Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold232
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: 2516017
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.33
Warning! 28201 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:140999 original size:107 final size:107
Alignment explanation
Indices: 140874--141103 Score: 284
Period size: 107 Copynumber: 2.1 Consensus size: 107
140864 AATAAAACCG
* * * * * *
140874 GGGTTAGAGTATTCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTAT-GAGAAATTAATATT
1 GGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATGGAG-AATTAATATT
* * * *
140938 TTAGAAATAAAGCCGGGGTTGGGGTATTCCCT-TGAAAATAACA
65 TTAGAAATAAAACCGGGGTTGGAGTATCCCCTCAG-AAATAACA
** *
140981 GGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATGGAGAATTGGTGTTT
1 GGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATGGAGAATTAATATTT
**
141046 TAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAATG
66 TAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACA
*
141088 GGGTTGGAGTATCCCC
1 GGGTTAGAGTATCCCC
141104 GATTATGAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
107 101 0.96
108 4 0.04
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (107 bp):
GGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATGGAGAATTAATATTT
TAGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACA
Found at i:141049 original size:186 final size:186
Alignment explanation
Indices: 140805--141182 Score: 535
Period size: 186 Copynumber: 2.0 Consensus size: 186
140795 GGATTGATGC
* * * *
140805 ATCCCCTAGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAA
1 ATCCCCTAGAAAATAACGAGATTAGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAA
* * *
140870 ACCGGGGTTAGAGTATTCCCTCGGAAATAATGGGGTTGGAGTATCCCCGATTATGAGAAATTAAT
66 ACCGGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT
* * * * *
140935 ATTTTAGAAATAAAGCCGGGGTTGGGGTATTCCCTTGAAAATAACAGGG-TTAGAGT
131 ATTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAAC-GGGATTAGAGT
* ** *
140991 ATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATG-GAGAATTGGTGTTTTAGAAATAA
1 ATCCCCTAGAAAATAACGAGATTAGAGTATCCCCGATTATGAGA-AATTAATATTTTAGAAATAA
* *
141055 AACCGGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGA
65 AACCGGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAA
* * *
141120 TGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGT
130 TATTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGT
141177 ATCCCC
1 ATCCCC
141183 GATGAAAAAT
Statistics
Matches: 169, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
185 5 0.03
186 164 0.97
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (186 bp):
ATCCCCTAGAAAATAACGAGATTAGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAA
ACCGGGGTTAGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT
ATTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGATTAGAGT
Found at i:141070 original size:79 final size:79
Alignment explanation
Indices: 140981--141230 Score: 373
Period size: 79 Copynumber: 3.2 Consensus size: 79
140971 GAAAATAACA
* * * * * *
140981 GGGTTAGAGTATCCCCTCGAAAATAACGAGATTAGAGTATCCCCGATTATGGAGAATTGGTGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTT
*
141046 TAGAAATAAAACCG
66 TAGAAATAAAATCG
* *
141060 GGGTTGGAGTATCCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
1 GGGTTGGAGTATCCCCTCGA-AAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTT
*
141124 TTAAAAATAAAATCG
65 TTAGAAATAAAATCG
141139 GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCG---ATGAAAAATTGATGTTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTT
141201 TAGAAATAAAATCG
66 TAGAAATAAAATCG
141215 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
141231 GATTGTGAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
76 46 0.29
78 1 0.01
79 108 0.69
80 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTT
TAGAAATAAAATCG
Found at i:141262 original size:51 final size:51
Alignment explanation
Indices: 141165--141334 Score: 161
Period size: 51 Copynumber: 3.4 Consensus size: 51
141155 TCGAAAATAA
* * *
141165 CGGGATTGGAGTATCCCCGA-T--GAAAAATTGATGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAAATGATGTTTTGGAAATAAAAT
** *
141213 CGGGGTTGGAGTATCCCCGATTGTGAAAAGACA-G-TGTTTTGGAAGTAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGAAAA-A-ATGATGTTTTGGAAATAAAAT
* * * * * *
141264 CAGAGTTGGAGTACCCCCAATTAAGAAAAAATGATGTTTCGGAAATGAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAAATGATGTTTTGGAAATAAAAT
* *
141315 CGGGATTGGAGTATTCCCGA
1 CGGGGTTGGAGTATCCCCGA
141335 GATGAAAAAT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
48 19 0.20
49 2 0.02
50 2 0.02
51 71 0.74
52 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTAAGAAAAAATGATGTTTTGGAAATAAAAT
Found at i:143738 original size:13 final size:13
Alignment explanation
Indices: 143720--143771 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
143710 AGCTTCGTAG
143720 CGATACATTGTAT
1 CGATACATTGTAT
143733 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
143752 CGATACATTGTAT
1 CGATACATTGTAT
143765 CGATACA
1 CGATACA
143772 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:143752 original size:19 final size:18
Alignment explanation
Indices: 143728--143788 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
143718 AGCGATACAT
143728 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
143747 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
143760 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
143779 TGTATCGATA
1 TGTATCGATA
143789 TATTTACGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:143761 original size:32 final size:32
Alignment explanation
Indices: 143720--143788 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
143710 AGCTTCGTAG
143720 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
143752 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
143784 CGATA
1 CGATA
143789 TATTTACGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:145089 original size:20 final size:21
Alignment explanation
Indices: 145064--145116 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
145054 ATTTTAGGCT
145064 TGTATCGATATATTCACT-TA
1 TGTATCGATATATTCACTATA
* * *
145084 TGTATCGATACATTTACTATT
1 TGTATCGATATATTCACTATA
*
145105 TGTATAGATATA
1 TGTATCGATATA
145117 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (21 bp):
TGTATCGATATATTCACTATA
Found at i:146011 original size:61 final size:61
Alignment explanation
Indices: 145620--146307 Score: 600
Period size: 61 Copynumber: 11.0 Consensus size: 61
145610 TAAAGTAGAT
* * * * *
145620 AGGTGCCACCAACTTGTGTGGGATTTGAGATAGAAAAGGAGTCTTGCTTTTTGAGGACCAAAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGA-AAAGAAAAGGCGTCTTGCTCTTTGAGGA-C-TAAA
* * * * *
145684 TAAGTGCCACCAACTTTTGTGGGCTTTTGAAAAAAAAAAAGAGACGCCCTGCTCTTTGAGGACTA
1 -AGGTGCCACCAACTTGTGTGGGC-TTTG--AAAAGAAAAG-G-CGTCTTGCTCTTTGAGGACTA
*
145749 GA
60 AA
* * *
145751 AGGTGTCACCAGA-TTGTGTGGGCTTT-AAAAGAAAAAAGAAGTGTCTTGCTCTTTGAAGACTAA
1 AGGTGCCACCA-ACTTGTGTGGGCTTTGAAAAG--AAAAG--GCGTCTTGCTCTTTGAGGACTAA
145814 A
61 A
* * * * *
145815 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGG-GTCCTGTTCTTTAAAGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCTTGCTCTTTGAGGACTAAA
* ** * * * *
145875 AGGTGCCACTAGGTTGTGTGGGCTTTGAAAAAAGGAAAAGACGTCATGCTTTTTGAGAACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTG--AAAA-GAAAAGGCGTCTTGCTCTTTGAGGACTAAA
* ** * * *
145939 ATGTGCCACCAACTTGTGTGAACTTTGAAAAGAAAATGCGTCTTGTTCTTTGAGGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCTTGCTCTTTGAGGACTAAA
* * * *
146000 AGCTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGT-TCTGCTTTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCT-TGCTCTTTGAGGACTAAA
** * *
146061 AGGTGCCACTGACTTGTGTGGCCTTT-AAAAGAAAAAGGCGT-TATACTCTTTGAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGGCGTCT-TGCTCTTTGAGGACTAAA
* * * * * * *
146122 AGGTGCCACCGACTTGTGTAGGCTTT-AAAAGGAAAAGGTGTCTTACTCTTTAAAGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAGGCGTCTTGCTCTTTGAGGACTAAA
* * * * *
146183 AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAAAG-ATCTTGCACTTTGAGGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGGCGTCTTGCTCTTTGAGGACTAAA
* * * * * *
146244 AGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAATGCGTCCTACTCTTTAAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCTTGCTCTTTGAGGACTAAA
146305 AGG
1 AGG
146308 ATAAAAGATT
Statistics
Matches: 509, Mismatches: 92, Indels: 48
0.78 0.14 0.07
Matches are distributed among these distances:
60 53 0.10
61 262 0.51
62 22 0.04
63 11 0.02
64 83 0.16
65 29 0.06
66 22 0.04
67 10 0.02
68 3 0.01
69 14 0.03
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (61 bp):
AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGGCGTCTTGCTCTTTGAGGACTAAA
Found at i:158295 original size:34 final size:34
Alignment explanation
Indices: 158252--158320 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
158242 AAATTTCCCA
158252 AATGTATCGATACAAAGATCAAATGTATCAATAC
1 AATGTATCGATACAAAGATCAAATGTATCAATAC
*
158286 AATGTATCGATACAAAGATCAAATGTATCGATAC
1 AATGTATCGATACAAAGATCAAATGTATCAATAC
158320 A
1 A
158321 TTGAGTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (34 bp):
AATGTATCGATACAAAGATCAAATGTATCAATAC
Found at i:158405 original size:32 final size:32
Alignment explanation
Indices: 158364--158434 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
158354 AGCTTCGTAG
158364 CGATACATTGTATCGATACAAAACTTATATAT
1 CGATACATTGTATCGATACAAAACTTATATAT
* *
158396 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATATAT
158428 CGATACA
1 CGATACA
158435 AATTATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATATAT
Found at i:158428 original size:19 final size:19
Alignment explanation
Indices: 158372--158435 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
158362 AGCGATACAT
*
158372 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
158391 TATATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
158404 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
158423 TGTATCGATACAA
1 TGTATCGATACAA
158436 ATTATTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.58
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:161145 original size:79 final size:78
Alignment explanation
Indices: 161035--161457 Score: 350
Period size: 79 Copynumber: 5.2 Consensus size: 78
161025 TGAAAAACTT
* *
161035 AATATTTTGGAGATAAAAACGAGG-TTGGAGTATCCTATCAAAAAAAACGGGGTTAGAGTATCCC
1 AATATTTTGGAAATAAAAACG-GGATTGGAGTATCCT-TCAAAAATAACGGGGTTAGAGTATCCC
* * *
161099 CAATGGTGAAAAATT
64 CGATGGTAAAAAATC
* * * ** *
161114 GATATTTTGGAAATAAAAACGGGATTTGAGTATCCCCTT-AGAAATAACGAAGTTAGAGTATCCT
1 AATATTTTGGAAATAAAAACGGGATTGGAGTAT--CCTTCAAAAATAACGGGGTTAGAGTATCCC
*
161178 CGATAGTAAAAAATC
64 CGATGGTAAAAAATC
* * * * *
161193 AATATTTTTGAAATAAAATC-GGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTAAAGTATCCC
1 AATATTTTGGAAATAAAAACGGGA-TTGGAGTAT-CCTTCAAAAATAACGGGGTTAGAGTATCCC
*
161257 CGATGGTGAAAAATC
64 CGATGGTAAAAAATC
* * * * * *
161272 ACTATTTTGGAAAAAAAAAGTCAAGG-TTGGAGTATCCCTTCAAAAATAATGGGATTGGAGTATC
1 AATATTTTGGAAATAAAAA--C-GGGATTGGAGTAT-CCTTCAAAAATAACGGGGTTAGAGTATC
*
161336 TCCGATGGTAAAAAAATC
62 CCCGATGGT-AAAAAATC
** * * * *
161354 AATATTTTAAAAATGAAAAAAATGTAGATTGGAGTATCTCTTTAAAAATAACGGGGTTGGAGTAT
1 AATATTTTGGAAAT---AAAAACG-GGATTGGAGTATC-CTTCAAAAATAACGGGGTTAGAGTAT
*
161419 CCCCAATGGTAAAAAAATC
61 CCCCGATGGT-AAAAAATC
* *
161438 GATATTTTGGTAATGAAAAA
1 AATATTTTGGAAAT-AAAAA
161458 AATCAATGAA
Statistics
Matches: 276, Mismatches: 52, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
78 9 0.03
79 132 0.48
80 1 0.00
81 44 0.16
82 22 0.08
83 4 0.01
84 59 0.21
85 5 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (78 bp):
AATATTTTGGAAATAAAAACGGGATTGGAGTATCCTTCAAAAATAACGGGGTTAGAGTATCCCCG
ATGGTAAAAAATC
Found at i:161209 original size:158 final size:159
Alignment explanation
Indices: 161035--161457 Score: 412
Period size: 158 Copynumber: 2.6 Consensus size: 159
161025 TGAAAAACTT
* * *
161035 AATATTTTGGAGATAAAAACGAGGTTGGAGTATCCTATCAAAAAAAACGGGGTTAGAGTATCCCC
1 AATATTTTAGAAATAAAAACGAGGTTGGAGTATCCT-TCAAAAATAACGGGGTTAGAGTATCCCC
* * *
161100 AATGGTGAAAAATTGATATTTTGGAAATAAAAA-C-GGGATTTGAGTATCCCCTT-AGAAATAAC
65 AATGGTGAAAAATTGATATTTTGGAAATAAAAAGCAAGG-TTGGAGTAT-CCCTTCAAAAATAAC
161162 GA-AGTTAGAGTATC-CTCGATAGT-AAAAAATC
128 GAGA-TTAGAGTATCTC-CGATAGTAAAAAAATC
* * * * *
161193 AATATTTTTGAAATAAAATCG-GAGTTGGAGTATCCCCTCAGAAATAACGGGGTTAAAGTATCCC
1 AATATTTTAGAAATAAAAACGAG-GTTGGAGTAT-CCTTCAAAAATAACGGGGTTAGAGTATCCC
* * *
161257 CGATGGTGAAAAA-TCACTATTTTGGAAAAAAAAAGTCAAGGTTGGAGTATCCCTTCAAAAATAA
64 CAATGGTGAAAAATTGA-TATTTTGGAAATAAAAAG-CAAGGTTGGAGTATCCCTTCAAAAATAA
* * * *
161321 TGGGATTGGAGTATCTCCGATGGTAAAAAAATC
127 CGAGATTAGAGTATCTCCGATAGTAAAAAAATC
* * * * *
161354 AATATTTTAAAAATGAAAAAAATGTAGATTGGAGTATCTCTTTAAAAATAACGGGGTTGGAGTAT
1 AATATTTTAGAAAT---AAAAACG-AGGTTGGAGTATC-CTTCAAAAATAACGGGGTTAGAGTAT
* * *
161419 CCCCAATGGTAAAAAAATCGATATTTTGGTAATGAAAAA
61 CCCCAATGGT-GAAAAATTGATATTTTGGAAAT-AAAAA
161458 AATCAATGAA
Statistics
Matches: 213, Mismatches: 33, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
157 3 0.01
158 80 0.38
159 7 0.03
160 32 0.15
161 24 0.11
164 6 0.03
165 39 0.18
166 16 0.08
167 6 0.03
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (159 bp):
AATATTTTAGAAATAAAAACGAGGTTGGAGTATCCTTCAAAAATAACGGGGTTAGAGTATCCCCA
ATGGTGAAAAATTGATATTTTGGAAATAAAAAGCAAGGTTGGAGTATCCCTTCAAAAATAACGAG
ATTAGAGTATCTCCGATAGTAAAAAAATC
Found at i:163905 original size:22 final size:20
Alignment explanation
Indices: 163856--163911 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
163846 AAAATCCCAG
*
163856 AATGTATTGATACAATGAGA
1 AATGTATCGATACAATGAGA
163876 AATGTATCGATACAATTGA-A
1 AATGTATCGATACAA-TGAGA
163896 AGCATGTATCGATACA
1 A--ATGTATCGATACA
163912 TTTATTTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
21 3 0.09
22 13 0.41
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:164473 original size:150 final size:150
Alignment explanation
Indices: 164202--164503 Score: 568
Period size: 150 Copynumber: 2.0 Consensus size: 150
164192 AAATGCTCTA
* * *
164202 ATAATCTAAAAGTACTTTTTCATTAAGTGTCAACGATCGTTGTCCCCATACCTTTCAACCTCTCC
1 ATAATCTAAAAGTACTTTTTCATCAAGCGTCAACGATCATTGTCCCCATACCTTTCAACCTCTCC
164267 ACCTAAACATGTTTTAAGTTGCTAGAAAATTGACCCGAACAAAATGAGGTGTCTACAATAATCAT
66 ACCTAAACATGTTTTAAGTTGCTAGAAAATTGACCCGAACAAAATGAGGTGTCTACAATAATCAT
164332 GATTAATATCATCTCTACTC
131 GATTAATATCATCTCTACTC
*
164352 ATAATCTAAAAGTACTTTTTCATCAAGCGTCAACGATCATTGTCCCCATACCTTTCGACCTCTCC
1 ATAATCTAAAAGTACTTTTTCATCAAGCGTCAACGATCATTGTCCCCATACCTTTCAACCTCTCC
164417 ACCTAAACATGTTTTAAGTTGCTAGAAAATTGACCCGAACAAAATGAGGTGTCTACAATAATCAT
66 ACCTAAACATGTTTTAAGTTGCTAGAAAATTGACCCGAACAAAATGAGGTGTCTACAATAATCAT
164482 GATTAATATCATCTCTACTC
131 GATTAATATCATCTCTACTC
164502 AT
1 AT
164504 CACATGCTTA
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (150 bp):
ATAATCTAAAAGTACTTTTTCATCAAGCGTCAACGATCATTGTCCCCATACCTTTCAACCTCTCC
ACCTAAACATGTTTTAAGTTGCTAGAAAATTGACCCGAACAAAATGAGGTGTCTACAATAATCAT
GATTAATATCATCTCTACTC
Found at i:165588 original size:147 final size:147
Alignment explanation
Indices: 165406--165699 Score: 570
Period size: 147 Copynumber: 2.0 Consensus size: 147
165396 AAATTGATTG
*
165406 ATTATGAGTGATATGCATATGAACTAAAAATTAAAAAATAGGTATCAATTATGCATATAGACAAC
1 ATTATGAGTGATATGCATATGAACTAAAAATTAAAAAATAGGCATCAATTATGCATATAGACAAC
165471 AATTAAAATTTATTTAATAATAATTGGAATGTCTTCTTTACTTATGATCTTGATTGTGCTTAAAA
66 AATTAAAATTTATTTAATAATAATTGGAATGTCTTCTTTACTTATGATCTTGATTGTGCTTAAAA
165536 GTCTATAAATGAATACA
131 GTCTATAAATGAATACA
165553 ATTATGAGTGATATGCATATGAACTAAAAATTAAAAAATAGGCATCAATTATGCATATAGACAAC
1 ATTATGAGTGATATGCATATGAACTAAAAATTAAAAAATAGGCATCAATTATGCATATAGACAAC
*
165618 AATTAAAATTTATTTAATAATAATTGGAATGTGTTCTTTACTTATGATCTTGATTGTGCTTAAAA
66 AATTAAAATTTATTTAATAATAATTGGAATGTCTTCTTTACTTATGATCTTGATTGTGCTTAAAA
165683 GTCTATAAATGAATACA
131 GTCTATAAATGAATACA
165700 TGAAATTTAA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (147 bp):
ATTATGAGTGATATGCATATGAACTAAAAATTAAAAAATAGGCATCAATTATGCATATAGACAAC
AATTAAAATTTATTTAATAATAATTGGAATGTCTTCTTTACTTATGATCTTGATTGTGCTTAAAA
GTCTATAAATGAATACA
Found at i:171460 original size:21 final size:21
Alignment explanation
Indices: 171436--171475 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
171426 TTGCGTTGCA
*
171436 TCCTTTGCTTTCCCAGTCATT
1 TCCTTTGCCTTCCCAGTCATT
*
171457 TCCTTTGCCTTCTCAGTCA
1 TCCTTTGCCTTCCCAGTCA
171476 CCTATCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.35, G:0.10, T:0.45
Consensus pattern (21 bp):
TCCTTTGCCTTCCCAGTCATT
Found at i:173135 original size:32 final size:31
Alignment explanation
Indices: 173054--173120 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
173044 ATCATAATTT
* ** * *
173054 TAAAAAATATTCAAAATATATAAAATTAAAA
1 TAAAAAATATTTAATGTTTATAAAACTAAAA
173085 TAAAAAATATTTGAATGTTTATAAAACTAAAA
1 TAAAAAATATTT-AATGTTTATAAAACTAAAA
173117 TAAA
1 TAAA
173121 TTAATAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
TAAAAAATATTTAATGTTTATAAAACTAAAA
Found at i:175292 original size:75 final size:74
Alignment explanation
Indices: 175170--175310 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 74
175160 AAGTCTTGAG
* * ** *
175170 TTTTTACTTATTAGAATAGGACTTAAATTATGATTATAAATATATTTTTAATTTTATTGTATTTA
1 TTTTTACTTATTAAAATAGAACTTAAATTACAATTATAAATATATTTTCAATTTTATTGTATTTA
175235 TTTATAATA
66 TTTATAATA
* * *
175244 TTTTTACTTATTAAAATAGAAGTTTAAATTACAATTATAAATATATTTTCGATTTTATTGTGTTT
1 TTTTTACTTATTAAAATAGAA-CTTAAATTACAATTATAAATATATTTTCAATTTTATTGTATTT
175309 AT
65 AT
175311 CGTGATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 19 0.33
75 39 0.67
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (74 bp):
TTTTTACTTATTAAAATAGAACTTAAATTACAATTATAAATATATTTTCAATTTTATTGTATTTA
TTTATAATA
Found at i:176841 original size:18 final size:18
Alignment explanation
Indices: 176800--176838 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
176790 ATATTACAAC
*
176800 AAAGATAAAAAAAAAAGT
1 AAAGATAAAAAAAAAACT
176818 AAAGATAAAGAAAAAAACT
1 AAAGATAAA-AAAAAAACT
176837 AA
1 AA
176839 GATTGACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAGATAAAAAAAAAACT
Found at i:181331 original size:58 final size:58
Alignment explanation
Indices: 181220--181331 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 58
181210 CATCAAATTA
* * * * *
181220 CATAATAGTCCCTAATTCATGAAAAATGACTAAAATGACCTAAGAATGTATGAAGTTG
1 CATAATAATCCCTAATGCACGAAAAATGACTAAAATGACATAAGAATGCATGAAGTTG
*
181278 CATAATAATCCCTTAATGCACGAAAAATGAACT-AAATGACATAA-TATGCATGAA
1 CATAATAATCCC-TAATGCACGAAAAATG-ACTAAAATGACATAAGAATGCATGAA
181332 ATTAGACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 19 0.41
59 24 0.52
60 3 0.07
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (58 bp):
CATAATAATCCCTAATGCACGAAAAATGACTAAAATGACATAAGAATGCATGAAGTTG
Found at i:186597 original size:1 final size:1
Alignment explanation
Indices: 186591--186633 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
186581 AAAGTGTTTG
***
186591 AAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
186634 TTAAATGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:186663 original size:21 final size:21
Alignment explanation
Indices: 186637--186693 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
186627 AAAAAAATTA
* *
186637 AATGTATCGATACATTTTTTG
1 AATGTATCGATACATTTGTGG
186658 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
186679 AATGTATCGATACAT
1 AATGTATCGATACAT
186694 CCTACAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Found at i:186773 original size:19 final size:19
Alignment explanation
Indices: 186749--186816 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
186739 AATTCAACAA
186749 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
186768 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
186783 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
186800 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
186817 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:186788 original size:13 final size:13
Alignment explanation
Indices: 186770--186794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186760 ACATAAGTTT
186770 TGTATCGATACAA
1 TGTATCGATACAA
186783 TGTATCGATACA
1 TGTATCGATACA
186795 TAAGTATTGT
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:186792 original size:32 final size:32
Alignment explanation
Indices: 186751--186813 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
186741 TTCAACAATT
*
186751 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
186783 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
186814 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:186874 original size:13 final size:13
Alignment explanation
Indices: 186856--186881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186846 CATTTTTCTG
186856 TGTATCGATACAT
1 TGTATCGATACAT
186869 TGTATCGATACAT
1 TGTATCGATACAT
186882 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:186878 original size:33 final size:33
Alignment explanation
Indices: 186836--186902 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
186826 GCCAAGGAAA
***
186836 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
186869 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
186902 T
1 T
186903 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:189417 original size:28 final size:27
Alignment explanation
Indices: 189350--189422 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
189340 CTTCACAATC
* *
189350 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
189377 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
189405 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
189423 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:189467 original size:51 final size:51
Alignment explanation
Indices: 189405--189575 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
189395 TTATTTCTGA
* * *
189405 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
189456 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
189509 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
189561 GAGGATACTCCAACC
1 GGGGATACTCCAACC
189576 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:189594 original size:28 final size:28
Alignment explanation
Indices: 189558--189639 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
189548 ATTTTTCACA
*
189558 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
189586 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
189614 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
189640 ATCTCTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:193414 original size:21 final size:22
Alignment explanation
Indices: 193388--193432 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
193378 GTGCATTGCT
193388 TGCTAATCTATGTC-ATGAATA
1 TGCTAATCTATGTCTATGAATA
193409 TGCTAATCTATGTCTATGAATA
1 TGCTAATCTATGTCTATGAATA
193431 TG
1 TG
193433 AATGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (22 bp):
TGCTAATCTATGTCTATGAATA
Found at i:195090 original size:61 final size:61
Alignment explanation
Indices: 195025--195148 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 61
195015 AAGAAAATAT
*
195025 TATCATCAAA-TATTTTCACAAT-CTCTTTTAAAAAGGATA-TTTTATTAGA-ATTCTCAAAGCC
1 TATCATCAAAGTATCTTCA-AATCCTCTTTT---AAGGATATTTTTATTAGAGATTCTCAAAGCC
* *
195086 TATCATTAAAGGTATCTTCAAATCCTCTTTTAAGGATATTTTTATTAGAGATTTTCAAAGCC
1 TATCATCAAA-GTATCTTCAAATCCTCTTTTAAGGATATTTTTATTAGAGATTCTCAAAGCC
195148 T
1 T
195149 TTTTCAAGGA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
60 7 0.13
61 19 0.35
62 15 0.27
63 14 0.25
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (61 bp):
TATCATCAAAGTATCTTCAAATCCTCTTTTAAGGATATTTTTATTAGAGATTCTCAAAGCC
Found at i:195182 original size:38 final size:37
Alignment explanation
Indices: 195102--195200 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 37
195092 TAAAGGTATC
* * * * *
195102 TTCAAATCCTCTTTTAAGGATATTTTTATTAGAGATT
1 TTCAAAGCCTCTTTTAAGGATATTCTAATAAGACATT
195139 TTCAAAGCCT-TTTTCAAGGATATTCTAATAAAGACATT
1 TTCAAAGCCTCTTTT-AAGGATATTCTAAT-AAGACATT
*
195177 TTCAAAGCTTCTCTTT-AGGATATT
1 TTCAAAGCCTCT-TTTAAGGATATT
195201 TCATCAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
36 4 0.08
37 21 0.40
38 23 0.44
39 1 0.02
40 3 0.06
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
TTCAAAGCCTCTTTTAAGGATATTCTAATAAGACATT
Found at i:195441 original size:36 final size:36
Alignment explanation
Indices: 195401--195580 Score: 143
Period size: 36 Copynumber: 5.0 Consensus size: 36
195391 ACATTTTCAA
*
195401 AGCCTCTTTTAAGGATATTTCATTATAGATTTTTAG
1 AGCCTCTTTTAAGGATATTTCATTAGAGATTTTTAG
* * *
195437 AGCCT-TTCTTAAGGATATTTCATTAAATATTTTCAG
1 AGCCTCTT-TTAAGGATATTTCATTAGAGATTTTTAG
* * *
195473 AGCTTCTTTTAAGGATATTTCGA-TA-AGGTTTTTCAA
1 AGCCTCTTTTAAGGATATTTC-ATTAGAGATTTTT-AG
* ** * *
195509 AGTCTCCCTTAAAGATGTTTCA-TAGAGATTTTTAG
1 AGCCTCTTTTAAGGATATTTCATTAGAGATTTTTAG
* * * * * *
195544 AGCATCTCTTGAGGAGATTTCATAAGATATTTTTAG
1 AGCCTCTTTTAAGGATATTTCATTAGAGATTTTTAG
195580 A
1 A
195581 CTTTCTCTCG
Statistics
Matches: 113, Mismatches: 25, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
35 26 0.23
36 84 0.74
37 3 0.03
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (36 bp):
AGCCTCTTTTAAGGATATTTCATTAGAGATTTTTAG
Found at i:195520 original size:72 final size:72
Alignment explanation
Indices: 195393--195531 Score: 165
Period size: 72 Copynumber: 1.9 Consensus size: 72
195383 TGATAAATAC
* ** *
195393 ATTTTCAAAGCCTCTTTTAAGGATATTTCATTATAGATTTTTAGAGCCTTTCTTAAGGATATTTC
1 ATTTTCAAAGCCTCTTTTAAGGATATTTCATTATAGATTTTTAAAGCCTCCCTTAAAGATATTTC
195458 ATTAAAT
66 ATTAAAT
* * * * *
195465 ATTTTCAGAGCTTCTTTTAAGGATATTTCGA-TA-AGGTTTTTCAAAGTCTCCCTTAAAGATGTT
1 ATTTTCAAAGCCTCTTTTAAGGATATTTC-ATTATAGATTTTT-AAAGCCTCCCTTAAAGATATT
195528 TCAT
64 TCAT
195532 AGAGATTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
71 7 0.12
72 48 0.86
73 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (72 bp):
ATTTTCAAAGCCTCTTTTAAGGATATTTCATTATAGATTTTTAAAGCCTCCCTTAAAGATATTTC
ATTAAAT
Found at i:195588 original size:36 final size:35
Alignment explanation
Indices: 195526--195600 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
195516 CTTAAAGATG
*
195526 TTTCATAGAGATTTTTAGAGCATCTCTTGAGGAGA
1 TTTCATAGAGATTTTTAGAGCATCTCTCGAGGAGA
* * *
195561 TTTCATAAGATATTTTTAGA-CTTTCTCTCGAGGATA
1 TTTCAT-AGAGATTTTTAGAGC-ATCTCTCGAGGAGA
195597 TTTC
1 TTTC
195601 CTTGGATGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (35 bp):
TTTCATAGAGATTTTTAGAGCATCTCTCGAGGAGA
Found at i:195595 original size:107 final size:108
Alignment explanation
Indices: 195394--195600 Score: 249
Period size: 107 Copynumber: 1.9 Consensus size: 108
195384 GATAAATACA
** * * * * *
195394 TTTTCAAAGCCTCTTTTAAGGATATTTCATTATAGATTTTTAGAGCCTTTCTTAAGGATATTTCA
1 TTTTCAAAGCCTCCCTTAAAGATATTTCATTAGAGATTTTTAGAGCATCTCTTAAGGAGATTTCA
* *
195459 TTAAATATTTTCAGAGCTTCTTTTAAGGATATTTCGATAAGGT
66 TTAAATATTTTCAGAGCTTCTCTCAAGGATATTTCGATAAGGT
* * *
195502 TTTTCAAAGTCTCCCTTAAAGATGTTTCA-TAGAGATTTTTAGAGCATCTCTTGAGGAGATTTCA
1 TTTTCAAAGCCTCCCTTAAAGATATTTCATTAGAGATTTTTAGAGCATCTCTTAAGGAGATTTCA
* *
195566 -TAAGATATTTTTAGA-CTTTCTCTCGAGGATATTTC
66 TTAA-ATATTTTCAGAGC-TTCTCTCAAGGATATTTC
195601 CTTGGATGTG
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
106 4 0.05
107 55 0.66
108 24 0.29
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (108 bp):
TTTTCAAAGCCTCCCTTAAAGATATTTCATTAGAGATTTTTAGAGCATCTCTTAAGGAGATTTCA
TTAAATATTTTCAGAGCTTCTCTCAAGGATATTTCGATAAGGT
Found at i:196018 original size:27 final size:27
Alignment explanation
Indices: 195977--196065 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
195967 AACCTCTTAG
195977 AATTTT-AATTGAACTTTCACACATAA
1 AATTTTCAATTGAACTTTCACACATAA
* * *
196003 AATTTTCAATTAAACTTTTTAAACAT-A
1 AATTTTCAATTGAAC-TTTCACACATAA
* **
196030 TATTTTTTATTGAACTTTCACACATGAA
1 AATTTTCAATTGAACTTTCACACAT-AA
*
196058 GATTTTCA
1 AATTTTCA
196066 TTAGACATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
26 14 0.30
27 19 0.40
28 14 0.30
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTTTCAATTGAACTTTCACACATAA
Found at i:196077 original size:54 final size:54
Alignment explanation
Indices: 195974--196094 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
195964 GCGAACCTCT
* *
195974 TAGAATTTTAATTGAACTTTCACACATAAAATTTTCAATTAAACTTTTTAAACA
1 TAGAATTTTTATTGAACTTTCACACATAAAATTTTCAATTAAACATTTTAAACA
* * * * *
196028 TATATTTTTTATTGAACTTTCACACATGAAGATTTTC-ATTAGACATTTTAAATA
1 TAGAATTTTTATTGAACTTTCACACAT-AAAATTTTCAATTAAACATTTTAAACA
196082 TAGAATTTTTATT
1 TAGAATTTTTATT
196095 TAAATTTTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 49 0.86
55 8 0.14
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (54 bp):
TAGAATTTTTATTGAACTTTCACACATAAAATTTTCAATTAAACATTTTAAACA
Found at i:196137 original size:54 final size:56
Alignment explanation
Indices: 196074--196205 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 56
196064 CATTAGACAT
* * * * *
196074 TTTAAATATAGAATTTTTATTTA-AATTTTTGCA-ATTGAAATTTTAATCTAA-CCC
1 TTTATATATAGAATTTTTAATTAGAATCTTGGCACA-TAAAATTTTAATCTAATCCC
** *
196128 TTTATATATAGGTTTTTTAATTAGAATCTTGGCACATAAAATTTTAATTTAATCCC
1 TTTATATATAGAATTTTTAATTAGAATCTTGGCACATAAAATTTTAATCTAATCCC
*
196184 TTCATATA-A-AATTTTTAATTAG
1 TTTATATATAGAATTTTTAATTAG
196206 GATTCCTACA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
54 30 0.47
55 23 0.36
56 11 0.17
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (56 bp):
TTTATATATAGAATTTTTAATTAGAATCTTGGCACATAAAATTTTAATCTAATCCC
Found at i:196923 original size:20 final size:21
Alignment explanation
Indices: 196900--196942 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
196890 GTTAAATTAA
196900 TTTAATT-TAAAATAATATTT
1 TTTAATTATAAAATAATATTT
* *
196920 TTTAATTATAATATTATATTT
1 TTTAATTATAAAATAATATTT
196941 TT
1 TT
196943 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTATAAAATAATATTT
Found at i:196941 original size:19 final size:20
Alignment explanation
Indices: 196900--196949 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
196890 GTTAAATTAA
*
196900 TTTAATTTAAAATAATATTT
1 TTTAATTTAAAATAATATAT
* *
196920 TTTAA-TTATAATATTATAT
1 TTTAATTTAAAATAATATAT
*
196939 TTTTATTTAAA
1 TTTAATTTAAA
196950 TTTAATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTTAAAATAATATAT
Found at i:196976 original size:22 final size:19
Alignment explanation
Indices: 196946--196987 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
196936 TATTTTTATT
196946 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
196967 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
196987 T
1 T
196988 TTTATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:197922 original size:104 final size:104
Alignment explanation
Indices: 197742--197950 Score: 330
Period size: 104 Copynumber: 2.0 Consensus size: 104
197732 CTTAAACTAT
* * * * *
197742 TTACGACCAAGAAAGTGAAAGAGTAGCAGTCTGTCCTGTTGTCTTGTCTTGGGGTTTATTAATGG
1 TTACGACCAACAAAGTGAAAGAGTAACAGTATGTCCTGATGTCTTGTCTTGAGGTTTATTAATGG
197807 CGTGCAAAAGTGAAATAAACAAGGCCACGAGGCTTTTGG
66 CGTGCAAAAGTGAAATAAACAAGGCCACGAGGCTTTTGG
* *
197846 TTACGACCAACAAAGTGTAAG-GATAACAGTATGTTCTGATGTCTTGTCTTGAGGTTTATTAATG
1 TTACGACCAACAAAGTGAAAGAG-TAACAGTATGTCCTGATGTCTTGTCTTGAGGTTTATTAATG
*
197910 GTGTGCAAAAGTGAAATAAACAAGGCCACGAGGCTTTTGG
65 GCGTGCAAAAGTGAAATAAACAAGGCCACGAGGCTTTTGG
197950 T
1 T
197951 ACAGGCGAGC
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
103 1 0.01
104 95 0.99
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (104 bp):
TTACGACCAACAAAGTGAAAGAGTAACAGTATGTCCTGATGTCTTGTCTTGAGGTTTATTAATGG
CGTGCAAAAGTGAAATAAACAAGGCCACGAGGCTTTTGG
Found at i:200002 original size:13 final size:13
Alignment explanation
Indices: 199984--200009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199974 CATTTTATGG
199984 TGTATCGATACAT
1 TGTATCGATACAT
199997 TGTATCGATACAT
1 TGTATCGATACAT
200010 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:200006 original size:33 final size:32
Alignment explanation
Indices: 199964--200027 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
199954 TACAAGCCAA
*
199964 TGTATCGATACAT-TTTATGGTGTATCGATACAT
1 TGTATCGATACATACTT-T-GTGTATCGATACAT
199997 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
200028 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 14 0.48
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:201872 original size:109 final size:104
Alignment explanation
Indices: 201686--201921 Score: 332
Period size: 109 Copynumber: 2.2 Consensus size: 104
201676 GTGAATACGA
*
201686 TCTATTTTCTGA--TTTTGTATTTCCTTAACGTCTTTTGTTATCTTCCATGCTTGGATTGGCTTA
1 TCTATTTTCTGATTTTTTGTATTTCCTTAAAGTCTTTTGTTATCTTCCATGCTTGGATTGGCTTA
* * *
201749 ATTATATTTTTGTTGGTGAATGCGATATATTCGTTTTAT
66 ATTATATTTATGTTGGTGAATGCGAAATATTCGTTTTAG
* *
201788 TCTATTTTCTGATTTTTTTTATTTCCTTAAAGTCTTTTGTTGTCTTCCATGTCATGCTTGGATTG
1 TCTATTTTCTGATTTTTTGTATTTCCTTAAAGTCTTTTGTTATCTT-C----CATGCTTGGATTG
* *
201853 GCTTAATTATATTTATGTTGGTGAATGCTAAATATTCTTTTTAG
61 GCTTAATTATATTTATGTTGGTGAATGCGAAATATTCGTTTTAG
*
201897 TCTATTTTCTTATTTTTTGTATTTC
1 TCTATTTTCTGATTTTTTGTATTTC
201922 TTTTTTTCAT
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
102 12 0.10
104 29 0.25
105 1 0.01
109 75 0.64
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (104 bp):
TCTATTTTCTGATTTTTTGTATTTCCTTAAAGTCTTTTGTTATCTTCCATGCTTGGATTGGCTTA
ATTATATTTATGTTGGTGAATGCGAAATATTCGTTTTAG
Found at i:203143 original size:10 final size:11
Alignment explanation
Indices: 203123--203147 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
203113 GTTTAACTTC
203123 TTTTTCTTTTT
1 TTTTTCTTTTT
203134 TTTTTCTTTTT
1 TTTTTCTTTTT
203145 TTT
1 TTT
203148 CTATTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:205895 original size:16 final size:16
Alignment explanation
Indices: 205874--205905 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
205864 ATACACCATT
205874 CAAAATCATCTTCTTG
1 CAAAATCATCTTCTTG
*
205890 CAAAATCATTTTCTTG
1 CAAAATCATCTTCTTG
205906 GCCTCTTTCT
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:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (16 bp):
CAAAATCATCTTCTTG
Found at i:214341 original size:2 final size:2
Alignment explanation
Indices: 214336--214364 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
214326 AAGGAGATTA
214336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
214365 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:214369 original size:2 final size:2
Alignment explanation
Indices: 214364--214410 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
214354 ATATATATAT
214364 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
214406 AG AG A
1 AG AG A
214411 TTGGGGAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:217559 original size:25 final size:26
Alignment explanation
Indices: 217525--217579 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
217515 TCCATATATG
*
217525 CCTTCCTCATCCGCCGAACAGCTTGT
1 CCTTCCTCATCCGCCAAACAGCTTGT
*
217551 CCTT-CTCATCGGCCAAACAGCTTGT
1 CCTTCCTCATCCGCCAAACAGCTTGT
217576 CCTT
1 CCTT
217580 TGATTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.16, C:0.40, G:0.15, T:0.29
Consensus pattern (26 bp):
CCTTCCTCATCCGCCAAACAGCTTGT
Found at i:217662 original size:12 final size:12
Alignment explanation
Indices: 217618--217661 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
217608 ATTTAGTTTA
217618 ATTTAAATTATT
1 ATTTAAATTATT
*
217630 ATTTAAA-TAAT
1 ATTTAAATTATT
* *
217641 ATTAAAATTTTT
1 ATTTAAATTATT
217653 ATTTAAATT
1 ATTTAAATT
217662 TAATTATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTAAATTATT
Found at i:217667 original size:23 final size:23
Alignment explanation
Indices: 217614--217676 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
217604 ATTAATTTAG
*
217614 TTTAATTTAAATTATTATTTAAA
1 TTTAATTAAAATTATTATTTAAA
* *
217637 -TAATATTAAAATTTTTATTTAAA
1 TTTA-ATTAAAATTATTATTTAAA
217660 TTTAATTATAAA-TATTA
1 TTTAATTA-AAATTATTA
217677 ATATAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.06
23 25 0.78
24 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAATTAAAATTATTATTTAAA
Found at i:218080 original size:29 final size:29
Alignment explanation
Indices: 218048--218114 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
218038 TTTTTAAAAA
218048 TATTTTCT-TTTTCTT-TCATTTTTTTTTCT
1 TATTTTCTCTTTTCTTGTC-TTTTTTTTT-T
218077 TATTTT-TCTTTTCTTGTCTTTTTTTTTT
1 TATTTTCTCTTTTCTTGTCTTTTTTTTTT
*
218105 TTTTTTCTCT
1 TATTTTCTCT
218115 CGCACTTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 7 0.21
29 25 0.74
30 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.81
Consensus pattern (29 bp):
TATTTTCTCTTTTCTTGTCTTTTTTTTTT
Found at i:219593 original size:20 final size:20
Alignment explanation
Indices: 219568--219622 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
219558 CTGCCAGTTT
**
219568 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
219588 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
*
219607 CATATATCGATACAAT
1 CATGTATCGATACAAT
219623 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:228637 original size:13 final size:13
Alignment explanation
Indices: 228619--228646 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
228609 ATACAAAGAT
228619 CAATGTATCGATA
1 CAATGTATCGATA
228632 CAATGTATCGATA
1 CAATGTATCGATA
228645 CA
1 CA
228647 TTTGAGTAAT
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:228728 original size:32 final size:33
Alignment explanation
Indices: 228687--228752 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
228677 AGTATCTTAA
*
228687 ATTGTATCGATACAACAC-TTATGTATTGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
*
228719 ATTGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
228752 A
1 A
228753 AATCATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:231025 original size:13 final size:13
Alignment explanation
Indices: 231007--231031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230997 CAATTCATCA
231007 TGTATCGATACAT
1 TGTATCGATACAT
231020 TGTATCGATACA
1 TGTATCGATACA
231032 ATGTGCCATG
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:231125 original size:19 final size:20
Alignment explanation
Indices: 231081--231133 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
231071 CTGCCAATTT
* **
231081 CATGTATTGATACAATTGTG
1 CATGTATCGATACAATTGAA
231101 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
231120 CATGTATCGATACA
1 CATGTATCGATACA
231134 TCTGGATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:231906 original size:17 final size:17
Alignment explanation
Indices: 231861--231910 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
231851 TTAATTAAGT
*
231861 ATGACTTAATTAAATAA
1 ATGACTTAATTAAATAG
* *
231878 AAGA-TAAATTAAATAG
1 ATGACTTAATTAAATAG
231894 ATGACTTAATTAAATAG
1 ATGACTTAATTAAATAG
231911 TTTAATTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (17 bp):
ATGACTTAATTAAATAG
Found at i:235761 original size:27 final size:27
Alignment explanation
Indices: 235731--235793 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
235721 ACGGGGTTGG
* *
235731 AGTATCCCCTCGAAAGAATGGGGTTAT
1 AGTATCCCCTCGAAAGAATAGAGTTAT
235758 AGTATCCCCTCGAAAGAATAGAGTTAT
1 AGTATCCCCTCGAAAGAATAGAGTTAT
235785 AGTATCCCC
1 AGTATCCCC
235794 GATGATGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (27 bp):
AGTATCCCCTCGAAAGAATAGAGTTAT
Found at i:235858 original size:124 final size:123
Alignment explanation
Indices: 235631--235889 Score: 324
Period size: 124 Copynumber: 2.1 Consensus size: 123
235621 AAAACGGGGC
* * * * * * *
235631 TAGATTATCCCCTTGGAAGAATAGGGTTAAAGTGTCCCTGATGATGATAATTTAGACAAAAATAA
1 TAGAGTATCCCCTCGAAAGAATAGAGTTAAAGTATCCCCGATGATGACAATTTAGACAAAAATAA
* * * *
235696 GATTTAAATCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCCTC-GAAAGAATGGGGT
66 AATTTAAATCTTAACAAGTTTAAAAACAGGGTTAGAGTATACCCTCTG-AAGAAT-GGGT
* *
235755 TATAGTATCCCCTCGAAAGAATAGAGTTATAGTATCCCCGATGATGACAATTTA-ACAAAAAATA
1 TAGAGTATCCCCTCGAAAGAATAGAGTTAAAGTATCCCCGATGATGACAATTTAGAC-AAAAATA
* * *
235819 AAATTTAAATCTTGACGAGTTTAAGAACAGGGTTAGAGTATACCCTCTGAAGAATGGGT
65 AAATTTAAATCTTAACAAGTTTAAAAACAGGGTTAGAGTATACCCTCTGAAGAATGGGT
*
235878 TGGAGTATCCCC
1 TAGAGTATCCCC
235890 GATAAATAAA
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
123 16 0.14
124 98 0.85
125 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (123 bp):
TAGAGTATCCCCTCGAAAGAATAGAGTTAAAGTATCCCCGATGATGACAATTTAGACAAAAATAA
AATTTAAATCTTAACAAGTTTAAAAACAGGGTTAGAGTATACCCTCTGAAGAATGGGT
Found at i:241120 original size:29 final size:29
Alignment explanation
Indices: 241046--241779 Score: 1017
Period size: 29 Copynumber: 25.4 Consensus size: 29
241036 CATTAACTTG
*
241046 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT
241076 CGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241107 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
241136 TGTAGGCTTTG-AAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241164 TACGTGGGCTTTG-AAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACT
* *
241194 TGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
241222 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241251 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
241279 AGCGTGAGCTTT-AAAAGGGTGCCACTGACTT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGAC-T
*
241310 GTGTGGGCTTTG-AAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
241339 TGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241367 TGTGAGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241396 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241424 TGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241453 TATGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* **
241482 TGTGGGCTTTG-AAAGGGTGTTACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
241510 TGTGGGCTTTGAAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241538 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241566 TGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
241595 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241624 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
241652 TGTGGGCTTTGAAAAGAGTGCTACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
241681 TGTGGGCTTTGAAAAGAGTGCTACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241710 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
241739 TGTGGGCTTTG-AAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
241767 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
241780 GAGATGAACG
Statistics
Matches: 639, Mismatches: 46, Indels: 37
0.89 0.06 0.05
Matches are distributed among these distances:
27 4 0.01
28 254 0.40
29 277 0.43
30 75 0.12
31 11 0.02
32 18 0.03
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:241255 original size:57 final size:57
Alignment explanation
Indices: 241046--241779 Score: 969
Period size: 57 Copynumber: 12.7 Consensus size: 57
241036 CATTAACTTG
* *
241046 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
241107 TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTAGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
241164 TACGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1 T--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
241222 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
241279 AGCGTGAGCTTT-AAAAGGGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACT
1 --TGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
241339 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGAGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
241396 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACT
* * **
241453 TATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGTTACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
241510 TGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
241566 TGTGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
241624 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCTACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
241681 TGTGGGCTTTGAAAAGAGTGCTACTGATTTGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACT
*
241739 TGTGGGCTTTG-AAAGAGTGCCACTAACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
241780 GAGATGAACG
Statistics
Matches: 601, Mismatches: 57, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
56 80 0.13
57 252 0.42
58 191 0.32
59 23 0.04
60 37 0.06
61 18 0.03
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:243023 original size:1 final size:1
Alignment explanation
Indices: 243019--243118 Score: 110
Period size: 1 Copynumber: 100.0 Consensus size: 1
243009 ATTTTTCTTG
* * * * * *
243019 TTTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
243084 GTTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
243119 GGGTGTAAAG
Statistics
Matches: 79, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:243023 original size:10 final size:9
Alignment explanation
Indices: 242999--243119 Score: 165
Period size: 9 Copynumber: 12.9 Consensus size: 9
242989 CCCATTTTTA
242999 TTTTTTTGCT
1 TTTTTTTG-T
243009 ATTTTTCTTGT
1 -TTTTT-TTGT
243020 TTTTTTT-T
1 TTTTTTTGT
243028 GTTTTTTTGTT
1 -TTTTTTTG-T
243039 TTTTTTTGT
1 TTTTTTTGT
243048 TTTTTTTGT
1 TTTTTTTGT
243057 TTTTTTTGTT
1 TTTTTTTG-T
243067 TTTTTTTGTT
1 TTTTTTTG-T
243077 TTTTTTTGT
1 TTTTTTTGT
243086 TTTTTTTGT
1 TTTTTTTGT
243095 TTTTTTTG-
1 TTTTTTTGT
243103 TTTTTTTGT
1 TTTTTTTGT
243112 TTTTTTTG
1 TTTTTTTG
243120 GGTGTAAAGG
Statistics
Matches: 104, Mismatches: 0, Indels: 14
0.88 0.00 0.12
Matches are distributed among these distances:
8 9 0.09
9 53 0.51
10 32 0.31
11 7 0.07
12 3 0.03
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.87
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:243035 original size:38 final size:36
Alignment explanation
Indices: 242999--243118 Score: 186
Period size: 38 Copynumber: 3.2 Consensus size: 36
242989 CCCATTTTTA
242999 TTTTTTTGCTATTTTTCTTGTTTTTTTTTGTTTTTTTGTT
1 TTTTTTTG-T-TTTTT-TTG-TTTTTTTTGTTTTTTTGTT
243039 TTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTGTT
1 TTTTTTTGTTTTTTTTGTTTTTTTTG--TTTTTTTGTT
243077 TTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTT
1 TTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTT
243113 TTTTTT
1 TTTTTT
243119 GGGTGTAAAG
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
36 25 0.32
37 3 0.04
38 41 0.53
39 1 0.01
40 8 0.10
ACGTcount: A:0.01, C:0.02, G:0.10, T:0.88
Consensus pattern (36 bp):
TTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTGTT
Found at i:247412 original size:13 final size:13
Alignment explanation
Indices: 247394--247418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
247384 CATAAAGTGT
247394 TGTATCGATACAA
1 TGTATCGATACAA
247407 TGTATCGATACA
1 TGTATCGATACA
247419 TATTTTTTTG
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:247416 original size:33 final size:33
Alignment explanation
Indices: 247374--247440 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
247364 TTCAACGATT
247374 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
247407 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
247440 T
1 T
247441 TCAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:247497 original size:13 final size:13
Alignment explanation
Indices: 247479--247505 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
247469 ACATTACTTA
247479 AATGTATCGATAC
1 AATGTATCGATAC
247492 AATGTATCGATAC
1 AATGTATCGATAC
247505 A
1 A
247506 CTGATCTTTG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:259689 original size:13 final size:13
Alignment explanation
Indices: 259671--259698 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
259661 ACAAATAGTA
259671 AATGTATCGATAC
1 AATGTATCGATAC
259684 AATGTATCGATAC
1 AATGTATCGATAC
259697 AA
1 AA
259699 AGCTACTGCC
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:263960 original size:18 final size:17
Alignment explanation
Indices: 263935--263970 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
263925 TCAAAAGTGA
263935 AAACACAAAAAAAAAAC
1 AAACACAAAAAAAAAAC
*
263952 AAACAACAAACAAAAAAC
1 AAAC-ACAAAAAAAAAAC
263970 A
1 A
263971 CAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (17 bp):
AAACACAAAAAAAAAAC
Found at i:265323 original size:33 final size:33
Alignment explanation
Indices: 265183--265667 Score: 657
Period size: 33 Copynumber: 15.0 Consensus size: 33
265173 CAAATTTCTC
* *
265183 TTCTT-AAAGTCCACAACTCAGTGGCATCTCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* * *
265215 TTC-TCAAAGTCGATGACTCCGTGGCATC--TT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
265245 TTCTTCAAAGTCCACAACTCAGTGGCATCTCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
265278 TTC-TCAAAGTCCATGACTCAGTGGCATCTCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* * *
265310 TTCTTCAAAGTCCATGACTTAGTGGCATTTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
265343 TTCTTCAAAGTCCAGGACTCAGTGGCATC-TCT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265375 TTC--CAAAGTCCACGATTCAGTGGCATC--TT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265404 TTCTTCAAAGTCCACGACTTAGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265437 TTCTTCAAAATCCACGACTCAGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265470 TTCTTCCAAGTCCACGACTCAGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
265503 TTCTTCAAAATCCACGACTTAGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265536 TTCTTCCAAGTCCACGACTCAGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
*
265569 TTCTTCAAAGTCCACGACTCAATGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
265602 TTCTTCCAAGTCCACGACTCGGTGGCATCTTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
* * *
265635 TTTTTCAAAGTCCACAACTCAGTGGCATATTTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
265668 CCCAAAGTCC
Statistics
Matches: 402, Mismatches: 42, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
29 4 0.01
30 27 0.07
31 44 0.11
32 57 0.14
33 270 0.67
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (33 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
Found at i:265736 original size:27 final size:27
Alignment explanation
Indices: 265699--265899 Score: 199
Period size: 27 Copynumber: 7.2 Consensus size: 27
265689 GCACCTTTTT
* * *
265699 CTTTTT-AGTCCAGAACTCTGTGACAC
1 CTTTTTAAGTCCACAACTCCGTGGCAC
265725 CTTTTTAAGTCCACAACTCCGTGGCAC
1 CTTTTTAAGTCCACAACTCCGTGGCAC
* *
265752 CCTTTCAAGTCCACAACTCCGTGGCACC
1 CTTTTTAAGTCCACAACTCCGTGGCA-C
* *
265780 TTTTTCTTTTTAAAGCCCACAACTCCATGGCAC
1 -----CTTTTT-AAGTCCACAACTCCGTGGCAC
*
265813 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CTTTTTAAGTCCACAACTCCGTGGCAC
*
265840 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CTTTTTAAGTCCACAACTCCGTGGCAC
* * *
265867 CCTTTTAAG-CCTACAAGTCAGTGGCAC
1 CTTTTTAAGTCC-ACAACTCCGTGGCAC
*
265894 CCTTTT
1 CTTTTT
265900 CAAAAGCCCA
Statistics
Matches: 152, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
26 8 0.05
27 115 0.76
28 6 0.04
33 5 0.03
34 18 0.12
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.30
Consensus pattern (27 bp):
CTTTTTAAGTCCACAACTCCGTGGCAC
Found at i:265841 original size:88 final size:86
Alignment explanation
Indices: 265672--265872 Score: 294
Period size: 88 Copynumber: 2.3 Consensus size: 86
265662 TATTTTCCCA
** * * ** *
265672 AAGTCCACAACTTTGTGGCACCTTTTTCTTTTTAGTCCAGAACTCTGTGACACCTTTTTAAGTCC
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAGCCCACAACTCCATGACACCCTTTTAAGTCC
265737 ACAACTCCGTGGCACCCTTTC
66 ACAACTCCGTGGCACCCTTTC
*
265758 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCATGGCACCCTTTTAAGT
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT--AGCCCACAACTCCATGACACCCTTTTAAGT
*
265823 CCACAACTCCGTGGCACCCTTTT
64 CCACAACTCCGTGGCACCCTTTC
*
265846 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT
265873 AAGCCTACAA
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
86 31 0.30
88 72 0.70
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.31
Consensus pattern (86 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAGCCCACAACTCCATGACACCCTTTTAAGTCC
ACAACTCCGTGGCACCCTTTC
Found at i:265923 original size:57 final size:57
Alignment explanation
Indices: 265735--265968 Score: 196
Period size: 54 Copynumber: 4.1 Consensus size: 57
265725 CTTTTTAAGT
* * * * *
265735 CCACAACTCCGTGGCACCCTTTCAAGTCC-ACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACCCTTTTAAG-CCTACAAGTCAGTGGCACCCTTTTC----AAAAGC
* * * *
265796 CCACAACTCCATGGCACCCTTTTAAGTCC-ACAACTCCGTGGCACCCTTTT---AAGT
1 CCACAACTCCGTGGCACCCTTTTAAG-CCTACAAGTCAGTGGCACCCTTTTCAAAAGC
265850 CCACAACTCCGTGGCACCCTTTTAAGCCTACAAGTCAGTGGCACCCTTTTCAAAAGC
1 CCACAACTCCGTGGCACCCTTTTAAGCCTACAAGTCAGTGGCACCCTTTTCAAAAGC
* * * * *
265907 CCACAAGTCGGTGGCACCCCTTTCAAAG-CTCACAAGTTAGTGGCAACC--TTCAAAAGC
1 CCACAACTCCGTGGCA-CCCTTT-TAAGCCT-ACAAGTCAGTGGCACCCTTTTCAAAAGC
*
265964 ACACA
1 CCACA
265969 GGTTGGTGCA
Statistics
Matches: 152, Mismatches: 14, Indels: 18
0.83 0.08 0.10
Matches are distributed among these distances:
53 2 0.01
54 47 0.31
57 30 0.20
58 8 0.05
59 18 0.12
61 47 0.31
ACGTcount: A:0.26, C:0.35, G:0.15, T:0.24
Consensus pattern (57 bp):
CCACAACTCCGTGGCACCCTTTTAAGCCTACAAGTCAGTGGCACCCTTTTCAAAAGC
Found at i:265949 original size:29 final size:30
Alignment explanation
Indices: 265879--266002 Score: 112
Period size: 29 Copynumber: 4.2 Consensus size: 30
265869 TTTTAAGCCT
* *
265879 ACAAGTCAGTGGCACCCTTTTCAAAAGCCC
1 ACAAGTCAGTGGCACCCCTTTCAAAAGCAC
* *
265909 ACAAGTCGGTGGCACCCCTTTC-AAAGCTC
1 ACAAGTCAGTGGCACCCCTTTCAAAAGCAC
* *
265938 ACAAGTTAGTGGCA-ACC-TTCAAAAGCAC
1 ACAAGTCAGTGGCACCCCTTTCAAAAGCAC
* ** *
265966 ACAGGTTGGT-GCAACCCTTTCAAAAGCCCAC
1 ACAAGTCAGTGGCACCCCTTTCAAAAG--CAC
265997 ACAAGT
1 ACAAGT
266003 TGGTGGCATC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.08
28 18 0.23
29 26 0.33
30 20 0.26
31 8 0.10
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (30 bp):
ACAAGTCAGTGGCACCCCTTTCAAAAGCAC
Found at i:265992 original size:57 final size:58
Alignment explanation
Indices: 265851--265997 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 58
265841 CTTTTAAGTC
* * * * * *
265851 CACAACTCCGTGGC-ACCCTTT-TAAGCCTACAAGTCAGTGGCACCCTTTTCAAAAGCC
1 CACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTCAGTGGCAACC-TTTCAAAAGCA
* * *
265908 CACAAGTCGGTGGCACCCCTTTCAAAGCTCACAAGTTAGTGGCAACC-TTCAAAAGCA
1 CACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCA
* *
265965 CACAGGTTGGT-GCAACCCTTTCAAAAGCCCACA
1 CACAAGTCGGTGGCAACCCTTTC-AAAGCCCACA
265998 CAAGTTGGTG
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
56 10 0.14
57 39 0.53
58 6 0.08
59 19 0.26
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (58 bp):
CACAAGTCGGTGGCAACCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAAGCA
Found at i:266000 original size:59 final size:58
Alignment explanation
Indices: 265879--266010 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 58
265869 TTTTAAGCCT
* * * * *
265879 ACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCGGTGGCACCCCTTTCAAAGCTC
1 ACAAGTTAGTGGCAACC-TTTCAAAAGCACACAAGTCGGTGGCAACCCTTTCAAAGCAC
* *
265938 ACAAGTTAGTGGCAACC-TTCAAAAGCACACAGGTTGGT-GCAACCCTTTCAAAAGCCCAC
1 ACAAGTTAGTGGCAACCTTTCAAAAGCACACAAGTCGGTGGCAACCCTTTC-AAAG--CAC
*
265997 ACAAGTTGGTGGCA
1 ACAAGTTAGTGGCA
266011 TCTTCTTCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
56 10 0.16
57 22 0.35
59 30 0.48
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (58 bp):
ACAAGTTAGTGGCAACCTTTCAAAAGCACACAAGTCGGTGGCAACCCTTTCAAAGCAC
Found at i:266086 original size:49 final size:49
Alignment explanation
Indices: 266014--266830 Score: 784
Period size: 49 Copynumber: 16.8 Consensus size: 49
266004 GGTGGCATCT
* * *
266014 TCTTCTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
266064 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
266113 TCTTTAAGTCTAATATCGCTGACCTTAAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
266165 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
266214 TTTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
*
266266 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGTACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
266315 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCA
* * * *
266367 TCTCTAAGACCAATGTTGCTGGCCTTCAATCAGCACATTGG------CA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
266410 ----TAAG-CCTAATATCGTTGGCCTTGAATCAGCATATTGGCACCTT-A
1 TCTTTAAGTCC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
266454 TCTTTAAGACCAATGTCGTCT-GCCTTGAATCAACACATTGG------CA
1 TCTTTAAGTCCAATGTCG-CTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
266497 -C---AAGCCCAATATCGATGGCCTTGAATCAGCATATTGGTACCTTCGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCA
* *
266545 TCTTTAATTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * *
266594 TCTTTAAGTCCGATATCGCTGGCTTTGAATTAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
266643 TCTTTAAGTCTAATGTCGCTGGTCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * * * *
266692 TCCTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * ** *
266741 ACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCT
1 TC-TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
266791 TCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATTG
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
266831 TCATTCTTCG
Statistics
Matches: 627, Mismatches: 100, Indels: 83
0.77 0.12 0.10
Matches are distributed among these distances:
38 3 0.00
39 58 0.09
42 1 0.00
43 3 0.00
44 1 0.00
47 30 0.05
48 30 0.05
49 299 0.48
50 10 0.02
51 4 0.01
52 188 0.30
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:266194 original size:101 final size:101
Alignment explanation
Indices: 266014--266830 Score: 957
Period size: 101 Copynumber: 8.4 Consensus size: 101
266004 GGTGGCATCT
* *
266014 TCTTCTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGACCA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCA
266076 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
65 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
266113 TCTTTAAGTCTAATATCGCTGACCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
266178 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
266214 TTTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
*
266279 TGTCGCTGGCCTTGAATCAGCACATTGGTACCTTCA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
266315 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTCTAAGACCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
* *
266380 TGTTGCTGGCCTTCAATCAGCACATTGG------CA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
266410 ----TAAG-CCTAATATCGTTGGCCTTGAATCAGCATATTGGCACC--T-T-ATCTTTAAGACCA
1 TCTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCA
*
266466 ATGTCGTCT-GCCTTGAATCAACACATTGG------CA
65 ATGTCG-CTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
266497 -C---AAGCCCAATATCGATGGCCTTGAATCAGCATATTGGTACCTTCGTCATCTTTAATTCCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
*
266558 TGTCGCTGGCCTTGAATCAACACATTGGCACCTTCA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
266594 TCTTTAAGTCCGATATCGCTGGCTTTGAATTAGCATATTGGCACC-TT-T-ATCTTTAAGTCTAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
*
266656 TGTCGCTGGTCTTGAATCAGCACATTGGCACCTTCA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * ** * *
266692 TCCTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACAT-TCCTAAGCCCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT-TTAAGTCCA
** *
266756 ATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCT
65 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * * *
266791 TCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATTG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
266831 TCATTCTTCG
Statistics
Matches: 631, Mismatches: 61, Indels: 52
0.85 0.08 0.07
Matches are distributed among these distances:
87 72 0.11
88 5 0.01
89 1 0.00
90 5 0.01
91 73 0.12
95 2 0.00
97 2 0.00
98 125 0.20
99 42 0.07
100 3 0.00
101 301 0.48
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAA
TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:266316 original size:150 final size:149
Alignment explanation
Indices: 266014--266830 Score: 796
Period size: 150 Copynumber: 5.6 Consensus size: 149
266004 GGTGGCATCT
* * *
266014 TCTTCTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
* * *
266079 TCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTTTAAGTCTAATATCGCTGACCTTAAA
65 TCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
*
266142 TCAGCATATTGGCGCCTTTGTCA
130 TCAGCATATTGGCACC--T-TCA
* * *
266165 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCCAATAT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGT
* * *
266230 CGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAA
66 CGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
* *
266295 TCAGCACATTGGTACCTTCA
130 TCAGCATATTGGCACCTTCA
* * * *
266315 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTCTAAGACCAA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAA
* * *
266380 TGTTGCTGGCCTTCAATCAGCACATT-G------G-CA----TAAG-CCTAATATCGTTGGCCTT
63 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCC-AATATCGCTGGCCTT
266432 GAATCAGCATATTGGCACCTT-A
127 GAATCAGCATATTGGCACCTTCA
* * * * *
266454 TCTTTAAGACCAATGTCGTCT-GCCTTGAATCAACACATTGG------CA-C---AAGCCCAATA
1 TCTTTAAGTCCAATATCG-CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
* * * * *
266508 TCGATGGCCTTGAATCAGCATATTGGTACCTTCGTCATCTTTAATTCCAATGTCGCTGGCCTTGA
65 TCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCATCTTTAAGTCCAATATCGCTGGCCTTGA
* *
266573 ATCAACACATTGGCACCTTCA
129 ATCAGCATATTGGCACCTTCA
* * * * * *
266594 TCTTTAAGTCCGATATCGCTGGCTTTGAATTAGCATATTGGCACCTTTATCTTTAAGTCTAATGT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGT
* * * *
266659 CGCTGGTCTTGAATCAGCACATTGGCACC-T-TCATCCTTAAGTCCGATATCGTTGGCCTTGAAT
66 CGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* *
266722 CAGCATATTGGCATCTTTA
131 CAGCATATTGGCACCTTCA
* * * ** * * *
266741 ACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTAA
1 TC-TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
*
266804 TGTCGCTGGCCATGAATCAGCACATTG
63 TGTCGCTGGCCTTGAATCAGCACATTG
266831 TCATTCTTCG
Statistics
Matches: 546, Mismatches: 83, Indels: 77
0.77 0.12 0.11
Matches are distributed among these distances:
126 28 0.05
127 1 0.00
129 1 0.00
130 2 0.00
134 1 0.00
135 2 0.00
139 74 0.14
140 72 0.13
144 2 0.00
145 1 0.00
146 1 0.00
147 45 0.08
148 41 0.08
149 1 0.00
150 191 0.35
151 5 0.01
152 3 0.01
153 75 0.14
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (149 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGT
CGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
CAGCATATTGGCACCTTCA
Found at i:266440 original size:39 final size:38
Alignment explanation
Indices: 266386--266533 Score: 109
Period size: 39 Copynumber: 3.6 Consensus size: 38
266376 CCAATGTTGC
*
266386 TGGCCTTCAATCAGCACATTGGCATAAGCCTAATATCGT
1 TGGCCTTGAATCAGCACATTGGCATAAGCC-AATATCGT
* *
266425 TGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGT
1 TGGCCTTGAATCAGCACATTGG---C--A----TAAG-CCAATATCGT
* * *
266473 CT-GCCTTGAATCAACACATTGGCACAAGCCCAATATCGA
1 -TGGCCTTGAATCAGCACATTGGCATAAG-CCAATATCGT
*
266512 TGGCCTTGAATCAGCATATTGG
1 TGGCCTTGAATCAGCACATTGG
266534 TACCTTCGTC
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
38 1 0.01
39 49 0.57
42 1 0.01
43 1 0.01
44 1 0.01
45 1 0.01
48 29 0.34
49 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (38 bp):
TGGCCTTGAATCAGCACATTGGCATAAGCCAATATCGT
Found at i:266587 original size:91 final size:90
Alignment explanation
Indices: 266324--266686 Score: 378
Period size: 87 Copynumber: 4.0 Consensus size: 90
266314 ATCTTTAAGT
* * * *
266324 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTCTAAGACCAATGTTGCTGG
1 CCAATATCGATGGCCTTGAATCAGCATATTGGCACC-TTGTCATCTTTAAGACCAATGTCGCTGG
* * *
266389 CCTTCAATCAGCACATTGGCATAAGC
65 CCTTGAATCAACACATTGGCACAAGC
* *
266415 CTAATATCGTTGGCCTTGAATCAGCATATTGGCACC-T-T-ATCTTTAAGACCAATGTCGTCT-G
1 CCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAAGACCAATGTCG-CTGG
266476 CCTTGAATCAACACATTGGCACAAGC
65 CCTTGAATCAACACATTGGCACAAGC
* **
266502 CCAATATCGATGGCCTTGAATCAGCATATTGGTACCTTCGTCATCTTTAATTCCAATGTCGCTGG
1 CCAATATCGATGGCCTTGAATCAGCATATTGGCACCTT-GTCATCTTTAAGACCAATGTCGCTGG
*
266567 CCTTGAATCAACACATTGGCACCTTCATCTTTAAGT
65 CCTTGAATCAACACATTGG------CA-C---AAGC
* * * * * * *
266603 CCGATATCGCTGGCTTTGAATTAGCATATTGGCACCTT-T-ATCTTTAAGTCTAATGTCGCTGGT
1 CCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAAGACCAATGTCGCTGGC
*
266666 CTTGAATCAGCACATTGGCAC
66 CTTGAATCAACACATTGGCAC
266687 CTTCATCCTT
Statistics
Matches: 233, Mismatches: 23, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
87 74 0.32
88 4 0.02
89 1 0.00
90 3 0.01
91 71 0.30
92 2 0.01
97 2 0.01
98 39 0.17
99 1 0.00
101 36 0.15
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (90 bp):
CCAATATCGATGGCCTTGAATCAGCATATTGGCACCTTGTCATCTTTAAGACCAATGTCGCTGGC
CTTGAATCAACACATTGGCACAAGC
Found at i:267655 original size:20 final size:20
Alignment explanation
Indices: 267630--267684 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
267620 CTGCCAAGAA
267630 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
*
267650 AATGTATCGATACATTGTTC
1 AATGTATCGATACATTATTC
**
267670 TTTGTATCGATACAT
1 AATGTATCGATACAT
267685 CTGGGAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:271251 original size:20 final size:20
Alignment explanation
Indices: 271226--271263 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
271216 GTAAAAACAC
271226 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
271246 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
271264 TGGGTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:272568 original size:52 final size:52
Alignment explanation
Indices: 272501--272599 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
272491 CATTAAAAAG
* * *
272501 TGTATTAATATATTTAGGTTAAAAACTCAAAACATATCGATACAATGGAGAA
1 TGTATTAATACATTTAGGTCAAAAACCCAAAACATATCGATACAATGGAGAA
* * * **
272553 TGTATTGATACATTTATGTCAAAAACCCAGAATGTATCGATACAATG
1 TGTATTAATACATTTAGGTCAAAAACCCAAAACATATCGATACAATG
272600 AAATATGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (52 bp):
TGTATTAATACATTTAGGTCAAAAACCCAAAACATATCGATACAATGGAGAA
Found at i:272694 original size:30 final size:30
Alignment explanation
Indices: 272659--272720 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
272649 TGGTCTTGTA
272659 TCGATAAATTTCAAGATTGTATCGATACAT
1 TCGATAAATTTCAAGATTGTATCGATACAT
272689 TCGATAAATTTCAAGATTGTATCGATACAT
1 TCGATAAATTTCAAGATTGTATCGATACAT
272719 TC
1 TC
272721 ACTTATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (30 bp):
TCGATAAATTTCAAGATTGTATCGATACAT
Found at i:272729 original size:20 final size:21
Alignment explanation
Indices: 272704--272758 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
272694 AAATTTCAAG
*
272704 ATTGTATCGATACATTCACTT
1 ATTGTATCGATACATTAACTT
272725 A-TGTATCGATACATTAACTT
1 ATTGTATCGATACATTAACTT
*
272745 ATTATATCGATACA
1 ATTGTATCGATACA
272759 AATTGCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTGTATCGATACATTAACTT
Found at i:274572 original size:13 final size:13
Alignment explanation
Indices: 274554--274579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
274544 CAATTTTTGG
274554 TGTATCGATACAT
1 TGTATCGATACAT
274567 TGTATCGATACAT
1 TGTATCGATACAT
274580 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:274591 original size:32 final size:33
Alignment explanation
Indices: 274534--274597 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
274524 TACAAGCCAA
**
274534 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
274567 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
274598 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:274604 original size:19 final size:18
Alignment explanation
Indices: 274534--274604 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
274524 TACAAGCCAA
274534 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
274554 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
274567 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
274586 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
274605 CTACTACCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:275318 original size:21 final size:21
Alignment explanation
Indices: 275277--275320 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
275267 CTCCCCTTTA
* *
275277 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
275298 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
275319 TC
1 TC
275321 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:277111 original size:13 final size:13
Alignment explanation
Indices: 277093--277118 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
277083 ATAATCACCC
277093 TGTATCGATACAA
1 TGTATCGATACAA
277106 TGTATCGATACAA
1 TGTATCGATACAA
277119 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:279209 original size:15 final size:15
Alignment explanation
Indices: 279189--279219 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
279179 ATTTCGTTTG
*
279189 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
279204 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
279219 G
1 G
279220 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:281069 original size:21 final size:21
Alignment explanation
Indices: 281022--281066 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
281012 AAGTTTTCAT
281022 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
281042 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
281064 TTT
1 TTT
281067 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:282747 original size:41 final size:41
Alignment explanation
Indices: 282690--282782 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
282680 ATTTTCAAAG
282690 TTGTTAGACTTTAAAAAAGGGAGCCAAAGCTTTAATATTAA
1 TTGTTAGACTTTAAAAAAGGGAGCCAAAGCTTTAATATTAA
282731 TTGTTAGACTTTAAAAAAGGGAGCCAAAGCTTTAATATTAA
1 TTGTTAGACTTTAAAAAAGGGAGCCAAAGCTTTAATATTAA
282772 TTGTTAGACTT
1 TTGTTAGACTT
282783 GGTGATAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (41 bp):
TTGTTAGACTTTAAAAAAGGGAGCCAAAGCTTTAATATTAA
Found at i:283985 original size:18 final size:19
Alignment explanation
Indices: 283959--283996 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
283949 TGTTCATCAC
283959 TATTCA-TGTATCGATACA
1 TATTCAGTGTATCGATACA
*
283977 TATTTATGTGTATCGATACA
1 TATTCA-GTGTATCGATACA
283997 GTGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (19 bp):
TATTCAGTGTATCGATACA
Found at i:284002 original size:13 final size:13
Alignment explanation
Indices: 283984--284009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283974 ACATATTTAT
283984 GTGTATCGATACA
1 GTGTATCGATACA
283997 GTGTATCGATACA
1 GTGTATCGATACA
284010 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:290786 original size:30 final size:30
Alignment explanation
Indices: 290752--290823 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
290742 CTTATATAAG
*
290752 TATAAATTAAAAATAAAGAGTTAATTTGAA
1 TATAAATTAAAAATAAAGAATTAATTTGAA
* * *
290782 TATAAAATTAAATATTAAGAATTTATTTGAA
1 TAT-AAATTAAAAATAAAGAATTAATTTGAA
*
290813 TTTAAATTAAA
1 TATAAATTAAA
290824 GGTTAATGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (30 bp):
TATAAATTAAAAATAAAGAATTAATTTGAA
Found at i:291723 original size:18 final size:19
Alignment explanation
Indices: 291653--291723 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 19
291643 TTTAAAAAAA
*
291653 AATTATATTAAT-ATTTAT
1 AATTAAATTAATAATTTAT
291671 AATTAAATTTAAATAATTTTTATT
1 AATTAAA-TT-AATAA--TTTA-T
*
291695 ATTTAAA-TAATAATTTA-
1 AATTAAATTAATAATTTAT
291712 AATTAAATTAAT
1 AATTAAATTAAT
291724 TCAAATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
17 6 0.14
18 10 0.23
19 6 0.14
20 3 0.07
21 6 0.14
22 1 0.02
23 4 0.09
24 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTAAATTAATAATTTAT
Found at i:292650 original size:2 final size:2
Alignment explanation
Indices: 292643--292667 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
292633 GGTGATGCAA
292643 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
292668 CAAAGAGATG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:293149 original size:20 final size:20
Alignment explanation
Indices: 293124--293161 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
293114 ACCTGCGATA
293124 GACACATACCAACATCAATG
1 GACACATACCAACATCAATG
*
293144 GACACATACCAATATCAA
1 GACACATACCAACATCAA
293162 ACACTCACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (20 bp):
GACACATACCAACATCAATG
Found at i:294627 original size:118 final size:118
Alignment explanation
Indices: 294498--294711 Score: 356
Period size: 118 Copynumber: 1.8 Consensus size: 118
294488 ACATAAAAAT
*
294498 ATAACTAAAGCACGACACGAAAAAAATAACATGAACACAATACGAATATACACACTTGCCAAAAT
1 ATAACTAAAGCACGACACGAAAAAAATAACATGAACACAATACGAATATACACACGTGCCAAAAT
* * *
294563 CTGTAACACAAATTATAATATATATATATATATATAAATATCTAACACATAAA
66 CTATAACACAAATTATAACATATATAAATATATATAAATATCTAACACATAAA
* * * *
294616 ATAACTAAAGCATGACATGAAAAAAATAACATGATCACAATATGAATATACACACGTGCCAAAAT
1 ATAACTAAAGCACGACACGAAAAAAATAACATGAACACAATACGAATATACACACGTGCCAAAAT
294681 CTATAACACAAATTATAACATATATAAATAT
66 CTATAACACAAATTATAACATATATAAATAT
294712 CTAGCACCTT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 88 1.00
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (118 bp):
ATAACTAAAGCACGACACGAAAAAAATAACATGAACACAATACGAATATACACACGTGCCAAAAT
CTATAACACAAATTATAACATATATAAATATATATAAATATCTAACACATAAA
Found at i:295634 original size:2 final size:2
Alignment explanation
Indices: 295627--295689 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
295617 TTGGAACATG
* * *
295627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC CA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
295669 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
295690 CCACAGATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:301575 original size:13 final size:13
Alignment explanation
Indices: 301559--301585 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
301549 TGATTAAAAT
301559 TATTTAAATTAAA
1 TATTTAAATTAAA
301572 TATTTAAATTAAA
1 TATTTAAATTAAA
301585 T
1 T
301586 TTAATTATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTAAATTAAA
Found at i:301585 original size:18 final size:19
Alignment explanation
Indices: 301562--301601 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
301552 TTAAAATTAT
*
301562 TTAAA-TTAAATATTTAAA
1 TTAAATTTAAATATTAAAA
*
301580 TTAAATTTAATTATTAAAA
1 TTAAATTTAAATATTAAAA
301599 TTA
1 TTA
301602 TTCGAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATTTAAATATTAAAA
Found at i:308623 original size:20 final size:22
Alignment explanation
Indices: 308595--308650 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
308585 CTGTTGGGCT
308595 AATTGTATCGATACAATTCTGG
1 AATTGTATCGATACAATTCTGG
*
308617 -A-TGTATCGATGC-ATTCTGG
1 AATTGTATCGATACAATTCTGG
*
308636 AATTGTATCAATACA
1 AATTGTATCGATACA
308651 TTCCTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 11 0.39
21 10 0.36
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (22 bp):
AATTGTATCGATACAATTCTGG
Found at i:308644 original size:21 final size:21
Alignment explanation
Indices: 308595--308674 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 21
308585 CTGTTGGGCT
308595 AATTGTATCGATACAATTCTGG
1 AATTGTATCGATAC-ATTCTGG
*
308617 -A-TGTATCGATGCATTCTGG
1 AATTGTATCGATACATTCTGG
*
308636 AATTGTATCAATACATTCCT--
1 AATTGTATCGATACATT-CTGG
308656 ATATATGTATCGATACATT
1 A-AT-TGTATCGATACATT
308675 TGAAGGGTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 7 0.14
20 12 0.24
21 15 0.31
22 15 0.31
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (21 bp):
AATTGTATCGATACATTCTGG
Found at i:309132 original size:20 final size:19
Alignment explanation
Indices: 309109--309173 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
309099 TTCATGTTAT
309109 TTATTTTATTTTCATTCTTG
1 TTATTTTATTTTCATT-TTG
** *
309129 TTA-TTTAAGTTCATATTTT
1 TTATTTTATTTTCAT-TTTG
*
309148 TTATTTTATTTTTATTTTTG
1 TTATTTTATTTTCA-TTTTG
309168 TTATTT
1 TTATTT
309174 ACGTTCAGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 14 0.40
20 20 0.57
21 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTTCATTTTG
Found at i:309134 original size:24 final size:25
Alignment explanation
Indices: 309084--309135 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
309074 ATTATTATTA
309084 TTATTATTATTTAAATTCATGTTAT
1 TTATTATTATTTAAATTCATGTTAT
** *
309109 TTATT-TTATTTTCATTCTTGTTAT
1 TTATTATTATTTAAATTCATGTTAT
309133 TTA
1 TTA
309136 AGTTCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (25 bp):
TTATTATTATTTAAATTCATGTTAT
Found at i:309174 original size:19 final size:19
Alignment explanation
Indices: 309113--309174 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
309103 TGTTATTTAT
*
309113 TTTATTTTCATTCTTGTTA
1 TTTATTTTCATTTTTGTTA
**
309132 TTTAAGTTCATATTTT-TTA
1 TTTATTTTCAT-TTTTGTTA
*
309151 TTTTATTTTTATTTTTGTTA
1 -TTTATTTTCATTTTTGTTA
309171 TTTA
1 TTTA
309175 CGTTCAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTATTTTCATTTTTGTTA
Found at i:309180 original size:39 final size:39
Alignment explanation
Indices: 309075--309180 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
309065 TTTAACTTTA
* * * *
309075 TTATTATTATTATTATTATTTAAATTCATGTTATTTATT
1 TTATTTTTATTATTGTTATTTAAGTTCATATTATTTATT
* * *
309114 TTATTTTCATTCTTGTTATTTAAGTTCATATTTTTTATT
1 TTATTTTTATTATTGTTATTTAAGTTCATATTATTTATT
* *
309153 TTATTTTTATTTTTGTTATTTACGTTCA
1 TTATTTTTATTATTGTTATTTAAGTTCA
309181 GACTTTACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.24, C:0.06, G:0.05, T:0.66
Consensus pattern (39 bp):
TTATTTTTATTATTGTTATTTAAGTTCATATTATTTATT
Found at i:310994 original size:20 final size:20
Alignment explanation
Indices: 310933--311009 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 20
310923 ACGATATAAA
* *
310933 TATATAATTATATAATATAAAT
1 TATATAAATATAT-A-ATAATT
*
310955 TAT-TAAGATAT-TAA-ATTT
1 TATATAA-ATATATAATAATT
310973 TATATAAATATATAATAATT
1 TATATAAATATATAATAATT
*
310993 TAAAT-AATATTATAATA
1 TATATAAATA-TATAATA
311010 TAAATATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 9 0.20
19 11 0.24
20 15 0.33
21 4 0.09
22 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
TATATAAATATATAATAATT
Found at i:311007 original size:17 final size:17
Alignment explanation
Indices: 310974--311015 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
310964 ATTAAATTTT
310974 ATATAAAT-ATATAATA
1 ATATAAATAATATAATA
* *
310990 ATTTAAATAATATTATA
1 ATATAAATAATATAATA
311007 ATATAAATA
1 ATATAAATA
311016 TAACATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAATAATATAATA
Found at i:311569 original size:20 final size:20
Alignment explanation
Indices: 311544--311581 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
311534 TATAAATCTT
311544 TTTAATTATTTTT-TTATTAA
1 TTTAA-TATTTTTATTATTAA
311564 TTTAATATTTTTATTATT
1 TTTAATATTTTTATTATT
311582 TTAACTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTAATATTTTTATTATTAA
Found at i:317021 original size:14 final size:16
Alignment explanation
Indices: 317002--317041 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 16
316992 GTTATTAGTG
317002 AGAAAAAAAGAA-G-A
1 AGAAAAAAAGAAGGAA
*
317016 AG-AAAAAGGAAGGAA
1 AGAAAAAAAGAAGGAA
317031 AGAAAAAAAGA
1 AGAAAAAAAGA
317042 TAAAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.38
14 3 0.14
15 3 0.14
16 7 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAGGAA
Done.