Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 92 of 175
Found at i:29437181 original size:20 final size:20
Alignment explanation
Indices: 29437156--29437235 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
29437146 GTATGGGATC
*
29437156 GCACTTTGGTGCCTTTGTTT
1 GCACTTTGGTGCCTCTGTTT
*
29437176 GCACTTTGATGCCTCTGTTT
1 GCACTTTGGTGCCTCTGTTT
*
29437196 GCACTTCGGGTGCCTCTGTTT
1 GCACTT-TGGTGCCTCTGTTT
**
29437217 GCACTACGGTGCCTCTGTT
1 GCACTTTGGTGCCTCTGTT
29437236 AGCATTTCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 36 0.68
21 17 0.32
ACGTcount: A:0.07, C:0.26, G:0.25, T:0.41
Consensus pattern (20 bp):
GCACTTTGGTGCCTCTGTTT
Found at i:29437211 original size:21 final size:21
Alignment explanation
Indices: 29437163--29437244 Score: 96
Period size: 20 Copynumber: 4.0 Consensus size: 21
29437153 ATCGCACTTT
* *
29437163 GGTGCCTTTGTTTGCACTT-T
1 GGTGCCTCTGTTTGCACTTCG
*
29437183 GATGCCTCTGTTTGCACTTCG
1 GGTGCCTCTGTTTGCACTTCG
*
29437204 GGTGCCTCTGTTTGCACTAC-
1 GGTGCCTCTGTTTGCACTTCG
* *
29437224 GGTGCCTCTGTTAGCATTTCG
1 GGTGCCTCTGTTTGCACTTCG
29437245 ATGCTCTCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
20 34 0.65
21 18 0.35
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (21 bp):
GGTGCCTCTGTTTGCACTTCG
Found at i:29437216 original size:41 final size:41
Alignment explanation
Indices: 29437163--29437244 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
29437153 ATCGCACTTT
* ** *
29437163 GGTGCCTTTGTTTGCACTTTGATGCCTCTGTTTGCACTTCG
1 GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
* *
29437204 GGTGCCTCTGTTTGCACTACGGTGCCTCTGTTAGCATTTCG
1 GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
29437245 ATGCTCTCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (41 bp):
GGTGCCTCTGTTTGCACTACGATGCCTCTGTTAGCACTTCG
Found at i:29437254 original size:41 final size:41
Alignment explanation
Indices: 29437156--29437254 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
29437146 GTATGGGATC
* * ** *
29437156 GCACTTTGG-TGCCTTTGTTTGCACTTTGATGCCTCTGTTT
1 GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
* *
29437196 GCACTTCGGGTGCCTCTGTTTGCACTACGGTGCCTCTGTTA
1 GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
*
29437237 GCATTTC-GATGCTCTCTG
1 GCACTTCGGATGC-CTCTG
29437255 ATGTGTTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 12 0.24
41 37 0.76
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.40
Consensus pattern (41 bp):
GCACTTCGGATGCCTCTGTTTGCACTACGATGCCTCTGTTA
Found at i:29438441 original size:42 final size:41
Alignment explanation
Indices: 29438358--29438442 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
29438348 CATGTTATCA
* * * *
29438358 CATATCGATGCCACTGTCCTAGACAGGGTCTTATATGAAAT
1 CATATCGATGCCAATGTCCCAGACAGAGTCTTACATGAAAT
*
29438399 CATATACGATGCCAATGTCCCAGACATAGTCTTACACT-AAAT
1 CATAT-CGATGCCAATGTCCCAGACAGAGTCTTACA-TGAAAT
29438441 CA
1 CA
29438443 CACCTCGGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 5 0.14
42 31 0.84
43 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAGACAGAGTCTTACATGAAAT
Found at i:29450131 original size:7 final size:6
Alignment explanation
Indices: 29450115--29450139 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29450105 GCAATTTAGT
29450115 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
29450140 ATAACTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:29461264 original size:23 final size:23
Alignment explanation
Indices: 29461236--29461287 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
29461226 TTGATAAAGA
29461236 TTTTGAAATGTGCCATTGATGAT
1 TTTTGAAATGTGCCATTGATGAT
29461259 TTTTGAAATGTGCCATTGATGAT
1 TTTTGAAATGTGCCATTGATGAT
29461282 TTTTGA
1 TTTTGA
29461288 TAAAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTTGAAATGTGCCATTGATGAT
Found at i:29461985 original size:43 final size:42
Alignment explanation
Indices: 29461934--29462060 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
29461924 AGGAACTCTG
29461934 ATATGTGTTTTCATGTAAGACCACGTCTAGGACATTGGCATCGA
1 ATATGTGTTTTCATGTAAGACCACGTCT-GGACATTGGCATC-A
* * * *
29461978 CT-TGTGTTTACGTGTAAGACC-CTGTCTGGAACAGTGGCATCA
1 ATATGTGTTTTCATGTAAGACCAC-GTCTGG-ACATTGGCATCA
*
29462020 ATATGTGATTAT-ATGTAAGACCACGTCTGGGACATTGGCAT
1 ATATGTG-TTTTCATGTAAGACCACGTCT-GGACATTGGCAT
29462061 TGTACAAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
42 5 0.07
43 57 0.84
44 6 0.09
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATATGTGTTTTCATGTAAGACCACGTCTGGACATTGGCATCA
Found at i:29464767 original size:41 final size:40
Alignment explanation
Indices: 29464701--29464777 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
29464691 TATATTCGTG
* *
29464701 GCGTTTGGAAAAAAACGTCACTATTGCTCGACTTTTAGCA
1 GCGTTTGGAAAAAAACGCCACTATTGCTCAACTTTTAGCA
*
29464741 GCGTTTGGACAAAAAACGCCATTATTGCTCAACTTTT
1 GCGTTTGGA-AAAAAACGCCACTATTGCTCAACTTTT
29464778 TTGCGGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 9 0.27
41 24 0.73
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (40 bp):
GCGTTTGGAAAAAAACGCCACTATTGCTCAACTTTTAGCA
Found at i:29465360 original size:7 final size:7
Alignment explanation
Indices: 29465329--29465389 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
29465319 ACTAATTAAT
29465329 CTAAACC
1 CTAAACC
29465336 CTAAATCC
1 CTAAA-CC
*
29465344 CTATTA-C
1 CTA-AACC
29465351 CTAAACC
1 CTAAACC
*
29465358 CTAAATC
1 CTAAACC
* *
29465365 ATAAAAC
1 CTAAACC
*
29465372 ATAAACC
1 CTAAACC
29465379 CTAAACC
1 CTAAACC
29465386 CTAA
1 CTAA
29465390 TCATAAAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 1 0.02
7 37 0.84
8 5 0.11
9 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:29465398 original size:21 final size:20
Alignment explanation
Indices: 29465325--29465406 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
29465315 AAACACTAAT
29465325 TAATC-TAAACCCTAAATCCC
1 TAATCATAAACCCTAAA-CCC
* * * *
29465345 TATTACCTAAACCCTAAATCA
1 TAAT-CATAAACCCTAAACCC
*
29465366 TAAAACATAAACCCTAAACCC
1 T-AATCATAAACCCTAAACCC
* *
29465387 TAATCATAAAACATAAACCC
1 TAATCATAAACCCTAAACCC
29465407 CTAAACCCCA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 19 0.40
21 17 0.35
22 12 0.25
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (20 bp):
TAATCATAAACCCTAAACCC
Found at i:29465399 original size:27 final size:29
Alignment explanation
Indices: 29465350--29465414 Score: 116
Period size: 28 Copynumber: 2.3 Consensus size: 29
29465340 ATCCCTATTA
29465350 CCTAAACCCTAAATCATAAAACATAAA-C
1 CCTAAACCCTAAATCATAAAACATAAACC
29465378 CCTAAACCCT-AATCATAAAACATAAACC
1 CCTAAACCCTAAATCATAAAACATAAACC
29465406 CCTAAACCC
1 CCTAAACCC
29465415 CAACCCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 16 0.44
28 20 0.56
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (29 bp):
CCTAAACCCTAAATCATAAAACATAAACC
Found at i:29465451 original size:15 final size:15
Alignment explanation
Indices: 29465428--29465463 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29465418 CCCTTAAGCC
29465428 ATAAA-CCATAATCT
1 ATAAACCCATAATCT
*
29465442 GTAAACCCATAATCT
1 ATAAACCCATAATCT
29465457 ATAAACC
1 ATAAACC
29465464 TTAAAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAACCCATAATCT
Found at i:29466000 original size:40 final size:40
Alignment explanation
Indices: 29465955--29466338 Score: 208
Period size: 40 Copynumber: 9.6 Consensus size: 40
29465945 TTTTGCGACT
* * * *
29465955 TTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
*
29465995 TTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
* * * ** ** * * *
29466035 TTCTAATGCCACTAAAGC-TCGCGTTGTGCTTAATTTTTTTGCGGCG
1 TT-T--T-TCA-AAAAGCGCCGC-TAATGCTCGA-TCTATAGCGGCG
* * * *
29466081 TTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
*
29466121 TTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
* * *
29466161 TTTTTCAAAAAGCGTCGCTAATGC-C-A-CTAAAGC-TC-
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
**** * * ** ** * * * *
29466196 AACAT-AAAACGACGGCG-TTGTGCTTAATTTTTTTGCAGCG
1 TTTTTCAAAAAG-CGCCGCTAATGCTCGA-TCTATAGCGGCG
* * * * * *
29466236 TTTTTCGAAAAGCACCGCTAATGGTCAACCTATAGCGGCA
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
* * *
29466276 TTTTTCAAAAAGCTCCGCTAATGCTCAATCTATAGTGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
*
29466316 TTTTTCAAAAAGCGCTGCTAATG
1 TTTTTCAAAAAGCGCCGCTAATG
29466339 TCACTAAAGC
Statistics
Matches: 248, Mismatches: 79, Indels: 34
0.69 0.22 0.09
Matches are distributed among these distances:
34 9 0.04
35 5 0.02
36 2 0.01
37 6 0.02
38 4 0.02
39 2 0.01
40 166 0.67
41 21 0.08
42 4 0.02
43 2 0.01
44 4 0.02
45 12 0.05
46 11 0.04
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
Found at i:29466073 original size:126 final size:126
Alignment explanation
Indices: 29465929--29466162 Score: 450
Period size: 126 Copynumber: 1.9 Consensus size: 126
29465919 TAAAGCGACA
*
29465929 GCGTTGTGCTTAATTTTTTTGCGACTTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
1 GCGTTGTGCTTAATTTTTTTGCGACGTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
29465994 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTCTAATGCCACTAAAGCTC
66 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTCTAATGCCACTAAAGCTC
*
29466055 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
1 GCGTTGTGCTTAATTTTTTTGCGACGTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
29466120 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTT
66 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTT
29466163 TTTCAAAAAG
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 106 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (126 bp):
GCGTTGTGCTTAATTTTTTTGCGACGTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTCTAATGCCACTAAAGCTC
Found at i:29466248 original size:75 final size:75
Alignment explanation
Indices: 29466155--29466489 Score: 314
Period size: 75 Copynumber: 4.4 Consensus size: 75
29466145 TCGATCTATA
*
29466155 GCGGCGTTTTTCAAAAAGCGTCGCTAATGCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCT
29466220 TAATTTTTTT
66 TAATTTTTTT
* * * * * * *** * **
29466230 GCAGCGTTTTTCGAAAAGCACCGCTAATGGTCAACCTATAGCGGCATTTTTCAAAAAG-CTCCGC
1 GCGGCGTTTTTCAAAAAGCGCCGCTAAT-G-CCA-CTAAAGC-TCA-ACAT-AAAACGACGGCG-
** * * * *
29466294 TAATGCTCAA-TCTATA
59 TTGTGCTTAATTTTTTT
* * * **
29466310 GTGGCGTTTTTCAAAAAGCGCTGCTAATGTCACTAAAGCTCAACATAAAACGATAGCGTTGTGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCT
29466375 TAATTTTTTT
66 TAATTTTTTT
* * * ***
29466385 GCGGCGTTTTTCAAAAAGCGTCGCTAGTGCCACTAAAGTTCAACATAAAACGACGAAATTGTGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCT
29466450 TAATTTTTTT
66 TAATTTTTTT
*
29466460 GCGGCGTTTTTCAAGAAGCGCCGCTAATGC
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGC
29466490 TCGATCTATA
Statistics
Matches: 196, Mismatches: 55, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
74 12 0.06
75 121 0.62
76 3 0.02
77 8 0.04
78 7 0.04
79 3 0.02
80 30 0.15
81 12 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (75 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCT
TAATTTTTTT
Found at i:29466410 original size:155 final size:155
Alignment explanation
Indices: 29466055--29466410 Score: 588
Period size: 155 Copynumber: 2.3 Consensus size: 155
29466045 ACTAAAGCTC
*
29466055 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGGTCGACCTATAGCGGC
1 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGGTCAACCTATAGCGGC
*
29466120 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGC
66 ATTTTTCAAAAAGCGCCACTAATGCTCAATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGC
*
29466185 CACTAAAGCTCAACATAAAACGACG
131 CACTAAAGCTCAACATAAAACGACA
* *
29466210 GCGTTGTGCTTAATTTTTTTGCAGCGTTTTTCGAAAAGCACCGCTAATGGTCAACCTATAGCGGC
1 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGGTCAACCTATAGCGGC
* * *
29466275 ATTTTTCAAAAAGCTCCGCTAATGCTCAATCTATAGTGGCGTTTTTCAAAAAGCG-CTGCTAATG
66 ATTTTTCAAAAAGCGCCACTAATGCTCAATCTATAGCGGCGTTTTTCAAAAAGCGTC-GCTAATG
* *
29466339 TCACTAAAGCTCAACATAAAACGATA
130 CCACTAAAGCTCAACATAAAACGACA
* *
29466365 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCAAAAAGCGTCGCTA
1 GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTA
29466411 GTGCCACTAA
Statistics
Matches: 186, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
154 1 0.01
155 185 0.99
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (155 bp):
GCGTTGTGCTTAATTTTTTTGCGGCGTTTTTCGAAAAGCGCCGCTAATGGTCAACCTATAGCGGC
ATTTTTCAAAAAGCGCCACTAATGCTCAATCTATAGCGGCGTTTTTCAAAAAGCGTCGCTAATGC
CACTAAAGCTCAACATAAAACGACA
Found at i:29473250 original size:59 final size:58
Alignment explanation
Indices: 29473183--29473296 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
29473173 TGAATGAATA
* * * *
29473183 ATCATATTCTTGTTTAAGTATAAACTTACCTATTGTGAACTGTGATTGACAGGAAAATG
1 ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGA-TGACAAGAAAATG
* *
29473242 ATCATATTCTTGTTTGAGTATAGACTCACCTACTATGAACTGTGATGACAAGAAA
1 ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGATGACAAGAAA
29473297 CTTTGATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 9 0.18
59 40 0.82
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (58 bp):
ATCATATTCTTGTTTAAGTATAAACTCACCTACTATGAACTGTGATGACAAGAAAATG
Found at i:29474664 original size:19 final size:21
Alignment explanation
Indices: 29474642--29474680 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
29474632 CTGCTAAACC
29474642 ATTTCA-TTGCAT-TTAGTTT
1 ATTTCATTTGCATATTAGTTT
29474661 ATTTCATTTGCATATTAGTT
1 ATTTCATTTGCATATTAGTT
29474681 CTTAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
ATTTCATTTGCATATTAGTTT
Found at i:29476622 original size:25 final size:25
Alignment explanation
Indices: 29476547--29476661 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
29476537 ATTCATGTAT
* *
29476547 GCTCATACGAGCTCTAAATC-AGTAT
1 GCTCATACGAGCTGTAAATCGAG-AA
* * * *
29476572 GCTC-TCACGAGCTATGAATTGGGAA
1 GCTCAT-ACGAGCTGTAAATCGAGAA
29476597 GCTCATACGAGCTGTAAATCGAGAA
1 GCTCATACGAGCTGTAAATCGAGAA
** *
29476622 GCTCATGTGAGCTGTAAATCAAGAA
1 GCTCATACGAGCTGTAAATCGAGAA
29476647 GCTCATACGAGCTGT
1 GCTCATACGAGCTGT
29476662 GGTGTGTCCG
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
24 1 0.01
25 70 0.96
26 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGTAAATCGAGAA
Found at i:29481712 original size:138 final size:138
Alignment explanation
Indices: 29481484--29481747 Score: 456
Period size: 138 Copynumber: 1.9 Consensus size: 138
29481474 TTTCCAAAAC
* * *
29481484 AATATTAATTTCCCTGTCTTTTATATTTTGGCTGAAATTAATTAATATAATTGTTTATATTAATA
1 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATTAATA
*** *
29481549 AATTCGGTAAAATATATGTAATTAATATTTTGTATGAATTAAATTCATATATTAATTATATTTTT
66 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTT
29481614 TACCAAAG
131 TACCAAAG
29481622 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATTAATA
1 AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATTAATA
*
29481687 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTTATATATTAATTATAT
66 AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATAT
29481748 CTATGTTCTC
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 118 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.47
Consensus pattern (138 bp):
AATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATATAATTGTTTATATTAATA
AATTCGGTAAAATATAAACAATTAATATTTTGTATGAATCAAATTCATATATTAATTATATTTTT
TACCAAAG
Found at i:29485207 original size:27 final size:27
Alignment explanation
Indices: 29485130--29485236 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 27
29485120 GGGTTATGGG
* * *
29485130 TTAGGGATTTAAAAAATAAATCAGGGT
1 TTAGGGTTTTAAAAAATAAATTAAGGT
*
29485157 TTAGGAATTTTAAAAAAATAAATTAAGGT
1 TTAGG-GTTTT-AAAAAATAAATTAAGGT
29485186 TTAGGGTTTTAAAAAATAAATTAAATTAGGGT
1 TTAGGGTTTTAAAAAATAAATT--A--A-GGT
*
29485218 TTAGGGTTTTTAAAAATAA
1 TTAGGGTTTTAAAAAATAA
29485237 TTTTGTATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
27 17 0.25
28 7 0.10
29 21 0.31
31 1 0.01
32 21 0.31
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.36
Consensus pattern (27 bp):
TTAGGGTTTTAAAAAATAAATTAAGGT
Found at i:29485219 original size:32 final size:30
Alignment explanation
Indices: 29485143--29485236 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 30
29485133 GGGATTTAAA
* *
29485143 AAATAAATCAGGGTTTAGGAATTTT-AAAA-
1 AAATAAATTAGGGTTTAGG-GTTTTAAAAAT
*
29485172 AAATAAATTAAGGTTTAGGGTTTTAAAAAAT
1 AAATAAATTAGGGTTTAGGGTTTT-AAAAAT
29485203 AAATTAAATTAGGGTTTAGGGTTTTTAAAAAT
1 AAA-TAAATTAGGGTTTAGGG-TTTTAAAAAT
29485235 AA
1 AA
29485237 TTTTGTATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.07
29 17 0.30
30 4 0.07
31 3 0.05
32 24 0.43
33 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.17, T:0.35
Consensus pattern (30 bp):
AAATAAATTAGGGTTTAGGGTTTTAAAAAT
Found at i:29485557 original size:125 final size:123
Alignment explanation
Indices: 29485330--29485625 Score: 434
Period size: 125 Copynumber: 2.4 Consensus size: 123
29485320 TTTTTTCGTC
* * * *
29485330 CAGTAATTTCT-AAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTTC
1 CAGTAGTTTCTGAAAAAA-TAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
* * *
29485394 AAGCAGGATGCACTATCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGACGCTCTTTTTCT
65 AAGCAGGATGCACTACCAGCAAAAGTACTGAAAAAAGCTCCCAC-TGGACGCACTTTTT-T
*
29485455 ACAGTAGTTTCTG-TAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
1 -CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTC
*
29485519 AAGCAGGATGCACTACCAGCAAAAGTACTGAAAAAAGCTCCCACTTGACGCACTTTTTT
65 AAGCAGGATGCACTACCAGCAAAAGTACTGAAAAAAGCTCCCACTGGACGCACTTTTTT
* * *
29485578 TAGTAGTTTCTGAAAAAATAATTTTGAAAACACGGCTCTAAAAAAATA
1 CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATA
29485626 ATTTTGAGAA
Statistics
Matches: 155, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
122 11 0.07
123 33 0.21
124 12 0.08
125 85 0.55
126 14 0.09
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (123 bp):
CAGTAGTTTCTGAAAAAATAATTTTGAAAAGACGGTTCTAAAAAAATAGTGTCAAAAACACTTCA
AGCAGGATGCACTACCAGCAAAAGTACTGAAAAAAGCTCCCACTGGACGCACTTTTTT
Found at i:29485649 original size:28 final size:28
Alignment explanation
Indices: 29485585--29485653 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
29485575 TTTTAGTAGT
*
29485585 TTCTGAAAAAATAATTTTGAAAACACGG
1 TTCTGAAAAAATAATTTTGAAAACACAG
* * * *
29485613 CTCTAAAAAAATAATTTTGAGAAGACAG
1 TTCTGAAAAAATAATTTTGAAAACACAG
29485641 TTCTGAAAAAATA
1 TTCTGAAAAAATA
29485654 GTGTCAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (28 bp):
TTCTGAAAAAATAATTTTGAAAACACAG
Found at i:29489257 original size:18 final size:18
Alignment explanation
Indices: 29489236--29489271 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29489226 GAAAGGAAAC
* *
29489236 ATATAATGGTTAGGATAT
1 ATATAAGGGATAGGATAT
29489254 ATATAAGGGATAGGATAT
1 ATATAAGGGATAGGATAT
29489272 GCACTTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
ATATAAGGGATAGGATAT
Found at i:29492076 original size:25 final size:25
Alignment explanation
Indices: 29492047--29492103 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
29492037 CATATGTTAG
29492047 TAATCGACATTAGAGTGGCATCTGT
1 TAATCGACATTAGAGTGGCATCTGT
*
29492072 TAATCGACATTAGCGTGGCATCTGT
1 TAATCGACATTAGAGTGGCATCTGT
29492097 TAA-CGAC
1 TAATCGAC
29492104 CATGTCAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (25 bp):
TAATCGACATTAGAGTGGCATCTGT
Found at i:29493212 original size:24 final size:22
Alignment explanation
Indices: 29493174--29493219 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
29493164 ATTGAAAAAC
29493174 CTAAAAAAATAAAAAGTATAAA
1 CTAAAAAAATAAAAAGTATAAA
*
29493196 CTAAAAAAATTACAAAATTATAAA
1 CTAAAAAAA-TA-AAAAGTATAAA
29493220 AAGATTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 10 0.48
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
CTAAAAAAATAAAAAGTATAAA
Found at i:29493226 original size:11 final size:10
Alignment explanation
Indices: 29493209--29493254 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
29493199 AAAAAATTAC
29493209 AAAATTATAA
1 AAAATTATAA
*
29493219 AAAGATTACAA
1 AAA-ATTATAA
29493230 AAAATTAT-A
1 AAAATTATAA
*
29493239 TAAA-TATAA
1 AAAATTATAA
29493248 AAAATTA
1 AAAATTA
29493255 CTAATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
8 3 0.10
9 8 0.28
10 9 0.31
11 9 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATTATAA
Found at i:29493232 original size:29 final size:28
Alignment explanation
Indices: 29493199--29493255 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
29493189 GTATAAACTA
29493199 AAAAAATTACA-AAATTATAAAAAGATTAC
1 AAAAAATTACATAAA-TATAAAAA-ATTAC
*
29493228 AAAAAATTATATAAATATAAAAAATTAC
1 AAAAAATTACATAAATATAAAAAATTAC
29493256 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 18 0.69
30 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAAAATTACATAAATATAAAAAATTAC
Found at i:29493799 original size:9 final size:9
Alignment explanation
Indices: 29493775--29493817 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
29493765 TTTTAAAAAG
29493775 TTTTAACATAT
1 TTTTAA-AT-T
29493786 TTTTAAATT
1 TTTTAAATT
29493795 TTTTAAATT
1 TTTTAAATT
*
29493804 TATTTATATT
1 T-TTTAAATT
29493814 TTTT
1 TTTT
29493818 TGTAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 14 0.47
10 10 0.33
11 6 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAAATT
Found at i:29497581 original size:18 final size:19
Alignment explanation
Indices: 29497560--29497601 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
29497550 AATTAATTTT
29497560 TATATGTAAAC-TGTAATC
1 TATATGTAAACTTGTAATC
* *
29497578 TATATTTATACTTGTAATC
1 TATATGTAAACTTGTAATC
*
29497597 AATAT
1 TATAT
29497602 TGAATTGGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (19 bp):
TATATGTAAACTTGTAATC
Found at i:29498994 original size:21 final size:21
Alignment explanation
Indices: 29498935--29498995 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
29498925 TTTTATTATA
*
29498935 TAATA-ATTAAATTTATATTT
1 TAATACATTATATTTATATTT
* *
29498955 GATATACATT-TATAATATATTT
1 TA-ATACATTATAT-TTATATTT
29498977 TAATACATTATATTTATAT
1 TAATACATTATATTTATAT
29498996 CAATAATCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 1 0.03
21 17 0.53
22 14 0.44
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATACATTATATTTATATTT
Found at i:29500474 original size:196 final size:197
Alignment explanation
Indices: 29500186--29500556 Score: 480
Period size: 196 Copynumber: 1.9 Consensus size: 197
29500176 AAACTAAAAC
* *
29500186 ATAGAGATTAAATTTCAAAATTGAGCATAACATAGGGACCAAAATTGAAATTTAACCATTGTTAT
1 ATAGAGATTAAATTTCAAAATTAAGCATAACATAGGGACCAAAATTGAAATTTAACCATTATTAT
* * **
29500251 ATAATTCGAAAGAAAAGAAAAAAGGTTGTGTATTTGGA-ATGTGTACGTCAAAATTTTAATTACA
66 ATAATTCGAAAGAAAAGAAAAAAGGTTGTGTATTTGGACATGCGCACGTCAAAATTTTAACCACA
* * *
29500315 ATAATGTATTTATACTAACAGTGACATTATAAAAGTTAAGGTACCGAATTATGTAAAAAATTAAA
131 ATAACGTATTTAGACTAACAATGACATTATAAAAGTTAAGGTACCGAATTATGTAAAAAATTAAA
29500380 GT
196 GT
* * * * * *
29500382 ATAGAGATTAAATTTCAAATTTAAGCATAATATAGGGACCAAAATTGGAATTTGACTATTATTGT
1 ATAGAGATTAAATTTCAAAATTAAGCATAACATAGGGACCAAAATTGAAATTTAACCATTATTAT
* * *
29500447 ATAATCTC-AAA-AATTAAG-TAAAAGGTTGTGTATTTGGACATGCGCACGTCAACATTTTAGCC
66 ATAAT-TCGAAAGAA--AAGAAAAAAGGTTGTGTATTTGGACATGCGCACGTCAAAATTTTAACC
* ** * *
29500509 AGAATGGCGTATTTAGATTAACAATGACATTATAAAAGTTGAGGTACC
128 ACAATAACGTATTTAGACTAACAATGACATTATAAAAGTTAAGGTACC
29500557 TGATGTTCCG
Statistics
Matches: 148, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
195 2 0.01
196 84 0.57
197 62 0.42
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (197 bp):
ATAGAGATTAAATTTCAAAATTAAGCATAACATAGGGACCAAAATTGAAATTTAACCATTATTAT
ATAATTCGAAAGAAAAGAAAAAAGGTTGTGTATTTGGACATGCGCACGTCAAAATTTTAACCACA
ATAACGTATTTAGACTAACAATGACATTATAAAAGTTAAGGTACCGAATTATGTAAAAAATTAAA
GT
Found at i:29502753 original size:23 final size:23
Alignment explanation
Indices: 29502727--29502772 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29502717 AAAAATCACA
29502727 CATAGT-GTGCCTTTACATATAAT
1 CATAGTCGTGCCTTTACAT-TAAT
* *
29502750 CATAGTCTTTCCTTTACATTAAT
1 CATAGTCGTGCCTTTACATTAAT
29502773 GCTCACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (23 bp):
CATAGTCGTGCCTTTACATTAAT
Found at i:29508928 original size:30 final size:30
Alignment explanation
Indices: 29508892--29508954 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
29508882 ATTTATTTTA
29508892 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
29508922 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
29508952 TTG
1 TTG
29508955 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:29509073 original size:18 final size:18
Alignment explanation
Indices: 29509037--29509075 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29509027 GAAATATTTA
*
29509037 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTATAGTAT
29509055 TTTTGATGTATTATA-TAT
1 TTTTGATGT-TTATAGTAT
29509073 TTT
1 TTT
29509076 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTGATGTTTATAGTAT
Found at i:29509099 original size:12 final size:12
Alignment explanation
Indices: 29509076--29509109 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29509066 TATATATTTT
29509076 AAAATT-ATATA
1 AAAATTAATATA
29509087 AAAATTAATATA
1 AAAATTAATATA
29509099 AAAATTAATAT
1 AAAATTAATAT
29509110 GGGCGGGCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:29509656 original size:30 final size:31
Alignment explanation
Indices: 29509622--29509687 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
29509612 TAAAATTTCA
29509622 AAATTCAAAATGTA-AGGGACTAAAATGGA-C
1 AAATTCAAAA-GTACAGGGACTAAAATGGATC
* * *
29509652 AAATTCAAAAGTACAGTGATTAAAATTGATC
1 AAATTCAAAAGTACAGGGACTAAAATGGATC
29509683 AAATT
1 AAATT
29509688 AAAGTATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 22 0.71
31 6 0.19
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (31 bp):
AAATTCAAAAGTACAGGGACTAAAATGGATC
Found at i:29510899 original size:23 final size:23
Alignment explanation
Indices: 29510852--29510903 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29510842 AACTATTTTT
*
29510852 TTATTTTAATTGCATACTTATTA
1 TTATTTTAATTGCATACTTACTA
29510875 TTATTTTCAATT-CATACGTT-CTA
1 TTATTTT-AATTGCATAC-TTACTA
29510898 TTATTT
1 TTATTT
29510904 ATTATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATTTTAATTGCATACTTACTA
Found at i:29518969 original size:14 final size:14
Alignment explanation
Indices: 29518950--29518986 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29518940 AATTTTCCTC
29518950 TTCTCTCTTTT-TT
1 TTCTCTCTTTTCTT
29518963 GTTCTCTCTTTTCTT
1 -TTCTCTCTTTTCTT
29518978 TTCT-TCTTT
1 TTCTCTCTTT
29518987 CGATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (14 bp):
TTCTCTCTTTTCTT
Found at i:29519790 original size:33 final size:33
Alignment explanation
Indices: 29519744--29519818 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
29519734 AGCTCCAAAG
* * *
29519744 TGTTCCCACCATAATGCCGTTCCAAAAGTTAGT
1 TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
* * *
29519777 TGTTCCTAACATAATATCGTTCCCAAGGTTAGT
1 TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
29519810 TGTTCCTAA
1 TGTTCCTAA
29519819 GATTACTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTTCCTAACATAATACCGTTCCAAAAGTTAGT
Found at i:29521555 original size:52 final size:53
Alignment explanation
Indices: 29521476--29521589 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 53
29521466 AAGGGGCTCT
* *
29521476 GTTTTTCGTGAACTTGGTTCGAATATCTTTGTTGACTCTG-TTTTTTGGGTTTC
1 GTTTTT-GTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
*
29521529 GTTTTTGTGAACTTGCTTCGACTATCTTTGTTGACTCCGTTTTTTTGGGTTTC
1 GTTTTTGTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
29521582 GTTTTTGT
1 GTTTTTGT
29521590 TTCTTTTTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 30 0.53
53 27 0.47
ACGTcount: A:0.10, C:0.14, G:0.22, T:0.54
Consensus pattern (53 bp):
GTTTTTGTGAACTTGCTTCGAATATCTTTGTTGACTCCGTTTTTTTGGGTTTC
Found at i:29525847 original size:13 final size:14
Alignment explanation
Indices: 29525822--29525850 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29525812 GAGTAATTTT
29525822 AAAAATTATATTAA
1 AAAAATTATATTAA
29525836 AAAAATTA-ATTAA
1 AAAAATTATATTAA
29525849 AA
1 AA
29525851 TTTATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTATATTAA
Found at i:29534525 original size:20 final size:20
Alignment explanation
Indices: 29534474--29534527 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
29534464 TGGATTGTTT
29534474 AAAAATTATAAATAAATTAGA
1 AAAAATTATAAAT-AATTAGA
* *
29534495 AGAGATATATAAAT-ATTAGA
1 AAAAAT-TATAAATAATTAGA
29534515 GAAAAATTATAAA
1 -AAAAATTATAAA
29534528 AAGATTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.44
21 8 0.30
22 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAATAATTAGA
Found at i:29534929 original size:11 final size:11
Alignment explanation
Indices: 29534915--29534940 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29534905 TTATTTTTAA
29534915 TTTTAAAATAC
1 TTTTAAAATAC
29534926 TTTTAAAATAC
1 TTTTAAAATAC
29534937 TTTT
1 TTTT
29534941 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:29535411 original size:17 final size:18
Alignment explanation
Indices: 29535383--29535417 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
29535373 TTTATTTATT
29535383 TATTTATAATTTTTAAAA
1 TATTTATAATTTTTAAAA
29535401 TATTTAT-ATTTTTAAAA
1 TATTTATAATTTTTAAAA
29535418 CAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATAATTTTTAAAA
Found at i:29535423 original size:18 final size:18
Alignment explanation
Indices: 29535384--29535423 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
29535374 TTATTTATTT
*
29535384 ATTTATAATTTTTAAAAT
1 ATTTATAATTTTTAAAAA
29535402 ATTTAT-ATTTTTAAAACA
1 ATTTATAATTTTTAAAA-A
29535420 ATTT
1 ATTT
29535424 TTTAGAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATAATTTTTAAAAA
Found at i:29559875 original size:5 final size:5
Alignment explanation
Indices: 29559865--29559903 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
29559855 TCCTAGGATG
* *
29559865 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
29559904 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:29571408 original size:20 final size:20
Alignment explanation
Indices: 29571383--29571424 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
29571373 ATTTATTGTT
29571383 GAACATTACTCACCTGTTGA
1 GAACATTACTCACCTGTTGA
29571403 GAACATTACTCACCTGTTGA
1 GAACATTACTCACCTGTTGA
29571423 GA
1 GA
29571425 GCTGTGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (20 bp):
GAACATTACTCACCTGTTGA
Found at i:29579980 original size:11 final size:11
Alignment explanation
Indices: 29579964--29579991 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29579954 AATCCATTTA
29579964 CCAAATTATCT
1 CCAAATTATCT
29579975 CCAAATTATCT
1 CCAAATTATCT
29579986 CCAAAT
1 CCAAAT
29579992 ATCCTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (11 bp):
CCAAATTATCT
Found at i:29580592 original size:19 final size:20
Alignment explanation
Indices: 29580560--29580597 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
29580550 TCCTAGATAT
*
29580560 TTTTTAAAATTTTATAATAA
1 TTTTTAAAATTTTAGAATAA
*
29580580 TTTTTCAAA-TTTAGAATA
1 TTTTTAAAATTTTAGAATA
29580598 GGGGACCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTTAAAATTTTAGAATAA
Found at i:29592524 original size:28 final size:28
Alignment explanation
Indices: 29592493--29592560 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
29592483 AAGAAATTAC
29592493 ATTAAGTTAATTTA-GATTAATTAATTTA
1 ATTAAGTTAATTTAGGA-TAATTAATTTA
*
29592521 ATTATA-TTATTTTAGGATAATTAATTTA
1 ATTA-AGTTAATTTAGGATAATTAATTTA
29592549 ATT-AGTTTAATT
1 ATTAAG-TTAATT
29592561 AATAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.03
28 30 0.88
29 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTAAGTTAATTTAGGATAATTAATTTA
Found at i:29601132 original size:29 final size:29
Alignment explanation
Indices: 29601096--29601170 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
29601086 CTATGAAGTG
* *
29601096 AAGCCTTTATGGCGATCACTATTAAATGA
1 AAGCCTTTGTGGCGATCACTATTAAATAA
* * *
29601125 AAGCCTTTGTGACAATCTCTATTAAATAA
1 AAGCCTTTGTGGCGATCACTATTAAATAA
*
29601154 AAGCCTTTGTGGGGATC
1 AAGCCTTTGTGGCGATC
29601171 TCTGAAAGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (29 bp):
AAGCCTTTGTGGCGATCACTATTAAATAA
Found at i:29601171 original size:29 final size:29
Alignment explanation
Indices: 29601071--29601223 Score: 108
Period size: 26 Copynumber: 5.6 Consensus size: 29
29601061 CGTATAAGTG
* * *
29601071 AGCCTTTGT-G-GATATCTATGAAGTG-A
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* *
29601097 AGCCTTTATGGCGATCACTATTAAATGAA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* * *
29601126 AGCCTTTGTGACAATCTCTATTAAATAAA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* * *
29601155 AGCCTTTGTGGGGATCTC--TGAAA-GGA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
* * *
29601181 AGCCTTTGTGGGGATCTC--TGAAA-GGA
1 AGCCTTTGTGGCGATCTCTATTAAATGAA
*
29601207 AGCCTTTGTGGCTATCT
1 AGCCTTTGTGGCGATCT
29601224 TAGCTAAATG
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
26 50 0.47
27 5 0.05
28 11 0.10
29 40 0.38
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (29 bp):
AGCCTTTGTGGCGATCTCTATTAAATGAA
Found at i:29606675 original size:26 final size:26
Alignment explanation
Indices: 29606600--29606675 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
29606590 GGTTATATTT
* *
29606600 AATGGCTATACGAAATAAATATATGA
1 AATGGTTATACGAAATAATTATATGA
** * * *
29606626 AATGGTTGCACAAAATACTAATATGA
1 AATGGTTATACGAAATAATTATATGA
* *
29606652 GATGGTTATACGAAATAGTTATAT
1 AATGGTTATACGAAATAATTATAT
29606676 AATTGGGTAT
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (26 bp):
AATGGTTATACGAAATAATTATATGA
Found at i:29617330 original size:14 final size:13
Alignment explanation
Indices: 29617311--29617349 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
29617301 AATTTCCAAA
29617311 TTTTCAAATTAAGG
1 TTTTCAAATTAA-G
29617325 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
29617339 CTTTCAAATTA
1 TTTTCAAATTA
29617350 CAAATACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:29621672 original size:21 final size:21
Alignment explanation
Indices: 29621648--29621703 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
29621638 ATGAACAATT
*
29621648 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
29621669 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
29621689 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
29621704 CGATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:29621689 original size:20 final size:23
Alignment explanation
Indices: 29621659--29621703 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
29621649 AGAAAAAGAG
29621659 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
29621680 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
29621702 AA
1 AA
29621704 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:29624543 original size:27 final size:29
Alignment explanation
Indices: 29624513--29624702 Score: 128
Period size: 32 Copynumber: 5.8 Consensus size: 29
29624503 GAAATAATAC
29624513 ATGAACAGGAGAGATTCCCTGCAAGAAATG
1 ATGAACAGGAGAGATTCCCTGCAAGAAA-G
29624543 ATGTGAACAGGAGAGATTCCCTGCAAGAAATG
1 A--TGAACAGGAGAGATTCCCTGCAAGAAA-G
* *
29624575 ATGTGAACAGGAAAGATTCCCTGCAACAAAATAATG
1 A--TGAACAGGAGAGATTCCCTG---CAAGA-AA-G
* *
29624611 TGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
1 -ATGAACAGGAGAGATTCCCTG---CAAGA-AA-G
* *
29624646 CGTGAACAGGAGAGATTCCCTACAAGAAATG
1 -ATGAACAGGAGAGATTCCCTGCAAGAAA-G
*
29624677 ATGTGAACAGGAAAGATTCCCTGCAA
1 A--TGAACAGGAGAGATTCCCTGCAA
29624703 CAGAATAATG
Statistics
Matches: 141, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.01
31 4 0.03
32 76 0.54
35 56 0.40
36 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.18
Consensus pattern (29 bp):
ATGAACAGGAGAGATTCCCTGCAAGAAAG
Found at i:29624627 original size:35 final size:35
Alignment explanation
Indices: 29624514--29624742 Score: 262
Period size: 35 Copynumber: 6.8 Consensus size: 35
29624504 AAATAATACA
* *
29624514 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
* *
29624546 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
*
29624578 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
*
29624613 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
*
29624648 TGAACAGGAGAGATTCCCT---ACAAGA-AATGATG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATG-TG
* * *
29624680 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
* * *
29624715 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAACAAAA
29624743 GACAAGTGAA
Statistics
Matches: 175, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
31 4 0.02
32 78 0.45
33 5 0.03
35 84 0.48
36 4 0.02
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (35 bp):
TGAACAGGAGAGATTCCCTGCAACAAAATAATGTG
Found at i:29624632 original size:67 final size:68
Alignment explanation
Indices: 29624504--29624742 Score: 260
Period size: 67 Copynumber: 3.5 Consensus size: 68
29624494 GTCCAAAAAG
* * * *
29624504 AAATAATACATGAACAGGAGAGATTCCCTGCAA-GAAATGA--TGTGAACAGGAGAGATTCCCTG
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTG
*
29624566 CAAG
65 CAAA
*
29624570 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGC
1 AAATAATCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGC
29624634 AACA
66 AA-A
* * *
29624638 AAATAATGCGTGAACAGGAGAGATTCCCT---ACAAGA-AATGATGTGAACAGGAAAGATTCCCT
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAACAAAATAATG-TGTGAACAGGAGAGATTCCCT
29624699 GCAACA
64 GCAA-A
* * *
29624705 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AAATAAT-CGTGAACAGGAAAGATTCCCTGCAACAAAA
29624743 GACAAGTGAA
Statistics
Matches: 148, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
64 22 0.15
65 5 0.03
66 10 0.07
67 82 0.55
68 6 0.04
70 23 0.16
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (68 bp):
AAATAATCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGC
AAA
Found at i:29624677 original size:102 final size:99
Alignment explanation
Indices: 29624504--29624742 Score: 361
Period size: 102 Copynumber: 2.4 Consensus size: 99
29624494 GTCCAAAAAG
* * * * *
29624504 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTACAA
29624569 GAAATGATGTGAACAGGAAAGATTCCCTGCAACA
66 GAAATGATGTGAACAGGAAAGATTCCCTGCAACA
*
29624603 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-AAAATAAT--GTGAACAGGAGAGATTCCCTA
29624668 CAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACA
63 CAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACA
* * *
29624705 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-AAAA
29624743 GACAAGTGAA
Statistics
Matches: 126, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
99 30 0.24
100 6 0.05
102 90 0.71
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (99 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTACAA
GAAATGATGTGAACAGGAAAGATTCCCTGCAACA
Found at i:29625007 original size:13 final size:13
Alignment explanation
Indices: 29624989--29625026 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
29624979 AATTTCCAAA
29624989 TTTTCAAATTAAG
1 TTTTCAAATTAAG
29625002 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
29625016 CTTTCAAATTA
1 TTTTCAAATTA
29625027 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:29633768 original size:68 final size:72
Alignment explanation
Indices: 29633684--29633838 Score: 228
Period size: 68 Copynumber: 2.2 Consensus size: 72
29633674 ACTTAGGTAA
*
29633684 TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTCTATTATAAGTATATTCTACAGG-CC-CA
1 TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTCTATTACAAGTATATTCTACAGGACCACA
29633747 C-AC-GC
66 CAACAGC
* * * *
29633752 TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTTTATTACAAGTCTCTTCTATAGGACCACA
1 TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTCTATTACAAGTATATTCTACAGGACCACA
29633817 CAAACAGC
66 C-AACAGC
29633825 TGTTTGGTTCAATG
1 TGTTTGGTTCAATG
29633839 GAATACCCTA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
68 54 0.70
69 2 0.03
70 3 0.04
72 2 0.03
73 16 0.21
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (72 bp):
TGTTTGGTTCAATGTAATGGCTATGCCATTACAAGTCTATTACAAGTATATTCTACAGGACCACA
CAACAGC
Found at i:29647243 original size:50 final size:50
Alignment explanation
Indices: 29647098--29647393 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
29647088 ATTTGGGTAA
* * * *
29647098 AGAGATCCCATGTAAGACCATGTCTAGGACATGGTATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
29647154 AGAGGTCCCATGTAAGA-CATGTCTAGGACATGGCATTGGCACCGAGGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
29647203 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
29647253 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
29647303 AGAACTCCCATGTAAGACCATTTCTGGGATATGGCATTGGTA--GTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
29647352 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29647394 TGTTATTATC
Statistics
Matches: 203, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
49 57 0.28
50 103 0.51
52 3 0.01
54 1 0.00
55 23 0.11
56 16 0.08
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:29649431 original size:26 final size:25
Alignment explanation
Indices: 29649401--29649451 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
29649391 ATTTTTTTAT
*
29649401 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATA-ATAACAATAA
*
29649427 TTTTATTAAAATTTAATAACAATAA
1 TTTTATTAAAATATAATAACAATAA
29649452 CAATAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTATTAAAATATAATAACAATAA
Found at i:29649641 original size:16 final size:16
Alignment explanation
Indices: 29649616--29649657 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
29649606 ATTGCAGTTT
* *
29649616 TATTCCATTACAGCTC
1 TATTCCATTACAACCC
*
29649632 TATTCAATTACAACCC
1 TATTCCATTACAACCC
29649648 TATTCCATTA
1 TATTCCATTA
29649658 TAGTGAACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.38
Consensus pattern (16 bp):
TATTCCATTACAACCC
Found at i:29651151 original size:56 final size:55
Alignment explanation
Indices: 29651004--29651153 Score: 178
Period size: 53 Copynumber: 2.7 Consensus size: 55
29650994 AAGGGGGTGT
* * ** * *
29651004 TAGGATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAGTGGGATTTTG
1 TAGGATATTATTATGGAAT-TTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
* ** *
29651060 TAAGATATTATTAT-GAA-TTATCCCTTAGCAATTTGATTCTTAATCAGATATTA
1 TAGGATATTATTATGGAATTTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
29651113 TAGGATATTATTATGGAATGTTATCTTTTAGCAATTTGATT
1 TAGGATATTATTATGGAAT-TTATCTTTTAGCAATTTGATT
29651154 TCTACATAAC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
53 41 0.53
54 3 0.04
55 2 0.03
56 32 0.41
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (55 bp):
TAGGATATTATTATGGAATTTATCTTTTAGCAATTTGATTCCTAATCAGATATTA
Found at i:29658605 original size:31 final size:31
Alignment explanation
Indices: 29658559--29658635 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
29658549 ATAATAAAAC
* * *
29658559 AATCATTGAACTATTTAAGAATTTTTATTTA
1 AATCATTAAATTATTTAAAAATTTTTATTTA
*
29658590 AATTATTAAATTATTTAAAAATTTTTATTTA
1 AATCATTAAATTATTTAAAAATTTTTATTTA
* *
29658621 AGTCATTAGATTATT
1 AATCATTAAATTATT
29658636 AACTTTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (31 bp):
AATCATTAAATTATTTAAAAATTTTTATTTA
Found at i:29660744 original size:48 final size:48
Alignment explanation
Indices: 29660674--29660847 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
29660664 ATCAGTGTGA
29660674 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
29660722 TGTGATATGTGATTTTCATGTAAGACCATATCTAGGATATGGCATCAG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
29660770 TGTGATATGTG-TTTTCGTGTAAGACCATAGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
***
29660817 TATGTGATATGTGACGAT-GTGTAAGACCATA
1 --TGTGATATGTGATTTTCGTGTAAGACCATA
29660848 GTTATACTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 30 0.27
48 56 0.50
49 24 0.22
50 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
Found at i:29661956 original size:48 final size:48
Alignment explanation
Indices: 29661886--29662059 Score: 235
Period size: 48 Copynumber: 3.6 Consensus size: 48
29661876 ATCAGTGTGA
29661886 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
29661934 TGTGATATGTGATTTTCATGTAAGACCATATCTAGGATATGGCATCAG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
* * *
29661982 TGTGATATGTG-TTTTCGTGTAAGACCATAGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
***
29662029 TATGTGATATGTGACGAT-GTGTAAGACCATA
1 --TGTGATATGTGATTTTCGTGTAAGACCATA
29662060 GTTATACTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 30 0.27
48 56 0.50
49 24 0.22
50 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATGGCATCGG
Found at i:29664683 original size:15 final size:16
Alignment explanation
Indices: 29664658--29664687 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29664648 TGTGTGGTTA
29664658 TAATAAAATATATATT
1 TAATAAAATATATATT
29664674 TAAT-AAATATATAT
1 TAATAAAATATATAT
29664688 ACATTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAAATATATATT
Found at i:29664708 original size:20 final size:20
Alignment explanation
Indices: 29664658--29664712 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
29664648 TGTGTGGTTA
29664658 TAATAAA-ATATAT-A-TT-
1 TAATAAATATATATAATTTG
29664674 TAATAAATATATATACATTTG
1 TAATAAATATATATA-ATTTG
*
29664695 TAAT-AATATGTATAATTT
1 TAATAAATATATATAATTT
29664713 ACTTATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
19 5 0.15
20 11 0.33
21 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (20 bp):
TAATAAATATATATAATTTG
Found at i:29671004 original size:24 final size:24
Alignment explanation
Indices: 29670889--29671017 Score: 89
Period size: 25 Copynumber: 5.2 Consensus size: 24
29670879 ACTTGTAAAC
* * * *
29670889 GGGAAGCTCTTTCGAGCCATAAACC
1 GGGAAGCTCATACGAGCCATTAA-T
**
29670914 GGGAAGCTCATGTGAGCCATGTAAT
1 GGGAAGCTCATACGAGCCAT-TAAT
* ** *
29670939 AGGAAGCTCATGTGAGCCATGTAAC
1 GGGAAGCTCATACGAGCCAT-TAAT
* * *
29670964 GAGAAGCT-TTAGAGAGCCATTAAT
1 GGGAAGCTCATA-CGAGCCATTAAT
*
29670988 GGGAAGCTCATACGAGCCAATAAT
1 GGGAAGCTCATACGAGCCATTAAT
29671012 GGGAAG
1 GGGAAG
29671018 TTCAAGTGAG
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
24 27 0.32
25 55 0.65
26 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.20
Consensus pattern (24 bp):
GGGAAGCTCATACGAGCCATTAAT
Found at i:29671093 original size:25 final size:25
Alignment explanation
Indices: 29670976--29671127 Score: 75
Period size: 25 Copynumber: 6.2 Consensus size: 25
29670966 GAAGCTTTAG
29670976 AGAGCC-ATTAAT-GGGAAGCTCATA
1 AGAGCCAATT-ATCGGGAAGCTCATA
* * *
29671000 CGAGCCAATAAT-GGGAAGTTCA-A
1 AGAGCCAATTATCGGGAAGCTCATA
* * * *
29671023 GTGAGGC-AGTATCGGGAAGCTCCAGA
1 -AGAGCCAATTATCGGGAAGCT-CATA
** *
29671049 A-AGCC-ATTAATCAAGTAGCTCATA
1 AGAGCCAATT-ATCGGGAAGCTCATA
* * **
29671073 AGATCCAGTTATCGGGAAGCTCCGA
1 AGAGCCAATTATCGGGAAGCTCATA
* *
29671098 AGAGCCAATTATCGGGACGCTTATA
1 AGAGCCAATTATCGGGAAGCTCATA
29671123 AGAGC
1 AGAGC
29671128 TTCTATGTGT
Statistics
Matches: 92, Mismatches: 28, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
23 4 0.04
24 36 0.39
25 49 0.53
26 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
AGAGCCAATTATCGGGAAGCTCATA
Found at i:29683241 original size:45 final size:44
Alignment explanation
Indices: 29683188--29683321 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 44
29683178 AGTGATACTC
* * *
29683188 GGTGGAATCAGCACATAGCAACCACCTTCATAATCAATAGTACCT
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACCT
*
29683233 GGTGGAATCAGCACACAATAACCACCTTTATAATCAATGATACCT
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCT
*
29683278 GGTGGAATCAACACACAACAACCACCTTTATAATCAATGGTACC
1 GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACC
29683322 CGGTACACGT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.01
45 79 0.98
46 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.22
Consensus pattern (44 bp):
GGTGGAATCAGCACACAACAACCACCTTTATAATCAATGTACCT
Found at i:29692463 original size:25 final size:23
Alignment explanation
Indices: 29692408--29692453 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29692398 GACTTAGGTC
29692408 ACACGGCCAAGTCACACACCCGT
1 ACACGGCCAAGTCACACACCCGT
29692431 ACACGGCCAAGTCACACACCCGT
1 ACACGGCCAAGTCACACACCCGT
29692454 GTGCTAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.43, G:0.17, T:0.09
Consensus pattern (23 bp):
ACACGGCCAAGTCACACACCCGT
Found at i:29693623 original size:25 final size:24
Alignment explanation
Indices: 29693580--29693674 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 24
29693570 AAAGCTCTTT
* *
29693580 CGAGCCATATACCGAGAAGCTTATA
1 CGAGCCAT-TAACGGGAAGCTTATA
* *
29693605 CGAACCATGTAACGGGAAGCTCTAGA
1 CGAGCCAT-TAACGGGAAGCT-TATA
*
29693631 -GAGCCATTAACGGGAAGCTCATA
1 CGAGCCATTAACGGGAAGCTTATA
*
29693654 CGAGCCAATTATCGGGAAGCT
1 CGAGCC-ATTAACGGGAAGCT
29693675 CTGAAGAGCC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 2 0.03
24 17 0.29
25 36 0.62
26 3 0.05
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (24 bp):
CGAGCCATTAACGGGAAGCTTATA
Found at i:29693670 original size:49 final size:50
Alignment explanation
Indices: 29693581--29693685 Score: 126
Period size: 49 Copynumber: 2.1 Consensus size: 50
29693571 AAGCTCTTTC
* *
29693581 GAGCCATATACCGAGAAGCTTATACGAACCATGTAACGGGAAGCTCT-AGA
1 GAGCCATATAACGAGAAGCTCATACGAACCATGTAACGGGAAGCTCTGA-A
* * *
29693631 GAGCCAT-TAACGGGAAGCTCATACGAGCCAAT-TATCGGGAAGCTCTGAA
1 GAGCCATATAACGAGAAGCTCATACGAACC-ATGTAACGGGAAGCTCTGAA
29693680 GAGCCA
1 GAGCCA
29693686 ATTATTGGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
49 38 0.79
50 10 0.21
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (50 bp):
GAGCCATATAACGAGAAGCTCATACGAACCATGTAACGGGAAGCTCTGAA
Found at i:29693675 original size:25 final size:23
Alignment explanation
Indices: 29693609--29693685 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 23
29693599 CTTATACGAA
29693609 CCATGTAACGGGAAGCTCTAGAGAG
1 CCAT-TAACGGGAAGCTCTA-AGAG
*
29693634 CCATTAACGGGAAGCTCATACGAG
1 CCATTAACGGGAAGCTC-TAAGAG
*
29693658 CCAATTATCGGGAAGCTCTGAAGAG
1 CC-ATTAACGGGAAGCTCT-AAGAG
29693683 CCA
1 CCA
29693686 ATTATTGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 20 0.43
25 26 0.57
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.17
Consensus pattern (23 bp):
CCATTAACGGGAAGCTCTAAGAG
Found at i:29693686 original size:25 final size:24
Alignment explanation
Indices: 29693617--29693695 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 24
29693607 AACCATGTAA
*
29693617 CGGGAAGCTCTAGAGAGCC-ATTAA
1 CGGGAAGCTCTA-AGAGCCAATTAT
*
29693641 CGGGAAGCTCATACGAGCCAATTAT
1 CGGGAAGCTC-TAAGAGCCAATTAT
29693666 CGGGAAGCTCTGAAGAGCCAATTAT
1 CGGGAAGCTCT-AAGAGCCAATTAT
*
29693691 TGGGA
1 CGGGA
29693696 TGCTTATAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 16 0.33
25 32 0.67
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCTAAGAGCCAATTAT
Found at i:29693786 original size:24 final size:25
Alignment explanation
Indices: 29693759--29693805 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29693749 GGATGCTCCG
*
29693759 AAGAGCTAT-TAACGAGAAGCTCAC
1 AAGAGCCATATAACGAGAAGCTCAC
*
29693783 AAGAGCCATATAACGGGAAGCTC
1 AAGAGCCATATAACGAGAAGCTC
29693806 GTGAGAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (25 bp):
AAGAGCCATATAACGAGAAGCTCAC
Found at i:29697038 original size:20 final size:20
Alignment explanation
Indices: 29697015--29697052 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29697005 AGAATAGTCT
29697015 TTGAACTGATAGAAAATTGA
1 TTGAACTGATAGAAAATTGA
29697035 TTGAACTGATAGAAAATT
1 TTGAACTGATAGAAAATT
29697053 ACCCAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGAACTGATAGAAAATTGA
Found at i:29704343 original size:45 final size:44
Alignment explanation
Indices: 29704247--29704397 Score: 178
Period size: 45 Copynumber: 3.4 Consensus size: 44
29704237 TATCTTTCAA
* * * *
29704247 CCATGGCCTTACTCATCTATA-TCATGATGCCATAGTATCTTTTAG
1 CCATGGTCTTACTCATCGATAGT-ATGATGCCATAGTGTCTTCT-G
**
29704292 TTATGGTCTTACTCATCGATAGTATGATGCCATAGTGTCATTCTG
1 CCATGGTCTTACTCATCGATAGTATGATGCCATAGTGTC-TTCTG
* * *
29704337 CCATGGTCTTACTTATCGATAGTGTGATGCCATGGTGTCTTTCTG
1 CCATGGTCTTACTCATCGATAGTATGATGCCATAGTGTC-TTCTG
29704382 CCATGGTCTTACTCAT
1 CCATGGTCTTACTCAT
29704398 GTTTAGGCTT
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 87 0.96
46 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.39
Consensus pattern (44 bp):
CCATGGTCTTACTCATCGATAGTATGATGCCATAGTGTCTTCTG
Found at i:29709762 original size:27 final size:27
Alignment explanation
Indices: 29709731--29709783 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29709721 AGGTAAGTTC
29709731 ATATTAGGGTTATTATCTTTATTAATG
1 ATATTAGGGTTATTATCTTTATTAATG
*
29709758 ATATTAGGGTTATTATGTTTATTAAT
1 ATATTAGGGTTATTATCTTTATTAAT
29709784 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (27 bp):
ATATTAGGGTTATTATCTTTATTAATG
Found at i:29720583 original size:44 final size:44
Alignment explanation
Indices: 29720495--29720585 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
29720485 GTAGGTCAAA
** * * **
29720495 TAATATTAAAATAACTTACACTAATCTGATTTTAAGTGGGAAAC
1 TAATATTAAAATAACTTACACTAATCAAAGTTTAAATGAAAAAC
29720539 TAATATTAAAATAA-TCTACACTAATCAAAGTTTAAATGAAAAAC
1 TAATATTAAAATAACT-TACACTAATCAAAGTTTAAATGAAAAAC
29720583 TAA
1 TAA
29720586 AAACAGAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACTTACACTAATCAAAGTTTAAATGAAAAAC
Found at i:29725646 original size:16 final size:16
Alignment explanation
Indices: 29725625--29725655 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29725615 TCCATTGTTT
*
29725625 CTTTTTGTTTTCTTTC
1 CTTTTTCTTTTCTTTC
29725641 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTT
29725656 TTTCTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (16 bp):
CTTTTTCTTTTCTTTC
Found at i:29725654 original size:27 final size:27
Alignment explanation
Indices: 29725622--29725673 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
29725612 TTTTCCATTG
29725622 TTTCTTTTTGT-TTTCTTTC-CTTTTTCT
1 TTTCTTTTT-TCTTT-TTTCTCTTTTTCT
29725649 TTTCTTTTTTCTTTTTTCTCTTTTT
1 TTTCTTTTTTCTTTTTTCTCTTTTT
29725674 TCTTGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTCTTTTTTCTTTTTTCTCTTTTTCT
Found at i:29725670 original size:16 final size:16
Alignment explanation
Indices: 29725651--29725683 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29725641 CTTTTTCTTT
*
29725651 TCTTTTTTCTTTTTTC
1 TCTTTTTTCTTGTTTC
29725667 TCTTTTTTCTTGTTTC
1 TCTTTTTTCTTGTTTC
29725683 T
1 T
29725684 ATAATTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (16 bp):
TCTTTTTTCTTGTTTC
Found at i:29726781 original size:13 final size:14
Alignment explanation
Indices: 29726756--29726784 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29726746 TCGAATTCAG
29726756 AAATTCAACACAAC
1 AAATTCAACACAAC
29726770 AAATTC-ACACAAC
1 AAATTCAACACAAC
29726783 AA
1 AA
29726785 TGCATCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATTCAACACAAC
Found at i:29732391 original size:22 final size:23
Alignment explanation
Indices: 29732352--29732399 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
29732342 TAAAACTAAT
29732352 TTTCCATTGTTT-CTTTTTTTTC
1 TTTCCATTGTTTCCTTTTTTTTC
* *
29732374 TTTCCTTTTTTTCCTTTTTTTTC
1 TTTCCATTGTTTCCTTTTTTTTC
29732397 TTT
1 TTT
29732400 TTTCTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTCCATTGTTTCCTTTTTTTTC
Found at i:29734788 original size:9 final size:9
Alignment explanation
Indices: 29734774--29734804 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29734764 GTTAAACGAA
29734774 TCGAGTTAT
1 TCGAGTTAT
*
29734783 TCGAGTTAA
1 TCGAGTTAT
29734792 TCGAGTTAT
1 TCGAGTTAT
29734801 TCGA
1 TCGA
29734805 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29735131 original size:30 final size:31
Alignment explanation
Indices: 29735097--29735156 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29735087 AAACCTTTTA
*
29735097 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
29735127 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
29735157 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:29737852 original size:3 final size:3
Alignment explanation
Indices: 29737844--29737886 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
29737834 ATATGTTCTT
29737844 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29737887 GCGATCATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29753407 original size:42 final size:42
Alignment explanation
Indices: 29753253--29753399 Score: 240
Period size: 42 Copynumber: 3.5 Consensus size: 42
29753243 GCGCTTAGAT
* * * *
29753253 AAGAACATGATCTTTAGCAGCGTTTTTATCTAAGCGCCTCTA
1 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
*
29753295 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTA
1 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
29753337 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
1 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
*
29753379 AAGAACATGTTCTTTAGCGGC
1 AAGAACATGGTCTTTAGCGGC
29753400 ACTTTTTTAC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (42 bp):
AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTA
Found at i:29753749 original size:21 final size:21
Alignment explanation
Indices: 29753725--29753791 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
29753715 TTTTGCTCTG
**
29753725 CTCTACTTCTTTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
*
29753746 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
29753767 CGT-TGCTTCCCTCGCTGCCGC
1 C-TCTACTTCCCTCGCTGCAGC
29753788 CTCT
1 CTCT
29753792 GCTTTAAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.04, C:0.45, G:0.18, T:0.33
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:29753794 original size:21 final size:21
Alignment explanation
Indices: 29753736--29753795 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
29753726 TCTACTTCTT
29753736 TCGCTGCAGCCTCTGCTTCCC
1 TCGCTGCAGCCTCTGCTTCCC
29753757 TCGCTGCAGCCGT-TGCTTCCC
1 TCGCTGCAGCC-TCTGCTTCCC
*
29753778 TCGCTGCCGCCTCTGCTT
1 TCGCTGCAGCCTCTGCTT
29753796 TAAGTTGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.03, C:0.45, G:0.22, T:0.30
Consensus pattern (21 bp):
TCGCTGCAGCCTCTGCTTCCC
Found at i:29759315 original size:9 final size:9
Alignment explanation
Indices: 29759301--29759518 Score: 207
Period size: 9 Copynumber: 24.9 Consensus size: 9
29759291 TTTTGATGTA
29759301 TTATGTAAG
1 TTATGTAAG
29759310 TTATGTAAG
1 TTATGTAAG
*
29759319 TTGTGT-A-
1 TTATGTAAG
*
29759326 TTATGTGAG
1 TTATGTAAG
*
29759335 TTATGTGAG
1 TTATGTAAG
*
29759344 TTATGTGAG
1 TTATGTAAG
29759353 TTATGTAAG
1 TTATGTAAG
*
29759362 TTATGGAAG
1 TTATGTAAG
* *
29759371 TTATTTAAT
1 TTATGTAAG
29759380 TTATGTAAG
1 TTATGTAAG
29759389 TTATGTAAG
1 TTATGTAAG
*
29759398 TTATGTAGG
1 TTATGTAAG
*
29759407 CTATGT-A-
1 TTATGTAAG
* *
29759414 TTATCTAAA
1 TTATGTAAG
* **
29759423 TAATGTTCG
1 TTATGTAAG
*
29759432 TTA-GGAAGG
1 TTATGTAA-G
29759441 TTATGT-A-
1 TTATGTAAG
29759448 TTATGTAAG
1 TTATGTAAG
*
29759457 TTATTTAAG
1 TTATGTAAG
* *
29759466 TTATTTAAT
1 TTATGTAAG
29759475 TTATGTAAG
1 TTATGTAAG
*
29759484 TTAAGTAAG
1 TTATGTAAG
29759493 TTATGTAAG
1 TTATGTAAG
29759502 TTATGTAAG
1 TTATGTAAG
29759511 TTATGTAA
1 TTATGTAA
29759519 TTAGAAATTT
Statistics
Matches: 171, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
7 15 0.09
8 5 0.03
9 150 0.88
10 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29759553 original size:20 final size:20
Alignment explanation
Indices: 29759530--29759568 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29759520 TAGAAATTTT
29759530 ATCTTAATATTATATAAGTA
1 ATCTTAATATTATATAAGTA
29759550 ATCTTAATATTATATAAGT
1 ATCTTAATATTATATAAGT
29759569 TATGTAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ATCTTAATATTATATAAGTA
Found at i:29759603 original size:37 final size:37
Alignment explanation
Indices: 29759550--29759913 Score: 326
Period size: 37 Copynumber: 9.7 Consensus size: 37
29759540 TATATAAGTA
29759550 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* * *
29759587 ACCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* * * *
29759624 ATCTTAACATTATATAAGTTATGTAATTTATGTAA-GTT
1 ATCTTAATATTATATAAGTTATGTAA-TT-CGAAATTTT
* * * * ** ** *
29759662 AT-GT-A-ATTAGA-AATTTTATCTTAATATTATAAAAGTA
1 ATCTTAATATTATATAA-GTTAT-GT-A-ATTCGAAATTTT
29759699 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* * * ** *
29759736 ATCTTAATATTATATAAGTAATCTTAATAT-TATATAAGTA
1 ATCTTAATATTATATAAGTTAT-GTAAT-TCGA-A-ATTTT
* *
29759776 ATCTTAATATTACATAAGTTATATAATTCGAAATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* * *
29759813 ATCTTAATATTGTATAAGTTATGTAATTCGATATTGT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
* *
29759850 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
*
29759887 ATCTTAACATTATATAAGTTATGTAAT
1 ATCTTAATATTATATAAGTTATGTAAT
29759914 ATTATATAAG
Statistics
Matches: 263, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
34 2 0.01
35 9 0.03
36 4 0.02
37 188 0.71
38 16 0.06
39 11 0.04
40 31 0.12
41 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (37 bp):
ATCTTAATATTATATAAGTTATGTAATTCGAAATTTT
Found at i:29759702 original size:20 final size:20
Alignment explanation
Indices: 29759679--29759794 Score: 123
Period size: 20 Copynumber: 6.0 Consensus size: 20
29759669 TAGAAATTTT
*
29759679 ATCTTAATATTATAAAAGTA
1 ATCTTAATATTATATAAGTA
*
29759699 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGTA
* * ** *
29759719 AT-GTAAT-TCGA-A-ATTTT
1 ATCTTAATAT-TATATAAGTA
29759736 ATCTTAATATTATATAAGTA
1 ATCTTAATATTATATAAGTA
29759756 ATCTTAATATTATATAAGTA
1 ATCTTAATATTATATAAGTA
*
29759776 ATCTTAATATTACATAAGT
1 ATCTTAATATTATATAAGT
29759795 TATATAATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
17 5 0.06
18 7 0.09
19 7 0.09
20 60 0.76
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (20 bp):
ATCTTAATATTATATAAGTA
Found at i:29759732 original size:57 final size:57
Alignment explanation
Indices: 29759589--29759774 Score: 286
Period size: 57 Copynumber: 3.3 Consensus size: 57
29759579 GAAATTTTAC
* * * *
29759589 CTTAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGTTAT
1 CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAAT
* * * *
29759646 -GTAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATAAAAGTAAT
1 CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAAT
29759701 CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAAT
1 CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAAT
29759758 CTTAATATTATATAAGT
1 CTTAATATTATATAAGT
29759775 AATCTTAATA
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
55 43 0.37
56 8 0.07
57 64 0.56
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (57 bp):
CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAAT
Found at i:29759922 original size:56 final size:57
Alignment explanation
Indices: 29759849--29759983 Score: 209
Period size: 56 Copynumber: 2.4 Consensus size: 57
29759839 TTCGATATTG
* * * *
29759849 TATCTTAATATTGTATAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGT
1 TATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGT
*
29759906 TAT-GTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGT
1 TATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGT
*
29759962 TATCTTAATATTATATAAGTTA
1 TATCGTAATATTATATAAGTTA
29759984 AGAAATTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
56 51 0.72
57 20 0.28
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (57 bp):
TATCGTAATATTATATAAGTTATGTAATTAGAAATTTTATCTTAACATTATATAAGT
Found at i:29762475 original size:19 final size:19
Alignment explanation
Indices: 29762451--29762494 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
29762441 GGACTACGTT
29762451 GGGGAATTGTTAGGGA-TTA
1 GGGGAATT-TTAGGGATTTA
29762470 GGGGAAATTTTAGGGATTTA
1 GGGG-AATTTTAGGGATTTA
29762490 GGGGA
1 GGGGA
29762495 GATGAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.43, T:0.30
Consensus pattern (19 bp):
GGGGAATTTTAGGGATTTA
Found at i:29762490 original size:20 final size:20
Alignment explanation
Indices: 29762451--29762494 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
29762441 GGACTACGTT
29762451 GGGG-AATTGTTAGGGATTA
1 GGGGAAATTGTTAGGGATTA
29762470 GGGGAAATT-TTAGGGATTTA
1 GGGGAAATTGTTAGGGA-TTA
29762490 GGGGA
1 GGGGA
29762495 GATGAGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.43, T:0.30
Consensus pattern (20 bp):
GGGGAAATTGTTAGGGATTA
Found at i:29763579 original size:21 final size:21
Alignment explanation
Indices: 29763555--29763631 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
29763545 ACCCTAAACT
*
29763555 CAAATCCCAAATCCCAAACCA
1 CAAACCCCAAATCCCAAACCA
* * *
29763576 CAAACCCCTAACCCCGAA-CA
1 CAAACCCCAAATCCCAAACCA
**
29763596 CTAAACCCCAAACTCAAAAACCA
1 C-AAACCCCAAA-TCCCAAACCA
* *
29763619 AAAATCCCAAATC
1 CAAACCCCAAATC
29763632 GTAATATTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.07
21 25 0.60
22 12 0.29
23 2 0.05
ACGTcount: A:0.48, C:0.42, G:0.01, T:0.09
Consensus pattern (21 bp):
CAAACCCCAAATCCCAAACCA
Found at i:29763620 original size:55 final size:57
Alignment explanation
Indices: 29763520--29763629 Score: 170
Period size: 55 Copynumber: 1.9 Consensus size: 57
29763510 CCCAAATTTC
* * *
29763520 CAAACCCCCTAACCCCGAACACTAAACCCTAAACTC-AAATCCCAAATCCCAAACCA
1 CAAACCCCCTAACCCCGAACACTAAACCCCAAACTCAAAAACCAAAATCCCAAACCA
29763576 CAAA-CCCCTAACCCCGAACACTAAACCCCAAACTCAAAAACCAAAAATCCCAAA
1 CAAACCCCCTAACCCCGAACACTAAACCCCAAACTCAAAAACC-AAAATCCCAAA
29763630 TCGTAATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
55 30 0.61
56 9 0.18
57 10 0.20
ACGTcount: A:0.46, C:0.43, G:0.02, T:0.09
Consensus pattern (57 bp):
CAAACCCCCTAACCCCGAACACTAAACCCCAAACTCAAAAACCAAAATCCCAAACCA
Found at i:29764719 original size:114 final size:112
Alignment explanation
Indices: 29764533--29764886 Score: 363
Period size: 114 Copynumber: 3.1 Consensus size: 112
29764523 CGCTTCCTAA
* * * * * *
29764533 AAAACGCCGCTAACGTCCGGATCATTAGCGACGCTTTTCACAAAACGCCGCTAAAGGCCCAAAAA
1 AAAACGCCGCTAAAGCCCGGAGCATTAGCGGCGCTTTTCAAAAAACGCCGC-AACGGCCCAAAAA
** *
29764598 AACAGAAAACGGCGTCGTTGGCCTTAGGTTTTTTTGCGGCGCTTTTCAG
65 CTCAG-AAACGACGTCGTTGGCCTTAGGTTTTTTTGCGGCGCTTTTCAG
* * * **
29764647 AAAACGCCGCTAAAGGCAGGAGCATTAGCGGTGCTTTTCAAAAAACGCCGCAACGCGGACAAAAA
1 AAAACGCCGCTAAAGCCCGGAGCATTAGCGGCGCTTTTCAAAAAACGCCGCAACG-GCCCAAAAA
* * *
29764712 CTCAGAAATGACGTCGTTGACCTTAGG-TTTTTTGCGGCGCTTTTTAG
65 CTCAGAAACGACGTCGTTGGCCTTAGGTTTTTTTGCGGCGCTTTTCAG
* * * * * *
29764759 AAATCGCCG-TTAAGTCCCCCGAGCATTAGCGGCG-TTTTTAGAAAAACGCCGCTACAGGTCCAA
1 AAAACGCCGCTAAAG--CCCGGAGCATTAGCGGCGCTTTTCA-AAAAACGCCGCAAC-GGCCCAA
* * *
29764822 AAACTCAGTAAACGACGTCGTTGGCCTTATGTTTTTTTGCGGTGCTTTTCAT
62 AAACTCAG-AAACGACGTCGTTGGCCTTAGGTTTTTTTGCGGCGCTTTTCAG
* *
29764874 AAATCGCTGCTAA
1 AAAACGCCGCTAA
29764887 TGCTTATTAT
Statistics
Matches: 198, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
111 4 0.02
112 32 0.16
113 61 0.31
114 74 0.37
115 25 0.13
116 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (112 bp):
AAAACGCCGCTAAAGCCCGGAGCATTAGCGGCGCTTTTCAAAAAACGCCGCAACGGCCCAAAAAC
TCAGAAACGACGTCGTTGGCCTTAGGTTTTTTTGCGGCGCTTTTCAG
Found at i:29764790 original size:113 final size:113
Alignment explanation
Indices: 29764555--29764886 Score: 325
Period size: 113 Copynumber: 2.9 Consensus size: 113
29764545 ACGTCCGGAT
* * ** ** * *
29764555 CATTAGCGACGCTTTTCA-CAAAACGCCGCTAA-AGGCCCAAAAAAACAGAAAACGGCGTCGTTG
1 CATTAGCGGCG-TTTTCAGAAAAACGCCGC-AACAGGGACAAAAACTCAGTAAACGACGTCGTTG
* * *
29764618 GCCTTAGGTTTTTTTGCGGCGCTTTTCAGAAAACGCCGCTAAAGGCAGGAG
64 GCCTTAGG-TTTTTTGCGGCGCTTTTCAGAAATCGCCGCTAAAGCCACGAG
* *
29764669 CATTAGCGGTGCTTTTCA-AAAAACGCCGCAAC-GCGGACAAAAACTCAG-AAATGACGTCGTTG
1 CATTAGCGGCG-TTTTCAGAAAAACGCCGCAACAG-GGACAAAAACTCAGTAAACGACGTCGTTG
* * * *
29764731 ACCTTAGGTTTTTTGCGGCGCTTTTTAGAAATCGCCG-TTAAGTCCCCCGAG
64 GCCTTAGGTTTTTTGCGGCGCTTTTCAGAAATCGCCGCTAAAG--CCACGAG
* * **
29764782 CATTAGCGGCGTTTTTAGAAAAACGCCGCTACAGGTCCAAAAACTCAGTAAACGACGTCGTTGGC
1 CATTAGCGGCGTTTTCAGAAAAACGCCGCAACAGGGACAAAAACTCAGTAAACGACGTCGTTGGC
* * * *
29764847 CTTATGTTTTTTTGCGGTGCTTTTCATAAATCGCTGCTAA
66 CTTA-GGTTTTTTGCGGCGCTTTTCAGAAATCGCCGCTAA
29764887 TGCTTATTAT
Statistics
Matches: 180, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
111 4 0.02
112 32 0.18
113 61 0.34
114 55 0.31
115 26 0.14
116 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (113 bp):
CATTAGCGGCGTTTTCAGAAAAACGCCGCAACAGGGACAAAAACTCAGTAAACGACGTCGTTGGC
CTTAGGTTTTTTGCGGCGCTTTTCAGAAATCGCCGCTAAAGCCACGAG
Found at i:29764946 original size:39 final size:39
Alignment explanation
Indices: 29764902--29764986 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 39
29764892 ATTATTAGCA
29764902 GCGTTTCCTAAATGCGCCGCTAAT-TCTCGATCTTTAGAG
1 GCGTTTCCTAAATGCGCCGCTAATGT-TCGATCTTTAGAG
** * * * *
29764941 GCGTTTTTGTAGATGCGCCGCTAGTGTTCGATTTTTAGCG
1 GCG-TTTCCTAAATGCGCCGCTAATGTTCGATCTTTAGAG
29764981 GCGTTT
1 GCGTTT
29764987 GTTGTCCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
39 6 0.16
40 31 0.82
41 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (39 bp):
GCGTTTCCTAAATGCGCCGCTAATGTTCGATCTTTAGAG
Found at i:29764958 original size:40 final size:41
Alignment explanation
Indices: 29764913--29764991 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
29764903 CGTTTCCTAA
29764913 ATGCGCCGCTAAT-TCTCGATCTTTAGAGGCGTTT-TTGTAG
1 ATGCGCCGCTAATGT-TCGATCTTTAGAGGCGTTTGTTGTAG
* * *
29764953 ATGCGCCGCTAGTGTTCGATTTTTAGCGGCGTTTGTTGT
1 ATGCGCCGCTAATGTTCGATCTTTAGAGGCGTTTGTTGT
29764992 CCAAACGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 29 0.85
41 5 0.15
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.39
Consensus pattern (41 bp):
ATGCGCCGCTAATGTTCGATCTTTAGAGGCGTTTGTTGTAG
Found at i:29776029 original size:15 final size:15
Alignment explanation
Indices: 29776009--29776038 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29775999 GAATCCTTCA
29776009 ATTAGGGTCTAAAAT
1 ATTAGGGTCTAAAAT
29776024 ATTAGGGTCTAAAAT
1 ATTAGGGTCTAAAAT
29776039 CAGGGTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
ATTAGGGTCTAAAAT
Found at i:29782352 original size:12 final size:13
Alignment explanation
Indices: 29782334--29782366 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
29782324 TCTTTTACCA
29782334 TATTTATTATTAC
1 TATTTATTATTAC
29782347 -ATTTATTATTAC
1 TATTTATTATTAC
29782359 TATTTATT
1 TATTTATT
29782367 TATATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATTATTAC
Found at i:29783469 original size:20 final size:18
Alignment explanation
Indices: 29783422--29783470 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
29783412 TAAATTTATA
*
29783422 ATCATTTTGTTGCATTTC
1 ATCATTTTGTTACATTTC
29783440 ATCTATTTTTGTTACGATCTTC
1 ATC-A-TTTTGTTAC-AT-TTC
29783462 ATCATTTTG
1 ATCATTTTG
29783471 GTTTATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 13 0.50
21 3 0.12
22 6 0.23
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (18 bp):
ATCATTTTGTTACATTTC
Found at i:29787041 original size:13 final size:12
Alignment explanation
Indices: 29787022--29787061 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
29787012 AAAGGTAAAG
29787022 AAAAGAAAAGAA
1 AAAAGAAAAGAA
29787034 AAACAGAAAA-AA
1 AAA-AGAAAAGAA
29787046 AAAAGAAACAGAA
1 AAAAGAAA-AGAA
29787059 AAA
1 AAA
29787062 GGAGAGGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:29787047 original size:17 final size:17
Alignment explanation
Indices: 29787007--29787061 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
29786997 ACTTCACTTT
* *
29787007 AAAAAAAAGGTAA-AGA
1 AAAAAAAAAGAAACAGA
29787023 AAAGAAAAGAA-AAACAGA
1 AAA-AAAA-AAGAAACAGA
29787041 AAAAAAAAAGAAACAGA
1 AAAAAAAAAGAAACAGA
29787058 AAAA
1 AAAA
29787062 GGAGAGGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 5 0.15
17 21 0.64
18 7 0.21
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAAACAGA
Found at i:29788208 original size:143 final size:143
Alignment explanation
Indices: 29787943--29788209 Score: 419
Period size: 143 Copynumber: 1.9 Consensus size: 143
29787933 GTCATCATGA
* * *
29787943 CGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTATAAATTATGGTGGATCTTATC
1 CGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATAGCGGATCTTATC
* * *
29788008 TTCCTGAAGTTATAATGGAGCAGATTGAAACCACCAGCCTTCTCTCCTTGAAATTGCAGCGAAGC
66 TTCCTGAAGTTACAATGGAGCAGATTGAAACCACCAGCCTTATCTCCCTGAAATTGCAGCGAAGC
29788073 AGACTGAAGACAG
131 AGACTGAAGACAG
* *
29788086 CGAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTACAAATTATAGCGGATCTTATC
1 CGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATAGCGGATCTTATC
* * *
29788151 TTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT-AAAGTTGCAG
66 TTCCTGAAGTTACAATGGAGCAGATTGAAACCACCAGCCTTATCTCCCTGAAA-TTGCAG
29788210 TTGGTTAGGA
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
142 3 0.03
143 109 0.97
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (143 bp):
CGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATAGCGGATCTTATC
TTCCTGAAGTTACAATGGAGCAGATTGAAACCACCAGCCTTATCTCCCTGAAATTGCAGCGAAGC
AGACTGAAGACAG
Found at i:29788284 original size:14 final size:14
Alignment explanation
Indices: 29788265--29788294 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29788255 AAGATTCGGC
29788265 TCGGCCGGGTAGAA
1 TCGGCCGGGTAGAA
29788279 TCGGCCGGGTAGAA
1 TCGGCCGGGTAGAA
29788293 TC
1 TC
29788295 AGCCCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (14 bp):
TCGGCCGGGTAGAA
Found at i:29789954 original size:12 final size:12
Alignment explanation
Indices: 29789939--29789963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29789929 GTTATCATCG
29789939 TTATTATTTATT
1 TTATTATTTATT
29789951 TTATTATTTATT
1 TTATTATTTATT
29789963 T
1 T
29789964 ATTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTATT
Done.