Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 4 of 52
Found at i:480225 original size:2 final size:2
Alignment explanation
Indices: 480220--480246 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
480210 CAGAATCAAT
480220 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
480247 GATGTTCCTT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:482151 original size:20 final size:21
Alignment explanation
Indices: 482105--482225 Score: 68
Period size: 22 Copynumber: 5.6 Consensus size: 21
482095 TGGTAAAATT
*
482105 TAATTTATAAATAA-ATTTTTA
1 TAATTTA-AAATAATATTTATA
* *
482126 TAAATTTAAATTATTATTTA-A
1 T-AATTTAAAATAATATTTATA
*
482147 TAA-TTAAAATAATATTTATT
1 TAATTTAAAATAATATTTATA
* **
482167 TAATTTAATAAAAATTATAAATA
1 TAATTTAA-AATAA-TATTTATA
* *
482190 TTAATATAAAAATAATATTTAAA
1 -TAAT-TTAAAATAATATTTATA
*
482213 TATTTTAATAATA
1 TAATTTAA-AATA
482226 TAACAAACCA
Statistics
Matches: 74, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
19 13 0.18
20 5 0.07
21 14 0.19
22 21 0.28
23 10 0.14
24 8 0.11
25 3 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATTTAAAATAATATTTATA
Found at i:482169 original size:23 final size:23
Alignment explanation
Indices: 482139--482210 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 23
482129 ATTTAAATTA
*
482139 TTATTTAATAATTAAAATAATAT
1 TTATTTAATAATAAAAATAATAT
* *
482162 TTATTTAATTTAATAAAAATTATAA
1 TTATTTAA--TAATAAAAATAATAT
*
482187 ATA-TTAAT-ATAAAAATAATAT
1 TTATTTAATAATAAAAATAATAT
482208 TTA
1 TTA
482211 AATATTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 13 0.32
22 1 0.03
23 8 0.20
24 4 0.10
25 14 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATTTAATAATAAAAATAATAT
Found at i:482191 original size:25 final size:26
Alignment explanation
Indices: 482163--482222 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 26
482153 AAATAATATT
*
482163 TATTTAATTTAATAAA-AAT-TATAAA
1 TATTTAATATAA-AAATAATATATAAA
*
482188 TA-TTAATATAAAAATAATATTTAAA
1 TATTTAATATAAAAATAATATATAAA
482213 TATTTTAATA
1 TA-TTTAATA
482223 ATATAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 3 0.10
24 11 0.38
25 9 0.31
27 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTTAATATAAAAATAATATATAAA
Found at i:482223 original size:25 final size:24
Alignment explanation
Indices: 482147--482223 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
482137 TATTATTTAA
* **
482147 TAATTAAAATAATATTTATTTAATT
1 TAATAAAAATAATATTTAAAT-ATT
482172 TAATAAAAAT--TA--TAAATATT
1 TAATAAAAATAATATTTAAATATT
*
482192 AATATAAAAATAATATTTAAATATTT
1 TA-ATAAAAATAATATTTAAATA-TT
482218 TAATAA
1 TAATAA
482224 TATAACAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
20 4 0.10
21 11 0.27
23 4 0.10
25 19 0.46
26 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAAAAATAATATTTAAATATT
Found at i:484549 original size:28 final size:28
Alignment explanation
Indices: 484495--484549 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
484485 GGATAGGTTA
* *
484495 AGATTAAATTCTTTCTACATGTAAACCT
1 AGATTAAATTCATTCTACATATAAACCT
* *
484523 AGATTAAATTCATTCTACGTATGAACC
1 AGATTAAATTCATTCTACATATAAACC
484550 GTGGGTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (28 bp):
AGATTAAATTCATTCTACATATAAACCT
Found at i:489796 original size:6 final size:6
Alignment explanation
Indices: 489787--489813 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
489777 TTATATTTTG
489787 AATTCA AATTCA AATTCA AATTCA AAT
1 AATTCA AATTCA AATTCA AATTCA AAT
489814 AAAAGGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCA
Found at i:494981 original size:2 final size:2
Alignment explanation
Indices: 494974--495008 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
494964 TTATTTAAAG
494974 TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
495009 TTGTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:494993 original size:14 final size:14
Alignment explanation
Indices: 494974--495008 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
494964 TTATTTAAAG
494974 TATATATATATATA
1 TATATATATATATA
494988 TATATAT-TATATA
1 TATATATATATATA
495001 T-TATATAT
1 TATATATAT
495009 TTGTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 8 0.40
14 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATATATATATA
Found at i:496402 original size:34 final size:35
Alignment explanation
Indices: 496331--496411 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
496321 AATCATTATA
* *
496331 ATAA-ATT-ATATAAAATAAAAAATAAATTGAGAC
1 ATAATATTAATATAAAATAAAAAATAAATTAAAAC
* *
496364 ATAATATTAATATAATATAAAAAAT-AATTAAAAT
1 ATAATATTAATATAAAATAAAAAATAAATTAAAAC
*
496398 ATAATATGAATATA
1 ATAATATTAATATA
496412 TGAACATTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 4 0.10
34 22 0.54
35 15 0.37
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (35 bp):
ATAATATTAATATAAAATAAAAAATAAATTAAAAC
Found at i:501557 original size:21 final size:23
Alignment explanation
Indices: 501531--501580 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
501521 AATTAAAAAA
501531 TTAATATTAAA-ATAA-ATAAT-T
1 TTAATATTAAATATAATA-AATAT
501552 TTAATATTAAATATAATAAATAT
1 TTAATATTAAATATAATAAATAT
501575 TTAATA
1 TTAATA
501581 AAAATATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 7 0.27
23 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATATTAAATATAATAAATAT
Found at i:501585 original size:22 final size:21
Alignment explanation
Indices: 501531--501587 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
501521 AATTAAAAAA
501531 TTAATATTAAAATA-AATAATT
1 TTAATA-TAAAATATAATAATT
*
501552 TTAATATTAAATATAATAAATAT
1 TTAATATAAAATATAAT-AAT-T
501575 TTAATA-AAAATAT
1 TTAATATAAAATAT
501588 TCATATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 9 0.29
22 9 0.29
23 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATATAAAATATAATAATT
Found at i:501689 original size:18 final size:19
Alignment explanation
Indices: 501659--501694 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
501649 CACTACATAT
501659 AATAAATTTAAAAATTAAA
1 AATAAATTTAAAAATTAAA
501678 AATAAA-TTAAAAATTAA
1 AATAAATTTAAAAATTAA
501695 TCTTTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAATTTAAAAATTAAA
Found at i:501753 original size:2 final size:2
Alignment explanation
Indices: 501746--501779 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
501736 AATTCTATGA
501746 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
501780 TATCAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:510294 original size:6 final size:6
Alignment explanation
Indices: 510280--510309 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
510270 TTGGTTTGAC
510280 TTTGAGT TTTGGT TTTGGT TTTGGT TTTGG
1 TTTG-GT TTTGGT TTTGGT TTTGGT TTTGG
510310 GTTCAGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (6 bp):
TTTGGT
Found at i:510469 original size:20 final size:21
Alignment explanation
Indices: 510433--510485 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
510423 TTATTTGTTA
*
510433 AAAAAATTAAAAT-ATAA-TAT
1 AAAAAA-TAATATAATAAGTAT
510453 AAAAAATAATATAATAAGTAT
1 AAAAAATAATATAATAAGTAT
*
510474 AATAAA-AATATA
1 AAAAAATAATATA
510486 TAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 16 0.55
21 8 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAATAATATAATAAGTAT
Found at i:511010 original size:10 final size:10
Alignment explanation
Indices: 510981--511016 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
510971 AATATATTTT
510981 TATTTTAAAA
1 TATTTTAAAA
*
510991 TATATT-AAA
1 TATTTTAAAA
511000 TATTTTAAAA
1 TATTTTAAAA
511010 TATTTTA
1 TATTTTA
511017 TTTTCTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:515812 original size:97 final size:97
Alignment explanation
Indices: 515646--515835 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 97
515636 TTGTCGGGAA
* * * * * *
515646 TACTCTAACCCCATTCTTGCGAGGGGATATTCTAATCTTGTTTTTAAACTCATCAAGGTTTAAAC
1 TACTCCAACCCCATTCTTCCGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAAC
* *
515711 CTTATTTTTGCTTAAATTGTCATCATCGAGGG
66 CTTATTTTCGCCTAAATTGTCATCATCGAGGG
* * ** *
515743 TACTCCAACCTCATTTTTCCGAGGGGATACTCCAATCTTCTTTTTAAACTTGTCAAGATTTAAAT
1 TACTCCAACCCCATTCTTCCGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAAC
*
515808 CTTATTTTCGCCTATATTGTCATCATCG
66 CTTATTTTCGCCTAAATTGTCATCATCG
515836 GGGACAGTCG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (97 bp):
TACTCCAACCCCATTCTTCCGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAAC
CTTATTTTCGCCTAAATTGTCATCATCGAGGG
Found at i:515864 original size:97 final size:97
Alignment explanation
Indices: 515665--515873 Score: 244
Period size: 97 Copynumber: 2.2 Consensus size: 97
515655 CCCATTCTTG
* * * * * *
515665 CGAGGGGATATTCTAATCTTGTTTTTAAACTCATCAAGGTTTAAACCTTATTTTTGCTTAAATTG
1 CGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAACCTTATTTTCGCCTAAATTG
*
515730 TCATCATCGAGGGTACTCCAACCTCATTTTTC
66 TCATCATCGAGGGTACTCCAACCTCATTTCTC
** * *
515762 CGAGGGGATACTCCAATCTTCTTTTTAAACTTGTCAAGATTTAAATCTTATTTTCGCCTATATTG
1 CGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAACCTTATTTTCGCCTAAATTG
*
515827 TCATCATCG-GGG-ACAGTCGAA-CTCCATTTCTC
66 TCATCATCGAGGGTAC--TCCAACCT-CATTTCTC
* *
515859 TGAGGGAATACTCCA
1 CGAGGGGATACTCCA
515874 TCCTTTTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
95 2 0.02
96 5 0.05
97 88 0.93
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (97 bp):
CGAGGGGATACTCCAATCTTCTTTTTAAACTCATCAAGATTTAAACCTTATTTTCGCCTAAATTG
TCATCATCGAGGGTACTCCAACCTCATTTCTC
Found at i:519403 original size:154 final size:153
Alignment explanation
Indices: 519157--519557 Score: 493
Period size: 153 Copynumber: 2.6 Consensus size: 153
519147 TTTTTTTCAG
* * * * * *
519157 ATTTTTCCTATTTTCAAAATATAAAGTTTTTTACTCCGTAAATTTTTT-AGTAGGATTTTTCTAA
1 ATTTTTTCTATTATCAAAATATGAAGTTTTCTACTCCGTAAATTTTTTCGGTACGATTTTTCTAA
* * * * **
519221 GTGTATGATTTTCATAATTCTTCAAATATTATTACTTAATTCACATTAAATCAGTTTTAAAGTAT
66 GTTTATAATTTTCAAAATTCTTCAAATATTATTACTTAATTCACATTAAATCAATTTTAAAAAAT
519286 TCAATT-TATTTTATGAGTTTTAGA
131 TCAATTAT-TTTTATGAGTTTTA-A
*
519310 ATTTTTTCTATTATAAAAATATGAAGTTTTCTACTCCGTAAATTTTTTCGGTACGATTTCTT-TA
1 ATTTTTTCTATTATCAAAATATGAAGTTTTCTACTCCGTAAATTTTTTCGGTACGATTT-TTCTA
* ** **
519374 AGTTTATAATTTTCAAAATTCTTCAAATATCATTGTTTAATTCTTATTAAATCAATTTTAAAAAA
65 AGTTTATAATTTTCAAAATTCTTCAAATATTATTACTTAATTCACATTAAATCAATTTTAAAAAA
*
519439 TTTAATTATTTTTATGAGTTTTAA
130 TTCAATTATTTTTATGAGTTTTAA
* * * * * ** *
519463 AATTTTTCTATTATCGAAATGTGGAGTTTTCTACTCTGTAAATTTTTTCGAAATGATTTTTCTAA
1 ATTTTTTCTATTATCAAAATATGAAGTTTTCTACTCCGTAAATTTTTTCGGTACGATTTTTCTAA
* *
519528 ATTTATAATTTCCAAAATTCTTCAAATATT
66 GTTTATAATTTTCAAAATTCTTCAAATATT
519558 GTGAAATTTT
Statistics
Matches: 213, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
152 2 0.01
153 124 0.58
154 84 0.39
155 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (153 bp):
ATTTTTTCTATTATCAAAATATGAAGTTTTCTACTCCGTAAATTTTTTCGGTACGATTTTTCTAA
GTTTATAATTTTCAAAATTCTTCAAATATTATTACTTAATTCACATTAAATCAATTTTAAAAAAT
TCAATTATTTTTATGAGTTTTAA
Found at i:521868 original size:235 final size:234
Alignment explanation
Indices: 521522--521953 Score: 531
Period size: 235 Copynumber: 1.8 Consensus size: 234
521512 AATGGGGTTG
* * *
521522 GAGTATTCCCTCGAAAATAACTGGTTGAGGTATCCCTAATGGTGAAAAATCAATGTTTTGAAAAT
1 GAGTATTCCCTCGAAAATAACGGGTTGAGGTATCCCGAATGGTGAAAAATCAATATTTTGAAAAT
* * *
521587 AAAATCGAGTTGGAGCATTCTCTCGAAAATAACGAGGTCAGAGTATCCTCGATGGAGAAAAATTC
66 AAAATCGAGTTGGAGCATCCTCTCAAAAATAACGAGGTCAGAGTATCCCCGATGGAGAAAAA-TC
*
521652 -ATATTTTGAAAATAAAAATCGGGTTAGAGTATCCCCTT-GAAAATAATAGGGTTGGAGTATCCC
130 GATATTTTGAAAATAAAAATCGGGTTAGAGTAT--CCTTAGAAAATAATAAGGTTGGAGTATCCC
521715 CGATGATAAAAAATCAATATTTCAAAAATAAAAACGGGATAC
193 CGATGATAAAAAATCAATATTTCAAAAATAAAAACGGGATAC
* *
521757 GAGTA-TCCCTTCGAAAATAACGGGGTTG-GAGTATCCCGGAT-GTGAAAAATCAATATTTTGGA
1 GAGTATTCCC-TCGAAAATAAC-GGGTTGAG-GTATCCCGAATGGTGAAAAATCAATATTTTGAA
* ** * *
521819 AATAAAAAT-G-GCTTGGAGTATCC-CTTCAAAAATAATC-AGGTTGGAGTATCCCCGATGGTGG
63 AAT-AAAATCGAG-TTGGAGCATCCTC-TCAAAAATAA-CGAGGTCAGAGTATCCCCGATGGAGA
* * * * *
521880 GAAATCGATATTTTGGAAATGAAAATGGGGTTGGAGTATCCTTAGAAAATAATAAGGTTGGAGTA
124 AAAATCGATATTTTGAAAATAAAAATCGGGTTAGAGTATCCTTAGAAAATAATAAGGTTGGAGTA
*
521945 TCCCTGATG
189 TCCCCGATG
521954 GTGAAAAGTC
Statistics
Matches: 168, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
233 4 0.02
234 36 0.21
235 108 0.64
236 20 0.12
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (234 bp):
GAGTATTCCCTCGAAAATAACGGGTTGAGGTATCCCGAATGGTGAAAAATCAATATTTTGAAAAT
AAAATCGAGTTGGAGCATCCTCTCAAAAATAACGAGGTCAGAGTATCCCCGATGGAGAAAAATCG
ATATTTTGAAAATAAAAATCGGGTTAGAGTATCCTTAGAAAATAATAAGGTTGGAGTATCCCCGA
TGATAAAAAATCAATATTTCAAAAATAAAAACGGGATAC
Found at i:521966 original size:78 final size:79
Alignment explanation
Indices: 521507--522026 Score: 431
Period size: 78 Copynumber: 6.7 Consensus size: 79
521497 TGTTTTGGGT
*
521507 ATAAAAATGGGGTTGGAGTATTCCC-TCGAAAATAACT--GGTT-GAGGTATCCCTAATGGTGAA
1 ATAAAAATGGGGTTGGAGTA-TCCCTTCGAAAATAA-TAAGGTTGGA-GTATCCCTGATGGTGAA
*
521568 AAATCAATGTTTTGAAA
63 AAATCAATATTTTGAAA
* * * * ** ** *
521585 AT-AAAATCGAGTTGGAGCAT-TCTCTCGAAAATAACGAGGTCAGAGTAT-CCTCGATGGAGAAA
1 ATAAAAATGGGGTTGGAGTATCCCT-TCGAAAATAATAAGGTTGGAGTATCCCT-GATGGTGAAA
521647 AATTC-ATATTTTGAAA
64 AA-TCAATATTTTGAAA
* * * * * *
521663 ATAAAAATCGGGTTAGAGTATCCCCTT-GAAAATAATAGGGTTGGAGTATCCCCGATGATAAAAA
1 ATAAAAATGGGGTTGGAGTAT-CCCTTCGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAA
**
521727 ATCAATATTTCAAAA
65 ATCAATATTTTGAAA
* * ** *** *
521742 ATAAAAACGGGATACGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCGGAT-GTGAAAAA
1 ATAAAAATGGGGTTGGAGTATCCCTTCGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAA
*
521806 TCAATATTTTGGAA
66 TCAATATTTTGAAA
* * * * **
521820 ATAAAAAT-GGCTTGGAGTATCCCTTCAAAAATAATCAGGTTGGAGTATCCCCGATGGTGGGAAA
1 ATAAAAATGGGGTTGGAGTATCCCTTCGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAA
* *
521884 TCGATATTTTGGAA
66 TCAATATTTTGAAA
* * *
521898 ATGAAAATGGGGTTGGAGTAT-CCTTAGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAG
1 ATAAAAATGGGGTTGGAGTATCCCTTCGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAA
* *
521962 TC--GATTTTGGAA
66 TCAATATTTTGAAA
* * ** * * *
521974 ATGAAAAT-AGGTTAAAGTATCCCTTTCGAAAATAACAAGGATAGAGTATCCCT
1 ATAAAAATGGGGTTGGAGTATCCC-TTCGAAAATAATAAGGTTGGAGTATCCCT
522027 TCGAAAATAA
Statistics
Matches: 359, Mismatches: 66, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
75 10 0.03
76 20 0.06
77 91 0.25
78 126 0.35
79 107 0.30
80 3 0.01
81 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (79 bp):
ATAAAAATGGGGTTGGAGTATCCCTTCGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAA
TCAATATTTTGAAA
Found at i:522036 original size:183 final size:185
Alignment explanation
Indices: 521834--522167 Score: 469
Period size: 183 Copynumber: 1.8 Consensus size: 185
521824 AAATGGCTTG
** * *
521834 GAGTATCCCTTCAAAAATAATCAGGTTGGAGTATCCCCGA-TGGTG-GGAAATCGATATTTTGGA
1 GAGTATCCCTTCAAAAATAATCAGGTTGGAGTAT-CCCGACT-GTGAAAAAATCAATATTTTAGA
* ** * * *
521897 AATGAAAATGGGGTTGGAGTATCC-TTAGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAA
64 AATAAAAACAGGGTTGGAGTATCCGTTAGAAAATAACAAGGTTGAAGTATCCCCGATGGTGAAAA
*
521961 GTCG-ATTTTGGAAATGAAAATAGGTTAAAGTATCCCTTTCGAAAATAACAAGGATA
129 ATCGAATTTTGGAAATGAAAATAGGTTAAAGTATCCCTTTCGAAAATAACAAGGATA
* **
522017 GAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCGACTGTGAAAAAATCAATATTTTAGAAA
1 GAGTATCCCTTCAAAAATAATCAGGTTGGAGTATCCCGACTGTGAAAAAATCAATATTTTAGAAA
* *
522082 TAAAAACAGGGTTGGAGTATCCGTTCGAAAATAACGAGGTTGAAGTATCCCCGATGGTGAAAAAT
66 TAAAAACAGGGTTGGAGTATCCGTTAGAAAATAACAAGGTTGAAGTATCCCCGATGGTGAAAAAT
522147 CGATATTTTGGAAATGAAAAT
131 CGA-ATTTTGGAAATGAAAAT
522168 GGGGTTGGAG
Statistics
Matches: 130, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
182 8 0.06
183 67 0.52
184 38 0.29
186 17 0.13
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (185 bp):
GAGTATCCCTTCAAAAATAATCAGGTTGGAGTATCCCGACTGTGAAAAAATCAATATTTTAGAAA
TAAAAACAGGGTTGGAGTATCCGTTAGAAAATAACAAGGTTGAAGTATCCCCGATGGTGAAAAAT
CGAATTTTGGAAATGAAAATAGGTTAAAGTATCCCTTTCGAAAATAACAAGGATA
Found at i:522129 original size:107 final size:105
Alignment explanation
Indices: 521908--522132 Score: 235
Period size: 107 Copynumber: 2.1 Consensus size: 105
521898 ATGAAAATGG
* * *
521908 GGTTGGAGTAT-CCTTAGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAGTCGATTTTGG
1 GGTTGAAGTATCCCTTAGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAATCGATTTTAG
* * *
521972 AAATGAAAATAGGTTAAAGTATCCCTTTCGAAAATAACAA
66 AAATAAAAACAGGTTAAAGTATCCCGTTCGAAAATAACAA
* * ** *
522012 GGAT-AGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCC-GACT-GTGAAAAAATCAATAT
1 GGTTGA-AGTATCCCTTAGAAAATAATAAGGTTGGAGTATCCCTGA-TGGTG-AAAAATC--GAT
** *
522074 TTTAGAAATAAAAACAGGGTTGGAGTAT-CCGTTCGAAAATAACGA
61 TTTAGAAATAAAAACA-GGTTAAAGTATCCCGTTCGAAAATAACAA
522119 GGTTGAAGTATCCC
1 GGTTGAAGTATCCC
522133 CGATGGTGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
104 13 0.13
105 34 0.35
107 41 0.42
108 10 0.10
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (105 bp):
GGTTGAAGTATCCCTTAGAAAATAATAAGGTTGGAGTATCCCTGATGGTGAAAAATCGATTTTAG
AAATAAAAACAGGTTAAAGTATCCCGTTCGAAAATAACAA
Found at i:522287 original size:80 final size:80
Alignment explanation
Indices: 522017--522327 Score: 337
Period size: 79 Copynumber: 3.9 Consensus size: 80
522007 AACAAGGATA
* * * *
522017 GAGTATCCCTTCGAAAATAATGGGGTTGGAGTAT-CCCGACT-GTGAAAAAATCAATATTTTAGA
1 GAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGA-TGGTGAAAAAATCGATATTTTGGA
*
522080 AATAAAAACAGGGTTG
65 AATAAAAACGGGGTTG
* *
522096 GAGTATCCGTTCGAAAATAACGAGGTTGAAGTATCCCCGATGGTG-AAAAATCGATATTTTGGAA
1 GAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATGGTGAAAAAATCGATATTTTGGAA
* *
522160 ATGAAAATGGGGTTG
66 ATAAAAACGGGGTTG
* * * * ***
522175 GAGTAT-CTTCTCAAAAATAACGAGATTAGAGTATTTTCGATGGT-AAAAAATCGATATTTTGAG
1 GAGTATCCCT-TCGAAAATAACGAGGTTGGAGTATCCCCGATGGTGAAAAAATCGATATTTTG-G
*
522238 AAATGAAAACGGGGTTG
64 AAATAAAAACGGGGTTG
* * * * *
522255 GAGTATCCCCTTC-AGAATAAAGGGGTTGGAGTATCTCCGATGGTGAAAAAAATTGATATTTTGG
1 GAGTAT-CCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATGGTG-AAAAAATCGATATTTTGG
522319 AAATAAAAA
64 AAATAAAAA
522328 AATTAATGAA
Statistics
Matches: 195, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
78 2 0.01
79 109 0.56
80 55 0.28
81 11 0.06
82 18 0.09
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (80 bp):
GAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATGGTGAAAAAATCGATATTTTGGAA
ATAAAAACGGGGTTG
Found at i:522788 original size:152 final size:151
Alignment explanation
Indices: 522512--522815 Score: 491
Period size: 152 Copynumber: 2.0 Consensus size: 151
522502 GGCTACACCT
* * *
522512 AAAAACAGGGGACAACATCGTGCTATCCCATTTTCTAAATTTATTATAGGTTGATTCGAGGGTTC
1 AAAAACAGGGGACAACATCGTGCTATCCCACTCTCTAAATTTATTATAGGTTGATTCGAGGATTC
*
522577 TAAAGGGTGGAAGAGGTACCATTAGAAAGGTGACTCGATGAGGGTCAATCTAAAAATATTTTAAA
66 TAAAGGGTGGAAGAGGTACCATTAGAAAGGTGACTCGATGAGAGTCAATCTAAAAATATTTTAAA
522642 AATTCTAAAGGAATCACTTTCC
131 AATTCTAAA-GAATCACTTTCC
* * ** * *
522664 AAAAACAGGGGACAGCATTGTGCTATCCTGCTCTCTGAATTTATTTTAGGTTGATTCGAGGATTC
1 AAAAACAGGGGACAACATCGTGCTATCCCACTCTCTAAATTTATTATAGGTTGATTCGAGGATTC
* *
522729 TAAAGGGTGGAAGAGGTATCATTAGAAAGGTGACTCGATGAGAGTCAATCTAAAAATATTTTTAA
66 TAAAGGGTGGAAGAGGTACCATTAGAAAGGTGACTCGATGAGAGTCAATCTAAAAATATTTTAAA
522794 AATTCTAAAGAATCACTTTCC
131 AATTCTAAAGAATCACTTTCC
522815 A
1 A
522816 GGGGAATAAA
Statistics
Matches: 140, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
151 13 0.09
152 127 0.91
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (151 bp):
AAAAACAGGGGACAACATCGTGCTATCCCACTCTCTAAATTTATTATAGGTTGATTCGAGGATTC
TAAAGGGTGGAAGAGGTACCATTAGAAAGGTGACTCGATGAGAGTCAATCTAAAAATATTTTAAA
AATTCTAAAGAATCACTTTCC
Found at i:522967 original size:24 final size:24
Alignment explanation
Indices: 522940--523001 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
522930 AACAATACCT
* *
522940 TTTTGAAAAGAAAAT-TTTACAAAA
1 TTTTGAAAA-AAAATATTCAAAAAA
* **
522964 TTTTTAGGAAAAATATTCAAAAAA
1 TTTTGAAAAAAAATATTCAAAAAA
522988 TTTTGAAAAAAAAT
1 TTTTGAAAAAAAAT
523002 CATCTAGTAG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (24 bp):
TTTTGAAAAAAAATATTCAAAAAA
Found at i:524291 original size:110 final size:110
Alignment explanation
Indices: 524093--524326 Score: 450
Period size: 110 Copynumber: 2.1 Consensus size: 110
524083 AATAGAAACC
524093 AAAACTGATGAAAGTAGAGAGGATATACCAAAAAGTTTGAGCTTTCTTTTTTTACTTAGAACAAA
1 AAAA-TGATGAAAGTAGAGAGGATATACCAAAAAGTTTGAGCTTTCTTTTTTTACTTAGAACAAA
524158 GGTTGTTGGCTTAGCTTTCTCCCTTTATTTACTATTATTTAGCAAG
65 GGTTGTTGGCTTAGCTTTCTCCCTTTATTTACTATTATTTAGCAAG
524204 AAAATGATGAAAGTAGAGAGGATATACCAAAAAGTTTGAGCTTTCTTTTTTTACTTAGAACAAAG
1 AAAATGATGAAAGTAGAGAGGATATACCAAAAAGTTTGAGCTTTCTTTTTTTACTTAGAACAAAG
524269 GTTGTTGGCTTAGCTTTCTCCCTTTATTTACTATTATTTAGCAAG
66 GTTGTTGGCTTAGCTTTCTCCCTTTATTTACTATTATTTAGCAAG
*
524314 AAAAAGATGAAAG
1 AAAATGATGAAAG
524327 AAGATAGCTT
Statistics
Matches: 122, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 118 0.97
111 4 0.03
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (110 bp):
AAAATGATGAAAGTAGAGAGGATATACCAAAAAGTTTGAGCTTTCTTTTTTTACTTAGAACAAAG
GTTGTTGGCTTAGCTTTCTCCCTTTATTTACTATTATTTAGCAAG
Found at i:525082 original size:20 final size:21
Alignment explanation
Indices: 525048--525101 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
525038 CGTTTTAGGC
* *
525048 ATGTATCAATGCATTCACT-T
1 ATGTATCGATACATTCACTGT
*
525068 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTCACTGT
*
525089 TTGTATCGATACA
1 ATGTATCGATACA
525102 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:525813 original size:156 final size:156
Alignment explanation
Indices: 525500--526089 Score: 749
Period size: 156 Copynumber: 3.8 Consensus size: 156
525490 AAATTATAAA
* * * *
525500 TATT-AAAAATTTTGTT-TCAAGGCCAAAAGTACTTGGTTGTATCTTGCTTGTAACTTTTGGATG
1 TATTCAAAAATCTTGTTCT-AAGGCCAAAAGTACTTGGCTGAATCTTCCTTGTAACTTTTGGATG
* * * *
525563 TGTTTTGTATGTTGATTTTGACTTCTTGGATG-TTAATTCTGTGTTTTTATTAGGTAAGGACTAA
65 TGTTTTGTATGCTGATTTTGATTTCTTGGATGTTTAATTTTGTGGTTTTATTAGGTAAGGACTAA
* * *
525627 CTTGCAAACTTAGAAAGTATAGGGATTT
130 CTTGCAAAATTAGAAAGTTTAAGGA-TT
*
525655 TATTCAAAAATCTTGTTCTAAGGCCAAATGTACTTGGCTGAATCTTCCTTGTAACTTTTGGATGT
1 TATTCAAAAATCTTGTTCTAAGGCCAAAAGTACTTGGCTGAATCTTCCTTGTAACTTTTGGATGT
* * * * *
525720 ATTTTGTATGTTGATTTTGATTTCTTGAATGTTTAATTTTGTGGTTTTATTAGATTAGGACTAAC
66 GTTTTGTATGCTGATTTTGATTTCTTGGATGTTTAATTTTGTGGTTTTATTAGGTAAGGACTAAC
*
525785 TTGCAAAATTAAAAAGTTTAAGGATT
131 TTGCAAAATTAGAAAGTTTAAGGATT
* * * * *
525811 TATTCGAAAATCTTGTTCTAAGGCCCAAAGTATTTGGTTGAATCTTCCTTGTAACTTTTAGATGT
1 TATTCAAAAATCTTGTTCTAAGGCCAAAAGTACTTGGCTGAATCTTCCTTGTAACTTTTGGATGT
* * *
525876 GTTTTGTATGCTGATTTTGATTTGTTGGATGTTTAATTTTGTGTTTTTATTAGGTAAGGACTAAT
66 GTTTTGTATGCTGATTTTGATTTCTTGGATGTTTAATTTTGTGGTTTTATTAGGTAAGGACTAAC
* *
525941 TTGCGAAATTAGAAAGTTTAAGGGGTT
131 TTGCAAAATTAGAAAGTTTAA-GGATT
* * * * * * **
525968 TGTTCAAAAATTTTATTCCAAGGCCAAAAGTGA-TTGGCCGAATCTTCCTTATAACTTTTTAATG
1 TATTCAAAAATCTTGTTCTAAGGCCAAAAGT-ACTTGGCTGAATCTTCCTTGTAACTTTTGGATG
* * *
526032 TGTTTTGTATGCTGATTTTGATTTCTTTGATGCTTAATTTTGT-GTTTTAATTACGTAA
65 TGTTTTGTATGCTGATTTTGATTTCTTGGATGTTTAATTTTGTGGTTTT-ATTAGGTAA
526090 AGACCTTTTT
Statistics
Matches: 380, Mismatches: 49, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
155 4 0.01
156 222 0.58
157 153 0.40
158 1 0.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (156 bp):
TATTCAAAAATCTTGTTCTAAGGCCAAAAGTACTTGGCTGAATCTTCCTTGTAACTTTTGGATGT
GTTTTGTATGCTGATTTTGATTTCTTGGATGTTTAATTTTGTGGTTTTATTAGGTAAGGACTAAC
TTGCAAAATTAGAAAGTTTAAGGATT
Found at i:529570 original size:154 final size:154
Alignment explanation
Indices: 529330--529698 Score: 445
Period size: 155 Copynumber: 2.4 Consensus size: 154
529320 GGTTAGGGAA
* * * * * *
529330 ATTTTCATAATTTTTTTAGAATCAAGTCCTAGGTTGTCACCAAGATCCTTTTATATCGAATGTGT
1 ATTTTCATAATTTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGATGCTTTTAT-GCCAATGTGT
* * **
529395 GCATTTAGGATATGTTCATCCCATTTATGATCATTTTAGTGTCCATTAGGGTAATCGAGATGTTT
65 GCATTTAGGATAGGTTCATCCCATTTATGATCATTTTAGTGTCCATTAAGGTAAT-GAGATACTT
* * **
529460 TCATGTCG-AAGATATATTCTAAGGGT
129 TCATGTCGAAAG-TATACTCAAAGGAC
* ** *
529486 ATTTTTATAA-TTTTTTAGAATCGAGTCTTAGGTTACCACCGGGATGCTTTTATGCCAATGTGTG
1 ATTTTCATAATTTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGATGCTTTTATGCCAATGTGTG
* * * *
529550 CATTTAGGATAGGTTTATCCCATTTATGATCATTTTAGTGTCTATTAAGGTTATGGGATACTTTC
66 CATTTAGGATAGGTTCATCCCATTTATGATCATTTTAGTGTCCATTAAGGTAATGAGATACTTTC
*
529615 ATGTTGAAAGTATACTCAAAGGAC
131 ATGTCGAAAGTATACTCAAAGGAC
* * **
529639 ATTTTCATAATTTTTTTTAAAATCGAGTCTTAGGTTGTGACTTGGATGCTTTTATGCCAA
1 ATTTTCATAA-TTTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGATGCTTTTATGCCAA
529699 AGGTCATTTT
Statistics
Matches: 180, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
153 32 0.18
154 61 0.34
155 78 0.43
156 9 0.05
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (154 bp):
ATTTTCATAATTTTTTTAGAATCGAGTCTTAGGTTGTCACCAGGATGCTTTTATGCCAATGTGTG
CATTTAGGATAGGTTCATCCCATTTATGATCATTTTAGTGTCCATTAAGGTAATGAGATACTTTC
ATGTCGAAAGTATACTCAAAGGAC
Found at i:531920 original size:23 final size:24
Alignment explanation
Indices: 531880--531930 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
531870 TTTTTAAAAA
*
531880 AATTATAAATAAAGAAATTTCA-T
1 AATTATAAATAAAGAAATATCATT
*
531903 AATTA-AAATAAAATAAATATCATT
1 AATTATAAAT-AAAGAAATATCATT
531927 AATT
1 AATT
531931 TTAGAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTATAAATAAAGAAATATCATT
Found at i:536869 original size:20 final size:20
Alignment explanation
Indices: 536828--536879 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
536818 GGACCCGTTG
*
536828 TATTAAAAAAG-AATTTAAA
1 TATTAAATAAGTAATTTAAA
**
536847 TATTAAATAAGTAATTTTTA
1 TATTAAATAAGTAATTTAAA
*
536867 TATTAACTAAGTA
1 TATTAAATAAGTA
536880 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (20 bp):
TATTAAATAAGTAATTTAAA
Found at i:545399 original size:18 final size:18
Alignment explanation
Indices: 545360--545397 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
545350 ACATTAATTA
545360 TTATTTTAATAAATTTTT
1 TTATTTTAATAAATTTTT
*
545378 TTATATTTAATATATTTTT
1 TTAT-TTTAATAAATTTTT
545397 T
1 T
545398 ATTAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTAATAAATTTTT
Found at i:545775 original size:3 final size:3
Alignment explanation
Indices: 545767--545791 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
545757 AAATTCATTG
545767 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
545792 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:545796 original size:3 final size:3
Alignment explanation
Indices: 545790--545814 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
545780 CTACTACTAC
545790 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
545815 TTGTTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:547972 original size:12 final size:12
Alignment explanation
Indices: 547951--547989 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
547941 TGATAGTTGT
547951 TATT-TATTATA
1 TATTATATTATA
547962 TATTATATTAT-
1 TATTATATTATA
547973 TATTTATATTATA
1 TA-TTATATTATA
547986 TATT
1 TATT
547990 GTTATTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.24
12 17 0.68
13 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTATATTATA
Found at i:547979 original size:19 final size:19
Alignment explanation
Indices: 547950--547995 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
547940 ATGATAGTTG
547950 TTATTTATTATATATTATATTA
1 TTATTTA-TAT-TA-TATATTA
*
547972 TTATTTATATTATATATTG
1 TTATTTATATTATATATTA
547991 TTATT
1 TTATT
547996 GTGATTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 2 0.09
21 3 0.13
22 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTATATTATATATTA
Found at i:548713 original size:12 final size:12
Alignment explanation
Indices: 548693--548743 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
548683 AATTGTGTCG
548693 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
548706 TCAATTTGAAAT
1 TCAATTTGAAAT
*
548718 AGTAAATATTGAAAT
1 --TCAAT-TTGAAAT
548733 TCAATTTGAAA
1 TCAATTTGAAA
548744 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:553450 original size:12 final size:12
Alignment explanation
Indices: 553430--553480 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
553420 AACTGTGTCG
553430 TCAACTTTGAAAT
1 TCAA-TTTGAAAT
553443 TCAATTTGAAAT
1 TCAATTTGAAAT
*
553455 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
553470 TCAATTTGAAA
1 TCAATTTGAAA
553481 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:553492 original size:27 final size:27
Alignment explanation
Indices: 553436--553492 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
553426 GTCGTCAACT
* *
553436 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
553463 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
553490 TTG
1 TTG
553493 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:561941 original size:13 final size:13
Alignment explanation
Indices: 561923--561948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
561913 CAATTTTTTG
561923 TGTATCGATACAT
1 TGTATCGATACAT
561936 TGTATCGATACAT
1 TGTATCGATACAT
561949 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:562688 original size:21 final size:21
Alignment explanation
Indices: 562647--562690 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
562637 CTCTCCTTTA
* *
562647 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
562668 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
562689 TC
1 TC
562691 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:564513 original size:13 final size:13
Alignment explanation
Indices: 564495--564533 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
564485 ATAATCACCC
564495 TGTATCGATACAA
1 TGTATCGATACAA
564508 TGTATCGATACAA
1 TGTATCGATACAA
564521 TGTATCGATACAA
1 TGTATCGATACAA
564534 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:566616 original size:15 final size:16
Alignment explanation
Indices: 566591--566625 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
566581 ATCACTTTCG
*
566591 TTTGAAGCTTCTTCAT
1 TTTGAAGCTTCCTCAT
566607 TTTG-AGCTTCCTCAT
1 TTTGAAGCTTCCTCAT
566622 TTTG
1 TTTG
566626 GACATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTGAAGCTTCCTCAT
Found at i:571091 original size:3 final size:3
Alignment explanation
Indices: 571064--571109 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
571054 TTTATCAATG
* * *
571064 TAT TTT TAT TAG TAT CTAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
571110 ATTTTTTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:571370 original size:12 final size:12
Alignment explanation
Indices: 571353--571382 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
571343 TATTTTTATC
571353 TATCATGGTTTA
1 TATCATGGTTTA
*
571365 TATCATGTTTTA
1 TATCATGGTTTA
571377 TATCAT
1 TATCAT
571383 ATAATCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (12 bp):
TATCATGGTTTA
Found at i:571821 original size:26 final size:25
Alignment explanation
Indices: 571795--571845 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
571785 ATTTATTATA
* *
571795 TTAAATGAATAAAAATTTTAAAAATAT
1 TTAAAT-AA-AAAAAATTAAAAAATAT
571822 TTAAATAAAAAAAATTAAAAAATA
1 TTAAATAAAAAAAATTAAAAAATA
571846 AAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 2 0.09
27 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TTAAATAAAAAAAATTAAAAAATAT
Found at i:571860 original size:14 final size:14
Alignment explanation
Indices: 571822--571862 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
571812 TTAAAAATAT
*
571822 TTAAATAAAAAAAA
1 TTAAATAAATAAAA
571836 TTAAA-AAATAAAA
1 TTAAATAAATAAAA
571849 -TAAATAATATAAAA
1 TTAAATAA-ATAAAA
571863 GCTTTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TTAAATAAATAAAA
Found at i:576464 original size:22 final size:22
Alignment explanation
Indices: 576436--576477 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
576426 TATTAAAATT
576436 AATTTTT-TAATAAAAATTTAGA
1 AATTTTTGTAA-AAAAATTTAGA
*
576458 AATTTTTGTAAAAATATTTA
1 AATTTTTGTAAAAAAATTTA
576478 TTTTAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTTTTGTAAAAAAATTTAGA
Found at i:577442 original size:56 final size:56
Alignment explanation
Indices: 577317--577480 Score: 169
Period size: 56 Copynumber: 3.0 Consensus size: 56
577307 ATATGTAGAA
* * * * * *
577317 TTTTTACACA-AAAATTTT-AATTAAATCTTTTACATATTAAAATTTTT-ATTAAAAC
1 TTTTTACACATGAAATTTTCAATTAAACCTTTGAAATA-TAGAATTTTTAATT-GAAC
* *
577372 --TTTACACATGAAATTTTCCAA-TAGACCTTTGAAATATAGAATTTTTCATTGAAC
1 TTTTTACACATGAAATTTT-CAATTAAACCTTTGAAATATAGAATTTTTAATTGAAC
* *
577426 TTTTTACACATGAAATTTTCAATTAAACTTTTTAAATATAGAATTTTTAATTGAA
1 TTTTTACACATGAAATTTTCAATTAAACCTTTGAAATATAGAATTTTTAATTGAA
577481 ATTCCATGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
53 8 0.09
54 19 0.21
55 17 0.19
56 47 0.52
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (56 bp):
TTTTTACACATGAAATTTTCAATTAAACCTTTGAAATATAGAATTTTTAATTGAAC
Found at i:577470 original size:28 final size:28
Alignment explanation
Indices: 577403--577477 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
577393 TAGACCTTTG
*
577403 AAATATAGAATTTTTC-ATTGAACTTTTT
1 AAATATAGAA-TTTTCAATTAAACTTTTT
* *
577431 ACACAT-GAAATTTTCAATTAAACTTTTT
1 AAATATAG-AATTTTCAATTAAACTTTTT
*
577459 AAATATAGAATTTTTAATT
1 AAATATAGAATTTTCAATT
577478 GAAATTCCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.16
28 31 0.82
29 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (28 bp):
AAATATAGAATTTTCAATTAAACTTTTT
Found at i:577568 original size:27 final size:27
Alignment explanation
Indices: 577527--577627 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
577517 TTGACATTTA
577527 CATATAGAATTTTTTAATTAAAATTTTTG
1 CATATAGAA--TTTTAATTAAAATTTTTG
* * * *
577556 CATGA-AGAATTTTAATCAAACTCTTTA
1 CAT-ATAGAATTTTAATTAAAATTTTTG
* *
577583 CATATAAAATTTTCGATT-AAATTTTTG
1 CATATAGAATTTT-AATTAAAATTTTTG
577610 CATATAGAATTTTTAATT
1 CATATAGAA-TTTTAATT
577628 GAACTTTAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
26 1 0.02
27 41 0.73
28 6 0.11
29 7 0.12
30 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.47
Consensus pattern (27 bp):
CATATAGAATTTTAATTAAAATTTTTG
Found at i:577569 original size:55 final size:55
Alignment explanation
Indices: 577522--577632 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 55
577512 TTAATTTGAC
* * *
577522 ATTTACATATAGAATTTTTTAATTAAAATTTTTGCATGA-AGAA-TTTTAATCAAACT
1 ATTTACATATA-AAATTTTCAATT-AAATTTTTGCAT-ATAGAATTTTTAATTAAACT
* * *
577578 CTTTACATATAAAATTTTCGATTAAATTTTTGCATATAGAATTTTTAATTGAACT
1 ATTTACATATAAAATTTTCAATTAAATTTTTGCATATAGAATTTTTAATTAAACT
577633 TTAAATGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
53 1 0.02
54 16 0.34
55 20 0.43
56 10 0.21
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (55 bp):
ATTTACATATAAAATTTTCAATTAAATTTTTGCATATAGAATTTTTAATTAAACT
Found at i:577769 original size:28 final size:27
Alignment explanation
Indices: 577738--577800 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
577728 CCAATTTAGG
*
577738 TTTTTACATA-TACAATTTTTAATTAGAC
1 TTTTTACA-AGTACAA-TTCTAATTAGAC
**
577766 TTTTTACAAGTTGAATTCTAATTAGAC
1 TTTTTACAAGTACAATTCTAATTAGAC
577793 TTTTTACA
1 TTTTTACA
577801 CATGGAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (27 bp):
TTTTTACAAGTACAATTCTAATTAGAC
Found at i:577808 original size:27 final size:27
Alignment explanation
Indices: 577757--577809 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
577747 ATACAATTTT
*
577757 TAATTAGACTTTTTACAAGTTGAATTC
1 TAATTAGACTTTTTACAAGTGGAATTC
577784 TAATTAGACTTTTTACACA-TGGAATT
1 TAATTAGACTTTTTACA-AGTGGAATT
577810 TTTTGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (27 bp):
TAATTAGACTTTTTACAAGTGGAATTC
Found at i:578832 original size:13 final size:13
Alignment explanation
Indices: 578814--578875 Score: 70
Period size: 13 Copynumber: 4.5 Consensus size: 13
578804 TTCAATCACC
578814 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
578827 AAAAAAAAGAAAG
1 AAAAAAAAAAAAG
578840 AAGAAAAAGAAAAAG
1 AA-AAAAA-AAAAAG
* *
578855 AGAAAAAACAAAG
1 AAAAAAAAAAAAG
578868 AAAGAAAA
1 AAA-AAAA
578876 TATTAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 21 0.51
14 14 0.34
15 6 0.15
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:578855 original size:28 final size:29
Alignment explanation
Indices: 578815--578875 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
578805 TCAATCACCA
*
578815 AAAAAAAAAAAGAAAAAAAAGAAAG-AAG
1 AAAAAAAAAAAGAAAAAAAACAAAGAAAG
* *
578843 AAAAAGAAAAAGAGAAAAAACAAAGAAAG
1 AAAAAAAAAAAGAAAAAAAACAAAGAAAG
578872 AAAA
1 AAAA
578876 TATTAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAGAAAAAAAACAAAGAAAG
Found at i:578996 original size:22 final size:22
Alignment explanation
Indices: 578962--579021 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
578952 TATATTTTAT
* * *
578962 TATGTCATGTCATGCATTCTAC
1 TATGTCTTTTCATGCATTATAC
*
578984 TATGTCTTTTCATG-ATTATAG
1 TATGTCTTTTCATGCATTATAC
579005 TATG-CTTTT-ATGACATT
1 TATGTCTTTTCATG-CATT
579022 TTCCACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 12 0.38
22 12 0.38
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (22 bp):
TATGTCTTTTCATGCATTATAC
Found at i:584088 original size:15 final size:17
Alignment explanation
Indices: 584059--584095 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
584049 AGATGTAATT
*
584059 TTTTTATATTGATTTTA
1 TTTTTATATTGATTTAA
584076 TTTTTAT-TT-ATTTAA
1 TTTTTATATTGATTTAA
584091 TTTTT
1 TTTTT
584096 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTATATTGATTTAA
Found at i:584093 original size:20 final size:20
Alignment explanation
Indices: 584057--584094 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
584047 GGAGATGTAA
*
584057 TTTTTTTATATTGATTTTAT
1 TTTTTTTATATTAATTTTAT
584077 TTTTATTTAT-TTAATTTT
1 TTTT-TTTATATTAATTTT
584095 TTGAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTTTTATATTAATTTTAT
Found at i:588087 original size:12 final size:12
Alignment explanation
Indices: 588070--588119 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
588060 CGTACAATTC
588070 AAAAAAAATTAT
1 AAAAAAAATTAT
588082 AAAAAAAATTA-
1 AAAAAAAATTAT
588093 AAAATAAAA-T-T
1 AAAA-AAAATTAT
*
588104 -CAAAAAATTAT
1 AAAAAAAATTAT
588115 AAAAA
1 AAAAA
588120 TTTATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 6 0.19
12 18 0.58
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAAAATTAT
Found at i:588108 original size:23 final size:23
Alignment explanation
Indices: 588065--588110 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
588055 AATGCCGTAC
* *
588065 AATTCAAAAAAAATTATAAAAAA
1 AATTAAAAAAAAATTACAAAAAA
588088 AATTAAAAATAAAATT-CAAAAAA
1 AATTAAAAA-AAAATTACAAAAAA
588111 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (23 bp):
AATTAAAAAAAAATTACAAAAAA
Found at i:588121 original size:18 final size:18
Alignment explanation
Indices: 588098--588349 Score: 72
Period size: 19 Copynumber: 13.3 Consensus size: 18
588088 AATTAAAAAT
588098 AAAATTCAAAAAATTATA
1 AAAATTCAAAAAATTATA
* **
588116 AAAATTTATGAAAATAAAAATA
1 AAAA--T-TCAAAA-AATTATA
* *
588138 AAATTTCAAAAAAATAT-
1 AAAATTCAAAAAATTATA
* **
588155 AAAATTGAAAATAAAAATA
1 AAAATTCAAAA-AATTATA
*
588174 AAAA-TCTATAAAATTATAA
1 AAAATTC-AAAAAATTAT-A
* * *
588193 AAAATTTAAAAAATAAAAA
1 AAAATTCAAAAAAT-TATA
588212 CAAAATTCAATAAAA-TATA
1 -AAAATTCAA-AAAATTATA
*
588231 TAAAATAT-ATAAAATTCA-A
1 -AAAAT-TCAAAAAATT-ATA
* * *
588250 AAACTTATAAAAAATTAAAACA
1 AAAATT-CAAAAAATT---ATA
*
588272 AAAATTCAAAAAATTACA
1 AAAATTCAAAAAATTATA
588290 AAATATT-ATGAAAAATCTAT-
1 AAA-ATTCA--AAAAAT-TATA
*
588310 AAAATTTAAAAAACTTATA
1 AAAATTCAAAAAA-TTATA
*
588329 AAAAGT-AAAAAA-TATA
1 AAAATTCAAAAAATTATA
588345 AAAAT
1 AAAAT
588350 AAAAATTTAG
Statistics
Matches: 177, Mismatches: 30, Indels: 56
0.67 0.11 0.21
Matches are distributed among these distances:
16 8 0.05
17 10 0.06
18 48 0.27
19 53 0.30
20 24 0.14
21 20 0.11
22 14 0.08
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATTCAAAAAATTATA
Found at i:588140 original size:39 final size:39
Alignment explanation
Indices: 588086--588235 Score: 166
Period size: 40 Copynumber: 3.8 Consensus size: 39
588076 AATTATAAAA
588086 AAAATTAAAAATAAAATTCAAAAAATTATAAAAATTTATG
1 AAAA-TAAAAATAAAATTCAAAAAATTATAAAAATTTATG
*
588126 AAAATAAAAATAAAATTTCAAAAAAATAT-AAAA--T-TG
1 AAAATAAAAATAAAA-TTCAAAAAATTATAAAAATTTATG
* * *
588162 AAAATAAAAATAAAAATCTATAAAATTATAAAAAATTTA-A
1 AAAATAAAAATAAAATTC-AAAAAATTAT-AAAAATTTATG
*
588202 AAAATAAAAACAAAATTCAATAAAATATATAAAA
1 AAAATAAAAATAAAATTCAA-AAAAT-TATAAAA
588236 TATATAAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
35 2 0.02
36 25 0.27
37 1 0.01
38 4 0.04
39 16 0.17
40 42 0.45
41 3 0.03
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (39 bp):
AAAATAAAAATAAAATTCAAAAAATTATAAAAATTTATG
Found at i:588141 original size:30 final size:28
Alignment explanation
Indices: 588107--588245 Score: 88
Period size: 30 Copynumber: 4.8 Consensus size: 28
588097 TAAAATTCAA
*
588107 AAAATTATAAAAATTTATGAAAATAAAAAT
1 AAAATT-TAAAAATATAT-AAAATAAAAAT
* *
588137 AAAATTTCAAAAAAATATAAAATTGAAAAT
1 AAAATTT-AAAAATATATAAAA-TAAAAAT
* * * *
588167 AAAA-ATAAAAATCTATAAAATTATAA-
1 AAAATTTAAAAATATATAAAATAAAAAT
*
588193 AAAATTTAAAAA-ATA-AAAACAAAATTCAAT
1 AAAATTTAAAAATATATAAAA-TAAA---AAT
*
588223 AAAATATATAAAATATATAAAAT
1 AAAATTTA-AAAATATATAAAAT
588246 TCAAAAACTT
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
25 4 0.05
26 7 0.08
27 10 0.12
28 12 0.14
29 8 0.10
30 31 0.37
31 4 0.05
32 3 0.04
33 4 0.05
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (28 bp):
AAAATTTAAAAATATATAAAATAAAAAT
Found at i:588146 original size:75 final size:74
Alignment explanation
Indices: 588065--588237 Score: 210
Period size: 76 Copynumber: 2.3 Consensus size: 74
588055 AATGCCGTAC
* *
588065 AATTCAAAAAAAATTATAAAA-AAAATTAAAAATAAAATTC-AAAAAATTAT-AAAAATTTATGA
1 AATTC-AAAAAAATTATAAAATAAAA-TAAAAATAAAAATCTAAAAAATTATAAAAAATTTA-AA
*
588127 AAATAAAAATAA
63 AAATAAAAACAA
*
588139 AATTTCAAAAAAA-TATAAAATTGAAAATAAAAATAAAAATCTATAAAATTATAAAAAATTTAAA
1 AA-TTCAAAAAAATTATAAAA-T-AAAATAAAAATAAAAATCTAAAAAATTATAAAAAATTTAAA
588203 AAATAAAAACAA
63 AAATAAAAACAA
*
588215 AATTCAATAAAATATATAAAATA
1 AATTCAAAAAAAT-TATAAAATA
588238 TATAAAATTC
Statistics
Matches: 86, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
73 7 0.08
74 9 0.10
75 26 0.30
76 28 0.33
77 16 0.19
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (74 bp):
AATTCAAAAAAATTATAAAATAAAATAAAAATAAAAATCTAAAAAATTATAAAAAATTTAAAAAA
TAAAAACAA
Found at i:588184 original size:16 final size:16
Alignment explanation
Indices: 588165--588211 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
588155 AAAATTGAAA
588165 ATAAAAATAAAAATCT
1 ATAAAAATAAAAATCT
*
588181 ATAAAATTATAAAAAATTT
1 ATAAAA--AT-AAAAATCT
588200 A-AAAAATAAAAA
1 ATAAAAATAAAAA
588212 CAAAATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
18 6 0.22
19 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATAAAAATCT
Found at i:588205 original size:9 final size:9
Alignment explanation
Indices: 588173--588372 Score: 61
Period size: 9 Copynumber: 21.4 Consensus size: 9
588163 AAATAAAAAT
*
588173 AAAAATCTA
1 AAAAATTTA
*
588182 TAAAATTATA
1 AAAAATT-TA
588192 AAAAATTTA
1 AAAAATTTA
**
588201 AAAAATAAAA
1 AAAAAT-TTA
*
588211 ACAAAATTCA
1 A-AAAATTTA
*
588221 ATAAAATATA
1 A-AAAATTTA
* *
588231 TAAAATATA
1 AAAAATTTA
* *
588240 TAAAATTCA
1 AAAAATTTA
*
588249 AAAACTTATA
1 AAAAATT-TA
*
588259 AAAAATTAAAA
1 AAAAATT--TA
*
588270 CAAAAATTCA
1 -AAAAATTTA
588280 AAAAA-TTA
1 AAAAATTTA
*
588288 CAAAATATTATG
1 -AAAA-ATT-TA
*
588300 AAAAATCTA
1 AAAAATTTA
*
588309 TAAAATTTA
1 AAAAATTTA
*
588318 AAAAACTTA
1 AAAAATTTA
*
588327 TAAAAA-GTA
1 -AAAAATTTA
*
588336 AAAAATAT-
1 AAAAATTTA
588344 AAAAA--T-
1 AAAAATTTA
588350 AAAAATTTA
1 AAAAATTTA
*
588359 GAAAATTATA
1 AAAAATT-TA
588369 AAAA
1 AAAA
588373 TTTCTAAAAT
Statistics
Matches: 144, Mismatches: 31, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
6 6 0.04
8 13 0.09
9 66 0.46
10 39 0.27
11 12 0.08
12 8 0.06
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.27
Consensus pattern (9 bp):
AAAAATTTA
Found at i:588236 original size:39 final size:38
Alignment explanation
Indices: 588084--588245 Score: 161
Period size: 39 Copynumber: 4.2 Consensus size: 38
588074 AAAATTATAA
588084 AAAAAATTAAAAATAAAATTCAAAAAAT-TATAAAAATTT
1 AAAAAA-TAAAAATAAAATTCAAAAAATATAT-AAAATTT
*
588123 ATGAAAATAAAAATAAAATTTCAAAAAA-ATATAAAA-TT
1 A-AAAAATAAAAATAAAA-TTCAAAAAATATATAAAATTT
* * * *
588161 -GAAAATAAAAATAAAAATCTATAAAATTATAAAAAATTT
1 AAAAAATAAAAATAAAATTC-A-AAAAATATATAAAATTT
* *
588200 AAAAAATAAAAACAAAATTCAATAAAATATATAAAATAT
1 AAAAAATAAAAATAAAATTCAA-AAAATATATAAAATTT
*
588239 ATAAAAT
1 AAAAAAT
588246 TCAAAAACTT
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.02
36 17 0.17
37 4 0.04
38 10 0.10
39 38 0.37
40 32 0.31
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (38 bp):
AAAAAATAAAAATAAAATTCAAAAAATATATAAAATTT
Found at i:588245 original size:58 final size:57
Alignment explanation
Indices: 588084--588322 Score: 191
Period size: 58 Copynumber: 4.1 Consensus size: 57
588074 AAAATTATAA
* * * *
588084 AAAAAATTAAAAATAAAATTCAAAAAATTATAAAAATTTATGAAAATAAAAATAAAATTT
1 AAAAAA-TAAAAACAAAATTCAAAAAATTAT-AAAATATATGAAAATTATAA-AAAATTT
* * * * ** *
588144 -CAAAA-AAATATAAAATTGAAAATAAAAATAAAAATCTAT-AAAATTATAAAAAATTT
1 AAAAAATAAAAACAAAATTCAAAA-AATTAT-AAAATATATGAAAATTATAAAAAATTT
* *
588200 AAAAAATAAAAACAAAATTCAATAAAATATATAAAATATAT-AAAATT-CAAAAACTTAT
1 AAAAAATAAAAACAAAATTCAA-AAAAT-TATAAAATATATGAAAATTATAAAAAATT-T
* * * * *
588258 AAAAAATTAAAACAAAAATTCAAAAAATTACAAAATATTATGAAAAATCTATAAAATTT
1 AAAAAATAAAAAC-AAAATTCAAAAAATTATAAAATA-TATGAAAATTATAAAAAATTT
588317 AAAAAA
1 AAAAAA
588323 CTTATAAAAA
Statistics
Matches: 146, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
56 7 0.05
57 42 0.29
58 62 0.42
59 29 0.20
60 6 0.04
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (57 bp):
AAAAAATAAAAACAAAATTCAAAAAATTATAAAATATATGAAAATTATAAAAAATTT
Found at i:588338 original size:16 final size:15
Alignment explanation
Indices: 588325--588354 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
588315 TTAAAAAACT
588325 TATAAAAAGTAAAAAA
1 TATAAAAA-TAAAAAA
588341 TATAAAAATAAAAA
1 TATAAAAATAAAAA
588355 TTTAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
TATAAAAATAAAAAA
Found at i:588373 original size:9 final size:9
Alignment explanation
Indices: 588271--588374 Score: 71
Period size: 9 Copynumber: 11.8 Consensus size: 9
588261 AAATTAAAAC
588271 AAAAATTCA-
1 AAAAATT-AT
*
588280 AAAAATTAC
1 AAAAATTAT
588289 AAAATATTAT
1 AAAA-ATTAT
588299 GAAAAATCTAT
1 -AAAAAT-TAT
*
588310 AAAATTTA-
1 AAAAATTAT
588318 AAAAACTTAT
1 AAAAA-TTAT
*
588328 AAAAAGTA-
1 AAAAATTAT
588336 AAAAA-TAT
1 AAAAATTAT
588344 -AAAA--AT
1 AAAAATTAT
588350 AAAAATT-T
1 AAAAATTAT
588358 AGAAAATTAT
1 A-AAAATTAT
588368 AAAAATT
1 AAAAATT
588375 TCTAAAATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.03
7 10 0.13
8 12 0.15
9 30 0.38
10 18 0.23
11 7 0.09
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:588466 original size:8 final size:8
Alignment explanation
Indices: 588450--588715 Score: 117
Period size: 8 Copynumber: 30.6 Consensus size: 8
588440 GCAAACATTA
*
588450 TATATTTT
1 TATAATTT
588458 TATAATTT
1 TATAATTT
*
588466 TTTAATTTT
1 TATAA-TTT
*
588475 TTTAATTT
1 TATAATTT
*
588483 TATATTTT
1 TATAATTT
588491 TA-AATTTT
1 TATAA-TTT
588499 TATAATTT
1 TATAATTT
*
588507 TTTGAATTT
1 TAT-AATTT
588516 TATAGATTTTTT
1 TATA-A---TTT
588528 TATAATTTTT
1 TATAA--TTT
*
588538 TGTAATTT
1 TATAATTT
*
588546 TCTAACTTT
1 TATAA-TTT
* *
588555 TTTATTTT
1 TATAATTT
588563 TATAATTT
1 TATAATTT
588571 TATAGATTTT
1 TATA-A-TTT
*
588581 TTTATATTT
1 TATA-ATTT
*
588590 TTTAATTT
1 TATAATTT
*
588598 TATTTTATTT
1 TA--TAATTT
*
588608 TGTATATTT
1 TATA-ATTT
*
588617 TTTAATTT
1 TATAATTT
588625 TATATATTT
1 TATA-ATTT
588634 TATAATTTT
1 TATAA-TTT
* *
588643 TGTGATTT
1 TATAATTT
*
588651 TTTAATTT
1 TATAATTT
588659 TAT--TTT
1 TATAATTT
588665 TA-AATTCT
1 TATAATT-T
588673 TAATAATTT
1 T-ATAATTT
*
588682 TTTAAATTT
1 TAT-AATTT
588691 TATAAATTTTT
1 TAT-AA--TTT
588702 TATAATTTT
1 TATAA-TTT
588711 TATAA
1 TATAA
588716 GTTCTTGAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 47
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.02
7 3 0.01
8 81 0.39
9 75 0.36
10 28 0.14
11 7 0.03
12 7 0.03
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.68
Consensus pattern (8 bp):
TATAATTT
Found at i:588467 original size:9 final size:9
Alignment explanation
Indices: 588447--588715 Score: 159
Period size: 9 Copynumber: 30.7 Consensus size: 9
588437 TTGGCAAACA
588447 TTATATATTT
1 TTATA-ATTT
588457 TTATAATTT
1 TTATAATTT
588466 TT-TAATTT
1 TTATAATTT
*
588474 TTTTAA-TT
1 TTATAATTT
588482 TTAT-ATTT
1 TTATAATTT
588490 TTA-AATTT
1 TTATAATTT
588498 TTATAATTT
1 TTATAATTT
588507 TT-TGAA-TT
1 TTAT-AATTT
588515 TTATAGATTTTT
1 TTATA-A--TTT
588527 TTATAATTTT
1 TTATAA-TTT
*
588537 TTGTAATTT
1 TTATAATTT
*
588546 TCTA-ACTTT
1 T-TATAATTT
588555 TT-T-ATTT
1 TTATAATTT
588562 TTATAA-TT
1 TTATAATTT
588570 TTATAGATTT
1 TTATA-ATTT
*
588580 TTTTATATTT
1 TTATA-ATTT
588590 TT-TAATTT
1 TTATAATTT
* *
588598 TATTTTATTT
1 T-TATAATTT
588608 TGTAT-ATTT
1 T-TATAATTT
588617 TT-TAA-TT
1 TTATAATTT
588624 TTAT-ATATT
1 TTATAAT-TT
588633 TTATAATTT
1 TTATAATTT
* *
588642 TTGTGATTT
1 TTATAATTT
588651 TT-TAA--T
1 TTATAATTT
588657 TT-T-ATTT
1 TTATAATTT
588664 TTA-AATTCT
1 TTATAATT-T
*
588673 TAATAATTT
1 TTATAATTT
*
588682 TT-TAAATT
1 TTATAATTT
588690 TTATAAATTTT
1 TTAT-AA-TTT
588701 TTATAATTT
1 TTATAATTT
588710 TTATAA
1 TTATAA
588716 GTTCTTGAAT
Statistics
Matches: 210, Mismatches: 17, Indels: 65
0.72 0.06 0.22
Matches are distributed among these distances:
5 1 0.00
6 4 0.02
7 15 0.07
8 60 0.29
9 71 0.34
10 45 0.21
11 7 0.03
12 7 0.03
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.68
Consensus pattern (9 bp):
TTATAATTT
Found at i:589354 original size:13 final size:13
Alignment explanation
Indices: 589336--589360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
589326 ATAATGCACA
589336 GTATCGATACATT
1 GTATCGATACATT
589349 GTATCGATACAT
1 GTATCGATACAT
589361 GACCACTATA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:589455 original size:19 final size:19
Alignment explanation
Indices: 589431--589500 Score: 115
Period size: 19 Copynumber: 3.6 Consensus size: 19
589421 TTAACTGTTA
589431 GTATCGATACATACAAGAT
1 GTATCGATACATACAAGAT
589450 GTATCGATACATACAAGAT
1 GTATCGATACATACAAGAT
589469 GTATCGATACATGACCAA-AT
1 GTATCGATACAT-A-CAAGAT
589489 GTATCGATACAT
1 GTATCGATACAT
589501 TGGCTTGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 31 0.63
20 15 0.31
21 3 0.06
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (19 bp):
GTATCGATACATACAAGAT
Found at i:597481 original size:20 final size:20
Alignment explanation
Indices: 597436--597487 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
597426 GTAGCCAAAC
* **
597436 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
597456 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
597475 TTGTATCGATACA
1 TTGTATCGATACA
597488 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:599736 original size:23 final size:22
Alignment explanation
Indices: 599694--599736 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
599684 TTGAAAAAAA
*
599694 TTTGAAAAAAAATTTTCTAAAC
1 TTTGAAAAAAAATTTGCTAAAC
*
599716 TTTGAGAAAAAATTTGGCTAA
1 TTTGAAAAAAAATTT-GCTAA
599737 TGAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (22 bp):
TTTGAAAAAAAATTTGCTAAAC
Found at i:603692 original size:13 final size:13
Alignment explanation
Indices: 603674--603712 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
603664 ACATTTTTCT
603674 TTGTATCGATACA
1 TTGTATCGATACA
603687 TTGTATCGATACA
1 TTGTATCGATACA
*
603700 CTGTATCGATACA
1 TTGTATCGATACA
603713 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:606265 original size:20 final size:20
Alignment explanation
Indices: 606220--606271 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
606210 GTAGCCAAAC
* **
606220 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
606240 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
606259 TTGTATCGATACA
1 TTGTATCGATACA
606272 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:612188 original size:59 final size:59
Alignment explanation
Indices: 612091--612210 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
612081 TGTAAATAAA
612091 TTTATGATTAAGGGGGAGAAAGAAACATGTAAGAAAACATGTGATTAAAGGAAATTGTT
1 TTTATGATTAAGGGGGAGAAAGAAACATGTAAGAAAACATGTGATTAAAGGAAATTGTT
* *
612150 TTTATGATTAAGGGGGAGAAAGAAACATGTGAGGAAACATGTGATTAAAGGAAATTGTT
1 TTTATGATTAAGGGGGAGAAAGAAACATGTAAGAAAACATGTGATTAAAGGAAATTGTT
612209 TT
1 TT
612211 ATTAAGGGGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.28
Consensus pattern (59 bp):
TTTATGATTAAGGGGGAGAAAGAAACATGTAAGAAAACATGTGATTAAAGGAAATTGTT
Found at i:612957 original size:33 final size:32
Alignment explanation
Indices: 612896--612963 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
612886 CCTTAACTGT
*
612896 TTGTATCGATACATACCAGATGTATCGATACA
1 TTGTATCGATACATACCAAATGTATCGATACA
*
612928 TTGTATCGATAGATGACCAAATGTATCGATACA
1 TTGTATCGATACAT-ACCAAATGTATCGATACA
612961 TTG
1 TTG
612964 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACCAAATGTATCGATACA
Found at i:616120 original size:27 final size:26
Alignment explanation
Indices: 616089--616151 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
616079 TGACTTTCTT
*
616089 ATATGAAATTTTAATTAACATTTCCAC
1 ATATGAAATTTTAATTAA-ATTCCCAC
* * *
616116 CTATGGAATTTTTAATTAAATTCCCAT
1 ATAT-GAAATTTTAATTAAATTCCCAC
616143 ATATGAAAT
1 ATATGAAAT
616152 CTTCACATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 4 0.14
27 12 0.41
28 13 0.45
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (26 bp):
ATATGAAATTTTAATTAAATTCCCAC
Found at i:619205 original size:3 final size:3
Alignment explanation
Indices: 619197--619222 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
619187 TAATTTTATG
619197 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
619223 TGATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:619597 original size:20 final size:21
Alignment explanation
Indices: 619574--619612 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
619564 ATCCACACAA
*
619574 TTTAAAAA-AATTATAAAAAG
1 TTTAAAAATAAATATAAAAAG
619594 TTTAAAAATAAATATAAAA
1 TTTAAAAATAAATATAAAA
619613 TTCAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
TTTAAAAATAAATATAAAAAG
Found at i:619625 original size:12 final size:12
Alignment explanation
Indices: 619604--619629 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
619594 TTTAAAAATA
619604 AATATAAAATTC
1 AATATAAAATTC
619616 AATATAAAATTC
1 AATATAAAATTC
619628 AA
1 AA
619630 AAAACTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATAAAATTC
Found at i:619643 original size:19 final size:19
Alignment explanation
Indices: 619621--619663 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
619611 AATTCAATAT
619621 AAAATTCAAAAAACTTAT-A
1 AAAATTCAAAAAA-TTATGA
619640 AAAATTCAAAAAATTATGA
1 AAAATTCAAAAAATTATGA
619659 AAAAT
1 AAAAT
619664 ATATAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATTCAAAAAATTATGA
Found at i:619684 original size:47 final size:45
Alignment explanation
Indices: 619552--619719 Score: 138
Period size: 47 Copynumber: 3.5 Consensus size: 45
619542 AAAATTAAAG
** * * * *
619552 AAAATATAAAAAATCCACACAATTTAAAAAAATTATAAAAAGTTTAA
1 AAAATATAAAAAATATATAAAATTCAAAAAACTTATAAAAAG--TAA
* * *
619599 AAATAAATATAAAATTCAATATAAAATTCAAAAAACTTATAAAAATTCAA
1 AAA-ATATA-AAAAAT--ATATAAAATTCAAAAAACTTATAAAAAGT-AA
* * *
619649 AAAATTATGAAAAATATATAACATTGAAAAAACTTATAAAAAGTAA
1 AAAA-TATAAAAAATATATAAAATTCAAAAAACTTATAAAAAGTAA
*
619695 AAAATATAAAAAAAATTATAAAATT
1 AAAATATAAAAAATA-TATAAAATT
619720 TGTAAAATTA
Statistics
Matches: 96, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
45 9 0.09
46 14 0.15
47 29 0.30
48 4 0.04
49 12 0.12
50 7 0.07
51 21 0.22
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (45 bp):
AAAATATAAAAAATATATAAAATTCAAAAAACTTATAAAAAGTAA
Found at i:619725 original size:30 final size:29
Alignment explanation
Indices: 619675--619749 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
619665 TATAACATTG
*
619675 AAAAAACTTATAAAA-AGTAAAA-AATATA
1 AAAAAAATTATAAAATAGTAAAATAAT-TA
*
619703 AAAAAAATTATAAAATTTGTAAAATTAATTA
1 AAAAAAATTATAAAA-TAGTAAAA-TAATTA
*
619734 TAAAAAATT-TAAAATA
1 AAAAAAATTATAAAATA
619750 AAATTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 14 0.36
29 1 0.03
30 11 0.28
31 10 0.26
32 3 0.08
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAAAATTATAAAATAGTAAAATAATTA
Found at i:619746 original size:21 final size:21
Alignment explanation
Indices: 619692--619751 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
619682 TTATAAAAAG
* *
619692 TAAAAAATATAAAAAAAATTA
1 TAAAAAATTTAAAATAAATTA
* *
619713 T-AAAATTTGTAAAATTAATTA
1 TAAAAAATT-TAAAATAAATTA
619734 TAAAAAATTTAAAATAAA
1 TAAAAAATTTAAAATAAA
619752 ATTGTGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 5 0.16
21 20 0.65
22 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAAAATTTAAAATAAATTA
Found at i:619817 original size:16 final size:15
Alignment explanation
Indices: 619796--619958 Score: 93
Period size: 17 Copynumber: 10.1 Consensus size: 15
619786 AAACATTATA
619796 TATTTTTGTAATTTTT
1 TATTTTT-TAATTTTT
619812 TATTTTTTTAATTTTT
1 TA-TTTTTTAATTTTT
619828 TAATTTTTATAATTTTCT
1 T-ATTTTT-TAATTTT-T
*
619846 AAGTTTTTT-ATTTTT
1 TA-TTTTTTAATTTTT
*
619861 TATAATTTTATAATTTTA
1 TAT--TTTT-TAATTTTT
*
619879 TAGATTTTTATATTTTT
1 TA-TTTTTTA-ATTTTT
619896 ATATTTTTTGAA--TTT
1 -TATTTTTT-AATTTTT
619911 TA-TTTTT-ATTTTAT
1 TATTTTTTAATTTT-T
*
619925 ATATTTTTTAATTTATA
1 -TATTTTTTAATTT-TT
*
619942 GATTTTTATAATTTTT
1 TATTTTT-TAATTTTT
619958 T
1 T
619959 GTAATTTTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
11 1 0.01
13 7 0.06
14 4 0.03
15 7 0.06
16 39 0.34
17 41 0.35
18 17 0.15
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTTTTAATTTTT
Found at i:619861 original size:34 final size:32
Alignment explanation
Indices: 619797--620008 Score: 138
Period size: 34 Copynumber: 6.5 Consensus size: 32
619787 AACATTATAT
* * *
619797 ATTTTTGTAATTTTTTATTTTTTTAATTTTTTA
1 ATTTTTATAA-TTTTTAGTTTTTTATTTTTTTA
619830 ATTTTTATAATTTTCTAAGTTTTTTATTTTTTATA
1 ATTTTTATAATTTT-T-AGTTTTTTATTTTTT-TA
* *
619865 A-TTTTATAATTTTATAGATTTTTATATTTTTA
1 ATTTTTATAATTTT-TAGTTTTTTATTTTTTTA
*
619897 TATTTTT-TGAA-TTTTA--TTTTTA-TTTTATA
1 -ATTTTTAT-AATTTTTAGTTTTTTATTTTTTTA
*
619926 TATTTTT-TAATTTATAGATTTTTATAATTTTTTGTA
1 -ATTTTTATAATTTTTAG-TTTTT-T-ATTTTTT-TA
* * *
619962 ATTTTTGTGAATTTTTA--ATTTTA-TTTTTAA
1 ATTTTTAT-AATTTTTAGTTTTTTATTTTTTTA
619992 ATTTTTAATAATTTTTA
1 ATTTTT-ATAATTTTTA
620009 AAATTTTATA
Statistics
Matches: 148, Mismatches: 14, Indels: 37
0.74 0.07 0.19
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 21 0.14
31 6 0.04
32 13 0.09
33 30 0.20
34 36 0.24
35 13 0.09
36 3 0.02
37 7 0.05
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (32 bp):
ATTTTTATAATTTTTAGTTTTTTATTTTTTTA
Found at i:619868 original size:10 final size:9
Alignment explanation
Indices: 619791--620040 Score: 152
Period size: 8 Copynumber: 27.7 Consensus size: 9
619781 TTGGAAAACA
619791 TTATATATTT
1 TTATA-ATTT
*
619801 TTGTAATTT
1 TTATAATTT
619810 TT-T-ATTT
1 TTATAATTT
*
619817 TTTTAATTT
1 TTATAATTT
619826 TT-TAATTT
1 TTATAATTT
619834 TTATAATTT
1 TTATAATTT
*
619843 TCTA-AGTTT
1 T-TATAATTT
*
619852 TT-TATTTT
1 TTATAATTT
619860 TTATAA-TT
1 TTATAATTT
619868 TTATAA-TT
1 TTATAATTT
619876 TTATAGATTT
1 TTATA-ATTT
619886 TTAT-ATTT
1 TTATAATTT
619894 TTAT-ATTT
1 TTATAATTT
619902 TT-TGAA-TT
1 TTAT-AATTT
**
619910 TTATTTTTATT
1 TTA-TAAT-TT
619921 TTATATATTT
1 TTATA-ATTT
619931 TT-TAA--T
1 TTATAATTT
619937 TTATAGATTT
1 TTATA-ATTT
619947 TTATAATTTT
1 TTATAA-TTT
*
619957 TTGTAATTT
1 TTATAATTT
*
619966 TTGTGAATTT
1 TTAT-AATTT
*
619976 TTAATTTTATTT
1 TT-A--TAATTT
619988 TTA-AATTT
1 TTATAATTT
619996 TTAATAATTT
1 TT-ATAATTT
*
620006 TTAAAATTT
1 TTATAATTT
*
620015 TATAAAATTTT
1 T-TATAA-TTT
620026 TTATAATTT
1 TTATAATTT
620035 TTATAA
1 TTATAA
620041 GTCTATGAAT
Statistics
Matches: 198, Mismatches: 14, Indels: 57
0.74 0.05 0.21
Matches are distributed among these distances:
6 3 0.02
7 9 0.05
8 58 0.29
9 55 0.28
10 55 0.28
11 11 0.06
12 6 0.03
13 1 0.01
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATAATTT
Found at i:619943 original size:61 final size:66
Alignment explanation
Indices: 619794--620036 Score: 213
Period size: 68 Copynumber: 3.7 Consensus size: 66
619784 GAAAACATTA
* * *
619794 TATATTTTTGTAATTTT-T-TATTTTTTTAA-TTTTT-TAATTTTTAT-AATTTTCTAAGTTTTT
1 TATATTTTT-TAATTTTATAGATTTTTATAATTTTTTATAATTTTTGTGAATTTT-T-A--TTTT
619854 TATTTTT
61 TA-TTTT
*
619861 TATAATTTTATAATTTTATAGATTTTTAT-A-TTTTTAT-ATTTTT-TGAA-TTTTATTTTTATT
1 TAT-ATTTTTTAATTTTATAGATTTTTATAATTTTTTATAATTTTTGTGAATTTTTATTTTTATT
619921 TT
65 TT
* *
619923 ATATATTTTTTAA-TTTATAGATTTTTATAATTTTTTGTAATTTTTGTGAATTTTTAATTTTATT
1 -TATATTTTTTAATTTTATAGATTTTTATAATTTTTTATAATTTTTGTGAATTTTTATTTTTATT
619987 TT
65 TT
* * *
619989 TAAATTTTTAATAATTTT-TAAAATTTTATAAAATTTTTTATAATTTTT
1 TATATTTTT--TAATTTTAT-AGATTTT-TATAATTTTTTATAATTTTT
620037 ATAAGTCTAT
Statistics
Matches: 150, Mismatches: 10, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
61 15 0.10
62 13 0.09
63 15 0.10
64 6 0.04
65 13 0.09
66 15 0.10
67 18 0.12
68 29 0.19
69 26 0.17
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (66 bp):
TATATTTTTTAATTTTATAGATTTTTATAATTTTTTATAATTTTTGTGAATTTTTATTTTTATTT
T
Found at i:620019 original size:17 final size:17
Alignment explanation
Indices: 619821--620019 Score: 70
Period size: 18 Copynumber: 11.6 Consensus size: 17
619811 TTATTTTTTT
* *
619821 AATTTTTTAATTTTTAT
1 AATTTTATAATTTTTAA
* *
619838 AATTTTCTAAGTTTTTTA
1 AATTTTATAA-TTTTTAA
** *
619856 TTTTTTATAA-TTTTAT
1 AATTTTATAATTTTTAA
*
619872 AATTTTATAGATTTTTAT
1 AATTTTATA-ATTTTTAA
* **
619890 ATTTTTAT-ATTTTTTG
1 AATTTTATAATTTTTAA
**
619906 AATTTTATTTTTATTTTATA
1 AATTTTA-TAAT-TTTTA-A
* * * *
619926 TATTTTTTAATTTATAG
1 AATTTTATAATTTTTAA
* *
619943 ATTTTTATAATTTTTTGTA
1 AATTTTATAA-TTTTT-AA
* *
619962 ATTTTTGTGAATTTTT--
1 AATTTTAT-AATTTTTAA
619978 AA-TTT-T-ATTTTTAA
1 AATTTTATAATTTTTAA
*
619992 ATTTTTAATAATTTTTAA
1 AATTTT-ATAATTTTTAA
620010 AATTTTATAA
1 AATTTTATAA
620020 AATTTTTTAT
Statistics
Matches: 133, Mismatches: 33, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
12 6 0.05
14 2 0.02
15 6 0.05
16 24 0.18
17 23 0.17
18 47 0.35
19 18 0.14
20 7 0.05
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.66
Consensus pattern (17 bp):
AATTTTATAATTTTTAA
Found at i:620275 original size:16 final size:17
Alignment explanation
Indices: 620243--620276 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
620233 GAATGAAAGT
620243 TTAAATATTTATTTAAG
1 TTAAATATTTATTTAAG
*
620260 TTAAAT-TTTTTTTAAG
1 TTAAATATTTATTTAAG
620276 T
1 T
620277 ATTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TTAAATATTTATTTAAG
Found at i:620504 original size:6 final size:7
Alignment explanation
Indices: 620489--620513 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
620479 TGCTGCAAGA
620489 TTTTGTT
1 TTTTGTT
620496 TTTTGTT
1 TTTTGTT
620503 TTTTGTT
1 TTTTGTT
620510 TTTT
1 TTTT
620514 TTCAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:621839 original size:2 final size:2
Alignment explanation
Indices: 621832--621860 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
621822 TGTTTAACAA
621832 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
621861 AGTGAGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:626954 original size:19 final size:20
Alignment explanation
Indices: 626919--626968 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
626909 GAAAATTGAA
626919 TATATATTTTTAATAATA-T
1 TATATATTTTTAATAATATT
*
626938 TATA-ATTTTATATTAATATT
1 TATATATTTT-TAATAATATT
626958 TATATATTTTT
1 TATATATTTTT
626969 TAAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 6 0.22
21 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATATTTTTAATAATATT
Found at i:626996 original size:15 final size:15
Alignment explanation
Indices: 626970--627012 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
626960 TATATTTTTT
626970 AAATTAAATTTAATAA
1 AAATT-AATTTAATAA
**
626986 AAATTAATTTAATTT
1 AAATTAATTTAATAA
*
627001 AAATTAACTTAA
1 AAATTAATTTAA
627013 ATAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTAATTTAATAA
Found at i:627003 original size:26 final size:26
Alignment explanation
Indices: 626967--627036 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
626957 TTATATATTT
*
626967 TTTAAATTAAATTTAA-TAAA-AATTAA
1 TTTAATTTAAATTTAACTAAATAA-T-A
626993 TTTAATTTAAA-TTAACTTAAATAATA
1 TTTAATTTAAATTTAAC-TAAATAATA
*
627019 TTTTATTTAAATTTAACT
1 TTTAATTTAAATTTAACT
627037 TAATTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 4 0.11
26 22 0.58
27 10 0.26
28 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTAATTTAAATTTAACTAAATAATA
Found at i:627045 original size:32 final size:31
Alignment explanation
Indices: 626967--627053 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
626957 TTATATATTT
* * * *
626967 TTTAAATTAAATTTAATAAAAATTAATTTAA
1 TTTAAATTAACTTAAATAAAATTTTATTTAA
*
626998 TTTAAATTAACTTAAATAATATTTTATTTAAA
1 TTTAAATTAACTTAAATAAAATTTTATTT-AA
* *
627030 TTTAACTTAATTTAAATAAAATTT
1 TTTAAATTAACTTAAATAAAATTT
627054 ATCAAATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 24 0.51
32 23 0.49
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTAAATTAACTTAAATAAAATTTTATTTAA
Found at i:629537 original size:158 final size:157
Alignment explanation
Indices: 628946--629726 Score: 676
Period size: 157 Copynumber: 5.0 Consensus size: 157
628936 CTTAATGGAT
* * * *
628946 CTTAA-AATGATCATAAATAGGG-TAAACCCATCTTAAAT-ACACATCTTTAGCATAAAAGCATC
1 CTTAAGAAGGATCATAAAT-GGGATAAACCTATCATAAATAAC-CACCTTTAGCATAAAAGCATC
*** * * * *
629008 TCGACAATAACTTATGACTCGATTCTAAAAAAATTATGAAAATGCCCCTATGGGTATACCTTCGA
64 TCGGTGATAACCTAAGACTCGATTCTAGAAAAATTATGAAAATGCCCTTATGGGTATACCTTCGA
629073 CATAAAAGTATCAT-GGTAACCCTAAAGAA
129 CATAAAAGTATC-TCGGTAACCCTAAAGAA
* * * * * * *
629102 CTTAAAAAGGATCATAAATGGGCTTAACCTATCATAGATACCCACCTTTGGTATAAAAGCATCCT
1 CTTAAGAAGGATCATAAATGGGATAAACCTATCATAAATAACCACCTTTAGCATAAAAGCAT-CT
* * *
629167 C-GTGACAACCTAAGACT-TAGTT-TTGAAAAAATTATGAAAATGCCCTTATGGGTATACCTTCG
65 CGGTGATAACCTAAGACTCGA-TTCTAG-AAAAATTATGAAAATGCCCTTATGGGTATACCTTCG
* * * ** *
629229 AAATGAAAGTATCCCGGTAATTCTAAA-AGG
128 ACATAAAAGTATCTCGGTAACCCTAAAGA-A
* * * * * *
629259 CTTAA-AAAGATCATAAATGGGATGAACCTATCATACATACCCACCGTTGGCATAAAAGCAT-TC
1 CTTAAGAAGGATCATAAATGGGATAAACCTATCATAAATAACCACCTTTAGCATAAAAGCATCT-
* * * * * * * * *
629322 CGGTTATAACCTATGACTCGATTTTGGAAAAATTA-CACAAATACCTTTGTGGGTATACTTTCGA
65 CGGTGATAACCTAAGACTCGATTCTAGAAAAATTATGA-AAATGCCCTTATGGGTATACCTTCGA
*
629386 CATAAAAGTATCTCGGTAACCCTAAAGGA
129 CATAAAAGTATCTCGGTAACCCTAAAGAA
** *
629415 CTTAAGAAGGATCATAAATAAGATAAACCTATTC-TAAATAACCACTTTTAGCATAAAAAGCATC
1 CTTAAGAAGGATCATAAATGGGATAAACCTA-TCATAAATAACCACCTTTAGCAT-AAAAGCATC
* * * * * *
629479 TTGGTGATAGCTTAAGACTTGATTCTAGAAAAATTATGAAAATGCCTTTATAGGTATACCTTCGA
64 TCGGTGATAACCTAAGACTCGATTCTAGAAAAATTATGAAAATGCCCTTATGGGTATACCTTCGA
* * ** *
629544 CATGAAAGTATCCCAATAATCCTAAAGAA
129 CATAAAAGTATCTCGGTAACCCTAAAGAA
* * * * *
629573 CTTAAGAAGTATCATAAATGGGATAAACCTATCTTAAAT-ACCTGCCATTAGCATAAAAACATCT
1 CTTAAGAAGGATCATAAATGGGATAAACCTATCATAAATAACC-ACCTTTAGCATAAAAGCATCT
* * * * * **
629637 CGGTGATAGCCTAAGACTCGGTTCTAAAAAAATTACGCAAAA-ACTCC-TATAAGTATACCTTCG
65 CGGTGATAACCTAAGACTCGATTCTAGAAAAATTATG-AAAATGC-CCTTATGGGTATACCTTCG
* *
629700 ACATGAAAA-TATCTTGGTAACCATAAA
128 ACAT-AAAAGTATCTCGGTAACCCTAAA
629727 TGACAGAAAA
Statistics
Matches: 502, Mismatches: 99, Indels: 47
0.77 0.15 0.07
Matches are distributed among these distances:
154 1 0.00
155 2 0.00
156 132 0.26
157 230 0.46
158 135 0.27
159 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (157 bp):
CTTAAGAAGGATCATAAATGGGATAAACCTATCATAAATAACCACCTTTAGCATAAAAGCATCTC
GGTGATAACCTAAGACTCGATTCTAGAAAAATTATGAAAATGCCCTTATGGGTATACCTTCGACA
TAAAAGTATCTCGGTAACCCTAAAGAA
Found at i:630126 original size:165 final size:166
Alignment explanation
Indices: 629815--630556 Score: 796
Period size: 165 Copynumber: 4.5 Consensus size: 166
629805 ATTACAATCA
* * **
629815 AGTCCTTAAA-TTTTG-AAATTACATTTCATACCCGACGAAAAAT-GA-A-AATGATACGAAAAG
1 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGATAAAAAATCGAGAGAAT-ATA--AAAA-
* * * * * *
629875 TTTTGAAAATTTT-TATATCCTTACAA-AAAGTCATAGGAATAATAGAAATTTAAAG-AAATGAC
62 TTTT-AAAATTTTCTAAACCCCTACAAGAAAGCCATAAGAATAATAGAAATTTAAAGAAAATGAA
* * *
629937 TAAGATGATTATTTTGT-TTCTAAAAACCAAATTTGCTATTT
126 TAAGATGATTATTTT-TCTTCTAAAAACTAGATTTACTATTT
* * * **
629978 AGTCTTTAAACTTTT-AAAAATTCTATTTCATA-TTGATGGAAAATCGAGAGAATATAAAAAGTT
1 AGTCCTTAAACTTTTGAAAATTTC-ATTTCATACTCGATAAAAAATCGAGAGAATATAAAAA-TT
*
630041 TTAAAATTTTCTAAACCCCTACGA-AAAGCCATAAGAATAATAGAAATTTAAAGAAAATGAATAA
64 TTAAAATTTTCTAAACCCCTACAAGAAAGCCATAAGAATAATAGAAATTTAAAGAAAATGAATAA
630105 GATGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
129 GATGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
* * * * *
630143 AGTCCTTATACTTTTGAAAA-TTCTATTTCATACTCGATAGAAAATCGAAATAATAAGAAAAATT
1 AGTCCTTAAACTTTTGAAAATTTC-ATTTCATACTCGATAAAAAATCGAGAGAAT-ATAAAAATT
* * ** *
630207 TTAAAAATTTCTAAACCCCTAC-AGAAGGCCATCGGAATAATAAAAATTTAAAGAAAAATGACA-
64 TTAAAATTTTCTAAACCCCTACAAGAAAGCCATAAGAATAATAGAAATTTAAAG-AAAATGA-AT
630270 AAGATGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
127 AAGATGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
* * * * * * * *
630310 AATCCTTAAACTTTTGAAAATTTCATTTCATACCCAATAAAAAACCAAGAGAACACAAAAAATTT
1 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGATAAAAAATCGAGAGAATATAAAAATTTT
* * * * * *
630375 AAAAATTTCTATATCCCTA-AAGAAATCCATAAGAATAATAGAAATTTAAAGCAAATGACTAAGA
66 AAAATTTTCTAAACCCCTACAAGAAAGCCATAAGAATAATAGAAATTTAAAGAAAATGAATAAGA
* * **
630439 AGATTATTTTTCTTTTAAAAACTAGATTGGCTATTT
131 TGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
** *
630475 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGACGAAAAATCGAGAGGATATGAAAAATTT
1 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGATAAAAAATCGAGAGAATAT-AAAAATTT
*
630540 TAAACTTTTCTAAACCC
65 TAAAATTTTCTAAACCC
630557 TTATGAAAGG
Statistics
Matches: 491, Mismatches: 69, Indels: 35
0.83 0.12 0.06
Matches are distributed among these distances:
163 17 0.03
164 63 0.13
165 166 0.34
166 145 0.30
167 96 0.20
168 4 0.01
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (166 bp):
AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGATAAAAAATCGAGAGAATATAAAAATTTT
AAAATTTTCTAAACCCCTACAAGAAAGCCATAAGAATAATAGAAATTTAAAGAAAATGAATAAGA
TGATTATTTTTCTTCTAAAAACTAGATTTACTATTT
Found at i:630321 original size:332 final size:330
Alignment explanation
Indices: 629815--630556 Score: 865
Period size: 332 Copynumber: 2.2 Consensus size: 330
629805 ATTACAATCA
* * * * *
629815 AGTCCTTAAA-TTTTG-AAATTACATTTCATACCCGACGAAAAAT-GAAA-ATGATACGAAAAGT
1 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGAAGAAAAATCGAAAGA--ATAAGAAAAAT
* * * * * * * * * * *
629876 TTTGAAAATTTTTATATCCTTACAAAAAGTCATAGGAATAATAGAAATTTAAAGAAATGACTAAG
64 TTTAAAAATTTCTAAACCCCTACAGAAGGCCATCGGAATAATAAAAATTTAAAGAAATGACAAAG
* * *
629941 ATGATTATTTTGTTTCTAAAAACCAAATTTGCTATTTAGTCTTTAAACTTTTAAAAA-TTCTATT
129 ATGATTATTTTGTTTCTAAAAACCAAATTTACTATTTAATCCTTAAACTTTTAAAAATTTC-ATT
*** ** * * * * * * *
630005 TCATA-TTGATGGAAAATCGAGAGAATATAAAAAGTTTTAAAATTTTCTAAACCCCT-ACGAAAA
193 TCATACCCAATAAAAAACCAAGAGAACACAAAAA-ATTTAAAAATTTCTAAACCCCTAAAG-AAA
*
630068 GCCATAAGAATAATAGAAATTTAAAGAAAATGAATAAGATGATTATTTTTCTTCTAAAAACTAGA
256 GCCATAAGAATAATAGAAATTTAAAGAAAATGAATAAGAAGATTATTTTTCTTCTAAAAACTAGA
*
630133 TTTACTATTT
321 TTGACTATTT
* *
630143 AGTCCTTATACTTTTGAAAA-TTCTATTTCATACTCGATAG-AAAATCGAAATAATAAGAAAAAT
1 AGTCCTTAAACTTTTGAAAATTTC-ATTTCATACTCGA-AGAAAAATCGAAAGAATAAGAAAAAT
630206 TTTAAAAATTTCTAAACCCCTACAGAAGGCCATCGGAATAATAAAAATTTAAAGAAAAATGACAA
64 TTTAAAAATTTCTAAACCCCTACAGAAGGCCATCGGAATAATAAAAATTTAAAG--AAATGACAA
* * *
630271 AGATGATTATTTT-TCTTCTAAAAACTAGATTTACTATTTAATCCTTAAACTTTTGAAAATTTCA
127 AGATGATTATTTTGT-TTCTAAAAACCAAATTTACTATTTAATCCTTAAACTTTTAAAAATTTCA
* *
630335 TTTCATACCCAATAAAAAACCAAGAGAACACAAAAAATTTAAAAATTTCTATATCCCTAAAGAAA
191 TTTCATACCCAATAAAAAACCAAGAGAACACAAAAAATTTAAAAATTTCTAAACCCCTAAAGAAA
* * * *
630400 TCCATAAGAATAATAGAAATTTAAAGCAAATGACTAAGAAGATTATTTTTCTTTTAAAAACTAGA
256 GCCATAAGAATAATAGAAATTTAAAGAAAATGAATAAGAAGATTATTTTTCTTCTAAAAACTAGA
*
630465 TTGGCTATTT
321 TTGACTATTT
* * * *
630475 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGACGAAAAATCGAGAGGATATGAAAAATTT
1 AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGAAGAAAAATCGAAAGAATAAGAAAAATTT
**
630540 TAAACTTTTCTAAACCC
66 TAAAAATTTCTAAACCC
630557 TTATGAAAGG
Statistics
Matches: 348, Mismatches: 52, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
328 9 0.03
329 7 0.02
330 73 0.21
331 7 0.02
332 225 0.65
333 27 0.08
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (330 bp):
AGTCCTTAAACTTTTGAAAATTTCATTTCATACTCGAAGAAAAATCGAAAGAATAAGAAAAATTT
TAAAAATTTCTAAACCCCTACAGAAGGCCATCGGAATAATAAAAATTTAAAGAAATGACAAAGAT
GATTATTTTGTTTCTAAAAACCAAATTTACTATTTAATCCTTAAACTTTTAAAAATTTCATTTCA
TACCCAATAAAAAACCAAGAGAACACAAAAAATTTAAAAATTTCTAAACCCCTAAAGAAAGCCAT
AAGAATAATAGAAATTTAAAGAAAATGAATAAGAAGATTATTTTTCTTCTAAAAACTAGATTGAC
TATTT
Found at i:632184 original size:28 final size:29
Alignment explanation
Indices: 632138--632193 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
632128 ATAGAAAAAA
632138 TTTTAAAACTAATAAAATA-AATTAAATT
1 TTTTAAAACTAATAAAATAGAATTAAATT
* **
632166 TTTTAAAACTGATTTAATATGAATTAAA
1 TTTTAAAACTAATAAAATA-GAATTAAA
632194 CAATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
30 7 0.30
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTTAAAACTAATAAAATAGAATTAAATT
Found at i:632444 original size:153 final size:151
Alignment explanation
Indices: 632121--632444 Score: 459
Period size: 153 Copynumber: 2.1 Consensus size: 151
632111 AAATCTATAC
632121 TTTGAAAATAGAAAAAATTTTAAAACTAATAAAATAAATTAAATTTTTTAAAACTGATTTAATAT
1 TTTGAAAATAG-AAAAATTTTAAAACTAATAAAATAAATTAAATTTTTTAAAACTGATTTAATAT
* * * * *
632186 GAATTAAACAATAATATTTGAAGAATTTTTAAAATTATAAGCTTAGAAAAATCCTACCAAAATTT
65 GAATTAAAAAATAATATTTGAAGAATTTTAAAAATTATAAGCTTAAAAAAATCCTAACAAAAATT
632251 TACAAAGTAAAAAACTTCGTAT
130 TACAAAGTAAAAAACTTCGTAT
* * * *
632273 TTCGATAACATAAAAAAAATTTAAAACTCATAAAATAAATTAAATTTTTTAAAACTGATTTAATA
1 TTTGA-AA-ATAGAAAAATTTTAAAACTAATAAAATAAATTAAATTTTTTAAAACTGATTTAATA
* *
632338 TGAATTAAAAAATAATATTTGAAGAATTTTAAAAATTATAAGCTCTAAAAAAATGCTAATAGAGA
64 TGAATTAAAAAATAATATTTGAAGAATTTTAAAAATTATAAGCT-TAAAAAAATCCTAACA-A-A
* * * *
632403 AATTTACGAAGTCAAAAATTTTGTAT
126 AATTTACAAAGTAAAAAACTTCGTAT
632429 TTTGAAAATAGAAAAA
1 TTTGAAAATAGAAAAA
632445 ATCTGAAAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
152 4 0.03
153 94 0.63
154 23 0.15
155 3 0.02
156 26 0.17
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.34
Consensus pattern (151 bp):
TTTGAAAATAGAAAAATTTTAAAACTAATAAAATAAATTAAATTTTTTAAAACTGATTTAATATG
AATTAAAAAATAATATTTGAAGAATTTTAAAAATTATAAGCTTAAAAAAATCCTAACAAAAATTT
ACAAAGTAAAAAACTTCGTAT
Found at i:635945 original size:51 final size:51
Alignment explanation
Indices: 635889--635986 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
635879 TCATTGATGT
* **
635889 TTTTA-TTTCTAAAACACCGATTTTCCACCATTGGGGATACTCCAACCCCGA
1 TTTTATTTTC-AAAACACCAATTTTCCACCATCAGGGATACTCCAACCCCGA
*
635940 TTTTATTTTCAAAACACCAATTTTCCACCATCAGGGATAGTCCAACC
1 TTTTATTTTCAAAACACCAATTTTCCACCATCAGGGATACTCCAACC
635987 TCGTTATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 38 0.90
52 4 0.10
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (51 bp):
TTTTATTTTCAAAACACCAATTTTCCACCATCAGGGATACTCCAACCCCGA
Found at i:636158 original size:79 final size:78
Alignment explanation
Indices: 635921--636179 Score: 274
Period size: 79 Copynumber: 3.3 Consensus size: 78
635911 TTCCACCATT
* * * * *
635921 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCACCATCAGGGATAGTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACCATCAGGGATACTCCAAC
*
635986 CTCGTTATTTTCGA
66 CCCGTTATTTT-GA
* * * * *
636000 AGAGATACTTCAACCCCGATTTT-TTTCTAAAACATCGA-TTTTCACCATCAGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACCATCAGGGATACTCCAAC
*
636063 CCCGTTATTTCCGA
66 CCCGTTATTT-TGA
* *
636077 GGGGATACTCCAA-CCCTAGTTTTATTTCCAAAACATCGATTTTTCACCATC-GAAGATACTCCA
1 GGGGATACTCCAACCCCGA-TTTTATTTCCAAAACATCGATTTTTCACCATCAG-GGATACTCCA
*
636140 ACCCCATTATTTATGA
64 ACCCCGTTATTT-TGA
* * *
636156 GGGAATACTCTAGCCCCGAATTTT
1 GGGGATACTCCAACCCCG-ATTTT
636180 CCACTATTGG
Statistics
Matches: 147, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
76 4 0.03
77 47 0.32
78 26 0.18
79 62 0.42
80 7 0.05
81 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACCATCAGGGATACTCCAAC
CCCGTTATTTTGA
Found at i:636303 original size:139 final size:139
Alignment explanation
Indices: 636050--636304 Score: 386
Period size: 139 Copynumber: 1.8 Consensus size: 139
636040 TTCACCATCA
* * * *
636050 GGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCTAGTTTTATTTCCAAAACATCG
1 GGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCTAGTTTTATTTCCAAAACACCG
*
636115 ATTTTTCACCATCGAAGATACTCCAACCCCATTATTTATGAGGGAATACTCTAGCCCCGAATTTT
66 ATTTTTCACCATCGAAGATACTCCAACCCCATTATTTACGAGGGAATACTCTAGCCCCGAATTTT
636180 CCACTATTG
131 CCACTATTG
* * *
636189 GGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCTAA-CCTCGGTTTTATTTTCAAAACACC
1 GGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCT-AGTTTTATTTCCAAAACACC
* * * *
636253 GATTTTTTACCATCGGAGATACTCCAACCCCATTATTTCCGAGGGGATACTC
65 GATTTTTCACCATCGAAGATACTCCAACCCCATTATTTACGAGGGAATACTC
636305 CAACCTTGAT
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
138 3 0.03
139 100 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (139 bp):
GGGATACTCCAACCCCGTTATTTCCGAGAGAATACTCCAACCCTAGTTTTATTTCCAAAACACCG
ATTTTTCACCATCGAAGATACTCCAACCCCATTATTTACGAGGGAATACTCTAGCCCCGAATTTT
CCACTATTG
Found at i:636310 original size:79 final size:79
Alignment explanation
Indices: 636191--636702 Score: 431
Period size: 79 Copynumber: 6.5 Consensus size: 79
636181 CACTATTGGG
** * * * * *
636191 GATACTCCAACCCCGTTATTTCCGAGAGAATACTCTAACCTCGGTTTTATTT-TCAAAACACCGA
1 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCT-AAAACACCAA
*
636255 TTTTTTACCATCGGA
65 TTTTTCACCATCGGA
* ** * * * ** *
636270 GATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCTTGATTTTATTTCTGAGACACTGAG
1 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAAT
* *
636335 TTTCCACCATCGAA
66 TTTTCACCATCGGA
* * * * *
636349 GATACTCCAACCCCATTATTTTTGAGGGAATACTCTAACCTC-AGTTTTATTTCTAAAACATCGA
1 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGA-TTTTATTTCTAAAACACCAA
*
636413 TTTTTCACCATCGGG
65 TTTTTCACCATCGGA
* ** * *
636428 GATACTGCAACCTTGTTATTTTTGAAGGGATACTCCAACCTC-ACTTTTATTTCTAAAACACTAA
1 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGA-TTTTATTTCTAAAACACCAA
* * *
636492 TTTTTCACAATTGAA
65 TTTTTCACCATCGGA
** ** * ** * *
636507 GATACTCCAACCCTATTATTTTTGAAAGGATACTCCAACCCCTTTTTTATTTCGAAAACATCAAT
1 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAAT
* *
636572 TTTTCACAATCGGG
66 TTTTCACCATCGGA
* * * * * * *
636586 GATACTCCAACCTCGTCATTTTTAAGGGGATACTTCAAACC-CGATTTTATTTCCAAGACACTAA
1 GATACTCCAACCCCGTTATTTTTGAGGGGATAC-TCCAACCTCGATTTTATTTCTAAAACACCAA
*
636650 TTTTTTACCATC-GA
65 TTTTTCACCATCGGA
* * * * *
636664 GGATACTCTAACCCCGTGATTTCTAAGGAGATACTCCAA
1 -GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAA
636703 TCCCATTTTT
Statistics
Matches: 352, Mismatches: 76, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
78 6 0.02
79 339 0.96
80 7 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAAT
TTTTCACCATCGGA
Found at i:636345 original size:218 final size:216
Alignment explanation
Indices: 635958--636385 Score: 571
Period size: 218 Copynumber: 2.0 Consensus size: 216
635948 TCAAAACACC
* * *
635958 AATTTTCCACCATCAGGGATAGTCCAACCTCGTTATTTTCGAAGAGATACTTCAACCCCGATTTT
1 AATTTTCCACCATCAGGGATACTCCAACCCCGTTATTTCCGAAGAGATACTTCAACCCCGATTTT
* * *
636023 TTTCTAAAACATCGATTTTCACCATCAGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCC
66 TTTCTAAAACACCGATTTTCACCATCAGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCC
* *
636088 AACCCTAGTTTTATTTCCAAAACATCGATTTTTCACCATCGAAGATACTCCAACCCCATTATTTA
131 AACCCTAGTTTTATTTCCAAAACATCGAGTTTCCACCATCGAAGATACTCCAACCCCATTATTTA
636153 TGAGGGAATACTCTAGCCCCG
196 TGAGGGAATACTCTAGCCCCG
* ** * *
636174 AATTTTCCACTATTGGGGATACTCCAACCCCGTTATTTCCG-AGAGAATAC-TCTAACCTCGGTT
1 AATTTTCCACCATCAGGGATACTCCAACCCCGTTATTTCCGAAGAG-ATACTTC-AACCCCGATT
*
636237 TTATTT-TCAAAACACCGATTTTTTACCATC-GGAGATACTCCAACCCCATTATTTCCGAGGGGA
64 TT-TTTCT-AAAACACCGA-TTTTCACCATCAGG-GATACTCCAACCCCATTATTTCCGAGGGGA
* ** *
636300 TACTCCAA-CCTTGATTTTATTTCTGAGACA-CTGAGTTTCCACCATCGAAGATACTCCAACCCC
125 TACTCCAACCCTAG-TTTTATTTCCAAAACATC-GAGTTTCCACCATCGAAGATACTCCAACCCC
*
636363 ATTATTTTTGAGGGAATACTCTA
188 ATTATTTATGAGGGAATACTCTA
636386 ACCTCAGTTT
Statistics
Matches: 185, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
215 6 0.03
216 50 0.27
217 19 0.10
218 110 0.59
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (216 bp):
AATTTTCCACCATCAGGGATACTCCAACCCCGTTATTTCCGAAGAGATACTTCAACCCCGATTTT
TTTCTAAAACACCGATTTTCACCATCAGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCC
AACCCTAGTTTTATTTCCAAAACATCGAGTTTCCACCATCGAAGATACTCCAACCCCATTATTTA
TGAGGGAATACTCTAGCCCCG
Found at i:636396 original size:158 final size:157
Alignment explanation
Indices: 636191--636678 Score: 557
Period size: 158 Copynumber: 3.1 Consensus size: 157
636181 CACTATTGGG
* ** * * *
636191 GATACTCCAACCCCGTTATTTCCGAGAGAATACTCTAACCTCGGTTTTATTTTC-AAAACACCGA
1 GATACTCCAACCCCATTATTTTTGAGGGAATACTCTAACCTCAGTTTTA-TTTCGAAAACATCGA
* * * * **
636255 TTTTTTACCATCGGAGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCTTGATTTTAT
65 TTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATACTCCAACC-TGATTTTAT
* * * *
636320 TTCTGAGACACTGAGTTTCCACCATCGAA
129 TTCTAAGACACTAATTTTTCACCATCGAA
*
636349 GATACTCCAACCCCATTATTTTTGAGGGAATACTCTAACCTCAGTTTTATTTCTAAAACATCGAT
1 GATACTCCAACCCCATTATTTTTGAGGGAATACTCTAACCTCAGTTTTATTTCGAAAACATCGAT
* * * *
636414 TTTTCACCATCGGGGATACTGCAACCTTGTTATTTTTGAAGGGATACTCCAACCTCACTTTTATT
66 TTTTCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATACTCCAACCTGA-TTTTATT
* * *
636479 TCTAAAACACTAATTTTTCACAATTGAA
130 TCTAAGACACTAATTTTTCACCATCGAA
* * * * ** *
636507 GATACTCCAACCCTATTATTTTTGAAAGG-ATACTCCAACCCCTTTTTTATTTCGAAAACATCAA
1 GATACTCCAACCCCATTATTTTTG-AGGGAATACTCTAACCTCAGTTTTATTTCGAAAACATCGA
* * * * *
636571 TTTTTCACAATCGGGGATACTCCAACCTCGTCATTTTTAAGGGGATACTTCAAACCCGATTTTAT
65 TTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATAC-TCCAACCTGATTTTAT
* * *
636636 TTCCAAGACACTAATTTTTTACCATCGAG
129 TTCTAAGACACTAATTTTTCACCATCGAA
*
636665 GATACTCTAACCCC
1 GATACTCCAACCCC
636679 GTGATTTCTA
Statistics
Matches: 278, Mismatches: 48, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
157 6 0.02
158 262 0.94
159 10 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (157 bp):
GATACTCCAACCCCATTATTTTTGAGGGAATACTCTAACCTCAGTTTTATTTCGAAAACATCGAT
TTTTCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATACTCCAACCTGATTTTATTT
CTAAGACACTAATTTTTCACCATCGAA
Found at i:640801 original size:60 final size:60
Alignment explanation
Indices: 640730--640879 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
640720 GAGATTGTTT
* * * *
640730 ATTAGCAAAGGTAACTCGATGTTACTTGTTGAGATGTCGATCAAACCTTTAAGGTCATTC
1 ATTAGCAAAGGTGACTCGATGTTACTTGCTAAGATGTCAATCAAACCTTTAAGGTCATTC
* * * * * * * **
640790 ATTGGCAAAGGTGACTCAATGTTACTTGCTAAGATGTTAATTAGACTTTTTAGGTTGTTC
1 ATTAGCAAAGGTGACTCGATGTTACTTGCTAAGATGTCAATCAAACCTTTAAGGTCATTC
*
640850 ATTAGCAAAGGTGACTCGATGTCACTTGCT
1 ATTAGCAAAGGTGACTCGATGTTACTTGCT
640880 TATATGCTGC
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (60 bp):
ATTAGCAAAGGTGACTCGATGTTACTTGCTAAGATGTCAATCAAACCTTTAAGGTCATTC
Found at i:642923 original size:13 final size:13
Alignment explanation
Indices: 642905--642931 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
642895 CATTACTCAA
642905 TGTATCGATACAT
1 TGTATCGATACAT
642918 TGTATCGATACAT
1 TGTATCGATACAT
642931 T
1 T
642932 TGATCTCTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:642948 original size:34 final size:32
Alignment explanation
Indices: 642885--642952 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 32
642875 GCCAAGGAAA
642885 TGTATCGATACATTACTCAATGTATCGATACAT
1 TGTATCGATACATTACTC-ATGTATCGATACAT
642918 TGTATCGATACATTTGATCTC-TGTATCGATACAT
1 TGTATCGATACA-TT-A-CTCATGTATCGATACAT
642952 T
1 T
642953 TGGGAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 12 0.38
34 16 0.50
35 1 0.03
36 3 0.09
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTACTCATGTATCGATACAT
Found at i:648256 original size:19 final size:20
Alignment explanation
Indices: 648232--648274 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
648222 TCTTTTTCCT
* *
648232 TTTTTTTCT-TTTTGATAAC
1 TTTTTTTCTCTTTTAACAAC
648251 TTTTTTTCTCTTTTAACAAC
1 TTTTTTTCTCTTTTAACAAC
648271 TTTT
1 TTTT
648275 GTTTTTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTTTCTCTTTTAACAAC
Found at i:648257 original size:21 final size:21
Alignment explanation
Indices: 648231--648283 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
648221 CTCTTTTTCC
* *
648231 TTTTTTTTCTTTTTGATAACT
1 TTTTTTTTCTTTTTAACAACT
*
648252 TTTTTTCTC-TTTTAACAACT
1 TTTTTTTTCTTTTTAACAACT
648272 TTTGTTTTTCTT
1 TTT-TTTTTCTT
648284 CCCCAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
21 13 0.50
22 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTTTTCTTTTTAACAACT
Found at i:649905 original size:79 final size:79
Alignment explanation
Indices: 649798--650132 Score: 415
Period size: 79 Copynumber: 4.2 Consensus size: 79
649788 GAGATAGTAA
* * *
649798 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTAAT-CCCGATTGTGAAAAATCAATG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGT-ATCCCCGATTATGAAAAATTAAT-
649862 ATTTGA-AAATAAAAC
64 ATTTGAGAAATAAAAC
* * * * *
649877 CGGGATTGGAGTATCCCCTCGGAGATAACGGGGTTTGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
* *
649942 TTTAGAAATAAAAT
66 TTGAGAAATAAAAC
* * * *
649956 CGGGGTTGGAGTATCCCCTCGAAAGTAACAGGGTTGGAGTATCCCCGATTACGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
*
650021 TTTAGAAATAAAAC
66 TTGAGAAATAAAAC
* * * **
650035 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAGGAAAATTGGTG
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT-TATGAAAAATTAAT-
*
650100 TTTTGA-AAATAAAAC
64 ATTTGAGAAATAAAAC
*
650115 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
650133 GATTGTGAAA
Statistics
Matches: 223, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
78 7 0.03
79 178 0.80
80 34 0.15
81 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
TTGAGAAATAAAAC
Done.