Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007877.1 Hibiscus syriacus cultivar Beakdansim tig00110253_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: 614694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:200865 original size:2 final size:2
Alignment explanation
Indices: 200858--200886 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
200848 ATAATAAAGA
200858 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200887 GGTTAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:202479 original size:30 final size:30
Alignment explanation
Indices: 202413--202481 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
202403 ATTTGAGTAC
* * * *
202413 TATGAGCTGCTATAGGTGTTGTGAGGTAAT
1 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
202443 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
1 TATGAGTTGCCATAGGTGCTGTGAGCTAAT
202473 TATGAGTTG
1 TATGAGTTG
202482 TCATGCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (30 bp):
TATGAGTTGCCATAGGTGCTGTGAGCTAAT
Found at i:203490 original size:18 final size:18
Alignment explanation
Indices: 203467--203505 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
203457 CCAATAAAAA
*
203467 TTATATTGTATTAAA-ATT
1 TTATATT-TATCAAATATT
203485 TTATATTTATCAAATATT
1 TTATATTTATCAAATATT
203503 TTA
1 TTA
203506 ATTATATCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTATATTTATCAAATATT
Found at i:208066 original size:18 final size:19
Alignment explanation
Indices: 208045--208093 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
208035 TTTTTGTTGG
* *
208045 TAAAAAAATTATGAT-TTT
1 TAAAAAAATTATGATAATC
* *
208063 TAAAATAATTATTATAATC
1 TAAAAAAATTATGATAATC
208082 TAAAAAAATTAT
1 TAAAAAAATTAT
208094 AAACAAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAAAATTATGATAATC
Found at i:222909 original size:42 final size:42
Alignment explanation
Indices: 222850--222984 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 42
222840 TGCAGCAGCA
222850 GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
1 GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
222892 GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
1 GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
*
222934 GCAGCAGAAACAGGAGAAATAGAAGAGC---TCCCACATGAT
1 GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
*
222973 GCAGCAGCAACA
1 GCAGCAGAAACA
222985 ACAGAAACAG
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
39 21 0.23
42 70 0.77
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.10
Consensus pattern (42 bp):
GCAGCAGAAACAGGAGAAATAGAAGAGCTGATCCAACATGAT
Found at i:223697 original size:10 final size:10
Alignment explanation
Indices: 223684--223718 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
223674 TATATTAAAA
223684 ATATAATTTT
1 ATATAATTTT
223694 ATATTAATATTT
1 ATA-TAAT-TTT
223706 ATATAATTTT
1 ATATAATTTT
223716 ATA
1 ATA
223719 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 8 0.35
12 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATAATTTT
Found at i:223712 original size:22 final size:22
Alignment explanation
Indices: 223684--223733 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
223674 TATATTAAAA
223684 ATATAATTTTAT-ATTAATATTT
1 ATATAATTTTATAATTAA-ATTT
223706 ATATAATTTTATAATTAAATTT
1 ATATAATTTTATAATTAAATTT
*
223728 AAATAA
1 ATATAA
223734 CATATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATAATTTTATAATTAAATTT
Found at i:228470 original size:134 final size:133
Alignment explanation
Indices: 228217--228707 Score: 668
Period size: 134 Copynumber: 3.7 Consensus size: 133
228207 GTTCGGGTCG
* * * *
228217 TCTAAGGGTGACAC-AGCTCCTACGTAATGAGGA--TCTAGTCAGGGG-ATGACACTGCTCATAT
1 TCTAAGGGTGACACGA-CTCCTACGTGATGAGGAGGTCTGGTC-GGGGAATGACACGGCTCATAC
* **
228278 GTGATGAAGAGATCTTGGCCATCTTTAGGAAAGG-TGATAACTCGGTTCCTACACGATGAGGACT
64 GTGATGAAGAGTTC-TGGCCATCTTTA-GAAAGGATGATAACTCGGTTCCTACGTGATGAGGA-T
228342 GCTGGTTA
126 GCTGGTTA
* *
228350 TCTATGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGGCACGGCTCATACGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACGGCTCATACGT
*
228415 GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGATGACTG
66 GATGAAGAGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGATG-CTG
228480 GTTA
130 GTTA
* * * * * *
228484 TCTATGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGGCACGGTTCATATGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACGGCTCATACGT
*
228549 GATGAAGAGTTCTGGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGATGGCTG
66 GATGAAGAGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGAT-GCTG
228614 GTTA
130 GTTA
* * * * * * *
228618 TCTAAGGGTGACACGACTCCTACGCGATGAGGAGATTTGGTCGGGGGATGATACGACTCATACAT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACGGCTCATACGT
228683 GATGAAGAGTTCTGGCCATCTTTAG
66 GATGAAGAGTTCTGGCCATCTTTAG
228708 GGATACTGGT
Statistics
Matches: 323, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
133 37 0.11
134 253 0.78
135 33 0.10
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (133 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGAATGACACGGCTCATACGT
GATGAAGAGTTCTGGCCATCTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGATGCTGG
TTA
Found at i:228775 original size:28 final size:28
Alignment explanation
Indices: 228722--228797 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
228712 ACTGGTTTTG
*
228722 AAAGAAA-ATGACTCAAATATAAGTTTCA
1 AAAGAAACAT-ACTCAAAGATAAGTTTCA
**
228750 AAAGAAACATACTCAAAGATTTGTTTCA
1 AAAGAAACATACTCAAAGATAAGTTTCA
*
228778 AGAA-AAACAAACTCAAAGAT
1 A-AAGAAACATACTCAAAGAT
228798 GATGTGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAGAAACATACTCAAAGATAAGTTTCA
Found at i:229301 original size:65 final size:63
Alignment explanation
Indices: 229202--229340 Score: 197
Period size: 65 Copynumber: 2.2 Consensus size: 63
229192 CAAAGATGAT
229202 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC--AAAAGAAACTATCTCAAAAGAGACA
* * * * * *
229267 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTTCAAAAGAAATTGTCTCAAGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACA
*
229330 AAACTTTGTTT
1 AAATTTTGTTT
229341 TTTCAGAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 32 0.48
65 35 0.52
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTATCTCAAAAGAGACA
Found at i:229339 original size:63 final size:64
Alignment explanation
Indices: 229206--229340 Score: 191
Period size: 63 Copynumber: 2.1 Consensus size: 64
229196 GATGATAAAT
*
229206 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTTAAAAGAAACTATCTCAAAAGAGACAAAAT
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC-TAAAAGAAACTATCTCAAAAGAGACAAAAC
* * * * * *
229271 TTTGTTTCCAAAGAAACATATTCAATGATTTTTC-AAAAGAAATTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACAAAAC
229334 TTTGTTT
1 TTTGTTT
229341 TTTCAGAACA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
63 32 0.51
65 31 0.49
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (64 bp):
TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAAGAAACTATCTCAAAAGAGACAAAAC
Found at i:229475 original size:32 final size:32
Alignment explanation
Indices: 229441--229562 Score: 95
Period size: 32 Copynumber: 3.8 Consensus size: 32
229431 TAAAACCTTG
* *
229441 TTTCCAGAGAAACAAACTCAAAGATGATATTG
1 TTTCAAGAGAAACAAACTCAAAGATGATATTA
* * * * *
229473 TTTTAAGAGAAA-ATGACTCAATAGTTAAAATTTA
1 TTTCAAGAGAAACA-AACTCAA-AGATGATA-TTA
* * * * *
229507 TTTCTAGGGAAAC-GACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAAACTCAAAGATGATATTA
229538 TTTCAAGAGAAACAAACTCAAAGAT
1 TTTCAAGAGAAACAAACTCAAAGAT
229563 TTTGTATTTC
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
31 15 0.22
32 29 0.43
33 12 0.18
34 11 0.16
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (32 bp):
TTTCAAGAGAAACAAACTCAAAGATGATATTA
Found at i:229540 original size:31 final size:30
Alignment explanation
Indices: 229503--229580 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
229493 ATAGTTAAAA
* *
229503 TTTATTTCTAGGGAAAC-GACTCAAAGATGGT
1 TTTATTTCTAGAGAAACAAACTCAAAGAT--T
*
229534 TTTATTTCAAGAGAAACAAACTCAAAGATT
1 TTTATTTCTAGAGAAACAAACTCAAAGATT
229564 TTGTATTTCTAGAGAAA
1 TT-TATTTCTAGAGAAA
229581 TTGTCTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 3 0.07
31 28 0.68
32 10 0.24
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTATTTCTAGAGAAACAAACTCAAAGATT
Found at i:229637 original size:30 final size:30
Alignment explanation
Indices: 229603--229676 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
229593 AAACAAAATT
* * * * *
229603 TGTTTTAATAGAAACGATCTCAAAGGTGGG
1 TGTTTCAAAAGAAACGAACTCAAAGATAGG
* *
229633 TGTTTCAAGAGAAACTAACTCAAAGATAGG
1 TGTTTCAAAAGAAACGAACTCAAAGATAGG
229663 TGTTTCAAAAGAAA
1 TGTTTCAAAAGAAA
229677 GGACTCACAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (30 bp):
TGTTTCAAAAGAAACGAACTCAAAGATAGG
Found at i:229945 original size:30 final size:31
Alignment explanation
Indices: 229890--229948 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
229880 GATTTGTCAT
**
229890 TTTGTTTCAAGTGAAACAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATCC
229921 TTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
229949 GATGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATCC
Found at i:229969 original size:32 final size:30
Alignment explanation
Indices: 229890--229971 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
229880 GATTTGTCAT
229890 TTTGTTTCAAGTGAAACAGACTCAAAGATCC
1 TTTGTTTCAAGTGAAACA-ACTCAAAGATCC
** **
229921 TTTGTTTCAAAAGAAACAACTCAAAGATGATG
1 TTTGTTTCAAGTGAAACAACTCAAAGAT--CC
*
229953 TTTGTTTCCAGTGAAACAA
1 TTTGTTTCAAGTGAAACAA
229972 ATTCATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 10 0.24
31 16 0.38
32 16 0.38
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (30 bp):
TTTGTTTCAAGTGAAACAACTCAAAGATCC
Found at i:230026 original size:36 final size:35
Alignment explanation
Indices: 229980--230123 Score: 123
Period size: 36 Copynumber: 4.0 Consensus size: 35
229970 AAATTCATAA
*
229980 TTTAGAAAATTGTCTCAAGTGAGACAACATTTGTT
1 TTTAGAAAATTGTCTCAAGCGAGACAACATTTGTT
* * * * * *
230015 TTTAAACAAATTGTCTCAAACAAGACAAAAATTATT
1 TTTAGA-AAATTGTCTCAAGCGAGACAACATTTGTT
*
230051 TTTAGAGAAATTGTCTTAAGCGAGACAA-AGTTTGTT
1 TTTAGA-AAATTGTCTCAAGCGAGACAACA-TTTGTT
* *
230087 TTTGAGAAAA-CGATCTCAAGTGAGATCAAC-TTTGTT
1 TTT-AGAAAATTG-TCTCAAGCGAGA-CAACATTTGTT
230123 T
1 T
230124 AATGTGAAAC
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
35 7 0.08
36 73 0.85
37 6 0.07
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (35 bp):
TTTAGAAAATTGTCTCAAGCGAGACAACATTTGTT
Found at i:230308 original size:109 final size:105
Alignment explanation
Indices: 230062--230309 Score: 276
Period size: 109 Copynumber: 2.3 Consensus size: 105
230052 TTAGAGAAAT
* * * *
230062 TGTCTTAAGCGAGACAAAGTTTGTTTT-TGAG-AA-AACGATCTCAAGTGAGATCAACTTTGTTT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAAATAACAATCTCAAGTGAGATCAACTTTGTTT
230124 AATGTGAAACAAATTCAAAATTTGTATTCTTAAAGGAAAAA
66 AATGTGAAACAAATTCAAAATTTGTATTC-TAAAGGAAAAA
* * * *
230165 TGTCTCAAACGAGACGAAATTTGTTTTGAA-AGAAATAACAATCTCAAGTGAGATTAATTTTTGT
1 TGTCTCAAGCGAGACGAAGTTTGTTTT-AAGAGAAATAACAATCTCAAGTGAGATCAA-CTTTGT
*
230229 TTCAA-GTGAATCAAATTCGAAAA-TTGTATATC-AAAGGAAAAAAAA
64 TT-AATGTGAAACAAATTC-AAAATTTGTAT-TCTAAAGG---AAAAA
*
230274 TGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAT
1 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAAAT
230310 TGTCTTAAAT
Statistics
Matches: 121, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
103 23 0.19
104 2 0.02
105 2 0.02
106 24 0.20
107 25 0.21
108 10 0.08
109 35 0.29
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (105 bp):
TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAAATAACAATCTCAAGTGAGATCAACTTTGTTT
AATGTGAAACAAATTCAAAATTTGTATTCTAAAGGAAAAA
Found at i:230845 original size:116 final size:117
Alignment explanation
Indices: 230699--230932 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 117
230689 GATCAAAATA
230699 ATGCATTTTTGACTGACTGTCTTGGATGTTATGATGGGTGTCAAGATGAAATTCATTTGATTTAT
1 ATGCATTTTTGACTGACTGTCTTGGATGTTATGATGGGTGTCAAGATGAAATTCATTTGATTTAT
230764 CCTCAAGTGCGGC-AAAAATGTTTTTAATATACATGATGATGAATGTTTGAT
66 CCTCAAGTGCGGCAAAAAATGTTTTTAATATACATGATGATGAATGTTTGAT
230815 ATGCATTTTTGACTGACTGTCTTGGATGTTATGATGGGTGTCAAGATGAAATTCATTTGATTTAT
1 ATGCATTTTTGACTGACTGTCTTGGATGTTATGATGGGTGTCAAGATGAAATTCATTTGATTTAT
230880 CCTCAAGTGCGGCAAAAAATGTTTTTAATATACATGATGATGAATGTTTGAT
66 CCTCAAGTGCGGCAAAAAATGTTTTTAATATACATGATGATGAATGTTTGAT
230932 A
1 A
230933 CAAAGATGCA
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 78 0.67
117 39 0.33
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.39
Consensus pattern (117 bp):
ATGCATTTTTGACTGACTGTCTTGGATGTTATGATGGGTGTCAAGATGAAATTCATTTGATTTAT
CCTCAAGTGCGGCAAAAAATGTTTTTAATATACATGATGATGAATGTTTGAT
Found at i:230976 original size:16 final size:16
Alignment explanation
Indices: 230955--230994 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
230945 CTCATGTAAT
**
230955 ATGTATGTATATGTTG
1 ATGTATGTATACATTG
*
230971 ATGTATGTATGCATTG
1 ATGTATGTATACATTG
230987 ATGTATGT
1 ATGTATGT
230995 TTTCTCGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (16 bp):
ATGTATGTATACATTG
Found at i:234724 original size:31 final size:32
Alignment explanation
Indices: 234664--234724 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
234654 TGACAAAATG
*
234664 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
234696 ACACAAACAAAAGAGAA-AAACAAGTTAGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGT
234725 ACATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
Found at i:238597 original size:21 final size:21
Alignment explanation
Indices: 238568--238620 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
238558 ATTCTGACTA
238568 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
238589 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
238610 TCGCAATGCGA
1 TCGCATTGCGA
238621 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:238635 original size:20 final size:20
Alignment explanation
Indices: 238610--238660 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
238600 TTTTCCGAAT
238610 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
238630 TCGCAATGCGAATATGTAAT
1 TCGCAATGCGAATATGTAAA
*
238650 TCGCAACGCGA
1 TCGCAATGCGA
238661 TTCTGATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:239351 original size:20 final size:20
Alignment explanation
Indices: 239288--239353 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
239278 AATTGCAATA
* *
239288 CGATTTT-AGTTTCGCGTTG
1 CGATTTTCATTTTCGTGTTG
**
239307 CGATAGTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
239327 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
239347 CGATTTT
1 CGATTTT
239354 AAGTTTTAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 5 0.12
20 35 0.88
ACGTcount: A:0.12, C:0.15, G:0.23, T:0.50
Consensus pattern (20 bp):
CGATTTTCATTTTCGTGTTG
Found at i:241095 original size:18 final size:18
Alignment explanation
Indices: 241072--241121 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
241062 TTTACTCGTA
241072 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
241090 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
241108 ATTTCACTTAGATT
1 ATTTCACTTAGATT
241122 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:241302 original size:20 final size:20
Alignment explanation
Indices: 241269--241356 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
241259 TAGTTTACTT
* *
241269 TCGCGACGCGAAAATGACTA
1 TCGCAACGCAAAAATGACTA
*
241289 TCGCAACGTAAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* * *
241309 TCACAATGCGAAAATGACTA
1 TCGCAACGCAAAAATGACTA
* **
241329 TCGCAACGCGAATTTGACTA
1 TCGCAACGCAAAAATGACTA
*
241349 TCACAACG
1 TCGCAACG
241357 AAAGAATCGC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
TCGCAACGCAAAAATGACTA
Found at i:241331 original size:40 final size:40
Alignment explanation
Indices: 241276--241354 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
241266 CTTTCGCGAC
*
241276 GCGAAAATGACTATCGCAACGTAAAAATGACTATCACAAT
1 GCGAAAATGACTATCGCAACGCAAAAATGACTATCACAAT
* **
241316 GCGAAAATGACTATCGCAACGCGAATTTGACTATCACAA
1 GCGAAAATGACTATCGCAACGCAAAAATGACTATCACAA
241355 CGAAAGAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (40 bp):
GCGAAAATGACTATCGCAACGCAAAAATGACTATCACAAT
Found at i:241424 original size:20 final size:20
Alignment explanation
Indices: 241399--241450 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
241389 GCGATTCTCT
241399 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
241419 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
241439 CGTTGCGATAGT
1 CGTTGCGATAGT
241451 TATTCGTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:241461 original size:18 final size:19
Alignment explanation
Indices: 241399--241462 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
241389 GCGATTCTCT
*
241399 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGT-ATATTCG
*
241419 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGT-ATATTCG
241439 CGTTGCGATAGT-TATTCG
1 CGTTGCGATAGTATATTCG
*
241457 TGTTGC
1 CGTTGC
241463 AATTTTAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.25
20 30 0.75
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTATATTCG
Found at i:242052 original size:42 final size:42
Alignment explanation
Indices: 241983--242062 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
241973 CCCCTATCGC
*
241983 TCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACAGT
1 TCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACAGT
* ** *
242025 TCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
242063 ACATTCTAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.20
Consensus pattern (42 bp):
TCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACAGT
Found at i:243917 original size:31 final size:32
Alignment explanation
Indices: 243857--243917 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
243847 TGACAAAATG
*
243857 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
243889 ACACAAACAAAAGAGAA-AAACAAGTTAGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGT
243918 ACATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.13
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
Found at i:247793 original size:21 final size:21
Alignment explanation
Indices: 247764--247816 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
247754 ATTCTGACTA
247764 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
247785 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
247806 TCGCAATGCGA
1 TCGCATTGCGA
247817 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:247831 original size:20 final size:20
Alignment explanation
Indices: 247806--247856 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
247796 TTTTCCGAAT
247806 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
247826 TCGCAATGCGAATATGTAAT
1 TCGCAATGCGAATATGTAAA
*
247846 TCGCAACGCGA
1 TCGCAATGCGA
247857 TTCTGATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:248551 original size:20 final size:20
Alignment explanation
Indices: 248481--248568 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
248471 AGAATTGCAA
*
248481 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
248500 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
248520 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
248540 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
248560 TGCGATTTT
1 TGCGATTTT
248569 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 7 0.12
20 52 0.88
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:248575 original size:20 final size:20
Alignment explanation
Indices: 248532--248575 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
248522 CGATAGTCAT
* *
248532 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
248552 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
248572 TTTC
1 TTTC
248576 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:250191 original size:18 final size:18
Alignment explanation
Indices: 250168--250217 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
250158 TTTACTCGTA
250168 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
250186 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
250204 ATTTCACTTAGATT
1 ATTTCACTTAGATT
250218 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:250393 original size:20 final size:20
Alignment explanation
Indices: 250365--250452 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
250355 TAGTTTACTT
*
250365 TCGCGACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
250385 TCGCAACGCAAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
250405 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
250425 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
*
250445 TCGGAACG
1 TCGCAACG
250453 AAAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:250544 original size:20 final size:20
Alignment explanation
Indices: 250500--250546 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
250490 TCTCTCGTTA
*
250500 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCATTG
**
250520 CGATAGTCATTTTCGCATTG
1 CGATAGTCAAATTCGCATTG
*
250540 TGATAGT
1 CGATAGT
250547 TATTCGTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
CGATAGTCAAATTCGCATTG
Found at i:251142 original size:21 final size:21
Alignment explanation
Indices: 251051--251155 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
251041 GACTCACCTG
*
251051 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
251073 T-ATCGCTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
251093 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
251114 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
251135 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
251156 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:251148 original size:42 final size:42
Alignment explanation
Indices: 251048--251158 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
251038 CCCGACTCAC
* * * *
251048 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGCTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGCTCAAGAGGCCA
* ** *
251090 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGCTCAAGAGGCCA
*
251132 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
251159 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.39, G:0.19, T:0.22
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGCTCAAGAGGCCA
Found at i:252579 original size:14 final size:14
Alignment explanation
Indices: 252560--252596 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
252550 GCTTGTTTAA
*
252560 TTGATTTGTAAAAT
1 TTGATTTGTAAAAG
252574 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
252588 TTGATTTGT
1 TTGATTTGT
252597 TTAATATTGA
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:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:252591 original size:28 final size:29
Alignment explanation
Indices: 252560--252614 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
252550 GCTTGTTTAA
*
252560 TTGATTTGTAAAAT-TTGATTTGTAAAAG
1 TTGATTTGTAAAATATTGATGTGTAAAAG
**
252588 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTAAAATATTGATGTGTAAA
252615 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (29 bp):
TTGATTTGTAAAATATTGATGTGTAAAAG
Found at i:252830 original size:20 final size:20
Alignment explanation
Indices: 252805--252873 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
252795 ACGATTTTCT
*
252805 CGTTGCGATAGTCGAATACC
1 CGTTGCGATAGTCAAATACC
* * *
252825 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACC
* * *
252845 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATACC
252865 CGTTGCGAT
1 CGTTGCGAT
252874 TTTTGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATACC
Found at i:252905 original size:20 final size:20
Alignment explanation
Indices: 252880--252935 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
252870 CGATTTTTGA
*
252880 GTTGCGATAATCAAATCCGT
1 GTTGCGATAATCAAATCCGC
* * *
252900 GTTGCGATAGTGAAATTCGC
1 GTTGCGATAATCAAATCCGC
*
252920 GTTGCGATATTCAAAT
1 GTTGCGATAATCAAAT
252936 GAATGTGTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGATAATCAAATCCGC
Found at i:256222 original size:20 final size:20
Alignment explanation
Indices: 256199--256317 Score: 193
Period size: 20 Copynumber: 6.0 Consensus size: 20
256189 GTGTTGCGCC
* *
256199 AGTCAGCATCGCGTTGTGAT
1 AGTCAGAATCGCGTTGCGAT
* *
256219 AGTCAGAATCTCATTGCGAT
1 AGTCAGAATCGCGTTGCGAT
256239 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
*
256259 AGTCAGAATCTCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
256279 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCGTTGCGAT
256299 AGTCAGAATCGCGTTGCGA
1 AGTCAGAATCGCGTTGCGA
256318 ATCTGGAAAC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 91 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (20 bp):
AGTCAGAATCGCGTTGCGAT
Found at i:257825 original size:28 final size:28
Alignment explanation
Indices: 257733--257831 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 28
257723 GGATACTTTT
* * *
257733 TTATTTTAATTTGTAAAAAATATAGGGTA
1 TTATTGTAATTTATAAAAATTATA-GGTA
* * * ** *
257762 TTATTGTAATTT-GAAAAATGCAGACCTT
1 TTATTGTAATTTATAAAAAT-TATAGGTA
257790 TTGA-TGTAATTTATAAAAATTATAGGTA
1 TT-ATTGTAATTTATAAAAATTATAGGTA
257818 TTATTGTAATTTAT
1 TTATTGTAATTTAT
257832 GAGAAGTTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
27 1 0.02
28 31 0.60
29 20 0.38
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.45
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAATTATAGGTA
Found at i:257881 original size:29 final size:28
Alignment explanation
Indices: 257794--257894 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
257784 GACCTTTTGA
* *
257794 TGTAATTTATAAAAATTATAGGTA-TTAT
1 TGTAATTTATAAAAGTT-TTGGTATTTAT
* * *
257822 TGTAATTTATGAGAAGTTTT-TTCTTTGAT
1 TGTAATTTAT-AAAAGTTTTGGTATTT-AT
257851 TGTAATTTATAAATAGTTTTGGTATTTAT
1 TGTAATTTATAAA-AGTTTTGGTATTTAT
*
257880 TGTAATATTAAAAAA
1 TGTAAT-TTATAAAA
257895 TTGACTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.02
28 15 0.26
29 32 0.55
30 10 0.17
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.50
Consensus pattern (28 bp):
TGTAATTTATAAAAGTTTTGGTATTTAT
Found at i:257969 original size:15 final size:15
Alignment explanation
Indices: 257940--257974 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
257930 TTTTATTGTA
*
257940 ATTTT-ATAATTTTT
1 ATTTTAATAATATTT
257954 ATTTTAATAATATTT
1 ATTTTAATAATATTT
257969 ATTTTA
1 ATTTTA
257975 GAAGTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTAATAATATTT
Found at i:259737 original size:14 final size:14
Alignment explanation
Indices: 259720--259759 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
259710 TTCGGTTATA
259720 TTCGTTTATGTTCG
1 TTCGTTTATGTTCG
* *
259734 TTCGTTTATATGCG
1 TTCGTTTATGTTCG
*
259748 TTCATTTATGTT
1 TTCGTTTATGTT
259760 TAACCCAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57
Consensus pattern (14 bp):
TTCGTTTATGTTCG
Found at i:261328 original size:10 final size:10
Alignment explanation
Indices: 261294--261354 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
261284 CAACGTTTAT
*
261294 GTTTGTGTTC
1 GTTTATGTTC
*
261304 ATTTATGTTC
1 GTTTATGTTC
*
261314 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
261326 GTTTATGTTC
1 GTTTATGTTC
*
261336 GTTTGTGTTC
1 GTTTATGTTC
261346 GTTTATGTT
1 GTTTATGTT
261355 TATTTATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
10 28 0.70
11 8 0.20
12 4 0.10
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.61
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:261355 original size:16 final size:16
Alignment explanation
Indices: 261289--261335 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
261279 GTCTCCAACG
261289 TTTATGTTTGTGTTCA
1 TTTATGTTTGTGTTCA
*
261305 TTTATGTTCGTGTTCA
1 TTTATGTTTGTGTTCA
*
261321 TTTATGTTTATGTTC
1 TTTATGTTTGTGTTC
261336 GTTTGTGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.13, C:0.09, G:0.17, T:0.62
Consensus pattern (16 bp):
TTTATGTTTGTGTTCA
Found at i:261357 original size:32 final size:32
Alignment explanation
Indices: 261287--261347 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
261277 GGGTCTCCAA
*
261287 CGTTTATGTTTGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTTATGTTCATTTATGTTCGTGTT
* * *
261319 CATTTATGTTTATGTTCGTTTGTGTTCGT
1 CGTTTATGTTTATGTTCATTTATGTTCGT
261348 TTATGTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (32 bp):
CGTTTATGTTTATGTTCATTTATGTTCGTGTT
Found at i:263207 original size:3 final size:3
Alignment explanation
Indices: 263199--263233 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
263189 ATTGTAAATA
263199 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
263234 ATAAATAAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:263570 original size:2 final size:2
Alignment explanation
Indices: 263563--263612 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
263553 TCGGAATTAA
263563 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
263605 AT AT AT AT
1 AT AT AT AT
263613 TAAAATATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268563 original size:21 final size:19
Alignment explanation
Indices: 268515--268569 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
268505 CTTTGCTAAC
*
268515 ACTTCTAACACTAACCGCT
1 ACTTCTAACACTAACCACT
*
268534 AATTACTAACACATAACCACT
1 ACTT-CTAACAC-TAACCACT
*
268555 ACCTTCTAAAACTAA
1 A-CTTCTAACACTAA
268570 TCGCTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.10
20 10 0.34
21 14 0.48
22 2 0.07
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (19 bp):
ACTTCTAACACTAACCACT
Found at i:268588 original size:4 final size:4
Alignment explanation
Indices: 268579--268613 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
268569 ATCGCTAATT
* *
268579 TTTA TTTA TTTA TTTA CTTA TTTA TTTA TATA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
268614 TATGTTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:274812 original size:102 final size:100
Alignment explanation
Indices: 274532--274842 Score: 387
Period size: 99 Copynumber: 3.1 Consensus size: 100
274522 TCTGTCACCT
* * * * *
274532 TTGAGATTGTTTCTCTCCAAACAAATTTCATCTCACTTTAGACAATTTTCCCTCGAAACACAAAT
1 TTGAGATTGTTT-TCT-AAAACAAATTTCATCTCGCTTGAGATAATTTTCCTTCGAAACACAAAT
274597 TTTGAAATTGTTTCACTTGAAACAAAATTTATCTCAC
64 TTTGAAATTGTTTCACTTGAAACAAAATTTATCTCAC
* * * *
274634 TTGAGATTGATATTT-TAAAA-AAA-ATCGTCTCGCTTGAGATAGTTTTCCCTT-AAAACACAAA
1 TTGAGATTG-T-TTTCTAAAACAAATTTCATCTCGCTTGAGATAATTTT-CCTTCGAAACACAAA
* *
274695 TTTTGAAATCGTTTCACTTGAAACAAAATTGATCTCAC
63 TTTTGAAATTGTTTCACTTGAAACAAAATTTATCTCAC
*
274733 TTGAGATTGTTTTCATAAAACCAAATTTTATCTCGCTTGAGATAATTTTCCTTCGAAACACAAAT
1 TTGAGATTGTTTTC-TAAAA-CAAATTTCATCTCGCTTGAGATAATTTTCCTTCGAAACACAAAT
* *
274798 TTTGAAATTATTTCACTCGAAACAAAATTTTATCTCAC
64 TTTGAAATTGTTTCACTTGAAACAAAA-TTTATCTCAC
*
274836 CTGAGAT
1 TTGAGAT
274843 AACTTCTTTA
Statistics
Matches: 178, Mismatches: 21, Indels: 19
0.82 0.10 0.09
Matches are distributed among these distances:
97 3 0.02
98 1 0.01
99 76 0.43
100 6 0.03
101 10 0.06
102 63 0.35
103 17 0.10
104 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (100 bp):
TTGAGATTGTTTTCTAAAACAAATTTCATCTCGCTTGAGATAATTTTCCTTCGAAACACAAATTT
TGAAATTGTTTCACTTGAAACAAAATTTATCTCAC
Found at i:275498 original size:139 final size:137
Alignment explanation
Indices: 275090--275606 Score: 588
Period size: 137 Copynumber: 3.7 Consensus size: 137
275080 TCGTTTTCAA
* * *
275090 AGTGTAATCCTCAGACAATCAGACTTCCTCAATGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
1 AGTGTCATCCTCAGACAATCAGACTTCCTAAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
* * *** * * * * * * *
275155 AAAATGAATAGTTTTCCTCACCAAGAAGGAATAATGTTGTGCACCGACCATATCTCCTCAACACG
66 AAAACGGATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACACG
275220 AAGGAGC
131 AAGGAGC
* * * * * * *
275227 AGTGTCATCCTCAAACAATCAGATTTCCTCAACGTGAATGAACCGTGTTATATCCAAATTATCCA
1 AGTGTCATCCTCAGACAATCAGACTTCCTAAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
* * * *
275292 AAAATGGATATACGT-CTGCAACACGAAGGAACAATGTCGTCCACTGATCAGATCTCCTCAACGC
66 AAAACGGATAGACGTCCT-CAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACAC
* *
275356 GAAGAAGA
130 GAAGGAGC
* *
275364 AATGTCATCCTCAGACAATCAGACTTCCTAAACGTGAAGGAACCGTGTTGTCTCCAAATTATCAC
1 AGTGTCATCCTCAGACAATCAGACTTCCTAAACGCGAAGGAACCGTGTTGTCTCCAAATTAT--C
* * *
275429 CAAATACGGATAGACGACCTCAGCACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACA
64 CAAAAACGGATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACA
*
275494 CGAAGGATC
129 CGAAGGAGC
* * * * *
275503 AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACTGTGTTGTCTCTAAATTATCTC
1 AGTGTCATCCTCAGACAATCAGACTTCCTAAACGCGAAGGAACCGTGTTGTCTCCAAATTA--TC
* * *
275568 CAAATAC-GACTAGATGTCCTCAACACGAAGGAAAAATGT
64 CAAAAACGGA-TAGACGTCCTCAACACGAAGGAACAATGT
275607 AACCAACTAG
Statistics
Matches: 321, Mismatches: 52, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
136 2 0.01
137 165 0.51
138 2 0.01
139 149 0.46
140 2 0.01
141 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (137 bp):
AGTGTCATCCTCAGACAATCAGACTTCCTAAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
AAAACGGATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACACG
AAGGAGC
Found at i:276020 original size:104 final size:104
Alignment explanation
Indices: 275826--276177 Score: 408
Period size: 104 Copynumber: 3.4 Consensus size: 104
275816 CTTAAACAAT
* * *
275826 ATATCATCTCCATATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGACCAA
1 ATATTATCTCCATATTGACCCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAA
*
275891 G-ACTCTTCAACATGGATGAGTAGTGTCGTTTTCAACACC
66 GAACTCTTCAACATGGATGAGCAGTGTC-TTTTCAACACC
* * * * *
275930 ATATTATCTCTATATTGACTCGACTTT-CTCAATGAGAAGGAAAAATGTCATATGAAA-CGACCA
1 ATATTATCTCCATATTGACCCGA-TTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCA
* * *
275993 AGAACACTTCAACATGGGTGAGCAGTGTTATTTTCAACACC
65 AGAACTCTTCAACATGGATGAGCAGTG-TCTTTTCAACACC
*** * * *
276034 ATATTATCTCTGGATTGACCCGATTTCCTCAACGAGAATGAACAATATCATATAAAAGCGGCC-A
1 ATATTATCTCCATATTGACCCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAA
* ** * *
276098 GAACTTTTCAACATGGATGAGCAGTGTCACTTGAACAAC
66 GAACTCTTCAACATGGATGAGCAGTGTCTTTTCAACACC
* * *
276137 AAATTATCTCCAAATTGA-TCGATTTCCTCAACGAGAAGGAA
1 ATATTATCTCCATATTGACCCGATTTCCTCAACGAGAAGGAA
276178 TAGTGTCATC
Statistics
Matches: 210, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
102 21 0.10
103 33 0.16
104 148 0.70
105 8 0.04
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (104 bp):
ATATTATCTCCATATTGACCCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAA
GAACTCTTCAACATGGATGAGCAGTGTCTTTTCAACACC
Found at i:276369 original size:3 final size:3
Alignment explanation
Indices: 276361--276405 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
276351 TTTTATCGGG
276361 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
276406 ATAATATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:278896 original size:24 final size:26
Alignment explanation
Indices: 278864--278911 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
278854 TCAAATTTTC
278864 AAATAAAGTCAT-AATT-AATTTTTAG
1 AAATAAAGTC-TCAATTCAATTTTTAG
278889 AAAT-AAGTCTCAATTCAATTTTT
1 AAATAAAGTCTCAATTCAATTTTT
278912 CCCAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 9 0.43
25 11 0.52
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
AAATAAAGTCTCAATTCAATTTTTAG
Found at i:280113 original size:154 final size:154
Alignment explanation
Indices: 279902--280194 Score: 480
Period size: 154 Copynumber: 1.9 Consensus size: 154
279892 CGATCACCAT
279902 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
1 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
* ** * * *
279967 CGATGGACGGCGGTGGATCGGAGAAAATAAGTT-GAACGGTTTTTGGCCTCTTGCCTGCGATCGG
66 CGATGGACGACGGCAGATCGGAGAAAATAA-TTCGAACGGTTTTTAGCCTCTTGCCGGCGATCAG
280031 GATCTCCGATTAACATTCCAAATGG
130 GATCTCCGATTAACATTCCAAATGG
*
280056 TCCGAACGGTCAAAAGTTGCGCGAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
1 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
* * *
280121 TGGTGGACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTTTTGCCGGCGATCAGG
66 CGATGGACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTCTTGCCGGCGATCAGG
280186 ATCTCCGAT
131 ATCTCCGAT
280195 CAATGTTCAA
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
153 2 0.02
154 126 0.98
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (154 bp):
TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
CGATGGACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTCTTGCCGGCGATCAGG
ATCTCCGATTAACATTCCAAATGG
Found at i:281027 original size:2 final size:2
Alignment explanation
Indices: 280978--281011 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
280968 TTTCGTACAT
280978 TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
281012 AGTTATAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:288031 original size:38 final size:38
Alignment explanation
Indices: 287980--288057 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
287970 TCTTTTCGAT
* **
287980 TTCATTTGGGTATTTTGATGAATTTATTTCTAGGGTTC
1 TTCATTTGGGTATTTTCAAAAATTTATTTCTAGGGTTC
*
288018 TTCATTTGGGTATTTTCAAAAATTTGTTTCTAGGGTTC
1 TTCATTTGGGTATTTTCAAAAATTTATTTCTAGGGTTC
288056 TT
1 TT
288058 TTCGATTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.53
Consensus pattern (38 bp):
TTCATTTGGGTATTTTCAAAAATTTATTTCTAGGGTTC
Found at i:288066 original size:23 final size:21
Alignment explanation
Indices: 288039--288092 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
288029 ATTTTCAAAA
288039 ATTTGTTTCTAGGGTTCTT-TTC
1 ATTTGTTT-TA-GGTTCTTGTTC
*
288061 GATTTGTATTTAGGTTTTTGTTC
1 -ATTTGT-TTTAGGTTCTTGTTC
288084 ATTTGTTTT
1 ATTTGTTTT
288093 GAACTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
23 11 0.39
24 2 0.07
ACGTcount: A:0.11, C:0.07, G:0.19, T:0.63
Consensus pattern (21 bp):
ATTTGTTTTAGGTTCTTGTTC
Found at i:289807 original size:19 final size:21
Alignment explanation
Indices: 289770--289808 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
289760 AAACAATGTA
289770 AAGATAAATCCTAAATTAAAG
1 AAGATAAATCCTAAATTAAAG
289791 AAGA-AAATCCT-AATTAAA
1 AAGATAAATCCTAAATTAAA
289809 ATACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (21 bp):
AAGATAAATCCTAAATTAAAG
Found at i:290462 original size:22 final size:22
Alignment explanation
Indices: 290437--290493 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
290427 AAGTTTGCTA
* *
290437 AAAATAAAATGAATTTAAAAAT
1 AAAATAAAACGAATTTAAAAAG
290459 AAAATAAAACGAATTTAAAAAG
1 AAAATAAAACGAATTTAAAAAG
290481 AAAATAAAACGAA
1 AAAATAAAACGAA
290494 ATGGGTTGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAATAAAACGAATTTAAAAAG
Found at i:291966 original size:73 final size:73
Alignment explanation
Indices: 291862--292009 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 73
291852 TGTGGAAAGA
* * *
291862 TCTCATTTTCAACCTAAATTGAAATTT-AAAAAACATGTAAAAACAAAATATTAGTGCACATTAA
1 TCTCATTTTCAACCT-AATTGAAATTTAAAAAAACATGTAAAAACAAAATATCAATACACATTAA
291926 ATAGAGAGG
65 ATAGAGAGG
291935 TCTCATTTTCAACCT-ATTGAAATTTAAAAAAAAAAACATGTAAAAACAAAATATCAATACACAT
1 TCTCATTTTCAACCTAATTGAAATTT----AAAAAAACATGTAAAAACAAAATATCAATACACAT
*
291999 TTAATAGAGAG
62 TAAATAGAGAG
292010 AATTACTGGC
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
71 10 0.15
73 15 0.23
76 41 0.62
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (73 bp):
TCTCATTTTCAACCTAATTGAAATTTAAAAAAACATGTAAAAACAAAATATCAATACACATTAAA
TAGAGAGG
Found at i:296417 original size:25 final size:24
Alignment explanation
Indices: 296371--296420 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
296361 ATATATATAT
**
296371 ATTAAAATTTTATTTATTAAAAAA
1 ATTAAAATTTTATTTAAGAAAAAA
*
296395 ATTAAAATATTTTTTTAAGAAAAAA
1 ATTAAAAT-TTTATTTAAGAAAAAA
296420 A
1 A
296421 ATCTTCCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTAAAATTTTATTTAAGAAAAAA
Found at i:323044 original size:20 final size:20
Alignment explanation
Indices: 323019--323058 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
323009 GTGAAGCTGC
323019 ACAAATCACCCA-AAAAATCA
1 ACAAAT-ACCCACAAAAATCA
*
323039 ACAAATACTCACAAAAATCA
1 ACAAATACCCACAAAAATCA
323059 TACTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (20 bp):
ACAAATACCCACAAAAATCA
Found at i:326911 original size:25 final size:25
Alignment explanation
Indices: 326877--326934 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
326867 GATCATCTTT
* *
326877 AATTTTAATCAATATTAAAATTTGA
1 AATTTTAATCAACATTAAAATTTCA
326902 AATTTTAATCAACATTAAAATTTCA
1 AATTTTAATCAACATTAAAATTTCA
326927 AATTTTAA
1 AATTTTAA
326935 AATATAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTTTAATCAACATTAAAATTTCA
Found at i:327160 original size:16 final size:15
Alignment explanation
Indices: 327132--327195 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 15
327122 GTGGAAGGAT
327132 TTATTTCTATATTATA
1 TTATTT-TATATTATA
327148 TCTATTTTATATTATA
1 T-TATTTTATATTATA
*
327164 TATATATATATATATATA
1 T-TAT-TTTATAT-TATA
327182 TTAATTTTTATATT
1 TT-A-TTTTATATT
327196 TTAATATTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 14 0.35
17 13 0.32
18 12 0.30
19 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTTATATTATA
Found at i:327711 original size:21 final size:20
Alignment explanation
Indices: 327682--327720 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
327672 AAGATTATTA
*
327682 AAATATATATTTTCTTTTACC
1 AAATATATATATT-TTTTACC
*
327703 AAATTTATATATTTTTTA
1 AAATATATATATTTTTTA
327721 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATATATATATTTTTTACC
Found at i:328305 original size:2 final size:2
Alignment explanation
Indices: 328300--328337 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
328290 GAAAAAACTC
328300 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
328338 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:331660 original size:28 final size:28
Alignment explanation
Indices: 331620--331680 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
331610 AAAAGAGCTT
331620 GTTGGTCTGGATGTTGTTTTGATTTAAA
1 GTTGGTCTGGATGTTGTTTTGATTTAAA
331648 GTTGGTCTGGATGTTGTTTTGATTTAAA
1 GTTGGTCTGGATGTTGTTTTGATTTAAA
331676 GTTGG
1 GTTGG
331681 GATGAAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.16, C:0.03, G:0.31, T:0.49
Consensus pattern (28 bp):
GTTGGTCTGGATGTTGTTTTGATTTAAA
Found at i:332466 original size:12 final size:12
Alignment explanation
Indices: 332451--332476 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
332441 TAATCAGATC
332451 CAGAATCAAGTT
1 CAGAATCAAGTT
332463 CAGAATCAAGTT
1 CAGAATCAAGTT
332475 CA
1 CA
332477 AGCGAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (12 bp):
CAGAATCAAGTT
Found at i:335006 original size:13 final size:12
Alignment explanation
Indices: 334985--335027 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
334975 GGCAGTCCAT
334985 TTTTAATTTTTAA
1 TTTT-ATTTTTAA
334998 TTTTGATTTTTAA
1 TTTT-ATTTTTAA
*
335011 -TTTATTTTTAT
1 TTTTATTTTTAA
335022 TTTTAT
1 TTTTAT
335028 CATTTTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 7 0.26
12 8 0.30
13 12 0.44
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:348487 original size:53 final size:52
Alignment explanation
Indices: 348413--348545 Score: 163
Period size: 53 Copynumber: 2.6 Consensus size: 52
348403 TTTATTTTTT
*
348413 TATATATATATATATATATATTATATAGTATATA-TAGTGTATA-TAGTATATTA
1 TATATATATATATATATATATTATATAGTATATAGTA-T-TATATTA-TAGATTA
348466 TATATATATATATATATATATTATA-A-TATATAGTATTATATTATAGATTA
1 TATATATATATATATATATATTATATAGTATATAGTATTATATTATAGATTA
*
348516 TAT-TATGTATAT-TATATA-TATCATAGTATA
1 TATATATATATATATATATATTAT-ATAGTATA
348546 CATTTATATA
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
47 3 0.04
48 7 0.10
49 9 0.12
50 17 0.23
51 9 0.12
52 3 0.04
53 25 0.34
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.50
Consensus pattern (52 bp):
TATATATATATATATATATATTATATAGTATATAGTATTATATTATAGATTA
Found at i:348518 original size:55 final size:54
Alignment explanation
Indices: 348413--348562 Score: 178
Period size: 55 Copynumber: 2.7 Consensus size: 54
348403 TTTATTTTTT
* *
348413 TATATATATATATATATATATTATATAGTATATATAGTGTATATAGTATATTATATA
1 TATATATATATATATATATAATATATAGTAT-TATA-T-TATAGAGTATATTATATA
* *
348470 TATATATATATATATATTATAATATATAGTATTATATTATAGATTATATTATGTA
1 TATATATATATATATA-TATAATATATAGTATTATATTATAGAGTATATTATATA
*
348525 TAT-TATATATATCATAGTATACATTTATA-TATTATATT
1 TATATATATATAT-ATA-TATA-ATATATAGTATTATATT
348563 TTTTATATTA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
54 9 0.11
55 34 0.40
56 7 0.08
57 20 0.24
58 14 0.17
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (54 bp):
TATATATATATATATATATAATATATAGTATTATATTATAGAGTATATTATATA
Found at i:348569 original size:64 final size:64
Alignment explanation
Indices: 348413--348594 Score: 170
Period size: 64 Copynumber: 3.0 Consensus size: 64
348403 TTTATTTTTT
* * *
348413 TATATATATATATATA-TATATTATATAGTA-TATA-T--AGTGTATA-TA-GTATATTATATA
1 TATATATATACATATATTATAATATATAGTATTATATTAGAGTATATATTATGTATATTATATA
* *
348470 TATATATATATATATATTATAATATATAGTATTATATTATAG-ATTATATTATGTATATTATATA
1 TATATATATACATATATTATAATATATAGTATTATATTAGAGTA-TATATTATGTATATTATATA
* * * *
348534 TATCATAGTATACATTTA-TATATTATAT-TTTTTATATTAGAGTATATATTAT-TAATATTAT
1 TAT-ATA-TATACATATATTATAATATATAGTATTATATTAGAGTATATATTATGT-ATATTAT
348595 TTATTTATTT
Statistics
Matches: 105, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
57 16 0.15
58 13 0.12
59 4 0.04
60 1 0.01
62 6 0.06
63 3 0.03
64 41 0.39
65 13 0.12
66 8 0.08
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (64 bp):
TATATATATACATATATTATAATATATAGTATTATATTAGAGTATATATTATGTATATTATATA
Found at i:348570 original size:34 final size:36
Alignment explanation
Indices: 348513--348579 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 36
348503 ATATTATAGA
*
348513 TTATATTATGTATATTATATATATCATAGTATACAT
1 TTATATTATGTATATTATATATATCAGAGTATACAT
* * *
348549 TTATA-TAT-TATATTTTTTATATTAGAGTATA
1 TTATATTATGTATATTATATATATCAGAGTATA
348580 TATTATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 19 0.70
35 3 0.11
36 5 0.19
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (36 bp):
TTATATTATGTATATTATATATATCAGAGTATACAT
Found at i:348581 original size:2 final size:2
Alignment explanation
Indices: 348413--348561 Score: 129
Period size: 2 Copynumber: 76.5 Consensus size: 2
348403 TTTATTTTTT
*
348413 TA TA TA TA TA TA TA TA TA TA T- TA TA TA GTA TA TA TA GTG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
348456 TA GTA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
348496 TA GTA T- TA TA T- TA TA GA T- TA TA T- TA TG TA TA T- 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
* *
348534 TA TCA TA GTA TA CA TT TA TA TA T- TA TA T
1 TA T-A TA -TA TA TA TA TA TA TA TA TA TA T
348562 TTTTTATATT
Statistics
Matches: 121, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
1 10 0.08
2 100 0.83
3 11 0.09
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:351508 original size:13 final size:13
Alignment explanation
Indices: 351490--351537 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
351480 AAACGAACAC
351490 AAATGAACATAAT
1 AAATGAACATAAT
351503 AAATGAAC---AT
1 AAATGAACATAAT
*
351513 AAATGAACACAAT
1 AAATGAACATAAT
*
351526 AAACGAACATAA
1 AAATGAACATAA
351538 ACGAACACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.62, C:0.12, G:0.08, T:0.17
Consensus pattern (13 bp):
AAATGAACATAAT
Found at i:351510 original size:23 final size:23
Alignment explanation
Indices: 351479--351561 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
351469 TAAACGAATG
* *
351479 TAAACGAACACAAATGAACATAA
1 TAAACGAACATAAATGAACACAA
*
351502 TAAATGAACATAAATGAACACAA
1 TAAACGAACATAAATGAACACAA
*
351525 TAAACGAACATAAACGAACACAA
1 TAAACGAACATAAATGAACACAA
351548 TAAACGAACATAAA
1 TAAACGAACATAAA
351562 CTAACAACAC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.61, C:0.17, G:0.08, T:0.13
Consensus pattern (23 bp):
TAAACGAACATAAATGAACACAA
Found at i:351537 original size:10 final size:10
Alignment explanation
Indices: 351468--351567 Score: 56
Period size: 10 Copynumber: 9.1 Consensus size: 10
351458 CATTTAAATG
*
351468 ATAAACGAAT
1 ATAAACGAAC
*
351478 GTAAACGAAC
1 ATAAACGAAC
* *
351488 ACAAATGAAC
1 ATAAACGAAC
*
351498 ATAATAAATGAAC
1 ---ATAAACGAAC
*
351511 ATAAATGAACAC
1 ATAAACG-A-AC
351523 AATAAACGAAC
1 -ATAAACGAAC
351534 ATAAACGAACAC
1 ATAAACG-A-AC
351546 AATAAACGAAC
1 -ATAAACGAAC
*
351557 ATAAACTAAC
1 ATAAACGAAC
351567 A
1 A
351568 ACACAAACAC
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
10 39 0.53
11 6 0.08
12 6 0.08
13 22 0.30
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.14
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:351550 original size:13 final size:13
Alignment explanation
Indices: 351511--351557 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
351501 ATAAATGAAC
*
351511 ATAAATGAACACA
1 ATAAACGAACACA
351524 ATAAACG-A-AC-
1 ATAAACGAACACA
351534 ATAAACGAACACA
1 ATAAACGAACACA
351547 ATAAACGAACA
1 ATAAACGAACA
351558 TAAACTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 3 0.10
13 17 0.57
ACGTcount: A:0.62, C:0.19, G:0.09, T:0.11
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:351575 original size:23 final size:23
Alignment explanation
Indices: 351480--351575 Score: 95
Period size: 23 Copynumber: 4.2 Consensus size: 23
351470 AAACGAATGT
* * * *
351480 AAACGAACACAAATGAACATAAT
1 AAACGAACATAAACGAACACAAC
* * *
351503 AAATGAACATAAATGAACACAAT
1 AAACGAACATAAACGAACACAAC
*
351526 AAACGAACATAAACGAACACAAT
1 AAACGAACATAAACGAACACAAC
*
351549 AAACGAACATAAACTAACA-ACAC
1 AAACGAACATAAACGAACACA-AC
351572 AAAC
1 AAAC
351576 ACAAACATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 1 0.02
23 64 0.98
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.11
Consensus pattern (23 bp):
AAACGAACATAAACGAACACAAC
Found at i:351881 original size:34 final size:34
Alignment explanation
Indices: 351838--351918 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
351828 CCTCTGTTCG
* *
351838 AACATAAATGAGCAAAAATGAACGAACATAAATA
1 AACATAAATGAACAAAAATAAACGAACATAAATA
* * * *
351872 AACATAAATGAACAGACATAAATGAACATAAATG
1 AACATAAATGAACAAAAATAAACGAACATAAATA
351906 AACATAAATGAAC
1 AACATAAATGAAC
351919 GAACATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.60, C:0.12, G:0.11, T:0.16
Consensus pattern (34 bp):
AACATAAATGAACAAAAATAAACGAACATAAATA
Found at i:351892 original size:14 final size:14
Alignment explanation
Indices: 351873--351899 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
351863 ACATAAATAA
351873 ACATAAATGAACAG
1 ACATAAATGAACAG
351887 ACATAAATGAACA
1 ACATAAATGAACA
351900 TAAATGAACA
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:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
ACATAAATGAACAG
Found at i:351909 original size:24 final size:25
Alignment explanation
Indices: 351837--351909 Score: 105
Period size: 24 Copynumber: 3.0 Consensus size: 25
351827 CCCTCTGTTC
* *
351837 GAACATAAATGAGCAAAAATGAAC-
1 GAACATAAATGAACATAAATGAACA
*
351861 GAACATAAATAAACATAAATGAACA
1 GAACATAAATGAACATAAATGAACA
351886 G-ACATAAATGAACATAAATGAACA
1 GAACATAAATGAACATAAATGAACA
351910 TAAATGAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (25 bp):
GAACATAAATGAACATAAATGAACA
Found at i:351915 original size:10 final size:10
Alignment explanation
Indices: 351861--351918 Score: 71
Period size: 10 Copynumber: 5.4 Consensus size: 10
351851 AAAAATGAAC
351861 GAACATAAAT
1 GAACATAAAT
*
351871 AAACATAAAT
1 GAACATAAAT
351881 GAACAGACATAAAT
1 G---A-ACATAAAT
351895 GAACATAAAT
1 GAACATAAAT
351905 GAACATAAAT
1 GAACATAAAT
351915 GAAC
1 GAAC
351919 GAACATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 31 0.74
11 1 0.02
13 1 0.02
14 9 0.21
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:351922 original size:24 final size:24
Alignment explanation
Indices: 351853--351925 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
351843 AAATGAGCAA
**
351853 AAATGAAC-GAACATAAATAAACAT
1 AAATGAACAGAA-ATAAACGAACAT
* *
351877 AAATGAACAGACATAAATGAACAT
1 AAATGAACAGAAATAAACGAACAT
* *
351901 AAATGAACATAAATGAACGAACAT
1 AAATGAACAGAAATAAACGAACAT
351925 A
1 A
351926 TAATCAAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.95
25 2 0.05
ACGTcount: A:0.60, C:0.12, G:0.11, T:0.16
Consensus pattern (24 bp):
AAATGAACAGAAATAAACGAACAT
Found at i:351924 original size:14 final size:13
Alignment explanation
Indices: 351853--351925 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 13
351843 AAATGAGCAA
351853 AAATGAACGAACAT
1 AAATGAAC-AACAT
351867 AAAT--A-AACAT
1 AAATGAACAACAT
351877 AAATGAACAGACAT
1 AAATGAACA-ACAT
351891 AAATG---AACAT
1 AAATGAACAACAT
351901 AAATG---AACAT
1 AAATGAACAACAT
351911 AAATGAACGAACAT
1 AAATGAAC-AACAT
351925 A
1 A
351926 TAATCAAACG
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
10 28 0.55
11 1 0.02
12 2 0.04
13 1 0.02
14 19 0.37
ACGTcount: A:0.60, C:0.12, G:0.11, T:0.16
Consensus pattern (13 bp):
AAATGAACAACAT
Found at i:358278 original size:7 final size:7
Alignment explanation
Indices: 358268--358686 Score: 203
Period size: 7 Copynumber: 57.9 Consensus size: 7
358258 TTTTTATTTT
358268 TTATATA
1 TTATATA
358275 TTATATA
1 TTATATA
*
358282 GTATATA
1 TTATATA
* *
358289 TAATGTA
1 TTATATA
358296 -TAGTATA
1 TTA-TATA
358303 -TATA-A
1 TTATATA
358308 TGTATAGTA
1 T-TATA-TA
358317 -TATATAA
1 TTATAT-A
358324 TGTATAGTA
1 T-TATA-TA
358333 -TATATA
1 TTATATA
358339 TTATAATA
1 TTAT-ATA
358347 TT-TAGTA
1 TTATA-TA
358354 TTATATTA
1 TTATA-TA
* *
358362 TATACATG
1 T-TATATA
358370 TTATATA
1 TTATATA
* *
358377 TTGTAGA
1 TTATATA
358384 -T-TATA
1 TTATATA
358389 TTATATA
1 TTATATA
358396 GTATATATA
1 -T-TATATA
358405 TTATTATA
1 TTA-TATA
358413 TTATATA
1 TTATATA
*
358420 ATATATA
1 TTATATA
*
358427 -TATGTA
1 TTATATA
358433 TTATAGTA
1 TTATA-TA
358441 CTATACTATA
1 -T-TA-TATA
*
358451 TAATATA
1 TTATATA
358458 TATATATA
1 T-TATATA
358466 TTATAT-
1 TTATATA
358472 TATATATA
1 T-TATATA
358480 TATATATA
1 T-TATATA
358488 TTAT-TA
1 TTATATA
358494 TTATATA
1 TTATATA
*
358501 GTAT-TA
1 TTATATA
358507 TATAGTATA
1 T-TA-TATA
358516 TT-TATA
1 TTATATA
358522 TTATATA
1 TTATATA
*
358529 GTATATA
1 TTATATA
358536 TATATATTA
1 T-TATA-TA
358545 TTATATA
1 TTATATA
*
358552 GTATTATA
1 TTA-TATA
358560 TTATAT-
1 TTATATA
358566 TTATAT-
1 TTATATA
*
358572 TATGTATA
1 T-TATATA
358580 TTATATA
1 TTATATA
358587 -TATCATA
1 TTAT-ATA
* *
358594 GTATACA
1 TTATATA
358601 TTTATATA
1 -TTATATA
*
358609 TTATATT
1 TTATATA
*
358616 TTTTATA
1 TTATATA
*
358623 TTAGAGTA
1 TTATA-TA
358631 -TATATTA
1 TTATA-TA
358638 TTA-ATA
1 TTATATA
358644 TTAT-TA
1 TTATATA
*
358650 ATATATTA
1 TTATA-TA
358658 TTATACT-
1 TTATA-TA
358665 TTATACTTA
1 TTATA--TA
*
358674 TTATTTA
1 TTATATA
358681 TTATAT
1 TTATAT
358687 TATTTTTTAT
Statistics
Matches: 322, Mismatches: 43, Indels: 94
0.70 0.09 0.20
Matches are distributed among these distances:
5 4 0.01
6 49 0.15
7 159 0.49
8 76 0.24
9 27 0.08
10 5 0.02
11 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (7 bp):
TTATATA
Found at i:358290 original size:16 final size:16
Alignment explanation
Indices: 358269--358638 Score: 246
Period size: 16 Copynumber: 22.6 Consensus size: 16
358259 TTTTATTTTT
358269 TATATATTATATAGTA
1 TATATATTATATAGTA
* *
358285 TATATAATGTATAGTA
1 TATATATTATATAGTA
* *
358301 TATATAATGTATAGTA
1 TATATATTATATAGTA
* *
358317 TATATAATGTATAGTA
1 TATATATTATATAGTA
358333 TATATATTATA-A-TA
1 TATATATTATATAGTA
*
358347 TTTAGTATTATATTA-TA
1 TATA-TATTATA-TAGTA
* *
358364 TACATGTTATATATTGTA
1 TATATATTATATA--GTA
*
358382 GATTATATTATATAGTA
1 TA-TATATTATATAGTA
*
358399 TATATATTATTATATTA
1 TATATATTA-TATAGTA
358416 TATA-ATATATATATGTA
1 TATATAT-TATATA-GTA
* *
358433 T-TATAGTACTATACTA
1 TATATATTA-TATAGTA
358449 TATA-ATATATATA-TA
1 TATATAT-TATATAGTA
*
358464 TATTATATTATATATATA
1 TA-TATATTATATA-GTA
*
358482 TATATATTAT-TATTA
1 TATATATTATATAGTA
358497 TATAGTATTATATAGTA
1 TATA-TATTATATAGTA
358514 TATTTATATTATATAGTA
1 TA--TATATTATATAGTA
*
358532 TATATA-TATATTATTA
1 TATATATTATA-TAGTA
358548 TATAGTATTATATTA-TA
1 TATA-TATTATA-TAGTA
* *
358565 TTTATATTATGTA-TA
1 TATATATTATATAGTA
358580 T-TATATATATCATAGTA
1 TATATAT-TAT-ATAGTA
* *
358597 TACAT-TTATATATTA
1 TATATATTATATAGTA
* *
358612 TATTTTTTATATTAG-A
1 TATATATTATA-TAGTA
358628 GTATATATTAT
1 -TATATATTAT
358639 TAATATTATT
Statistics
Matches: 292, Mismatches: 30, Indels: 63
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.03
15 40 0.14
16 131 0.45
17 70 0.24
18 30 0.10
19 11 0.04
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATATTATATAGTA
Found at i:358451 original size:33 final size:31
Alignment explanation
Indices: 358278--358614 Score: 182
Period size: 31 Copynumber: 10.7 Consensus size: 31
358268 TTATATATTA
* * *
358278 TATAGTATATATAATGTATAGTATATATAAT-G
1 TATA-TATATATAATATATA-TATGTATTATAG
* *
358310 TATAGTATATATAATGTATAGTATATATATTATAA
1 TATA-TATATATAA--TATA-TATATGTATTATAG
* * * *
358345 TATTTAGTATTATATTATATACATGTTATATATTG
1 TATATA-TA-TATAATATATATATG-TAT-TATAG
* * *
358380 TAGAT-TATATTATATAGTATATATATTAT--
1 TATATATATATAATATA-TATATGTATTATAG
358409 TATAT-TATATAATATATATATGTATTATAG
1 TATATATATATAATATATATATGTATTATAG
* *
358439 TACTATACTATATAATATATATATATATTATAT
1 TA-TATA-TATATAATATATATATGTATTATAG
358472 TATATATATAT-ATATAT-TAT-TATTATA-
1 TATATATATATAATATATATATGTATTATAG
*
358499 TAGTAT-TATATAGTATATTTATAT-TA-TATAG
1 TA-TATATATATA--ATATATATATGTATTATAG
* *
358530 TATATATATATATTAT-TATATAGTATTATAT
1 TATATATATATAATATATATAT-GTATTATAG
* * * *
358561 TATATTTATATTATGTATATTATATATATCATAG
1 TATATATATA-TA-ATATA-TATATGTATTATAG
* *
358595 TATACATTTAT-ATAT-TATAT
1 TATATATATATAATATATATAT
358615 TTTTTATATT
Statistics
Matches: 245, Mismatches: 32, Indels: 59
0.73 0.10 0.18
Matches are distributed among these distances:
27 7 0.03
28 26 0.11
29 25 0.10
30 22 0.09
31 40 0.16
32 30 0.12
33 39 0.16
34 34 0.14
35 18 0.07
36 4 0.02
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (31 bp):
TATATATATATAATATATATATGTATTATAG
Found at i:358615 original size:49 final size:47
Alignment explanation
Indices: 358326--358690 Score: 221
Period size: 53 Copynumber: 7.3 Consensus size: 47
358316 ATATATAATG
* *
358326 TATAGTATATATATTATA-ATATT-TAGTATTATATTATATACATGTTATA
1 TATA-TATATATATTATATATATTATA-TATTATATT-TATA-TTATTATA
* * *
358375 TATTGTAGATTATATTATATAGTA-TATATATTATTATATTATATAATATATA
1 TA-TATATA-TATATTATATA-TATTATATATTA-TAT-TTATATTAT-TATA
* * *
358427 TATGTATTATAGTACTATACTATATAATATATATATATATTATATTATATATA
1 TATATA-TATA-TATTATA-TATATTATATAT-TATAT-TTATATTAT-TATA
*
358480 TATATATATTATTATTATATAGTATTATATAGTATATTTATATTA-TATA
1 TATATATA-TA-TATTATATA-TATTATATATTATATTTATATTATTATA
*
358529 GTATATATATATATTATTATATAGTATTATATTATATTTATATTATGTATA
1 -TATATATATATATTA-TATATATTA-TATATTATATTTATATTAT-TATA
* *
358580 TTATATATATCATAGTATACAT-TTATATATTATATTT-T-TTA-TAT-
1 -TATATATAT-ATATTATATATATTATATATTATATTTATATTATTATA
* * *
358624 TAGAGTATATATTATTAATATTATTAATATATTATTATACTTTATACTTATTATT
1 TATA-TATATA-TATT-ATA-TA-TATTATA-TATTATA-TTTATA-TTATTATA
358679 TAT-TATAT-TATT
1 TATATATATATATT
358691 TTTTATTTAA
Statistics
Matches: 257, Mismatches: 25, Indels: 66
0.74 0.07 0.19
Matches are distributed among these distances:
43 4 0.02
44 8 0.03
45 6 0.02
46 1 0.00
47 4 0.02
48 14 0.05
49 51 0.20
50 23 0.09
51 44 0.17
52 40 0.16
53 55 0.21
54 5 0.02
55 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (47 bp):
TATATATATATATTATATATATTATATATTATATTTATATTATTATA
Found at i:358634 original size:2 final size:2
Alignment explanation
Indices: 358269--358614 Score: 207
Period size: 2 Copynumber: 181.5 Consensus size: 2
358259 TTTTATTTTT
* *
358269 TA TA TA T- TA TA TA GTA TA TA TA -A TG TA TA GTA TA TA TA -A TG
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
358310 TA TA GTA TA TA TA -A TG TA TA GTA TA TA TA T- TA TA -A TA TT TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * *
358351 GTA T- TA TA T- TA TA TA CA TG T- TA TA TA T- TG TA GA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
358389 T- TA TA TA GTA TA TA TA T- TA T- TA TA T- TA TA TA -A 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
*
358427 TA TG TA T- TA TA GTA CTA TA CTA 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 TA
358467 TA TA T- TA TA TA TA TA TA TA TA T- TA T- TA T- TA TA TA GTA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
358505 TA TA TA GTA TA TT TA TA T- TA TA TA GTA TA TA TA TA TA T- TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
358546 TA TA TA GTA T- TA TA T- TA TA TT TA TA T- TA TG TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
358585 TA TA TCA TA GTA TA CA TT TA TA TA T- TA TA T
1 TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA T
358615 TTTTTATATT
Statistics
Matches: 271, Mismatches: 27, Indels: 92
0.69 0.07 0.24
Matches are distributed among these distances:
1 32 0.12
2 209 0.77
3 30 0.11
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:358655 original size:20 final size:20
Alignment explanation
Indices: 358400--358660 Score: 73
Period size: 20 Copynumber: 12.6 Consensus size: 20
358390 TATATAGTAT
358400 ATATATTATT-ATATTATATA
1 ATATATTATTAATATTAT-TA
* *
358420 ATATATATATGTATTA-TAGTA
1 ATATAT-TAT-TAATATTATTA
* *
358441 CTATACTATATAATA-TA-TA
1 ATATATTAT-TAATATTATTA
*
358460 TATATATTATATTATATATATATA
1 -ATATATTAT-TAATAT-TAT-TA
*
358484 TATATTATTATTATATAGTATT-
1 -ATA-TATTATTA-ATATTATTA
*
358506 ATATAGTATATTTATATTATATA
1 ATATA-T-TATTAATATTAT-TA
*
358529 GTATA-TA-TATATATTATT-
1 ATATATTATTA-ATATTATTA
*
358547 ATATAGTATT-ATATTA-TA
1 ATATATTATTAATATTATTA
*
358565 TTTATATTATGT-ATATTATATA
1 -ATATATTAT-TAATATTAT-TA
*
358587 TATCATAGTA-TACAT-TTATATA
1 -AT-ATATTATTA-ATATTAT-TA
* * * *
358609 TTATATTTTTTATATTA-GA
1 ATATATTATTAATATTATTA
358628 GTATATATTATTAATATTATTA
1 --ATATATTATTAATATTATTA
358650 ATATATTATTA
1 ATATATTATTA
358661 TACTTTATAC
Statistics
Matches: 182, Mismatches: 29, Indels: 60
0.67 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 10 0.05
19 14 0.08
20 63 0.35
21 39 0.21
22 22 0.12
23 14 0.08
24 10 0.05
25 9 0.05
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
ATATATTATTAATATTATTA
Found at i:358703 original size:15 final size:15
Alignment explanation
Indices: 358464--358697 Score: 87
Period size: 15 Copynumber: 15.3 Consensus size: 15
358454 TATATATATA
*
358464 TATTATATTATATATA
1 TATTATATTAT-TATT
358480 TATATATATTATTA-T
1 TAT-TATATTATTATT
* *
358495 TA-TATAGTATTATA
1 TATTATATTATTATT
*
358509 TAGTATA-T-TTATAT
1 TATTATATTATTAT-T
358523 TATATAGTATATATATATAT
1 TAT-TA-TAT-TAT-TAT-T
*
358543 TATTATA-TAGTATT
1 TATTATATTATTATT
358557 ATATTATA-T-TTATAT
1 -TATTATATTATTAT-T
*
358572 TATGTATATTA-TATA
1 TAT-TATATTATTATT
* * *
358587 TATCATAGTATACATT
1 TATTATATTAT-TATT
358603 TA-TATATTA-TATT
1 TATTATATTATTATT
* * *
358616 TTTTATATTAGAGTATA
1 TATTATATT--ATTATT
*
358633 TATTATTAATATTA-T
1 TATTA-TATTATTATT
* *
358648 TAATATATTATTATAC
1 TATTATATTATTAT-T
358664 T-TTATACTTATTATT
1 TATTATA-TTATTATT
*
358679 TATTATATTATTTTT
1 TATTATATTATTATT
358694 TATT
1 TATT
358698 TAATTAATTA
Statistics
Matches: 165, Mismatches: 27, Indels: 53
0.67 0.11 0.22
Matches are distributed among these distances:
13 17 0.10
14 30 0.18
15 52 0.32
16 34 0.21
17 15 0.09
18 6 0.04
19 3 0.02
20 8 0.05
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTATATTATTATT
Found at i:360690 original size:46 final size:46
Alignment explanation
Indices: 360593--360705 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 46
360583 TTACCATCCT
* *
360593 GTAAGGATGCACCAACCTGT-AATACAGTAATTGGGATTATAATCC
1 GTAAGGATGCACCAACCTGTAAATACAATAATTGGGATTATAATCA
* *
360638 GCTAAGGATGCACCATCCTGTAAAT-CAATAATT-GGATTTATCATCTA
1 G-TAAGGATGCACCAACCTGTAAATACAATAATTGGGA-TTATAATC-A
* *
360685 GTAAGGATGCATCAGCCTGTA
1 GTAAGGATGCACCAACCTGTA
360706 TTTTGGTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
45 4 0.07
46 50 0.86
47 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (46 bp):
GTAAGGATGCACCAACCTGTAAATACAATAATTGGGATTATAATCA
Found at i:361869 original size:131 final size:131
Alignment explanation
Indices: 361634--361872 Score: 352
Period size: 131 Copynumber: 1.8 Consensus size: 131
361624 ATAATTCTAA
* * * * * *
361634 GAGAGGAAACGATAATATCTAATTATTTTCGATCAAGAATAAATGACCTCTTATGCCTTAAAGTA
1 GAGAGAAAACGATAATATATAATTATTTACAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
361699 GTCATTTATTGCTCCAATCAAAATGAAGAGATATCACTATTTTATCTTAAAAATCAATATTGATT
66 ATCATTTATTACTCCAACCAAAATGAAAAGATATCACTATTTTATCTTAAAAATCAATATTGATT
361764 C
131 C
*
361765 GAGAGAAAACGATAATATATAATTATTTACAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATATAATTATTTACAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
361830 ATCATTTATTACTTCAACCGAAATGAAAAGATATTACTATTTT
66 ATCATTTATTACTCCAACCAAAATGAAAAGATATCACTATTTT
361873 CAATATTAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 94 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATATAATTATTTACAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
ATCATTTATTACTCCAACCAAAATGAAAAGATATCACTATTTTATCTTAAAAATCAATATTGATT
C
Found at i:364200 original size:17 final size:16
Alignment explanation
Indices: 364157--364214 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
364147 TTGGGCCTGC
*
364157 AATAAAATATAAACAA
1 AATAAAATAAAAACAA
364173 AATAAAGATAAAAACTAA
1 AATAAA-ATAAAAAC-AA
*
364191 AATAAAATAAAACCAAA
1 AATAAAATAAAAAC-AA
364208 AATAAAA
1 AATAAAA
364215 ATTAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.16
17 23 0.62
18 8 0.22
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AATAAAATAAAAACAA
Found at i:386124 original size:191 final size:191
Alignment explanation
Indices: 385800--386177 Score: 756
Period size: 191 Copynumber: 2.0 Consensus size: 191
385790 AGAGAGAGAG
385800 TGAGAGAGGCTTGTGGTTACGCAAATGATAAAAAAATTATTGTTATCATATGATTCATATAGATA
1 TGAGAGAGGCTTGTGGTTACGCAAATGATAAAAAAATTATTGTTATCATATGATTCATATAGATA
385865 GGTCTATGGTTTTAAAGAAAAATGGATTAATAACCTTTAAAGTCCCTAAACTTCTTTAAGTTCAG
66 GGTCTATGGTTTTAAAGAAAAATGGATTAATAACCTTTAAAGTCCCTAAACTTCTTTAAGTTCAG
385930 GAAAAAAATCAAGAATCCTCTATAACTTTATTTTGGTTCCTAAATTTTGCAAGATTCTAAT
131 GAAAAAAATCAAGAATCCTCTATAACTTTATTTTGGTTCCTAAATTTTGCAAGATTCTAAT
385991 TGAGAGAGGCTTGTGGTTACGCAAATGATAAAAAAATTATTGTTATCATATGATTCATATAGATA
1 TGAGAGAGGCTTGTGGTTACGCAAATGATAAAAAAATTATTGTTATCATATGATTCATATAGATA
386056 GGTCTATGGTTTTAAAGAAAAATGGATTAATAACCTTTAAAGTCCCTAAACTTCTTTAAGTTCAG
66 GGTCTATGGTTTTAAAGAAAAATGGATTAATAACCTTTAAAGTCCCTAAACTTCTTTAAGTTCAG
386121 GAAAAAAATCAAGAATCCTCTATAACTTTATTTTGGTTCCTAAATTTTGCAAGATTC
131 GAAAAAAATCAAGAATCCTCTATAACTTTATTTTGGTTCCTAAATTTTGCAAGATTC
386178 ACATAATCTA
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 187 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (191 bp):
TGAGAGAGGCTTGTGGTTACGCAAATGATAAAAAAATTATTGTTATCATATGATTCATATAGATA
GGTCTATGGTTTTAAAGAAAAATGGATTAATAACCTTTAAAGTCCCTAAACTTCTTTAAGTTCAG
GAAAAAAATCAAGAATCCTCTATAACTTTATTTTGGTTCCTAAATTTTGCAAGATTCTAAT
Found at i:386565 original size:45 final size:46
Alignment explanation
Indices: 386485--386578 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 46
386475 AAAATGTCGA
* * *
386485 TATCTATAGCGGCGTTTTTGGAACAAATGCCACAAAAGGTCATATC
1 TATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGACAGATC
* *
386531 TATCTATAGCGGTG-TTTTGGAACAAACGCTACAAAAGGACAGATC
1 TATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGACAGATC
386576 TAT
1 TAT
386579 GGCATCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 30 0.70
46 13 0.30
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (46 bp):
TATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGACAGATC
Found at i:387175 original size:25 final size:25
Alignment explanation
Indices: 387141--387188 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
387131 GTCGTACATT
387141 TGATTTTGATGGGTGAGTCTTCCGA
1 TGATTTTGATGGGTGAGTCTTCCGA
*
387166 TGATTTTGATGGGTGAGTTTTCC
1 TGATTTTGATGGGTGAGTCTTCC
387189 AGTAAGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (25 bp):
TGATTTTGATGGGTGAGTCTTCCGA
Found at i:389259 original size:19 final size:19
Alignment explanation
Indices: 389232--389274 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
389222 AATTTATCCC
389232 AAAAA-TTATGGAAAATAA
1 AAAAATTTATGGAAAATAA
389250 AAAAATTTATGGAAAATAA
1 AAAAATTTATGGAAAATAA
*
389269 ATAAAT
1 AAAAAT
389275 AAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (19 bp):
AAAAATTTATGGAAAATAA
Found at i:389985 original size:18 final size:19
Alignment explanation
Indices: 389960--390043 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
389950 AAATTTAGTT
389960 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* *
389978 TGTATATTATAAATT-TGATT-
1 T-T-TA-TATTAATTATAATTC
**
389998 TTTATATTAATTCCAATTC
1 TTTATATTAATTATAATTC
*
390017 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
390036 -TTATATTA
1 TTTATATTA
390044 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.13
18 14 0.26
19 18 0.34
20 7 0.13
21 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:390057 original size:13 final size:14
Alignment explanation
Indices: 390023--390059 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
390013 ATTCTTTATA
390023 TTATTTAT-AATTC
1 TTATTTATAAATTC
390036 TTATATTATAAATT-
1 TTAT-TTATAAATTC
390050 TTATTTATAA
1 TTATTTATAA
390060 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:390390 original size:54 final size:54
Alignment explanation
Indices: 390308--390415 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
390298 TCTCACCAAG
390308 AGTACTTGTTTAAACTTAAGATGTAATGGTTATAGAGCAACTAGTCATTTAGGT
1 AGTACTTGTTTAAACTTAAGATGTAATGGTTATAGAGCAACTAGTCATTTAGGT
390362 AGTACTTGTTTAAACTTAAGATGTAATGGTTATAGAGCAACTAGTCATTTAGGT
1 AGTACTTGTTTAAACTTAAGATGTAATGGTTATAGAGCAACTAGTCATTTAGGT
390416 TCTATGGACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (54 bp):
AGTACTTGTTTAAACTTAAGATGTAATGGTTATAGAGCAACTAGTCATTTAGGT
Found at i:392956 original size:6 final size:6
Alignment explanation
Indices: 392919--393019 Score: 54
Period size: 6 Copynumber: 16.3 Consensus size: 6
392909 ACTATTTATA
392919 ATTAAT ATTAAAAT AATTATAT ATT-AT AATTAAT ATTAAAAT AATTATAT
1 ATTAAT ATT--AAT -ATTA-AT ATTAAT -ATTAAT ATT--AAT -ATTA-AT
*
392969 ATT-AT AATTAAT ATTAAT A-T-A- ATTAAT ATTAAT ATTAA- CTT-AT
1 ATTAAT -ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
393012 ATTAAT AT
1 ATTAAT AT
393020 AATCTAGTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 34
0.68 0.02 0.30
Matches are distributed among these distances:
3 1 0.01
4 3 0.04
5 10 0.13
6 34 0.45
7 12 0.16
8 10 0.13
9 6 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:392965 original size:43 final size:43
Alignment explanation
Indices: 392916--393053 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 43
392906 TAAACTATTT
392916 ATAATTAATATTAAAATAATTATATATTATAATTAATATTAAA
1 ATAATTAATATTAAAATAATTATATATTATAATTAATATTAAA
* *
392959 ATAATTATATATTATAATTAA-TAT-TAATATAATTAATATTAATA
1 ATAATTA-ATATTA-AAATAATTATATATTATAATTAATATTAA-A
* *
393003 TTAACTT-ATATTAATATAATCTAGTTTATAATTTATAATTAATA-TAAA
1 ATAA-TTAATATTAAAATAAT-TA---TAT-A-TTATAATTAATATTAAA
393051 ATA
1 ATA
393054 TAGTCTATCA
Statistics
Matches: 76, Mismatches: 7, Indels: 19
0.75 0.07 0.19
Matches are distributed among these distances:
42 4 0.05
43 30 0.39
44 15 0.20
45 7 0.09
47 1 0.01
48 4 0.05
49 4 0.05
50 11 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (43 bp):
ATAATTAATATTAAAATAATTATATATTATAATTAATATTAAA
Found at i:393020 original size:31 final size:28
Alignment explanation
Indices: 392914--392999 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
392904 AATAAACTAT
392914 TTATAATTAATATTAAAATAATTATATA
1 TTATAATTAATATTAAAATAATTATATA
392942 TTATAATTAATATTAAAATAATTATATA
1 TTATAATTAATATTAAAATAATTATATA
*
392970 TTATAATTAATATTAATATAATTA-ATA
1 TTATAATTAATATTAAAATAATTATATA
392997 TTA
1 TTA
393000 ATATTAACTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 6 0.11
28 51 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTATAATTAATATTAAAATAATTATATA
Found at i:393230 original size:51 final size:51
Alignment explanation
Indices: 393175--393306 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 51
393165 ATTAATAAAT
*
393175 TAATATATAGTTTATTTATACTATATAGTTTATATACACTAATGAACTATA
1 TAATATATAGTTTATTTATACTATATAGGTTATATACACTAATGAACTATA
*
393226 TAATATATAGTTTGTATATATCATATACTATATAGGTTATATATACTAATGAACTATA
1 TAATATATAG--T-T-TAT-T--TATACTATATAGGTTATATACACTAATGAACTATA
*
393284 TAATATATAGTTTATATATACTA
1 TAATATATAGTTTATTTATACTA
393307 ATGAACTATA
Statistics
Matches: 71, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
51 17 0.24
53 1 0.01
54 4 0.06
55 4 0.06
56 2 0.03
58 43 0.61
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (51 bp):
TAATATATAGTTTATTTATACTATATAGGTTATATACACTAATGAACTATA
Found at i:393233 original size:33 final size:33
Alignment explanation
Indices: 393191--393428 Score: 234
Period size: 33 Copynumber: 7.5 Consensus size: 33
393181 ATAGTTTATT
* *
393191 TATACTATATAGTTTATATACACTAATGAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
*
393224 TATAATATATAG-TT-TGTATA-T-AT---C-A
1 TATAATATATAGTTTATATATACTAATGAACTA
* *
393249 TATACTATATAGGTTATATATACTAATGAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
393282 TATAATATATAGTTTATATATACTAATGAAC--
1 TATAATATATAGTTTATATATACTAATGAACTA
393313 TATAATATATAG-TT-TATATA-TAATGAACTA
1 TATAATATATAGTTTATATATACTAATGAACTA
* * *
393343 TATAAATGTATAGTTTATATATACGATAT-AGTCTA
1 TAT-AATATATAGTTTATATATACTA-ATGA-ACTA
* *
393378 TATATGTTATATAGTTTATATATACTAATAAACTA
1 TATA--ATATATAGTTTATATATACTAATGAACTA
*
393413 TATAATGTATAGTTTA
1 TATAATATATAGTTTA
393429 GGGTTTAGGG
Statistics
Matches: 170, Mismatches: 16, Indels: 38
0.76 0.07 0.17
Matches are distributed among these distances:
25 12 0.07
26 3 0.02
27 5 0.03
28 9 0.05
29 10 0.06
30 6 0.04
31 24 0.14
32 5 0.03
33 57 0.34
34 3 0.02
35 17 0.10
36 19 0.11
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.43
Consensus pattern (33 bp):
TATAATATATAGTTTATATATACTAATGAACTA
Found at i:393257 original size:25 final size:25
Alignment explanation
Indices: 393223--393270 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
393213 CTAATGAACT
* *
393223 ATATAATATATAGTTTGTATATATC
1 ATATAATATATAGGTTATATATATC
*
393248 ATATACTATATAGGTTATATATA
1 ATATAATATATAGGTTATATATA
393271 CTAATGAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATATC
Found at i:393259 original size:58 final size:57
Alignment explanation
Indices: 393191--393390 Score: 210
Period size: 58 Copynumber: 3.4 Consensus size: 57
393181 ATAGTTTATT
*
393191 TATACTATATAGTTTATATACACTAATGAACTATATAATATATAGTTTGTATATATCA
1 TATACTATATAGTTTATATA-ACTAATGAACTATATAATATATAGTTTATATATATCA
* *
393249 TATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAA
1 TATACTATATAGTTTATATA-ACTAATGAACTATATAATATATAG-TT-TATATA-T-AT-CA
* *
393312 CTATAATATATAGTTTATAT-A-TAATGAACTATATAAATGTATAGTTTATATATA-CGA
1 -TATACTATATAGTTTATATAACTAATGAACTATAT-AATATATAGTTTATATATATC-A
393369 TATAGTCTATATA-TGTTATATA
1 TATA--CTATATAGT-TTATATA
393391 GTTTATATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
56 4 0.03
57 2 0.02
58 56 0.46
59 3 0.02
60 11 0.09
61 16 0.13
62 11 0.09
63 1 0.01
64 17 0.14
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (57 bp):
TATACTATATAGTTTATATAACTAATGAACTATATAATATATAGTTTATATATATCA
Found at i:393334 original size:18 final size:18
Alignment explanation
Indices: 393175--393401 Score: 83
Period size: 18 Copynumber: 13.1 Consensus size: 18
393165 ATTAATAAAT
*
393175 TAATATATAGTTTATTTA
1 TAATATATAGTTTATATA
*
393193 TACTATATAGTTTATATA
1 TAATATATAGTTTATATA
* * *
393211 CACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
*
393226 TAATATATAGTTTGTATA
1 TAATATATAGTTTATATA
* *
393244 T-ATCATATACTATATAGGT-
1 TAAT-ATATAGTTTATA--TA
* **
393263 TATATATACTAATGAACTATA
1 TA-ATATA-TAGTTTA-TATA
393284 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
*
393302 TACTA-AT-G---A-ACTA
1 TAATATATAGTTTATA-TA
393315 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
* *
393333 TAAT-GA-A--CTATATA
1 TAATATATAGTTTATATA
*
393347 -AATGTATAGTTTATATA
1 TAATATATAGTTTATATA
** *
393364 TACGATATAGTCTATATA
1 TAATATATAGTTTATATA
**
393382 TGTTATATAGTTTATATA
1 TAATATATAGTTTATATA
393400 TA
1 TA
393402 CTAATAAACT
Statistics
Matches: 152, Mismatches: 32, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
12 1 0.01
13 10 0.07
14 10 0.07
15 9 0.06
16 5 0.03
17 14 0.09
18 77 0.51
19 6 0.04
20 10 0.07
21 8 0.05
22 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:393457 original size:2 final size:2
Alignment explanation
Indices: 393450--393563 Score: 60
Period size: 2 Copynumber: 56.0 Consensus size: 2
393440 TTAGGATTTT
* * *
393450 TA TA TA TA TT TCA TA TG TA AA T- TA TA CTA TA TA GTA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* *
393492 -A TT TA TA TA TA TA -A TA TA TA GTT TA TA TA TA TA -A 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
*
393532 GTA TA TGA -A TA -A AA CTA TA GTA TA TA TA TA TA
1 -TA TA T-A TA TA TA TA -TA TA -TA TA TA TA TA TA
393564 GGTCATATGC
Statistics
Matches: 87, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
1 6 0.07
2 69 0.79
3 12 0.14
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:393498 original size:11 final size:11
Alignment explanation
Indices: 393448--393522 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
393438 GTTTAGGATT
393448 TTTATATAT-A
1 TTTATATATAA
*
393458 TTTCATATGTAA
1 TTT-ATATATAA
*
393470 ATTATACTAT-A
1 TTTATA-TATAA
*
393481 TAGTATATATAA
1 T-TTATATATAA
393493 TTTATATAT-A
1 TTTATATATAA
* *
393503 -TAATATATAG
1 TTTATATATAA
393513 TTTATATATA
1 TTTATATATA
393523 TAATATATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
9 7 0.14
10 4 0.08
11 27 0.55
12 11 0.22
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (11 bp):
TTTATATATAA
Done.