Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold369
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: 402231
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 19069 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:216158 original size:15 final size:15
Alignment explanation
Indices: 216112--216158 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
216102 TTTATTTGAC
*
216112 TATTATTATTATCAT
1 TATTATTATTATCTT
*
216127 TATTATTATCAGT-TT
1 TATTATTATTA-TCTT
*
216142 TATTTTTATTATCTT
1 TATTATTATTATCTT
216157 TA
1 TA
216159 GTATAATGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTATTATTATCTT
Found at i:220403 original size:6 final size:6
Alignment explanation
Indices: 220389--220442 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
220379 AAATAAGTCT
* * *
220389 ATAAAA ATAACA ATAAACA A-AAAC ATAAAA GTAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
220437 ATAAAA
1 ATAAAA
220443 CAAATAAGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 1 0.03
6 37 0.93
7 2 0.05
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:221998 original size:26 final size:26
Alignment explanation
Indices: 221950--221999 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
221940 ACATTAAAAC
* *
221950 AAATAATAATGAGAACATTAAGAAGA
1 AAATAATAATAAGAACATGAAGAAGA
* *
221976 AAATAATAATAAGTATATGAAGAA
1 AAATAATAATAAGAACATGAAGAA
222000 AATATGACAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.22
Consensus pattern (26 bp):
AAATAATAATAAGAACATGAAGAAGA
Found at i:222097 original size:19 final size:20
Alignment explanation
Indices: 222073--222117 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
222063 AACAGATACT
*
222073 AGAAAAATAAACA-AAAT-A
1 AGAAAAATAAAAAGAAATAA
222091 AGAAAAATAAAAAGAAATAA
1 AGAAAAATAAAAAGAAATAA
222111 AGAAAAA
1 AGAAAAA
222118 AAATATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 8 0.33
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (20 bp):
AGAAAAATAAAAAGAAATAA
Found at i:229995 original size:30 final size:30
Alignment explanation
Indices: 229949--230005 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
229939 CACGGGTTGG
*
229949 CACATGGGCATGTGGCCAGCCAGTGTGTCT
1 CACACGGGCATGTGGCCAGCCAGTGTGTCT
* *
229979 CACACGGGCGTGTGGCCAGCCCGTGTG
1 CACACGGGCATGTGGCCAGCCAGTGTG
230006 GAAATGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.30, G:0.37, T:0.19
Consensus pattern (30 bp):
CACACGGGCATGTGGCCAGCCAGTGTGTCT
Found at i:230834 original size:16 final size:17
Alignment explanation
Indices: 230815--230855 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
230805 AAAAAGGAGG
230815 AAAAAATAAAAAATA-A
1 AAAAAATAAAAAATATA
230831 AAAAAATAAAAAATATA
1 AAAAAATAAAAAATATA
230848 AAAAAATA
1 AAAAAATA
230856 TTTGATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAAAATATA
Found at i:230841 original size:23 final size:24
Alignment explanation
Indices: 230789--230851 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
230779 TTTTTAAATC
* *
230789 AATAAAAAAT-CAAAATAAAAAGG
1 AATAAAAAATAAAAAATAAAAAGA
**
230812 AGGAAAAAATAAAAAATAAAAA-A
1 AATAAAAAATAAAAAATAAAAAGA
230835 AATAAAAAATATAAAAA
1 AATAAAAAATA-AAAAA
230852 AATATTTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (24 bp):
AATAAAAAATAAAAAATAAAAAGA
Found at i:230856 original size:10 final size:9
Alignment explanation
Indices: 230822--230853 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
230812 AGGAAAAAAT
230822 AAAAAATAA
1 AAAAAATAA
230831 AAAAAATAA
1 AAAAAATAA
*
230840 AAAATATAA
1 AAAAAATAA
230849 AAAAA
1 AAAAA
230854 TATTTGATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:240005 original size:11 final size:11
Alignment explanation
Indices: 239989--240014 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
239979 AACTAATAGT
239989 AAAAAATAAAA
1 AAAAAATAAAA
240000 AAAAAATAAAA
1 AAAAAATAAAA
240011 AAAA
1 AAAA
240015 TTAAGAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:240217 original size:14 final size:15
Alignment explanation
Indices: 240184--240217 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
240174 ATGAGAATAT
240184 AAAAATAGAAAAACC
1 AAAAATAGAAAAACC
**
240199 AAAAATAGAGGAACC
1 AAAAATAGAAAAACC
240214 AAAA
1 AAAA
240218 CTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAATAGAAAAACC
Found at i:241360 original size:47 final size:47
Alignment explanation
Indices: 241302--241392 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
241292 TAATTCCACT
*
241302 TGACAATCTCAAATTATAGTTAAAATTTTAAATTAGTTCCTAAAACA
1 TGACAACCTCAAATTATAGTTAAAATTTTAAATTAGTTCCTAAAACA
*
241349 TGACAACCTCAAATTATCGTTAAAATTTTAAATTAGTTCCTAAA
1 TGACAACCTCAAATTATAGTTAAAATTTTAAATTAGTTCCTAAA
241393 GCAATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (47 bp):
TGACAACCTCAAATTATAGTTAAAATTTTAAATTAGTTCCTAAAACA
Found at i:242413 original size:13 final size:13
Alignment explanation
Indices: 242397--242422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
242387 TGGGGGGTGG
242397 GGAGAAGAGATTA
1 GGAGAAGAGATTA
242410 GGAGAAGAGATTA
1 GGAGAAGAGATTA
242423 AGGAAGAACC
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:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (13 bp):
GGAGAAGAGATTA
Found at i:247384 original size:24 final size:24
Alignment explanation
Indices: 247357--247414 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
247347 TGAGATACCG
*
247357 ACCTTTTCGTTGATATCCTTTTCA
1 ACCTTTTCATTGATATCCTTTTCA
*
247381 ACCTTTTCATTTATATCCTTTTCA
1 ACCTTTTCATTGATATCCTTTTCA
247405 ACCTTCTTCA
1 ACCTT-TTCA
247415 ATGGATTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (24 bp):
ACCTTTTCATTGATATCCTTTTCA
Found at i:247589 original size:36 final size:36
Alignment explanation
Indices: 247493--247819 Score: 172
Period size: 36 Copynumber: 8.8 Consensus size: 36
247483 GTAACAAAGT
*
247493 TTTGCGCCCAACACTAGTCGGATAAACCGACGATAGA
1 TTTGCGCCCAACACTAGTCGGATAAACCGACAAT-GA
* ** * * *
247530 --TGTGCCCTGCACTAGTTGAATAAACCGACAATGT
1 TTTGCGCCCAACACTAGTCGGATAAACCGACAATGA
* * *
247564 TTTGCGCCCAACGCTAGTCGGATAAACTGACGATATCAAA
1 TTTGCGCCCAACACTAGTCGGATAAACCGAC-A-AT--GA
* * * *
247604 TGTGTGCCCAACACTAGTCAGATAAACCGACAATGT
1 TTTGCGCCCAACACTAGTCGGATAAACCGACAATGA
* * ** * * *
247640 TTTGCTCCCAGCGTTAGTCAGATAAATCGACGATATCAAA
1 TTTGCGCCCAACACTAGTCGGATAAACCGAC-A-AT--GA
* **
247680 TGTGTACCCAACACTAGTCGGATAAACCGACAATGA
1 TTTGCGCCCAACACTAGTCGGATAAACCGACAATGA
* * * * ** ** *
247716 GTTACGCCCAGCGCTAGTTAGATAAATTGACGATATCA
1 TTTGCGCCCAACACTAGTCGGATAAACCGAC-A-ATGA
** * * *
247754 AATGTGCCCAACACTAGTCGGATAAATCAACAATGA
1 TTTGCGCCCAACACTAGTCGGATAAACCGACAATGA
* * *
247790 TTTGCGCCTAGCGCTAGTCGGATAAACCGA
1 TTTGCGCCCAACACTAGTCGGATAAACCGA
247820 AAAATACATA
Statistics
Matches: 206, Mismatches: 72, Indels: 25
0.68 0.24 0.08
Matches are distributed among these distances:
34 1 0.00
35 26 0.13
36 92 0.45
37 4 0.02
38 32 0.16
39 2 0.01
40 49 0.24
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (36 bp):
TTTGCGCCCAACACTAGTCGGATAAACCGACAATGA
Found at i:247621 original size:40 final size:39
Alignment explanation
Indices: 247569--247779 Score: 134
Period size: 40 Copynumber: 5.5 Consensus size: 39
247559 AATGTTTTGC
* *
247569 GCCCAACGCTAGTCGGATAAACTGACGATATCAAATGTGT
1 GCCCAACACTAGTCAGATAAACTGACGATATCAAAT-TGT
* ***
247609 GCCCAACACTAGTCAGATAAACCGAC-A-AT-GTTTTGCT
1 GCCCAACACTAGTCAGATAAACTGACGATATCAAATTG-T
* **
247646 -CCCAGCGTTAGTCAGATAAA-TCGACGATATCAAATGTGT
1 GCCCAACACTAGTCAGATAAACT-GACGATATCAAAT-TGT
* * * * * **
247685 ACCCAACACTAGTCGGATAAACCGAC-A-AT-GAGTTAC
1 GCCCAACACTAGTCAGATAAACTGACGATATCAAATTGT
* * * *
247721 GCCCAGCGCTAGTTAGATAAATTGACGATATCAAA-TGT
1 GCCCAACACTAGTCAGATAAACTGACGATATCAAATTGT
*
247759 GCCCAACACTAGTCGGATAAA
1 GCCCAACACTAGTCAGATAAA
247780 TCAACAATGA
Statistics
Matches: 123, Mismatches: 37, Indels: 24
0.67 0.20 0.13
Matches are distributed among these distances:
36 42 0.34
37 6 0.05
38 26 0.21
39 5 0.04
40 44 0.36
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (39 bp):
GCCCAACACTAGTCAGATAAACTGACGATATCAAATTGT
Found at i:247658 original size:76 final size:76
Alignment explanation
Indices: 247530--247816 Score: 364
Period size: 76 Copynumber: 3.8 Consensus size: 76
247520 CGACGATAGA
** * * * * *
247530 TGTGCCCTGCACTAGTTGAATAAACCGACAATGTTTTGCGCCCAACGCTAGTCGGATAAACTGAC
1 TGTGCCCAACACTAGTCGGATAAACCGACAATGATTTGCGCCCAGCGCTAGTCAGATAAACTGAC
247595 GATATCAAATG
66 GATATCAAATG
* * * *
247606 TGTGCCCAACACTAGTCAGATAAACCGACAATGTTTTGCTCCCAGCGTTAGTCAGATAAA-TCGA
1 TGTGCCCAACACTAGTCGGATAAACCGACAATGATTTGCGCCCAGCGCTAGTCAGATAAACT-GA
247670 CGATATCAAATG
65 CGATATCAAATG
* * * * *
247682 TGTACCCAACACTAGTCGGATAAACCGACAATGAGTTACGCCCAGCGCTAGTTAGATAAATTGAC
1 TGTGCCCAACACTAGTCGGATAAACCGACAATGATTTGCGCCCAGCGCTAGTCAGATAAACTGAC
247747 GATATCAAA--
66 GATATCAAATG
* * * *
247756 TGTGCCCAACACTAGTCGGATAAATCAACAATGATTTGCGCCTAGCGCTAGTCGGATAAAC
1 TGTGCCCAACACTAGTCGGATAAACCGACAATGATTTGCGCCCAGCGCTAGTCAGATAAAC
247817 CGAAAAATAC
Statistics
Matches: 183, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
74 52 0.28
75 1 0.01
76 129 0.70
77 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (76 bp):
TGTGCCCAACACTAGTCGGATAAACCGACAATGATTTGCGCCCAGCGCTAGTCAGATAAACTGAC
GATATCAAATG
Found at i:254804 original size:41 final size:41
Alignment explanation
Indices: 254744--254842 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
254734 CTATATGATT
* *
254744 AGCACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAACG
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
*
254784 AGCACTAAGTGTGCGAAATTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
*
254825 GGCACTAAGTGTGCGAAA
1 AGCACTAAGTGTGCGAAA
254843 CCGAGATCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 15 0.28
41 39 0.72
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.24
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAATTAAATAATGAGGTTAAATAACG
Found at i:255984 original size:4 final size:4
Alignment explanation
Indices: 255977--256002 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
255967 TAATACATAG
255977 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
256003 TATATATATA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:262257 original size:41 final size:41
Alignment explanation
Indices: 262212--262356 Score: 245
Period size: 41 Copynumber: 3.5 Consensus size: 41
262202 GACTTTAAGT
262212 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
262253 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAAGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
262294 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
262335 CTAGCAGGCTAAGTGTCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
262357 ATATGTTAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:263035 original size:164 final size:165
Alignment explanation
Indices: 262759--263091 Score: 596
Period size: 164 Copynumber: 2.0 Consensus size: 165
262749 TGTTCGTTTA
262759 TATGTATTTTAGATATGCTATAAACTTACTAAGCTATAAAAGCTTACTTTGATTGTTTTTGTCCA
1 TATGTATTTTAGATATGCTATAAACTTACTAAGCTATAAAAGCTTACTTTGATTGTTTTTGTCCA
262824 TTTGTTTTATAGATAAAAACCAAGCTGCAGACTCGAGGATCGTTAGCGAAGATCATCACTCTATC
66 TTTGTTTTATAGATAAAAACCAAGCTGCAGACTCGAGGATCGTTAGCGAAGATCATCACTCTATC
* * *
262889 TACTGTCTCGGTATTAAAACGTTTAAATTTTAACT
131 TACTGTCTCGATATTAAAAAGTTCAAATTTTAACT
262924 TATG-ATTTTAGATATGCTATAAACTTACTAAGCTATAAAAGCTTACTTTGATTGTTTTTGTCCA
1 TATGTATTTTAGATATGCTATAAACTTACTAAGCTATAAAAGCTTACTTTGATTGTTTTTGTCCA
* *
262988 TTTGTTTTATAGATAAAAACCAAGCTGCAGACTCGGGGATCGTTAGCGAAGTTCATCACTCTATC
66 TTTGTTTTATAGATAAAAACCAAGCTGCAGACTCGAGGATCGTTAGCGAAGATCATCACTCTATC
* *
263053 TATTGTCTCGATATTAAAAAGTTCGAATTTTAACT
131 TACTGTCTCGATATTAAAAAGTTCAAATTTTAACT
263088 TATG
1 TATG
263092 GAATGTATAG
Statistics
Matches: 161, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
164 157 0.98
165 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (165 bp):
TATGTATTTTAGATATGCTATAAACTTACTAAGCTATAAAAGCTTACTTTGATTGTTTTTGTCCA
TTTGTTTTATAGATAAAAACCAAGCTGCAGACTCGAGGATCGTTAGCGAAGATCATCACTCTATC
TACTGTCTCGATATTAAAAAGTTCAAATTTTAACT
Found at i:267246 original size:37 final size:38
Alignment explanation
Indices: 267189--267263 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
267179 TTCTTCAATC
267189 TAGCCCAATTGCTTCTCTTTTTTCTCTTTTGACCCCAA
1 TAGCCCAATTGCTTCTCTTTTTTCTCTTTTGACCCCAA
267227 TAGCCCAATT-CTTCTCTTTTTTCTCTTTTGACCCCAA
1 TAGCCCAATTGCTTCTCTTTTTTCTCTTTTGACCCCAA
267264 ATTGCACCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 27 0.73
38 10 0.27
ACGTcount: A:0.16, C:0.32, G:0.07, T:0.45
Consensus pattern (38 bp):
TAGCCCAATTGCTTCTCTTTTTTCTCTTTTGACCCCAA
Found at i:268744 original size:11 final size:11
Alignment explanation
Indices: 268730--268754 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
268720 ACTCATCATC
268730 AACACAAAATT
1 AACACAAAATT
268741 AACACAAAATT
1 AACACAAAATT
268752 AAC
1 AAC
268755 TCATATAATA
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:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (11 bp):
AACACAAAATT
Found at i:283502 original size:21 final size:20
Alignment explanation
Indices: 283476--283515 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
283466 ACTTATTATA
283476 GAAATTTTTGAAGATTTTTTT
1 GAAATTTTTGAA-ATTTTTTT
*
283497 GAAATTTTTGTAATTTTTT
1 GAAATTTTTGAAATTTTTT
283516 AGAGCGGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (20 bp):
GAAATTTTTGAAATTTTTTT
Found at i:287887 original size:4 final size:4
Alignment explanation
Indices: 287878--287913 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
287868 GACCGACTTC
*
287878 AAAG AAAG AAAG AAAG AAAG AAAAG CAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAA
287914 ATTTACCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:287907 original size:13 final size:13
Alignment explanation
Indices: 287878--287914 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
287868 GACCGACTTC
287878 AAAGAAAG-AAAG
1 AAAGAAAGAAAAG
287890 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
*
287903 CAAGAAAGAAAA
1 AAAGAAAGAAAA
287915 TTTACCTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.76, C:0.03, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:289326 original size:11 final size:11
Alignment explanation
Indices: 289310--289482 Score: 123
Period size: 11 Copynumber: 15.9 Consensus size: 11
289300 TATTTTTTAA
289310 TTTTAAAATAT
1 TTTTAAAATAT
289321 TTTTAAAATACT
1 TTTTAAAATA-T
* *
289333 TTTT---TTAA
1 TTTTAAAATAT
289341 TTTTAAAATAT
1 TTTTAAAATAT
289352 TTTTAAAATAT
1 TTTTAAAATAT
289363 TTTTAAAATACTT
1 TTTTAAAATA--T
** *
289376 TTTTAATTTTTT
1 TTTTAA-AATAT
289388 ATTTTAAAATAT
1 -TTTTAAAATAT
289400 TTTTAAAATACT
1 TTTTAAAATA-T
**
289412 TTTTTTAAT-T
1 TTTTAAAATAT
*
289422 TTTT----TAA
1 TTTTAAAATAT
289429 TTTTAAAATAT
1 TTTTAAAATAT
289440 TTTTAAAATACT
1 TTTTAAAATA-T
*
289452 TTTTTAAATACT
1 TTTTAAAATA-T
289464 TTTT-AAA-AT
1 TTTTAAAATAT
289473 TTTTAAAATA
1 TTTTAAAATA
289483 AATTTTTGGT
Statistics
Matches: 130, Mismatches: 15, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.03
8 4 0.03
9 7 0.05
10 9 0.07
11 59 0.45
12 32 0.25
13 13 0.10
14 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:289340 original size:31 final size:30
Alignment explanation
Indices: 289302--289366 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 30
289292 AATATATTTA
289302 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATA-T
289333 TTTTTTAATTTTAAAATATTTTTAAAATAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAT
289363 TTTT
1 TTTT
289367 AAAATACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAT
Found at i:289392 original size:79 final size:78
Alignment explanation
Indices: 289301--289458 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 78
289291 AAATATATTT
*
289301 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAAATATTTTTAAAATATTTT
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTT--AATAATTTTAAAATATTTT
289366 TAAAATACTTTTTTA
64 TAAAATACTTTTTTA
**
289381 ATTTTTT-ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTA
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAATAATTTTAAAATATTTTTA
289445 AAATACTTTTTTA
66 AAATACTTTTTTA
289458 A
1 A
289459 ATACTTTTTA
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
77 32 0.43
79 36 0.48
80 7 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (78 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAATAATTTTAAAATATTTTTA
AAATACTTTTTTA
Found at i:291238 original size:10 final size:9
Alignment explanation
Indices: 291225--291257 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
291215 AAACAAAATA
291225 GAAAAATTT
1 GAAAAATTT
291234 AGAAAAATTT
1 -GAAAAATTT
291244 G-AAAATTT
1 GAAAAATTT
291252 GAAAAA
1 GAAAAA
291258 CAGGTGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (9 bp):
GAAAAATTT
Found at i:291972 original size:10 final size:9
Alignment explanation
Indices: 291959--291991 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
291949 AAACAAAATA
291959 GAAAAATTT
1 GAAAAATTT
291968 AGAAAAATTT
1 -GAAAAATTT
291978 G-AAAATTT
1 GAAAAATTT
291986 GAAAAA
1 GAAAAA
291992 CAGGTGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (9 bp):
GAAAAATTT
Found at i:292368 original size:64 final size:64
Alignment explanation
Indices: 292267--292394 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
292257 CTACAGGTTT
* * *
292267 ACCAAATAAATATCAGGATTTCCATTTATACATAAGATTTCATATTCCAAGATTGCAAAACATA
1 ACCAAATAAACATCAGGATTTCCATTTATACATAAGATTTCATATTCCAACATTACAAAACATA
* *
292331 ACCAAATAAACATCATGATTTCCATTTATACATAAGATTTCATATTCCAACATTATAAAACATA
1 ACCAAATAAACATCAGGATTTCCATTTATACATAAGATTTCATATTCCAACATTACAAAACATA
292395 CTCAAAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (64 bp):
ACCAAATAAACATCAGGATTTCCATTTATACATAAGATTTCATATTCCAACATTACAAAACATA
Found at i:292930 original size:20 final size:20
Alignment explanation
Indices: 292902--292952 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
292892 CATAGATGCA
292902 AAACAGGGGCACAAATGTGC
1 AAACAGGGGCACAAATGTGC
** **
292922 AGTCAGGGGCACTGATGTGC
1 AAACAGGGGCACAAATGTGC
292942 AAACAGGGGCA
1 AAACAGGGGCA
292953 GCGAAGTGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (20 bp):
AAACAGGGGCACAAATGTGC
Found at i:293287 original size:179 final size:181
Alignment explanation
Indices: 292941--293305 Score: 671
Period size: 179 Copynumber: 2.0 Consensus size: 181
292931 CACTGATGTG
292941 CAAACAGGGGCAGCGAAGTGTGTACATAAATAATTGCAATTCATATGGTTATATAAATAACCAAA
1 CAAACAGGGGCAGCGAAGTGTGTACATAAATAATTGCAATTCATATGGTTATATAAATAACCAAA
293006 ATAATTTCACATTTATATATATATATCAATTAACTAGAAATCAATAATCTAAAACACAAATAAAT
66 ATAATTTCACATTTATATATATATATCAATTAACTAGAAATCAATAATCTAAAACACAAATAAAT
*
293071 TACAAATCTAAAGAAAAACATTCTAATCTTACCTACGATCCATTCCCAATT
131 TACAAATCTAAAGAAAAACATTATAATCTTACCTACGATCCATTCCCAATT
*
293122 CAAATAGGGGCAGCGAAGTGTGTACATAAATAATTGCAATTCATATGGTTATATAAATAACCAAA
1 CAAACAGGGGCAGCGAAGTGTGTACATAAATAATTGCAATTCATATGGTTATATAAATAACCAAA
*
293187 ATAATTTCACATTTATATATA-A-ATCAATTAACTAGAAATCAGTAATCTAAAACACAAATAAAT
66 ATAATTTCACATTTATATATATATATCAATTAACTAGAAATCAATAATCTAAAACACAAATAAAT
* *
293250 TACAAATCTAAAGAAAAACATTATAATCTTTCCTACGATCCATTCCGAATT
131 TACAAATCTAAAGAAAAACATTATAATCTTACCTACGATCCATTCCCAATT
293301 CAAAC
1 CAAAC
293306 GCAAGGACTA
Statistics
Matches: 178, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
179 92 0.52
180 1 0.01
181 85 0.48
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (181 bp):
CAAACAGGGGCAGCGAAGTGTGTACATAAATAATTGCAATTCATATGGTTATATAAATAACCAAA
ATAATTTCACATTTATATATATATATCAATTAACTAGAAATCAATAATCTAAAACACAAATAAAT
TACAAATCTAAAGAAAAACATTATAATCTTACCTACGATCCATTCCCAATT
Found at i:294116 original size:108 final size:108
Alignment explanation
Indices: 293927--294142 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
293917 ATTTTGGTTG
293927 CTATTAGAGAAAGATGATGATTCATCATTTGTATTTTATTTCTTTTAGTTTTATTTTATAATTAC
1 CTATTAGAGAAAGATGATGATTCATCATTTGTATTTTATTTCTTTTAGTTTTATTTTATAATTAC
293992 AATTTTATAGTTAGTTCTAAACTTACAATTTTAACAATTAATA
66 AATTTTATAGTTAGTTCTAAACTTACAATTTTAACAATTAATA
294035 CTATTAGAGAAAGATGATGATTCATCATTTGTATTTTATTTTCTTTTAG-TTTATTTTATAATTA
1 CTATTAGAGAAAGATGATGATTCATCATTTGTATTTTA-TTTCTTTTAGTTTTATTTTATAATTA
294099 CAATTTTATAGTTAGTTCTAAACTTACAATTTTAACAATTAATA
65 CAATTTTATAGTTAGTTCTAAACTTACAATTTTAACAATTAATA
294143 GGCCCATAAC
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 97 0.91
109 10 0.09
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (108 bp):
CTATTAGAGAAAGATGATGATTCATCATTTGTATTTTATTTCTTTTAGTTTTATTTTATAATTAC
AATTTTATAGTTAGTTCTAAACTTACAATTTTAACAATTAATA
Found at i:294927 original size:29 final size:29
Alignment explanation
Indices: 294885--294947 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
294875 AAATTTTACC
* *
294885 TAAAACTATACTCATATATATTATTATTA
1 TAAAACAATACTCATATATATTATTATCA
294914 TAAAACAATACTCATATATATTATTATCA
1 TAAAACAATACTCATATATATTATTATCA
294943 TAAAA
1 TAAAA
294948 ATTTCAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAACAATACTCATATATATTATTATCA
Found at i:296307 original size:44 final size:44
Alignment explanation
Indices: 296253--296347 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
296243 ATGGTCCAAC
* *
296253 CATGGTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
296297 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
296341 CATGGAC
1 CATGGAC
296348 CTTGAGATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:296430 original size:3 final size:3
Alignment explanation
Indices: 296422--296471 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
296412 TCACATAACT
296422 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
296470 TA
1 TA
296472 GCAACAATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:301180 original size:17 final size:17
Alignment explanation
Indices: 301158--301205 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
301148 TTTTTATGTT
*
301158 TTATATATATTATTTTA
1 TTATATATATTATTATA
301175 TTATATAATATATATTATA
1 TTATAT-ATAT-TATTATA
301194 TTATATTATATT
1 TTATA-TATATT
301206 GTTTNNNNNN
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 5 0.19
19 15 0.56
20 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATATATTATTATA
Found at i:301185 original size:5 final size:5
Alignment explanation
Indices: 301158--301205 Score: 59
Period size: 5 Copynumber: 10.4 Consensus size: 5
301148 TTTTTATGTT
*
301158 TTATA -TATA TTAT- TT-TA TTATA TAATA -TATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
301204 TT
1 TT
301206 GTTTNNNNNN
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 1 0.03
4 11 0.30
5 25 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:301186 original size:24 final size:24
Alignment explanation
Indices: 301160--301204 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
301150 TTTATGTTTT
301160 ATATATATTAT-TT-TATTATATA
1 ATATATATTATATTATATTATATA
301182 ATATATATTATATTATATTATAT
1 ATATATATTATATTATATTATAT
301205 TGTTTNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATATTATATTATATTATATA
Found at i:302610 original size:37 final size:39
Alignment explanation
Indices: 302551--302646 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
302541 CGGATAGATT
* * * *
302551 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
302588 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
302627 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
302647 TATTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:304912 original size:187 final size:188
Alignment explanation
Indices: 304586--304961 Score: 745
Period size: 187 Copynumber: 2.0 Consensus size: 188
304576 AAACTGGATT
304586 TCTAAAATATAACGGTTTTAAGACTTCCACTGTAAATTATGTTTTGGTAAATAAATGAATTAAAT
1 TCTAAAATATAACGGTTTTAAGACTTCCACTGTAAATTATGTTTTGGTAAATAAATGAATTAAAT
304651 AACACTTTCGAAAATGGTTATAAACGAATACGAACTATGAATCTTGAATGATTTGACGAAACAAC
66 AACACTTTCGAAAATGGTTATAAACGAATACGAACTATGAATCTTGAATGATTTGACGAAACAAC
304716 CCTATTTTCAAAACCCTACCTTGTGACAACTCCAGATTCAGCCATCATGTTTAGGCCA
131 CCTATTTTCAAAACCCTACCTTGTGACAACTCCAGATTCAGCCATCATGTTTAGGCCA
304774 TCTAAAATAT-ACGGTTTTAAGACTTCCACTGTAAATTATGTTTTGGTAAATAAATGAATTAAAT
1 TCTAAAATATAACGGTTTTAAGACTTCCACTGTAAATTATGTTTTGGTAAATAAATGAATTAAAT
304838 AACACTTTCGAAAATGGTTATAAACGAATACGAACTATGAATCTTGAATGATTTGACGAAACAAC
66 AACACTTTCGAAAATGGTTATAAACGAATACGAACTATGAATCTTGAATGATTTGACGAAACAAC
304903 CCTATTTTCAAAACCCTACCTTGTGACAACTCCAGATTCAGCCATCATGTTTAGGCCA
131 CCTATTTTCAAAACCCTACCTTGTGACAACTCCAGATTCAGCCATCATGTTTAGGCCA
304961 T
1 T
304962 GTTTGGGGTG
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 178 0.95
188 10 0.05
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (188 bp):
TCTAAAATATAACGGTTTTAAGACTTCCACTGTAAATTATGTTTTGGTAAATAAATGAATTAAAT
AACACTTTCGAAAATGGTTATAAACGAATACGAACTATGAATCTTGAATGATTTGACGAAACAAC
CCTATTTTCAAAACCCTACCTTGTGACAACTCCAGATTCAGCCATCATGTTTAGGCCA
Found at i:312706 original size:22 final size:22
Alignment explanation
Indices: 312681--312727 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
312671 CATCAATTTC
*
312681 CATTGTCAATTCGTTTTTTTTT
1 CATTGTCAATTCATTTTTTTTT
312703 CATTGTCAATTCATTTTTTTTT
1 CATTGTCAATTCATTTTTTTTT
312725 CAT
1 CAT
312728 AATCAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (22 bp):
CATTGTCAATTCATTTTTTTTT
Found at i:312733 original size:22 final size:22
Alignment explanation
Indices: 312686--312735 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
312676 ATTTCCATTG
* **
312686 TCAATTCGTTTTTTTTTCATTG
1 TCAATTCATTTTTTTTTCATAA
312708 TCAATTCATTTTTTTTTCATAA
1 TCAATTCATTTTTTTTTCATAA
312730 TCAATT
1 TCAATT
312736 TACAGTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.04, T:0.60
Consensus pattern (22 bp):
TCAATTCATTTTTTTTTCATAA
Found at i:313195 original size:45 final size:45
Alignment explanation
Indices: 313120--313295 Score: 289
Period size: 45 Copynumber: 3.9 Consensus size: 45
313110 NNNNNNNNNN
* *
313120 TATTCGACACACAAAGTGCCGAGTCAGTAACAGTAACAGTAACAG
1 TATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAG
* * *
313165 TATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAG
1 TATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAG
*
313210 TATTCAACACACAAAGTGCCGAATCGGTAACAGTAACAGTAACAG
1 TATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAG
*
313255 TATTCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTA
1 TATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTA
313296 GTCGGCACAT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 121 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (45 bp):
TATTCAACACACAAAGTGCCGAATCAGTAACAGTAACAGTAACAG
Found at i:313319 original size:38 final size:39
Alignment explanation
Indices: 313123--313322 Score: 141
Period size: 45 Copynumber: 4.7 Consensus size: 39
313113 NNNNNNNTAT
*
313123 TCGACACACAAAGTGCCGAGTCAGTAACAGTAACAGTAACAGTAT
1 TCGACACACAAAGTGCCGA---A-T--CAGTAACAGTAACAGTAG
* * * *
313168 TCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTAT
1 TCGACACACAAAGTGCCGAA----T--CAGTAACAGTAACAGTAG
* *
313213 TCAACACACAAAGTGCCGAATCGGTAACAGTAACAGTAACAGTAT
1 TCGACACACAAAGTGCCGAA----T--CAGTAACAGTAACAGTAG
313258 TCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAG
1 TCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAG
* * *
313297 TCGGCACA-TAAGTGCCTAATCAGTAA
1 TCGACACACAAAGTGCCGAATCAGTAA
313323 GCCGGCAAAT
Statistics
Matches: 141, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
38 16 0.11
39 24 0.17
41 1 0.01
42 1 0.01
45 99 0.70
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (39 bp):
TCGACACACAAAGTGCCGAATCAGTAACAGTAACAGTAG
Found at i:315119 original size:16 final size:16
Alignment explanation
Indices: 315098--315137 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
315088 TTATTAAGTA
315098 AATTTTGCAATATTCC
1 AATTTTGCAATATTCC
315114 AATTTTGCAATATTCC
1 AATTTTGCAATATTCC
315130 AATTTTGC
1 AATTTTGC
315138 CCTTAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (16 bp):
AATTTTGCAATATTCC
Found at i:315367 original size:32 final size:32
Alignment explanation
Indices: 315329--315390 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
315319 GCCCGTTTTT
* **
315329 AAATAAATACCAAAAATTTATTTTAAAAATTA
1 AAATAAAAACCAAAAAAGTATTTTAAAAATTA
**
315361 AAATAAAAATTAAAAAAGTATTTTAAAAAT
1 AAATAAAAACCAAAAAAGTATTTTAAAAAT
315391 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (32 bp):
AAATAAAAACCAAAAAAGTATTTTAAAAATTA
Found at i:319516 original size:14 final size:14
Alignment explanation
Indices: 319497--319525 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
319487 GAGTTGCTGC
319497 GACGTGGGAGCAAT
1 GACGTGGGAGCAAT
319511 GACGTGGGAGCAAT
1 GACGTGGGAGCAAT
319525 G
1 G
319526 GGGGTGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.45, T:0.14
Consensus pattern (14 bp):
GACGTGGGAGCAAT
Found at i:324293 original size:23 final size:24
Alignment explanation
Indices: 324265--324321 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
324255 AGCCTCTCCA
324265 TTTTTACTTTTTC-CAT-TTTTTAT
1 TTTTTACTTTTTCACATCTTTTT-T
324288 TTTTTA-TTTTTCACATCTTTTTT
1 TTTTTACTTTTTCACATCTTTTTT
*
324311 TTCTT-CTTTTT
1 TTTTTACTTTTT
324322 TTTTGTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 19 0.63
24 5 0.17
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTACTTTTTCACATCTTTTTT
Found at i:324792 original size:6 final size:6
Alignment explanation
Indices: 324781--324818 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
324771 CCCAGCAGGG
324781 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT TTCTTT T
324819 CCCCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:324843 original size:15 final size:15
Alignment explanation
Indices: 324823--324865 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
324813 TCTTTTCCCC
*
324823 CTTTTTTTATTTTTTT
1 CTTTTTTT-TTGTTTT
324839 CTTTTTTTTTGTTTT
1 CTTTTTTTTTGTTTT
324854 CTCTCTTTTTTT
1 CT-T-TTTTTTT
324866 TTGGATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (15 bp):
CTTTTTTTTTGTTTT
Found at i:324847 original size:35 final size:36
Alignment explanation
Indices: 324790--324865 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
324780 GTTCTTTTTC
*
324790 TTTTTCTTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
1 TTTTTATTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
* * *
324826 TTTTTATTTTT-TTCTTT-TTTTTTGTTTTCTCTCTT
1 TTTTTATTTTTCTT-TTTCTTTTTTCTTTTCCCCCTT
324861 TTTTT
1 TTTTT
324866 TTGGATTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (36 bp):
TTTTTATTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
Found at i:324868 original size:19 final size:18
Alignment explanation
Indices: 324781--324867 Score: 72
Period size: 19 Copynumber: 4.8 Consensus size: 18
324771 CCCAGCAGGG
324781 TTCT-TTTTCTTTTTCTTT
1 TTCTCTTTT-TTTTTCTTT
*
324799 TTCTTTTTCTTTTTTCTTT
1 TTCTCTTT-TTTTTTCTTT
* * *
324818 TCCCCCTTTTTTTAT-TTT
1 T-TCTCTTTTTTTTTCTTT
*
324836 TT-TCTTTTTTTTTGTTT
1 TTCTCTTTTTTTTTCTTT
324853 TCTCTCTTTTTTTTT
1 T-TCTCTTTTTTTTT
324868 GGATTGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.16
17 4 0.07
18 9 0.16
19 29 0.52
20 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (18 bp):
TTCTCTTTTTTTTTCTTT
Found at i:332971 original size:3 final size:3
Alignment explanation
Indices: 332963--333004 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
332953 TAGTCCCGTT
*
332963 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
333005 AGCTAATCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:334962 original size:30 final size:30
Alignment explanation
Indices: 334906--334962 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
334896 AATTTAATTC
* *
334906 TTTTTTTTAAATATTTACGATGAAATTAGA
1 TTTTTTTTAAATATTTACAATCAAATTAGA
334936 TTTTTTTTAAA-ATTTGACAATCAAATT
1 TTTTTTTTAAATATTT-ACAATCAAATT
334963 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTTTTTTAAATATTTACAATCAAATTAGA
Found at i:338555 original size:18 final size:20
Alignment explanation
Indices: 338534--338580 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
338524 TGTAAAATTG
338534 AAATAAA-T-TTAGAGCTGC
1 AAATAAACTATTAGAGCTGC
338552 AAATAAAACTAATTAGAGCTGC
1 AAAT-AAACT-ATTAGAGCTGC
338574 AAATAAA
1 AAATAAA
338581 AGCTGTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 1 0.04
21 3 0.12
22 14 0.56
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (20 bp):
AAATAAACTATTAGAGCTGC
Found at i:339762 original size:107 final size:107
Alignment explanation
Indices: 339635--340222 Score: 665
Period size: 110 Copynumber: 5.6 Consensus size: 107
339625 TTTTTTTTAC
* *
339635 TTTTTTTAATTTTTTT-GTATATTTATATTTTACTCTGACACGAAAAAAAAG-AATTTTTTTTAA
1 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAA
* *
339698 ATTTGTACTAGGTGCCGGCCATTGACAGACCAGCACCCCAAAA
66 ATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAA
*
339741 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAAGAAATTTTTTTTT
1 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACAC-GAAAAAAAAGAAA---TTTTTT
339806 TTAAATTTGTACTGGGTGCCGGCCATT---------G-ACCCAAAA
62 TTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
339842 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAA
1 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAA
339907 A-TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAAA
66 ATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC---AAAA
***
339951 TTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACG-----AAA-TTTTTTTTTTTA
1 -TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTT-
* *
340010 AAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCTAAATT
64 -AAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-A
* ****
340056 TTTTTTTAAAATTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAAAAAAATT
1 TTTTTTT--AATTTTTTTCGTATATTTATATCTGACTCTGACACG-AAAAAAAAG-AAATTTTTT
340121 TT-AA-TTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
62 TTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
* *
340165 -----TT--TTTTTTTCGTATATTTATATCTGATTCTGACACAAAAAAAAAGTAAAATTTTTTTT
1 TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAG--AAATTTTTTTT
340223 TACTATTGGG
Statistics
Matches: 420, Mismatches: 27, Indels: 76
0.80 0.05 0.15
Matches are distributed among these distances:
96 21 0.05
97 11 0.03
99 9 0.02
100 51 0.12
101 49 0.12
102 1 0.00
103 1 0.00
104 20 0.05
105 4 0.01
106 58 0.14
107 58 0.14
108 9 0.02
109 6 0.01
110 81 0.19
111 2 0.00
112 35 0.08
114 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (107 bp):
TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAA
ATTTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
Found at i:339860 original size:101 final size:102
Alignment explanation
Indices: 339734--340113 Score: 387
Period size: 101 Copynumber: 3.6 Consensus size: 102
339724 AGACCAGCAC
339734 CCCAAAA-TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAAGAAAT
1 CCCAAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACAC-AAAAAAAAAGAAAT
339798 TTTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTG-A
65 TTTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGCA
*
339835 CCCAAAA-TTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACGAAAAAAAAGAAA--
1 CCCAAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAAATT
339897 -TTTTTTTTAAA-TTGTACTGGGTGCCGGCCATTGACAGGCCAGCA
66 TTTTTTTTTAAATTTGTACTGGGTGCCGGCCATT---------GCA
339941 CCCAAAAAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACAC---------GAA
1 CCC---AAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAA
339997 ATTTTTTTTTTTAAAAATTTGTACTGGGTGCCGGCCATTGACA
63 ATTTTTTTTTTT--AAATTTGTACTGGGTGCCGGCCATTG-CA
*
340040 GGCCAGCACCTAAATTTTTTTTTAAAATTTTTTTTGTATATTTATATCTGACTCTGACACGAAAA
1 --CC--CA---AAA-TTTTTTTT--AATTTTTTTCGTATATTTATATCTGACTCTGACAC-AAAA
340105 AAAAAGAAA
55 AAAAAGAAA
340114 AAAAATTTTA
Statistics
Matches: 236, Mismatches: 2, Indels: 67
0.77 0.01 0.22
Matches are distributed among these distances:
96 21 0.09
97 11 0.05
98 1 0.00
99 2 0.01
100 13 0.06
101 55 0.23
103 4 0.02
104 16 0.07
105 1 0.00
106 41 0.17
107 21 0.09
109 4 0.02
110 42 0.18
116 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (102 bp):
CCCAAAATTTTTTTTAATTTTTTTCGTATATTTATATCTGACTCTGACACAAAAAAAAAGAAATT
TTTTTTTTTAAATTTGTACTGGGTGCCGGCCATTGCA
Found at i:340269 original size:100 final size:98
Alignment explanation
Indices: 340063--340270 Score: 253
Period size: 98 Copynumber: 2.1 Consensus size: 98
340053 ATTTTTTTTT
340063 AAAA-TTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAAAAAAATTTTAATT
1 AAAATTTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAG-AAAAAAATTTTAATT
* * *
340127 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
65 CTACTGGGTGCCGGCCATTCAAAGGCCAGCACCC
* * * **
340161 AAAATTTTTTTTTCGTATATTTATATCTGATTCTGACAC-AAAAAAAAAG-TAAAATTTTTTTTT
1 AAAATTTTTTTTT-GTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAAAAAATTTTAATT
* * *
340224 ACTATTGGGTGCTGGCC-TGTCAAAGGCCGGCACCC
65 -CTACTGGGTGCCGGCCAT-TCAAAGGCCAGCACCC
340259 AAAATTTTTTTT
1 AAAATTTTTTTT
340271 CTTTTTCGTA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
97 11 0.12
98 42 0.44
99 18 0.19
100 24 0.25
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (98 bp):
AAAATTTTTTTTTGTATATTTATATCTGACTCTGACACGAAAAAAAAAGAAAAAAATTTTAATTC
TACTGGGTGCCGGCCATTCAAAGGCCAGCACCC
Found at i:343269 original size:14 final size:14
Alignment explanation
Indices: 343250--343286 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
343240 TACAATATCT
343250 AAATAATAACAACA
1 AAATAATAACAACA
*
343264 AAATAATAGCAACA
1 AAATAATAACAACA
*
343278 TAATAATAA
1 AAATAATAA
343287 AATGGTTGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:347448 original size:24 final size:24
Alignment explanation
Indices: 347421--347537 Score: 92
Period size: 24 Copynumber: 5.2 Consensus size: 24
347411 CTATACCCGT
347421 GTCATTGATGAAACTCAAGCTGAG
1 GTCATTGATGAAACTCAAGCTGAG
* *
347445 GTCA-T-A--AGACTCCAA-ATGAG
1 GTCATTGATGAAACT-CAAGCTGAG
*
347465 GTAATTGATGAAACTCAAGCTGAG
1 GTCATTGATGAAACTCAAGCTGAG
* *
347489 GTCA-T-A--AGACTCCAA-ATGAG
1 GTCATTGATGAAACT-CAAGCTGAG
*
347509 GTAATTGATGAAACTCAAGCTGAG
1 GTCATTGATGAAACTCAAGCTGAG
347533 GTCAT
1 GTCAT
347538 AAGACTCCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
20 22 0.32
21 8 0.12
22 4 0.06
23 8 0.12
24 27 0.39
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (24 bp):
GTCATTGATGAAACTCAAGCTGAG
Found at i:347464 original size:20 final size:20
Alignment explanation
Indices: 347441--347554 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
347431 AAACTCAAGC
347441 TGAGGTCATAAGACTCCAAA
1 TGAGGTCATAAGACTCCAAA
* * *
347461 TGAGGTAATTGATGAAACT-CAAGC
1 TGAGGTCA-T-A--AGACTCCAA-A
347485 TGAGGTCATAAGACTCCAAA
1 TGAGGTCATAAGACTCCAAA
* * *
347505 TGAGGTAATTGATGAAACT-CAAGC
1 TGAGGTCA-T-A--AGACTCCAA-A
347529 TGAGGTCATAAGACTCCAAA
1 TGAGGTCATAAGACTCCAAA
347549 TGAGGT
1 TGAGGT
347555 ATATACATGC
Statistics
Matches: 70, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
20 28 0.40
21 8 0.11
22 4 0.06
23 8 0.11
24 22 0.31
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (20 bp):
TGAGGTCATAAGACTCCAAA
Found at i:347487 original size:44 final size:44
Alignment explanation
Indices: 347424--347555 Score: 264
Period size: 44 Copynumber: 3.0 Consensus size: 44
347414 TACCCGTGTC
347424 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
1 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
347468 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
1 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
347512 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
1 ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
347556 TATACATGCA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 88 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (44 bp):
ATTGATGAAACTCAAGCTGAGGTCATAAGACTCCAAATGAGGTA
Found at i:349017 original size:12 final size:12
Alignment explanation
Indices: 349000--349030 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
348990 ATGGTGAAGA
349000 GTGGTGGCTGTG
1 GTGGTGGCTGTG
349012 GTGGTGGCTGTG
1 GTGGTGGCTGTG
349024 GTGGTGG
1 GTGGTGG
349031 TTGCGGTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.61, T:0.32
Consensus pattern (12 bp):
GTGGTGGCTGTG
Found at i:349042 original size:24 final size:24
Alignment explanation
Indices: 349000--349057 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
348990 ATGGTGAAGA
* * * *
349000 GTGGTGGCTGTGGTGGTGGCTGTG
1 GTGGTGGTTGCGGTAGTGGCTGCG
*
349024 GTGGTGGTTGCGGTAGTGGGTGCG
1 GTGGTGGTTGCGGTAGTGGCTGCG
*
349048 GGGGTGGTTG
1 GTGGTGGTTG
349058 TGGAAGCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.02, C:0.07, G:0.60, T:0.31
Consensus pattern (24 bp):
GTGGTGGTTGCGGTAGTGGCTGCG
Found at i:349060 original size:75 final size:75
Alignment explanation
Indices: 348900--349072 Score: 193
Period size: 75 Copynumber: 2.3 Consensus size: 75
348890 TGGTTGTGGT
* * * *
348900 GCTGGATGTGGAAACGTGGTGAAGAGTGGTGGTTGTGGTAGTGGCTGCGGCAGTGGATGTGGGGG
1 GCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGCTGCGGCAGTGGATGCGGGAG
* * *
348965 TGGTTGTGGT
66 TGGGTGCGGG
* * ** * *
348975 GCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTGGCTGTGGTGGTGGTTGCGGTAG
1 GCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGCTGCGGCAGTGGATGCGGGAG
349040 TGGGTGCGGG
66 TGGGTGCGGG
* * * *
349050 GGTGGTTGTGGAAGCATAGTGAA
1 GCTGGATGTGGAAACATGGTGAA
349073 TAGCGGCAGT
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.14, C:0.07, G:0.51, T:0.27
Consensus pattern (75 bp):
GCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGCTGCGGCAGTGGATGCGGGAG
TGGGTGCGGG
Found at i:349199 original size:60 final size:60
Alignment explanation
Indices: 349039--349207 Score: 257
Period size: 60 Copynumber: 2.8 Consensus size: 60
349029 GGTTGCGGTA
* * * * **
349039 GTGGGTGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGTTGTGGCTCTGGCTGTG
1 GTGGGTGCGGCGGAGGTTGTGGAAGCATGGTGAATAGCAGTGGTTGTGGCTCTGGCTGTG
* * *
349099 GTGGGTGTGGCGGAGGTTGCGGAAGCATGGTGAATAGCAGTGGCTGTGGCTCTGGCTGTG
1 GTGGGTGCGGCGGAGGTTGTGGAAGCATGGTGAATAGCAGTGGTTGTGGCTCTGGCTGTG
349159 GTGGGTGCGGCGGAGGTTGTGGAAGCATGGTGAATAGCAGTGGTTGTGG
1 GTGGGTGCGGCGGAGGTTGTGGAAGCATGGTGAATAGCAGTGGTTGTGG
349208 ACTCAAGGAG
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.14, C:0.11, G:0.49, T:0.25
Consensus pattern (60 bp):
GTGGGTGCGGCGGAGGTTGTGGAAGCATGGTGAATAGCAGTGGTTGTGGCTCTGGCTGTG
Found at i:356292 original size:13 final size:13
Alignment explanation
Indices: 356274--356313 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
356264 AGTTCTTCAT
356274 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
356287 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
356300 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
356313 T
1 T
356314 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:360603 original size:19 final size:19
Alignment explanation
Indices: 360579--360616 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
360569 TGAATTGTTG
*
360579 CTTTTATCTGTGTTTTTCT
1 CTTTTATCTATGTTTTTCT
360598 CTTTTATCTATGTTTTTCT
1 CTTTTATCTATGTTTTTCT
360617 TTCATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (19 bp):
CTTTTATCTATGTTTTTCT
Found at i:366620 original size:17 final size:18
Alignment explanation
Indices: 366587--366620 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
366577 GATATTAAGT
366587 AAATTAATTTGTTTTAAA
1 AAATTAATTTGTTTTAAA
366605 AAATTAATTT-TTTTAA
1 AAATTAATTTGTTTTAA
366621 TTTTCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATTAATTTGTTTTAAA
Found at i:373343 original size:39 final size:39
Alignment explanation
Indices: 373300--373378 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
373290 TCATCAATAT
373300 CCCCTGCATAATTACTATCAATATACCCAAAAAAATTAA
1 CCCCTGCATAATTACTATCAATATACCCAAAAAAATTAA
*
373339 CCCCTGCATAATTACTATCAGTATACCCAAAAAAATTAA
1 CCCCTGCATAATTACTATCAATATACCCAAAAAAATTAA
373378 C
1 C
373379 ATCAATATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.27, G:0.04, T:0.25
Consensus pattern (39 bp):
CCCCTGCATAATTACTATCAATATACCCAAAAAAATTAA
Found at i:375996 original size:3 final size:3
Alignment explanation
Indices: 375988--376076 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
375978 TATATCTCAT
375988 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
376036 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
376077 TTAAAATTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:377144 original size:21 final size:21
Alignment explanation
Indices: 377119--377161 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
377109 CATGAACTAT
377119 TTTAAACTTCAAAGGAAATAA
1 TTTAAACTTCAAAGGAAATAA
377140 TTTAAACTTCAAAGGAAATAA
1 TTTAAACTTCAAAGGAAATAA
377161 T
1 T
377162 ATGTTTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (21 bp):
TTTAAACTTCAAAGGAAATAA
Found at i:381366 original size:18 final size:18
Alignment explanation
Indices: 381345--381386 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
381335 TATAATTATA
*
381345 ATTATATTTATCTATTCT
1 ATTATATTTATATATTCT
381363 ATTATA--TATATATTCT
1 ATTATATTTATATATTCT
*
381379 AATATATT
1 ATTATATT
381387 GTTGATTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 14 0.70
18 6 0.30
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATATTTATATATTCT
Found at i:381967 original size:33 final size:33
Alignment explanation
Indices: 381925--381988 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
381915 AGGAAATCTA
* *
381925 CACAACTTGCCATCCCCTTGTCCGCCTGATGTC
1 CACAACTTGCCATCCCCTCGTCCGCCAGATGTC
*
381958 CACAACTTGCCATCCTCTCGTCCGCCAGATG
1 CACAACTTGCCATCCCCTCGTCCGCCAGATG
381989 GCCATAGCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.42, G:0.16, T:0.25
Consensus pattern (33 bp):
CACAACTTGCCATCCCCTCGTCCGCCAGATGTC
Found at i:382003 original size:33 final size:33
Alignment explanation
Indices: 381925--382004 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
381915 AGGAAATCTA
* * * *
381925 CACAACTTGCCATCCCCTTGTCCGCCTGATGTC
1 CACAACTCGCCATCCCCTCGTCCGCCAGATGGC
* *
381958 CACAACTTGCCATCCTCTCGTCCGCCAGATGGC
1 CACAACTCGCCATCCCCTCGTCCGCCAGATGGC
* *
381991 CATAGCTCGCCATC
1 CACAACTCGCCATC
382005 TCCTTATTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.17, C:0.42, G:0.16, T:0.24
Consensus pattern (33 bp):
CACAACTCGCCATCCCCTCGTCCGCCAGATGGC
Found at i:384832 original size:31 final size:31
Alignment explanation
Indices: 384785--384845 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
384775 AAAGAAGGGT
384785 AAAAATAACAGTGCAAAAACAATTTGA-TTTTC
1 AAAAATAACAGTGC-AAAAC-ATTTGACTTTTC
384817 AAAAATAA-AGTGCAAAACATTTGACTTTT
1 AAAAATAACAGTGCAAAACATTTGACTTTT
384846 TATACTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.21
30 9 0.32
31 5 0.18
32 8 0.29
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (31 bp):
AAAAATAACAGTGCAAAACATTTGACTTTTC
Found at i:388352 original size:20 final size:21
Alignment explanation
Indices: 388327--388366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
388317 TTATAAGATA
*
388327 AACTA-TACAAATTATCATTC
1 AACTATTAAAAATTATCATTC
*
388347 AACTATTAAAAATTTTCATT
1 AACTATTAAAAATTATCATT
388367 TTAAACTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (21 bp):
AACTATTAAAAATTATCATTC
Found at i:394236 original size:106 final size:106
Alignment explanation
Indices: 394059--394268 Score: 339
Period size: 106 Copynumber: 2.0 Consensus size: 106
394049 CTTTAAAATT
* * * * *
394059 TTAAGAGGATATTTGGCTATTTGGTCGAACAAGAAATCGGAACCCAGCACGTTAGGGCATGTTTT
1 TTAAAAGGATATTTAGCTATTTGGTCAAACAAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
394124 CCCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAACC
66 CCCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAACC
*
394165 TTAAAAGGATATTTAGCTATTTGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
1 TTAAAAGGATATTTAGCTATTTGGTCAAACAAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
* * *
394230 CTCGAATTTTCAAACGCAAAATATTGTCTTACTTTGAAA
66 CCCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
394269 TTTTCATTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
TTAAAAGGATATTTAGCTATTTGGTCAAACAAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
CCCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAACC
Found at i:394642 original size:21 final size:21
Alignment explanation
Indices: 394601--394642 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
394591 CGAAATATAT
*
394601 ATAAATTAAAAAATAATAAAA
1 ATAAATTAAAAAACAATAAAA
* *
394622 ATAAA-TAAATAACAATGAAA
1 ATAAATTAAAAAACAATAAAA
394642 A
1 A
394643 CAATTAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAATTAAAAAACAATAAAA
Found at i:396388 original size:45 final size:45
Alignment explanation
Indices: 396315--396403 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
396305 GCTCTAATGT
396315 AACTTCAGAGAGATAAGATCTATGTTTTTTAATCCGCTCCACTAC
1 AACTTCAGAGAGATAAGATCTATGTTTTTTAATCCGCTCCACTAC
* * * * *
396360 AACTTCAGGGAGATAGGAT-TAGTTTTTTTTTATCCGCTTCACTA
1 AACTTCAGAGAGATAAGATCTA-TGTTTTTTAATCCGCTCCACTA
396404 TCAGTACAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (45 bp):
AACTTCAGAGAGATAAGATCTATGTTTTTTAATCCGCTCCACTAC
Found at i:396437 original size:7 final size:7
Alignment explanation
Indices: 396422--396453 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
396412 GGAAGACAAG
*
396422 ATCTGCA
1 ATCTCCA
396429 ATCTCCA
1 ATCTCCA
396436 ATCTCCA
1 ATCTCCA
396443 ATCTCCA
1 ATCTCCA
396450 ATCT
1 ATCT
396454 ACTTCGCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.28, C:0.38, G:0.03, T:0.31
Consensus pattern (7 bp):
ATCTCCA
Found at i:396580 original size:45 final size:45
Alignment explanation
Indices: 396450--396754 Score: 348
Period size: 45 Copynumber: 6.8 Consensus size: 45
396440 CCAATCTCCA
* *
396450 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCG
* * * ** ** * *
396495 ACCTACTCCACTG-CTGTTTAGGGAGACAAGATATGCTATCTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCG
*
396539 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTC-
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCG
*
396583 AGTCTACTTCACTGCCAATACAGGAAGACAAGA-CTTGCTATCTTCG
1 A-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTTCG
* * * *
396629 ATCTACTTCGCTGCCAATACAGGAAGATAAGATATGTTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCG
* * *
396674 ATCTACTTTGCTACCAATACAGGAAGACAATA-CTTGCTATCTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTTCG
* * *
396719 ATCTATTTCGCTGCCAATACAGGAAAATAAGATCTG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
396755 TTGTTTTTAG
Statistics
Matches: 212, Mismatches: 41, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
44 35 0.17
45 175 0.83
46 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCG
Found at i:396654 original size:90 final size:90
Alignment explanation
Indices: 396450--396754 Score: 400
Period size: 90 Copynumber: 3.4 Consensus size: 90
396440 CCAATCTCCA
* * * * * ** *
396450 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACAATCTTC-GACCTACTCCACTG-CTGTT
1 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAG-TCTACTTCACTGCCAATA
* *
396513 TAGGGAGACAAGA-TATGCTATCTTCG
65 CAGGAAGACAAGACT-TGCTATCTTCG
396539 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATAC
1 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATAC
396604 AGGAAGACAAGACTTGCTATCTTCG
66 AGGAAGACAAGACTTGCTATCTTCG
* * * ** *
396629 ATCTACTTCGCTGCCAATACAGGAAGATAAGATATGTTATCTTCAATCTACTTTGCTACCAATAC
1 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATAC
*
396694 AGGAAGACAATACTTGCTATCTTCG
66 AGGAAGACAAGACTTGCTATCTTCG
* *
396719 ATCTATTTCGCTGCCAATACAGGAAAATAAGATCTG
1 ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTG
396755 TTGTTTTTAG
Statistics
Matches: 193, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
89 51 0.26
90 141 0.73
91 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (90 bp):
ATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTTCACTGCCAATAC
AGGAAGACAAGACTTGCTATCTTCG
Found at i:396792 original size:135 final size:135
Alignment explanation
Indices: 396451--396793 Score: 324
Period size: 135 Copynumber: 2.5 Consensus size: 135
396441 CAATCTCCAA
* * * * * * * **
396451 TCTACTTCGCTGCCAATACAGGAAGACAAGA-TCTACAATCTTCGACCTACTCCACTG-CTGTTT
1 TCTACTTCACTGCCAATACAGGAAAACAAGACT-TGCTATCTTAGATCTACTCCGCTGACAATTT
* * * *
396514 AGGGAGACAAGATATGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTAT
65 AGGGAGATAAGATATGCTATCTTCAATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTAT
396579 CTTCAG
130 CTTCAG
* * * * **
396585 TCTACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCGCTGCCAATACA
1 TCTACTTCACTGCCAATACAGGAAAACAAGACTTGCTATCTTAGATCTACTCCGCTGACAATTTA
* * * *
396650 GGAAGATAAGATATGTTATCTTCAATCTACTTTGCTACCAATACAGGAAGACAATA-CTTGCTAT
66 GGGAGATAAGATATGCTATCTTCAATCTACTTCGCTACCAATACAGGAAGACAAGATC-TGCTAT
396714 CTTC-G
130 CTTCAG
* * * *
396719 ATCTATTTCGCTGCCAATACAGGAAAATAAGATCTGTTG-T-TTTTAG-TCTACTCCGCT-ACAA
1 -TCTACTTCACTGCCAATACAGGAAAACAAGA-C--TTGCTATCTTAGATCTACTCCGCTGACAA
396780 TTTTAGGGAGATAA
62 -TTTAGGGAGATAA
396794 TACTTGATAT
Statistics
Matches: 172, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
134 54 0.31
135 109 0.63
136 5 0.03
137 1 0.01
138 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (135 bp):
TCTACTTCACTGCCAATACAGGAAAACAAGACTTGCTATCTTAGATCTACTCCGCTGACAATTTA
GGGAGATAAGATATGCTATCTTCAATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATC
TTCAG
Done.