Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007880.1 Hibiscus syriacus cultivar Beakdansim tig00110258_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1382630
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 5
Found at i:308838 original size:2 final size:2
Alignment explanation
Indices: 308831--308857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
308821 TACTCAATCC
308831 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
308858 CAATTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:313089 original size:2 final size:2
Alignment explanation
Indices: 313084--313115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
313074 ACACACACAC
313084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
313116 GAGTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314087 original size:16 final size:16
Alignment explanation
Indices: 314066--314117 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
314056 TGTGACTCAA
*
314066 CTCGTTGCTCGTTAAG
1 CTCGTTACTCGTTAAG
* *
314082 CTCGTTACTTGTTAAT
1 CTCGTTACTCGTTAAG
**
314098 CTTATTACTCGTTAAG
1 CTCGTTACTCGTTAAG
314114 CTCG
1 CTCG
314118 ATGCTCATTG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (16 bp):
CTCGTTACTCGTTAAG
Found at i:316403 original size:16 final size:16
Alignment explanation
Indices: 316382--316426 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
316372 TGTGGCTCAA
*
316382 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCATTAAG
316398 CTCGTTGCTCATTAAG
1 CTCGTTGCTCATTAAG
*
316414 CTCGATGCTCATT
1 CTCGTTGCTCATT
316427 GCTCGCCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:317891 original size:10 final size:10
Alignment explanation
Indices: 317862--317930 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
317852 GCTGCTGGAA
317862 AACCGGTTTG
1 AACCGGTTTG
*
317872 -ACCAGTTTTG
1 AACC-GGTTTG
317882 AACCGGTTTG
1 AACCGGTTTG
*
317892 -ACCGGTTCG
1 AACCGGTTTG
*
317901 AACTGGTTTG
1 AACCGGTTTG
*
317911 -ACCGGTCTG
1 AACCGGTTTG
*
317920 AACCGGGTTG
1 AACCGGTTTG
317930 A
1 A
317931 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:317908 original size:19 final size:19
Alignment explanation
Indices: 317862--317932 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
317852 GCTGCTGGAA
* *
317862 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
317882 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
*
317901 AACTGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
317920 AACCGGGTTGACC
1 AACCGGTTTGACC
317933 CGACCCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.04
19 30 0.67
20 13 0.29
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:317949 original size:17 final size:17
Alignment explanation
Indices: 317927--317983 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
317917 CTGAACCGGG
*
317927 TTGACCCGACCCGACTA
1 TTGACCCGACCCGACCA
*
317944 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCA
*
317961 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCA
317978 TTGACC
1 TTGACC
317984 GTTGACCGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (17 bp):
TTGACCCGACCCGACCA
Found at i:317983 original size:7 final size:7
Alignment explanation
Indices: 317973--318009 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
317963 GACCCGACCC
317973 GACCGTT
1 GACCGTT
317980 GACCGTT
1 GACCGTT
317987 GACCG-T
1 GACCGTT
317993 GACCGTT
1 GACCGTT
318000 GACCGTT
1 GACCGTT
318007 GAC
1 GAC
318010 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:317997 original size:13 final size:13
Alignment explanation
Indices: 317973--318005 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
317963 GACCCGACCC
317973 GACCGTTGACCGTT
1 GACCG-TGACCGTT
317987 GACCGTGACCGTT
1 GACCGTGACCGTT
318000 GACCGT
1 GACCGT
318006 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:324509 original size:10 final size:10
Alignment explanation
Indices: 324480--324567 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
324470 GCTGCTGGAA
324480 AACCGGTTTG
1 AACCGGTTTG
*
324490 -ACCAGTTTTG
1 AACC-GGTTTG
324500 AACCGGTTTG
1 AACCGGTTTG
*
324510 -ACCGGTTCG
1 AACCGGTTTG
324519 AACCGGTTTG
1 AACCGGTTTG
*
324529 -ACCGGTCTG
1 AACCGGTTTG
324538 AACCGGTTTG
1 AACCGGTTTG
*
324548 -ACCGGTCTG
1 AACCGGTTTG
*
324557 AACCGGGTTG
1 AACCGGTTTG
324567 A
1 A
324568 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:324523 original size:19 final size:19
Alignment explanation
Indices: 324480--324569 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
324470 GCTGCTGGAA
* *
324480 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
324500 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
324519 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
324538 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
324557 AACCGGGTTGACC
1 AACCGGTTTGACC
324570 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:324586 original size:17 final size:17
Alignment explanation
Indices: 324564--324620 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
324554 CTGAACCGGG
*
324564 TTGACCCGACCCGACTA
1 TTGACCCGACCCGACCA
*
324581 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCA
*
324598 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCA
324615 TTGACC
1 TTGACC
324621 GTTGACCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (17 bp):
TTGACCCGACCCGACCA
Found at i:324620 original size:7 final size:7
Alignment explanation
Indices: 324610--324653 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
324600 GACCCGACCC
324610 GACCGTT
1 GACCGTT
324617 GACCGTT
1 GACCGTT
*
324624 GACCATT
1 GACCGTT
324631 GACCG-T
1 GACCGTT
324637 GACCGTT
1 GACCGTT
324644 GACCGTT
1 GACCGTT
324651 GAC
1 GAC
324654 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:324641 original size:20 final size:21
Alignment explanation
Indices: 324610--324653 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
324600 GACCCGACCC
324610 GACCGTTGACCGTTGACCATT
1 GACCGTTGACCGTTGACCATT
*
324631 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCGTTGACCATT
324651 GAC
1 GAC
324654 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (21 bp):
GACCGTTGACCGTTGACCATT
Found at i:326487 original size:2 final size:2
Alignment explanation
Indices: 326482--326551 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
326472 TTTTCTCTCT
*
326482 CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
326524 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
326552 TATATATATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:326556 original size:2 final size:2
Alignment explanation
Indices: 326551--326578 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
326541 ACACACACAC
326551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
326579 GATTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332285 original size:23 final size:23
Alignment explanation
Indices: 332255--332320 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
332245 CCATGCATCT
332255 ACCTTCTGGAAGCTGCTGACTGG
1 ACCTTCTGGAAGCTGCTGACTGG
*
332278 ACCTTCTGGAAGCTACTGACTGG
1 ACCTTCTGGAAGCTGCTGACTGG
* * *
332301 ATCATCTAGAAGCTGCTGAC
1 ACCTTCTGGAAGCTGCTGAC
332321 GTGGCAGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
ACCTTCTGGAAGCTGCTGACTGG
Found at i:338529 original size:17 final size:17
Alignment explanation
Indices: 338507--338551 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
338497 CATTCCTATA
338507 TGAGTTATCAGTAATAT
1 TGAGTTATCAGTAATAT
338524 TGAGTTATCAGTAATAT
1 TGAGTTATCAGTAATAT
338541 TGAGTTATCAG
1 TGAGTTATCAG
338552 CTGTCATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (17 bp):
TGAGTTATCAGTAATAT
Found at i:342855 original size:2 final size:2
Alignment explanation
Indices: 342848--342877 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
342838 CTAAAAGAGT
342848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
342878 CTCTATCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:342903 original size:123 final size:122
Alignment explanation
Indices: 342756--342978 Score: 349
Period size: 123 Copynumber: 1.8 Consensus size: 122
342746 CTATCTCTCT
* *
342756 CTCTCTCTCCTTTTTTTTCCATTAAATATTTTCATATTTCCAACTATTAATTTCATTCATTTATT
1 CTCTATCTCCTTTTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTATT
342821 TTTACTCTCCTAC-GATCCTAAAAGAGTTATATATATATATATATATATATATATATA
66 TTTACTCTCCTACAG-TCCTAAAAGAGTTATATATATATATATATATATATATATATA
* * * *
342878 CTCTATCTCCTTGTTTTTTTCATTAAATATTTTTACATTTCCGACTGTTAATTTCATTCATTTAT
1 CTCTATCTCCTT-TTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTAT
* *
342943 TTTTACTCTTCTACAGTCCTAGAAGAGTTATATATA
65 TTTTACTCTCCTACAGTCCTAAAAGAGTTATATATA
342979 GTAGAATCTA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
122 11 0.12
123 79 0.87
124 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (122 bp):
CTCTATCTCCTTTTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTATT
TTTACTCTCCTACAGTCCTAAAAGAGTTATATATATATATATATATATATATATATA
Found at i:347704 original size:404 final size:400
Alignment explanation
Indices: 346934--347740 Score: 1461
Period size: 404 Copynumber: 2.0 Consensus size: 400
346924 AGGCTATACC
* *
346934 AAAACAATTGGCCAAACTATATCACCTTTTTCAAATAGGTGCCTAAATTATTTTTTGACTCATCC
1 AAAACAAGTGGCCAAACTATATCACCTTTTCCAAATAGGTGCCTAAATTATTTTTTGACTCATCC
*
346999 ATGTACTTAACATTATAAACGTTATCCATTTAGGTGTTCGGACCGTCAACGTCGTTAATTTCTCC
66 AGGTACTTAACATTATAAACGTTATCCATTTAGGTGTTCGGACCGTCAACGTCGTTAATTTCTCC
347064 CATTAAATGACATGTGGCACAATCTGATAGTTTTGAAATTTATTTTTTTAAAAATATTATGATAT
131 CATTAAATGACATGTGGCACAATCTGATAGTTTTGAAATTTATTTTTTTAAAAATATTATGATAT
* *
347129 ATATATATATTTTTATAAAAAAACATTAACTTTTCTTATATTATAAAACAACCTCAAAATCTCAA
196 ATATATATATTTTTATAAAAAAACATTAACTTTTCTTATATTATAAAACAACCCCAAAATCCCAA
* * *
347194 ATGCTAACCTTAATCTGCGTTGTCGCTCTTTCCAGCCACGATTACCACCATCGACATAGTCCATG
261 ATACTAACCTTAATCTGCGTTGTCGCCCTTTCCAGCCACGATCACCACCATCGACATAGTCCATG
347259 TCATCCTCCTACTCATACGTCGTCTTAGTTTTCGTCTATTAGCTACCGGAACTGCCGATGTGAGT
326 TCATCCTCCTACTCATACGTCGTCTTAGTTTTCGTCTATTAGCTACCGGAACTGCCGATGTGAGT
347324 TTAGGTATTG
391 TTAGGTATTG
347334 AAAACAAGTGGCCAAACTATATCACCTTTTCCAAATAGGTGCCTAAATTATTTTTTGACTCATCC
1 AAAACAAGTGGCCAAACTATATCACCTTTTCCAAATAGGTGCCTAAATTATTTTTTGACTCATCC
*
347399 AGGTACTTAACATTATAAACGTTATCCATTTAGGTGTTCGGGCCGTCAACGTCGTTAATTTCTCC
66 AGGTACTTAACATTATAAACGTTATCCATTTAGGTGTTCGGACCGTCAACGTCGTTAATTTCTCC
* *
347464 CATTAAATGACATGTGGCACAATCTGATAGTTTTGAATTTTTTTTTAAATATTAAAAATATTATG
131 CATTAAATGACATGTGGCACAATCTGATAGTTTTGAAATTTATTTT---T-TTAAAAATATTATG
*
347529 ATATATATATATATTTTTATAAAAAAACATTAACTTTTCTTATATTATAAAACAGCCCCAAAATC
192 ATATATATATATATTTTTATAAAAAAACATTAACTTTTCTTATATTATAAAACAACCCCAAAATC
*
347594 CCAAATACTAACCTTAATCTGCGTTGTCGCCCTTTCCAGCCACGATCACCGCCATCGACATAGTC
257 CCAAATACTAACCTTAATCTGCGTTGTCGCCCTTTCCAGCCACGATCACCACCATCGACATAGTC
347659 CATGTCATCCTCCTACTCATACGTCGTCTTAGTTTTCGTCTATTAGCTACCGGAACTGCCGATGT
322 CATGTCATCCTCCTACTCATACGTCGTCTTAGTTTTCGTCTATTAGCTACCGGAACTGCCGATGT
347724 GAGTTTAGGTATTG
387 GAGTTTAGGTATTG
347738 AAA
1 AAA
347741 TGAAGGTTTT
Statistics
Matches: 390, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
400 170 0.44
403 1 0.00
404 219 0.56
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (400 bp):
AAAACAAGTGGCCAAACTATATCACCTTTTCCAAATAGGTGCCTAAATTATTTTTTGACTCATCC
AGGTACTTAACATTATAAACGTTATCCATTTAGGTGTTCGGACCGTCAACGTCGTTAATTTCTCC
CATTAAATGACATGTGGCACAATCTGATAGTTTTGAAATTTATTTTTTTAAAAATATTATGATAT
ATATATATATTTTTATAAAAAAACATTAACTTTTCTTATATTATAAAACAACCCCAAAATCCCAA
ATACTAACCTTAATCTGCGTTGTCGCCCTTTCCAGCCACGATCACCACCATCGACATAGTCCATG
TCATCCTCCTACTCATACGTCGTCTTAGTTTTCGTCTATTAGCTACCGGAACTGCCGATGTGAGT
TTAGGTATTG
Found at i:350728 original size:2 final size:2
Alignment explanation
Indices: 350723--350752 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
350713 TTTATTATGC
*
350723 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350753 CATACTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:355051 original size:19 final size:19
Alignment explanation
Indices: 355029--355066 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
355019 ATTCCTAGAA
*
355029 ATTGCCATGCACCCTACAC
1 ATTGCCATGCACACTACAC
*
355048 ATTGCCCTGCACACTACAC
1 ATTGCCATGCACACTACAC
355067 GGCCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.21
Consensus pattern (19 bp):
ATTGCCATGCACACTACAC
Found at i:367915 original size:16 final size:18
Alignment explanation
Indices: 367892--367933 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
367882 AAATTGAGAA
367892 AAGAAAAAAG-A-AAAAG
1 AAGAAAAAAGAATAAAAG
*
367908 AGGAAAAAAGAATAAAAG
1 AAGAAAAAAGAATAAAAG
367926 AAGAAAAA
1 AAGAAAAA
367934 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 12 0.55
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAGAATAAAAG
Found at i:367924 original size:8 final size:7
Alignment explanation
Indices: 367890--367932 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
367880 CTAAATTGAG
367890 AAAAGAA
1 AAAAGAA
367897 AAAAGAA
1 AAAAGAA
367904 AAAGAGGAA
1 AAA-A-GAA
367913 AAAAGAA
1 AAAAGAA
367920 TAAAAGAA
1 -AAAAGAA
367928 GAAAA
1 -AAAA
367933 ATAAGGTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 13 0.41
8 13 0.41
9 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:368871 original size:105 final size:105
Alignment explanation
Indices: 368687--369563 Score: 1466
Period size: 105 Copynumber: 8.3 Consensus size: 105
368677 AGGTTTTACC
*
368687 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
368752 ATGAAGGGACCACTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
368792 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
368857 ACGAAGGGACCACTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
368897 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
368962 ACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
369002 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
369067 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
369107 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
369172 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
369212 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACCCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
369277 ACGAAGGGACCGCTGGTTGTCAACAAACAACCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
369318 CAGAGCCAATTTCAACTTCATAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
369383 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
369424 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
369489 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
369530 CGGAGCCAATTTTAACTTCACAGCGAAGGATATT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATT
369564 CAACTCAAAG
Statistics
Matches: 740, Mismatches: 31, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 500 0.68
106 240 0.32
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:370103 original size:2 final size:2
Alignment explanation
Indices: 370096--370126 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
370086 TGAAATAAAC
370096 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
370127 TGTACAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:371253 original size:2 final size:2
Alignment explanation
Indices: 371248--371288 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
371238 TTAACATTTG
371248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
371289 TATTATTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:373237 original size:23 final size:23
Alignment explanation
Indices: 373211--373278 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
373201 TTTTTAATAA
*
373211 TTCTTTCTTTATGACACGTTTTC
1 TTCTATCTTTATGACACGTTTTC
* *
373234 TTCTATCTTTATGATACATTTTC
1 TTCTATCTTTATGACACGTTTTC
*
373257 TTCTGTCTTTATGACACGTTTT
1 TTCTATCTTTATGACACGTTTT
373279 TCGTTATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (23 bp):
TTCTATCTTTATGACACGTTTTC
Found at i:373302 original size:46 final size:46
Alignment explanation
Indices: 373211--373302 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
373201 TTTTTAATAA
* * * * * *
373211 TTCTTTCTTTATGACACGTTTTCTTCTATCTTTATGATACATTTTC
1 TTCTGTCTTTATGACACGTTTTCGTCTATATATACGACACATTTTC
*
373257 TTCTGTCTTTATGACACGTTTTTCGT-TATATATACGACACGTTTTC
1 TTCTGTCTTTATGACACG-TTTTCGTCTATATATACGACACATTTTC
373303 AATCGTTTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 32 0.84
47 6 0.16
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (46 bp):
TTCTGTCTTTATGACACGTTTTCGTCTATATATACGACACATTTTC
Found at i:387478 original size:2 final size:2
Alignment explanation
Indices: 387471--387517 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
387461 TACTCAATCC
387471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
387513 TA TA T
1 TA TA T
387518 CAATTCAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:390250 original size:16 final size:16
Alignment explanation
Indices: 390229--390286 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
390219 TGTGGCTCAA
390229 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCGTTAAG
*
390245 CTCGTTGCTCATTAAG
1 CTCGTTGCTCGTTAAG
* *
390261 CTTGTTACTCGTTAAG
1 CTCGTTGCTCGTTAAG
*
390277 CTCGATGCTC
1 CTCGTTGCTC
390287 ATTGCTCGCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.38
Consensus pattern (16 bp):
CTCGTTGCTCGTTAAG
Found at i:391309 original size:2 final size:2
Alignment explanation
Indices: 391304--391331 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
391294 ACACACAAAC
391304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391332 GAGTAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:392271 original size:35 final size:35
Alignment explanation
Indices: 392232--392313 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
392222 CTCAACTTGT
*
392232 TGCTCGTAAAACTTGTTAAAATTTTGCTTGACTAG
1 TGCTCGTAAAACTCGTTAAAATTTTGCTTGACTAG
* *
392267 TGCTCGTTAAACTCGTTAAAATTTTGCTTGACTTG
1 TGCTCGTAAAACTCGTTAAAATTTTGCTTGACTAG
392302 TGCTCGTTAAAA
1 TGCTCG-TAAAA
392314 AAACTTGTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 38 0.90
36 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (35 bp):
TGCTCGTAAAACTCGTTAAAATTTTGCTTGACTAG
Found at i:392351 original size:16 final size:16
Alignment explanation
Indices: 392330--392395 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
392320 GTGGCTCAAC
392330 TCGTTGCTAGTTAAGT
1 TCGTTGCTAGTTAAGT
*
392346 TCGTTGCTAGTTAAGC
1 TCGTTGCTAGTTAAGT
392362 TCGTTGCTCA-TTAAGCT
1 TCGTTGCT-AGTTAAG-T
* *
392379 T-GTTACTCGTTAAGT
1 TCGTTGCTAGTTAAGT
392394 TC
1 TC
392396 AATGCTCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.05
16 38 0.90
17 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (16 bp):
TCGTTGCTAGTTAAGT
Found at i:394454 original size:32 final size:31
Alignment explanation
Indices: 394418--394494 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
394408 CGGGGCCGTG
*
394418 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
394450 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
394481 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
394495 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:394477 original size:63 final size:63
Alignment explanation
Indices: 394371--394494 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
394361 CCCTAAGGGA
* * ** *
394371 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
394434 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
394495 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:395405 original size:22 final size:22
Alignment explanation
Indices: 395377--395419 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
395367 AACGGTCAAC
*
395377 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGATCGGGTCG
395399 GGTCAACGGTCGGATCGGGTC
1 GGTCAACGGTCGGATCGGGTC
395420 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGATCGGGTCG
Found at i:395440 original size:19 final size:19
Alignment explanation
Indices: 395418--395534 Score: 121
Period size: 19 Copynumber: 6.1 Consensus size: 19
395408 TCGGATCGGG
*
395418 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGT
*
395437 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
395456 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
395475 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
395494 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
395514 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
395534 T
1 T
395535 TCCAGCAGCC
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
18 3 0.04
19 55 0.65
20 17 0.20
21 9 0.11
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:395492 original size:29 final size:28
Alignment explanation
Indices: 395429--395533 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 28
395419 CAGACCGGTC
* * * *
395429 AAACCGGCTCAGACCGGTCAAACCGATTC
1 AAACCGG-TCAAACCGGTCGAACCGGTTG
*
395458 AGACCGGTCAAACCGGTTCGAACCGGTTG
1 AAACCGGTCAAACCGG-TCGAACCGGTTG
395487 AAACCGGTCAAACCGGTCAGAACCGGTTG
1 AAACCGGTCAAACCGGTC-GAACCGGTTG
*
395516 AAAACCGGTTAAACCGGT
1 -AAACCGGTCAAACCGGT
395534 TTCCAGCAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.15
29 40 0.61
30 16 0.24
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (28 bp):
AAACCGGTCAAACCGGTCGAACCGGTTG
Found at i:395534 original size:9 final size:9
Alignment explanation
Indices: 395416--395533 Score: 101
Period size: 9 Copynumber: 12.3 Consensus size: 9
395406 GGTCGGATCG
*
395416 GGTCAGACC
1 GGTCAAACC
395425 GGTCAAACC
1 GGTCAAACC
*
395434 GGCTCAGACC
1 GG-TCAAACC
395444 GGTCAAACC
1 GGTCAAACC
* *
395453 GATTCAGACC
1 G-GTCAAACC
395463 GGTCAAACC
1 GGTCAAACC
*
395472 GGTTCGAACC
1 GG-TCAAACC
*
395482 GGTTGAAACC
1 GG-TCAAACC
395492 GGTCAAACC
1 GGTCAAACC
395501 GGTCAGAACC
1 GGTCA-AACC
*
395511 GGTTGAAAACC
1 GG-T-CAAACC
*
395522 GGTTAAACC
1 GGTCAAACC
395531 GGT
1 GGT
395534 TTCCAGCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
9 44 0.49
10 38 0.42
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:401785 original size:102 final size:102
Alignment explanation
Indices: 401648--401835 Score: 288
Period size: 102 Copynumber: 1.8 Consensus size: 102
401638 TCTCTCTCTC
* *
401648 TTTTCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTATTTTTACTCTCCTACGA
1 TTTTCATTAAATATTTTCACATTTCCAACTATTAATCTCATTCATTTATTTTTACTCTCCTACAA
*
401713 TCCTAAAAGAGTTATATATATACTCTTTCTCCTTGTT
66 TCATAAAAGAGTTATATATATACTCTTTCTCCTTGTT
* ** *
401750 TTTTTATTAAATAATTTT-ACATTTCTGACTGTTAATCTCATTCATTTATTTTTACTCTCCTACA
1 TTTTCATTAAAT-ATTTTCACATTTCCAACTATTAATCTCATTCATTTATTTTTACTCTCCTACA
*
401814 ATCATAGAAGAGTTATATATAT
65 ATCATAAAAGAGTTATATATAT
401836 TAGAAAATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 72 0.94
103 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (102 bp):
TTTTCATTAAATATTTTCACATTTCCAACTATTAATCTCATTCATTTATTTTTACTCTCCTACAA
TCATAAAAGAGTTATATATATACTCTTTCTCCTTGTT
Found at i:412515 original size:19 final size:19
Alignment explanation
Indices: 412493--412530 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
412483 ATTCCTAGAA
*
412493 ATTGCCATGCACCCTACAC
1 ATTGCCATGCACACTACAC
*
412512 ATTGCCCTGCACACTACAC
1 ATTGCCATGCACACTACAC
412531 GGCCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.21
Consensus pattern (19 bp):
ATTGCCATGCACACTACAC
Found at i:414407 original size:2 final size:2
Alignment explanation
Indices: 414400--414442 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
414390 CATTTGTATT
414400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
414442 T
1 T
414443 TATTTCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:425367 original size:16 final size:17
Alignment explanation
Indices: 425344--425384 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
425334 AAATTGAGAA
425344 AAGAAAAAAGAA-AAAG
1 AAGAAAAAAGAATAAAG
*
425360 AGGAAAAAAGAATAAAG
1 AAGAAAAAAGAATAAAG
425377 AAGAAAAA
1 AAGAAAAA
425385 TAAGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAGAATAAAG
Found at i:426514 original size:104 final size:105
Alignment explanation
Indices: 426124--426986 Score: 1331
Period size: 105 Copynumber: 8.3 Consensus size: 105
426114 AGGTTTTACC
*
426124 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
426189 ATGAAGGGACCACTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
426229 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
426294 ACGAAGGGACCACTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
426334 CGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
426399 ACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
426439 CAGAGCCAATTTCAACTTCACAACGAA-GATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
426503 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
426543 CAGAGCCAATTTCAAC-TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
426607 ACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
426646 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CCCGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
426710 ACGAA-GGACCGCTGGTTGTCAACAAAACA-ACCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAAC-AAACATTTCTCAATTT
* * *
426749 CAGAG-CAATTT-TACTTCATAGCGAA--ATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
426810 ACGAAGGGACCGCTGGTTGTCAACAAACAATTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * *
426850 CGGAGCCCAATTTCAACTT--CAGCGAAGGATATTGGACTCGAGA-TACGCAAGTTCAACTTCAC
1 CAGAG-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
426912 G-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * *
426953 CGGAGCCAATTTTAACTTCACAGCGAAGGATATT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATT
426987 CAACTCAAAG
Statistics
Matches: 712, Mismatches: 31, Indels: 31
0.92 0.04 0.04
Matches are distributed among these distances:
99 9 0.01
100 34 0.05
101 40 0.06
102 69 0.10
103 123 0.17
104 209 0.29
105 228 0.32
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:426850 original size:307 final size:312
Alignment explanation
Indices: 426124--426986 Score: 1339
Period size: 307 Copynumber: 2.8 Consensus size: 312
426114 AGGTTTTACC
*
426124 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAA-GATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
426189 ATGAAGGGACCACTGGTTGTCAATAAACATTTCTTAATTTCGGAGCCAATTTCAACTTCACAACG
65 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCGGAGCCAATTTCAAC-TCACAACG
* * *
426254 AAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATA
129 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-C
* *
426319 AACATTTCTTAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGC
193 AACATTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
***
426384 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATTT
258 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGAACCTCAATTT
426439 CAGAGCCAATTTCAACTTCACAACGAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 CAGAGCCAATTTCAACTTCACAACGAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
426504 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTCACAACGAA
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCGGAGCCAATTTCAACTCACAACGAA
426569 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC
131 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC
* * *
426634 ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-CCCGACAACGTAAG
196 ATTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
426698 TTCAACTTCACGACGAA-GGACCGCTGGTTGTCAACAAAAC-AACCTCAATTT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AAACGAACCTCAATTT
* * *
426749 CAGAG-CAATTT-TACTTCATAGCGAA-ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 CAGAGCCAATTTCAACTTCACAACGAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
426811 CGAAGGGACCGCTGGTTGTCAACAAACAATTCCCAATTTCGGAGCCCAATTTCAACT-TCAGCGA
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCGGAG-CCAATTTCAACTCACAACGA
* *
426875 AGGATATTGGACTCGAGA-TACGCAAGTTCAACTTCACG-CGAAGGGACCGCTGGTTGTCAACAA
130 AGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-A
* * *
426938 ACAACTTCTCAATTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATT
194 AC-ATTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATT
426987 CAACTCAAAG
Statistics
Matches: 513, Mismatches: 31, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
305 23 0.04
306 22 0.04
307 142 0.28
308 23 0.04
309 6 0.01
310 31 0.06
311 32 0.06
312 51 0.10
313 69 0.13
314 87 0.17
315 27 0.05
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (312 bp):
CAGAGCCAATTTCAACTTCACAACGAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCGGAGCCAATTTCAACTCACAACGAA
GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC
ATTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACGAACCTCAATTT
Found at i:428647 original size:2 final size:2
Alignment explanation
Indices: 428642--428678 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
428632 TTTAACATTG
428642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
428679 TTTATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:428857 original size:18 final size:18
Alignment explanation
Indices: 428836--428870 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
428826 CCACATAACG
428836 TTATTACATAGATATATT
1 TTATTACATAGATATATT
* *
428854 TTATTATATATATATAT
1 TTATTACATAGATATAT
428871 ATATCGTTTG
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:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATTACATAGATATATT
Found at i:430290 original size:23 final size:23
Alignment explanation
Indices: 430261--430323 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
430251 TAATATTATT
430261 TCTTTATGACACGTTTTCTTCTA
1 TCTTTATGACACGTTTTCTTCTA
* * *
430284 TCTTTATGATACATTTTCTTCTG
1 TCTTTATGACACGTTTTCTTCTA
430307 TCTTTATGACACGTTTT
1 TCTTTATGACACGTTTT
430324 TCGTTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (23 bp):
TCTTTATGACACGTTTTCTTCTA
Found at i:434189 original size:69 final size:69
Alignment explanation
Indices: 434078--434212 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 69
434068 GGATGTAAGT
* *
434078 GTGATGTAAGATTTGTTAAAGGAACTAGACTTCCATTGAGTCGATTGTTAGACAAATCTAACTCA
1 GTGATGTAAGATTTGTTAAAGGAACTAGACTTCCATTGAGTCGATTGTCAGACAAATATAACTCA
434143 CCAA
66 CCAA
* * * *
434147 GTGATGTAAGATTTGTTAAAGGAATTAGATTTCCATTGAGTCGATTGTCGGACATATATAACTCA
1 GTGATGTAAGATTTGTTAAAGGAACTAGACTTCCATTGAGTCGATTGTCAGACAAATATAACTCA
434212 C
66 C
434213 GAAGAGAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (69 bp):
GTGATGTAAGATTTGTTAAAGGAACTAGACTTCCATTGAGTCGATTGTCAGACAAATATAACTCA
CCAA
Found at i:443281 original size:6 final size:6
Alignment explanation
Indices: 443270--443330 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
443260 GACACGTATT
* * *
443270 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
443318 ACCACG ACCACG A
1 ACCACG ACCACG A
443331 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:443338 original size:5 final size:5
Alignment explanation
Indices: 443328--443376 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
443318 ACCACGACCA
* * * *
443328 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
443377 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:448453 original size:6 final size:6
Alignment explanation
Indices: 448442--448522 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
448432 GACACGTATT
448442 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
448490 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
448523 GAGCCGAGCC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:448531 original size:5 final size:5
Alignment explanation
Indices: 448521--448570 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
448511 ACGACCACGA
* * * * *
448521 CCGAG CCGAG CCGAG CCGAG CCGTG CCGTG CCGTG CCGTG CCGAG ACGAG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG
448571 ACGGACGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.14, C:0.38, G:0.40, T:0.08
Consensus pattern (5 bp):
CCGAG
Found at i:448541 original size:15 final size:15
Alignment explanation
Indices: 448521--448570 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
448511 ACGACCACGA
*
448521 CCGAGCCGAGCCGAG
1 CCGAGCCGTGCCGAG
*
448536 CCGAGCCGTGCCGTG
1 CCGAGCCGTGCCGAG
*
448551 CCGTGCCGTGCCGAG
1 CCGAGCCGTGCCGAG
*
448566 ACGAG
1 CCGAG
448571 ACGGACGGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.14, C:0.38, G:0.40, T:0.08
Consensus pattern (15 bp):
CCGAGCCGTGCCGAG
Found at i:450883 original size:16 final size:16
Alignment explanation
Indices: 450862--450913 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
450852 TGTGGCTCAA
*
450862 CTCGTTGCTCGTTAAG
1 CTCGTTACTCGTTAAG
* *
450878 CTCGTTACTTGTTAAT
1 CTCGTTACTCGTTAAG
**
450894 CTTATTACTCGTTAAG
1 CTCGTTACTCGTTAAG
450910 CTCG
1 CTCG
450914 ATGCTCATTG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (16 bp):
CTCGTTACTCGTTAAG
Found at i:452221 original size:2 final size:2
Alignment explanation
Indices: 452216--452260 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
452206 TGTGTGTGTG
452216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452258 TA T
1 TA T
452261 GAGTAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:453219 original size:16 final size:16
Alignment explanation
Indices: 453198--453242 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
453188 TGTGGCTCAA
*
453198 CTCGTTGCTCGTTAAG
1 CTCGTTGCTCATTAAG
453214 CTCGTTGCTCATTAAG
1 CTCGTTGCTCATTAAG
*
453230 CTCGATGCTCATT
1 CTCGTTGCTCATT
453243 GCTCGCCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:453359 original size:13 final size:13
Alignment explanation
Indices: 453341--453367 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
453331 TATAAACATA
453341 AATTAAAAAATTT
1 AATTAAAAAATTT
453354 AATTAAAAAATTT
1 AATTAAAAAATTT
453367 A
1 A
453368 TCAAAAGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTAAAAAATTT
Found at i:454251 original size:2 final size:2
Alignment explanation
Indices: 454246--454279 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
454236 TTTTCTCTCT
*
454246 CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
454280 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:454284 original size:2 final size:2
Alignment explanation
Indices: 454279--454328 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
454269 ACACACACAC
454279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
454321 AT AT AT AT
1 AT AT AT AT
454329 GATTAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:460040 original size:23 final size:23
Alignment explanation
Indices: 460010--460073 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
460000 ATGCATCTAA
460010 CTTCTGGAAGCTGCTGACTGGAC
1 CTTCTGGAAGCTGCTGACTGGAC
* *
460033 CTTCTGGAAGCTACTGACTGGAT
1 CTTCTGGAAGCTGCTGACTGGAC
* *
460056 CATCTAGAAGCTGCTGAC
1 CTTCTGGAAGCTGCTGAC
460074 GTGGCAGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
CTTCTGGAAGCTGCTGACTGGAC
Found at i:466303 original size:17 final size:17
Alignment explanation
Indices: 466281--466324 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
466271 CATTCCTATA
466281 TGAGTTATCAGTAATAT
1 TGAGTTATCAGTAATAT
466298 TGAGTTATCAGTAATAT
1 TGAGTTATCAGTAATAT
466315 TGAGTTATCA
1 TGAGTTATCA
466325 TCTGTCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (17 bp):
TGAGTTATCAGTAATAT
Found at i:470647 original size:113 final size:113
Alignment explanation
Indices: 470525--470738 Score: 315
Period size: 113 Copynumber: 1.9 Consensus size: 113
470515 TATACTCTAT
* *
470525 CTCTCTCTCTCCT-TTTTTTCCATTAAATATTTTCATATTTCCAACTATTAATTTCATTCATTTA
1 CTCTATCTCT-CTGTTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTA
470589 TTTTTACTCTCCTAC-GATCCTAAAAGAGTTATATATATATATATATATA
65 TTTTTACTCTCCTACAG-TCCTAAAAGAGTTATATATATATATATATATA
* * * * *
470638 CTCTATCTCTTTGTTTTTTTCATTAAATATTTTTACATTTCCGACTGTTAATTTCATTCATTTAT
1 CTCTATCTCTCTGTTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTAT
* *
470703 TTTTACTCTTCTACAGTCCTAGAAGAGTTATATATA
66 TTTTACTCTCCTACAGTCCTAAAAGAGTTATATATA
470739 GTAGAATCTA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 1 0.01
113 88 0.98
114 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (113 bp):
CTCTATCTCTCTGTTTTTTCCATTAAATATTTTCACATTTCCAACTATTAATTTCATTCATTTAT
TTTTACTCTCCTACAGTCCTAAAAGAGTTATATATATATATATATATA
Found at i:476456 original size:3 final size:3
Alignment explanation
Indices: 476448--476486 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
476438 AAGGATAAAG
* *
476448 ATT ATT ATT ATT AGT AGT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
476487 GTTGTTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:486263 original size:30 final size:29
Alignment explanation
Indices: 486229--486285 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
486219 ATTCTAACTC
* *
486229 AAATTAATCTTTTAAACTTTTGAACATTCT
1 AAATTAATC-CTTAAAATTTTGAACATTCT
**
486259 AAATTGGTCCTTAAAATTTTGAACATT
1 AAATTAATCCTTAAAATTTTGAACATT
486286 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (29 bp):
AAATTAATCCTTAAAATTTTGAACATTCT
Found at i:488103 original size:21 final size:21
Alignment explanation
Indices: 488090--488136 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
488080 AATACAAGCG
*
488090 GTGAATAGACAAATCAATGGT
1 GTGAAGAGACAAATCAATGGT
488111 GTGAAGAGACAAATCAATGGT
1 GTGAAGAGACAAATCAATGGT
488132 GTGAA
1 GTGAA
488137 TAAGAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (21 bp):
GTGAAGAGACAAATCAATGGT
Found at i:489172 original size:45 final size:45
Alignment explanation
Indices: 489058--489184 Score: 182
Period size: 45 Copynumber: 2.8 Consensus size: 45
489048 GGGGATGTTA
* **
489058 TTGGTACGTTCAAAAGTTTGGGGACCAATTTAGAATGGGGTAAAT
1 TTGGAACGTTCAAAAGTTTGGGGATTAATTTAGAATGGGGTAAAT
* *
489103 TTGGAACGTTCAAGAGTTTGGGGATTAATTTAGAATGGGGTGAAT
1 TTGGAACGTTCAAAAGTTTGGGGATTAATTTAGAATGGGGTAAAT
* * *
489148 TTGGAATGTTCAACAGTTTGGGGATTAATTTAAAATG
1 TTGGAACGTTCAAAAGTTTGGGGATTAATTTAGAATG
489185 ATAGCCATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (45 bp):
TTGGAACGTTCAAAAGTTTGGGGATTAATTTAGAATGGGGTAAAT
Found at i:489184 original size:29 final size:29
Alignment explanation
Indices: 489152--489244 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
489142 GTGAATTTGG
*
489152 AATGTTCAACAGTTTGGGGATTAATTTAA
1 AATGTTCAAAAGTTTGGGGATTAATTTAA
* * * * * *
489181 AATGATAGCCATAA-TTTGAGGATAAAATTAG
1 AATG-T--TCAAAAGTTTGGGGATTAATTTAA
* *
489212 AATGTTTAAAAGTTTAGGGATTAATTTAA
1 AATGTTCAAAAGTTTGGGGATTAATTTAA
489241 AATG
1 AATG
489245 AGGTTTGAGG
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
28 3 0.07
29 20 0.44
30 2 0.04
31 17 0.38
32 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.35
Consensus pattern (29 bp):
AATGTTCAAAAGTTTGGGGATTAATTTAA
Found at i:495745 original size:27 final size:25
Alignment explanation
Indices: 495702--495752 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
495692 TTTTAATCTG
*
495702 AAAATGGCCTATTGGAATTATCAAC
1 AAAATGGCCTATGGGAATTATCAAC
495727 AAAATGGGTCCTATGGGAATTATCAA
1 AAAAT-GG-CCTATGGGAATTATCAA
495753 ACTCAAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 16 0.70
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (25 bp):
AAAATGGCCTATGGGAATTATCAAC
Found at i:497504 original size:15 final size:16
Alignment explanation
Indices: 497486--497518 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
497476 GTGGCAGATC
497486 AAAATCTAG-ACGGGA
1 AAAATCTAGAACGGGA
497501 AAAATCTAGAACGGGA
1 AAAATCTAGAACGGGA
497517 AA
1 AA
497519 GAAAGATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAATCTAGAACGGGA
Found at i:500532 original size:25 final size:25
Alignment explanation
Indices: 500498--500549 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
500488 TCTAGCAAAG
500498 AATCCGTCTTTTCATTCCAGGACGA
1 AATCCGTCTTTTCATTCCAGGACGA
500523 AATCCGTCTTTTCATTCCAGGACGA
1 AATCCGTCTTTTCATTCCAGGACGA
500548 AA
1 AA
500550 CACATACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (25 bp):
AATCCGTCTTTTCATTCCAGGACGA
Found at i:500837 original size:35 final size:37
Alignment explanation
Indices: 500791--500879 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
500781 TTGTTAAAAG
* *
500791 TTTCAAAGTTTGG-CAA-CCAACTTTGGAAAATATTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATTT
****
500826 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATATTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATTT
500863 TTTCAAAGTTTGGTAAA
1 TTTCAAAGTTTGGTAAA
500880 ATATTGGTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 13 0.28
36 2 0.04
37 31 0.67
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (37 bp):
TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATTT
Found at i:514892 original size:14 final size:14
Alignment explanation
Indices: 514873--514899 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
514863 CGATGTTAAA
514873 AACTTAACGGAAGC
1 AACTTAACGGAAGC
514887 AACTTAACGGAAG
1 AACTTAACGGAAG
514900 TGTTGTACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (14 bp):
AACTTAACGGAAGC
Found at i:515105 original size:13 final size:15
Alignment explanation
Indices: 515076--515108 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
515066 TTAATAATAA
515076 AAAATTTCATGTAAT
1 AAAATTTCATGTAAT
515091 AAAATTT-AT-TAAT
1 AAAATTTCATGTAAT
515104 AAAAT
1 AAAAT
515109 AAATTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATTTCATGTAAT
Found at i:519158 original size:24 final size:24
Alignment explanation
Indices: 519097--519158 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
519087 AGAAAATAAT
*
519097 ATTTAAAACAAAAAGATAATTCCTAA
1 ATTT-AAA-AAAAAGATAAATCCTAA
**
519123 AAATAAAAAAAAGATAAATCCT-A
1 ATTTAAAAAAAAGATAAATCCTAA
519146 ATTTAAAATAAAA
1 ATTTAAAA-AAAA
519159 AATTCGGCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 7 0.23
24 18 0.60
25 3 0.10
26 2 0.07
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (24 bp):
ATTTAAAAAAAAGATAAATCCTAA
Found at i:519242 original size:23 final size:23
Alignment explanation
Indices: 519172--519258 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
519162 TCGGCTAGGG
* *
519172 CACCATGTCACCTGCCATGTCAT
1 CACCACGTCAGCTGCCATGTCAT
* * * ** *
519195 CGCCATG-CTAGCTACCACATTAT
1 CACCACGTC-AGCTGCCATGTCAT
519218 CACCACGTCAGCTGCCATGTCAT
1 CACCACGTCAGCTGCCATGTCAT
519241 CACCACGTCAGCTGCCAT
1 CACCACGTCAGCTGCCAT
519259 ATCAATCGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.02
23 48 0.96
24 1 0.02
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (23 bp):
CACCACGTCAGCTGCCATGTCAT
Found at i:530620 original size:2 final size:2
Alignment explanation
Indices: 530615--530664 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
530605 AAAATTATTG
530615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
530657 AT AT AT AT
1 AT AT AT AT
530665 TTTATAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:532692 original size:31 final size:31
Alignment explanation
Indices: 532657--532718 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
532647 TTATTCGGTG
532657 AATTCAATACGT-CTTTCTCACTAGGAACTCC
1 AATTCAATACGTCCTTT-TCACTAGGAACTCC
*
532688 AATTCAATATGTCCTTTTCACTAGGAACTCC
1 AATTCAATACGTCCTTTTCACTAGGAACTCC
532719 CAAACTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (31 bp):
AATTCAATACGTCCTTTTCACTAGGAACTCC
Found at i:545099 original size:298 final size:294
Alignment explanation
Indices: 544643--545739 Score: 1300
Period size: 298 Copynumber: 3.7 Consensus size: 294
544633 CCCGACCCAT
* * * * *
544643 CCTGACCCCAAAAAAATTGTAATTTTACCTATACATTTAAGGATAATTGCAAGAATACTCATCTA
1 CCTGA-CCC-AAAAAATTATAATTTTACTTATATATTTAGGGATAATTGCAATAATACTCATCTA
* *
544708 TATATTATTTTTCTTTTAATTAAATCACTATTTTTATTGAATAAAAATAATATTTTTCAATAAAT
64 TATATTA-TTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAAT
* * *
544773 ATATTATTTCGGGTTGGGTCTGGTCGGGTTCGAATTTTATCTCAAAAAATCGAGTTGGGTTCAGG
128 ATATTATTTCGGATCGGGTCTGGTCGAGTTCGAATTTTATCTCAAAAAATCGAGTT-GGTTCAGG
*
544838 TTGGGTGGAAGGTGTATATTTTTCGGGTCCAGTTCGAGTCGGGTCAAAATCGAGTTTTTAAGGTT
192 TTGGGTGGAAGGTGTATATTTTTCGGGTCCA-TTCGAGT-GGGTC-AGATCGAGTTTTTAAGGTT
*
544903 ATGTTTGGGTCAGGTCGGGTTCGGATTTAGGGTGAAAAATA
254 ATGTTTGGGTCGGGTCGGGTTCGGATTTAGGGTGAAAAATA
*
544944 CCTGACCCAAAAAATTGA-AATTTTACATTATATATTTAGGGATATTTGCAATAATACTCCA-CT
1 CCTGACCCAAAAAATT-ATAATTTTAC-TTATATATTTAGGGATAATTGCAATAATACT-CATCT
545007 ATATATTA-TTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAAT
63 ATATATTATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAAT
* * * * *
545071 ATATTATTTCGGGTTGGGTCTTGTCGGGTTC-AGATTTTATCTCAAAAAATCGAGTCGGGTTCAG
128 ATATTATTTCGGATCGGGTCTGGTCGAGTTCGA-ATTTTATCTCAAAAAATCGAGT-TGGTTCAG
*
545135 GTTGGGTGGAAGGTGTATATTTTTCGGGTCCAATTCGAGTAGGTTCAGATCGAGTTTTTAAGGTT
191 GTTGGGTGGAAGGTGTATATTTTTCGGGTCC-ATTCGAGT-GGGTCAGATCGAGTTTTTAAGGTT
*
545200 ATGTTAGGGTCGGGTCGGGTTCGGATTTAGGGTG-AAAATA
254 ATGTTTGGGTCGGGTCGGGTTCGGATTTAGGGTGAAAAATA
* * *
545240 CCCGACCCAAAAGATTATAATTTTACCTTATATATTTAGGGATAATTACAATAATACTCCA-CTA
1 CCTGACCCAAAAAATTATAATTTTA-CTTATATATTTAGGGATAATTGCAATAATACT-CATCTA
* * *
545304 TATATTA-TTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTTTAAT--ACA
64 TATATTATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAATA
* * * *
545366 TATTATTTTGGATCGGGTCGGGTCGAGTTTGAATTTTATCTCAAAAAATC-A--------A-GTC
129 TATTATTTCGGATCGGGTCTGGTCGAGTTCGAATTTTATCTCAAAAAATCGAGTTGGTTCAGGTT
* *
545421 GGGTGGAAGGTGTATATTTTTC-GG--C--T----TGGGTCAGATCGAGTTATTAAGGTTATATT
194 GGGTGGAAGGTGTATATTTTTCGGGTCCATTCGAGTGGGTCAGATCGAGTTTTTAAGGTTATGTT
**
545477 TGGGTCGGGTTAGGTTCGGATTTAGGGTGACAAAAATCTGA
259 TGGGTCGGGTCGGGTTCGGATTTAGGGTG--AAAAA--T-A
* *
545518 CCCAACTCGAACCAAAAAATTATAATTTTATCTTATATATTTAGAGATAATTGCAATAATACTCA
1 --C--CT-GACCCAAAAAATTATAATTTTA-CTTATATATTTAGGGATAATTGCAATAATACTCA
*
545583 TCTATATTTTATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTT-AATA
60 TCTATATATTATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATA
* ** * * * *
545647 TATATATTATTTCAAATCGAGGTCTTGTCGAGTTCGGATTTTATCTCAGAAAATCGAGTCTTGTT
125 AATATATTATTTCGGATCG-GGTCTGGTCGAGTTCGAATTTTATCTCAAAAAATCGAGT-TGGTT
*
545712 C-GGATTGGGTGGAAGGTGCATACTTTTT
188 CAGG-TTGGGTGGAAGGTGTATA-TTTTT
545740 GAGTCGGGTG
Statistics
Matches: 703, Mismatches: 55, Indels: 79
0.84 0.07 0.09
Matches are distributed among these distances:
272 52 0.07
273 1 0.00
275 4 0.01
277 2 0.00
278 1 0.00
280 2 0.00
282 5 0.01
283 86 0.12
284 48 0.07
285 14 0.02
286 30 0.04
287 1 0.00
293 1 0.00
294 43 0.06
295 2 0.00
296 120 0.17
297 68 0.10
298 160 0.23
299 17 0.02
300 39 0.06
301 7 0.01
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (294 bp):
CCTGACCCAAAAAATTATAATTTTACTTATATATTTAGGGATAATTGCAATAATACTCATCTATA
TATTATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAATATA
TTATTTCGGATCGGGTCTGGTCGAGTTCGAATTTTATCTCAAAAAATCGAGTTGGTTCAGGTTGG
GTGGAAGGTGTATATTTTTCGGGTCCATTCGAGTGGGTCAGATCGAGTTTTTAAGGTTATGTTTG
GGTCGGGTCGGGTTCGGATTTAGGGTGAAAAATA
Found at i:545771 original size:284 final size:277
Alignment explanation
Indices: 544950--545706 Score: 653
Period size: 296 Copynumber: 2.6 Consensus size: 277
544940 AATACCTGAC
* * * *
544950 CCAAAAAATTGA-AATTTTACATTATATATTTAGGGATATTTGCAATAATACTCCACTATATATT
1 CCAAAAAATT-ATAATTTTACCTTATATATTTAGAGATAATTACAATAATACTCCACTATATATT
* * *
545014 ATTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTCAATAAATATATTATT
65 ATTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTT-AA-ATACATATTATT
*** * ** * *
545079 TCGGGTTGGGTCTTGTCGGGTTC-AGATTTTATCTCAAAAAATCGAGTCGGGTTCAGGTTGGGTG
128 TCAAATCGGGTCGGGTCGAGTTCGA-ATTTTATCTCAAAAAATC-A---------A-GTCGGGTG
* * *
545143 GAAGGTGTATATTTTTCGGGTCCAATTCGAGTAGGTTCAGATCGAGTTTTTAAGGT-TATGTTAG
181 GAAGGTGCATATTTTTC-GG--C---TC--G--GG-T-AGA-C--GTTATTAA-GTATAT-TT-C
** *
545207 GGTCGGGTCGGGTTCGGATTTAGGGTG---AAAA--T-A--C--C-CGAC
228 GGTCGGGTTAGGTTCGGATTTAGGGTGACAAAAATCTGACCCAACTCGAA
* *
545246 CCAAAAGATTATAATTTTACCTTATATATTTAGGGATAATTACAATAATACTCCACTATATATTA
1 CCAAAAAATTATAATTTTACCTTATATATTTAGAGATAATTACAATAATACTCCACTATATATTA
* **
545311 TTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTTTAATACATATTATTTTG
66 TTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTTAAATACATATTATTTCA
* * *
545376 GATCGGGTCGGGTCGAGTTTGAATTTTATCTCAAAAAATCAAGTCGGGTGGAAGGTGTATATTTT
131 AATCGGGTCGGGTCGAGTTCGAATTTTATCTCAAAAAATCAAGTCGGGTGGAAGGTGCATATTTT
* *
545441 TCGGCTTGGGTCAGATCGAGTTATTAAGGTTATATTTGGGTCGGGTTAGGTTCGGATTTAGGGTG
196 TCGGCTCGGGT-AGA-C--GTTATTAA-G-TATATTTCGGTCGGGTTAGGTTCGGATTTAGGGTG
545506 ACAAAAATCTGACCCAACTCGAA
255 ACAAAAATCTGACCCAACTCGAA
* * *
545529 CCAAAAAATTATAATTTTATCTTATATATTTAGAGATAATTGCAATAATACT-CATCTATATTTT
1 CCAAAAAATTATAATTTTACCTTATATATTTAGAGATAATTACAATAATACTCCA-CTATATATT
* *
545593 ATTTTCTTTCAATTAAATCCCTATTTTTATTGAATAAAAATAATATTTTTAATATATATATTATT
65 A-TTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTTAA-ATACATATTATT
** * * *
545658 TCAAATCGAGGTCTTGTCGAGTTCGGATTTTATCTCAGAAAATCGAGTC
128 TCAAATCG-GGTCGGGTCGAGTTCGAATTTTATCTCAAAAAATCAAGTC
545707 TTGTTCGGAT
Statistics
Matches: 404, Mismatches: 38, Indels: 48
0.82 0.08 0.10
Matches are distributed among these distances:
272 44 0.11
273 5 0.01
274 3 0.01
275 5 0.01
277 2 0.00
278 1 0.00
280 2 0.00
282 5 0.01
283 84 0.21
284 49 0.12
285 16 0.04
286 34 0.08
293 1 0.00
294 44 0.11
295 3 0.01
296 106 0.26
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (277 bp):
CCAAAAAATTATAATTTTACCTTATATATTTAGAGATAATTACAATAATACTCCACTATATATTA
TTTCTTTCAATTAAATCCCTATTTTTATTAAATAAAAATAATATTTTTAAATACATATTATTTCA
AATCGGGTCGGGTCGAGTTCGAATTTTATCTCAAAAAATCAAGTCGGGTGGAAGGTGCATATTTT
TCGGCTCGGGTAGACGTTATTAAGTATATTTCGGTCGGGTTAGGTTCGGATTTAGGGTGACAAAA
ATCTGACCCAACTCGAA
Found at i:549701 original size:2 final size:2
Alignment explanation
Indices: 549694--549728 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
549684 ATTAATGTTG
549694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549729 AGCTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:553339 original size:26 final size:28
Alignment explanation
Indices: 553310--553369 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
553300 TGCAATTAAT
553310 AAGGAA-A-CGTAAATGCATGCGTCCAA
1 AAGGAACAGCGTAAATGCATGCGTCCAA
553336 AAGGAAACAGCGTAAATGCATGCGTCCAA
1 AAGG-AACAGCGTAAATGCATGCGTCCAA
553365 AAGGA
1 AAGGA
553370 GATAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.13
27 2 0.06
28 2 0.06
29 23 0.74
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.13
Consensus pattern (28 bp):
AAGGAACAGCGTAAATGCATGCGTCCAA
Found at i:558780 original size:20 final size:20
Alignment explanation
Indices: 558755--558792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
558745 CAGTTAACTC
558755 GTTGACCCGACCGTTGACAT
1 GTTGACCCGACCGTTGACAT
*
558775 GTTGACCCGACTGTTGAC
1 GTTGACCCGACCGTTGAC
558793 CGATTGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (20 bp):
GTTGACCCGACCGTTGACAT
Found at i:559691 original size:60 final size:60
Alignment explanation
Indices: 559559--559696 Score: 195
Period size: 60 Copynumber: 2.3 Consensus size: 60
559549 TGGCTAGGGT
* * * * * *
559559 GTCCTTATGGATACATGTATCTTATATATTGGACTTCTAGATCCTAGTGGTCTAGGGCAA
1 GTCCTTATGGATGCCTGTATCTTACATATTGGACTCCTAGATCCAAGGGGTCTAGGGCAA
* *
559619 GTCCTTATGGATGCCTGTATCTTCCATATTGGACTCCTAGATCCAAGGGGTCTAGGGTAA
1 GTCCTTATGGATGCCTGTATCTTACATATTGGACTCCTAGATCCAAGGGGTCTAGGGCAA
*
559679 GTTCTTATGGATGCCTGT
1 GTCCTTATGGATGCCTGT
559697 TATGGGGTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (60 bp):
GTCCTTATGGATGCCTGTATCTTACATATTGGACTCCTAGATCCAAGGGGTCTAGGGCAA
Found at i:561750 original size:19 final size:20
Alignment explanation
Indices: 561726--561776 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
561716 ATAAATAAAT
561726 ATTAAATAAAAAGG-AAAAA
1 ATTAAATAAAAAGGTAAAAA
561745 ATTAAA-AAAAAGGTTTAAAAA
1 ATTAAATAAAAAGG--TAAAAA
*
561766 ATAAAATAAAA
1 ATTAAATAAAA
561777 TCAAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 6 0.22
21 10 0.37
22 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.20
Consensus pattern (20 bp):
ATTAAATAAAAAGGTAAAAA
Found at i:563206 original size:5 final size:5
Alignment explanation
Indices: 563192--563513 Score: 197
Period size: 5 Copynumber: 62.4 Consensus size: 5
563182 AAAAAAAACA
**
563192 AATA- AATAT AATAT ATATAT AATAAT AATAT AATAT -ATAT GTTAT AA-AT
1 AATAT AATAT AATAT A-ATAT AAT-AT AATAT AATAT AATAT AATAT AATAT
*
563241 AA-AT TATA- ATATAT AATA- AATAT AATAT ATATAT AGTATAT AATAT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT A-ATAT A--ATAT AATAT
* *
563287 AGATAT ACTAT AATAT AAAAT AA-AT -ATAAT AATAT AATAT ATATAT
1 A-ATAT AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT A-ATAT
* *
563333 ACTAGAT AATAT AAATAT ATTAT AACATAT AATAT -ATAT ATATAT AATAT
1 A--ATAT AATAT -AATAT AATAT -A-ATAT AATAT AATAT A-ATAT AATAT
*
563383 AATAT AAATAT ACTAT AATAT -ATAAT AATAT AATAT -ATAT ACTATAT
1 AATAT -AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT A--ATAT
* *
563430 AATAT AAATAT ACTAT AATAT -ATAAT AA-AT AA-AT AATAT TATAAT
1 AATAT -AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AAT-AT
* * *
563475 ACATAT AAAAT -ATAT TATAT AAATAT ACTAT ACATAT AA
1 A-ATAT AATAT AATAT AATAT -AATAT AATAT A-ATAT AA
563514 ACTATATATA
Statistics
Matches: 259, Mismatches: 23, Indels: 71
0.73 0.07 0.20
Matches are distributed among these distances:
3 1 0.00
4 44 0.17
5 127 0.49
6 66 0.25
7 21 0.08
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:563207 original size:2 final size:2
Alignment explanation
Indices: 563197--563532 Score: 191
Period size: 2 Copynumber: 181.0 Consensus size: 2
563187 AAACAAATAA
*
563197 AT AT A- AT AT AT AT AT A- AT A- AT A- AT AT A- AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
563234 -T AT AA AT AA AT -T AT A- AT AT AT A- AT AA AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
563271 AT AT AGT AT AT A- AT AT AG AT AT ACT AT A- AT AT A- AA AT AA AT
1 AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
563312 AT A- AT A- AT AT A- AT AT AT AT AT ACT AG AT A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
563351 AT -T AT A- AC AT AT A- AT AT AT AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
563388 AA AT AT ACT AT A- AT AT AT A- AT A- AT AT A- AT AT AT AT ACT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
563428 AT A- AT AT AA AT AT ACT AT A- AT AT AT A- AT AA AT AA AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
563467 AT -T AT A- AT AC AT AT A- AA AT AT AT -T AT AT AA AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
563506 AC AT AT AA ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT
563533 TAAAAAAGAT
Statistics
Matches: 258, Mismatches: 34, Indels: 84
0.69 0.09 0.22
Matches are distributed among these distances:
1 34 0.13
2 209 0.81
3 15 0.06
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:563213 original size:11 final size:11
Alignment explanation
Indices: 563197--563531 Score: 238
Period size: 11 Copynumber: 30.5 Consensus size: 11
563187 AAACAAATAA
563197 ATATAATATAT
1 ATATAATATAT
563208 ATATAATA-AT
1 ATATAATATAT
563218 AATATAATATAT
1 -ATATAATATAT
* * *
563230 ATGTTATAAAT
1 ATATAATATAT
* *
563241 AAATTATA-AT
1 ATATAATATAT
563251 ATATAATA-A-
1 ATATAATATAT
563260 ATATAATATAT
1 ATATAATATAT
*
563271 ATATAGTATAT
1 ATATAATATAT
563282 AATATAGATATA-
1 -ATATA-ATATAT
*
563294 CTATAATATA-
1 ATATAATATAT
*
563304 AAATAAATATAAT
1 ATAT-AATAT-AT
563317 AATATAATATAT
1 -ATATAATATAT
* *
563329 ATATACTAGAT
1 ATATAATATAT
563340 AATATAA-ATAT
1 -ATATAATATAT
*
563351 ATTATAACATAT
1 A-TATAATATAT
563363 A-ATATATATAT
1 ATATA-ATATAT
563374 ATATAATATA-
1 ATATAATATAT
563384 ATATAA-ATAT
1 ATATAATATAT
563394 ACTATAATATAT
1 A-TATAATATAT
563406 A-ATAATATA-
1 ATATAATATAT
563415 ATAT-ATATACT
1 ATATAATATA-T
*
563426 ATATAATATAA
1 ATATAATATAT
*
563437 ATATACTATAAT
1 ATATAATAT-AT
563449 ATATAATA-A-
1 ATATAATATAT
563458 ATA-AATA-AT
1 ATATAATATAT
*
563467 ATTATAATACAT
1 A-TATAATATAT
*
563479 ATAAAATATATT
1 ATATAATATA-T
563491 ATATAA-ATAT
1 ATATAATATAT
*
563501 ACTATACATATAA
1 A-TATA-ATATAT
563514 ACTATATATATAT
1 A-TATA-ATATAT
563527 ATATA
1 ATATA
563532 TTAAAAAAGA
Statistics
Matches: 265, Mismatches: 28, Indels: 61
0.75 0.08 0.17
Matches are distributed among these distances:
8 5 0.02
9 21 0.08
10 45 0.17
11 112 0.42
12 55 0.21
13 24 0.09
14 3 0.01
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
ATATAATATAT
Found at i:563486 original size:47 final size:45
Alignment explanation
Indices: 563191--563529 Score: 247
Period size: 43 Copynumber: 7.4 Consensus size: 45
563181 CAAAAAAAAC
* * *
563191 AAATAAATATAATATATATATAATA-ATAATATAATAT-ATATGTTAT
1 AAATAAATAT-ATAT-TATATAATATA-AATATACTATAATATATAAT
* * *
563237 AAATAAAT-TATAATATAT-A-ATAAATATAATAT-ATATATAGT
1 AAATAAATATATATTATATAATATAAATATACTATAATATATAAT
* * *
563278 ATAT-AATATAGATATACTATAATATAAA-ATA-AAT-ATA-ATAAT
1 AAATAAATATATAT-TA-TATAATATAAATATACTATAATATATAAT
* * * * *
563320 ATAATATATATATACTAGATAATATAAATATATTATAACATATAAT
1 A-AATAAATATATATTATATAATATAAATATACTATAATATATAAT
* *
563366 --ATATATATATATAATATAATATAAATATACTATAATATATAAT
1 AAATAAATATATATTATATAATATAAATATACTATAATATATAAT
*
563409 AATATAATATATATACTATATAATATAAATATACTATAATATATAAT
1 AA-ATAA-ATATATATTATATAATATAAATATACTATAATATATAAT
* *
563456 AAATAAATA-ATATTATAATACATATAAAATATATTATATAAATATACTAT
1 AAATAAATATATATTAT-ATA-ATAT-AAATATACTATA-ATATATA--AT
563506 ACATATAAACTATATATATATATA
1 A-A-ATAAA-TATATAT-TATATA
563530 TATTAAAAAA
Statistics
Matches: 239, Mismatches: 27, Indels: 46
0.77 0.09 0.15
Matches are distributed among these distances:
40 3 0.01
41 23 0.10
42 19 0.08
43 58 0.24
44 21 0.09
45 14 0.06
46 24 0.10
47 50 0.21
48 6 0.03
50 3 0.01
51 1 0.00
52 5 0.02
53 2 0.01
54 7 0.03
55 3 0.01
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (45 bp):
AAATAAATATATATTATATAATATAAATATACTATAATATATAAT
Found at i:564402 original size:16 final size:16
Alignment explanation
Indices: 564383--564414 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
564373 AAAAAGTTTT
564383 GAAAAATAAAATAAAA
1 GAAAAATAAAATAAAA
*
564399 GAAAGATAAAATAAAA
1 GAAAAATAAAATAAAA
564415 ACAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
GAAAAATAAAATAAAA
Found at i:564451 original size:27 final size:27
Alignment explanation
Indices: 564421--564510 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
564411 AAAAACAATA
564421 AAAAAGAATGAAGAAAATTTAAATTTT
1 AAAAAGAATGAAGAAAATTTAAATTTT
* ** *
564448 AAAATA-AATAAAGAAAAAATAAA--TA
1 AAAA-AGAATGAAGAAAATTTAAATTTT
* *
564473 AAGAAAAAAGTGAAGAAAATGTTAATTTTT
1 AA-AAAGAA-TGAAGAAAAT-TTAAATTTT
564503 AAAAAGAA
1 AAAAAGAA
564511 AAAAGAAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
25 4 0.09
26 4 0.09
27 26 0.57
28 4 0.09
29 5 0.11
30 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (27 bp):
AAAAAGAATGAAGAAAATTTAAATTTT
Found at i:564468 original size:15 final size:15
Alignment explanation
Indices: 564448--564481 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
564438 TTTAAATTTT
564448 AAAATAAATAAAGAA
1 AAAATAAATAAAGAA
564463 AAAATAAATAAAGAA
1 AAAATAAATAAAGAA
564478 AAAA
1 AAAA
564482 GTGAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAATAAATAAAGAA
Found at i:564516 original size:55 final size:54
Alignment explanation
Indices: 564389--564571 Score: 167
Period size: 57 Copynumber: 3.2 Consensus size: 54
564379 TTTTGAAAAA
* *
564389 TAAAATAAAAGAAAGATAAAATAAAAACAATAAAAAAGAATGAAGAAAAT-TTAAATTT
1 TAAAATAAAA-AAAGAAAAAATAAATA-AA-AAAAAAG--TGAAGAAAATGTTAAATTT
* *
564447 TAAAATAAATAAAGAAAAAATAAATAAAGAAAAAAGTGAAGAAAATGTTAATTTT
1 TAAAATAAAAAAAGAAAAAATAAATAAA-AAAAAAGTGAAGAAAATGTTAAATTT
*
564502 TAAAA-AGAAAAAAGAAACAAAATAAATAAAAAAGAAAG-AAAG-AAATGTTAAAATTT
1 TAAAATA-AAAAAAG-AA-AAAATAAATAAAAAA-AAAGTGAAGAAAATGTT-AAATTT
* *
564558 GAAAGTAATAAAAA
1 TAAAATAA-AAAAA
564572 ATAACAGAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
54 11 0.10
55 25 0.23
56 26 0.24
57 36 0.34
58 9 0.08
ACGTcount: A:0.69, C:0.01, G:0.10, T:0.20
Consensus pattern (54 bp):
TAAAATAAAAAAAGAAAAAATAAATAAAAAAAAAGTGAAGAAAATGTTAAATTT
Found at i:564534 original size:54 final size:52
Alignment explanation
Indices: 564417--564546 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 52
564407 AAATAAAAAC
*
564417 AATAAAAAAGAATGAAGAAAATTTAAATTTTAAAATAAATAAAGAAAAAATA
1 AATAAAAAAGAATGAAGAAAATTTAAATTTTAAAATAAAAAAAGAAAAAATA
* *
564469 AATAAAGAAAAAAGTGAAGAAAATGTTAATTTTTAAAA-AGAAAAAAGAAACAAAATA
1 AATAAA-AAAGAA-TGAAGAAAAT-TTAAATTTTAAAATA-AAAAAAG-AA-AAAATA
*
564526 AATAAAAAAGAAAGAAAGAAA
1 AATAAAAAAGAATG-AAGAAA
564547 TGTTAAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
52 6 0.09
53 5 0.08
54 11 0.17
55 19 0.29
56 13 0.20
57 12 0.18
ACGTcount: A:0.70, C:0.01, G:0.11, T:0.18
Consensus pattern (52 bp):
AATAAAAAAGAATGAAGAAAATTTAAATTTTAAAATAAAAAAAGAAAAAATA
Found at i:569461 original size:46 final size:47
Alignment explanation
Indices: 569351--569473 Score: 194
Period size: 47 Copynumber: 2.6 Consensus size: 47
569341 GAATAAATGT
*
569351 ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGC
*
569398 ATGCGAACTAGAAATCATGCGGTTATGTTTATTTTCTCGAAC-AAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGC
* * *
569444 ATGCGAATTAGATATCATGCGATTAGGTTT
1 ATGCGAACTAGAAATCATGCGGTTAGGTTT
569474 TCTTTTTGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 30 0.43
47 40 0.57
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (47 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAAGC
Found at i:574112 original size:125 final size:125
Alignment explanation
Indices: 573874--574113 Score: 270
Period size: 125 Copynumber: 1.9 Consensus size: 125
573864 TAGGATATGT
*
573874 TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCCAGACCAAAGAGGAATGAAGAAC
1 TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCAAGACCAAAGAGGAATGAAGAAC
**
573939 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGACGATGA
66 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCCACACCAGTATGAGACGATGA
* ** * ** *
573999 TGGGGTACGACTGAACCCAC-ATCATGTTGAGATGATGAGATTAAGACC-AAGAAGGCATTG-AG
1 TGGGGCACGACTGAACCC-CTATCATGTTGAGATGACAAAACCAAGACCAAAG-AGG-AATGAAG
* * * * * * * *
574061 AATGAGCCTTACAATTTGAGGTGTTGGGGCGTTTTGAAGGCCCATATCAGTAT
63 AACGAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCCACACCAGTAT
574114 AAGATAATGT
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
124 3 0.03
125 87 0.93
126 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.21
Consensus pattern (125 bp):
TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCAAGACCAAAGAGGAATGAAGAAC
GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCCACACCAGTATGAGACGATGA
Found at i:575342 original size:36 final size:36
Alignment explanation
Indices: 575300--575421 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
575290 AGCAAAGTCA
575300 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
* * * * * *
575336 GTCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
** * * *
575372 ATCTTGTGTCTTCA-TCAAAGAGTCGTGAAGGAAATCC
1 ATCTTAAGCCTTCACT-AAAGAGTAGTGAAGCAAA-CC
*
575409 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
575422 TCATAAGAGT
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
36 52 0.83
37 11 0.17
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
Found at i:575934 original size:54 final size:54
Alignment explanation
Indices: 575792--576483 Score: 918
Period size: 54 Copynumber: 12.9 Consensus size: 54
575782 AGTGAAGCAA
* * *
575792 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
575846 AAG-A-TTGTTCGAGTTTCATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTG
* * ** * * *
575898 AAGAAGAGGTACGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
575952 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
576006 AAGAAAATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
576060 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
576114 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
576168 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
576222 AAGAAGATTTCCAAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCG--TG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
576274 -TGAAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
**
576327 AA-AAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
576380 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--T-
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* * * * *
576432 AAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCG
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG
576484 ATTGTTGAAG
Statistics
Matches: 571, Mismatches: 56, Indels: 23
0.88 0.09 0.04
Matches are distributed among these distances:
51 43 0.08
52 54 0.09
53 74 0.13
54 396 0.69
55 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:576603 original size:55 final size:55
Alignment explanation
Indices: 576434--576705 Score: 320
Period size: 55 Copynumber: 4.9 Consensus size: 55
576424 AACCCCGTAA
* * * *
576434 GAAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAAGAGGGAGC-GAACCCGATTGTT
1 GAAGATTGTTCGAGTCT-TATACT-CTCTG-AAGAAATAGGGAGCAG-ACACGATCGTT
*
576490 GAAGATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGA-CTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGAAATAGGGAGCAGACACGATC-GTT
576547 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * **
576602 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * * *
576657 GAAGATTGTTTGAGTCTTATACTCTATGAA-AGAATAGAGAGCGGACACG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACG
576706 TTTTCCGAAG
Statistics
Matches: 193, Mismatches: 15, Indels: 17
0.86 0.07 0.08
Matches are distributed among these distances:
55 125 0.65
56 19 0.10
57 43 0.22
58 6 0.03
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
Found at i:580015 original size:3 final size:3
Alignment explanation
Indices: 580007--580067 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
579997 TTATCATCCC
580007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
580055 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
580068 ATTAGTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:585372 original size:24 final size:21
Alignment explanation
Indices: 585322--585377 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
585312 GAGATTCTTC
585322 TGAAGAAGAACCAGCACATGA
1 TGAAGAAGAACCAGCACATGA
585343 TGAAGAAGAACCAGCACATGA
1 TGAAGAAGAACCAGCACATGA
*
585364 TGAACAAGAACCAG
1 TGAAGAAGAACCAG
585378 AGAGTTCTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.09
Consensus pattern (21 bp):
TGAAGAAGAACCAGCACATGA
Found at i:587151 original size:18 final size:18
Alignment explanation
Indices: 587124--587173 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
587114 AGATTGTTGA
587124 AAGTTGCACCGAATGTGC
1 AAGTTGCACCGAATGTGC
*
587142 AAGTTACACCGAATGTGC
1 AAGTTGCACCGAATGTGC
587160 AAGTTGCACCGAAT
1 AAGTTGCACCGAAT
587174 ATTGAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (18 bp):
AAGTTGCACCGAATGTGC
Found at i:588197 original size:17 final size:18
Alignment explanation
Indices: 588169--588208 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
588159 CCTTGTTTCC
588169 TTTAATATAAATAAAAAT
1 TTTAATATAAATAAAAAT
*
588187 TTTAA-ATAAATGAAAAT
1 TTTAATATAAATAAAAAT
588204 TTTAA
1 TTTAA
588209 GGGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TTTAATATAAATAAAAAT
Found at i:590806 original size:2 final size:2
Alignment explanation
Indices: 590799--590832 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
590789 AGTTTCTTTG
*
590799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
590833 CACACACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:602249 original size:24 final size:24
Alignment explanation
Indices: 602183--602256 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
602173 ATTTTTGATT
* *
602183 TGGATTTTGATATGATAATTGACC
1 TGGATTTTGATATGATACTTAACC
*
602207 TGGATTTTTATATGATACTTAACC
1 TGGATTTTGATATGATACTTAACC
* *
602231 TGGATTTTGATCTGCTACTTAACC
1 TGGATTTTGATATGATACTTAACC
602255 TG
1 TG
602257 AATTATGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.43
Consensus pattern (24 bp):
TGGATTTTGATATGATACTTAACC
Found at i:607008 original size:75 final size:75
Alignment explanation
Indices: 606885--607036 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
606875 CTTGTTCTGA
606885 CATGTGTCCAAGTTTCTGATGCCATAGAATTACAGAATCTGAACTACATGAGGCAACAGAGGCTT
1 CATGTGTCCAAGTTTCTGATGCCATAGAATTACAGAATCTGAACTACATGAGGCAACAGAGGCTT
606950 CTGCTTCTAG
66 CTGCTTCTAG
606960 CATGTGTCCAAGTTTCTGATGCCATAGAATTACAGAATCTGAACTACATGAGGCAACAGAGGCTT
1 CATGTGTCCAAGTTTCTGATGCCATAGAATTACAGAATCTGAACTACATGAGGCAACAGAGGCTT
607025 CTGCTTCTAG
66 CTGCTTCTAG
607035 CA
1 CA
607037 AAAAGGACTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (75 bp):
CATGTGTCCAAGTTTCTGATGCCATAGAATTACAGAATCTGAACTACATGAGGCAACAGAGGCTT
CTGCTTCTAG
Found at i:612144 original size:36 final size:36
Alignment explanation
Indices: 611961--612150 Score: 220
Period size: 36 Copynumber: 5.3 Consensus size: 36
611951 TGAATAAGAA
* * * *
611961 GAACGAAAGAAAGCATC-ACACTTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* *
611996 GAACGAAAGGAAGCATCGGCACTTCCGACTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* * *
612032 GAACGGAATGAAGCATCGACACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* * *
612068 GAACTGAAGGAAACATCGGCACTTCCAATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
* * * *
612104 GAACGGAAGGAAGTATCGGCATTTCCGATTCAATTT
1 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
*
612140 GAACGGGAGGA
1 GAACGGAAGGA
612151 TGTATCACAT
Statistics
Matches: 131, Mismatches: 23, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
35 16 0.12
36 115 0.88
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
Found at i:614975 original size:13 final size:13
Alignment explanation
Indices: 614957--614981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614947 AGTGTTAATG
614957 AATTTTAAGATTA
1 AATTTTAAGATTA
614970 AATTTTAAGATT
1 AATTTTAAGATT
614982 TTATATTCGA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTTAAGATTA
Found at i:615017 original size:17 final size:18
Alignment explanation
Indices: 614983--615019 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
614973 TTTAAGATTT
614983 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
615002 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
615019 T
1 T
615020 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:620923 original size:17 final size:18
Alignment explanation
Indices: 620895--620934 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
620885 CCTTGTTTCC
620895 TTTAATATAAAT-AAAGAT
1 TTTAATATAAATGAAA-AT
620913 TTTAA-ATAAATGAAAAT
1 TTTAATATAAATGAAAAT
620930 TTTAA
1 TTTAA
620935 GGGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
TTTAATATAAATGAAAAT
Found at i:626251 original size:17 final size:17
Alignment explanation
Indices: 626231--626266 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
626221 CATGTTTTTT
*
626231 AATTTTTAAAAAATTAA
1 AATTATTAAAAAATTAA
626248 AATTATTAAAAAATTAA
1 AATTATTAAAAAATTAA
626265 AA
1 AA
626267 GCAGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATTAAAAAATTAA
Found at i:628739 original size:2 final size:2
Alignment explanation
Indices: 628734--628766 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
628724 TATTTGTGTG
628734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
628767 TTTGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:628999 original size:39 final size:41
Alignment explanation
Indices: 628904--628999 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 41
628894 CCTTAGATTT
* * *
628904 CATGTCCTCAAACAAACAATCAAGTCATTCAAACACGATTA
1 CATGTCCTCAAACAAACAATCAAGTCATCCAAACACAACTA
* * * *
628945 GATGACCTCATACAAA-GATCAA-TCATCCAAACACAACTA
1 CATGTCCTCAAACAAACAATCAAGTCATCCAAACACAACTA
*
628984 CATGTCCACAAACAAA
1 CATGTCCTCAAACAAA
629000 TGAGCATTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
39 26 0.59
40 5 0.11
41 13 0.30
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.19
Consensus pattern (41 bp):
CATGTCCTCAAACAAACAATCAAGTCATCCAAACACAACTA
Found at i:629343 original size:38 final size:37
Alignment explanation
Indices: 629301--629438 Score: 136
Period size: 37 Copynumber: 3.7 Consensus size: 37
629291 ATTAAAATTT
* * *
629301 GAATATGTTATTTTTAAAGTTATATTCGATTGAAATAG
1 GAATATATTATTTTTAAATTTATATTCGATT-AAATAC
* *
629339 GAATAT-TTTTTTTATAAATTTATATTTGATTAAATAC
1 GAATATATTATTTT-TAAATTTATATTCGATTAAATAC
* * * *
629376 AAATATATTATTTATAAATTTATATTCAATTAAAATAT
1 GAATATATTATTTTTAAATTTATATTCGATT-AAATAC
**
629414 GAATATATTA-TTACAAATTTATATT
1 GAATATATTATTTTTAAATTTATATT
629439 GAGTAAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
37 45 0.53
38 40 0.47
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (37 bp):
GAATATATTATTTTTAAATTTATATTCGATTAAATAC
Found at i:629390 original size:37 final size:38
Alignment explanation
Indices: 629280--629448 Score: 164
Period size: 38 Copynumber: 4.5 Consensus size: 38
629270 TTATTTGAGG
* * ** * *
629280 ATTTATGTTCAATTAAAATTTGAATATGTTATTTTTAA
1 ATTTATATTCGATTAAAATACGAATATATTATTTATAA
* * * * *
629318 AGTTATATTCGATTGAAATAGGAATATTTTTTTTATAA
1 ATTTATATTCGATTAAAATACGAATATATTATTTATAA
* *
629356 ATTTATATTTGATT-AAATACAAATATATTATTTATAA
1 ATTTATATTCGATTAAAATACGAATATATTATTTATAA
* * *
629393 ATTTATATTCAATTAAAATATGAATATATTA-TTACAA
1 ATTTATATTCGATTAAAATACGAATATATTATTTATAA
*
629430 ATTTATATT-GAGTAAAATA
1 ATTTATATTCGATTAAAATA
629449 TGGTATTGTA
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
36 8 0.07
37 45 0.42
38 55 0.51
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (38 bp):
ATTTATATTCGATTAAAATACGAATATATTATTTATAA
Found at i:630225 original size:95 final size:95
Alignment explanation
Indices: 630059--630464 Score: 569
Period size: 95 Copynumber: 4.3 Consensus size: 95
630049 CTTTAAGCTG
* *
630059 CAAGTTCTTCTCATTATGAACTCTTTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
1 CAAGTTCTTCTCATTATGAATTCTCTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
* * *
630124 TGAAATGTTGTGAATTGAGCAAAGGTTGAA
66 CGAAATGTCGTGAATCGAGCAAAGGTTGAA
* * *
630154 CAAGTTCTTCTCATTATAAATTCTCTCCTGGAAATGTTGGTCCCTCGAGTGAGGTATCGCTGATT
1 CAAGTTCTTCTCATTATGAATTCTCTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
*
630219 CAAAATGTCGTGAATCGAGCAAAGGTTGAA
66 CGAAATGTCGTGAATCGAGCAAAGGTTGAA
* * * **
630249 CAAGTTCTTCTCATTATGAATTCTCTACTAGAAATGTCGGTCTCTCGAGTGAGGCGCCGCTGATT
1 CAAGTTCTTCTCATTATGAATTCTCTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
* * *
630314 CGAAATGCCGTGAATTGAGCAAAGGTTGGA
66 CGAAATGTCGTGAATCGAGCAAAGGTTGAA
* ** * *
630344 CAAGTTCTTCTCATTATGAATTCTCTACTGAAAATGTTGGTGTCTCAAGTGAGGCGTCGCTGATT
1 CAAGTTCTTCTCATTATGAATTCTCTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
* *
630409 CGAAATGTCATGAATCGAGCAATAGGTCGAA
66 CGAAATGTCGTGAATCGAGCAA-AGGTTGAA
*
630440 CAAGTTCTTATCATTATGAACTTCT
1 CAAGTTCTTCTCATTATGAA-TTCT
630465 TCTCCCTCTA
Statistics
Matches: 276, Mismatches: 33, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
95 247 0.89
96 25 0.09
97 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (95 bp):
CAAGTTCTTCTCATTATGAATTCTCTACTGGAAATGTTGGTCCCTCGAGTGAGGCATCGCTGATT
CGAAATGTCGTGAATCGAGCAAAGGTTGAA
Found at i:631156 original size:75 final size:75
Alignment explanation
Indices: 630928--631157 Score: 334
Period size: 75 Copynumber: 3.1 Consensus size: 75
630918 GGAAACTTTA
* * *
630928 TCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCGAGTGAAATAAAATTTCTTGTTTCGAG
1 TCAAGCGAGATGAAATTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTC-TGTTTCGAG
630993 TAAAAACTGTC
65 TAAAAACTGTC
* * * *
631004 TCAAGCGAGAAGAAATTTGTTTTAAGAAAAATAATATCAAGTAAGATAAAATTTCTGTTGCGAGT
1 TCAAGCGAGATGAAATTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTCTGTTTCGAGT
** *
631069 GGAAACTATC
66 AAAAACTGTC
* *
631079 TCAAGCGGGATGAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTCTGTTTCGAGT
1 TCAAGCGAGATGAAATTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTCTGTTTCGAGT
*
631144 AAAAATTGTC
66 AAAAACTGTC
631154 TCAA
1 TCAA
631158 CTGACGGTGG
Statistics
Matches: 134, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 85 0.63
76 49 0.37
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (75 bp):
TCAAGCGAGATGAAATTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAAATTTCTGTTTCGAGT
AAAAACTGTC
Found at i:631810 original size:57 final size:56
Alignment explanation
Indices: 631694--631810 Score: 123
Period size: 57 Copynumber: 2.1 Consensus size: 56
631684 GTATATTTTA
* *
631694 TTTTATTTTAATTTTGGCATGATAGTTTGATTATTTATGCCTTAGTCCTACTTTTAT
1 TTTTATTTTAATTTTGGCATGATAGTTTGATTATTTAT-CCTTAGTCCTACATTAAT
* * *
631751 TTTTATTTTAATTTTTGCATG-TTGTTTGCATATTAATTTAT-TTTAGTCCTA-ATTAAT
1 TTTTATTTTAATTTTGGCATGATAGTTTG---ATT-ATTTATCCTTAGTCCTACATTAAT
631808 TTT
1 TTT
631811 GTATGATAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
56 6 0.12
57 27 0.53
58 9 0.18
59 3 0.06
60 6 0.12
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (56 bp):
TTTTATTTTAATTTTGGCATGATAGTTTGATTATTTATCCTTAGTCCTACATTAAT
Done.