Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001592.1 Hibiscus syriacus cultivar Beakdansim tig00003172_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: 193584
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3058 original size:14 final size:14
Alignment explanation
Indices: 3039--3078 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
3029 CCTTTGGTAT
3039 CAGTATCATATGAA
1 CAGTATCATATGAA
3053 CAGTATCATATGAA
1 CAGTATCATATGAA
3067 CAGTATCGATAT
1 CAGTATC-ATAT
3079 TATTCATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (14 bp):
CAGTATCATATGAA
Found at i:8011 original size:20 final size:20
Alignment explanation
Indices: 7955--8011 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
7945 CAATGTAGGT
*
7955 AGTATCGATACTACCCAGTG
1 AGTATCGATACTACCCTGTG
7975 AGTATCGATACTACCCTGTG
1 AGTATCGATACTACCCTGTG
*
7995 AGTATCGATACTTCCCT
1 AGTATCGATACTACCCT
8012 TACCTTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTACCCTGTG
Found at i:10744 original size:3 final size:3
Alignment explanation
Indices: 10736--10769 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10726 TTACCAATAT
10736 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
10770 GTTTTTGTTT
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):
TTA
Found at i:15941 original size:203 final size:203
Alignment explanation
Indices: 15586--16056 Score: 705
Period size: 203 Copynumber: 2.3 Consensus size: 203
15576 AGGTCGGTGC
* *
15586 TATTCCAACTCCTTATGTGATGGAAACGAGCTAAGGTTAAACAAATTCTTCTCATTATGAACTTC
1 TATT-CAACTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
15651 TTCTCCATCATCGGATGTGTTCTTCTCATTATGAACCCTTCCATTGGAAATGTTGATCCACCTCC
65 TTCTCCATCATCGGATGAGTTCTTCTCATTATGAACCCTTCCACTGGAAATGTTGATCCACCTCC
* * * *
15716 TTCTATGATGGAATCGAACAAAGTGATGATGATGATCCAACTCC-TTATGCGATGGATGAGCCAA
130 TTCTATGATGGAATCGAACAAAGTGATGATGATGATCAAACTCCATT-TGCGATGGATCAACAAA
15780 GTATTAGT-T
194 GTATTAGTGT
*
15789 ATATTACAACTCCTTATGTGATGGAAATGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
1 -TATT-CAACTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* *
15854 CTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTC-TCCACTGGAAATGTTGATCCACCTC
64 CTTCTCCATCATCGGATGAGTTCTTCTCATTATGAACCCTTCCACTGGAAATGTTGATCCACCTC
* * ** *
15918 CTTCTGTGATGGATTTTAACAAAGTGATGATGCTGATCAAACTCCATTTGCGATGGATCAACAAA
129 CTTCTATGATGGAATCGAACAAAGTGATGATGATGATCAAACTCCATTTGCGATGGATCAACAAA
*
15983 GTATTGGTGT
194 GTATTAGTGT
* *
15993 TGTTCTAACTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTATTCTCATTATGAACTT
1 TATTC-AACTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTT
16057 ATTCATTGGG
Statistics
Matches: 243, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
202 1 0.00
203 143 0.59
204 99 0.41
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (203 bp):
TATTCAACTCCTTATGTGATGGAAACGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTCCATCATCGGATGAGTTCTTCTCATTATGAACCCTTCCACTGGAAATGTTGATCCACCTCCT
TCTATGATGGAATCGAACAAAGTGATGATGATGATCAAACTCCATTTGCGATGGATCAACAAAGT
ATTAGTGT
Found at i:17312 original size:24 final size:24
Alignment explanation
Indices: 17280--17367 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
17270 GATATCAGAA
*
17280 ATCAAAACAGAATTCAGATAAGAT
1 ATCAGAACAGAATTCAGATAAGAT
* * *
17304 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATAAGAT
* *
17328 ATCAGAACAGAATTCAGGTAATAT
1 ATCAGAACAGAATTCAGATAAGAT
17352 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
17368 AGTCGGAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATAAGAT
Found at i:17337 original size:48 final size:48
Alignment explanation
Indices: 17273--17364 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
17263 AAACAGAGAT
17273 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
* * *
17321 ATCAGAAATCAGAACAGAATTCAGGTAATATATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAAT
17365 TCAAGTCGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:17344 original size:12 final size:12
Alignment explanation
Indices: 17275--17344 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
17265 ACAGAGATAT
* *
17275 CAGAAATCAAAA
1 CAGAATTCAGAA
17287 CAGAATTCAGATA
1 CAGAATTCAGA-A
17300 -AG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
17311 CAGAATCCAGAT
1 CAGAATTCAGAA
*
17323 CAGAAATCAGAA
1 CAGAATTCAGAA
17335 CAGAATTCAG
1 CAGAATTCAG
17345 GTAATATATC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.07
12 40 0.87
13 3 0.07
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:17377 original size:48 final size:48
Alignment explanation
Indices: 17273--17377 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
17263 AAACAGAGAT
*
17273 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
* * *
17321 ATCAGAAATCAGAACAGAATTCAGGTAATATATCAGAACAGAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAA-TCAAG
*
17370 -TCGGAAAT
1 ATCAGAAAT
17378 AAGATAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 47 0.92
49 4 0.08
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:20014 original size:35 final size:35
Alignment explanation
Indices: 19966--20043 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
19956 TTTTTAATAA
*
19966 AAATAAAATCAACAATCAAGTATAACATTATAATT
1 AAATAAAACCAACAATCAAGTATAACATTATAATT
* * *
20001 AAATACAACCAACAATCAAGTTTAACGTTATAATT
1 AAATAAAACCAACAATCAAGTATAACATTATAATT
20036 AAATAAAA
1 AAATAAAA
20044 TTTATTCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (35 bp):
AAATAAAACCAACAATCAAGTATAACATTATAATT
Found at i:22774 original size:9 final size:9
Alignment explanation
Indices: 22760--22786 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
22750 CATATGAGTT
22760 TGTATATAA
1 TGTATATAA
22769 TGTATATAA
1 TGTATATAA
22778 TGTATATAA
1 TGTATATAA
22787 ATTTATTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
TGTATATAA
Found at i:26250 original size:19 final size:20
Alignment explanation
Indices: 26213--26249 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
26203 GAGTAGCTGG
26213 AAATTTGATTTATTATTTTA
1 AAATTTGATTTATTATTTTA
26233 AAATTT-ATTT-TTATTTT
1 AAATTTGATTTATTATTTT
26250 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
AAATTTGATTTATTATTTTA
Found at i:29361 original size:31 final size:31
Alignment explanation
Indices: 29293--29379 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
29283 AAATAAGCAA
* *
29293 TTGCCACTAAGGCCACACAAGCAATTGCACTT
1 TTGCCACTAAGGCCA-ACAAGCAAATCCACTT
* * **
29325 ATGCCACTAAGGCCAAGAATTAAATCCACTT
1 TTGCCACTAAGGCCAACAAGCAAATCCACTT
*
29356 TTGCCACTAAGGCCAA-AAACAAAT
1 TTGCCACTAAGGCCAACAAGCAAAT
29380 ACTCCTACAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
30 6 0.13
31 26 0.57
32 14 0.30
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (31 bp):
TTGCCACTAAGGCCAACAAGCAAATCCACTT
Found at i:37411 original size:12 final size:12
Alignment explanation
Indices: 37394--37418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37384 AGGTAGTATA
37394 TAGTGTAAAATT
1 TAGTGTAAAATT
37406 TAGTGTAAAATT
1 TAGTGTAAAATT
37418 T
1 T
37419 GGTGATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TAGTGTAAAATT
Found at i:39057 original size:19 final size:19
Alignment explanation
Indices: 39011--39065 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
39001 GTTAAGGATA
*
39011 AAAAATTAAACAAATTATT
1 AAAAATTAAATAAATTATT
* *
39030 --TATTTAAATAAATTATT
1 AAAAATTAAATAAATTATT
39047 AAAAATTAAATAAATTATT
1 AAAAATTAAATAAATTATT
39066 CACGACTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTAAATAAATTATT
Found at i:40628 original size:3 final size:3
Alignment explanation
Indices: 40615--40689 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
40605 AAAGATCTAA
* * *
40615 TAT TAT T-T TAT TAT TAT TAT TAT TAT CAT TAT TAG TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
40662 TAT TAT TAG TAG TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40690 TTCGTTTGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:42288 original size:2 final size:2
Alignment explanation
Indices: 42281--42319 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
42271 TGAATGAATT
*
42281 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42320 ATTTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44263 original size:20 final size:20
Alignment explanation
Indices: 44232--44272 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
44222 TGCATTCTCG
44232 TTTTGCATTTGCTTAT-TAA
1 TTTTGCATTTGCTTATATAA
44251 TTTTGCTATTTGCTTATATAA
1 TTTTGC-ATTTGCTTATATAA
44272 T
1 T
44273 AATCTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTTGCATTTGCTTATATAA
Found at i:48076 original size:2 final size:2
Alignment explanation
Indices: 48069--48264 Score: 329
Period size: 2 Copynumber: 98.0 Consensus size: 2
48059 ATCTCGTTAT
48069 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
48111 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
48153 AC AC AC AC GC AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
48195 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * ** *
48237 AT GC AC AC AC AC AC GT GC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
48265 GTGCATGCGT
Statistics
Matches: 182, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 182 1.00
ACGTcount: A:0.47, C:0.49, G:0.03, T:0.01
Consensus pattern (2 bp):
AC
Found at i:48290 original size:32 final size:32
Alignment explanation
Indices: 48254--48326 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
48244 CACACACGTG
*
48254 CACACACACACGTGCATGCGTGTATACATGCA
1 CACACACACACGTGCATGCGTGCATACATGCA
*
48286 CACACACACATGTGCATGCGTGCATACATGCA
1 CACACACACACGTGCATGCGTGCATACATGCA
48318 CACACACAC
1 CACACACAC
48327 TCACGCGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.34, G:0.16, T:0.16
Consensus pattern (32 bp):
CACACACACACGTGCATGCGTGCATACATGCA
Found at i:49015 original size:150 final size:149
Alignment explanation
Indices: 48755--49061 Score: 418
Period size: 150 Copynumber: 2.1 Consensus size: 149
48745 TAAGTTTTTT
* * * * *
48755 GGACCATCCATAAGACCTTTGGGCAGGATGTTTAGACGTATGTGTCTAAAATGAGAAAAGCTTCT
1 GGACCATCCACAAGACCTTTGGGCAGGATGTTTACACGTATCTGTCAAAAAAGAGAAAAGCTTCT
* * *
48820 CATTTAAATAAAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAGC-TAGTAAATTGCAT
66 CATTTAAATAAAAAAATTGAAATTTTTAAAAAGTAAGAAAGGTTTCTT-GCATAGTAAAGTACAT
*
48884 CCAAAATTGGTAAGTCCTTC
130 CCAAAATTGATAAGTCCTTC
* * * * *
48904 GGGCCATCCACAAGACCTTTGGGTAGGATGTTTTCACGTATCTGTCCAAAAAAGAGAAATGTTTC
1 GGACCATCCACAAGACCTTTGGGCAGGATGTTTACACGTATCTGT-CAAAAAAGAGAAAAGCTTC
** * **
48969 TCATTTAAATCTAAAAATTGAAATTTTTAAAAAGTAAGAAAGGTTTCTTTCATAGTAAAGTATTT
65 TCATTTAAATAAAAAAATTGAAATTTTTAAAAAGTAAGAAAGGTTTCTTGCATAGTAAAGTACAT
49034 CCAAAATTGATAAGTCCTTC
130 CCAAAATTGATAAGTCCTTC
49054 GGACCATC
1 GGACCATC
49062 AATAAGTCTT
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
149 40 0.29
150 96 0.71
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (149 bp):
GGACCATCCACAAGACCTTTGGGCAGGATGTTTACACGTATCTGTCAAAAAAGAGAAAAGCTTCT
CATTTAAATAAAAAAATTGAAATTTTTAAAAAGTAAGAAAGGTTTCTTGCATAGTAAAGTACATC
CAAAATTGATAAGTCCTTC
Found at i:49313 original size:233 final size:233
Alignment explanation
Indices: 48894--51063 Score: 2652
Period size: 232 Copynumber: 9.3 Consensus size: 233
48884 CCAAAATTGG
* * * * * * * * * *
48894 TAAGTCCTTCGGGCCATCCACAAGACCTTTGGGTAGGATGTTTTCACGTATCTGTCCAAAAAAGA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
* * * *
48959 GAAATGTTTCTCATTTAAATCTAAAAATTGAAATTTTTAAAAAGTAAGAAAGGTTTCTTTCATAG
66 GAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAG
* * * * * * *
49024 TAAAGTATTTCCAAAATTGATAAGTCCTTCGGACCATCAATAAGTCTTTTGAGCATGATTCTTAA
131 TAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAA
* * * * * *
49089 ATTCTTTGAGTTATCTGTAAGTCTTCCGAGAAAGATGA
196 ATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * ** *
49127 TAAGTCATTCGGGCCATTCATAAGACCTTCGGGAAGGATGTTTTCACATGTTTTTTTAAAATTGA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
* * *
49192 GAAAAGTTTCTCATTTGAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAG
66 GAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAG
*
49257 TAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTACGTCTTTCGAGCATGATGCTTAA
131 TAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAA
*
49322 ATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
196 ATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * *
49360 TAAGTCCTTCGGGCCAATT-ATAAGACCTTTGGGCATGATG-TTTCATATGTTTTTCGAAAAATG
1 TAAGTCCTTCGGGCC-ATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATG
* * *
49423 AGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGATTTCTTACTTA
65 AGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
* * ** * *
49488 GTAAATTGTTTTCAAAATCAGTAAGTCCTTCGAGCCATCAGTAAGTCTTTCGACCATGATGCTTA
130 GTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
** *
49553 AATTATTCGGGTCACCTGTAAGTCTTTCGAGCAAGATGA
195 AATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * * * *
49592 TAAGTCTTTCGTGCCA-TCTATAAGACTTTCGGGCAGAATGTTTTCAC--GTTTCTATCTAGAAA
1 TAAGTCCTTCGGGCCATTC-ATAAGACCTTCGGGCAGGATGTTTTCACATGTTT-T-TCGA-AAA
*
49654 A-GAGAAAAGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
62 ATGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
*
49718 CTAGT-AACATGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG-ACTAAT
127 CTAGTAAAC-TGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA-TGAT
* * * * *
49781 GCTTAAATCCTTTGGGTTATCTGTAAGTCTTTTGAGAAAAATGA
190 GCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * * **** * * *
49825 TAAGTCCTTCCGGCCATCCACAAGA-CTTCATATAGGATGTTTT--CATGTATCTGTCTAAAAAA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGT-T-TTTCGAAAAAT
49887 GAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAA-TAAGAAAGGTTTCTTACCT
64 GAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCT
* * *
49951 AGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCAATCAGTAAGTCTTTCGAGCATGATGCTT
129 AGTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
*
50016 AAATCCTTCGGGTCATCTGTAAGTCTTTC-AGGCAAGTTGA
194 AAATCCTTCGGGTCATCTGTAAGTCTTTCGA-GCAAGATGA
* * * * * * * *
50056 TAA-TCCTTCGGGCTATCCATAAGACCTTCGGGTAGGATGTTTTCACGTATCTGTCTAAAAAAT-
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTC-GAAAAATG
* * *
50119 AGAAAGGTTTCTCATTTAAATCTAAAAATTGAAAATTTTGAGAGGTAAGAAAGGTTTCTTACCTA
65 AGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
* * * * * * *
50184 GTAAACTATTTCCAAACTTGATAAGTCCTTCAGGCCATCAATAAGT-TATTTGAGCATGATTCTT
130 GTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCT-TTCGAGCATGATGCTT
* * * * *
50248 AAATTCTTCGAGTCATCTGTAAGTCTTCCGAGAAAGAAGA
194 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
** * *
50288 TAAGTTTTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTTGAAAATTGA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
* * * *
50353 GAAAGGTTTCTCATTTGAATCTGAAAATTAAAATTTTTTGAAAAGTAATAAAGGTTTCTTACCTA
66 GAAAGGTTTCTCATTTAAATCTAAAAATTGAAA-TTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
* * **
50418 GTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGACCATCAGTAAGTCTTTTC-ATAATGATGCTT
130 GTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTC-TTTCGAGCATGATGCTT
* * *
50482 AAATCCTTCGAGTCATTTGTAAGTCTTTCGAGCAAGATAA
194 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * * *
50522 TAAGTCCTTCAGGCCATTTATAAGACCTTCGGGCATGATGTTTTCACATGTTTTTTCAAAAAATG
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATG-TTTTTCGAAAAATG
* * *
50587 AGAAAGGTTTCTCATTTAAATTTGAGAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
65 AGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTA
** *
50652 GTAAACTGTTTCCAAAATT-AAAAGTCCTTCGGGCCATAAGTAAGTCTTT-GAGCATGATGCTTA
130 GTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
* * *
50715 AATCCTTCGGGTCATCTGTTAGTATTTCGATCAAGATGA
195 AATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* ** * * * *
50754 TAAGTTCTTCGAACCATTCATAAGACCTTCAGGCAGGATGTTTTCACATGTGTTTCGAAAATTAA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
* * * *
50819 GAAAGGTTTCTCATTTAATTCT-CAAATTGAAATTTTTTTTAAAAGTTAGAAAGGTTTCTTACCT
66 GAAAGGTTTCTCATTTAAATCTAAAAATTGAAA--TTTTTGAAAAGTAAGAAAGGTTTCTTACCT
* * * * *
50883 AGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAGTAATTCTTTTGAGCATGATTCTT
129 AGTAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
* *
50948 AAATCCTTCAGGTTATCTGTAAGTCTTTCGAGCAAGATGA
194 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
* * * * * * **
50988 TAAGTCATTCGAGCCATCCATAAGACCTTCGGGCATGATGTTTTCACATGTCTCTAAAAAAATGA
1 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
51053 GAAAGGTTTCT
66 GAAAGGTTTCT
51064 TACCAAGTAA
Statistics
Matches: 1667, Mismatches: 234, Indels: 71
0.85 0.12 0.04
Matches are distributed among these distances:
230 29 0.02
231 210 0.13
232 531 0.32
233 531 0.32
234 322 0.19
235 43 0.03
236 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (233 bp):
TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA
GAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAG
TAAACTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAA
ATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA
Found at i:49527 original size:20 final size:19
Alignment explanation
Indices: 49504--49544 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
49494 TGTTTTCAAA
49504 ATCAGTAAGTCCTTCGAGCC
1 ATCAGTAAGTCCTTCGA-CC
*
49524 ATCAGTAAGTCTTTCGACC
1 ATCAGTAAGTCCTTCGACC
49543 AT
1 AT
49545 GATGCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (19 bp):
ATCAGTAAGTCCTTCGACC
Found at i:51180 original size:186 final size:186
Alignment explanation
Indices: 50866--51247 Score: 674
Period size: 186 Copynumber: 2.1 Consensus size: 186
50856 TTTAAAAGTT
* *
50866 AGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAGTAATTC
1 AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTC
*
50931 TTTTGAGCATGATTCTTAAATCCTTCAGGTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
66 TTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
* *
50996 TCGAGCCATCCATAAGACCTTCGGGCATGATGTTTTCACATGTCTCTAAAAAAATG
131 TCGAGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTCTCTAAAAAAATG
*
51052 AGAAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTC
1 AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTC
51117 TTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
66 TTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
* **
51182 TCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTCTCTCGAAAAATG
131 TCGAGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTCTCTAAAAAAATG
*
51238 AGTAAGGTTT
1 AGAAAGGTTT
51248 TTCATTTAAT
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
186 186 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (186 bp):
AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTC
TTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
TCGAGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTCTCTAAAAAAATG
Found at i:51407 original size:652 final size:652
Alignment explanation
Indices: 50402--51715 Score: 1748
Period size: 652 Copynumber: 2.0 Consensus size: 652
50392 GAAAAGTAAT
* * *
50402 AAAGGTTTCTTACCTAGTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGACCATCAGTAAGTCTT
1 AAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTCGGACCATCAATAAGTCTT
* * *
50467 TTCATAATGATGCTTAAATCCTTCGAGTCATTTGTAAGTCTTTCGAGCAAGATAATAAGTCCTTC
66 TTCAGAATGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCATTC
** * * * *
50532 AGGCCATTTATAAGACCTTCGGGCATGATGTTTTCACATGTTTTTTCAAAAAATGAGAAAGGTTT
131 AGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTTCTCTCAAAAAATGAGAAAGGTTT
* *
50597 CTCATTTAAATTTGAGAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTGTT
196 CTCATTTAAATTTGAAAACTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTGTT
* *
50662 TCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCTTTGAGCATGATGCTTAAATCCTTCGGGT
261 TCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCTTTGAACATGATGCTTAAATCCTTCAGGT
* * * *
50727 CATCTGTTAGTATTTCGATCAAGATGATAAGTTC-TTC-GAACCATTCATAAGACCTTCAGGCAG
326 CATATGTAAGTATTTCGAGCAAGATGATAAG-TCATTCAG-ACCATTCATAAGACCTTCAAGCAG
* *
50790 GATGTTTTCACATGTGTTTCGAAAATTAAGAAAGGTTTCTCATTT-AATTCTCAAA-TTGAAATT
389 GATGTTTTCACATGTGTTTCAAAAACTAAGAAAGGTTTCTCATTTAAATT-TCAAATTTG-AATT
* * * * * * *
50853 TTTTTTAAAAGTTAGAAAGGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTTGGG
452 TTTTTTAAAAGTAAGAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATCGATAAGTCATTCGAG
* ** * * **
50918 CCATCAGTAATTCTTT-TGAGCATGATT-CTTAAATCCTTCAGGTTATCTGTAAGTCTTTCGAGC
517 CCATCAGTAAGTCTTTCT-AGCATG-TTGAGTAAATCCTTCAGGTCATCTATAAACCTTTCGAGC
* * *
50981 AAGATGATAAGTCATTCGAGCCATCCATAAGACCTTCGGGCATGATGTTTTCACATGTCTCTAAA
580 AAGAAGATAAGTCATTCGAGCCATCCATAAGACATTCGGGCAAGATGTTTTCACATGTCTCTAAA
51046 AAAATGAG
645 AAAATGAG
* * *
51054 AAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTCTT
1 AAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTCGGACCATCAATAAGTCTT
* * * *
51119 TTGAGCATGATTCTTAAATCCTTC-AGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATT
66 TTCAGAATGATGCTTAAATCCTTCGA-GTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCATT
* * *
51183 CGGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATG-TCTCTCGAAAAATGAGTAAGGTT
130 CAGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTTCTCTCAAAAAATGAGAAAGGTT
* * *
51247 TTTCATTT-AATTCTGAAAACTGAAATTTTTGAAAAGTAAGAAATGTTTCTTACCTAGTAAATTG
195 TCTCATTTAAATT-TGAAAACTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTG
* ** * *
51311 TTTCCGAAATTGGTAAGTCCTTCGGGCCATCAGTAA-TCTTTCGAATATGATGCTTAAATCCTTC
259 TTTCCAAAATT-AAAAGTCCTTCGGGCCATAAGTAAGTCTTT-GAACATGATGCTTAAATCCTTC
*
51375 AGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATTCAGACCATTCATAAGACCTTCAAGC
322 AGGTCATATGTAAGTATTTCGAGCAAGATGATAAGTCATTCAGACCATTCATAAGACCTTCAAGC
* * * * * * *
51440 ATGATGTTTTTACATGTTTTTTAAAAACTGAGAAAGGTTTCTCATTTAAATTTGAAATTTGATTT
387 AGGATGTTTTCACATGTGTTTCAAAAACTAAGAAAGGTTTCTCATTTAAATTTCAAATTTGAATT
* *
51505 TTTTTTAAATGTAAGAAAGGTTTCTTACCTAGTAAAATGTTTCCAAAATCGATAAGTCATTCGAG
452 TTTTTTAAAAGTAAGAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATCGATAAGTCATTCGAG
* * ** * *
51570 CCATCAGTCAGTCTTTCTAGCATGTTGAGTAAATCTTTTGGGTCATTTATAAACCTTTCGAGCAC
517 CCATCAGTAAGTCTTTCTAGCATGTTGAGTAAATCCTTCAGGTCATCTATAAACCTTTCGAGCAA
* * * * **
51635 GAAGATAAGTCTTTCGGGCCATCCATAAGACATTCGGGCAAGATGTTTTCACATGTTTTTACCAA
582 GAAGATAAGTCATTCGAGCCATCCATAAGACATTCGGGCAAGATGTTTTCACATGTCTCTAAAAA
51700 AATGAG
647 AATGAG
*
51706 AAAAGTTTCT
1 AAAGGTTTCT
51716 CATTTAAATC
Statistics
Matches: 572, Mismatches: 80, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
650 4 0.01
651 93 0.16
652 466 0.81
653 9 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (652 bp):
AAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTCGGACCATCAATAAGTCTT
TTCAGAATGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATAATAAGTCATTC
AGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTTCTCTCAAAAAATGAGAAAGGTTT
CTCATTTAAATTTGAAAACTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTGTT
TCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCTTTGAACATGATGCTTAAATCCTTCAGGT
CATATGTAAGTATTTCGAGCAAGATGATAAGTCATTCAGACCATTCATAAGACCTTCAAGCAGGA
TGTTTTCACATGTGTTTCAAAAACTAAGAAAGGTTTCTCATTTAAATTTCAAATTTGAATTTTTT
TTAAAAGTAAGAAAGGTTTCTTACCTAGTAAAATATTTCCAAAATCGATAAGTCATTCGAGCCAT
CAGTAAGTCTTTCTAGCATGTTGAGTAAATCCTTCAGGTCATCTATAAACCTTTCGAGCAAGAAG
ATAAGTCATTCGAGCCATCCATAAGACATTCGGGCAAGATGTTTTCACATGTCTCTAAAAAAATG
AG
Found at i:51474 original size:418 final size:417
Alignment explanation
Indices: 50634--51481 Score: 1186
Period size: 418 Copynumber: 2.0 Consensus size: 417
50624 TTGAAAAGTA
* *
50634 AGAAAGGTTTCTTACCTAGTAAACTGTTTCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCT
1 AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCT
* * *
50699 TTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTTAGTATTTCGATCAAGATGATAAGTTCTTC
66 TTGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTATTTCGAGCAAGATGATAAGTTCTTC
* * * *
50764 GAACCATTCATAAGACCTTCAGGCAGGATGTTTTCACATGTGTTTCGAAAATTAAGAAAGGTTTC
131 GAACCATCCATAAGACCTTCAGGCAGGATGTTTTCACATGTCTCTCGAAAAATAAGAAAGGTTTC
* * * *
50829 TCATTTAATTCTCAAATTGAAATTTTTTTTAAAAGTTAGAAAGGTTTCTTACCTAGTAAACTATT
196 TCATTTAATTCTAAAACTGAAA-TTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATT
* * * *
50894 TCCAAAATTGGTAAGTCCTTTGGGCCATCAGTAATTCTTTTGAGCATGATTCTTAAATCCTTCAG
260 TCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAATTCTTTCGAACATGATGCTTAAATCCTTCAG
* * **
50959 GTTATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATCCATAAGACCTTCGGGCAT
325 GTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATCCATAAGACCTTCAAGCAT
51024 GATGTTTTCACATGTCTCTAAAAAAATG
390 GATGTTTTCACATGTCTCTAAAAAAATG
* ** * *
51052 AGAAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAA-TAATT
1 AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATT-AAAAGTCCTTCGGGCCAT-AAGTAAGT
* *
51116 CTTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAG-TC
64 C-TTTGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTATTTCGAGCAAGATGATAAGTTC
** * *
51180 ATTCGGGCCATCCATAAGACCTTC-GAGCAGGATGTTTTCACATGTCTCTCGAAAAATGAGTAAG
128 -TTCGAACCATCCATAAGACCTTCAG-GCAGGATGTTTTCACATGTCTCTCGAAAAATAAGAAAG
* *
51244 GTTTTTCATTTAATTCTGAAAACTGAAA-TTTTTGAAAAGTAAGAAATGTTTCTTACCTAGTAAA
191 GTTTCTCATTTAATTCT-AAAACTGAAATTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAA
* * * *
51308 TTGTTTCCGAAATTGGTAAGTCCTTCGGGCCATCAGTAA-TCTTTCGAATATGATGCTTAAATCC
255 CTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAATTCTTTCGAACATGATGCTTAAATCC
*
51372 TTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATTC-AGACCATTCATAAGACCTTC
320 TTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGAG-CCATCCATAAGACCTTC
* * * * *
51436 AAGCATGATGTTTTTACATGTTTTTTAAAAACTG
384 AAGCATGATGTTTTCACATGTCTCTAAAAAAATG
51470 AGAAAGGTTTCT
1 AGAAAGGTTTCT
51482 CATTTAAATT
Statistics
Matches: 379, Mismatches: 44, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
417 2 0.01
418 152 0.40
419 91 0.24
420 126 0.33
421 8 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (417 bp):
AGAAAGGTTTCTTACCAAGTAAACTATTTCCAAAATTAAAAGTCCTTCGGGCCATAAGTAAGTCT
TTGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGTATTTCGAGCAAGATGATAAGTTCTTC
GAACCATCCATAAGACCTTCAGGCAGGATGTTTTCACATGTCTCTCGAAAAATAAGAAAGGTTTC
TCATTTAATTCTAAAACTGAAATTTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTATTT
CCAAAATTGGTAAGTCCTTCGGGCCATCAGTAATTCTTTCGAACATGATGCTTAAATCCTTCAGG
TCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGAGCCATCCATAAGACCTTCAAGCATG
ATGTTTTCACATGTCTCTAAAAAAATG
Found at i:51479 original size:232 final size:232
Alignment explanation
Indices: 51052--51730 Score: 797
Period size: 233 Copynumber: 2.9 Consensus size: 232
51042 TAAAAAAATG
* * * *
51052 AGAAAGGTTTCTTACCAAGTAAATTATTTCCAAAATTGGTAAGTCCTTTGGGCCATCAATAATTC
1 AGAAAGGTTTCTTACCTAGTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAA-TC
* * *
51117 TTTTGAGCATGATTCTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCAT
65 TTTCGAGCATGATGCTTAAATCCTTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCAT
* * ** *
51182 TCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTTCACATGTCTCTCGAAAAATGAGTAAGGTT
130 TCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGT-TTTTTAAAAATGAGAAAGGTT
*
51247 TTTCATTTAATTCTGAAAACTGA-AATTTTTGAAAAGTA
194 TCTCATTTAATTCTGAAAACTGATAATTTTTGAAAAGTA
* *
51285 AGAAATGTTTCTTACCTAGTAAATTGTTTCCGAAATTGGTAAGTCCTTCGGGCCATCAGTAATCT
1 AGAAAGGTTTCTTACCTAGTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAATCT
**
51350 TTCGAATATGATGCTTAAATCCTTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATT
66 TTCGAGCATGATGCTTAAATCCTTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATT
* * * * * *
51415 CAGACCATTCATAAGACCTTCAAGCATGATGTTTTTACATGTTTTTTAAAAACTGAGAAAGGTTT
131 CGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTTTTTTAAAAA-TGAGAAAGGTTT
** ** * *
51480 CTCATTTAAATT-TGAAATTTGATTTTTTTTTAAATGTA
195 CTCATTT-AATTCTGAAAACTGATAATTTTTGAAAAGTA
* * * * * *
51518 AGAAAGGTTTCTTACCTAGTAAAATGTTTCCAAAATCGATAAGTCATTCGAGCCATCAGTCAGTC
1 AGAAAGGTTTCTTACCTAGTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGT-AATC
* * ** * ** * * ** * * *
51583 TTTCTAGCATGTTGAGTAAATCTTTTGGGTCATTTATAAACCTTTCGAGCACGAAGATAAGTCTT
65 TTTCGAGCATGATGCTTAAATCCTTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCAT
* * *
51648 TCGGGCCATCCATAAGACATTCGGGCAAGATGTTTTCACATG-TTTTTACCAAAATGAGAAAAGT
130 TCGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTTTTTTA--AAAATGAGAAAGGT
*
51712 TTCTCATTTAAATCTGAAA
193 TTCTCATTTAATTCTGAAA
51731 TTTTTAATTC
Statistics
Matches: 377, Mismatches: 62, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
231 7 0.02
232 124 0.33
233 133 0.35
234 109 0.29
235 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (232 bp):
AGAAAGGTTTCTTACCTAGTAAATTGTTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAATCT
TTCGAGCATGATGCTTAAATCCTTCAGGTCATATGTAAGTCTTTCGAGCAAGATGATAAGTCATT
CGGGCCATCCATAAGACCTTCGAGCAAGATGTTTTCACATGTTTTTTAAAAATGAGAAAGGTTTC
TCATTTAATTCTGAAAACTGATAATTTTTGAAAAGTA
Found at i:52528 original size:133 final size:131
Alignment explanation
Indices: 52000--52834 Score: 677
Period size: 133 Copynumber: 6.3 Consensus size: 131
51990 CAAATTGAAC
* * * *
52000 TCGATTCAATCTTTCCTGAGTGACAGT---ATAAATCAAC-TCCCCGAGATCTGATTTTCCGTCA
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCC-AGATCTGATTTTCCCTCA
* * * * *
52061 GGAAGAAGTGGAACTTATCCCTAATCTTTTCAGATTGGATTTTCCTTGAGTAACAGTGAAACAAG
65 AGAAGAAGTGGAACATAT--CT--TCTTTTCAGATTTGATATTCCTTGAGTAACAGCGAAACAAG
* *
52126 TGTGCC
126 TCTGCT
* * * * * *
52132 TCGATTCAATTTTTCCTGAATGACAGTGGAATGAATTAACATCCCCATATCTGATTTTCCCTCAA
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
* * * * **
52197 GAAGAAGCGTAAAAAATCCCTATCTTTTCAGATTTGATATT-CTCTGAGTAACAATGAAACAAGT
66 GAAGAAGTGGAACATAT--CT-TCTTTTCAGATTTGATATTCCT-TGAGTAACAGCGAAACAAGT
*
52261 CTGCC
127 CTGCT
* * *
52266 TCGATTTAATCTTCCCTGAAG-AACAGTGGAATAAATCAAC-TCCCTAGATCTGATTTTCCCTCA
1 TCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCA
* * * * * *
52329 A-AAGGAAGTGGTATAGATCTCTTTTTTTCATATTTGATGTTCCCTT-AGTGAAAAAG-G-AACA
65 AGAA-GAAGTGG-A-ACATATCTTCTTTTCAGATTTGATATT-CCTTGAGT--AACAGCGAAACA
52390 AGTCTGCT
124 AGTCTGCT
* * * *
52398 TCGATTCAATCTTCCCTGAGCAACAGTGAAATAAATCAACATCCCCAGATCTGATTTTCCCTCAG
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
*
52463 GAAGAAGTGGAACATATCTTCTCTTTCAAGATTTGATATTCCTTGAGTAATAGCGAAACAAGTCT
66 GAAGAAGTGGAACATATCTTCT-TTTC-AGATTTGATATTCCTTGAGTAACAGCGAAACAAGTCT
52528 GCCT
129 G-CT
* * ** *
52532 T-GATTCAATCTTGCCTGAATAATTGGGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
** * * *
52596 GAAGAAGCAGAACATATCTTTCTTTTTAGATTTAATATT-CTCTGAGTAATAGC-AGAACAAGTC
66 GAAGAAGTGGAACATATC-TTCTTTTCAGATTTGATATTCCT-TGAGTAACAGCGA-AACAAGTC
*
52659 TACCT
128 T-GCT
* * * * * * * *
52664 T-GATTCGATCTTCCTTGAATAACACT-GAATGAATCAACGTCCCCATATTTAATTTTCCCTCAA
1 TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
* * * * *
52727 GAAGAAGTAGAATATATC-TCTTATCTTCAATATTTGATATTCCCTGAGTAACAGTGGAAA-AA-
66 GAAGAAGTGGAACATATCTTC-T-T-TTC-AGATTTGATATTCCTTGAGTAACAG-CGAAACAAG
*
52789 TCT-AT
126 TCTGCT
*
52794 GTCGATTCAATCTTCCCTAAAG-AACAGTGGAATGAATCAAC
1 -TCGATTCAATCTTCCCT-GAGTAACAGTGGAATGAATCAAC
52835 GTTTATTGAT
Statistics
Matches: 581, Mismatches: 85, Indels: 73
0.79 0.12 0.10
Matches are distributed among these distances:
129 2 0.00
130 2 0.00
131 68 0.12
132 177 0.30
133 192 0.33
134 90 0.15
135 45 0.08
136 5 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (131 bp):
TCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATCTGATTTTCCCTCAA
GAAGAAGTGGAACATATCTTCTTTTCAGATTTGATATTCCTTGAGTAACAGCGAAACAAGTCTGC
T
Found at i:52677 original size:265 final size:263
Alignment explanation
Indices: 52132--52834 Score: 672
Period size: 265 Copynumber: 2.7 Consensus size: 263
52122 CAAGTGTGCC
* * ** *
52132 TCGATTCAATTTTTCCTGAATGACAGTGGAATGAATTAACATCCCCATATCTGATTTTCCCTCAA
1 TCGATTCAATCTTCCCTGAACAACAGT-GAATGAATCAACATCCCCATATCTGATTTTCCCTCAA
* * * *
52197 GAAGAAGCGTAAAAAATCCCTATCTTTTC-AGATTTGATATT-CTCTGAGTAACAATGAAACAAG
65 GAAGAAGTGGAAAATAT--CT-TCTTTTCAAGATTTGATATTCCT-TGAGTAACAACGAAACAAG
* * *
52260 TCTGCCTCGATTTAATCTTCCCTGAAGAACAGTGGAATAAATCAACTCCCTAGATCTGATTTTCC
126 TCTGCCTCGATTCAATCTTCCCTGAAGAACAGGGGAATAAATCAACTCCCCAGATCTGATTTTCC
** * * * * * *
52325 CTCAAAAGGAAGTGGTATAGATCTCTTTTTTTCATATTTGATGTTCCCTTAGTGAAAAAGGAACA
191 CTCAAAAGGAAGCAGTATACATATCTTTTTTTCAGATTTAATATTCCCTGAGTGAAAAAGGAACA
*
52390 AGTCTGCT
256 AGTCTCCT
* * * *
52398 TCGATTCAATCTTCCCTGAGCAACAGTGAAATAAATCAACATCCCCAGATCTGATTTTCCCTCAG
1 TCGATTCAATCTTCCCTGAACAACAGTG-AATGAATCAACATCCCCATATCTGATTTTCCCTCAA
* * *
52463 GAAGAAGTGGAACATATCTTCTCTTTCAAGATTTGATATTCCTTGAGTAATAGCGAAACAAGTCT
65 GAAGAAGTGGAAAATATCTTCT-TTTCAAGATTTGATATTCCTTGAGTAACAACGAAACAAGTCT
* * * ** *
52528 GCCTTGATTCAATCTTGCCTGAATAATTGGGGAATGAATCAACATCCCCAGATCTGATTTTCCCT
129 GCCTCGATTCAATCTTCCCTGAAGAACAGGGGAATAAATCAAC-TCCCCAGATCTGATTTTCCCT
* * *
52593 CAAGAA-GAAGCAG-A-ACATATCTTTCTTTTTAGATTTAATATTCTCTGAGT--AATAGCAGAA
193 CAA-AAGGAAGCAGTATACATATCTTT-TTTTCAGATTTAATATTCCCTGAGTGAAAAAG--GAA
52653 CAAGTCTACCT
254 CAAGTCT-CCT
* * * * * * *
52664 T-GATTCGATCTTCCTTGAATAACACTGAATGAATCAACGTCCCCATATTTAATTTTCCCTCAAG
1 TCGATTCAATCTTCCCTGAACAACAGTGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAG
* * * * **
52728 AAGAAGTAGAATATATC-TCTTATCTTCAATATTTGATATTCCCTGAGTAACAGTGGAAA-AA-T
66 AAGAAGTGGAAAATATCTTC-T-T-TTCAAGATTTGATATTCCTTGAGTAACA-ACGAAACAAGT
*** * * *
52790 CTATGTCGATTCAATCTTCCCTAAAGAACAGTGGAATGAATCAAC
127 CTGCCTCGATTCAATCTTCCCTGAAGAACAGGGGAATAAATCAAC
52835 GTTTATTGAT
Statistics
Matches: 358, Mismatches: 66, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
263 9 0.03
264 98 0.27
265 145 0.41
266 104 0.29
267 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (263 bp):
TCGATTCAATCTTCCCTGAACAACAGTGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAG
AAGAAGTGGAAAATATCTTCTTTTCAAGATTTGATATTCCTTGAGTAACAACGAAACAAGTCTGC
CTCGATTCAATCTTCCCTGAAGAACAGGGGAATAAATCAACTCCCCAGATCTGATTTTCCCTCAA
AAGGAAGCAGTATACATATCTTTTTTTCAGATTTAATATTCCCTGAGTGAAAAAGGAACAAGTCT
CCT
Found at i:54698 original size:65 final size:65
Alignment explanation
Indices: 54588--54718 Score: 205
Period size: 65 Copynumber: 2.0 Consensus size: 65
54578 ATCAAATGTA
54588 TATTTGAATTTGCCAATTCATATTTAGATGAGGTATAATCGTTAGG-TACCGATTTCGGGCGTTG
1 TATTTGAATTTGCCAATTCATATTTA-ATGAGGTATAATCGTTAGGTTACCGATTTCGGGCGTTG
54652 T
65 T
54653 TATTTGAATTTGCCAATTTCAATATTT-A-GAGGTATAATCGTTTAGGTTACCGATTTCGGGCGT
1 TATTTGAATTTGCCAA-TTC-ATATTTAATGAGGTATAATCG-TTAGGTTACCGATTTCGGGCGT
54716 TGT
63 TGT
54719 GGGGTGCTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
64 12 0.19
65 22 0.35
66 22 0.35
67 6 0.10
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (65 bp):
TATTTGAATTTGCCAATTCATATTTAATGAGGTATAATCGTTAGGTTACCGATTTCGGGCGTTGT
Found at i:58341 original size:88 final size:86
Alignment explanation
Indices: 58221--58390 Score: 268
Period size: 88 Copynumber: 2.0 Consensus size: 86
58211 TCCAGAATAT
* * *
58221 TTAATTTCAATTAATCAAATAGATTTAATTAATTTGAAATAATAAATCCCTAATCTGATTAGGGT
1 TTAAATTCAATTAATCAAATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGT
58286 AACTTGGATATAAAAGGATTA
66 AACTTGGATATAAAAGGATTA
* *
58307 TTAAATTCTAATTAATTAATATATATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
1 TTAAATTC-AATTAATCAA-ATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
*
58372 GTAACTTGGCTATAAAAGG
64 GTAACTTGGATATAAAAGG
58391 GTGTGTTATG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 7 0.09
87 9 0.12
88 60 0.79
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (86 bp):
TTAAATTCAATTAATCAAATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGT
AACTTGGATATAAAAGGATTA
Found at i:68488 original size:30 final size:31
Alignment explanation
Indices: 68436--68498 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
68426 CTTACCAAGG
68436 AAGAAAATTCAAACGAAAATGAAGGCCTCAA
1 AAGAAAATTCAAACGAAAATGAAGGCCTCAA
68467 AAGAAAATTCAAACG-AAATGAAGGCCTCAA
1 AAGAAAATTCAAACGAAAATGAAGGCCTCAA
68497 AA
1 AA
68499 ATGAACCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.13
Consensus pattern (31 bp):
AAGAAAATTCAAACGAAAATGAAGGCCTCAA
Found at i:68818 original size:21 final size:21
Alignment explanation
Indices: 68794--68835 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68784 TATGAGAAAT
*
68794 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
68815 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
68836 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:72644 original size:21 final size:21
Alignment explanation
Indices: 72618--72681 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
72608 TTTTGGTGCA
*
72618 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
72639 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
72660 GAAGGGGAACCGATACCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
72682 CAGGGGAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 18 0.53
22 1 0.03
23 15 0.44
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.14
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:72688 original size:21 final size:21
Alignment explanation
Indices: 72662--72701 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
72652 CCCCCTTTGA
72662 AGGGGAACCGATACCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
72683 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
72702 TGGGGTTCTG
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:0.28, C:0.40, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:83051 original size:27 final size:27
Alignment explanation
Indices: 83013--83076 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
83003 ACGAGCCGAG
83013 TCGAACTTGAGTATTGCTAAGCTCGAC
1 TCGAACTTGAGTATTGCTAAGCTCGAC
83040 TCGAACTTGAGTATTGCTAAGCTCGAC
1 TCGAACTTGAGTATTGCTAAGCTCGAC
83067 TCGAACTTGA
1 TCGAACTTGA
83077 AAACTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (27 bp):
TCGAACTTGAGTATTGCTAAGCTCGAC
Found at i:85926 original size:22 final size:22
Alignment explanation
Indices: 85899--85947 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
85889 AAAATTATAT
* *
85899 TATTTACGTTTATGTGTAAAAA
1 TATTTACATTTATGCGTAAAAA
85921 TATTTACATTTATGCGTAAAAA
1 TATTTACATTTATGCGTAAAAA
85943 T-TTTA
1 TATTTA
85948 TTGTGTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (22 bp):
TATTTACATTTATGCGTAAAAA
Found at i:89300 original size:35 final size:34
Alignment explanation
Indices: 89216--89302 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
89206 AAAATAATTT
*
89216 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
89250 TAAATAATAAAAAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
89288 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
89303 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:89315 original size:13 final size:13
Alignment explanation
Indices: 89297--89321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89287 GTAATAAACA
89297 AAATTAACAAAAT
1 AAATTAACAAAAT
89310 AAATTAACAAAA
1 AAATTAACAAAA
89322 AGTCAAACAA
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:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:89368 original size:33 final size:34
Alignment explanation
Indices: 89292--89379 Score: 151
Period size: 33 Copynumber: 2.6 Consensus size: 34
89282 AAATGGTAAT
89292 AAACAAAATTAACAAAATAAATTAACAAAAAGTC
1 AAACAAAATTAACAAAATAAATTAACAAAAAGTC
89326 AAACAAAATTAACAAAATAAATTAA-AAAAAGTC
1 AAACAAAATTAACAAAATAAATTAACAAAAAGTC
* *
89359 CAACCAAATTAACAAAATAAA
1 AAACAAAATTAACAAAATAAA
89380 GTAAGTATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.17
Consensus pattern (34 bp):
AAACAAAATTAACAAAATAAATTAACAAAAAGTC
Found at i:90154 original size:20 final size:20
Alignment explanation
Indices: 90129--90179 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
90119 GGAGCGTGGG
90129 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
*
90149 GGGGAATCAGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
90169 GGGGAATCGGT
1 GGGGAATCGGT
90180 TCCCTAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:92970 original size:21 final size:21
Alignment explanation
Indices: 92946--92986 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
92936 CAGAACCCCA
*
92946 TGGGGGGTATCGATTCCCCTG
1 TGGGGGGAATCGATTCCCCTG
*
92967 TGGGGGGAATCGGTTCCCCT
1 TGGGGGGAATCGATTCCCCT
92987 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.24, G:0.39, T:0.27
Consensus pattern (21 bp):
TGGGGGGAATCGATTCCCCTG
Found at i:93021 original size:20 final size:21
Alignment explanation
Indices: 92969--93029 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
92959 TTCCCCTGTG
92969 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
92992 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
93012 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
93030 TGCACTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:99166 original size:3 final size:3
Alignment explanation
Indices: 99160--99200 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
99150 ATCATCATCA
* * *
99160 TCG TCG TCG TCG TCG TCG TCG TCG TCA TTG TCA TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
99201 AGGAGCAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.05, C:0.32, G:0.27, T:0.37
Consensus pattern (3 bp):
TCG
Found at i:99510 original size:20 final size:20
Alignment explanation
Indices: 99485--99526 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
99475 GGCGGCGTCT
99485 GGTAAGGGAAAGCCGGTAGC
1 GGTAAGGGAAAGCCGGTAGC
99505 GGTAAGGGAAAGCCGGTAGC
1 GGTAAGGGAAAGCCGGTAGC
99525 GG
1 GG
99527 CATCATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.48, T:0.10
Consensus pattern (20 bp):
GGTAAGGGAAAGCCGGTAGC
Found at i:100134 original size:29 final size:31
Alignment explanation
Indices: 100098--100156 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
100088 GAAAAAATTT
*
100098 AATTAAATAAAATATTAA-AAAA-ATTAAAG
1 AATTAAATAAAATACTAACAAAATATTAAAG
100127 AATTAAATAAAATACTAACAAAATATTAAA
1 AATTAAATAAAATACTAACAAAATATTAAA
100157 TATAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.63
30 4 0.15
31 6 0.22
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (31 bp):
AATTAAATAAAATACTAACAAAATATTAAAG
Found at i:109230 original size:60 final size:60
Alignment explanation
Indices: 109157--109301 Score: 254
Period size: 60 Copynumber: 2.4 Consensus size: 60
109147 AAAATTGTAT
*
109157 TTCAATGATTAAAAGTTACAAAATGGTCTCCTAATTATAGGATGTTGCTTTGTTGAGTCA
1 TTCAATGATTAAAAGTTACAAAATGGTCTCCTAATTATAGGATGTTGATTTGTTGAGTCA
* *
109217 TTCAATGATTAAAAGTTACAAAGTAGTCTCCTAATTATAGGATGTTGATTTGTTGAGTCA
1 TTCAATGATTAAAAGTTACAAAATGGTCTCCTAATTATAGGATGTTGATTTGTTGAGTCA
*
109277 TTCAACGATTAAAAGTTACAAAATG
1 TTCAATGATTAAAAGTTACAAAATG
109302 ATCATTCGAC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (60 bp):
TTCAATGATTAAAAGTTACAAAATGGTCTCCTAATTATAGGATGTTGATTTGTTGAGTCA
Found at i:110084 original size:51 final size:51
Alignment explanation
Indices: 110018--110114 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
110008 TGGTGAGTCG
*
110018 CTTTCTTTCTTTCTTTGCATTTGCCTCACCACCCAAATATTGTTATTCTTT
1 CTTTCTTTCTTTCTTTGCATTTGCCTCACCACCCAAATATAGTTATTCTTT
**
110069 CTTTCTTTCTTTCTTTGCATTTGCCTCGGCACCCAAATATAGTTAT
1 CTTTCTTTCTTTCTTTGCATTTGCCTCACCACCCAAATATAGTTAT
110115 CTTGAAGGCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.16, C:0.27, G:0.08, T:0.48
Consensus pattern (51 bp):
CTTTCTTTCTTTCTTTGCATTTGCCTCACCACCCAAATATAGTTATTCTTT
Found at i:110194 original size:167 final size:159
Alignment explanation
Indices: 109918--110267 Score: 443
Period size: 167 Copynumber: 2.2 Consensus size: 159
109908 AAATCATGAA
* * *
109918 GCATTTGCCTCAACACCCAAATATTGTTACCTTGAAGGCTACTTATCAGGATGAAAATGTGGTCT
1 GCATTTGCCTCAGCACCCAAATATAGTTACCTTGAAGGCTACTTATCAGGATGAAAATGTGGTCC
* *
109983 ATTTGGTTATTGAGTTGTGTGAAGATGGTGAGTCGCTTTCTTTCTTTCTTTGCATTTGCCTCACC
66 ATTTGGTTATTGAGTTGTGTGAAGATGGTGAGT--C--ACATTCTTTCTTTGCATTTGCCTCACC
* *
110048 ACCCAAATATTGTTATTCTTTCTTTCTTTCTTTCTTT
127 AACCAAATATTGTTATTATTTCTTTC-TTC---CTTT
* * * ***
110085 GCATTTGCCTCGGCACCCAAATATAGTTATCTTGAAGGCTACTTATGAGGATGACTTTGCT-GTC
1 GCATTTGCCTCAGCACCCAAATATAGTTACCTTGAAGGCTACTTATCAGGATGAAAATG-TGGTC
* *
110149 CATTTGGTTA-TGCAGTTGTGTGAAGGTGGTGAGTCACATTCTTTCTTTGCATTTGCCTCAGCAA
65 CATTTGGTTATTG-AGTTGTGTGAAGATGGTGAGTCACATTCTTTCTTTGCATTTGCCTCACCAA
*
110213 CTAAATATTGTTATTATTTCTTTCTTCCTTT
129 CCAAATATTGTTATTATTTCTTTCTTCCTTT
*
110244 GCATTTGCCTCAGCCCCCAAATAT
1 GCATTTGCCTCAGCACCCAAATAT
110268 TAAAAATTGC
Statistics
Matches: 163, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
159 26 0.16
162 3 0.02
163 47 0.29
165 1 0.01
166 2 0.01
167 83 0.51
168 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (159 bp):
GCATTTGCCTCAGCACCCAAATATAGTTACCTTGAAGGCTACTTATCAGGATGAAAATGTGGTCC
ATTTGGTTATTGAGTTGTGTGAAGATGGTGAGTCACATTCTTTCTTTGCATTTGCCTCACCAACC
AAATATTGTTATTATTTCTTTCTTCCTTT
Found at i:111608 original size:15 final size:15
Alignment explanation
Indices: 111588--111617 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111578 CATTCTGGGA
*
111588 TGGTTGGTCCTTCCG
1 TGGTTGGACCTTCCG
111603 TGGTTGGACCTTCCG
1 TGGTTGGACCTTCCG
111618 AAGACTGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.27, G:0.33, T:0.37
Consensus pattern (15 bp):
TGGTTGGACCTTCCG
Found at i:114750 original size:17 final size:20
Alignment explanation
Indices: 114727--114777 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
114717 GGGCCTGTAG
114727 TAATATT-TAA-AATAATAA
1 TAATATTATAATAATAATAA
*
114745 -AATATTATAATAATCATAA
1 TAATATTATAATAATAATAA
114764 TAATATTAATAATA
1 TAATATT-ATAATA
114778 CTTATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.21
18 3 0.11
19 7 0.25
20 6 0.21
21 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATATTATAATAATAATAA
Found at i:116025 original size:21 final size:21
Alignment explanation
Indices: 115983--116025 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
115973 TTTCTGGGCT
*
115983 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
116004 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
116025 A
1 A
116026 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:116729 original size:103 final size:103
Alignment explanation
Indices: 116545--116762 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
116535 GTAGAGGGTC
* * *
116545 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
* *
116610 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGGATATGATTCTTAAGGAATGA
116648 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
116713 TTGATCCTTGGCATATGGATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGGATATGATTCTTAAGGAATGA
116751 TATGTGGTCCTT
1 TATGTGGTCCTT
116763 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
TTGATCCTTGGCATATGGATATGATTCTTAAGGAATGA
Found at i:116812 original size:23 final size:23
Alignment explanation
Indices: 116780--116846 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
116770 TTATTATATT
116780 GCACTACGGTGCAATTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
* * *
116803 GCACTCCGGTGCAATTCTAAGTG
1 GCACTACGGTGCAATTCTACGCG
*
116826 GCACTTA-GGTGCAATTATACG
1 GCAC-TACGGTGCAATTCTACG
116847 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:122686 original size:21 final size:21
Alignment explanation
Indices: 122644--122686 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
122634 TTCCTGGGCT
*
122644 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
122665 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
122686 A
1 A
122687 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:122749 original size:19 final size:20
Alignment explanation
Indices: 122711--122751 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
122701 CCAGAACGCT
*
122711 AGGGGGGAATCGATACCCCC
1 AGGGGGGAACCGATACCCCC
*
122731 AGGGGGGAACCGATTCCCCC
1 AGGGGGGAACCGATACCCCC
122751 A
1 A
122752 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (20 bp):
AGGGGGGAACCGATACCCCC
Found at i:123434 original size:103 final size:103
Alignment explanation
Indices: 123209--123426 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
123199 GTAGAGGGTC
* *
123209 TATGTGGTCCTTCGGGACATATATGTATTGTTTGGAACATTTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
123274 TTGATCCTTGGTATATGTGTATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
123312 TATGTGGTCCTTCGGGACATATATGTATTCTTTTGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
123377 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
123415 TATGTGGTCCTT
1 TATGTGGTCCTT
123427 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:123476 original size:23 final size:23
Alignment explanation
Indices: 123443--123510 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
123433 ATTATTATAT
123443 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
123466 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTACGGTGCAATTCTACGC
*
123489 GGCACTTA-GGTGCAATTATACG
1 GGCAC-TACGGTGCAATTCTACG
123511 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:124312 original size:66 final size:66
Alignment explanation
Indices: 124204--124654 Score: 583
Period size: 67 Copynumber: 6.8 Consensus size: 66
124194 TAGGGATAAA
* * * * *
124204 TTTGTTTCAAGAGAAAATGTCTCAAGAGAGATAAAA-TCTGTTTCGAGGGAAACAATCACAAAGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT-TGTTTCAAGGGAAACAATCTCAAAGA
124268 TT
65 TT
* * *
124270 TGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAATTG-
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAA-AGA
124334 TT
65 TT
* * * * *
124336 TAAT-TTTCAAGAGAAATTGTCTCGAGAGAGACAAAACTTGTTTCAAGAGAAACAAACTCAAAGA
1 T-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGA
124400 TT
65 TT
124402 TTTGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAACTTTGTTTCAAGGGAAACAGA-CTCAAAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAACA-ATCTCAAAG
124464 ATT
64 ATT
* *
124467 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAAC-ATACTCAAAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAACTTGTTTCAAGGGAAACAAT-CTCAAAG
124531 ATT
64 ATT
* *
124534 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACCAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAACAATCTCAAAGA
124599 TT
65 TT
* * * *
124601 TTTGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTTATTTCAAGAGAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAAC
124655 TGTCTAAAGA
Statistics
Matches: 343, Mismatches: 28, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
64 11 0.03
65 52 0.15
66 134 0.39
67 141 0.41
68 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (66 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGAT
T
Found at i:124520 original size:37 final size:36
Alignment explanation
Indices: 124340--124690 Score: 171
Period size: 30 Copynumber: 10.4 Consensus size: 36
124330 ATTGTTTAAT
* * * *
124340 TTTCAAGAGAAATTGTCTCGAGAGAGACAAAACTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
*** **
124376 TTTCAAGAGAAACAAACTC-A-A-AG---ATTTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
* *
124406 TTTCAAGAGAAACTGTCTCAAGAGA-CAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
* * * *
124441 TTTCAAGGGAAACAGACTC-A-A-AG----ATTTGTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATT-TG
124471 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATTTG
* * **
124508 TTTCAAGGGAAACAT-ACTC-A-A-AG---ATTTTTG
1 TTTCAAGAGAAAC-TGTCTCAAGAGAGAAAAAATTTG
* *
124538 TTTCAAGAGAAACTGTCTCAAGAGAGACCAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATTTG
* *** **
124575 TTTCAAGGGAAACAAACTC-A-A-AG---ATTTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
* * *
124605 TTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATTTG
* *
124642 TTTCAAGAGAAACTGTCTAAAGAGAGAAAACATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
*
124678 TTCCAAGAGAAAC
1 TTTCAAGAGAAAC
124691 AATCTCAAAG
Statistics
Matches: 237, Mismatches: 46, Indels: 64
0.68 0.13 0.18
Matches are distributed among these distances:
29 4 0.02
30 79 0.33
31 4 0.02
32 5 0.02
33 10 0.04
34 6 0.03
35 24 0.10
36 35 0.15
37 66 0.28
38 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTG
Found at i:124520 original size:132 final size:133
Alignment explanation
Indices: 124206--124654 Score: 597
Period size: 132 Copynumber: 3.4 Consensus size: 133
124196 GGGATAAATT
* * * * * * * *
124206 TGTTTCAAGAGAAAATGTCTCAAGAGAGA-TAAAATCTGTTTCGAGGGAAACAATCACAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACAAACTCAAAGATT
* * *
124270 TGTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGGGAAACAATCTCAATTG
66 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAA-CTCAA-AG
124334 -TTTAA
129 ATTT-A
* * *
124339 T-TTTCAAGAGAAATTGTCTCGAGAGAGAC-AAAACTTGTTTCAAGAGAAACAAACTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACAAACTCAAAGATT
124402 TTTGTTTCAAGAGAAACTGTCTC-A-AGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGA
66 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACA-ACTCAAAGA
*
124465 TTTG
130 TTTA
* *
124469 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACATACTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACAAACTCAAAGATT
*
124534 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACCAAACTTTGTTTCAAGGGAAACAAACTCAAAGA
66 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-AACTCAAAGA
*
124599 TTTT
130 TTTA
* * * *
124603 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTTATTTCAAGAGAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAAC
124655 TGTCTAAAGA
Statistics
Matches: 282, Mismatches: 25, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
130 13 0.05
131 52 0.18
132 128 0.45
133 2 0.01
134 86 0.30
135 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (133 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACAAACTCAAAGATT
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAACTCAAAGAT
TTA
Found at i:125090 original size:34 final size:34
Alignment explanation
Indices: 125012--125122 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 34
125002 TCTCCAAGGA
* * *
125012 AAAATATCTCAAGCGAGATGATATTTGTTTTAAGAG
1 AAAATGTCTCAAGCGAGA-CA-ATTTGTTTTTAGAG
125048 AAAATGTCTCAAGCGAGACAATTT-TTTTTAGAG
1 AAAATGTCTCAAGCGAGACAATTTGTTTTTAGAG
*
125081 AAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAGAA
1 AAAA-TGTCTCAAGCGAGAC--AATTTGTTTTTAGAG
125118 AAAAT
1 AAAAT
125123 TTATCAAGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
33 12 0.18
34 19 0.28
35 1 0.01
36 23 0.34
37 12 0.18
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (34 bp):
AAAATGTCTCAAGCGAGACAATTTGTTTTTAGAG
Found at i:125215 original size:60 final size:60
Alignment explanation
Indices: 125097--125217 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
125087 GTCTCAAGCG
* * * *
125097 AGACAAAATTTGTTTTTAGAAAAAATTTATCAAGTGAAACCAAGTTTGTTTTGCAGAGAA
1 AGACAAAATTTGTTTTTAGAAAAAATATATCAAGTGAAACAAAATTTGTTTCGCAGAGAA
* * *
125157 AGACAAAATTTGTTTTTAGAGAAAACTATCTCAAGTGATACAAAATTTGTTTCG-AGAGAA
1 AGACAAAATTTGTTTTTAGA-AAAAATATATCAAGTGAAACAAAATTTGTTTCGCAGAGAA
125217 A
1 A
125218 CAACCCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
60 27 0.51
61 26 0.49
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (60 bp):
AGACAAAATTTGTTTTTAGAAAAAATATATCAAGTGAAACAAAATTTGTTTCGCAGAGAA
Found at i:132941 original size:13 final size:13
Alignment explanation
Indices: 132923--132947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
132913 TTGGAAACAC
132923 AACTTTGCTTAGA
1 AACTTTGCTTAGA
132936 AACTTTGCTTAG
1 AACTTTGCTTAG
132948 GGTCAGGATT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
AACTTTGCTTAGA
Found at i:137969 original size:42 final size:41
Alignment explanation
Indices: 137868--138324 Score: 630
Period size: 42 Copynumber: 10.8 Consensus size: 41
137858 CTATACACCA
* *
137868 GTAAGGCTTAACCTGTGCACAAAG--AAGAGGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAG-GGA-CCT-GGGAAACT
* * *
137912 GTAAGGTTTATCCTTGCACACAACAAAAGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
137954 GTATGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
137996 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
* *
138038 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
138080 GTAAGGGTTACCTTCGCACACAGTAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
138122 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
138164 GTAAGGGTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
138206 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
138248 GTAAGGCTTACCTTCGTACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
138290 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
138325 ATAATACTTC
Statistics
Matches: 374, Mismatches: 29, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
41 16 0.04
42 319 0.85
43 23 0.06
44 14 0.04
45 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:138015 original size:84 final size:84
Alignment explanation
Indices: 137868--138324 Score: 724
Period size: 84 Copynumber: 5.4 Consensus size: 84
137858 CTATACACCA
* * * *
137868 GTAAGGCTTAACCTGTGCACAAAG--AAGAGGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCA
1 GTAAGGCTTACCCT-TGCACACAGCAAAG-GGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCA
* *
137930 CACAACAAAAGGACCTGGGAAACT
61 CACAGCAAAGGGACCTGGGAAACT
*
137954 GTATGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
138019 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
* *
138038 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGGTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
*
138103 TAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
138122 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGGTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
138187 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
138206 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGTACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
138271 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
138290 GTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGACCTG
138325 ATAATACTTC
Statistics
Matches: 352, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
83 8 0.02
84 315 0.89
85 11 0.03
86 15 0.04
87 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:139299 original size:10 final size:10
Alignment explanation
Indices: 139286--139368 Score: 68
Period size: 10 Copynumber: 8.5 Consensus size: 10
139276 CGGGTCGGGT
*
139286 CGGTTCAGAC
1 CGGTTCAAAC
139296 CGG-TCAAAC
1 CGGTTCAAAC
*
139305 TGGTTCAAAC
1 CGGTTCAAAC
139315 CGG-TCAAAAC
1 CGGTTC-AAAC
139325 CGGTT-AAAC
1 CGGTTCAAAC
*
139334 CTG-TCAAAAC
1 CGGTTC-AAAC
139344 CGGTTCAAAAC
1 CGGTTC-AAAC
*
139355 TGGTT-AAAC
1 CGGTTCAAAC
139364 CGGTT
1 CGGTT
139369 TTCCAGTTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
8 1 0.02
9 23 0.38
10 24 0.40
11 12 0.20
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (10 bp):
CGGTTCAAAC
Found at i:139333 original size:19 final size:20
Alignment explanation
Indices: 139286--139352 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 20
139276 CGGGTCGGGT
*
139286 CGGTTCAGACCGGTC-AAAC
1 CGGTTCAAACCGGTCAAAAC
*
139305 TGGTTCAAACCGGTCAAAAC
1 CGGTTCAAACCGGTCAAAAC
*
139325 CGGTT-AAACCTGTCAAAAC
1 CGGTTCAAACCGGTCAAAAC
139344 CGGTTCAAA
1 CGGTTCAAA
139353 ACTGGTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 31 0.74
20 11 0.26
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
CGGTTCAAACCGGTCAAAAC
Found at i:145429 original size:42 final size:41
Alignment explanation
Indices: 145343--145712 Score: 483
Period size: 42 Copynumber: 8.8 Consensus size: 41
145333 CTATACACTA
* *
145343 GTAAGGCTTAACCTGTGCACA-AAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAA-CAAAGGGA-CCT-GGGAAACT
* *
145387 GTAAGGTTTATCCTTTCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
* *
145429 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
145471 GTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTACC-TTGCACACAACAAAGGGACCTGGGAAACT
* *
145513 ATAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
*
145555 GTAAGGCTTACCTTCGCACACAACAAAAGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAACAAAGGGACCTGGGAAACT
* *
145597 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAACAAAGGGACCTGGGAAACT
* *
145639 GTAAGGCTTACCTTCGCACACAGCAAAGGGACTTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAACAAAGGGACCTGGGAAACT
*
145681 GTAAGGCTTACCTTCGCACACAGCAAAGGGAC
1 GTAAGGCTTACCTT-GCACACAACAAAGGGAC
145713 ATGATAATAC
Statistics
Matches: 297, Mismatches: 21, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
41 10 0.03
42 253 0.85
43 18 0.06
44 16 0.05
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAACAAAGGGACCTGGGAAACT
Found at i:145475 original size:84 final size:84
Alignment explanation
Indices: 145343--145712 Score: 566
Period size: 84 Copynumber: 4.4 Consensus size: 84
145333 CTATACACTA
* * * * * *
145343 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-TCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
145406 ACAACAAAGGGACCTGGGAAACT
62 ACAACAAAGGGACCTGGGAAACT
*
145429 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTTGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
145494 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
* *
145513 ATAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
*
145578 CAAAAGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
145597 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
*
145662 CAAAGGGACTTGGGAAACT
66 CAAAGGGACCTGGGAAACT
145681 GTAAGGCTTA-CCTTCGCACACAGCAAAGGGAC
1 GTAAGGCTTACCCTT-GCACACAGCAAAGGGAC
145713 ATGATAATAC
Statistics
Matches: 266, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
83 8 0.03
84 228 0.86
85 14 0.05
86 16 0.06
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
CAAAGGGACCTGGGAAACT
Found at i:157525 original size:15 final size:15
Alignment explanation
Indices: 157505--157535 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
157495 AGTACACACA
157505 ATCAGGAATTAGACC
1 ATCAGGAATTAGACC
157520 ATCAGGAATTAGACC
1 ATCAGGAATTAGACC
157535 A
1 A
157536 GTTACAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
ATCAGGAATTAGACC
Found at i:158491 original size:13 final size:13
Alignment explanation
Indices: 158460--158498 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
158450 TAGCCTTCTG
*
158460 CCTCCGCCTTCAT
1 CCTCCCCCTTCAT
158473 CCTCCCCCTTCAT
1 CCTCCCCCTTCAT
*
158486 CCTCCCCCATCAT
1 CCTCCCCCTTCAT
158499 TGTCTGAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.10, C:0.59, G:0.03, T:0.28
Consensus pattern (13 bp):
CCTCCCCCTTCAT
Found at i:165837 original size:38 final size:38
Alignment explanation
Indices: 165784--165866 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
165774 ATTGTTATTG
*
165784 TTTTCTCCTTATTAGATCAAGAGAAGTTGTAATT-TCTA
1 TTTTCTCCTTATTAGACCAAGAGAAGTTGTAATTCT-TA
* * *
165822 TTTTCTCTTTGTTAGACCGAGAGAAGTTGTAATTCTTA
1 TTTTCTCCTTATTAGACCAAGAGAAGTTGTAATTCTTA
165860 TTTTCTC
1 TTTTCTC
165867 ACAGTGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 39 0.98
39 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (38 bp):
TTTTCTCCTTATTAGACCAAGAGAAGTTGTAATTCTTA
Found at i:172153 original size:20 final size:20
Alignment explanation
Indices: 172128--172167 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
172118 TTCAAGCAGC
172128 AGTTTGGTCTCACCCAGATT
1 AGTTTGGTCTCACCCAGATT
172148 AGTTTGGTCTCACCCAGATT
1 AGTTTGGTCTCACCCAGATT
172168 TAGAACAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (20 bp):
AGTTTGGTCTCACCCAGATT
Found at i:174433 original size:3 final size:3
Alignment explanation
Indices: 174425--174461 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
174415 AAAAAATATC
174425 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
174462 AATACATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:176109 original size:2 final size:2
Alignment explanation
Indices: 176104--176149 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
176094 GTTATGAATA
176104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176146 AT AT
1 AT AT
176150 GTTAAAGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:178687 original size:21 final size:20
Alignment explanation
Indices: 178662--178701 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
178652 AATAAATGGA
*
178662 ATGCAAGTGCAAAATGCAAAG
1 ATGCAAATGC-AAATGCAAAG
*
178683 ATGCAAATGCAGATGCAAA
1 ATGCAAATGCAAATGCAAA
178702 AAATATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAG
Found at i:181262 original size:16 final size:16
Alignment explanation
Indices: 181243--181287 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
181233 AATCTTAGGT
181243 GTTAGAAAAGTTAACA
1 GTTAGAAAAGTTAACA
181259 GTTAGAAAAGTTAACA
1 GTTAGAAAAGTTAACA
181275 GTTAGAAAAGTTA
1 GTTAGAAAAGTTA
181288 GCGGTTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (16 bp):
GTTAGAAAAGTTAACA
Found at i:181294 original size:16 final size:16
Alignment explanation
Indices: 181221--181295 Score: 87
Period size: 16 Copynumber: 4.7 Consensus size: 16
181211 TAGTTAGTAA
**
181221 TTAGCAGTTAGAAATC
1 TTAGCAGTTAGAAAAG
**
181237 TTAGGTGTTAGAAAAG
1 TTAGCAGTTAGAAAAG
*
181253 TTAACAGTTAGAAAAG
1 TTAGCAGTTAGAAAAG
*
181269 TTAACAGTTAGAAAAG
1 TTAGCAGTTAGAAAAG
*
181285 TTAGCGGTTAG
1 TTAGCAGTTAG
181296 CAGAGTTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (16 bp):
TTAGCAGTTAGAAAAG
Found at i:181531 original size:113 final size:113
Alignment explanation
Indices: 181414--181620 Score: 326
Period size: 113 Copynumber: 1.8 Consensus size: 113
181404 AGCTAATGGT
* *
181414 TAGCAGAGTTCGAACCATAATAATATGGATCATACCCTAAATCGGGTCACCACAAGGTCG-ATTC
1 TAGCAGAGTCCGAACCATAATAATATGGATCATACCCCAAATCGGGTCACCACAAGGTCGAATT-
*
181478 AAATATTAGAAACAATAAATATATAAATAATGGTTAGAGTGCAATAAAA
65 AAATATTAGAAACAATAAATAAATAAATAATGGTTAGAGTGCAATAAAA
** * * *
181527 TAGCAGAGTCCGAACCATAATAATATGGATCATACCCCGGATCTGGTCACCACAAGGTTGAATTG
1 TAGCAGAGTCCGAACCATAATAATATGGATCATACCCCAAATCGGGTCACCACAAGGTCGAATTA
181592 AATATTAGAAACAATAAATAAATAAATAA
66 AATATTAGAAACAATAAATAAATAAATAA
181621 CAATGGATAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
113 82 0.96
114 3 0.04
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (113 bp):
TAGCAGAGTCCGAACCATAATAATATGGATCATACCCCAAATCGGGTCACCACAAGGTCGAATTA
AATATTAGAAACAATAAATAAATAAATAATGGTTAGAGTGCAATAAAA
Found at i:183832 original size:4 final size:4
Alignment explanation
Indices: 183823--183895 Score: 73
Period size: 4 Copynumber: 18.2 Consensus size: 4
183813 AGTCACATTC
*
183823 TCTT TCTT TCTTT TCTT T-TT TCTT T-TT TTTCT TCTT TC-T TCTTT TCTTT
1 TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCT-T TCTT TCTT TC-TT TC-TT
183872 TCTT TCTT TC-T TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
183896 GCATTTTCCT
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
3 12 0.20
4 34 0.56
5 15 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:183845 original size:7 final size:7
Alignment explanation
Indices: 183833--183895 Score: 54
Period size: 7 Copynumber: 8.1 Consensus size: 7
183823 TCTTTCTTTC
183833 TTTTCTT
1 TTTTCTT
183840 TTTTCTTTT
1 TTTTC--TT
183849 TTTTCTT
1 TTTTCTT
*
183856 CTTTCTT
1 TTTTCTT
183863 CTTTTCTTT
1 -TTTTC-TT
183872 TCTTTCTT
1 T-TTTCTT
*
183880 TCTTCTT
1 TTTTCTT
183887 TCTTTCTT
1 T-TTTCTT
183895 T
1 T
183896 GCATTTTCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 19 0.41
8 14 0.30
9 13 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:183859 original size:24 final size:24
Alignment explanation
Indices: 183823--183895 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
183813 AGTCACATTC
183823 TCTTTCTTTCTTTTCTTTTTTCTTT
1 TCTTTC-TTCTTTTCTTTTTTCTTT
*
183848 TTTTTCTTC-TTTCTTCTTTTCTTT
1 TCTTTCTTCTTTTCTT-TTTTCTTT
*
183872 TCTTTCTT-TCTTCTTTCTTTCTTT
1 TCTTTCTTCTTTTCTTT-TTTCTTT
183896 GCATTTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 7 0.17
24 30 0.71
25 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTCTTCTTTTCTTTTTTCTTT
Found at i:183862 original size:28 final size:27
Alignment explanation
Indices: 183826--183895 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
183816 CACATTCTCT
*
183826 TTCTTTCTTTTCTTTTTTCTTTTTTTTC
1 TTCTTTCTTTTCTTTTTTC-TTTCTTTC
183854 TTCTTTCTTCTT-TTCTTTTCTTTCTTTC
1 TTCTTTCTT-TTCTT-TTTTCTTTCTTTC
183882 TTCTTTC-TTTCTTT
1 TTCTTTCTTTTCTTT
183896 GCATTTTCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 25 0.66
29 7 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (27 bp):
TTCTTTCTTTTCTTTTTTCTTTCTTTC
Found at i:192149 original size:4 final size:4
Alignment explanation
Indices: 192136--192175 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
192126 TGTTCAATAT
192136 TTTC -TTC TTTC TTTC -TTC TCTTC TTTC TTTC TTT- TTTC TT
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TT
192176 GTTTGGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 9 0.28
4 19 0.59
5 4 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:192152 original size:11 final size:11
Alignment explanation
Indices: 192136--192175 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
192126 TGTTCAATAT
192136 TTTCTTCTTTC
1 TTTCTTCTTTC
192147 TTTCTTCTCTTC
1 TTTCTTCT-TTC
192159 TTTCTTTCTTT-
1 TTTC-TTCTTTC
192170 TTTCTT
1 TTTCTT
192176 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.07
11 12 0.44
12 9 0.33
13 4 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:192159 original size:16 final size:16
Alignment explanation
Indices: 192138--192168 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
192128 TTCAATATTT
192138 TCTTCTTTCTTTCTTC
1 TCTTCTTTCTTTCTTC
192154 TCTTCTTTCTTTCTT
1 TCTTCTTTCTTTCTT
192169 TTTTCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TCTTCTTTCTTTCTTC
Done.