Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 67 of 103
Found at i:25183909 original size:10 final size:10
Alignment explanation
Indices: 25183894--25183932 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
25183884 GTGGCTGAAA
25183894 TTGATGATAT
1 TTGATGATAT
25183904 TTGATGATATT
1 TTGATGATA-T
*
25183915 TTGGTGATAT
1 TTGATGATAT
*
25183925 TTAATGAT
1 TTGATGAT
25183933 TGGTGAGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (10 bp):
TTGATGATAT
Found at i:25183922 original size:11 final size:11
Alignment explanation
Indices: 25183894--25183926 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25183884 GTGGCTGAAA
25183894 TTGATGATA-T
1 TTGATGATATT
25183904 TTGATGATATT
1 TTGATGATATT
*
25183915 TTGGTGATATT
1 TTGATGATATT
25183926 T
1 T
25183927 AATGATTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (11 bp):
TTGATGATATT
Found at i:25186930 original size:174 final size:173
Alignment explanation
Indices: 25186610--25186931 Score: 405
Period size: 174 Copynumber: 1.8 Consensus size: 173
25186600 ATAAACACTT
* * * * *
25186610 AACACATAAGTCTTGTCGTTAGTTAATTATCAATATTTTTATTAATTTTATGACATGATAATCTT
1 AACACATAAATCTTGTCGTTAGTTAATTATCAATATTTTCATTAATTTGATAACATGATAATATT
* * * * *
25186675 TTTAATATAAGTTTATTTTTTAATAATTTCAAATTATTGTTAAATAAATTATAATTTTTATTTTT
66 ATTAATATAAGTTTACTCTTTAATAATTTAAAATTATTATTAAATAAATTATAATTTTTA-TTTT
*** *
25186740 TTTAAAAAATTCAATCACTTTTGTCTAAAAAAATATTTTCGTTG
130 AAAAAAAAAATCAATCACTTTTGTCTAAAAAAATATTTTCGTTG
* * *
25186784 AACACATAAATTTTGTCGTTAGTTAATTGTCGATATTTTCATTAATTTGATAACATGATAATATT
1 AACACATAAATCTTGTCGTTAGTTAATTATCAATATTTTCATTAATTTGATAACATGATAATATT
* * * *
25186849 ATTAA-AGTCATTTTACTCTTTATTAATTTTAAAAATTATTATTAAATAGATTATAATTTTTA-T
66 ATTAATA-TAAGTTTACTCTTTAATAA-TTT-AAAATTATTATTAAATAAATTATAATTTTTATT
25186912 TTAAAAAAAAAATCAATCAC
128 TTAAAAAAAAAATCAATCAC
25186932 CCCGTGCCCA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
173 1 0.01
174 92 0.74
175 3 0.02
176 28 0.23
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.48
Consensus pattern (173 bp):
AACACATAAATCTTGTCGTTAGTTAATTATCAATATTTTCATTAATTTGATAACATGATAATATT
ATTAATATAAGTTTACTCTTTAATAATTTAAAATTATTATTAAATAAATTATAATTTTTATTTTA
AAAAAAAAATCAATCACTTTTGTCTAAAAAAATATTTTCGTTG
Found at i:25187168 original size:7 final size:7
Alignment explanation
Indices: 25187156--25187223 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
25187146 ATATATTTTA
25187156 AATATTT
1 AATATTT
25187163 AATATTT
1 AATATTT
25187170 AATATTATT
1 AATA-T-TT
*
25187179 ATTATTT
1 AATATTT
25187186 AATATTT
1 AATATTT
*
25187193 TA-ATTT
1 AATATTT
*
25187199 AATCTTAT
1 AATATT-T
25187207 AA-ATTATT
1 AATA-T-TT
25187215 AATATTT
1 AATATTT
25187222 AA
1 AA
25187224 AAAATAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
6 5 0.10
7 26 0.54
8 10 0.21
9 7 0.15
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (7 bp):
AATATTT
Found at i:25187175 original size:23 final size:23
Alignment explanation
Indices: 25187148--25187192 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25187138 ATAAAAAAAT
25187148 ATATT-TTAAATATTTAATATTTA
1 ATATTATT-AATATTTAATATTTA
*
25187171 ATATTATTATTATTTAATATTT
1 ATATTATTAATATTTAATATTT
25187193 TAATTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTATTAATATTTAATATTTA
Found at i:25187184 original size:16 final size:16
Alignment explanation
Indices: 25187165--25187220 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
25187155 AAATATTTAA
25187165 TATTTAATATTATTAT
1 TATTTAATATTATTAT
25187181 TATTTAATATT-TTA-
1 TATTTAATATTATTAT
* *
25187195 -ATTTAATCTTATAAAT
1 TATTTAATATTAT-TAT
25187211 TA-TTAATATT
1 TATTTAATATT
25187221 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 4 0.12
16 18 0.55
17 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTAATATTATTAT
Found at i:25187206 original size:23 final size:23
Alignment explanation
Indices: 25187158--25187206 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
25187148 ATATTTTAAA
*
25187158 TATTTAATATTTAATATTATTAT
1 TATTTAATATTTAATATTAATAT
*
25187181 TATTTAATATTTTAAT-TTAATCT
1 TATTTAATA-TTTAATATTAATAT
25187204 TAT
1 TAT
25187207 AAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTAATATTTAATATTAATAT
Found at i:25189662 original size:19 final size:19
Alignment explanation
Indices: 25189638--25189688 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
25189628 ATTTACATAA
25189638 AAAAAATATATAA-TATTTT
1 AAAAAATATA-AATTATTTT
*
25189657 AAAAAATTTAAATTATTTT
1 AAAAAATATAAATTATTTT
*
25189676 AAAAAATTTAAAT
1 AAAAAATATAAAT
25189689 AAGTCATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 2 0.07
19 28 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAAATATAAATTATTTT
Found at i:25189833 original size:33 final size:33
Alignment explanation
Indices: 25189791--25189884 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
25189781 GTTGATGTGG
*
25189791 CATGTTAACATATCATAATTGATGATGATGTAA
1 CATGCTAACATATCATAATTGATGATGATGTAA
25189824 CATGCTAACATATCATAATTGATGATGATGTAA
1 CATGCTAACATATCATAATTGATGATGATGTAA
*
25189857 CATGCTAACATATCATAATTGATTATGA
1 CATGCTAACATATCATAATTGATGATGA
25189885 CATGATATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (33 bp):
CATGCTAACATATCATAATTGATGATGATGTAA
Found at i:25190089 original size:29 final size:29
Alignment explanation
Indices: 25190057--25190112 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
25190047 ATATAAAAGC
* *
25190057 TTGATTGAACGTAATAAAAATATAAAGAT
1 TTGATTGAACGCAATAAAAACATAAAGAT
* *
25190086 TTGATTGAATGCAATTAAAACATAAAG
1 TTGATTGAACGCAATAAAAACATAAAG
25190113 GCTTATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.30
Consensus pattern (29 bp):
TTGATTGAACGCAATAAAAACATAAAGAT
Found at i:25217163 original size:18 final size:18
Alignment explanation
Indices: 25217140--25217175 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25217130 CTATAAATGG
25217140 GTCTACAAGATCAAGCTT
1 GTCTACAAGATCAAGCTT
25217158 GTCTACAAGATCAAGCTT
1 GTCTACAAGATCAAGCTT
25217176 CTTGCTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
GTCTACAAGATCAAGCTT
Found at i:25224145 original size:11 final size:11
Alignment explanation
Indices: 25224129--25224168 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
25224119 AAATAGTCAT
25224129 TCTATTCCCTC
1 TCTATTCCCTC
*
25224140 TCTATTCCAT-
1 TCTATTCCCTC
25224150 TCTATTCCCTC
1 TCTATTCCCTC
25224161 TCTATTCC
1 TCTATTCC
25224169 ATTCCACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.47
Consensus pattern (11 bp):
TCTATTCCCTC
Found at i:25224150 original size:21 final size:21
Alignment explanation
Indices: 25224126--25224172 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
25224116 ACAAAATAGT
25224126 CATTCTATTCCCTCTCTATTC
1 CATTCTATTCCCTCTCTATTC
25224147 CATTCTATTCCCTCTCTATTC
1 CATTCTATTCCCTCTCTATTC
25224168 CATTC
1 CATTC
25224173 CACGAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (21 bp):
CATTCTATTCCCTCTCTATTC
Found at i:25225914 original size:66 final size:66
Alignment explanation
Indices: 25225808--25225939 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
25225798 ATATCCAAAA
25225808 TTATATAAAATAAATGAGAAATGAAAAGTGATTTTAAAAGATAATTTAAAGTTATTAAATATTTT
1 TTATATAAAATAAATGAGAAATGAAAAGTGATTTTAAAAGATAATTTAAAGTTATTAAATATTTT
25225873 T
66 T
*
25225874 TTATATAAAATAAATGAGTAATGAAAAGTGATTTTAAAAGATAATTTAAAGTTATTAAATATTTT
1 TTATATAAAATAAATGAGAAATGAAAAGTGATTTTAAAAGATAATTTAAAGTTATTAAATATTTT
25225939 T
66 T
25225940 AAAGTAAATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (66 bp):
TTATATAAAATAAATGAGAAATGAAAAGTGATTTTAAAAGATAATTTAAAGTTATTAAATATTTT
T
Found at i:25227212 original size:14 final size:13
Alignment explanation
Indices: 25227176--25227200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25227166 ACAGCATTTT
25227176 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
25227189 TTAAAAAAAAAA
1 TTAAAAAAAAAA
25227201 GCTTAAAGAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TTAAAAAAAAAAA
Found at i:25233205 original size:19 final size:19
Alignment explanation
Indices: 25233181--25233218 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25233171 CTGCCAAACC
*
25233181 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
25233200 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
25233219 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:25239188 original size:13 final size:13
Alignment explanation
Indices: 25239170--25239194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25239160 GGAGAAATTG
25239170 TGATTTTATAAAA
1 TGATTTTATAAAA
25239183 TGATTTTATAAA
1 TGATTTTATAAA
25239195 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:25241435 original size:22 final size:22
Alignment explanation
Indices: 25241410--25241459 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
25241400 GTGACTTAAT
* *
25241410 CATTACATCTTTGGAACTTAGG
1 CATTACATATGTGGAACTTAGG
* *
25241432 CATTGCATATGTGGAACTTGGG
1 CATTACATATGTGGAACTTAGG
25241454 CATTAC
1 CATTAC
25241460 GTGACTGGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (22 bp):
CATTACATATGTGGAACTTAGG
Found at i:25241657 original size:22 final size:22
Alignment explanation
Indices: 25241609--25241666 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
25241599 TTTAGGGTAC
*
25241609 TTAGGCATTACGTGACTAAGCT
1 TTAGGCATTACATGACTAAGCT
* * **
25241631 ATAGGTATTACATGACTAATTT
1 TTAGGCATTACATGACTAAGCT
25241653 TTAGGCATTACATG
1 TTAGGCATTACATG
25241667 TCTGATTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (22 bp):
TTAGGCATTACATGACTAAGCT
Found at i:25244902 original size:16 final size:16
Alignment explanation
Indices: 25244869--25244904 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25244859 TCTTGGGTTT
*
25244869 TTAGGTATTGCGTAAC
1 TTAGGTATTGCATAAC
*
25244885 TTAGGTATTGCATGAC
1 TTAGGTATTGCATAAC
25244901 TTAG
1 TTAG
25244905 ACATTGTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (16 bp):
TTAGGTATTGCATAAC
Found at i:25245009 original size:23 final size:23
Alignment explanation
Indices: 25244981--25245046 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
25244971 CTTAAAGACT
25244981 AGTCATGCAATGCCCTATCAATC
1 AGTCATGCAATGCCCTATCAATC
* **
25245004 AGTCATGCAAT-ACCTAAAAATC
1 AGTCATGCAATGCCCTATCAATC
* **
25245026 AGTTACACAATGCCCTATCAA
1 AGTCATGCAATGCCCTATCAA
25245047 CTAGTTACAC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (23 bp):
AGTCATGCAATGCCCTATCAATC
Found at i:25245025 original size:22 final size:23
Alignment explanation
Indices: 25244981--25245028 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
25244971 CTTAAAGACT
* **
25244981 AGTCATGCAATGCCCTATCAATC
1 AGTCATGCAATGACCTAAAAATC
25245004 AGTCATGCAAT-ACCTAAAAATC
1 AGTCATGCAATGACCTAAAAATC
25245026 AGT
1 AGT
25245029 TACACAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (23 bp):
AGTCATGCAATGACCTAAAAATC
Found at i:25245036 original size:22 final size:22
Alignment explanation
Indices: 25245011--25245133 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
25245001 ATCAGTCATG
25245011 CAATACCTAAAAATCAGTTACA
1 CAATACCTAAAAATCAGTTACA
* **
25245033 CAATGCCCTATCAA-CTAGTTACA
1 CAAT-ACCTAAAAATC-AGTTACA
** * * * *
25245056 CAATGTCTAAAAATTAATAATA
1 CAATACCTAAAAATCAGTTACA
* * * *
25245078 TAATACCCAAAAA-CTAGTCACG
1 CAATACCTAAAAATC-AGTTACA
* *
25245100 CAATAACTAAAAATTAGTTACA
1 CAATACCTAAAAATCAGTTACA
25245122 CAATACCTAAAA
1 CAATACCTAAAA
25245134 GCCATCAAAA
Statistics
Matches: 69, Mismatches: 27, Indels: 10
0.65 0.25 0.09
Matches are distributed among these distances:
22 52 0.75
23 17 0.25
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (22 bp):
CAATACCTAAAAATCAGTTACA
Found at i:25245127 original size:44 final size:44
Alignment explanation
Indices: 25245004--25245133 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 44
25244994 CCTATCAATC
* * * * **
25245004 AGTCATGCAATACCTAAAAATCAGTTACACAATGCCCTATCAACT
1 AGTCACGCAATAACTAAAAATTAGTTACACAATACCC-AAAAACT
* * ** * * * *
25245049 AGTTACACAATGTCTAAAAATTAATAATATAATACCCAAAAACT
1 AGTCACGCAATAACTAAAAATTAGTTACACAATACCCAAAAACT
*
25245093 AGTCACGCAATAACTAAAAATTAGTTACACAATACCTAAAA
1 AGTCACGCAATAACTAAAAATTAGTTACACAATACCCAAAA
25245134 GCCATCAAAA
Statistics
Matches: 63, Mismatches: 22, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
44 37 0.59
45 26 0.41
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (44 bp):
AGTCACGCAATAACTAAAAATTAGTTACACAATACCCAAAAACT
Found at i:25245361 original size:60 final size:60
Alignment explanation
Indices: 25245250--25245426 Score: 196
Period size: 61 Copynumber: 3.0 Consensus size: 60
25245240 GCTCAAAATG
* ** * **
25245250 CTCAAAGGTTTTTCTTCGTATAT-AAAAAATACTCCAAAATGCTTAACATGCTTAAAACC
1 CTCAAAGATTTTTCTTCGTATATCAAAACCTACTCCAAAATGCTTAAAATGCTTAAAAAA
* *
25245309 CTCAAAGATTTTTCTTTGTATATCAAAACCTACTCCAAAATGCTTAAAATGCTCAAAAAAA
1 CTCAAAGATTTTTCTTCGTATATCAAAACCTACTCCAAAATGCTTAAAATGCT-TAAAAAA
* * * * * *
25245370 CTCAAATATTTTTCTTCATGTATCAAAAACC-ACTCTAAAATGCTCAAAACGCTTAAA
1 CTCAAAGATTTTTCTTCGTATATC-AAAACCTACTCCAAAATGCTTAAAATGCTTAAA
25245427 GGTTTTTCTT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
59 21 0.21
60 29 0.29
61 43 0.43
62 6 0.06
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (60 bp):
CTCAAAGATTTTTCTTCGTATATCAAAACCTACTCCAAAATGCTTAAAATGCTTAAAAAA
Found at i:25248484 original size:33 final size:33
Alignment explanation
Indices: 25248426--25248494 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
25248416 TGATTTTAAC
**
25248426 TTTTTCAATATTATATTATGTGATTTCTTTTTT
1 TTTTTCAATATTATATTATGTGATTTAATTTTT
*
25248459 TTTTTCAAT-TTGTATTCTATG-GATTTAATTTTT
1 TTTTTCAATATTATA-T-TATGTGATTTAATTTTT
25248492 TTT
1 TTT
25248495 AATTAATACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 4 0.13
33 23 0.74
34 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.07, T:0.67
Consensus pattern (33 bp):
TTTTTCAATATTATATTATGTGATTTAATTTTT
Found at i:25251842 original size:17 final size:17
Alignment explanation
Indices: 25251820--25251852 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25251810 AACTCTTGTG
*
25251820 TCAATCTTTGTTCATTA
1 TCAATCCTTGTTCATTA
25251837 TCAATCCTTGTTCATT
1 TCAATCCTTGTTCATT
25251853 CTCATGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (17 bp):
TCAATCCTTGTTCATTA
Found at i:25265945 original size:26 final size:26
Alignment explanation
Indices: 25265907--25265956 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
25265897 TTCAATCAAC
* *
25265907 TTGCAAGATTGCTTTTGGGTTTTTAA
1 TTGCAAGACTGCTTTTGGGATTTTAA
25265933 TTGCAAGACTGCTTTTGGGATTTT
1 TTGCAAGACTGCTTTTGGGATTTT
25265957 GAGAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.48
Consensus pattern (26 bp):
TTGCAAGACTGCTTTTGGGATTTTAA
Found at i:25270096 original size:12 final size:12
Alignment explanation
Indices: 25270079--25270108 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25270069 CAAAAATCTA
25270079 TTTTTTCTTTTT
1 TTTTTTCTTTTT
*
25270091 TTTTTTGTTTTT
1 TTTTTTCTTTTT
25270103 TTTTTT
1 TTTTTT
25270109 TGGGTGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:25270102 original size:13 final size:13
Alignment explanation
Indices: 25270086--25270110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25270076 CTATTTTTTC
25270086 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
25270099 TTTTTTTTTTTG
1 TTTTTTTTTTTG
25270111 GGTGTGGGTG
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:25271532 original size:133 final size:133
Alignment explanation
Indices: 25271294--25271554 Score: 369
Period size: 133 Copynumber: 2.0 Consensus size: 133
25271284 GCAAAATCTC
* * * *
25271294 AGCTAGGGAAGAACAAGGGCGTGGGGCTTCGGGCGACATCAAGGCAGCTGGCAGGGCGTGGTTGT
1 AGCTAGGGAAGAACAAGGGCATGGGGCTTCGGGCGACACCAAGGCAGCCGGCAGGGCGTGGCTGT
* * ** * * *
25271359 GGTTGGGCAGCTGGGGAGAAAAGAAAGATGAATCAATGAAGGAGCTGAGCGTGGCGTGGTAGGCT
66 GGCTAGGCAGCTGGACAGAAAAAAAAGATGAACCAATGAAGGAGCAGAGCGTGGCGTGGTAGGCT
25271424 AGT
131 AGT
* * *
25271427 AGCTAGGGAAGAACAAGGGCATGGGGCTTGGGGCGACACCAAGGTAGCCGGTAGGGCGTGGCTGT
1 AGCTAGGGAAGAACAAGGGCATGGGGCTTCGGGCGACACCAAGGCAGCCGGCAGGGCGTGGCTGT
* * *
25271492 GGCTAGGCGGCTGGACAGAAAAAAAAGATGAACCGATGAAGGAGCAGAGCTTGGCGTGGTAGG
66 GGCTAGGCAGCTGGACAGAAAAAAAAGATGAACCAATGAAGGAGCAGAGCGTGGCGTGGTAGG
25271555 TCGGCAGCTG
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
133 111 1.00
ACGTcount: A:0.27, C:0.15, G:0.43, T:0.15
Consensus pattern (133 bp):
AGCTAGGGAAGAACAAGGGCATGGGGCTTCGGGCGACACCAAGGCAGCCGGCAGGGCGTGGCTGT
GGCTAGGCAGCTGGACAGAAAAAAAAGATGAACCAATGAAGGAGCAGAGCGTGGCGTGGTAGGCT
AGT
Found at i:25291413 original size:23 final size:23
Alignment explanation
Indices: 25291387--25291431 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
25291377 AGAGTTTGTG
*
25291387 ACACGACATGTTAGGAATGTGTA
1 ACACGACATGGTAGGAATGTGTA
*
25291410 ACACGACATGGTGGGAATGTGT
1 ACACGACATGGTAGGAATGTGT
25291432 GGCAGGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (23 bp):
ACACGACATGGTAGGAATGTGTA
Found at i:25291485 original size:23 final size:23
Alignment explanation
Indices: 25291459--25291541 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
25291449 GTAGGTTTTA
*
25291459 GAATTTGTGACACGACATGGTTG
1 GAATGTGTGACACGACATGGTTG
* *
25291482 GAATGTGTGACACGACAGGGTTTA
1 GAATGTGTGACACGACATGG-TTG
* * * *
25291506 GAGTTTGTGACACGCCATGGTGG
1 GAATGTGTGACACGACATGGTTG
25291529 GAATGTGTGACAC
1 GAATGTGTGACAC
25291542 ATCAGCGTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 30 0.62
24 18 0.38
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (23 bp):
GAATGTGTGACACGACATGGTTG
Found at i:25291525 original size:47 final size:47
Alignment explanation
Indices: 25291455--25291756 Score: 265
Period size: 47 Copynumber: 6.5 Consensus size: 47
25291445 TACGGTAGGT
* * ** * *
25291455 TTTAGAATTTGTGACACGACATGGTTGGAATGTGTGACACGACAGGG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGCG
* *
25291502 TTTAGAGTTTGTGACACGCCATGGTGGGAATGTGTGACAC-ATCAGCG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGA-CAGCG
* * * * * *
25291549 TTCAGAGTTGGTGACACGCCATTGAGGGAATCTGTGACATGCCAACG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGCG
* * * *
25291596 TTTAGAGTTGGTGACACACCATGGAGGGAATCTGTGAGACGCCAGCG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGCG
* * * * **
25291643 TTTAGAG-TCGTGACACGCCACGAAGGGAATCTGTGACACGTCAATG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGCG
* * * * *
25291689 TTCAGAGTTTGTCAAACTCCATGGA--G-ATCTGTGACACGGCA-CGG
1 TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGC-G
* *
25291733 TTTAGAGTGTGTGACACGACATGG
1 TTTAGAGTTTGTGACACGCCATGG
25291757 TAATTGATGG
Statistics
Matches: 210, Mismatches: 41, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
44 33 0.16
45 1 0.00
46 38 0.18
47 138 0.66
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (47 bp):
TTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGCG
Found at i:25292406 original size:31 final size:31
Alignment explanation
Indices: 25292368--25292565 Score: 244
Period size: 31 Copynumber: 6.5 Consensus size: 31
25292358 ATTGGCGTGT
*
25292368 TGGCGTGTTACTACATTTTACGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
**
25292399 TGGCGTGTTACCACAGCTTACG-T-TAT--A
1 TGGCGTGTTACCACATTTTACGTTATATGCA
* *
25292426 T-GCGTGTTACCACAGTTTATGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
*
25292456 TGGCGTGTTACCACATTCTACGTTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
* * *
25292487 TGGCGTGTTACCATAGTTTACATTATATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
* * *
25292518 TGGCATGTTACCACATTCTACGTTACATGCA
1 TGGCGTGTTACCACATTTTACGTTATATGCA
*
25292549 TGGCGTGCTACCACATT
1 TGGCGTGTTACCACATT
25292566 ATAGGTTAAC
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
26 18 0.13
27 3 0.02
28 3 0.02
29 3 0.02
30 3 0.02
31 112 0.79
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (31 bp):
TGGCGTGTTACCACATTTTACGTTATATGCA
Found at i:25292437 original size:26 final size:26
Alignment explanation
Indices: 25292401--25292454 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
25292391 TATATGCATG
25292401 GCGTGTTACCACAGCTTACGTTATAT
1 GCGTGTTACCACAGCTTACGTTATAT
* *
25292427 GCGTGTTACCACAGTTTATGTTATAT
1 GCGTGTTACCACAGCTTACGTTATAT
25292453 GC
1 GC
25292455 ATGGCGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (26 bp):
GCGTGTTACCACAGCTTACGTTATAT
Found at i:25293436 original size:13 final size:13
Alignment explanation
Indices: 25293418--25293444 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25293408 CTGAATAGTT
25293418 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
25293431 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
25293444 A
1 A
25293445 GTACTGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:25295306 original size:20 final size:19
Alignment explanation
Indices: 25295256--25295324 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
25295246 TTTTAATTTT
25295256 AAATAAATAAAAATATAATGA
1 AAATAAA-AAAAATATAAT-A
*
25295277 AAAAATAAAAAAATATAATA
1 AAATA-AAAAAAATATAATA
* *
25295297 ATAATAAAAATAATAAAATAA
1 A-AATAAAAAAAATATAAT-A
25295318 AAATAAA
1 AAATAAA
25295325 CTTCAAAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 19 0.46
21 20 0.49
22 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (19 bp):
AAATAAAAAAAATATAATA
Found at i:25302696 original size:31 final size:31
Alignment explanation
Indices: 25302648--25302756 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
25302638 TTTGTCAGTC
* *
25302648 ATGTTGTAACACGCCATGCATATAACGTATA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
*
25302679 ATGTGGTAACTTC-CCATGCATATAACGTAAA
1 ATGTGGTAAC-ACGCCATGCATATAACGTAAA
*
25302710 ATGTGGTAACACGCCATGCATATAATGTAAA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
*
25302741 ATGTTGTAACACGCCA
1 ATGTGGTAACACGCCA
25302757 ACGCTGACAC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
30 1 0.01
31 68 0.97
32 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (31 bp):
ATGTGGTAACACGCCATGCATATAACGTAAA
Found at i:25303214 original size:63 final size:63
Alignment explanation
Indices: 25303108--25303231 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
25303098 ATCACGGCCC
* * *
25303108 GATGACGATGGTGCTCAATAAAGAGTTGACAGAGCTCATACAGTTCAGAGAGCTGAGAGAGCT
1 GATGACGATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAAAGAGCT
* * * * *
25303171 GATGACGATGGTGCTCAACAGAGAGTTGGCAGAGTTGAGACAGTTCAGAGAGTTGAAAGAG
1 GATGACGATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAAAGAG
25303232 AAAGATGATC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (63 bp):
GATGACGATGGTGCTCAACAAAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAAAGAGCT
Found at i:25308130 original size:2 final size:2
Alignment explanation
Indices: 25308125--25308159 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25308115 ATATATATAA
25308125 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25308160 AATTATTATT
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25327334 original size:2 final size:2
Alignment explanation
Indices: 25327322--25327351 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25327312 ATCTGCTATC
*
25327322 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25327352 AACTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:25331362 original size:343 final size:343
Alignment explanation
Indices: 25330731--25331405 Score: 1071
Period size: 343 Copynumber: 2.0 Consensus size: 343
25330721 AAAGGTTTAA
* * *
25330731 TTTAGAGAAAAATAATTGATAATAATGGAACTTTTATTCATGTATTCTACAAGAATTCTTTTTAG
1 TTTAAAGAAAAATAATTGATAATAATGGAACTTTTATTCATGTATTCTACAAAAATGCTTTTTAG
25330796 AGTAATTATGGCACTAATAACTCATTATGATTTAGAGCCACACAAAATGGATGTTAAGATTGTCT
66 AGTAATTATGGCACTAATAACTCATTATGATTTAGAGCCACACAAAATGGATGTTAAGATTGTCT
* * * *
25330861 TCTTGAATGAGAATCTTGTTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGGGTATGGTT
131 TCTTGAATGAGAATCCTATTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATAGTT
* *
25330926 AAGATCATCTTTTGTGTAGACTTAAAGTGTATTTATGAGTTTAAACAAGCTTCTCGTCAGTAGTA
196 AAGATCATCTTTTGTGTAGACTCAAAGTGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
* *
25330991 TTTTAAATTTGATGAATTGATAATCTCTTTTGATTTTGTTAAGAACAAAATAGACTGATACATAT
261 TCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTGTTAAGAACAAAATAGACTAATACATAT
*
25331056 TTTTGAAGATTGTGGAAC
326 TTCTGAAGATTGTGGAAC
* * *
25331074 TTTAAAGAAAAATAATTGATAATAATGGAGCTTTTTTTCCTGTATTCTACAAAAATGCTTTTTAG
1 TTTAAAGAAAAATAATTGATAATAATGGAACTTTTATTCATGTATTCTACAAAAATGCTTTTTAG
* * * ** *
25331139 AGTAATTATGGCACTAGTAGCTCATTATGATTTAGGGCCGTACAAAATGGATGTTAAGATTGTTT
66 AGTAATTATGGCACTAATAACTCATTATGATTTAGAGCCACACAAAATGGATGTTAAGATTGTCT
* *
25331204 TCTTGAATGAGAATCCTATTAGAGAGGTCTATATGTTGTAACTTAAGTGTTTAAAGAGTATAGTT
131 TCTTGAATGAGAATCCTATTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATAGTT
* * *
25331269 ACGATCATCTTTTGTGTAGACTCAAAGTGTATTTATGAGTTCAAACAAGTTTTTCGTCAGTAGTA
196 AAGATCATCTTTTGTGTAGACTCAAAGTGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
* * * * *
25331334 TCTTAAATTTTATGAATTGATAATCTCTTTTGATTTTGTTGAGAACAAAGTAGATTAATGCATAT
261 TCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTGTTAAGAACAAAATAGACTAATACATAT
25331399 TTCTGAA
326 TTCTGAA
25331406 AACCGTGGAA
Statistics
Matches: 301, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
343 301 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.39
Consensus pattern (343 bp):
TTTAAAGAAAAATAATTGATAATAATGGAACTTTTATTCATGTATTCTACAAAAATGCTTTTTAG
AGTAATTATGGCACTAATAACTCATTATGATTTAGAGCCACACAAAATGGATGTTAAGATTGTCT
TCTTGAATGAGAATCCTATTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATAGTT
AAGATCATCTTTTGTGTAGACTCAAAGTGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
TCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTGTTAAGAACAAAATAGACTAATACATAT
TTCTGAAGATTGTGGAAC
Found at i:25336358 original size:18 final size:18
Alignment explanation
Indices: 25336337--25336371 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25336327 TTAGTTGAGT
*
25336337 AATTTTTAGTTTAATTAG
1 AATTTATAGTTTAATTAG
*
25336355 AATTTATATTTTAATTA
1 AATTTATAGTTTAATTA
25336372 TTTGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTATAGTTTAATTAG
Found at i:25348843 original size:73 final size:74
Alignment explanation
Indices: 25348763--25348918 Score: 206
Period size: 74 Copynumber: 2.1 Consensus size: 74
25348753 AAACCTATAC
* * *
25348763 TTATAAATATGTATTCATTAAATAACAATTATTGAAATATT-TTTATTTTAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTCTTTATTATAATTATTAGTAAGAT
25348827 TTAAACCAA
66 TTAAACCAA
* * ** *
25348836 TTATAAATGTGTATTCATCAAATGATGATCATTGGAATATTCTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTCTTTATTATAATTATTAGTAAGAT
** *
25348901 TTATTCCAT
66 TTAAACCAA
25348910 TTATAAATA
1 TTATAAATA
25348919 AAAAATTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 34 0.49
74 36 0.51
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTCTTTATTATAATTATTAGTAAGAT
TTAAACCAA
Found at i:25349011 original size:13 final size:14
Alignment explanation
Indices: 25348993--25349022 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25348983 TAATTTAAAT
25348993 ATTAA-TATTTTAA
1 ATTAATTATTTTAA
25349006 ATTAATTATTTTAA
1 ATTAATTATTTTAA
25349020 ATT
1 ATT
25349023 TTAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAATTATTTTAA
Found at i:25349443 original size:28 final size:28
Alignment explanation
Indices: 25349406--25349501 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
25349396 ATGGGCTCAT
*
25349406 CACAAACCCATGGTTTTAACAAGTTCAC
1 CACAAACCCATGGTTTTAACGAGTTCAC
** *
25349434 CACAAACCCATAATTTTAATGAGTTCAC
1 CACAAACCCATGGTTTTAACGAGTTCAC
* *
25349462 CACAAACCCATGGTTTTTAACGGGATCAC
1 CACAAACCCATGG-TTTTAACGAGTTCAC
*
25349491 TACAAACCCAT
1 CACAAACCCAT
25349502 ACATGAACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 35 0.61
29 22 0.39
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.25
Consensus pattern (28 bp):
CACAAACCCATGGTTTTAACGAGTTCAC
Found at i:25358608 original size:3 final size:3
Alignment explanation
Indices: 25358600--25358689 Score: 51
Period size: 3 Copynumber: 29.3 Consensus size: 3
25358590 TATTTTTTAG
* *
25358600 TTA TTA TTAA TTAA TTA TTA TTT TTG TT- TTA TTA TATA TT- TTA TTA
1 TTA TTA TT-A TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * * *
25358646 TCA -TA TTT TCTA TTC TTA TTTC TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
25358690 ACTTTACATT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
2 5 0.07
3 49 0.72
4 14 0.21
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25374882 original size:2 final size:2
Alignment explanation
Indices: 25374875--25374905 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25374865 NNNNNNNNNN
25374875 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 T
25374906 ACCCATGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25375005 original size:76 final size:76
Alignment explanation
Indices: 25374877--25375025 Score: 262
Period size: 76 Copynumber: 2.0 Consensus size: 76
25374867 NNNNNNNNTC
**
25374877 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGGTAACCCAAGCACCAGATC
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATC
25374942 CAGCGCCGACT
66 CAGCGCCGACT
* *
25374953 TCTCTCTCTCTCTCTCTCTCTCTTTCTCTACCCATGCTAACCGCCGACAACCCAAGCACCAGATC
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATC
25375018 CAGCGCCG
66 CAGCGCCG
25375026 GTAGGGCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.18, C:0.44, G:0.11, T:0.26
Consensus pattern (76 bp):
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATC
CAGCGCCGACT
Found at i:25375040 original size:76 final size:76
Alignment explanation
Indices: 25374878--25375050 Score: 242
Period size: 76 Copynumber: 2.3 Consensus size: 76
25374868 NNNNNNNTCT
**
25374878 CTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGGTAACCCAAGCACCAGATCC
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATCC
**
25374943 AGCGCCGACTT
66 AGCGCCGACGG
* *
25374954 CTCTCTCTCTCTCTCTCTCTCTTTCTCTACCCATGCTAACCGCCGACAACCCAAGCACCAGATCC
1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATCC
*
25375019 AGCGCCGGTAGGG
66 AGCGCC-G-ACGG
*
25375032 CT-TC-CTCTCTCTCACTCTC
1 CTCTCTCTCTCTCTCTCTCTC
25375051 CTCCTGCCGA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
76 81 0.93
77 3 0.03
78 3 0.03
ACGTcount: A:0.17, C:0.44, G:0.12, T:0.27
Consensus pattern (76 bp):
CTCTCTCTCTCTCTCTCTCTCTCTCTCTACCCATGCTAACCGACGACAACCCAAGCACCAGATCC
AGCGCCGACGG
Found at i:25375501 original size:14 final size:14
Alignment explanation
Indices: 25375480--25375516 Score: 53
Period size: 11 Copynumber: 2.9 Consensus size: 14
25375470 CCCTCTTTTT
25375480 TTCATTTTTTTT--
1 TTCATTTTTTTTAA
25375492 TT-ATTTTTTTTAA
1 TTCATTTTTTTTAA
25375505 TTCATTTTTTTT
1 TTCATTTTTTTT
25375517 GTTTATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 2 0.09
14 9 0.41
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCATTTTTTTTAA
Found at i:25376620 original size:67 final size:66
Alignment explanation
Indices: 25376497--25376863 Score: 429
Period size: 67 Copynumber: 5.5 Consensus size: 66
25376487 ATCATAATCT
* *
25376497 AAAAAAATTCAATGGTTGATAACTAT--A-CAT-CATAATCATATCAAGCCATATCAACCTTAGT
1 AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACCTTA-T
25376558 AC
65 AC
* * * * *
25376560 AAAAAAATTCAAAGGTCGATAACTAAACACCATATAAAATCATATTAACCCATATCAACCTTTAT
1 AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACC-TTAT
25376625 AC
65 AC
* * * * * * * **
25376627 AAAAAAATTCAAAAGTTGTTAACTATACATCGTATATGATTATATCAAGCCATATTAAGTTTAAT
1 AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACCTT-AT
25376692 AC
65 AC
*
25376694 AAAAAAATTCAAAGGTTGATAACTATACGCCATATATAATCATATCAAGCCATATCAACCTTAAT
1 AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACCTT-AT
25376759 AC
65 AC
* * * * *
25376761 AAAAAAAAAATCAAAAGTTAATAATTATAAACCATATATAATCATATCAAGCCATATCAACCTT-
1 --AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACCTTA
25376825 TAC
64 TAC
25376828 ACAAAAAATTACAAAGGTTGATAACTATACACCATA
1 A-AAAAAATT-CAAAGGTTGATAACTATACACCATA
25376864 ACTATATCAA
Statistics
Matches: 252, Mismatches: 42, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
63 23 0.09
65 2 0.01
66 12 0.05
67 156 0.62
68 3 0.01
69 56 0.22
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (66 bp):
AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAAGCCATATCAACCTTATA
C
Found at i:25376866 original size:13 final size:15
Alignment explanation
Indices: 25376848--25376880 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
25376838 ACAAAGGTTG
25376848 ATAACTATA-C-ACC
1 ATAACTATATCAACC
25376861 ATAACTATATCAACC
1 ATAACTATATCAACC
25376876 ATAAC
1 ATAAC
25376881 ACCAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 1 0.06
15 8 0.44
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAACTATATCAACC
Found at i:25379099 original size:15 final size:15
Alignment explanation
Indices: 25379065--25379099 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
25379055 AATTACTATT
*
25379065 ATATATATACTTTTA
1 ATATATATACTTTAA
*
25379080 GTATATATACTTTAA
1 ATATATATACTTTAA
25379095 ATATA
1 ATATA
25379100 AACATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:25380403 original size:15 final size:15
Alignment explanation
Indices: 25380365--25380403 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
25380355 GAATAGAATT
25380365 AAAAAAATATAAATA
1 AAAAAAATATAAATA
** *
25380380 CTAATAATATAAATA
1 AAAAAAATATAAATA
25380395 AAAAAAATA
1 AAAAAAATA
25380404 AATTTTTTTT
Statistics
Matches: 18, Mismatches: 6, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAATATAAATA
Found at i:25387134 original size:11 final size:12
Alignment explanation
Indices: 25387115--25387149 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
25387105 ACAAAGTTTG
25387115 GTAGAAGAGAAA
1 GTAGAAGAGAAA
25387127 GT-GAAGAGAAA
1 GTAGAAGAGAAA
25387138 GTAGAAG-GAAA
1 GTAGAAGAGAAA
25387149 G
1 G
25387150 AGAGTGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (12 bp):
GTAGAAGAGAAA
Found at i:25402969 original size:25 final size:25
Alignment explanation
Indices: 25402941--25403027 Score: 101
Period size: 25 Copynumber: 3.5 Consensus size: 25
25402931 ATGGACTTCT
25402941 CCCATTTCTT-TTTGATTGGACCATG
1 CCCATTTCTTCTTT-ATTGGACCATG
25402966 CCCA-TTCTTCCTTTATTGGACCATG
1 CCCATTTCTT-CTTTATTGGACCATG
*
25402991 TCCATTT-TTCCTTTATTGGACCATG
1 CCCATTTCTT-CTTTATTGGACCATG
*
25403016 TCCATTT-TTCTT
1 CCCATTTCTTCTT
25403028 GCTTGTTGGG
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
24 8 0.14
25 45 0.78
26 5 0.09
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.47
Consensus pattern (25 bp):
CCCATTTCTTCTTTATTGGACCATG
Found at i:25403047 original size:27 final size:25
Alignment explanation
Indices: 25402955--25403055 Score: 123
Period size: 25 Copynumber: 4.0 Consensus size: 25
25402945 TTTCTTTTTG
*
25402955 ATTGGACCATGCCCATTCTTCCTTT
1 ATTGGACCATGCCCATTTTTCCTTT
*
25402980 ATTGGACCATGTCCATTTTTCCTTT
1 ATTGGACCATGCCCATTTTTCCTTT
* *
25403005 ATTGGACCATGTCCATTTTTCTTGCTT
1 ATTGGACCATGCCCATTTTTCCT--TT
* *
25403032 GTTGGGCCATGCCCA-TTTTCCTTT
1 ATTGGACCATGCCCATTTTTCCTTT
25403056 CTTGTTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.03
25 45 0.67
26 6 0.09
27 14 0.21
ACGTcount: A:0.14, C:0.27, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTGGACCATGCCCATTTTTCCTTT
Found at i:25403281 original size:34 final size:34
Alignment explanation
Indices: 25403212--25403297 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
25403202 CTTTCAATTT
* *
25403212 TTCAGTAGCTAAAGCTGCTTATATTGGCTCCAAAA
1 TTCAGTAGCT-AAGCTGCTTATATTGCCTCAAAAA
* *
25403247 -TCAGTAGCTAAGCTGCTTTATTTTTCCTCAAAAA
1 TTCAGTAGCTAAGCTGC-TTATATTGCCTCAAAAA
**
25403281 TTCAACAGCTAAGCTGC
1 TTCAGTAGCTAAGCTGC
25403298 ACTTTTCTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.16
34 22 0.51
35 14 0.33
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (34 bp):
TTCAGTAGCTAAGCTGCTTATATTGCCTCAAAAA
Found at i:25403606 original size:27 final size:29
Alignment explanation
Indices: 25403549--25403619 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
25403539 CTCTTTTCCT
*
25403549 TTTGTTTTTCTTTCTCTCTCGGTTTTCTC
1 TTTGTTTTTCTTTCTCTCTCGGTCTTCTC
*
25403578 TTTGTTTTTGTTT-T-TCTCGGCTCTT-TC
1 TTTGTTTTTCTTTCTCTCTCGG-TCTTCTC
25403605 TTTGTTCTTTCTTTC
1 TTTGTT-TTTCTTTC
25403620 CTTTTCTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 14 0.39
28 10 0.28
29 12 0.33
ACGTcount: A:0.00, C:0.21, G:0.11, T:0.68
Consensus pattern (29 bp):
TTTGTTTTTCTTTCTCTCTCGGTCTTCTC
Found at i:25404695 original size:10 final size:11
Alignment explanation
Indices: 25404677--25404713 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
25404667 GAGGCTGAAA
25404677 TTGATGATATT
1 TTGATGATATT
25404688 TT-ATGATATT
1 TTGATGATATT
*
25404698 TTGGTGATA-T
1 TTGATGATATT
25404708 TTGATG
1 TTGATG
25404714 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:25406216 original size:22 final size:23
Alignment explanation
Indices: 25406173--25406217 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
25406163 AACTTTTACG
25406173 CTAAAAAAATTATTTACGTATAACT
1 CTAAAAAAATTATTTA--TATAACT
*
25406198 CTAAAAATATTATTT-TATAA
1 CTAAAAAAATTATTTATATAA
25406218 GAAAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
25 14 0.74
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
CTAAAAAAATTATTTATATAACT
Found at i:25407243 original size:19 final size:19
Alignment explanation
Indices: 25407219--25407264 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
25407209 TTAATATTTT
25407219 AATATTATTTTATT-AATAA
1 AATATTATTTTATTCAA-AA
25407238 AATATTATTTTATTCAAAA
1 AATATTATTTTATTCAAAA
*
25407257 AATTTTAT
1 AATATTAT
25407265 CTTGTCTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTATTTTATTCAAAA
Found at i:25410486 original size:29 final size:28
Alignment explanation
Indices: 25410441--25410502 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
25410431 TATGGGCAAT
* * *
25410441 TTTTTCAGTTTTTGGGGTAAAAATGTAA
1 TTTTTCACTTTTAGGGGCAAAAATGTAA
25410469 TTTTTCACTTTATAGGGGCAAAAATGTAA
1 TTTTTCACTTT-TAGGGGCAAAAATGTAA
25410498 TTTTT
1 TTTTT
25410503 AAAAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (28 bp):
TTTTTCACTTTTAGGGGCAAAAATGTAA
Found at i:25414511 original size:129 final size:129
Alignment explanation
Indices: 25414280--25414540 Score: 373
Period size: 129 Copynumber: 2.0 Consensus size: 129
25414270 GTGGCCTGAA
* *
25414280 CGTGAGGTTCACTCAAATCATACCTCAGGAGATACTTCACCCAACATCTCCCCTCGGAGGTAAAT
1 CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCTCGGAGGTAAAT
* * * * * * *
25414345 ATATAATTGAGTTACCGTGCTCCTCTCATAGGTAGTCCACGGAAACCCCCACCACTGCAGTGAC
66 ATATAATTGAGTTACCATACCCCTATCATAAGCAGTCCACGGAAACCCCCACCACTACAGTGAC
* * * *
25414409 CGTGAGGTGCATTCAAATCTTACCTCAAGAGATACTTCATCCAACATCTCCCC-CTGGAGGTAAG
1 CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCTC-GGAGGTAAA
25414473 TATATAATT-AGGTTACCATACCCCTATCATAAGCAGTCCACGGAAACCCCCACCACTACAGTGA
65 TATATAATTGA-GTTACCATACCCCTATCATAAGCAGTCCACGGAAACCCCCACCACTACAGTGA
25414537 C
129 C
25414538 CGT
1 CGT
25414541 TTAATATACC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 2 0.02
129 115 0.98
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (129 bp):
CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCTCGGAGGTAAAT
ATATAATTGAGTTACCATACCCCTATCATAAGCAGTCCACGGAAACCCCCACCACTACAGTGAC
Found at i:25415974 original size:28 final size:29
Alignment explanation
Indices: 25415916--25415981 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
25415906 GTAAATTTTT
** *
25415916 AAAAATTACACTTTTACTCCCGTAAAGTG
1 AAAAATTACACTTTTACTCCCAAAAACTG
*
25415945 AAAAATTACATTTTTAC-CCCAAAAACTG
1 AAAAATTACACTTTTACTCCCAAAAACTG
25415973 AAAAATTAC
1 AAAAATTAC
25415982 CCACAGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTACTCCCAAAAACTG
Found at i:25417893 original size:22 final size:22
Alignment explanation
Indices: 25417852--25417906 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
25417842 AATTTATTAT
25417852 TTAATTTTAA--TTTCACTTTA
1 TTAATTTTAATTTTTCACTTTA
25417872 TTAATTTTAATTTTTCTA-TTTA
1 TTAATTTTAATTTTTC-ACTTTA
* *
25417894 ATAATTTAAATTT
1 TTAATTTTAATTT
25417907 AATTGTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
22 19 0.63
23 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAATTTTAATTTTTCACTTTA
Found at i:25420265 original size:3 final size:3
Alignment explanation
Indices: 25420257--25420296 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25420247 CTAATTAATA
25420257 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25420297 CAATTATGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:25421086 original size:21 final size:22
Alignment explanation
Indices: 25421022--25421103 Score: 62
Period size: 24 Copynumber: 3.6 Consensus size: 22
25421012 GTTGTGTCAT
* **
25421022 TAATTTCATATATACATAATAAAG
1 TAATTT-ATATATA-ATATTATTG
25421046 TAATATTATATATACATATT-TT-
1 TAAT-TTATATATA-ATATTATTG
25421068 TAATTTATATATAAGTATTATTG
1 TAATTTATATATAA-TATTATTG
*
25421091 TAACTTATA-ATAA
1 TAATTTATATATAA
25421104 ACTTTATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 1 0.02
21 13 0.26
22 10 0.20
23 8 0.16
24 16 0.32
25 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATTTATATATAATATTATTG
Found at i:25421098 original size:23 final size:20
Alignment explanation
Indices: 25421051--25421103 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
25421041 TAAAGTAATA
*
25421051 TTATATATACATATTTTTAAT
1 TTATATATA-ATATTTTTAAC
25421072 TTATATATAAGTATTATTGTAAC
1 TTATATATAA-TATT-TT-TAAC
25421095 TTATA-ATAA
1 TTATATATAA
25421104 ACTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 13 0.46
22 6 0.21
23 8 0.29
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
TTATATATAATATTTTTAAC
Found at i:25425213 original size:60 final size:60
Alignment explanation
Indices: 25425138--25425255 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
25425128 GACTTGATTG
* * * **
25425138 GAATATCATCTTGTTGTGTGTTTATCCTATTAGAAGATATGTTAATCTTTTGAGATGTTA
1 GAATATCATCATGTTGTATGTTCATCCTATTAGAAGATATGTTAATCCCTTGAGATGTTA
* * * *
25425198 GAATATCTTCATGTTGTATGTTCATCTTATTAGAGGATATGTTGATCCCTTGAGATGT
1 GAATATCATCATGTTGTATGTTCATCCTATTAGAAGATATGTTAATCCCTTGAGATGT
25425256 GTTGATCTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.45
Consensus pattern (60 bp):
GAATATCATCATGTTGTATGTTCATCCTATTAGAAGATATGTTAATCCCTTGAGATGTTA
Found at i:25427214 original size:19 final size:19
Alignment explanation
Indices: 25427190--25427227 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25427180 CCATTTAACT
*
25427190 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
25427209 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
25427228 GGTTTGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:25428602 original size:13 final size:13
Alignment explanation
Indices: 25428584--25428608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25428574 AGAGAAATTG
25428584 TGATTTTATAAAA
1 TGATTTTATAAAA
25428597 TGATTTTATAAA
1 TGATTTTATAAA
25428609 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:25429091 original size:19 final size:20
Alignment explanation
Indices: 25429064--25429109 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
25429054 AGGAGACAAG
*
25429064 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
25429083 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
25429102 ATAATATT
1 ATAATATT
25429110 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:25430801 original size:13 final size:13
Alignment explanation
Indices: 25430783--25430807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25430773 AGAGAAATTG
25430783 TGATTTTATAAAA
1 TGATTTTATAAAA
25430796 TGATTTTATAAA
1 TGATTTTATAAA
25430808 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:25436722 original size:2 final size:2
Alignment explanation
Indices: 25436715--25436742 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25436705 ATTTGTTCGT
25436715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25436743 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25437055 original size:2 final size:2
Alignment explanation
Indices: 25437048--25437092 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
25437038 AATTTATTTC
* * *
25437048 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25437090 AT A
1 AT A
25437093 ATCTTCTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:25444520 original size:13 final size:13
Alignment explanation
Indices: 25444502--25444526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25444492 GGAGAAATTG
25444502 TGATTTTATAAAA
1 TGATTTTATAAAA
25444515 TGATTTTATAAA
1 TGATTTTATAAA
25444527 TTTTTTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:25447114 original size:16 final size:17
Alignment explanation
Indices: 25447093--25447127 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
25447083 CAGTACCTTT
*
25447093 TTAATCGATTAAA-TTG
1 TTAATCAATTAAACTTG
25447109 TTAATCAATTAAACTTG
1 TTAATCAATTAAACTTG
25447126 TT
1 TT
25447128 CCCGTAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (17 bp):
TTAATCAATTAAACTTG
Found at i:25476033 original size:19 final size:19
Alignment explanation
Indices: 25476009--25476046 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25475999 CTGCCAAACC
*
25476009 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
25476028 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
25476047 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:25483866 original size:26 final size:26
Alignment explanation
Indices: 25483830--25483891 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
25483820 AGATACTATT
25483830 TAAAGATTTTCTCTCTTTTTCATCAA
1 TAAAGATTTTCTCTCTTTTTCATCAA
25483856 TAAAGATTTTCTCTCTTTTTCATCAA
1 TAAAGATTTTCTCTCTTTTTCATCAA
*
25483882 AAAAGATTTT
1 TAAAGATTTT
25483892 AATATTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (26 bp):
TAAAGATTTTCTCTCTTTTTCATCAA
Found at i:25484747 original size:31 final size:31
Alignment explanation
Indices: 25484712--25484773 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
25484702 AATGATGATT
* **
25484712 GTCACAATCCAAACTTGAGGGTCCATGATCG
1 GTCACAACCCAAACCCGAGGGTCCATGATCG
25484743 GTCACAACCCAAACCCGAGGGTCCATGATCG
1 GTCACAACCCAAACCCGAGGGTCCATGATCG
25484774 ACACACGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.18
Consensus pattern (31 bp):
GTCACAACCCAAACCCGAGGGTCCATGATCG
Found at i:25490892 original size:2 final size:2
Alignment explanation
Indices: 25490887--25490913 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25490877 TAGGTTTCCA
25490887 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
25490914 AGTTTCTTAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:25501558 original size:3 final size:3
Alignment explanation
Indices: 25501550--25501579 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25501540 ATAAGCTTGA
25501550 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25501580 GAAGAGTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25513007 original size:33 final size:33
Alignment explanation
Indices: 25512965--25513045 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
25512955 GGTAAAGAAC
25512965 ATTTTATAGTCCTCTATGTCACGTCTTGTCCCT
1 ATTTTATAGTCCTCTATGTCACGTCTTGTCCCT
25512998 ATTTTATAGTCCTCTATGTCACGTCTTGTCCCT
1 ATTTTATAGTCCTCTATGTCACGTCTTGTCCCT
*
25513031 ATTTTGTAGTCCTCT
1 ATTTTATAGTCCTCT
25513046 GGGTCAATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.15, C:0.26, G:0.12, T:0.47
Consensus pattern (33 bp):
ATTTTATAGTCCTCTATGTCACGTCTTGTCCCT
Found at i:25513691 original size:9 final size:9
Alignment explanation
Indices: 25513669--25513730 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
25513659 TTTATATTAT
25513669 TATTTTTTA
1 TATTTTTTA
25513678 TATTTATTTA
1 TATTT-TTTA
25513688 -ATTTTTTA
1 TATTTTTTA
25513696 TATTTATTCTA
1 TATTT-TT-TA
*
25513707 TTTTTTTTA
1 TATTTTTTA
*
25513716 TATATTTTA
1 TATTTTTTA
*
25513725 AATTTT
1 TATTTT
25513731 AATAGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 4 0.09
9 26 0.59
10 8 0.18
11 6 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTTTA
Found at i:25513712 original size:20 final size:19
Alignment explanation
Indices: 25513658--25513718 Score: 79
Period size: 18 Copynumber: 3.1 Consensus size: 19
25513648 TTTTCTTTCA
25513658 ATTTATATTATTATTTTTTAT
1 ATTTAT-TTATT-TTTTTTAT
*
25513679 ATTTATTTA-ATTTTTTAT
1 ATTTATTTATTTTTTTTAT
25513697 ATTTATTCTATTTTTTTTAT
1 ATTTATT-TATTTTTTTTAT
25513717 AT
1 AT
25513719 ATTTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 15 0.42
19 2 0.06
20 13 0.36
21 6 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTATTTATTTTTTTTAT
Found at i:25531633 original size:24 final size:25
Alignment explanation
Indices: 25531606--25531659 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
25531596 TTCAAAAATA
25531606 ATTTTAATAAAA-TTTT-T-TTTTT
1 ATTTTAATAAAATTTTTATATTTTT
*
25531628 ATATTTAATTAAATTTTTATATTTTT
1 AT-TTTAATAAAATTTTTATATTTTT
25531654 ATTTTA
1 ATTTTA
25531660 CGTTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 4 0.15
25 5 0.19
26 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
ATTTTAATAAAATTTTTATATTTTT
Found at i:25531700 original size:17 final size:17
Alignment explanation
Indices: 25531678--25531718 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
25531668 TAAGAACTAT
25531678 AAAAAAAA-TATTTAAA
1 AAAAAAAAGTATTTAAA
25531694 AAGAAAAAAGTATTTAAA
1 AA-AAAAAAGTATTTAAA
25531712 AAAAAAA
1 AAAAAAA
25531719 TTTAAGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.48
18 10 0.43
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
AAAAAAAAGTATTTAAA
Found at i:25531725 original size:21 final size:18
Alignment explanation
Indices: 25531678--25531718 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25531668 TAAGAACTAT
25531678 AAAAAAAA-TATTTAAAA
1 AAAAAAAAGTATTTAAAA
*
25531695 AGAAAAAAGTATTTAAAA
1 AAAAAAAAGTATTTAAAA
25531713 AAAAAA
1 AAAAAA
25531719 TTTAAGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAAAAAGTATTTAAAA
Found at i:25531869 original size:17 final size:17
Alignment explanation
Indices: 25531829--25531869 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
25531819 ATGAATAGAT
*
25531829 TAAATTCAATCTTAATC
1 TAAATTTAATCTTAATC
25531846 T-AATTTAATC-TATATC
1 TAAATTTAATCTTA-ATC
25531862 TAAATTTA
1 TAAATTTA
25531870 GATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAATCTTAATC
Found at i:25533708 original size:50 final size:52
Alignment explanation
Indices: 25533611--25533711 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
25533601 ATACAGCTTC
*
25533611 AGATAACTAAATCAATTTAACTAAAAATAAATAAAACACTTACATGCATTTT
1 AGATAACTAAATCAACTTAACTAAAAATAAATAAAACACTTACATGCATTTT
* ***
25533663 AGATCACTAAATCAACTTAACTGTGAA-AAA-AAAACACTTACATGCATTT
1 AGATAACTAAATCAACTTAACTAAAAATAAATAAAACACTTACATGCATTT
25533712 GGATGTGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 19 0.43
51 3 0.07
52 22 0.50
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (52 bp):
AGATAACTAAATCAACTTAACTAAAAATAAATAAAACACTTACATGCATTTT
Found at i:25534126 original size:90 final size:93
Alignment explanation
Indices: 25534032--25534214 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 93
25534022 TTCATATCAT
* * * * *
25534032 TTTTCAATGTTAAATGTAATTAATATAAAAT-GTACATATCAGA-TAGCTAAAGGTAAGATTTT-
1 TTTTCAATGCTAAATGTAATTAATAAAAAATGGTACATATCAAATTAGCTAAAGATAAAATTTTA
* *
25534094 GAGAGAGAATGAGTTACTACATATTCTA
66 AAAAGAGAATGAGTTACTACATATTCTA
25534122 TTTTCAATGCTAAATGTAATTAATAAAAAATGGTACATATCAAATTAGCTAAAGATAAAATTTTA
1 TTTTCAATGCTAAATGTAATTAATAAAAAATGGTACATATCAAATTAGCTAAAGATAAAATTTTA
*
25534187 AAAAGAGATTGAGTTACTACATATTCTA
66 AAAAGAGAATGAGTTACTACATATTCTA
25534215 CTCTAAATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 29 0.35
91 11 0.13
92 17 0.21
93 25 0.30
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (93 bp):
TTTTCAATGCTAAATGTAATTAATAAAAAATGGTACATATCAAATTAGCTAAAGATAAAATTTTA
AAAAGAGAATGAGTTACTACATATTCTA
Found at i:25548626 original size:27 final size:28
Alignment explanation
Indices: 25548570--25548670 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 28
25548560 TGGTTCATAA
* *
25548570 GTAACAACAACATTTTAGACATTAA-A-GT
1 GTAACAACAATATTTTTGA-A-TAAGACGT
*
25548598 GTAACAA-AATATTTTTGAATATGACGT
1 GTAACAACAATATTTTTGAATAAGACGT
* * * *
25548625 GTAATAATAATATTTTTTTAATAAGGCGT
1 GTAACAACAATA-TTTTTGAATAAGACGT
25548654 GTAACAACAATATTTTT
1 GTAACAACAATATTTTT
25548671 TTTTAACATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 17 0.28
28 16 0.27
29 23 0.38
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (28 bp):
GTAACAACAATATTTTTGAATAAGACGT
Found at i:25548654 original size:29 final size:28
Alignment explanation
Indices: 25548596--25548672 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
25548586 AGACATTAAA
* *
25548596 GTGTAACAAAATA-TTTTTGAATATGAC
1 GTGTAACAAAATATTTTTTTAATAAGAC
* *
25548623 GTGTAATAATAATATTTTTTTAATAAGGC
1 GTGTAACAA-AATATTTTTTTAATAAGAC
25548652 GTGTAACAACAATATTTTTTT
1 GTGTAACAA-AATATTTTTTT
25548673 TTAACATGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 8 0.19
28 4 0.10
29 30 0.71
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (28 bp):
GTGTAACAAAATATTTTTTTAATAAGAC
Found at i:25548706 original size:26 final size:25
Alignment explanation
Indices: 25548669--25548744 Score: 95
Period size: 25 Copynumber: 3.0 Consensus size: 25
25548659 AACAATATTT
25548669 TTTTTTAACATGGCGTGTAACAACC
1 TTTTTTAACATGGCGTGTAACAACC
*
25548694 TTTTTTAACCATGGCGTGTAATATA--
1 TTTTTTAA-CATGGCGTGTAACA-ACC
25548719 TTTTTGT-ACATGGCGTGTAACAACC
1 TTTTT-TAACATGGCGTGTAACAACC
25548744 T
1 T
25548745 AACCATGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
23 1 0.02
24 13 0.30
25 15 0.34
26 14 0.32
27 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (25 bp):
TTTTTTAACATGGCGTGTAACAACC
Found at i:25548750 original size:45 final size:45
Alignment explanation
Indices: 25548676--25548874 Score: 193
Period size: 45 Copynumber: 4.2 Consensus size: 45
25548666 TTTTTTTTTA
* *
25548676 ACATGGCGTGTAACAACCTTTTTTAACCATGGCGTGTAATATATTTTTGT
1 ACATGGCGTGTAACAACC-----TAACCATGGCGTGTCACATATTTTTGT
**
25548726 ACATGGCGTGTAACAACCTAACCATGATGTGTCACATATTTTTGT
1 ACATGGCGTGTAACAACCTAACCATGGCGTGTCACATATTTTTGT
* **** * *
25548771 ATATGGCGTGTCATATGTTTCTATA-CATGGCGTGTCACATGTTTCTGT
1 ACATGGCGTGT-A-A-CAACCTA-ACCATGGCGTGTCACATATTTTTGT
* *
25548819 ACATGGTGTGTAACAACCTAACCATGGAGTGTCACATATTTTTGT
1 ACATGGCGTGTAACAACCTAACCATGGCGTGTCACATATTTTTGT
25548864 ACATGGCGTGT
1 ACATGGCGTGT
25548875 CACATGTTTC
Statistics
Matches: 121, Mismatches: 23, Indels: 15
0.76 0.14 0.09
Matches are distributed among these distances:
44 1 0.01
45 66 0.55
46 2 0.02
47 2 0.02
48 31 0.26
49 1 0.01
50 18 0.15
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (45 bp):
ACATGGCGTGTAACAACCTAACCATGGCGTGTCACATATTTTTGT
Found at i:25548800 original size:24 final size:24
Alignment explanation
Indices: 25548754--25549105 Score: 178
Period size: 24 Copynumber: 15.2 Consensus size: 24
25548744 TAACCATGAT
* * * *
25548754 GTGTCACATATTTTTGTATATGGC
1 GTGTCACATGTTTCTATACATGGC
*
25548778 GTGTCATATGTTTCTATACATGGC
1 GTGTCACATGTTTCTATACATGGC
* *
25548802 GTGTCACATGTTTCTGTACATGGT
1 GTGTCACATGTTTCTATACATGGC
* ** *
25548826 GTGTAACA---ACCTA-ACCATGGA
1 GTGTCACATGTTTCTATA-CATGGC
* * *
25548847 GTGTCACATATTTTTGTACATGGC
1 GTGTCACATGTTTCTATACATGGC
* *
25548871 GTGTCACATGTTTCTGTACATAGC
1 GTGTCACATGTTTCTATACATGGC
* **
25548895 GTGTAACA---ACCTA-ACAATGGC
1 GTGTCACATGTTTCTATAC-ATGGC
* ** *
25548916 GTGTAACA---ACCTA-ACAATGAC
1 GTGTCACATGTTTCTATAC-ATGGC
*
25548937 GTGTCACATGTTTTTATACATGGC
1 GTGTCACATGTTTCTATACATGGC
*
25548961 GTGTCACATGTTTCTATACATGGT
1 GTGTCACATGTTTCTATACATGGC
* * * *
25548985 ATATCACATGTTTCTGTATATGGC
1 GTGTCACATGTTTCTATACATGGC
* * *
25549009 GTGTCATATGTTTCTGTACATGGT
1 GTGTCACATGTTTCTATACATGGC
* ** *
25549033 GTGTAACA---ACCTA-ACCATGAC
1 GTGTCACATGTTTCTATA-CATGGC
* * * *
25549054 GTGTCACATATTTTTGTACACGGC
1 GTGTCACATGTTTCTATACATGGC
* *
25549078 GTGTCACATGTTTCTGTACATGGT
1 GTGTCACATGTTTCTATACATGGC
25549102 GTGT
1 GTGT
25549106 AACAACCTAA
Statistics
Matches: 250, Mismatches: 63, Indels: 30
0.73 0.18 0.09
Matches are distributed among these distances:
20 4 0.02
21 60 0.24
24 182 0.73
25 4 0.02
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (24 bp):
GTGTCACATGTTTCTATACATGGC
Found at i:25548830 original size:93 final size:92
Alignment explanation
Indices: 25548703--25549012 Score: 376
Period size: 93 Copynumber: 3.4 Consensus size: 92
25548693 CTTTTTTAAC
* * *
25548703 CATGGCGTGTAATATATTTTTGTACATGGCGTGTAACAACCTAACCATGATGTGTCACATATTTT
1 CATGGCGTGTAACATGTTTCTGTACATGGCGTGTAACAACCTAACCATGA-GTGTCACATATTTT
* *
25548768 TGTATATGGCGTGTCATATGTTTCTATA
65 TGTACATGGCGTGTCACATGTTTCTATA
* *
25548796 CATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACCTAACCATGGAGTGTCACATATTTT
1 CATGGCGTGTAACATGTTTCTGTACATGGCGTGTAACAACCTAACCAT-GAGTGTCACATATTTT
*
25548861 TGTACATGGCGTGTCACATGTTTCTGTA
65 TGTACATGGCGTGTCACATGTTTCTATA
* ** * * *
25548889 CATAGCGTGTAACA---ACCT-AACAATGGCGTGTAACAACCTAACAATGACGTGTCACATGTTT
1 CATGGCGTGTAACATGTTTCTGTAC-ATGGCGTGTAACAACCTAACCATGA-GTGTCACATATTT
*
25548950 TTATACATGGCGTGTCACATGTTTCTATA
64 TTGTACATGGCGTGTCACATGTTTCTATA
** * * *
25548979 CATGGTATATCACATGTTTCTGTATATGGCGTGT
1 CATGGCGTGTAACATGTTTCTGTACATGGCGTGT
25549013 CATATGTTTC
Statistics
Matches: 183, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
89 4 0.02
90 71 0.39
93 105 0.57
94 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (92 bp):
CATGGCGTGTAACATGTTTCTGTACATGGCGTGTAACAACCTAACCATGAGTGTCACATATTTTT
GTACATGGCGTGTCACATGTTTCTATA
Found at i:25548867 original size:69 final size:69
Alignment explanation
Indices: 25548773--25549120 Score: 359
Period size: 69 Copynumber: 5.0 Consensus size: 69
25548763 ATTTTTGTAT
* * * *
25548773 ATGGCGTGTCATATGTTTCTATACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACCT
1 ATGGAGTGTCACATATTTCTGTACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACCT
25548838 AACC
66 AACC
* * *
25548842 ATGGAGTGTCACATATTTTTGTACATGGCGTGTCACATGTTTCTGTACATAGCGTGTAACAACCT
1 ATGGAGTGTCACATATTTCTGTACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACCT
*
25548907 AACA
66 AACC
* * * * * * * * *
25548911 ATGGCGTGTAACA-A--CCT-AACAATGACGTGTCACATGTTTTTATACATGGCGTGTCACATGT
1 ATGGAGTGTCACATATTTCTGTAC-ATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACA---
**
25548972 TTCTATA-C
62 ACCTA-ACC
* * * *
25548980 ATGGTA-TATCACATGTTTCTGTATATGGCGTGTCATATGTTTCTGTACATGGTGTGTAACAACC
1 ATGG-AGTGTCACATATTTCTGTACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
25549044 TAACC
65 TAACC
* *
25549049 AT-GACGTGTCACATATTTTTGTACACGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
1 ATGGA-GTGTCACATATTTCTGTACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACC
25549113 TAACC
65 TAACC
25549118 ATG
1 ATG
25549121 ACATGTAACA
Statistics
Matches: 223, Mismatches: 42, Indels: 27
0.76 0.14 0.09
Matches are distributed among these distances:
65 2 0.01
66 33 0.15
67 1 0.00
68 3 0.01
69 149 0.67
70 1 0.00
72 33 0.15
73 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (69 bp):
ATGGAGTGTCACATATTTCTGTACATGGCGTGTCACATGTTTCTGTACATGGTGTGTAACAACCT
AACC
Found at i:25548919 original size:21 final size:21
Alignment explanation
Indices: 25548893--25548940 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
25548883 TCTGTACATA
25548893 GCGTGTAACAACCTAACAATG
1 GCGTGTAACAACCTAACAATG
25548914 GCGTGTAACAACCTAACAATG
1 GCGTGTAACAACCTAACAATG
*
25548935 ACGTGT
1 GCGTGT
25548941 CACATGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GCGTGTAACAACCTAACAATG
Found at i:25553087 original size:11 final size:11
Alignment explanation
Indices: 25553071--25553099 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
25553061 TTAAAGACTC
25553071 AATTGAAAAAA
1 AATTGAAAAAA
25553082 AATTG-AAAAA
1 AATTGAAAAAA
25553092 AATTGAAA
1 AATTGAAA
25553100 CATCCTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (11 bp):
AATTGAAAAAA
Found at i:25573873 original size:44 final size:44
Alignment explanation
Indices: 25573791--25574359 Score: 468
Period size: 44 Copynumber: 12.9 Consensus size: 44
25573781 ATGGAAAAAA
* * *
25573791 CTCCTTATCTA-AATTAGGCTACGTAACTTTAAAGAAAGAATAAA
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAA-AAAGAATAAG
* * * *
25573835 CTCCTCATTTAGAATAAGGTTACATAACTTTAAAAAAGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * * * *
25573879 CTCATCATATGGAATGAGGCTATGTAACTTT-ACAAAGGATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * * * * *
25573922 CTCATCATCTAAAATAAGGCTACATGACTTT-TAAAAGGATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * ** * * *
25573965 CTCATCATCTAGAATGAGGTTATATAACTTTACAAAGGAATAAA
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * *
25574009 CTCTTCATCTGGAATGAGGTTACGTAACTTTAAAAAGGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * *
25574053 CTCTTTATCTAGAATAAGGTTACGTAACTTTAAAAAAGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * * *
25574097 CTCCTAAT-TTGAAATGAGGCTACGCAACTTTAAAAATGAAGAAG
1 CTCCTCATCTAG-AATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * * ** *
25574141 TTCTTCATCTGGAATGAGGCTATGTAAAATT-AAAATGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * * * *
25574184 CTACTTATTTGGAATGAGGCTACGTAACTTTAAAAAGGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
* * *
25574228 CTCCTTATCTAGAATGAGGCTACGTAACTATGTAACTTTAAAATAAATAAA
1 CTCCTCATCTAGAATGAGGCTACGTAACT-T-TAA----AAAA-GAATAAG
* * * *
25574279 CTCCTCATCTAAAATGAGGTTACATAACTTT-AAAATGAATAAG
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
*
25574322 CTCCTCATCTAGAATGAGGCTATGTAAC-TTAAAAAAGA
1 CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGA
25574360 TTTCTAAACA
Statistics
Matches: 425, Mismatches: 87, Indels: 27
0.79 0.16 0.05
Matches are distributed among these distances:
42 2 0.00
43 141 0.33
44 221 0.52
45 22 0.05
46 3 0.01
48 1 0.00
49 1 0.00
50 4 0.01
51 30 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (44 bp):
CTCCTCATCTAGAATGAGGCTACGTAACTTTAAAAAAGAATAAG
Found at i:25574216 original size:175 final size:179
Alignment explanation
Indices: 25573928--25574348 Score: 478
Period size: 175 Copynumber: 2.4 Consensus size: 179
25573918 TAAGCTCATC
* ** * * * * *
25573928 ATCTAAAATAAGGCTACATGACTTTTAAAA-GGATAAGCTCATCATCTAGAATGAGGTTATATAA
1 ATCTAAAATGAGGCTACACAAC-TTTAAAATGAAGAAGCTCCTCATCTAGAATGAGGCTATGTAA
** * *
25573992 CTTTACAAAGGAATAAACTCTTCATCTGGAATGAGGTTACGTAACTTTAAAAAGGAATAAGCTCT
65 AATTACAAAGGAATAAACTCTTCATCTGGAATGAGGCTACGTAACTTTAAAAAGGAATAAGCTCC
* * *
25574057 TTATCTAGAATAAGGTTACGTAACT-T-TAA-AAAA-GAATAAGCTCCTA
130 TTATCTAGAATAAGGCTACGTAACTATGTAATAAAATAAATAAACTCCTA
* * * * * *
25574103 ATTTGAAATGAGGCTACGCAACTTTAAAAATGAAGAAGTTCTTCATCTGGAATGAGGCTATGTAA
1 ATCTAAAATGAGGCTACACAACTTT-AAAATGAAGAAGCTCCTCATCTAGAATGAGGCTATGTAA
* * *
25574168 AATTA-AAATGAATAAGCTACTT-ATTTGGAATGAGGCTACGTAACTTTAAAAAGGAATAAGCTC
65 AATTACAAAGGAATAAACT-CTTCATCTGGAATGAGGCTACGTAACTTTAAAAAGGAATAAGCTC
* *
25574231 CTTATCTAGAATGAGGCTACGTAACTATGTAACTTTAAAATAAATAAACTCCTC
129 CTTATCTAGAATAAGGCTACGTAACTATGTAA---TAAAATAAATAAACTCCTA
* * *
25574285 ATCTAAAATGAGGTTACATAACTTTAAAATGAATAAGCTCCTCATCTAGAATGAGGCTATGTAA
1 ATCTAAAATGAGGCTACACAACTTTAAAATGAAGAAGCTCCTCATCTAGAATGAGGCTATGTAA
25574349 CTTAAAAAAG
Statistics
Matches: 202, Mismatches: 34, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
174 3 0.01
175 93 0.46
176 34 0.17
177 3 0.01
181 39 0.19
182 30 0.15
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (179 bp):
ATCTAAAATGAGGCTACACAACTTTAAAATGAAGAAGCTCCTCATCTAGAATGAGGCTATGTAAA
ATTACAAAGGAATAAACTCTTCATCTGGAATGAGGCTACGTAACTTTAAAAAGGAATAAGCTCCT
TATCTAGAATAAGGCTACGTAACTATGTAATAAAATAAATAAACTCCTA
Found at i:25574289 original size:51 final size:49
Alignment explanation
Indices: 25574207--25574350 Score: 158
Period size: 43 Copynumber: 3.0 Consensus size: 49
25574197 ATGAGGCTAC
*
25574207 GTAACTTTAAAA-AGGAATAAGCTCCTTATCTAGAATGAGGCTACGTAACTA
1 GTAACTTTAAAATA--AATAAGCTCCTCATCTAGAATGAGGCTA-GTAACTA
* *
25574258 TGTAACTTTAAAATAAATAAACTCCTCATCTAAAATGAGG-T--T-AC-A
1 -GTAACTTTAAAATAAATAAGCTCCTCATCTAGAATGAGGCTAGTAACTA
*
25574303 -TAACTTTAAAATGAATAAGCTCCTCATCTAGAATGAGGCTATGTAACT
1 GTAACTTTAAAATAAATAAGCTCCTCATCTAGAATGAGGCTA-GTAACT
25574351 TAAAAAAGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
43 35 0.44
44 1 0.01
45 1 0.01
46 2 0.03
47 2 0.03
48 2 0.03
50 1 0.01
51 22 0.28
52 12 0.15
53 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (49 bp):
GTAACTTTAAAATAAATAAGCTCCTCATCTAGAATGAGGCTAGTAACTA
Found at i:25575190 original size:6 final size:6
Alignment explanation
Indices: 25575181--25575214 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
25575171 TGAAAATTAA
25575181 AAAACT AAAACT AAAACAT AAAACT AAAAC- AAAA
1 AAAACT AAAACT AAAAC-T AAAACT AAAACT AAAA
25575215 GTAACAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAACT
Found at i:25575202 original size:13 final size:13
Alignment explanation
Indices: 25575181--25575211 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25575171 TGAAAATTAA
25575181 AAAAC-TAAAACT
1 AAAACATAAAACT
25575193 AAAACATAAAACT
1 AAAACATAAAACT
25575206 AAAACA
1 AAAACA
25575212 AAAGTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAACATAAAACT
Found at i:25576270 original size:16 final size:16
Alignment explanation
Indices: 25576249--25576283 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
25576239 TGAACTGGGC
25576249 AAAGTGGTAAACATCA
1 AAAGTGGTAAACATCA
25576265 AAAGTGGTAAACATCA
1 AAAGTGGTAAACATCA
25576281 AAA
1 AAA
25576284 TTTGTAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAGTGGTAAACATCA
Found at i:25580481 original size:30 final size:30
Alignment explanation
Indices: 25580442--25580501 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
25580432 TAACAGCATC
25580442 TGTAAACACAAATTTTGTCCTATCGAAGGA
1 TGTAAACACAAATTTTGTCCTATCGAAGGA
*
25580472 TGTAGACACAAATTTTGTCCTATCGAAGGA
1 TGTAAACACAAATTTTGTCCTATCGAAGGA
25580502 ACCATTTGTA
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:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (30 bp):
TGTAAACACAAATTTTGTCCTATCGAAGGA
Found at i:25581469 original size:25 final size:26
Alignment explanation
Indices: 25581432--25581487 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
25581422 AAAAAAAGTA
* * *
25581432 AAAAAATTTAATT-AGTAAATTAAATT
1 AAAAAATTAAATTAAGGAAAGTAAA-T
25581458 AAAAAA-TAAATTAAGGAAAGTAAAT
1 AAAAAATTAAATTAAGGAAAGTAAAT
25581483 AAAAA
1 AAAAA
25581488 TGAATTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (26 bp):
AAAAAATTAAATTAAGGAAAGTAAAT
Found at i:25586518 original size:27 final size:27
Alignment explanation
Indices: 25586480--25586536 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
25586470 TAAGTAAGAT
25586480 ATATTGAATATCCATTATAACTACCAC
1 ATATTGAATATCCATTATAACTACCAC
*
25586507 ATATTGAATATCCATTATAACTAGCAC
1 ATATTGAATATCCATTATAACTACCAC
25586534 ATA
1 ATA
25586537 ATATTCAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATTGAATATCCATTATAACTACCAC
Found at i:25594390 original size:31 final size:30
Alignment explanation
Indices: 25594322--25594391 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
25594312 AAATATTTAT
*
25594322 AATATCTATAGTAGCTAAACAAGATATATG
1 AATATCCATAGTAGCTAAACAAGATATATG
* *
25594352 -ATATCCATAGTAGCTAAGCAAGGTATATTG
1 AATATCCATAGTAGCTAAACAAGATATA-TG
25594382 AATATCCATA
1 AATATCCATA
25594392 ATAACTAGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 24 0.69
30 2 0.06
31 9 0.26
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (30 bp):
AATATCCATAGTAGCTAAACAAGATATATG
Found at i:25607274 original size:32 final size:34
Alignment explanation
Indices: 25607215--25607281 Score: 111
Period size: 32 Copynumber: 2.0 Consensus size: 34
25607205 TATATAAAGT
*
25607215 TGTATGTAAACATATATGTATTAACTCATATACA
1 TGTATGTAAACATATATATATTAACTCATATACA
25607249 TGTATGTAAACA-A-ATATATTAACTCATATACA
1 TGTATGTAAACATATATATATTAACTCATATACA
25607281 T
1 T
25607282 AAAGTTGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 19 0.59
33 1 0.03
34 12 0.38
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.37
Consensus pattern (34 bp):
TGTATGTAAACATATATATATTAACTCATATACA
Found at i:25607343 original size:146 final size:144
Alignment explanation
Indices: 25607175--25607650 Score: 742
Period size: 151 Copynumber: 3.2 Consensus size: 144
25607165 TTGAATAATG
25607175 CATACA-TATATATTAACTTAATTATAAAGTTATATAAAGTTGTATGTAAACATATATGTATTAA
1 CATACATTATATATTAACTTAATTATAAAGTTATATAAAGTTGTATGTAAACATATATGTATTAA
* *
25607239 CTCATATACATGTATGTAAACAAATATATTAACTCATATACATAAAGTTGTATGCATAC-TGTAA
66 CTCATATACATGTATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATACATAT-A
*
25607303 GGTATGTAAGCATATA
130 TGTATGTAA-CATATA
* ** *
25607319 CATACATGTATATATTAACTTAATTATAAAGTTATAGAAAGTTGTATGTAAATGTATATGAATTA
1 CATACAT-TATATATTAACTTAATTATAAAGTTATATAAAGTTGTATGTAAACATATATGTATTA
*
25607384 ACTCATATACATATATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATACATATA
65 ACTCATATACATGTATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATACATATA
*
25607449 TGTATTTAACATATA
130 TGTATGTAACATATA
*
25607464 CATACATATATATATATATATTAACTTAGTTATAAAGTTATATAAAGTTGTATGTAAACATATAT
1 CATAC------AT-TATATATTAACTTAATTATAAAGTTATATAAAGTTGTATGTAAACATATAT
25607529 GTATTAACTCATATACATGTATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATA
59 GTATTAACTCATATACATGTATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATA
25607594 CATATATGTATGTAAACATATA
124 CATATATGTATGT-AACATATA
25607616 CATACA-TATATATTAACTTAATTATAAAGTTATAT
1 CATACATTATATATTAACTTAATTATAAAGTTATAT
25607651 CAATTAAAGA
Statistics
Matches: 304, Mismatches: 18, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
144 34 0.11
145 11 0.04
146 120 0.39
147 2 0.01
151 124 0.41
152 13 0.04
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (144 bp):
CATACATTATATATTAACTTAATTATAAAGTTATATAAAGTTGTATGTAAACATATATGTATTAA
CTCATATACATGTATGTAAACATATATATTAACTCATATACATAAAGTTGTATGCATACATATAT
GTATGTAACATATA
Found at i:25607550 original size:18 final size:18
Alignment explanation
Indices: 25607527--25607578 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
25607517 GTAAACATAT
25607527 ATGTATTAACTCATATAC
1 ATGTATTAACTCATATAC
*
25607545 ATGTATGTAA-ACATAT--
1 ATGTAT-TAACTCATATAC
25607561 A--TATTAACTCATATAC
1 ATGTATTAACTCATATAC
25607577 AT
1 AT
25607579 AAAGTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 11
0.68 0.05 0.28
Matches are distributed among these distances:
13 3 0.11
14 8 0.30
16 2 0.07
18 11 0.41
19 3 0.11
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (18 bp):
ATGTATTAACTCATATAC
Found at i:25607571 original size:32 final size:33
Alignment explanation
Indices: 25607512--25607578 Score: 118
Period size: 32 Copynumber: 2.0 Consensus size: 33
25607502 TATATAAAGT
25607512 TGTATGTAAACATATATGTATTAACTCATATACA
1 TGTATGTAAACATATA-GTATTAACTCATATACA
25607546 TGTATGTAAACATATA-TATTAACTCATATACA
1 TGTATGTAAACATATAGTATTAACTCATATACA
25607578 T
1 T
25607579 AAAGTTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.52
34 16 0.48
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (33 bp):
TGTATGTAAACATATAGTATTAACTCATATACA
Found at i:25608372 original size:13 final size:13
Alignment explanation
Indices: 25608351--25608385 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
25608341 GAAATCCGTT
25608351 GAAAATTTCCAAC
1 GAAAATTTCCAAC
*
25608364 GAAATTTTCCAAC
1 GAAAATTTCCAAC
25608377 GGAAAATTT
1 -GAAAATTT
25608386 TTCGTTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (13 bp):
GAAAATTTCCAAC
Found at i:25615373 original size:18 final size:17
Alignment explanation
Indices: 25615347--25615427 Score: 58
Period size: 18 Copynumber: 4.7 Consensus size: 17
25615337 AAATTATTAA
*
25615347 TTAAATTTATGTTATAAT
1 TTAATTTTAT-TTATAAT
*
25615365 TTAATTTTATTTCA-AAA
1 TTAATTTTATTT-ATAAT
* * *
25615382 GTAA-TTAATTTGTAAT
1 TTAATTTTATTTATAAT
**
25615398 AAAATTTTATATTATAAT
1 TTAATTTTAT-TTATAAT
25615416 TTAATTTTATTT
1 TTAATTTTATTT
25615428 CAAAAATGAT
Statistics
Matches: 47, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.21
17 13 0.28
18 24 0.51
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTAATTTTATTTATAAT
Found at i:25615407 original size:51 final size:50
Alignment explanation
Indices: 25615344--25615443 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 50
25615334 TTTAAATTAT
* * *
25615344 TAATTAAATTTATGTTATAATTTAATTTTATTTCAAAAGTAATTAATTTG
1 TAATAAAATTTATATTATAATTTAATTTTATTTCAAAAATAATTAATTTG
*
25615394 TAATAAAATTTTATATTATAATTTAATTTTATTTCAAAAATGATTAATTT
1 TAATAAAA-TTTATATTATAATTTAATTTTATTTCAAAAATAATTAATTT
25615444 TTTACTCTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 7 0.16
51 38 0.84
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (50 bp):
TAATAAAATTTATATTATAATTTAATTTTATTTCAAAAATAATTAATTTG
Done.