Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 19
Found at i:3511077 original size:28 final size:29
Alignment explanation
Indices: 3511007--3511091 Score: 109
Period size: 28 Copynumber: 2.9 Consensus size: 29
3510997 AACTATATAT
* * *
3511007 TATACGTTTCCAAAACTATTTTAAAAATTA
1 TATATGTTTTCAAAATTATTTTAAAAA-TA
*
3511037 TATATGTTTTCAAAATTATTTTAAAAA-C
1 TATATGTTTTCAAAATTATTTTAAAAATA
*
3511065 TATATGTTTTCAAAATCATTTTAAAAA
1 TATATGTTTTCAAAATTATTTTAAAAA
3511092 AAAACATATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 26 0.52
30 24 0.48
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (29 bp):
TATATGTTTTCAAAATTATTTTAAAAATA
Found at i:3511124 original size:38 final size:41
Alignment explanation
Indices: 3511065--3511156 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 41
3511055 TTTTAAAAAC
3511065 TATATGTTTTC-AAAATCA-TTTTAAAAAAAAAC-ATATAT
1 TATATGTTTTCAAAAATCATTTTTAAAAAAAAACTATATAT
* *
3511103 TATACGTTTTCAAAAAT-ATTTTTAAAAAAAATCTATATAT
1 TATATGTTTTCAAAAATCATTTTTAAAAAAAAACTATATAT
3511143 TATATGTTTTCAAA
1 TATATGTTTTCAAA
3511157 TTTATCTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 11 0.23
39 18 0.38
40 19 0.40
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (41 bp):
TATATGTTTTCAAAAATCATTTTTAAAAAAAAACTATATAT
Found at i:3511169 original size:38 final size:38
Alignment explanation
Indices: 3511065--3511169 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 38
3511055 TTTTAAAAAC
*
3511065 TATATGTTTTCAAAATCATTTTAAAAAAAAACATATAT
1 TATATGTTTTCAAAATTATTTTAAAAAAAAACATATAT
* * *
3511103 TATACGTTTTCAAAAATATTTTTAAAAAAAATCTATATAT
1 TATATGTTTTCAAAATTA-TTTTAAAAAAAAAC-ATATAT
* *
3511143 TATATGTTTTCAAATTTATCTTAAAAA
1 TATATGTTTTCAAAATTATTTTAAAAA
3511170 CTATATGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 15 0.26
39 21 0.37
40 21 0.37
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (38 bp):
TATATGTTTTCAAAATTATTTTAAAAAAAAACATATAT
Found at i:3511174 original size:28 final size:28
Alignment explanation
Indices: 3511143--3511203 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3511133 ATCTATATAT
3511143 TATATGTTTTC-AAAT-TTATCTTAAAAAC
1 TATATGTTTTCAAAATCTT-T-TTAAAAAC
3511171 TATATGTTTTCAAAATCTTTTTAAAAAC
1 TATATGTTTTCAAAATCTTTTTAAAAAC
3511199 TATAT
1 TATAT
3511204 ATTATACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 24 0.77
29 5 0.16
30 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (28 bp):
TATATGTTTTCAAAATCTTTTTAAAAAC
Found at i:3513269 original size:5 final size:5
Alignment explanation
Indices: 3513259--3513287 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3513249 CAAACAACCC
3513259 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3513288 GCCTCTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3516903 original size:42 final size:42
Alignment explanation
Indices: 3516852--3516955 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
3516842 GCCCAAAGGT
* *
3516852 CTTAAAGATGGCCAGAAGGATTTAAACATGATGCTCGAAAGA
1 CTTATAGATGGCCAGAAGGATTTAAACATCATGCTCGAAAGA
* * *
3516894 CTTATAGATGACCCA-AAAGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATG-GCCAGAAGGATTTAAACATCATGCTCGAAAGA
3516936 CTTACTA-ATGGCTC-GAAGGA
1 CTTA-TAGATGGC-CAGAAGGA
3516956 CTTACTAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
41 1 0.02
42 45 0.88
43 5 0.10
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (42 bp):
CTTATAGATGGCCAGAAGGATTTAAACATCATGCTCGAAAGA
Found at i:3516951 original size:20 final size:20
Alignment explanation
Indices: 3516926--3516963 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3516916 TAAGCATCAT
3516926 GCTCGAAAGACTTACTAATG
1 GCTCGAAAGACTTACTAATG
*
3516946 GCTCGAAGGACTTACTAA
1 GCTCGAAAGACTTACTAA
3516964 GTAAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GCTCGAAAGACTTACTAATG
Found at i:3517397 original size:242 final size:240
Alignment explanation
Indices: 3516831--3517622 Score: 1038
Period size: 242 Copynumber: 3.3 Consensus size: 240
3516821 ATCACCATAC
* * * * * *
3516831 GAAAACATCCTGCCCAAAGGTCTTAAAGATGGCCAGAAGGATTTAAACATGATGCTCGAAAGACT
1 GAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACT
** * * * * *
3516896 TATAGATGACCCAAAAGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCTCGAAGGACTTAC
66 TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
* * *
3516961 TAAGTAAAAAACTTTGGGAATCGTTTTCTTAC-TTA-AA-AAAAATCAATTTTCTAAAAAGATTT
131 TAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTACAAGAAAAATCAATTTTC-AAAAAGATTT
* *
3517023 AAATGAAAAACTTTGGAAATCGCTTTCTCATTTTTTGGAAATCATGT
195 AAATGAGAAACTTTGGAAATCGCTTTCTCA-TTTTTGAAAATCATGT
** * * * * *
3517070 GAAAACATTATGCCCGAAGTTCTTATGGATGGCCCGAATGACTT-ATCATCTTGCTCGAAAGACT
1 GAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACT
* * *
3517134 TATAGATAACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACTGGTGTCCCGAAGGACTTAC
66 TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
* * *
3517199 TAAGTAAGAAACTTTGGAAATTATTTTCTTGCTTTACAAGAAAAATCAATTTTCAAAAAAATAAT
131 TAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTACAAGAAAAATCAATTTTCAAAAAGAT--T
* *
3517264 TAAATGAGAAACTTTGGAATTCGCTTTCTCATTTTTGAAAATTATGT
194 TAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAAATCATGT
* * * *
3517311 GAAAACATCCTTCCCGAAGGTCTTATAGATGGCCCGAAGAACTTAAGCATCATGCTCAAAAGACA
1 GAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACT
* *
3517376 TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACATACTGATGGCCTGAAGGACTTAC
66 TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
*
3517441 TAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGATTT
131 TAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTACAAGAAAAATCAATTTTCA-AAAAGATTT
* * * *
3517506 AAATGAGAAACTTTGGAAATCACTTTCACAATTTCGAAAATCATGT
195 AAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAAATCATGT
* * * * * *
3517552 G--AACATCTTGCCTGAAGGTCTTATGGATGGCTCGAAGGACTTAAGCATAATACTCGAAAGACT
1 GAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACT
*
3517615 TATTGATG
66 TATAGATG
3517623 TCCCAAAGGA
Statistics
Matches: 477, Mismatches: 69, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
238 99 0.21
239 97 0.20
240 9 0.02
241 108 0.23
242 158 0.33
243 6 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (240 bp):
GAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACT
TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAC
TAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTACAAGAAAAATCAATTTTCAAAAAGATTTA
AATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAAATCATGT
Found at i:3517404 original size:42 final size:42
Alignment explanation
Indices: 3517334--3517439 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
3517324 CCGAAGGTCT
* * *
3517334 TATAGATGGCCCGAAGAACTTAAGCATCATGCTCAAAAGACA
1 TATAGATGGCCTGAAGGACTTAAACATCATGCTCAAAAGACA
* *
3517376 TATAGATGACCTGAAGGATTTAAACATCATGCTCAAAAGACA
1 TATAGATGGCCTGAAGGACTTAAACATCATGCTCAAAAGACA
3517418 TACT-GATGGCCTGAAGGACTTA
1 TA-TAGATGGCCTGAAGGACTTA
3517440 CTAAGTAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 55 0.98
43 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (42 bp):
TATAGATGGCCTGAAGGACTTAAACATCATGCTCAAAAGACA
Found at i:3519889 original size:29 final size:29
Alignment explanation
Indices: 3519846--3519904 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3519836 GAAGGCTATC
* *
3519846 TTGATCCCTAAAAAAGTGGGGTATGATAT
1 TTGATCCCTAAAAAAGAGGGGCATGATAT
* *
3519875 TTGATCCCTACAAAAGAGGGGCATGGTAT
1 TTGATCCCTAAAAAAGAGGGGCATGATAT
3519904 T
1 T
3519905 CGAGTGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (29 bp):
TTGATCCCTAAAAAAGAGGGGCATGATAT
Found at i:3527557 original size:18 final size:18
Alignment explanation
Indices: 3527534--3527568 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3527524 TCAAATTTGT
3527534 TATTTTAATTAAAATTAA
1 TATTTTAATTAAAATTAA
*
3527552 TATTTTTATTAAAATTA
1 TATTTTAATTAAAATTA
3527569 CAAAATACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTAATTAAAATTAA
Found at i:3529246 original size:6 final size:6
Alignment explanation
Indices: 3529235--3529282 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
3529225 ATTAACACCT
*
3529235 TTTGCA TTTGCA TTTGGCA TTTCACA TTTGCA TTT-CTA TTTGCA TTTG
1 TTTGCA TTTGCA TTT-GCA TTT-GCA TTTGCA TTTGC-A TTTGCA TTTG
3529283 TATTATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 1 0.03
6 23 0.64
7 12 0.33
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:3532004 original size:11 final size:10
Alignment explanation
Indices: 3531984--3532079 Score: 54
Period size: 11 Copynumber: 9.3 Consensus size: 10
3531974 GAAAATAAAT
*
3531984 AAAAATAAGA
1 AAAAAAAAGA
3531994 ACAAAAAAAGA
1 A-AAAAAAAGA
3532005 AAAAAAAA-A
1 AAAAAAAAGA
*
3532014 ATGATAAAAAA-T
1 A--A-AAAAAAGA
*
3532026 AGAAAAAAGA
1 AAAAAAAAGA
*
3532036 GAAAAAAAGGA
1 -AAAAAAAAGA
3532047 AAAAAAAAGGA
1 AAAAAAAA-GA
**
3532058 AAAAGGAA-A
1 AAAAAAAAGA
*
3532067 AAAAAAACGA
1 AAAAAAAAGA
3532077 AAA
1 AAA
3532080 GAGAGAAAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
9 14 0.21
10 19 0.29
11 26 0.39
12 7 0.11
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:3532040 original size:18 final size:19
Alignment explanation
Indices: 3532009--3532069 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
3531999 AAAAGAAAAA
*
3532009 AAAAAATGATAAAAAATA-G
1 AAAAAATGAGAAAAAA-AGG
3532028 AAAAAA-GAGAAAAAAAGG
1 AAAAAATGAGAAAAAAAGG
** *
3532046 AAAAAAAAAG-GAAAAAGG
1 AAAAAATGAGAAAAAAAGG
3532064 AAAAAA
1 AAAAAA
3532070 AAAACGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.76
19 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAATGAGAAAAAAAGG
Found at i:3532088 original size:19 final size:19
Alignment explanation
Indices: 3532039--3532079 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3532029 AAAAAGAGAA
*
3532039 AAAAAGG-AAAAAAAAAGG
1 AAAAAGGAAAAAAAAAACG
3532057 AAAAAGGAAAAAAAAAACG
1 AAAAAGGAAAAAAAAAACG
3532076 AAAA
1 AAAA
3532080 GAGAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAGGAAAAAAAAAACG
Found at i:3535076 original size:45 final size:45
Alignment explanation
Indices: 3535026--3535202 Score: 157
Period size: 45 Copynumber: 4.0 Consensus size: 45
3535016 GTCTTCCTTT
* *
3535026 ACTTTCTCGTGAAGAAGAGT-AGATCTTTTAGTGGTGTCATTCTTG
1 ACTTTCTCGTGAAGAAGAGTCA-ACCTTTTAGTGATGTCATTCTTG
* * *
3535071 ACTTTCTCATGAAGAGGAGTCAACCTTTTAGTGATTTCATTCTTG
1 ACTTTCTCGTGAAGAAGAGTCAACCTTTTAGTGATGTCATTCTTG
* * * *
3535116 ACTTTCTCGTAAAG-AGAAGTCAATCTTTCAGTG-T-TCTATTTTTG
1 ACTTTCTCGTGAAGAAG-AGTCAACCTTTTAGTGATGTC-ATTCTTG
* *** *
3535160 AATTTCT-AAAAAAAAGAAGTCAACCTTTTAGTGATGTCATTCT
1 ACTTTCTCGTGAAGAAG-AGTCAACCTTTTAGTGATGTCATTCT
3535203 CAATTTGACT
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
43 5 0.05
44 31 0.29
45 69 0.64
46 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (45 bp):
ACTTTCTCGTGAAGAAGAGTCAACCTTTTAGTGATGTCATTCTTG
Found at i:3535208 original size:44 final size:43
Alignment explanation
Indices: 3535088--3535208 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 43
3535078 CATGAAGAGG
* *** *
3535088 AGTCAACCTTTTAGTGATTTCATTCTTGACTTTCTCGTAAAGAGA
1 AGTCAACCTTTTAGTGA-TTCATTC-TGAATTTCTAAAAAAAAGA
* * *
3535133 AGTCAATCTTTCAGTG-TTCTATTTTTGAATTTCTAAAAAAAAGA
1 AGTCAACCTTTTAGTGATTC-A-TTCTGAATTTCTAAAAAAAAGA
*
3535177 AGTCAACCTTTTAGTGATGTCATTCTCAATTT
1 AGTCAACCTTTTAGTGAT-TCATTCTGAATTT
3535209 GACTTTCTCG
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
43 3 0.05
44 37 0.62
45 18 0.30
46 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (43 bp):
AGTCAACCTTTTAGTGATTCATTCTGAATTTCTAAAAAAAAGA
Found at i:3535231 original size:50 final size:51
Alignment explanation
Indices: 3535174--3535269 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
3535164 TCTAAAAAAA
* *
3535174 AGAAGTCAACCTTTT-AGT-GATGTCA-TTCTCAATTTGACTTTCTCGCGGAG
1 AGAAGTCAA-CTTTTCAGTAG-TATCATTTCTCAACTTGACTTTCTCGCGGAG
3535224 AGAAGTCAACTTTTCAGTAGTATCATTTCTCAACTTGACTTTCTCG
1 AGAAGTCAACTTTTCAGTAGTATCATTTCTCAACTTGACTTTCTCG
3535270 TGTGGAGGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
49 5 0.12
50 16 0.39
51 20 0.49
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (51 bp):
AGAAGTCAACTTTTCAGTAGTATCATTTCTCAACTTGACTTTCTCGCGGAG
Found at i:3536045 original size:55 final size:55
Alignment explanation
Indices: 3535961--3536336 Score: 481
Period size: 55 Copynumber: 6.9 Consensus size: 55
3535951 AAGAGTTCTT
* *
3535961 GAGTCTTATCTCCCTAAAAGAAGAATGGAGCAGACCCATCTTCCAAAGATTTTTC
1 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * *
3536016 GAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTT
1 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * *
3536071 GAGTCTTATCT-CCTGGAAAGAA-AGTTGAGCAGACCCGTTTTCCAAAGATTTTTC
1 GAGTCTTATCTCCCT-AAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * * *
3536125 GAGTCTTATCTCACTTAAAGAAGAGTGGACCATACCCGTCTTCCAAAGATTTTTC
1 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * *
3536180 GAGTCTTATCTCCCTAAAA-AAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTC
1 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * ** *
3536234 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGTAAACATGTCTTCCAAAGA-TTTCC
1 GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
* * * *
3536288 TGAGTCTGATCTCCCCTCAAAGAAGACTGGAGCAGATCCGTCTTCCAAA
1 -GAGTCTTATCT-CCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAA
3536337 ATTGATCTAA
Statistics
Matches: 278, Mismatches: 37, Indels: 11
0.85 0.11 0.03
Matches are distributed among these distances:
54 101 0.36
55 148 0.53
56 29 0.10
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (55 bp):
GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
Found at i:3536149 original size:109 final size:109
Alignment explanation
Indices: 3535950--3536336 Score: 483
Period size: 109 Copynumber: 3.5 Consensus size: 109
3535940 AAGTGGATCA
* * *
3535950 AAAGAGTTCTTGAGTCTTATCTCCCTAAAAGAAGAATGGAGCAGACCCATCTTCCAAAGATTTTT
1 AAAGATTTCTTGAGTCTTATCTCCCT-AAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTT
* * *
3536015 CGAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGACCCGTCTTCC
65 CGAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAAACCCGTCTTCC
* * *
3536060 AAAGATTTTTTGAGTCTTATCT-CCTGGAAAGAA-AGTTGAGCAGACCCGTTTTCCAAAGATTTT
1 AAAGATTTCTTGAGTCTTATCTCCCT--AAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTT
* * * *
3536123 TCGAGTCTTATCTCACTTAAAGAAGAGTGGACCATACCCGTCTTCC
64 TCGAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAAACCCGTCTTCC
* * * *
3536169 AAAGATTT-TTCGAGTCTTATCTCCCTAAAAAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCT
1 AAAGATTTCTT-GAGTCTTATCTCCCTAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTT
* **
3536233 CGAGTCTTATCTCCCTAAAAGAAGAGTGGAGTAAACATGTCTTCC
65 CGAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAAACCCGTCTTCC
* * * *
3536278 AAAGATTTCCTGAGTCTGATCTCCCCTCAAAGAAGACTGGAGCAGATCCGTCTTCCAAA
1 AAAGATTTCTTGAGTCTTATCT-CCCT-AAAGAAGAGTGGAGCAGACCCGTCTTCCAAA
3536337 ATTGATCTAA
Statistics
Matches: 238, Mismatches: 32, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
108 7 0.03
109 171 0.72
110 34 0.14
111 26 0.11
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (109 bp):
AAAGATTTCTTGAGTCTTATCTCCCTAAAGAAGAGTGGAGCAGACCCGTCTTCCAAAGATTTTTC
GAGTCTTATCTCCCTAAAAGAAGAGTGGAGCAAACCCGTCTTCC
Found at i:3541577 original size:131 final size:131
Alignment explanation
Indices: 3541334--3541701 Score: 470
Period size: 131 Copynumber: 2.8 Consensus size: 131
3541324 TAATTTTAAG
* * *** *
3541334 AGAGAAAATGATTATATCTAATTATTTCCAATCTAGAATAAATGTTTTCTCATGCCTTAAAACAA
1 AGAGAAAATGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAA
* * *
3541399 TCATTTATTACTCCAATCGAAGT-AGAGAGATATTACTATTTCATCTTAAAATTCAATATCGATT
66 TCATTTATTACTCCAATCGAAGTGA-AAAGATATTACTATTCCATCTTAAAAATCAATATCGATT
*
3541463 CG
130 CA
** * *
3541465 ATTGAAAATGATAATATCTAATGATTTCCAATCAAGAATAAATGACCTCTCATACCTTAAAGCAA
1 AGAGAAAATGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAA
* * * * *
3541530 TCATTTATTATTCCAATCGAAGTGAACAGATATCACTATTCCGTCTTAAAAATCAATATTGATTC
66 TCATTTATTACTCCAATCGAAGTGAAAAGATATTACTATTCCATCTTAAAAATCAATATCGATTC
3541595 A
131 A
* * * * * *
3541596 AGAGAAAATGGTAATATCAAATTATTTCCAATCGAGAATAAATGACCACTCATGCCTCAAAGCAG
1 AGAGAAAATGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAA
*
3541661 TCATTTATTACTCCAA-CTGAAATGAAAAGATATTACTATTC
66 TCATTTATTACTCCAATC-GAAGTGAAAAGATATTACTATTC
3541702 TCAATATCGA
Statistics
Matches: 203, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
130 1 0.00
131 201 0.99
132 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (131 bp):
AGAGAAAATGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCAA
TCATTTATTACTCCAATCGAAGTGAAAAGATATTACTATTCCATCTTAAAAATCAATATCGATTC
A
Found at i:3543840 original size:3 final size:3
Alignment explanation
Indices: 3543832--3543954 Score: 104
Period size: 3 Copynumber: 39.7 Consensus size: 3
3543822 TATTTTATTT
* * *
3543832 ATA ATA ATA ATA ATA ATTA CTC ATA ATA ATA ATA ATA ACA ATA AT-
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
3543877 CTA ATA ATA TTG ATA ATA ATA ATA ACTA TTA ATA AAA ACTA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA
*
3543924 ATA ACTA ATTA ATA ATA ATA ATA ACA ATA AT
1 ATA A-TA A-TA ATA ATA ATA ATA ATA ATA AT
3543955 TATAGCGGGA
Statistics
Matches: 94, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
2 1 0.01
3 82 0.87
4 11 0.12
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3543892 original size:26 final size:26
Alignment explanation
Indices: 3543832--3543954 Score: 126
Period size: 26 Copynumber: 4.8 Consensus size: 26
3543822 TATTTTATTT
* *
3543832 ATAATAATAATAATAATTA-CTCATA
1 ATAATAATAATAATAATAATCTAATA
*
3543857 ATAATAATAATAACAATAATCTAATA
1 ATAATAATAATAATAATAATCTAATA
* * *
3543883 ATATTGATAATAATAATAA-CTATTA
1 ATAATAATAATAATAATAATCTAATA
* *
3543908 ATAAAAACTAGTAATAATAA-CTAATTA
1 ATAATAA-TAATAATAATAATCTAA-TA
*
3543935 ATAATAATAATAACAATAAT
1 ATAATAATAATAATAATAAT
3543955 TATAGCGGGA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
25 26 0.33
26 45 0.57
27 8 0.10
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATAATAATAATAATAATCTAATA
Found at i:3547473 original size:23 final size:23
Alignment explanation
Indices: 3547429--3547473 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3547419 TGTTGAAGCA
*
3547429 GCAGGTGGTAGCGTGTTAGAGCT
1 GCAGGTGGTAGCGTGCTAGAGCT
*
3547452 GCAGGTGGTAGCGTGCTGGAGC
1 GCAGGTGGTAGCGTGCTAGAGC
3547474 AGCAAGCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.47, T:0.22
Consensus pattern (23 bp):
GCAGGTGGTAGCGTGCTAGAGCT
Found at i:3553967 original size:24 final size:23
Alignment explanation
Indices: 3553940--3554037 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
3553930 GAAAGACCGT
3553940 GTAGAATTTGTCCCGAAGGACCAC
1 GTAGAA-TTGTCCCGAAGGACCAC
* * *
3553964 GTAGAAATATCCCGAATGACCAC
1 GTAGAATTGTCCCGAAGGACCAC
* * * *
3553987 ATAGAAATATCCCGAAGAACCAC
1 GTAGAATTGTCCCGAAGGACCAC
* *
3554010 ATAG-ATTGTCCCGAAGGACTAC
1 GTAGAATTGTCCCGAAGGACCAC
3554032 GTAGAA
1 GTAGAA
3554038 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 17 0.27
23 39 0.63
24 6 0.10
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (23 bp):
GTAGAATTGTCCCGAAGGACCAC
Found at i:3553984 original size:23 final size:23
Alignment explanation
Indices: 3553950--3554037 Score: 106
Period size: 23 Copynumber: 3.9 Consensus size: 23
3553940 GTAGAATTTG
*
3553950 TCCCGAAGGACCACGTAGAAATA
1 TCCCGAAGGACCACATAGAAATA
*
3553973 TCCCGAATGACCACATAGAAATA
1 TCCCGAAGGACCACATAGAAATA
* * *
3553996 TCCCGAAGAACCACATAG-ATTG
1 TCCCGAAGGACCACATAGAAATA
* *
3554018 TCCCGAAGGACTACGTAGAA
1 TCCCGAAGGACCACATAGAA
3554038 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.31
23 38 0.69
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGAAATA
Found at i:3555769 original size:64 final size:63
Alignment explanation
Indices: 3555681--3555839 Score: 203
Period size: 64 Copynumber: 2.5 Consensus size: 63
3555671 TACACTAAGA
* * * * * *
3555681 GTGCACCGATGCATGAAGTGCATTCGATGTTTCAAACAAGCCAGAGTGCATCGATGCATGGCCT
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAAA-AACCCAGAGTGCATCGATGCATGGCAT
* * *
3555745 GTGCATCGATGCATAAAATACATTCGATGTTTTCATAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATACATTCGATG-TTTCAAAAACCCAGAGTGCATCGATGCATGGCAT
3555809 GTGCATCGATGCATAAAATGA-ATTCGATGTT
1 GTGCATCGATGCATAAAAT-ACATTCGATGTT
3555840 CAATTTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 2 0.02
64 75 0.89
65 7 0.08
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTCAAAAACCCAGAGTGCATCGATGCATGGCAT
Found at i:3564400 original size:64 final size:63
Alignment explanation
Indices: 3564313--3564470 Score: 226
Period size: 64 Copynumber: 2.5 Consensus size: 63
3564303 TCTTAGTGCA
* * * * * *
3564313 TGCACCGATGCATGAAGTGCATTCAATGTTTCAAACAAGCCAGAGTGCATCGATGCATGGTCTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAA-AACCCAGAGTGCATCGATGCATGGTATG
* *
3564377 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAAACCCTGAGTGCATCGATGCATGGTATG
1 TGCATCGATGCATAAAATGCATTCGATG-TTTCAAAAACCCAGAGTGCATCGATGCATGGTATG
3564441 TGCATCGATGCATAAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
3564471 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
63 2 0.02
64 77 0.91
65 6 0.07
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAAAACCCAGAGTGCATCGATGCATGGTATG
Found at i:3566364 original size:19 final size:19
Alignment explanation
Indices: 3566342--3566382 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3566332 TCCTTATATA
*
3566342 TATATATATATATTATTTT
1 TATAGATATATATTATTTT
* *
3566361 TATAGATTTTTATTATTTT
1 TATAGATATATATTATTTT
3566380 TAT
1 TAT
3566383 TTGCAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TATAGATATATATTATTTT
Found at i:3567893 original size:17 final size:17
Alignment explanation
Indices: 3567871--3567910 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3567861 ACATACATAT
3567871 ATTTAGGTTAATTATAC
1 ATTTAGGTTAATTATAC
3567888 ATTTAGGTTAATTATAC
1 ATTTAGGTTAATTATAC
3567905 ATTTAG
1 ATTTAG
3567911 TCCCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (17 bp):
ATTTAGGTTAATTATAC
Found at i:3569237 original size:46 final size:47
Alignment explanation
Indices: 3569158--3569250 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
3569148 TTATATTATT
* * * *
3569158 TTATTTTTTTGAATAAATGCATGCGAACTAGAAATCATGCGGTTAGG
1 TTATTTTTCTGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
*
3569205 TTATTTTTCCTGAACAAA-GCATG-GGACTAGAAAGCATGAGGTTAGG
1 TTATTTTT-CTGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
3569251 ATATGATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
46 20 0.50
47 13 0.32
48 7 0.17
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (47 bp):
TTATTTTTCTGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
Found at i:3578674 original size:20 final size:20
Alignment explanation
Indices: 3578649--3578686 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3578639 TTTTGGTGCA
*
3578649 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
3578669 GAGGGAACCGATACCCCC
1 GAGGGAACCGATACCCCC
3578687 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:3582344 original size:23 final size:23
Alignment explanation
Indices: 3582318--3582366 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
3582308 TACATTTTGC
* *
3582318 AAGAATGATAGATTGTCTTTTTA
1 AAGAATGATAGATTCTCTTTTCA
3582341 AAG-ATGATAGATTCTCTTTTCA
1 AAGAATGATAGATTCTCTTTTCA
3582363 AAGA
1 AAGA
3582367 CAAAAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (23 bp):
AAGAATGATAGATTCTCTTTTCA
Found at i:3585380 original size:38 final size:38
Alignment explanation
Indices: 3585337--3585444 Score: 89
Period size: 38 Copynumber: 3.2 Consensus size: 38
3585327 CATAATTTGA
3585337 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
1 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
* * *
3585375 T-A-AT-A--TCTACA-T-AATAC-ATAAT----TTGA-
1 TAATATAATTTCAATATTAAATGCTATAATAAGATT-AT
3585401 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
1 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
3585439 TAATAT
1 TAATAT
3585445 CTATGTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 28
0.60 0.07 0.33
Matches are distributed among these distances:
26 3 0.06
27 2 0.04
28 2 0.04
29 1 0.02
30 5 0.10
31 8 0.16
32 2 0.04
33 8 0.16
34 5 0.10
35 1 0.02
36 2 0.04
37 2 0.04
38 9 0.18
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (38 bp):
TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
Found at i:3585392 original size:64 final size:64
Alignment explanation
Indices: 3585318--3585447 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
3585308 TTTATTGTTA
3585318 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
1 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
3585382 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
1 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
3585446 TA
1 TA
3585448 TGTTAAATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (64 bp):
TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
Found at i:3586171 original size:18 final size:18
Alignment explanation
Indices: 3586150--3586188 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
3586140 AATTATTAGG
3586150 AAATAA-AAAAAGTTCAAA
1 AAATAAGAAAAA-TTCAAA
3586168 AAATAAGTAAAAATTCAAA
1 AAATAAG-AAAAATTCAAA
3586187 AA
1 AA
3586189 TATCAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAATAAGAAAAATTCAAA
Found at i:3589893 original size:22 final size:22
Alignment explanation
Indices: 3589818--3589893 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
3589808 ACGGAGATGA
*
3589818 CTTAGCACTCATACTAAAGTGC
1 CTTAGCACTGATACTAAAGTGC
* * * *
3589840 CTCAGCACTAATACGAAGGTGC
1 CTTAGCACTGATACTAAAGTGC
* * *
3589862 ATTCGCACTGATACTAAAGTTC
1 CTTAGCACTGATACTAAAGTGC
3589884 CTTAGCACTG
1 CTTAGCACTG
3589894 CTGGTATATA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (22 bp):
CTTAGCACTGATACTAAAGTGC
Found at i:3594194 original size:19 final size:19
Alignment explanation
Indices: 3594170--3594211 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
3594160 TTTGTTACCT
3594170 GCTGCTTTTATTCGTGACA
1 GCTGCTTTTATTCGTGACA
3594189 GCTGCTTTTATTCGTGACA
1 GCTGCTTTTATTCGTGACA
3594208 GCTG
1 GCTG
3594212 GTTTATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
GCTGCTTTTATTCGTGACA
Found at i:3594218 original size:18 final size:19
Alignment explanation
Indices: 3594170--3594218 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
3594160 TTTGTTACCT
*
3594170 GCTGCTTTTATTCGTGACA
1 GCTGCGTTTATTCGTGACA
*
3594189 GCTGCTTTTATTCGTGACA
1 GCTGCGTTTATTCGTGACA
3594208 GCTG-GTTTATT
1 GCTGCGTTTATT
3594219 TGTTGTTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (19 bp):
GCTGCGTTTATTCGTGACA
Found at i:3598682 original size:40 final size:40
Alignment explanation
Indices: 3598638--3598737 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
3598628 GCGAAGTTGA
* *
3598638 CATCTTTGGTTGGTGGCTAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
* * *
3598678 CATCTTTGGTAGGTGACCAACTTGTACATATTTGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
3598718 CATCTTTGGTAGGTGGCCAA
1 CATCTTTGGTAGGTGGCCAA
3598738 ACTTTTGCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATTGGAAAATT
Found at i:3599604 original size:46 final size:46
Alignment explanation
Indices: 3599554--3599857 Score: 437
Period size: 46 Copynumber: 6.6 Consensus size: 46
3599544 ACGAAACTTC
* ** *
3599554 TGCATCCTTTCATATATTTTAGTTATGGCATCCTTTCATGCGTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
*
3599600 TGCATCCCTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * *
3599646 TGCATCCGTTCTTGCATTTTAGTTATGACATCCTTTCATTCCTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * * *
3599692 TGCATTCGTTCATGCATTTTAATTATGACATCCTTTCATTCCTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
3599738 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * * *
3599784 TCCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATGTCTTAA
1 TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * *
3599830 TGCATCCTTTCATGTATTTTAATTATGG
1 TGCATCCGTTCATGCATTTTAGTTATGG
3599858 ATTCGGTTTG
Statistics
Matches: 235, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 235 1.00
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (46 bp):
TGCATCCGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
Found at i:3601725 original size:46 final size:46
Alignment explanation
Indices: 3601656--3602004 Score: 430
Period size: 46 Copynumber: 7.5 Consensus size: 46
3601646 GTGTTGTTTG
* *
3601656 TGAAAGGATGCCATAATTAAAATGCATGAACGGATGCATTAAGGCG
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* *
3601702 TGAAAGGATGCCATAACTGAAATGCATGAATGAATGAATGCATTAAGGCA
1 TGAAAGGATGCCATAACTAAAATGCATGAACG---G-ATGCATTAAGGCA
* *
3601752 TGAAAAGATGCCATAACTAAAATGCATGAAGGGATGCATTAAGGCA
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* *
3601798 TGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCATTAAGGCA
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* * * * *
3601844 TTAAAGGATGACATAATTAAAATTCATGAACGGATGCATTAAGACA
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* * * *
3601890 TGAGAGGATGCCATAACCAAAATGCATGAAAGGATGCATTAGGGCA
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* * * * *
3601936 TGAAAGGATGTCATGATTAAAATGCATGAACGGATGTATTAATGCA
1 TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
* *
3601982 TGAAAAGA-GACCAGAACTAAAAT
1 TGAAAGGATG-CCATAACTAAAAT
3602005 TAAAGAATAA
Statistics
Matches: 259, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
45 1 0.00
46 215 0.83
47 1 0.00
49 1 0.00
50 41 0.16
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
TGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGCA
Found at i:3601787 original size:26 final size:26
Alignment explanation
Indices: 3601656--3601834 Score: 109
Period size: 26 Copynumber: 7.4 Consensus size: 26
3601646 GTGTTGTTTG
*
3601656 TGAAAGGATGCCATAATTAAAATGCA
1 TGAAAGGATGCCATAACTAAAATGCA
* * *
3601682 TGAACGGATG-CAT---T--AAGGCG
1 TGAAAGGATGCCATAACTAAAATGCA
*
3601702 TGAAAGGATGCCATAACTGAAATGCA
1 TGAAAGGATGCCATAACTAAAATGCA
* * * * * *
3601728 TGAATGAATG-AAT-GC-ATTAAGGCA
1 TGAAAGGATGCCATAACTA-AAATGCA
*
3601752 TGAAAAGATGCCATAACTAAAATGCA
1 TGAAAGGATGCCATAACTAAAATGCA
* *
3601778 TGAAGGGATG-CAT---T--AAGGCA
1 TGAAAGGATGCCATAACTAAAATGCA
*
3601798 TGAAAGGATGTCATAACTAAAATGCA
1 TGAAAGGATGCCATAACTAAAATGCA
3601824 TGAAAGGATGC
1 TGAAAGGATGC
3601835 ATTAAGGCAT
Statistics
Matches: 111, Mismatches: 26, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
20 27 0.24
21 6 0.05
22 2 0.02
24 15 0.14
25 10 0.09
26 50 0.45
27 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (26 bp):
TGAAAGGATGCCATAACTAAAATGCA
Found at i:3601800 original size:20 final size:20
Alignment explanation
Indices: 3601775--3601945 Score: 81
Period size: 20 Copynumber: 7.7 Consensus size: 20
3601765 TAACTAAAAT
*
3601775 GCATGAAGGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
3601795 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
3601821 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3601841 GCATTAAAGGATGACATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
3601867 TCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * * *
3601887 ACATGAGAGGATGCCATAACCAAAAT
1 GCATGAAAGGATG-CAT-----TAAG
*
3601913 GCATGAAAGGATGCATTAGG
1 GCATGAAAGGATGCATTAAG
3601933 GCATGAAAGGATG
1 GCATGAAAGGATG
3601946 TCATGATTAA
Statistics
Matches: 114, Mismatches: 19, Indels: 36
0.67 0.11 0.21
Matches are distributed among these distances:
20 52 0.46
21 7 0.06
22 4 0.04
24 4 0.04
25 7 0.06
26 40 0.35
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:3602465 original size:16 final size:16
Alignment explanation
Indices: 3602444--3602508 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
3602434 TAATAAATAA
3602444 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3602460 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
3602476 ACGACCATAAATGAAC
1 ACGAACATAAACGAAC
*
3602492 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3602508 A
1 A
3602509 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3603621 original size:24 final size:24
Alignment explanation
Indices: 3603585--3603694 Score: 157
Period size: 24 Copynumber: 4.6 Consensus size: 24
3603575 AGATTGGTTA
** *
3603585 AACATAAATGAACGAACATAAACA
1 AACATAACCGAACGAACATAAACG
*
3603609 AACATAACCGAACGAACATAAATG
1 AACATAACCGAACGAACATAAACG
*
3603633 AACTTAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
*
3603657 AACTTAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
*
3603681 AACATAACTGAACG
1 AACATAACCGAACG
3603695 TTCACGAACG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.54, C:0.22, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:3603649 original size:14 final size:14
Alignment explanation
Indices: 3603609--3603683 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
3603599 AACATAAACA
3603609 AACATAACCGAACG
1 AACATAACCGAACG
*
3603623 AACAT-A---AATG
1 AACATAACCGAACG
*
3603633 AACTTAACCGAACG
1 AACATAACCGAACG
3603647 AACAT-A---AACG
1 AACATAACCGAACG
*
3603657 AACTTAACCGAACG
1 AACATAACCGAACG
*
3603671 AACATAAACGAAC
1 AACATAACCGAAC
3603684 ATAACTGAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
10 15 0.33
11 2 0.04
13 2 0.04
14 27 0.59
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:3603703 original size:34 final size:34
Alignment explanation
Indices: 3603643--3603717 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
3603633 AACTTAACCG
3603643 AACGAACATAAACGAACTTAACCGAACG-AACATA
1 AACGAACATAAACGAACTTAACCGAACGTAA-ATA
* *
3603677 AACGAACAT-AACTGAACGTTCA-CGAACGTAAATG
1 AACGAACATAAAC-GAAC-TTAACCGAACGTAAATA
3603711 AACGAAC
1 AACGAAC
3603718 GAGACCTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 3 0.08
34 28 0.78
35 5 0.14
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (34 bp):
AACGAACATAAACGAACTTAACCGAACGTAAATA
Found at i:3607678 original size:15 final size:14
Alignment explanation
Indices: 3607654--3607684 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3607644 GTTAGTATTA
3607654 TTAATATTTCAAGT
1 TTAATATTTCAAGT
3607668 TTAATTATTTCAAGT
1 TTAA-TATTTCAAGT
3607683 TT
1 TT
3607685 GTTTTGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
TTAATATTTCAAGT
Found at i:3607806 original size:66 final size:66
Alignment explanation
Indices: 3607724--3607853 Score: 260
Period size: 66 Copynumber: 2.0 Consensus size: 66
3607714 GGACTCTTAG
3607724 TAAATGTTCTAGTTTCTACTAGAGAATCTTAGTAAGAGTTTTACAATAAATACTCTACTATAGGA
1 TAAATGTTCTAGTTTCTACTAGAGAATCTTAGTAAGAGTTTTACAATAAATACTCTACTATAGGA
3607789 T
66 T
3607790 TAAATGTTCTAGTTTCTACTAGAGAATCTTAGTAAGAGTTTTACAATAAATACTCTACTATAGG
1 TAAATGTTCTAGTTTCTACTAGAGAATCTTAGTAAGAGTTTTACAATAAATACTCTACTATAGG
3607854 GTTATTACAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (66 bp):
TAAATGTTCTAGTTTCTACTAGAGAATCTTAGTAAGAGTTTTACAATAAATACTCTACTATAGGA
T
Found at i:3608209 original size:2 final size:2
Alignment explanation
Indices: 3608202--3608226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3608192 CGCACTTTTA
3608202 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
3608227 CAGATTTTAC
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:3611922 original size:19 final size:19
Alignment explanation
Indices: 3611900--3611955 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
3611890 GATTGCTATT
3611900 TTTAAAAATATATATATAA
1 TTTAAAAATATATATATAA
* *
3611919 TTTAAAATTAAATATAAATAA
1 TTTAAAA--ATATATATATAA
* *
3611940 TTTAATATTATATATA
1 TTTAAAAATATATATA
3611956 ACACAGTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAAAATATATATATAA
Found at i:3611933 original size:21 final size:21
Alignment explanation
Indices: 3611909--3611956 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3611899 TTTTAAAAAT
*
3611909 ATATATATAATTTAAAATTAA
1 ATATAAATAATTTAAAATTAA
* *
3611930 ATATAAATAATTTAATATTAT
1 ATATAAATAATTTAAAATTAA
3611951 ATATAA
1 ATATAA
3611957 CACAGTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAATAATTTAAAATTAA
Found at i:3614927 original size:14 final size:13
Alignment explanation
Indices: 3614905--3614944 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
3614895 TTAGTCATCT
3614905 TTTTATTATTTTA
1 TTTTATTATTTTA
*
3614918 TTTCTATTATGGTTA
1 TTT-TATTAT-TTTA
3614933 TTTTATTATTTT
1 TTTTATTATTTT
3614945 TTAAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:3617197 original size:29 final size:30
Alignment explanation
Indices: 3617133--3617213 Score: 137
Period size: 29 Copynumber: 2.7 Consensus size: 30
3617123 TTAAATATAC
*
3617133 AATAACATAAAATACTATACCAAAAATTAA
1 AATAACATAAAATACAATACCAAAAATTAA
*
3617163 AATAACATAAAATACAATATC-AAAATTAA
1 AATAACATAAAATACAATACCAAAAATTAA
3617192 AATAACATAAAATACAATACCA
1 AATAACATAAAATACAATACCA
3617214 TAGATACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 28 0.60
30 19 0.40
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (30 bp):
AATAACATAAAATACAATACCAAAAATTAA
Found at i:3629200 original size:22 final size:23
Alignment explanation
Indices: 3629175--3629218 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3629165 AATTAAGTTT
3629175 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
3629197 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
3629219 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:3629359 original size:22 final size:22
Alignment explanation
Indices: 3629333--3629388 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
3629323 CTCGGAGGGA
*
3629333 ACCGATTCCCCTCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
3629355 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
3629377 ACCGATTCCCCC
1 ACCGATTCCCCC
3629389 TGATCAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.43, G:0.23, T:0.16
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:3631336 original size:21 final size:21
Alignment explanation
Indices: 3631311--3631350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3631301 AAGACTCTAT
3631311 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
3631332 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
3631351 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:3635193 original size:22 final size:21
Alignment explanation
Indices: 3635162--3635240 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
3635152 TTTAGTGCAG
3635162 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* * *
3635183 AGGGAAATCGATTCCCCTTTCA
1 AGGG-AATCGATACCCCCTTGA
* *
3635205 ATGGGAACCGATTCCCTCCTTG-
1 A-GGGAATCGATACCC-CCTTGA
3635227 AGGGAATCGATACC
1 AGGGAATCGATACC
3635241 TCCCATGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 15 0.32
22 26 0.55
23 6 0.13
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:3641218 original size:21 final size:21
Alignment explanation
Indices: 3641194--3641240 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3641184 ATTTCAGAGA
* *
3641194 TACTTACCAAGGTACTTCATC
1 TACTTACCAAGGTAATTCACC
3641215 TACTTACCAAGGTAATTCACC
1 TACTTACCAAGGTAATTCACC
3641236 TACTT
1 TACTT
3641241 TCACTTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (21 bp):
TACTTACCAAGGTAATTCACC
Found at i:3649256 original size:173 final size:168
Alignment explanation
Indices: 3649042--3649794 Score: 657
Period size: 166 Copynumber: 4.5 Consensus size: 168
3649032 ATAAAAACAT
* * * * *
3649042 ATATATGTGCAAATAATGTCTCCCTTCGGGGAAATATTCATCCCAACAACTCTCATGCTTGATGG
1 ATATATGTACAGATAATGT-TCCCTTCAGGGAACTATTCATCCCAACAACTCTCATGCCTGATGG
* * * * * * *
3649107 GATGAGATATTATGACATGGTAGAGACTCCCTACAAAAAGTGAAAGAATTTCTTGTGAAAAGTGT
65 GATGAGACACTATGACATGGCAGAGATTCCCTACAAAAAGTGAAAGAACTTCTTGTGAAAAGAGC
* * * *
3649172 CTTCCCCTTGATTTCAGAGATTCTCTACATATTCCAGAAATAT
130 CTT-CCATT-TTTTCAAAGATTCTCTACATATTCCA-AAA-AC
* * * **
3649215 ATATATGTACAGATAATGTTCCCCTTCAGGGAATTATTCATCCTAACAACTCTCATTCCTGATAA
1 ATATATGTACAGATAATGTT-CCCTTCAGGGAACTATTCATCCCAACAACTCTCATGCCTGATGG
* * * * * *
3649280 GATGAGACATTATGATATGACAAATATTCCAC-ACAAAAGGTGAAA-ACACTTCTTGTGAAAAGA
65 GATGAGACACTATGACATGGCAGAGATTCC-CTACAAAAAGTGAAAGA-ACTTCTTGTGAAAAGA
*
3649343 G--TTCCATTTTTT-AAAGATTCTATACATATTCCAAAAAC
128 GCCTTCCATTTTTTCAAAGATTCTCTACATATTCCAAAAAC
* * * * * *
3649381 ATATTTATACAGATAAAGTTACCATTCAAGTAA-TATTTCATCCCAACAACTCTCATGCCTGATG
1 ATATATGTACAGATAATGTT-CCCTTCAGGGAACTA-TTCATCCCAACAACTCTCATGCCTGATG
* * * * * * ** *
3649445 GGATGAGGCACTATGACATGGCGGTGATTTCTTA-AGAAAG-GTAAACTCACTTCTTGTGAAAGG
64 GGATGAGACACTATGACATGGCAGAGATTCCCTACAAAAAGTG-AAA-GAACTTCTTGTGAAAAG
* * *
3649508 AGCCTTCCTTTTTTTCAAATATTCTCTACATATTTCAAAAAC
127 AGCCTTCCATTTTTTCAAAGATTCTCTACATATTCCAAAAAC
* * * ** * * *
3649550 ATATTTATACATATAATGTT--CTTTGGGGAACTA-TCGATCTCAACAACTCTTATGCTTGATGG
1 ATATATGTACAGATAATGTTCCCTTCAGGGAACTATTC-ATCCCAACAACTCTCATGCCTGATGG
* * * * * * * *
3649612 GATGAGACACTATGACATGGAAGAGATTTCCTGCAAAAGGTGAAAGAGCTACTTATGAAAAAAGC
65 GATGAGACACTATGACATGGCAGAGATTCCCTACAAAAAGTGAAAGAACTTCTTGTGAAAAGAGC
* ** *
3649677 CTTCCATTTTTCTCAAAGATTCTCTAAATGCTCCAGAAAC
130 CTTCCATTTTT-TCAAAGATTCTCTACATATTCCAAAAAC
** * *
3649717 ATATATGTACAGATAATGTTCCCTT-TTGAAACTATTCATCCCAACAACTCTCATGCCTAATGGG
1 ATATATGTACAGATAATGTTCCCTTCAGGGAACTATTCATCCCAACAACTCTCATGCCTGATGGG
*
3649781 ATGACACACTATGA
66 ATGAGACACTATGA
3649795 ATAGGCAAAG
Statistics
Matches: 465, Mismatches: 96, Indels: 43
0.77 0.16 0.07
Matches are distributed among these distances:
164 1 0.00
165 11 0.02
166 168 0.36
167 51 0.11
168 72 0.15
169 49 0.11
170 4 0.01
171 2 0.00
172 2 0.00
173 104 0.22
174 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (168 bp):
ATATATGTACAGATAATGTTCCCTTCAGGGAACTATTCATCCCAACAACTCTCATGCCTGATGGG
ATGAGACACTATGACATGGCAGAGATTCCCTACAAAAAGTGAAAGAACTTCTTGTGAAAAGAGCC
TTCCATTTTTTCAAAGATTCTCTACATATTCCAAAAAC
Found at i:3651913 original size:94 final size:94
Alignment explanation
Indices: 3651749--3651935 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 94
3651739 AATACTAGTA
* * **
3651749 ATGATAAATATTGAACAAGAGTTCATTATGTTTTAAGTTAAGATGGTAAAACATTTAATATAATA
1 ATGATAAATAGTGAACAAGAGATCATTATGTTTTAAGCAAAGATGGTAAAACATTTAATATAATA
*
3651814 AGAAAAAGTTGAAAGATCTTTTAACCATG
66 AGAAAAAGTTAAAAGATCTTTTAACCATG
*
3651843 ATGATAAATAGTGAACAAGAGATCATTATGTTTTAAGCAAAGATGGTAAAGCATTTAATATAATA
1 ATGATAAATAGTGAACAAGAGATCATTATGTTTTAAGCAAAGATGGTAAAACATTTAATATAATA
*
3651908 GGAAAAAGTTAAAAGATCTTTTAACCAT
66 AGAAAAAGTTAAAAGATCTTTTAACCAT
3651936 CTTTATATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (94 bp):
ATGATAAATAGTGAACAAGAGATCATTATGTTTTAAGCAAAGATGGTAAAACATTTAATATAATA
AGAAAAAGTTAAAAGATCTTTTAACCATG
Found at i:3653050 original size:31 final size:31
Alignment explanation
Indices: 3652998--3653069 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
3652988 AAATTTTATC
* *
3652998 TTTTG-AAAGTTTAATAGCC-AAAGTATAAAT
1 TTTTGAAAAGTTTAAGAGCCAAAAATAT-AAT
3653028 TTTTGAAAAGTTTAAG-GACCAAAAATATAAT
1 TTTTGAAAAGTTTAAGAG-CCAAAAATATAAT
3653059 TTTT-AAAAGTT
1 TTTTGAAAAGTT
3653070 ATATATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 13 0.35
31 18 0.49
32 6 0.16
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (31 bp):
TTTTGAAAAGTTTAAGAGCCAAAAATATAAT
Found at i:3655174 original size:24 final size:24
Alignment explanation
Indices: 3655138--3655184 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3655128 ATCATGCCAA
** *
3655138 GAGTACATGAATGTATTAATACAT
1 GAGTACACAAATGTACTAATACAT
3655162 GAGTACACAAATGTACTAATACA
1 GAGTACACAAATGTACTAATACA
3655185 GAATCAATCG
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:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (24 bp):
GAGTACACAAATGTACTAATACAT
Found at i:3657176 original size:45 final size:46
Alignment explanation
Indices: 3657091--3657178 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
3657081 AAATAGCCTG
* *
3657091 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
3657137 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
3657179 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:3665375 original size:45 final size:46
Alignment explanation
Indices: 3665299--3665386 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
3665289 AAATAGCTTG
** * *
3665299 AGTGCATCGATGTGTGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
3665345 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
3665387 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 22 0.58
46 16 0.42
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:3669379 original size:15 final size:17
Alignment explanation
Indices: 3669359--3669390 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3669349 CATAATATAA
3669359 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
3669374 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
3669391 AAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:3676618 original size:23 final size:23
Alignment explanation
Indices: 3676589--3676664 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
3676579 TGAAAAGTAC
3676589 AAAGATTAAAATAAAATTTTATA
1 AAAGATTAAAATAAAATTTTATA
* * *
3676612 AAAGATTAGGAATGAAAA--GTA-C
1 AAAGATTA-AAAT-AAAATTTTATA
3676634 AAAGATTAAAATAAAATTTTATA
1 AAAGATTAAAATAAAATTTTATA
3676657 AAAGATTA
1 AAAGATTA
3676665 CTATAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 4 0.10
21 3 0.07
22 10 0.24
23 18 0.43
24 3 0.07
25 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.11, T:0.29
Consensus pattern (23 bp):
AAAGATTAAAATAAAATTTTATA
Found at i:3676629 original size:45 final size:45
Alignment explanation
Indices: 3676574--3676664 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
3676564 TAAATTAAAA
3676574 AGGAATGAAAAGTACAAAGATTAAAATAAAATTTTATAAAAGATT
1 AGGAATGAAAAGTACAAAGATTAAAATAAAATTTTATAAAAGATT
3676619 AGGAATGAAAAGTACAAAGATTAAAATAAAATTTTATAAAAGATT
1 AGGAATGAAAAGTACAAAGATTAAAATAAAATTTTATAAAAGATT
3676664 A
1 A
3676665 CTATAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (45 bp):
AGGAATGAAAAGTACAAAGATTAAAATAAAATTTTATAAAAGATT
Found at i:3676846 original size:22 final size:21
Alignment explanation
Indices: 3676814--3676854 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3676804 TGATAAATGC
3676814 TTATAATTTAAAA-TTTAAAA
1 TTATAATTTAAAACTTTAAAA
3676834 TTATAGATATTAAAACTTTAA
1 TTATA-AT-TTAAAACTTTAA
3676855 TTTTTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 6 0.33
23 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAATTTAAAACTTTAAAA
Found at i:3678517 original size:22 final size:22
Alignment explanation
Indices: 3678492--3678540 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3678482 CAAAATTTAG
* *
3678492 CGAAACTGAAAGTAACTCGAAC
1 CGAAACCGAAAGTAACCCGAAC
* *
3678514 CGAAACCGAAATTATCCCGAAC
1 CGAAACCGAAAGTAACCCGAAC
3678536 CGAAA
1 CGAAA
3678541 GCAACTGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.27, G:0.16, T:0.12
Consensus pattern (22 bp):
CGAAACCGAAAGTAACCCGAAC
Found at i:3678576 original size:33 final size:32
Alignment explanation
Indices: 3678549--3678612 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3678539 AAGCAACTGG
3678549 AACCGAATTTTAACCTGATATGAAAGCAACCCA
1 AACCGAA-TTTAACCTGATATGAAAGCAACCCA
* *
3678582 AATCGAATTTAACCTGATCTGAAAGCAACCC
1 AACCGAATTTAACCTGATATGAAAGCAACCC
3678613 GAACATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (32 bp):
AACCGAATTTAACCTGATATGAAAGCAACCCA
Found at i:3678703 original size:20 final size:20
Alignment explanation
Indices: 3678647--3678703 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 20
3678637 TAATAAATTA
* *
3678647 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAAATAATAG
3678665 ATTTAT--TAAAAA-AATTAG
1 ATTTATAATAAAAATAA-TAG
3678683 ATTTATAATAAAAATAATAG
1 ATTTATAATAAAAATAATAG
3678703 A
1 A
3678704 AAATTTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 1 0.03
17 7 0.23
18 11 0.35
20 10 0.32
21 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTTATAATAAAAATAATAG
Found at i:3679370 original size:32 final size:32
Alignment explanation
Indices: 3679292--3679374 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
3679282 ACCTAAACCG
*
3679292 AAAATCAAACGATCCGATATTAACCTGACCCA
1 AAAATCAACCGATCCGATATTAACCTGACCCA
* * * **
3679324 AAAATCAACTGATCCGATATTGATCTGAACTGA
1 AAAATCAACCGATCCGATATTAACCTG-ACCCA
3679357 AAAAT-AACCGATCCGATA
1 AAAATCAACCGATCCGATA
3679375 ATCGCCCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 35 0.81
33 8 0.19
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (32 bp):
AAAATCAACCGATCCGATATTAACCTGACCCA
Found at i:3680393 original size:37 final size:36
Alignment explanation
Indices: 3680253--3680508 Score: 223
Period size: 37 Copynumber: 6.9 Consensus size: 36
3680243 TTTTTTTATT
* *
3680253 TATATATTATATAATTTTGAAAACATTTTG-AAA-A
1 TATATAATATATAATTTTTAAAACATTTTGAAAAGA
* * *
3680287 TATATGATATATAATTTTTAAAACATTTTAAAAACA
1 TATATAATATATAATTTTTAAAACATTTTGAAAAGA
* * *
3680323 TTTAT-ATATTATATAGTTTTAAAACGTTTTTGAAAAGA
1 TATATAATA-TATA-ATTTTTAAAAC-ATTTTGAAAAGA
* * * *
3680361 AATATAATATATAGTTTTCAAAACATTTTTGAAAATA
1 TATATAATATATAATTTTTAAAACA-TTTTGAAAAGA
* * * * *
3680398 TACATATTATATAGTTTTTAAAACGTTTTGAAAATAAA
1 TATATAATATATAATTTTTAAAACATTTTG-AAA-AGA
3680436 TATATAATATATAATTTTTTGAAAAACATTTTG-AAAGCA
1 TATATAATATATAA-TTTTT--AAAACATTTTGAAAAG-A
* *
3680475 TATATAATATGTAATTTTTAAAACATTTTTAAAA
1 TATATAATATATAATTTTTAAAACATTTTGAAAA
3680509 ATTATATGGT
Statistics
Matches: 179, Mismatches: 29, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
34 26 0.15
35 6 0.03
36 24 0.13
37 54 0.30
38 35 0.20
39 24 0.13
41 10 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (36 bp):
TATATAATATATAATTTTTAAAACATTTTGAAAAGA
Found at i:3680544 original size:34 final size:34
Alignment explanation
Indices: 3680494--3680561 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
3680484 TGTAATTTTT
* *
3680494 AAAACATTTTTAAAAATTATATGGTTTTTAAAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTAAAAA
* *
3680528 AAAACACTTTTGAAAATTATATAGTTTTTTAAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTAAAAA
3680562 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (34 bp):
AAAACACTTTTAAAAATTATATAGTTTTTAAAAA
Found at i:3680647 original size:23 final size:23
Alignment explanation
Indices: 3680621--3680694 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
3680611 TAAAAATGTA
*
3680621 TATTA-TATAATTTTTATATTTAT
1 TATTATTATAATTATT-TATTTAT
*
3680644 TATTATTATTATTATTTATTTAT
1 TATTATTATAATTATTTATTTAT
* *
3680667 TATT-TT-TTATTACTTATTTTAT
1 TATTATTATAATTATTTA-TTTAT
3680689 T-TTATT
1 TATTATT
3680695 TTTTCCCGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
21 11 0.24
22 10 0.22
23 16 0.36
24 8 0.18
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTATAATTATTTATTTAT
Found at i:3680648 original size:3 final size:3
Alignment explanation
Indices: 3680640--3680694 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
3680630 ATTTTTATAT
3680640 TTA TTA TTA TTA TTA TTA TTTA TTTA TTA TT- TT- TTA TTA CTTA TT-
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA -TTA TTA
3680685 TTA TT- TTA TT
1 TTA TTA TTA TT
3680695 TTTTCCCGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.17
3 29 0.62
4 10 0.21
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:3680668 original size:14 final size:14
Alignment explanation
Indices: 3680640--3680677 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3680630 ATTTTTATAT
3680640 TTATTA-TTA-TTA
1 TTATTATTTATTTA
3680652 TTATTATTTATTTA
1 TTATTATTTATTTA
*
3680666 TTATTTTTTATT
1 TTATTATTTATT
3680678 ACTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 6 0.26
13 3 0.13
14 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTATTTA
Found at i:3680677 original size:30 final size:30
Alignment explanation
Indices: 3680633--3680695 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
3680623 TTATATAATT
3680633 TTTATATTTATTATTA-TTATTATTA-TTTA
1 TTTATATTTATTATTACTTATT-TTATTTTA
*
3680662 TTTATTATTTTTTATTACTTATTTTATTTTA
1 TTTA-TATTTATTATTACTTATTTTATTTTA
3680693 TTT
1 TTT
3680696 TTTCCCGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 14 0.47
31 12 0.40
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTATATTTATTATTACTTATTTTATTTTA
Found at i:3680683 original size:14 final size:13
Alignment explanation
Indices: 3680646--3680698 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 13
3680636 ATATTTATTA
*
3680646 TTATTATTATTAT
1 TTATTATTATTTT
3680659 TTATTTATTATTTT
1 TTA-TTATTATTTT
3680673 TTATTACTTA--TT
1 TTATTA-TTATTTT
3680685 TTATT-TTATTTT
1 TTATTATTATTTT
3680697 TT
1 TT
3680699 CCCGTTTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.09
12 11 0.31
13 6 0.17
14 15 0.43
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:3680691 original size:17 final size:17
Alignment explanation
Indices: 3680634--3680694 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
3680624 TATATAATTT
3680634 TTATATTTATTATTATTA
1 TTAT-TTTATTATTATTA
*
3680652 TTATTAT-TTATTTATTA
1 TTATTTTATTA-TTATTA
3680669 TT-TTTTATTACTTATT-
1 TTATTTTATTA-TTATTA
3680685 TTATTTTATT
1 TTATTTTATT
3680695 TTTTCCCGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.22
17 25 0.68
18 4 0.11
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTATTATTATTA
Found at i:3681844 original size:16 final size:16
Alignment explanation
Indices: 3681823--3681853 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3681813 TTAGTCAGTG
3681823 TTTTATTTATTTATTA
1 TTTTATTTATTTATTA
3681839 TTTTATTTATTTATT
1 TTTTATTTATTTATT
3681854 TTGGCTCATT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:3681845 original size:12 final size:13
Alignment explanation
Indices: 3681824--3681855 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3681814 TAGTCAGTGT
3681824 TTTA-TTTATTTA
1 TTTATTTTATTTA
3681836 -TTATTTTATTTA
1 TTTATTTTATTTA
3681848 TTTATTTT
1 TTTATTTT
3681856 GGCTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 8 0.44
13 7 0.39
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:3681989 original size:3 final size:3
Alignment explanation
Indices: 3681981--3682012 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3681971 TTATTTACTT
3681981 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3682013 TTTTGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3683830 original size:18 final size:19
Alignment explanation
Indices: 3683809--3683853 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3683799 ATTTAGACAT
3683809 TTTGCATTTT-TTATTTTC
1 TTTGCATTTTGTTATTTTC
3683827 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
3683846 TTTGCATT
1 TTTGCATT
3683854 CACATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:3687714 original size:168 final size:165
Alignment explanation
Indices: 3687256--3687974 Score: 1090
Period size: 164 Copynumber: 4.4 Consensus size: 165
3687246 TAAACAAACT
*
3687256 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * **
3687320 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA-GGTTATCTG-TGACCAAAAGAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
* * *
3687383 CTTTGAGTTCGACTACGCTCAGCTCAATGACATATC
130 CTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
*
3687419 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
3687484 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
3687548 TTTGAGTTCGACTACGCTCAGCTCTAA-GGCACATC
131 TTTGAGTTCGACTACGCTCAGCTC-AACGGCACATC
* * * **
3687583 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
*
3687648 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAA-CAAA
62 CTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
*
3687712 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACGTC
127 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* * *
3687751 ATTTGCAGTATAGCTTAAGTTGAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
3687816 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
* *
3687881 TTCGAGTTCGACTACACTCAGCTCAACGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
* * ** *
3687916 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCTAAAGACCTTCGAGTTCAATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
3687975 TATTCAACTT
Statistics
Matches: 510, Mismatches: 36, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
163 43 0.08
164 209 0.41
165 105 0.21
167 2 0.00
168 148 0.29
169 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCAACGGCACATC
Found at i:3687857 original size:332 final size:329
Alignment explanation
Indices: 3687256--3687974 Score: 1106
Period size: 332 Copynumber: 2.2 Consensus size: 329
3687246 TAAACAAACT
* *
3687256 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCCAAAGACCCCGAGTTCGATTACACTCA
* ** *
3687320 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGTTATCTGTGACCAAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGTTATCTGCCAACAAAAGACCT
* *
3687385 TTGAGTTCGACTACGCTCAGCTCAATGACATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
131 TTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
*
3687450 ATCTGCCAAAGACCCCCGAGTTCGATTACACTTAGCTTCGAGGGCACATCATTTGCAGCATAACT
196 ATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACT
* *
3687515 TAAGTCGAGAAGGGTTATCTG-CAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAA-GGC
261 TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTC-AACGGC
3687578 ACATC
325 ACATC
* * *
3687583 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CCAAAGACC-CCGAGTTCGATTACA
* * * *
3687648 CTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAAC-AAA
62 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAA-GGTTATCTGCCAACAAAA
* * * *
3687712 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACGTCATTTGCAGTATAGCTTAAGTTGAGAA
126 GACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAA
*
3687777 GGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCA
191 GGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCA
3687842 TAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAA
256 TAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAA
3687907 CGGCACATC
321 CGGCACATC
* * *
3687916 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-CTAAAGACCTTCGAGTTCAATTA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCCAAAGACC-CCGAGTTCGATTA
3687975 TATTCAACTT
Statistics
Matches: 357, Mismatches: 27, Indels: 14
0.90 0.07 0.04
Matches are distributed among these distances:
327 34 0.10
329 20 0.06
331 8 0.02
332 207 0.58
333 88 0.25
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (329 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCCAAAGACCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGTTATCTGCCAACAAAAGACCT
TTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
ATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCAACGGCA
CATC
Found at i:3688650 original size:72 final size:74
Alignment explanation
Indices: 3688585--3688788 Score: 229
Period size: 74 Copynumber: 2.8 Consensus size: 74
3688575 TTTTTTTTTT
* * *
3688585 ATTTATATATTATATAATTTTGAAAAC-ATTTTG-AAA-ATATATGATATATAATTTTTAAAACA
1 ATTTATATATTATATAATTTT-AAAACGATTTTGAAAAGAAATATAATATATAATTTTCAAAACA
*
3688647 TTTTAAAAAC
65 TTTTTAAAAC
* * *
3688657 ATTTATATATTATATAGTTTTAAAACGTTTTTGAAAAGAAATATAATATATAGTTTTCAAAACAT
1 ATTTATATATTATATAATTTTAAAACGATTTTGAAAAGAAATATAATATATAATTTTCAAAACAT
*
3688722 TTTTGAAA-
66 TTTTAAAAC
* * * *
3688730 ATATACATATTATATAGTTTTTAAAACG-TTTTGAAAATAAATATATAATATATAATTTT
1 ATTTATATATTATATA-ATTTTAAAACGATTTTGAAAA-GAA-ATATAATATATAATTTT
3688789 TTGAAAAATA
Statistics
Matches: 113, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
71 5 0.04
72 25 0.22
73 26 0.23
74 41 0.36
75 16 0.14
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (74 bp):
ATTTATATATTATATAATTTTAAAACGATTTTGAAAAGAAATATAATATATAATTTTCAAAACAT
TTTTAAAAC
Found at i:3688810 original size:38 final size:35
Alignment explanation
Indices: 3688588--3688811 Score: 182
Period size: 37 Copynumber: 6.1 Consensus size: 35
3688578 TTTTTTTATT
* *
3688588 TATATATTATATAATTTTGAAAACATTTTG-AAAA
1 TATATAATATATAATTTTTAAAACATTTTGAAAAA
*
3688622 TATATGATATATAATTTTTAAAACATTTT-AAAAA
1 TATATAATATATAATTTTTAAAACATTTTGAAAAA
* * * *
3688656 CATTTATATATTATATAGTTTTAAAACGTTTTTGAAAAGA
1 TATATA-ATA-TATA-ATTTTTAAAAC-ATTTTGAAAA-A
* * *
3688696 AATATAATATATAGTTTTCAAAACATTTTTGAAAATA
1 TATATAATATATAATTTTTAAAACA-TTTTGAAAA-A
* * * *
3688733 TACATATTATATAGTTTTTAAAACGTTTTGAAAATAAA
1 TATATAATATATAATTTTTAAAACATTTTG--AA-AAA
*
3688771 TATATAATATATAATTTTTTGAAAAATATTTTGAAAAA
1 TATATAATATATAA-TTTTT--AAAACATTTTGAAAAA
3688809 TAT
1 TAT
3688812 TTTGAAAGCA
Statistics
Matches: 151, Mismatches: 25, Indels: 24
0.75 0.12 0.12
Matches are distributed among these distances:
34 33 0.22
35 3 0.02
36 9 0.06
37 48 0.32
38 28 0.19
39 16 0.11
40 5 0.03
41 9 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAATTTTTAAAACATTTTGAAAAA
Found at i:3688824 original size:13 final size:12
Alignment explanation
Indices: 3688787--3688818 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3688777 ATATATAATT
3688787 TTTTGAAAAATA
1 TTTTGAAAAATA
3688799 TTTTGAAAAATA
1 TTTTGAAAAATA
3688811 TTTTGAAA
1 TTTTGAAA
3688819 GCATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (12 bp):
TTTTGAAAAATA
Found at i:3688889 original size:32 final size:32
Alignment explanation
Indices: 3688841--3688906 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
3688831 TGTAATTTTT
* *
3688841 AAAACATTTTTAAAAATTATATGGTTTTTAAA
1 AAAACACTTTTAAAAATTATATAGTTTTTAAA
* *
3688873 AAAACACTTTTGAAAATTATATAGTTTTTTAA
1 AAAACACTTTTAAAAATTATATAGTTTTTAAA
3688905 AA
1 AA
3688907 TGTTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (32 bp):
AAAACACTTTTAAAAATTATATAGTTTTTAAA
Found at i:3688993 original size:3 final size:3
Alignment explanation
Indices: 3688985--3689044 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
3688975 ATTTTTATAT
3688985 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
3689029 CTTA TT- TTA TT- TTA TT
1 -TTA TTA TTA TTA TTA TT
3689045 TTTTCCCGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.15
3 38 0.73
4 6 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:3689046 original size:10 final size:11
Alignment explanation
Indices: 3688988--3689044 Score: 68
Period size: 10 Copynumber: 5.5 Consensus size: 11
3688978 TTTATATTTA
3688988 TTATTATTATT
1 TTATTATTATT
3688999 ATTATTATTA-T
1 -TTATTATTATT
3689010 TTATTATTATT
1 TTATTATTATT
*
3689021 TT-TTATTA-C
1 TTATTATTATT
3689030 TTATT-TTATT
1 TTATTATTATT
3689040 TTATT
1 TTATT
3689045 TTTTCCCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 5 0.12
10 22 0.55
11 4 0.10
12 9 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTATT
Found at i:3689047 original size:25 final size:25
Alignment explanation
Indices: 3688979--3689048 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
3688969 TATATAATTT
*
3688979 TTATATTTATTATTATTATTATTATTA
1 TTAT-TTTATTATTATT-TTTTTATTA
3689006 TTA-TTTATTATTA-TTTTTTATTA
1 TTATTTTATTATTATTTTTTTATTA
3689029 CTTATTTTATT-TTATTTTTT
1 -TTATTTTATTATTATTTTTT
3689049 CCCGTTTCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 21 0.54
27 3 0.08
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTTTATTATTATTTTTTTATTA
Found at i:3690912 original size:9 final size:10
Alignment explanation
Indices: 3690886--3690910 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3690876 TTAGTAATTT
3690886 TTAAAATTAA
1 TTAAAATTAA
3690896 TTAAAATTAA
1 TTAAAATTAA
3690906 TTAAA
1 TTAAA
3690911 TTTTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAATTAA
Found at i:3694839 original size:42 final size:42
Alignment explanation
Indices: 3694780--3694859 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
3694770 ATTAGGTATG
3694780 TAAAATTAAAATAACTAATGGTAAATATCTATATACCATACC
1 TAAAATTAAAATAACTAATGGTAAATATCTATATACCATACC
*
3694822 TAAAATTAAAATAACTAATGGTAGATATCTATATACCA
1 TAAAATTAAAATAACTAATGGTAAATATCTATATACCA
3694860 CTCTTGTCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (42 bp):
TAAAATTAAAATAACTAATGGTAAATATCTATATACCATACC
Found at i:3697082 original size:19 final size:19
Alignment explanation
Indices: 3697054--3697101 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3697044 ACTACTGGTG
*
3697054 CAAACAATTAATTATGCCT
1 CAAACTATTAATTATGCCT
3697073 CAAACTATTAATTATGCCT
1 CAAACTATTAATTATGCCT
*
3697092 CAGACTATTA
1 CAAACTATTA
3697102 TTAACAGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (19 bp):
CAAACTATTAATTATGCCT
Found at i:3698315 original size:15 final size:15
Alignment explanation
Indices: 3698295--3698326 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3698285 GAACAAGCTA
3698295 TCTGACTAGCGGGGT
1 TCTGACTAGCGGGGT
3698310 TCTGACTAGCGGGGT
1 TCTGACTAGCGGGGT
3698325 TC
1 TC
3698327 ATTCGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.22, G:0.38, T:0.28
Consensus pattern (15 bp):
TCTGACTAGCGGGGT
Found at i:3704432 original size:35 final size:35
Alignment explanation
Indices: 3704340--3704411 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3704330 CCAAAAAAGA
3704340 AGAGTTGGATTAGGACTTAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTTAAATACTAGTCTAAAAT
*
3704375 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTTAAATACTAGTCTAAAAT
3704410 AG
1 AG
3704412 GGTTTTTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTTAAATACTAGTCTAAAAT
Found at i:3704877 original size:2 final size:2
Alignment explanation
Indices: 3704870--3704915 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3704860 TTATTATTAT
3704870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3704912 -A TA T
1 TA TA T
3704916 TTTACTTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3705085 original size:2 final size:2
Alignment explanation
Indices: 3705080--3705112 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3705070 CTTCTAACTT
3705080 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 T
3705113 TATTTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3705275 original size:41 final size:39
Alignment explanation
Indices: 3705230--3705306 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
3705220 AGGGCCCATT
* *
3705230 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
3705271 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
3705307 GGTGAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:3705396 original size:2 final size:2
Alignment explanation
Indices: 3705389--3705424 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3705379 TAATACTTTG
3705389 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
3705425 TATCCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3705495 original size:9 final size:9
Alignment explanation
Indices: 3705475--3705550 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
3705465 TATTTTTTCC
*
3705475 TTATCTTAT
1 TTATTTTAT
3705484 TTA-TTTATT
1 TTATTTTA-T
3705493 TTATTTTAT
1 TTATTTTAT
3705502 TTATTTT-T
1 TTATTTTAT
*
3705510 TTCCTTTTATT
1 TT-ATTTTA-T
* *
3705521 TTATTCTCT
1 TTATTTTAT
*
3705530 TTATCTTAT
1 TTATTTTAT
*
3705539 TTATTTTCT
1 TTATTTTAT
3705548 TTA
1 TTA
3705551 CCTTGTTTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
8 6 0.12
9 36 0.69
10 7 0.13
11 3 0.06
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:3705501 original size:18 final size:17
Alignment explanation
Indices: 3705475--3705560 Score: 73
Period size: 18 Copynumber: 4.8 Consensus size: 17
3705465 TATTTTTTCC
3705475 TTATCTTATTTATTTATT
1 TTATCTTATTTATTT-TT
*
3705493 TTATTTTATTTATTTTT
1 TTATCTTATTTATTTTT
* * *
3705510 TTCCTTTTATTTTATTCTCT
1 TT-ATCTTA-TTTATT-TTT
3705530 TTATCTTATTTATTTTCT
1 TTATCTTATTTATTTT-T
* *
3705548 TTACCTTGTTTAT
1 TTATCTTATTTAT
3705561 CTAACACATT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.09
18 37 0.66
19 10 0.18
20 4 0.07
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.72
Consensus pattern (17 bp):
TTATCTTATTTATTTTT
Found at i:3705502 original size:14 final size:14
Alignment explanation
Indices: 3705483--3705544 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
3705473 CCTTATCTTA
3705483 TTTATTTATTTTAT
1 TTTATTTATTTTAT
3705497 TTTATTTATTTT-T
1 TTTATTTATTTTAT
3705510 TTCCT-TTTATTTTAT
1 TT--TATTTATTTTAT
* * *
3705525 TCTCTTTATCTTA-
1 TTTATTTATTTTAT
3705538 TTTATTT
1 TTTATTT
3705545 TCTTTACCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 9 0.22
14 28 0.70
15 3 0.08
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:3713888 original size:95 final size:99
Alignment explanation
Indices: 3713696--3714424 Score: 423
Period size: 103 Copynumber: 7.2 Consensus size: 99
3713686 GATTTTAGCT
* * ** * *
3713696 AGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAGGACAACACAAG-------TCACAA
* *
3713761 CGAAGGAACGGCTGGTTGTCAACAAACAATTTCCCAATTTC
59 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
* * *
3713802 AGAGCCAATTTCAACTTCACATCGAAGGATGTTGGAC-TCGGACAAC-CAAG-CACAACGAAGGG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAGGACAACACAAGTCACAACGAAGGG
*
3713864 ACGACTGG-TGTCAATAAACAATTTCCCAATTTC
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTC
* *
3713897 AGAGTCACTTTCAACTTCACAGCGAAGGATATTGGACTTAGGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAGGACAACACAAG-------TCACAA
*
3713962 CGAA-GGACGACTGGTTGTCAACAAACAATCTCCCAA-TTC
59 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
*
3714001 AGAG-C-----CAA--T---AGCGAAGGATATTGGAC-TAGAGACGACACAAGTTCACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAG-GACAACACAAG------TCACAA
* * * *
3714054 CGAGGGGACGACTGGTTGTTAACAAACAA-TTCCTAAGTTTT
59 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAA-TTTC
* * * * * * *
3714095 AGGGTCAATTTCAACTTCACATCGAAGGATATTGAAC-TCGAGACCAACAAGTTAACTTCACAAC
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAG-GA-CAAC-A--CAA-GTCACAAC
* *
3714159 GAAGGGACGGCTGGTTGTCAAC-AATAATTT-CCAATTTC
60 GAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
* * *
3714197 ATAGCC-ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATGAC-ACAAGTTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-TAG--GACAAC-A---CAA-GTCACA
*
3714260 ACGAAGGGACG---GGTTGTCAACAAACAATTTCCTAATTTC
58 ACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
* * * * * * * * *
3714299 AGGGTCAATTTTAACTTTACATCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-TAG---G-ACAA-CACAA-GTCACAA
* ** * *** * *
3714364 CGAAGGGGCGGTTGGCTGTCAACAAACAATTTTTGAGTTCC
59 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
3714405 AGAGCCAATTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
3714425 GTGGAAGATA
Statistics
Matches: 503, Mismatches: 74, Indels: 92
0.75 0.11 0.14
Matches are distributed among these distances:
92 21 0.04
93 50 0.10
94 5 0.01
95 58 0.12
96 27 0.05
97 4 0.01
98 3 0.01
100 13 0.03
101 35 0.07
102 21 0.04
103 81 0.16
104 52 0.10
105 56 0.11
106 73 0.15
107 2 0.00
109 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (99 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTAGGACAACACAAGTCACAACGAAGGG
ACGACTGGTTGTCAACAAACAATTTCCCAATTTC
Found at i:3714266 original size:299 final size:292
Alignment explanation
Indices: 3713720--3714424 Score: 769
Period size: 293 Copynumber: 2.3 Consensus size: 292
3713710 CTGCACAGTA
*
3713720 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGACTGGTTGTCAACA
* *
3713785 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGACAACCA
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGGACAACCA
*
3713850 AGCACAACGAAGGGACGACTGGTGTCAATAAACAATTTCCCAATTTCAGAGTCACTTTCAACTTC
131 AGCACAACGAAGGGACGACTGGTGTCAATAAACAATTTCCCAATTTCAGAGCCACTTTCAACTTC
* *
3713915 ACAGCGAAGGATATTGGACTTAGGACAACACAAGTTCAACTTCACAACGAAGGACGACTGGTTGT
196 ACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAAGG--GACGGGTTGT
3713980 CAACAAACAATCTCCCAATTCAGAGCCAATAGCG
259 CAACAAACAATCTCCCAATTCAGAGCCAATAGCG
* * * *
3714014 AAGGATATTGGACT-AGAGACGACACAAGTTC-ACTTCACAACGAGGGGACGACTGGTTGTTAAC
1 AAGGATATTGGACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGAACGACTGGTTGTCAAC
* * * *
3714077 AAACAA-TTCCTAAGTTTTAGGGTCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACCA
65 AAACAATTTCCCAA-TTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCG-GA-CA
* * * *
3714141 A-CAAGTTAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAATAATTT-CCAATTTCATAGCC
127 ACCAAG-------CACAACGAAGGGACGACTGG-TGTCAATAAACAATTTCCCAATTTCAGAGCC
**
3714203 A-TTTCAACTTCACAGCGAAGGATATTGGACTCGA-GATGACACAAGTTCAACTTCACAACGAAG
184 ACTTTCAACTTCACAGCGAAGGATATTGGACT-GAGGACAACACAAGTTCAACTTCACAACGAAG
* * * * *
3714266 GGACGGGTTGTCAACAAACAATTTCCTAATTTCAGGGTCAATTTTAACTTTACATCG
248 GGACGGGTTGTCAACAAACAATCTCCCAA-TTCAGAG-C-----CAA---T--AGCG
* * * ** ** *
3714323 AAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGACTGGTTGTCAACA
*** * *
3714388 AACAATTTTTGAGTTCCAGAGCCAATTTCAACTTCAC
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
3714425 GTGGAAGATA
Statistics
Matches: 340, Mismatches: 43, Indels: 40
0.80 0.10 0.09
Matches are distributed among these distances:
292 6 0.02
293 74 0.22
294 34 0.10
295 3 0.01
297 25 0.07
298 6 0.02
299 59 0.17
300 14 0.04
301 26 0.08
302 6 0.02
304 2 0.01
307 1 0.00
309 28 0.08
310 53 0.16
311 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (292 bp):
AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGACTGGTTGTCAACA
AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGGACAACCA
AGCACAACGAAGGGACGACTGGTGTCAATAAACAATTTCCCAATTTCAGAGCCACTTTCAACTTC
ACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAAGGGACGGGTTGTCA
ACAAACAATCTCCCAATTCAGAGCCAATAGCG
Found at i:3714325 original size:103 final size:105
Alignment explanation
Indices: 3714012--3714395 Score: 464
Period size: 103 Copynumber: 3.7 Consensus size: 105
3714002 GAGCCAATAG
* * * * *
3714012 CGAAGGATATTGGACTAGAGACGACACAAGTTC-ACTTCACAACGAGGGGACGACTGGTTGTTAA
1 CGAAGGATATTGGACTCGAGACCACACAAGTTCAACTTCACAACGAAGGGACG-GTGGTTGTCAA
*
3714076 CAAACAA-TTCCTAAGTTTTAGGGTCAATTTCAACTTCACAT
65 CAAACAATTTCCTAA-TTTCAGGGTCAATTTCAACTTCACAT
*
3714117 CGAAGGATATTGAACTCGAGACCA-ACAAGTT-AACTTCACAACGAAGGGACGGCTGGTTGTCAA
1 CGAAGGATATTGGACTCGAGACCACACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTCAA
* ** * *
3714180 C-AATAATTTCC-AATTTCATAG-CCATTTCAACTTCACAG
65 CAAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACAT
**
3714218 CGAAGGATATTGGACTCGAGATGACACAAGTTCAACTTCACAACGAAGGGAC-G-GGTTGTCAAC
1 CGAAGGATATTGGACTCGAGACCACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCAAC
* *
3714281 AAACAATTTCCTAATTTCAGGGTCAATTTTAACTTTACAT
66 AAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACAT
* * * * *
3714321 CGAAGGATATTAGACTCAAGA-CAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCA
1 CGAAGGATATTGGACTCGAGACCA-CACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTCA
3714385 ACAAACAATTT
64 ACAAACAATTT
3714396 TTGAGTTCCA
Statistics
Matches: 239, Mismatches: 28, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
100 10 0.04
101 45 0.19
102 22 0.09
103 83 0.35
104 40 0.17
105 21 0.09
106 18 0.08
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (105 bp):
CGAAGGATATTGGACTCGAGACCACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCAAC
AAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACAT
Found at i:3714962 original size:33 final size:35
Alignment explanation
Indices: 3714919--3714988 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 35
3714909 ACCAAAAAGA
3714919 AGAGTTGGATTAGGACTC-AATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCGAATACTAGTCTAAAAT
3714953 AGAG-TGGATTAGGACTCGAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCGAATACTAGTCTAAAAT
3714987 AG
1 AG
3714989 GGTTTTTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCGAATACTAGTCTAAAAT
Found at i:3715655 original size:2 final size:2
Alignment explanation
Indices: 3715648--3715682 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3715638 ACTTTATTAT
3715648 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 T
3715683 TATTTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3715835 original size:41 final size:38
Alignment explanation
Indices: 3715791--3715865 Score: 107
Period size: 41 Copynumber: 1.9 Consensus size: 38
3715781 AGGGCCCATT
3715791 TTTTTGT-TTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-C-CCCACTTTCCTC
*
3715831 TTTTTGTCTTATTTCTGACTAAAGCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCACTTTC
3715866 AGTGAAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 9 0.27
39 1 0.03
40 8 0.24
41 15 0.45
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (38 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCACTTTCCTC
Found at i:3715955 original size:2 final size:2
Alignment explanation
Indices: 3715948--3716006 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
3715938 ATACTTGATG
*
3715948 TA TA TA TA TA TA TA TA T- TA TA GA TA TA TA TA TA 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 TA
3715989 TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3716007 TCCTTTTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3715975 original size:21 final size:20
Alignment explanation
Indices: 3715949--3716007 Score: 100
Period size: 21 Copynumber: 2.9 Consensus size: 20
3715939 TACTTGATGT
3715949 ATATATATATATATATTATA
1 ATATATATATATATATTATA
3715969 GATATATATATATATATATATA
1 -ATATATATATATATAT-TATA
3715991 ATATATATATATATATT
1 ATATATATATATATATT
3716008 CCTTTTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.86
22 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATATATATATATATTATA
Found at i:3715982 original size:25 final size:25
Alignment explanation
Indices: 3715948--3716006 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
3715938 ATACTTGATG
*
3715948 TATATATATATATATATTATAGATA
1 TATATATATATATATATAATAGATA
*
3715973 TATATATATATATATATAATATATA
1 TATATATATATATATATAATAGATA
3715998 TATATATAT
1 TATATATAT
3716007 TCCTTTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TATATATATATATATATAATAGATA
Found at i:3716108 original size:14 final size:14
Alignment explanation
Indices: 3716078--3716122 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
3716068 TATTATTTAT
*
3716078 TTTATTTT-TTCTT
1 TTTATTTTATTCTC
3716091 TTTATTTTATTCTC
1 TTTATTTTATTCTC
* *
3716105 TTTATATTATTTTC
1 TTTATTTTATTCTC
3716119 TTTA
1 TTTA
3716123 CCTTGTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTATTCTC
Found at i:3716112 original size:16 final size:13
Alignment explanation
Indices: 3716077--3716121 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3716067 TTATTATTTA
3716077 TTTTATTTTTTCT
1 TTTTATTTTTTCT
3716090 TTTTATTTTATTCT
1 TTTTATTTT-TTCT
3716104 CTTTATATTATTTTCT
1 -TTT-TATT-TTTTCT
3716120 TT
1 TT
3716122 ACCTTGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 4 0.14
15 5 0.18
16 8 0.29
17 2 0.07
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTCT
Found at i:3724332 original size:2 final size:2
Alignment explanation
Indices: 3724325--3724361 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3724315 TTTTACCTAT
3724325 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 T
3724362 GAGTAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3728860 original size:2 final size:2
Alignment explanation
Indices: 3728853--3728889 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3728843 CATTTTTACC
3728853 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 T
3728890 GAGTAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.