Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2231931 original size:25 final size:26
Alignment explanation
Indices: 2231854--2231932 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
2231844 AAATTTAACC
*
2231854 TTTT-TTATTATTTTTTATTTTATTTCG
1 TTTTCTTATTA-TTTTTATTTTATTT-A
2231881 TTTTCTTATT-TTTTTATTTTCA-TTA
1 TTTTCTTATTATTTTTATTTT-ATTTA
*
2231906 TTTTCTTATTATTTTTCTTTT-TTTA
1 TTTTCTTATTATTTTTATTTTATTTA
2231931 TT
1 TT
2231933 ACTTCATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
25 15 0.33
26 21 0.46
27 5 0.11
28 5 0.11
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTCTTATTATTTTTATTTTATTTA
Found at i:2235358 original size:60 final size:61
Alignment explanation
Indices: 2235289--2235426 Score: 194
Period size: 60 Copynumber: 2.3 Consensus size: 61
2235279 AATTATTCTT
* * * *
2235289 ATTTTATCCTTAAATTATGA-CTATCATTTTAAATT-AGTCCTCAAA-TTTTTGAACATTTCA
1 ATTTCATCCTCAAATTATGATCT-TCATTCTAAATTGA-TCCCCAAACTTTTTGAACATTTCA
2235349 ATTTCATCCTCAAATTATGATCTTCATTCTAAATTGATCCCCAAACTTTTTGAACATTTCA
1 ATTTCATCCTCAAATTATGATCTTCATTCTAAATTGATCCCCAAACTTTTTGAACATTTCA
2235410 ATTTCATCC-CAAATTAT
1 ATTTCATCCTCAAATTAT
2235427 ATGTACATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
60 44 0.62
61 27 0.38
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (61 bp):
ATTTCATCCTCAAATTATGATCTTCATTCTAAATTGATCCCCAAACTTTTTGAACATTTCA
Found at i:2235645 original size:59 final size:59
Alignment explanation
Indices: 2235553--2235667 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
2235543 GATAAATTTA
* ** * **
2235553 GGATGAAATTGGAAGATTCAAAAGTTTGGGGACTAATTTGGAATGAGAGTCATAGTTTG
1 GGATGAAATTAGAAGATTCAAAAGTTTAAGGACTAATCTAAAATGAGAGTCATAGTTTG
* *
2235612 GGATGAAATTAGAATG-TTTAAAAGTTTAAGGACTAATCTAAAATGAGGGTCATAGT
1 GGATGAAATTAGAA-GATTCAAAAGTTTAAGGACTAATCTAAAATGAGAGTCATAGT
2235668 CTGAGGATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 46 0.98
60 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.30
Consensus pattern (59 bp):
GGATGAAATTAGAAGATTCAAAAGTTTAAGGACTAATCTAAAATGAGAGTCATAGTTTG
Found at i:2237711 original size:45 final size:45
Alignment explanation
Indices: 2237660--2238005 Score: 380
Period size: 45 Copynumber: 7.7 Consensus size: 45
2237650 TTTGTAACAT
* * *
2237660 CTTTTCCT-TTGATAATGCACCCATATACATTTCAACTGTAGTATA
1 CTTTT-CTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
*
2237705 CTTTTCCT-TTGATAATGTACCCATATACATTTTAAC-CATAGCATA
1 CTTTT-CTGTTGATAATGTACCCATATACATTTCAACTC-TAGCATA
*
2237750 CTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCAT-
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* * * *
2237794 GTTCTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGCATA
1 CTT-TTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* * * *
2237840 CTTATCTGTTGATAATGCACCCATATGCATTCCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
** * *
2237885 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTAAAGTATG
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
* *
2237930 TTTTTCTGTTGTTAATGTACCCATATACATTTCAAC-CATAGCAT-
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTC-TAGCATA
* * * * *
2237974 CCTTTCATGCTAATAATGCACCCATATGCATT
1 CTTTTC-TGTTGATAATGTACCCATATACATT
2238006 AGTATTTTCA
Statistics
Matches: 262, Mismatches: 32, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
44 8 0.03
45 251 0.96
46 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
Found at i:2237841 original size:135 final size:135
Alignment explanation
Indices: 2237668--2238005 Score: 432
Period size: 135 Copynumber: 2.5 Consensus size: 135
2237658 ATCTTTTCCT
* * *
2237668 TTGATAATGCACCCATATACATTTCAACTGTAGTATACTTTTCCT-TTGATAATGTACCCATATA
1 TTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTT-CTGTTGATAATGCACCCATATA
** **
2237732 CATTTTAAC-CATAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATGT
65 CATTCCAACTC-TAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAACTAAAGCATGT
2237796 TCTTCTA
129 TCTTCTA
* * *
2237803 TTGATAATGCACCCATATGCATTTCAACTCTAGCATACTTATCTGTTGATAATGCACCCATATGC
1 TTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATAC
* * *
2237868 ATTCCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAAAGTATGTTT
66 ATTCCAACTCTAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAACTAAAGCATGTTC
*
2237933 TTCTG
131 TTCTA
* * * * *
2237938 TTGTTAATGTACCCATATACATTTCAAC-CATAGCAT-CCTTTCATGCTAATAATGCACCCATAT
1 TTGATAATGCACCCATATACATTTCAACTC-TAGCATACTTTTC-TGTTGATAATGCACCCATAT
*
2238001 GCATT
64 ACATT
2238006 AGTATTTTCA
Statistics
Matches: 178, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
134 7 0.04
135 170 0.96
136 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (135 bp):
TTGATAATGCACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATAC
ATTCCAACTCTAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAACTAAAGCATGTTC
TTCTA
Found at i:2238440 original size:20 final size:20
Alignment explanation
Indices: 2238412--2238466 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
2238402 TGGCCCTTCA
*
2238412 GTATCGATACCCCTACTATG
1 GTATTGATACCCCTACTATG
*
2238432 GTATTGATACTACCCTATTATG
1 GTATTGATAC--CCCTACTATG
2238454 GTATTGATACCCC
1 GTATTGATACCCC
2238467 CTTCCAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
22 19 0.61
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
GTATTGATACCCCTACTATG
Found at i:2238453 original size:22 final size:22
Alignment explanation
Indices: 2238422--2238463 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2238412 GTATCGATAC
2238422 CCCTACTATGGTATTGATACTA
1 CCCTACTATGGTATTGATACTA
*
2238444 CCCTATTATGGTATTGATAC
1 CCCTACTATGGTATTGATAC
2238464 CCCCTTCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (22 bp):
CCCTACTATGGTATTGATACTA
Found at i:2238532 original size:95 final size:93
Alignment explanation
Indices: 2238412--2238633 Score: 229
Period size: 94 Copynumber: 2.4 Consensus size: 93
2238402 TGGCCCTTCA
* * **
2238412 GTATCGATACCC-CTACTATGGTATTGATACTACCCTAT-TATGGTATTGATACCCCCTTCCA-G
1 GTATCGATACCCTC-ACCATGGTATTGATAC--CACTATCTATGGTACCGATACCCCCTT--AGG
2238474 TATCAATACCAAAATTA-ACTTCGATGTAAT-ATG
61 TATCAATACCAAAATTAGA-TTCGATGT-ATCATG
* *
2238507 GTATCGATACCCTCACCATGTTATTGATACCACTATGCTATGGTACCGATACCCCCTTAGGTATT
1 GTATCGATACCCTCACCATGGTATTGATACCACTAT-CTATGGTACCGATACCCCCTTAGGTATC
* * *
2238572 GATACCAAAATTAGATTCGATGTTTCTTG
65 AATACCAAAATTAGATTCGATGTATCATG
* **
2238601 GTATCGATACCCTTACCATGGTATCAATACCAC
1 GTATCGATACCCTCACCATGGTATTGATACCAC
2238634 ATCGCTTGGA
Statistics
Matches: 108, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
93 7 0.06
94 55 0.51
95 45 0.42
96 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (93 bp):
GTATCGATACCCTCACCATGGTATTGATACCACTATCTATGGTACCGATACCCCCTTAGGTATCA
ATACCAAAATTAGATTCGATGTATCATG
Found at i:2238613 original size:94 final size:94
Alignment explanation
Indices: 2238479--2238651 Score: 228
Period size: 94 Copynumber: 1.8 Consensus size: 94
2238469 TCCAGTATCA
* **
2238479 ATACCAAAATTAACTTCGATGTAATATGGTATCGATACCCTCACCATGTTATTGATACCACTAT-
1 ATACCAAAATTAACTTCGATGTAATATGGTATCGATACCCTCACCATGGTATCAATACCAC-ATC
2238543 GCTATGG-TACCGATACCCCCTTAGGTATTG
65 GCT-TGGATACCGATACCCCCTTAGGTATTG
* * *
2238573 ATACCAAAATTAGA-TTCGATGT-TTCTTGGTATCGATACCCTTACCATGGTATCAATACCACAT
1 ATACCAAAATTA-ACTTCGATGTAAT-ATGGTATCGATACCCTCACCATGGTATCAATACCACAT
2238636 CGCTTGGATACCGATA
64 CGCTTGGATACCGATA
2238652 ATGATTGAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
93 6 0.09
94 62 0.90
95 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (94 bp):
ATACCAAAATTAACTTCGATGTAATATGGTATCGATACCCTCACCATGGTATCAATACCACATCG
CTTGGATACCGATACCCCCTTAGGTATTG
Found at i:2244939 original size:127 final size:127
Alignment explanation
Indices: 2244762--2245080 Score: 394
Period size: 127 Copynumber: 2.5 Consensus size: 127
2244752 CATCTTTAGG
* * *
2244762 AAGGATGATAAC-TCGGTTCCTACGTGATGAGGACGACTGGTTATTTGGGTTGACACAGTTCCTA
1 AAGGGTGATAACAT-GGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTA
* * ** * * * *
2244826 CATAATGAGGAAATCTGGTCGGGTGATGACACGGTTCCTACGCGATGAGGACG-CAT-TCCATCT
65 CATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGA-GTC-TGACCACCT
* * *
2244889 AAGGGTGATAACATGGTTCCTACGTGATAAGGACGATTGGTTATCTGGGTTGACACAACTCCTAC
1 AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
* * *
2244954 ATAATGAGGAGATCTGGTCAGTTGATAACACGACTCATACGTGATGAAGAGTTCTGACCACCT
66 ATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGAG-TCTGACCACCT
* * *
2245017 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTAGTTATCT-GGTTGACACAATTCCTAC
1 AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
2245081 GCTATAAGGA
Statistics
Matches: 165, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
126 1 0.01
127 116 0.70
128 48 0.29
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (127 bp):
AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
ATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGAGTCTGACCACCT
Found at i:2245330 original size:35 final size:34
Alignment explanation
Indices: 2245221--2245345 Score: 118
Period size: 35 Copynumber: 3.8 Consensus size: 34
2245211 GACAAAATTC
* *
2245221 GTTTCAAGGG-AATGACTCAAAGATG---GTTAT
1 GTTTCAAGGGAAACGACTCAAAGATGTTTGTTTT
* **
2245251 GTTTCAAGAGAAACAGACTCAAAGA--TTTAATTT
1 GTTTCAAGGGAAAC-GACTCAAAGATGTTTGTTTT
*
2245284 GTTTCATGGGAAACGATCTCAAAGATGTTTGTTTT
1 GTTTCAAGGGAAACGA-CTCAAAGATGTTTGTTTT
*
2245319 GTTTCAAGGGAAACATACTCAAAGATG
1 GTTTCAAGGGAAAC-GACTCAAAGATG
2245346 GGTGTTTCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
30 9 0.12
31 2 0.03
32 12 0.16
33 22 0.29
35 29 0.39
36 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (34 bp):
GTTTCAAGGGAAACGACTCAAAGATGTTTGTTTT
Found at i:2245531 original size:33 final size:34
Alignment explanation
Indices: 2245456--2245535 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
2245446 ATAAGATTTG
* ** *
2245456 TTTCAAGAGAAAC-GATCTCAAAGATGGTTGTTG
1 TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
* *
2245489 TTTCCAGTGAAACAGA-CTCAAAGATAATTTTTA
1 TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
2245522 TTTCAAGTGAAACA
1 TTTCAAGTGAAACA
2245536 ATTTCAGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (34 bp):
TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
Found at i:2245891 original size:34 final size:34
Alignment explanation
Indices: 2245848--2245914 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2245838 AAAGGAAAAA
**
2245848 TGTCTCAAGCGAGATGAAATTTGTTTTGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAT
*
2245882 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAA
2245915 AACACCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAT
Found at i:2247297 original size:2 final size:2
Alignment explanation
Indices: 2247290--2247314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2247280 TCAGCTTTAT
2247290 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2247315 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2251430 original size:30 final size:29
Alignment explanation
Indices: 2251395--2251509 Score: 97
Period size: 30 Copynumber: 3.9 Consensus size: 29
2251385 ATAAATCTTG
* * *
2251395 AAAACATGAACTTAAAGGATTAAAATAACA
1 AAAACA-GAATTTAAAGGACTAAAATAGCA
* * *
2251425 TAAACAGAAGTTAAGAGG-CTAAAATAGTA
1 AAAACAGAATTTAA-AGGACTAAAATAGCA
* *
2251454 AAAACAGAAATTTAAAAGACCAAAATAGCA
1 AAAACAG-AATTTAAAGGACTAAAATAGCA
* *
2251484 CAAACATGAATTTAAAGGATTAAAAT
1 AAAACA-GAATTTAAAGGACTAAAAT
2251510 GGAAAAAATA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 23 0.34
30 43 0.64
31 1 0.01
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (29 bp):
AAAACAGAATTTAAAGGACTAAAATAGCA
Found at i:2252100 original size:21 final size:21
Alignment explanation
Indices: 2252048--2252093 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2252038 ACAAACAGAA
2252048 AAGTAAAATTTAAGAAGTACC
1 AAGTAAAATTTAAGAAGTACC
2252069 AAGTAAAATTTAAGAAGTACC
1 AAGTAAAATTTAAGAAGTACC
2252090 AAGT
1 AAGT
2252094 GGAATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGTAAAATTTAAGAAGTACC
Found at i:2253353 original size:127 final size:126
Alignment explanation
Indices: 2252934--2253355 Score: 417
Period size: 123 Copynumber: 3.3 Consensus size: 126
2252924 GTGACACGAC
* ** * *
2252934 TCCTACATAATGAGGAGATCTAGTTGGGGGATAACAT-TCCTCATACTTGATGAAGAGTTCTTGG
1 TCCTACATAATGAGGAG-TCT-GGTCAGGGATGACATGT-CTCATACGTGATGAAGAGTTC-TGG
* * **
2252998 CCATCTTTAGGAAGGGTGATAACTCGATTCCTACGTGATGAGGATAACTGGTTATCTGGGTTGAC
62 CCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGTTGAC
2253063 ACAGT
122 ACAGT
* * * * * ** **
2253068 TCCTACATAATGAGGAAATCTGGTC-GGG-TGACACGGT-TCCTACGCGATGAGGA-TGGTAACC
1 TCCTACATAATGAGG-AGTCTGGTCAGGGATGACA-TGTCTCATACGTGATGAAGAGTTCTGGCC
* * *
2253129 ATCT-AAGGTGATAACACGGTTCCTACGTGATGAGGACGGATGGTTATCTGGGTTGACACAGC
64 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGTTGACACAGT
*
2253191 TCCTACATAATGAGGAGATCTGGTCAGTTGATGACATGTCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACATAATGAGGAG-TCTGGTCAG-GGATGACATGTCTCATACGTGATGAAGAGTTCTGGCC
*
2253256 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTAGTTATCT-GGTTGACACAGT
64 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGTTGACACAGT
*** *
2253318 TCCTACGCGATGAGGATGGCTGGTCAAGGGATGACATG
1 TCCTACATAATGAGGA-GTCTGGTC-AGGGATGACATG
2253356 GTTCCTACGC
Statistics
Matches: 237, Mismatches: 39, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
122 1 0.00
123 71 0.30
124 3 0.01
125 3 0.01
126 18 0.08
127 48 0.20
128 45 0.19
129 6 0.03
130 1 0.00
131 16 0.07
132 3 0.01
133 3 0.01
134 18 0.08
135 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (126 bp):
TCCTACATAATGAGGAGTCTGGTCAGGGATGACATGTCTCATACGTGATGAAGAGTTCTGGCCAT
CTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTATCTGGGTTGACACAGT
Found at i:2253364 original size:40 final size:40
Alignment explanation
Indices: 2253274--2253420 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
2253264 GTGATAACAC
* * * ** * *
2253274 GGTTCCTACGTGATGAGGATGGCTAGTTATCTGGTTGACAC
1 GGTTCCTACGCGATGAGGATGGCTGGTCA-AGGGATGACAT
*
2253315 AGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACAT
1 GGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACAT
2253355 GGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACAT
1 GGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACAT
* * *
2253395 GGTTTCTACGTGATGAGGACGGCTGG
1 GGTTCCTACGCGATGAGGATGGCTGG
2253421 CCATCTTTAG
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 69 0.73
41 25 0.27
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (40 bp):
GGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACAT
Found at i:2253370 original size:127 final size:126
Alignment explanation
Indices: 2252982--2253370 Score: 430
Period size: 123 Copynumber: 3.0 Consensus size: 126
2252972 CCTCATACTT
* * **
2252982 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTACGTGATGAGGATAACT
1 GATGAAGAGTTC-TGGCCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGATGGCT
* *
2253047 GGTTATCTGGGTTGACACAGTTCCTACATAATGAGGAAATCTGGTC-GGG-TGACACGGTTCCTA
60 GGTTATCTGGGTTGACACAGTTCCTACATAATGAGG-AGTCTGGTCAGGGATGACATGGTTCCTA
2253110 CGC
124 CGC
* ** ** * *
2253113 GATGAGGA-TGGTAACCATCT-AAGGTGATAACACGGTTCCTACGTGATGAGGACGGATGGTTAT
1 GATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTAT
* * * *
2253176 CTGGGTTGACACAGCTCCTACATAATGAGGAGATCTGGTCAGTTGATGACAT-GTCTCATACGT
66 CTGGGTTGACACAGTTCCTACATAATGAGGAG-TCTGGTCAG-GGATGACATGGT-TCCTACGC
*
2253239 GATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTAGTTAT
1 GATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTAT
*** *
2253304 CT-GGTTGACACAGTTCCTACGCGATGAGGATGGCTGGTCAAGGGATGACATGGTTCCTACGC
66 CTGGGTTGACACAGTTCCTACATAATGAGGA-GTCTGGTC-AGGGATGACATGGTTCCTACGC
2253366 GATGA
1 GATGA
2253371 GGATGGCTGG
Statistics
Matches: 215, Mismatches: 33, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
122 1 0.00
123 71 0.33
124 3 0.01
125 3 0.01
126 18 0.08
127 58 0.27
128 47 0.22
129 6 0.03
130 1 0.00
131 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (126 bp):
GATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTGGTTAT
CTGGGTTGACACAGTTCCTACATAATGAGGAGTCTGGTCAGGGATGACATGGTTCCTACGC
Found at i:2253390 original size:21 final size:21
Alignment explanation
Indices: 2253326--2253391 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
2253316 GTTCCTACGC
2253326 GATGAGGATGGCTGGTCAAGG
1 GATGAGGATGGCTGGTCAAGG
* * ** * *
2253347 GATGA-CATGGTTCCT-ACGC
1 GATGAGGATGGCTGGTCAAGG
2253366 GATGAGGATGGCTGGTCAAGG
1 GATGAGGATGGCTGGTCAAGG
2253387 GATGA
1 GATGA
2253392 CATGGTTTCT
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 7 0.23
20 12 0.39
21 12 0.39
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.21
Consensus pattern (21 bp):
GATGAGGATGGCTGGTCAAGG
Found at i:2253607 original size:35 final size:34
Alignment explanation
Indices: 2253529--2253628 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 34
2253519 CTTAAAGATG
* *
2253529 GTTTTGTTTCAAGAGAAACAGACTCAGAGA--TTT
1 GTTTTGTTTCAAGGGAAACA-ACTCAAAGATGTTT
**
2253562 AATTTGTTTCAAGGGAAACAATCTCAAAGATGTTT
1 GTTTTGTTTCAAGGGAAACAA-CTCAAAGATGTTT
2253597 GTTTTGTTTCAAGGGAAACAAACTCAAAGATG
1 GTTTTGTTTCAAGGGAAAC-AACTCAAAGATG
2253629 GGTATGTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
32 1 0.02
33 24 0.42
35 30 0.53
36 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (34 bp):
GTTTTGTTTCAAGGGAAACAACTCAAAGATGTTT
Found at i:2254298 original size:22 final size:20
Alignment explanation
Indices: 2254251--2254325 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 20
2254241 CAATGTAATC
**
2254251 TGGTATCGATACC-CTCACCA
1 TGGTATCGATACCACT-ATTA
2254271 TGGTATCGATACCACTATGATA
1 TGGTATCGATACCACTAT--TA
* *
2254293 TGGTATCGATACCCCTCTTA
1 TGGTATCGATACCACTATTA
2254313 -GGTATCGATACCA
1 TGGTATCGATACCA
2254326 AAATTAGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 12 0.26
20 16 0.34
21 2 0.04
22 17 0.36
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
TGGTATCGATACCACTATTA
Found at i:2257404 original size:85 final size:83
Alignment explanation
Indices: 2257299--2257467 Score: 320
Period size: 85 Copynumber: 2.0 Consensus size: 83
2257289 TCAATCTAAA
2257299 AATAAAATAATACTATTCTTTATTTATTTTTATTTTTTTTAAAATCAAGCTCCTTGTCATATCCA
1 AATAAAATAATACTATTCTTTATTTATTTTTATTTTTTTTAAAATCAAGCTCCTTGTCATATCCA
2257364 CGTCCAATTTTTTAATTT
66 CGTCCAATTTTTTAATTT
2257382 AATAAAATAATATACTATTCTTTATTTATTTTTATTTTTTTTAAAATCAAGCTCCTTGTCATATC
1 AATAAAAT-A-ATACTATTCTTTATTTATTTTTATTTTTTTTAAAATCAAGCTCCTTGTCATATC
2257447 CACGTCCAATTTTTTAATTT
64 CACGTCCAATTTTTTAATTT
2257467 A
1 A
2257468 TTCTCTTAGT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
83 8 0.10
84 1 0.01
85 75 0.89
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (83 bp):
AATAAAATAATACTATTCTTTATTTATTTTTATTTTTTTTAAAATCAAGCTCCTTGTCATATCCA
CGTCCAATTTTTTAATTT
Found at i:2260252 original size:4 final size:4
Alignment explanation
Indices: 2260243--2260275 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
2260233 TTTCCAGGTA
2260243 TTTC TTTC TTTC TTTC TTTC TTTC -TTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
2260276 CAATTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:2261956 original size:18 final size:16
Alignment explanation
Indices: 2261924--2261957 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2261914 TATTAATGGA
2261924 GTAAAAAAATAAAAAG
1 GTAAAAAAATAAAAAG
2261940 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAA-TAAAAAG
2261958 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
GTAAAAAAATAAAAAG
Found at i:2262097 original size:16 final size:17
Alignment explanation
Indices: 2262065--2262118 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2262055 TATTAAGAAA
2262065 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
2262082 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
2262098 ATAATATATA-AATAAAT
1 AAAATA-ATAGAAAAAAT
2262115 AAAA
1 AAAA
2262119 ACAAAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.43
17 16 0.53
18 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:2262140 original size:16 final size:16
Alignment explanation
Indices: 2262121--2262176 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
2262111 AAATAAAAAC
*
2262121 AAAAATAGATATTAAG
1 AAAAATATATATTAAG
*
2262137 AAAATATATATATAAAAAG
1 AAAA-ATATATAT--TAAG
*
2262156 TAAAATATATATTAAG
1 AAAAATATATATTAAG
2262172 AAAAA
1 AAAAA
2262177 ATACATACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 11 0.34
17 7 0.22
18 8 0.25
19 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
AAAAATATATATTAAG
Found at i:2262244 original size:2 final size:2
Alignment explanation
Indices: 2262207--2262310 Score: 120
Period size: 2 Copynumber: 52.0 Consensus size: 2
2262197 AAAAAAAATC
* * * * *
2262207 TA TA CTA TA CA TA TA CA TA TA CA TA CA TA CA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2262250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2262291 TA TA TA AA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2262311 AATAAAAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.01
2 84 0.97
3 2 0.02
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
TA
Found at i:2262320 original size:21 final size:21
Alignment explanation
Indices: 2262277--2262337 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
2262267 ATATATATAT
*
2262277 ATATATATATAAGATATATAAAA
1 ATATATATATAA-ATA-AAAAAA
2262300 ATATATATATAAATAAAAAAA
1 ATATATATATAAATAAAAAAA
**
2262321 GGA-ATATAGTAAATAAA
1 ATATATATA-TAAATAAA
2262338 TAAATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.15
21 14 0.41
22 3 0.09
23 12 0.35
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
ATATATATATAAATAAAAAAA
Found at i:2273825 original size:302 final size:302
Alignment explanation
Indices: 2273276--2273879 Score: 1190
Period size: 302 Copynumber: 2.0 Consensus size: 302
2273266 TTCTAAAACT
2273276 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
1 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
2273341 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
66 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
2273406 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
131 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
*
2273471 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAT
196 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
2273536 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
261 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
2273578 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
1 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
2273643 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
66 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
2273708 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
131 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
*
2273773 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAATCCCCTCGATATCTATTTAC
196 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
2273838 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
261 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
2273880 ATCTACTCAA
Statistics
Matches: 300, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
302 300 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (302 bp):
TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
Found at i:2274211 original size:122 final size:124
Alignment explanation
Indices: 2273992--2274369 Score: 392
Period size: 110 Copynumber: 3.2 Consensus size: 124
2273982 ATGTCAAACA
* * * * *
2273992 CCACAAAATGGTAACATTAGCGACGGTTTTTCTAAAAATGTCGCTATAGACTCATCTTTTACGGC
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCAAAAAACGCCGCTATAAACTCATCTTTTACGGC
* * *
2274057 ATTTTTAAAATAAATGCCGCAATAAATTAGTGCATTAGTGGCATTTTT-AATACAAATG
66 ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
* * * * *
2274115 CCACAAAATGGTAATATTAGCGA-AGTTTTTCAAAAAACGCCGTTATAAACTCGTCTTTTGCGGT
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCAAAAAACGCCGCTATAAACTCATCTTTTACGGC
* *
2274179 ATTTTTAAAACAAATACCTCAATAAATCAGTGCATTAGTGGCGTTTTTAAATACAAATG
66 ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
* * * * * *
2274238 TCACAAAATGGTAACATTAGTGGCA--TTTTC--TATA----GC-AT----T-ATCTTTTGCGGC
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCAAAAAACGCCGCTATAAACTCATCTTTTACGGC
* ** * * * *
2274289 TTTTTTAAAACAAGCACCGCAATAAATCAGTGCATTAGTGGCGTTTTTAGATTCAAACG
66 ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
2274348 CCACAAAATGGTAACATTAGCG
1 CCACAAAATGGTAACATTAGCG
2274370 GTGTTTTTAT
Statistics
Matches: 220, Mismatches: 33, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
110 82 0.37
111 1 0.00
115 2 0.01
116 1 0.00
120 2 0.01
122 80 0.36
123 51 0.23
124 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (124 bp):
CCACAAAATGGTAACATTAGCGACAGTTTTTCAAAAAACGCCGCTATAAACTCATCTTTTACGGC
ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
Found at i:2274458 original size:232 final size:232
Alignment explanation
Indices: 2274045--2274467 Score: 562
Period size: 232 Copynumber: 1.8 Consensus size: 232
2274035 CTATAGACTC
* ** *
2274045 ATCTTTTACGGCATTTTTAAAATAAATGCCGCAATAAATTAGTGCATTAGTGGCATTTTTAATAC
1 ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTAATAC
* *
2274110 AAATGCCACAAAATGGTAATATTAGCGAAGTTTTTCAAAAAACGCCGTTATAAACTCGTCTTTTG
66 AAACGCCACAAAATGGTAACATTAGCGAAGTTTTTCAAAAAACGCCGTTATAAACTCGTCTTTTG
* * * *
2274175 CGGTATTTTTAAAACAAATACCTCAATAAATCAGTGCATTAGTGGCGTTTTTAAATACAAATGTC
131 CGGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAATGTC
2274240 ACAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
196 ACAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
* * * * *
2274277 ATCTTTTGCGGCTTTTTTAAAACAAGCACCGCAATAAATCAGTGCATTAGTGGCGTTTTTAGATT
1 ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTA-ATA
** * * ** *
2274342 CAAACGCCACAAAATGGTAACATTAGCGGTGTTTTT-ATATAAACGTCGTTATTGACTTGTCTTT
65 CAAACGCCACAAAATGGTAACATTAGCGAAGTTTTTCA-AAAAACGCCGTTATAAACTCGTCTTT
* * ** **
2274406 TGTGGTGTTTTT-AAACAAACGTCGCAATAGGTCAGTGAATTAGTGACGTTTTTAAATACAAA
129 TGCGGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAA
2274468 CGCCGCAAGT
Statistics
Matches: 161, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
232 96 0.60
233 65 0.40
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (232 bp):
ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTAATAC
AAACGCCACAAAATGGTAACATTAGCGAAGTTTTTCAAAAAACGCCGTTATAAACTCGTCTTTTG
CGGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAATGTC
ACAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
Found at i:2276086 original size:51 final size:51
Alignment explanation
Indices: 2276010--2276108 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
2276000 TTAAAAGTTG
* *
2276010 ATGTTTCTTATCTGTCCTAAAAATGGGTGGAAGAGACTACATTTTATGTTT
1 ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATGTTT
*
2276061 ATGTTTCTTTTATGTCATAAAAATGGGTGGAAGAGACTACATTTTATG
1 ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATG
2276109 AAGATAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (51 bp):
ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATGTTT
Found at i:2277453 original size:2 final size:2
Alignment explanation
Indices: 2277446--2277481 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2277436 ACATAAATGC
2277446 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
2277482 TTACACTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2279585 original size:4 final size:4
Alignment explanation
Indices: 2279576--2279604 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2279566 TAAATGTGTC
2279576 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
2279605 ACAAGGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:2283527 original size:6 final size:6
Alignment explanation
Indices: 2283515--2283564 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
2283505 TCTATGAATG
* *
2283515 TATGTA CATGTA CATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
2283563 TA
1 TA
2283565 AAAAGATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (6 bp):
TATGTA
Found at i:2284679 original size:25 final size:26
Alignment explanation
Indices: 2284651--2284699 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2284641 TTTTAACTAC
2284651 ACAAA-TTTATTAATATT-TTATTAAA
1 ACAAACTTT-TTAATATTATTATTAAA
*
2284676 ACAAACTTTTTTATATTATTATTA
1 ACAAACTTTTTAATATTATTATTA
2284700 TTATTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (26 bp):
ACAAACTTTTTAATATTATTATTAAA
Found at i:2288114 original size:27 final size:27
Alignment explanation
Indices: 2288076--2288139 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
2288066 AATGACTCTG
*
2288076 AATCATTCAAAATGTAC-TCATGTGTTA
1 AATCATTCAAAATATACTTC-TGTGTTA
*
2288103 AATCATTCAAAATATACTTCTGTGTTG
1 AATCATTCAAAATATACTTCTGTGTTA
2288130 AATCATTCAA
1 AATCATTCAA
2288140 TATTGTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (27 bp):
AATCATTCAAAATATACTTCTGTGTTA
Found at i:2289474 original size:30 final size:30
Alignment explanation
Indices: 2289440--2289512 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
2289430 GATACATGAA
2289440 TTTAGATAAAATA-CTATTTTGATCC-TAAAC
1 TTTAGATAAAATATC-ATTTTGA-CCTTAAAC
* *
2289470 TTTAGATGAAATATCATTTTGACCTTTTAAC
1 TTTAGATAAAATATCATTTTGACC-TTAAAC
2289501 TTTAGATAAAAT
1 TTTAGATAAAAT
2289513 GTCAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.05
30 19 0.51
31 16 0.43
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTAGATAAAATATCATTTTGACCTTAAAC
Found at i:2290809 original size:60 final size:59
Alignment explanation
Indices: 2290668--2290810 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 59
2290658 AAGGGTATAG
* * *
2290668 TACACAAATGGTCCCTTGACTATAGGGTCTTACTTTGTTGAGCCCTCTGACTATTAAAAGT
1 TACA-AAATGGTCCC-TGACTATAGGGACTTACTTTGTTGAGCACTCTGACTAGTAAAAGT
* * * *
2290729 TACAAAATGATCCTCCGACTATA-GGACGTTGCTTTGTTGAGTCATTC-GACTAGTAAAAGT
1 TACAAAATGGTCC-CTGACTATAGGGAC-TTACTTTGTTGAG-CACTCTGACTAGTAAAAGT
2290789 TACAAAATGGTCACCTGACTAT
1 TACAAAATGGTC-CCTGACTAT
2290811 TCATATATTC
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
59 3 0.04
60 57 0.83
61 9 0.13
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (59 bp):
TACAAAATGGTCCCTGACTATAGGGACTTACTTTGTTGAGCACTCTGACTAGTAAAAGT
Found at i:2292778 original size:25 final size:25
Alignment explanation
Indices: 2292740--2292797 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
2292730 TAAATTTAGA
* *
2292740 AAAATATATAAAAAATTTAGAGACAT
1 AAAAT-TATAAAAAATTTAAAAACAT
* *
2292766 AAAATTATAAAAATTTTAAAAATAT
1 AAAATTATAAAAAATTTAAAAACAT
2292791 AAAATTA
1 AAAATTA
2292798 AATCATCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 23 0.82
26 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (25 bp):
AAAATTATAAAAAATTTAAAAACAT
Found at i:2294227 original size:21 final size:21
Alignment explanation
Indices: 2294189--2294228 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2294179 ACGCTACGTA
* **
2294189 AAATGTTAATTTTTCTACCGG
1 AAATATTAATTTCGCTACCGG
2294210 AAATATTAATTTCGCTACC
1 AAATATTAATTTCGCTACC
2294229 AAAATGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (21 bp):
AAATATTAATTTCGCTACCGG
Found at i:2300601 original size:71 final size:71
Alignment explanation
Indices: 2300456--2300604 Score: 160
Period size: 71 Copynumber: 2.1 Consensus size: 71
2300446 TCTCCCTAAA
* * * *
2300456 TTTTTTGGTTTAATTATTTTTTAAGACATTATCAGTTTCAAAATTAAATGAAATTAAGTCTTGTC
1 TTTTTTGGTTTAATTATCTTTCAAGACATGATCAGTTTCAAAATTAAATGAAATTAAGTCTTATC
2300521 CTTAAT
66 CTTAAT
* * * * *
2300527 TTTTTTGGTTTGATTATCTTTCAGGACATGA-CGGTTTTAAAATT-AGTGAAATTAAG-CTTCAA
1 TTTTTTGGTTTAATTATCTTTCAAGACATGATCAGTTTCAAAATTAAATGAAATTAAGTCTT--A
*
2300589 TCCTCTATT
64 TCCT-TAAT
2300598 TTTTTTG
1 TTTTTTG
2300605 TGGTTTCAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
68 3 0.05
69 11 0.17
70 15 0.23
71 36 0.55
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (71 bp):
TTTTTTGGTTTAATTATCTTTCAAGACATGATCAGTTTCAAAATTAAATGAAATTAAGTCTTATC
CTTAAT
Found at i:2300696 original size:117 final size:117
Alignment explanation
Indices: 2300490--2300715 Score: 400
Period size: 117 Copynumber: 1.9 Consensus size: 117
2300480 GACATTATCA
*
2300490 GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTTGGTTTGATTATCTTTCAGGACA
1 GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTTGGTTTGATTATCTTGCAGGACA
* *
2300555 TGACGGTTTTAAAATTAGTGAAATTAAGCTTCAATCCTCTATTTTTTTTGTG
66 CGACGGTTATAAAATTAGTGAAATTAAGCTTCAATCCTCTATTTTTTTTGTG
2300607 GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAACTTTTTTTGGTTTGATTATCTTGCAGGAC
1 GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAA-TTTTTTTGGTTTGATTATCTTGCAGGAC
*
2300672 ACGACGGTTAT-AAATTAGTGAAATTAAGCTTCAATCTTCTATTT
65 ACGACGGTTATAAAATTAGTGAAATTAAGCTTCAATCCTCTATTT
2300716 ATTTATGGTT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
117 68 0.65
118 36 0.35
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (117 bp):
GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTTGGTTTGATTATCTTGCAGGACA
CGACGGTTATAAAATTAGTGAAATTAAGCTTCAATCCTCTATTTTTTTTGTG
Found at i:2302273 original size:60 final size:58
Alignment explanation
Indices: 2302200--2302330 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 58
2302190 GTAATAGGAT
**
2302200 AAAGTATAC-AAATAGACCCTCGACTATAGGGTGATGCTTTGTTGAG-TCATTAGACTATTA
1 AAAGT-TACAAAATAGACCCTCGACTA-A-GGTGATGCTTTGTTGAGTTC-CCAGACTATTA
** * * *
2302260 AAAGTTACAAAATAGTTCTTCGACTAAGGTGTTGCTTTGTTGAGTTCCCCGACTATTA
1 AAAGTTACAAAATAGACCCTCGACTAAGGTGATGCTTTGTTGAGTTCCCAGACTATTA
*
2302318 AAAGCTACAAAAT
1 AAAGTTACAAAAT
2302331 GGTCACCCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 36 0.59
59 6 0.10
60 19 0.31
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (58 bp):
AAAGTTACAAAATAGACCCTCGACTAAGGTGATGCTTTGTTGAGTTCCCAGACTATTA
Found at i:2306222 original size:22 final size:22
Alignment explanation
Indices: 2306172--2306223 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
2306162 CGTGAATATG
* *
2306172 TTCGTTTAGCGTTCATTTAGTG
1 TTCGTTTAGCATTCATTTAGTA
* * *
2306194 TTAGTTTAGCATTTATTTATTA
1 TTCGTTTAGCATTCATTTAGTA
2306216 TTCGTTTA
1 TTCGTTTA
2306224 TCGTTCGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.10, G:0.15, T:0.56
Consensus pattern (22 bp):
TTCGTTTAGCATTCATTTAGTA
Found at i:2311359 original size:21 final size:20
Alignment explanation
Indices: 2311292--2311430 Score: 89
Period size: 21 Copynumber: 6.8 Consensus size: 20
2311282 AAATGACCAA
***
2311292 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** * *
2311312 CAGAATCGCAAATCAATTTC
1 CAAAATCGCAACGCGATTTT
2311332 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2311353 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2311374 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2311394 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2311415 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2311431 ACACATAAAT
Statistics
Matches: 90, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
20 44 0.49
21 46 0.51
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2311446 original size:40 final size:40
Alignment explanation
Indices: 2311397--2311551 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
2311387 CGATTTTCCA
* ** *
2311397 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
2311437 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
2311477 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
2311517 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2311552 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:2311459 original size:20 final size:20
Alignment explanation
Indices: 2311397--2311550 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
2311387 CGATTTTCCA
* ** *
2311397 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2311417 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2311437 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2311457 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2311477 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2311497 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2311517 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2311538 AAATCGCAACGCG
1 AAATCGCAACGCG
2311551 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2311972 original size:33 final size:33
Alignment explanation
Indices: 2311933--2312003 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2311923 TTCACTTAGA
*
2311933 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2311966 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2311999 TTTCA
1 TTTCA
2312004 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2312109 original size:21 final size:20
Alignment explanation
Indices: 2312083--2312188 Score: 82
Period size: 21 Copynumber: 5.5 Consensus size: 20
2312073 TGCAGAAGAG
2312083 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
2312104 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
*
2312124 TCACAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
2312145 TCGCAACTAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
2312159 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
2312178 TCGCAACGAGA
1 TCGCAACGAGA
2312189 GAATCGCAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
14 10 0.16
16 2 0.03
17 2 0.03
19 11 0.17
20 15 0.23
21 24 0.38
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:2312143 original size:41 final size:35
Alignment explanation
Indices: 2312083--2312199 Score: 139
Period size: 33 Copynumber: 3.2 Consensus size: 35
2312073 TGCAGAAGAG
*
2312083 TCGCAACGAGATAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA
*
2312118 TGACTGTCACAACGAGAGAAATGAAAATCGCAACTAGAGAA
1 T--C-G---CAACGAGAGAAATGAAAATCGCAACGAGAGAA
*
2312159 TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA
2312192 TCGCAACG
1 TCGCAACG
2312200 CGAAACCAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
33 31 0.44
35 5 0.07
37 1 0.01
38 2 0.03
39 1 0.01
41 31 0.44
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (35 bp):
TCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA
Found at i:2312172 original size:33 final size:33
Alignment explanation
Indices: 2312135--2312215 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2312125 CACAACGAGA
*
2312135 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2312168 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2312201 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2312216 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2312195 original size:14 final size:14
Alignment explanation
Indices: 2312143--2312199 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2312133 GAGAAATGAA
*
2312143 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
2312157 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2312176 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2312190 AATCGCAACG
1 AATCGCAACG
2312200 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2312233 original size:19 final size:19
Alignment explanation
Indices: 2312211--2312294 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
2312201 GAAACCAAAA
*
2312211 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2312230 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2312249 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
2312263 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2312282 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2312295 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.16
16 3 0.05
17 3 0.05
19 40 0.73
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2312276 original size:33 final size:33
Alignment explanation
Indices: 2312234--2312316 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
2312224 TTCATTTCGC
2312234 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
*
2312267 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
2312300 GTTGCGATTTTCATTTC
1 GTTGCGATTTTCATTTC
2312317 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTCTA
Found at i:2312304 original size:14 final size:14
Alignment explanation
Indices: 2312252--2312308 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2312242 TTTCATTTCG
2312252 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
2312266 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2312285 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2312299 CGTTGCGATT
1 CGTTGCGATT
2312309 TTCATTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2314062 original size:19 final size:19
Alignment explanation
Indices: 2314035--2314169 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2314025 CTTAGTAAAA
*
2314035 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2314054 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
2314070 T--CGTTGCGATTTTCAGT
1 TCGCGTTGCGATTTTCATT
* *
2314087 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2314103 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2314120 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2314139 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2314159 TCGTGTTGCGA
1 TCGCGTTGCGA
2314170 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 10 0.11
19 46 0.49
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2314076 original size:14 final size:14
Alignment explanation
Indices: 2314057--2314113 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2314047 TTTCATTTCG
2314057 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
2314071 CGTTGCGATTTTCAGTT
1 CGTTGCGA--TTC-TTT
*
2314088 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2314104 CGTTGCGATT
1 CGTTGCGATT
2314114 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2314077 original size:33 final size:33
Alignment explanation
Indices: 2314040--2314132 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2314030 TAAAATCGCA
*
2314040 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
2314073 TTGCGATTTTCAGTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2314106 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2314133 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2316113 original size:14 final size:14
Alignment explanation
Indices: 2316094--2316129 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2316084 ATTGTTTAAT
2316094 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2316108 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2316122 TGATTTGT
1 TGATTTGT
2316130 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2316260 original size:19 final size:19
Alignment explanation
Indices: 2316236--2316333 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2316226 AAAATTGACT
2316236 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2316255 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2316274 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2316288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2316307 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2316327 ATCGCAA
1 ATCGCAA
2316334 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2316365 original size:53 final size:53
Alignment explanation
Indices: 2316236--2316352 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
2316226 AAAATTGACT
2316236 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
2316288 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2316341 ATCGCAATGCGA
1 ATCGCAATGCGA
2316353 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2316370 original size:19 final size:19
Alignment explanation
Indices: 2316342--2316530 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
2316332 AACGGGAGAA
* *
2316342 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
2316361 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2316377 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2316394 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2316413 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2316429 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2316446 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2316465 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2316484 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
2316502 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2316518 TCGCATTGCGATT
1 TCGCATTGCGATT
2316531 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 14 0.10
18 1 0.01
19 76 0.52
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2316405 original size:52 final size:52
Alignment explanation
Indices: 2316342--2316544 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
2316332 AACGGGAGAA
* *
2316342 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2316394 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
2316446 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
2316502 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
2316545 GTAATTTCCG
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 2 0.01
50 2 0.01
51 3 0.02
52 80 0.57
53 24 0.17
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2316552 original size:33 final size:33
Alignment explanation
Indices: 2316399--2316544 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
2316389 TCATTTCGCA
2316399 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2316432 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
2316468 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
2316504 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
2316537 TTGCGATT
1 TTGCGATT
2316545 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2319001 original size:24 final size:24
Alignment explanation
Indices: 2318967--2319013 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2318957 CTGAAACATC
2318967 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2318991 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2319014 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2319723 original size:20 final size:20
Alignment explanation
Indices: 2319695--2320004 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
2319685 AAATTTCAGT
* *
2319695 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
2319715 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
2319735 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
2319755 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
2319775 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
2319795 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
2319815 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
2319835 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
2319855 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
2319875 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
2319895 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
2319915 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
2319935 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
2319955 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
2319975 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
2319995 GTTGCGATTT
1 GTTGCGATTT
2320005 TGGAAACTGA
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:2321060 original size:11 final size:11
Alignment explanation
Indices: 2321044--2321096 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
2321034 ATTTTAAAAA
2321044 ATTTAATAATT
1 ATTTAATAATT
*
2321055 ATTTAATAATA
1 ATTTAATAATT
2321066 ATTT-AT--TT
1 ATTTAATAATT
2321074 AATTTAATAATT
1 -ATTTAATAATT
2321086 ATTTAATAATT
1 ATTTAATAATT
2321097 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 1 0.03
9 4 0.11
10 4 0.11
11 25 0.69
12 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:2324527 original size:67 final size:68
Alignment explanation
Indices: 2324453--2324579 Score: 202
Period size: 68 Copynumber: 1.9 Consensus size: 68
2324443 CACTATGACC
2324453 ACTCAACTAAACCCTATCAAAC-ATGTGGCCATCTAAGAATTTTTACCATCAATTTGGCCACACA
1 ACTCAACTAAACCCTATCAAACAATGTGGCCATCTAAGAATTTTTACCATCAATTTGGCCACACA
2324517 AGT
66 AGT
** * * *
2324520 ACTCAACTGTACCCTATCAAACAATGTGGCCATTTAAGAATTTTTGCTATCAATTTGGCC
1 ACTCAACTAAACCCTATCAAACAATGTGGCCATCTAAGAATTTTTACCATCAATTTGGCC
2324580 TCTCAACTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 20 0.37
68 34 0.63
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (68 bp):
ACTCAACTAAACCCTATCAAACAATGTGGCCATCTAAGAATTTTTACCATCAATTTGGCCACACA
AGT
Found at i:2327959 original size:16 final size:16
Alignment explanation
Indices: 2327897--2327958 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
2327887 TAAATAAACT
2327897 AACATAAACGAACACG
1 AACATAAACGAACACG
2327913 AACATAAACGAACACG
1 AACATAAACGAACACG
* *
2327929 AACATAAATGAACATG
1 AACATAAACGAACACG
2327945 AACATAAACGAACA
1 AACATAAACGAACA
2327959 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:2328214 original size:11 final size:11
Alignment explanation
Indices: 2328198--2328239 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2328188 TCGAGACTCG
2328198 AGCTCGATTGA
1 AGCTCGATTGA
2328209 AGCTCGATTCTG-
1 AGCTCGA-T-TGA
*
2328221 AGCTCGATTCA
1 AGCTCGATTGA
2328232 AGCTCGAT
1 AGCTCGAT
2328240 ATTGCCTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 8 0.30
13 2 0.07
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:2328227 original size:23 final size:24
Alignment explanation
Indices: 2328173--2328240 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
2328163 AAAAAATTAA
* *
2328173 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAGCTCGATACTC
* *
2328197 GAGCTCGATTGAAGCTCGATTCT-
1 GAGCTCGATTAAAGCTCGATACTC
*
2328220 GAGCTCGATTCAAGCTCGATA
1 GAGCTCGATTAAAGCTCGATA
2328241 TTGCCTCAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGATACTC
Found at i:2329562 original size:30 final size:30
Alignment explanation
Indices: 2329493--2329569 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
2329483 ATGATCTTCA
* *
2329493 GATAAAATATCTAGTTGACCCTTAAACTTT
1 GATAAAATATCAATTTGACCCTTAAACTTT
* * * *
2329523 AACTAAAATATCAATTTGATCCTTGAATTTT
1 GA-TAAAATATCAATTTGACCCTTAAACTTT
2329554 GATAAAATATCAATTT
1 GATAAAATATCAATTT
2329570 AACTCATGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 15 0.38
31 24 0.62
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (30 bp):
GATAAAATATCAATTTGACCCTTAAACTTT
Found at i:2329930 original size:29 final size:29
Alignment explanation
Indices: 2329888--2329943 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2329878 TATCCGTCGG
* *
2329888 AAGTGGCCGGAAACATAGTGCGACTTCGA
1 AAGTCGCCGGAAACATAATGCGACTTCGA
*
2329917 AAGTCGCCGGAAACATAATGCGTCTTC
1 AAGTCGCCGGAAACATAATGCGACTTC
2329944 AGTTTTGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (29 bp):
AAGTCGCCGGAAACATAATGCGACTTCGA
Found at i:2330057 original size:32 final size:32
Alignment explanation
Indices: 2330013--2330087 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
2330003 AGATGCATTA
*
2330013 TGTTCCCAACGTCTTTTCCAAAAGACGTATTG
1 TGTTCCCGACGTCTTTTCCAAAAGACGTATTG
*
2330045 TGTTCCCGACGTCTTTTTCAAAAGACGTATTG
1 TGTTCCCGACGTCTTTTCCAAAAGACGTATTG
2330077 TGTTCCCGACG
1 TGTTCCCGACG
2330088 ACTCTTCGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTTCCCGACGTCTTTTCCAAAAGACGTATTG
Found at i:2330921 original size:29 final size:29
Alignment explanation
Indices: 2330877--2331018 Score: 84
Period size: 29 Copynumber: 4.9 Consensus size: 29
2330867 ATGTCAACAT
2330877 ATTATTGTT-AAA-ATTTTAATAA-AAA-A
1 ATTATT-TTAAAATATTTTAATAATAAATA
*
2330903 ATATATATTTAAAATATTTAAATATATAAATA
1 AT-TAT-TTTAAAATATTTTAATA-ATAAATA
*
2330935 ATTATTTTATAAT-TTTTAATAATAAATA
1 ATTATTTTAAAATATTTTAATAATAAATA
** *
2330963 GATT-TAATAAAATAATATTCT-ATAATTAAAAA
1 -ATTATTTTAAAAT-AT-TT-TAATAA-TAAATA
* *
2330995 ATTATTTTATAA-ATTCTAATAATA
1 ATTATTTTAAAATATTTTAATAATA
2331019 GAAACTCAGT
Statistics
Matches: 90, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
26 2 0.02
27 5 0.06
28 20 0.22
29 23 0.26
30 11 0.12
31 15 0.17
32 14 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTATTTTAAAATATTTTAATAATAAATA
Found at i:2331837 original size:37 final size:37
Alignment explanation
Indices: 2331787--2331863 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
2331777 GCATGGACTT
2331787 GTATTTGATTGCATTGATGAGAGGATACAATATAGTC
1 GTATTTGATTGCATTGATGAGAGGATACAATATAGTC
*
2331824 GTATTTGATTGCATTGATGAGAGTATACAATATAGTC
1 GTATTTGATTGCATTGATGAGAGGATACAATATAGTC
2331861 GTA
1 GTA
2331864 ATATCGTACC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.36
Consensus pattern (37 bp):
GTATTTGATTGCATTGATGAGAGGATACAATATAGTC
Found at i:2347241 original size:15 final size:16
Alignment explanation
Indices: 2347210--2347247 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
2347200 TTTTTTTTTA
2347210 TTGTGGAAAATTGAGT
1 TTGTGGAAAATTGAGT
2347226 TTGTGGAAAA-TGAGT
1 TTGTGGAAAATTGAGT
2347241 TTGTGGA
1 TTGTGGA
2347248 GGGAGGGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (16 bp):
TTGTGGAAAATTGAGT
Found at i:2348466 original size:20 final size:20
Alignment explanation
Indices: 2348441--2348478 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2348431 AGAAGATTTA
2348441 TTGATGTTTTTGAAAATAAT
1 TTGATGTTTTTGAAAATAAT
2348461 TTGATGTTTTTGAAAATA
1 TTGATGTTTTTGAAAATA
2348479 CGTACGGAAG
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:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGATGTTTTTGAAAATAAT
Found at i:2350496 original size:3 final size:3
Alignment explanation
Indices: 2350478--2350511 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2350468 TCTTAATTAT
*
2350478 ATA ATA TATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
2350512 TCATATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2351339 original size:21 final size:21
Alignment explanation
Indices: 2351301--2351352 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2351291 TGCGATAGTA
2351301 CAAATTCGCATTGCGATTTTC
1 CAAATTCGCATTGCGATTTTC
2351322 CAAATTCGCATTGCGATTTTC
1 CAAATTCGCATTGCGATTTTC
2351343 CAGAA-TCGCA
1 CA-AATTCGCA
2351353 ACGCGAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (21 bp):
CAAATTCGCATTGCGATTTTC
Found at i:2351358 original size:21 final size:21
Alignment explanation
Indices: 2351279--2351358 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
2351269 AAATCAGTTC
**
2351279 CCAGAATCGCAATGCGATAGT
1 CCAGAATCGCAATGCGATTTT
* *
2351300 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATTTT
*
2351321 CCA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATTTT
*
2351342 CCAGAATCGCAACGCGA
1 CCAGAATCGCAATGCGA
2351359 ACATATAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.04
21 46 0.92
22 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATTTT
Found at i:2351434 original size:20 final size:20
Alignment explanation
Indices: 2351387--2351617 Score: 193
Period size: 20 Copynumber: 11.6 Consensus size: 20
2351377 GATTCTGACT
*
2351387 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
2351408 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
2351428 ATTGCAACAAC-AATACGTAA
1 ATCGCAAC-GCGTATCCGTAA
*
2351448 ATCGCAA-GCATATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * * *
2351467 ATTGAAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2351487 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * * *
2351507 ATCCCATCGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2351527 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
2351547 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
2351568 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
2351588 ATCGCAACGCG-AT-CGATAA
1 ATCGCAACGCGTATCCG-TAA
*
2351607 TTCGCAACGCG
1 ATCGCAACGCG
2351618 ATCTCCGGTA
Statistics
Matches: 164, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
18 3 0.02
19 27 0.16
20 99 0.60
21 35 0.21
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:2351518 original size:40 final size:40
Alignment explanation
Indices: 2351387--2351617 Score: 270
Period size: 40 Copynumber: 5.8 Consensus size: 40
2351377 GATTCTGACT
** *
2351387 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGT-AAATCGCAACGCGTATCCGTAA
* * *
2351428 ATTGCAACAACAATACGTAAATCGCAA-GCATATCCGTAA
1 ATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAA
* * * *
2351467 ATTGAAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAA
* * * *
2351507 ATCCCATCGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAA
2351547 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGT-AAATCGCAACGCGTATCCGTAA
* *
2351588 ATCGCAACG-CGAT-CGATAATTCGCAACGCG
1 ATCGCAACGACAATACG-TAAATCGCAACGCG
2351618 ATCTCCGGTA
Statistics
Matches: 164, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 49 0.30
40 72 0.44
41 43 0.26
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
ATCGCAACGACAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:2351613 original size:19 final size:18
Alignment explanation
Indices: 2351364--2351620 Score: 131
Period size: 20 Copynumber: 12.9 Consensus size: 18
2351354 CGCGAACATA
2351364 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGCGA-TCG
* *
2351382 TGACTATCGCAACGAGTATCCG
1 T-A-AATCGCAACGCG-AT-CG
2351404 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCG-AT-CG
* * *
2351425 TAAATTGCAACAACAATACG
1 TAAATCGCAAC-GCGAT-CG
*
2351445 TAAATCGCAA-GCATATCCG
1 TAAATCGCAACGC-GAT-CG
* * *
2351464 TAAATTGAAACGAGAATACG
1 TAAATCGCAACGCG-AT-CG
2351484 TAAATCGCAACGCGTATCTG
1 TAAATCGCAACGCG-ATC-G
* * *
2351504 TAAATCCCATCGAGAATACG
1 TAAATCGCAACGCG-AT-CG
*
2351524 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCG-AT-CG
*
2351544 TAAATCGCAACGACAATACG
1 TAAATCGCAACG-CGAT-CG
2351564 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCG-AT-CG
2351585 TAAATCGCAACGCGATCG
1 TAAATCGCAACGCGATCG
*
2351603 ATAATTCGCAACGCGATC
1 -TAAATCGCAACGCGATC
2351621 TCCGGTATCG
Statistics
Matches: 186, Mismatches: 38, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
18 4 0.02
19 32 0.17
20 110 0.59
21 38 0.20
22 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (18 bp):
TAAATCGCAACGCGATCG
Found at i:2351697 original size:21 final size:21
Alignment explanation
Indices: 2351668--2351714 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2351658 ATTCTGACTA
2351668 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2351689 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
2351710 TCGCA
1 TCGCA
2351715 ACGCGATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2351720 original size:21 final size:20
Alignment explanation
Indices: 2351704--2351760 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2351694 TTGCGATTTT
*
2351704 CCTAATTCGCAACGCGATTA
1 CCTAAATCGCAACGCGATTA
* *
2351724 CGTAAATCGCAACGCGAATA
1 CCTAAATCGCAACGCGATTA
*
2351744 CGTAAATCGCAACGCGA
1 CCTAAATCGCAACGCGA
2351761 ATCTGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
CCTAAATCGCAACGCGATTA
Found at i:2351735 original size:20 final size:20
Alignment explanation
Indices: 2351710--2351811 Score: 120
Period size: 20 Copynumber: 5.1 Consensus size: 20
2351700 TTTTCCTAAT
*
2351710 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
2351730 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
2351750 TCGCAACGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
* *
2351770 TCGCAATGCAAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
*
2351790 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
2351810 TC
1 TC
2351812 ACAATGAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
19 1 0.01
20 76 0.99
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:2351756 original size:40 final size:40
Alignment explanation
Indices: 2351710--2351811 Score: 136
Period size: 40 Copynumber: 2.5 Consensus size: 40
2351700 TTTTCCTAAT
* *
2351710 TCGCAACGCGATTAC-GTAAATCGCAACGCGAATAC-GTAAA
1 TCGCAACGCGAAT-CTGTAAATCGCAACGCAAAT-CTGTAAA
*
2351750 TCGCAACGCGAATCTGTAAATCGCAATGCAAATCTGTAAA
1 TCGCAACGCGAATCTGTAAATCGCAACGCAAATCTGTAAA
*
2351790 TCGCAATGCGAATCTGTAAATC
1 TCGCAACGCGAATCTGTAAATC
2351812 ACAATGAGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 2 0.04
40 54 0.96
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (40 bp):
TCGCAACGCGAATCTGTAAATCGCAACGCAAATCTGTAAA
Found at i:2351816 original size:20 final size:20
Alignment explanation
Indices: 2351725--2351817 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
2351715 ACGCGATTAC
*
2351725 GTAAATCGCAACGCGAATAC-
1 GTAAATCGCAATGCGAAT-CT
*
2351745 GTAAATCGCAACGCGAATCT
1 GTAAATCGCAATGCGAATCT
*
2351765 GTAAATCGCAATGCAAATCT
1 GTAAATCGCAATGCGAATCT
2351785 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAATGCGAATCT
*
2351805 GTAAATCACAATG
1 GTAAATCGCAATG
2351818 AGATTCTGAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 1 0.01
20 67 0.99
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
GTAAATCGCAATGCGAATCT
Found at i:2355089 original size:20 final size:21
Alignment explanation
Indices: 2355058--2355152 Score: 126
Period size: 20 Copynumber: 4.7 Consensus size: 21
2355048 GACATTCATT
2355058 TGACTCATCGCAACGC-GAATA
1 TGACT-ATCGCAACGCGGAATA
* *
2355079 TGACTATCGCAACAC-GAAAA
1 TGACTATCGCAACGCGGAATA
*
2355099 TGACTATCGCAATGCGGAAT-
1 TGACTATCGCAACGCGGAATA
2355119 TGACTATCGCAACGCGGAA-A
1 TGACTATCGCAACGCGGAATA
2355139 TGACTATCGCAACG
1 TGACTATCGCAACG
2355153 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
20 58 0.88
21 8 0.12
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:2355180 original size:60 final size:61
Alignment explanation
Indices: 2355057--2355180 Score: 132
Period size: 60 Copynumber: 2.0 Consensus size: 61
2355047 TGACATTCAT
* * **
2355057 TTGACTCATCGCAACGCGAATATGACTATCGCAACACGAAAATGACTATCGCAATGCGGAA
1 TTGACTCATCGCAACGCGAATATGACTATCGCAACACGAAAATGACAATCGAAATGCAAAA
*
2355118 TTGACT-ATCGCAACGCGGAA-ATGACTATCGCAACGA-GAGAATCG-CAATGCGAAATG-AAAA
1 TTGACTCATCGCAACGC-GAATATGACTATCGCAAC-ACGAAAAT-GACAAT-CGAAATGCAAAA
2355178 TTG
1 TTG
2355181 CAATGCAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
60 37 0.69
61 17 0.31
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (61 bp):
TTGACTCATCGCAACGCGAATATGACTATCGCAACACGAAAATGACAATCGAAATGCAAAA
Found at i:2355185 original size:19 final size:18
Alignment explanation
Indices: 2355161--2355196 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2355151 CGAGAGAATC
*
2355161 GCAATGCGAAATGAAAATT
1 GCAATGC-AAATAAAAATT
2355180 GCAATGCAAATAAAAAT
1 GCAATGCAAATAAAAAT
2355197 CGTAACGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (18 bp):
GCAATGCAAATAAAAATT
Found at i:2355319 original size:32 final size:33
Alignment explanation
Indices: 2355252--2355345 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
2355242 ATTAGTTTCG
2355252 CGTTGCGA-TTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
2355285 CGTTGCGATTTTCATTTCGCATTG-GATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
2355317 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
2355346 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 22 0.41
33 24 0.44
34 8 0.15
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.41
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:2357526 original size:19 final size:17
Alignment explanation
Indices: 2357483--2357531 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 17
2357473 CGCGACTATA
2357483 GTTCGCGTTGCGATTTT
1 GTTCGCGTTGCGATTTT
2357500 G-T--CGTTGCGATTTT
1 GTTCGCGTTGCGATTTT
2357514 GGTTTCGCGTTGCGATTT
1 -G-TTCGCGTTGCGATTT
2357532 CTCATTGCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 12 0.44
15 1 0.04
16 1 0.04
17 2 0.07
19 11 0.41
ACGTcount: A:0.06, C:0.16, G:0.31, T:0.47
Consensus pattern (17 bp):
GTTCGCGTTGCGATTTT
Found at i:2357810 original size:93 final size:94
Alignment explanation
Indices: 2357645--2358009 Score: 460
Period size: 92 Copynumber: 4.1 Consensus size: 94
2357635 AATGGATGCA
* *
2357645 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATA-TAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
**
2357708 TTAATAGAATTGGCAGCAACCAAACAAAT
66 TTAGCAGAATTGGCAGCAACCAAACAAAT
2357737 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* **
2357801 TTAGCAGAATTGGTAGCAACTGAAC-AAT
66 TTAGCAGAATTGGCAGCAACCAAACAAAT
2357829 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAA-TTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2357893 TTAGCAGAATTGGCAGCAAACC-GATAAAT
66 TTAGCAGAATTGGCAGC-AACCAAACAAAT
*
2357922 TTAC-TTCAACCAAAAG-----AC-----CAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-
* * * *
2357976 TTTATCAGTA-TGACAGCAACCAAATAAAT
65 TTTAGCAGAATTGGCAGCAACCAAACAAAT
2358005 TTACT
1 TTACT
2358010 AAGCAATCTA
Statistics
Matches: 248, Mismatches: 16, Indels: 26
0.86 0.06 0.09
Matches are distributed among these distances:
82 14 0.06
83 39 0.16
84 8 0.03
87 2 0.01
91 24 0.10
92 75 0.30
93 60 0.24
94 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCAAACAAAT
Found at i:2358003 original size:83 final size:81
Alignment explanation
Indices: 2357853--2358009 Score: 219
Period size: 83 Copynumber: 1.9 Consensus size: 81
2357843 AAGACAAAAC
* * *
2357853 AAAGACAAATACTAATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAT
1 AAAGACAAATACTAATTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGACAGCAAACCAAT
2357918 AAATTTACTTCAACCA
66 AAATTTACTTCAACCA
* *
2357934 AAAGACCAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTTATCAGTA-TGACAGC-AACC
1 AAAGA-CAAATACTAA-TTCACAGTGTTAAAGAATAAACAG-TTTAGCAGAATTGACAGCAAACC
2357997 AAATAAATTTACT
63 -AATAAATTTACT
2358010 AAGCAATCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
81 5 0.07
82 14 0.21
83 40 0.60
84 8 0.12
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (81 bp):
AAAGACAAATACTAATTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGACAGCAAACCAAT
AAATTTACTTCAACCA
Found at i:2359580 original size:79 final size:79
Alignment explanation
Indices: 2359437--2359594 Score: 284
Period size: 78 Copynumber: 2.0 Consensus size: 79
2359427 TTTCTTTGTG
2359437 CAGGTGAAAGCTTCGAAGCAATTGTAGTGCTAGGCTAACTTTATCCTTAATGGTCAATGAAGCCG
1 CAGGTGAAAGCTTCGAAGCAATTGTAGTGCTAGGCTAACTTTATCCTTAATGGTCAATGAAGCCG
2359502 -AAAAAATTTCTAC
66 AAAAAAATTTCTAC
2359515 CAGGTGAAAGCTTCGAAGCAATTGTAGTGGCTAGGCTAACTTTATTCCTTAAT-GTCAATGAAGC
1 CAGGTGAAAGCTTCGAAGCAATTGTAGT-GCTAGGCTAACTTTA-TCCTTAATGGTCAATGAAGC
2359579 CGAAAAAAATTTCTAC
64 CGAAAAAAATTTCTAC
2359595 AAAAACAATA
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
78 28 0.36
79 28 0.36
80 21 0.27
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (79 bp):
CAGGTGAAAGCTTCGAAGCAATTGTAGTGCTAGGCTAACTTTATCCTTAATGGTCAATGAAGCCG
AAAAAAATTTCTAC
Found at i:2359791 original size:14 final size:14
Alignment explanation
Indices: 2359772--2359808 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2359762 GGAAATGACT
2359772 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2359786 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2359800 ATCGTAACG
1 ATCGCAACG
2359809 CGAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2359827 original size:19 final size:19
Alignment explanation
Indices: 2359799--2359849 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2359789 GCAACGAGAG
* *
2359799 AATCGTAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
2359818 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2359837 AATCGCAATGCGA
1 AATCGCAACGCGA
2359850 TTTTGGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2359883 original size:14 final size:14
Alignment explanation
Indices: 2359861--2359912 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2359851 TTTGGTTTCG
*
2359861 CGTTACGATTATCT
1 CGTTGCGATTATCT
*
2359875 CGTTGCGATTTTCAT
1 CGTTGCGATTATC-T
* *
2359890 -TTTGCGATTCTCT
1 CGTTGCGATTATCT
2359903 CGTTGCGATT
1 CGTTGCGATT
2359913 TTCATTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2359898 original size:28 final size:28
Alignment explanation
Indices: 2359866--2359920 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2359856 TTTCGCGTTA
2359866 CGATTATCTCGTTGCGATTTTCATTTTG
1 CGATTATCTCGTTGCGATTTTCATTTTG
*
2359894 CGATTCTCTCGTTGCGATTTTCATTTT
1 CGATTATCTCGTTGCGATTTTCATTTT
2359921 TATGTTGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.16, T:0.51
Consensus pattern (28 bp):
CGATTATCTCGTTGCGATTTTCATTTTG
Found at i:2360517 original size:20 final size:20
Alignment explanation
Indices: 2360492--2360705 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
2360482 CTTTAAAAAT
2360492 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2360512 CGCGTTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2360532 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
2360553 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2360573 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
2360593 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2360613 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2360633 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2360653 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
2360674 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2360695 CTCGTTGCGAT
1 CGCGTTGCGAT
2360706 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
20 108 0.68
21 52 0.32
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2360578 original size:40 final size:41
Alignment explanation
Indices: 2360494--2360705 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
2360484 TTAAAAATCG
* *
2360494 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2360535 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2360575 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2360615 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2360656 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2360697 CGTTGCGAT
1 CGTTGCGAT
2360706 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2360866 original size:20 final size:20
Alignment explanation
Indices: 2360821--2360870 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2360811 TTCATAATTA
2360821 CGTTGCGATTCTGGGAACTG
1 CGTTGCGATTCTGGGAACTG
** *
2360841 ATTTGCGATTCTGGAGATC-G
1 CGTTGCGATTCTGG-GAACTG
2360861 CGTTGCGATT
1 CGTTGCGATT
2360871 TTTATTTCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTCTGGGAACTG
Found at i:2361351 original size:20 final size:20
Alignment explanation
Indices: 2361328--2361367 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2361318 TTTAATTAAG
*
2361328 AATATTAAATTTTAAAAATT
1 AATATGAAATTTTAAAAATT
*
2361348 AATATGAATTTTTAAAAATT
1 AATATGAAATTTTAAAAATT
2361368 TTGTAGCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATGAAATTTTAAAAATT
Found at i:2361484 original size:16 final size:16
Alignment explanation
Indices: 2361459--2361496 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2361449 GTTTATGTTA
2361459 TCTTCCGTCGCTCACT
1 TCTTCCGTCGCTCACT
*
2361475 TCTTCTGTCGCTCACT
1 TCTTCCGTCGCTCACT
*
2361491 TTTTCC
1 TCTTCC
2361497 CTATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.05, C:0.39, G:0.11, T:0.45
Consensus pattern (16 bp):
TCTTCCGTCGCTCACT
Found at i:2362611 original size:33 final size:33
Alignment explanation
Indices: 2362569--2362637 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
2362559 GCTTCTGTTG
2362569 GTTAATTACTTTAAAGGCTGCATGGTTCTATTT
1 GTTAATTACTTTAAAGGCTGCATGGTTCTATTT
*
2362602 GTTAATTACTTTAAAGGCTGCATGGTTCTGTTT
1 GTTAATTACTTTAAAGGCTGCATGGTTCTATTT
2362635 GTT
1 GTT
2362638 TACCTTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (33 bp):
GTTAATTACTTTAAAGGCTGCATGGTTCTATTT
Found at i:2364123 original size:19 final size:19
Alignment explanation
Indices: 2364099--2364163 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
2364089 TTTAAACGGG
2364099 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2364118 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2364137 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
2364156 TACATCGA
1 TGCATCGA
2364164 CATTAATGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2372146 original size:175 final size:176
Alignment explanation
Indices: 2371954--2372305 Score: 688
Period size: 176 Copynumber: 2.0 Consensus size: 176
2371944 GATTGTGGTG
2371954 AGAGTAATCGATTTTTTTTTTT-TAATCGTTCTAAACAAGAGAAAACTAGACCATAGATCCTCTA
1 AGAGTAATCGATTTTTTTTTTTATAATCGTTCTAAACAAGAGAAAACTAGACCATAGATCCTCTA
2372018 GTTTTTAATATGTTCAATTCAGTCCCTACATGTAGATCTAATTATTATGATTTCATATTTATTTA
66 GTTTTTAATATGTTCAATTCAGTCCCTACATGTAGATCTAATTATTATGATTTCATATTTATTTA
2372083 GGTTTGGATCAAAATCAGGGATTCATTTTTATGATTCTATGGATAA
131 GGTTTGGATCAAAATCAGGGATTCATTTTTATGATTCTATGGATAA
2372129 AGAGTAATCGATTTTTTTTTTTATAATCGTTCTAAACAAGAGAAAACTAGACCATAGATCCTCTA
1 AGAGTAATCGATTTTTTTTTTTATAATCGTTCTAAACAAGAGAAAACTAGACCATAGATCCTCTA
2372194 GTTTTTAATATGTTCAATTCAGTCCCTACATGTAGATCTAATTATTATGATTTCATATTTATTTA
66 GTTTTTAATATGTTCAATTCAGTCCCTACATGTAGATCTAATTATTATGATTTCATATTTATTTA
*
2372259 TGTTTGGATCAAAATCAGGGATTCATTTTTATGATTCTATGGATAA
131 GGTTTGGATCAAAATCAGGGATTCATTTTTATGATTCTATGGATAA
2372305 A
1 A
2372306 CGTTTACATG
Statistics
Matches: 175, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
175 22 0.13
176 153 0.87
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (176 bp):
AGAGTAATCGATTTTTTTTTTTATAATCGTTCTAAACAAGAGAAAACTAGACCATAGATCCTCTA
GTTTTTAATATGTTCAATTCAGTCCCTACATGTAGATCTAATTATTATGATTTCATATTTATTTA
GGTTTGGATCAAAATCAGGGATTCATTTTTATGATTCTATGGATAA
Found at i:2372568 original size:46 final size:46
Alignment explanation
Indices: 2372518--2372659 Score: 275
Period size: 46 Copynumber: 3.1 Consensus size: 46
2372508 CAATTTATGA
2372518 ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
1 ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
2372564 ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
1 ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
*
2372610 ACTGTATCGTTTATACCATTAAACTTTTATTTTTGTCAATTATAGC
1 ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
2372656 ACTG
1 ACTG
2372660 AATTTTGATT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 95 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (46 bp):
ACTGTATCGTTTATACCATTAAACTTTTAATTTTGTCAATTATAGC
Found at i:2372670 original size:29 final size:29
Alignment explanation
Indices: 2372634--2372693 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
2372624 ACCATTAAAC
*
2372634 TTTTATTTTTG-TCAATTATAG-CACTGAA
1 TTTTATTTTCGCTCAATTAT-GCCACTGAA
2372662 TTTTGATTTTCGCTTCAATTATGCCACTGAA
1 TTTT-ATTTTCGC-TCAATTATGCCACTGAA
2372693 T
1 T
2372694 CGTTAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.15
29 6 0.22
30 1 0.04
31 16 0.59
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTTATTTTCGCTCAATTATGCCACTGAA
Found at i:2373584 original size:43 final size:43
Alignment explanation
Indices: 2373528--2373620 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 43
2373518 ACTTAAAACT
* * * * *
2373528 AAGCATTGAATATAATTAGAGTGTTTATTAAATATAAAATTTA
1 AAGCATAGAATATAATTAGAGTGATCAATAAATACAAAATTTA
* * *
2373571 AAGCATAGGATATAATTAGAGTGATCAATAAATGCAAATTTTA
1 AAGCATAGAATATAATTAGAGTGATCAATAAATACAAAATTTA
2373614 AAGCATA
1 AAGCATA
2373621 ATATAGGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.33
Consensus pattern (43 bp):
AAGCATAGAATATAATTAGAGTGATCAATAAATACAAAATTTA
Found at i:2377070 original size:21 final size:22
Alignment explanation
Indices: 2377016--2377070 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
2377006 TGTGTAGAGT
* *
2377016 TTTAGGATTT-AAGGTTTAGAG
1 TTTAGGATTTAAAGGTTGAGAA
*
2377037 TTTAGGGTTTAAAGGTTGA-AA
1 TTTAGGATTTAAAGGTTGAGAA
2377058 TTTAGGATTTAAA
1 TTTAGGATTTAAA
2377071 TTATATGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (22 bp):
TTTAGGATTTAAAGGTTGAGAA
Found at i:2377808 original size:48 final size:49
Alignment explanation
Indices: 2377735--2377835 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 49
2377725 GAGCTCTATC
*
2377735 ATGGGAAGATGAATGACGTGGGGAAGAAGAAA-GAAGAAGAGATTGATG
1 ATGGGAAGATGAATGACGTGCGGAAGAAGAAAGGAAGAAGAGATTGATG
* *
2377783 ATGGGAAGATGGATGACGTGCGGAAGAAGAAAGCGGATGAAGAGATTGATG
1 ATGGGAAGATGAATGACGTGCGGAAGAAGAAA--GGAAGAAGAGATTGATG
2377834 AT
1 AT
2377836 AGGATATTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
48 30 0.64
51 17 0.36
ACGTcount: A:0.41, C:0.04, G:0.40, T:0.16
Consensus pattern (49 bp):
ATGGGAAGATGAATGACGTGCGGAAGAAGAAAGGAAGAAGAGATTGATG
Found at i:2396249 original size:27 final size:27
Alignment explanation
Indices: 2396190--2396243 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2396180 TCGACCTGAT
2396190 CAAGTTTTCAGGATACTCAATATTTAA
1 CAAGTTTTCAGGATACTCAATATTTAA
2396217 CAAGTTTTCAGGATACTCAATATTTAA
1 CAAGTTTTCAGGATACTCAATATTTAA
2396244 ACAGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (27 bp):
CAAGTTTTCAGGATACTCAATATTTAA
Found at i:2400329 original size:21 final size:21
Alignment explanation
Indices: 2400305--2400345 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2400295 ATGTTTAATG
2400305 AAAAAGATATCAATTATTAAC
1 AAAAAGATATCAATTATTAAC
* *
2400326 AAAAGGATATCAATTGTTAA
1 AAAAAGATATCAATTATTAA
2400346 AAAGATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (21 bp):
AAAAAGATATCAATTATTAAC
Found at i:2400352 original size:18 final size:19
Alignment explanation
Indices: 2400305--2400361 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
2400295 ATGTTTAATG
*
2400305 AAAAAGATATCAATTATTA
1 AAAAAGATATCAATTGTTA
2400324 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
*
2400344 AAAAAGATACCAATTGTT
1 AAAAAGATATCAATTGTT
2400362 GGAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:2407842 original size:16 final size:16
Alignment explanation
Indices: 2407821--2407853 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2407811 TATTTAATAA
*
2407821 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2407837 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2407853 A
1 A
2407854 AAAAAAATTT
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:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Done.