Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008936.1 Hibiscus syriacus cultivar Beakdansim tig00112254_pilon, whole genome shotgun sequence
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: 973811
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:220137 original size:26 final size:28
Alignment explanation
Indices: 220099--220151 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
220089 ATAAGAATAT
*
220099 AGTATCATATATTATTATAATATAATTG
1 AGTATCATATATTATAATAATATAATTG
*
220127 AGTAT-AT-TATTGTAATAATATAATT
1 AGTATCATATATTATAATAATATAATT
220152 ATTATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 2 0.09
28 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (28 bp):
AGTATCATATATTATAATAATATAATTG
Found at i:220188 original size:22 final size:24
Alignment explanation
Indices: 220163--220210 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
220153 TTATTATTTA
220163 TTAAAAATATTAATAA-T-ATATT
1 TTAAAAATATTAATAATTAATATT
* *
220185 TTAAATATGTTAATAATTAATATT
1 TTAAAAATATTAATAATTAATATT
220209 TT
1 TT
220211 TATTAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 1 0.05
24 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTAAAAATATTAATAATTAATATT
Found at i:221607 original size:151 final size:151
Alignment explanation
Indices: 221333--221635 Score: 597
Period size: 151 Copynumber: 2.0 Consensus size: 151
221323 GTTCAGACGA
221333 AAGGTTGTTCCGTATTAGGCATCAAAATGCTGATATAATTTCGAAGAACCTTTTCTGCTGTTGCA
1 AAGGTTGTTCCGTATTAGGCATCAAAATGCTGATATAATTTCGAAGAACCTTTTCTGCTGTTGCA
221398 TTCCAACAAAACAAATGTTCCAATCTATATAAACTTTATATTATAAAGATAAGTGCAAGGTTTAA
66 TTCCAACAAAACAAATGTTCCAATCTATATAAACTTTATATTATAAAGATAAGTGCAAGGTTTAA
221463 TATAAAAAAATCCCCCAAATT
131 TATAAAAAAATCCCCCAAATT
221484 AAGGTTGTTCCGTATTAGGCATCAAAATGCTGATATAATTTCGAAGAACCTTTTCTGCTGTTGCA
1 AAGGTTGTTCCGTATTAGGCATCAAAATGCTGATATAATTTCGAAGAACCTTTTCTGCTGTTGCA
221549 TTCCAACAAAACAAATGTTCCAATCTATATAAACTTTATATTATAAAGATAAGTGCAAGGTTTAA
66 TTCCAACAAAACAAATGTTCCAATCTATATAAACTTTATATTATAAAGATAAGTGCAAGGTTTAA
*
221614 TATGAAAAAATCCCCCAAATT
131 TATAAAAAAATCCCCCAAATT
221635 A
1 A
221636 CACCCTTTTT
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (151 bp):
AAGGTTGTTCCGTATTAGGCATCAAAATGCTGATATAATTTCGAAGAACCTTTTCTGCTGTTGCA
TTCCAACAAAACAAATGTTCCAATCTATATAAACTTTATATTATAAAGATAAGTGCAAGGTTTAA
TATAAAAAAATCCCCCAAATT
Found at i:222043 original size:24 final size:24
Alignment explanation
Indices: 222016--222076 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
222006 TTTAAATATC
222016 TAAATTCCTAAAATTTCAAACATT
1 TAAATTCCTAAAATTTCAAACATT
*
222040 TAAATAT-TTAAAATTTCAAACATT
1 TAAAT-TCCTAAAATTTCAAACATT
*
222064 CAAA-TCTCTAAAA
1 TAAATTC-CTAAAA
222077 ATCTCATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATTCCTAAAATTTCAAACATT
Found at i:224661 original size:15 final size:14
Alignment explanation
Indices: 224641--224697 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
224631 ATTTAATCCT
224641 TTTTATTATTATTTA
1 TTTTATTATT-TTTA
224656 TTTTATCT-TTTTTA
1 TTTTAT-TATTTTTA
*
224670 TTTTAATATTTTTTA
1 TTTTATTA-TTTTTA
224685 TTATTATTATTTT
1 TT-TTATTATTTT
224698 GTTTATACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 1 0.03
14 9 0.25
15 20 0.56
16 6 0.17
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:224724 original size:2 final size:2
Alignment explanation
Indices: 224717--224748 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
224707 TTGTTTAAAG
224717 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
224749 CTATTACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224738 original size:13 final size:13
Alignment explanation
Indices: 224720--224745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
224710 TTTAAAGATA
224720 TATATATATATAT
1 TATATATATATAT
224733 TATATATATATAT
1 TATATATATATAT
224746 ATACTATTAC
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:224738 original size:15 final size:15
Alignment explanation
Indices: 224718--224747 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
224708 TGTTTAAAGA
224718 TATATATATATATAT
1 TATATATATATATAT
224733 TATATATATATATAT
1 TATATATATATATAT
224748 ACTATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:224939 original size:26 final size:25
Alignment explanation
Indices: 224893--224957 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 25
224883 TTTTACTTTC
*
224893 TTTTTATTTATTTAGTATATGTCTTA
1 TTTTTATTTATTTAGTATATGT-ATA
* *
224919 TTTTTATTT-TTTTGTTTTATGTATA
1 TTTTTATTTATTTAG-TATATGTATA
*
224944 TTTTTTAATTATTT
1 -TTTTTATTTATTT
224958 TTTATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 6 0.19
26 23 0.72
27 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTTATTTATTTAGTATATGTATA
Found at i:224968 original size:21 final size:21
Alignment explanation
Indices: 224940--224988 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
224930 TTGTTTTATG
* *
224940 TATATTTTTTAATTA-TTTTT
1 TATATTTTTTTATTACCTTTT
*
224960 TATATTTTTTTTTTACCTTTT
1 TATATTTTTTTATTACCTTTT
224981 TATATTTT
1 TATATTTT
224989 ATTTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (21 bp):
TATATTTTTTTATTACCTTTT
Found at i:224969 original size:22 final size:21
Alignment explanation
Indices: 224916--225022 Score: 87
Period size: 22 Copynumber: 5.0 Consensus size: 21
224906 AGTATATGTC
*
224916 TTAT-TTTTATTTTTTTGTTTT
1 TTATATTTTA-TTTTTTATTTT
**
224937 ATGTATATTTT-TTAATTATTTT
1 -T-TATATTTTATTTTTTATTTT
*
224959 TTATATTTT-TTTTTTACCTTT
1 TTATATTTTATTTTTTA-TTTT
224980 TTATATTTTATTTTTCT-TTCTT
1 TTATATTTTATTTTT-TATT-TT
225002 TTATATTTTATTTTGTTATTT
1 TTATATTTTATTTT-TTATTT
225023 GCATTATCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
20 13 0.19
21 14 0.20
22 32 0.46
23 7 0.10
24 4 0.06
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.77
Consensus pattern (21 bp):
TTATATTTTATTTTTTATTTT
Found at i:224993 original size:21 final size:21
Alignment explanation
Indices: 224956--225015 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
224946 TTTTAATTAT
*
224956 TTTTTATATTTTTTTTTTAC-C
1 TTTTTATATTTTATTTTT-CTC
*
224977 TTTTTATATTTTATTTTTCTT
1 TTTTTATATTTTATTTTTCTC
224998 TCTTTTATATTTTATTTT
1 T-TTTTATATTTTATTTT
225016 GTTATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
22 16 0.46
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTATATTTTATTTTTCTC
Found at i:225072 original size:3 final size:3
Alignment explanation
Indices: 225064--225097 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
225054 GCTATGTATA
225064 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
225098 TCATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:231435 original size:15 final size:15
Alignment explanation
Indices: 231408--231444 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
231398 GTCCTAAATT
231408 GAAAAAAAGGAAAAA
1 GAAAAAAAGGAAAAA
231423 GAGAAAAAA-GAAAAA
1 GA-AAAAAAGGAAAAA
231438 GAAAAAA
1 GAAAAAA
231445 TATGGGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
GAAAAAAAGGAAAAA
Found at i:232764 original size:110 final size:109
Alignment explanation
Indices: 232560--232820 Score: 298
Period size: 110 Copynumber: 2.4 Consensus size: 109
232550 GGGCTTCCCA
* * * *
232560 ATTTCAGAGCCAATTTTAACTTTACAGCGAATGATATTGGACTCAAGACAACACAAGCTCAACTT
1 ATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTT
* * *
232625 CACAATGAATGGGCGACTGATTGTTAACAAACAACTTT-AAAGTTTC
65 CACAACGAAGGGGCGACTGATTGTCAACAAACAA-TTTCAAAG-TTC
* *
232671 ATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAACTCAACTTC
1 ATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTTC
* * * **
232736 ACAGCGAAGGGGC-AGCTGGTTGTCAACAAATAATTTCTTAGTTC
66 ACAACGAAGGGGCGA-CTGATTGTCAACAAACAATTTCAAAGTTC
* * *
232780 ---CAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCA
1 ATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
232821 GAGCAATACA
Statistics
Matches: 129, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
106 36 0.28
109 7 0.05
110 82 0.64
111 4 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (109 bp):
ATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTTC
ACAACGAAGGGGCGACTGATTGTCAACAAACAATTTCAAAGTTC
Found at i:233532 original size:241 final size:241
Alignment explanation
Indices: 233097--233600 Score: 927
Period size: 241 Copynumber: 2.1 Consensus size: 241
233087 TACATTGGAT
* * *
233097 TTTCAACTTCACGACGAAGAATATCCAATTCCTAGGCTCAACTTCATGACGAATGGGCCATATAC
1 TTTCAATTTCAAGACGAAGGATATCCAATTCCTAGGCTCAACTTCATGACGAATGGGCCATATAC
* *
233162 ATATACAACTTCACAACGAATGGTGTCGTACCCTAACATATTGACCCAACTTCACAACGAAGGAG
66 ATATACAACTTCACAACGAATGGTATCGTACCCTAACAGATTGACCCAACTTCACAACGAAGGAG
*
233227 TCATCTGTAACACAACAACACCGAAGTCTTCAGGACAGGTTTCACCTCCACGCTGAAGTATCTTA
131 TCATCTGTAACACAACAACACCGAAGTCTTCAGGACAGGTTTCACCTCCACGATGAAGTATCTTA
*
233292 AGCTAGAAGACAATCCAGGAGTTACTGGTTAAAGCTTTGAGTTCGA
196 AGCCAGAAGACAATCCAGGAGTTACTGGTTAAAGCTTTGAGTTCGA
*
233338 TTTCAATTTCAAGACGAAGGATATCCAATTCCTAGGCTCAACTTCATGACGAATGGGCTATATAC
1 TTTCAATTTCAAGACGAAGGATATCCAATTCCTAGGCTCAACTTCATGACGAATGGGCCATATAC
233403 ATATACAACTTCACAACGAATGGTATCGTACCCTAACAGATTGACCCAACTTCACAACGAAGGAG
66 ATATACAACTTCACAACGAATGGTATCGTACCCTAACAGATTGACCCAACTTCACAACGAAGGAG
*
233468 TCATCTGTAACACAACAACACCGAAGTCTTCATGACAGGTTTCACCTCCACGATGAAGTATCTTA
131 TCATCTGTAACACAACAACACCGAAGTCTTCAGGACAGGTTTCACCTCCACGATGAAGTATCTTA
233533 AGCCAGAAGACAATCCAGGAGTTACTGGTTAAAGCTTTGAGTTCGA
196 AGCCAGAAGACAATCCAGGAGTTACTGGTTAAAGCTTTGAGTTCGA
233579 TTTCAATTTCAAGACGAAGGAT
1 TTTCAATTTCAAGACGAAGGAT
233601 TTGTGCTAAG
Statistics
Matches: 254, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 254 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (241 bp):
TTTCAATTTCAAGACGAAGGATATCCAATTCCTAGGCTCAACTTCATGACGAATGGGCCATATAC
ATATACAACTTCACAACGAATGGTATCGTACCCTAACAGATTGACCCAACTTCACAACGAAGGAG
TCATCTGTAACACAACAACACCGAAGTCTTCAGGACAGGTTTCACCTCCACGATGAAGTATCTTA
AGCCAGAAGACAATCCAGGAGTTACTGGTTAAAGCTTTGAGTTCGA
Found at i:234836 original size:3 final size:3
Alignment explanation
Indices: 234828--234886 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
234818 TTAATCCTTT
*
234828 TTA TTA TTA TTTA TT- TTA TCT- TT- TTA TT- TTA ATA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA
234872 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
234887 GTTTTTGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
2 7 0.15
3 35 0.73
4 6 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:235121 original size:32 final size:35
Alignment explanation
Indices: 235085--235166 Score: 89
Period size: 36 Copynumber: 2.4 Consensus size: 35
235075 TTTTACTTTC
*
235085 TTTTTATTTATTT-ATTTA-GTATA-TGTCTTATT
1 TTTTTATTTATTTGATTTATGTATATTATCTTATT
* * *
235117 TTTTTATTTTTTTGTTTTATGTATATTTATTTTATT
1 TTTTTATTTATTTGATTTATGTATA-TTATCTTATT
235153 TTTTTATTATATTT
1 TTTTTATT-TATTT
235167 TTTTTTACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 12 0.30
33 4 0.10
34 5 0.12
36 15 0.38
37 4 0.10
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.74
Consensus pattern (35 bp):
TTTTTATTTATTTGATTTATGTATATTATCTTATT
Found at i:235136 original size:13 final size:13
Alignment explanation
Indices: 235118--235170 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
235108 TGTCTTATTT
*
235118 TTTTATTTTTTTG
1 TTTTATTTTTTTA
*
235131 TTTTATGTATATTTA
1 TTTTAT-T-TTTTTA
235146 TTTTATTTTTTTA
1 TTTTATTTTTTTA
*
235159 TTATATTTTTTT
1 TTTTATTTTTTT
235171 TTACCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 22 0.65
14 2 0.06
15 10 0.29
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:235148 original size:23 final size:21
Alignment explanation
Indices: 235119--235172 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 21
235109 GTCTTATTTT
235119 TTTATTTTTTTGTTTTATGTATA
1 TTTATTTTTTT-TTTTAT-TATA
235142 TTTATTTTATTTTTTTATTATA
1 TTTATTTT-TTTTTTTATTATA
235164 TTT-TTTTTT
1 TTTATTTTTT
235173 ACCTTTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 7 0.23
23 14 0.47
24 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTATTTTTTTTTTTATTATA
Found at i:235156 original size:22 final size:23
Alignment explanation
Indices: 235086--235171 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
235076 TTTACTTTCT
*
235086 TTTTATT-TATTTATTTAGTATATG
1 TTTTATTATATTTATTT--TATTTG
* *
235110 TCTTATT-TTTTTATTTT-TTTG
1 TTTTATTATATTTATTTTATTTG
235131 TTTTATGTATATTTATTTTATTT-
1 TTTTAT-TATATTTATTTTATTTG
*
235154 TTTTATTATATTTTTTTT
1 TTTTATTATATTTATTTT
235172 TACCTTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.15
22 13 0.25
23 15 0.28
24 17 0.32
ACGTcount: A:0.19, C:0.01, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTATTATATTTATTTTATTTG
Found at i:235173 original size:28 final size:28
Alignment explanation
Indices: 235087--235173 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
235077 TTACTTTCTT
* * *
235087 TTTA-TTTATTTATTTAGTATATGTCTTA
1 TTTATTTTATTTTTTTATTATAT-TTTTA
* * * *
235115 TTT-TTTTATTTTTTTGTTTTATGTATA
1 TTTATTTTATTTTTTTATTATATTTTTA
*
235142 TTTATTTTATTTTTTTATTATATTTTTT
1 TTTATTTTATTTTTTTATTATATTTTTA
235170 TTTA
1 TTTA
235174 CCTTTTTACC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTATTTTATTTTTTTATTATATTTTTA
Found at i:235179 original size:23 final size:23
Alignment explanation
Indices: 235131--235181 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
235121 TATTTTTTTG
**
235131 TTTTATGTATATTTATTTTATTT
1 TTTTATGTATATTTATTTTACCT
*
235154 TTTTAT-TATATTTTTTTTTACCT
1 TTTTATGTATA-TTTATTTTACCT
235177 TTTTA
1 TTTTA
235182 CCTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTATGTATATTTATTTTACCT
Found at i:235209 original size:22 final size:21
Alignment explanation
Indices: 235123--235214 Score: 62
Period size: 22 Copynumber: 4.3 Consensus size: 21
235113 TATTTTTTTA
* *
235123 TTTTTTTGTTTTATGTATATTT
1 TTTTTTTCTTTT-TTTATATTT
*
235145 ATTTTATTT-TTTTATTATATTT
1 -TTTT-TTTCTTTTTTTATATTT
* * **
235167 TTTTTTAC-CTTTTTACCTTT
1 TTTTTTTCTTTTTTTATATTT
235187 TTTTTTTCTTTCTTTTATATTT
1 TTTTTTTCTTT-TTTTATATTT
*
235209 TATTTT
1 TTTTTT
235215 GTTATTTGCA
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
20 17 0.32
21 5 0.09
22 20 0.38
23 8 0.15
24 3 0.06
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTATATTT
Found at i:235229 original size:30 final size:31
Alignment explanation
Indices: 235195--235254 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
235185 TTTTTTTTTC
*
235195 TTTCTT-TTATATTTTATTTTGTTATTTGCA
1 TTTCTTCTTATATTTTATTTAGTTATTTGCA
* * *
235225 TTTCTTCTTATTTTTTGTTTAGTTGTTTGC
1 TTTCTTCTTATATTTTATTTAGTTATTTGC
235255 TATGTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.70
Consensus pattern (31 bp):
TTTCTTCTTATATTTTATTTAGTTATTTGCA
Found at i:237409 original size:17 final size:17
Alignment explanation
Indices: 237387--237421 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
237377 ATCACATAAA
237387 TTTCATGTTTGACGCCG
1 TTTCATGTTTGACGCCG
*
237404 TTTCATGTTTGATGCCG
1 TTTCATGTTTGACGCCG
237421 T
1 T
237422 GGAAACTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TTTCATGTTTGACGCCG
Found at i:237573 original size:20 final size:19
Alignment explanation
Indices: 237548--237589 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
237538 ATATTTTTAA
237548 TAAAATATAAATAAAATATT
1 TAAAATAT-AATAAAATATT
* *
237568 TAAAATATATTAAAATTTT
1 TAAAATATAATAAAATATT
237587 TAA
1 TAA
237590 GAGAACGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATATAATAAAATATT
Found at i:238182 original size:29 final size:29
Alignment explanation
Indices: 238149--238248 Score: 191
Period size: 29 Copynumber: 3.4 Consensus size: 29
238139 AAGTATCTTC
238149 TGAATTTATATTTACTATAGATTAATTAT
1 TGAATTTATATTTACTATAGATTAATTAT
238178 TGAATTTATATTTACTATAGATTAATTAT
1 TGAATTTATATTTACTATAGATTAATTAT
*
238207 TGAATTTATATTTATTATAGATTAATTAT
1 TGAATTTATATTTACTATAGATTAATTAT
238236 TGAATTTATATTT
1 TGAATTTATATTT
238249 TTTTATAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (29 bp):
TGAATTTATATTTACTATAGATTAATTAT
Found at i:238435 original size:59 final size:60
Alignment explanation
Indices: 238370--238504 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 60
238360 TTAAATGGTA
* * *
238370 ACTCTCATTTTAAATTACTTCTTAAATTTTTAAATATT-TCAATTTTATCCCT-AACTATG
1 ACTCTCATTTTAAATTACTCCTTAAATTTTTAAATATTCT-AATTTAATCCATAAACTATG
* * *
238429 ACTCTCATTCTAAATTAGTCCTTAAATTTTTGAATATTCTAATTTAATCCATAAACTATG
1 ACTCTCATTTTAAATTACTCCTTAAATTTTTAAATATTCTAATTTAATCCATAAACTATG
*
238489 ACCCTC-TTTCTAAATT
1 ACTCTCATTT-TAAATT
238505 GATCCCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 46 0.71
60 19 0.29
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.46
Consensus pattern (60 bp):
ACTCTCATTTTAAATTACTCCTTAAATTTTTAAATATTCTAATTTAATCCATAAACTATG
Found at i:238520 original size:60 final size:59
Alignment explanation
Indices: 238397--238532 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 59
238387 CTTCTTAAAT
* * * * ** *
238397 TTTTAAATATT-TCAATTTTATCCCTAACTATGACTCTCATTCTAAATTAGTCCTTAAAT
1 TTTTGAATATTCT-AATTTAATCCATAACTATGACCCTCATTCTAAATTAGTCCCCAAAC
*
238456 TTTTGAATATTCTAATTTAATCCATAAACTATGACCCTCTTTCTAAATT-GATCCCCAAAC
1 TTTTGAATATTCTAATTTAATCCAT-AACTATGACCCTCATTCTAAATTAG-TCCCCAAAC
* *
238516 TTTTGAATCTTCCAATT
1 TTTTGAATATTCTAATT
238533 ACATTCCCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 21 0.33
60 43 0.67
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
TTTTGAATATTCTAATTTAATCCATAACTATGACCCTCATTCTAAATTAGTCCCCAAAC
Found at i:238759 original size:60 final size:59
Alignment explanation
Indices: 238666--238821 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 59
238656 ATATATACAT
* * * *
238666 ATAGTTTGGGATAAAATTGGAATGTTCTAAAAGTTTGGA-AACCAATTTAGAAT-AAAGGTC
1 ATAGTTTGGGATGAAATTGAAATATT-TAAAAGTTT-GATAACCAATTTAGAATGAAA-GTA
* ** *
238726 ATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTGATGATTAATTTAGAATGATAGTA
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTTTGATAACCAATTTAGAATGAAAGTA
* * *
238786 ATAGTTTAGGAATGAAATTAAAACATTTAAAAGTTT
1 ATAGTTT-GGGATGAAATTGAAATATTTAAAAGTTT
238822 AAGAACTAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.02
60 61 0.75
61 18 0.22
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATATTTAAAAGTTTGATAACCAATTTAGAATGAAAGTA
Found at i:238832 original size:60 final size:60
Alignment explanation
Indices: 238693--238840 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
238683 TGGAATGTTC
* * * * * *
238693 TAAAAGTTTGGAA-ACCAATTTAGAATAAAGGTCATAGTTTGGGGATGAAATTGAAATATT
1 TAAAAGTTT-GAAGACTAATTTAGAATAAAGGTAATAGTTTAGGAATGAAATTAAAACATT
* * *
238753 TAAAAGTTTGATGATTAATTTAGAATGATA-GTAATAGTTTAGGAATGAAATTAAAACATT
1 TAAAAGTTTGAAGACTAATTTAGAAT-AAAGGTAATAGTTTAGGAATGAAATTAAAACATT
*
238813 TAAAAGTTT-AAGAACTAATTTAAAATAA
1 TAAAAGTTTGAAG-ACTAATTTAGAATAA
238841 CGATAATACT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
59 5 0.07
60 65 0.90
61 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (60 bp):
TAAAAGTTTGAAGACTAATTTAGAATAAAGGTAATAGTTTAGGAATGAAATTAAAACATT
Found at i:238940 original size:21 final size:22
Alignment explanation
Indices: 238916--238956 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
238906 TTTTTCACAT
*
238916 TTTTATCTCTTT-TTTTTTTCC
1 TTTTATCTATTTCTTTTTTTCC
*
238937 TTTTATTTATTTCTTTTTTT
1 TTTTATCTATTTCTTTTTTT
238957 GGGGGGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTATCTATTTCTTTTTTTCC
Found at i:240741 original size:19 final size:20
Alignment explanation
Indices: 240704--240742 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
240694 ATTTTTAAAA
240704 TATTAAAATGATTTATTTAT
1 TATTAAAATGATTTATTTAT
*
240724 TATTAAAAT-ATTTTTTTAT
1 TATTAAAATGATTTATTTAT
240743 AATTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTAAAATGATTTATTTAT
Found at i:240913 original size:24 final size:23
Alignment explanation
Indices: 240886--240931 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
240876 TTCAATATTT
240886 TGATAATT-AATATTTTGATTAAAA
1 TGAT-ATTAAATATTTT-ATTAAAA
240910 TGATATTAAAATATTTTATTAA
1 TGATATT-AAATATTTTATTAA
240932 TATTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (23 bp):
TGATATTAAATATTTTATTAAAA
Found at i:245514 original size:20 final size:21
Alignment explanation
Indices: 245485--245528 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
245475 CAGTTGTCTT
* *
245485 AATTACAAAAATTAAAAGTTA
1 AATTACAAAAATAAAAAATTA
245506 AATTA-AAAAATAAAAAATTA
1 AATTACAAAAATAAAAAATTA
245526 AAT
1 AAT
245529 CCAAATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AATTACAAAAATAAAAAATTA
Found at i:246191 original size:505 final size:506
Alignment explanation
Indices: 245241--246231 Score: 1894
Period size: 505 Copynumber: 2.0 Consensus size: 506
245231 AGTGATAATT
245241 GTCGTAACCATCCTTTGGGTGGGTCCGAAATTGAGCTTCGACTTAAATAAATAGGTTAGAGCCGC
1 GTCGTAACCATCCTTTGGGTGGGTCCGAAATTGAGCTTCGACTTAAATAAATAGGTTAGAGCCGC
245306 CACTGATCATTTATTTTTAAAAACAAATAAAAATTAGGTTGACCAGACACCTCGGTTTACTCTCT
66 CACTGATCATTTATTTTTAAAAACAAATAAAAATTAGGTTGACCAGACACCTCGGTTTACTCTCT
245371 TACATGATCTGCATCTTACCAAAAATATGTCGGGTTCGGGAGTCGGTTACAGTCAAGGAAGGATT
131 TACATGATCTGCATCTTACCAAAAATATGTCGGGTTCGGGAGTCGGTTACAGTCAAGGAAGGATT
*
245436 AGAACCCTTGTACTGTCATTTTGGTACTAATTTAATTTTCAGTTGTCTTAATTACAAAAATTAAA
196 AGAACCCTTGTACTGCCATTTTGGTACTAATTTAATTTTCAGTTGTCTTAATTACAAAAATTAAA
*
245501 AGTTAAATTAAAAAATAAAAAATTAAATCCAAATTACTTACCTTTAATCGATTTAATGTAACCCT
261 AGTTAAATTAAAAAATAAAAAATTAAATCCAAATTACTTACCTTTAATCGATTTAATATAACCCT
245566 AAAAGGTCAGAAAGATGTTAAAAAAATAAAAATATTAAGTGATTCAAAAAGAAGAATTAACAAAA
326 AAAAGGTCAGAAAGATGTTAAAAAAATAAAAATATTAAGTGATTCAAAAAGAAGAATTAACAAAA
245631 ACTAAATTTTAATACTTTAAATAAAGAAAAAAAAAAGAAATACGTACATAC-AAAAAAACATGGA
391 ACTAAATTTTAATACTTTAAATAAAGAAAAAAAAAAGAAATACGTACATACAAAAAAAACATGGA
245695 CATAAAATTAACAGAATGAAATGCCAAAAAAAATAAATTGCAAAGAATAAG
456 CATAAAATTAACAGAATGAAATGCCAAAAAAAATAAATTGCAAAGAATAAG
* * *
245746 GTCGTAACCATCCTTTGGGTGGGTCCGAAATTGGGCTTCGACTTAAATAAATGGGTTAGAGCCGT
1 GTCGTAACCATCCTTTGGGTGGGTCCGAAATTGAGCTTCGACTTAAATAAATAGGTTAGAGCCGC
245811 CACTGATCATTTATTTTTAAAAACAAATAAAAATTAGGTTGACCAGACACCTCGGTTTACTCTCT
66 CACTGATCATTTATTTTTAAAAACAAATAAAAATTAGGTTGACCAGACACCTCGGTTTACTCTCT
245876 TACATGATCTGCATCTTACCAAAAATATGTCGGGTTCGGGAGTCGGTTACAGTCAAGGAAGGATT
131 TACATGATCTGCATCTTACCAAAAATATGTCGGGTTCGGGAGTCGGTTACAGTCAAGGAAGGATT
*
245941 AGAACCCTTGTACTGCCATTTTGGTACTAATTTAATTTTCAGTTGTCTTAATTACGAAAATTAAA
196 AGAACCCTTGTACTGCCATTTTGGTACTAATTTAATTTTCAGTTGTCTTAATTACAAAAATTAAA
246006 AGTTAAATTAAAAAATAAAAAATTAAATCCAAATTACTTACCTTTAATCGATTTAATATAACCCT
261 AGTTAAATTAAAAAATAAAAAATTAAATCCAAATTACTTACCTTTAATCGATTTAATATAACCCT
246071 AAAAGGTCAGAAAGATGTTAAAAAAATAAAAATATTAAGTGATTCAAAAAGAAGAATTAACAAAA
326 AAAAGGTCAGAAAGATGTTAAAAAAATAAAAATATTAAGTGATTCAAAAAGAAGAATTAACAAAA
* *
246136 TCTAAATTTTAATACTTTAAATAAAGAAAAAAAAAAGAAATACGTACATACAAAAAAAAATATGG
391 ACTAAATTTTAATACTTTAAATAAAGAAAAAAAAAAGAAATACGTACATAC-AAAAAAAACATGG
246201 ACATAAAATTAACAGAATGAAATGCCAAAAA
455 ACATAAAATTAACAGAATGAAATGCCAAAAA
246232 CCAATAGAAC
Statistics
Matches: 476, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
505 434 0.91
507 42 0.09
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (506 bp):
GTCGTAACCATCCTTTGGGTGGGTCCGAAATTGAGCTTCGACTTAAATAAATAGGTTAGAGCCGC
CACTGATCATTTATTTTTAAAAACAAATAAAAATTAGGTTGACCAGACACCTCGGTTTACTCTCT
TACATGATCTGCATCTTACCAAAAATATGTCGGGTTCGGGAGTCGGTTACAGTCAAGGAAGGATT
AGAACCCTTGTACTGCCATTTTGGTACTAATTTAATTTTCAGTTGTCTTAATTACAAAAATTAAA
AGTTAAATTAAAAAATAAAAAATTAAATCCAAATTACTTACCTTTAATCGATTTAATATAACCCT
AAAAGGTCAGAAAGATGTTAAAAAAATAAAAATATTAAGTGATTCAAAAAGAAGAATTAACAAAA
ACTAAATTTTAATACTTTAAATAAAGAAAAAAAAAAGAAATACGTACATACAAAAAAAACATGGA
CATAAAATTAACAGAATGAAATGCCAAAAAAAATAAATTGCAAAGAATAAG
Found at i:246204 original size:20 final size:21
Alignment explanation
Indices: 246166--246205 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
246156 ATAAAGAAAA
*
246166 AAAAAAGAAATACGTACATAC
1 AAAAAAGAAATACGGACATAC
*
246187 AAAAAA-AAATATGGACATA
1 AAAAAAGAAATACGGACATA
246206 AAATTAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAAAAGAAATACGGACATAC
Found at i:247344 original size:13 final size:14
Alignment explanation
Indices: 247288--247358 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
247278 TTAACTAATA
247288 ACATAT-AATAATAGT
1 ACATATGAAT-ATA-T
* *
247303 ACATGTAAATATAT
1 ACATATGAATATAT
*
247317 A-ATGATGTATATAT
1 ACAT-ATGAATATAT
*
247331 ACATAT-ACTATAT
1 ACATATGAATATAT
247344 A-ATATGAATATAT
1 ACATATGAATATAT
247357 AC
1 AC
247359 GACACAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
12 4 0.09
13 15 0.34
14 12 0.27
15 10 0.23
16 3 0.07
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
ACATATGAATATAT
Found at i:247393 original size:13 final size:13
Alignment explanation
Indices: 247375--247410 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
247365 ATATATACAC
*
247375 TATATAATGTAAA
1 TATATAATATAAA
*
247388 TATATATTATAAA
1 TATATAATATAAA
247401 TATATAATAT
1 TATATAATAT
247411 GTATGTACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:248410 original size:14 final size:15
Alignment explanation
Indices: 248384--248421 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
248374 TTTTGACGAA
248384 CTTGATATTCTGATT
1 CTTGATATTCTGATT
248399 CTTGAT-TTCTGATT
1 CTTGATATTCTGATT
248413 -TCTGATATT
1 CT-TGATATT
248422 TGGTTTGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 12 0.57
15 8 0.38
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (15 bp):
CTTGATATTCTGATT
Found at i:248473 original size:17 final size:17
Alignment explanation
Indices: 248451--248483 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
248441 GGAGTTTCGT
248451 TAAAGAAACTTTATCTC
1 TAAAGAAACTTTATCTC
248468 TAAAGAAACTTTATCT
1 TAAAGAAACTTTATCT
248484 ATAGTCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (17 bp):
TAAAGAAACTTTATCTC
Found at i:254465 original size:18 final size:18
Alignment explanation
Indices: 254442--254498 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
254432 TATATTTTCC
254442 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
254460 AACAATTGATATCCTTTTGTT
1 AACAATTGGTAT-C-TTT-TT
254481 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
254499 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:254484 original size:21 final size:20
Alignment explanation
Indices: 254442--254498 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
254432 TATATTTTCC
254442 AACAATTGGTAT-C-TTTTT
1 AACAATTGGTATCCTTTTTT
*
254460 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATCCTTTT-TT
254481 AACAATTGGTAT-CTTTTT
1 AACAATTGGTATCCTTTTT
254499 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.32
19 2 0.06
20 8 0.24
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (20 bp):
AACAATTGGTATCCTTTTTT
Found at i:254752 original size:20 final size:21
Alignment explanation
Indices: 254727--254774 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
254717 AACATTAATA
254727 AACAGTACT-GATACTATATG
1 AACAGTACTCGATACTATATG
*
254747 AACAGTA-TCGATACTATGTG
1 AACAGTACTCGATACTATATG
254767 AACAGTAC
1 AACAGTAC
254775 AATACTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (21 bp):
AACAGTACTCGATACTATATG
Found at i:254785 original size:19 final size:20
Alignment explanation
Indices: 254737--254789 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
254727 AACAGTACTG
* *
254737 ATACTATATGAACAGTATCG
1 ATACTATGTGAACAGTATCA
254757 ATACTATGTGAACAGTA-CA
1 ATACTATGTGAACAGTATCA
*
254776 ATACTGTGTGAACA
1 ATACTATGTGAACA
254790 TTAATGAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
ATACTATGTGAACAGTATCA
Found at i:255245 original size:34 final size:34
Alignment explanation
Indices: 255205--255287 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
255195 TCATTGTAAA
* *
255205 AGGGAAAGGTTCTAGCTAAGCCCGTGTAAAATCT
1 AGGGAAAGGTTCTAGCTAAGCCCATGTAAAAGCT
255239 AGGGAAAGGTTCTAGCTAAGCCCATGTAAAAGCT
1 AGGGAAAGGTTCTAGCTAAGCCCATGTAAAAGCT
*
255273 AGGGACAGGTTCTAG
1 AGGGAAAGGTTCTAG
255288 TTTATCCGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.22
Consensus pattern (34 bp):
AGGGAAAGGTTCTAGCTAAGCCCATGTAAAAGCT
Found at i:271880 original size:131 final size:131
Alignment explanation
Indices: 271629--271996 Score: 417
Period size: 131 Copynumber: 2.8 Consensus size: 131
271619 GGAAATATTT
* * * * * * *
271629 AATTATCTTCT-ATCGAGAAGAAACGACATCTCATGCTTTAAAACAATCATTTCTTACTCC-AAT
1 AATTAT-TTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTCATTTATTAC-CCAAAT
* * * ** *
271692 CAAAAT-AA-ATA-ATTACTATTTCCTTCTAAGATTTGATATTAATTCGAGAGAAAACAATAATA
64 CAAAATGAAGAGATATTACTATTTCCTCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATA
*
271754 TCT
129 TCC
*
271757 AATTATTT-TCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCAGTT-ATTTATTACCCAAAT
1 AATTATTTCT-AATCGAGAATAAATGACCTCTCATGCCTTAAAGCA-TTCATTTATTACCCAAAT
** *
271820 TGAAATGAAGAGATATTACTATTTCGTCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATA
64 CAAAATGAAGAGATATTACTATTTCCTCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATA
271885 TCC
129 TCC
* * * * *
271888 AATTATTTCTAATCGAGAATAAATGACCTTTCATTCCTTAGAGCATTCATTTATTACTCTAATCA
1 AATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTCATTTATTACCCAAATCA
* * *
271953 AAATTAAGAGATGTTACTATTTCCTCCTAAAATTCAATATTAAT
66 AAATGAAGAGATATTACTATTTCCTCCTAAAATTAAATATTAAT
271997 TCAAATGTTA
Statistics
Matches: 201, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
126 1 0.00
127 4 0.02
128 49 0.24
129 3 0.01
130 4 0.02
131 139 0.69
132 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (131 bp):
AATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTCATTTATTACCCAAATCA
AAATGAAGAGATATTACTATTTCCTCCTAAAATTAAATATTAATCCGAGAGAAAACAATAATATC
C
Found at i:274111 original size:3 final size:3
Alignment explanation
Indices: 274103--274145 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
274093 CTGAAAAACA
274103 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
274146 TCCCATACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:274750 original size:180 final size:179
Alignment explanation
Indices: 274424--274756 Score: 470
Period size: 180 Copynumber: 1.9 Consensus size: 179
274414 TATTTAAATG
* *
274424 AGAAACTTTAGAAATCGTTTTCTCATTTCGAAAAACATGTGAAAACATCTAGCCCGAAGGTTTTA
1 AGAAACTTTAGAAATCGTTTTCTCATTTCGAAAAACATGTGAAAACATCTAGCCCAAAGGTCTTA
* * * *
274489 TGAATGATCCGAATGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAACCA
66 TGAATGACCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAAGATTTAACCA
* *
274554 TCAAGTTGGAAAGACTTACTGATGATCCGAAAGACTTACTAATTAAGTA
131 TCAAGCTCGAAAGACTTACTGATGATCCGAAAGACTTACTAATTAAGTA
* * * *
274603 AGAAACTTTGGAAATCGTTTTCTCACTTTTC-AAAATCATGTGAAAACATCTTGCCTAAAGGTCT
1 AGAAACTTTAGAAATCGTTTTCTCA--TTTCGAAAAACATGTGAAAACATCTAGCCCAAAGGTCT
* * * *
274667 TATGGATGGCCCGAAGGACTTATCTTCTTGCTCAAAAGGCTTATAGATGACCCGAAAGATTTAAG
64 TATGAATGACCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAAGATTTAAC
* * *
274732 CATCATGCTCGTAAGACTTATTGAT
129 CATCAAGCTCGAAAGACTTACTGAT
274757 AGCCCGAAGG
Statistics
Matches: 133, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
179 24 0.18
180 105 0.79
181 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (179 bp):
AGAAACTTTAGAAATCGTTTTCTCATTTCGAAAAACATGTGAAAACATCTAGCCCAAAGGTCTTA
TGAATGACCCGAAGGACTTATCATCTTGCTCAAAAGGCTTATAGATGACCCGAAAGATTTAACCA
TCAAGCTCGAAAGACTTACTGATGATCCGAAAGACTTACTAATTAAGTA
Found at i:275026 original size:42 final size:41
Alignment explanation
Indices: 274931--275031 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 41
274921 AGGTCATATG
274931 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATA
1 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATA
* * *
274972 GATGACCTGAAGGATTTAATCAT-TATGCTCGAAAGACTTACT-
1 GATGGCCCGAAGGACTT-ATCATCT-TGCTCGAAAGACTTA-TA
275014 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
275032 CCAATTTTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 16 0.31
42 34 0.67
43 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATA
Found at i:275146 original size:260 final size:260
Alignment explanation
Indices: 274603--275156 Score: 812
Period size: 260 Copynumber: 2.1 Consensus size: 260
274593 TAATTAAGTA
* * * * * * * *
274603 AGAAACTTTGGAAATCGTTTTCTCACTTTTC-AAAATCATGTGAAAACATCTTGCCTAAAGGTCT
1 AGAAACTTTGGAAATCGTCTTCTTATTTTTCAAAAAACATGTGAAAACATCCTACCCAAAGGTCA
* *
274667 TATGGATGGCCCGAAGGACTTATCTTCTTGCTCAAAAGGCTTATAGATGACCCGAAAGATTTAAG
66 TATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAAGATTTAAG
* * * *
274732 CATCATGCTCGTAAGACTTATTGATAGCCCGAAGGTCTTACCAATTTTCGAAATAGTTTACTACG
131 CATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACCAATTTTCGAAATAATTTACTACG
* *
274797 TAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTCAGAAAAGATTTAAATG
196 TAAGAAAATTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTCAAAAAAGATTTAAATG
*
274862 AGAAACTTTGGAAATCG-GTTCTTATTTTTCAAAAAAACATGTGAAAACATCCTACCCAAAGGTC
1 AGAAACTTTGGAAATCGTCTTCTTATTTTTC-AAAAAACATGTGAAAACATCCTACCCAAAGGTC
* * *
274926 ATATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCTGAAGGATTTAA
65 ATATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAAGATTTAA
* * *
274991 TCATTATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTT-GAAATAATTTACTA-
130 GCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACCAATTTTCGAAATAATTTACTAC
*
275054 GTTAAGAAAATTTGGAAAT-AGTTTTCTTACTTTTCAAAAATTTTAATTTTCAAAAAAGATTTAA
195 G-TAAGAAAATTTGGAAATCA-TTTTCTTACTTTTCAAAAATTTCAATTTTCAAAAAAGATTTAA
*
275118 ATT
258 ATG
*
275121 AGAAACTTTGGAAATCGTCTTCTTATTTTTCGAAAA
1 AGAAACTTTGGAAATCGTCTTCTTATTTTTCAAAAA
275157 TCATAAAAAC
Statistics
Matches: 264, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
258 12 0.05
259 110 0.42
260 142 0.54
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (260 bp):
AGAAACTTTGGAAATCGTCTTCTTATTTTTCAAAAAACATGTGAAAACATCCTACCCAAAGGTCA
TATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAAGATTTAAG
CATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTACCAATTTTCGAAATAATTTACTACG
TAAGAAAATTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTCAAAAAAGATTTAAATG
Found at i:283155 original size:21 final size:20
Alignment explanation
Indices: 283127--283165 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
283117 TACTACATGA
*
283127 ATTTATAGCATCGACAAAAG
1 ATTTATAGCATCAACAAAAG
*
283147 ATTTCATAGCTTCAACAAA
1 ATTT-ATAGCATCAACAAA
283166 GACCATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
ATTTATAGCATCAACAAAAG
Found at i:294151 original size:18 final size:18
Alignment explanation
Indices: 294094--294171 Score: 81
Period size: 18 Copynumber: 4.4 Consensus size: 18
294084 ATTAATTTGT
294094 ATCTGATAACTGTAAAAT-
1 ATCTGATAACTGT-AAATC
* * * *
294112 GTCTTAT-ATTGT-AATT
1 ATCTGATAACTGTAAATC
294128 ATCTGATAACTGTAAATC
1 ATCTGATAACTGTAAATC
*
294146 ATCTGATAACTGAAAATC
1 ATCTGATAACTGTAAATC
294164 ATCTGATA
1 ATCTGATA
294172 TCTATAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
15 3 0.06
16 5 0.10
17 8 0.16
18 33 0.67
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
ATCTGATAACTGTAAATC
Found at i:294180 original size:18 final size:18
Alignment explanation
Indices: 294128--294180 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
294118 TATTGTAATT
*
294128 ATCTGATAACTGTAAATC
1 ATCTGATAACTATAAATC
294146 ATCTGATAACTGA-AAATC
1 ATCTGATAACT-ATAAATC
*
294164 ATCTGATATCTATAAAT
1 ATCTGATAACTATAAAT
294181 ATTTAGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCTGATAACTATAAATC
Found at i:299494 original size:131 final size:131
Alignment explanation
Indices: 299287--299650 Score: 458
Period size: 131 Copynumber: 2.8 Consensus size: 131
299277 ATTATCTTCT
* * * * * * *
299287 ATCGAGAAGAAACGACCTCCCATGCCTTAAAGCAATCATTTCTTACTTCAATCAAAATAAAAAAA
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCAATCAAAATGAAAAGA
* ** * * *
299352 TATTACTATTTCCTTCTAAGATTTGATATTATTTCGAGAGAAAACAATAATATCTAATTATTTCC
66 TATTACTATTTCCTTCTAAAATTAAATATTAATTCGAGAGAAAACAATAATATCCAACTATTTCC
299417 A
131 A
* * * *
299418 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACCCCAATCGAAATGAAGAGA
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCAATCAAAATGAAAAGA
* * * * * * * *
299483 TATTAATATTTCGTCCTAAAATTAAATACTAATCCTAGAGAAAACGATAATATCCGACTATTTCC
66 TATTACTATTTCCTTCTAAAATTAAATATTAATTCGAGAGAAAACAATAATATCCAACTATTTCC
299548 A
131 A
* * * *
299549 ATCGAGAATAAATGGCCTCTCATGCCTTAGAGCAATCATTTATTACTCCAACCAAAATGAATAGA
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCAATCAAAATGAAAAGA
*
299614 TATTACTATTTCCTTCTAAAATTCAATATTAATTCGA
66 TATTACTATTTCCTTCTAAAATTAAATATTAATTCGA
299651 ATGTTATTAT
Statistics
Matches: 194, Mismatches: 39, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
131 194 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (131 bp):
ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCAATCAAAATGAAAAGA
TATTACTATTTCCTTCTAAAATTAAATATTAATTCGAGAGAAAACAATAATATCCAACTATTTCC
A
Found at i:300943 original size:5 final size:5
Alignment explanation
Indices: 300929--301075 Score: 55
Period size: 5 Copynumber: 26.6 Consensus size: 5
300919 GTTAAAAGAG
* *
300929 AAAAT AAAAAT AAAAC AAAAC AAAAT AAAAT AAAA- AAGAAGT GAGAAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AA-T ---AAAAT
* * * * **
300979 AAAGAT AAAAC AAAAT AAAAT AAAAGTGTT AAATTT TAAAG AAAAT ACAAGG
1 AAA-AT AAAAT AAAAT AAAAT AAAA----T AAA-AT AAAAT AAAAT A-AAAT
*
301031 AAAGAA AAAAT AAAAGGT -AAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAA-AT AAAAT AAAA--T AAAAT AAAAT AAAAT AAAAT AAAAT AAA
301076 TAATAAATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
4 3 0.03
5 74 0.68
6 22 0.20
7 1 0.01
8 1 0.01
9 6 0.06
10 2 0.02
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:301148 original size:18 final size:18
Alignment explanation
Indices: 301127--301169 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
301117 GTTGTTTTTA
*
301127 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAATT
301145 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
301163 AAATAAA
1 AAATAAA
301170 TAATCTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:304482 original size:63 final size:63
Alignment explanation
Indices: 304415--304574 Score: 196
Period size: 63 Copynumber: 2.5 Consensus size: 63
304405 TCTTTAACAT
* * *
304415 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
* * ** *
304478 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
* *
304542 GTACATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
304575 ACTGAACAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
62 2 0.02
63 44 0.53
64 34 0.41
65 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:307324 original size:21 final size:21
Alignment explanation
Indices: 307300--307357 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
307290 TCATAGAATT
*
307300 TGTCCCGAAGGACTACGTAGA
1 TGTCCCAAAGGACTACGTAGA
*
307321 TGTCCCAAAGGACCACGTAGA
1 TGTCCCAAAGGACTACGTAGA
307342 TGTCCCAAAGGACTAC
1 TGTCCCAAAGGACTAC
307358 ATATAACACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (21 bp):
TGTCCCAAAGGACTACGTAGA
Found at i:307399 original size:18 final size:18
Alignment explanation
Indices: 307372--307432 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
307362 AACACATATT
* *
307372 TCCCAAAGGACAACTATG
1 TCCCGAAGGACCACTATG
*
307390 TCCCGGAGGACCACTATG
1 TCCCGAAGGACCACTATG
307408 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
307426 TCCCGAA
1 TCCCGAA
307433 CGACTGTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.16
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:308263 original size:63 final size:62
Alignment explanation
Indices: 308194--308333 Score: 167
Period size: 62 Copynumber: 2.2 Consensus size: 62
308184 TCTTTAACAT
* *
308194 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGAT--ACCAATCACATTCGATGTTTCCATTTTTAAGGG
* * * ** *
308257 GTGCATCGATGCACTCCTTATGCATCGATGCTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTCATGCATCGATACCAATCACATTCGATGTTTCCATTTTTAAGGG
308319 GTGCATCGATGCACT
1 GTGCATCGATGCACT
308334 TCTTGTGCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
61 17 0.25
62 25 0.37
63 25 0.37
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTCATGCATCGATACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:311155 original size:18 final size:18
Alignment explanation
Indices: 311121--311192 Score: 83
Period size: 18 Copynumber: 4.0 Consensus size: 18
311111 ATATAACACA
* *
311121 TATGTCCCGAAGGACCAC
1 TATGTCCCAAATGACCAC
*
311139 TATGTTCCAAA-GAACCAC
1 TATGTCCCAAATG-ACCAC
311157 TATGTCCCAAATGACCAC
1 TATGTCCCAAATGACCAC
* *
311175 TATGTCCCGAAGGACCAC
1 TATGTCCCAAATGACCAC
311193 GTAGACCCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 1 0.02
18 45 0.96
19 1 0.02
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (18 bp):
TATGTCCCAAATGACCAC
Found at i:311192 original size:36 final size:36
Alignment explanation
Indices: 311121--311192 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
311111 ATATAACACA
* *
311121 TATGTCCCGAAGGACCACTATGTTCCAAAGAACCAC
1 TATGTCCCAAAGGACCACTATGTCCCAAAGAACCAC
* * *
311157 TATGTCCCAAATGACCACTATGTCCCGAAGGACCAC
1 TATGTCCCAAAGGACCACTATGTCCCAAAGAACCAC
311193 GTAGACCCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (36 bp):
TATGTCCCAAAGGACCACTATGTCCCAAAGAACCAC
Found at i:311972 original size:20 final size:20
Alignment explanation
Indices: 311947--311984 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
311937 TTCCCCTTGA
311947 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
311967 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
311985 TTAAAAAGTA
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:312083 original size:64 final size:64
Alignment explanation
Indices: 311995--312152 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
311985 TTAAAAAGTA
* ** * * *
311995 CATCGATGCACTACCCATGTATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGAGGTG
1 CATCGATGCACTTCTTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGG-GGTG
* * ** *
312059 CATCGATGCAC-TCTTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGGTG
1 CATCGATGCACTTC-TTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGGGTG
* *
312123 CATCGATGCACTTCTTGTGCAACGATACAC
1 CATCGATGCACTTCTTATGCATCGATACAC
312153 ACTGAACAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
63 1 0.01
64 67 0.87
65 9 0.12
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (64 bp):
CATCGATGCACTTCTTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGGGTG
Found at i:313954 original size:85 final size:84
Alignment explanation
Indices: 313791--313969 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 84
313781 TGACGCGCAA
* * * *
313791 TTATGTGTCATAAATCTATGACGCGCATCTATGACGCTCATTGCGTGTCATTGAAGCCCCTGTCA
1 TTATGTGTCATAAATCTATGACACGCATCTATGACGCTCATTGCGTGTCATTGAAGACACTGCCA
313856 TAAATGAAAATGACACACAT
66 TAAA-GAAAATGACACACAT
* * * * *
313876 TTATGTGTCATAAATTTATGACACGCATGTATGAC-TTACATTGTGTGTCTTTGAAGAACAC-GC
1 TTATGTGTCATAAATCTATGACACGCATCTATGACGCT-CATTGCGTGTCATTGAAG-ACACTGC
313939 CATTAAA-AAATATGACACACAT
64 CA-TAAAGAAA-ATGACACACAT
313961 TCT-TGTGTC
1 T-TATGTGTC
313970 GTGATTGTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
84 4 0.05
85 69 0.86
86 7 0.09
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (84 bp):
TTATGTGTCATAAATCTATGACACGCATCTATGACGCTCATTGCGTGTCATTGAAGACACTGCCA
TAAAGAAAATGACACACAT
Found at i:313996 original size:2 final size:2
Alignment explanation
Indices: 313989--314042 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
313979 TTTCGTAAAT
313989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
314030 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
314043 CAATCATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:319966 original size:10 final size:10
Alignment explanation
Indices: 319945--320011 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 10
319935 ATTAAAAGAG
319945 AAAATAAAAT
1 AAAATAAAAT
319955 AAAATAAAAT
1 AAAATAAAAT
319965 AAAA-AAAA-
1 AAAATAAAAT
319973 AAGAATTGGGAAAAT
1 AA-AA-T---AAAAT
*
319988 AAAGATAAAAC
1 AAA-ATAAAAT
319999 AAAAT-AAAT
1 AAAATAAAAT
320008 AAAA
1 AAAA
320012 AAGAAGTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
8 2 0.04
9 13 0.28
10 16 0.34
11 7 0.15
14 6 0.13
15 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.15
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:320079 original size:12 final size:12
Alignment explanation
Indices: 320051--320092 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
320041 AGGAAAGAAA
320051 AAAAT-AAAGGT
1 AAAATAAAAGGT
320062 AAAATAAAAGGT
1 AAAATAAAAGGT
*
320074 ATAATAAAA--T
1 AAAATAAAAGGT
320084 AAAATAAAA
1 AAAATAAAA
320093 TAAAAGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 5 0.18
12 14 0.50
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (12 bp):
AAAATAAAAGGT
Found at i:320084 original size:5 final size:5
Alignment explanation
Indices: 320051--320107 Score: 51
Period size: 5 Copynumber: 10.4 Consensus size: 5
320041 AGGAAAGAAA
* *
320051 AAAAT AAAGGT AAAAT AAAAGGT ATAAT AAAAT AAAAT AAAAT AAAAGAT
1 AAAAT AAA-AT AAAAT AAAA--T AAAAT AAAAT AAAAT AAAAT -AAA-AT
320101 AAAAT AA
1 AAAAT AA
320108 TAAATAACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 27 0.63
6 10 0.23
7 6 0.14
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:320096 original size:27 final size:28
Alignment explanation
Indices: 320051--320107 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
320041 AGGAAAGAAA
* * *
320051 AAAATAAAGGTAAAATAAAAGGTATAAT
1 AAAATAAAGATAAAATAAAAGATAAAAT
320079 AAAATAAA-ATAAAATAAAAGATAAAAT
1 AAAATAAAGATAAAATAAAAGATAAAAT
320106 AA
1 AA
320108 TAAATAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (28 bp):
AAAATAAAGATAAAATAAAAGATAAAAT
Found at i:320114 original size:12 final size:11
Alignment explanation
Indices: 320076--320114 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
320066 TAAAAGGTAT
320076 AATAAAAT-AA
1 AATAAAATAAA
320086 AATAAAATAAA
1 AATAAAATAAA
320097 AGATAAAATAATA
1 A-ATAAAATAA-A
320110 AATAA
1 AATAA
320115 CAGTAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 3 0.12
12 13 0.50
13 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:320178 original size:18 final size:18
Alignment explanation
Indices: 320157--320199 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
320147 GTTATTTTTA
*
320157 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
320175 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
320193 AAATAAA
1 AAATAAA
320200 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:320815 original size:12 final size:13
Alignment explanation
Indices: 320800--320828 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
320790 AAAGATAAAA
320800 TAAAATAATAT-T
1 TAAAATAATATCT
320812 TAAAATAATATCT
1 TAAAATAATATCT
320825 TAAA
1 TAAA
320829 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:322760 original size:26 final size:24
Alignment explanation
Indices: 322715--322762 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
322705 GTCCCATTTT
322715 ATGTGATATTATATATTGTATATC
1 ATGTGATATTATATATTGTATATC
*
322739 ATGTGATTTATATCATATTGTATA
1 ATGTGATAT-TAT-ATATTGTATA
322763 CACGTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATGTGATATTATATATTGTATATC
Found at i:322794 original size:2 final size:2
Alignment explanation
Indices: 322783--322816 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
322773 ATTACGTATT
322783 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
322817 TACATTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:323818 original size:21 final size:21
Alignment explanation
Indices: 323793--323838 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
323783 AATTTTACCA
323793 TTTATTTTCT-TTTCTTATTTT
1 TTTA-TTTCTGTTTCTTATTTT
*
323814 TTTATTTCTGGTTTCTTTTTTT
1 TTTATTTCT-GTTTCTTATTTT
323836 TTT
1 TTT
323839 CCTAACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTATTTCTGTTTCTTATTTT
Found at i:323948 original size:2 final size:2
Alignment explanation
Indices: 323941--323966 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
323931 TGTATCTAGC
323941 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
323967 TTGTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323973 original size:14 final size:14
Alignment explanation
Indices: 323942--323984 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
323932 GTATCTAGCA
* *
323942 TATATATATATATA
1 TATATATATATTTG
323956 TATATATATATTTG
1 TATATATATATTTG
* *
323970 TATATTTGTATTTG
1 TATATATATATTTG
323984 T
1 T
323985 TTTTCTTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (14 bp):
TATATATATATTTG
Found at i:324013 original size:46 final size:45
Alignment explanation
Indices: 323963--324059 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 45
323953 ATATATATAT
*
323963 ATATTTGTATATTTGTATT-TGT-TTTTCTTACCTTTCGTTTTGTTTC
1 ATATTTATATATTTGTATTAT-TATTTT-TTACCTTTC-TTTTGTTTC
* *
324009 ATATTTATATATTTTTATTATTACTTTTTTTCCTTTCTTTTGTTTC
1 ATATTTATATATTTGTATTATTA-TTTTTTACCTTTCTTTTGTTTC
324055 -TATTT
1 ATATTT
324060 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
45 5 0.11
46 27 0.60
47 9 0.20
48 4 0.09
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.68
Consensus pattern (45 bp):
ATATTTATATATTTGTATTATTATTTTTTACCTTTCTTTTGTTTC
Found at i:324075 original size:5 final size:5
Alignment explanation
Indices: 324067--324105 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
324057 TTTTTTTATT
*
324067 TTTTA TTTTA TTTTA TTTTA TTTGTT TTTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA TTTT
324106 TTTCCTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.73
6 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:324075 original size:15 final size:14
Alignment explanation
Indices: 324055--324108 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
324045 CTTTTGTTTC
324055 TATTTTTTTATTTTT
1 TATTTTTTT-TTTTT
*
324070 TATTTTATTTTATTT
1 TATTTT-TTTTTTTT
*
324085 TATTTGTTTTTTATT
1 TATTT-TTTTTTTTT
324100 TATTTTTTT
1 TATTTTTTT
324109 CCTCTCCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (14 bp):
TATTTTTTTTTTTT
Found at i:324075 original size:26 final size:26
Alignment explanation
Indices: 324046--324105 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
324036 TTTTCCTTTC
*
324046 TTTTGTTTCTATTTT-TTTATTTTTTA
1 TTTTATTT-TATTTTATTTATTTTTTA
*
324072 TTTTATTTTATTTTATTTGTTTTTTA
1 TTTTATTTTATTTTATTTATTTTTTA
324098 -TTTATTTT
1 TTTTATTTT
324106 TTTCCTCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.13, C:0.02, G:0.03, T:0.82
Consensus pattern (26 bp):
TTTTATTTTATTTTATTTATTTTTTA
Found at i:327467 original size:23 final size:23
Alignment explanation
Indices: 327413--327467 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
327403 TCATACTTTG
* *
327413 CATTTTATTTTCCATGTTTATTT
1 CATTCTATTTTCCATGTTTATTA
**
327436 TTTTCTATTTTCCATGTTT-TTA
1 CATTCTATTTTCCATGTTTATTA
327458 CATTCATATT
1 CATTC-TATT
327468 AACCAATAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.18, C:0.15, G:0.04, T:0.64
Consensus pattern (23 bp):
CATTCTATTTTCCATGTTTATTA
Found at i:331652 original size:18 final size:17
Alignment explanation
Indices: 331598--331646 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
331588 TTGGACTTCT
* *
331598 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
331616 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
331634 AGTGCATTCGATG
1 AGTGCA-TCGATG
331647 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:331733 original size:21 final size:21
Alignment explanation
Indices: 331709--331748 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
331699 CAATTTATTC
331709 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
331730 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
331749 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:334337 original size:24 final size:23
Alignment explanation
Indices: 334266--334345 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
334256 CATGGTCTTG
*
334266 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
334289 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
334310 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
*
334334 TGCATTGATGCA
1 TGCATCGATGCA
334346 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.24
24 16 0.35
25 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:334358 original size:44 final size:42
Alignment explanation
Indices: 334243--334365 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
334233 AAAACCCGAC
* *
334243 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * **
334286 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
* *
334331 GGATGCATTGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
334366 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 17 0.27
44 28 0.44
45 18 0.29
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:337895 original size:24 final size:24
Alignment explanation
Indices: 337868--337920 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
337858 TAATGATTTT
337868 TCTATTAGAGGTTCTTTGGGGACC
1 TCTATTAGAGGTTCTTTGGGGACC
337892 TCTATTAGAGGTTCTTTGGGGACC
1 TCTATTAGAGGTTCTTTGGGGACC
337916 TCTAT
1 TCTAT
337921 GATTGTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (24 bp):
TCTATTAGAGGTTCTTTGGGGACC
Found at i:339737 original size:64 final size:65
Alignment explanation
Indices: 339669--339832 Score: 206
Period size: 64 Copynumber: 2.5 Consensus size: 65
339659 AAATAGCCTG
* *
339669 GTGCATCGATGCATGGATTGTACATCGATGCATC-AAATGCATTCGATGTTTTAATTAAATCAAA
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCGAAATGCATTCGATGTTTTAATTAAATCAAA
** * * * **
339733 GTGCATCGATGCATGGAGAGTGCATCGGTGCA-CGGAATGCATTCGATGTTTTAATTTATTCATT
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCGAAATGCATTCGATGTTTTAATTAAATCAAA
339797 GATGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 G-TGCATCGATGCATGG-ATTG-TGCATCGGTGCAT
339833 GCCTTTGAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.01
64 54 0.64
65 15 0.18
66 2 0.02
67 12 0.14
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATGGATTGTGCATCGGTGCATCGAAATGCATTCGATGTTTTAATTAAATCAAA
Found at i:339818 original size:21 final size:21
Alignment explanation
Indices: 339794--339833 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
339784 TAATTTATTC
339794 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
339815 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
339834 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:345627 original size:46 final size:46
Alignment explanation
Indices: 345574--345667 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
345564 AAATTTTGTA
*
345574 CAAGTCAGCCCAAGAAATTATCGATCTGGAAGGTAAACCATTGAGC
1 CAAGTCAGCCCAAGAAATTATCGATCCGGAAGGTAAACCATTGAGC
*
345620 CAAGTCAGCCCAAGAAATTATCGATCCGGAAGGTAATCCATTGAGC
1 CAAGTCAGCCCAAGAAATTATCGATCCGGAAGGTAAACCATTGAGC
345666 CA
1 CA
345668 TGCCCTGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (46 bp):
CAAGTCAGCCCAAGAAATTATCGATCCGGAAGGTAAACCATTGAGC
Found at i:350847 original size:11 final size:11
Alignment explanation
Indices: 350831--350856 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
350821 CCTAAGTCGA
350831 AAAAGAAAAAG
1 AAAAGAAAAAG
350842 AAAAGAAAAAG
1 AAAAGAAAAAG
350853 AAAA
1 AAAA
350857 TGTTTTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:350913 original size:8 final size:8
Alignment explanation
Indices: 350896--350945 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
350886 CCTAAATTAG
350896 AAAAAA-A
1 AAAAAAGA
350903 AAAAAAG-
1 AAAAAAGA
350910 -AAAAAGA
1 AAAAAAGA
350917 AAAAAAGA
1 AAAAAAGA
350925 GAAAAAAGA
1 -AAAAAAGA
350934 AAAAAAGA
1 AAAAAAGA
350942 AAAA
1 AAAA
350946 GAAAAATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 19 0.49
9 8 0.21
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:350913 original size:14 final size:15
Alignment explanation
Indices: 350894--350951 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
350884 ACCCTAAATT
350894 AGAAAAA-AAAAAAA
1 AGAAAAAGAAAAAAA
350908 AGAAAAAGAAAAAAA
1 AGAAAAAGAAAAAAA
350923 GAGAAAAA-AGAAAAAA
1 -AGAAAAAGA-AAAAAA
350939 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
350952 TAAGGTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.17
15 19 0.47
16 14 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAAAAA
Found at i:350921 original size:17 final size:17
Alignment explanation
Indices: 350899--350951 Score: 67
Period size: 16 Copynumber: 3.3 Consensus size: 17
350889 AAATTAGAAA
350899 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
*
350916 -AAAAAAAGAG-AAAA-
1 AAAAAAAAAAGAAAAAG
*
350930 AAGAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
350947 AAAAA
1 AAAAA
350952 TAAGGTGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 12 0.41
16 13 0.45
17 4 0.14
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:350937 original size:31 final size:30
Alignment explanation
Indices: 350894--350951 Score: 107
Period size: 31 Copynumber: 1.9 Consensus size: 30
350884 ACCCTAAATT
350894 AGAAAAAAAAAAAAAGAAAAAGAAAAAAAG
1 AGAAAAAAAAAAAAAGAAAAAGAAAAAAAG
350924 AGAAAAAAGAAAAAAAGAAAAAGAAAAA
1 AGAAAAAA-AAAAAAAGAAAAAGAAAAA
350952 TAAGGTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (30 bp):
AGAAAAAAAAAAAAAGAAAAAGAAAAAAAG
Found at i:353896 original size:4 final size:4
Alignment explanation
Indices: 353887--353935 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
353877 TTCCTAACAT
* * *
353887 TTTA TTTA TTCA TATA -TTG TTTA TTTA -TTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
353933 TTT
1 TTT
353936 TCCTCTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 4 0.11
4 33 0.89
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:353909 original size:19 final size:19
Alignment explanation
Indices: 353887--353934 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
353877 TTCCTAACAT
*
353887 TTTATTTATTCATATA-TTG
1 TTTATTTATT-ATATATTTA
*
353906 TTTATTTATTATTTATTTA
1 TTTATTTATTATATATTTA
353925 TTTATTTATT
1 TTTATTTATT
353935 TTCCTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTATTATATATTTA
Found at i:354115 original size:19 final size:18
Alignment explanation
Indices: 354093--354154 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
354083 TTTCCCTTTC
*
354093 TTTTGTTTCTATTTCTTTA
1 TTTTGTTT-TATTTATTTA
*
354112 TTTTGTATTTTTTTATTTAA
1 TTTTGT-TTTATTTATTT-A
*
354132 TTTGTTTTTTATTTATTTA
1 TTT-TGTTTTATTTATTTA
354151 TTTT
1 TTTT
354155 TCCTCTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 1 0.03
19 17 0.47
20 16 0.44
21 2 0.06
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTGTTTTATTTATTTA
Found at i:354141 original size:16 final size:15
Alignment explanation
Indices: 354102--354155 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
354092 CTTTTGTTTC
*
354102 TATTTCTTTATTT-TG
1 TATTT-TTTATTTATT
354117 TATTTTTTTATTTAATT
1 TA-TTTTTTATTT-ATT
*
354134 TGTTTTTTATTTATT
1 TATTTTTTATTTATT
354149 TATTTTT
1 TATTTTT
354156 CCTCTCCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 18 0.55
16 13 0.39
17 2 0.06
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (15 bp):
TATTTTTTATTTATT
Found at i:354199 original size:13 final size:13
Alignment explanation
Indices: 354177--354210 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
354167 TTTTTTTCTT
*
354177 TTTATATTCTGTA
1 TTTATTTTCTGTA
*
354190 TTTATTTTCTTTA
1 TTTATTTTCTGTA
354203 TTTATTTT
1 TTTATTTT
354211 GTACATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTTCTGTA
Found at i:354221 original size:24 final size:23
Alignment explanation
Indices: 354168--354221 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
354158 TCTCCTTGGT
*
354168 TTTTTTCTTTTTATATTCTGTAT
1 TTTTTTCTTTTTATATTCTGTAA
*
354191 TTATTTTCTTTATT-TATTTTGTACA
1 TT-TTTTCTTT-TTATATTCTGTA-A
354216 TTTTTT
1 TTTTTT
354222 GTTCTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.08
24 20 0.77
25 4 0.15
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTTTCTTTTTATATTCTGTAA
Found at i:357314 original size:28 final size:27
Alignment explanation
Indices: 357268--357332 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
357258 TCATTTACGT
* * *
357268 TTTAATATTACATATAAAAATTATATAG
1 TTTAATATAAAATAAAAAAATTAT-TAG
* *
357296 TTTAATATAAAATAAAAAATTTATTAT
1 TTTAATATAAAATAAAAAAATTATTAG
357323 TTTCAATATA
1 TTT-AATATA
357333 TGCAATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTAATATAAAATAAAAAAATTATTAG
Found at i:359860 original size:29 final size:27
Alignment explanation
Indices: 359791--359863 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 27
359781 ATATTTTCAA
* *
359791 AATAAAAATTCGGTTCGATTCACGGTT
1 AATAAAAATTAGGTTCGATTAACGGTT
359818 AA-AAAAA--AGAGTTCGATTAATTCGGTT
1 AATAAAAATTAG-GTTCGATTAA--CGGTT
*
359845 AATAAAAATTTGGTTCGAT
1 AATAAAAATTAGGTTCGAT
359864 CAGCGGCCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 1 0.03
25 9 0.24
26 5 0.14
27 9 0.24
28 5 0.14
29 7 0.19
30 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (27 bp):
AATAAAAATTAGGTTCGATTAACGGTT
Found at i:363172 original size:35 final size:35
Alignment explanation
Indices: 363132--363204 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
363122 TGCTATCACA
* *
363132 ATAAACACCATAGTACTTAAAATGCATCTATGATC
1 ATAAACACCATAGGACTTAAAATGAATCTATGATC
363167 ATAAACACCATAGGACTTAAAATGAATCTATGATC
1 ATAAACACCATAGGACTTAAAATGAATCTATGATC
363202 ATA
1 ATA
363205 GGTGTATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (35 bp):
ATAAACACCATAGGACTTAAAATGAATCTATGATC
Found at i:365190 original size:4 final size:4
Alignment explanation
Indices: 365181--365253 Score: 53
Period size: 4 Copynumber: 17.5 Consensus size: 4
365171 TAATATTAAC
* *
365181 AAAT AAAT AAAAT AAA- GAAT CAAAT -AAT GAAT AAAT AAA- AAAT ATAAT
1 AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
365229 GAAAT ATAAT AAAT AAAT AATAT AA
1 -AAAT A-AAT AAAT AAAT AA-AT AA
365254 TATATAATAG
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
3 8 0.14
4 27 0.47
5 21 0.37
6 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:365215 original size:28 final size:26
Alignment explanation
Indices: 365182--365250 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
365172 AATATTAACA
365182 AATAAATAAAATAA-AGAATCAAATAAT
1 AATAAATAAAA-AATAGAATCAAAT-AT
* *
365209 GAATAAATAAAAAATATAATGAAATAT
1 -AATAAATAAAAAATAGAATCAAATAT
*
365236 AATAAATAAATAATA
1 AATAAATAAAAAATA
365251 TAATATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 14 0.38
27 4 0.11
28 19 0.51
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (26 bp):
AATAAATAAAAAATAGAATCAAATAT
Found at i:365258 original size:23 final size:24
Alignment explanation
Indices: 365210--365262 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
365200 TCAAATAATG
365210 AATAAATAAAAAATATAATGAAATAT
1 AATAAATAAAAAATATAAT--AATAT
*
365236 AATAAATAAATAATATAAT-ATAT
1 AATAAATAAAAAATATAATAATAT
365259 AATA
1 AATA
365263 GTAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.31
26 18 0.69
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAAATAAAAAATATAATAATAT
Found at i:365260 original size:16 final size:18
Alignment explanation
Indices: 365231--365270 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
365221 AATATAATGA
365231 AATATAATAAATAA-A-T
1 AATATAATAAATAATAGT
*
365247 AATATAATATATAATAGT
1 AATATAATAAATAATAGT
365265 AATATA
1 AATATA
365271 TACGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AATATAATAAATAATAGT
Found at i:365267 original size:13 final size:12
Alignment explanation
Indices: 365232--365272 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
365222 ATATAATGAA
365232 ATATAATA-AAT
1 ATATAATATAAT
*
365243 AAATAATATAAT
1 ATATAATATAAT
365255 ATATAATAGTAAT
1 ATATAATA-TAAT
365268 ATATA
1 ATATA
365273 CGTATATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 7 0.27
12 10 0.38
13 9 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:366656 original size:23 final size:24
Alignment explanation
Indices: 366605--366657 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
366595 GTTAGGGGAT
* **
366605 TAGGG-TTGAAACCCTAATCTATT
1 TAGGGTTTGAAACCCTAATATAAA
366628 TAGGGTTTGAAACCCTAATATAAA
1 TAGGGTTTGAAACCCTAATATAAA
366652 T-GGGTT
1 TAGGGTT
366658 CTCTTGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (24 bp):
TAGGGTTTGAAACCCTAATATAAA
Found at i:367165 original size:40 final size:42
Alignment explanation
Indices: 367095--367309 Score: 156
Period size: 40 Copynumber: 5.0 Consensus size: 42
367085 ACGGCTGGTT
* * *
367095 ATCTAGGGG-TGACACGACTCCTACGCGATGAGGAGATCTGG
1 ATCTAGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
* * *
367136 -TC-GGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 ATCTAGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
* * * *
367176 CCATCTTTAGGAAGGGCAATAACATGGTTCCTACGTGATGAGGATG-TCTGG
1 --ATC--TA-G--GGG--ATGACACGGCTCCTACGTGATGAAGA-GATCTGG
367227 TTATCTAGGGG-TGACACGGCTCCTACGTGATGAAGAGATCTGG
1 --ATCTAGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
* * *
367270 -TC-AGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 ATCTAGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
367310 CAATCTCTAG
Statistics
Matches: 138, Mismatches: 21, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
39 8 0.06
40 61 0.44
42 1 0.01
43 28 0.20
46 3 0.02
47 1 0.01
48 1 0.01
49 5 0.04
51 29 0.21
52 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
ATCTAGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
Found at i:367250 original size:134 final size:134
Alignment explanation
Indices: 366960--367320 Score: 535
Period size: 134 Copynumber: 2.7 Consensus size: 134
366950 AGTTCGAGTC
* * * * * *
366960 ATCTAAGGGTGACACGGATCCTACATGATGAGGACATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
**
367025 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCAATAACTCGGTTCCTACGCGATGAGGACGGC
367090 TGGTT
130 TGGTT
* *
367095 ATCTAGGGGTGACACGACTCCTACGCGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
* * *
367160 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCAATAACAT-GGTTCCTACGTGATGAGGATGTC
66 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCAATAAC-TCGGTTCCTACGCGATGAGGACGGC
367224 TGGTT
130 TGGTT
* * *
367229 ATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCAGGAGATGACACGGCTCATACG
1 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
* *
367294 TGATGAAGAGTTCTGGCAATCTCTAGG
66 TGATGAAGAGTTCTGGCCATCTTTAGG
367321 GATAATGATT
Statistics
Matches: 205, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
134 134 0.65
135 71 0.35
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (134 bp):
ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACG
TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCAATAACTCGGTTCCTACGCGATGAGGACGGCT
GGTT
Found at i:367473 original size:162 final size:163
Alignment explanation
Indices: 367206--367530 Score: 634
Period size: 162 Copynumber: 2.0 Consensus size: 163
367196 AACATGGTTC
*
367206 CTACGTGATGAGGATGTCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
1 CTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
367271 CAGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCAATCTCTAGGGATAATGATTTCAAA
66 CAGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCAATCTCTAGGGATAATGATTTCAAA
367336 AGAAACCGACTCAAA-ATGATGTTTCAAAAGAA
131 AGAAACCGACTCAAAGATGATGTTTCAAAAGAA
367368 CTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
1 CTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
367433 CAGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCAATCTCTAGGGATAATGATTTCAAA
66 CAGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCAATCTCTAGGGATAATGATTTCAAA
367498 AGAAACCGACTCAAAGATGATGTTTCAAAAGAA
131 AGAAACCGACTCAAAGATGATGTTTCAAAAGAA
367531 GCAGACTCAA
Statistics
Matches: 161, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
162 144 0.89
163 17 0.11
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.24
Consensus pattern (163 bp):
CTACGTGATGAGGACGTCTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
CAGGAGATGACACGGCTCATACGTGATGAAGAGTTCTGGCAATCTCTAGGGATAATGATTTCAAA
AGAAACCGACTCAAAGATGATGTTTCAAAAGAA
Found at i:367766 original size:20 final size:21
Alignment explanation
Indices: 367741--367785 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
367731 TTTCTCACGA
* *
367741 AAAAC-TGTTTCAAGAGAGAC
1 AAAACTTGTTTCAAAAGAAAC
367761 AAAACTTTGTTTCAAAAGAAAC
1 AAAAC-TTGTTTCAAAAGAAAC
367783 AAA
1 AAA
367786 CTCAAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
22 16 0.76
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (21 bp):
AAAACTTGTTTCAAAAGAAAC
Found at i:367818 original size:29 final size:30
Alignment explanation
Indices: 367769--368008 Score: 121
Period size: 29 Copynumber: 8.0 Consensus size: 30
367759 ACAAAACTTT
367769 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
367799 GTTTCAAAAGAAA-TGACTCAAAGA-TTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
367826 -TTTCACGAAATTGTCTTAAGAGAAA--CAAA-ACTTTG
1 GTTTCA--AAA--G----AA-ACAAACTCAAAGATTTTG
* * * *
367861 G-TT-AAAAAAAATAGACTCAAAGAATTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
367888 -TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
367916 ATTTCAAAAGAAAC-AACTCACAGACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
* * *
367945 GTTTCAAGAGAAACTAACTCAAAGATAGGTTTT
1 GTTTCAAAAGAAACAAACTCAAAGAT---TTTG
*
367978 GTTTCAAAAGAAACAATCTCAAAGATGTTTG
1 GTTTCAAAAGAAACAAACTCAAAGAT-TTTG
368009 TTTTAAGAGA
Statistics
Matches: 164, Mismatches: 20, Indels: 51
0.70 0.09 0.22
Matches are distributed among these distances:
25 3 0.02
26 7 0.04
27 18 0.11
28 17 0.10
29 44 0.27
30 27 0.16
31 4 0.02
32 6 0.04
33 24 0.15
34 10 0.06
35 3 0.02
36 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:367921 original size:91 final size:91
Alignment explanation
Indices: 367690--367915 Score: 257
Period size: 91 Copynumber: 2.5 Consensus size: 91
367680 GTTAAGAGAC
* * *
367690 ACAATCTCAAAG-A-TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCACGAAAAACTGTTTCA
1 ACAAACTCAAAGAATTTTTTCAAAAGAAACA-ACTCAAAGATTTTTTTCACG-AAAACTGTTTCA
* * *
367753 AGAGAGACAAAACTTTGTTTCAAAAGAA
64 AGAGAAACAAAACTTTGGTTCAAAAAAA
* ** *
367781 ACAAACTCAAAGATTTTGGTTTCAAAAGAAATGACTCAAAGA-TTTTTTCACG-AAATTGTCTT-
1 ACAAACTCAAAGAATTT--TTTCAAAAGAAACAACTCAAAGATTTTTTTCACGAAAACTGT-TTC
367843 AAGAGAAACAAAACTTTGGTT-AAAAAAA
63 AAGAGAAACAAAACTTTGGTTCAAAAAAA
* *
367871 ATAGACTCAAAGAATTTTTTCAAAAGAAACAACTCAAAGATTTTT
1 ACAAACTCAAAGAATTTTTTCAAAAGAAACAACTCAAAGATTTTT
367916 ATTTCAAAAG
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
88 21 0.18
89 4 0.04
90 20 0.18
91 36 0.32
92 2 0.02
93 11 0.10
94 9 0.08
95 11 0.10
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (91 bp):
ACAAACTCAAAGAATTTTTTCAAAAGAAACAACTCAAAGATTTTTTTCACGAAAACTGTTTCAAG
AGAAACAAAACTTTGGTTCAAAAAAA
Found at i:367983 original size:33 final size:30
Alignment explanation
Indices: 367888--368020 Score: 155
Period size: 29 Copynumber: 4.4 Consensus size: 30
367878 CAAAGAATTT
*
367888 TTTCAAAAGAAACAACTCAAAGAT-TTTTA
1 TTTCAAAAGAAACAACTCAAAGATGTTTTG
* *
367917 TTTCAAAAGAAACAACTCACAGA-CTTTTG
1 TTTCAAAAGAAACAACTCAAAGATGTTTTG
*
367946 TTTCAAGAGAAACTAACTCAAAGATAGGTTTTG
1 TTTCAAAAGAAAC-AACTCAAAGAT--GTTTTG
367979 TTTCAAAAGAAACAATCTCAAAGATG-TTTG
1 TTTCAAAAGAAACAA-CTCAAAGATGTTTTG
* *
368009 TTTTAAGAGAAA
1 TTTCAAAAGAAA
368021 TTGTCTCAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
29 38 0.42
30 23 0.26
31 1 0.01
32 2 0.02
33 26 0.29
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.30
Consensus pattern (30 bp):
TTTCAAAAGAAACAACTCAAAGATGTTTTG
Done.