATATATAAAT
*
5338196 ATAATTATGATATAAAA
1 ATAA-TAT-ATATAAAT
5338213 ATAATATATATAAAT
1 ATAATATATATAAAT
5338228 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 5 0.19
17 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAATATATATAAAT
Found at i:5338310 original size:21 final size:21
Alignment explanation
Indices: 5338286--5338328 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5338276 TAACTTTTAA
5338286 AGTAGAGAATA-AATATAAAAT
1 AGTAGA-AATATAATATAAAAT
* *
5338307 AGTATAAATATAATATGAAAT
1 AGTAGAAATATAATATAAAAT
5338328 A
1 A
5338329 TTAATCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (21 bp):
AGTAGAAATATAATATAAAAT
Found at i:5339685 original size:17 final size:18
Alignment explanation
Indices: 5339663--5339702 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5339653 TGATATTATG
5339663 AATTTAAAA-AAAAAAAA
1 AATTTAAAATAAAAAAAA
*
5339680 AATTTAAAATTAAAAAATA
1 AATTTAAAA-TAAAAAAAA
5339699 AATT
1 AATT
5339703 ACATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTTAAAATAAAAAAAA
Found at i:5340473 original size:17 final size:18
Alignment explanation
Indices: 5340448--5340492 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5340438 AAAATATTTT
*
5340448 TTATTTTATAAATTT-TGA
1 TTATATTATAAATTTAT-A
5340466 TT-TATTATAAATTTATA
1 TTATATTATAAATTTATA
5340483 TTATATTATA
1 TTATATTATA
5340493 TTTTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATATTATAAATTTATA
Found at i:5341517 original size:17 final size:17
Alignment explanation
Indices: 5341495--5341528 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5341485 TAAATGATTT
5341495 ATAAAAA-AATAATTTTA
1 ATAAAAATAAT-ATTTTA
5341512 ATAAAAATAATATTTTA
1 ATAAAAATAATATTTTA
5341529 TGTGATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATAATATTTTA
Found at i:5344581 original size:18 final size:18
Alignment explanation
Indices: 5344547--5344580 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5344537 TCAAAACTTA
*
5344547 TTTTTTGTTTTTGTTTTG
1 TTTTGTGTTTTTGTTTTG
5344565 TTTTGTGTTTTT-TTTT
1 TTTTGTGTTTTTGTTTT
5344581 TAGATTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (18 bp):
TTTTGTGTTTTTGTTTTG
Found at i:5345622 original size:2 final size:2
Alignment explanation
Indices: 5345615--5345639 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5345605 ATGTCAGGTA
5345615 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5345640 GCACTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5348660 original size:2 final size:2
Alignment explanation
Indices: 5348647--5348689 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5348637 TCCATTAACC
*
5348647 TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5348689 T
1 T
5348690 ATTACATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5353945 original size:3 final size:3
Alignment explanation
Indices: 5353937--5353970 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
5353927 TTAAGTTTTC
* *
5353937 ATA ATA ATA ATA ATA AAA AAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5353971 AAAAACGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:5353962 original size:15 final size:16
Alignment explanation
Indices: 5353942--5353974 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5353932 TTTTCATAAT
5353942 AATAATAATAA-AAAA
1 AATAATAATAATAAAA
5353957 AATAATAATAATAAAA
1 AATAATAATAATAAAA
5353973 AA
1 AA
5353975 ACGAAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAATAATAATAAAA
Found at i:5353962 original size:18 final size:18
Alignment explanation
Indices: 5353939--5353975 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5353929 AAGTTTTCAT
5353939 AATAATAATAATAAAAAA
1 AATAATAATAATAAAAAA
5353957 AATAATAATAATAAAAAA
1 AATAATAATAATAAAAAA
5353975 A
1 A
5353976 CGAAAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAATAATAATAAAAAA
Found at i:5353963 original size:21 final size:20
Alignment explanation
Indices: 5353937--5353975 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5353927 TTAAGTTTTC
5353937 ATAATAATAATAATAAAAAAA
1 ATAATAATAATAA-AAAAAAA
5353958 ATAATAATAATAAAAAAA
1 ATAATAATAATAAAAAAA
5353976 CGAAAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAATAATAATAAAAAAAAA
Found at i:5355417 original size:16 final size:16
Alignment explanation
Indices: 5355396--5355427 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5355386 ATTATTATAT
*
5355396 ATATAAAATAATTAAA
1 ATATAAAATAAATAAA
5355412 ATATAAAATAAATAAA
1 ATATAAAATAAATAAA
5355428 TATCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATAAAATAAATAAA
Found at i:5359978 original size:2 final size:2
Alignment explanation
Indices: 5359971--5360005 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5359961 AATGGGAACT
5359971 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5360006 GTGGTGCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5364616 original size:51 final size:51
Alignment explanation
Indices: 5364557--5364658 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
5364547 TGCTGCAAGT
* *
5364557 AGGAAGATAGATGTACTTGTAGTAGCTTATATTTGGTGG-TTCACTTTTGAC
1 AGGAAGATAAATGTACCTGTAGTAGCTTATATTTGGTGGATT-ACTTTTGAC
5364608 AGGAAGATAAATGTACCTGTAGTAGCTTATATTTGGTGGATTACTTTTGAC
1 AGGAAGATAAATGTACCTGTAGTAGCTTATATTTGGTGGATTACTTTTGAC
5364659 TAAAATGTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 46 0.96
52 2 0.04
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (51 bp):
AGGAAGATAAATGTACCTGTAGTAGCTTATATTTGGTGGATTACTTTTGAC
Found at i:5364735 original size:42 final size:40
Alignment explanation
Indices: 5364644--5364739 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
5364634 TTATATTTGG
* *
5364644 TGGATTACTTTTGACTAAAATGTGATATTTGAAATATAGA
1 TGGATTACTTTTAACTAAAATGTGATATTTGAAACATAGA
* *
5364684 TGGATTACTTTTAACTAAAATGTGATATATTTAAAGCATGGA
1 TGGATTACTTTTAACTAAAATGTGATAT-TTGAAA-CATAGA
5364726 T-GATATACTTTTAA
1 TGGAT-TACTTTTAA
5364740 GTCTGTCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 27 0.55
41 8 0.16
42 14 0.29
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (40 bp):
TGGATTACTTTTAACTAAAATGTGATATTTGAAACATAGA
Found at i:5368068 original size:19 final size:19
Alignment explanation
Indices: 5368044--5368103 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
5368034 TTTGAATTTC
5368044 AACAATTTGTATCGATACA
1 AACAATTTGTATCGATACA
*
5368063 AACAATAAATGTATCGATACA
1 AACAAT--TTGTATCGATACA
**
5368084 TAA-GTTTTGTATCGATACA
1 -AACAATTTGTATCGATACA
5368103 A
1 A
5368104 TATATGGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
21 13 0.38
22 2 0.06
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (19 bp):
AACAATTTGTATCGATACA
Found at i:5368134 original size:19 final size:18
Alignment explanation
Indices: 5368072--5368134 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
5368062 AAACAATAAA
5368072 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
5368091 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
* *
5368104 TATATGGATACATAAGTGT
1 TGTATCGATACATAAGT-T
5368123 TGTATCGATACA
1 TGTATCGATACA
5368135 ATGTATCGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
17 2 0.06
19 21 0.62
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:5368189 original size:20 final size:20
Alignment explanation
Indices: 5368164--5368218 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5368154 CTGCTAAGGA
5368164 AATGTATCGATACATT-ACTC
1 AATGTATCGATACATTGAC-C
5368184 AATGTATCGATACATTGACC
1 AATGTATCGATACATTGACC
**
5368204 TTTGTATCGATACAT
1 AATGTATCGATACAT
5368219 CTAGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGACC
Found at i:5373469 original size:32 final size:33
Alignment explanation
Indices: 5373414--5373477 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
5373404 TTCAACGATT
5373414 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
5373447 TGTATCGATATAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
5373478 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:5373471 original size:19 final size:19
Alignment explanation
Indices: 5373413--5373496 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
5373403 TTTCAACGAT
5373413 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
5373433 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
5373447 -TGTATCGATATATAAGTG
1 TTGTATCGATACATAAGTG
*
5373465 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
5373484 TTGTATCGATACA
1 TTGTATCGATACA
5373497 ATGTATCGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
19 29 0.53
20 12 0.22
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:5373709 original size:52 final size:52
Alignment explanation
Indices: 5373584--5373710 Score: 193
Period size: 52 Copynumber: 2.4 Consensus size: 52
5373574 CTGATCTTTA
* *
5373584 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGACAAATTTGCCCAGATATATCGATACACTATGAAATG
*
5373636 TATCGATACATACA-AGCAAATTTGCCCAGATATATCGATACACTATGAAATG
1 TATCGATACATGCAGA-CAAATTTGCCCAGATATATCGATACACTATGAAATG
* *
5373688 TATCGATACACGCAGATAAATTT
1 TATCGATACATGCAGACAAATTT
5373711 TCATATTTCG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 66 0.99
53 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (52 bp):
TATCGATACATGCAGACAAATTTGCCCAGATATATCGATACACTATGAAATG
Found at i:5374411 original size:13 final size:13
Alignment explanation
Indices: 5374393--5374417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5374383 CATAAAGTGT
5374393 TGTATCGATACAA
1 TGTATCGATACAA
5374406 TGTATCGATACA
1 TGTATCGATACA
5374418 TGTTTTTTTG
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5374498 original size:13 final size:13
Alignment explanation
Indices: 5374480--5374504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5374470 ATCACTTAAA
5374480 TGTATCGATACAT
1 TGTATCGATACAT
5374493 TGTATCGATACA
1 TGTATCGATACA
5374505 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5374557 original size:52 final size:52
Alignment explanation
Indices: 5374513--5374693 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
5374503 CACTGATCTT
5374513 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
5374565 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
5374617 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
5374669 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
5374694 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:5382800 original size:41 final size:41
Alignment explanation
Indices: 5382755--5382944 Score: 190
Period size: 41 Copynumber: 4.6 Consensus size: 41
5382745 CAAATAACAA
*
5382755 TAGCGACGTTT-ATTAATAAAACG-CTGTTAATATTCATGACT
1 TAGCGACGTTTGATTAAT-AAACGTC-GCTAATATTCATGACT
* * * * *
5382796 TAGCGTCGTTTGGTTAATAAACATCGTTAATATTCATGACG
1 TAGCGACGTTTGATTAATAAACGTCGCTAATATTCATGACT
* *
5382837 TAGC-ACCGTTTGGTTAATAAACGTTGCTAATATTCATGACT
1 TAGCGA-CGTTTGATTAATAAACGTCGCTAATATTCATGACT
* *
5382878 TAGCGGCGTTTGCATT-ATAAATGTCGCTAATATTCATGACT
1 TAGCGACGTTTG-ATTAATAAACGTCGCTAATATTCATGACT
* * **
5382919 TAGCGGCATTTTCTTAATAAACGTCG
1 TAGCGACGTTTGATTAATAAACGTCG
5382945 TTAAAATTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.02
41 116 0.92
42 8 0.06
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (41 bp):
TAGCGACGTTTGATTAATAAACGTCGCTAATATTCATGACT
Found at i:5382898 original size:82 final size:83
Alignment explanation
Indices: 5382767--5382922 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 83
5382757 GCGACGTTTA
* * * *
5382767 TTAATAAAACGCTGTTAATATTCATGACTTAGCGTCGTTTGGTTAATAAACATCGTTAATATTCA
1 TTAATAAAACGCTGCTAATATTCATGACTTAGCGGCGTTTGATTAATAAACATCGCTAATATTCA
5382832 TGACGTAGCACCGTTTGG
66 TGACGTAGCACCGTTTGG
* **
5382850 TTAAT-AAACGTTGCTAATATTCATGACTTAGCGGCGTTTGCATT-ATAAATGTCGCTAATATTC
1 TTAATAAAACGCTGCTAATATTCATGACTTAGCGGCGTTTG-ATTAATAAACATCGCTAATATTC
*
5382913 ATGACTTAGC
65 ATGACGTAGC
5382923 GGCATTTTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
82 57 0.89
83 7 0.11
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (83 bp):
TTAATAAAACGCTGCTAATATTCATGACTTAGCGGCGTTTGATTAATAAACATCGCTAATATTCA
TGACGTAGCACCGTTTGG
Found at i:5382936 original size:82 final size:82
Alignment explanation
Indices: 5382767--5382942 Score: 210
Period size: 82 Copynumber: 2.1 Consensus size: 82
5382757 GCGACGTTTA
* * * * *
5382767 TTAATAAAACGCTGTTAATATTCATGACTTAGCGTCGTTTGGTTAATAAACATCGTTAATATTCA
1 TTAAT-AAACGTTGCTAATATTCATGACTTAGCGGCGTTTGATTAATAAACATCGCTAATATTCA
* *
5382832 TGACGTAGCACCGTTTGG
65 TGACGTAGCACCATTTGC
**
5382850 TTAATAAACGTTGCTAATATTCATGACTTAGCGGCGTTTGCATT-ATAAATGTCGCTAATATTCA
1 TTAATAAACGTTGCTAATATTCATGACTTAGCGGCGTTTG-ATTAATAAACATCGCTAATATTCA
* ** *
5382914 TGACTTAGCGGCATTTTC
65 TGACGTAGCACCATTTGC
5382932 TTAATAAACGT
1 TTAATAAACGT
5382943 CGTTAAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
82 72 0.91
83 7 0.09
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (82 bp):
TTAATAAACGTTGCTAATATTCATGACTTAGCGGCGTTTGATTAATAAACATCGCTAATATTCAT
GACGTAGCACCATTTGC
Found at i:5387050 original size:20 final size:20
Alignment explanation
Indices: 5387007--5387058 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5386997 GTAGCCAAAC
*
5387007 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
*
5387027 -TGTATTGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
5387046 TTGTATCGATACA
1 TTGTATCGATACA
5387059 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:5388985 original size:22 final size:22
Alignment explanation
Indices: 5388957--5389014 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
5388947 TAAATTATTT
5388957 ATATGTTTAATAAAGATTTAAA
1 ATATGTTTAATAAAGATTTAAA
5388979 ATATGTTTAATAAAGATTTAAA
1 ATATGTTTAATAAAGATTTAAA
*
5389001 ATATGTCTAATAAA
1 ATATGTTTAATAAA
5389015 ATATAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.40
Consensus pattern (22 bp):
ATATGTTTAATAAAGATTTAAA
Found at i:5392727 original size:79 final size:78
Alignment explanation
Indices: 5392452--5392750 Score: 309
Period size: 79 Copynumber: 3.8 Consensus size: 78
5392442 ACAACGGGGC
* ** *
5392452 TGGAGTATCCCCGATTATGAAAAAT-TAGTGTTCCAGAAATAAAATCGGGGTCGGAGTATCCCCT
1 TGGAGTATCCCCGATTATGAAAAATCGA-TGTTTTAGAAAT-AAATCGGGGTTGGAGTATCCCCT
*
5392516 CAGAAATAACAGGGT
64 CGGAAATAACAGGGT
* * *
5392531 TGGAGTATCCCTGATTAT-AAAAATCGATATTTT-GAAAACGAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTATGAAAAATCGATGTTTTAG-AAA-TAAATCGGGGTTGGAGTATCCCCT
* *
5392594 CGAAAATAACGGGGT
64 CGGAAATAACAGGGT
* ** ** * * *
5392609 TGGAGTATCCCCGATTGTGAAAAATCGATGACTTAGAAATAAGGCCAGGGTTGAAGTATCCCCTT
1 TGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAA-ATCGGGGTTGGAGTATCCCCTC
5392674 GGAAATAACAGGGT
65 GGAAATAACAGGGT
* * * *
5392688 TGGAGTATCCCCGATTGTGAAAAGTC-AGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TGGAGTATCCCCGATTATGAAAAATCGA-TGTTTTAGAAAT-AAATCGGGGTTGGAGTATCCCC
5392751 GATTATGGAA
Statistics
Matches: 180, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
77 1 0.01
78 65 0.36
79 111 0.62
80 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (78 bp):
TGGAGTATCCCCGATTATGAAAAATCGATGTTTTAGAAATAAATCGGGGTTGGAGTATCCCCTCG
GAAATAACAGGGT
Found at i:5392746 original size:51 final size:49
Alignment explanation
Indices: 5392686--5392862 Score: 169
Period size: 51 Copynumber: 3.5 Consensus size: 49
5392676 AAATAACAGG
*
5392686 GTTGGAGTATCCCCGATTGTGAAAAGTCAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAA-T-AGTGTTTTGGAAATAAAATCGGA
* * *
5392737 GTTGGAGTATCCCCGATTATGGAAAATGGGTATTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-GAAAAT-AGTGTTTTGGAAATAAAATCGGA
* * * * * *
5392788 GTTTGAGTATCCCCAATTAAGAAAAATTGATGTCTTGGAAATGAAATCGG-
1 GTTGGAGTATCCCCGATTATG-AAAATAG-TGTTTTGGAAATAAAATCGGA
* *
5392838 GATTAGAGTATCCCCGA-GATGAAAA
1 G-TTGGAGTATCCCCGATTATGAAAA
5392863 ATCTAGAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
49 4 0.04
50 5 0.05
51 91 0.87
52 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTATGAAAATAGTGTTTTGGAAATAAAATCGGA
Found at i:5395238 original size:13 final size:13
Alignment explanation
Indices: 5395220--5395247 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5395210 ATACAAAGAT
5395220 CAATGTATCGATA
1 CAATGTATCGATA
5395233 CAATGTATCGATA
1 CAATGTATCGATA
5395246 CA
1 CA
5395248 TTTAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:5395445 original size:21 final size:21
Alignment explanation
Indices: 5395389--5395445 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
5395379 GTTGGGACCT
*
5395389 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATTTTAGAAA
5395410 TGTATCGATACATTTTAGAAA
1 TGTATCGATACATTTTAGAAA
5395431 TGTATCGATACATTT
1 TGTATCGATACATTT
5395446 GGATAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTTAGAAA
Found at i:5404970 original size:2 final size:2
Alignment explanation
Indices: 5404965--5404989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5404955 TTTTAAATGG
5404965 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5404990 AAGTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5408853 original size:2 final size:2
Alignment explanation
Indices: 5408836--5408885 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
5408826 CAAACAGTCA
* *
5408836 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5408878 AT AT AT AT
1 AT AT AT AT
5408886 TCTCAGACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5416115 original size:12 final size:12
Alignment explanation
Indices: 5416098--5416122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5416088 ATGCCTTGCA
5416098 TATGTTTCATAT
1 TATGTTTCATAT
5416110 TATGTTTCATAT
1 TATGTTTCATAT
5416122 T
1 T
5416123 TTCTCTAGAC
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TATGTTTCATAT
Found at i:5427531 original size:31 final size:31
Alignment explanation
Indices: 5427466--5427532 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
5427456 TTAAAAAAAC
* * * *
5427466 AAAAA-TTCAAATTCAAAAAAATTTGATATG
1 AAAAAGTTCAAACTCAAAAAAATCTGAAATA
5427496 AAAAAGTTCAAACTCAAAAAAATCT-AAATCA
1 AAAAAGTTCAAACTCAAAAAAATCTGAAAT-A
5427527 AAAAAG
1 AAAAAG
5427533 CTTCGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.22
Consensus pattern (31 bp):
AAAAAGTTCAAACTCAAAAAAATCTGAAATA
Found at i:5429522 original size:14 final size:15
Alignment explanation
Indices: 5429503--5429531 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5429493 ATATTTACTA
5429503 AATTTTAA-AATTTT
1 AATTTTAATAATTTT
5429517 AATTTTAATAATTTT
1 AATTTTAATAATTTT
5429532 GTCACTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTTTAATAATTTT
Found at i:5429658 original size:16 final size:16
Alignment explanation
Indices: 5429624--5429670 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5429614 TATCTAAGTC
*
5429624 AATCCAAACTT-AAACT
1 AATCCAAA-TTCAAAAT
5429640 AATCCAAATTCAAAAT
1 AATCCAAATTCAAAAT
**
5429656 AATTTAAATTCAAAA
1 AATCCAAATTCAAAA
5429671 AAATTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (16 bp):
AATCCAAATTCAAAAT
Found at i:5429675 original size:16 final size:16
Alignment explanation
Indices: 5429645--5429677 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5429635 AAACTAATCC
*
5429645 AAATTCAAAATAATTT
1 AAATTCAAAAAAATTT
5429661 AAATTCAAAAAAATTT
1 AAATTCAAAAAAATTT
5429677 A
1 A
5429678 TATATGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTCAAAAAAATTT
Found at i:5429770 original size:33 final size:33
Alignment explanation
Indices: 5429733--5429799 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
5429723 AACTTAAATC
* * *
5429733 TAAAATAATTTAAATTTAAAATA-AATTTAAACT
1 TAAAAGAATTTAAACTTAAAA-ACAATCTAAACT
5429766 TAAAAGAATTTAAACTTAAAAACAATCTAAACT
1 TAAAAGAATTTAAACTTAAAAACAATCTAAACT
5429799 T
1 T
5429800 GTTGGTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.34
Consensus pattern (33 bp):
TAAAAGAATTTAAACTTAAAAACAATCTAAACT
Found at i:5429787 original size:17 final size:16
Alignment explanation
Indices: 5429718--5429799 Score: 85
Period size: 16 Copynumber: 5.0 Consensus size: 16
5429708 TAAATTAGAA
*
5429718 AAAAAAACTTAAA-TCT
1 AAAAAAATTTAAACT-T
* *
5429734 AAAATAATTTAAATTT
1 AAAAAAATTTAAACTT
5429750 AAAATAAATTTAAACTT
1 AAAA-AAATTTAAACTT
*
5429767 AAAAGAATTTAAACTT
1 AAAAAAATTTAAACTT
*
5429783 AAAAACAATCTAAACTT
1 AAAAA-AATTTAAACTT
5429800 GTTGGTTTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
16 31 0.55
17 25 0.45
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.32
Consensus pattern (16 bp):
AAAAAAATTTAAACTT
Found at i:5431157 original size:22 final size:22
Alignment explanation
Indices: 5431111--5431157 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
5431101 TTATTAGATG
*
5431111 AAAAATTACAATTTTTATAGTA
1 AAAAATTACAATTTTTATAGAA
5431133 AAAAATTATC-ATTATTTAT-GAA
1 AAAAATTA-CAATT-TTTATAGAA
5431155 AAA
1 AAA
5431158 GCTTTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAATTACAATTTTTATAGAA
Found at i:5433156 original size:2 final size:2
Alignment explanation
Indices: 5433149--5433181 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5433139 GTTATCTATC
5433149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5433182 TGGCAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5437456 original size:4 final size:4
Alignment explanation
Indices: 5437449--5437477 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5437439 ATATGTATGC
5437449 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
5437478 TAGATTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:5443298 original size:51 final size:51
Alignment explanation
Indices: 5443232--5443350 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
5443222 TGAAAATAAT
* * *
5443232 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCC
*
5443283 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCC
5443334 GGGGTTGAAGTATCCCC
1 GGGGTTGAAGTATCCCC
5443351 TAGGAAATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (51 bp):
GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCC
Found at i:5443373 original size:28 final size:28
Alignment explanation
Indices: 5443334--5443406 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
5443324 AAATAAAGCC
* *
5443334 GGGGTTGAAGTATCCCCTAGGAAATAAT
1 GGGGTTGGAGTATCCCCAAGGAAATAAT
* * *
5443362 GGGGTTGGAGTATCTCCAATGAACTAAT
1 GGGGTTGGAGTATCCCCAAGGAAATAAT
*
5443390 GGGGTTAGAGTATCCCC
1 GGGGTTGGAGTATCCCC
5443407 GATTGTGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.26
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCAAGGAAATAAT
Found at i:5443455 original size:158 final size:157
Alignment explanation
Indices: 5443228--5443532 Score: 387
Period size: 158 Copynumber: 1.9 Consensus size: 157
5443218 TCCGTGAAAA
* * ** *
5443228 TAATGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTGAAG
1 TAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACCGGAGTTGAAG
* * *
5443293 TATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAGCCGGGGTTGAAGTATCCCCT-AGGAA
66 TATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAA-ACGAGGTTGAAGTATCCCCTCA-GAA
* *
5443357 ATAATGGGGTTGGAGTATCTCCAATGAAC
129 ATAACGGGATTGGAGTATCTCCAATGAAC
** * * *
5443386 TAATGGGGTTAGAGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTGAAG
1 TAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACCGGAGTTGAAG
* * * * * * *
5443451 TATCCCTGATTGTGGAGAATTAGTGTTTTAGAAATAAAACGAGGTTGGAGTATCCCCTCAGAAAT
66 TATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACGAGGTTGAAGTATCCCCTCAGAAAT
5443516 AACGGGATTGGAGTATC
131 AACGGGATTGGAGTATC
5443533 CTTGATTATG
Statistics
Matches: 124, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
157 37 0.30
158 87 0.70
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (157 bp):
TAATGGGGTTAGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACCGGAGTTGAAG
TATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAACGAGGTTGAAGTATCCCCTCAGAAAT
AACGGGATTGGAGTATCTCCAATGAAC
Found at i:5443478 original size:51 final size:50
Alignment explanation
Indices: 5443398--5443507 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 50
5443388 ATGGGGTTAG
*
5443398 AGTATCCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCG-GAGTTGA
1 AGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAA-CGAG-GTTGA
* * * *
5443449 AGTATCCCTGATTGTGGAGAATT-AGTGTTTTAGAAATAAAACGAGGTTGG
1 AGTATCCCCGATTGTGAAAAATTGA-TGTTTTAGAAATAAAACGAGGTTGA
5443499 AGTATCCCC
1 AGTATCCCC
5443508 TCAGAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
50 15 0.29
51 36 0.71
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (50 bp):
AGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACGAGGTTGA
Found at i:5445850 original size:20 final size:20
Alignment explanation
Indices: 5445825--5445901 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
5445815 CAAAAAAGCC
5445825 AAAATGTATCGATACATTAT
1 AAAATGTATCGATACATTAT
5445845 AAAATGTATCGATACA--AT
1 AAAATGTATCGATACATTAT
* * **
5445863 GAGCAATGTATCGATACAATGC
1 -A-AAATGTATCGATACATTAT
5445885 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
5445902 CTGGGTAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 44 0.92
21 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAATGTATCGATACATTAT
Found at i:5445943 original size:20 final size:20
Alignment explanation
Indices: 5445918--5445972 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
5445908 AAACTTCCTA
5445918 GATGTATCGATACAAAGATC
1 GATGTATCGATACAAAGATC
5445938 GATGTATCGATACAAAGATC
1 GATGTATCGATACAAAGATC
*
5445958 GATATATCGATACAA
1 GATGTATCGATACAA
5445973 TGTATTGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (20 bp):
GATGTATCGATACAAAGATC
Found at i:5446930 original size:41 final size:45
Alignment explanation
Indices: 5446879--5446971 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
5446869 TGCTGTTTTC
*
5446879 TGAGGACAAAAGA-AAAA-AA-AAATA-AAGTGTGTCCTGCTCTT
1 TGAGGACAAAAGAGAAAATAAGAAAAAGAAGTGTGTCCTGCTCTT
*
5446920 TGAGGACAAAAGAGAAAATAAGAAAAAGAAGTGTGTCCTGCTTTT
1 TGAGGACAAAAGAGAAAATAAGAAAAAGAAGTGTGTCCTGCTCTT
*
5446965 TAAGGAC
1 TGAGGAC
5446972 TGAAAAGTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 13 0.29
42 4 0.09
43 2 0.04
44 4 0.09
45 22 0.49
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (45 bp):
TGAGGACAAAAGAGAAAATAAGAAAAAGAAGTGTGTCCTGCTCTT
Found at i:5447043 original size:61 final size:59
Alignment explanation
Indices: 5446954--5447309 Score: 340
Period size: 61 Copynumber: 5.9 Consensus size: 59
5446944 AAAGAAGTGT
* * * *
5446954 GTCCTGCTTTTTAAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAGGC
1 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGAGCTTT-AAAAGAAAAGGC
* * * *
5447015 GTCCTACCCTTTGAGGATTGGAAGGTGCCACCAACTTGTGCGAGCTTTGCAAAA-AGAAA-GC
1 GTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGAGCTTT--AAAAGA-AAAGGC
* * * * * * *
5447076 ATCCTGCACTTTGAGGACTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAGGAGAAGAC
1 GTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGAGCTTTAAAA-GAAAAGGC
* * *
5447137 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTTGA-CTTTAAAAGGAGAAGGT
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTG-TGAGCTTTAAAA-GAAAAGGC
* * * * *
5447197 GTCCTGCTCTTTGAGGACTAAAGGTGCCACTAGCTTATGTGGGCTTTAAAAGAAAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAG--AAAAGGC
* * * *
5447258 ATCCTGCTATTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAG
1 GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAG
5447310 GCATCCTGCT
Statistics
Matches: 246, Mismatches: 38, Indels: 22
0.80 0.12 0.07
Matches are distributed among these distances:
59 7 0.03
60 78 0.32
61 153 0.62
62 8 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (59 bp):
GTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGAGCTTTAAAAGAAAAGGC
Found at i:5447263 original size:121 final size:120
Alignment explanation
Indices: 5446946--5447310 Score: 405
Period size: 121 Copynumber: 3.0 Consensus size: 120
5446936 AATAAGAAAA
* * * *
5446946 AGAAGTGTGTCCTGCTTTTTAAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAA
1 AGAAG-GTGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAA
* * * *
5447011 AGGCGTCCTACCCTTTGAGGATTGGAAGGTGCCACCAACTTGTG-CGAGCTTTGCAAAA--
64 AGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTCGA-CTTT--AAAAGG
* ** * * *
5447069 AGAAAGCATCCTGCACTTTGAGGACTGAAAAGTACCACCAACTTGTGTGGGCTTTAAAAGGAGAA
1 AGAAGGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAA
* *
5447134 GACGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTTGACTTTAAAAGG
65 GGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTCGACTTTAAAAGG
* * * *
5447190 AGAAGGTGTCCTGCTCTTTGAGGACT-AAAGGTGCCACTAGCTTATGTGGGCTTTAAAAGAAAAA
1 AGAAGGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAG--AAA
* * * *
5447254 AGGCATCCTGCTATTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGG
64 AGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTCGACTTTAAAAGG
5447311 CATCCTGCTC
Statistics
Matches: 205, Mismatches: 31, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
119 5 0.02
120 27 0.13
121 103 0.50
122 66 0.32
123 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (120 bp):
AGAAGGTGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
GCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTCGACTTTAAAAGG
Found at i:5447463 original size:60 final size:61
Alignment explanation
Indices: 5447351--5447739 Score: 450
Period size: 60 Copynumber: 6.4 Consensus size: 61
5447341 AGGAGAGAGA
* *
5447351 GTCCTGCTCTTTGAGGACT--AGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGG--GTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGC
* * ** *
5447412 GTCCTGCTCTTTGAGGACTACA-GGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGC
* ** *
5447472 GTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAA-AAAAAAGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGC
* * * *
5447532 GTCCTGCTTTTTAAGGACTAAA-GGTGCCACCAACTCATGTGAGCTTTAAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGGC
* * * * * * *
5447593 ATCCTACTCATTGAGGACTAAAGGGTGCTACCAACTTGTGTGGGCTTGAAAAAGGAAAAA-AC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTT-TAAAA-GAAAAAGGC
* * * *
5447655 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-GAAGGAGAAGAC
1 GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGC
5447715 GTCCTGCTCTTTGAGGACTAAAGGG
1 GTCCTGCTCTTTGAGGACTAAAGGG
5447740 CTAAAAGAGA
Statistics
Matches: 279, Mismatches: 40, Indels: 19
0.83 0.12 0.06
Matches are distributed among these distances:
59 27 0.10
60 109 0.39
61 68 0.24
62 68 0.24
63 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (61 bp):
GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGC
Found at i:5447501 original size:215 final size:214
Alignment explanation
Indices: 5447125--5447523 Score: 615
Period size: 215 Copynumber: 1.9 Consensus size: 214
5447115 GTGGGCTTTA
* * *
5447125 AAAGGAGAAGACGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTTGACTTTAAAAGG
1 AAAGGAGAAGACGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGA
* * *
5447190 AGAAGGTGTCCTGCTCTTTGAGGACTAAAGGTGCCACTAGCTTATGTGGGCTTTAAAAGAAAAAA
66 AGAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAA
* *
5447255 GGCATCCTGCTATTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCT
131 GGCATCCTGCTATTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCATCCTGCT
5447320 CTTTGAGGACAAAAAGGCG
196 CTTTGAGGACAAAAAGGCG
*
5447339 AAAGGAGAGAGA-GTCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAA
1 AAAGGAGA-AGACGTCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGACTTTAAA
*
5447402 AGAAGAAGGCGTCCTGCTCTTTGAGGACTACAGGTGCCACCAGCTTATGTAGGCTTTAAAAG-AA
63 AGAAGAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTATGTAGGCTTTAAAAGAAA
* * * *
5447466 AAAGGCGTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAA
128 AAAGGCATCCTGCTATTTGAGGACT-GAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
5447524 AAAAAAGCGT
Statistics
Matches: 167, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
214 51 0.31
215 113 0.68
216 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (214 bp):
AAAGGAGAAGACGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGACTTTAAAAGA
AGAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAA
GGCATCCTGCTATTTGAGGACTGAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGCATCCTGCT
CTTTGAGGACAAAAAGGCG
Found at i:5447584 original size:121 final size:120
Alignment explanation
Indices: 5447351--5447731 Score: 453
Period size: 121 Copynumber: 3.1 Consensus size: 120
5447341 AGGAGAGAGA
* * * *
5447351 GTCCTGCTCTTTGAGGACTAGGA-AGTGCCACCAACTTGTGTGGGCTTTAAAAGAAGAAGGCGTC
1 GTCCTGCTCTTTGAGGA-TTGGAGGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAAAGCGTC
* * *
5447415 CTGCTCTTTGAGGACTACAGGTGCCACCAGCTTATGT-AGGCTTTAAAAGAAAAAGGC
64 CTGCTCTTTGAGGACTAAAGGTGCCACCAACTCATGTGA-GCTTTAAAAGAAAAAGGC
*
5447472 GTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAAAAAAGCGTCCT
1 GTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAGCGTCCT
* *
5447537 GCTTTTTAAGGACTAAAGGTGCCACCAACTCATGTGAGCTTTAAAAAGAAAAAGGC
66 GCTCTTTGAGGACTAAAGGTGCCACCAACTCATGTGAGCTTT-AAAAGAAAAAGGC
* * * * ** * * *
5447593 ATCCTACTCATTGAGGACTAAAGGGTGCTACCAACTTGTGTGGGCTTGAAAAAGGAAAAAACGTC
1 GTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAA--AAAAAGCGTC
* * * * * *
5447658 CTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTT-GAAGGAGAAGAC
64 CTGCTCTTTGAGGACTAAA-GGTGCCACCAACTCATGTGAGCTTTAAAAGAAAAAGGC
5447715 GTCCTGCTCTTTGAGGA
1 GTCCTGCTCTTTGAGGA
5447732 CTAAAGGGCT
Statistics
Matches: 223, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
120 50 0.22
121 102 0.46
122 22 0.10
123 26 0.12
124 23 0.10
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (120 bp):
GTCCTGCTCTTTGAGGATTGGAGGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAGCGTCCT
GCTCTTTGAGGACTAAAGGTGCCACCAACTCATGTGAGCTTTAAAAGAAAAAGGC
Found at i:5455584 original size:20 final size:19
Alignment explanation
Indices: 5455559--5455630 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
5455549 AAAATGCTTG
*
5455559 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
* *
5455579 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGA-A
5455599 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
5455619 AATGTATCGATA
1 AATGTATCGATA
5455631 GATCTGGGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:5462046 original size:15 final size:15
Alignment explanation
Indices: 5462009--5462078 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 15
5461999 TATATTTTAA
*
5462009 TTAATTT-TTAAAAT
1 TTAATTTATTATAAT
*
5462023 TT-TTTTATTATAAT
1 TTAATTTATTATAAT
5462037 TTAATTTATTACATAAT
1 TTAATTTATT--ATAAT
* *
5462054 TT-TTTTATTATAAC
1 TTAATTTATTATAAT
5462068 TTAATTTATTA
1 TTAATTTATTA
5462079 CGTAAATGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 3 0.07
14 16 0.36
15 13 0.29
16 6 0.13
17 7 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTTATTATAAT
Found at i:5462058 original size:31 final size:29
Alignment explanation
Indices: 5462001--5462079 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 29
5461991 TATCGTATTA
*
5462001 TATTTTAATTAATTT-TTA-AAATTTTTT
1 TATTATAATTAATTTATTACAAATTTTTT
5462028 TATTATAATTTAATTTATTACATAATTTTTT
1 TATTATAA-TTAATTTATTACA-AATTTTTT
5462059 TATTATAACTTAATTTATTAC
1 TATTATAA-TTAATTTATTAC
5462080 GTAAATGCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 7 0.15
28 7 0.15
29 3 0.07
30 1 0.02
31 28 0.61
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTATAATTAATTTATTACAAATTTTTT
Found at i:5462487 original size:16 final size:17
Alignment explanation
Indices: 5462455--5462488 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5462445 ATAAATATTT
*
5462455 TAAAATTTATATAAATA
1 TAAAATATATATAAATA
5462472 TAAAATATAT-TAAATA
1 TAAAATATATATAAATA
5462488 T
1 T
5462489 GATCATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATATATATAAATA
Found at i:5465013 original size:16 final size:16
Alignment explanation
Indices: 5464993--5465040 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
5464983 ATCATTTGAG
5464993 ATTTGAGTTATTTTAA
1 ATTTGAGTTATTTTAA
* * *
5465009 GTTTGAATTATTTCAA
1 ATTTGAGTTATTTTAA
*
5465025 ATTTGAGTCATTTTAA
1 ATTTGAGTTATTTTAA
5465041 TTTCGATCTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTGAGTTATTTTAA
Found at i:5467917 original size:20 final size:21
Alignment explanation
Indices: 5467892--5467937 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5467882 ATTGATCATA
* *
5467892 TATTTAATTATTTAT-TAATT
1 TATTTAAATACTTATATAATT
*
5467912 TATTTAAATACTTATATATTT
1 TATTTAAATACTTATATAATT
5467933 TATTT
1 TATTT
5467938 GTATGTTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTAAATACTTATATAATT
Found at i:5468947 original size:13 final size:13
Alignment explanation
Indices: 5468929--5468953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5468919 TATGCTAAAT
5468929 ATAATAAATTATA
1 ATAATAAATTATA
5468942 ATAATAAATTAT
1 ATAATAAATTAT
5468954 GTTATATGAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAAATTATA
Found at i:5471539 original size:187 final size:189
Alignment explanation
Indices: 5471197--5471567 Score: 444
Period size: 187 Copynumber: 2.0 Consensus size: 189
5471187 ACTTCCAATC
* * * *
5471197 CATTTTAAACTCTATTCTAAGGTAAACATTGATAATTGCCATGGCCATTGCACATTTTTGATTAG
1 CATTTTAAACTCTATGCTAAGGTAAAC--T-ATAATTACCATGGCCATTGCACATTTTTAATTAA
* *
5471262 TTCAAACAGATTTTTCTAGTCCAAGCAATTCAAATTCATTTTTAACTCCATATTAATGCACACAT
63 TTCAAACAGATGTTTCTAGTCCAAGCAATTCAAATTCATTTTTAACTCCATACTAATGCACACAT
* * * ** * * * *
5471327 TCGTCATTAGACTGGTAATCATATATTTCTATCAATTCAAACAAGTTTTTAGGTCTAAAATT
128 TCATAACTAGACTAATAACCATATATTTCTAGCAATGCAAACAAATTTTTAGGTCTAAAATT
*
5471389 CATTTTAAACTCTATGCTAAGGTAAAC-AT-ATTACCATGGCCATTGCACATTTTTAATTAATTT
1 CATTTTAAACTCTATGCTAAGGTAAACTATAATTACCATGGCCATTGCACATTTTTAATTAATTC
* * * * * *
5471452 AAATATA-GTTTCTAGATCCAAGCAGTTCAAATAT-ATTTTTAATTCCATGCTAATGTACACATT
66 AAACAGATGTTTCTAG-TCCAAGCAATTCAAAT-TCATTTTTAACTCCATACTAATGCACACATT
* * *
5471515 CATAACTAGACTAATTACCATATATTTCTAGCAGTGCAAGCAAATTTTTAGGT
129 CATAACTAGACTAATAACCATATATTTCTAGCAATGCAAACAAATTTTTAGGT
5471568 TCACGATAAA
Statistics
Matches: 152, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
186 7 0.05
187 116 0.76
188 3 0.02
192 26 0.17
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (189 bp):
CATTTTAAACTCTATGCTAAGGTAAACTATAATTACCATGGCCATTGCACATTTTTAATTAATTC
AAACAGATGTTTCTAGTCCAAGCAATTCAAATTCATTTTTAACTCCATACTAATGCACACATTCA
TAACTAGACTAATAACCATATATTTCTAGCAATGCAAACAAATTTTTAGGTCTAAAATT
Found at i:5474796 original size:24 final size:24
Alignment explanation
Indices: 5474769--5474820 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5474759 TTTTAATCAC
5474769 TATTCAACATAAATATAAGTTT-AT
1 TATTCAACAT-AATATAAGTTTAAT
* * *
5474793 TATTTAATATAATATAATTTTAAT
1 TATTCAACATAATATAAGTTTAAT
5474817 TATT
1 TATT
5474821 TTAAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTCAACATAATATAAGTTTAAT
Found at i:5474829 original size:21 final size:22
Alignment explanation
Indices: 5474777--5474839 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
5474767 ACTATTCAAC
*
5474777 ATAAATATAAGTTT-ATTATTT
1 ATAAATATAATTTTAATTATTT
5474798 AATATAATATAATTTTAATTATTT
1 -ATA-AATATAATTTTAATTATTT
5474822 -TAAATATAATTTTTAATT
1 ATAAATATAA-TTTTAATT
5474840 TGTTATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 7 0.19
22 13 0.35
23 10 0.27
24 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATAAATATAATTTTAATTATTT
Found at i:5474851 original size:22 final size:21
Alignment explanation
Indices: 5474803--5474844 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5474793 TATTTAATAT
*
5474803 AATATAATTTTAATTATTTTA
1 AATATAATTTTAATTATGTTA
5474824 AATATAATTTTTAATT-TGTTA
1 AATATAA-TTTTAATTATGTTA
5474845 TTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AATATAATTTTAATTATGTTA
Found at i:5477446 original size:28 final size:29
Alignment explanation
Indices: 5477391--5477454 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
5477381 GAAAAAATTT
* *
5477391 AAAAGACATTTATCTCTCTAAATTTTTATA
1 AAAATACATTTATCTCTCTAAATGTTTA-A
5477421 AAAATACATTTATCTCT-T-AATGTTTAA
1 AAAATACATTTATCTCTCTAAATGTTTAA
*
5477448 AGAATAC
1 AAAATAC
5477455 TCATTTACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
28 7 0.23
29 1 0.03
30 16 0.52
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAATACATTTATCTCTCTAAATGTTTAA
Done.