Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008983.1 Hibiscus syriacus cultivar Beakdansim tig00112347_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: 1350231
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:185470 original size:2 final size:2
Alignment explanation
Indices: 185465--185489 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
185455 AAAAAAAATA
185465 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
185490 GTTTTTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:188300 original size:5 final size:5
Alignment explanation
Indices: 188290--188328 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
188280 TGTTCCAGAG
*
188290 TTCTC TTCTC TTCTC TTCTC TTCTC GTCTC TTCTC TTCT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
188329 TCATTCTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.38, G:0.03, T:0.59
Consensus pattern (5 bp):
TTCTC
Found at i:188336 original size:15 final size:15
Alignment explanation
Indices: 188290--188337 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
188280 TGTTCCAGAG
*
188290 TTCTCTTCTCTTCTC
1 TTCTCTTCTCATCTC
*
188305 TTCTCTTCTCGTCTC
1 TTCTCTTCTCATCTC
188320 TTCTCTTCTTCAT-TC
1 TTCTCTTC-TCATCTC
188335 TTC
1 TTC
188338 ATACGTGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.58
Consensus pattern (15 bp):
TTCTCTTCTCATCTC
Found at i:188992 original size:20 final size:22
Alignment explanation
Indices: 188947--189004 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
188937 GCATGGGTAG
188947 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
188971 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
188991 TGTATCGATGCACT
1 TGCATCGATGCACT
189005 TGAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:193199 original size:14 final size:14
Alignment explanation
Indices: 193182--193213 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
193172 AATGAACATA
193182 AACGAACATAACCG
1 AACGAACATAACCG
193196 AACGAACATAACCG
1 AACGAACATAACCG
193210 AACG
1 AACG
193214 TTCACGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:193273 original size:43 final size:41
Alignment explanation
Indices: 193223--193315 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
193213 GTTCACGAAC
* *
193223 TTAAATGAACGAACGAGACCTATGTTCATGTTCGTTCATTTAA
1 TTAAATGAACG-ACAAAACCT-TGTTCATGTTCGTTCATTTAA
*
193266 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 TTAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
*
193306 -TAAATAAACG
1 TTAAATGAACG
193316 CACATAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 8 0.18
40 21 0.47
41 6 0.13
43 10 0.22
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (41 bp):
TTAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:194333 original size:2 final size:2
Alignment explanation
Indices: 194326--194359 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
194316 TCTACTTTTA
194326 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
194360 GAATGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194619 original size:22 final size:22
Alignment explanation
Indices: 194593--194649 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
194583 AAATTGGTAA
194593 CTCTAACCCATAACCCCATATC
1 CTCTAACCCATAACCCCATATC
194615 CTCTAACCCATAACCCCATATC
1 CTCTAACCCATAACCCCATATC
*
194637 TTCTGAA-CCATAA
1 CTCT-AACCCATAA
194650 ACCTTAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.25
Consensus pattern (22 bp):
CTCTAACCCATAACCCCATATC
Found at i:202068 original size:8 final size:9
Alignment explanation
Indices: 202048--202078 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
202038 GATTAGAACC
202048 AAAAA-AAT
1 AAAAATAAT
202056 AAAAATAAT
1 AAAAATAAT
202065 AAAAATAAT
1 AAAAATAAT
202074 AAAAA
1 AAAAA
202079 CAAAGACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATAAT
Found at i:204745 original size:12 final size:12
Alignment explanation
Indices: 204728--204766 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
204718 AGCGATCTCT
*
204728 TTCTCTTTCCCG
1 TTCTCTATCCCG
*
204740 TTCTCTATCTCG
1 TTCTCTATCCCG
*
204752 CTCTCTATCCCG
1 TTCTCTATCCCG
204764 TTC
1 TTC
204767 CCTTTCTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.05, C:0.41, G:0.08, T:0.46
Consensus pattern (12 bp):
TTCTCTATCCCG
Found at i:204756 original size:24 final size:24
Alignment explanation
Indices: 204729--204775 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
204719 GCGATCTCTT
* *
204729 TCTCTTTCCCGTTCTCTATCTCGC
1 TCTCTATCCCGTTCCCTATCTCGC
*
204753 TCTCTATCCCGTTCCCTTTCTCG
1 TCTCTATCCCGTTCCCTATCTCG
204776 ATCTAGATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.43, G:0.09, T:0.45
Consensus pattern (24 bp):
TCTCTATCCCGTTCCCTATCTCGC
Found at i:204785 original size:24 final size:24
Alignment explanation
Indices: 204735--204785 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
204725 TCTTTCTCTT
* * **
204735 TCCCGTTCTCTATCTCGCTCTCTA
1 TCCCGTTCCCTATCTCGATCTAGA
*
204759 TCCCGTTCCCTTTCTCGATCTAGA
1 TCCCGTTCCCTATCTCGATCTAGA
204783 TCC
1 TCC
204786 TTCTTTCGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.41, G:0.10, T:0.39
Consensus pattern (24 bp):
TCCCGTTCCCTATCTCGATCTAGA
Found at i:205303 original size:19 final size:18
Alignment explanation
Indices: 205281--205324 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
205271 TTTCTCTCTG
205281 CCTTCTTTCTCCCTCTTCT
1 CCTTCTTTCTCCCTCTT-T
* *
205300 CCTTATCTCTCCCTCTTT
1 CCTTCTTTCTCCCTCTTT
205318 CC-TCTTT
1 CCTTCTTT
205325 TTGTGCTCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 3 0.14
18 3 0.14
19 15 0.71
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (18 bp):
CCTTCTTTCTCCCTCTTT
Found at i:205662 original size:22 final size:23
Alignment explanation
Indices: 205619--205662 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
205609 CTCACTACCG
**
205619 ATTTGGTAACAAATAATTTATTA
1 ATTTGGTAACAAATAAAATATTA
*
205642 ATTT-GTAATAAATAAAATATT
1 ATTTGGTAACAAATAAAATATT
205663 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTTGGTAACAAATAAAATATTA
Found at i:210952 original size:15 final size:16
Alignment explanation
Indices: 210926--210961 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
210916 TAGACATAGA
210926 TTATTGTTATAAATAT
1 TTATTGTTATAAATAT
*
210942 TTATT-TTATAACTAT
1 TTATTGTTATAAATAT
210957 TTATT
1 TTATT
210962 ATAATTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATTGTTATAAATAT
Found at i:210976 original size:21 final size:20
Alignment explanation
Indices: 210952--210991 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
210942 TTATTTTATA
*
210952 ACTATTTATTATAATTAGATC
1 ACTATTTATTA-AATAAGATC
210973 ACTATTTATTAAATAAGAT
1 ACTATTTATTAAATAAGAT
210992 TTTGATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
ACTATTTATTAAATAAGATC
Found at i:217876 original size:24 final size:24
Alignment explanation
Indices: 217832--217881 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
217822 ATAAAGAACC
*
217832 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
217856 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
217880 AA
1 AA
217882 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:224228 original size:135 final size:134
Alignment explanation
Indices: 223987--224256 Score: 477
Period size: 135 Copynumber: 2.0 Consensus size: 134
223977 AATTGTATTC
* * *
223987 AGGATTTTGATAAATGCTCTAGTAATACAGTCCAACATTTTAGATAAAAGGCGGTTAATCATTTA
1 AGGATTCTGATAAATGCTCTAGTAATACAATCCAACATTTTAGATAAAAGACGGTTAATCATTTA
*
224052 CACTTATGTTTGTGATTTCATCAAGTCTATCTTAACATAAACCACAAATCATGAATATGAAATCA
66 CACTTATGTTTGTAATTTCATCAAGTCTATCTTAACATAAACCACAAATCATGAATATGAAATCA
224117 TTAA
131 TTAA
*
224121 AGGATTCTGATAAATGCTCTTGTAATACAATCCAACATTTTAGATAAAAAGACGGTTAATCATTT
1 AGGATTCTGATAAATGCTCTAGTAATACAATCCAACATTTTAGAT-AAAAGACGGTTAATCATTT
*
224186 ACACTTATGTTTGTAATTTCATCAAGTCTATCTTAACATAAACTACAAATCATGAATATGAAATC
65 ACACTTATGTTTGTAATTTCATCAAGTCTATCTTAACATAAACCACAAATCATGAATATGAAATC
224251 ATTAA
130 ATTAA
224256 A
1 A
224257 AGCATTTCTA
Statistics
Matches: 129, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
134 42 0.33
135 87 0.67
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (134 bp):
AGGATTCTGATAAATGCTCTAGTAATACAATCCAACATTTTAGATAAAAGACGGTTAATCATTTA
CACTTATGTTTGTAATTTCATCAAGTCTATCTTAACATAAACCACAAATCATGAATATGAAATCA
TTAA
Found at i:226928 original size:23 final size:23
Alignment explanation
Indices: 226902--226976 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
226892 GAGTCAAGGG
226902 ATTCTACGCGGTCCTTCGGGACA
1 ATTCTACGCGGTCCTTCGGGACA
* **
226925 ATTCTATGTAGTCCTTCGGGACA
1 ATTCTACGCGGTCCTTCGGGACA
*
226948 ATTCTACGCGGTTCTTCGGGACA
1 ATTCTACGCGGTCCTTCGGGACA
*
226971 AATCTA
1 ATTCTA
226977 TGTGGCACTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (23 bp):
ATTCTACGCGGTCCTTCGGGACA
Found at i:226987 original size:23 final size:22
Alignment explanation
Indices: 226914--226987 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
226904 TCTACGCGGT
*
226914 CCTTCGGGACAATTCTATGTAGT
1 CCTTCGGGACAATTCTATGT-GG
* *
226937 CCTTCGGGACAATTCTACGCGG
1 CCTTCGGGACAATTCTATGTGG
* *
226959 TTCTTCGGGACAAATCTATGTGG
1 -CCTTCGGGACAATTCTATGTGG
226982 CACTTC
1 C-CTTC
226988 AGTGCAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (22 bp):
CCTTCGGGACAATTCTATGTGG
Found at i:227007 original size:24 final size:24
Alignment explanation
Indices: 226980--227031 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
226970 AAATCTATGT
*
226980 GGCACTTCAGTGCAAATTCTACAC
1 GGCACTTCAGTACAAATTCTACAC
*
227004 GGCACTTCGGTACAAATTCTACAC
1 GGCACTTCAGTACAAATTCTACAC
227028 GGCA
1 GGCA
227032 ATTTCGACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (24 bp):
GGCACTTCAGTACAAATTCTACAC
Found at i:229764 original size:41 final size:41
Alignment explanation
Indices: 229707--229791 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
229697 ACTACTTGAA
*
229707 ATGAAAAGAATACTTATGAGAAGCATGATATTGCATGTCGG
1 ATGAAAAGAATACTTATGAGAAGCATGATATTGCATGTAGG
229748 ATGAAAAGAATACTTATGAGAAGCATGATATTGCATGTAGG
1 ATGAAAAGAATACTTATGAGAAGCATGATATTGCATGTAGG
229789 ATG
1 ATG
229792 CTATCTACCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (41 bp):
ATGAAAAGAATACTTATGAGAAGCATGATATTGCATGTAGG
Found at i:237007 original size:33 final size:33
Alignment explanation
Indices: 236965--237035 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
236955 CCAAAAAGAG
236965 AGATCTTTTAACTGGAAGCTAAAGAACACAAGT
1 AGATCTTTTAACTGGAAGCTAAAGAACACAAGT
*
236998 AGATCTTTTAGCTGGAAGCTAAAGAACACAAGT
1 AGATCTTTTAACTGGAAGCTAAAGAACACAAGT
237031 AGATC
1 AGATC
237036 AACCACTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (33 bp):
AGATCTTTTAACTGGAAGCTAAAGAACACAAGT
Found at i:243539 original size:16 final size:16
Alignment explanation
Indices: 243518--243549 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
243508 CCCAAGGTCC
*
243518 GAAACCAACGTAAGTG
1 GAAACCAACATAAGTG
243534 GAAACCAACATAAGTG
1 GAAACCAACATAAGTG
243550 TCTAAATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (16 bp):
GAAACCAACATAAGTG
Found at i:245837 original size:3 final size:3
Alignment explanation
Indices: 245831--245876 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
245821 AATTCACGTG
* * *
245831 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCA TCT TCT TAT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
245877 TTTCCCATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:248057 original size:120 final size:120
Alignment explanation
Indices: 247902--248159 Score: 338
Period size: 120 Copynumber: 2.2 Consensus size: 120
247892 GCCTTATGCT
* * * *
247902 CTAA-GTAAGTCCTTATGGTCCAATGGGCACACCCCTCGGGTGGGCACCTACGCTTAGGTTAGGG
1 CTAAGGTAAGTCCTTATGGGCCAATGGGCACACCCCTCAGGTAGGCACCTACGCTTAGGCTAGGG
* * *
247966 TAAGACCTTATGGTCCCAAGATGTTCCCTTAGGTAGGCTCTTACGCTCTTTGGGC
66 TAAGACCTTATAGACCCAAGATGTTCCCTTAGGTAGGCTCTTACGCCCTTTGGGC
* * * * * *
248021 CTAAGGTAAGTCTTTATGGGCCAGTGGGCACACCCCTCATGTAGGCACCTATGTTTCGGCTAGGG
1 CTAAGGTAAGTCCTTATGGGCCAATGGGCACACCCCTCAGGTAGGCACCTACGCTTAGGCTAGGG
* * * *
248086 TAAGACCTTGTAGACCCAAGGTGTTCCTTTAGGTTGGCTCTTACGCCCTTTGGGC
66 TAAGACCTTATAGACCCAAGATGTTCCCTTAGGTAGGCTCTTACGCCCTTTGGGC
* *
248141 TTAGGGTAAGTCCTTATGG
1 CTAAGGTAAGTCCTTATGG
248160 ATACAGTTCT
Statistics
Matches: 118, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
119 4 0.03
120 114 0.97
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (120 bp):
CTAAGGTAAGTCCTTATGGGCCAATGGGCACACCCCTCAGGTAGGCACCTACGCTTAGGCTAGGG
TAAGACCTTATAGACCCAAGATGTTCCCTTAGGTAGGCTCTTACGCCCTTTGGGC
Found at i:248584 original size:2 final size:2
Alignment explanation
Indices: 248577--248615 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
248567 CATTTATGGT
248577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
248616 TACTTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:249518 original size:2 final size:2
Alignment explanation
Indices: 249511--249578 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
249501 CAAAATTACG
249511 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
249553 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
249579 GCACGTTAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250716 original size:28 final size:30
Alignment explanation
Indices: 250685--250745 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
250675 TTTGAAAATA
250685 TTTTGAAAACATATAT-ATATA-ATATAGT
1 TTTTGAAAACATATATAATATATATATAGT
*
250713 TTTTGAAAATATATATAATATATTATATAGT
1 TTTTGAAAACATATATAATATA-TATATAGT
250744 TT
1 TT
250746 CGAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 15 0.52
29 5 0.17
31 9 0.31
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTTGAAAACATATATAATATATATATAGT
Found at i:250824 original size:14 final size:14
Alignment explanation
Indices: 250805--250848 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
250795 TTTAAAACAT
250805 ATTATTTTTCATTA
1 ATTATTTTTCATTA
250819 ATTATTTTTCATTA
1 ATTATTTTTCATTA
250833 ATTA-TTTT-ATTA
1 ATTATTTTTCATTA
250845 ATTA
1 ATTA
250849 ATATTTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.27
13 4 0.13
14 18 0.60
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTTTTCATTA
Found at i:252103 original size:13 final size:13
Alignment explanation
Indices: 252078--252103 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
252068 CTTTTATTCC
252078 TTTTATTTACTTT
1 TTTTATTTACTTT
252091 TTTTATTTACTTT
1 TTTTATTTACTTT
252104 ATTTCGATCT
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTACTTT
Found at i:256258 original size:99 final size:99
Alignment explanation
Indices: 256010--256284 Score: 397
Period size: 99 Copynumber: 2.8 Consensus size: 99
256000 ATGTATACAG
* * * **
256010 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCTGGCTTTATAAATAAGATTCAGC
1 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGGATAAGATTCAGC
* *
256075 TAGCATGATAAAGGTGATTATAATATATATACAA
66 TAGCCTGATAAAGGTGATTATAATATATATAAAA
*
256109 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGATTTATGGATAAGATTCAGC
1 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGGATAAGATTCAGC
256174 TAGCCTGATAAAGGTGATTATAATATATATAAAA
66 TAGCCTGATAAAGGTGATTATAATATATATAAAA
* * * * * * * **
256208 TAAATCTTGAGCTGTCCCTCTAGAGTATTTAGTTAAATGCCCCAGCTTTATGGATAACATTCAAT
1 TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGGATAAGATTCAGC
256273 TAGCCTGATAAA
66 TAGCCTGATAAA
256285 CGCAAATTAC
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 158 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (99 bp):
TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTATGGATAAGATTCAGC
TAGCCTGATAAAGGTGATTATAATATATATAAAA
Found at i:257621 original size:86 final size:86
Alignment explanation
Indices: 257516--257981 Score: 605
Period size: 86 Copynumber: 5.4 Consensus size: 86
257506 GAAGAACATT
* * *
257516 TCACAT-GCTTTCCCATGAAGGGGAGTCATCCAAAGATCATCTTACTTGCTTCAGACCCACGAAG
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAG
257580 GAGAACCACCTGAGGAATATA
66 GAGAACCACCTGAGGAATATA
* * * *
257601 TCACATAGTTTTCCCGTGAAGGGGAGTCATTCAAAGATCATCTCATTTGGTTCAGACCCACGAAG
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAG
*
257666 GGGAACCACCTGAGGAATATA
66 GAGAACCACCTGAGGAATATA
* *
257687 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTTAGACCCGCGAAG
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAG
* *
257752 GGGAACCACTTGAGGAATATA
66 GAGAACCACCTGAGGAATATA
* **
257773 TTACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGTGAA-
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAG
*
257837 GAGGAATCACCTGAGGAATATA
66 GA-GAACCACCTGAGGAATATA
* * * ***
257859 TCACATGGCTTTCCCATGGAA-GGGAGCCATTCAAAGATCATCTCACTTGGTTCAGACTTGCGAA
1 TCACATGGCTTTCCCGT-GAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAA
* ***
257923 GGGGAATTGCCTGAGGAATATA
65 GGAGAACCACCTGAGGAATATA
* * * * * *
257945 CCACTTGGCTTTCCCGTAAAGAGGATTCATCTAAAGA
1 TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGA
257982 ATTATGACCA
Statistics
Matches: 337, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
85 9 0.03
86 324 0.96
87 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (86 bp):
TCACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCACGAAG
GAGAACCACCTGAGGAATATA
Found at i:258468 original size:200 final size:200
Alignment explanation
Indices: 258037--258516 Score: 602
Period size: 200 Copynumber: 2.4 Consensus size: 200
258027 GAGGAACAGT
* * * *
258037 TTACAGCATAACTCAAGGCTAGAA-GTGTTATCTGTCAACAAAACCTTCGAGTTCAATTTCATTC
1 TTACAGCATAGCTCAAGACGAGAACG-GTTATCTGTCAAAAAAACCTTCGAGTTCAATTTCATTC
* * * *
258101 AGTTTGAAGGCATATCAACCGTATGGTAGCAACGAGGAACTACTTTCCGGTTAAAGCTTAAACTG
65 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGATTAAAGCTTAAACTG
* * * * * * *
258166 AGGTCTTTAAGTCAAGAAGAAGACCTGGGTTGGCTGCAATTTAGCAACAAAGAATTATATCCCAT
130 AGGTATTTAAGTCAAGAAGAAGACCTAGGTTAGCTACAATTTAGAAACAAAGAACTATATCCCAG
258231 CCAAAA
195 CCAAAA
* ** * * * * * *
258237 TTACAGTATAGCTCAAGGTGAGAAGGGTTATCTTTCAATAAAACTTTCGAGTTCGATTCCATTCA
1 TTACAGCATAGCTCAAGACGAGAACGGTTATCTGTCAAAAAAACCTTCGAGTTCAATTTCATTCA
* * *
258302 GCTCGAAGGCATATCAACTGCATGGTAGCAACGAGGAACTACTTTCCGATTGAAGTTTAAACTGA
66 GCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGATTAAAGCTTAAACTGA
* ** * *
258367 GGTATTTAAGTCAAGAAGAAGTCCTAGGTTAGCTATGATTTAGAAACAAGGAACTATCTCCCAGC
131 GGTATTTAAGTCAAGAAGAAGACCTAGGTTAGCTACAATTTAGAAACAAAGAACTATATCCCAGC
*
258432 CAAAT
196 CAAAA
* * *
258437 TTATAGCATAGTTCAAGACGATAACGGTTATCTGTCAACAAAAACCTTCGAGTTCAATTTCATTC
1 TTACAGCATAGCTCAAGACGAGAACGGTTATCTGTCAA-AAAAACCTTCGAGTTCAATTTCATTC
*
258502 AGCTCGAGGGCATAT
65 AGCTCGAAGGCATAT
258517 TTTCTGGTTG
Statistics
Matches: 236, Mismatches: 42, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
200 199 0.84
201 37 0.16
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (200 bp):
TTACAGCATAGCTCAAGACGAGAACGGTTATCTGTCAAAAAAACCTTCGAGTTCAATTTCATTCA
GCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGATTAAAGCTTAAACTGA
GGTATTTAAGTCAAGAAGAAGACCTAGGTTAGCTACAATTTAGAAACAAAGAACTATATCCCAGC
CAAAA
Found at i:258835 original size:35 final size:34
Alignment explanation
Indices: 258796--258920 Score: 139
Period size: 33 Copynumber: 3.6 Consensus size: 34
258786 ATATATATTA
* *
258796 ATATAGTATAGTTTTTGAAAATATTTTGAAAACATAT
1 ATATAATATAGTTTTTGAAAACATTTTG-AAA-A-AT
*
258833 ATATATATATAGTTTTTG-AAACGTTTTG-AAAAT
1 ATATA-ATATAGTTTTTGAAAACATTTTGAAAAAT
*
258866 ATATAATATAGTTTTTGAAAACATTTCGAAAATAT
1 ATATAATATAGTTTTTGAAAACATTTTGAAAA-AT
*
258901 ATATTATATAG-TTTTGAAAA
1 ATATAATATAGTTTTTGAAAA
258921 TAATTTTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.15
33 15 0.19
34 13 0.17
35 14 0.18
37 13 0.17
38 11 0.14
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (34 bp):
ATATAATATAGTTTTTGAAAACATTTTGAAAAAT
Found at i:258850 original size:38 final size:36
Alignment explanation
Indices: 258796--258953 Score: 157
Period size: 38 Copynumber: 4.4 Consensus size: 36
258786 ATATATATTA
*
258796 ATATAGTATAGTTTTTGAAAATATTTTGAAAACATATAT
1 ATATA-TATAGTTTTTGAAAACATTTTG-AAA-ATATAT
*
258835 ATATATATAGTTTTTG-AAACGTTTTG-AAA-ATAT
1 ATATATATAGTTTTTGAAAACATTTTGAAAATATAT
*
258868 ATA-ATATAGTTTTTGAAAACATTTCGAAAATATAT
1 ATATATATAGTTTTTGAAAACATTTTGAAAATATAT
* ***
258903 AT-TATATAG-TTTTGAAAATAATTTTTGAAAGCGTAT
1 ATATATATAGTTTTTGAAAA-CA-TTTTGAAAATATAT
258939 ATCATATATAGTTTT
1 AT-ATATATAGTTTT
258954 AAAAATGATT
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
32 12 0.12
33 15 0.15
34 13 0.13
35 15 0.15
36 12 0.12
37 8 0.08
38 18 0.18
39 8 0.08
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (36 bp):
ATATATATAGTTTTTGAAAACATTTTGAAAATATAT
Found at i:260329 original size:23 final size:23
Alignment explanation
Indices: 260294--260338 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
260284 TAACTCTTTG
* * *
260294 TTTTGTTTGTTTTGTTTTTTTAA
1 TTTTATTTGTTTTATCTTTTTAA
*
260317 TTTTATTTTTTTTATCTTTTTA
1 TTTTATTTGTTTTATCTTTTTA
260339 GGACAATTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (23 bp):
TTTTATTTGTTTTATCTTTTTAA
Found at i:261933 original size:24 final size:23
Alignment explanation
Indices: 261906--261950 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
261896 AAGATATAGG
261906 ATATG-ATATACATGATTATATGCA
1 ATATGTAT-TACATG-TTATATGCA
261930 ATATGTATTACATGTTATATG
1 ATATGTATTACATGTTATATG
261951 AAATGACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 11 0.55
25 2 0.10
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (23 bp):
ATATGTATTACATGTTATATGCA
Found at i:262368 original size:25 final size:27
Alignment explanation
Indices: 262339--262400 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
262329 ACTCGAATTC
*
262339 AATAAGAAT-AGT-GTATGTATTTTGT
1 AATAAGAATAAATAGTATGTATTTTGT
262364 AATAAGAATTAAATAGTATGTATTTTGT
1 AATAAGAA-TAAATAGTATGTATTTTGT
262392 AATAAGAAT
1 AATAAGAAT
262401 TGTGGTTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 8 0.24
26 1 0.03
27 3 0.09
28 21 0.64
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (27 bp):
AATAAGAATAAATAGTATGTATTTTGT
Found at i:262610 original size:12 final size:12
Alignment explanation
Indices: 262593--262646 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
262583 GAAAGTTTTC
*
262593 ACTGTTTATGGT
1 ACTGTTCATGGT
*
262605 ACTGTTCACGGT
1 ACTGTTCATGGT
262617 ACTGTT-AT--T
1 ACTGTTCATGGT
262626 ACTGTTCATGGT
1 ACTGTTCATGGT
*
262638 ATTGTTCAT
1 ACTGTTCAT
262647 ACAGTATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 1 0.03
12 25 0.71
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:262630 original size:21 final size:21
Alignment explanation
Indices: 262604--262643 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
262594 CTGTTTATGG
262604 TACTGTTCACGGTACTGTTAT
1 TACTGTTCACGGTACTGTTAT
* *
262625 TACTGTTCATGGTATTGTT
1 TACTGTTCACGGTACTGTT
262644 CATACAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (21 bp):
TACTGTTCACGGTACTGTTAT
Found at i:265741 original size:14 final size:14
Alignment explanation
Indices: 265722--265748 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
265712 TTGCTTTGAC
265722 TCGATTCTAATTCT
1 TCGATTCTAATTCT
265736 TCGATTCTAATTC
1 TCGATTCTAATTC
265749 ATCTAAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TCGATTCTAATTCT
Found at i:270712 original size:22 final size:22
Alignment explanation
Indices: 270686--270740 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
270676 TTGTGTTTGG
270686 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
*
270708 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTAATGC
270730 TCAAAGGTTTG
1 TCAAAGGTTTG
270741 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:271374 original size:14 final size:14
Alignment explanation
Indices: 271357--271407 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
271347 TTCTTTTTGA
271357 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
271371 TTTTTGTTC-TTCT
1 TTTTTGTTCTTTCT
271384 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
271400 TTTTTGTT
1 TTTTTGTT
271408 TTTGCCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.29
14 12 0.35
15 2 0.06
16 10 0.29
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:275455 original size:2 final size:2
Alignment explanation
Indices: 275448--275474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
275438 GAACATACGC
275448 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
275475 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:275625 original size:12 final size:12
Alignment explanation
Indices: 275603--275647 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
275593 GAATAAAAGG
275603 AAAATATAATAGT
1 AAAA-ATAATAGT
*
275616 AAAAATAATAAT
1 AAAAATAATAGT
*
275628 AAATATAATAGT
1 AAAAATAATAGT
*
275640 AATAATAA
1 AAAAATAA
275648 AAATACAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:275631 original size:24 final size:24
Alignment explanation
Indices: 275604--275652 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
275594 AATAAAAGGA
*
275604 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
275628 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
275652 A
1 A
275653 CAAAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:276284 original size:37 final size:37
Alignment explanation
Indices: 276210--276303 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
276200 GGATCCTATC
* * * * * *
276210 TTTAGGAATTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGCAAAACTATATCATATT
*
276247 TTTAGGAGTTTAAATCCTAGCAAAATTATATCATATT
1 TTTAGGAGTTTAAATCCTAGCAAAACTATATCATATT
* *
276284 TTTAGAAGTTTGAATCCTAG
1 TTTAGGAGTTTAAATCCTAG
276304 TAGGACGAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGCAAAACTATATCATATT
Found at i:277623 original size:20 final size:20
Alignment explanation
Indices: 277600--277641 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
277590 CAACGCGAAC
*
277600 TCCAATTTCACAACACAGTT
1 TCCAAATTCACAACACAGTT
* *
277620 TCCAAATTCGCAACTCAGTT
1 TCCAAATTCACAACACAGTT
277640 TC
1 TC
277642 TGAAATCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (20 bp):
TCCAAATTCACAACACAGTT
Found at i:277670 original size:20 final size:19
Alignment explanation
Indices: 277647--277716 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
277637 GTTTCTGAAA
277647 TCGCAACGCGATTTTAAAAT
1 TCGCAACGCGATTTT-AAAT
* *
277667 TCGCAACACTGAATTTCAAAT
1 TCGCAACGC-G-ATTTTAAAT
* *
277688 TCGCAACTCGATTTCTGAAT
1 TCGCAACGCGATTT-TAAAT
277708 TCGCAACGC
1 TCGCAACGC
277717 AAATTTCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 4 0.10
20 20 0.49
21 13 0.32
22 4 0.10
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (19 bp):
TCGCAACGCGATTTTAAAT
Found at i:277731 original size:19 final size:20
Alignment explanation
Indices: 277707--277781 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
277697 GATTTCTGAA
*
277707 TTCGCAACGCAAATTT-CTT
1 TTCGCAACACAAATTTCCTT
*
277726 TTCGCAACACAAGTTTCCTT
1 TTCGCAACACAAATTTCCTT
* * *
277746 TTCGCAACA-ATATTTTCTAA
1 TTCGCAACACAAATTTCCT-T
*
277766 TTCGCAACACGAATTT
1 TTCGCAACACAAATTT
277782 TGTTTTCGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 20 0.44
20 21 0.47
21 4 0.09
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (20 bp):
TTCGCAACACAAATTTCCTT
Found at i:278802 original size:24 final size:24
Alignment explanation
Indices: 278744--278790 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
278734 AGTCAGTATT
* * *
278744 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTCGTCAATACC
278768 CGAACTTTGATATTCGTCAATAC
1 CGAACTTTGATATTCGTCAATAC
278791 TCGGATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATATTCGTCAATACC
Found at i:284216 original size:21 final size:21
Alignment explanation
Indices: 284158--284223 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
284148 ATCCTGAATA
* *
284158 ATGGAAGGGGCCTCTTAAACG
1 ATGGGAGGGGCCTCTTGAACG
* *
284179 ATGGGATGGGCCTCTTGGACG
1 ATGGGAGGGGCCTCTTGAACG
*
284200 ATGGGAGGGGCCTCTTGAATG
1 ATGGGAGGGGCCTCTTGAACG
284221 ATG
1 ATG
284224 ACAGGTGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (21 bp):
ATGGGAGGGGCCTCTTGAACG
Found at i:284273 original size:21 final size:21
Alignment explanation
Indices: 284226--284273 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
284216 GAATGATGAC
*
284226 AGGTGAATCATGAACAATGGG
1 AGGTGGATCATGAACAATGGG
*
284247 AGGTGGATCATGAACAATGGT
1 AGGTGGATCATGAACAATGGG
284268 AGGTGG
1 AGGTGG
284274 GTCAGGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.38, T:0.21
Consensus pattern (21 bp):
AGGTGGATCATGAACAATGGG
Found at i:284429 original size:12 final size:12
Alignment explanation
Indices: 284410--284451 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
284400 GGGCCACTAA
284410 AAATAAATTAAT
1 AAATAAATTAAT
* *
284422 ACATAAATTAGT
1 AAATAAATTAAT
*
284434 AAATAAATAAAT
1 AAATAAATTAAT
284446 AAATAA
1 AAATAA
284452 TGCCGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:284890 original size:42 final size:42
Alignment explanation
Indices: 284831--284927 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
284821 GATGGAATAT
* * * * *
284831 GTGATGGCTCTCGGTGTCTAGGTGTATAATCGGCTTGATCAG
1 GTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATCAG
284873 GTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATCAG
1 GTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATCAG
284915 GTGATGGCTCTCG
1 GTGATGGCTCTCG
284928 AAGTAGGGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.30
Consensus pattern (42 bp):
GTGATGGCTCTCGGTGTCGAGCTATAGAATCGGCTCGATCAG
Found at i:286090 original size:20 final size:20
Alignment explanation
Indices: 286067--286151 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
286057 TTTGAAACTT
*
286067 AAATTCGCAACATGAAAATG
1 AAATTCGCAACACGAAAATG
** *
286087 AAATTTTCAACACGAAAATA
1 AAATTCGCAACACGAAAATG
* * *
286107 AAATTCACAACGCAAAAATG
1 AAATTCGCAACACGAAAATG
**
286127 AAATTCGCAACGTGAAAACTG
1 AAATTCGCAACACGAAAA-TG
286148 AAAT
1 AAAT
286152 CGCGTTGCGA
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 46 0.88
21 6 0.12
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:286736 original size:20 final size:21
Alignment explanation
Indices: 286711--286781 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
286701 TAAACGCGCT
*
286711 TTGCGAATT-ACAAATTCGCG
1 TTGCGAATTCAGAAATTCGCG
* * *
286731 TTGCGATTTCAGAAACT-GAG
1 TTGCGAATTCAGAAATTCGCG
**
286751 TTGCGAATTTGGGAAATTCGCG
1 TTGCGAA-TTCAGAAATTCGCG
286773 TTGCGAATT
1 TTGCGAATT
286782 TGGAAACTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 16 0.41
21 14 0.36
22 9 0.23
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (21 bp):
TTGCGAATTCAGAAATTCGCG
Found at i:286766 original size:21 final size:20
Alignment explanation
Indices: 286742--286802 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
286732 TGCGATTTCA
286742 GAAACTGAGTTGCGAATTTGG
1 GAAACTGAGTTGCGAATTT-G
* *
286763 GAAATTCGCGTTGCGAATTTG
1 GAAACT-GAGTTGCGAATTTG
*
286784 GAAACTGTGTTGCGGAATT
1 GAAACTGAGTTGC-GAATT
286803 GGAGTTCGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 16 0.47
22 12 0.35
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.31
Consensus pattern (20 bp):
GAAACTGAGTTGCGAATTTG
Found at i:286772 original size:42 final size:40
Alignment explanation
Indices: 286722--286818 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 40
286712 TGCGAATTAC
286722 AAATTCGCGTTGCGATTTCAGAAACTGAGTTGC-GAATTTGGG
1 AAATTCGCGTTGCGATTT-AGAAACTGAGTTGCGGAA-TT-GG
* *
286764 AAATTCGCGTTGCGAATTTGGAAACTGTGTTGCGGAATTGG
1 AAATTCGCGTTGCG-ATTTAGAAACTGAGTTGCGGAATTGG
*
286805 -AGTTCGCGTTGCGA
1 AAATTCGCGTTGCGA
286819 ATTTGTTGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 1 0.02
40 12 0.24
41 2 0.04
42 28 0.56
43 7 0.14
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (40 bp):
AAATTCGCGTTGCGATTTAGAAACTGAGTTGCGGAATTGG
Found at i:287345 original size:60 final size:59
Alignment explanation
Indices: 287297--287407 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
287287 ATAGTACCTT
* *
287297 GACTATTGGGTGAT-ATTTTATTGAGTCCCTCGATTATTAAAAGTTACAAAATAATCCCC
1 GACTATAGGGTGATGA-TTTATTGAGTCCCTCGACTATTAAAAGTTACAAAATAATCCCC
* * *
287356 GACTATAGGGTGTTGATTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAAT
1 GACTATAGGGTGATGATTTATTGAGTCCCTCGACTATTAAAAGTTACAAAAT
287408 GGTCAACCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (59 bp):
GACTATAGGGTGATGATTTATTGAGTCCCTCGACTATTAAAAGTTACAAAATAATCCCC
Found at i:291415 original size:2 final size:2
Alignment explanation
Indices: 291408--291469 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
291398 TATATTGTTA
291408 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
291450 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
291470 TTATTTATCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:292385 original size:23 final size:23
Alignment explanation
Indices: 292334--292409 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
292324 TTTCTCTTGC
*
292334 AAATGAAAATGTT--CAACAAC-
1 AAATGAAAATGTTCGCAAAAACT
292354 AAATGAAAATGTTCGCAAAAACT
1 AAATGAAAATGTTCGCAAAAACT
* *
292377 AAATAAAAATGTTCGCAAAAGCT
1 AAATGAAAATGTTCGCAAAAACT
292400 AAATGAAAAT
1 AAATGAAAAT
292410 ATTCACTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 13 0.27
22 6 0.12
23 30 0.61
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (23 bp):
AAATGAAAATGTTCGCAAAAACT
Found at i:292987 original size:263 final size:263
Alignment explanation
Indices: 292503--293018 Score: 930
Period size: 263 Copynumber: 2.0 Consensus size: 263
292493 TCTCGAATGC
*
292503 TAAACGAACGAACATGACCTTCAAAAATAAATATATGAACACGAATTTGAACATGATATTAAAAA
1 TAAACGAACGAACATGACCTTCAAAAATAAATATATGAACACGAATTTAAACATGATATTAAAAA
* * *
292568 TTTAAATAAATATCGATCGAATATAAACATTTTTAAAAACAAACAAATAAACAAAAACGAACATA
66 TTTAAATAAATATCGATCAAATATAAACACTTTTAAAAACAAAAAAATAAACAAAAACGAACATA
*
292633 ATTTTATTCGTTCAAACTCAATTTATTTACACCCCTAATTATATTACAAAGGGTATATCTACGTC
131 ATTTTATTCGTTCAAACTCAATTTATTTACACCCCTAATTATATTACAAAAGGTATATCTACGTC
* *
292698 CTCAATAAATTAAAAAATAAAATAATAATATTAGGTAAAAGACAAATAGGGCTACCTCTAAATTT
196 CTCAATAAATTAAAAAATAAAATAATAATATTAGGTAAAAGACAAAAAGGGCTACCCCTAAATTT
292763 GCT
261 GCT
*
292766 TAAACGAACGAATATGACCTTCAAAAATAAATATATGAACACGAATTTAAACATGATATTAAAAA
1 TAAACGAACGAACATGACCTTCAAAAATAAATATATGAACACGAATTTAAACATGATATTAAAAA
292831 TTTAAATAAATATCGATCAAATATAAACACTTTTAAAAACAAAAAAATAAACAAAAACGAACATA
66 TTTAAATAAATATCGATCAAATATAAACACTTTTAAAAACAAAAAAATAAACAAAAACGAACATA
*
292896 ATTTTATT-GTTCAAACTCAATTTATTTA-A-TCCTAATTATATTACAAAAGGTATATCTACGTC
131 ATTTTATTCGTTCAAACTCAATTTATTTACACCCCTAATTATATTACAAAAGGTATATCTACGTC
292958 CTCAATAAATTAAAAAATAAAATAATAATATTAGGTAAAAGACAAAAAGGGCTACCCCTAA
196 CTCAATAAATTAAAAAATAAAATAATAATATTAGGTAAAAGACAAAAAGGGCTACCCCTAA
293019 TTATTTTTAC
Statistics
Matches: 244, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
260 90 0.37
261 1 0.00
262 20 0.08
263 133 0.55
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (263 bp):
TAAACGAACGAACATGACCTTCAAAAATAAATATATGAACACGAATTTAAACATGATATTAAAAA
TTTAAATAAATATCGATCAAATATAAACACTTTTAAAAACAAAAAAATAAACAAAAACGAACATA
ATTTTATTCGTTCAAACTCAATTTATTTACACCCCTAATTATATTACAAAAGGTATATCTACGTC
CTCAATAAATTAAAAAATAAAATAATAATATTAGGTAAAAGACAAAAAGGGCTACCCCTAAATTT
GCT
Found at i:297655 original size:18 final size:20
Alignment explanation
Indices: 297632--297679 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
297622 AAAATACGAA
*
297632 CATCGAATGC-C-ATTAGTG
1 CATCGAATGCACAAGTAGTG
297650 CATCG-ATGCACAAGTAGTG
1 CATCGAATGCACAAGTAGTG
297669 CAT-GAATGCAC
1 CATCGAATGCAC
297680 CCCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 15 0.58
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
CATCGAATGCACAAGTAGTG
Found at i:309558 original size:2 final size:2
Alignment explanation
Indices: 309551--309581 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
309541 GGTTAATTCA
309551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
309582 GGATTAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:314375 original size:31 final size:31
Alignment explanation
Indices: 314340--314400 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
314330 TTGATATTAA
*
314340 TAAATAAAAATATATTAAAATTTTAATAATT
1 TAAATAAAAATAAATTAAAATTTTAATAATT
* * *
314371 TAAATAAAACTAAATTATAATTTTTATAAT
1 TAAATAAAAATAAATTAAAATTTTAATAAT
314401 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATAAAAATAAATTAAAATTTTAATAATT
Found at i:314503 original size:2 final size:2
Alignment explanation
Indices: 314498--314531 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
314488 ATTTTTTTAA
*
314498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
314532 GACTAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:315912 original size:3 final size:3
Alignment explanation
Indices: 315904--315940 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
315894 ATATATATAT
*
315904 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
315941 GTATGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:315921 original size:14 final size:14
Alignment explanation
Indices: 315904--315931 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
315894 ATATATATAT
315904 TAATAATAATAATA
1 TAATAATAATAATA
315918 TAATAATAATAATA
1 TAATAATAATAATA
315932 ATAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:315924 original size:17 final size:17
Alignment explanation
Indices: 315898--315934 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
315888 ATATATATAT
*
315898 ATATATTAATAATAATA
1 ATATAATAATAATAATA
315915 ATATAATAATAATAATA
1 ATATAATAATAATAATA
315932 ATA
1 ATA
315935 AAAATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATAATAATAATA
Found at i:316218 original size:76 final size:76
Alignment explanation
Indices: 316092--316898 Score: 1478
Period size: 76 Copynumber: 10.6 Consensus size: 76
316082 GGTCTTATGA
* * * *
316092 ATGACCCTG-AGGGTTTGAAAACATTAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTG
316156 AAGGACTTACAG
65 AAGGACTTACAG
*
316168 ATGACCCGAAGGATTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316233 AGGACTTACAG
66 AGGACTTACAG
316244 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316309 AGGACTTACAG
66 AGGACTTACAG
*
316320 ATGACCCGAAGGTTTTGAAAATATCAAAAAGTTCCCGAAGGCTTTTT-GAATACATCATGCACTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAA-ACATCATGCACTG
*
316384 AAGGGCTTACAG
65 AAGGACTTACAG
316396 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
316461 AGGGCTTACAG
66 AGGACTTACAG
316472 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316537 AGGACTTACAG
66 AGGACTTACAG
316548 ATGACCCGAAGGTTTTGAAAACATC-AAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316612 AGGACTTACAG
66 AGGACTTACAG
316623 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTT-GAATACATCATGCACTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAA-ACATCATGCACTG
*
316687 AAGGGCTTACAG
65 AAGGACTTACAG
316699 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316764 AGGACTTACAG
66 AGGACTTACAG
316775 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
316840 AGGACTTACAG
66 AGGACTTACAG
316851 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTG
316899 AATATGCACT
Statistics
Matches: 714, Mismatches: 11, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
75 82 0.11
76 626 0.88
77 6 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (76 bp):
ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:316919 original size:31 final size:31
Alignment explanation
Indices: 316884--316946 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
316874 TCAAAAAGTT
316884 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
1 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
316915 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
1 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
316946 C
1 C
316947 TTACAGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGAATATGCACTGAAGGG
Found at i:316958 original size:102 final size:106
Alignment explanation
Indices: 316808--317000 Score: 340
Period size: 102 Copynumber: 1.8 Consensus size: 106
316798 TCAAAAAGTT
316808 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
316873 ATCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
65 ATCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
*
316915 CCCGAAGGCTTTTT-G-A-AT-ATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTTGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA
316976 TCAAAAAGTTCCCGAAGGCTTTTTG
66 TCAAAAAGTTCCCGAAGGCTTTTTG
317001 GAAACATCAT
Statistics
Matches: 85, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
102 67 0.79
103 2 0.02
104 1 0.01
106 1 0.01
107 14 0.16
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (106 bp):
CCCGAAGGCTTTTTGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA
TCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
Found at i:317897 original size:22 final size:22
Alignment explanation
Indices: 317872--317926 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
317862 CATAAAGCTT
317872 TCATCTTTGAAAAGAGAAACTA
1 TCATCTTTGAAAAGAGAAACTA
* *
317894 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAAACTA
317916 TCATCTTTGAA
1 TCATCTTTGAA
317927 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAAACTA
Found at i:318431 original size:54 final size:54
Alignment explanation
Indices: 318289--318550 Score: 429
Period size: 54 Copynumber: 4.9 Consensus size: 54
318279 AGAATAGCAG
* * *
318289 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTT-TGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGG-TTTCTGTTCAGAT
*
318343 GTTCGT-AAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
*
318396 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTATTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
* *
318450 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTAAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
*
318504 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG
318551 CCAAGATTTC
Statistics
Matches: 195, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
52 3 0.02
53 45 0.23
54 147 0.75
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
Found at i:323250 original size:18 final size:18
Alignment explanation
Indices: 323200--323252 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
323190 TGTTTTTTGT
* *
323200 TTTTTTTTATTTATTTCCC
1 TTTTTTTTCTTT-TTTCCA
323219 TTTTTTTTC-TTTTTCCA
1 TTTTTTTTCTTTTTTCCA
323236 TTTTTTTTCTTTTTTCC
1 TTTTTTTTCTTTTTTCC
323253 TTTCTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 14 0.45
18 9 0.29
19 8 0.26
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCCA
Found at i:323269 original size:27 final size:26
Alignment explanation
Indices: 323239--323292 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
323229 TTTTCCATTT
323239 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTT-CTTTCTTTGCTGGA
323266 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
323292 T
1 T
323293 GAGTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:323586 original size:2 final size:2
Alignment explanation
Indices: 323579--323606 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323569 ACAACAAAGG
323579 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
323607 TATTAAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:328613 original size:31 final size:31
Alignment explanation
Indices: 328578--328638 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
328568 TTGATATTAA
*
328578 TAAATAAAAATATATTAAAATTTTAATAATT
1 TAAATAAAAATAAATTAAAATTTTAATAATT
* * *
328609 TAAATAAAACTAAATTATAATTTTTATAAT
1 TAAATAAAAATAAATTAAAATTTTAATAAT
328639 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
TAAATAAAAATAAATTAAAATTTTAATAATT
Found at i:328742 original size:2 final size:2
Alignment explanation
Indices: 328735--328772 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
328725 TATTTTTAAA
*
328735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328773 GACTAAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:330131 original size:2 final size:2
Alignment explanation
Indices: 330124--330167 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
330114 TGGGCCTTTG
*
330124 TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA -A TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
330162 TA TA TA
1 TA TA TA
330168 ATAATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:330158 original size:3 final size:3
Alignment explanation
Indices: 330150--330188 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
330140 TATATATATT
*
330150 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
330189 GTATGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:330169 original size:16 final size:16
Alignment explanation
Indices: 330125--330188 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
330115 GGGCCTTTGT
330125 ATATATATATATATATATA
1 ATATATA-ATA-ATA-ATA
*
330144 TATATTTAATAATAATA
1 -ATATATAATAATAATA
330161 ATATATAATAATAATA
1 ATATATAATAATAATA
*
330177 ATA-ATAAAAATA
1 ATATATAATAATA
330189 GTATGAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.20
16 18 0.44
17 3 0.07
18 3 0.07
19 3 0.07
20 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATAATAATAATA
Found at i:330469 original size:76 final size:76
Alignment explanation
Indices: 330343--331150 Score: 1487
Period size: 76 Copynumber: 10.6 Consensus size: 76
330333 GGTCTTATGA
* * * *
330343 ATGACCCTG-AGGGTTTGAAAACATTAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTG
330407 AAGGACTTACAG
65 AAGGACTTACAG
*
330419 ATGACCCGAAGGATTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
330484 AGGACTTACAG
66 AGGACTTACAG
330495 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
330560 AGGACTTACAG
66 AGGACTTACAG
*
330571 ATGACCCGAAGGTTTTGAAAATATCAAAAAGTTCCCGAAGGCTTTTT-GAATACATCATGCACTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAA-ACATCATGCACTG
*
330635 AAGGGCTTACAG
65 AAGGACTTACAG
330647 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
330712 AGGGCTTACAG
66 AGGACTTACAG
330723 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
330788 AGGACTTACAG
66 AGGACTTACAG
330799 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
330864 AGGACTTACAG
66 AGGACTTACAG
330875 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTT-GAATACATCATGCACTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAA-ACATCATGCACTG
*
330939 AAGGGCTTACAG
65 AAGGACTTACAG
330951 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
331016 AGGACTTACAG
66 AGGACTTACAG
331027 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
331092 AGGACTTACAG
66 AGGACTTACAG
331103 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTG
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTG
331151 AATATGCACT
Statistics
Matches: 716, Mismatches: 11, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
75 7 0.01
76 703 0.98
77 6 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (76 bp):
ATGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:331171 original size:31 final size:31
Alignment explanation
Indices: 331136--331198 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
331126 TCAAAAAGTT
331136 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
1 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
331167 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
1 CCCGAAGGCTTTTTGAATATGCACTGAAGGG
331198 C
1 C
331199 TTACAGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGAATATGCACTGAAGGG
Found at i:331210 original size:102 final size:106
Alignment explanation
Indices: 331060--331252 Score: 340
Period size: 102 Copynumber: 1.8 Consensus size: 106
331050 TCAAAAAGTT
331060 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAC
331125 ATCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
65 ATCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
*
331167 CCCGAAGGCTTTTT-G-A-AT-ATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTTGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA
331228 TCAAAAAGTTCCCGAAGGCTTTTTG
66 TCAAAAAGTTCCCGAAGGCTTTTTG
331253 GAAACATCAT
Statistics
Matches: 85, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
102 67 0.79
103 2 0.02
104 1 0.01
106 1 0.01
107 14 0.16
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (106 bp):
CCCGAAGGCTTTTTGGAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACA
TCAAAAAGTTCCCGAAGGCTTTTTGAATATGCACTGAAGGG
Found at i:332152 original size:22 final size:22
Alignment explanation
Indices: 332127--332181 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
332117 CATAAAGCTT
332127 TCATCTTTGAAAAGAGAAACTA
1 TCATCTTTGAAAAGAGAAACTA
* *
332149 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAAACTA
332171 TCATCTTTGAA
1 TCATCTTTGAA
332182 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAAACTA
Found at i:332626 original size:54 final size:54
Alignment explanation
Indices: 332544--332806 Score: 447
Period size: 54 Copynumber: 4.9 Consensus size: 54
332534 AGAATAGCAG
* * *
332544 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTT-TGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGG-TTTCTGTTCAGAT
*
332598 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTTAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
332652 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
* *
332706 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTAAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
*
332760 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG
332807 CCAAGATTTC
Statistics
Matches: 199, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
53 3 0.02
54 196 0.98
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
Found at i:337474 original size:17 final size:17
Alignment explanation
Indices: 337453--337507 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
337443 GTTTTTTGTT
*
337453 TTTTTTTATTTATTTCCC
1 TTTTTTT-TCTATTTCCC
*
337471 TTTTTTTTCTTTTTCCC
1 TTTTTTTTCTATTTCCC
* *
337488 TTTTTTTTCTTTTTTCC
1 TTTTTTTTCTATTTCCC
337505 TTT
1 TTT
337508 CTTTGCTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 27 0.79
18 7 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTTCTATTTCCC
Found at i:337474 original size:18 final size:17
Alignment explanation
Indices: 337465--337507 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
337455 TTTTTATTTA
337465 TTTCCCTTTTTTTTCTT
1 TTTCCCTTTTTTTTCTT
337482 TTTCCCTTTTTTTTCTT
1 TTTCCCTTTTTTTTCTT
*
337499 TTTTCCTTT
1 TTTCCCTTT
337508 CTTTGCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCCCTTTTTTTTCTT
Found at i:337521 original size:27 final size:26
Alignment explanation
Indices: 337491--337544 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
337481 TTTTCCCTTT
337491 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTT-CTTTCTTTGCTGGA
337518 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
337544 T
1 T
337545 GAGTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:337998 original size:3 final size:3
Alignment explanation
Indices: 337990--338053 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
337980 TTTATTTATT
337990 TAA TAA TAA TAA TATA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
338037 TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TA
338054 GTATGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:338011 original size:16 final size:16
Alignment explanation
Indices: 337990--338048 Score: 111
Period size: 16 Copynumber: 3.8 Consensus size: 16
337980 TTTATTTATT
337990 TAATAATAATAATATA
1 TAATAATAATAATATA
338006 TAATAATAATAATATA
1 TAATAATAATAATATA
338022 TAATAATAATAATA-A
1 TAATAATAATAATATA
338037 TAATAATAATAA
1 TAATAATAATAA
338049 AAATAGTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 13 0.30
16 30 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:346126 original size:22 final size:22
Alignment explanation
Indices: 346076--346133 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
346066 TCGGTTGAGG
* * *
346076 GGGTATCGATTCCTCTTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
346098 -GGTACCGATTCCCCCTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
346119 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
346134 TAACCCAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.31
Consensus pattern (22 bp):
GGGTACCGATTCCCCCTTGAAT
Found at i:358800 original size:24 final size:24
Alignment explanation
Indices: 358773--358836 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
358763 TTCGCTTTAG
358773 TTGAACTCAAATTTTAGGCTTCAA
1 TTGAACTCAAATTTTAGGCTTCAA
** *
358797 TTGAGTTTAAATTTTAGGCTTCAA
1 TTGAACTCAAATTTTAGGCTTCAA
* *
358821 TCGAACTTCTAATTTT
1 TTGAAC-TCAAATTTT
358837 TTTTTTGAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (24 bp):
TTGAACTCAAATTTTAGGCTTCAA
Found at i:361365 original size:16 final size:16
Alignment explanation
Indices: 361344--361376 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
361334 TTACTACCTC
361344 TGTAAAGTTTCAGAAT
1 TGTAAAGTTTCAGAAT
361360 TGTAAAGTTTCAGAAT
1 TGTAAAGTTTCAGAAT
361376 T
1 T
361377 TAGTAACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TGTAAAGTTTCAGAAT
Found at i:362151 original size:64 final size:63
Alignment explanation
Indices: 362054--362194 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
362044 CACATTCAAT
* * *
362054 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAA-TTGATGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTG-TGCATCGATGCAT-AGGTA
* * * *
362117 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTTGTGCATCGATGCATAGGTA
362181 GTGCATCGATGCAC
1 GTGCATCGATGCAC
362195 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 18 0.27
64 46 0.69
65 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTTGTGCATCGATGCATAGGTA
Found at i:362209 original size:24 final size:20
Alignment explanation
Indices: 362182--362239 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
362172 GCATGGGTAG
362182 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
362206 TGCATCGATGCACTGTGGAA
1 TGCATCGATGCACTGTAGAA
362226 TGCATCGATGCACT
1 TGCATCGATGCACT
362240 TCAAGGGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:363134 original size:18 final size:18
Alignment explanation
Indices: 363047--363124 Score: 138
Period size: 18 Copynumber: 4.3 Consensus size: 18
363037 GAGGGTCTAC
*
363047 GTGGTACTTCGGGACATA
1 GTGGTCCTTCGGGACATA
363065 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
363083 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
363101 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
363119 GTGGTC
1 GTGGTC
363125 ATACGAGACA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:376029 original size:168 final size:168
Alignment explanation
Indices: 375739--376088 Score: 486
Period size: 168 Copynumber: 2.1 Consensus size: 168
375729 AATTTGAGTA
* * * * *
375739 TTGAAATTTTAGGGATTTAAAGGATTGATGCGACAATGAGTGCGATGATTGGTCATTGGATGGGC
1 TTGAGATTTTA-GGATTTAAAAGATTGATGCGACAAGGAGTGCGATGATTGATCATTAGATGGGC
* * *
375804 AATGACGGCTGGGTAGCTATTTGACAATAATGGTGACGACCGACGATGGCTAGTGATGGTAATTG
65 AATAACGGCTGGGTAGCTATTTGACAATAATAGTGACAACCGACGATGGCTAGTGATGGTAATTG
* * *
375869 GGGGTTTGAAATTAAAAG-TTTTAAGGGTTTGAAGATATT
130 AGGGTTAGAAATT-AAAGTTTTTAAGGGCTTGAAGATATT
* **
375908 TTGAGATTTTAGGATTTAAAAGATTGATGTGACGGGGAGTGCGATGATTGATCATTAGATGGGCA
1 TTGAGATTTTAGGATTTAAAAGATTGATGCGACAAGGAGTGCGATGATTGATCATTAGATGGGCA
* * * * *
375973 ATAACGGGTGGGTGGTTATTTGACAATAATAGTTACAACCGACGGTGGCTAGTGATGGTAATTGA
66 ATAACGGCTGGGTAGCTATTTGACAATAATAGTGACAACCGACGATGGCTAGTGATGGTAATTGA
* *
376038 GGGTTAGAAATTAAGGTTTTTAGGGGCTTGAAGATATT
131 GGGTTAGAAATTAAAGTTTTTAAGGGCTTGAAGATATT
376076 TTGAGATTTTAGG
1 TTGAGATTTTAGG
376089 GAAATTTTGA
Statistics
Matches: 159, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
167 3 0.02
168 146 0.92
169 10 0.06
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.32
Consensus pattern (168 bp):
TTGAGATTTTAGGATTTAAAAGATTGATGCGACAAGGAGTGCGATGATTGATCATTAGATGGGCA
ATAACGGCTGGGTAGCTATTTGACAATAATAGTGACAACCGACGATGGCTAGTGATGGTAATTGA
GGGTTAGAAATTAAAGTTTTTAAGGGCTTGAAGATATT
Found at i:378658 original size:24 final size:24
Alignment explanation
Indices: 378623--378679 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
378613 AAAAAATCTT
378623 AAACTT-AACTAGATTGAAGCCTC
1 AAACTTGAACTAGATTGAAGCCTC
378646 AAACTTGAACTAGATTGAAGCCTC
1 AAACTTGAACTAGATTGAAGCCTC
378670 AAACTTGAAC
1 AAACTTGAAC
378680 ATAAACCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (24 bp):
AAACTTGAACTAGATTGAAGCCTC
Found at i:386925 original size:18 final size:19
Alignment explanation
Indices: 386890--386926 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
386880 CACGGAATGT
386890 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
386910 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
386927 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:387097 original size:14 final size:14
Alignment explanation
Indices: 387078--387109 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
387068 GCGAAATTTT
387078 AAATATTTAAATAA
1 AAATATTTAAATAA
*
387092 AAATATTTATATAA
1 AAATATTTAAATAA
387106 AAAT
1 AAAT
387110 TCTATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTTAAATAA
Found at i:389133 original size:93 final size:95
Alignment explanation
Indices: 388972--389161 Score: 276
Period size: 93 Copynumber: 2.0 Consensus size: 95
388962 CTATGTTTCG
* *
388972 AGTAGCAAGCACATGAACACTTGAAAAACTTTTTACAGTTGCCACTGAGACAAGAGGAAACACGA
1 AGTAGCAAACACATGAACACTTGAAAAACTTTTTACAATTGCCACTGAGACAAGAGGAAACACGA
*
389037 AACAAGGAAAACCAATAACATAAATGCATA
66 AACAAGGAAAACCAACAACATAAATGCATA
* * * *
389067 AGTAGCAAACACATGAACAC-T-AGACACTTTTTACAATTGCCGCTGAGACAAGCGGAAACACGA
1 AGTAGCAAACACATGAACACTTGAAAAACTTTTTACAATTGCCACTGAGACAAGAGGAAACACGA
** *
389130 AACAAGGAAAAGTAACAGCATAAATGCATA
66 AACAAGGAAAACCAACAACATAAATGCATA
389160 AG
1 AG
389162 AAGCTTCAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 65 0.76
94 1 0.01
95 19 0.22
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.16
Consensus pattern (95 bp):
AGTAGCAAACACATGAACACTTGAAAAACTTTTTACAATTGCCACTGAGACAAGAGGAAACACGA
AACAAGGAAAACCAACAACATAAATGCATA
Found at i:391059 original size:21 final size:19
Alignment explanation
Indices: 391014--391064 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
391004 CCAAAATAAT
391014 AAAAAAAT-ATGATTTTTC
1 AAAAAAATAATGATTTTTC
*
391032 AATAAAAATAATGATTTAATTG
1 AA-AAAAATAATGATTT--TTC
391054 AAAAAAATAAT
1 AAAAAAATAAT
391065 ATATATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 6 0.21
20 7 0.25
21 9 0.32
22 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAAAAATAATGATTTTTC
Found at i:400148 original size:18 final size:18
Alignment explanation
Indices: 400121--400156 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
400111 ATCCTGAGTG
400121 GGTGGCGAATATTGTCCC
1 GGTGGCGAATATTGTCCC
*
400139 GGTGGTGAATATTGTCCC
1 GGTGGCGAATATTGTCCC
400157 AGTGCCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
GGTGGCGAATATTGTCCC
Found at i:402476 original size:19 final size:18
Alignment explanation
Indices: 402457--402606 Score: 99
Period size: 19 Copynumber: 7.9 Consensus size: 18
402447 AAAGAGCAAG
*
402457 AAAAAAATAAAAAATGAA
1 AAAAAAAAAAAAAATGAA
**
402475 GAAAAAAAATGAAAAT-AA
1 -AAAAAAAAAAAAAATGAA
* *
402493 AAAAAGAGAGAAAAAAGGAA
1 AAAAA-A-AAAAAAAATGAA
402513 AAAAAAGAAAAAAAATGAA
1 AAAAAA-AAAAAAAATGAA
*
402532 AAAAAAGAAAAAAAAGGAA
1 AAAAAA-AAAAAAAATGAA
402551 AAAAAAAGAAGAAAAA-GAA
1 AAAAAAA-AA-AAAAATGAA
* *
402570 GAAGAGAAAAATAAAAA-CAA
1 -AA-A-AAAAAAAAAAATGAA
* *
402590 AATAAAACAAAAAATGA
1 AAAAAAAAAAAAAATGA
402607 GGGTTCAAGA
Statistics
Matches: 106, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
17 14 0.13
18 5 0.05
19 60 0.57
20 21 0.20
21 2 0.02
22 4 0.04
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAAAATGAA
Found at i:402506 original size:25 final size:26
Alignment explanation
Indices: 402460--402546 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
402450 GAGCAAGAAA
* *
402460 AAAATAAAAAATGAAGAAAAAAAATG
1 AAAATAAAAAAAGAAGAAAAAAAAGG
*
402486 AAAATAAAAAAAG-AGAGAAAAAAGG
1 AAAATAAAAAAAGAAGAAAAAAAAGG
* *
402511 AAAAAAAAGAAAAAAAATGAAAAAAAA-G
1 -AAAATAA-AAAAAGAA-GAAAAAAAAGG
402539 AAAA-AAAA
1 AAAATAAAA
402547 GGAAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.24
26 20 0.39
27 9 0.18
28 2 0.04
29 8 0.16
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.06
Consensus pattern (26 bp):
AAAATAAAAAAAGAAGAAAAAAAAGG
Found at i:402518 original size:29 final size:29
Alignment explanation
Indices: 402457--402586 Score: 108
Period size: 29 Copynumber: 4.4 Consensus size: 29
402447 AAAGAGCAAG
*
402457 AAAAAAATAAAAAATGA-AG-AAAAAA-A
1 AAAAAAATAAAAAAAGAGAGAAAAAAAGA
** *
402483 ATGAAAATAAAAAAAGAGAGAAAAAAGGA
1 AAAAAAATAAAAAAAGAGAGAAAAAAAGA
*
402512 AAAAAAAGAAAAAAA-ATGA-AAAAAAAGA
1 AAAAAAATAAAAAAAGA-GAGAAAAAAAGA
* *
402540 AAAAAAAGGAAAAAAAAAGAAGAAAAAGAAGA
1 AAAAAAA-TAAAAAAAGAG-AGAAAAA-AAGA
402572 AGAGAAAAATAAAAA
1 A-A-AAAAATAAAAA
402587 CAAAATAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
26 14 0.17
27 2 0.02
28 21 0.25
29 24 0.29
30 2 0.02
31 5 0.06
32 5 0.06
33 6 0.07
34 5 0.06
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.05
Consensus pattern (29 bp):
AAAAAAATAAAAAAAGAGAGAAAAAAAGA
Found at i:402518 original size:38 final size:37
Alignment explanation
Indices: 402460--402580 Score: 67
Period size: 37 Copynumber: 3.3 Consensus size: 37
402450 GAGCAAGAAA
*
402460 AAAAT-AAAAAATGAAGAAAAAAAATGAAAATAAAAAAAG
1 AAAATGAAAAAA--AAGAAAAAAAAGGAAAA-AAAAAAAG
* *
402499 -AGA-G-AAAAAAGGAAAAAAAA-GAAAAAAAATGAAA-
1 AAAATGAAAAAAAAGAAAAAAAAGGAAAAAAAA--AAAG
* * * *
402533 AAAAAGAAAAAAAAGGAAAAAAAAAGAAGAAAAAGAAG
1 AAAATGAAAAAAAA-GAAAAAAAAGGAAAAAAAAAAAG
*
402571 AAGA-GAAAAA
1 AAAATGAAAAA
402581 TAAAAACAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
33 4 0.06
34 5 0.08
35 15 0.23
36 1 0.02
37 19 0.29
38 14 0.21
39 8 0.12
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (37 bp):
AAAATGAAAAAAAAGAAAAAAAAGGAAAAAAAAAAAG
Found at i:402572 original size:9 final size:9
Alignment explanation
Indices: 402457--402569 Score: 104
Period size: 9 Copynumber: 12.1 Consensus size: 9
402447 AAAGAGCAAG
*
402457 AAAAAAATA
1 AAAAAAAGA
402466 AAAAATGAAGA
1 AAAAA--AAGA
402477 AAAAAAATGA
1 AAAAAAA-GA
*
402487 AAATAAA-A
1 AAAAAAAGA
* *
402495 AAAGAGAG-
1 AAAAAAAGA
*
402503 AAAAAAGGA
1 AAAAAAAGA
402512 AAAAAAAGA
1 AAAAAAAGA
402521 AAAAAAATGA
1 AAAAAAA-GA
402531 AAAAAAAGA
1 AAAAAAAGA
402540 AAAAAAAGGAA
1 AAAAAAA-G-A
402551 AAAAAAAGA
1 AAAAAAAGA
*
402560 AGAAAAAGA
1 AAAAAAAGA
402569 A
1 A
402570 GAAGAGAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
8 11 0.13
9 41 0.47
10 19 0.22
11 16 0.18
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:402602 original size:11 final size:10
Alignment explanation
Indices: 402457--402602 Score: 62
Period size: 10 Copynumber: 13.7 Consensus size: 10
402447 AAAGAGCAAG
402457 AAAAAAATAA
1 AAAAAAATAA
* *
402467 AAAATGAA-GA
1 AAAA-AAATAA
402477 AAAAAAATGAA
1 AAAAAAAT-AA
*
402488 AATAAAAAAAGA
1 AA-AAAAATA-A
**
402500 GAGAAAAAAGGA
1 -A-AAAAAATAA
*
402512 AAAAAAA-GA
1 AAAAAAATAA
*
402521 AAAAAAATGA
1 AAAAAAATAA
*
402531 AAAAAAAGAA
1 AAAAAAATAA
**
402541 AAAAAAGGAA
1 AAAAAAATAA
*
402551 AAAAAAAGAA
1 AAAAAAATAA
*
402561 GAAAAAGAAGAA
1 -AAAAA-AATAA
*
402573 GAGAAAAATAA
1 -AAAAAAATAA
402584 AAACAAAATAA
1 AAA-AAAATAA
402595 AACAAAAA
1 AA-AAAAA
402603 ATGAGGGTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
9 11 0.10
10 45 0.41
11 29 0.26
12 18 0.16
13 6 0.05
14 1 0.01
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:404073 original size:108 final size:107
Alignment explanation
Indices: 403884--404184 Score: 458
Period size: 108 Copynumber: 2.8 Consensus size: 107
403874 TGAGGCAAAA
* *
403884 GAAGATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGTGATTGATGAAGATTGTG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTGTG
403949 GGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATCGTT
66 GGTCTTATACTCTCTGAAGAAATAGGGGACA-ACGCGATCGTT
* * *
403992 GAAGATTGTTCGAGTTTTATACTCTCCGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTGTG
* *
404057 GGTCTTATACTCTCTGAAGAAATAGGGGGCAACGCGATTGTT
66 GGTCTTATACTCTCTGAAGAAATAGGGGACAACGCGATCGTT
* * * * *
404099 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGCGTAGACACGATTGTTAAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTG-T
*
404164 CGAGTCTTATACTCTCTGAAG
65 -GGGTCTTATACTCTCTGAAG
404185 GACTATGGAG
Statistics
Matches: 176, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
107 66 0.38
108 91 0.52
109 19 0.11
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (107 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGCGATTGATGAAGATTGTG
GGTCTTATACTCTCTGAAGAAATAGGGGACAACGCGATCGTT
Found at i:404214 original size:55 final size:55
Alignment explanation
Indices: 403884--404222 Score: 438
Period size: 55 Copynumber: 6.3 Consensus size: 55
403874 TGAGGCAAAA
* * * *
403884 GAAGATGGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGAAGACGTGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
* * *
403939 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
* * *
403992 GAAGATTGTTCGAGTTTTATACTCTCCGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
*
404047 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCA-ACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
* * *
404099 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGCGTAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
* * * * * * * *
404154 AAAGATTGTTCGAGTCTTATACTCTCTGAAGGACTATGGAGCTGACGTGATTTTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
404209 GAAGA-TGTTCGAGT
1 GAAGATTGTTCGAGT
404223 GCTATTCTCC
Statistics
Matches: 247, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
52 18 0.07
53 76 0.31
54 41 0.17
55 112 0.45
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTT
Found at i:404947 original size:17 final size:17
Alignment explanation
Indices: 404925--404967 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
404915 GTCGGCCACC
404925 CCCGTGACCAGCTCGCG
1 CCCGTGACCAGCTCGCG
*
404942 CCCGTGACCAGCTTGCG
1 CCCGTGACCAGCTCGCG
404959 CCCGTGACC
1 CCCGTGACC
404968 TACAAAGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.47, G:0.28, T:0.14
Consensus pattern (17 bp):
CCCGTGACCAGCTCGCG
Found at i:407919 original size:21 final size:21
Alignment explanation
Indices: 407895--407934 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
407885 TATCTTCAAA
407895 TTTT-AAAAATATTATAAAAGG
1 TTTTCAAAAAT-TTATAAAAGG
*
407916 TTTTCATAAATTTATAAAA
1 TTTTCAAAAATTTATAAAA
407935 ATATAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTTCAAAAATTTATAAAAGG
Found at i:407964 original size:2 final size:2
Alignment explanation
Indices: 407957--407987 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
407947 CCATAAGCTG
407957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
407988 ACATACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413744 original size:4 final size:4
Alignment explanation
Indices: 413735--413850 Score: 133
Period size: 4 Copynumber: 29.0 Consensus size: 4
413725 GTTAGAAATT
* * * * *
413735 TGTA TGTA TGTA TGTA TGTA TGCA TGCA TGCA TGTA TGCA TGCA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * *
413783 TGTA TGTA TGTA TGTA TGTA TGCA TGCA TGTA TGTA TGCA TGCA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
413831 TGTA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA
413851 CGAAGTAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (4 bp):
TGTA
Found at i:413756 original size:16 final size:16
Alignment explanation
Indices: 413735--413850 Score: 187
Period size: 16 Copynumber: 7.2 Consensus size: 16
413725 GTTAGAAATT
* *
413735 TGTATGTATGTATGTA
1 TGTATGCATGCATGTA
*
413751 TGTATGCATGCATGCA
1 TGTATGCATGCATGTA
413767 TGTATGCATGCATGTA
1 TGTATGCATGCATGTA
* *
413783 TGTATGTATGTATGTA
1 TGTATGCATGCATGTA
413799 TGTATGCATGCATGTA
1 TGTATGCATGCATGTA
413815 TGTATGCATGCATGTA
1 TGTATGCATGCATGTA
413831 TGTATGCATGCATGTA
1 TGTATGCATGCATGTA
413847 TGTA
1 TGTA
413851 CGAAGTAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 92 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (16 bp):
TGTATGCATGCATGTA
Done.