Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold333
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: 1398653
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.32
Warning! 76431 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:287939 original size:11 final size:11
Alignment explanation
Indices: 287923--287957 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
287913 ATAAAAGCTG
*
287923 AATTATAATTA
1 AATTATAAGTA
287934 AATTATAAGTA
1 AATTATAAGTA
*
287945 AATTATATGTA
1 AATTATAAGTA
287956 AA
1 AA
287958 GGGACTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (11 bp):
AATTATAAGTA
Found at i:289334 original size:17 final size:17
Alignment explanation
Indices: 289312--289345 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
289302 TTTGAAATGG
*
289312 AAAATGTTATTGAAATA
1 AAAATGCTATTGAAATA
289329 AAAATGCTATTGAAATA
1 AAAATGCTATTGAAATA
289346 GAAAGTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATGCTATTGAAATA
Found at i:290276 original size:21 final size:21
Alignment explanation
Indices: 290252--290293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
290242 ATTTTATCAC
290252 TTTTGAAATAAGGTATCGATA
1 TTTTGAAATAAGGTATCGATA
* **
290273 TTTTGACATTTGGTATCGATA
1 TTTTGAAATAAGGTATCGATA
290294 CCTGACCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTTGAAATAAGGTATCGATA
Found at i:298817 original size:32 final size:32
Alignment explanation
Indices: 298776--298839 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
298766 AGCCTTGGCC
298776 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
1 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
*
298808 TCTCTTGGGTATGATCCTCAGGGTATTCACTT
1 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
298840 ACTTCGTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (32 bp):
TCTCTTGGGTATGATCCTCAGAGTATTCACTT
Found at i:305306 original size:21 final size:21
Alignment explanation
Indices: 305280--305328 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
305270 TACTCCAGGC
* *
305280 CTCGAGATAGGAACCCCTTTT
1 CTCGAGAAAGGAACCCCTTGT
*
305301 CTCGAGAAATGAACCCCTTGT
1 CTCGAGAAAGGAACCCCTTGT
305322 CTCGAGA
1 CTCGAGA
305329 CATTCAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
CTCGAGAAAGGAACCCCTTGT
Found at i:305429 original size:22 final size:22
Alignment explanation
Indices: 305384--305436 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
305374 TCGAGAGTCA
*
305384 GTCTCGAGACTTGAGAATTCAT
1 GTCTCGAGACATGAGAATTCAT
*
305406 GTCTCGAGACATG-GATTTCAAT
1 GTCTCGAGACATGAGAATTC-AT
*
305428 GTCTTGAGA
1 GTCTCGAGA
305437 TGTGTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (22 bp):
GTCTCGAGACATGAGAATTCAT
Found at i:306084 original size:222 final size:222
Alignment explanation
Indices: 305697--306144 Score: 815
Period size: 222 Copynumber: 2.0 Consensus size: 222
305687 GAAATATTCT
* *
305697 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAACTCATGTGTGGGG
1 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
305762 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
66 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
* *
305827 AAACCTACTTATACTTACAGAATTGGATTGTCAATAAAAGTAAGCATTGGTATATGATGAACTAT
131 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
305892 TTGTAGTAAGAAATCCTAAATAGAATG
196 TTGTAGTAAGAAATCCTAAATAGAATG
305919 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
1 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
* * *
305984 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAATGGATAAGTAATCCGTTGATAG
66 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
306049 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
131 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
* *
306114 TTTTAGTGAGAAATCCTAAATAGAATG
196 TTGTAGTAAGAAATCCTAAATAGAATG
306141 GAGT
1 GAGT
306145 AAAAAATTTC
Statistics
Matches: 217, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 217 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (222 bp):
GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
TTGTAGTAAGAAATCCTAAATAGAATG
Found at i:306443 original size:29 final size:29
Alignment explanation
Indices: 306411--306553 Score: 144
Period size: 29 Copynumber: 5.0 Consensus size: 29
306401 TGGAAAATCT
* * *
306411 AAAGTACAATCTAAAGTGGTGGGCAGTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
** * * * * *
306440 AAAGTGTAAGTCAAAGTGATAGCCATTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
*
306469 AAAGTGCAAGCCAAAGTGGTGGACAGTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
* * *
306498 AAAGTACAAGCCAAAGTGGCGAACAATCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
*
306527 -AAGTACAAGCCAAAGTGGTAGACAGTC
1 AAAGTACAAGCCAAAGTGGTGGACAGTC
306554 TAACTACGAA
Statistics
Matches: 91, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
28 23 0.25
29 68 0.75
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (29 bp):
AAAGTACAAGCCAAAGTGGTGGACAGTCC
Found at i:311278 original size:25 final size:25
Alignment explanation
Indices: 311248--311302 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
311238 TATTTGCGCA
311248 ATTTTTATTATTATCGTTATTATATT
1 ATTTTTATT-TTATCGTTATTATATT
* * *
311274 ATTTTTATTTTCTTGTTATTTTATT
1 ATTTTTATTTTATCGTTATTATATT
311299 ATTT
1 ATTT
311303 CTTTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
ATTTTTATTTTATCGTTATTATATT
Found at i:314657 original size:7 final size:7
Alignment explanation
Indices: 314631--314681 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
314621 CTTATTCATC
314631 ATCACAT
1 ATCACAT
* * *
314638 CTCATAA
1 ATCACAT
314645 ATCACAT
1 ATCACAT
314652 ATCACAT
1 ATCACAT
314659 ATCACAT
1 ATCACAT
314666 ATCACAT
1 ATCACAT
314673 ATCACAT
1 ATCACAT
314680 AT
1 AT
314682 TGATGGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCACAT
Found at i:316233 original size:29 final size:29
Alignment explanation
Indices: 316199--316297 Score: 128
Period size: 29 Copynumber: 3.4 Consensus size: 29
316189 ACGAACTATT
*
316199 TGGCAGACAGTCCAAAATACAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
* * **
316228 TGGCAGGCAGTTCAAAGTGTAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
*
316257 TGGCAGACAATCCAAAGTACAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
316286 TGGC-GAACAGTC
1 TGGCAG-ACAGTC
316298 TAACTACGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (29 bp):
TGGCAGACAGTCCAAAGTACAAGCCAAAG
Found at i:331218 original size:31 final size:32
Alignment explanation
Indices: 331182--331246 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
331172 CTTAGATAAT
*
331182 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
331213 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
331245 TT
1 TT
331247 GTAATTTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGAATTCAATTACTC
Found at i:332635 original size:24 final size:24
Alignment explanation
Indices: 332607--332654 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
332597 TGACTTTGAA
332607 AATAATTTAATTGAGTCGATTTAT
1 AATAATTTAATTGAGTCGATTTAT
*
332631 AATAATTTAATTGAGTTGATTTAT
1 AATAATTTAATTGAGTCGATTTAT
332655 TCGATGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
AATAATTTAATTGAGTCGATTTAT
Found at i:337946 original size:24 final size:24
Alignment explanation
Indices: 337919--337974 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
337909 TAAATATGGA
**
337919 AATAAATAACAAAGATTTTATGCT
1 AATAAATAACAAAGATACTATGCT
** *
337943 AATAAATGTCAAATATACTATGCT
1 AATAAATAACAAAGATACTATGCT
337967 AATAAATA
1 AATAAATA
337975 CTAAATCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (24 bp):
AATAAATAACAAAGATACTATGCT
Found at i:346588 original size:13 final size:13
Alignment explanation
Indices: 346570--346595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
346560 AAAAAAGTTT
346570 TTTTATTTTTTTA
1 TTTTATTTTTTTA
346583 TTTTATTTTTTTA
1 TTTTATTTTTTTA
346596 GTCTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:346606 original size:21 final size:21
Alignment explanation
Indices: 346567--346608 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
346557 ATAAAAAAAG
* * *
346567 TTTTTTTATTTTTTTATTTTA
1 TTTTTTTAGTCTTTAATTTTA
346588 TTTTTTTAGTCTTTAATTTTA
1 TTTTTTTAGTCTTTAATTTTA
346609 CATTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTAGTCTTTAATTTTA
Found at i:360440 original size:18 final size:19
Alignment explanation
Indices: 360419--360464 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
360409 TTTACTTTTT
360419 TATTTTTTA-TTTT-ATAA
1 TATTTTTTAGTTTTCATAA
360436 -ATATTTTTAGTTTTCATAA
1 TAT-TTTTTAGTTTTCATAA
360455 TACTTTTTTA
1 TA-TTTTTTA
360465 AGCCAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.08
17 6 0.25
18 4 0.17
19 4 0.17
20 7 0.29
21 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTTAGTTTTCATAA
Found at i:363593 original size:55 final size:55
Alignment explanation
Indices: 363531--363663 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
363521 TAAGTTGTTT
* * * *
363531 TATGTTTAAATCGATTGTCATGTTGGAATACTACTTCTTTTAAATCA-ATTATTTA
1 TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAAT-AGACTATTTA
* * * *
363586 TATGTTTAAATCTATTGTTATGTTGGAATACTGCTACATTTGAATAGACTGTTTA
1 TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAATAGACTATTTA
*
363641 TATGTTTAAATTGATTGTTATGT
1 TATGTTTAAATCGATTGTTATGT
363664 AGCATGTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 1 0.01
55 66 0.99
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAATAGACTATTTA
Found at i:368256 original size:161 final size:161
Alignment explanation
Indices: 368072--368386 Score: 612
Period size: 161 Copynumber: 2.0 Consensus size: 161
368062 CTTGAATTTC
*
368072 TTTCTCTTAGTTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
1 TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
368137 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
66 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
368202 TCCATGAATGAGTCATTATAATTAGCTAGGG
131 TCCATGAATGAGTCATTATAATTAGCTAGGG
*
368233 TTTCTCTTAGCTAGGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
1 TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
368298 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
66 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
368363 TCCATGAATGAGTCATTATAATTA
131 TCCATGAATGAGTCATTATAATTA
368387 TCTACTAACT
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (161 bp):
TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
TCCATGAATGAGTCATTATAATTAGCTAGGG
Found at i:373325 original size:15 final size:15
Alignment explanation
Indices: 373305--373340 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
373295 AACAACATGA
*
373305 AATAATAGGAATAAT
1 AATAATAGCAATAAT
373320 AATAATAGCAATAAT
1 AATAATAGCAATAAT
373335 AATAAT
1 AATAAT
373341 GATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (15 bp):
AATAATAGCAATAAT
Found at i:377114 original size:24 final size:25
Alignment explanation
Indices: 377086--377153 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
377076 CTTTCTAATA
377086 TTGGCTCTCTTGAGCTTCCC-AT-T
1 TTGGCTCTCTTGAGCTTCCCGATAT
377109 TATGGCTCT-TATGAGCTTCCCGATAT
1 T-TGGCTCTCT-TGAGCTTCCCGATAT
* *
377135 TTGGCTCGCATGAGCTTCC
1 TTGGCTCTCTTGAGCTTCC
377154 AGTTACATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 2 0.05
24 17 0.45
25 17 0.45
26 2 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (25 bp):
TTGGCTCTCTTGAGCTTCCCGATAT
Found at i:377147 original size:25 final size:23
Alignment explanation
Indices: 377086--377153 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
377076 CTTTCTAATA
*
377086 TTGGCTCTCTTGAGCTTCCCATT
1 TTGGCTCTCATGAGCTTCCCATT
*
377109 TATGGCTCTTATGAGCTTCCCGATAT
1 T-TGGCTCTCATGAGCTTCCC-AT-T
*
377135 TTGGCTCGCATGAGCTTCC
1 TTGGCTCTCATGAGCTTCC
377154 AGTTACATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 17 0.45
25 18 0.47
26 2 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (23 bp):
TTGGCTCTCATGAGCTTCCCATT
Found at i:377164 original size:25 final size:25
Alignment explanation
Indices: 377136--377192 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
377126 TCCCGATATT
* *
377136 TGGCTCGCATGAGCTTCCAGTTACA
1 TGGCTCGCATGAACTTCCAGTTAAA
* *
377161 TGGCTCACATGAACTTCCTGTTAAA
1 TGGCTCGCATGAACTTCCAGTTAAA
377186 TGGCTCG
1 TGGCTCG
377193 TAAGAGCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (25 bp):
TGGCTCGCATGAACTTCCAGTTAAA
Found at i:378923 original size:38 final size:39
Alignment explanation
Indices: 378820--378959 Score: 210
Period size: 39 Copynumber: 3.6 Consensus size: 39
378810 CATGTTTTTT
* *
378820 TGAGTATTGTGATATATGCTTGAATATTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
378859 TGGGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
378898 TGAGTATTGT-ATATATGTTTCAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
378936 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
378960 AGTGAATATA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 34 0.38
39 56 0.62
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:384138 original size:55 final size:55
Alignment explanation
Indices: 384072--384208 Score: 168
Period size: 55 Copynumber: 2.5 Consensus size: 55
384062 ATTTCCCAAA
* * * * *
384072 AATATTGCTTCTTTTGGATTGATTTTTTTTATATTTAAATCGACTT-TCGTGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGA-TTATCATGTTGG
*
384127 AATATTGCTTCTTTTGAATCGATTGTTTATATCTTTAAATCGATTATCATGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTATCATGTTGG
* * * *
384182 AATACTACTTATTTTGAATCAATTGTT
1 AATATTGCTTCTTTTGAATCGATTGTT
384209 ATGGATGAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 2 0.03
55 69 0.97
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (55 bp):
AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTATCATGTTGG
Found at i:384289 original size:61 final size:60
Alignment explanation
Indices: 384194--384350 Score: 208
Period size: 61 Copynumber: 2.6 Consensus size: 60
384184 TACTACTTAT
* * * *
384194 TTTGAATCAATTGTTATGGAT-GAATACTACTTCTTCTTCTTTTGAATTGATTGTTTATATG
1 TTTGAATCGATTGTTATGG-TGGAATA-TTCTTCTTCTTCTTTTGAATCGACTGTTTATATG
*
384255 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTCTTTTGAATCGACTGTTTGTATG
1 TTTGAATCGATTGTTATGGTGGAATATT-CTTCTTCTTCTTTTGAATCGACTGTTTATATG
* *
384316 TTTAAATCGATTGTTATGTTGGAATACTTCTTCTT
1 TTTGAATCGATTGTTATGGTGGAATA-TTCTTCTT
384351 TTGAATCGAT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
60 2 0.02
61 82 0.95
62 2 0.02
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (60 bp):
TTTGAATCGATTGTTATGGTGGAATATTCTTCTTCTTCTTTTGAATCGACTGTTTATATG
Found at i:384363 original size:34 final size:36
Alignment explanation
Indices: 384320--384404 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 36
384310 TGTATGTTTA
384320 AATCGATTGTTA-TGTTGGAATA-CTTCTTC-TTTTG
1 AATCGATTGTTATTG-TGGAATATCTTCTTCTTTTTG
384354 AATCGATTGTTATTGTGGAATATTGCTTCTTCTTATTTTG
1 AATCGATTGTTATTGTGGAATA-T-CTTCTTC-T-TTTTG
384394 AATCGATTGTT
1 AATCGATTGTT
384405 TATATATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
34 19 0.43
35 2 0.05
37 7 0.16
40 16 0.36
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (36 bp):
AATCGATTGTTATTGTGGAATATCTTCTTCTTTTTG
Found at i:384372 original size:95 final size:95
Alignment explanation
Indices: 384255--384459 Score: 338
Period size: 95 Copynumber: 2.2 Consensus size: 95
384245 TGTTTATATG
* * *
384255 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTCTTTTGAATCGACTGTTTGTATGTTTA
1 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
384320 AATCGATTGTTATGTTGGAATACTTCTTCT
66 AATCGATTGTTATGTTGGAATACTTCTTCT
* *
384350 TTTGAATCGATTGTTATTGTGGAATATTGCTTCTTCTTATTTTGAATCGATTGTTTATATATTTA
1 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
* *
384415 AATCGATTGTTATGTTGGATTATTTCTTCT
66 AATCGATTGTTATGTTGGAATACTTCTTCT
*
384445 ATTGAATCGATTGTT
1 TTTGAATCGATTGTT
384460 TATATGTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (95 bp):
TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
AATCGATTGTTATGTTGGAATACTTCTTCT
Found at i:384450 original size:55 final size:55
Alignment explanation
Indices: 384391--384514 Score: 176
Period size: 55 Copynumber: 2.3 Consensus size: 55
384381 TCTTCTTATT
* * * * *
384391 TTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGATTATTTCTTCTA
1 TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
* *
384446 TTGAATCGATTGTTTATATGTTTAAATCGATTATTATGTTAGAATACTGCTTCTT
1 TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
*
384501 TTGAATCAATTGTT
1 TTGAATCGATTGTT
384515 ATGGTGGAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.51
Consensus pattern (55 bp):
TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
Found at i:384501 original size:150 final size:150
Alignment explanation
Indices: 384079--384635 Score: 722
Period size: 156 Copynumber: 3.7 Consensus size: 150
384069 AAAAATATTG
* * * * ** *
384079 CTTCTTTTGGATTGATTTTTTTTATATTTAAATCGACTT-TCGTGTTGGAATATTGCTTCTTTTG
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGA-TTGTTATGTTGGAATATTTCTTCTTTTG
* * *
384143 AATCGATTGTTTATATCTTTAAATCGATTATCATGTTGGAATACTACTTATTTTGAATCAATTGT
65 AATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGT
* *
384208 TATGGAT-GAATACTACTTCTT
130 TATGG-TGGAATATTGCTTCTT
* * * *
384229 CTTCTTTTGAATTGATTGTTTATATGTTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTC
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATA-----T-TTCTTC
* * * * *
384294 TTTTGAATCGACTGTTTGTATGTTTAAATCGATTGTTATGTTGGAATACTTCTTCTTTTGAATCG
60 TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCA
*
384359 ATTGTTATTGTGGAATATTGCTTCTT
125 ATTGTTATGGTGGAATATTGCTTCTT
* * *
384385 CTTATTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGATTATTTCTTCTATTGA
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
* *
384450 ATCGATTGTTTATATGTTTAAATCGATTATTATGTTAGAATACTGCTTCTTTTGAATCAATTGTT
66 ATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGTT
*
384515 ATGGTGGAATATTGCTTTTTT
131 ATGGTGGAATATTGC-TTCTT
* *
384536 TTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTACTTCTTTTGA
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
* * *
384601 ATTGATTGTTTATATGTTCAAATCGATTGTTATGT
66 ATCGATTGTTTATATGTTTAAATCGATTATTATGT
384636 AGCACGTCTA
Statistics
Matches: 355, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
149 2 0.01
150 125 0.35
151 97 0.27
155 2 0.01
156 129 0.36
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (150 bp):
CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
ATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGTT
ATGGTGGAATATTGCTTCTT
Found at i:386776 original size:39 final size:39
Alignment explanation
Indices: 386733--386868 Score: 152
Period size: 39 Copynumber: 3.5 Consensus size: 39
386723 CATTTTCACT
*
386733 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
386772 TTTAAGCATATATCAGAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
386811 TTCAAGCATATAT-ATCAACA-ATCATGTAATCACATAACA
1 TTTAAGCATATATCA-CAATACA-CATATAATCACATAACA
* * *
386850 TTCAAGAATAT-TCTCAATA
1 TTTAAGCATATATCACAATA
386869 TTCAAAAACA
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.07
39 77 0.93
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:387812 original size:170 final size:170
Alignment explanation
Indices: 387530--387846 Score: 616
Period size: 170 Copynumber: 1.9 Consensus size: 170
387520 CTACGCTATG
*
387530 TTCAAAAATCAATTAGGAACTCACCACAAGCAATCAAAAACATAAGCCTAAGCTATGTTCCCATA
1 TTCAAAAATCAACTAGGAACTCACCACAAGCAATCAAAAACATAAGCCTAAGCTATGTTCCCATA
387595 TAACCGAAACATTTAACATAACAATCTTTACATTCGAATATATTGGTCTATACTCAATCTTTTTG
66 TAACCGAAACATTTAACATAACAATCTTTACATTCGAATATATTGGTCTATACTCAATCTTTTTG
387660 CCTAAAACCAATTCCGTACAACAATTCACACAATAATATA
131 CCTAAAACCAATTCCGTACAACAATTCACACAATAATATA
*
387700 TTCAAAAATCAACTAGGAACTCACCACAAGCAATCAAAAATATAAGCCTAAGCTATGTTCCCATA
1 TTCAAAAATCAACTAGGAACTCACCACAAGCAATCAAAAACATAAGCCTAAGCTATGTTCCCATA
387765 TAACCGAAACATTTAACATAACAATCTTTACATTCGAATATATTGGTCTATACTCAATCTTTTTG
66 TAACCGAAACATTTAACATAACAATCTTTACATTCGAATATATTGGTCTATACTCAATCTTTTTG
387830 CCTAAAACCAATTCCGT
131 CCTAAAACCAATTCCGT
387847 TCATCTTTTA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 145 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (170 bp):
TTCAAAAATCAACTAGGAACTCACCACAAGCAATCAAAAACATAAGCCTAAGCTATGTTCCCATA
TAACCGAAACATTTAACATAACAATCTTTACATTCGAATATATTGGTCTATACTCAATCTTTTTG
CCTAAAACCAATTCCGTACAACAATTCACACAATAATATA
Found at i:389675 original size:16 final size:16
Alignment explanation
Indices: 389654--389686 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
389644 AAGTTAAAAC
*
389654 TTAATCGACAACTTTA
1 TTAATCCACAACTTTA
389670 TTAATCCACAACTTTA
1 TTAATCCACAACTTTA
389686 T
1 T
389687 ATTTCAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAATCCACAACTTTA
Found at i:389849 original size:20 final size:20
Alignment explanation
Indices: 389817--389859 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
389807 AGATAAAATC
389817 ATTTTCAACCATCCTCTTTT
1 ATTTTCAACCATCCTCTTTT
389837 ATTTTGCAA-CATCCTCTTTT
1 ATTTT-CAACCATCCTCTTTT
389857 ATT
1 ATT
389860 GTACAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTCAACCATCCTCTTTT
Found at i:394612 original size:3 final size:3
Alignment explanation
Indices: 394604--394633 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
394594 TATTAGTTAA
*
394604 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
394634 CACGATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:398394 original size:19 final size:19
Alignment explanation
Indices: 398372--398411 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
398362 GAAGGGTGGC
*
398372 AATATCAAATCTGGGTGAA
1 AATATCAAATCCGGGTGAA
*
398391 AATATCATATCCGGGTGAA
1 AATATCAAATCCGGGTGAA
398410 AA
1 AA
398412 GAGGTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
AATATCAAATCCGGGTGAA
Found at i:405157 original size:205 final size:205
Alignment explanation
Indices: 404805--405214 Score: 820
Period size: 205 Copynumber: 2.0 Consensus size: 205
404795 AAAAGGATTT
404805 TTGTAAGTTTCGGTGCTAAAAGGTTGGGCTGCCTCTGTGCTATATCTGACTCTATCTATTTATTT
1 TTGTAAGTTTCGGTGCTAAAAGGTTGGGCTGCCTCTGTGCTATATCTGACTCTATCTATTTATTT
404870 ATCTAAGTGGCATTGTTTAGCTTTGGTAATGAGAAATGACAAGGGACAAATGTCAGAAACGGACT
66 ATCTAAGTGGCATTGTTTAGCTTTGGTAATGAGAAATGACAAGGGACAAATGTCAGAAACGGACT
404935 AATTGTTGGAAGCAAGTTGCAGAGATCGTTGTGTCAGACTCCAGTTGCAACATCTGATCGTATAA
131 AATTGTTGGAAGCAAGTTGCAGAGATCGTTGTGTCAGACTCCAGTTGCAACATCTGATCGTATAA
405000 CCGATAATGC
196 CCGATAATGC
405010 TTGTAAGTTTCGGTGCTAAAAGGTTGGGCTGCCTCTGTGCTATATCTGACTCTATCTATTTATTT
1 TTGTAAGTTTCGGTGCTAAAAGGTTGGGCTGCCTCTGTGCTATATCTGACTCTATCTATTTATTT
405075 ATCTAAGTGGCATTGTTTAGCTTTGGTAATGAGAAATGACAAGGGACAAATGTCAGAAACGGACT
66 ATCTAAGTGGCATTGTTTAGCTTTGGTAATGAGAAATGACAAGGGACAAATGTCAGAAACGGACT
405140 AATTGTTGGAAGCAAGTTGCAGAGATCGTTGTGTCAGACTCCAGTTGCAACATCTGATCGTATAA
131 AATTGTTGGAAGCAAGTTGCAGAGATCGTTGTGTCAGACTCCAGTTGCAACATCTGATCGTATAA
405205 CCGATAATGC
196 CCGATAATGC
405215 AAAATGAGAA
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 205 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (205 bp):
TTGTAAGTTTCGGTGCTAAAAGGTTGGGCTGCCTCTGTGCTATATCTGACTCTATCTATTTATTT
ATCTAAGTGGCATTGTTTAGCTTTGGTAATGAGAAATGACAAGGGACAAATGTCAGAAACGGACT
AATTGTTGGAAGCAAGTTGCAGAGATCGTTGTGTCAGACTCCAGTTGCAACATCTGATCGTATAA
CCGATAATGC
Found at i:423425 original size:25 final size:24
Alignment explanation
Indices: 423276--423422 Score: 68
Period size: 25 Copynumber: 5.9 Consensus size: 24
423266 CTTATGACCG
*
423276 TCCTGATATATGGCTCTTCGTGAGCT
1 TCCTGATA-ATGGCTCTTCG-GAACT
* * **
423302 TCCTGATTAAAGGCTTTTTATGAACT
1 TCCTGA-TAATGGC-TCTTCGGAACT
* *
423328 TCCTGAGTAATGGATCTCCGGAACT
1 TCCTGA-TAATGGCTCTTCGGAACT
*
423353 TCCCGAT-ATGGCTCGCTT--GAACT
1 TCCTGATAATGGCT--CTTCGGAACT
* * * *
423376 TCCCGATATATGACT-ATCTGGAGCT
1 TCCTGATA-ATGGCTCTTC-GGAACT
423401 TCCTGATTAATGGCTCTTCGGA
1 TCCTGA-TAATGGCTCTTCGGA
423423 GCTACCCGTT
Statistics
Matches: 89, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
22 1 0.01
23 17 0.19
24 1 0.01
25 36 0.40
26 29 0.33
27 5 0.06
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (24 bp):
TCCTGATAATGGCTCTTCGGAACT
Found at i:423473 original size:73 final size:73
Alignment explanation
Indices: 423319--423478 Score: 171
Period size: 73 Copynumber: 2.2 Consensus size: 73
423309 TAAAGGCTTT
* * * *
423319 TTATGAACTTCCTGAGTAATGGATCTCCGGAACTTCCCGATATGGCTCGCTTGAACTTCCCGATA
1 TTATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATATGGCTCGCATGAACTTCCCGAAA
423384 TATGACTA
66 TATGACTA
* * * * * * *
423392 TCT-GGAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGTTATTGGCTCGCATGAACTT-CCTA
1 T-TATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATA-TGGCTCGCATGAACTTCCCGA
* *
423455 AATATGGCTC
64 AATATGACTA
423465 TTATGAGCTTCCTG
1 TTATGAGCTTCCTG
423479 TTATACAGCC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
72 1 0.01
73 53 0.76
74 16 0.23
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (73 bp):
TTATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATATGGCTCGCATGAACTTCCCGAAA
TATGACTA
Found at i:426514 original size:3 final size:3
Alignment explanation
Indices: 426499--426549 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
426489 TACTATGACC
*
426499 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426547 TTA
1 TTA
426550 CTGTACATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:426824 original size:16 final size:16
Alignment explanation
Indices: 426791--426824 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
426781 TATTGTACAC
**
426791 ATATATATGTATTTGA
1 ATATATATGTATGCGA
426807 ATATATATGTATGCGA
1 ATATATATGTATGCGA
426823 AT
1 AT
426825 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:431707 original size:8 final size:7
Alignment explanation
Indices: 431672--431706 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
431662 AAAAGTGATG
431672 TGAAAAA
1 TGAAAAA
431679 TGAAAAGA
1 TGAAAA-A
431687 TG-AAAA
1 TGAAAAA
431693 TGAAAAA
1 TGAAAAA
431700 TGAAAAA
1 TGAAAAA
431707 AAATGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:438028 original size:16 final size:16
Alignment explanation
Indices: 437995--438028 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
437985 TATTGTACAC
**
437995 ATATATATGTATTTGA
1 ATATATATGTATGCGA
438011 ATATATATGTATGCGA
1 ATATATATGTATGCGA
438027 AT
1 AT
438029 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:441869 original size:7 final size:7
Alignment explanation
Indices: 441857--441896 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
441847 AAAAGTGATG
441857 TGAAAAA
1 TGAAAAA
441864 TGAAAAGA
1 TGAAAA-A
441872 T-AAAAA
1 TGAAAAA
441878 TGAAAAA
1 TGAAAAA
441885 TGAAAAA
1 TGAAAAA
441892 -GAAAA
1 TGAAAA
441897 TGGAGAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 7 0.23
7 22 0.71
8 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
TGAAAAA
Found at i:443268 original size:45 final size:44
Alignment explanation
Indices: 443133--443268 Score: 130
Period size: 45 Copynumber: 3.1 Consensus size: 44
443123 GATCAGTGAT
* *
443133 GATAACAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAA
1 GATAACAGATCTTGCCTTCCT-CATAGACAGTGGAGCAGATCGAA
* * * * * ** * *
443178 GACACCA-ACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAA
1 GATAACAGATCTTGCCTTCCTCATAGACAGTGGAGCAGATCGAA
* *
443221 GATAACAGATCTTGCCTTCCTCCATAGACAGCGGAGCAGATCAAA
1 GATAACAGATCTTGCCTTCCT-CATAGACAGTGGAGCAGATCGAA
443266 GAT
1 GAT
443269 GGTAAATTTT
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
43 22 0.33
44 20 0.30
45 25 0.37
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (44 bp):
GATAACAGATCTTGCCTTCCTCATAGACAGTGGAGCAGATCGAA
Found at i:443415 original size:132 final size:132
Alignment explanation
Indices: 443253--443499 Score: 397
Period size: 132 Copynumber: 1.9 Consensus size: 132
443243 CATAGACAGC
* *
443253 GGAGCAGATCAAAGATGGTAAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
443318 ATTCTACTTCCCT-GGTTAGCAGTGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGT
66 ATTCTACTTCCCTAGG-CAGCAGCGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGT
443382 AGT
130 AGT
* *
443385 GGAGCAGATCAAAGATGGTGAATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
443450 GTTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTG
66 ATTCTACTTCCCTAGGCAGCAGCGGAATAGATTAAAGATTTAAGATCTTG
443500 CCTTTCTGTA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
132 103 0.98
133 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTAGGCAGCAGCGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGTA
GT
Found at i:443571 original size:227 final size:227
Alignment explanation
Indices: 443305--443725 Score: 639
Period size: 227 Copynumber: 1.9 Consensus size: 227
443295 AGTGGAGTAC
** * * *
443305 ATTGAAGCCAGTAATTCTACTTCCCTGGTTAGCAGTGGAATAGATTAAAGATTTAAGATCTTGTC
1 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTATC
* * * *
443370 TCCCCAAGCAGTAGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCACTGTGGTTACAGTGGAG
66 TCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAG-ATTTTACCTCACCGTGGTTACAGTGGAG
* * *
443434 TACATTGAAGCCAGTAGTTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTT
130 TACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTT
443499 GCCTTTCTGTATAGACAGTGGAGCAAATCAAAG
195 GCCTTTCTGTATAGACAGTGGAGCAAATCAAAG
* * *
443532 ATTGATGCCAGTAATTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTAT
1 ATTGAAGCCAGTAATTCTACT-TCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTAT
* *
443596 CTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAG
65 CTCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCACCGTGGTTACAGTGGAG
* *
443661 TACATTGAAGCCAATAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTT
130 TACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTT
443726 CAAGCAGTAG
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
226 1 0.01
227 171 0.99
228 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (227 bp):
ATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTATC
TCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCACCGTGGTTACAGTGGAGT
ACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTTG
CCTTTCTGTATAGACAGTGGAGCAAATCAAAG
Found at i:443827 original size:125 final size:129
Alignment explanation
Indices: 443532--443814 Score: 384
Period size: 125 Copynumber: 2.2 Consensus size: 129
443522 CAAATCAAAG
*
443532 ATTGATGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTATC
1 ATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATC-T-TC
443597 TCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAGT
64 T-CCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAGT
443662 AC
128 AC
* *
443664 ATTGAAGCCAATAATTCTA-CTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATC-T-T
1 ATTGAAGCCAGTAATTCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTCT
* * * *
443726 -C-AAGCAGTAGTGGAGCAGATCAAAGATGG-TGAATTTTCCCTC-CCTGTGGTTACAGTGGAGT
65 CCTAAACAGTAGTGGAGCAAATCAAAGATGGCAG-ATTTTACCTCTCC-GTGGTTACAGTGGAGT
443787 AC
128 AC
443789 ATTGAAGCCAGT-ATTCTTATCTCCCT
1 ATTGAAGCCAGTAATTC-TATCTCCCT
443815 AAGCAGTAGT
Statistics
Matches: 138, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
124 7 0.05
125 71 0.51
126 2 0.01
128 1 0.01
129 1 0.01
131 1 0.01
132 55 0.40
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (129 bp):
ATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTCTC
CTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAGTAC
Found at i:450193 original size:71 final size:71
Alignment explanation
Indices: 450077--450211 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 71
450067 GGGCTTCCAA
* * *
450077 TTCACGGTGGTTATATAGTCACGGGTTGAAGTATAACTAGGGCTCTCAATTGACTATGGTTATGT
1 TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATGT
450142 GGTTAG
66 GGTTAG
* * *
450148 TTCACGATGGTTATATGGTCACGGGTTGAACTATAACTAGGGCTCTTAGTTGACAATGGTTATG
1 TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATG
450212 CGATCACGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (71 bp):
TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATGT
GGTTAG
Found at i:450598 original size:107 final size:107
Alignment explanation
Indices: 450477--450685 Score: 323
Period size: 107 Copynumber: 2.0 Consensus size: 107
450467 GGGTAAAAAA
* * *
450477 AAGGTATCAAGACCTAGATCTCGTAAAACTGAGT-TGAAAATATTTTTATAAATATTTATGAAGT
1 AAGGTATCAAGACCTAGATCTCATAAAACTGAGTCAG-AAATATTTTTATAAATATTTATGAAAT
450541 GTTAGTAAT-ATGATATTAAAATTTCGTTAGAAAATTTTTACGT
65 GTTAGTAATGATG-TATTAAAATTTCGTTAGAAAATTTTTACGT
* *
450584 AAGGTATCGAGACCTCGATCTCATAAAACTGAGTCAGAAATATTTTTATAAATATTTATGAAATG
1 AAGGTATCAAGACCTAGATCTCATAAAACTGAGTCAGAAATATTTTTATAAATATTTATGAAATG
* *
450649 TTAGTAATGTTGTATTAAAATTTTGTTAGAAAATTTT
66 TTAGTAATGATGTATTAAAATTTCGTTAGAAAATTTT
450686 AATGTTTGGG
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 90 0.97
108 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (107 bp):
AAGGTATCAAGACCTAGATCTCATAAAACTGAGTCAGAAATATTTTTATAAATATTTATGAAATG
TTAGTAATGATGTATTAAAATTTCGTTAGAAAATTTTTACGT
Found at i:452714 original size:74 final size:74
Alignment explanation
Indices: 452588--452737 Score: 210
Period size: 74 Copynumber: 2.0 Consensus size: 74
452578 CCAGCTGTAA
* * **
452588 AGATAAGGTTCGCGGGAGTGAGCTCTCCGAAATGGAAATGTGTGCACATGAATATGAATTGACGG
1 AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
*
452653 ACCCGGAAT
66 ACCCAGAAT
* * * * *
452662 AGATGAGGTTTGCAGGAGTGTGCTTTCTGAAATGAAAATGTGCACACATGAATATGAATTGACGG
1 AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
452727 ACCCAGAAT
66 ACCCAGAAT
452736 AG
1 AG
452738 TACGCTAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (74 bp):
AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
ACCCAGAAT
Found at i:468614 original size:21 final size:22
Alignment explanation
Indices: 468589--468639 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
468579 TAACACATAA
468589 AGTGCCTGAA-ACGACACACAT
1 AGTGCCTGAATACGACACACAT
* *
468610 GGTGCCT-AATACGACACATAT
1 AGTGCCTGAATACGACACACAT
468631 AGTGCCTGA
1 AGTGCCTGA
468640 TCGGCAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (22 bp):
AGTGCCTGAATACGACACACAT
Found at i:469129 original size:17 final size:18
Alignment explanation
Indices: 469095--469130 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
469085 TGAATTTTTA
469095 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
469113 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
469130 T
1 T
469131 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:469614 original size:3 final size:3
Alignment explanation
Indices: 469599--469644 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
469589 ATATATTAGT
* *
469599 TAA TAA TAT TAA TAA TAA TACA TTA TAA TAA T-A TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
469643 TA
1 TA
469645 TTTAATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:469645 original size:13 final size:13
Alignment explanation
Indices: 469599--469645 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
469589 ATATATTAGT
*
469599 TAATAATATTA-A
1 TAATAATATAATA
* *
469611 TAATAATACATTA
1 TAATAATATAATA
469624 TAATAATATAATA
1 TAATAATATAATA
469637 TAATAATAT
1 TAATAATAT
469646 TTAATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:471707 original size:22 final size:24
Alignment explanation
Indices: 471679--471738 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
471669 TTAAGGAAAC
471679 GAACTGT-GTTGCA-TAATACTGT
1 GAACTGTAGTTGCAGTAATACTGT
* *
471701 GAACTGTATTTGTAGTAATACTGT
1 GAACTGTAGTTGCAGTAATACTGT
* *
471725 GAATTGTATTTGCA
1 GAACTGTAGTTGCA
471739 AAAATGTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.22
23 4 0.12
24 21 0.66
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (24 bp):
GAACTGTAGTTGCAGTAATACTGT
Found at i:471924 original size:24 final size:24
Alignment explanation
Indices: 471843--471933 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
471833 GAATATCGCA
* ***
471843 AACTGTATTTGCAGAAATGTTGCG
1 AACTGTATTTACAGAAATGTAATG
* * * *
471867 AACTGTATTTGCA-AAATTTTATTTT
1 AACTGTATTTACAGAAA-TGTA-ATG
471892 AACTGTATTTACAGAAATGTAATG
1 AACTGTATTTACAGAAATGTAATG
*
471916 AACTGTATTTACACAAAT
1 AACTGTATTTACAGAAAT
471934 TCCGTGAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.06
24 33 0.61
25 15 0.28
26 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (24 bp):
AACTGTATTTACAGAAATGTAATG
Found at i:472093 original size:47 final size:47
Alignment explanation
Indices: 471968--472122 Score: 156
Period size: 46 Copynumber: 3.3 Consensus size: 47
471958 CTGTGAATTG
* * *
471968 TATTTGCATAAATG-TCGCAAATTGTATCGTAGAACATTACGAACTA
1 TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
* * * * * *
472014 TATTTACA-AAA-ACATCGTGAACTGTTTTGTAGAATTATTGCGAACTA
1 TATTTGCATAAATGC-TCGCGAATTGTATCGTAGAA-TATTGCGAACTA
* *
472061 TATTTGCATAAATGCT-GCGAATTGTATCGTAGAATATTGCGAATTG
1 TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
*
472107 TTTTTGCATAAATGCT
1 TATTTGCATAAATGCT
472123 GCAAACTGTA
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
45 3 0.03
46 47 0.55
47 31 0.36
48 4 0.05
49 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (47 bp):
TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
Found at i:472113 original size:46 final size:47
Alignment explanation
Indices: 471949--472133 Score: 148
Period size: 46 Copynumber: 4.0 Consensus size: 47
471939 GAATTGTTCT
* * * * *
471949 GTAGAATTACTGTGAATTGTATTTGCATAAATG-TCGCAAATTGTATC
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCT-GCAAACTGTATC
* * * * * *
471996 GTAGAA-CATTACGAACTATATTTACAAAAACAT-CGTG--AACTGTTTT
1 GTAGAATTATTGCGAACTATATTTGC-ATAA-ATGC-TGCAAACTGTATC
* *
472042 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCGAATTGTATC
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTATC
* * *
472089 GTAGAA-TATTGCGAATTGTTTTTGCATAAATGCTGCAAACTGTAT
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTAT
472134 TTACAGAAAT
Statistics
Matches: 107, Mismatches: 23, Indels: 17
0.73 0.16 0.12
Matches are distributed among these distances:
45 4 0.04
46 62 0.58
47 37 0.35
48 3 0.03
49 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (47 bp):
GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTATC
Found at i:472569 original size:54 final size:54
Alignment explanation
Indices: 472358--472772 Score: 316
Period size: 54 Copynumber: 7.9 Consensus size: 54
472348 ACAAACCGTA
* * * * *
472358 AGATTCGTAAAATCTCAAAAGT---AGGTCGTGATTGTATATCAACGGACAAGG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * *
472409 AGATTCGTAAAAT-TTAGAAAGTAGAAGGACATGATCT-TAAATCAGCGAACCATG
1 AGATTCGTAAAATCTCA-AAAGTAGAAGGTCATGAT-TGTAAATCAGCGGACCATG
* * * *
472463 AGATTCGTGAAATCTC----G-A-AAGGTCATGATTGTAAATTAGCAGACCGTG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * ** *
472511 AGATTCGTAAAATCTCAAAAGTTGAAGGTCGTGATCGTAAATCAATGGACCATA
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * ** ** *
472565 AGATTCCTAAAATCTCAAAAGTAGAAGGTCATGATCGTAAACCAGCAAACGGTT
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* ** *
472619 AGATTCGTAAAATCTCGAAAGTAGAAGG-CAATGATTGTAAATCAGTAGACTATG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTC-ATGATTGTAAATCAGCGGACCATG
** * ** * * * *
472673 ACCTTTGTAAAATCTCGAAAA-TAGAAGGTTGTGATTGTAAATCAGTGAACCGTA
1 AGATTCGTAAAATCTC-AAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * *
472727 AGATTCATAAAATTTCTAATGTAGAAGGTCATGATTGTAAATCAGC
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGC
472773 ATGACAACCC
Statistics
Matches: 281, Mismatches: 66, Indels: 31
0.74 0.17 0.08
Matches are distributed among these distances:
47 1 0.00
48 38 0.14
49 1 0.00
50 3 0.01
51 18 0.06
52 1 0.00
53 3 0.01
54 211 0.75
55 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (54 bp):
AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
Found at i:477153 original size:31 final size:31
Alignment explanation
Indices: 477118--477191 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
477108 TCAAATAACT
477118 AAGTACTAATTTGAACCACAGAA-CCAAATTC
1 AAGTACTAATTTGAACCA-AGAAGCCAAATTC
* * * *
477149 AAGTACCAATTTGAATCAAGAAGCTAAGTTC
1 AAGTACTAATTTGAACCAAGAAGCCAAATTC
477180 AAGTATCTAATT
1 AAGTA-CTAATT
477192 GGACCAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 27 0.75
32 5 0.14
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (31 bp):
AAGTACTAATTTGAACCAAGAAGCCAAATTC
Found at i:478515 original size:22 final size:21
Alignment explanation
Indices: 478481--478521 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
478471 TTTCCCCCCC
*
478481 AATTGATAGAAAATGAAAAAAA
1 AATTGAAAGAAAA-GAAAAAAA
*
478503 AATTGAAATAAAAGAAAAA
1 AATTGAAAGAAAAGAAAAA
478522 CAGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
AATTGAAAGAAAAGAAAAAAA
Found at i:478830 original size:13 final size:13
Alignment explanation
Indices: 478812--478843 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
478802 CTTTCTAGCC
478812 TTCTACTTTTCCA
1 TTCTACTTTTCCA
478825 TTCTACTTTTCCA
1 TTCTACTTTTCCA
*
478838 CTCTAC
1 TTCTAC
478844 CAAACACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCTACTTTTCCA
Found at i:485707 original size:18 final size:19
Alignment explanation
Indices: 485667--485710 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
485657 GATTAAGTTA
485667 AAAATGTTTTAATTATGATT
1 AAAAT-TTTTAATTATGATT
*
485687 AAAATTTTTAATTATTA-T
1 AAAATTTTTAATTATGATT
485705 AAAATT
1 AAAATT
485711 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AAAATTTTTAATTATGATT
Found at i:486600 original size:18 final size:19
Alignment explanation
Indices: 486574--486617 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
486564 TATTCTTTAG
486574 AATTTTTTT-AAAAATATA
1 AATTTTTTTAAAAAATATA
486592 TAATTTTTTTAAAAAATATA
1 -AATTTTTTTAAAAAATATA
486612 AATTTT
1 AATTTT
486618 GGAATTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTTTTAAAAAATATA
Found at i:486655 original size:18 final size:18
Alignment explanation
Indices: 486632--486676 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
486622 TTTTTCTAAA
486632 TATTTTGAATTTAAAAAT
1 TATTTTGAATTTAAAAAT
* *
486650 TATTTTAAAATTTGAAAAT
1 TATTTT-GAATTTAAAAAT
486669 TATTTTGA
1 TATTTTGA
486677 TTCTTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TATTTTGAATTTAAAAAT
Found at i:488514 original size:30 final size:31
Alignment explanation
Indices: 488478--488546 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
488468 TGATTTCAAT
488478 TCAGTCACTCAACT-TT-CAAAAAA-TGACAAA
1 TCAGTCACT-AA-TGTTACAAAAAAGTGACAAA
*
488508 TCAGTCACTAATGTTATAAAAAAGTGACAAA
1 TCAGTCACTAATGTTACAAAAAAGTGACAAA
488539 TCAGTCAC
1 TCAGTCAC
488547 CCACAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 15 0.43
31 15 0.43
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (31 bp):
TCAGTCACTAATGTTACAAAAAAGTGACAAA
Found at i:490316 original size:21 final size:21
Alignment explanation
Indices: 490290--490416 Score: 105
Period size: 21 Copynumber: 6.0 Consensus size: 21
490280 TTTGGGTGGA
**
490290 TCAGCTTTCATAAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
490311 TCAGCTTTCACGAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
*
490332 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
* * *
490353 TTAGCTCTT-ACGAGTTTTTGT
1 TCAGCT-TTCACGAGCTTCTGT
* * * **
490374 TTAGCTTTTATGATTTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
* *
490395 TCAG-TTCTTATGAGCTTCTGT
1 TCAGCTT-TCACGAGCTTCTGT
490416 T
1 T
490417 GGAGTGTTCG
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
20 4 0.04
21 85 0.94
22 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TCAGCTTTCACGAGCTTCTGT
Found at i:500397 original size:2 final size:2
Alignment explanation
Indices: 500379--500413 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
500369 AGTTATATGT
*
500379 TA TA T- TA TA TT 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
500414 GTGAACTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:507845 original size:25 final size:24
Alignment explanation
Indices: 507794--507844 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
507784 TTGAATATTA
* *
507794 TTTAATATTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTATATAAT
507818 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTATATAAT
507842 TTT
1 TTT
507845 TTATAGCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTATATAAT
Found at i:509197 original size:42 final size:42
Alignment explanation
Indices: 509138--509234 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
509128 GCCCGTGTGG
* *
509138 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCTGTGTC
1 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
509180 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
1 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
509222 TCAGGCCGTGTGG
1 TCAGGCCGTGTGG
509235 GCTTTCGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.21, C:0.31, G:0.30, T:0.19
Consensus pattern (42 bp):
TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
Found at i:510417 original size:33 final size:34
Alignment explanation
Indices: 510362--510437 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
510352 TGGCCCTACC
* * * *
510362 ATGGTCTTA-CATTCGTAGTGCCATAACCCAATT
1 ATGGTCTTATCATTAGTAATGCCACAACCCAACT
* *
510395 ATGGTCTTATCATTAG-AATGCCACAGCCCAGCT
1 ATGGTCTTATCATTAGTAATGCCACAACCCAACT
510428 ATGGTCTTAT
1 ATGGTCTTAT
510438 GTGCAAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 31 0.86
34 5 0.14
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (34 bp):
ATGGTCTTATCATTAGTAATGCCACAACCCAACT
Found at i:510978 original size:19 final size:20
Alignment explanation
Indices: 510949--510989 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
510939 CATAATTTCC
510949 ATGTATCAACATATCAAGAT
1 ATGTATCAACATATCAAGAT
510969 ATGTAT-AACATATCAAGAT
1 ATGTATCAACATATCAAGAT
510988 AT
1 AT
510990 TAATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (20 bp):
ATGTATCAACATATCAAGAT
Found at i:511015 original size:12 final size:12
Alignment explanation
Indices: 510998--511032 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
510988 ATTAATATAT
510998 ATACATATCATG
1 ATACATATCATG
511010 ATACATATCATG
1 ATACATATCATG
511022 ATACATATCAT
1 ATACATATCAT
511033 TCTCTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (12 bp):
ATACATATCATG
Found at i:511177 original size:21 final size:21
Alignment explanation
Indices: 511153--511211 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
511143 CAAAAACTTG
*
511153 TAAGAGCTGAACAGAAACTCA
1 TAAGAGCTAAACAGAAACTCA
* *
511174 TAAGAGTTAAACAGAAGCTCGA
1 TAAGAGCTAAACAGAAACTC-A
*
511196 -AAGAACTAAACAGAAA
1 TAAGAGCTAAACAGAAA
511212 GTAAAACATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.19, T:0.14
Consensus pattern (21 bp):
TAAGAGCTAAACAGAAACTCA
Found at i:516218 original size:127 final size:126
Alignment explanation
Indices: 515989--516509 Score: 619
Period size: 127 Copynumber: 4.2 Consensus size: 126
515979 TAAGGCCAAG
* * * *
515989 CAGAAACTATTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCTGTAATTTTGCTGACAGTGC
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
516054 ATCTTGCTTAAAGCGTTTTTGGCACTATTTTTTCAGAATAGCCTTCTCAAAATTATTTTTT
66 ATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * *
516115 CA-AGAACTACTGTATAAAAAGAGCGTCTACATGGGAGCTTTTTTCAGTAATTTTTGTTGACAGT
1 CAGA-AACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAA-TTTTGCTGACAGT
* * *
516179 GCAT-TCTGCTTGAAGCGTTTTTAACACTATTTTTTCAGAACCGTCTTTTCAAAATTATTTTTT
64 GCATCT-TGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * * * *
516242 CGGAAACTATTGTAAAAAAAGAGCGTCCACGTGGGAGGTTTTTT-AGTAATTTTGCTGACAGTGC
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * * *
516306 ATCATGTTTGAAGCGTTTTTGACA-TAATTTTTTTTAGAAT-TTCTTCT--TAATTATTTTTT
66 ATCTTGCTTGAAGCGTTTTTGACACT-A-TTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * * * *
516365 CAGAAACTACTATAGAAAAATAACGTCCA-AGTGGGAG-TTTTTTCAGTACTTTTGCTAACAGTG
1 CAGAAACTACTGTAGAAAAAGAGCGTCCACA-TGGGAGCTTTTTTCAGTAATTTTGCTGACAGTG
* * * *
516428 CATCTTGCTTGAAGCGTTTTTGTCACTATTTTTTCATAATCGTTTTCTCAAAATTAATTTTT
65 CATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
*
516490 CAGAAACTACTATAGAAAAA
1 CAGAAACTACTGTAGAAAAA
516510 AAAAAATACA
Statistics
Matches: 335, Mismatches: 47, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
122 16 0.05
123 85 0.25
124 2 0.01
125 71 0.21
126 58 0.17
127 102 0.30
128 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (126 bp):
CAGAAACTACTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTT
Found at i:516706 original size:27 final size:28
Alignment explanation
Indices: 516669--516746 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
516659 TTAATTAATG
* *
516669 TTTTTT-AAAT-CTTAAACCCTGATTTA
1 TTTTTTAAAATCCCTAAACCCTAATTTA
*
516695 TTTTTTAAAATCCCCAAACCCTAATTTA
1 TTTTTTAAAATCCCTAAACCCTAATTTA
516723 TTTTTTAAAATCCCTAAACCCTAA
1 TTTTTTAAAATCCCTAAACCCTAA
516747 ATAAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.13
27 4 0.09
28 36 0.78
ACGTcount: A:0.35, C:0.22, G:0.01, T:0.42
Consensus pattern (28 bp):
TTTTTTAAAATCCCTAAACCCTAATTTA
Found at i:522538 original size:10 final size:11
Alignment explanation
Indices: 522483--522569 Score: 79
Period size: 11 Copynumber: 7.9 Consensus size: 11
522473 TTTTGTAGGT
522483 TTTTGGTGCTG
1 TTTTGGTGCTG
* *
522494 TTTTGTTGTTG
1 TTTTGGTGCTG
* *
522505 TTGGTGATGCTG
1 TT-TTGGTGCTG
*
522517 TTTTTTGTGCTG
1 -TTTTGGTGCTG
522529 -TTTGGTGCTG
1 TTTTGGTGCTG
*
522539 TTTTGATGCTG
1 TTTTGGTGCTG
*
522550 TTTTGGTGTTG
1 TTTTGGTGCTG
522561 TTTT-GTGCT
1 TTTTGGTGCT
522570 ACTTTTTGTG
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
10 13 0.22
11 33 0.55
12 12 0.20
13 2 0.03
ACGTcount: A:0.02, C:0.07, G:0.32, T:0.59
Consensus pattern (11 bp):
TTTTGGTGCTG
Found at i:522575 original size:22 final size:22
Alignment explanation
Indices: 522529--522586 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
522519 TTTTGTGCTG
*
522529 TTTGGTGCTGTTTTGATGCTGT
1 TTTGGTGCTGTTTTGATGCTCT
*
522551 TTTGGTGTTGTTTTG-TGCTACT
1 TTTGGTGCTGTTTTGATGCT-CT
* *
522573 TTTTGTGGTGTTTT
1 TTTGGTGCTGTTTT
522587 ATTGTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.03, C:0.07, G:0.29, T:0.60
Consensus pattern (22 bp):
TTTGGTGCTGTTTTGATGCTCT
Found at i:523114 original size:3 final size:3
Alignment explanation
Indices: 523100--523130 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
523090 CCAATAAATA
*
523100 ATG ATG ACG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
523131 AAACAAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:524905 original size:29 final size:30
Alignment explanation
Indices: 524873--524938 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
524863 TATCGTTATC
524873 TTTTAATAAAATTTATATAATTTTTAAT-T
1 TTTTAATAAAATTTATATAATTTTTAATAT
* * * *
524902 TTTTTATAAATTTTTTATGATTTTTAATAAT
1 TTTTAATAAAATTTATATAATTTTTAAT-AT
524933 TTTTAA
1 TTTTAA
524939 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 24 0.80
31 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTAATAAAATTTATATAATTTTTAATAT
Found at i:524907 original size:20 final size:20
Alignment explanation
Indices: 524884--524943 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
524874 TTTAATAAAA
524884 TTTATATAATTTTTAATTTT
1 TTTATATAATTTTTAATTTT
* *
524904 TTTATA-AATTTTTTATGATT
1 TTTATATAATTTTTAAT-TTT
524924 TTTA-ATAATTTTTAAATTTT
1 TTTATATAATTTTT-AATTTT
524944 AAAAAGACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 10 0.30
20 21 0.64
21 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATATAATTTTTAATTTT
Found at i:524937 original size:10 final size:10
Alignment explanation
Indices: 524873--524938 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
524863 TATCGTTATC
*
524873 TTTTAATAAA
1 TTTTAATAAT
*
524883 ATTTATATAAT
1 TTTTA-ATAAT
524894 TTTTAAT--T
1 TTTTAATAAT
*
524902 TTTTTATAAAT
1 TTTTAAT-AAT
* *
524913 TTTTTATGAT
1 TTTTAATAAT
524923 TTTTAATAAT
1 TTTTAATAAT
524933 TTTTAA
1 TTTTAA
524939 ATTTTAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
8 7 0.16
10 22 0.49
11 16 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:524973 original size:7 final size:7
Alignment explanation
Indices: 524961--524986 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
524951 CTTAATTGAT
524961 TTTTAAA
1 TTTTAAA
524968 TTTTAAA
1 TTTTAAA
524975 TTTTAAA
1 TTTTAAA
524982 TTTTA
1 TTTTA
524987 GTCTTATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:526589 original size:2 final size:2
Alignment explanation
Indices: 526582--526620 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
526572 CCAATACATC
526582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
526621 ACATTTTCAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:533772 original size:15 final size:15
Alignment explanation
Indices: 533752--533804 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
533742 TTAGCTAAAT
533752 TTAAAATTATAAAAA
1 TTAAAATTATAAAAA
*
533767 TTAAAAATTTTAAAAA
1 TT-AAAATTATAAAAA
*
533783 ATAAAATTATAAAAA
1 TTAAAATTATAAAAA
533798 -TAAAATT
1 TTAAAATT
533805 TAACATAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 13 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATTATAAAAA
Found at i:533773 original size:16 final size:16
Alignment explanation
Indices: 533748--533802 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
533738 TATTTTAGCT
*
533748 AAATTTAAAATTATAA
1 AAATTAAAAATTATAA
*
533764 AAATTAAAAATTTTAA
1 AAATTAAAAATTATAA
*
533780 AAAAT-AAAATTATAA
1 AAATTAAAAATTATAA
533795 AAA-TAAAA
1 AAATTAAAA
533803 TTTAACATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 1 0.03
15 15 0.44
16 18 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAAATTATAA
Found at i:533917 original size:16 final size:16
Alignment explanation
Indices: 533896--533926 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
533886 AATTAAAATG
533896 CATTCATATCACCAAC
1 CATTCATATCACCAAC
533912 CATTCATATCACCAA
1 CATTCATATCACCAA
533927 TATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
CATTCATATCACCAAC
Found at i:536601 original size:14 final size:15
Alignment explanation
Indices: 536579--536655 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
536569 CATCCAAACG
536579 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
536593 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
536608 ACAGAAAAATAAAACATTTT
1 CCAG-AAAAT----CATTTT
536628 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
536642 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
536656 ACTGGCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 12 0.24
16 4 0.08
18 5 0.10
20 8 0.16
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:536639 original size:34 final size:35
Alignment explanation
Indices: 536583--536649 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
536573 CAAACGCCAG
* *
536583 AAAATATTTTCCAGTAAATCATTTTACAGAAAAAT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAAT
*
536618 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
536650 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAAT
Found at i:538277 original size:14 final size:14
Alignment explanation
Indices: 538258--538284 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
538248 CAGAAGTTGG
538258 GAAATTGGGGAAAA
1 GAAATTGGGGAAAA
538272 GAAATTGGGGAAA
1 GAAATTGGGGAAA
538285 TCTAATTTGG
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:0.48, C:0.00, G:0.37, T:0.15
Consensus pattern (14 bp):
GAAATTGGGGAAAA
Found at i:538602 original size:10 final size:11
Alignment explanation
Indices: 538580--538604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
538570 GTTGCTAAGC
538580 TTTAAATTTTT
1 TTTAAATTTTT
538591 TTTAAATTTTT
1 TTTAAATTTTT
538602 TTT
1 TTT
538605 CTCTGATAAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTAAATTTTT
Found at i:539069 original size:41 final size:42
Alignment explanation
Indices: 539002--539100 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 42
538992 TAAAATAATT
** *
539002 TTTTGCGGCGTTTTTCTCATGTACGCCGCTACT-GCT-TAACC
1 TTTTGCGGCGTTTTTCTCATAAACGCCACTA-TAGCTCTAACC
* * *
539043 TTTTGCGGCATTTTTCTCATAAACGCCATTATAGCTCTAATC
1 TTTTGCGGCGTTTTTCTCATAAACGCCACTATAGCTCTAACC
539085 TTTTGCGGCGTTTTTC
1 TTTTGCGGCGTTTTTC
539101 GATTAGCGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.02
41 29 0.59
42 19 0.39
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.42
Consensus pattern (42 bp):
TTTTGCGGCGTTTTTCTCATAAACGCCACTATAGCTCTAACC
Found at i:539507 original size:34 final size:37
Alignment explanation
Indices: 539464--539531 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
539454 GATGTTGTTT
*
539464 TTAATAA-TTTTAATTTATTAT-TAT-TTTATAATTC
1 TTAATAATTTTTAATTAATTATCTATGTTTATAATTC
*
539498 TTAATAATTTTTAATTAATTCTCTATGTTTATAA
1 TTAATAATTTTTAATTAATTATCTATGTTTATAA
539532 ATATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 7 0.24
35 12 0.41
36 3 0.10
37 7 0.24
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (37 bp):
TTAATAATTTTTAATTAATTATCTATGTTTATAATTC
Found at i:555572 original size:17 final size:17
Alignment explanation
Indices: 555536--555583 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
555526 CATTGTCCCC
* *
555536 AATGTACTGAC-ATTAA
1 AATGTAATGACAATAAA
555552 AATGTAATGACAATAAA
1 AATGTAATGACAATAAA
* *
555569 AATGAAATTACAATA
1 AATGTAATGACAATA
555584 TATACTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (17 bp):
AATGTAATGACAATAAA
Found at i:566179 original size:45 final size:45
Alignment explanation
Indices: 566128--566217 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
566118 TTGCTTGCAA
*
566128 ACATCACAAATCTCTCAAGGTTAGTAATTTCACATATACGAAAAC
1 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
566173 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
1 ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
566218 GTGTAACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (45 bp):
ACATCACAAATCTCACAAGGTTAGTAATTTCACATATACGAAAAC
Found at i:566517 original size:25 final size:25
Alignment explanation
Indices: 566485--566552 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
566475 ACATAAGAAT
* *
566485 AATGCTCACACAAGCTGTAATTGTA
1 AATGCTCACACAAGCTGTAACTATA
* ** *
566510 ATTGCTCACATGAGTTGTAACTATA
1 AATGCTCACACAAGCTGTAACTATA
566535 AATGCTCACACAAGCTGT
1 AATGCTCACACAAGCTGT
566553 GAAATGGGAC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (25 bp):
AATGCTCACACAAGCTGTAACTATA
Found at i:577061 original size:4 final size:4
Alignment explanation
Indices: 577052--577137 Score: 99
Period size: 4 Copynumber: 21.5 Consensus size: 4
577042 TAAATTAAGA
577052 AATT AATT AATT AA-- AATT AATT AATT AAATT AATT AA-- AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT -AATT AATT AATT AATT AATT
*
577097 AATT AAATT AATT AAATT AATT AATT AAATT AATT GATT AA
1 AATT -AATT AATT -AATT AATT AATT -AATT AATT AATT AA
577138 AAATATTTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
2 4 0.06
4 52 0.72
5 16 0.22
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (4 bp):
AATT
Found at i:577083 original size:13 final size:13
Alignment explanation
Indices: 577051--577138 Score: 109
Period size: 13 Copynumber: 7.2 Consensus size: 13
577041 TTAAATTAAG
577051 AAATTAATTAATT
1 AAATTAATTAATT
577064 AAAATTAATTAATT
1 -AAATTAATTAATT
577078 AAATTAATT-A--
1 AAATTAATTAATT
577088 AAATTAATTAATT
1 AAATTAATTAATT
577101 --A--AATTAATT
1 AAATTAATTAATT
577110 AAATTAATTAATT
1 AAATTAATTAATT
*
577123 AAATTAATTGATT
1 AAATTAATTAATT
577136 AAA
1 AAA
577139 AATATTTATT
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
9 8 0.12
10 9 0.14
11 3 0.05
12 1 0.02
13 32 0.48
14 13 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:577084 original size:9 final size:9
Alignment explanation
Indices: 577035--577138 Score: 93
Period size: 9 Copynumber: 12.3 Consensus size: 9
577025 CGAATTGAGA
577035 AAATT-ATT
1 AAATTAATT
*
577043 AAATTAA-G
1 AAATTAATT
577051 AAATTAATT
1 AAATTAATT
577060 -AATTAAAATT
1 AAATT--AATT
577070 -AATTAATT
1 AAATTAATT
577078 AAATTAATT
1 AAATTAATT
577087 -AA--AATT
1 AAATTAATT
577093 -AATTAATT
1 AAATTAATT
577101 AAATTAATT
1 AAATTAATT
577110 AAATTAATT
1 AAATTAATT
577119 -AATTAAATT
1 AAATT-AATT
*
577128 -AATTGATT
1 AAATTAATT
577136 AAA
1 AAA
577139 AATATTTATT
Statistics
Matches: 83, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
6 6 0.07
8 33 0.40
9 36 0.43
10 8 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:579015 original size:13 final size:13
Alignment explanation
Indices: 578993--579022 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
578983 GTTAAGAAAA
*
578993 TAATTGAATTAAT
1 TAATTAAATTAAT
579006 TAATTAAATTAAT
1 TAATTAAATTAAT
579019 TAAT
1 TAAT
579023 ATTATGGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:584814 original size:19 final size:18
Alignment explanation
Indices: 584779--584814 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
584769 TTGCTATGTT
*
584779 ATTTTATATTATGTTTAA
1 ATTTTATATTATATTTAA
584797 ATTTTATGATTATATTTA
1 ATTTTAT-ATTATATTTA
584815 TTAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATTTTATATTATATTTAA
Found at i:588296 original size:33 final size:33
Alignment explanation
Indices: 588254--588330 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
588244 TGACATTCAC
**
588254 AGAGTAAGTCTATTAGGATAATAAACACAGCAT
1 AGAGTAAGTCTATTAGGATAATAAACACAAAAT
* * *
588287 AGAGTAAGTCGATTCGGATAGTAAACACAAAAT
1 AGAGTAAGTCTATTAGGATAATAAACACAAAAT
*
588320 AGATTAAGTCT
1 AGAGTAAGTCT
588331 GACAGGACAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (33 bp):
AGAGTAAGTCTATTAGGATAATAAACACAAAAT
Found at i:590516 original size:21 final size:21
Alignment explanation
Indices: 590490--590536 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
590480 TCAAAGCAGT
* *
590490 GGTATCGCGAGATCCCCTTAG
1 GGTATCACGAGATCCCCCTAG
*
590511 GGTATCACTAGATCCCCCTAG
1 GGTATCACGAGATCCCCCTAG
590532 GGTAT
1 GGTAT
590537 TGCAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTATCACGAGATCCCCCTAG
Found at i:594099 original size:21 final size:21
Alignment explanation
Indices: 594075--594115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
594065 ATTTTAGGAA
594075 AATTATTTAATATGAAAAATT
1 AATTATTTAATATGAAAAATT
* * *
594096 AATTGTTTAATTTGGAAAAT
1 AATTATTTAATATGAAAAAT
594116 AGAGAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
AATTATTTAATATGAAAAATT
Found at i:598168 original size:22 final size:23
Alignment explanation
Indices: 598129--598171 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
598119 ATAGAACAAG
598129 TGAAAAAATCATTAAATTTTCTA
1 TGAAAAAATCATTAAATTTTCTA
*
598152 TGAAAAACTCATT-AATTTTC
1 TGAAAAAATCATTAAATTTTC
598172 AGAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (23 bp):
TGAAAAAATCATTAAATTTTCTA
Found at i:613914 original size:26 final size:26
Alignment explanation
Indices: 613879--613953 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
613869 ACATATATTG
613879 TTACTGGCAGCTTTGCTGCGATACTGA
1 TTACTGGCAGCTTTGCTGCGATACT-A
* **
613906 -TACTAGCAGCTTCACTGCGATACTA
1 TTACTGGCAGCTTTGCTGCGATACTA
*
613931 TTACTGGCAACTTTGCTGCGATA
1 TTACTGGCAGCTTTGCTGCGATA
613954 TTGGTGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGATACTA
Found at i:619185 original size:15 final size:15
Alignment explanation
Indices: 619165--619194 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
619155 TTTCCCATTG
619165 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
619180 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
619195 ATACAATTTC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:631603 original size:61 final size:62
Alignment explanation
Indices: 631481--631603 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 62
631471 AGCACACTGC
631481 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
1 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
* * * * ** * * *
631543 AACTGGAAAGGCTATATAGAATATTGTTGC-AGTAGAATCAGATCATTTTGCTAATGGAAAT
1 AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
631604 GCTATAGCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
61 26 0.50
62 26 0.50
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (62 bp):
AACTGGAAAGGCTATACAAAATACTATTGCAAAAAAAATCAGATCAATTTGCTAATAGAAAT
Found at i:647282 original size:27 final size:27
Alignment explanation
Indices: 647244--647297 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
647234 AAGTGAAGGC
647244 CATAATTTGAATATGTCTTCTGCAATT
1 CATAATTTGAATATGTCTTCTGCAATT
647271 CATAATTTGAATATGTCTTCTGCAATT
1 CATAATTTGAATATGTCTTCTGCAATT
647298 AACTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (27 bp):
CATAATTTGAATATGTCTTCTGCAATT
Found at i:647490 original size:44 final size:44
Alignment explanation
Indices: 647382--647471 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
647372 TAATTGTAAT
* * * * *
647382 TTAAATTCTAATTATTTTTAAATGTGTATTTATCACAACTTCTA
1 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
*
647426 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTTTA
1 TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
647470 TT
1 TT
647472 TTATTTAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (44 bp):
TTAAATTATAACTATTTTTAAATATATAATTATCACAACTTCTA
Found at i:672011 original size:23 final size:23
Alignment explanation
Indices: 671985--672036 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
671975 TTGACTATTT
* *
671985 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
672008 CTGTAATACCCCAAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
*
672031 CAGTAA
1 CTGTAA
672037 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCAAAAATTACTA
Found at i:675214 original size:24 final size:25
Alignment explanation
Indices: 675182--675228 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
675172 GTGTATATGC
675182 ATGTCATAAAATTTATGA-TATAAGT
1 ATGTCATAAAA-TTATGATTATAAGT
*
675207 ATGT-ATAATATTATGATTATAA
1 ATGTCATAAAATTATGATTATAA
675229 TTATACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (25 bp):
ATGTCATAAAATTATGATTATAAGT
Found at i:676390 original size:30 final size:30
Alignment explanation
Indices: 676352--676434 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
676342 GAGAATATAA
* * * *
676352 TGCTCACACAAGCTGATAGTATATCAGGGT
1 TGCTCACACAAGCTAACAGTATAACAGAGT
* * *
676382 TTCTCACACAGGCTAACATTATAACAGAGT
1 TGCTCACACAAGCTAACAGTATAACAGAGT
*
676412 TGCTCACACAAGCTAACATTATA
1 TGCTCACACAAGCTAACAGTATA
676435 TTGAGACTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (30 bp):
TGCTCACACAAGCTAACAGTATAACAGAGT
Found at i:685222 original size:25 final size:25
Alignment explanation
Indices: 685194--685245 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
685184 CACTAATAGT
685194 GTGGAAAGAGTTGGGTGGTGGTTAG
1 GTGGAAAGAGTTGGGTGGTGGTTAG
685219 GTGGAAAGAGTTGGGTGGTGGTTAG
1 GTGGAAAGAGTTGGGTGGTGGTTAG
685244 GT
1 GT
685246 CAGATAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (25 bp):
GTGGAAAGAGTTGGGTGGTGGTTAG
Found at i:695608 original size:18 final size:18
Alignment explanation
Indices: 695585--695627 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
695575 TGCCAGATGC
* *
695585 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
695603 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
695621 GTTTCCT
1 GTATCCT
695628 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:695893 original size:21 final size:21
Alignment explanation
Indices: 695868--695915 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
695858 CCAACACCGA
695868 CAACCAG-ATCCCCTACCGGAG
1 CAACCAGAATCCCC-ACCGGAG
* *
695889 GAACCAGAATCCCCGCCGGAG
1 CAACCAGAATCCCCACCGGAG
695910 CAACCA
1 CAACCA
695916 CAACCCTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (21 bp):
CAACCAGAATCCCCACCGGAG
Found at i:695926 original size:21 final size:21
Alignment explanation
Indices: 695883--695929 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
695873 AGATCCCCTA
* *
695883 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAATCCCCG
695904 CCGGAGCAACCACAA-CCCTCG
1 CCGGAGCAACCACAATCCC-CG
695925 CCGGA
1 CCGGA
695930 AGCTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.28, C:0.43, G:0.26, T:0.04
Consensus pattern (21 bp):
CCGGAGCAACCACAATCCCCG
Found at i:696701 original size:96 final size:94
Alignment explanation
Indices: 696560--696852 Score: 347
Period size: 96 Copynumber: 3.1 Consensus size: 94
696550 AACCTCAAAT
*
696560 CCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTTAACCCTAATCTAATTTTTTAAAAA
1 CCTAATTTATTTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTAAAAA
696625 TCTATAATTAATTTAATCAAGTAACCCTAAAC
64 T-TATAATTAATTTAATCAAGTAACCCTAAAC
* * * *
696657 CCTAATTTATTTGATTTTTCCTTAAAAACCCTTAACTCTAAACCCTAATCTAACTTTTTAAAAAA
1 CCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTAAAAAT
* * *
696722 AATTAATTAAATTACTCAAGTAACCCTAAAC
65 TA-TAATTAATTTAATCAAGTAACCCTAAAC
* ** * * *
696753 CCTAATTTAATTT-ATTTTTTCTTAAAAAACAATAAACACGAAA-CCTAATCCAATTTTGAAAAA
1 CCTAATTT-ATTTGATTTTTACTT-AAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAA
** **
696816 TTATAATTAATTTAATTGACAAACCCTAAAC
64 TTATAATTAATTTAATCAAGTAACCCTAAAC
696847 CCTAAT
1 CCTAAT
696853 CCCTTATTTA
Statistics
Matches: 168, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
94 28 0.17
95 11 0.07
96 97 0.58
97 32 0.19
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.37
Consensus pattern (94 bp):
CCTAATTTATTTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAAAAATT
ATAATTAATTTAATCAAGTAACCCTAAAC
Found at i:698323 original size:22 final size:21
Alignment explanation
Indices: 698293--698333 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
698283 GATGATTTAT
698293 AAATATCAAAAATTTAAATAG
1 AAATATCAAAAATTTAAATAG
**
698314 AAATAATCAATTATTTAAAT
1 AAAT-ATCAAAAATTTAAAT
698334 TAGTCTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATCAAAAATTTAAATAG
Done.