Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 75 of 103
Found at i:28011305 original size:2 final size:2
Alignment explanation
Indices: 28011294--28011365 Score: 105
Period size: 2 Copynumber: 37.0 Consensus size: 2
28011284 CATAGTTTGT
*
28011294 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA NT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
28011334 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
28011366 GTTTTTCTAA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
1 3 0.05
2 60 0.94
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28013304 original size:19 final size:18
Alignment explanation
Indices: 28013277--28013312 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28013267 TCAATCAAGG
28013277 GGGTGTTTTTGGTCTTTTT
1 GGGTGTTTTTGGT-TTTTT
*
28013296 GGGTTTTTTTGGTTTTT
1 GGGTGTTTTTGGTTTTT
28013313 GTATGCGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.00, C:0.03, G:0.31, T:0.67
Consensus pattern (18 bp):
GGGTGTTTTTGGTTTTTT
Found at i:28017888 original size:15 final size:15
Alignment explanation
Indices: 28017864--28017899 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
28017854 TTTTAGAGAC
28017864 TAAA-TTAAAAAATA
1 TAAATTTAAAAAATA
*
28017878 TATATTTAAAAAATA
1 TAAATTTAAAAAATA
28017893 TAAATTT
1 TAAATTT
28017900 TTAAGTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATTTAAAAAATA
Found at i:28018560 original size:18 final size:19
Alignment explanation
Indices: 28018537--28018583 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
28018527 ATGTAATTTG
* *
28018537 AAATATTAAACA-AAATAA
1 AAATATTAAAAATAAACAA
*
28018555 AAATATAAAAAATAAACAA
1 AAATATTAAAAATAAACAA
28018574 AAA-ATTAAAA
1 AAATATTAAAA
28018584 GGATGGGGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATATTAAAAATAAACAA
Found at i:28020836 original size:30 final size:29
Alignment explanation
Indices: 28020800--28020885 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
28020790 TGTTTGATTC
28020800 AAAATAAAAATATAAAAATTTATTTAACTT
1 AAAATAAAAATATAAAAATTTATTTAA-TT
* * * *
28020830 AAAATAAAAATATAAGAGTATGATTGAATT
1 AAAATAAAAATATAAAAAT-TTATTTAATT
*
28020860 -CAATAAAAATATAAAAATTTATTTAA
1 AAAATAAAAATATAAAAATTTATTTAA
28020886 AATTTTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 6 0.13
29 15 0.33
30 19 0.41
31 6 0.13
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATAAAAATATAAAAATTTATTTAATT
Found at i:28024936 original size:22 final size:21
Alignment explanation
Indices: 28024904--28024945 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
28024894 TTGACAAAAT
28024904 AAAAAATATTTATAAATTTTA
1 AAAAAATATTTATAAATTTTA
28024925 AAAATAATATTTATAAATTTT
1 AAAA-AATATTTATAAATTTT
28024946 GAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAAATATTTATAAATTTTA
Found at i:28030200 original size:8 final size:8
Alignment explanation
Indices: 28030187--28030218 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
28030177 ATTAATATTT
28030187 CATTAATA
1 CATTAATA
28030195 CATTAATA
1 CATTAATA
28030203 CATTAATA
1 CATTAATA
28030211 CATTAATA
1 CATTAATA
28030219 AAGACCAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
CATTAATA
Found at i:28036704 original size:48 final size:48
Alignment explanation
Indices: 28036633--28036728 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
28036623 TTAATAAGCC
28036633 TGCAAACTTTGTTCTCACTTCCTTTATCTTCAAAACCTTCAGGTTGCT
1 TGCAAACTTTGTTCTCACTTCCTTTATCTTCAAAACCTTCAGGTTGCT
*
28036681 TGCAAACTTTGTTCTCACTTCCTTTCTCTTCAAAACCTTCAGGTTGCT
1 TGCAAACTTTGTTCTCACTTCCTTTATCTTCAAAACCTTCAGGTTGCT
28036729 CAATGTAGAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (48 bp):
TGCAAACTTTGTTCTCACTTCCTTTATCTTCAAAACCTTCAGGTTGCT
Found at i:28041897 original size:2 final size:2
Alignment explanation
Indices: 28041890--28041915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28041880 TGATAGGCTA
28041890 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
28041916 TAAATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28042536 original size:17 final size:19
Alignment explanation
Indices: 28042502--28042547 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
28042492 GCTTACGAAA
28042502 AAATATAATAATAATAAAG
1 AAATATAATAATAATAAAG
*
28042521 AAATATAA-AA-AATAAAT
1 AAATATAATAATAATAAAG
28042538 AAATAATAAT
1 AAAT-ATAAT
28042548 TAAATGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATATAATAATAATAAAG
Found at i:28042552 original size:28 final size:29
Alignment explanation
Indices: 28042499--28042557 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
28042489 ATTGCTTACG
28042499 AAAAAATATAATAATAATAAAGAAAT-AT
1 AAAAAATATAATAATAATAAAGAAATGAT
**
28042527 AAAAAATA-AATAAATAATAATTAAATGAT
1 AAAAAATATAAT-AATAATAAAGAAATGAT
28042556 AA
1 AA
28042558 TAATAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 3 0.11
28 20 0.74
29 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAAAATATAATAATAATAAAGAAATGAT
Found at i:28045151 original size:9 final size:9
Alignment explanation
Indices: 28045139--28045170 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28045129 AATAACGCGT
28045139 TTAACACGA
1 TTAACACGA
*
28045148 TTAACACGT
1 TTAACACGA
28045157 TTAACACGA
1 TTAACACGA
28045166 TTAAC
1 TTAAC
28045171 TAAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
TTAACACGA
Found at i:28045157 original size:18 final size:18
Alignment explanation
Indices: 28045131--28045170 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
28045121 ACACGATTAA
*
28045131 TAACGCGTTTAACACGAT
1 TAACACGTTTAACACGAT
28045149 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
28045167 TAAC
1 TAAC
28045171 TAAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:28045439 original size:18 final size:18
Alignment explanation
Indices: 28045416--28045452 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28045406 AACGTGTCAT
*
28045416 GTATACACGTTTAAACAC
1 GTATACACATTTAAACAC
28045434 GTATACACATTTAAACAC
1 GTATACACATTTAAACAC
28045452 G
1 G
28045453 ATAACGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
GTATACACATTTAAACAC
Found at i:28065921 original size:15 final size:14
Alignment explanation
Indices: 28065890--28065934 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
28065880 AATTATAACT
28065890 GAAAACAGAAAAAG
1 GAAAACAGAAAAAG
*
28065904 GAAAATAGAAAGAAG
1 GAAAACAGAAA-AAG
*
28065919 GAAAGCAGAAAAAG
1 GAAAACAGAAAAAG
28065933 GA
1 GA
28065935 GAGTTTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (14 bp):
GAAAACAGAAAAAG
Found at i:28100222 original size:5 final size:5
Alignment explanation
Indices: 28100214--28100241 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28100204 AAAAGAAGTT
28100214 GGTTG GGTTG GGTTG GGTTG GGTTG GGT
1 GGTTG GGTTG GGTTG GGTTG GGTTG GGT
28100242 ACGGCCCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (5 bp):
GGTTG
Found at i:28103407 original size:28 final size:29
Alignment explanation
Indices: 28103348--28103419 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
28103338 CTATTTAAGC
* *
28103348 ATAAAATACTAAATA-TTAAACTATAATTT
1 ATAAAATA-TAAATAGTTAAACTACAATAT
28103377 ATAAAATATAAATAGTTAAA-TACAATAT
1 ATAAAATATAAATAGTTAAACTACAATAT
*
28103405 ATAGAAT-T-AATAGTT
1 ATAAAATATAAATAGTT
28103420 TTCTCTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 18 0.46
29 13 0.33
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (29 bp):
ATAAAATATAAATAGTTAAACTACAATAT
Found at i:28107395 original size:29 final size:29
Alignment explanation
Indices: 28107355--28107414 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
28107345 GGACACAATG
*
28107355 TTTTTTTCACGTATCAAATTAAATCTTTT
1 TTTTTTTCACGTAACAAATTAAATCTTTT
*
28107384 TTTTTTTTACGTAACAAATTAAATCTTTT
1 TTTTTTTCACGTAACAAATTAAATCTTTT
28107413 TT
1 TT
28107415 AATTAAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTTTTCACGTAACAAATTAAATCTTTT
Found at i:28123379 original size:22 final size:22
Alignment explanation
Indices: 28123337--28123381 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
28123327 TTCTCCACCC
*
28123337 CTCTTTCTCTCTCTTTCTTTTT
1 CTCTTTCTCTCACTTTCTTTTT
*
28123359 CTCTTTCTCTTCACTTTTTTTTT
1 CTCTTTCTC-TCACTTTCTTTTT
28123382 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (22 bp):
CTCTTTCTCTCACTTTCTTTTT
Found at i:28123572 original size:16 final size:17
Alignment explanation
Indices: 28123543--28123575 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
28123533 TTCTTTTTTT
28123543 TATTTATATTATTTAAC
1 TATTTATATTATTTAAC
28123560 TATTTAT-TTATTTAAC
1 TATTTATATTATTTAAC
28123576 CATTGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATATTATTTAAC
Found at i:28124801 original size:258 final size:257
Alignment explanation
Indices: 28124346--28124852 Score: 838
Period size: 258 Copynumber: 2.0 Consensus size: 257
28124336 TATTTTTTTA
*
28124346 AAGAAGTAAAAATTTGACATGTTTTTTAACTTAAATAATTTTATATAAAAAATAGATTTTTGTTA
1 AAGAAGTAAAAATTTGACATGTTTTTCAACTTAAATAATTTTATATAAAAAATAGATTTTTGTTA
28124411 TGACTGAATTATTAGTTTCAATTATTTTATGAAATTTTGTAATAAATTCATGATTATATTTCAAT
66 TGACTGAATTATTAGTTTCAATTATTTTATGAAATTTTGTAATAAATTCATGATTATATTTCAAT
* *
28124476 AATTGTTTGTCCAGCTTTGTTGTGTATGGACATCAAATAGCATCTGTACAACTTCTAACAAAATA
131 AATTGTTTGTCCAGCTTTGTTGTGTATGGACATCAAATAGCATCCGTACAACTTCGAACAAAATA
*
28124541 TAAGTGTTATTG-CATTAAAAAATTTATTTAATGATAGATGTATGTATTATTTAGTTTGCCG
196 TAAGTATTATTGTCATTAAAAAATTTATTTAATGATAGATGTATGTATTATTTAGTTTGCCG
* *
28124602 AAGAAGTAAAAATTTGACATGTTTTTCAATTTAAATAATTTTATATAAAAAATAGAATTTTTTTT
1 AAGAAGTAAAAATTTGACATGTTTTTCAACTTAAATAATTTTATATAAAAAATAG-ATTTTTGTT
* *
28124667 ATGACTGAATTATTTGTTTCAATTATTTTATGAAAATTTAT-TAATAAATTTATGATTATATTTC
65 ATGACTGAATTATTAGTTTCAATTATTTTATG-AAATTT-TGTAATAAATTCATGATTATATTTC
* * *
28124731 AATAGTTGTTTGTCTAGCTTTGTTGTGTATGGACATCAAATAGCATCCGTACAACTTCGAATAAA
128 AATAATTGTTTGTCCAGCTTTGTTGTGTATGGACATCAAATAGCATCCGTACAACTTCGAACAAA
** * *
28124796 ATATAAGTATTATTGTTTTTAAAAATTTTATTTGATGATAGATGTATGTATTATTTA
193 ATATAAGTATTATTGTCATTAAAAAATTTATTTAATGATAGATGTATGTATTATTTA
28124853 CTCAAAAAAT
Statistics
Matches: 232, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
256 53 0.23
257 39 0.17
258 102 0.44
259 38 0.16
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (257 bp):
AAGAAGTAAAAATTTGACATGTTTTTCAACTTAAATAATTTTATATAAAAAATAGATTTTTGTTA
TGACTGAATTATTAGTTTCAATTATTTTATGAAATTTTGTAATAAATTCATGATTATATTTCAAT
AATTGTTTGTCCAGCTTTGTTGTGTATGGACATCAAATAGCATCCGTACAACTTCGAACAAAATA
TAAGTATTATTGTCATTAAAAAATTTATTTAATGATAGATGTATGTATTATTTAGTTTGCCG
Found at i:28127021 original size:2 final size:2
Alignment explanation
Indices: 28127014--28127044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28127004 TGTATAACAC
28127014 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28127045 TAGCTCCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28138180 original size:16 final size:16
Alignment explanation
Indices: 28138159--28138191 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28138149 TACTATTTGG
*
28138159 TCATATTGTCTTTGTA
1 TCATATTATCTTTGTA
28138175 TCATATTATCTTTGTA
1 TCATATTATCTTTGTA
28138191 T
1 T
28138192 TAATGCATTA
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:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TCATATTATCTTTGTA
Found at i:28156244 original size:27 final size:27
Alignment explanation
Indices: 28156214--28156330 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
28156204 GTAATATTTT
* *
28156214 AAAATTTAATTATTACATATCATGTTA
1 AAAATTTAATTATCACACATCATGTTA
* * *
28156241 AAAATTTAGTTATCACACATCTTGTTG
1 AAAATTTAATTATCACACATCATGTTA
* * * *
28156268 AAAATTAAATTATCACACGTTATGTTG
1 AAAATTTAATTATCACACATCATGTTA
* *
28156295 AAAATTTAATTATAACAC-TCCATATTA
1 AAAATTTAATTATCACACAT-CATGTTA
28156322 AAAATTTAA
1 AAAATTTAA
28156331 AATACATGTC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 73 0.99
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (27 bp):
AAAATTTAATTATCACACATCATGTTA
Found at i:28166931 original size:37 final size:36
Alignment explanation
Indices: 28166865--28166936 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 36
28166855 TTGATCAAAG
* *
28166865 TTCAATACAATGCCTTTTATGGATCAAGCATAACCT
1 TTCAATACAATGCCTTTTATGGATAAAGCACAACCT
** *
28166901 TTCAATACAATGTTTTTTTATGGTTAAAGCACAACC
1 TTCAATACAATG-CCTTTTATGGATAAAGCACAACC
28166937 ATTTTACCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (36 bp):
TTCAATACAATGCCTTTTATGGATAAAGCACAACCT
Found at i:28170474 original size:16 final size:16
Alignment explanation
Indices: 28170449--28170481 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28170439 TATTAAAAAT
28170449 ATTTTTACTTT-TTAA
1 ATTTTTACTTTGTTAA
28170464 ATTTGTTACTTTGTTAA
1 ATTT-TTACTTTGTTAA
28170481 A
1 A
28170482 AATATTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTTACTTTGTTAA
Found at i:28170653 original size:32 final size:32
Alignment explanation
Indices: 28170597--28170681 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
28170587 TAAAAAAATT
* * *
28170597 AAAATAAAACATATAATATAAAAAATTGTATTA
1 AAAATAAAA-ATAAAATATAAAAAATTATAATA
*
28170630 AGAAATGAAAATAAAATATAAAAAATTATAATA
1 A-AAATAAAAATAAAATATAAAAAATTATAATA
28170663 AAAATAAAAATAAAATATA
1 AAAATAAAAATAAAATATA
28170682 TGACATTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 17 0.37
33 22 0.48
34 7 0.15
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATTATAATA
Found at i:28170655 original size:20 final size:19
Alignment explanation
Indices: 28170632--28170672 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
28170622 TTGTATTAAG
28170632 AAATGAAAATAAAATATAAA
1 AAATGAAAATAAAA-ATAAA
* *
28170652 AAATTATAATAAAAATAAA
1 AAATGAAAATAAAAATAAA
28170671 AA
1 AA
28170673 TAAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATGAAAATAAAAATAAA
Found at i:28171272 original size:33 final size:32
Alignment explanation
Indices: 28171228--28171305 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 32
28171218 AAATATCATA
*
28171228 TATTTTA-TTTTTATTATAAT-TTTGTATATTT
1 TATTTTATTTTTTAATATAATATTT-TATATTT
28171259 TATTTTCATTTTTTAATATAATATTTTATATTT
1 TATTTT-ATTTTTTAATATAATATTTTATATTT
28171292 TATTTTAATTTTTT
1 TATTTT-ATTTTTT
28171306 TAAAAGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 6 0.14
32 1 0.02
33 32 0.76
34 3 0.07
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (32 bp):
TATTTTATTTTTTAATATAATATTTTATATTT
Found at i:28171305 original size:20 final size:20
Alignment explanation
Indices: 28171230--28171305 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
28171220 ATATCATATA
*
28171230 TTTTAT-TTTTATTATAATT
1 TTTTATATTTTATTTTAATT
* *
28171249 TTGTATATTTTATTTTCATT
1 TTTTATATTTTATTTTAATT
*
28171269 TTTTA-A---TA---TAATA
1 TTTTATATTTTATTTTAATT
28171282 TTTTATATTTTATTTTAATT
1 TTTTATATTTTATTTTAATT
28171302 TTTT
1 TTTT
28171306 TAAAAGATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 15
0.66 0.11 0.23
Matches are distributed among these distances:
13 8 0.19
14 1 0.02
16 2 0.05
17 2 0.05
19 6 0.14
20 23 0.55
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (20 bp):
TTTTATATTTTATTTTAATT
Found at i:28172674 original size:5 final size:5
Alignment explanation
Indices: 28172664--28172690 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28172654 TAAAAGTTGT
28172664 GATGG GATGG GATGG GATGG GATGG GA
1 GATGG GATGG GATGG GATGG GATGG GA
28172691 AGGAAGGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.59, T:0.19
Consensus pattern (5 bp):
GATGG
Found at i:28173868 original size:16 final size:17
Alignment explanation
Indices: 28173847--28173882 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28173837 TCTTCGTTCC
*
28173847 TTCTCTTTCTCTC-TCT
1 TTCTCTTTCGCTCTTCT
28173863 TTCTCTTTCGCTCTTCT
1 TTCTCTTTCGCTCTTCT
28173880 TTC
1 TTC
28173883 ACAAAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (17 bp):
TTCTCTTTCGCTCTTCT
Found at i:28188867 original size:2 final size:2
Alignment explanation
Indices: 28188860--28188913 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
28188850 GGACTATTTA
** * * *
28188860 AT AT AT AT AT AT AT AT CG AT AT AT AT AT AT AT CT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28188902 AT -T AT AT AT AT A
1 AT AT AT AT AT AT A
28188914 AATCCTAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28188903 original size:16 final size:16
Alignment explanation
Indices: 28188862--28188892 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28188852 ACTATTTAAT
28188862 ATATATATATATATCG
1 ATATATATATATATCG
28188878 ATATATATATATATC
1 ATATATATATATATC
28188893 TGTGTATATA
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:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATATATATATATCG
Found at i:28192727 original size:2 final size:2
Alignment explanation
Indices: 28192720--28192751 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28192710 TTAATCCCTC
28192720 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28192752 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28192756 original size:2 final size:2
Alignment explanation
Indices: 28192751--28192794 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
28192741 TCTCTCTCTC
*
28192751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28192793 TA
1 TA
28192795 CTGCTAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28192904 original size:2 final size:2
Alignment explanation
Indices: 28192888--28192944 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
28192878 CAATTCATAC
*
28192888 AT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28192929 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
28192945 TAACATTGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28200408 original size:19 final size:18
Alignment explanation
Indices: 28200386--28200441 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
28200376 ATAAATTAAT
28200386 TAAAAACAAAAGACAAATG
1 TAAAAA-AAAAGACAAATG
*
28200405 TAAAAATAAATAAACAAAT-
1 TAAAAA-AAA-AGACAAATG
28200424 TAAAAAAAAAGACAAATG
1 TAAAAAAAAAGACAAATG
28200442 AAGAAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.22
18 3 0.09
19 15 0.47
20 7 0.22
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (18 bp):
TAAAAAAAAAGACAAATG
Found at i:28200410 original size:20 final size:19
Alignment explanation
Indices: 28200386--28200441 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
28200376 ATAAATTAAT
*
28200386 TAAAAACAAAAGACAAATG
1 TAAAAAAAAAAGACAAATG
28200405 TAAAAATAAATAA-ACAAAT-
1 TAAAAA-AAA-AAGACAAATG
28200424 T-AAAAAAAAAGACAAATG
1 TAAAAAAAAAAGACAAATG
28200442 AAGAAAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 2 0.06
17 9 0.28
18 4 0.12
19 7 0.22
20 8 0.25
21 2 0.06
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (19 bp):
TAAAAAAAAAAGACAAATG
Found at i:28200425 original size:38 final size:38
Alignment explanation
Indices: 28200361--28200441 Score: 128
Period size: 38 Copynumber: 2.1 Consensus size: 38
28200351 ATAATAGAAA
**
28200361 AAATGTAAAAAGTAAATAAATTAATTAAAAACAAAAGAC
1 AAATGTAAAAAGTAAATAAACAAATTAAAAA-AAAAGAC
28200400 AAATGTAAAAA-TAAATAAACAAATTAAAAAAAAAGAC
1 AAATGTAAAAAGTAAATAAACAAATTAAAAAAAAAGAC
28200437 AAATG
1 AAATG
28200442 AAGAAAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 12 0.30
38 17 0.43
39 11 0.28
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (38 bp):
AAATGTAAAAAGTAAATAAACAAATTAAAAAAAAAGAC
Found at i:28200448 original size:17 final size:17
Alignment explanation
Indices: 28200387--28200449 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
28200377 TAAATTAATT
28200387 AAAAACAAAAGACAAATG
1 AAAAA-AAAAGACAAATG
* *
28200405 TAAAAATAAATAAACAAATT
1 -AAAAA-AAA-AGACAAATG
28200425 AAAAAAAAAGACAAATG
1 AAAAAAAAAGACAAATG
*
28200442 AAGAAAAA
1 AAAAAAAA
28200450 CAAATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 14 0.38
18 3 0.08
19 13 0.35
20 7 0.19
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAGACAAATG
Found at i:28223923 original size:16 final size:16
Alignment explanation
Indices: 28223895--28223936 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
28223885 AATTTATTAT
28223895 ATTAAAAATATATACAA
1 ATTAAAAATATATA-AA
28223912 ATTAAAAA-ATATAAA
1 ATTAAAAATATATAAA
*
28223927 AATAAAAATA
1 ATTAAAAATA
28223937 ATTGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.39
16 6 0.26
17 8 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAAATATATAAA
Found at i:28225408 original size:39 final size:39
Alignment explanation
Indices: 28225360--28225493 Score: 227
Period size: 37 Copynumber: 3.4 Consensus size: 39
28225350 TCAATTGTTT
28225360 AAAGAGAACAAGAGAAGCAATTTAAAAAAAAAAAAAACA
1 AAAGAGAACAAGAGAAGCAATTTAAAAAAAAAAAAAACA
*
28225399 AAAGAGAACAAGAGAAGCAATTT--CAAAAAAAAAAACA
1 AAAGAGAACAAGAGAAGCAATTTAAAAAAAAAAAAAACA
28225436 AAAGAGAACAAGAGAAGCAATTTCAACAAAAAAAAAAAACA
1 AAAGAGAACAAGAGAAGCAATTT-AA-AAAAAAAAAAAACA
28225477 AAAGAGAACAAGAGAAG
1 AAAGAGAACAAGAGAAG
28225494 GGTTAGAGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
37 36 0.40
39 23 0.26
41 30 0.34
ACGTcount: A:0.69, C:0.10, G:0.15, T:0.07
Consensus pattern (39 bp):
AAAGAGAACAAGAGAAGCAATTTAAAAAAAAAAAAAACA
Found at i:28244499 original size:18 final size:19
Alignment explanation
Indices: 28244477--28244527 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
28244467 AATAAAAAGC
28244477 AAAAAGCAAAAAAAAAT-A
1 AAAAAGCAAAAAAAAATAA
* **
28244495 GAAAA-CTAAAACCAAATAA
1 AAAAAGC-AAAAAAAAATAA
28244514 AAAAAGCAAAAAAA
1 AAAAAGCAAAAAAA
28244528 TAAAAGTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.50
19 10 0.42
20 1 0.04
ACGTcount: A:0.78, C:0.10, G:0.06, T:0.06
Consensus pattern (19 bp):
AAAAAGCAAAAAAAAATAA
Found at i:28244505 original size:24 final size:24
Alignment explanation
Indices: 28244461--28244517 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
28244451 GCAAAAAAAG
* *
28244461 AAAAAGAATAAAAAGCAAAAAGCA
1 AAAAAAAATAAAAAGCAAAAACCA
*
28244485 AAAAAAAATAGAAAA-CTAAAACCA
1 AAAAAAAATA-AAAAGCAAAAACCA
28244509 AATAAAAAA
1 AA-AAAAAA
28244518 AGCAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.77, C:0.09, G:0.07, T:0.07
Consensus pattern (24 bp):
AAAAAAAATAAAAAGCAAAAACCA
Found at i:28244740 original size:2 final size:2
Alignment explanation
Indices: 28244733--28244785 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28244723 ATACCATCAC
28244733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28244775 AT AT AT AT AT A
1 AT AT AT AT AT A
28244786 ACTGAATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28245535 original size:21 final size:21
Alignment explanation
Indices: 28245511--28245576 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
28245501 ATGATTAAGA
*
28245511 TTACTTGAATGATCTTTGAAC
1 TTACTTGAATGATTTTTGAAC
* * *
28245532 TTACTTGAATTATTTTTAAAG
1 TTACTTGAATGATTTTTGAAC
*
28245553 TTATTTGAATGAGTTTTTGAAC
1 TTACTTGAATGA-TTTTTGAAC
28245575 TT
1 TT
28245577 GTTTAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 27 0.75
22 9 0.25
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.50
Consensus pattern (21 bp):
TTACTTGAATGATTTTTGAAC
Found at i:28254307 original size:37 final size:38
Alignment explanation
Indices: 28254265--28254336 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
28254255 ATTTTTATGG
28254265 GTCGCTAATCATATGAAAAAAA-ACCTAAATATATTAC
1 GTCGCTAATCATATGAAAAAAATACCTAAATATATTAC
* *
28254302 GTCGCTGATCATTTGAAAAAAATACCTAAATATAT
1 GTCGCTAATCATATGAAAAAAATACCTAAATATAT
28254337 AACGCCGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (38 bp):
GTCGCTAATCATATGAAAAAAATACCTAAATATATTAC
Found at i:28264945 original size:71 final size:72
Alignment explanation
Indices: 28264790--28264957 Score: 205
Period size: 71 Copynumber: 2.3 Consensus size: 72
28264780 GACAAAAATT
* * * * * * * **
28264790 TTTCCAACGGAATTTCTGTTGGAAAAATTTTTGGTGAGCCAAAAAAAAAGGAGACAAGCATTTTT
1 TTTCCAACGAAATTTCTGTTGGAAAAAGTTTTGGGGAGCCAAAAAAAAAGAAAACAACCATATCA
28264855 GACGAAA
66 GACGAAA
* *
28264862 TTTCCAATGAAATTTCTGTTGGAAAAAGTTTTGGGGAG-CAAAAATAAAA-AAAACCACCATATC
1 TTTCCAACGAAATTTCTGTTGGAAAAAGTTTTGGGGAGCCAAAAA-AAAAGAAAACAACCATATC
28264925 AGACGAAA
65 AGACGAAA
*
28264933 TTTCCAACGAAATTTCCGTTGGAAA
1 TTTCCAACGAAATTTCTGTTGGAAA
28264958 TCTATCGGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
71 44 0.54
72 38 0.46
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (72 bp):
TTTCCAACGAAATTTCTGTTGGAAAAAGTTTTGGGGAGCCAAAAAAAAAGAAAACAACCATATCA
GACGAAA
Found at i:28272895 original size:175 final size:176
Alignment explanation
Indices: 28272594--28272947 Score: 514
Period size: 175 Copynumber: 2.0 Consensus size: 176
28272584 ATTCCTTTTC
* * * *
28272594 TCCTCTCCCTTCATTTTCTTATTTCCCTTTCTCTCCCTACCCACAGCCACCTTCTCACTTTTCTC
1 TCCTCTCCATTCATTTTCTTATTTCCCTTTCTCTCCCTAACCACAACCACCTTCTCACTTCTCTC
* * * * *
28272659 TAAACTTTTCCCTCCGTCGGTCGCTTTCTCCTTCTCTCTCACCTTTCTCTCAACTGGTGGCTTGA
66 TAAACTTTTCCCTCCCTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCTCGCAACCGGTGGCTTGA
28272724 AGCTCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACCGACAA
131 AGCTCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACCGACAA
* * * * *
28272770 TCCT-TCCATTCATTTTCTTCTTTCCCTTTCTCTCTCTAATCGCAACCTCCTTCTCACTTCTCTC
1 TCCTCTCCATTCATTTTCTTATTTCCCTTTCTCTCCCTAACCACAACCACCTTCTCACTTCTCTC
* * * *
28272834 TAAACTTTTCCCTCCACT-GGCCGTTTTGTCCTTCTCTGTCACCTTCCTCGCCACCGGTGGCTTG
66 TAAACTTTTCCCTCC-CTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCTCGCAACCGGTGGCTTG
*
28272898 AAGCTCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACCGATAA
130 AAGCTCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACCGACAA
28272945 TCC
1 TCC
28272948 ATAGATTTGA
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
175 153 0.97
176 5 0.03
ACGTcount: A:0.16, C:0.40, G:0.08, T:0.36
Consensus pattern (176 bp):
TCCTCTCCATTCATTTTCTTATTTCCCTTTCTCTCCCTAACCACAACCACCTTCTCACTTCTCTC
TAAACTTTTCCCTCCCTCGGCCGCTTTCTCCTTCTCTCTCACCTTCCTCGCAACCGGTGGCTTGA
AGCTCGGTCACCCAAAACCCTAAATATCTCTTCCCTCCACCGACAA
Found at i:28274194 original size:14 final size:14
Alignment explanation
Indices: 28274166--28274209 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28274156 CCAACGGGTC
*
28274166 ATTTTTATTAATAA
1 ATTTTTATTTATAA
*
28274180 ATTTTTATTTTTAAA
1 ATTTTTATTTAT-AA
*
28274195 ATTGTTATTTATAA
1 ATTTTTATTTATAA
28274209 A
1 A
28274210 AATAAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
ATTTTTATTTATAA
Found at i:28279703 original size:18 final size:18
Alignment explanation
Indices: 28279680--28279714 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28279670 CATGGAAGGA
28279680 GATGAA-AATGAAGATGAC
1 GATGAAGAA-GAAGATGAC
28279698 GATGAAGAAGAAGATGA
1 GATGAAGAAGAAGATGA
28279715 ACTTGAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.51, C:0.03, G:0.31, T:0.14
Consensus pattern (18 bp):
GATGAAGAAGAAGATGAC
Found at i:28280485 original size:19 final size:20
Alignment explanation
Indices: 28280440--28280477 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28280430 AGGATATTTC
28280440 TAATATTTGTTAATGAAATTG
1 TAATATTTGTTAA-GAAATTG
*
28280461 TTATATTTGTTAA-AAAT
1 TAATATTTGTTAAGAAAT
28280478 ATTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
21 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
TAATATTTGTTAAGAAATTG
Found at i:28281912 original size:50 final size:50
Alignment explanation
Indices: 28281837--28281938 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
28281827 TCTGCACAAG
*
28281837 TAAGATCACATTTCATGATATGATGTTAAAGTTTCACTGCTACACTGAGA
1 TAAGATCACATTTCATGATATGATGTCAAAGTTTCACTGCTACACTGAGA
*
28281887 TAAGATCACATTTCATGATATGATGTCAATGTTTCACTGCTACACTGAGA
1 TAAGATCACATTTCATGATATGATGTCAAAGTTTCACTGCTACACTGAGA
28281937 TA
1 TA
28281939 CTTTTTAGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (50 bp):
TAAGATCACATTTCATGATATGATGTCAAAGTTTCACTGCTACACTGAGA
Found at i:28282300 original size:45 final size:45
Alignment explanation
Indices: 28282235--28282338 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
28282225 AATATGAAAC
* * *
28282235 AATTCCGTTGGAAACCAATTTCCAACTG-AATTGCTTCCAATGGAA
1 AATTCTGTTGGAAACAAATTTCCAAC-GAAATTACTTCCAATGGAA
* *
28282280 AATTCTGTTGGAAACAAATTTCCAACGAAATTATTTCTAATGGAA
1 AATTCTGTTGGAAACAAATTTCCAACGAAATTACTTCCAATGGAA
28282325 AATT-TCGTTGGAAA
1 AATTCT-GTTGGAAA
28282339 TTTCCAACGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 2 0.04
45 50 0.96
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (45 bp):
AATTCTGTTGGAAACAAATTTCCAACGAAATTACTTCCAATGGAA
Found at i:28282868 original size:18 final size:18
Alignment explanation
Indices: 28282845--28282880 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28282835 ACGAGAGCTC
28282845 TTTAGAGCTTTTCTTTAA
1 TTTAGAGCTTTTCTTTAA
28282863 TTTAGAGCTTTTCTTTAA
1 TTTAGAGCTTTTCTTTAA
28282881 GTTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (18 bp):
TTTAGAGCTTTTCTTTAA
Found at i:28290723 original size:2 final size:2
Alignment explanation
Indices: 28290716--28290752 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
28290706 ATAGATCTTT
*
28290716 TA TA TA TA TA AA TA TA TA -A TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28290753 GTAAAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:28292080 original size:3 final size:3
Alignment explanation
Indices: 28292072--28292106 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28292062 ATATATAAAG
28292072 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28292107 GGAATGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28293270 original size:27 final size:28
Alignment explanation
Indices: 28293201--28293270 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
28293191 TGGTTCATAA
28293201 ATAACAATAACATTTTAAGCATTAAATT
1 ATAACAATAACATTTTAAGCATTAAATT
* * *
28293229 GTAA-AA-AAAATTTTTGAA-CATTACA-T
1 ATAACAATAACA-TTTT-AAGCATTAAATT
28293255 ATAACAATAACATTTT
1 ATAACAATAACATTTT
28293271 TTCAACATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
26 7 0.21
27 18 0.55
28 8 0.24
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (28 bp):
ATAACAATAACATTTTAAGCATTAAATT
Found at i:28293277 original size:29 final size:30
Alignment explanation
Indices: 28293239--28293310 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
28293229 GTAAAAAAAA
* * *
28293239 TTTTTGAACATTACATATAACAATAACA-T
1 TTTTTCAACATGACATATAACAACAACATT
* * *
28293268 TTTTTCAACATGACGTGTAACAACAATATT
1 TTTTTCAACATGACATATAACAACAACATT
28293298 TTTTTCAACATGA
1 TTTTTCAACATGA
28293311 TGTGTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTTCAACATGACATATAACAACAACATT
Found at i:28293396 original size:26 final size:26
Alignment explanation
Indices: 28293342--28293396 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
28293332 TTGCGTGTAA
* * *
28293342 TAATAATTTTTTTTCAACATTACGCG
1 TAATAATCTTTTTTCAACATGACACG
* *
28293368 TAATAATCTTTTTTCAGCATGACATG
1 TAATAATCTTTTTTCAACATGACACG
28293394 TAA
1 TAA
28293397 CATATTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (26 bp):
TAATAATCTTTTTTCAACATGACACG
Found at i:28293408 original size:79 final size:79
Alignment explanation
Indices: 28293256--28293842 Score: 502
Period size: 79 Copynumber: 7.3 Consensus size: 79
28293246 ACATTACATA
** * * *
28293256 TAACAATAACATTTTTTCAACATGACGTGTAACAACAATATTTTTTTCAA-CATGATGTGTAATA
1 TAACAATAATTTTTTTTCAACATTACGTGTAACAAC----TTTTTTT-AACCATGACGTGTAACA
* *
28293320 TATTTTTGTACATTGCGTG
61 TATTTTTGTACATGGTGTG
* * * * * *
28293339 TAATAATAATTTTTTTTCAACATTACGCGTAATAA-TCTTTTTTCAGCATGACATGTAACATATT
1 TAACAATAATTTTTTTTCAACATTACGTGTAACAACT-TTTTTTAACCATGACGTGTAACATATT
**
28293403 TTTGTACATGGCATG
65 TTTGTACATGGTGTG
* ** * * * *
28293418 CAACAATAATTTTTTTCTCAACA-TGGGTTGTAATAACATTTTTTAACCATGACGTATAACATGT
1 TAACAATAATTTTTTT-TCAACATTACG-TGTAACAACTTTTTTTAACCATGACGTGTAACATAT
*
28293482 TTTTGTATATGGTGTG
64 TTTTGTACATGGTGTG
* * * * * ** * *
28293498 TAATAACAATTTTTTTTC-ACATTATGTGTAACAACCTTTTTTTAACCACGGCGTACAATATGTT
1 TAACAATAATTTTTTTTCAACATTACGTGTAACAA-CTTTTTTTAACCATGACGTGTAACATATT
*
28293562 TTTGTACATGATGTG
65 TTTGTACATGGTGTG
* * * * * * * *
28293577 TAATAACAAATTTTTTTTCAACATGACGTATAACAAC-CTTTTTAACCATAACATGTAACATGTT
1 TAACAA-TAATTTTTTTTCAACATTACGTGTAACAACTTTTTTTAACCATGACGTGTAACATATT
28293641 TTTGTACATGGTGTG
65 TTTGTACATGGTGTG
** * * * *
28293656 TAACAATAATTTTTTTAAAAAAAATATGGCATGTAACAACCTTTTTTAACCATGACGTGTAACAT
1 TAACAATAATTTTTTT--TCAACAT-T-ACGTGTAACAACTTTTTTTAACCATGACGTGTAACAT
28293721 ATTTTT-TACATGGTGTG
62 ATTTTTGTACATGGTGTG
* * *
28293738 TAACAATAATATTTTTTTTCAATATTGCGTGTAACAACTTTTTTTAACCATGATGTGTAACATAT
1 TAACAAT-A-ATTTTTTTTCAACATTACGTGTAACAACTTTTTTTAACCATGACGTGTAACATAT
**
28293803 TTTTGTACATGACGTG
64 TTTTGTACATGGTGTG
*
28293819 TAACAATAATATTTTTTTTAACAT
1 TAACAATAAT-TTTTTTTCAACAT
28293843 GGTATGTAAC
Statistics
Matches: 411, Mismatches: 75, Indels: 39
0.78 0.14 0.07
Matches are distributed among these distances:
78 21 0.05
79 137 0.33
80 128 0.31
81 30 0.07
82 31 0.08
83 56 0.14
84 8 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (79 bp):
TAACAATAATTTTTTTTCAACATTACGTGTAACAACTTTTTTTAACCATGACGTGTAACATATTT
TTGTACATGGTGTG
Found at i:28293726 original size:26 final size:26
Alignment explanation
Indices: 28293687--28293823 Score: 83
Period size: 26 Copynumber: 5.3 Consensus size: 26
28293677 AAATATGGCA
*
28293687 TGTAACA-ACCTTTTTTAACCATGACG
1 TGTAACATACTTTTTTTAA-CATGACG
**
28293713 TGTAACATA--TTTTTT-ACATGGTG
1 TGTAACATACTTTTTTTAACATGACG
* *
28293736 TGTAACAATAATATTTTTTTTCAATATTG-CG
1 TGTAAC----ATACTTTTTTT-AACA-TGACG
*
28293767 TGTAACA-ACTTTTTTTAACCATGATG
1 TGTAACATACTTTTTTTAA-CATGACG
*
28293793 TGTAACATA-TTTTTGT-ACATGACG
1 TGTAACATACTTTTTTTAACATGACG
28293817 TGTAACA
1 TGTAACA
28293824 ATAATATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
23 11 0.12
24 14 0.16
25 11 0.12
26 30 0.34
27 6 0.07
29 6 0.07
31 9 0.10
32 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (26 bp):
TGTAACATACTTTTTTTAACATGACG
Found at i:28301105 original size:16 final size:16
Alignment explanation
Indices: 28301074--28301119 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
28301064 ACTAATTTTG
28301074 AATAATCATTTATTATTA
1 AATAATCA--TATTATTA
28301092 AATAATCATATTATTA
1 AATAATCATATTATTA
*
28301108 ATTAATCA-ATTA
1 AATAATCATATTA
28301120 ATCAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
18 8 0.30
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATCATATTATTA
Found at i:28301567 original size:22 final size:23
Alignment explanation
Indices: 28301531--28301577 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28301521 TCAATTAATT
28301531 AATTTAGTAATTTAA-CAAATCA
1 AATTTAGTAATTTAATCAAATCA
*
28301553 AATTATAGTAA-TTAATCAATTCA
1 AATT-TAGTAATTTAATCAAATCA
28301576 AA
1 AA
28301578 ATGTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (23 bp):
AATTTAGTAATTTAATCAAATCA
Found at i:28301850 original size:397 final size:398
Alignment explanation
Indices: 28301108--28302092 Score: 1517
Period size: 398 Copynumber: 2.5 Consensus size: 398
28301098 CATATTATTA
* *
28301108 ATTAATCAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAATAATTAATAAAT
1 ATTAA-CAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAGTAATTAATCAAT
*
28301173 TCAAAATGTATTAGTAAATTTAGTAAAATTTAAAACTATTTACATTAATTAAAGTTTTATTAAAT
65 TCAAAATGTATTAGTAAATTTAGTAAAATTTAAAAGTATTTACATTAATTAAAGTTTTATTAAAT
* * * *
28301238 TAATTAAATGATTTAACTAATCAAATGAAAAAAAGTTTTAGTAGTTAAGGAATAAACTAAATTAG
130 TAATTAAATAATTTAACTAATAAAATG---AAAAGTTTTAGTAGTTAAGCAATAAATTAAATTAG
* * * *
28301303 TAATATTATTTAATTTTAAAAATATTTAAATAAATTAAGGTGTTTAGTGAGGTAATTAAATAATT
192 TAATATTATTTAATTTTAAAAATATTTAAATAAATTAAGGTGTTTAGCGACGTAATTAAAGAATA
* *
28301368 TAGTTAATTAAGTATTAGGATGTTATAAGTAATTAAGAAATTACTTAAATTAGTAATATTGTATA
257 TAGTTAATTAAGTATTAGGATGTTATAAGTAATTAAGAAATTAATTAAATTAGTAATATTATATA
* *
28301433 ATATTATTTTTTATTTAAATTAATTAAG-GGGTTAGGGAATTAATTAAAAAATTTAACTAATTCT
322 ATATTATTTTTTATTTAAATTAAGTAAGAAGGTTAGGGAATTAATTAAAAAATTTAACTAATTCT
28301497 GAAAAATCATGT
387 GAAAAATCATGT
* * *
28301509 ATTAGCAATTAATCAATTAATTAATTTAGTAATTTAACAAATCAAATTATAGTAATTAATCAATT
1 ATTAACAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAGTAATTAATCAATT
**
28301574 CAAAATGTATTAAAAAATTTAGTAAAATTTAAAAGTATTTACATTAATTAAAGTTTTATTAAATT
66 CAAAATGTATTAGTAAATTTAGTAAAATTTAAAAGTATTTACATTAATTAAAGTTTTATTAAATT
*
28301639 AATTAAATAATATAACTAATAAAATGAAAAGTTTTAGTAGTTAAGCAATAAATTAAATTAGTAAT
131 AATTAAATAATTTAACTAATAAAATGAAAAGTTTTAGTAGTTAAGCAATAAATTAAATTAGTAAT
*
28301704 ATTATTTAATTTTAAAAATATTTAAATAAATTAAGGTGTTTAGCGACGTAATTAAGGAATATAGT
196 ATTATTTAATTTTAAAAATATTTAAATAAATTAAGGTGTTTAGCGACGTAATTAAAGAATATAGT
* * * *
28301769 TCATTAAGTGTTAGGGTGTTTTAAGTAATTAACG-AATTAATTAAATTAGTAATATTATATAATA
261 TAATTAAGTATTAGGATGTTATAAGTAATTAA-GAAATTAATTAAATTAGTAATATTATATAATA
* * * *
28301833 TTATTTTTTATTTAAATTAAGTAAGAAGTTTAGGGAATTACTTACAAAATTTAACTAATTTTGAA
325 TTATTTTTTATTTAAATTAAGTAAGAAGGTTAGGGAATTAATTAAAAAATTTAACTAATTCTGAA
28301898 AAATCATGT
390 AAATCATGT
* * * *
28301907 GTTAATAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAACGATAGTACTTAATCAATT
1 ATTAACAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAGTAATTAATCAATT
* * *
28301972 CAAAATGTATTAGTAAATTGAGTAAAATTTAAAAGCATTTACTTTAATTAAAGTTTTATTAAATT
66 CAAAATGTATTAGTAAATTTAGTAAAATTTAAAAGTATTTACATTAATTAAAGTTTTATTAAATT
**
28302037 AATTAAATAATTTAACTAATCAAATAAAAAAAGTTTTA-TAAGTTAAGCAATTAAAT
131 AATTAAATAATTTAACTAAT-AAA-ATGAAAAGTTTTAGT-AGTTAAGCAA-TAAAT
28302093 AATTCTTGTA
Statistics
Matches: 533, Mismatches: 45, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
397 177 0.33
398 181 0.34
399 4 0.01
400 162 0.30
401 9 0.02
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (398 bp):
ATTAACAATTAATCAATTAATTAAATTAGTAATTTAACAAATCAAATGATAGTAATTAATCAATT
CAAAATGTATTAGTAAATTTAGTAAAATTTAAAAGTATTTACATTAATTAAAGTTTTATTAAATT
AATTAAATAATTTAACTAATAAAATGAAAAGTTTTAGTAGTTAAGCAATAAATTAAATTAGTAAT
ATTATTTAATTTTAAAAATATTTAAATAAATTAAGGTGTTTAGCGACGTAATTAAAGAATATAGT
TAATTAAGTATTAGGATGTTATAAGTAATTAAGAAATTAATTAAATTAGTAATATTATATAATAT
TATTTTTTATTTAAATTAAGTAAGAAGGTTAGGGAATTAATTAAAAAATTTAACTAATTCTGAAA
AATCATGT
Found at i:28303161 original size:14 final size:14
Alignment explanation
Indices: 28303142--28303169 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28303132 TTAAGTCTAA
28303142 TAACCAAACTACCT
1 TAACCAAACTACCT
28303156 TAACCAAACTACCT
1 TAACCAAACTACCT
28303170 AAATAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
TAACCAAACTACCT
Found at i:28309344 original size:2 final size:2
Alignment explanation
Indices: 28309337--28309379 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28309327 CTTTTATTTA
28309337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28309379 A
1 A
28309380 CATACACTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28319345 original size:3 final size:3
Alignment explanation
Indices: 28319339--28319366 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28319329 AAAGTTACTG
28319339 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28319367 AGCATTCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28320175 original size:14 final size:14
Alignment explanation
Indices: 28320156--28320196 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
28320146 TTCTAAATTC
28320156 ATACATA-ATCATAT
1 ATACATATAT-ATAT
28320170 ATACATATATATAT
1 ATACATATATATAT
*
28320184 ATATATATA-ATAT
1 ATACATATATATAT
28320197 GTTTGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 19 0.76
15 2 0.08
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATACATATATATAT
Found at i:28325499 original size:15 final size:14
Alignment explanation
Indices: 28325470--28325497 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28325460 AAACTATCTA
28325470 AAACTTTTTTCTTT
1 AAACTTTTTTCTTT
28325484 AAACTTTTTTCTTT
1 AAACTTTTTTCTTT
28325498 TATTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
AAACTTTTTTCTTT
Found at i:28330210 original size:26 final size:26
Alignment explanation
Indices: 28330180--28330238 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
28330170 ACATTCAAAT
28330180 ATTAATAATTAAATTATAAATAAAAA
1 ATTAATAATTAAATTATAAATAAAAA
*
28330206 ATTAATAATTAAATTATAAATAAAAT
1 ATTAATAATTAAATTATAAATAAAAA
28330232 ATTAATA
1 ATTAATA
28330239 TTTAGATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTAATAATTAAATTATAAATAAAAA
Found at i:28330383 original size:132 final size:136
Alignment explanation
Indices: 28330225--28330558 Score: 391
Period size: 140 Copynumber: 2.5 Consensus size: 136
28330215 TAAATTATAA
* *
28330225 ATAAAATATTAATA-TTTAGATGATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAC
1 ATAAAATATTAATATTTTA-ATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAA
* * *
28330289 TTAAAAATTAATAATCATAATAACATTTAACTTATAAATAAAACAATAATATT-T-T-TA-AAT-
65 AT-AAAA-TAAAAATCATAATAACATTTAAATTA-AAATAAAACAATAATATTATATATACAATG
28330349 ATT-AATGAT
127 ATTAAATGAT
*
28330358 -TAAAATATTAATATTTTAATTATCAATTATTAATATTTTTTAATAAATTATAAA-TATTTAA-A
1 ATAAAATATTAATATTTTAATTATCAATTATTAATA-TTTTAAATAAATTATAAATTA-TTAATA
* *
28330420 AATAAAATAAAAATCATAATAATATTTAAATTAAAATAAAATAATAATATTATATAATACTAATG
64 AATAAAATAAAAATCATAATAACATTTAAATTAAAATAAAACAATAATATTATAT-ATAC-AATG
*
28330485 ATTAAATTAT
127 ATTAAATGAT
* * * *
28330495 AAATAAAATATTAACATTTAAATTATCAATTATTAATATATTAAACAAATTATAAATTATTAAT
1 --ATAAAATATTAATATTTTAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAAT
28330559 GTTTTAAAAA
Statistics
Matches: 171, Mismatches: 14, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
129 17 0.10
130 24 0.14
131 5 0.03
132 33 0.19
133 27 0.16
135 3 0.02
136 3 0.02
137 5 0.03
139 19 0.11
140 35 0.20
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (136 bp):
ATAAAATATTAATATTTTAATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATAAA
TAAAATAAAAATCATAATAACATTTAAATTAAAATAAAACAATAATATTATATATACAATGATTA
AATGAT
Found at i:28330433 original size:28 final size:29
Alignment explanation
Indices: 28330410--28330468 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
28330400 ATAAATTATA
28330410 AATATTTAAAAATAAAATAAAAATCATAAT
1 AATATTT-AAAATAAAATAAAAATCATAAT
* *
28330440 AATATTTAAATTAAAAT-AAAATAATAAT
1 AATATTTAAAATAAAATAAAAATCATAAT
28330468 A
1 A
28330469 TTATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.41
29 9 0.33
30 7 0.26
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
AATATTTAAAATAAAATAAAAATCATAAT
Found at i:28350933 original size:2 final size:2
Alignment explanation
Indices: 28350926--28350950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28350916 CTTTTAAGTC
28350926 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 T
28350951 TAATTTTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28355682 original size:39 final size:38
Alignment explanation
Indices: 28355615--28355691 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
28355605 AAATTTCTAA
* *
28355615 TTCCTTTTAATTCTATGAGGAAGTAGAATTGGGTTAGTG
1 TTCCTTTTAATTCTATAAGGAAGAAGAATT-GGTTAGTG
* *
28355654 TTCCTTTTAATTCTGTAAGGATGAAGAATTGGTTAGTG
1 TTCCTTTTAATTCTATAAGGAAGAAGAATTGGTTAGTG
28355692 CTGTCATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 8 0.24
39 26 0.76
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (38 bp):
TTCCTTTTAATTCTATAAGGAAGAAGAATTGGTTAGTG
Found at i:28371753 original size:21 final size:21
Alignment explanation
Indices: 28371727--28371773 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
28371717 CTAAATCCAA
28371727 AACTACTATCAAATCAAGAAC
1 AACTACTATCAAATCAAGAAC
28371748 AACTACTATCAAATCAAGAAC
1 AACTACTATCAAATCAAGAAC
28371769 AACTA
1 AACTA
28371774 ACAATCCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.19
Consensus pattern (21 bp):
AACTACTATCAAATCAAGAAC
Found at i:28372155 original size:2 final size:2
Alignment explanation
Indices: 28372148--28372204 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
28372138 AAAAATTAAA
* *
28372148 AG AG AG AG AG AG AG CA- AG AG AG AG AG AG AC AG AG AG AG AG AA
1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
28372190 AG AG AA AG A- AG AG AG
1 AG AG AG AG AG AG AG AG
28372205 CAGACTGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 43 0.93
3 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.42, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28382862 original size:34 final size:34
Alignment explanation
Indices: 28382824--28382889 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
28382814 TGTTAAATAT
28382824 TTGTTAGATAAACTTAACTCAAATCATATATTGG
1 TTGTTAGATAAACTTAACTCAAATCATATATTGG
28382858 TTGTTAGATAAACTTAACTCAAATCATATATT
1 TTGTTAGATAAACTTAACTCAAATCATATATT
28382890 TGGTATTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (34 bp):
TTGTTAGATAAACTTAACTCAAATCATATATTGG
Found at i:28389311 original size:25 final size:25
Alignment explanation
Indices: 28389294--28389348 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
28389284 GCTTAATTCT
*
28389294 TATAAGATGTAAGTAGCTCAACTTC
1 TATAAAATGTAAGTAGCTCAACTTC
** * *
28389319 TATAAAATGTAAACACCTCAATTTC
1 TATAAAATGTAAGTAGCTCAACTTC
28389344 TATAA
1 TATAA
28389349 TATATGAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (25 bp):
TATAAAATGTAAGTAGCTCAACTTC
Found at i:28390167 original size:26 final size:26
Alignment explanation
Indices: 28390129--28390186 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
28390119 TCACCAAAGT
* *
28390129 ATAG-TTGTTTTAACTCTAACTAGAA
1 ATAGATTGCTTTAACTCTAACGAGAA
*
28390154 GTAGATTGCTTTAACTCTAACGAGAA
1 ATAGATTGCTTTAACTCTAACGAGAA
28390180 ATAGATT
1 ATAGATT
28390187 TAAATCCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (26 bp):
ATAGATTGCTTTAACTCTAACGAGAA
Found at i:28391414 original size:21 final size:21
Alignment explanation
Indices: 28391353--28391414 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
28391343 ACATTACAAC
* *
28391353 AATGTATTGATAGA-CGGGAT
1 AATGTATCGATAGATCGGGCT
* * *
28391373 AATTTATCGATACATGGGGCT
1 AATGTATCGATAGATCGGGCT
*
28391394 AATGTATCGATAGATCAGGCT
1 AATGTATCGATAGATCGGGCT
28391415 TATTTTGAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (21 bp):
AATGTATCGATAGATCGGGCT
Found at i:28393039 original size:16 final size:17
Alignment explanation
Indices: 28393015--28393050 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
28393005 AATTTCACAC
28393015 AATGATTAAAT-ATATA
1 AATGATTAAATAATATA
*
28393031 AATGGTTAAATAATATA
1 AATGATTAAATAATATA
28393048 AAT
1 AAT
28393051 TGAAAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AATGATTAAATAATATA
Found at i:28413075 original size:29 final size:29
Alignment explanation
Indices: 28413011--28413087 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
28413001 ATAAGTGTTT
* *
28413011 CTCTCTCATAGCTTTTCACTCTTACCTTA
1 CTCTTTCATACCTTTTCACTCTTACCTTA
* * * * *
28413040 CTGTTTCATATCTTTTCATTTTTACCTTG
1 CTCTTTCATACCTTTTCACTCTTACCTTA
*
28413069 TTCTTTCATACCTTATTCA
1 CTCTTTCATACCTT-TTCA
28413088 ATCTCATATC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 34 0.89
30 4 0.11
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (29 bp):
CTCTTTCATACCTTTTCACTCTTACCTTA
Found at i:28416959 original size:2 final size:2
Alignment explanation
Indices: 28416954--28416979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28416944 TAATATATGA
28416954 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
28416980 GTTATATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28417485 original size:2 final size:2
Alignment explanation
Indices: 28417478--28417518 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28417468 ATTCAATCAT
28417478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28417519 CTGAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28422771 original size:2 final size:2
Alignment explanation
Indices: 28422764--28422790 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28422754 AGCAAATACG
28422764 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28422791 AGCAACCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28430785 original size:20 final size:20
Alignment explanation
Indices: 28430760--28430813 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
28430750 ATATATCAAA
* *
28430760 TTATTCACTAATTTATTAGT
1 TTATTCACTAATTTACTAAT
**
28430780 TTATTCACTAATAAACTAAT
1 TTATTCACTAATTTACTAAT
28430800 TTATTCACTAATTT
1 TTATTCACTAATTT
28430814 CCTTTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (20 bp):
TTATTCACTAATTTACTAAT
Found at i:28430973 original size:13 final size:13
Alignment explanation
Indices: 28430955--28430979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28430945 CGCACATATG
28430955 AATGATTATATTA
1 AATGATTATATTA
28430968 AATGATTATATT
1 AATGATTATATT
28430980 TGGTAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATGATTATATTA
Found at i:28431959 original size:31 final size:31
Alignment explanation
Indices: 28431921--28431985 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
28431911 TTCTAGTTCC
28431921 AATAATGTTCCAATAGCACATATAAAGAAAA
1 AATAATGTTCCAATAGCACATATAAAGAAAA
* *
28431952 AATAATGTTGCAATAGCACATATAAAGGAAA
1 AATAATGTTCCAATAGCACATATAAAGAAAA
28431983 AAT
1 AAT
28431986 TGAACTGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (31 bp):
AATAATGTTCCAATAGCACATATAAAGAAAA
Found at i:28433647 original size:64 final size:64
Alignment explanation
Indices: 28433564--28433721 Score: 228
Period size: 64 Copynumber: 2.5 Consensus size: 64
28433554 AGATTTTTTG
28433564 TGTTCAAGACTATTTGTTATTGTTTTTATCCATTGTTGGAA-ACTATTAATGATTTGCTGTTATT
1 TGTTCAAGACTATTTGTTATTGTTTTTATCCATTGTT-GAATACTATTAATGATTTGCTGTTATT
* * * * *
28433628 TGTTGAAGATTATTTGTTATTGTTTTTATCCATTGTTGAATATTGTTAATGATTTGTTGTTATT
1 TGTTCAAGACTATTTGTTATTGTTTTTATCCATTGTTGAATACTATTAATGATTTGCTGTTATT
* * *
28433692 TGCTCAAGACTATTTATTGTTGTTTTTATC
1 TGTTCAAGACTATTTGTTATTGTTTTTATC
28433722 TATGTTTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 3 0.04
64 80 0.96
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (64 bp):
TGTTCAAGACTATTTGTTATTGTTTTTATCCATTGTTGAATACTATTAATGATTTGCTGTTATT
Found at i:28440657 original size:24 final size:25
Alignment explanation
Indices: 28440630--28440678 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
28440620 AATTGTCTCA
*
28440630 TAAATAATT-ATTTTTATATTTAAT
1 TAAATAATTAATTATTATATTTAAT
28440654 TAAATAATTCAATTATTATATTTAA
1 TAAATAATT-AATTATTATATTTAA
28440679 ATTTTAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAATAATTAATTATTATATTTAAT
Found at i:28450309 original size:22 final size:23
Alignment explanation
Indices: 28450284--28450347 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
28450274 TGGAATGATC
28450284 AAAAAT-AAGTTTTGAT-CTTAGA
1 AAAAATCAAGTTTTGATGC-TAGA
* *
28450306 AAAATTCATGTTTTGATGCTAGA
1 AAAAATCAAGTTTTGATGCTAGA
* *
28450329 AAAATTCATGTTTTGATGC
1 AAAAATCAAGTTTTGATGC
28450348 ATTAAAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 5 0.13
23 32 0.84
24 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (23 bp):
AAAAATCAAGTTTTGATGCTAGA
Found at i:28450354 original size:23 final size:23
Alignment explanation
Indices: 28450292--28450347 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
28450282 TCAAAAATAA
28450292 GTTTTGAT-CTTAGAAAAATTCAT
1 GTTTTGATGC-TAGAAAAATTCAT
28450315 GTTTTGATGCTAGAAAAATTCAT
1 GTTTTGATGCTAGAAAAATTCAT
28450338 GTTTTGATGC
1 GTTTTGATGC
28450348 ATTAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (23 bp):
GTTTTGATGCTAGAAAAATTCAT
Found at i:28450529 original size:20 final size:20
Alignment explanation
Indices: 28450504--28450557 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
28450494 CCTGAAGAAC
*
28450504 ATCTATGGATAGATGAG-CAG
1 ATCTATCGATAGATG-GCCAG
*
28450524 ATCTATCCATAGATGGCCAG
1 ATCTATCGATAGATGGCCAG
28450544 ATCTATCGATAGAT
1 ATCTATCGATAGAT
28450558 AGCTCCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (20 bp):
ATCTATCGATAGATGGCCAG
Found at i:28453728 original size:11 final size:10
Alignment explanation
Indices: 28453687--28453781 Score: 51
Period size: 11 Copynumber: 9.6 Consensus size: 10
28453677 TTTTGCTGTT
28453687 TAAAAAATAAA
1 TAAAAAAT-AA
* *
28453698 TAAATATATGA
1 TAAA-AAATAA
28453709 TAAAAAATAA
1 TAAAAAATAA
*
28453719 TAAAATAATAG
1 TAAAA-AATAA
28453730 TAAACAAA-AGA
1 TAAA-AAATA-A
*
28453741 TAAACAATAA
1 TAAAAAATAA
28453751 -ACAAAAA-AA
1 TA-AAAAATAA
28453760 T-AAAAAT-A
1 TAAAAAATAA
28453768 -AAAAAATAA
1 TAAAAAATAA
28453777 -AAAAA
1 TAAAAA
28453782 GAGAAGGAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
8 12 0.18
9 9 0.14
10 17 0.26
11 24 0.36
12 4 0.06
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:28453753 original size:18 final size:17
Alignment explanation
Indices: 28453720--28453773 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
28453710 AAAAAATAAT
* *
28453720 AAAATAATAGTAAACAA
1 AAAATAAAAATAAACAA
*
28453737 AAGATAAACAATAAACAAA
1 AAAATAAA-AATAAAC-AA
28453756 AAAATAAAAATAAA-AA
1 AAAATAAAAATAAACAA
28453772 AA
1 AA
28453774 TAAAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 4 0.13
17 6 0.19
18 12 0.39
19 9 0.29
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.13
Consensus pattern (17 bp):
AAAATAAAAATAAACAA
Found at i:28453772 original size:7 final size:7
Alignment explanation
Indices: 28453687--28453780 Score: 50
Period size: 7 Copynumber: 13.0 Consensus size: 7
28453677 TTTTGCTGTT
28453687 TAAAAAA
1 TAAAAAA
28453694 TAAATAAA
1 TAAA-AAA
* **
28453702 TATATGA
1 TAAAAAA
28453709 TAAAAAA
1 TAAAAAA
28453716 TAATAAAA
1 TAA-AAAA
28453724 TAATAGTAAA
1 TAA-A--AAA
* *
28453734 CAAAAGA
1 TAAAAAA
*
28453741 TAAACAA
1 TAAAAAA
*
28453748 T-AAACA
1 TAAAAAA
28453754 -AAAAAA
1 TAAAAAA
28453760 T-AAAAA
1 TAAAAAA
28453766 TAAAAAAA
1 T-AAAAAA
28453774 TAAAAAA
1 TAAAAAA
28453781 AGAGAAGGAG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
6 13 0.20
7 25 0.38
8 21 0.32
9 1 0.02
10 5 0.08
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (7 bp):
TAAAAAA
Found at i:28454081 original size:14 final size:14
Alignment explanation
Indices: 28454062--28454088 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28454052 AATCAAAGAA
28454062 ATATACCAAAAAAT
1 ATATACCAAAAAAT
28454076 ATATACCAAAAAA
1 ATATACCAAAAAA
28454089 ATTCGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (14 bp):
ATATACCAAAAAAT
Found at i:28454311 original size:20 final size:20
Alignment explanation
Indices: 28454285--28454336 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 20
28454275 GAGAGCCGAT
*
28454285 CGTTGGGGAGCGACGTCGTC
1 CGTTGGGGAGCGACGTCGAC
*
28454305 GGTTGGGGA--GA-GTCGAC
1 CGTTGGGGAGCGACGTCGAC
28454322 CGTTGGGGAGCGACG
1 CGTTGGGGAGCGACG
28454337 CCGGCGTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.50
18 2 0.08
19 2 0.08
20 9 0.35
ACGTcount: A:0.13, C:0.19, G:0.50, T:0.17
Consensus pattern (20 bp):
CGTTGGGGAGCGACGTCGAC
Found at i:28454326 original size:17 final size:17
Alignment explanation
Indices: 28454273--28454331 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
28454263 GATCTATTTT
* *
28454273 GGGAGAGCCGATCGTTG
1 GGGAGAGTCGACCGTTG
* *
28454290 GGGAGCGACGTCGTCGGTTG
1 GGGA--GA-GTCGACCGTTG
28454310 GGGAGAGTCGACCGTTG
1 GGGAGAGTCGACCGTTG
28454327 GGGAG
1 GGGAG
28454332 CGACGCCGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.15, C:0.17, G:0.51, T:0.17
Consensus pattern (17 bp):
GGGAGAGTCGACCGTTG
Found at i:28456000 original size:22 final size:22
Alignment explanation
Indices: 28455972--28456027 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
28455962 TAGAATATAA
*
28455972 AAAAAATAAAATATAGGAGAAT
1 AAAAAATAAAATATACGAGAAT
* *
28455994 AAAAAATAAAAAATACGATAAT
1 AAAAAATAAAATATACGAGAAT
**
28456016 ATGAAATAAAAT
1 AAAAAATAAAAT
28456028 GAAAATAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAAAATAAAATATACGAGAAT
Found at i:28456035 original size:21 final size:20
Alignment explanation
Indices: 28456011--28456058 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
28456001 AAAAAATACG
28456011 ATAATATGAAATAAAATGA-AA
1 ATAATAT-AAA-AAAATGACAA
28456032 ATAATAATAAAAAAATGACAA
1 ATAAT-ATAAAAAAATGACAA
*
28456053 AAAATA
1 ATAATA
28456059 GATAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (20 bp):
ATAATATAAAAAAATGACAA
Found at i:28456046 original size:20 final size:22
Alignment explanation
Indices: 28456023--28456063 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
28456013 AATATGAAAT
*
28456023 AAAATGA-AAATAATA-ATAAA
1 AAAATGACAAAAAATAGATAAA
28456043 AAAATGACAAAAAATAGATAA
1 AAAATGACAAAAAATAGATAA
28456064 TTATATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAATGACAAAAAATAGATAAA
Found at i:28461969 original size:40 final size:40
Alignment explanation
Indices: 28461925--28462003 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
28461915 TCCCTAAACC
*
28461925 TTTCCCCTGTAAAGATGACAAAGCTGTCCCGTGGAACTAT
1 TTTCCCCTGCAAAGATGACAAAGCTGTCCCGTGGAACTAT
*
28461965 TTTCCCCTGCAAAGATGGCAAAGCTGTCCCGTGGAACTA
1 TTTCCCCTGCAAAGATGACAAAGCTGTCCCGTGGAACTA
28462004 CAATTGCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTTCCCCTGCAAAGATGACAAAGCTGTCCCGTGGAACTAT
Found at i:28468037 original size:37 final size:37
Alignment explanation
Indices: 28467981--28468281 Score: 306
Period size: 37 Copynumber: 8.1 Consensus size: 37
28467971 TAGTTTCAAG
* *
28467981 ATTTTTAAAATCTCATTGCCTCAATTTTGAGGAATTC
1 ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
* *
28468018 ATTTTTAAAGTCTCGTTGCCTCAATTTTGAGGAGTTA
1 ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
*
28468055 ATTATTTTAAAAGTCTCATTGCTTCAATTTTGAGGAGTTC
1 A-T-TTTT-AAAGTCTCATTGCCTCAATTTTGAGGAGTTC
* * *
28468095 -TATTTAAAAGT-TCCGTTGCCTCAATTTTGAGGAGTTT
1 AT-TTTTAAAGTCT-CATTGCCTCAATTTTGAGGAGTTC
* * * *
28468132 ACTTTTAAAGTTTCGTTGCCTCAATTTTTAGGAGTT-
1 ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
* * * * *
28468168 -TTTTTAAAGTTTCATTGCTTCAATTTTGAAGATTTT
1 ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
* * *
28468204 ATTTTTAAAGTTTCATTGCCTCAATCTTGAGGAGTTT
1 ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
* *
28468241 ATTTTAAAAAG-CTTCATTGCCTCAATTTTGAGAAGTTC
1 ATTTT-TAAAGTC-TCATTGCCTCAATTTTGAGGAGTTC
28468279 ATT
1 ATT
28468282 AAAAAAAAAA
Statistics
Matches: 225, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
35 29 0.13
36 1 0.00
37 127 0.56
38 36 0.16
39 4 0.02
40 28 0.12
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (37 bp):
ATTTTTAAAGTCTCATTGCCTCAATTTTGAGGAGTTC
Found at i:28468240 original size:109 final size:113
Alignment explanation
Indices: 28467981--28468282 Score: 364
Period size: 114 Copynumber: 2.7 Consensus size: 113
28467971 TAGTTTCAAG
* * * * *
28467981 ATTTTTAAAATCTCATTGCCTCAATTTTGAGGAATTCATTTTTAAAGTCTCGTTGCCTCAATTTT
1 ATTTTTAAAGTTTCATTGCCTCAATTTTGAGGAGTTTA-TTTTAAAGTTTCGTTGCCTCAATTTT
*
28468046 GAGGAGTTAATTATTTTAAAAGTCTCATTGCTTCAATTTTGAGGAGTTCT
65 GAGGAGTT-ATTATTTTAAAAGTCTCATTGCTTCAATTTTGAAGAGTTCT
* * *
28468096 A-TTTAAAAGTTCCGTTGCCTCAATTTTGAGGAGTTTACTTTTAAAGTTTCGTTGCCTCAATTTT
1 ATTTTTAAAGTTTCATTGCCTCAATTTTGAGGAGTTTA-TTTTAAAGTTTCGTTGCCTCAATTTT
* * *
28468160 TAGGAG-T-TT-TTTT-AAAGTTTCATTGCTTCAATTTTGAAGA-TTTT
65 GAGGAGTTATTATTTTAAAAGTCTCATTGCTTCAATTTTGAAGAGTTCT
* * *
28468204 ATTTTTAAAGTTTCATTGCCTCAATCTTGAGGAGTTTATTTTAAAAAGCTTCATTGCCTCAATTT
1 ATTTTTAAAGTTTCATTGCCTCAATTTTGAGGAGTTTATTTT--AAAGTTTCGTTGCCTCAATTT
*
28468269 TGAGAAGTTCATTA
64 TGAGGAGTT-ATTA
28468283 AAAAAAAAAG
Statistics
Matches: 159, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
108 8 0.05
109 57 0.36
110 28 0.18
111 3 0.02
113 3 0.02
114 59 0.37
115 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (113 bp):
ATTTTTAAAGTTTCATTGCCTCAATTTTGAGGAGTTTATTTTAAAGTTTCGTTGCCTCAATTTTG
AGGAGTTATTATTTTAAAAGTCTCATTGCTTCAATTTTGAAGAGTTCT
Found at i:28468288 original size:38 final size:38
Alignment explanation
Indices: 28468210--28468288 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
28468200 TTTTATTTTT
* * * **
28468210 AAAGTTTCATTGCCTCAATCTTGAGGAGTTTATTTTAA
1 AAAGCTTCATTGCCTCAATCTTGAGAAGTTCATTAAAA
*
28468248 AAAGCTTCATTGCCTCAATTTTGAGAAGTTCATTAAAA
1 AAAGCTTCATTGCCTCAATCTTGAGAAGTTCATTAAAA
28468286 AAA
1 AAA
28468289 AAAGAGCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (38 bp):
AAAGCTTCATTGCCTCAATCTTGAGAAGTTCATTAAAA
Found at i:28470477 original size:17 final size:18
Alignment explanation
Indices: 28470451--28470488 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28470441 AAGATTATTC
*
28470451 AATAAAAATA-ATAAATA
1 AATAAAAATAGATAAAAA
*
28470468 AATAACAATAGATAAAAA
1 AATAAAAATAGATAAAAA
28470486 AAT
1 AAT
28470489 GATGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAAAATAGATAAAAA
Found at i:28470592 original size:11 final size:11
Alignment explanation
Indices: 28470563--28470607 Score: 58
Period size: 10 Copynumber: 4.1 Consensus size: 11
28470553 TACATGACAT
28470563 TAAATAAATAGGA
1 TAAATAAATA--A
28470576 -AAATAAATAA
1 TAAATAAATAA
28470586 TAAATAAATAA
1 TAAATAAATAA
28470597 T-AATAAATAA
1 TAAATAAATAA
28470607 T
1 T
28470608 CTAAGACGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.35
11 11 0.35
12 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:28470844 original size:26 final size:26
Alignment explanation
Indices: 28470797--28470847 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28470787 AAATAGATAA
*
28470797 TTGCATTAGCATAGCATATACATATG
1 TTGCATCAGCATAGCATATACATATG
*
28470823 TTGCATCATGCATATCAT-TACATAT
1 TTGCATCA-GCATAGCATATACATAT
28470848 AAATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (26 bp):
TTGCATCAGCATAGCATATACATATG
Found at i:28473227 original size:15 final size:14
Alignment explanation
Indices: 28473202--28473236 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28473192 AGCTTGCAAA
28473202 AAATAAAATAAATAAT
1 AAAT-AAATAAAT-AT
28473218 AAATAAATAAATAT
1 AAATAAATAAATAT
28473232 AAATA
1 AAATA
28473237 TACATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATAAATAT
Found at i:28473308 original size:25 final size:26
Alignment explanation
Indices: 28473271--28473353 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 26
28473261 TTTGGATAAA
* *
28473271 AAAATTAATTAAATAAA-AAATATAT
1 AAAATAAAATAAATAAATAAATATAT
28473296 AAAATAAAATAAA-AAATAATGATAGTAAT
1 AAAATAAAATAAATAAATAA--ATA-T-AT
28473325 AAAATGAAAA-AAATAAATAAATAATAT
1 AAAAT-AAAATAAATAAATAAAT-ATAT
28473352 AA
1 AA
28473354 TTGGAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 3 0.06
25 13 0.27
27 7 0.15
28 4 0.08
29 11 0.23
30 10 0.21
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAATAAAATAAATAAATAAATATAT
Found at i:28486868 original size:158 final size:158
Alignment explanation
Indices: 28486576--28486898 Score: 398
Period size: 158 Copynumber: 2.0 Consensus size: 158
28486566 CCATCTCACT
* * * *
28486576 CCTTGTAATGGTTCTTGGTATATACTTATAAAATCTCGTAAACTCTTTATAGAGAGTGAACAATT
1 CCTTGTAATGGTTCTTAGTATATACTTATAAAATATCGTAAACTCTTTATAAAGAGTGAACAATC
* * * * **
28486641 GACAAATTGTTGAACTGCCTCACTGGTAAAAGTATGTTTGTGGCTAACCATCTAAGGTTGCCCTT
66 GACAAATTGTTGAACTGCCTCACTGGTAAAAGTATATTTGTAGCTAACCATCTAAGGCTACCCCC
* *
28486706 ATGGCCCGACGATAACA-ATTCTTTGTCC
131 ATGGCCCGACAATAACACA-TCTTGGTCC
* * *
28486734 CCTTGTAATGGTTCTTAGTATATACTTGTAAAATATCGTAAACTCTTTATAAAG-GATGAGCAGT
1 CCTTGTAATGGTTCTTAGTATATACTTATAAAATATCGTAAACTCTTTATAAAGAG-TGAACAAT
**** * * *
28486798 CGGTGGATTGTTGGATTGCCTCACTGGTAAAAGTATATTTGTAGCTAACCATTTAAGGCTACCCC
65 CGACAAATTGTTGAACTGCCTCACTGGTAAAAGTATATTTGTAGCTAACCATCTAAGGCTACCCC
*
28486863 CATGGCCCTACAATAACACATCTTGGTCC
130 CATGGCCCGACAATAACACATCTTGGTCC
*
28486892 CTTTGTA
1 CCTTGTA
28486899 CTTATCTCGA
Statistics
Matches: 139, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
157 1 0.01
158 137 0.99
159 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (158 bp):
CCTTGTAATGGTTCTTAGTATATACTTATAAAATATCGTAAACTCTTTATAAAGAGTGAACAATC
GACAAATTGTTGAACTGCCTCACTGGTAAAAGTATATTTGTAGCTAACCATCTAAGGCTACCCCC
ATGGCCCGACAATAACACATCTTGGTCC
Found at i:28490220 original size:4 final size:4
Alignment explanation
Indices: 28490211--28490265 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
28490201 TTAAGGGATG
28490211 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
28490259 CTTT CTT
1 CTTT CTT
28490266 CACCAGTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:28497852 original size:16 final size:16
Alignment explanation
Indices: 28497831--28497885 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
28497821 TGAATTCAAA
28497831 TTAAATTATTTTGAAT
1 TTAAATTATTTTGAAT
*
28497847 TTAAATTATTTCGAAT
1 TTAAATTATTTTGAAT
* * * *
28497863 TTGAGTCAGTTTGAAT
1 TTAAATTATTTTGAAT
28497879 TTAAATT
1 TTAAATT
28497886 CAAATTATCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (16 bp):
TTAAATTATTTTGAAT
Found at i:28499326 original size:28 final size:29
Alignment explanation
Indices: 28499295--28499349 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28499285 TAATAAATAA
28499295 ATTTTATATATTA-TATTTTACCATAAGT
1 ATTTTATATATTATTATTTTACCATAAGT
* * *
28499323 ATTTTTTATTTTATTTTTTTACCATAA
1 ATTTTATATATTATTATTTTACCATAA
28499350 TATGAATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTATATATTATTATTTTACCATAAGT
Found at i:28500039 original size:3 final size:3
Alignment explanation
Indices: 28500031--28500060 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28500021 ACGAATTACC
*
28500031 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28500061 TTTTAAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:28502888 original size:4 final size:4
Alignment explanation
Indices: 28502879--28502944 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
28502869 CCCCACTAGC
* *
28502879 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
28502927 ATAC ATAT ACAT ATAT AT
1 ATAT ATAT ATAT ATAT AT
28502945 TATTTAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:28502890 original size:6 final size:6
Alignment explanation
Indices: 28502879--28502944 Score: 96
Period size: 6 Copynumber: 11.0 Consensus size: 6
28502869 CCCCACTAGC
* *
28502879 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAC ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
28502927 ATACAT ATACAT ATATAT
1 ATATAT ATATAT ATATAT
28502945 TATTTAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATAT
Done.