Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold323
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: 1512004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:479194 original size:19 final size:20
Alignment explanation
Indices: 479170--479207 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
479160 TTGAGAGGGA
479170 AAAAAAAAG-AAAGAAAAGG
1 AAAAAAAAGAAAAGAAAAGG
*
479189 AAAAAAGAGAAAAGAAAAG
1 AAAAAAAAGAAAAGAAAAG
479208 AGATTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAGAAAAGG
Found at i:482639 original size:38 final size:38
Alignment explanation
Indices: 482597--482672 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
482587 AATTGGTTTC
* * *
482597 AAACCATGCCATCAG-TTAAGAATAATGGTTTTTGTATT
1 AAACCATGCCA-CAGAATAAGAATAATGATTTTTATATT
*
482635 AAACCATGCCACAGAATAAGAATAGTGATTTTTATATT
1 AAACCATGCCACAGAATAAGAATAATGATTTTTATATT
482673 GAACTGTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 3 0.09
38 30 0.91
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (38 bp):
AAACCATGCCACAGAATAAGAATAATGATTTTTATATT
Found at i:483074 original size:19 final size:19
Alignment explanation
Indices: 483050--483099 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
483040 AAACCGTAAA
*
483050 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
483069 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
483088 TGTATCGATACA
1 TGTATCGATACA
483100 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:483150 original size:21 final size:21
Alignment explanation
Indices: 483124--483164 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
483114 AGCTACTGCC
483124 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
483145 AAGGAAATGTATCGATACAT
1 AAGGAAATGTATCGATACAT
483165 CGATCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:485614 original size:51 final size:51
Alignment explanation
Indices: 485525--485757 Score: 256
Period size: 51 Copynumber: 4.6 Consensus size: 51
485515 TTAAGTTTCT
* * * *
485525 CAATTTTTCATAATCGGGGGTACTTCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
* * * * *
485576 TAATTTTTCACAATTGGGGATACTCCAACTCCGATTTTATTTTTGAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
* * *
485627 CAATTTTCCACAATCGGGGATACTCCAAC-CGCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTC-CGATTTTATTTCT-AAAACAC
* * * *
485678 CAA-TTTTCTATAATTGGGGACACTCCAACTCCAATTTTATTTCCAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
* *
485729 CGACTTTTCATAATCGGGGATACTCCAAC
1 CAATTTTTCATAATCGGGGATACTCCAAC
485758 CCCGTTATTT
Statistics
Matches: 152, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
50 6 0.04
51 140 0.92
52 6 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAACAC
Found at i:485693 original size:102 final size:101
Alignment explanation
Indices: 485529--485761 Score: 308
Period size: 102 Copynumber: 2.3 Consensus size: 101
485519 GTTTCTCAAT
* * *
485529 TTTTCATAATCGGGGGTACTTCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCACAATTGGG
1 TTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATTGGG
* * ***
485594 GATACTCCAACTCCGATTTTATTTTTGAAACACCAA
66 GACACTCCAACTCCAATTTTATTTCCAAAACACCAA
* * *
485630 TTTTCCACAATCGGGGATACTCCAACCGCGGTTTTATTT-TCAAAACACCAA-TTTTCTATAATT
1 TTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTTC-ACAATT
*
485693 GGGGACACTCCAACTCCAATTTTATTTCCAAAACACCGAC
63 GGGGACACTCCAACTCCAATTTTATTTCCAAAACACC-AA
485733 TTTTCATAATCGGGGATACTCCAACCCCG
1 TTTTCATAATCGGGGATACTCCAACCCCG
485762 TTATTTTCGA
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
101 10 0.09
102 99 0.87
103 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (101 bp):
TTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATTGGG
GACACTCCAACTCCAATTTTATTTCCAAAACACCAA
Found at i:485785 original size:79 final size:76
Alignment explanation
Indices: 485693--485863 Score: 209
Period size: 76 Copynumber: 2.2 Consensus size: 76
485683 TTCTATAATT
* *
485693 GGGGACACTCCAACTCCAATTTTATTTCCAAAACACCGACTTTTCATAATCGGGGATACTCCAAC
1 GGGGACACTCCAACTCCAATTTCATTTCCAAAACACC-AATTTT--TAATCGGGGATACTCCAAC
485758 CCCGTTATTTTCGA
63 CCCGTTATTTTCGA
* ** * * * * *
485772 GGGGACACTCCAACCCCGGTTTCATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAATCCT
1 GGGGACACTCCAACTCCAATTTCATTTCCAAAACACCAATTTTTAATCGGGGATACTCCAACCCC
485837 GTTATTTTCGA
66 GTTATTTTCGA
*
485848 GGGGATACTCC-ACTCC
1 GGGGACACTCCAACTCC
485864 CGTTATTTTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
75 4 0.05
76 40 0.50
78 5 0.06
79 31 0.39
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.30
Consensus pattern (76 bp):
GGGGACACTCCAACTCCAATTTCATTTCCAAAACACCAATTTTTAATCGGGGATACTCCAACCCC
GTTATTTTCGA
Found at i:485852 original size:28 final size:28
Alignment explanation
Indices: 485820--485893 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
485810 ATTTTTCATC
485820 GGGGATACTCCAATCCTGTTATTTTCGA
1 GGGGATACTCCAATCCTGTTATTTTCGA
* *
485848 GGGGATACTCCACTCCCGTTATTTTCGA
1 GGGGATACTCCAATCCTGTTATTTTCGA
* *
485876 GGGGATACCCCAACCCTG
1 GGGGATACTCCAATCCTG
485894 GCTTTATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAATCCTGTTATTTTCGA
Found at i:485926 original size:183 final size:185
Alignment explanation
Indices: 485713--486128 Score: 475
Period size: 188 Copynumber: 2.2 Consensus size: 185
485703 CAACTCCAAT
* * * * * *
485713 TTTATTTCCAAAACACCGACTTT-TCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
1 TTTATTTCTAAAATACC-AATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAAGGGA
* * * *
485777 CACTCCAACCCC-GGTTTCATTTCT-AAAACATCA-ATTTT-TCATCGGGGATACTCCAATCCTG
65 CACTCCAACCCCAGCTTT-ATATCTAAAAACATCATATTTTATAATCGGGGATACTCCAACCCTG
* * **
485838 TTATTTTCGA-GGGGATACTCCACTCCCGTTATTTTCGAGGGGATACCCCAACCCTGGC
129 TTA-TTTC-ATGGGGATACTCCAATCCCGTTATTTTCGAAGGGATACCCCAACCCTAAC
** * * *
485896 TTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCTAACCCTGTTATCTCCGAAGGGAT
1 TTTATTTCTAAAATACCAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAAGGGAC
* * * *
485961 ACTCCAACCCCAGCTTTATATCTAAAAATATTATTTTTTTGATAATCGGGGGTACTCCAACCCTG
66 ACTCCAACCCCAGCTTTATATCTAAAAACATCA-TATTTT-ATAATCGGGGATACTCCAACCCTG
* * *
486026 TTATTTCATTGGGGATACTCCAATCTCGTTATTTTCGAAGGGATACTCCAACCCTAAT
129 TTATTTCA-TGGGGATACTCCAATCCCGTTATTTTCGAAGGGATACCCCAACCCTAAC
* *
486084 TTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 TTTATTTCTAAAATACCAATTTCTCATAATCGGGGATACTCCAAC
486129 TCCGATTTTA
Statistics
Matches: 193, Mismatches: 31, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
182 4 0.02
183 65 0.34
184 11 0.06
186 5 0.03
187 4 0.02
188 104 0.54
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (185 bp):
TTTATTTCTAAAATACCAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCCGAAGGGAC
ACTCCAACCCCAGCTTTATATCTAAAAACATCATATTTTATAATCGGGGATACTCCAACCCTGTT
ATTTCATGGGGATACTCCAATCCCGTTATTTTCGAAGGGATACCCCAACCCTAAC
Found at i:485979 original size:79 final size:81
Alignment explanation
Indices: 485848--486029 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 81
485838 TTATTTTCGA
* * * * ** *
485848 GGGGATACTCC-ACTCCCGTTATTTTCGAGGGGATACCCCAACCCTGGCTTTATTTCT-AAAATA
1 GGGGATACTCCAAC-CCTGTTATCTCCGAAGGGATACCCCAACCCCAGCTTTATATCTAAAAATA
485911 TTA-ATTTCTCATAATC
65 TTATATTTCTCATAATC
* *
485927 GGGGATACTCTAACCCTGTTATCTCCGAAGGGATACTCCAACCCCAGCTTTATATCTAAAAATAT
1 GGGGATACTCCAACCCTGTTATCTCCGAAGGGATACCCCAACCCCAGCTTTATATCTAAAAATAT
* * *
485992 TATTTTTTTGATAATC
66 TATATTTCTCATAATC
*
486008 GGGGGTACTCCAACCCTGTTAT
1 GGGGATACTCCAACCCTGTTAT
486030 TTCATTGGGG
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 45 0.52
80 11 0.13
81 30 0.35
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (81 bp):
GGGGATACTCCAACCCTGTTATCTCCGAAGGGATACCCCAACCCCAGCTTTATATCTAAAAATAT
TATATTTCTCATAATC
Found at i:486041 original size:81 final size:79
Alignment explanation
Indices: 485848--486048 Score: 208
Period size: 81 Copynumber: 2.5 Consensus size: 79
485838 TTATTTTCGA
* * * ** *
485848 GGGGATACTCC-ACTCCCGTTATTTTC-GAGGGGATACCCCAACCCTGGCTTTATTTCTAAAATA
1 GGGGATACTCCAAC-CCTGTTA-TCTCAGAGGGGATACTCCAACCCCAGCTTTATATCTAAAATA
485911 TTAATTTCTCATAATC
64 TTAATTTCTCATAATC
* * *
485927 GGGGATACTCTAACCCTGTTATCTCCGAAGGGATACTCCAACCCCAGCTTTATATCTAAAAATAT
1 GGGGATACTCCAACCCTGTTATCTCAGAGGGGATACTCCAACCCCAGCTTTATATCT-AAAATAT
* * *
485992 TATTTTTTTGATAATC
65 TA-ATTTCTCATAATC
* * **
486008 GGGGGTACTCCAACCCTGTTATTTCATTGGGGATACTCCAA
1 GGGGATACTCCAACCCTGTTATCTCAGAGGGGATACTCCAA
486049 TCTCGTTATT
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
78 3 0.03
79 42 0.42
80 11 0.11
81 44 0.44
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCTGTTATCTCAGAGGGGATACTCCAACCCCAGCTTTATATCTAAAATATT
AATTTCTCATAATC
Found at i:486127 original size:51 final size:51
Alignment explanation
Indices: 486065--486230 Score: 212
Period size: 51 Copynumber: 3.3 Consensus size: 51
486055 TATTTTCGAA
* *
486065 GGGATACTCCAACCCTAATTTTATTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCG
* * *
486116 GGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTCTCATAATCG
1 GGGATACTCCAAC-CCTGATTTTATTTCTAAAATACCAATTTTTCATAATCG
* *
486167 GGGATACTCCAACCCTGATTTTATTT-TCAAAATACCGA-TTTTCTATAATCA
1 GGGATACTCCAACCCTGATTTTATTTCT-AAAATACCAATTTTTC-ATAATCG
*
486218 GGCATACTCCAAC
1 GGGATACTCCAAC
486231 TCTATTTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
50 6 0.06
51 92 0.92
52 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCG
Found at i:488352 original size:33 final size:32
Alignment explanation
Indices: 488314--488380 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
488304 GTTACAAGCT
488314 ATGTATCGATATAATTCAT-CATGTATTGATACA
1 ATGTATCGATA-AATT-ATACATGTATTGATACA
*
488347 ATGTATCGATACATTATACCATGTATTGATACA
1 ATGTATCGATAAATTATA-CATGTATTGATACA
488380 A
1 A
488381 ACAGTGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.10
33 26 0.84
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (32 bp):
ATGTATCGATAAATTATACATGTATTGATACA
Found at i:488370 original size:20 final size:20
Alignment explanation
Indices: 488342--488379 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
488332 TCATGTATTG
488342 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
* *
488362 ATACCATGTATTGATACA
1 ATACAATGTATCGATACA
488380 AACAGTGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:494701 original size:20 final size:22
Alignment explanation
Indices: 494668--494716 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
494658 TAAAAATTAT
*
494668 TTTCAGCT-AAAATAA-AAAAA
1 TTTCAGTTAAAAATAATAAAAA
*
494688 TTT-AGTTAAAAATAATATAAA
1 TTTCAGTTAAAAATAATAAAAA
494709 TTTCAGTT
1 TTTCAGTT
494717 TTATTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 7 0.29
22 4 0.17
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (22 bp):
TTTCAGTTAAAAATAATAAAAA
Found at i:495640 original size:38 final size:38
Alignment explanation
Indices: 495584--495700 Score: 137
Period size: 38 Copynumber: 3.1 Consensus size: 38
495574 CATGACATCG
* * *
495584 GTTAAGAATTGTAGTTTTTATATTGAACCGTACCACCA
1 GTTAAGAATAGTAGTTTTTATATTGAACCGTGCCACTA
* * *
495622 GTTAAGAATAGT-GATTTTTATATTAAACTGTGCCGCTA
1 GTTAAGAATAGTAG-TTTTTATATTGAACCGTGCCACTA
** *
495660 AATAAGAATAGTAGTTTTTGTATTGAACCGTGCCACTA
1 GTTAAGAATAGTAGTTTTTATATTGAACCGTGCCACTA
495698 GTT
1 GTT
495701 TATAATAATG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
37 1 0.02
38 61 0.97
39 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (38 bp):
GTTAAGAATAGTAGTTTTTATATTGAACCGTGCCACTA
Found at i:495782 original size:38 final size:37
Alignment explanation
Indices: 495698--495828 Score: 120
Period size: 38 Copynumber: 3.5 Consensus size: 37
495688 CGTGCCACTA
* * * *
495698 GTTTATAATAATGGTTTTCATTTCGAACATGCTATCG
1 GTTTAGAATAATGATTTTCATTTCGAACGTGCCATCG
**
495735 GTTTAGAATAATGATTTTTGTTTCGAATCGTGCCATCG
1 GTTTAGAATAATGATTTTCATTTCGAA-CGTGCCATCG
* * * *
495773 GTTTAGAATAGT-AGTTTTCATTTCAAACCGCGCCATCA
1 GTTTAGAATAATGA-TTTTCATTTCGAA-CGTGCCATCG
* *
495811 GTTTAAAATAGTGATTTT
1 GTTTAGAATAATGATTTT
495829 TGTTAATAGC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
37 24 0.31
38 52 0.68
39 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (37 bp):
GTTTAGAATAATGATTTTCATTTCGAACGTGCCATCG
Found at i:500494 original size:177 final size:177
Alignment explanation
Indices: 500192--500540 Score: 563
Period size: 177 Copynumber: 2.0 Consensus size: 177
500182 TTATTCACCT
* * * *
500192 TATAAACTATTATTAAGCAAAATGTTTAAGGGTCGTTGGTCACCAAAGAAGTAACAGACTGATTA
1 TATAAACTACTATTAAGCAAAATGTTTAAGGGCCATTGGTCACCAAAGAAGTAACAGACTGATCA
* * *
500257 GTTAACTCCAACACATCAACTATTAAAGAATCTTTGAACAAGACCTAAATTTGGTTGTTCACTAC
66 GTTAACTCCAACACATCAACTATCAAAGAATCTTTGAACAAGACCTAAATTCGATTGTTCACTAC
* *
500322 ATTTGAGTAATTGTGAAACATTTTCTAGCCACTGAAATGCTTCCGTA
131 ATTTGAGTAATTATGAAACATCTTCTAGCCACTGAAATGCTTCCGTA
*
500369 TATAAACTACTATTAAGCAAAATGTTTAAGGGCCATTGGTCACCAAGGAAGTAACAGACTGATCA
1 TATAAACTACTATTAAGCAAAATGTTTAAGGGCCATTGGTCACCAAAGAAGTAACAGACTGATCA
* * * * *
500434 GTTAACTCCAACATATTAACTATCAAAGAATCTTTGAATAAGACCTAACTTCGATTGTTCACTGC
66 GTTAACTCCAACACATCAACTATCAAAGAATCTTTGAACAAGACCTAAATTCGATTGTTCACTAC
500499 ATTTGAGTAATTATGAAACATCTTCTAGCCACTGAAATGCTT
131 ATTTGAGTAATTATGAAACATCTTCTAGCCACTGAAATGCTT
500541 TCACGTAATA
Statistics
Matches: 157, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 157 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (177 bp):
TATAAACTACTATTAAGCAAAATGTTTAAGGGCCATTGGTCACCAAAGAAGTAACAGACTGATCA
GTTAACTCCAACACATCAACTATCAAAGAATCTTTGAACAAGACCTAAATTCGATTGTTCACTAC
ATTTGAGTAATTATGAAACATCTTCTAGCCACTGAAATGCTTCCGTA
Found at i:506087 original size:20 final size:20
Alignment explanation
Indices: 506034--506088 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
506024 AAATTTCCAG
** *
506034 ATGTATCGATACAAAGATTA
1 ATGTATCGATACATTGAATA
506054 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
506074 ATGTATCGATACATT
1 ATGTATCGATACATT
506089 TCCTTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:512180 original size:38 final size:38
Alignment explanation
Indices: 512145--512246 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 38
512135 ATAGCATAAG
*
512145 TCAAAACAAAAACTACTATTTT-AATTCGGTGGCATAGT
1 TCAAAACAAAAACTACTATTTTAAATT-GGTGGCATAGA
* *
512183 TCGAAACAAAAA-T-CATAATTTTCAAATTGGTGGCATGGA
1 TCAAAACAAAAACTAC-T-ATTTT-AAATTGGTGGCATAGA
*
512222 TCAAAAC-AAAACTACTATTCTAAAT
1 TCAAAACAAAAACTACTATTTTAAAT
512247 CAATGGTTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
36 1 0.02
37 6 0.11
38 24 0.45
39 17 0.32
40 5 0.09
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (38 bp):
TCAAAACAAAAACTACTATTTTAAATTGGTGGCATAGA
Found at i:513779 original size:32 final size:32
Alignment explanation
Indices: 513734--513802 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
513724 ACAGTAACTA
*
513734 TATCGATACATAAGTATTGTATAGATATAATG
1 TATCGATACATAAGTATTGTATAGATACAATG
* * *
513766 TATCGATAGATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTATTGTATAGATACAATG
513798 TATCG
1 TATCG
513803 CTATGAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATAGATACAATG
Found at i:522852 original size:13 final size:13
Alignment explanation
Indices: 522834--522861 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
522824 ATACAAAGAT
522834 CAATGTATCGATA
1 CAATGTATCGATA
522847 CAATGTATCGATA
1 CAATGTATCGATA
522860 CA
1 CA
522862 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:524620 original size:52 final size:49
Alignment explanation
Indices: 524516--524699 Score: 176
Period size: 49 Copynumber: 3.7 Consensus size: 49
524506 AATGATAATG
* * ** *
524516 TGCTGATTCATGGCCAGCGACATTTAGACTTGAAG--GAAAATGCCAATG
1 TGCTGATTCAAGGCCAGCGACA-TTGGACTCAAAGATGAAAATGCCAATA
** *
524564 TGCTGAGGCAAGGCCAGCGACATTGGGCTCAGAA-ATGTTAAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTCA-AAGATG--AAA-ATGCCAATA
* * * *
524616 TGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGACTCAAAGATGAAAATGCCAATA
* *
524665 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA
1 TGCTGATTCAAGGCCAGCGACATTGGACTCAAAGA
524700 CAAGGTGCCA
Statistics
Matches: 110, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
47 5 0.05
48 21 0.19
49 41 0.37
50 3 0.03
51 5 0.05
52 35 0.32
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTCAAAGATGAAAATGCCAATA
Found at i:524729 original size:48 final size:47
Alignment explanation
Indices: 524516--525183 Score: 361
Period size: 48 Copynumber: 14.5 Consensus size: 47
524506 AATGATAATG
* * * * * *
524516 TGCTGATTCATGGCCAGCGACATTTAGACTTGAAGGAAA-ATGCCAATG
1 TGCTGATTCAAGGCCAGCGACA-TTGGTCTT-AAAGAAAGGTGCCAATA
** ** *
524564 TGCTGAGGCAAGGCCAGCGACATTGGGCTCAGAAATGTTAAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATT-GG-TCTTAAA-G--AAAGGTGCCAATA
* * * * **
524616 TGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAATGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA--AAGGTGCCAATA
*
524665 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACA
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-AAGGTGCCAATA
* * * * *
524713 TGCCGATTCAAAGCCAGTGATATTAGG-CTT------A--TGCCAATG
1 TGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGAAAGGTGCCAATA
* * *
524752 TGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGATAAGGTGCCAACA
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-AAGGTGCCAATA
* * * *
524800 TG-TCGATTCAAAGCCAGCGATATTGGGCTT------A--TGCCAATG
1 TGCT-GATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATA
* * *
524839 TGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACA
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-AAGGTGCCAATA
* * * *
524887 TG-TCGATTCAAAGCCAGCGATATTGGGCTT------A--TGCCAATG
1 TGCT-GATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATA
* * *
524926 TGCTTATTCAAGGCCAGCAACATTGGT-TTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA--AAGGTGCCAATA
*
524974 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-AAGGTGCCAATA
* * * * * *
525022 TGCTGATTCAAAGCCAGTGATATTGGGCTT------A--TGCCGATG
1 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATA
* * * *
525061 TGCTGATTCAAGGCCAGCAACATTGGT-TATAAAGACAAAGTGTCAGTA
1 TGCTGATTCAAGGCCAGCGACATTGGTCT-TAAAGA-AAGGTGCCAATA
* *
525109 TGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAG--AAAGGTGCCAATA
*
525159 TGCTTG-TTCAAGGCCAGCGATATTG
1 TGC-TGATTCAAGGCCAGCGACATTG
525184 AACTTAGAAG
Statistics
Matches: 471, Mismatches: 91, Indels: 115
0.70 0.13 0.17
Matches are distributed among these distances:
38 5 0.01
39 111 0.24
40 2 0.00
41 4 0.01
46 4 0.01
47 5 0.01
48 207 0.44
49 63 0.13
50 35 0.07
51 8 0.02
52 27 0.06
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (47 bp):
TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATA
Found at i:524807 original size:87 final size:87
Alignment explanation
Indices: 524656--525004 Score: 542
Period size: 87 Copynumber: 4.0 Consensus size: 87
524646 AAAGATGAAA
* * * *
524656 ATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAACATGCCGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATT
* *
524721 CAAAGCCAGTGATATTAGGCTT
66 CAAAGCCAGCGATATTGGGCTT
*
524743 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGATAAGGTGCCAACATGTCGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATT
524808 CAAAGCCAGCGATATTGGGCTT
66 CAAAGCCAGCGATATTGGGCTT
524830 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATT
524895 CAAAGCCAGCGATATTGGGCTT
66 CAAAGCCAGCGATATTGGGCTT
* *
524917 ATGCCAATGTGCTTATTCAAGGCCAGCAACATTGG-TTTAAAGATGAAGGTGCC-A-ATGTGCTG
1 ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGA-CAAGGTGCCAACATGT-C-G
* * *
524979 ATTCAAGGCCAGCGACATTGGTCTT
63 ATTCAAAGCCAGCGATATTGGGCTT
525004 A
1 A
525005 AAGACAAAGT
Statistics
Matches: 246, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
85 4 0.02
86 10 0.04
87 232 0.94
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (87 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATT
CAAAGCCAGCGATATTGGGCTT
Found at i:524998 original size:135 final size:135
Alignment explanation
Indices: 524831--525183 Score: 496
Period size: 135 Copynumber: 2.6 Consensus size: 135
524821 ATTGGGCTTA
* *
524831 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTTTAAAGACAAGGTGCCAACATGTCGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCCAATATGTCGATTC
*
524896 AAAGCCAGCGATATTGGGCTTATGCCAATGTGCTTATTCAAGGCCAGCAACATTGGTT-TAAAGA
66 AAAGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAGA
* *
524960 TGAAGG
131 -CAAAG
* *
524966 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGTGCCAATATG-CTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCCAATATGTC-GATT
* *
525030 CAAAGCCAGTGATATTGGGCTTATGCCGATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAG
65 CAAAGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAG
525095 ACAAAG
130 ACAAAG
* * * * * *
525101 TGTCAGTATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGCCAATATGCTTG-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTTTTAAAGA-CAAGGTGCCAATATG-TCGA
*
525165 TTCAAGGCCAGCGATATTG
63 TTCAAAGCCAGCGATATTG
525184 AACTTAGAAG
Statistics
Matches: 193, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
134 1 0.01
135 145 0.75
136 16 0.08
137 30 0.16
138 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (135 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCCAATATGTCGATTC
AAAGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAGA
CAAAG
Found at i:525069 original size:87 final size:87
Alignment explanation
Indices: 524966--525135 Score: 270
Period size: 87 Copynumber: 2.0 Consensus size: 87
524956 AAGATGAAGG
*
524966 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT-TAAAGACAAAGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGT-TATAAAGACAAAGTGCCAATATGCTGATT
*
525030 CAAAGCCAGTGATATTGGGCTTA
65 CAAAGCCAGCGATATTGGGCTTA
* * *
525053 TGCCGATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAGACAAAGTGTCAGTATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAGACAAAGTGCCAATATGCTGATTC
*
525118 AAGGCCAGCGATATTGGG
66 AAAGCCAGCGATATTGGG
525136 TTTTAAAGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 1 0.01
87 75 0.99
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTTATAAAGACAAAGTGCCAATATGCTGATTC
AAAGCCAGCGATATTGGGCTTA
Found at i:525174 original size:50 final size:49
Alignment explanation
Indices: 525061--525183 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 49
525051 TATGCCGATG
* * * *
525061 TGCTGATTCAAGGCCAGCAACATT-GGTTATAAAGACAAAGTGTCAGTA
1 TGCTGATTCAAGGCCAGCGATATTGGGTTATAAAGACAAAGTGCCAATA
* *
525109 TGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGGTTATAAAGACAAA-GTGCCAATA
525159 TGCTTG-TTCAAGGCCAGCGATATTG
1 TGC-TGATTCAAGGCCAGCGATATTG
525184 AACTTAGAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
48 22 0.33
49 13 0.20
50 29 0.44
51 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCGATATTGGGTTATAAAGACAAAGTGCCAATA
Found at i:525383 original size:29 final size:28
Alignment explanation
Indices: 525237--525539 Score: 308
Period size: 28 Copynumber: 10.7 Consensus size: 28
525227 GGTTGTATTA
* * * *
525237 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTGGAAAGATGCCACTG
* * *
525265 ACTTATGGGCTTT-GAAAGAATACCACTA
1 ACTTGTGGGCTTTGGAAAG-ATGCCACTG
* *
525293 ACTTGTGGGC-TT-GAAAGGGGTGCCGCTG
1 ACTTGTGGGCTTTGGAAA--GATGCCACTG
** *
525321 ACTTGTGCACTTTTG-AAGATTGCCACTG
1 ACTTGTGGGCTTTGGAAAGA-TGCCACTG
*
525349 ACTTGTGGGCTTTGGAAAAGATGCCACTA
1 ACTTGTGGGCTTTGG-AAAGATGCCACTG
* * * * *
525378 ACTTGTAGCCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTGGAAAGATGCCACTG
525406 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGG-AAAGATGCCACTG
525435 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGG-AAAGATGCCACTG
* * *
525464 ACTTGTGGGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTGGAAAGATGCCACTG
525492 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGG-AAAGATGCCACTG
*
525521 ACTTGTGGGCTTTGTAAAG
1 ACTTGTGGGCTTTGGAAAG
525540 GTGAGGAATG
Statistics
Matches: 228, Mismatches: 37, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
27 11 0.05
28 109 0.48
29 103 0.45
30 5 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (28 bp):
ACTTGTGGGCTTTGGAAAGATGCCACTG
Found at i:525391 original size:57 final size:57
Alignment explanation
Indices: 525257--525534 Score: 298
Period size: 57 Copynumber: 4.9 Consensus size: 57
525247 TTTTGAAGGT
* * * * * *
525257 TGCCACTGACTTATGGGCTTT-GAAAGAATACCACTAACTTGTGGGC-TT-GAAAGGGG
1 TGCCACTGACTTGTGGCCTTTGGAAAG-ATGCCACTGACTTGTGGGCTTTGGAAA-AGA
* *
525313 TGCCGCTGACTTGT-GCACTTTTG-AAGATTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGC-CTTTGGAAAGA-TGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * * *
525370 TGCCACTAACTTGTAGCCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGCCTTTGGAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * *
525427 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGCCTTTGG-AAAGATGCCACTGACTTGTGGGCTTTGGAAAAGA
*
525484 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTG
1 TGCCACTGACTTGTGGCCTTTGG-AAAGATGCCACTGACTTGTGGGCTTTG
525535 TAAAGGTGAG
Statistics
Matches: 193, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.01
56 35 0.18
57 123 0.64
58 33 0.17
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (57 bp):
TGCCACTGACTTGTGGCCTTTGGAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:525443 original size:86 final size:86
Alignment explanation
Indices: 525257--525534 Score: 388
Period size: 86 Copynumber: 3.3 Consensus size: 86
525247 TTTTGAAGGT
* * * *
525257 TGCCACTGACTTATGGGCTTT-G-AAAGAATACCACTAACTTGTGGGC--TTGAAAGGGGTGCCG
1 TGCCACTGACTTGTGGGCTTTGGAAAAG-ATGCCACTAACTTGTGGGCTTTTG-AA-GGTTGCCA
** *
525318 CTGACTTGTGCACTTTTG--AAGA
63 CTGACTTGTGGGCTTTGGAAAAGA
* *
525340 TTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTAGCCTTTTGAAGGTTGCCACT
1 -TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACT
525405 GACTTGTGGGCTTTGGAAAAGA
65 GACTTGTGGGCTTTGGAAAAGA
*
525427 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTG
525492 ACTTGTGGGCTTTGGAAAAGA
66 ACTTGTGGGCTTTGGAAAAGA
525513 TGCCACTGACTTGTGGGCTTTG
1 TGCCACTGACTTGTGGGCTTTG
525535 TAAAGGTGAG
Statistics
Matches: 176, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
84 20 0.11
85 38 0.22
86 111 0.63
87 7 0.04
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (86 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTG
ACTTGTGGGCTTTGGAAAAGA
Found at i:526980 original size:1 final size:1
Alignment explanation
Indices: 526976--527148 Score: 85
Period size: 1 Copynumber: 173.0 Consensus size: 1
526966 CTTTTTGTTG
* * * * * * * * *
526976 TTTTTTTTTTCTTTTTTTATTTTTTTCTGTTTTGTTTGTTTTTTTTGTTTGTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * * * *
527041 CTTTTTTGTTTGTTTGTTTGTTTTTTTCTTCTTTTTTTTCTTTTTTCTTCTTTTTCTTTGTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
527106 TTGTTTTTTTCTTCTTTTTTTCTTCTTTATTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
527149 GCGGAGGACG
Statistics
Matches: 114, Mismatches: 58, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 114 1.00
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (1 bp):
T
Found at i:526990 original size:8 final size:8
Alignment explanation
Indices: 526979--527145 Score: 96
Period size: 8 Copynumber: 20.9 Consensus size: 8
526969 TTTGTTGTTT
526979 TTTTTTTC
1 TTTTTTTC
*
526987 TTTTTTTA
1 TTTTTTTC
526995 TTTTTTTC
1 TTTTTTTC
527003 TGTTTTGTT-
1 T-TTTT-TTC
*
527012 TGTTTTT-
1 TTTTTTTC
* *
527019 TTTGTTTG
1 TTTTTTTC
527027 TTTTTTT-
1 TTTTTTTC
*
527034 TATTTTTC
1 TTTTTTTC
*
527042 -TTTTTTG
1 TTTTTTTC
* *
527049 TTTGTTTG
1 TTTTTTTC
*
527057 TTTGTTT-
1 TTTTTTTC
*
527064 TTTTCTTC
1 TTTTTTTC
527072 TTTTTTT-
1 TTTTTTTC
527079 TCTTTTTTC
1 T-TTTTTTC
527088 TTCTTTTTC
1 TT-TTTTTC
* *
527097 TTTGTTTG
1 TTTTTTTC
*
527105 TTTGTTT-
1 TTTTTTTC
*
527112 TTTTCTTC
1 TTTTTTTC
527120 TTTTTTTC
1 TTTTTTTC
527128 TTCTTTATTTC
1 -T-TTT-TTTC
527139 TTTTTTT
1 TTTTTTT
527146 TTTGCGGAGG
Statistics
Matches: 128, Mismatches: 18, Indels: 26
0.74 0.10 0.15
Matches are distributed among these distances:
7 29 0.23
8 71 0.55
9 18 0.14
10 6 0.05
11 4 0.03
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:527024 original size:47 final size:47
Alignment explanation
Indices: 526976--527145 Score: 195
Period size: 47 Copynumber: 3.6 Consensus size: 47
526966 CTTTTTGTTG
*
526976 TTTTTTTTTTCTTTTTTTATTTTTTTCTGTTTTGTTTGTTTTTTT-T
1 TTTTTTTTTTCTTTTTTTCTTTTTTTCTGTTTTGTTTGTTTTTTTCT
* *
527022 GTTTGTTTTTTT-TATTTTTCTTTTTTGTTTG-TTTGTTTGTTTTTTTCT
1 -TTT-TTTTTTTCTTTTTTTCTTTTTT-TCTGTTTTGTTTGTTTTTTTCT
* *
527070 TCTTTTTTTTC-TTTTTTCTTCTTTTTCTTTGTTTGTTTGTTTTTTTCT
1 TTTTTTTTTTCTTTTTTTCTT-TTTTTCTGT-TTTGTTTGTTTTTTTCT
*
527118 TCTTTTTTTCTTCTTTATTTCTTTTTTT
1 T-TTTTTTT-TTCTTTTTTTCTTTTTTT
527146 TTTGCGGAGG
Statistics
Matches: 104, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
46 17 0.16
47 36 0.35
48 29 0.28
49 6 0.06
50 8 0.08
51 8 0.08
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (47 bp):
TTTTTTTTTTCTTTTTTTCTTTTTTTCTGTTTTGTTTGTTTTTTTCT
Found at i:527031 original size:39 final size:37
Alignment explanation
Indices: 526967--527125 Score: 155
Period size: 39 Copynumber: 4.1 Consensus size: 37
526957 ATCCGGACCC
526967 TTTTTG-TTGTTTTTTTT-TTCTTTTTTTATTTTTTTCT
1 TTTTTGTTTGTTTTTTTTGTT-TTTTTTT-TTTTTTTCT
*
527004 GTTTTGTTTGTTTTTTTTGTTTGTTTTTTTTATTTTTCT
1 TTTTTGTTTGTTTTTTTTGTTT-TTTTTTTT-TTTTTCT
*
527043 TTTTTGTTTGTTTGTTTGTT-TTTTTCTTCTTTTTTTTCT
1 TTTTTGTTTGTTT-TTT-TTGTTTTT-TTTTTTTTTTTCT
* * *
527082 TTTTTCTTCT-TTTTCTTTGTTTGTTTGTTTTTTTCTTCT
1 TTTTTGTT-TGTTTTTTTTGTTT-TTT-TTTTTTTTTTCT
527121 TTTTT
1 TTTTT
527126 TCTTCTTTAT
Statistics
Matches: 104, Mismatches: 7, Indels: 20
0.79 0.05 0.15
Matches are distributed among these distances:
37 7 0.07
38 20 0.19
39 63 0.61
40 12 0.12
41 2 0.02
ACGTcount: A:0.01, C:0.07, G:0.09, T:0.83
Consensus pattern (37 bp):
TTTTTGTTTGTTTTTTTTGTTTTTTTTTTTTTTTTCT
Found at i:527040 original size:48 final size:45
Alignment explanation
Indices: 526967--527146 Score: 152
Period size: 48 Copynumber: 3.7 Consensus size: 45
526957 ATCCGGACCC
*
526967 TTTTTGTTGTTTTTTTTTTCTTTTTTTATTTTTTTCTGTTTTGTTTG
1 TTTTTTTTGTTTTTTTTTT-TTTTTTT-TTTTTTTCTGTTTTGTTTG
527014 TTTTTTTTGTTTGTTTTTTTTATTTTTCTTTTTTGTT-TG-TTTGTTTG
1 TTTTTTTTGTTT-TTTTTTTT-TTTTT-TTTTTT-TTCTGTTTTGTTTG
* * *
527061 TTTTTTTCT-TCTTTTTTTTCTTTTTTCTTCTTTTTCTTTGTTTGTTTG
1 TTTTTTT-TGT-TTTTTTTT-TTTTTTTTTTTTTTTCTGT-TTTGTTTG
527109 TTTTTTTCT-TCTTTTTTTCTTCTTTATTTCTTTTTTTT
1 TTTTTTT-TGT-TTTTTTT-TT-TTT-TTT-TTTTTTTT
527147 TTGCGGAGGA
Statistics
Matches: 113, Mismatches: 6, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
45 2 0.02
46 6 0.05
47 38 0.34
48 51 0.45
49 7 0.06
50 2 0.02
51 7 0.06
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.83
Consensus pattern (45 bp):
TTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTCTGTTTTGTTTG
Found at i:527143 original size:78 final size:78
Alignment explanation
Indices: 526995--527145 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 78
526985 TCTTTTTTTA
* * * *
526995 TTTTTTTCTGTTTTGTTTGTTTTTTTTGTTTGTTTTTTTTATTTTTCTTTTTTGTTTGTTTGTTT
1 TTTTTTTCTGTTTTGTTTCTTTTTTTTGTTTGTTTTTTTTATTCTTCTTTTTTGTTTCTTTATTT
*
527060 GTTTTTTTCTTCT
66 CTTTTTTTCTTCT
527073 TTTTTTTCT-TTTT-TCTTCTTTTTCTTTGTTTGTTTGTTTTT-TTCTTCTTTTTT-TCTTCTTT
1 TTTTTTTCTGTTTTGT-TTCTTTTT-TTTGTTTGTTT-TTTTTATTCTTCTTTTTTGT-TTCTTT
527134 ATTTCTTTTTTT
62 ATTTCTTTTTTT
527146 TTTGCGGAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
76 1 0.02
77 12 0.19
78 46 0.72
79 5 0.08
ACGTcount: A:0.01, C:0.09, G:0.08, T:0.82
Consensus pattern (78 bp):
TTTTTTTCTGTTTTGTTTCTTTTTTTTGTTTGTTTTTTTTATTCTTCTTTTTTGTTTCTTTATTT
CTTTTTTTCTTCT
Found at i:539102 original size:13 final size:13
Alignment explanation
Indices: 539084--539108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
539074 CAAAGATCAG
539084 TGTATCGATACAA
1 TGTATCGATACAA
539097 TGTATCGATACA
1 TGTATCGATACA
539109 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:544546 original size:32 final size:32
Alignment explanation
Indices: 544503--544573 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
544493 AGCTTCGTAG
544503 CGATACATTGTATCAATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
* *
544535 CGATACGTTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCAATACAACACTTATGTAT
544567 CGATACA
1 CGATACA
544574 GTTACTTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCAATACAACACTTATGTAT
Found at i:544567 original size:19 final size:19
Alignment explanation
Indices: 544511--544573 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
544501 AGCGATACAT
*
544511 TGTATCAATACAACACTTA
1 TGTATCGATACAACACTTA
*
544530 TGTATCGAT-----ACGT-
1 TGTATCGATACAACACTTA
544543 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
544562 TGTATCGATACA
1 TGTATCGATACA
544574 GTTACTTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
18 3 0.09
19 20 0.57
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:551548 original size:19 final size:19
Alignment explanation
Indices: 551524--551563 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
551514 GCTATGTATG
551524 AGCTAGGGAGGAAGTGTTT
1 AGCTAGGGAGGAAGTGTTT
551543 AGCTAGGGAGGAAGTGTTT
1 AGCTAGGGAGGAAGTGTTT
551562 AG
1 AG
551564 AGGTGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.42, T:0.25
Consensus pattern (19 bp):
AGCTAGGGAGGAAGTGTTT
Found at i:552081 original size:20 final size:20
Alignment explanation
Indices: 552056--552112 Score: 87
Period size: 22 Copynumber: 2.8 Consensus size: 20
552046 TTTGCCTTGC
*
552056 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAAGA
552076 ATGTATCGATACAATTTGAAGA
1 ATGTATCGATAC-A-TTGAAGA
552098 ATGTATCGATACATT
1 ATGTATCGATACATT
552113 TTTGTTAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 14 0.41
21 2 0.06
22 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:554160 original size:15 final size:15
Alignment explanation
Indices: 554140--554174 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
554130 AACCATCAAA
554140 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
554155 GATGATGATGATAAT
1 GATGATGAAGATAAT
554170 GATGA
1 GATGA
554175 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:558453 original size:79 final size:80
Alignment explanation
Indices: 558370--558706 Score: 393
Period size: 79 Copynumber: 4.3 Consensus size: 80
558360 AAATAGGGTC
* * * * *
558370 GGAGTACCCCCTCAGAAATAACGGGGTTGGAGTATTCCCAATGGTGAAAAATCGA-TGTTTTAGA
1 GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAGTATTTTAGA
558434 AATAAAATCGAGGTT
66 AATAAAATCGAGGTT
* * *
558449 GGAGTATTCCCTC-GAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAATTC-AGTATTTTAG
1 GGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAGTATTTTAG
558512 AAATAAAATC-ATGGTT
65 AAATAAAATCGA-GGTT
* * * * *
558528 GGAGTATCCCTTCAAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAAT-TAGTTTTTTAGA
1 GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAGTATTTTAGA
*
558592 AATAAAACTGGA-GTT
66 AATAAAA-TCGAGGTT
* * * * * *
558607 AGAGTATCCCCTCAAAAATATCGGGGATGGAGTATCCCCTATTGTGAAAAATTGA-TATTTT-GA
1 GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAGTATTTTAGA
558670 GAATAAAATCGAGGTT
66 -AATAAAATCGAGGTT
*
558686 GGAGTATCCCCTTAGAAATAA
1 GGAGTATCCCCTCAGAAATAA
558707 AAACATGAAT
Statistics
Matches: 219, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
78 8 0.04
79 208 0.95
80 2 0.01
81 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (80 bp):
GGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGAGTATTTTAGA
AATAAAATCGAGGTT
Found at i:561140 original size:20 final size:20
Alignment explanation
Indices: 561117--561168 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
561107 TAAAACTCAG
*
561117 AATGTATTGATAAAATGAAC
1 AATGTATCGATAAAATGAAC
* *
561137 AATGTATCGACACAATGAAC
1 AATGTATCGATAAAATGAAC
561157 AATGTATCGATA
1 AATGTATCGATA
561169 CATCTGGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATAAAATGAAC
Found at i:561180 original size:70 final size:71
Alignment explanation
Indices: 561067--561203 Score: 206
Period size: 70 Copynumber: 1.9 Consensus size: 71
561057 AAAATGCCTG
* * * *
561067 AATGTATCGATACATTGAGAAATGTATCGATACATCTAGGTAAAACTCAGAATGTATTGATA-AA
1 AATGTATCGACACAATGAGAAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATACAA
561131 ATGAAC
66 ATGAAC
*
561137 AATGTATCGACACAATGA-ACAATGTATCGATACATCTGGGTAAAACCCAGAATGTATCGATACA
1 AATGTATCGACACAATGAGA-AATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATACA
561201 AAT
65 AAT
561204 TGTGAAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
69 1 0.02
70 55 0.92
71 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (71 bp):
AATGTATCGACACAATGAGAAATGTATCGATACATCTAGGTAAAACCCAGAATGTATCGATACAA
ATGAAC
Found at i:561631 original size:3 final size:3
Alignment explanation
Indices: 561619--561679 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
561609 CATTCGACTT
561619 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
561666 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
561680 TGGGTAGATT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:562010 original size:41 final size:41
Alignment explanation
Indices: 561926--562025 Score: 139
Period size: 41 Copynumber: 2.4 Consensus size: 41
561916 ATTAAATGTG
* * *
561926 TCCTACTCTTTGAGGATGAAAGAGAAAAGGAAATAAAGTGCA
1 TCCTGCTCTTTGAGGA-CAAAGAGAAAAGGAAATAAAGCGCA
*
561968 TCCTGCTCTTTGAGGACAAAGGGAAAAGGAAA-AGAAGCGCA
1 TCCTGCTCTTTGAGGACAAAGAGAAAAGGAAATA-AAGCGCA
562009 TCCTGCTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
562026 TAGAAGGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.02
41 37 0.70
42 15 0.28
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGACAAAGAGAAAAGGAAATAAAGCGCA
Found at i:562111 original size:61 final size:60
Alignment explanation
Indices: 562009--562623 Score: 716
Period size: 61 Copynumber: 10.2 Consensus size: 60
561999 AAGAAGCGCA
* **
562009 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGTAAGGAGAAAGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGCG
* * * * *
562070 TCCTGCTTTTTGAGGACTAAAAGGTGCCACC-AGTTCATGTGGGCTTTAAAAAGGAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTT-GTGTGGGCTTT-AAAAGGAAAAGCG
* * * * *
562131 TCTTGCTTTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGCG
* * * *
562192 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGTTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-CG
* * *
562253 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAA-TTGTGTGGGCTTTGAAAGG-AAAGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCG
* ** * * *
562311 TCCTGCTCTTTGAGGATTGGAAGGTGCCACCAATTTGTATGGGCTTTAAAAGGAAAATGAG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCG
* * *
562372 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAGG-AAAGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCG
* * * * ** * *
562431 TCCTACTTTTTAAGAACTGGAAGGTTCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCG
* * * *
562492 TCATGCTCTTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCG
* * * *
562553 TCCTACTCTTTGAGAACTAAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCG
562614 TCCTGCTCTT
1 TCCTGCTCTT
562624 CAAAGACTGA
Statistics
Matches: 477, Mismatches: 67, Indels: 20
0.85 0.12 0.04
Matches are distributed among these distances:
58 33 0.07
59 67 0.14
60 39 0.08
61 330 0.69
62 8 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCG
Found at i:563600 original size:17 final size:16
Alignment explanation
Indices: 563578--563647 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 16
563568 AAGCAGGTTA
563578 TTTTCTTTTCTCTTTTT
1 TTTTCTTTTCT-TTTTT
563595 TTTTCTTTT-TTCATTTT
1 TTTTCTTTTCTT--TTTT
*
563612 TTTTGTTGTTCTTTTTT
1 TTTTCTT-TTCTTTTTT
*
563629 GTTTCTTTT-TTTTTT
1 TTTTCTTTTCTTTTTT
563644 TTTT
1 TTTT
563648 TGAAAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
15 10 0.22
16 3 0.07
17 28 0.62
18 2 0.04
19 2 0.04
ACGTcount: A:0.01, C:0.10, G:0.04, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTCTTTTTT
Found at i:563626 original size:13 final size:11
Alignment explanation
Indices: 563588--563649 Score: 60
Period size: 10 Copynumber: 5.8 Consensus size: 11
563578 TTTTCTTTTC
563588 TCTTTTTT-TT
1 TCTTTTTTGTT
**
563598 TCTTTTTTCAT
1 TCTTTTTTGTT
563609 T-TTTTTTGTTGT
1 TCTTTTTTG-T-T
563621 TCTTTTTTGTT
1 TCTTTTTTGTT
563632 TCTTTTTT-TT
1 TCTTTTTTGTT
563642 T-TTTTTTG
1 TCTTTTTTG
563650 AAAAAAAGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
9 6 0.14
10 17 0.39
11 11 0.25
12 3 0.07
13 7 0.16
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.84
Consensus pattern (11 bp):
TCTTTTTTGTT
Found at i:568427 original size:13 final size:13
Alignment explanation
Indices: 568409--568435 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
568399 ACATTATGCT
568409 TTGTATCGATACA
1 TTGTATCGATACA
568422 TTGTATCGATACA
1 TTGTATCGATACA
568435 T
1 T
568436 GATCATTGTA
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):
TTGTATCGATACA
Found at i:568444 original size:19 final size:19
Alignment explanation
Indices: 568420--568476 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
568410 TGTATCGATA
568420 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
*
568439 CATTGTATCGATACATACAT
1 CATTGTATCGATACAT-GAT
*
568459 AATTGTATCGATACATGA
1 CATTGTATCGATACATGA
568477 ATCTGGCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:568450 original size:32 final size:33
Alignment explanation
Indices: 568390--568454 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
568380 TACATTCAGA
* * *
568390 TGTATTGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
568423 TGTATCGATACATGAT-CATTGTATCGATACAT
1 TGTATCGATACATGATGCATTGTATCGATACAT
568455 ACATAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGATGCATTGTATCGATACAT
Found at i:568465 original size:20 final size:19
Alignment explanation
Indices: 568421--568474 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
568411 GTATCGATAC
* *
568421 ATTGTATCGATACATGATC
1 ATTGTATCGATACATCATA
568440 ATTGTATCGATACATACATA
1 ATTGTATCGATACAT-CATA
568460 ATTGTATCGATACAT
1 ATTGTATCGATACAT
568475 GAATCTGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (19 bp):
ATTGTATCGATACATCATA
Found at i:572520 original size:36 final size:38
Alignment explanation
Indices: 572478--572579 Score: 172
Period size: 38 Copynumber: 2.7 Consensus size: 38
572468 TTTAAATGTT
572478 ATTTAAATGTTAATTTCTAAAAATTTTAG-TTAC-AAA
1 ATTTAAATGTTAATTTCTAAAAATTTTAGTTTACAAAA
*
572514 ATTTAAATGTTAATTTCTAAAAATTTTTGTTTACAAAA
1 ATTTAAATGTTAATTTCTAAAAATTTTAGTTTACAAAA
*
572552 ATTCAAATGTTAATTTCTAAAAATTTTA
1 ATTTAAATGTTAATTTCTAAAAATTTTA
572580 ATGAGGCCAC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 28 0.46
37 4 0.07
38 29 0.48
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (38 bp):
ATTTAAATGTTAATTTCTAAAAATTTTAGTTTACAAAA
Found at i:572536 original size:22 final size:22
Alignment explanation
Indices: 572511--572582 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
572501 TTTTAGTTAC
572511 AAAATTTAAATGTTAATTTCTA
1 AAAATTTAAATGTTAATTTCTA
* *
572533 AAAATTT--TTG-T--TTAC-A
1 AAAATTTAAATGTTAATTTCTA
*
572549 AAAATTCAAATGTTAATTTCTA
1 AAAATTTAAATGTTAATTTCTA
*
572571 AAAATTTTAATG
1 AAAATTTAAATG
572583 AGGCCACATG
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
16 7 0.19
17 3 0.08
18 2 0.05
19 2 0.05
20 2 0.05
21 3 0.08
22 18 0.49
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (22 bp):
AAAATTTAAATGTTAATTTCTA
Found at i:572954 original size:32 final size:33
Alignment explanation
Indices: 572894--572955 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
572884 CTTTCAGATG
* *
572894 TATCGATACATTATGCTTTGTATTGATACAATT
1 TATCGATACATTATGCATTGTATCGATACAATT
572927 TATCGATACATGT-T-CATTGTATCGATACA
1 TATCGATACAT-TATGCATTGTATCGATACA
572956 TGAACAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.50
33 12 0.46
34 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATACAATT
Found at i:582278 original size:21 final size:21
Alignment explanation
Indices: 582254--582297 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
582244 ATAGTAATTC
*
582254 TTTTAGTTAATGTTATATTTT
1 TTTTAGCTAATGTTATATTTT
* * *
582275 TTTTTGCTAATGTTTTGTTTT
1 TTTTAGCTAATGTTATATTTT
582296 TT
1 TT
582298 CAACACAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.02, G:0.11, T:0.70
Consensus pattern (21 bp):
TTTTAGCTAATGTTATATTTT
Found at i:583046 original size:16 final size:18
Alignment explanation
Indices: 583025--583058 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
583015 AAATTCATCA
583025 ATCAA-TTTA-TTAAAAT
1 ATCAATTTTATTTAAAAT
583041 ATCAATTTTATTTAAAAT
1 ATCAATTTTATTTAAAAT
583059 TATAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCAATTTTATTTAAAAT
Found at i:583220 original size:2 final size:2
Alignment explanation
Indices: 583208--583252 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
583198 CATAAACAAC
583208 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
583249 AT AT
1 AT AT
583253 GTAAATGGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:584074 original size:16 final size:17
Alignment explanation
Indices: 584043--584074 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
584033 TACATGTATC
584043 GTTAAATACTTTGAATG
1 GTTAAATACTTTGAATG
584060 GTTAAATAC-TTGAAT
1 GTTAAATACTTTGAAT
584075 ATGAGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (17 bp):
GTTAAATACTTTGAATG
Found at i:586287 original size:92 final size:92
Alignment explanation
Indices: 586115--586295 Score: 202
Period size: 92 Copynumber: 2.0 Consensus size: 92
586105 ATGGTTGTTA
* * * * * *
586115 TTGTAATTCAATGAGATTTCAAATTTACAATATATTTAGTTTATTATAATAGTTATTTATTTAAA
1 TTGTAATTCAATGAGACTTCAAATTTACAACATATCTAGTTCATTATAATAGCTATTTAATTAAA
* * *
586180 AGTTGATTTAGTACATTATTGTGACTT
66 AGTTGATATAATACATTATAGTGACTT
* *** * * *
586207 TTGTAATTTAATGAGACTTCAAATTTATTGCATGTCTAGTTCATTGTAATAGCTATTTAATTACA
1 TTGTAATTCAATGAGACTTCAAATTTACAACATATCTAGTTCATTATAATAGCTATTTAATTAAA
586272 AGTT-AGTATAATACATTATAGTGA
66 AGTTGA-TATAATACATTATAGTGA
586296 TGCATTTGTT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
91 1 0.01
92 71 0.99
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (92 bp):
TTGTAATTCAATGAGACTTCAAATTTACAACATATCTAGTTCATTATAATAGCTATTTAATTAAA
AGTTGATATAATACATTATAGTGACTT
Found at i:587244 original size:20 final size:21
Alignment explanation
Indices: 587221--587260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
587211 AAGATTGAAT
587221 AAAATCG-AAA-AAGATTTTGA
1 AAAATCGTAAACAAG-TTTTGA
587241 AAAATCGTAAACAAGTTTTG
1 AAAATCGTAAACAAGTTTTG
587261 TTCGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 8 0.44
22 3 0.17
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAATCGTAAACAAGTTTTGA
Found at i:587567 original size:20 final size:19
Alignment explanation
Indices: 587502--587577 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
587492 TTGTATCGAT
* * *
587502 ACATTGTATCAATTCATGT
1 ACATTGTATCGATACATGC
* *
587521 TCATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
587540 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
587559 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
587578 AAACTGGCAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 35 0.69
20 16 0.31
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:593820 original size:13 final size:13
Alignment explanation
Indices: 593802--593841 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
593792 ACAATATTCT
593802 TTGTATCGATACA
1 TTGTATCGATACA
*
593815 TTGTATTGATACA
1 TTGTATCGATACA
*
593828 ATGTATCGATACA
1 TTGTATCGATACA
593841 T
1 T
593842 AGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:595720 original size:30 final size:33
Alignment explanation
Indices: 595658--595733 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 33
595648 CTATAACAAA
595658 AAGGGGGAGAAATGTTTGAAAATAAATTTTTATC
1 AAGGGGGAGAAATGTTT-AAAATAAATTTTTATC
* *
595692 AAGGGGGAGAAAT-TTT-TAATTAA-TTTTATC
1 AAGGGGGAGAAATGTTTAAAATAAATTTTTATC
595722 AAGGGGGAGAAA
1 AAGGGGGAGAAA
595734 AATGAAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 19 0.47
31 5 0.12
33 3 0.08
34 13 0.32
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (33 bp):
AAGGGGGAGAAATGTTTAAAATAAATTTTTATC
Found at i:596288 original size:13 final size:13
Alignment explanation
Indices: 596270--596296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
596260 GCATTATGCT
596270 TTGTATCGATACA
1 TTGTATCGATACA
596283 TTGTATCGATACA
1 TTGTATCGATACA
596296 T
1 T
596297 GTTCATTGTA
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):
TTGTATCGATACA
Found at i:596326 original size:20 final size:19
Alignment explanation
Indices: 596280--596332 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
596270 TTGTATCGAT
* *
596280 ACATTGTATCGATACATGT
1 ACATTGTATCAATACATGC
*
596299 TCATTGTATCAATACATGC
1 ACATTGTATCAATACATGC
596318 ACAATTGTATCAATA
1 AC-ATTGTATCAATA
596333 TATAAAACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
ACATTGTATCAATACATGC
Found at i:605365 original size:155 final size:155
Alignment explanation
Indices: 605059--605345 Score: 389
Period size: 155 Copynumber: 1.9 Consensus size: 155
605049 ACTATTTTGT
* * *
605059 AATTTTAAAAAGTTTAGGGGCTAAATTATAAAAAGTTCAAACTTTTTTTTTTTGTATATCCTTGC
1 AATTTTAAAAAGTTTAGGGACTAAATTATAAAAAGTTCAAACTTTTTTTTTTGGGATATCCTTGC
* * * * *
605124 TTAGCCAAGAGTCCCTACTACTATAAGTTGACTATTTCATGCATTTCTAAACATATTTTAGGCCT
66 TTAGCCAAGAGTCCCTACCACCATAAGTGGACTACTTCATGCATTACTAAACATATTTTAGGCCT
* *
605189 TTAGCATGTTAGAGACCTTTTTGCG
131 TTAACATATTAGAGACCTTTTTGCG
* *
605214 AATTTTAAAAAGTTTAGGGACTAAATTATAAGAAGTTTTAAA-TTTTTTTGTTTGGGA-ATCCTT
1 AATTTTAAAAAGTTTAGGGACTAAATTATAAAAAG-TTCAAACTTTTTTT-TTTGGGATATCCTT
** ** *
605277 GCTTAGCTGAGAGTCCCTACCACCATCGGTGGACTACTTCATGCATTACTAAACATATTTTAGGT
64 GCTTAGCCAAGAGTCCCTACCACCATAAGTGGACTACTTCATGCATTACTAAACATATTTTAGGC
605342 CTTT
129 CTTT
605346 TAATTTATTA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
155 105 0.91
156 10 0.09
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (155 bp):
AATTTTAAAAAGTTTAGGGACTAAATTATAAAAAGTTCAAACTTTTTTTTTTGGGATATCCTTGC
TTAGCCAAGAGTCCCTACCACCATAAGTGGACTACTTCATGCATTACTAAACATATTTTAGGCCT
TTAACATATTAGAGACCTTTTTGCG
Found at i:609846 original size:160 final size:162
Alignment explanation
Indices: 609674--610126 Score: 712
Period size: 162 Copynumber: 2.8 Consensus size: 162
609664 TTAATTCAAT
* * * *
609674 TTAATTTTATTTATTTTTGAAAATACCATTTTGTATCCTAATGGAAGCCTAAAAGAATGCAAAAG
1 TTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGCCTAAAAGAATACAAAAG
* *
609739 GTTTTTGAAATCTTTTATACCCCTATGGATGCCCATAGGAATATAAAAGATTAG-AAAAATAAAT
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
* *
609803 ACTAGTATTTATC-CAATAATACCAATTTAAG
131 ACTAGAATTTATCACAACAATACCAATTTAAG
* * * **
609834 TTAATTTTATTTATTTTTGAAAATATCGTTTCGTACCCTAATGAAAGCCTGAAAGAATATGAAAG
1 TTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGCCTAAAAGAATACAAAAG
609899 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
* *
609964 ATTAGAATTTATCAGAACAATACCAATTTAAG
131 ACTAGAATTTATCACAACAATACCAATTTAAG
* * *
609996 TTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAACCCAAAAGGATACAAAAG
1 TTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGCCTAAAAGAATACAAAAG
* *
610061 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCAGAGGAAAATAAAAGATTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
610126 A
131 A
610127 TTGTTTAATT
Statistics
Matches: 266, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
160 108 0.41
161 21 0.08
162 137 0.52
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (162 bp):
TTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGCCTAAAAGAATACAAAAG
GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
ACTAGAATTTATCACAACAATACCAATTTAAG
Found at i:611074 original size:31 final size:31
Alignment explanation
Indices: 611030--611090 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
611020 ACTAGCTTTG
611030 TTTTTCTA-ATTTTTCTACT-TATTTCTTTCTA
1 TTTTTCTATATTTTTCT-CTCTATTT-TTTCTA
* *
611061 TTTTTCTCTTTTTTTCTCTCTATTTTTTCT
1 TTTTTCTATATTTTTCTCTCTATTTTTTCT
611091 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTTCTATATTTTTCTCTCTATTTTTTCTA
Found at i:611088 original size:13 final size:12
Alignment explanation
Indices: 611061--611101 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
611051 TTTCTTTCTA
611061 TTTT-TCTCTTT
1 TTTTCTCTCTTT
611072 TTTTCTCTCTATT
1 TTTTCTCTCT-TT
611085 TTTTCTCTCTTT
1 TTTTCTCTCTTT
611097 TTTTC
1 TTTTC
611102 AACTGGACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.14
12 12 0.43
13 12 0.43
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTCTCTTT
Found at i:611091 original size:23 final size:22
Alignment explanation
Indices: 611038--611099 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
611028 TGTTTTTCTA
* *
611038 ATTTTTCTAC-TTATTTCTTTCT
1 ATTTTTCT-CTTTTTTTCTCTCT
611060 ATTTTTCTCTTTTTTTCTCTCT
1 ATTTTTCTCTTTTTTTCTCTCT
611082 ATTTTTTCTCTCTTTTTT
1 A-TTTTTCTCT-TTTTTT
611100 TCAACTGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 9 0.26
24 6 0.17
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (22 bp):
ATTTTTCTCTTTTTTTCTCTCT
Found at i:612898 original size:41 final size:40
Alignment explanation
Indices: 612853--612935 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
612843 ATGTTTTGAA
* *
612853 AAGATAGTGTAATTATAAATGCCAAATGTTATTGGGTTTAC
1 AAGATAGTGTAATGA-AAATGCCAAATGTTATTAGGTTTAC
* *
612894 AAGATAGTGTGATGACAATGCCAAATGTTATTAGGTTTAC
1 AAGATAGTGTAATGAAAATGCCAAATGTTATTAGGTTTAC
612934 AA
1 AA
612936 TATTTTATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
40 25 0.66
41 13 0.34
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (40 bp):
AAGATAGTGTAATGAAAATGCCAAATGTTATTAGGTTTAC
Found at i:612962 original size:38 final size:38
Alignment explanation
Indices: 612867--612964 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 38
612857 TAGTGTAATT
* *
612867 ATAAATGCCAAATGTTATTGGGTTTACAAGATAGTGTG
1 ATAAATGCCAAATGTTATTAGGTTTACAAGATAGTATG
* **
612905 ATGACAATGCCAAATGTTATTAGGTTTACAATATTTTATG
1 AT-A-AATGCCAAATGTTATTAGGTTTACAAGATAGTATG
* *
612945 CTAAATGCCAAAGGTTATTA
1 ATAAATGCCAAATGTTATTA
612965 AGTTCAGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
38 18 0.35
39 2 0.04
40 31 0.61
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (38 bp):
ATAAATGCCAAATGTTATTAGGTTTACAAGATAGTATG
Found at i:613868 original size:59 final size:59
Alignment explanation
Indices: 613773--613940 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 59
613763 TAGCTATTTA
* * * * * *
613773 AGGAGGTTAAGCCATATAGATACCTACTTTTG-GAGGTTAAGCCTTATAGATAGCTG-TG
1 AGGAGGTTAAGCCTTATAGATACTTGC-TTAGAGAGGTTAAGCCTTATAAATACCTGTTG
*
613831 AGAGAGGTTAAGCCTTATAGATACTTGCTTAGAGAGGTTAAG-CTCTATAAATACCTGTTT
1 AG-GAGGTTAAGCCTTATAGATACTTGCTTAGAGAGGTTAAGCCT-TATAAATACCTGTTG
* * * *
613891 AGGAGATTAAGCCTTATAAACACTTGTTTA-AGGAGGTTAAGCCTTATAAA
1 AGGAGGTTAAGCCTTATAGATACTTGCTTAGA-GAGGTTAAGCCTTATAAA
613941 GAAAGAAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
58 8 0.09
59 80 0.86
60 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32
Consensus pattern (59 bp):
AGGAGGTTAAGCCTTATAGATACTTGCTTAGAGAGGTTAAGCCTTATAAATACCTGTTG
Found at i:613939 original size:30 final size:29
Alignment explanation
Indices: 613773--613940 Score: 153
Period size: 30 Copynumber: 5.7 Consensus size: 29
613763 TAGCTATTTA
* * **
613773 AGGAGGTTAAGCCATATAGATACCTACTTT
1 AGGAGGTTAAGCCTTATAAATA-CTTGTTT
* * *
613803 TGGAGGTTAAGCCTTATAGATAGC-TG-TG
1 AGGAGGTTAAGCCTTATAAATA-CTTGTTT
* *
613831 AGAGAGGTTAAGCCTTATAGATACTTGCTT
1 AG-GAGGTTAAGCCTTATAAATACTTGTTT
*
613861 AGAGAGGTTAAG-CTCTATAAATACCTGTTT
1 AG-GAGGTTAAGCCT-TATAAATACTTGTTT
* *
613891 AGGAGATTAAGCCTTATAAACACTTGTTT
1 AGGAGGTTAAGCCTTATAAATACTTGTTT
613920 AAGGAGGTTAAGCCTTATAAA
1 -AGGAGGTTAAGCCTTATAAA
613941 GAAAGAAAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
28 3 0.03
29 45 0.38
30 69 0.59
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32
Consensus pattern (29 bp):
AGGAGGTTAAGCCTTATAAATACTTGTTT
Found at i:614323 original size:42 final size:42
Alignment explanation
Indices: 614235--614335 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
614225 CGTAGAGAGG
* * * * *
614235 TTAAACCTTAGAAAAAGCCTTATAAACATTTGCCTAGGTAGG
1 TTAAGCCTTAGGAAAAGCCTTATAAAAACTTGCCTAGGTAGA
**
614277 TTAAGCCTTAGGAAAAGCCTTATAAAAACTTGGTTAAGG-AGA
1 TTAAGCCTTAGGAAAAGCCTTATAAAAACTTGCCT-AGGTAGA
* *
614319 TTAAGACTTAAGAAAAG
1 TTAAGCCTTAGGAAAAG
614336 GCCAGTTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 46 0.94
43 3 0.06
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.27
Consensus pattern (42 bp):
TTAAGCCTTAGGAAAAGCCTTATAAAAACTTGCCTAGGTAGA
Found at i:615971 original size:13 final size:13
Alignment explanation
Indices: 615953--615980 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
615943 TGCCATAAAA
615953 GATGAAATTAAGT
1 GATGAAATTAAGT
615966 GATGAAATTAAGT
1 GATGAAATTAAGT
615979 GA
1 GA
615981 CTTAGGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (13 bp):
GATGAAATTAAGT
Found at i:617996 original size:13 final size:13
Alignment explanation
Indices: 617978--618002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617968 CATTTTATGG
617978 TGTATCGATACAA
1 TGTATCGATACAA
617991 TGTATCGATACA
1 TGTATCGATACA
618003 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:620567 original size:13 final size:13
Alignment explanation
Indices: 620549--620587 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
620539 ATAATCCCCC
*
620549 TGTATCGATACAG
1 TGTATCGATACAA
620562 TGTATCGATACAA
1 TGTATCGATACAA
*
620575 TGTATCGCTACAA
1 TGTATCGATACAA
620588 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:624578 original size:16 final size:17
Alignment explanation
Indices: 624554--624587 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
624544 CTTGCAATTC
624554 ATTTATTTTCTTT-TTA
1 ATTTATTTTCTTTCTTA
*
624570 ATTTTTTTTCTTTCTTA
1 ATTTATTTTCTTTCTTA
624587 A
1 A
624588 GCGCGTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTATTTTCTTTCTTA
Found at i:634028 original size:154 final size:152
Alignment explanation
Indices: 633513--634203 Score: 692
Period size: 149 Copynumber: 4.6 Consensus size: 152
633503 GTTGTTTCAC
* * * * *
633513 AGGACTAGGTTTTGGAG-AAAATGCTTAAAGGTCCCTAAGGTCTACCA-TCACTTAAAAGTGCTC
1 AGGACTAGGTTTAGGAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGCTC
* * * * * *
633576 GGTAATCCTAAAGGACTTGAAAAAGATAAAAATAAATCTACTCCTAATTCATACCTTCGACATAA
66 AGTGATCCTAGAGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGACATAA
* * *
633641 AAGTAGA-CTCGGTAATTTCAT
131 AAGTAGACCTCGATAGTTTTAT
** * * *
633662 AGGGTTAGGTTT-CGAGAAAAATGCTAAAATATCCCTAA-GTTTACCATTGACTTAGAAGTGCTT
1 AGGACTAGGTTTAGGAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGC-T
* * **
633725 CA-TGATCTTA-AGGGACTTGAAAAAGATAAAAATAAACCTACTCCTAATTCATACCTTTGATGT
65 CAGTGATCCTAGA-GGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGACAT
* *
633788 AGAAGCAGACC-CGATAGTTTTCAT
129 AAAAGTAGACCTCGATAGTTTT-AT
* * * * *
633812 AGGTCTAGGTTTAGAGAAAAAAATGCTAAAAGATCGCTAAGGTCTACCATCGACTTAGAAGTGCC
1 AGGACTAGGTTTAG-GAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGCT
* *
633877 CAGTGATCCTAGAGGACTT-AGAAAAGATAAAAACAAACCTGCTCCTAATTCATACCTTTGGCAT
65 CAGTGATCCTAGAGGACTTGA-AAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGACAT
*
633941 AAAAGTGGACCCTCGATAGTTTTAT
129 AAAAGTAGA-CCTCGATAGTTTTAT
* *
633966 AGGACTAGGTTTCAGGAGAAAAATGCTAAAAGGTCCATAAGGTCTACCATTGACTTAGAAGTGCT
1 AGGACTAGGTTT-AGGAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGCT
* * * * * ***
634031 CGGTGATCCTAGAGGACTTGGAAAAGATAAAAACAAATCTACTCCTAATTAATACCTTCGTTGTA
65 CAGTGATCCTAGAGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGACATA
* * *
634096 GAAGCAGACC-AG-TAGTTTTAT
130 AAAGTAGACCTCGATAGTTTTAT
* * * ** * *
634117 AGGACTAAGTTTTA-G-GAAAAATGCTAACATATCTTTAAGGTTTACCATCGACTTAGAAGTGC-
1 AGGACT-AGGTTTAGGAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGCT
* *
634179 CTAGTGATTCGA-AGGGACTTGAAAA
65 C-AGTGATCCTAGA-GGACTTGAAAA
634204 GGGTTGCAAA
Statistics
Matches: 452, Mismatches: 71, Indels: 38
0.81 0.13 0.07
Matches are distributed among these distances:
148 13 0.03
149 164 0.36
150 16 0.04
151 16 0.04
152 31 0.07
153 80 0.18
154 120 0.27
155 12 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (152 bp):
AGGACTAGGTTTAGGAGAAAAATGCTAAAAGATCCCTAAGGTCTACCATTGACTTAGAAGTGCTC
AGTGATCCTAGAGGACTTGAAAAAGATAAAAACAAACCTACTCCTAATTCATACCTTTGACATAA
AAGTAGACCTCGATAGTTTTAT
Found at i:635883 original size:18 final size:20
Alignment explanation
Indices: 635852--635888 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
635842 TAATCTTTTT
*
635852 ATTTAAAGTACCA-TATTTA
1 ATTTAAAATACCATTATTTA
635871 ATTTAAAAT-CCATTATTT
1 ATTTAAAATACCATTATTT
635889 TATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.19
19 13 0.81
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTTAAAATACCATTATTTA
Found at i:647253 original size:12 final size:12
Alignment explanation
Indices: 647232--647263 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
647222 ATCAGCATAC
*
647232 GACTACTCCTAT
1 GACTAATCCTAT
647244 GACTAATCCTAT
1 GACTAATCCTAT
647256 GACTAATC
1 GACTAATC
647264 GTCACTCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (12 bp):
GACTAATCCTAT
Found at i:653356 original size:18 final size:18
Alignment explanation
Indices: 653335--653370 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
653325 TGAGTCAACT
653335 TCATCATCACCATCATTG
1 TCATCATCACCATCATTG
* *
653353 TCATCTTCATCATCATTG
1 TCATCATCACCATCATTG
653371 ATAGTTGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCATCACCATCATTG
Found at i:654972 original size:32 final size:33
Alignment explanation
Indices: 654931--654995 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
654921 ACAATTCAAT
654931 ATGTATCGATACCAAG-AACATATATCGATACA
1 ATGTATCGATACCAAGCAACATATATCGATACA
* * *
654963 ATGTATCGATACTAAGCAATATGTATCGATACA
1 ATGTATCGATACCAAGCAACATATATCGATACA
654996 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACCAAGCAACATATATCGATACA
Found at i:658478 original size:28 final size:28
Alignment explanation
Indices: 658358--658917 Score: 450
Period size: 28 Copynumber: 19.5 Consensus size: 28
658348 CCAGCGACAT
*
658358 TGGG-TTTAGAAAGGTTGCCACTAACTTGTG
1 TGGGCTTTA-AAAGGATGCCACTAAC-T-TG
* *
658388 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTTA-A-AAGGATGCCACTAAC-T-TG
* * *
658420 TGGGCTTTAGAAGGGCTGCCCCTAACTTG
1 TGGGCTTTA-AAAGGATGCCACTAACTTG
* * *
658449 TGGGCTTTAAAAGGATGCCATTGATTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
** * *
658477 TGGGCTTCGAAAGGGTACCACTAACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* * * *
658505 TGGGCTTTGAAAGGTTGCCATTAACTTA
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* *
658533 TGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* *
658561 TGGGCTTTGAAAGGTTGCCACTAACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* * * *
658589 TGGGTTTTGAAAGGGTGTCACTAACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* * * * *
658617 TGGGCTTTGAGAGAGGTTGCAATTGACTTG
1 TGGGCTTT-A-AAAGGATGCCACTAACTTG
* *
658647 TGGGCTTTGAGAAGGATGCCACT-ATTTG
1 TGGGCTTT-AAAAGGATGCCACTAACTTG
*
658675 TGGGCTTTGAAAA-GATGCCACTAACTGG
1 TGGGCTTT-AAAAGGATGCCACTAACTTG
658703 TGGGCTTTGAAAA-GATGCCACTAACTTG
1 TGGGCTTT-AAAAGGATGCCACTAACTTG
*
658731 TGGGCTTTGAAAA-GATGCCACTAACGTG
1 TGGGCTTT-AAAAGGATGCCACTAACTTG
* * *
658759 TGGGCTTTGAAATGATGCCA-TCGACTTGTG
1 TGGGCTTTAAAAGGATGCCACT-AAC-T-TG
* *
658789 TGGGGGTTTCGAAAAGG-TGCCACTGACTTG
1 T-GGGCTTT--AAAAGGATGCCACTAACTTG
* *
658819 TGGGCTTTTAAAGGTTGCCACTAACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* * *
658847 TGGGCTTTGAAAGGATGCCACTGACTTA
1 TGGGCTTTAAAAGGATGCCACTAACTTG
* * * *
658875 TGGGTTTTTAAAGGTTGCCACTGACTTG
1 TGGGCTTTAAAAGGATGCCACTAACTTG
658903 TGGGCTTTGAAAAGG
1 TGGGCTTT-AAAAGG
658918 TGAACGTTCT
Statistics
Matches: 447, Mismatches: 68, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
27 18 0.04
28 298 0.67
29 30 0.07
30 34 0.08
31 24 0.05
32 38 0.09
33 5 0.01
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (28 bp):
TGGGCTTTAAAAGGATGCCACTAACTTG
Found at i:658510 original size:56 final size:57
Alignment explanation
Indices: 658358--658917 Score: 546
Period size: 56 Copynumber: 9.8 Consensus size: 57
658348 CCAGCGACAT
* * * *
658358 TGGG-TTTAGAAAGGTTGCCACTAACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTT-GAAAGGATGCCACTAAC-T-TGTGGGCTTT-GAAAAGGATGCCACTAAC-T-TG
* * * * * *
658420 TGGGCTTTAGAAGGGCTGCCCCTAACTTGTGGGCTTT-AAAAGGATGCCATTGATTTG
1 TGGGCTTT-GAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* * * * * *
658477 TGGGCTTCGAAAGGGTACCACTAACTTGTGGGCTTTG-AAAGGTTGCCATTAACTTA
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* *
658533 TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG-AAAGGTTGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* * * * * * * *
658589 TGGGTTTTGAAAGGGTGTCACTAACTTGTGGGCTTTGAGAGAGGTTGCAATTGACTTG
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGA-AAAGGATGCCACTAACTTG
* *
658647 TGGGCTTTGAGAAGGATGCCACT-ATTTGTGGGCTTTGAAAA-GATGCCACTAACTGG
1 TGGGCTTTGA-AAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* *
658703 TGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAA-GATGCCACTAACGTG
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* * * *
658759 TGGGCTTTGAAATGATGCCA-TCGACTTGTGTGGGGGTTTCGAAAAGG-TGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACT-AAC-T-TGT-GGGCTTT-GAAAAGGATGCCACTAACTTG
* * * *
658819 TGGGCTTTTAAAGGTTGCCACTAACTTGTGGGCTTTG-AAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
* * * *
658875 TGGGTTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGG
1 TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGG
658918 TGAACGTTCT
Statistics
Matches: 428, Mismatches: 55, Indels: 35
0.83 0.11 0.07
Matches are distributed among these distances:
55 17 0.04
56 245 0.57
57 23 0.05
58 45 0.11
59 28 0.07
60 35 0.08
61 12 0.03
62 5 0.01
63 18 0.04
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (57 bp):
TGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGATGCCACTAACTTG
Found at i:658537 original size:84 final size:85
Alignment explanation
Indices: 658367--658914 Score: 552
Period size: 84 Copynumber: 6.4 Consensus size: 85
658357 TTGGGTTTAG
* * * *
658367 AAAGGTTGCCACTAACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAA
1 AAAGGATGCCACTGAC-T-TGTGGGCTTT-GA-AAGGATGCCACTAAC-T-TGTGGGCTTT-GAA
* * *
658432 GGGCTGCCCCTAACTTGTGGGCTTT-A
59 AGGATGCCACTAACTTGTGGGCTTTGA
* * * * * *
658458 AAAGGATGCCATTGATTTGTGGGCTTCGAAAGGGTACCACTAACTTGTGGGCTTTGAAAGGTTGC
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGC
* *
658523 CATTAACTTATGGGCTTTG-
66 CACTAACTTGTGGGCTTTGA
* * * * * *
658542 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGTTTTGAAAGGGTGT
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGC
658607 CACTAACTTGTGGGCTTTGA
66 CACTAACTTGTGGGCTTTGA
* * * * * *
658627 GAGAGGTTGCAATTGACTTGTGGGCTTTGAGAAGGATGCCACT-ATTTGTGGGCTTTGAAAAGAT
1 -AAAGGATGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTAACTTGTGGGCTTTGAAAGGAT
*
658691 GCCACTAACTGGTGGGCTTTGA
64 GCCACTAACTTGTGGGCTTTGA
* * * *
658713 AAA-GATGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTAACGTGTGGGCTTTGAAATGATGC
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGC
* *
658777 CA-TCGACTTGTGTGGGGGTTTCGA
66 CACT-AAC-T-TGT-GGGCTTT-GA
* *
658801 AAAGG-TGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAACTTGTGGGCTTTGAAAGGATGC
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGC
* * **
658865 CACTGACTTATGGG-TTTTT
66 CACTAACTTGTGGGCTTTGA
*
658884 AAAGGTTGCCACTGACTTGTGGGCTTTGAAA
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAA
658915 AGGTGAACGT
Statistics
Matches: 385, Mismatches: 59, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
83 17 0.04
84 167 0.43
85 16 0.04
86 66 0.17
87 30 0.08
88 65 0.17
89 11 0.03
90 1 0.00
91 12 0.03
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (85 bp):
AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGC
CACTAACTTGTGGGCTTTGA
Found at i:659986 original size:13 final size:13
Alignment explanation
Indices: 659965--659995 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
659955 CGATACATGG
*
659965 TACAATGTATCGA
1 TACATTGTATCGA
659978 TACATTGTATCGA
1 TACATTGTATCGA
659991 TACAT
1 TACAT
659996 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:667996 original size:16 final size:17
Alignment explanation
Indices: 667964--667998 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
667954 AGGAGGAGAT
667964 AATTGTTTAAGGGGGAG
1 AATTGTTTAAGGGGGAG
*
667981 AATTTTTTAA-GGGGAG
1 AATTGTTTAAGGGGGAG
667997 AA
1 AA
667999 AAACGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (17 bp):
AATTGTTTAAGGGGGAG
Found at i:668492 original size:39 final size:39
Alignment explanation
Indices: 668437--668579 Score: 151
Period size: 39 Copynumber: 3.4 Consensus size: 39
668427 TGGGGACGAA
*
668437 TTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCC
1 TTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCC
* * *
668476 TTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCC
1 TTGAATCAGCACATTGGCA---------TAAGCCCAATATCGCTGGCC
*
668524 TTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCC
1 TTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCC
*
668563 TTGAATCAGCATATTGG
1 TTGAATCAGCACATTGG
668580 TAACTTCGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
39 51 0.59
48 35 0.41
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (39 bp):
TTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCC
Found at i:668548 original size:87 final size:88
Alignment explanation
Indices: 668437--668735 Score: 366
Period size: 101 Copynumber: 3.2 Consensus size: 88
668427 TGGGGACGAA
* * *
668437 TTGAATCAGCACATTGGCATAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTG-T
1 TTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTGAT
668501 CTTTAAGACCAATGTCGCTGGCC
66 CTTTAAGACCAATGTCGCTGGCC
*
668524 TTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTCGT
1 TTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTT-G-
* *
668589 CATCTTTAAGTCCAATGTCGCTGGCT
64 -ATCTTTAAGACCAATGTCGCTGGCC
* **
668615 TTGAATCAGTACATTGGCACCTTCATCTTTTAATCCAATATCGCTGGCCTTGAATCAGCATATTG
1 TTGAATCAGCACATTGGCA----CA------AGCCCAATATCGCTGGCCTTGAATCAGCATATTG
668680 GTACCTTTGTCATCTTTAAGACCAATGTCGCTGGCC
56 GTACC-TTG--ATCTTTAAGACCAATGTCGCTGGCC
668716 TTGAATCAGCACATTGGCAC
1 TTGAATCAGCACATTGGCAC
668736 CTTCATCTTT
Statistics
Matches: 184, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
87 58 0.32
88 1 0.01
91 40 0.22
95 2 0.01
97 1 0.01
101 80 0.43
102 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (88 bp):
TTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTGAT
CTTTAAGACCAATGTCGCTGGCC
Found at i:668660 original size:49 final size:50
Alignment explanation
Indices: 668548--668878 Score: 298
Period size: 52 Copynumber: 6.6 Consensus size: 50
668538 TGGCACAAGC
* * * *
668548 CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTCGTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-T-TTTAAGT
* * *
668600 CCAATGTCGCTGGCTTTGAATCAGTACATTGGCACCTTCATCTTTTAA-T
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGT
* * *
668649 CCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCATC-TTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTTAAGT
*
668701 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAA-T
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGT
* * * * * * *
668750 CCAATATCGCTGGCCTTGAATCATCATATTGGCATCTTTAACATTCCTAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-TT-TTAAGT
** ** * *
668802 CCAACGTCGCTGGCCTTGTCTCAGCACATTGG-A--TTCTTC-TTCAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGT
* * * *
668848 CTAATGTCGTTGGCCATGAATCAGCACATTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTG
668879 TCATTCTTTG
Statistics
Matches: 228, Mismatches: 43, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
46 28 0.12
47 1 0.00
49 76 0.33
50 13 0.06
51 11 0.05
52 99 0.43
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.34
Consensus pattern (50 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGT
Found at i:668811 original size:101 final size:101
Alignment explanation
Indices: 668548--668833 Score: 421
Period size: 101 Copynumber: 2.8 Consensus size: 101
668538 TGGCACAAGC
* *
668548 CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTCGTCATCTTTAAGTCCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTTGTCATCTTTAAGACCAATGTCGCTGG
* *
668613 CTTTGAATCAGTACATTGGCACCTTCATCTTTTAAT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTTAAT
*
668649 CCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTGTCATCTTTAAGACCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTTGTCATCTTTAAGACCAATGTCGCTGG
668714 CCTTGAATCAGCACATTGGCACCTTCATCTTTTAAT
66 CCTTGAATCAGCACATTGGCACCTTCATCTTTTAAT
* * * ** * * *
668750 CCAATATCGCTGGCCTTGAATCATCATATTGGCATCTTTAACAT-TCCTAAGCCCAACGTCGCTG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTTGTCATCT-TTAAGACCAATGTCGCTG
**
668814 GCCTTGTCTCAGCACATTGG
65 GCCTTGAATCAGCACATTGG
668834 ATTCTTCTTC
Statistics
Matches: 169, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 1 0.01
101 168 0.99
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (101 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGTAACTTTGTCATCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCACCTTCATCTTTTAAT
Found at i:672833 original size:13 final size:13
Alignment explanation
Indices: 672815--672841 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
672805 ACATGCTGCT
672815 TTGTATCGATACA
1 TTGTATCGATACA
672828 TTGTATCGATACA
1 TTGTATCGATACA
672841 T
1 T
672842 ATTCATTGTA
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):
TTGTATCGATACA
Found at i:672850 original size:19 final size:19
Alignment explanation
Indices: 672825--672880 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
672815 TTGTATCGAT
*
672825 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATAG
* * *
672844 TCATTGTATCGATAGATGG
1 ACATTGTATCGATACATAG
672863 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
672881 GAAACTGGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATAG
Found at i:674321 original size:13 final size:13
Alignment explanation
Indices: 674281--674345 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 13
674271 ATCTGGACCC
674281 TTTTTTGTTTGTT
1 TTTTTTGTTTGTT
674294 TATTTTT-TTTGTT
1 T-TTTTTGTTTGTT
*
674307 TTTTTT-TTT-TG
1 TTTTTTGTTTGTT
674318 TTTTTTGTTTGTT
1 TTTTTTGTTTGTT
*
674331 TTTTTGGTTT-TT
1 TTTTTTGTTTGTT
674343 TTT
1 TTT
674346 AGTATGAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
11 7 0.15
12 16 0.35
13 18 0.39
14 5 0.11
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (13 bp):
TTTTTTGTTTGTT
Found at i:674323 original size:20 final size:20
Alignment explanation
Indices: 674281--674343 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
674271 ATCTGGACCC
*
674281 TTTTTTGTTTG-TTTATT--
1 TTTTTTGTTTGTTTTTTTGG
* *
674298 TTTTTTGTTTTTTTTTTTTG
1 TTTTTTGTTTGTTTTTTTGG
674318 TTTTTTGTTTGTTTTTTTGG
1 TTTTTTGTTTGTTTTTTTGG
674338 TTTTTT
1 TTTTTT
674344 TTAGTATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
17 10 0.26
18 5 0.13
20 24 0.62
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.86
Consensus pattern (20 bp):
TTTTTTGTTTGTTTTTTTGG
Found at i:678621 original size:19 final size:19
Alignment explanation
Indices: 678597--678650 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
678587 ATTCAACGAT
* *
678597 TTGTATCGATCCATAAGTG
1 TTGTATCGATACATAAGTA
678616 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
678635 TTGTATCGATACATAA
1 TTGTATCGATACATAA
678651 TTAGCTACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:689671 original size:20 final size:20
Alignment explanation
Indices: 689642--689718 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
689632 GTAAAAAGAC
689642 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* * *
689662 AGAATATATCGAAACATTCA
1 AGAATGTATCGATACATTGA
* *
689682 TA-CATTTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
689702 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
689719 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:691476 original size:33 final size:32
Alignment explanation
Indices: 691434--691497 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
691424 TACAAGCCAA
* *
691434 TGTATCGATACATTTTGGGATGTTTCGATACAT
1 TGTATCGATACATATTGGG-TGTATCGATACAT
*
691467 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
691498 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAT
Found at i:691587 original size:20 final size:21
Alignment explanation
Indices: 691539--691590 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
691529 ACCAATCACC
691539 TGTATCGATACATTCTCAACA
1 TGTATCGATACATTCTCAACA
** * *
691560 ACTATCGATACATT-TGATCA
1 TGTATCGATACATTCTCAACA
691580 TGTATCGATAC
1 TGTATCGATAC
691591 GATGTATCGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTCAACA
Found at i:691597 original size:13 final size:13
Alignment explanation
Indices: 691579--691603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
691569 ACATTTGATC
691579 ATGTATCGATACG
1 ATGTATCGATACG
691592 ATGTATCGATAC
1 ATGTATCGATAC
691604 TATGCAATAT
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:0.20, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACG
Found at i:691708 original size:20 final size:20
Alignment explanation
Indices: 691683--691734 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
691673 GTCAACCTTA
*
691683 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACAT
691703 ATGTATCGATACAAATACAT
1 ATGTATCGATACAAATACAT
691723 ATGTATCGATAC
1 ATGTATCGATAC
691735 TTTGATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAATACAT
Found at i:694106 original size:13 final size:13
Alignment explanation
Indices: 694088--694125 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
694078 ATAAACCCTT
694088 TGTATCGATACAC
1 TGTATCGATACAC
694101 TGTATCGATACAC
1 TGTATCGATACAC
*
694114 TATATCGATACA
1 TGTATCGATACA
694126 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:700289 original size:13 final size:13
Alignment explanation
Indices: 700271--700296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
700261 ACATTTTGGG
700271 ATGTATCGATACA
1 ATGTATCGATACA
700284 ATGTATCGATACA
1 ATGTATCGATACA
700297 TAGTGTGTAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:700402 original size:20 final size:21
Alignment explanation
Indices: 700355--700407 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
700345 GCCAATCACC
*
700355 TGTATCGATACATTCTTAACA
1 TGTATCGATACATTCTGAACA
* *
700376 AGTATCGATACATT-TGATCA
1 TGTATCGATACATTCTGAACA
700396 TGTATCGATACA
1 TGTATCGATACA
700408 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTGAACA
Found at i:705373 original size:6 final size:7
Alignment explanation
Indices: 705354--705386 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
705344 TATTATACGT
705354 TAAAAAA
1 TAAAAAA
705361 TAAAAAAA
1 T-AAAAAA
705369 TAAAAAA
1 TAAAAAA
705376 TAAAAAA
1 TAAAAAA
705383 TAAA
1 TAAA
705387 TTGAGTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:706110 original size:164 final size:160
Alignment explanation
Indices: 705424--706261 Score: 491
Period size: 166 Copynumber: 5.1 Consensus size: 160
705414 AATTAATAAA
* * * *
705424 AATATTAGATG-AATTTAAAAAATTTTAAATAAAAGAATATC-CCCTGAAAATATTTATGGAATA
1 AATATTTGATGAAATTT-AAAAATTATAAATAAAA-AA-ATCTCCC--AAAAAATTTATGGAGTA
* * * * *
705487 AAAAACTCAAT-TTTTCAAAAATAAAGAAATTTTAAAAAAGAAAAAAATCAAAACTCTTGAAAAT
61 AAAAACTCTATATTTT-AGAAAT-AAGAAAATTT-CAAAA-AAAAAGA--AAAACTCTTG-AAAT
* * * * * * * *
705551 GAATG-AATTTTTCAAAGCTGTTTTACTGTGAATCAAATTAT
119 AAAAGAAATTTTTCAAAACTGATTTAATATGAATTAAATGAT
* ** **
705592 AATATTTGAT-AAATTTAAAAAATT-TAAAATCGATAAAAATCCTTTCAAAAAAAATTTACAGAG
1 AATATTTGATGAAATTT-AAAAATTAT-AAAT--AAAAAAAT-C--TCCCAAAAAATTTATGGAG
* * * * * * * * * * *
705655 -AAGGAAACTCTGTATTTTGGAAATGAGAGGAATTTTATGAAAAAATGAAAAACTCATGAAGTTG
59 TAA-AAAACTCTATATTTTAGAAATAAGA-AAATTTCA-AAAAAAAAGAAAAACTCTTGAA-ATA
* * *
705719 AAA-TAATTTTTCAAAAATGATTTAATATGAATCAAATGAT
120 AAAGAAATTTTTCAAAACTGATTTAATATGAATTAAATGAT
* * * * * *
705759 AATATTTGATGAATTTTAAAAATTTTCAATCAATGAAAATCCTCCTGAAAAAAATTATGGAG-AA
1 AATATTTGATGAAATTTAAAAATTATAAAT-AA-AAAAAT-CTCC-CAAAAAATTTATGGAGTAA
* * * * * ** * **
705823 TAAAACTCTATATTTCAAAAACAAGAGGAA-TTCTAAGGAAAACTGAAAAACATATAAAAAT-AA
62 -AAAACTCTATATTTTAGAAATAAGA-AAATTTC-AA-AAAAAAAGAAAAAC-TCTTGAAATAAA
* * * *
705886 ATAAATTTTTTAAAACTAATTTACTATGAATTAAATGAT
122 AGAAATTTTTCAAAACTGATTTAATATGAATTAAATGAT
705925 AATATTTGATG-AATATTAAAAATTATAAACTAAGAAAAATCTCCCAAAAAATGTTTATGGAGTA
1 AATATTTGATGAAAT-TTAAAAATTATAAA-TAA-AAAAATCTCCCAAAAAA--TTTATGGAGTA
* *
705989 AAAAACTCTGTATTTTAGAAATAAGAAAATTTCAAAAAAAAAGAAAAACCCTTGAAATAAAAGAA
61 AAAAACTCTATATTTTAGAAATAAGAAAATTTCAAAAAAAAAGAAAAACTCTTGAAATAAAAGAA
* * *
706054 AATTTTCAAAACTGATTTAATGTGAATTAAATAAT
126 ATTTTTCAAAACTGATTTAATATGAATTAAATGAT
* * * * ** *
706089 AATATTTGATGAAATTTAAAAATTAAAAACAAAAAAATCCCCTCGAAAACATTTACAGAGTAGAA
1 AATATTTGATGAAATTTAAAAATTATAAATAAAAAAATCTCC-C-AAAAAATTTATGGAGTAAAA
* * * * *
706154 AACTCTATATTTT-GAAAATAGGAAAATTTCAAGGAAGAAAGGAAAAACTCAT-AAA-AATGAAT
64 AACTCTATATTTTAG-AAATAAGAAAATTTCAA--AAAAAAAGAAAAACTCTTGAAATAA--AAG
* *
706216 AAATTTTTGAAAATTGATTTAATATGAATTAAATGAT
124 AAATTTTTCAAAACTGATTTAATATGAATTAAATGAT
*
706253 GATATTTGA
1 AATATTTGA
706262 AAAATTTTAA
Statistics
Matches: 525, Mismatches: 108, Indels: 78
0.74 0.15 0.11
Matches are distributed among these distances:
161 1 0.00
162 50 0.10
163 11 0.02
164 136 0.26
165 20 0.04
166 146 0.28
167 77 0.15
168 34 0.06
169 14 0.03
170 31 0.06
171 4 0.01
172 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.31
Consensus pattern (160 bp):
AATATTTGATGAAATTTAAAAATTATAAATAAAAAAATCTCCCAAAAAATTTATGGAGTAAAAAA
CTCTATATTTTAGAAATAAGAAAATTTCAAAAAAAAAGAAAAACTCTTGAAATAAAAGAAATTTT
TCAAAACTGATTTAATATGAATTAAATGAT
Found at i:710830 original size:19 final size:19
Alignment explanation
Indices: 710784--710840 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
710774 TTCCCTTTAA
*
710784 TTAAAAAATTTTCTCTCCC
1 TTAAAAAAATTTCTCTCCC
*
710803 TTAATAAAATTTCT-TCCC
1 TTAAAAAAATTTCTCTCCC
*
710821 TTAAAAAAAATATCTCTCCC
1 TT-AAAAAAATTTCTCTCCC
710841 CCTTTTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 6 0.19
19 22 0.69
20 4 0.12
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAAAATTTCTCTCCC
Found at i:710910 original size:57 final size:57
Alignment explanation
Indices: 710815--710928 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
710805 AATAAAATTT
710815 CTTCCCTTAAAAAAAATATCTCTCCCCCTTTTTGTTTCCAAAATAATCTCTTTTATA
1 CTTCCCTTAAAAAAAATATCTCTCCCCCTTTTTGTTTCCAAAATAATCTCTTTTATA
* * *
710872 CTTCTCTTTAAAAAAATATCTCTCCCCTTTTTTGTTTCCAAAATAATCTCTTTTATA
1 CTTCCCTTAAAAAAAATATCTCTCCCCCTTTTTGTTTCCAAAATAATCTCTTTTATA
710929 AAATTAGTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.45
Consensus pattern (57 bp):
CTTCCCTTAAAAAAAATATCTCTCCCCCTTTTTGTTTCCAAAATAATCTCTTTTATA
Found at i:712248 original size:20 final size:20
Alignment explanation
Indices: 712223--712270 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
712213 GTGGGAGCTG
712223 GCCGGTTGTGACTTGAGTGT
1 GCCGGTTGTGACTTGAGTGT
712243 GCCGGTTGTGACTTGAGTGT
1 GCCGGTTGTGACTTGAGTGT
*
712263 GCCAGTTG
1 GCCGGTTG
712271 CGACCTGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.10, C:0.17, G:0.40, T:0.33
Consensus pattern (20 bp):
GCCGGTTGTGACTTGAGTGT
Found at i:719011 original size:20 final size:19
Alignment explanation
Indices: 718965--719014 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
718955 CAATTCGCTG
*
718965 TGTATCGATACCAAGATCA
1 TGTATCGATACAAAGATCA
*
718984 TATATCGATACAAAGCAAT-A
1 TGTATCGATACAAAG--ATCA
719004 TGTATCGATAC
1 TGTATCGATAC
719015 TTCTGAGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 11 0.42
21 2 0.08
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (19 bp):
TGTATCGATACAAAGATCA
Found at i:720108 original size:67 final size:65
Alignment explanation
Indices: 720034--720183 Score: 160
Period size: 67 Copynumber: 2.3 Consensus size: 65
720024 CTAAAACGAA
* *
720034 CTTAAAATCTCTTATTTTATGCAAAATTAACTAGCCTTAATATCTTAATGGCGCCAGCTAAATAA
1 CTTAAAATCTCTTATTTTA-GCAAAATTAACTAGCCTTAACATCTTAATAGCGCCAGC-AAATAA
*
720099 GG
64 AG
* * * * * * *
720101 CTTAAAATC-CTTAATCTTGAGCCAACTTAGCTAGGCTTAACATCTTAATAGTGCTAGCAAATAA
1 CTTAAAATCTCTT-AT-TTTAGCAAAATTAACTAGCCTTAACATCTTAATAGCGCCAGCAAATAA
720165 AG
64 AG
720167 C-TAAAATCTCTTATTTT
1 CTTAAAATCTCTTATTTT
720184 GTGCTGATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
64 2 0.03
65 9 0.13
66 14 0.20
67 41 0.59
68 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (65 bp):
CTTAAAATCTCTTATTTTAGCAAAATTAACTAGCCTTAACATCTTAATAGCGCCAGCAAATAAAG
Found at i:720816 original size:19 final size:20
Alignment explanation
Indices: 720792--720834 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
720782 TTTCAGTAAA
*
720792 ACATACTTAA-AGTATCGAT
1 ACATACGTAATAGTATCGAT
*
720811 ACATACGTAATTGTATCGAT
1 ACATACGTAATAGTATCGAT
720831 ACAT
1 ACAT
720835 TATGGTTGAC
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:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (20 bp):
ACATACGTAATAGTATCGAT
Found at i:720931 original size:13 final size:13
Alignment explanation
Indices: 720913--720937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
720903 CATGCTGCTT
720913 TGTATCGATACAA
1 TGTATCGATACAA
720926 TGTATCGATACA
1 TGTATCGATACA
720938 TGTTCATTGA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:720934 original size:33 final size:32
Alignment explanation
Indices: 720892--720956 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
720882 ACACACCCAG
* *
720892 ATGTATCGATACATGCTGCTTTGTATCGATACA
1 ATGTATCGATACATG-TGCATTGAATCGATACA
*
720925 ATGTATCGATACATGTTCATTGAATCGATACA
1 ATGTATCGATACATGTGCATTGAATCGATACA
720957 TGGACAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACATGTGCATTGAATCGATACA
Done.