Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008214.1 Hibiscus syriacus cultivar Beakdansim tig00110840_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: 2117680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:189162 original size:20 final size:21
Alignment explanation
Indices: 189124--189162 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
189114 ACGACGAATA
*
189124 TTCTAAGATAAAGATATTTTT
1 TTCTAAAATAAAGATATTTTT
189145 TTCTAAAATAAA-ATATTT
1 TTCTAAAATAAAGATATTT
189163 GACATCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (21 bp):
TTCTAAAATAAAGATATTTTT
Found at i:190255 original size:14 final size:14
Alignment explanation
Indices: 190236--190272 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
190226 AATTCTAAAC
190236 AAATTAATTTACTT
1 AAATTAATTTACTT
190250 AAATTAATTTACTT
1 AAATTAATTTACTT
190264 AAATTAATT
1 AAATTAATT
190273 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTAATTTACTT
Found at i:191650 original size:16 final size:16
Alignment explanation
Indices: 191631--191703 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
191621 TTTAATTTTA
191631 AATTATAATTAT-ATTC
1 AATT-TAATTATAATTC
191647 AATTTTAATTATAATTC
1 AA-TTTAATTATAATTC
* *
191664 TATTTAATTACAATT-
1 AATTTAATTATAATTC
* *
191679 AAATTAATTA-AAGTC
1 AATTTAATTATAATTC
191694 ATATTTAATT
1 A-ATTTAATT
191704 TCAATTTAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.06
15 9 0.19
16 28 0.60
17 7 0.15
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (16 bp):
AATTTAATTATAATTC
Found at i:191656 original size:22 final size:23
Alignment explanation
Indices: 191607--191672 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
191597 TCTATAATTC
* *
191607 AAATTACAATT-TATTTTAATTTT
1 AAATTATAATTATA-TTCAATTTT
191630 AAATTATAATTATATTCAATTTT
1 AAATTATAATTATATTCAATTTT
* *
191653 -AATTATAATTCTATTTAATT
1 AAATTATAATTATATTCAATT
191673 ACAATTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 18 0.47
23 18 0.47
24 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
AAATTATAATTATATTCAATTTT
Found at i:191678 original size:22 final size:22
Alignment explanation
Indices: 191590--191683 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
191580 CTAATTCTAC
191590 TTATAATTCTA--TAATT-CAAA
1 TTATAATTCTATTTAATTAC-AA
*
191610 TTACAATT-TATTTTAATTTTA-AA
1 TTATAATTCTA-TTTAA--TTACAA
* * **
191633 TTATAATTATATTCAATTTTAA
1 TTATAATTCTATTTAATTACAA
191655 TTATAATTCTATTTAATTACAA
1 TTATAATTCTATTTAATTACAA
191677 TTA-AATT
1 TTATAATT
191684 AATTAAAGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
19 2 0.03
20 7 0.12
21 6 0.10
22 26 0.45
23 13 0.22
24 4 0.07
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAATTCTATTTAATTACAA
Found at i:191699 original size:31 final size:31
Alignment explanation
Indices: 191651--191709 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
191641 ATATTCAATT
*
191651 TTAATTATAATTCTATTTAATTACAATTAAA
1 TTAATTATAAGTCTATTTAATTACAATTAAA
*
191682 TTAATTA-AAGTCATATTTAATTTCAATT
1 TTAATTATAAGTC-TATTTAATTACAATT
191710 TAACTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (31 bp):
TTAATTATAAGTCTATTTAATTACAATTAAA
Found at i:192321 original size:21 final size:20
Alignment explanation
Indices: 192281--192322 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
192271 TGACCGTTTA
*
192281 TAGCCGTTGGGGATGATTTC
1 TAGCCGTTGGGAATGATTTC
*
192301 TAGCCGTTTGGGAATGTTTTC
1 TAGCCG-TTGGGAATGATTTC
192322 T
1 T
192323 CTACAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (20 bp):
TAGCCGTTGGGAATGATTTC
Found at i:194243 original size:18 final size:19
Alignment explanation
Indices: 194196--194243 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
194186 GTTGTCTGTT
*
194196 TCAT-CTTCATCATTGGAT
1 TCATACTTCATCATTGGAG
*
194214 TCATA-TTTATCATTGGAG
1 TCATACTTCATCATTGGAG
194232 TCA-ACTTCATCA
1 TCATACTTCATCA
194244 CTCCAAGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (19 bp):
TCATACTTCATCATTGGAG
Found at i:196114 original size:65 final size:65
Alignment explanation
Indices: 196025--196181 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
196015 ATAAGACCTA
* * * * **
196025 GTGCATCGGTACACTAATTACATTCGATATTTCAA-AATAGCCAG-GAGTGCATCGATGCATGGT
1 GTGCATCGGTACACAAAATGCATTCGATATTTCAATAA-AACC-GTGAACGCATCGATGCATGGT
196088 CT
64 CT
* * * * *
196090 GTGCATTGGTACAGAAAATGCATTCGATGTTTCAATAAAATCGTGAACGCATCGATGCATGGTTT
1 GTGCATCGGTACACAAAATGCATTCGATATTTCAATAAAACCGTGAACGCATCGATGCATGGTCT
196155 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
196182 ATTAGGGTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 1 0.01
65 74 0.96
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATATTTCAATAAAACCGTGAACGCATCGATGCATGGTCT
Found at i:198717 original size:2 final size:2
Alignment explanation
Indices: 198710--198748 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
198700 TATTTATGAC
198710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
198749 TGCATAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:203803 original size:31 final size:31
Alignment explanation
Indices: 203768--203967 Score: 224
Period size: 31 Copynumber: 6.5 Consensus size: 31
203758 CAATGTCCAT
*
203768 GTGACCAAAACTTAACAAAACAATAACGTAA
1 GTGACCAAAACTTAATAAAACAATAACGTAA
* *
203799 GTGACCAAAACTTAATAAAACGATAACATAA
1 GTGACCAAAACTTAATAAAACAATAACGTAA
* * *
203830 GTGACCAAAATTTAGTAAAACAATAACATAA
1 GTGACCAAAACTTAATAAAACAATAACGTAA
******* *
203861 GTGACCAAAACTT-ATGTTTTTTTAACGAAAA
1 GTGACCAAAACTTAATAAAACAATAACG-TAA
*
203892 GTGACCAAAACTTAATAAAACAATAACGCAA
1 GTGACCAAAACTTAATAAAACAATAACGTAA
*
203923 GTGACC-AAACTTTAATAAAACAATAATGTAA
1 GTGACCAAAAC-TTAATAAAACAATAACGTAA
203954 GTGACCAAAACTTA
1 GTGACCAAAACTTA
203968 TATTTTCAAA
Statistics
Matches: 138, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
30 9 0.07
31 118 0.86
32 11 0.08
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (31 bp):
GTGACCAAAACTTAATAAAACAATAACGTAA
Found at i:203927 original size:93 final size:92
Alignment explanation
Indices: 203797--203998 Score: 289
Period size: 93 Copynumber: 2.2 Consensus size: 92
203787 ACAATAACGT
* * *
203797 AAGTGACCAAAACTTAATAAAACGATAACATAAGTGACCAAAATTTAGTAAAACAATAACATAAG
1 AAGTGACCAAAACTTAATAAAACAATAACACAAGTGACCAAAATTTAATAAAACAATAACATAAG
* **
203862 TGACCAAAACTTATGTTTTTTTAACGAA
66 TGACCAAAACTTAT-ATTTTCAAACGAA
* * **
203890 AAGTGACCAAAACTTAATAAAACAATAACGCAAGTGACCAAACTTTAATAAAACAATAATGTAAG
1 AAGTGACCAAAACTTAATAAAACAATAACACAAGTGACCAAAATTTAATAAAACAATAACATAAG
*
203955 TGACCAAAACTTATATTTTCAAAGGAA
66 TGACCAAAACTTATATTTTCAAACGAA
203982 AA-TGACCAAAACTTAAT
1 AAGTGACCAAAACTTAAT
203999 CCACGTATTG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 15 0.15
92 11 0.11
93 72 0.73
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.24
Consensus pattern (92 bp):
AAGTGACCAAAACTTAATAAAACAATAACACAAGTGACCAAAATTTAATAAAACAATAACATAAG
TGACCAAAACTTATATTTTCAAACGAA
Found at i:204605 original size:18 final size:18
Alignment explanation
Indices: 204563--204606 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
204553 TCATGGAATG
*
204563 TAAGATTACCATTGAGAA
1 TAAGATTACCAGTGAGAA
*
204581 T-AGATTACCAGTGGGAA
1 TAAGATTACCAGTGAGAA
204598 TAAGATTAC
1 TAAGATTAC
204607 TGGGAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (18 bp):
TAAGATTACCAGTGAGAA
Found at i:210960 original size:60 final size:60
Alignment explanation
Indices: 210822--210990 Score: 156
Period size: 60 Copynumber: 2.8 Consensus size: 60
210812 ATATTTATTT
* * * *
210822 TAAATTAGTCCGTAAACTTTTAAACATTT-AATTTCCT-T-CTTAAAATACGACTATCATTC
1 TAAATTAGTCCCTAAACTTTTAAACATTTCAA-TT-CTATCCTCAAACTATGACTATCATTC
*
210881 TAAATTCA-T-CCTCAAACTTTTAAACATTTCAATTCTATCCTCAAACTATGATCT-TCGTTC
1 TAAATT-AGTCCCT-AAACTTTTAAACATTTCAATTCTATCCTCAAACTATGA-CTATCATTC
* *
210941 TAAATTAGTCCCTAAACTTTTTGAACATTCCAATT-TCATCC-CAAACTATG
1 TAAATTAGTCCCTAAAC-TTTTAAACATTTCAATTCT-ATCCTCAAACTATG
210991 TGTATATCCT
Statistics
Matches: 93, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
58 4 0.04
59 27 0.29
60 38 0.41
61 24 0.26
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (60 bp):
TAAATTAGTCCCTAAACTTTTAAACATTTCAATTCTATCCTCAAACTATGACTATCATTC
Found at i:216713 original size:19 final size:19
Alignment explanation
Indices: 216689--216734 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
216679 TTTGTGTACT
216689 GATACATAGGTAGTATATC
1 GATACATAGGTAGTATATC
216708 GATACATAGGTAGTATATC
1 GATACATAGGTAGTATATC
216727 GATACATA
1 GATACATA
216735 TGTTAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (19 bp):
GATACATAGGTAGTATATC
Found at i:231179 original size:34 final size:35
Alignment explanation
Indices: 231136--231211 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
231126 AACACAGTCA
231136 TCAATTACATTCTAAAC-CCAAAATCCAAAATACT
1 TCAATTACATTCTAAACTCCAAAATCCAAAATACT
* *
231170 TCAATTACATTCTAAACTTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACTCCAAAATCCAAAATACT
231205 TCAATTA
1 TCAATTA
231212 TAAGCCCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 17 0.44
35 22 0.56
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
TCAATTACATTCTAAACTCCAAAATCCAAAATACT
Found at i:231228 original size:35 final size:35
Alignment explanation
Indices: 231152--231230 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 35
231142 ACATTCTAAA
* ** *
231152 CCCAAAATCCAAAATACTTCAATTACATTCTAAAC
1 CCCAAATTCCAAAATACTTCAATTACAAGCCAAAC
** * *
231187 TTCAAATTCCAAAATACTTCAATTATAAGCCCAAC
1 CCCAAATTCCAAAATACTTCAATTACAAGCCAAAC
231222 CCCAAATTC
1 CCCAAATTC
231231 ATAATCCATT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (35 bp):
CCCAAATTCCAAAATACTTCAATTACAAGCCAAAC
Found at i:231611 original size:148 final size:144
Alignment explanation
Indices: 231406--231677 Score: 409
Period size: 148 Copynumber: 1.9 Consensus size: 144
231396 TTTATAAAAG
* * * *
231406 TTGACTCGAATTTTTTTCGATTTGAGTTTATAAAATTTAAGTCAAGTCGAATTGAATTGAATTTT
1 TTGACTCGAATTTTTTTCGATTTAAGTTTATAAAATTTAAATAAAGTCGAACTGAATTGAATTTT
* * * *
231471 CGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTTATTCTAATTCA
66 CGA----CTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAATTCA
231536 GTTCAATTTATAAAATAA
127 GTTCAATTTATAAAATAA
** *
231554 TTGACTCGAATTTTTTTTTATTTAATTTTATAAAATTTAAATAAAGTCGAACTGAATTGAATTTT
1 TTGACTCGAATTTTTTTCGATTTAAGTTTATAAAATTTAAATAAAGTCGAACTGAATTGAATTTT
231619 CGACTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAATT
66 CGACTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAATT
231678 TAAATAGTAT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 52 0.46
148 61 0.54
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (144 bp):
TTGACTCGAATTTTTTTCGATTTAAGTTTATAAAATTTAAATAAAGTCGAACTGAATTGAATTTT
CGACTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTATAATTCAGTTC
AATTTATAAAATAA
Found at i:232658 original size:37 final size:38
Alignment explanation
Indices: 232608--232680 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
232598 TTTATTTTGT
* *
232608 TCGGGTTGGG-TTTTTTAAGTGTGATATTTGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
232645 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCG
232681 GGTTGGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 9 0.27
38 24 0.73
ACGTcount: A:0.12, C:0.08, G:0.37, T:0.42
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:233569 original size:35 final size:36
Alignment explanation
Indices: 233482--233579 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 36
233472 TGAGAATGGA
* * * *
233482 TTATGAATTTGTGGTTGAGCATGTAATTGAAGTATT
1 TTATGAATTTGAGGTTTAGAATGTAATTGAAATATT
233518 TT-TGAAATTTGAGGTTTAGAATGTAATTGAAATATT
1 TTATG-AATTTGAGGTTTAGAATGTAATTGAAATATT
* * *
233554 TTAT-AATTTGGGGTTTATAATATAAT
1 TTATGAATTTGAGGTTTAGAATGTAAT
233580 GGATGATTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
35 21 0.40
36 31 0.58
37 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (36 bp):
TTATGAATTTGAGGTTTAGAATGTAATTGAAATATT
Found at i:234280 original size:37 final size:36
Alignment explanation
Indices: 234239--234356 Score: 103
Period size: 37 Copynumber: 3.1 Consensus size: 36
234229 TAATATGATT
234239 ATTTTTTAAAAGTTAAAACAATTTGTTAGTTAAGATA
1 ATTTTTTAAAAGTTAAAA-AATTTGTTAGTTAAGATA
* * * *
234276 ATTTTTTAACAA-TTAAATAAATTATGATAATTAATATG
1 ATTTTTTAA-AAGTTAAA-AAATT-TGTTAGTTAAGATA
* *
234314 ATTACTCTTTAAAAGTTAAAATAAATTGTTAGTTATGATA
1 ATT--T-TTTAAAAGTTAAAA-AATTTGTTAGTTAAGATA
234354 ATT
1 ATT
234357 AAATTAATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
37 18 0.29
38 16 0.25
40 16 0.25
41 13 0.21
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (36 bp):
ATTTTTTAAAAGTTAAAAAATTTGTTAGTTAAGATA
Found at i:234306 original size:78 final size:79
Alignment explanation
Indices: 234207--234356 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 79
234197 GAGATTTTGA
* * * *
234207 AATTATAATAAACTATTATAATTAATATGATTATTTTTTAAAAGTTAAAACAATTTGTTAGTTAA
1 AATTATAATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGTTAA
234272 GATAATTTTTTAAC
66 GATAATTTTTTAAC
* * *
234286 AATTA-AATAAATTATGATAATTAATATGATTACTCTTTAAAAGTTAAAATAAATTGTTAGTTAT
1 AATTATAATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGTTAA
234350 GATAATT
66 GATAATT
234357 AAATTAATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 59 0.92
79 5 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (79 bp):
AATTATAATAAACTATGATAATTAATATGATTACTCTTTAAAAGTTAAAACAAATTGTTAGTTAA
GATAATTTTTTAAC
Found at i:234550 original size:23 final size:23
Alignment explanation
Indices: 234524--234567 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
234514 TATGTACTAA
234524 TTAA-TTAATAATTTAAATATAAT
1 TTAACTTAA-AATTTAAATATAAT
*
234547 TTAACTTAAAATTTTAATATA
1 TTAACTTAAAATTTAAATATA
234568 TATATATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAACTTAAAATTTAAATATAAT
Found at i:234648 original size:2 final size:2
Alignment explanation
Indices: 234641--234666 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
234631 AAAATAAACA
234641 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
234667 TCACATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234942 original size:77 final size:77
Alignment explanation
Indices: 234744--235201 Score: 602
Period size: 77 Copynumber: 6.0 Consensus size: 77
234734 ATAGTATATT
* *
234744 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACATTTTG---AGTATATATATAATGTAT
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACATTTTGAAAAATATATATATAATATAT
234804 AGTTTTTGAAAACA
65 AGTTTTT-AAAACA
234818 TTTTGAAAAAATATATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATATAATA
1 TTTTG--AAAATATATATATAATATATAGTTTTT-AAAACATTTTG-AAAAATATATATATAATA
234883 TATAGTTTTTAAAACA
62 TATAGTTTTTAAAACA
* * *
234899 TTTTGAACA-CT-TATATAATATATAGTTTTTAAAAATATTTTGAAAAA-ATATATATAATATAT
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACATTTTGAAAAATATATATATAATATAT
*
234961 GGTTTTTAAAACA
65 AGTTTTTAAAACA
* *
234974 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACATTTTG-AAAATATGTATATAATATATA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAAATATATATATAATATATA
235038 GTTTTTAAAACA
66 GTTTTTAAAACA
*
235050 TTTTGAATATATATATATATATATATAGTTTTTAAAACATTTTGAAAAA-ATATATATAATATAT
1 TTTTGAAAATATATATATA-ATATATAGTTTTTAAAACATTTTGAAAAATATATATATAATATAT
235114 AGTTTTTAAAACA
65 AGTTTTTAAAACA
* * * *
235127 TTTTGAAAAAATATATATAATATATAG-TTTTAAAATATTTTTG-AATATATAT-TATATTATAT
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA-TTTTGAAAAATATATATATAATATAT
*
235189 -GATTTTGAAAACA
65 AG-TTTTTAAAACA
235202 ATTATTTTAA
Statistics
Matches: 347, Mismatches: 21, Indels: 31
0.87 0.05 0.08
Matches are distributed among these distances:
74 6 0.02
75 70 0.20
76 76 0.22
77 119 0.34
78 39 0.11
79 3 0.01
81 11 0.03
82 23 0.07
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (77 bp):
TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAAATATATATATAATATATA
GTTTTTAAAACA
Found at i:234991 original size:38 final size:38
Alignment explanation
Indices: 234744--235201 Score: 610
Period size: 38 Copynumber: 12.0 Consensus size: 38
234734 ATAGTATATT
234744 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACA
* *
234781 TTTTG--AGTATATATATAATGTATAGTTTTTGAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACA
234818 TTTTGAAAAAATATATATATAATATATAGTTTTTGAAAACA
1 TTTTG--AAAATATATATATAATATATAGTTTTT-AAAACA
234859 TTTTGAAAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTG--AAAATATATATATAATATATAGTTTTTAAAACA
* * *
234899 TTTTGAACA-CT-TATATAATATATAGTTTTTAAAAATA
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACA
* *
234936 TTTTGAAAAAATATATATAATATATGGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
234974 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
235012 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
235050 TTTTGAATATATATATATATATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATA-ATATATAGTTTTTAAAACA
*
235089 TTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
* *
235127 TTTTGAAAAAATATATATAATATATAG-TTTTAAAATA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
* * *
235164 TTTTTGAATATATAT-TATATTATAT-GATTTTGAAAACA
1 -TTTTGAAAATATATATATAATATATAG-TTTTTAAAACA
235202 ATTATTTTAA
Statistics
Matches: 385, Mismatches: 24, Indels: 23
0.89 0.06 0.05
Matches are distributed among these distances:
36 21 0.05
37 70 0.18
38 165 0.43
39 54 0.14
40 11 0.03
41 64 0.17
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (38 bp):
TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
Found at i:235042 original size:115 final size:114
Alignment explanation
Indices: 234744--235201 Score: 601
Period size: 115 Copynumber: 4.0 Consensus size: 114
234734 ATAGTATATT
* *
234744 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACATTTTG--AGTATATATATAATGTATA
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACATTTTGAAAATATATATATAATATATA
234805 GTTTTTGAAAACATTTTGAAAAAATATATATATAATATATAGTTTTTGAAAACA
65 GTTTTT-AAAACATTTTG-AAAAA-ATATATATAATATATAGTTTTT-AAAACA
* *
234859 TTTTGAAAAAATATATATATAATATATAGTTTTTAAAACATTTTGAACA-CT-TATATAATATAT
1 TTTTG--AAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATAT
* *
234922 AGTTTTTAAAAATATTTTGAAAAAATATATATAATATATGGTTTTTAAAACA
64 AGTTTTT-AAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
* *
234974 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACATTTTGAAAATATGTATATAATATATAG
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAG
* *
235039 TTTTTAAAACATTTTGAATATATATATATATATATATAGTTTTTAAAACA
66 TTTTTAAAACATTTTGAAAAAATATATATA-ATATATAGTTTTTAAAACA
* *
235089 TTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAG
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAG
* * * * *
235154 -TTTTAAAATATTTTTGAATATATAT-TATATTATAT-GATTTTGAAAACA
66 TTTTTAAAACA-TTTTGAAAAAATATATATAATATATAG-TTTTTAAAACA
235202 ATTATTTTAA
Statistics
Matches: 311, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
112 1 0.00
113 55 0.18
114 36 0.12
115 128 0.41
116 21 0.07
117 5 0.02
118 42 0.14
119 23 0.07
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (114 bp):
TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAG
TTTTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:235255 original size:3 final size:3
Alignment explanation
Indices: 235247--235284 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
235237 AAAAATTTAT
*
235247 TTA TTA TTA TTA TTA TATA TTA -TA TTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
235285 TATTTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:235272 original size:21 final size:20
Alignment explanation
Indices: 235244--235290 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
235234 TTTAAAAATT
*
235244 TATTTATTATTATTATTATA
1 TATTTATTATTATTAGTATA
*
235264 TATTATATTATTATTAGTATT
1 TATT-TATTATTATTAGTATA
235285 TATTTA
1 TATTTA
235291 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTATTATTATTAGTATA
Found at i:235287 original size:18 final size:17
Alignment explanation
Indices: 235244--235287 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 17
235234 TTTAAAAATT
235244 TATTTATTATTATTATTA
1 TATTTA-TATTATTATTA
235262 TATATTATATTATTATTA
1 TAT-TTATATTATTATTA
235280 GTATTTAT
1 -TATTTAT
235288 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTTATATTATTATTA
Found at i:235302 original size:18 final size:19
Alignment explanation
Indices: 235241--235304 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
235231 AATTTTAAAA
235241 ATTTATTT-ATTATTA-TT
1 ATTTATTTAATTATTATTT
235258 ATTATATATTATATTATTATTAGT
1 ATT-TAT-TTA-ATTATTATT--T
235282 ATTTATTTAATT-TTATTT
1 ATTTATTTAATTATTATTT
235300 ATTTA
1 ATTTA
235305 CTTTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.08
18 9 0.22
19 2 0.05
20 5 0.12
21 10 0.25
22 4 0.10
23 3 0.08
24 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTAATTATTATTT
Found at i:245688 original size:23 final size:23
Alignment explanation
Indices: 245635--245759 Score: 156
Period size: 23 Copynumber: 5.7 Consensus size: 23
245625 TCGAAATGGA
245635 GTGCATGGATGCACTA----CATG
1 GTGCATGGATGCACTAGTGGCA-G
*
245655 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
245678 GTGCATGGATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
*
245701 GTGCATGAATGCACTAGTGGCAG
1 GTGCATGGATGCACTAGTGGCAG
*
245724 GTGCATGGATGTACT-GTAGG--G
1 GTGCATGGATGCACTAGT-GGCAG
245745 GTGCATGGATGCACT
1 GTGCATGGATGCACT
245760 TTGACACCCT
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
20 15 0.16
21 15 0.16
22 2 0.02
23 60 0.64
24 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (23 bp):
GTGCATGGATGCACTAGTGGCAG
Found at i:246005 original size:21 final size:21
Alignment explanation
Indices: 245981--246020 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
245971 ATGTTTAATG
*
245981 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATAGTTAAC
* *
246002 AAAATGATATCAATAGTTA
1 AAAAAGATACCAATAGTTA
246021 CCAATTGTTT
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:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (21 bp):
AAAAAGATACCAATAGTTAAC
Found at i:249315 original size:2 final size:2
Alignment explanation
Indices: 249308--249362 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
249298 TAGCTTAAGC
249308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
249350 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
249363 TTAAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:251182 original size:3 final size:3
Alignment explanation
Indices: 251174--251263 Score: 50
Period size: 3 Copynumber: 30.7 Consensus size: 3
251164 TTCATTTTCT
* * *
251174 TTA TTA TTA TTA TTA TTA TTA TTTA TTTA TT- TTC TGA TTTA TTTA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA -TTA -TTA TTA
*
251222 TCT- TT- TTA CT- TTA TT- TTA TT- TTA TTA TT- TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
251262 TT
1 TT
251264 TTCCTTTCAT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
2 12 0.17
3 45 0.63
4 14 0.20
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:251277 original size:37 final size:34
Alignment explanation
Indices: 251177--251279 Score: 91
Period size: 37 Copynumber: 2.8 Consensus size: 34
251167 ATTTTCTTTA
* *
251177 TTATTATTATTATTATTATTTATTTATTTTCTGAT
1 TTATTATTATTATT-TTCTTTATTTATTTTATGAT
* *
251212 TTATTTAATATCT-TTTTACTTTATTTTATTTTATTATT
1 TTA-TTATTAT-TATTTT-CTTTA-TTTATTTTATGA-T
251250 TTATTATTATTATTTTCCTTTCATTTATTT
1 TTATTATTATTATTTT-CTTT-ATTTATTT
251280 AACATTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
35 5 0.09
36 13 0.24
37 32 0.58
38 5 0.09
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (34 bp):
TTATTATTATTATTTTCTTTATTTATTTTATGAT
Found at i:252116 original size:20 final size:20
Alignment explanation
Indices: 252088--252128 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
252078 TGGATTTTTA
*
252088 AAATTTATTTTTGAAA-TTAT
1 AAATATATTTTT-AAAGTTAT
252108 AAATATATTTTTAAAGTTAT
1 AAATATATTTTTAAAGTTAT
252128 A
1 A
252129 TTTAAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATATATTTTTAAAGTTAT
Found at i:252784 original size:9 final size:10
Alignment explanation
Indices: 252756--252783 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
252746 TTGGTTTTCT
252756 ATTTTTTTTA
1 ATTTTTTTTA
252766 ATTTTTTTTA
1 ATTTTTTTTA
252776 ATTTTTTT
1 ATTTTTTT
252784 ATTTCAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:253011 original size:2 final size:2
Alignment explanation
Indices: 253006--253040 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
252996 TATACTTATG
253006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
253041 TTGTGTACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:253146 original size:40 final size:41
Alignment explanation
Indices: 253081--253159 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
253071 TCTATATACT
* *
253081 TATATTGTATACTTACAAGTATAATGTG-AA-TATATTAAG
1 TATAATGTATACTTACAAATATAATGTGTAATTATATTAAG
*
253120 TATAATGTATACATTATAAATATAATGTGTAATTATATTA
1 TATAATGTATAC-TTACAAATATAATGTGTAATTATATTA
253160 TATAGTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.32
40 14 0.41
41 2 0.06
42 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (41 bp):
TATAATGTATACTTACAAATATAATGTGTAATTATATTAAG
Found at i:253162 original size:20 final size:20
Alignment explanation
Indices: 253100--253163 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
253090 TACTTACAAG
253100 TATAATGTG-AA-TATATTAA
1 TATAATGTGTAATTATATT-A
* *
253119 GTATAATGTATACATTATA-AA
1 -TATAATGTGTA-ATTATATTA
253140 TATAATGTGTAATTATATTA
1 TATAATGTGTAATTATATTA
253160 TATA
1 TATA
253164 GTTATAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.17
20 23 0.64
21 2 0.06
22 1 0.03
23 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (20 bp):
TATAATGTGTAATTATATTA
Found at i:253526 original size:14 final size:14
Alignment explanation
Indices: 253507--253535 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
253497 TTAATTTATT
253507 TAATTTTTTGTTTG
1 TAATTTTTTGTTTG
253521 TAATTTTTTGTTTG
1 TAATTTTTTGTTTG
253535 T
1 T
253536 TCAATGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TAATTTTTTGTTTG
Found at i:253996 original size:20 final size:20
Alignment explanation
Indices: 253959--253997 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
253949 TGTGCTGTAT
*
253959 CTGATTTCACATTACCAAAC
1 CTGATTTCACATCACCAAAC
* *
253979 CTGATTTTACATCGCCAAA
1 CTGATTTCACATCACCAAA
253998 GAAGACTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (20 bp):
CTGATTTCACATCACCAAAC
Found at i:254445 original size:21 final size:24
Alignment explanation
Indices: 254394--254453 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 24
254384 ATATTTTTAA
254394 ATTAAGTTAATAGTAAAATATATAT
1 ATTAAGTTAATA-TAAAATATATAT
*
254419 AATAAGTTAATATAAAA-ATAT-T
1 ATTAAGTTAATATAAAATATATAT
254441 -TTAAGTTAATATA
1 ATTAAGTTAATATA
254454 TATAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 4 0.12
24 5 0.15
25 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (24 bp):
ATTAAGTTAATATAAAATATATAT
Found at i:254576 original size:2 final size:2
Alignment explanation
Indices: 254527--254563 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
254517 TTCATTAAAT
254527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
254564 TAAGAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:254777 original size:39 final size:39
Alignment explanation
Indices: 254734--254839 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
254724 TTTAAAAACT
*
254734 AATTTAGAATGTTAATATGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
*
254773 AATTTAGAACGTT-ATGGTGTCAAAT--TTTAAGAAATTAAG
1 AATTTAGAATGTTAAT-GTG--AAATAATTTAAGAAATTAAG
*
254812 ATTTTAGAATGTTAGA-GTGAAATAATTT
1 AATTTAGAATGTTA-ATGTGAAATAATTT
254840 GAGGATTATG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
37 4 0.07
38 2 0.04
39 45 0.80
41 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:255264 original size:31 final size:31
Alignment explanation
Indices: 255222--255290 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
255212 GGGTGACCAC
* *
255222 ATCTTAATTAAATAAAAATGAAAGTGATCAT
1 ATCTTATTTAAATAAAAACGAAAGTGATCAT
* *
255253 ATCTTATTTAAATAAAAACGTAAGTGATTAT
1 ATCTTATTTAAATAAAAACGAAAGTGATCAT
255284 ATCTTAT
1 ATCTTAT
255291 ATATTTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (31 bp):
ATCTTATTTAAATAAAAACGAAAGTGATCAT
Found at i:257406 original size:23 final size:24
Alignment explanation
Indices: 257371--257424 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
257361 TAGAGGACAA
*
257371 AAAAATATGTAATATATAA-AA-TTT
1 AAAAATATCTAAT-TA-AATAATTTT
257395 AAAAAT-TCTAATTAAATAATTTT
1 AAAAATATCTAATTAAATAATTTT
257418 AAAAATA
1 AAAAATA
257425 AAAAGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.08
22 4 0.15
23 14 0.54
24 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAAATATCTAATTAAATAATTTT
Found at i:257582 original size:18 final size:19
Alignment explanation
Indices: 257543--257584 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
257533 AAGAATTGAG
257543 AATAAAAAAATCAGTATAA
1 AATAAAAAAATCAGTATAA
257562 AATAAAAAAAT-A-TATATA
1 AATAAAAAAATCAGTATA-A
257580 AATAA
1 AATAA
257585 TCGAGTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 7 0.32
19 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AATAAAAAAATCAGTATAA
Found at i:258389 original size:64 final size:64
Alignment explanation
Indices: 258312--258471 Score: 248
Period size: 64 Copynumber: 2.5 Consensus size: 64
258302 ATTGCTACAG
* * * *
258312 TGAAGATGGTTGGTTTACAAGCCGCCTTCATTGTTAATATTTATTATCTTAAAAAAAGCAACAA
1 TGAAGAAGGTTGGTTTACAAGTCGCCTTCACTGTTAATATTTATTATCTTAAAAAAAACAACAA
* * *
258376 TGAAGAAGGTTGGTTTACAAGTCACCTTCACTGTTAATATTTATTATCTTAAAAAAAACTAGAA
1 TGAAGAAGGTTGGTTTACAAGTCGCCTTCACTGTTAATATTTATTATCTTAAAAAAAACAACAA
*
258440 TGAAGAAGATTGGTTTACAAGTCGCCTTCACT
1 TGAAGAAGGTTGGTTTACAAGTCGCCTTCACT
258472 ATTCATAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 87 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (64 bp):
TGAAGAAGGTTGGTTTACAAGTCGCCTTCACTGTTAATATTTATTATCTTAAAAAAAACAACAA
Found at i:258505 original size:118 final size:118
Alignment explanation
Indices: 258376--258602 Score: 321
Period size: 118 Copynumber: 1.9 Consensus size: 118
258366 AAAGCAACAA
** * * * * *
258376 TGAAGAAGGTTGGTTTACAAGTCACCTTCACTGTTAATATTTATTATCTTAAAAAAAACTAGAAT
1 TGAAGAAGGTTGGTTTACAAACCACATTCACCGTTAATATTTACTATATTAAAAAAAACTACAAT
*
258441 GAAGAA-GATTGGTTTACAAGTCGCCTTCACTATTCATAAAAAAAGTGCTACAC
66 GAAGAATGA-TGGTTTACAAGCCGCCTTCACTATTCATAAAAAAAGTGCTACAC
* * *
258494 TGAAGATGGTTGGTTTACAAACCGCATTCACCGTTCATATTTACTATATTAAAAAAAACTACAAT
1 TGAAGAAGGTTGGTTTACAAACCACATTCACCGTTAATATTTACTATATTAAAAAAAACTACAAT
* *
258559 GAAGAATGATGGTTTCCAAGCCGCCTTCATTATTCATAAAAAAA
66 GAAGAATGATGGTTTACAAGCCGCCTTCACTATTCATAAAAAAA
258603 TGTAAAGGGT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 93 0.98
119 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (118 bp):
TGAAGAAGGTTGGTTTACAAACCACATTCACCGTTAATATTTACTATATTAAAAAAAACTACAAT
GAAGAATGATGGTTTACAAGCCGCCTTCACTATTCATAAAAAAAGTGCTACAC
Found at i:259067 original size:13 final size:13
Alignment explanation
Indices: 259049--259073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259039 TAGTAAGTTG
259049 ATTTAATTTTTTA
1 ATTTAATTTTTTA
259062 ATTTAATTTTTT
1 ATTTAATTTTTT
259074 TTATATGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTAATTTTTTA
Found at i:269746 original size:2 final size:2
Alignment explanation
Indices: 269739--269765 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
269729 CCAGAAAAGC
269739 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
269766 TTCTGACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:269901 original size:2 final size:2
Alignment explanation
Indices: 269894--269968 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
269884 ACAAACAACC
269894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
269936 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
269969 TCTGACATCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:271114 original size:24 final size:24
Alignment explanation
Indices: 271082--271128 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
271072 TTGTCCTTAG
*
271082 TTTTCGACATTTATTAGGACATAA
1 TTTTCGACATCTATTAGGACATAA
271106 TTTTCGACATCTATTAGGACATA
1 TTTTCGACATCTATTAGGACATA
271129 CATAAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (24 bp):
TTTTCGACATCTATTAGGACATAA
Found at i:272475 original size:55 final size:55
Alignment explanation
Indices: 272415--272523 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 55
272405 TTACATGGGT
* *
272415 TGCACACTTAATATCAATAAGGAAATTCATAAACTTAATATGAATTTCTTAGTTC
1 TGCACACATAATACCAATAAGGAAATTCATAAACTTAATATGAATTTCTTAGTTC
* * * * *
272470 TGCACACATATTGCCCATAAGGAATTTCATAAACTTATTATGAATTTCTTAGTT
1 TGCACACATAATACCAATAAGGAAATTCATAAACTTAATATGAATTTCTTAGTT
272524 TTTAAACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (55 bp):
TGCACACATAATACCAATAAGGAAATTCATAAACTTAATATGAATTTCTTAGTTC
Found at i:275280 original size:12 final size:12
Alignment explanation
Indices: 275249--275289 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
275239 TAACTATAAT
*
275249 ATATAATTTAAA
1 ATATAATTAAAA
275261 A-A-AATTAAAA
1 ATATAATTAAAA
275271 ATATAATTAAAA
1 ATATAATTAAAA
275283 ATATAAT
1 ATATAAT
275290 ATTACATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 16 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAATTAAAA
Found at i:275298 original size:22 final size:21
Alignment explanation
Indices: 275273--275317 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
275263 AATTAAAAAT
*
275273 ATAATTAAAAATATAATATTAC
1 ATAATTAAAAATAAAATA-TAC
275295 ATAATTAAAAATAAAATATAC
1 ATAATTAAAAATAAAATATAC
275316 AT
1 AT
275318 TCACTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATTAAAAATAAAATATAC
Found at i:278959 original size:30 final size:30
Alignment explanation
Indices: 278925--279063 Score: 116
Period size: 28 Copynumber: 4.8 Consensus size: 30
278915 AAAATTATAG
278925 TTAAGATAAAAATAAAATATATTTATTAAA
1 TTAAGATAAAAATAAAATATATTTATTAAA
*
278955 TTAAGATAAGAATAAAATATAAATTT-TTAAA
1 TTAAGATAAAAATAAAATAT--ATTTATTAAA
*
278986 TT-A-A-AATAA-AAAATATATTT-TTAAA
1 TTAAGATAAAAATAAAATATATTTATTAAA
* * *
279011 CTAATATAAAAAT-AAATAATATTTAAT-AA
1 TTAAGATAAAAATAAAAT-ATATTTATTAAA
* * *
279040 TTTAGGT-AAAATATAATATATTTA
1 TTAAGATAAAAATAAAATATATTTA
279064 ATAATTTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
25 10 0.11
26 1 0.01
27 8 0.09
28 24 0.27
29 15 0.17
30 21 0.23
31 7 0.08
32 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (30 bp):
TTAAGATAAAAATAAAATATATTTATTAAA
Found at i:279026 original size:31 final size:30
Alignment explanation
Indices: 278930--279032 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 30
278920 TATAGTTAAG
*
278930 ATAAAAAT--AAAATATATTTATTAAATTAAG
1 ATAAAAATAAAAAATATATTT-TTAAA-TAAT
* * *
278960 ATAAGAATAAAATATAAATTTTT--A-AAT
1 ATAAAAATAAAAAATATATTTTTAAATAAT
278987 -T-AAAATAAAAAATATATTTTTAAACTAAT
1 ATAAAAATAAAAAATATATTTTTAAA-TAAT
*
279016 ATAAAAATAAATAATAT
1 ATAAAAATAAAAAATAT
279033 TTAATAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
25 17 0.30
26 1 0.02
27 3 0.05
29 4 0.07
30 8 0.14
31 15 0.26
32 9 0.16
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (30 bp):
ATAAAAATAAAAAATATATTTTTAAATAAT
Found at i:279099 original size:29 final size:29
Alignment explanation
Indices: 279063--279127 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
279053 TAATATATTT
* *
279063 AATA-ATTTATAAGTTAATATAAGATTAA
1 AATATATTTATAAGTCAATATAAGAATAA
* *
279091 AATATATTTTTTAGTCAATATAAGAATAA
1 AATATATTTATAAGTCAATATAAGAATAA
279120 AATATATT
1 AATATATT
279128 CAATAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (29 bp):
AATATATTTATAAGTCAATATAAGAATAA
Found at i:280831 original size:18 final size:17
Alignment explanation
Indices: 280810--280849 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
280800 TATATTTTAT
280810 TAAAGAAATAAAAATAAA
1 TAAAGAAAT-AAAATAAA
*
280828 TAAAATAAATAAAATAAA
1 T-AAAGAAATAAAATAAA
280846 TAAA
1 TAAA
280850 AAGGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 10 0.50
19 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
TAAAGAAATAAAATAAA
Found at i:280834 original size:9 final size:9
Alignment explanation
Indices: 280815--280850 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
280805 TTTATTAAAG
280815 AAATAAAAAT
1 AAAT-AAAAT
280825 AAATAAAAT
1 AAATAAAAT
280834 AAATAAAAT
1 AAATAAAAT
280843 AAATAAAA
1 AAATAAAA
280851 AGGAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:285825 original size:15 final size:15
Alignment explanation
Indices: 285805--285834 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
285795 TTTATTAAGA
285805 ATTTAAATCAAATAT
1 ATTTAAATCAAATAT
285820 ATTTAAATCAAATAT
1 ATTTAAATCAAATAT
285835 TAATCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAATCAAATAT
Found at i:287818 original size:3 final size:3
Alignment explanation
Indices: 287797--287909 Score: 181
Period size: 3 Copynumber: 37.7 Consensus size: 3
287787 TTTTTACCCA
* *
287797 TAT TAT AAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
287845 TAT TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
287893 TAT TAT CAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
287910 AATATATATT
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:287921 original size:11 final size:10
Alignment explanation
Indices: 287905--287945 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
287895 TTATCATTAT
287905 TATTAAATATA
1 TATTAAATA-A
287916 TATTAAATACA
1 TATTAAATA-A
287927 TATATAAATAA
1 TAT-TAAATAA
287938 TATTAAAT
1 TATTAAAT
287946 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:289361 original size:17 final size:17
Alignment explanation
Indices: 289339--289378 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
289329 TTATGTAGTC
289339 ATAAATATATATAATAA
1 ATAAATATATATAATAA
* **
289356 ATAAATATTTATTTTAA
1 ATAAATATATATAATAA
289373 ATAAAT
1 ATAAAT
289379 TATTTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATATATAATAA
Found at i:289373 original size:13 final size:13
Alignment explanation
Indices: 289357--289394 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
289347 ATATAATAAA
289357 TAAATATTTATTT
1 TAAATATTTATTT
*
289370 TAAATAAATTATTT
1 TAAAT-ATTTATTT
289384 T-AATATTTATT
1 TAAATATTTATT
289395 ATCGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:290054 original size:29 final size:28
Alignment explanation
Indices: 290012--290121 Score: 73
Period size: 28 Copynumber: 3.9 Consensus size: 28
290002 AAAAGTTCAT
* *
290012 ATATTTAATTTTTAATTATTTCTTTTCAAA
1 ATATTT-ATATTTAATTA-TTATTTTCAAA
* * *
290042 ATTTTTATATTTACTTATTATTTTCATA
1 ATATTTATATTTAATTATTATTTTCAAA
* *
290070 ATATTTATATGTTTTATT-TTATTTGC-AA
1 ATATTTATA--TTTAATTATTATTTTCAAA
* *
290098 GTATTT-TATTTCATTATTTATTTT
1 ATATTTATATTTAATTA-TTATTTT
290122 TCTGTCAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
25 6 0.10
27 8 0.13
28 23 0.37
29 16 0.25
30 10 0.16
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (28 bp):
ATATTTATATTTAATTATTATTTTCAAA
Found at i:292740 original size:113 final size:113
Alignment explanation
Indices: 292532--293776 Score: 1782
Period size: 114 Copynumber: 10.9 Consensus size: 113
292522 CAAAGATTCA
* * * *
292532 AATTTATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
292597 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
*
292645 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
292710 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
*
292758 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
292823 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCCTG
* * *
292872 AATTCATCACTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
292937 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCCTG
292986 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
*
293051 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * *
293099 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
* *
293164 AAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * *
293213 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
*
293278 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
293327 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
* * *
293392 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
293441 AATTCATCATTTGATGGATCA-ATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAGCT-TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCT
* * *
293504 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * * *
293557 AGTTCATCATTTGATGGATCA-ATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAGCT-TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCT
* * *
293620 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
293673 AATTCATCA-TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTTATCTG
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTC---ATCTG
* *
293736 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
293777 TAATTCTATC
Statistics
Matches: 1089, Mismatches: 32, Indels: 20
0.95 0.03 0.02
Matches are distributed among these distances:
112 5 0.00
113 265 0.24
114 551 0.51
115 86 0.08
116 182 0.17
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
Found at i:294107 original size:3 final size:3
Alignment explanation
Indices: 294092--294222 Score: 217
Period size: 3 Copynumber: 43.7 Consensus size: 3
294082 TTTTTACCCA
* *
294092 TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
294140 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
294188 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
294223 AATATATATT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:294247 original size:10 final size:10
Alignment explanation
Indices: 294218--294256 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
294208 TTATTATTAT
294218 TATTAAATATA
1 TATTAAATA-A
294229 TATTAAATACA
1 TATTAAATA-A
294240 TA-TAAATAA
1 TATTAAATAA
294249 TATTAAAT
1 TATTAAAT
294257 TACAAAGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 3 0.12
10 11 0.42
11 12 0.46
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:294371 original size:14 final size:14
Alignment explanation
Indices: 294352--294389 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
294342 ATCCCATGCT
294352 CAGCCGCCTCTAGC
1 CAGCCGCCTCTAGC
294366 CAGCCGCCTCTAGC
1 CAGCCGCCTCTAGC
294380 CAGCCGCCTC
1 CAGCCGCCTC
294390 AGACTGACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.13, C:0.53, G:0.21, T:0.13
Consensus pattern (14 bp):
CAGCCGCCTCTAGC
Found at i:295097 original size:9 final size:10
Alignment explanation
Indices: 295085--295123 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
295075 TTATTATTAT
295085 TATTAAAT-A
1 TATTAAATAA
295094 TATTAAATACA
1 TATTAAATA-A
295105 TATATAAATAA
1 TAT-TAAATAA
295116 TATTAAAT
1 TATTAAAT
295124 TACAAAGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:295802 original size:17 final size:17
Alignment explanation
Indices: 295780--295819 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
295770 TTATGTAGTC
295780 ATAAATATATATAATAA
1 ATAAATATATATAATAA
* **
295797 ATAAATATTTATTTTAA
1 ATAAATATATATAATAA
295814 ATAAAT
1 ATAAAT
295820 TATTTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATATATAATAA
Found at i:295814 original size:13 final size:13
Alignment explanation
Indices: 295798--295835 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
295788 ATATAATAAA
295798 TAAATATTTATTT
1 TAAATATTTATTT
*
295811 TAAATAAATTATTT
1 TAAAT-ATTTATTT
295825 T-AATATTTATT
1 TAAATATTTATT
295836 ATCGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:301167 original size:17 final size:18
Alignment explanation
Indices: 301145--301178 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
301135 TCAGCCGGTC
301145 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
301162 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
301179 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:305210 original size:6 final size:6
Alignment explanation
Indices: 305199--305224 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
305189 TTGGTCTCAT
305199 CTTTTC CTTTTC CTTTTC CTTTTC CT
1 CTTTTC CTTTTC CTTTTC CTTTTC CT
305225 AATTAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
CTTTTC
Found at i:306284 original size:20 final size:20
Alignment explanation
Indices: 306259--306319 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
306249 ATTTTTCAAA
306259 GAAAACATTTACCAAACTTT
1 GAAAACATTTACCAAACTTT
*
306279 GAAAACTATTT-TCAAA----
1 GAAAAC-ATTTACCAAACTTT
306295 G-AAACATTTACCAAACTTT
1 GAAAACATTTACCAAACTTT
306314 GAAAAC
1 GAAAAC
306320 CACTTTTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 4 0.12
15 8 0.25
16 1 0.03
19 1 0.03
20 14 0.44
21 4 0.12
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.28
Consensus pattern (20 bp):
GAAAACATTTACCAAACTTT
Found at i:306307 original size:35 final size:37
Alignment explanation
Indices: 306225--306332 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 37
306215 TTTTCAACAG
*
306225 ACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAA
1 ACATTTACCAAACTTTG-AAAACTATTTTTCAAAGAAA
306263 ACATTTACCAAACTTTGAAAACTA-TTTTCAAAG-AA
1 ACATTTACCAAACTTTGAAAACTATTTTTCAAAGAAA
*
306298 ACATTTACCAAACTTTGAAAACCACTTTTTCAAAG
1 ACATTTACCAAACTTTGAAAACTA-TTTTTCAAAG
306333 TTGGTTACCA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
35 25 0.38
36 9 0.14
37 16 0.24
38 16 0.24
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (37 bp):
ACATTTACCAAACTTTGAAAACTATTTTTCAAAGAAA
Found at i:310923 original size:35 final size:36
Alignment explanation
Indices: 310836--310951 Score: 164
Period size: 35 Copynumber: 3.2 Consensus size: 36
310826 TTATCTCATT
* *
310836 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
310871 AACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
310908 ATCA-TTTTCAAAGAAACATTTACCAAACTTTAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
310943 ACCATTTTT
1 ATCATTTTT
310952 TTAAAGTTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 35 0.49
36 12 0.17
37 25 0.35
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:311508 original size:14 final size:15
Alignment explanation
Indices: 311483--311514 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
311473 TTAGTTAAAA
311483 ATTTGAAGATAAATT
1 ATTTGAAGATAAATT
311498 ATTTGAA-ATAAATT
1 ATTTGAAGATAAATT
311512 ATT
1 ATT
311515 AATGTAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (15 bp):
ATTTGAAGATAAATT
Found at i:313367 original size:115 final size:115
Alignment explanation
Indices: 313165--313377 Score: 372
Period size: 115 Copynumber: 1.9 Consensus size: 115
313155 ATAATTAATT
* * * *
313165 TTTTTATGAGACAAAAAACTCTAGTTATTAATTTTATTTTAATATTTAATTATAACTTGATGCAT
1 TTTTTATGAGACAAAAAAATATAGTTATTAATTTTATTTTAAGATTTAATCATAACTTGATGCAT
* *
313230 AGATATAGTGAAATGATAATATTTAAAAATTCAACTATTATTGTTAACTA
66 AGATACAGTGAAACGATAATATTTAAAAATTCAACTATTATTGTTAACTA
313280 TTTTTATGAGACAAAAAAATATAGTTATTAATTTTATTTTAAGATTTAATCATAACTTGATGCAT
1 TTTTTATGAGACAAAAAAATATAGTTATTAATTTTATTTTAAGATTTAATCATAACTTGATGCAT
313345 AGATACAGTGAAACGATAATATTTAAAAATTCA
66 AGATACAGTGAAACGATAATATTTAAAAATTCA
313378 TGATAAATTT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 92 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.41
Consensus pattern (115 bp):
TTTTTATGAGACAAAAAAATATAGTTATTAATTTTATTTTAAGATTTAATCATAACTTGATGCAT
AGATACAGTGAAACGATAATATTTAAAAATTCAACTATTATTGTTAACTA
Found at i:320478 original size:22 final size:22
Alignment explanation
Indices: 320453--320503 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
320443 GTTATTTTTT
**
320453 TATAATTAT-TTTTAAATAATAA
1 TATAATTATATTAAAAATAA-AA
320475 TATAAATTATATTAAAAATAAAA
1 TAT-AATTATATTAAAAATAAAA
320498 TATAAT
1 TATAAT
320504 AAGATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 11 0.44
24 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAATTATATTAAAAATAAAA
Found at i:320544 original size:111 final size:112
Alignment explanation
Indices: 320417--320770 Score: 430
Period size: 111 Copynumber: 3.2 Consensus size: 112
320407 GTAAGACTTA
*
320417 AAAATAAAAATGAGTTTAATATTTTTGTT-ATTTTTTTATAATTATTTTTAAATAATAATATAAA
1 AAAATAAAAATAAGTTTAATATTTTTGTTAATTTTTTTA-AATTATTTTTAAATAATAATATAAA
* *
320481 TTATATTAAAAATAAAATATAATAAGATTATTTAGAGAATCCAATCAC
65 TTATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCCAATCAC
*
320529 AAAAT-AAAATAAGTTTAATATTTTAT-TTAAATTTTTTACAA-T-TTTTTAAATAATAATATAG
1 AAAATAAAAATAAGTTTAATATTTT-TGTTAATTTTTTTA-AATTATTTTTAAATAATAATAT--
*
320590 AAATTATATTAAAAATAAAAT-TATTAAAATTATTTAGAGATTACCAATCAC
62 AAATTATATTAAAAATAAAATATATTAAAATTATTTAGAGAAT-CCAATCAC
* *
320641 AAAAT-AAAATAAGTTTAATA-TTTTGATTTAAATTATTTTAAGTTA-TTTTAAATAATAATATA
1 AAAATAAAAATAAGTTTAATATTTTTG--TT-AATTTTTTTAAATTATTTTTAAATAAT-A-ATA
*
320703 TAAATTATATTAAAAAT----TATATTAAAATTATTTAGAGAATCCAAATCAT
61 TAAATTATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCC-AATCAC
320752 AAAATAAAAATAA-TTTAAT
1 AAAATAAAAATAAGTTTAAT
320771 TAAAAAATAA
Statistics
Matches: 215, Mismatches: 11, Indels: 33
0.83 0.04 0.13
Matches are distributed among these distances:
110 21 0.10
111 78 0.36
112 72 0.33
113 3 0.01
114 36 0.17
115 1 0.00
116 4 0.02
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (112 bp):
AAAATAAAAATAAGTTTAATATTTTTGTTAATTTTTTTAAATTATTTTTAAATAATAATATAAAT
TATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCCAATCAC
Found at i:320596 original size:112 final size:111
Alignment explanation
Indices: 320417--320770 Score: 460
Period size: 112 Copynumber: 3.2 Consensus size: 111
320407 GTAAGACTTA
* *
320417 AAAATAAAAATGAGTTTAATATTTT-TGTT-ATTTTTTTATAATTATTTTTAAATAATAATAT-A
1 AAAATAAAAATAAGTTTAATATTTTAT-TTAAATTTTTTA-AA-T-TTTTTAAATAATAATATAA
* *
320479 AATTATATTAAAAATAAAATATAATAAGATTATTTAGAGAATCCAATCAC
62 AATTATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCCAATCAC
320529 AAAAT-AAAATAAGTTTAATATTTTATTTAAATTTTTTACAATTTTTTAAATAATAATATAGAAA
1 AAAATAAAAATAAGTTTAATATTTTATTTAAATTTTTTA-AATTTTTTAAATAATAATATA-AAA
*
320593 TTATATTAAAAATAAAAT-TATTAAAATTATTTAGAGATTACCAATCAC
64 TTATATTAAAAATAAAATATATTAAAATTATTTAGAGAAT-CCAATCAC
*
320641 AAAAT-AAAATAAGTTTAATATTTTGATTTAAATTATTTTAAGTTATTTTAAATAATAATATATA
1 AAAATAAAAATAAGTTTAATATTTT-ATTTAAATT-TTTTAAATT-TTTTAAATAATAATATA-A
*
320705 AATTATATTAAAAAT----TATATTAAAATTATTTAGAGAATCCAAATCAT
62 AATTATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCC-AATCAC
320752 AAAATAAAAATAA-TTTAAT
1 AAAATAAAAATAAGTTTAAT
320771 TAAAAAATAA
Statistics
Matches: 221, Mismatches: 10, Indels: 23
0.87 0.04 0.09
Matches are distributed among these distances:
110 20 0.09
111 75 0.34
112 76 0.34
113 12 0.05
114 38 0.17
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (111 bp):
AAAATAAAAATAAGTTTAATATTTTATTTAAATTTTTTAAATTTTTTAAATAATAATATAAAATT
ATATTAAAAATAAAATATATTAAAATTATTTAGAGAATCCAATCAC
Found at i:320729 original size:11 final size:12
Alignment explanation
Indices: 320704--320733 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
320694 AATAATATAT
320704 AAATTATATTAA
1 AAATTATATTAA
320716 AAATTATATT-A
1 AAATTATATTAA
320727 AAATTAT
1 AAATTAT
320734 TTAGAGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATTATATTAA
Found at i:320730 original size:23 final size:23
Alignment explanation
Indices: 320670--320733 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
320660 ATTTTGATTT
* * *
320670 AAATTAT-TTTAAGTTATTTTAA
1 AAATTATATTAAAATTATATTAA
*
320692 ATAATAATA-TATAAATTATATTAA
1 A-AATTATATTA-AAATTATATTAA
320716 AAATTATATTAAAATTAT
1 AAATTATATTAAAATTAT
320734 TTAGAGAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 1 0.03
23 19 0.58
24 13 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATTATATTAAAATTATATTAA
Found at i:322389 original size:188 final size:186
Alignment explanation
Indices: 322015--322390 Score: 707
Period size: 188 Copynumber: 2.0 Consensus size: 186
322005 TCTTTATATT
322015 TCATTTTTTTTCAAGTTGCCTTCGCTTTTCTCTCTGTTTTCCCTATAAAGTTTCCAAATCGATGA
1 TCATTTTTTTTCAAGTTGCCTTCGCTTTTCTCTCTGTTTTCCCTATAAAGTTTCCAAATCGATGA
322080 TTGTGACATAGCTCTGCAATTTTCTTATTTCAAATTTTAAATCAAAATTCAATATTGTAAGTATT
66 TTGTGACATAGCTCTGCAATTTTCTTATTTCAAATTTTAAATCAAAATTCAATATTGTAAGTATT
322145 TTCTTTTCGGTTGCATCTGTTTAACGAGCCCATTGCATTCTATATAGTTTTTTTTTTC
131 TTCTTTTCGGTTGCATCTGTTTAACGAGCCCATTGCATTCTATATAG--TTTTTTTTC
322203 TCATTTTTTTTCAAGTTGCCTTCGCTTTTCTCTCTGTTTTCCCTATAAAGTTTCCAAATCGATGA
1 TCATTTTTTTTCAAGTTGCCTTCGCTTTTCTCTCTGTTTTCCCTATAAAGTTTCCAAATCGATGA
322268 TTGTGACATAGCTCTGCAATTTTCTTATTTCAAATTTTAAATCAAAATTCAATATTTGTAAGTAT
66 TTGTGACATAGCTCTGCAATTTTCTTATTTCAAATTTTAAATCAAAATTCAATA-TTGTAAGTA-
322333 TTTTCTTTTCGGTTGCATCTGTTTATACGAGCCCATTGCATTCTATATAGTTTTTTTT
129 TTTTCTTTTCGGTTGCATCTGTTTA-ACGAGCCCATTGCATTCTATATAGTTTTTTTT
322391 TGTGGCAAAT
Statistics
Matches: 185, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
188 119 0.64
189 17 0.09
190 25 0.14
191 24 0.13
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (186 bp):
TCATTTTTTTTCAAGTTGCCTTCGCTTTTCTCTCTGTTTTCCCTATAAAGTTTCCAAATCGATGA
TTGTGACATAGCTCTGCAATTTTCTTATTTCAAATTTTAAATCAAAATTCAATATTGTAAGTATT
TTCTTTTCGGTTGCATCTGTTTAACGAGCCCATTGCATTCTATATAGTTTTTTTTC
Found at i:327052 original size:12 final size:12
Alignment explanation
Indices: 327037--327064 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
327027 TTAATTAGGA
327037 TTTAAAATATTT
1 TTTAAAATATTT
327049 TTTAAAATATTT
1 TTTAAAATATTT
327061 TTTA
1 TTTA
327065 GGTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTAAAATATTT
Found at i:327066 original size:68 final size:71
Alignment explanation
Indices: 326991--327133 Score: 229
Period size: 68 Copynumber: 2.1 Consensus size: 71
326981 ATATTTTTCC
326991 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATT-TTTTAAA
1 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTTAAA
327055 -A-TAT
66 TATTAT
* * **
327059 TTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAGGATTTAGGATATTATTTTAAA
1 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTTAAA
327124 TATTAT
66 TATTAT
327130 TTTT
1 TTTT
327134 GTTTTAGATA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
68 53 0.78
69 7 0.10
70 1 0.01
71 7 0.10
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (71 bp):
TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTTAAA
TATTAT
Found at i:327894 original size:38 final size:38
Alignment explanation
Indices: 327849--327921 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
327839 ATTTAAAACC
327849 CCCTTTTA-TAATTATTA-CTATTTATTATTTTATTATTT
1 CCCTTTTATTAATTATTATCTA-TT-TTATTTTATTATTT
* *
327887 CCCTTTTATTTATTTTTATCTATTTTATTTTATTA
1 CCCTTTTATTAATTATTATCTATTTTATTTTATTA
327922 AATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 19 0.61
39 9 0.29
40 3 0.10
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (38 bp):
CCCTTTTATTAATTATTATCTATTTTATTTTATTATTT
Found at i:327895 original size:19 final size:20
Alignment explanation
Indices: 327873--327921 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
327863 TTACTATTTA
*
327873 TTATTTTATTATT-TCCCTT
1 TTATTTTATTATTATCCATT
* *
327892 TTA-TTTATTTTTATCTATT
1 TTATTTTATTATTATCCATT
327911 TTATTTTATTA
1 TTATTTTATTA
327922 AATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTATTATCCATT
Found at i:332009 original size:28 final size:27
Alignment explanation
Indices: 331977--332044 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 27
331967 TTGTTTACTT
*
331977 TTTCGAACAGTAGAAAAAAAGTTCAATG
1 TTTCGAACAG-AGAAAAAAAGTCCAATG
*
332005 TTTCGAAC----AAAAAAAGTCCATTG
1 TTTCGAACAGAGAAAAAAAGTCCAATG
332028 TTTCGAACAGAGAAAAA
1 TTTCGAACAGAGAAAAA
332045 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
23 21 0.62
27 5 0.15
28 8 0.24
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (27 bp):
TTTCGAACAGAGAAAAAAAGTCCAATG
Found at i:332995 original size:69 final size:68
Alignment explanation
Indices: 332922--333118 Score: 211
Period size: 69 Copynumber: 2.8 Consensus size: 68
332912 AGGATAATAT
* * *
332922 TTTAAACATTATAATTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTTTTTTAATT
1 TTTAAA-ATTATAATTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATT
332987 AGGA
65 AGGA
*
332991 TTTAAAA-TATTATTTAAAATATTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAA
1 TTTAAAATTATAATTT---ATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAA
333054 TTAGGA
63 TTAGGA
* * *
333060 TTTAGGATATTATTTTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAATTA-GTTTTA
1 TTTA--A-A--ATTAT-AAT-TTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
333119 ATTAGGATTT
Statistics
Matches: 108, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
67 7 0.06
68 1 0.01
69 53 0.49
70 5 0.05
71 1 0.01
72 1 0.01
74 12 0.11
75 24 0.22
76 2 0.02
77 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (68 bp):
TTTAAAATTATAATTTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTA
GGA
Found at i:333048 original size:24 final size:23
Alignment explanation
Indices: 332945--333052 Score: 71
Period size: 25 Copynumber: 4.6 Consensus size: 23
332935 ATTTATCTTT
332945 GTTTTAGATATTTTAGTTTAAATAG
1 GTTTTAG-TATTTTA-TTTAAATAG
*
332970 GTTTTAG---TTT-TTTAATTAG
1 GTTTTAGTATTTTATTTAAATAG
* ** * *
332989 GATTTAAAATATTATTTAAAATATT
1 GTTTTAGTATTTTATTT-AAATA-G
*
333014 TTTTTAGGTATTTTAGTTTAAATAG
1 GTTTTA-GTATTTTA-TTTAAATAG
333039 GTTTTAGTATTTTA
1 GTTTTAGTATTTTA
333053 ATTAGGATTT
Statistics
Matches: 62, Mismatches: 13, Indels: 17
0.67 0.14 0.18
Matches are distributed among these distances:
19 13 0.21
21 3 0.05
22 2 0.03
23 3 0.05
24 12 0.19
25 16 0.26
26 10 0.16
27 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (23 bp):
GTTTTAGTATTTTATTTAAATAG
Found at i:333845 original size:15 final size:16
Alignment explanation
Indices: 333827--333869 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
333817 ATTACTATTA
333827 TTTTATTATTTTT-TC
1 TTTTATTATTTTTATC
333842 TTTTATTTATTTTTATC
1 TTTTA-TTATTTTTATC
*
333859 TATT-TTATTTT
1 TTTTATTATTTT
333870 ATTAAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTATTTTTATC
Found at i:333864 original size:19 final size:18
Alignment explanation
Indices: 333825--333868 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
333815 TTATTACTAT
333825 TATTTTA-TTATTTTTTC
1 TATTTTATTTATTTTTTC
333842 --TTTTATTTATTTTTATC
1 TATTTTATTTATTTTT-TC
333859 TATTTTATTT
1 TATTTTATTT
333869 TATTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 2 0.09
19 8 0.35
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTATTTATTTTTTC
Found at i:337231 original size:17 final size:17
Alignment explanation
Indices: 337209--337241 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
337199 AGATATCATA
337209 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
337226 ATATTATATTTTATAT
1 ATATTATATTTTATAT
337242 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:338057 original size:21 final size:21
Alignment explanation
Indices: 338027--338078 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
338017 ATACAATTTT
* *
338027 AGTATTGATACTCCCAGGT-GG
1 AGTATCGATACTCCC-GATAGG
338048 AGTATCGATACTCCCGATAGG
1 AGTATCGATACTCCCGATAGG
338069 AGTATCGATA
1 AGTATCGATA
338079 TTGGGGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (21 bp):
AGTATCGATACTCCCGATAGG
Found at i:356818 original size:20 final size:19
Alignment explanation
Indices: 356772--356822 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
356762 AACTGTGGAT
* *
356772 CAGTATCGGTACTGATTGG
1 CAGTATCGATACTGAATGG
356791 -AGGTATCGATACTGAAATGG
1 CA-GTATCGATACTG-AATGG
356811 CAGTATCGATAC
1 CAGTATCGATAC
356823 CAAAGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 11 0.41
20 14 0.52
21 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (19 bp):
CAGTATCGATACTGAATGG
Found at i:366376 original size:21 final size:22
Alignment explanation
Indices: 366330--366398 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
366320 AGAGTCGAGG
*
366330 GTGGTCATTCAGGACAAAACTAT
1 GTGGTCATTCGGGAC-AAACTAT
366353 GTGGTCATTCGGGACAAA-TAT
1 GTGGTCATTCGGGACAAACTAT
* *
366374 GTGG-CACTTCGGTACAAATTAT
1 GTGGTCA-TTCGGGACAAACTAT
366396 GTG
1 GTG
366399 AGTTGTGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 2 0.05
21 17 0.40
22 9 0.21
23 14 0.33
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (22 bp):
GTGGTCATTCGGGACAAACTAT
Found at i:369407 original size:13 final size:13
Alignment explanation
Indices: 369389--369417 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
369379 AAGCAAAGTA
369389 TTAAACATATATC
1 TTAAACATATATC
369402 TTAAACATATATC
1 TTAAACATATATC
369415 TTA
1 TTA
369418 GTGAGACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAACATATATC
Found at i:373860 original size:29 final size:30
Alignment explanation
Indices: 373809--373900 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 30
373799 TATAAATACG
* *
373809 CTCTCAACCCGTAAACAT-TCACAGCAATC
1 CTCTCAACCCGTAAAAATCACACAGCAATC
* *
373838 CTCTCAACCCG-AAAAATCACACAACAAAC
1 CTCTCAACCCGTAAAAATCACACAGCAATC
* * *
373867 CTTTCAACCCGTAAATATCAC-CCGACAATC
1 CTCTCAACCCGTAAAAATCACACAG-CAATC
373897 CTCT
1 CTCT
373901 TATATTTGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.10
29 30 0.60
30 15 0.30
ACGTcount: A:0.37, C:0.38, G:0.05, T:0.20
Consensus pattern (30 bp):
CTCTCAACCCGTAAAAATCACACAGCAATC
Found at i:380058 original size:17 final size:18
Alignment explanation
Indices: 380024--380100 Score: 131
Period size: 17 Copynumber: 4.4 Consensus size: 18
380014 AAATATTTAA
380024 GGAAAATGTGATTTTTCG
1 GGAAAATGTGATTTTTCG
*
380042 AGAAAATGTGA-TTTTCG
1 GGAAAATGTGATTTTTCG
380059 GGAAAATGTGA-TTTTCG
1 GGAAAATGTGATTTTTCG
380076 GGAAAATGTGATTTTTCG
1 GGAAAATGTGATTTTTCG
380094 GGAAAAT
1 GGAAAAT
380101 AACCATCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
17 33 0.59
18 23 0.41
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (18 bp):
GGAAAATGTGATTTTTCG
Found at i:380070 original size:35 final size:35
Alignment explanation
Indices: 380024--380100 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
380014 AAATATTTAA
380024 GGAAAATGTGATTTTTCGAGAAAATGTGA-TTTTCG
1 GGAAAATGTGA-TTTTCGAGAAAATGTGATTTTTCG
*
380059 GGAAAATGTGATTTTCGGGAAAATGTGATTTTTCG
1 GGAAAATGTGATTTTCGAGAAAATGTGATTTTTCG
380094 GGAAAAT
1 GGAAAAT
380101 AACCATCTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 16 0.40
35 24 0.60
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (35 bp):
GGAAAATGTGATTTTCGAGAAAATGTGATTTTTCG
Found at i:390283 original size:23 final size:21
Alignment explanation
Indices: 390227--390288 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
390217 TTTTGGTGCA
*
390227 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
390247 GAGGGAACCAATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
390268 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
390289 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:390296 original size:21 final size:21
Alignment explanation
Indices: 390270--390309 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
390260 CCCCCTTTGA
*
390270 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
390291 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
390310 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:392882 original size:17 final size:19
Alignment explanation
Indices: 392850--392885 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
392840 ACTCAAAGTG
392850 TAAAATTAAGTTTTAAAAT
1 TAAAATTAAGTTTTAAAAT
392869 TAAAA-TAA-TTTTAAAAT
1 TAAAATTAAGTTTTAAAAT
392886 AATTTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATTAAGTTTTAAAAT
Found at i:392884 original size:11 final size:11
Alignment explanation
Indices: 392868--392892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
392858 AGTTTTAAAA
392868 TTAAAATAATT
1 TTAAAATAATT
392879 TTAAAATAATT
1 TTAAAATAATT
392890 TTA
1 TTA
392893 CAAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:394927 original size:35 final size:34
Alignment explanation
Indices: 394842--394928 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
394832 AATATAATTT
*
394842 TAAATACAACAAACTTACAATAAATATTAAATGG
1 TAAATACAACAAAATTACAATAAATATTAAATGG
*
394876 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA---ATATTAAATGG
394914 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
394929 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 3 0.07
38 12 0.27
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAATATTAAATGG
Found at i:394996 original size:34 final size:35
Alignment explanation
Indices: 394919--394997 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
394909 AATGGTAATA
* *
394919 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
394954 AACAAATTTAA-CAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACCAAAATAAATTAACAA-AAAGTCC
394987 AACCAAATTTA
1 AA-CAAATTTA
394998 TGAAATAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 7 0.17
34 23 0.57
35 10 0.25
ACGTcount: A:0.61, C:0.16, G:0.01, T:0.22
Consensus pattern (35 bp):
AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
Found at i:395567 original size:33 final size:33
Alignment explanation
Indices: 395528--395602 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
395518 CATAAAACCA
*
395528 GGTGGCGGCGGTGGCATCGGGTAAGGGAACGGC
1 GGTGGCGGCGGCGGCATCGGGTAAGGGAACGGC
395561 GGTGGCGGCGGCGGCATCGGGTAAGGGAACGGC
1 GGTGGCGGCGGCGGCATCGGGTAAGGGAACGGC
395594 GGTGGCGGC
1 GGTGGCGGC
395603 ATCACATATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.20, G:0.56, T:0.11
Consensus pattern (33 bp):
GGTGGCGGCGGCGGCATCGGGTAAGGGAACGGC
Found at i:397344 original size:17 final size:17
Alignment explanation
Indices: 397324--397385 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
397314 ATTAATTAAA
397324 TAAAATATTAAAAAATT
1 TAAAATATTAAAAAATT
397341 T-AAATACTTAAATAAA-T
1 TAAAATA-TTAAA-AAATT
*
397358 TAAAA-A-TAAAATATT
1 TAAAATATTAAAAAATT
* *
397373 TAATATAATAAAA
1 TAAAATATTAAAA
397386 TATATCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 6 0.16
17 14 0.38
18 6 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATATTAAAAAATT
Found at i:399333 original size:45 final size:44
Alignment explanation
Indices: 399283--399372 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 44
399273 TGTTTATAAC
*
399283 TCACAAATATCAAGGAAATGGGTATCTTCCAAATACTTTAATGTA
1 TCACAAATATCAAGAAAATGGGTATCTTCCAAATACTTT-ATGTA
399328 TCACAAATATCAAGAAAATGGGTATCTTCCAAATACTTTATGTA
1 TCACAAATATCAAGAAAATGGGTATCTTCCAAATACTTTATGTA
399372 T
1 T
399373 TCAACTTCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 6 0.14
45 38 0.86
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (44 bp):
TCACAAATATCAAGAAAATGGGTATCTTCCAAATACTTTATGTA
Found at i:399507 original size:91 final size:90
Alignment explanation
Indices: 399412--399579 Score: 264
Period size: 90 Copynumber: 1.9 Consensus size: 90
399402 AAAAAGTTTT
* * *
399412 TTTTTTTTTTTGCAAAGGTCGAAAATTTAGTTTGCCCAATTAATAACGTGAGAGAACAAACATAC
1 TTTTTTTTTTTGCAAAGGTC-AAAATTTAGTTTACCCAATTAATAACGTAAGAGAACAAACACAC
*
399477 TTAATTTAAAAATGGGTGATTAAAGA
65 TTAATTAAAAAATGGGTGATTAAAGA
* * *
399503 TTTTTTTTTTTGCAAAGGTCAAAATTTAGTTTACCCAATTAATAACGTAAGTGACCAAACACATT
1 TTTTTTTTTTTGCAAAGGTCAAAATTTAGTTTACCCAATTAATAACGTAAGAGAACAAACACACT
399568 TAATTAAAAAAT
66 TAATTAAAAAAT
399580 TGATAATTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 50 0.71
91 20 0.29
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (90 bp):
TTTTTTTTTTTGCAAAGGTCAAAATTTAGTTTACCCAATTAATAACGTAAGAGAACAAACACACT
TAATTAAAAAATGGGTGATTAAAGA
Found at i:406664 original size:36 final size:33
Alignment explanation
Indices: 406624--406693 Score: 77
Period size: 36 Copynumber: 2.0 Consensus size: 33
406614 AAAGATCTAA
*
406624 TTAAAAAAACAAAGAGATATATTATAATAATTATCT
1 TTAAAAAAACAAA-AGA-AAATTAT-ATAATTATCT
* * *
406660 TTAAATAAATAAAAGAAAATTATATTATTATCT
1 TTAAAAAAACAAAAGAAAATTATATAATTATCT
406693 T
1 T
406694 AAATCAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
33 10 0.33
34 6 0.20
35 3 0.10
36 11 0.37
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (33 bp):
TTAAAAAAACAAAAGAAAATTATATAATTATCT
Found at i:407402 original size:22 final size:23
Alignment explanation
Indices: 407361--407404 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
407351 TATATAACTA
*
407361 AAAACAATTTCTAACATTTTATT
1 AAAACAATCTCTAACATTTTATT
*
407384 AAAACAATCT-TAACCTTTTAT
1 AAAACAATCTCTAACATTTTAT
407405 CGAATACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAACAATCTCTAACATTTTATT
Found at i:417293 original size:15 final size:16
Alignment explanation
Indices: 417273--417302 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
417263 ATATTTAATT
417273 TATTTTTTGT-ATTAG
1 TATTTTTTGTGATTAG
417288 TATTTTTTGTGATTA
1 TATTTTTTGTGATTA
417303 TTATCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (16 bp):
TATTTTTTGTGATTAG
Found at i:439011 original size:55 final size:55
Alignment explanation
Indices: 438927--439246 Score: 383
Period size: 55 Copynumber: 5.8 Consensus size: 55
438917 GGAGTTATCA
*
438927 ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTAATGAATAACCGT
1 ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
* *
438982 ACATGCAATATGTGTACAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
1 ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
*
439037 ACAAT-CACTATGTGTGTAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
1 AC-ATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
* * * * * *
439092 GCATGCACTATCTGTGCAATTCCGCAGAATTAATCATGAGTTGATGAATAACTGT
1 ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
* * ** * * * *
439147 ACAAGCACTATGTGTGCAATTCTATAGAATTCATCATGACTTTATAAATAATCGT
1 ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
* * * ** **
439202 ATAGTG-ATTAGGTGTGCAAAACCACAAAATTCATCATGAGTTGAT
1 ACA-TGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGAT
439247 AAATTATCGT
Statistics
Matches: 226, Mismatches: 36, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
54 2 0.01
55 221 0.98
56 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (55 bp):
ACATGCACTATGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAACCGT
Done.