Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold302
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: 592491
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.31
Warning! 22277 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:169483 original size:26 final size:26
Alignment explanation
Indices: 169412--169494 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 26
169402 CTTATCCATT
*
169412 GAACCAACAGGCTCACTCTTGACACA
1 GAACCAACAGGCTCATTCTTGACACA
169438 GATTAACGC-ACAGGCTCATTCTTGACACA
1 G---AAC-CAACAGGCTCATTCTTGACACA
*
169467 GAACCAACAGACTCATTCTTGACACA
1 GAACCAACAGGCTCATTCTTGACACA
169493 GA
1 GA
169495 TTAACGCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.02
26 25 0.50
29 23 0.46
30 1 0.02
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (26 bp):
GAACCAACAGGCTCATTCTTGACACA
Found at i:169911 original size:22 final size:22
Alignment explanation
Indices: 169886--169939 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
169876 CTCAAATCGA
* *
169886 GCATTTGACCCAAAAAATTAGG
1 GCATTCGAACCAAAAAATTAGG
*
169908 GCATTCGAACCAAAACATTAGG
1 GCATTCGAACCAAAAAATTAGG
169930 GCATTC-AACC
1 GCATTCGAACC
169940 CTTGCATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (22 bp):
GCATTCGAACCAAAAAATTAGG
Found at i:182543 original size:19 final size:18
Alignment explanation
Indices: 182520--182565 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
182510 TAATTTAGCC
*
182520 ATTTTTATTTCTATTATA
1 ATTTTTATTTCTAGTATA
182538 ATTTTTATTTCTAGTATA
1 ATTTTTATTTCTAGTATA
*
182556 AATTTTATTT
1 ATTTTTATTT
182566 TGTTTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTATTTCTAGTATA
Found at i:182575 original size:23 final size:23
Alignment explanation
Indices: 182540--182585 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
182530 CTATTATAAT
182540 TTTTATTTCTAGTATAAATTTTA
1 TTTTATTTCTAGTATAAATTTTA
* * * *
182563 TTTTGTTTTTAGTTTAATTTTTA
1 TTTTATTTCTAGTATAAATTTTA
182586 CATTCTAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTATTTCTAGTATAAATTTTA
Found at i:186523 original size:6 final size:6
Alignment explanation
Indices: 186514--186580 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
186504 TTTGTTTTCT
* * * *
186514 TTTTAG TTTTAG TTTTA- TTTTA- TGTCTA- TGATTAT TTTTAT TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG T-TTTAG T-TTTAG TTTTAG TTTTAG
186561 TTTTAG TTTTAG TTTTAG TT
1 TTTTAG TTTTAG TTTTAG TT
186581 GTTTTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 6 0.11
6 47 0.87
7 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.12, T:0.69
Consensus pattern (6 bp):
TTTTAG
Found at i:186591 original size:6 final size:6
Alignment explanation
Indices: 186508--186596 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
186498 ATTTTATTTG
* * * * * **
186508 TTTTCT TTTTAG TTTTAG TTTTA- TTTTAT GTCTAT GATTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
186555 TTTTAG TTTTAG TTTTAG TTTTAGTT GTTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT TTTTAT TTT
186597 CTTAGACTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
5 5 0.07
6 58 0.84
7 1 0.01
9 5 0.07
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:188196 original size:22 final size:23
Alignment explanation
Indices: 188170--188216 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
188160 TTCCTAATGA
* *
188170 ATGGCTCTC-CGAGCTTCCCGAT
1 ATGGCTCGCTCGAACTTCCCGAT
*
188192 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTCGAACTTCCCGAT
188215 AT
1 AT
188217 ATGGCTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (23 bp):
ATGGCTCGCTCGAACTTCCCGAT
Found at i:188234 original size:25 final size:23
Alignment explanation
Indices: 188180--188235 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
188170 ATGGCTCTCC
* *
188180 GAGCTTCCCGATATGGCTCGCTT
1 GAGCTTCCCGATATGGCTAGCTG
* *
188203 GAACTTCCCGATATATGGCTATCTG
1 GAGCTTCCCG--ATATGGCTAGCTG
188228 GAGCTTCC
1 GAGCTTCC
188236 TGATTAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 9 0.35
25 17 0.65
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (23 bp):
GAGCTTCCCGATATGGCTAGCTG
Found at i:191528 original size:30 final size:30
Alignment explanation
Indices: 191492--191580 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
191482 AGCTTCAGGG
* *
191492 GCCACACGGGTTGGGCACATGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
* *
191522 GCCACACGGGCTGGCCATACGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
191552 GCCACACGGGCTGGCCACATGCCCATGTG
1 GCCACACGGGCTGGCCACATGCCCATGTG
191581 CTAGCCCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (30 bp):
GCCACACGGGCTGGCCACATGCCCATGTGA
Found at i:203188 original size:14 final size:14
Alignment explanation
Indices: 203155--203191 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
203145 GCATGGTATG
*
203155 GGTTTATGGGTTTT
1 GGTTTATAGGTTTT
203169 GG-TTATAGGTTTT
1 GGTTTATAGGTTTT
203182 GGTTTATAGG
1 GGTTTATAGG
203192 CAAATGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (14 bp):
GGTTTATAGGTTTT
Found at i:210868 original size:2 final size:2
Alignment explanation
Indices: 210861--210885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
210851 GAGTAAAATT
210861 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
210886 GGTTTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212858 original size:23 final size:25
Alignment explanation
Indices: 212823--212874 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
212813 AAAAGGTAGC
212823 AAAATAGTGAAAAAAAATAACAA-G
1 AAAATAGTGAAAAAAAATAACAAGG
*
212847 AAAATAGT-AAAAAAAATAGCAAGG
1 AAAATAGTGAAAAAAAATAACAAGG
212871 AAAA
1 AAAA
212875 GCAGCAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.12
Consensus pattern (25 bp):
AAAATAGTGAAAAAAAATAACAAGG
Found at i:213230 original size:19 final size:20
Alignment explanation
Indices: 213206--213265 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
213196 ATTCTTTACA
213206 TTTTATAATTTTTTAC-AAT
1 TTTTATAATTTTTTACTAAT
* *
213225 TTTTAT-GTTTTTTTCTAAT
1 TTTTATAATTTTTTACTAAT
* *
213244 TTTTAATAACTTTTTAATAAT
1 TTTT-ATAATTTTTTACTAAT
213265 T
1 T
213266 GAATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.22
19 13 0.41
20 2 0.06
21 10 0.31
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTTTACTAAT
Found at i:213566 original size:92 final size:90
Alignment explanation
Indices: 213345--213577 Score: 274
Period size: 92 Copynumber: 2.5 Consensus size: 90
213335 AATTTTTAAT
*
213345 AAAAGTAGGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGA
1 AAAAG-AGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAG-CTTTTTGATGCATTTTGAAAGA
* * *
213410 TCAAGTGCCTAATTTGAGTGCAAAAAAA
63 TCAAGTACCCAATATGAGTGCAAAAAAA
* * **
213438 AATA-A-GGGCTTAATTTCTTTTTTTTTTTTAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAG
1 AAAAGAGGGGCTTAATTGC---TTTTTTTGAAAAGTTTGAGAG-CTTTTTGATGCATTTTGAAAG
*
213501 TTCAAGTACCCAA-ATGAGTGCAAAAAAA
62 ATCAAGTACCCAATATGAGTGCAAAAAAA
*
213529 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAATGTTTGAGTGCTTTTTG
1 AAAAG-AGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAGCTTTTTG
213578 CACCCTTAAG
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
90 11 0.09
91 35 0.30
92 47 0.40
93 14 0.12
94 11 0.09
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (90 bp):
AAAAGAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCTTTTTGATGCATTTTGAAAGATCA
AGTACCCAATATGAGTGCAAAAAAA
Found at i:216617 original size:27 final size:26
Alignment explanation
Indices: 216587--216642 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
216577 AGGCTATCCC
216587 TTCATAATT-CACCACAAAGGCATTCAT
1 TTCAT-ATTGCACCACAAAGGCATTC-T
* *
216614 TTCATATTGCGCCACAAAGGCTTTCT
1 TTCATATTGCACCACAAAGGCATTCT
216640 TTC
1 TTC
216643 TTTCCTGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
TTCATATTGCACCACAAAGGCATTCT
Found at i:218723 original size:34 final size:35
Alignment explanation
Indices: 218591--218722 Score: 101
Period size: 34 Copynumber: 3.8 Consensus size: 35
218581 AATATGACGC
* *
218591 ATTGGCGTTGTGGTGGGATATTGATT-AATGAAGT
1 ATTGGCGTTGTGGCGGGATATTAATTGAATGAAGT
** * * *
218625 -TCTGGCGTTGTGGCAAGATGTTGATTGAATGATGT
1 AT-TGGCGTTGTGGCGGGATATTAATTGAATGAAGT
** * * *
218660 ATCAGTGTTGTGGTGGAATGA-TAATTGAA-GAAGT
1 ATTGGCGTTGTGGCGGGAT-ATTAATTGAATGAAGT
*
218694 ATTGGTGTTGTGGCGGGATATTAATTGAA
1 ATTGGCGTTGTGGCGGGATATTAATTGAA
218723 GGAGGACTAG
Statistics
Matches: 74, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
33 2 0.03
34 47 0.64
35 24 0.32
36 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.34, T:0.36
Consensus pattern (35 bp):
ATTGGCGTTGTGGCGGGATATTAATTGAATGAAGT
Found at i:220878 original size:116 final size:123
Alignment explanation
Indices: 220748--220988 Score: 363
Period size: 129 Copynumber: 2.0 Consensus size: 123
220738 ATCATGTGTC
220748 ATAATTAATTTAATTAAGAGATTCA-T-T-AATAAAA-A-T-AAA-ATAATATTAAGTAAATTAA
1 ATAATTAATTTAATTAAGAGATTCATTATAAATAAAATACTAAAAGATAATATTAAGTAAATTAA
220806 TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATT-AAAAAAAGTGAAATT
66 TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGAAATT
220863 ATAATTTAATTTAATTAAGAGATTCATTAATAAAAATAAAATACTTAAAAGTGATAATATTAAGT
1 ATAA-TTAATTTAATTAAGAGATTCATT-AT--AAATAAAATAC-TAAAA--GATAATATTAAGT
220928 AAATTAATAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGA
59 AAATTAATAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGA
220989 GAATAATACA
Statistics
Matches: 111, Mismatches: 0, Indels: 15
0.88 0.00 0.12
Matches are distributed among these distances:
115 4 0.04
116 21 0.19
117 1 0.01
119 1 0.01
122 7 0.06
123 1 0.01
125 1 0.01
126 3 0.03
129 61 0.55
130 11 0.10
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.34
Consensus pattern (123 bp):
ATAATTAATTTAATTAAGAGATTCATTATAAATAAAATACTAAAAGATAATATTAAGTAAATTAA
TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGAAATT
Found at i:224231 original size:12 final size:12
Alignment explanation
Indices: 224214--224256 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
224204 TAAGGGAAGA
224214 GAGCCCAAGCAT
1 GAGCCCAAGCAT
*
224226 GAGCCCAAGTAT
1 GAGCCCAAGCAT
224238 GAGCCCAAGCAT
1 GAGCCCAAGCAT
224250 GAGCCCA
1 GAGCCCA
224257 GGTATGTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.09
Consensus pattern (12 bp):
GAGCCCAAGCAT
Found at i:224246 original size:24 final size:24
Alignment explanation
Indices: 224214--224262 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
224204 TAAGGGAAGA
224214 GAGCCCAAGCATGAGCCCAAGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
*
224238 GAGCCCAAGCATGAGCCCAGGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
224262 G
1 G
224263 TCGCCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.12
Consensus pattern (24 bp):
GAGCCCAAGCATGAGCCCAAGTAT
Found at i:230835 original size:19 final size:19
Alignment explanation
Indices: 230797--230835 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
230787 AAATAGTGAG
*
230797 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
230816 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
230835 A
1 A
230836 CAATTCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:233410 original size:13 final size:13
Alignment explanation
Indices: 233392--233426 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
233382 TTTAATTGGG
*
233392 TAATTAATTTAGT
1 TAATTAATTTAAT
*
233405 TAATTAAATTAAT
1 TAATTAATTTAAT
233418 TAATTAATT
1 TAATTAATT
233427 AATATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TAATTAATTTAAT
Found at i:235422 original size:43 final size:43
Alignment explanation
Indices: 235353--235469 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
235343 TTACAAACAA
* **
235353 AAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTT-TCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACG-TTTCTCCCAC
* **
235396 AAACGCCGCTAAAGAACATGACCTTTAGCGATGTTTCTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACGTTTCTCCCAC
* *
235439 AAACGCCGCAAAAGAACA-AACCTTTAGCGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGAC
235470 ACTTGTAGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 14 0.22
43 50 0.78
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGACGTTTCTCCCAC
Found at i:238020 original size:25 final size:25
Alignment explanation
Indices: 237992--238050 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
237982 ATCTCCCAAC
237992 AATTGATAAACCAATA-ATATGATCA
1 AATT-ATAAACCAATACATATGATCA
* **
238017 AATTATAACCCCTTACATATGATCA
1 AATTATAAACCAATACATATGATCA
238042 AATTATAAA
1 AATTATAAA
238051 TCACTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (25 bp):
AATTATAAACCAATACATATGATCA
Found at i:247327 original size:9 final size:9
Alignment explanation
Indices: 247313--247337 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
247303 GAAAACTAAC
247313 AACTAACTT
1 AACTAACTT
247322 AACTAACTT
1 AACTAACTT
247331 AACTAAC
1 AACTAAC
247338 AACTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (9 bp):
AACTAACTT
Found at i:251524 original size:26 final size:27
Alignment explanation
Indices: 251459--251521 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
251449 ATACGTCAGG
*
251459 AAAGGAAGCCTTTGTGGATAACTCTAA
1 AAAGGAAGCCTTTGTGGACAACTCTAA
* * *
251486 AAAGAAAGCCTTTGTGGCCAACTTTAA
1 AAAGGAAGCCTTTGTGGACAACTCTAA
251513 AAAGGAAGC
1 AAAGGAAGC
251522 TTTCATGGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGACAACTCTAA
Found at i:251530 original size:27 final size:27
Alignment explanation
Indices: 251459--251536 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
251449 ATACGTCAGG
* * **
251459 AAAGGAAGCCTTTGTGGATAACTCTAA
1 AAAGAAAGCCTTTATGGCCAACTCTAA
* *
251486 AAAGAAAGCCTTTGTGGCCAACTTTAA
1 AAAGAAAGCCTTTATGGCCAACTCTAA
* *
251513 AAAGGAAG-CTTTCATGGCGAACTC
1 AAAGAAAGCCTTT-ATGGCCAACTC
251537 CAAAGGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (27 bp):
AAAGAAAGCCTTTATGGCCAACTCTAA
Found at i:262318 original size:15 final size:15
Alignment explanation
Indices: 262298--262329 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
262288 AATTTCACTA
*
262298 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
262313 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
262328 TT
1 TT
262330 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:265819 original size:5 final size:5
Alignment explanation
Indices: 265805--265859 Score: 92
Period size: 5 Copynumber: 11.0 Consensus size: 5
265795 AATATATATA
* *
265805 TCAAT TCAAT CCAAT TCAAT TCAAT CCAAT TCAAT TCAAT TCAAT TCAAT
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT
265855 TCAAT
1 TCAAT
265860 AATCAATACA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:267171 original size:37 final size:37
Alignment explanation
Indices: 267130--267473 Score: 329
Period size: 37 Copynumber: 9.2 Consensus size: 37
267120 TTGAACAACT
* * *
267130 TTCAGTATATTTAGTAGACATTGCTCTTTTGAGCATG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
*
267167 TTCAGTATAATTAGTAGATATTGCT-TGTTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A-TG
* * * *
267205 TTCAATATAATCAGTAGACATTGCTCTTTTAAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
*
267242 TTTAGTATAATCAGTAGATATTGCT-TATTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A-TG
* * ** *
267280 TTCAGTATAATCAATAGACATTATTCTTTTGAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* *
267317 TTCAATATAATCAGTAGATATTGCTCGTTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGC-A-TG
* *
267355 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* * * * **
267392 TCCAGTATAATTAGAAGATATTGCTCGTTTGAGCACA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* * * *
267429 TTCAGTATAATAAGTAGATACTGCTCATTTGAGCATA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
267466 TTCAGTAT
1 TTCAGTAT
267474 TTAATCGATT
Statistics
Matches: 253, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
36 2 0.01
37 159 0.63
38 89 0.35
39 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (37 bp):
TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
Found at i:267249 original size:75 final size:75
Alignment explanation
Indices: 267116--267473 Score: 484
Period size: 75 Copynumber: 4.8 Consensus size: 75
267106 ACAATATCGT
* * * * *
267116 TCGTTTGAACAACTTTCAGTATATTTAGTAGACATTGCTCTTTTGAGCATGTTCAGTATAATTAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
267181 TAGATATTGC
66 TAGATATTGC
* * * *
267191 TTGTTTGAGCAACTTTCAATATAATCAGTAGACATTGCTCTTTTAAGCACGTTTAGTATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
267256 TAGATATTGC
66 TAGATATTGC
** * ** *
267266 TTATTTGAGCAACTTTCAGTATAATCAATAGACATTATTCTTTTGAGCACGTTCAATATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
267331 TAGATATTGC
66 TAGATATTGC
* *
267341 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAGTATAATTAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
*
267406 AAGATATTGC
66 TAGATATTGC
* * * * * **
267416 TCGTTTGAGC-ACATTCAGTATAATAAGTAGATACTGCTCATTTGAGCATATTCAGTAT
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTAT
267474 TTAATCGATT
Statistics
Matches: 249, Mismatches: 34, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
74 40 0.16
75 209 0.84
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (75 bp):
TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
TAGATATTGC
Found at i:271239 original size:37 final size:39
Alignment explanation
Indices: 271198--271293 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 39
271188 ATATTATTTT
271198 AATAGTTTAATATTAAATTTAAT-TT-AA-T-ACTTATCTA
1 AATAGTTTAATATT-AATTTAATATTAAAGTGA-TTATCTA
* *
271235 AATAGTATT-CTATTAATTTAATATTAAAGTGATTATCTT
1 AATAGT-TTAATATTAATTTAATATTAAAGTGATTATCTA
271274 AATA-TTTAAT-TTAATTTAAT
1 AATAGTTTAATATTAATTTAAT
271294 GTTTATCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
36 8 0.16
37 24 0.48
38 6 0.12
39 11 0.22
40 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (39 bp):
AATAGTTTAATATTAATTTAATATTAAAGTGATTATCTA
Found at i:271347 original size:62 final size:59
Alignment explanation
Indices: 271272--271519 Score: 244
Period size: 62 Copynumber: 3.9 Consensus size: 59
271262 AGTGATTATC
* * * * *
271272 TTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTATTTTAATAAGAT
*
271334 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATT-ATTT--TAAT-AA--G--
271399 TAT
58 -AT
* * * * *
271402 CTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 -TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTATTTTAATAAGAT
*
271465 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTATTTTAATA
271520 TTAAAGTCAT
Statistics
Matches: 155, Mismatches: 18, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
59 32 0.21
60 8 0.05
61 2 0.01
62 55 0.35
63 4 0.03
65 1 0.01
66 1 0.01
68 4 0.03
69 29 0.19
70 1 0.01
71 6 0.04
72 12 0.08
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTATTTTAATAAGAT
Found at i:271388 original size:32 final size:32
Alignment explanation
Indices: 271346--271521 Score: 87
Period size: 32 Copynumber: 5.4 Consensus size: 32
271336 AATATTAAAT
*
271346 TTAATCTAATATTTATCTTAATAAACATTATA
1 TTAATTTAATATTTATCTTAATAAACATTATA
* * * * *
271378 TTAATTTAATATTAAAGTGATTATCTTAATATT-TAA
1 TTAATTTAATATT-TA-T-CTTA-ATAAACATTAT-A
* * *
271414 TTTAATTTAATGTTTATCTTGTAGATAAATATTCTA
1 -TTAATTTAATATTTATC-T-TA-ATAAACATTATA
* ** *
271450 TTATTTTAATA-AGAT-TTAAT----ATTAAA
1 TTAATTTAATATTTATCTTAATAAACATTATA
*
271476 TTTAATCTAATATTTATCTTAATAAACATTATA
1 -TTAATTTAATATTTATCTTAATAAACATTATA
271509 TTAATTTAATATT
1 TTAATTTAATATT
271522 AAAGTCATTA
Statistics
Matches: 104, Mismatches: 24, Indels: 32
0.65 0.15 0.20
Matches are distributed among these distances:
26 4 0.04
27 9 0.09
28 2 0.02
29 5 0.05
30 2 0.02
31 2 0.02
32 25 0.24
33 6 0.06
34 3 0.03
35 15 0.14
36 18 0.17
37 13 0.12
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (32 bp):
TTAATTTAATATTTATCTTAATAAACATTATA
Found at i:271412 original size:131 final size:131
Alignment explanation
Indices: 271189--271531 Score: 602
Period size: 131 Copynumber: 2.6 Consensus size: 131
271179 TCAAAAATAA
* * * ** *
271189 TATTATTTTAAT-AG-TTTAATATTAAATTTAATTTAATACTTATCTAAAT-AGTATTCTATTAA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
271251 TTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATT
66 TTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATT
271316 C
131 C
271317 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
271382 TTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATT
66 TTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATT
271447 C
131 C
271448 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
1 TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
*
271513 TTTAATATTAAAGTCATTA
66 TTTAATATTAAAGTGATTA
271532 AGTTTAATCA
Statistics
Matches: 205, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
128 12 0.06
129 2 0.01
130 32 0.16
131 159 0.78
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (131 bp):
TATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAA
TTTAATATTAAAGTGATTATCTTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATT
C
Found at i:274932 original size:45 final size:45
Alignment explanation
Indices: 274863--274963 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
274853 GATGTGTTCG
* * *
274863 TATAACAGGTTTGGATATCGTAAATGAGCTTACACACGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
* * *
274908 TATAACAGATCTGGATATCATAAATGGGCTTGCACATGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
274953 TATAACAGATC
1 TATAACAGATC
274964 ACTCTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
Found at i:275579 original size:25 final size:25
Alignment explanation
Indices: 275540--275596 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
275530 TGCAAATTTT
275540 TTAAGAATTACAAAAAGTTAT-AAAAA
1 TTAA-AATTAC-AAAAGTTATCAAAAA
* *
275566 TTAAAATTATAAAATTTATCAAAAA
1 TTAAAATTACAAAAGTTATCAAAAA
*
275591 TAAAAA
1 TTAAAA
275597 ATGTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAATTACAAAAGTTATCAAAAA
Found at i:289377 original size:40 final size:40
Alignment explanation
Indices: 289333--289426 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 40
289323 GCTTCCTCAA
289333 GGACGCGATTTCCT-TCTACGT-CAG-CAGGTCGCGCTGACGT
1 GGACGCGATTTCCTGTC-ACGTCCAGACA--TCGCGCTGACGT
* *
289373 GGACGCGATGTCCTGTCACGTACCCTGACATCGCGCTGACGT
1 GGACGCGATTTCCTGTCACGT--CCAGACATCGCGCTGACGT
289415 GGACGCGATTTC
1 GGACGCGATTTC
289427 GGGGAAAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 17 0.37
41 2 0.04
42 23 0.50
43 2 0.04
44 2 0.04
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (40 bp):
GGACGCGATTTCCTGTCACGTCCAGACATCGCGCTGACGT
Found at i:297696 original size:6 final size:6
Alignment explanation
Indices: 297685--297712 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
297675 ACAGTGGAGG
297685 TTTGAC TTTGAC TTTGAC TTTGAC TTTG
1 TTTGAC TTTGAC TTTGAC TTTGAC TTTG
297713 GTCTCCGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (6 bp):
TTTGAC
Found at i:302071 original size:22 final size:21
Alignment explanation
Indices: 302022--302076 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
302012 AAATAATAAA
** *
302022 ATATTAAAAATATATTATTTT
1 ATATTAAATTTATATTATTTG
302043 ATATTAATATTTATA-TATTTG
1 ATATTAA-ATTTATATTATTTG
302064 ATATTTAAATTTA
1 ATA-TTAAATTTA
302077 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATTAAATTTATATTATTTG
Found at i:302278 original size:29 final size:30
Alignment explanation
Indices: 302237--302315 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
302227 AATTAAATCA
* * *
302237 AATCAAAATTTCAAGTATAAATTTATACA-T
1 AATC-AAATTTCATGTATAAAATTACACATT
*
302267 AATCAAAGTTCATGTATAAAATTACACATT
1 AATCAAATTTCATGTATAAAATTACACATT
302297 AGATCAAATTTCATGTATA
1 A-ATCAAATTTCATGTATA
302316 TTTTTGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.48
30 6 0.14
31 16 0.38
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (30 bp):
AATCAAATTTCATGTATAAAATTACACATT
Found at i:302397 original size:20 final size:21
Alignment explanation
Indices: 302355--302398 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
302345 GTATGTTTTA
*
302355 ATATTTACATTGTAATACTAT
1 ATATTTACATTGTAATACAAT
* *
302376 ATATTTA-ATTTTTATACAAT
1 ATATTTACATTGTAATACAAT
302396 ATA
1 ATA
302399 AAATACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTACATTGTAATACAAT
Found at i:304475 original size:11 final size:11
Alignment explanation
Indices: 304459--304483 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
304449 GTCACCAGCG
304459 GGTTGGATAAA
1 GGTTGGATAAA
304470 GGTTGGATAAA
1 GGTTGGATAAA
304481 GGT
1 GGT
304484 AAACACTAGT
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:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (11 bp):
GGTTGGATAAA
Found at i:314939 original size:14 final size:14
Alignment explanation
Indices: 314920--314947 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
314910 AGCATAACAA
314920 CTGGATTATATAAT
1 CTGGATTATATAAT
314934 CTGGATTATATAAT
1 CTGGATTATATAAT
314948 TTTCTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CTGGATTATATAAT
Found at i:316821 original size:15 final size:15
Alignment explanation
Indices: 316803--316834 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
316793 TCAATGTCAC
316803 TACTGCTTTTATGTT
1 TACTGCTTTTATGTT
316818 TACTGCTTTTATGTT
1 TACTGCTTTTATGTT
316833 TA
1 TA
316835 AGTGTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (15 bp):
TACTGCTTTTATGTT
Found at i:323227 original size:11 final size:11
Alignment explanation
Indices: 323204--323241 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
323194 GTAAGATGGC
323204 TTTTCTT-TCT
1 TTTTCTTCTCT
323214 TTTTCTTCTCT
1 TTTTCTTCTCT
*
323225 TTTTTTTCT-T
1 TTTTCTTCTCT
323235 TTTTCTT
1 TTTTCTT
323242 TTTTCTGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:323232 original size:14 final size:13
Alignment explanation
Indices: 323205--323247 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
323195 TAAGATGGCT
323205 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
323219 TTCTCTTTTTTTTC
1 TT-TCTTTTTTTTC
*
323233 TTTTTTCTTTTTTC
1 TTTCTT-TTTTTTC
323247 T
1 T
323248 GTAGTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.69
15 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:325349 original size:12 final size:12
Alignment explanation
Indices: 325332--325361 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
325322 ACAAAATTCG
325332 AATTTAATTTCC
1 AATTTAATTTCC
*
325344 AATTTAATTTCT
1 AATTTAATTTCC
325356 AATTTA
1 AATTTA
325362 TTTATGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:330432 original size:12 final size:12
Alignment explanation
Indices: 330415--330447 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
330405 ACAAAATCCG
330415 AATTTAATTTCC
1 AATTTAATTTCC
*
330427 AATTTAATTTCT
1 AATTTAATTTCC
330439 AATTTAATT
1 AATTTAATT
330448 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:330870 original size:6 final size:6
Alignment explanation
Indices: 330859--330883 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
330849 GCTTTTTTAT
330859 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
330884 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:331197 original size:30 final size:29
Alignment explanation
Indices: 331134--331211 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
331124 TAATCTTGTT
* * *
331134 TAGTTGGATGACCAATTTAAAAAAATTCA
1 TAGTTGGGTGACAAATTTAAAAAAATCCA
* *
331163 TAGTTGGGTGACAAATTTGAGACAAATCCA
1 TAGTTGGGTGACAAATTT-AAAAAAATCCA
* *
331193 TAGTTAGGTAATCAAATTT
1 TAGTTGGGTGA-CAAATTT
331212 TTTTTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.40
30 17 0.43
31 7 0.17
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (29 bp):
TAGTTGGGTGACAAATTTAAAAAAATCCA
Found at i:332650 original size:18 final size:18
Alignment explanation
Indices: 332623--332657 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
332613 AGCACCAAAG
332623 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
332641 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
332658 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:338166 original size:34 final size:33
Alignment explanation
Indices: 338061--338166 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
338051 TTTAGTGTTC
* *
338061 TTTTTT-AAAAATTAATTAAATTAGGGTTTAGG
1 TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
** *
338093 AGTTTTAAATTAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
*
338127 GTTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
338161 TTTTTT
1 TTTTTT
338167 TAAAGGCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.06
33 2 0.03
34 55 0.89
35 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:339900 original size:40 final size:40
Alignment explanation
Indices: 339856--339935 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
339846 GTCAACGTAG
339856 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
1 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
**
339896 TTGACCGTTAAAAATGGTTTGATTTTTAAAAAAACTGTAA
1 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
339936 CGTTGAGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (40 bp):
TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
Found at i:340523 original size:126 final size:125
Alignment explanation
Indices: 340097--340614 Score: 665
Period size: 126 Copynumber: 4.2 Consensus size: 125
340087 GATTTTGGTT
* * * * ** * *
340097 TTTTTCTACGGTAGTTCCTGAAAAAATAATTTTAAGAAGATGGTTCCCAACAAATAGTCTTAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* *
340162 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAACTCCCACGTGGA-AGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCTCCCACGTGGACA-CTC
** * *
340222 ---TTCTACAACAGTTCTTGAAAAAATAATTTTAAGAAGACAG-TTCTAAACAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGAC-GTTTCTGAACAAATAGTGTCAAA
* *
340283 AACGCTTCAAGCA-GATGCACTGTCAACAAAATTGATGAAAAAAGCTCCTACGTGGACACT-
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ATGAAAAAAGCTCCCACGTGGACACTC
* * * *
340343 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* *
340408 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTGAAGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ATGAAAAAAGCTCCCACGTGGACACTC
* * * *
340469 TTTTTCTATAGTAGTTCATGAAAAAATAATTTTGAGAAAACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* * *
340534 ACACTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCTCCCACGTGGACACTC
340595 TTTTTCTACAGTAGTTCATG
1 TTTTTCTACAGTAGTTCATG
340615 TTTGGCCTTA
Statistics
Matches: 350, Mismatches: 32, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
121 20 0.06
122 82 0.23
123 3 0.01
124 64 0.18
125 45 0.13
126 136 0.39
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTATGAAAAAAGCTCCCACGTGGACACTC
Found at i:340811 original size:28 final size:28
Alignment explanation
Indices: 340780--340841 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
340770 CGGCGTTATT
340780 TTTTTATCGGAGAACACAACGCGAATAA
1 TTTTTATCGGAGAACACAACGCGAATAA
*
340808 TTTTTATCGGAGAACACAACGCGAATTA
1 TTTTTATCGGAGAACACAACGCGAATAA
340836 TTTTTA
1 TTTTTA
340842 ACTAGACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (28 bp):
TTTTTATCGGAGAACACAACGCGAATAA
Found at i:343757 original size:24 final size:23
Alignment explanation
Indices: 343701--343757 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
343691 AAGAACTTCT
*
343701 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
343724 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
343749 ACTTTTATT
1 A-TTTTATT
343758 TTATTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:344161 original size:18 final size:18
Alignment explanation
Indices: 344138--344174 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
344128 GGGAAAAGGA
* *
344138 ATATAAGGGTTATGATAC
1 ATATAAGGGCTAGGATAC
344156 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
344174 A
1 A
344175 CACCTGGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:345952 original size:30 final size:30
Alignment explanation
Indices: 345918--345986 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
345908 ATTAATTAAA
345918 GAGAGTTTTGAGAAATTTA-AGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAGA-GAGAAATTT
*
345948 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAGAGAGAAATTT
*
345978 GAAAGTTTT
1 GAGAGTTTT
345987 TTTTGCTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAGAGAGAAATTT
Found at i:347076 original size:38 final size:38
Alignment explanation
Indices: 347025--347100 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
347015 ATTATATGTG
347025 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
*
347063 CTTATTTTTCTAGATTAGTTCATATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
347101 TATACATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.57
Consensus pattern (38 bp):
CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
Found at i:347098 original size:20 final size:20
Alignment explanation
Indices: 347037--347098 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
347027 TATTTTTCTA
*
347037 GATTAGTTCAGATTTAAATT
1 GATTAGTTCATATTTAAATT
* *** *
347057 GATT--TTCTTATTTTTCTA
1 GATTAGTTCATATTTAAATT
347075 GATTAGTTCATATTTAAATT
1 GATTAGTTCATATTTAAATT
347095 GATT
1 GATT
347099 TTTATACATT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
18 12 0.41
20 17 0.59
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTAGTTCATATTTAAATT
Found at i:370554 original size:14 final size:14
Alignment explanation
Indices: 370535--370562 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
370525 ACCCTAGTAG
370535 TAATTAACAAGAAA
1 TAATTAACAAGAAA
370549 TAATTAACAAGAAA
1 TAATTAACAAGAAA
370563 GTCGCTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:374317 original size:23 final size:24
Alignment explanation
Indices: 374291--374336 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
374281 TACAAGTCTA
374291 GTTTAGTAA-TATATTGAATTATG
1 GTTTAGTAATTATATTGAATTATG
*
374314 GTTTAGTAATTTTATTGAATTAT
1 GTTTAGTAATTATATTGAATTAT
374337 AATTAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (24 bp):
GTTTAGTAATTATATTGAATTATG
Found at i:376204 original size:17 final size:17
Alignment explanation
Indices: 376179--376226 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
376169 TGATGTGTTC
*
376179 TTCAGTAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
376196 TTCAATAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
*
376213 TTCGATAAAAGAAA
1 TTCAATAAAAGAAA
376227 AGTAGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (17 bp):
TTCAATAAAAGAAAGAA
Found at i:382758 original size:38 final size:38
Alignment explanation
Indices: 382705--382781 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
382695 AAATACTAAG
382705 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
** **
382743 TGATAAATTTGTTTAGCATGCTTGTTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
382781 T
1 T
382782 TTTGTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (38 bp):
TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
Found at i:384728 original size:17 final size:18
Alignment explanation
Indices: 384706--384742 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
384696 CAAAACTAAG
384706 GTTCATTTGGTGTT-CAT
1 GTTCATTTGGTGTTCCAT
384723 GTTCATTTGGTGTTCCAT
1 GTTCATTTGGTGTTCCAT
384741 GT
1 GT
384743 CAGGATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.51
Consensus pattern (18 bp):
GTTCATTTGGTGTTCCAT
Found at i:395675 original size:77 final size:76
Alignment explanation
Indices: 395548--395770 Score: 247
Period size: 77 Copynumber: 2.9 Consensus size: 76
395538 CAATTCTCCA
* *
395548 CATGGTATCAAATGTTTTTGGTTCTTTCCTTATAAGTGTTTTTTTTCTGGTCGAACTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTT-CTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTC
*
395613 TCATGTTTATTC
65 TCATGTTCATTC
* *
395625 CATGGTATCAGATGTTTTTGGTT-TTT-TTCCTAAGTGTTTTCTTTTCCTGGTTGAAATCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCTT-ATAAGTGTTTT-TTTT-CTGGTCGAAATCTTGCT
*
395688 TCTCTTGTTCATTC
63 TCTCATGTTCATTC
* * * *
395702 CATGGTATCAGAT-TTTTCTGGTTCCTTAC-TATGAAGAGTTTTTTTTTCTTGGTCGAATTATTG
1 CATGGTATCAGATGTTTT-TGGTT-CTTTCTTAT-AAGTG-TTTTTTTTC-TGGTCGAAATCTTG
395765 CTTCTC
61 CTTCTC
395771 CTATTCTATT
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
74 2 0.02
75 10 0.08
76 11 0.09
77 67 0.54
78 2 0.02
79 28 0.23
80 4 0.03
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (76 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTCT
CATGTTCATTC
Found at i:408101 original size:6 final size:7
Alignment explanation
Indices: 408086--408111 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
408076 CTTCCGTTAA
408086 TTTTATT
1 TTTTATT
408093 TTTTATT
1 TTTTATT
408100 TTTTATT
1 TTTTATT
408107 TTTTA
1 TTTTA
408112 AAATTTATTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:409297 original size:36 final size:30
Alignment explanation
Indices: 409229--409288 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
409219 GCTCGATAAG
409229 AATCTTAAATATTAATATTGATACTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
*
409259 AATCTTAAATATTAATATTGATATTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
409289 TAAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
AATCTTAAATATTAATATTGATACTAAGTT
Found at i:409368 original size:31 final size:27
Alignment explanation
Indices: 409330--409391 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
409320 AAATAATCAT
409330 TCAACTATGATAGTGTTTTTATTTTAGTCA
1 TCAACTAT-A-AGTGTTTTTA-TTTAGTCA
* *
409360 CTCAACTATAATTTTTTTTATTTAGTCA
1 -TCAACTATAAGTGTTTTTATTTAGTCA
409388 TCAA
1 TCAA
409392 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 8 0.28
30 1 0.03
31 8 0.28
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TCAACTATAAGTGTTTTTATTTAGTCA
Found at i:415791 original size:20 final size:21
Alignment explanation
Indices: 415750--415792 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
415740 ACCAATAGAT
*
415750 AATTGTGGACAATGCCACCAG
1 AATTGTAGACAATGCCACCAG
*
415771 AATTGTAGACAA-GCTACCAG
1 AATTGTAGACAATGCCACCAG
415791 AA
1 AA
415793 CAAATATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
AATTGTAGACAATGCCACCAG
Found at i:416307 original size:71 final size:71
Alignment explanation
Indices: 416226--416370 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
416216 CACGAGATAA
416226 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
1 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
416291 TACTTG
66 TACTTG
*
416297 AACACACACCTTAAACCAACGATCCAAAATCAGCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
1 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
416362 TACTTG
66 TACTTG
416368 AAC
1 AAC
416371 CACTTATTAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (71 bp):
AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
TACTTG
Found at i:416690 original size:56 final size:56
Alignment explanation
Indices: 416627--416740 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
416617 GACAAAAAGG
*
416627 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGATGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
416683 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
416739 AA
1 AA
416741 GAAGCATAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (56 bp):
AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
Found at i:418955 original size:16 final size:16
Alignment explanation
Indices: 418903--418965 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
418893 GTTTAGTTCA
418903 CTGTAATGGAATAG-G
1 CTGTAATGGAATAGAG
* * *
418918 ACTATAATGTAATAGAA
1 -CTGTAATGGAATAGAG
*
418935 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
418951 CTGTAATAGAATAGA
1 CTGTAATGGAATAGA
418966 ACTTTAATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:418973 original size:16 final size:16
Alignment explanation
Indices: 418906--418974 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
418896 TAGTTCACTG
* * *
418906 TAATGGAATAGGACTA
1 TAATAGAATAGAACTT
418922 TAAT-GTAATAGAA-TT
1 TAATAG-AATAGAACTT
* * *
418937 GTAATGGAATAGAGCTG
1 -TAATAGAATAGAACTT
418954 TAATAGAATAGAACTT
1 TAATAGAATAGAACTT
418970 TAATA
1 TAATA
418975 AGTAATCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 38 0.90
17 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.30
Consensus pattern (16 bp):
TAATAGAATAGAACTT
Found at i:421322 original size:96 final size:97
Alignment explanation
Indices: 421147--421339 Score: 370
Period size: 96 Copynumber: 2.0 Consensus size: 97
421137 AAGGAAGGAC
421147 TTAGGTAATAAATATATCAAAATTTATATAGTGGGGCTTAGAGGTGCTCATGGGTCGTGATGCGG
1 TTAGGTAAT-AATATATCAAAATTTATATAGTGGGGCTTAGAGGTGCTCATGGGTCGTGATGCGG
421212 AACCCCGGATCTAGACACAAGAGAAACACAAAT
65 AACCCCGGATCTAGACACAAGAGAAACACAAAT
421245 TTAGGTAAT-ATATATCAAAATTTATATAGTGGGGCTTAGAGGTGCTCATGGGTCGTGATGCGGA
1 TTAGGTAATAATATATCAAAATTTATATAGTGGGGCTTAGAGGTGCTCATGGGTCGTGATGCGGA
421309 ACCCCGGATCTAGACACAAGAGAAACACAAA
66 ACCCCGGATCTAGACACAAGAGAAACACAAA
421340 AAAGAAATAA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 86 0.91
98 9 0.09
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (97 bp):
TTAGGTAATAATATATCAAAATTTATATAGTGGGGCTTAGAGGTGCTCATGGGTCGTGATGCGGA
ACCCCGGATCTAGACACAAGAGAAACACAAAT
Found at i:421383 original size:3 final size:3
Alignment explanation
Indices: 421375--421400 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
421365 AAATTAGTTA
421375 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
421401 AAGAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:423008 original size:18 final size:18
Alignment explanation
Indices: 422985--423027 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
422975 GAATAGGTTT
422985 TTAATTAAACAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
423003 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
423021 TTAATTA
1 TTAATTA
423028 CACATTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:424986 original size:3 final size:3
Alignment explanation
Indices: 424980--425006 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
424970 TTTTTAAAAC
424980 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
425007 TTTTTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:427595 original size:6 final size:6
Alignment explanation
Indices: 427584--427628 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
427574 AGAGAGTATA
*
427584 TATATG TATATGTG TTTATG TATATG TATATG TATATG TATATG T
1 TATATG TATA--TG TATATG TATATG TATATG TATATG TATATG T
427629 GTTTTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 30 0.86
8 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (6 bp):
TATATG
Found at i:427944 original size:21 final size:21
Alignment explanation
Indices: 427928--427973 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
427918 ATTGTTTCTT
427928 TTGTTCTCGTTCTTGTTGTTC
1 TTGTTCTCGTTCTTGTTGTTC
* *
427949 TTGTTCTTGTTCTTGTTGTTG
1 TTGTTCTCGTTCTTGTTGTTC
427970 TTGT
1 TTGT
427974 GTCTGTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.22, T:0.65
Consensus pattern (21 bp):
TTGTTCTCGTTCTTGTTGTTC
Found at i:427967 original size:15 final size:15
Alignment explanation
Indices: 427923--427973 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
427913 TTTTGATTGT
*
427923 TTCTT-TTGTTCTCG
1 TTCTTGTTGTTCTTG
427937 TTCTTGTTGTTCTTG
1 TTCTTGTTGTTCTTG
* *
427952 TTCTTGTTCTTGTTG
1 TTCTTGTTGTTCTTG
*
427967 TTGTTGT
1 TTCTTGT
427974 GTCTGTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.00, C:0.14, G:0.20, T:0.67
Consensus pattern (15 bp):
TTCTTGTTGTTCTTG
Found at i:427980 original size:21 final size:20
Alignment explanation
Indices: 427928--427980 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
427918 ATTGTTTCTT
427928 TTGTTCTCGTTCTTGTTGTTC
1 TTGTTCT-GTTCTTGTTGTTC
*
427949 TTGTTCTTGTTCTTGTTGTTG
1 TTGTTC-TGTTCTTGTTGTTC
427970 TTGTGTCTGTT
1 TTGT-TCTGTT
427981 TGTTTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.00, C:0.13, G:0.23, T:0.64
Consensus pattern (20 bp):
TTGTTCTGTTCTTGTTGTTC
Found at i:429114 original size:29 final size:25
Alignment explanation
Indices: 429063--429115 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
429053 AAGATTACTT
429063 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
*
429088 ATTTGAATTTAATTACAAACAATCA
1 ATTTGAATTTAATTACAAACAATTA
429113 ATT
1 ATT
429116 CTTAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:432019 original size:21 final size:21
Alignment explanation
Indices: 431993--432040 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
431983 ATTAGGTGGA
*
431993 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
432014 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
432035 TTAGCT
1 TCAGCT
432041 TTTGAGCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:442442 original size:42 final size:43
Alignment explanation
Indices: 442340--442444 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 43
442330 AATGCCAACG
* * * * *
442340 TCCCAGACGTGGTCTTACATGTAATTAATTATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGTAATTAATTATCGACGCCAATA
* *
442383 TCCCAAACAGGGTCTTACACGTAATT-ATATAT-GACGCCAATA
1 TCCCAGACATGGTCTTACACGTAATTAAT-TATCGACGCCAATA
442425 TCCCAGACATGGTCTTACAC
1 TCCCAGACATGGTCTTACAC
442445 ATAAATCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 27 0.52
43 25 0.48
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATTAATTATCGACGCCAATA
Found at i:443447 original size:15 final size:15
Alignment explanation
Indices: 443427--443457 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
443417 ATAAATTAAA
443427 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
443442 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
443457 A
1 A
443458 TAAGGCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AGGTATAATTTCAAC
Found at i:454707 original size:9 final size:9
Alignment explanation
Indices: 454693--454733 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
454683 AACTTGGTGC
454693 ATTTTGTTT
1 ATTTTGTTT
454702 ATTTTGTTT
1 ATTTTGTTT
*
454711 ATTTTATTT
1 ATTTTGTTT
454720 ATTTTGTTT
1 ATTTTGTTT
454729 ATTTT
1 ATTTT
454734 TAATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:454814 original size:23 final size:23
Alignment explanation
Indices: 454784--454835 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
454774 TGCAACTTGG
454784 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
454807 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
454830 TTTCAT
1 TTTCAT
454836 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:454847 original size:59 final size:59
Alignment explanation
Indices: 454784--454899 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
454774 TGCAACTTGG
*
454784 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTATAATGCTTTCATCTTTTGC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
* * *
454843 TTTCATAATGATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTT
454900 TAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
Found at i:454868 original size:23 final size:23
Alignment explanation
Indices: 454840--454894 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
454830 TTTCATCTTT
454840 TGCTTTCATAATGATAGCTA-ATA
1 TGCTTTCATAATGATAGCTACA-A
* *
454863 TGCTTTCATAATGGTAGTTACAA
1 TGCTTTCATAATGATAGCTACAA
454886 TGCTTTCAT
1 TGCTTTCAT
454895 CTTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
TGCTTTCATAATGATAGCTACAA
Found at i:459249 original size:17 final size:17
Alignment explanation
Indices: 459227--459261 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
459217 TAGGCTTGGG
459227 TTAGTCTT-TTACAAATA
1 TTAGTCTTGTTA-AAATA
459244 TTAGTCTTGTTAAAATA
1 TTAGTCTTGTTAAAATA
459261 T
1 T
459262 GGCTCGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (17 bp):
TTAGTCTTGTTAAAATA
Found at i:459380 original size:8 final size:8
Alignment explanation
Indices: 459367--459392 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
459357 TAAAAAAGTA
459367 TATTAAAT
1 TATTAAAT
459375 TATTAAAT
1 TATTAAAT
459383 TATTAAAT
1 TATTAAAT
459391 TA
1 TA
459393 AAGCAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TATTAAAT
Found at i:459413 original size:232 final size:232
Alignment explanation
Indices: 459011--459476 Score: 898
Period size: 232 Copynumber: 2.0 Consensus size: 232
459001 GGGCAAAAAA
459011 ATTAGTCTTGTTAAAATATGGCTCAGGTTATAAAAATTAGATTTATGGTAATATATAATACTATA
1 ATTAGTCTTGTTAAAATATGGCTCAGGTTATAAAAATTAGATTTATGGTAATATATAATACTATA
459076 ATGTAAATTAGAAAAATGTTAAGTTGTCTATACATAAAATTCTAATAAATAAAAAAGTATATTAA
66 ATGTAAATTAGAAAAATGTTAAGTTGTCTATACATAAAATTCTAATAAATAAAAAAGTATATTAA
459141 ATTATTAAATATTAAATTAAAAGCAATATAAATTTTTTTTCAAAAAAAATTTAAAAAAATATGGA
131 ATTATTAAATATTAAATTAAAAGCAATATAAATTTTTTTTCAAAAAAAATTTAAAAAAATATGGA
459206 GGAGCTTAAAATAGGCTTGGGTTAGTCTTTTACAAAT
196 GGAGCTTAAAATAGGCTTGGGTTAGTCTTTTACAAAT
* *
459243 ATTAGTCTTGTTAAAATATGGCTCGGGTTATAAAAATTAGGTTTATGGTAATATATAATACTATA
1 ATTAGTCTTGTTAAAATATGGCTCAGGTTATAAAAATTAGATTTATGGTAATATATAATACTATA
459308 ATGTAAATTAGAAAAATGTTAAGTTGTCTATACATAAAATTCTAATAAATAAAAAAGTATATTAA
66 ATGTAAATTAGAAAAATGTTAAGTTGTCTATACATAAAATTCTAATAAATAAAAAAGTATATTAA
459373 ATTATTAAATTATTAAATT-AAAGCAATATAAATTTTTTTTCAAAAAAAATTTAAAAAAATATGG
131 ATTATTAAA-TATTAAATTAAAAGCAATATAAATTTTTTTTCAAAAAAAATTTAAAAAAATATGG
459437 AGGAGCTTAAAATAGGCTTGGGTTAGTCTTTTACAAAT
195 AGGAGCTTAAAATAGGCTTGGGTTAGTCTTTTACAAAT
459475 AT
1 AT
459477 ACGCGGACCT
Statistics
Matches: 231, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
232 222 0.96
233 9 0.04
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (232 bp):
ATTAGTCTTGTTAAAATATGGCTCAGGTTATAAAAATTAGATTTATGGTAATATATAATACTATA
ATGTAAATTAGAAAAATGTTAAGTTGTCTATACATAAAATTCTAATAAATAAAAAAGTATATTAA
ATTATTAAATATTAAATTAAAAGCAATATAAATTTTTTTTCAAAAAAAATTTAAAAAAATATGGA
GGAGCTTAAAATAGGCTTGGGTTAGTCTTTTACAAAT
Found at i:460117 original size:13 final size:13
Alignment explanation
Indices: 460099--460123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460089 ATTTCTGGTC
460099 TTTACTCAAGTTT
1 TTTACTCAAGTTT
460112 TTTACTCAAGTT
1 TTTACTCAAGTT
460124 CTTAAGCTGA
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:464597 original size:13 final size:13
Alignment explanation
Indices: 464579--464603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
464569 ATTTCTGGTC
464579 TTTACTCAAGTTT
1 TTTACTCAAGTTT
464592 TTTACTCAAGTT
1 TTTACTCAAGTT
464604 CTTAAGCTGA
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:470580 original size:46 final size:46
Alignment explanation
Indices: 470513--470605 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
470503 AAGATACAAG
470513 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
470559 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
470605 A
1 A
470606 ATGCTCCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (46 bp):
ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
Found at i:471314 original size:22 final size:22
Alignment explanation
Indices: 471289--471342 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
471279 TTGTTTTTAA
* *
471289 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATTAA-TAT
*
471311 AAAAGTATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
*
471333 AACATTATAT
1 AAAATTATAT
471343 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:471460 original size:29 final size:28
Alignment explanation
Indices: 471402--471460 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
471392 TATGTAAAAT
* * **
471402 ATATTAATATTAATCTTTTATTATGTTA
1 ATATTAAAATTAATATTTTATTATACTA
*
471430 ATATTAAAATTATATATTTTATTTTACTA
1 ATATTAAAATTA-ATATTTTATTATACTA
471459 AT
1 AT
471461 TATCATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAAAATTAATATTTTATTATACTA
Found at i:475781 original size:18 final size:20
Alignment explanation
Indices: 475724--475786 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
475714 AAAAAAATTA
475724 ATTTTC-CTATTATTATTATTT
1 ATTTTCACTATT-TTATT-TTT
*
475745 ATTTTTACTATTTTA-TTTT
1 ATTTTCACTATTTTATTTTT
475764 ATTTTCA-T-TTTTATTTTT
1 ATTTTCACTATTTTATTTTT
475782 ATTTT
1 ATTTT
475787 TGCAGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 9 0.24
20 1 0.03
21 8 0.21
22 5 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTCACTATTTTATTTTT
Found at i:475785 original size:6 final size:6
Alignment explanation
Indices: 475731--475787 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
475721 TTAATTTTCC
* *
475731 TATTAT TATTATT TATTTT TACTATTT TA-TTT TATTTT CATTTT TATTTT
1 TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT TATTTT
475781 TATTTT T
1 TATTTT T
475788 GCAGGAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 6 0.14
8 5 0.11
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:482361 original size:48 final size:48
Alignment explanation
Indices: 482305--482491 Score: 374
Period size: 48 Copynumber: 3.9 Consensus size: 48
482295 CTTCGGTAAG
482305 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
1 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
482353 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
1 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
482401 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
1 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
482449 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAA
1 TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAA
482492 AGTCACTTTT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 139 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (48 bp):
TCCTAAAAATTATACATTCTTTACTGGGTAAATTATAAAAAAAGGAAA
Found at i:505844 original size:4 final size:4
Alignment explanation
Indices: 505835--505860 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
505825 ACATGCTTCA
505835 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
505861 TTGTAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:507409 original size:7 final size:7
Alignment explanation
Indices: 507329--507426 Score: 81
Period size: 7 Copynumber: 14.0 Consensus size: 7
507319 TCCTTTTCAA
*
507329 CTCAATA
1 CTCAATT
**
507336 CTCAACC
1 CTCAATT
507343 CTCAATT
1 CTCAATT
*
507350 CTAAATT
1 CTCAATT
* *
507357 CTCACTC
1 CTCAATT
507364 CTCAATT
1 CTCAATT
*
507371 TTC-ATT
1 CTCAATT
507377 CCTCAATT
1 -CTCAATT
* *
507385 TTCAATC
1 CTCAATT
* *
507392 CTGAATC
1 CTCAATT
507399 CTCAATT
1 CTCAATT
507406 CTCAATT
1 CTCAATT
507413 CTCAATT
1 CTCAATT
507420 CTCAATT
1 CTCAATT
507427 ATTATTTTTA
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
6 3 0.04
7 65 0.92
8 3 0.04
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.39
Consensus pattern (7 bp):
CTCAATT
Found at i:511849 original size:42 final size:41
Alignment explanation
Indices: 511718--511858 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 41
511708 GAAGCCCGAA
* * *
511718 GGTTGAACAGAAGCTCATGAGAGCTAAACAAAAACTCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAAC-AAAACTCATAAG
* * * * *
511760 GGTTGAACGGAAGCTCGTAAGAGATGAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAACA-AAACTCATAAG
* *
511802 GGTTAAACAGAAGCTCAAAAGAGCTGAACGAAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTGAAC-AAAACTCATAAG
* *
511844 AGTTAAAGAGAAGCT
1 GGTTAAACAGAAGCT
511859 TGTGAGAGCT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 80 0.98
43 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (41 bp):
GGTTAAACAGAAGCTCATAAGAGCTGAACAAAACTCATAAG
Found at i:517901 original size:20 final size:21
Alignment explanation
Indices: 517873--517920 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
517863 TACGGCGGCG
* *
517873 CCGGTGCCGGCGGCCGGTAA-
1 CCGGCGCCGGCGCCCGGTAAC
517893 CCGGCGCCGGCGCCCGGTAAC
1 CCGGCGCCGGCGCCCGGTAAC
517914 CCGGCGC
1 CCGGCGC
517921 GGGGCATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.08, C:0.44, G:0.42, T:0.06
Consensus pattern (21 bp):
CCGGCGCCGGCGCCCGGTAAC
Found at i:518405 original size:11 final size:12
Alignment explanation
Indices: 518391--518419 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
518381 TTAATTAATA
518391 ATATTATTATT-
1 ATATTATTATTG
518402 ATATTATTATTG
1 ATATTATTATTG
518414 ATATTA
1 ATATTA
518420 CAATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATATTATTATTG
Found at i:519901 original size:21 final size:21
Alignment explanation
Indices: 519877--519946 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
519867 AGATTATTTG
519877 CACCGTTGAGTGGTTTATCCA
1 CACCGTTGAGTGGTTTATCCA
*** *
519898 CACCGTTTGAGCAATTTATCTA
1 CACCG-TTGAGTGGTTTATCCA
** *
519920 CATTGTTTAGTGGTTTATCCA
1 CACCGTTGAGTGGTTTATCCA
519941 CACCGT
1 CACCGT
519947 ATTAGCAGTT
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (21 bp):
CACCGTTGAGTGGTTTATCCA
Found at i:519957 original size:22 final size:21
Alignment explanation
Indices: 519889--519957 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
519879 CCGTTGAGTG
519889 GTTTATCCACACCGTTTGAGCA
1 GTTTATCCACACCGTTT-AGCA
* * ** **
519911 ATTTATCTACATTGTTTAGTG
1 GTTTATCCACACCGTTTAGCA
519932 GTTTATCCACACCGTATTAGCA
1 GTTTATCCACACCGT-TTAGCA
519954 GTTT
1 GTTT
519958 TAATCTACAA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTTATCCACACCGTTTAGCA
Found at i:524914 original size:13 final size:14
Alignment explanation
Indices: 524896--524924 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
524886 TAAAGACTTG
524896 ATATG-ATTAACCA
1 ATATGAATTAACCA
524909 ATATGAATTAACCA
1 ATATGAATTAACCA
524923 AT
1 AT
524925 GTCACCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
ATATGAATTAACCA
Found at i:537080 original size:5 final size:5
Alignment explanation
Indices: 537070--537096 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
537060 AATTAATCTA
537070 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
537097 TATTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:539470 original size:18 final size:18
Alignment explanation
Indices: 539434--539478 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
539424 ACAAATGCCT
539434 TTAA-AATAGTAACAAAA
1 TTAACAATAGTAACAAAA
539451 TTAACAATAG-AACAATAA
1 TTAACAATAGTAACAA-AA
539469 TTATACAATA
1 TTA-ACAATA
539479 TCCAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAACAATAGTAACAAAA
Found at i:539580 original size:20 final size:21
Alignment explanation
Indices: 539528--539583 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
539518 TAGTGAAAAA
*
539528 AAAACAACAATAAAATAGCAAG
1 AAAACAATAA-AAAATAGCAAG
*
539550 AAAATAATAAAAAATAGCAAG
1 AAAACAATAAAAAATAGCAAG
*
539571 -AAACAGTAAAAAA
1 AAAACAATAAAAAA
539584 AAAGTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAACAATAAAAAATAGCAAG
Found at i:539988 original size:31 final size:31
Alignment explanation
Indices: 539930--539995 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
539920 CGTGTAATTA
* **
539930 TATACATGAAACTTTAATTGTGGTTCAAATG
1 TATACATGAAACATTAATTGTAATTCAAATG
* *
539961 TATATATGAAACATTAATTTTAATTC-AAT-
1 TATACATGAAACATTAATTGTAATTCAAATG
539990 TATACA
1 TATACA
539996 CATTTAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 5 0.17
30 3 0.10
31 21 0.72
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
TATACATGAAACATTAATTGTAATTCAAATG
Found at i:558896 original size:18 final size:18
Alignment explanation
Indices: 558875--558927 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
558865 ATAATTATAA
558875 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
558893 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
*
558911 TATTTAATTAAAAAAAT
1 TA-TTAATTAATAAAAT
558928 CATTTAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:564493 original size:41 final size:41
Alignment explanation
Indices: 564436--564750 Score: 225
Period size: 41 Copynumber: 7.7 Consensus size: 41
564426 ACCTTTCGGG
564436 GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
* * * ** * *
564477 GCTTTAGCGGTGTTTTTGAAGAAGCGTCGCTAATATTCGGG
1 GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
* *
564518 GTTTTAGCGGCGTTTTTAAA-AAGCGCCGC-AACTGCGCAGA
1 GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAA-TGCTCAGA
* * * * *
564558 GCTTTAGCGGCGTTTTTCAGGAAGCGCCGCTAATACTCGGG
1 GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
* * ** * *
564599 GTTTTAGCGACGTTTTTGAAA-AAATGCCGCTAATGCTCTGG
1 GCTTTAGCGGCGTTTTT-AAAGAAGCGCCGCTAATGCTCAGA
* * * *
564640 GTTTTAGCGGCGCTTTTGT-AA-AACCGCCGTTAATGCTC-GTG
1 GCTTTAGCGGCG-TTTT-TAAAGAAGCGCCGCTAATGCTCAG-A
* * * * *
564681 GTTTTAGAGGCATTTTTTGAA-AAGCGCAGCTAATGCTCAG-
1 GCTTTAGCGGC-GTTTTTAAAGAAGCGCCGCTAATGCTCAGA
* *
564721 GATTTAGTGGCGTTTTTGAAA-AAGCGCCGC
1 GCTTTAGCGGCGTTTTT-AAAGAAGCGCCGC
564751 AAAAACATTT
Statistics
Matches: 218, Mismatches: 45, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
39 7 0.03
40 49 0.22
41 153 0.70
42 8 0.04
43 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
GCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGA
Found at i:564573 original size:81 final size:81
Alignment explanation
Indices: 564430--564750 Score: 308
Period size: 82 Copynumber: 3.9 Consensus size: 81
564420 AACATAACCT
* * * *
564430 TTCGGGGCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCAGAGCTTTAGCGGTGTTTTTG
1 TTCGGGGTTTTAGCGGCGTTTTTAAA-AAGCGCCGCTAATGCGCAGAGCTTTAGCGGCGTTTTTC
*
564495 AAGAAGCGTCGCTAATA
65 AAGAAGCGCCGCTAATA
564512 TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGC-AACTGCGCAGAGCTTTAGCGGCGTTTTTC
1 TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCTAA-TGCGCAGAGCTTTAGCGGCGTTTTTC
*
564576 AGGAAGCGCCGCTAATA
65 AAGAAGCGCCGCTAATA
* * ** * * * *
564593 CTCGGGGTTTTAGCGACGTTTTTGAAAAAATGCCGCTAATGCTCTGGGTTTTAGCGGCGCTTTTG
1 TTCGGGGTTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCGCAGAGCTTTAGCGGCG-TTTT-
* * *
564658 T-AA-AACCGCCGTTAATG
63 TCAAGAAGCGCCGCTAATA
* * * * * * * * * *
564675 CTCGTGGTTTTAGAGGCATTTTTTGAAAAGCGCAGCTAATGCTCAG-GATTTAGTGGCGTTTTTG
1 TTCGGGGTTTTAGCGGC-GTTTTTAAAAAGCGCCGCTAATGCGCAGAGCTTTAGCGGCGTTTTTC
*
564739 AAAAAGCGCCGC
65 AAGAAGCGCCGC
564751 AAAAACATTT
Statistics
Matches: 200, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.00
80 8 0.04
81 85 0.43
82 93 0.47
83 12 0.06
84 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (81 bp):
TTCGGGGTTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCGCAGAGCTTTAGCGGCGTTTTTCA
AGAAGCGCCGCTAATA
Found at i:565268 original size:21 final size:21
Alignment explanation
Indices: 565224--565268 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
565214 GATTTAAGGT
* * *
565224 TTATGGGTTAGGGGCTAGGGG
1 TTATGGGTTAGAGGCTAAGAG
*
565245 TTATGGGTTAGAGGTTAAGAG
1 TTATGGGTTAGAGGCTAAGAG
565266 TTA
1 TTA
565269 GGGATTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.42, T:0.33
Consensus pattern (21 bp):
TTATGGGTTAGAGGCTAAGAG
Found at i:565408 original size:15 final size:15
Alignment explanation
Indices: 565385--565421 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
565375 GTGTTATGGG
*
565385 TTAGAGTTTAAGGGT
1 TTAGGGTTTAAGGGT
565400 TTAGGGTTTAAGGGT
1 TTAGGGTTTAAGGGT
*
565415 TAAGGGT
1 TTAGGGT
565422 CGAATTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (15 bp):
TTAGGGTTTAAGGGT
Found at i:565413 original size:8 final size:8
Alignment explanation
Indices: 565390--565421 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
565380 ATGGGTTAGA
565390 GTTTAAGG
1 GTTTAAGG
565398 GTTT-AGG
1 GTTTAAGG
565405 GTTTAAGG
1 GTTTAAGG
565413 G-TTAAGG
1 GTTTAAGG
565420 GT
1 GT
565422 CGAATTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.64
8 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.38
Consensus pattern (8 bp):
GTTTAAGG
Found at i:565539 original size:21 final size:21
Alignment explanation
Indices: 565515--565554 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
565505 GGGGTTTGGG
565515 GTTAGAGA-TTAGAGGTTTATA
1 GTTAGAGATTTAG-GGTTTATA
*
565536 GTTAGTGATTTAGGGTTTA
1 GTTAGAGATTTAGGGTTTA
565555 AAGATTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (21 bp):
GTTAGAGATTTAGGGTTTATA
Done.