Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008044.1 Hibiscus syriacus cultivar Beakdansim tig00110532_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 979496
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:344414 original size:183 final size:185
Alignment explanation
Indices: 344106--344474 Score: 715
Period size: 183 Copynumber: 2.0 Consensus size: 185
344096 GATAATCTCC
344106 TTACTCCGATTATATCAAAACCAACGTGTGAAATTAATACACACTAAGTAATTTCTTAGTGATGC
1 TTACTCCGATTATATCAAAACCAACGTGTGAAATTAATACACACTAAGTAATTTCTTAGTGATGC
344171 ATAAATAACCATAAACAAACTTATAAACACGAGTATAACATAACAAGTCTAATATCAAGTAACTC
66 ATAAATAACCATAAACAAACTTATAAACACGAGTATAACATAACAAGTCTAATATCAAGTAACTC
344236 TTTTAATTTATTATAAACGTTATAA-TTT-TACCCGTAGTGCTAACATGGTAATT
131 TTTTAATTTATTATAAACGTTATAATTTTGTACCCGTAGTGCTAACATGGTAATT
344289 TTACTCCGATTATATCAAAACCAACGTGTGAAATTAATACACACTAAGTAATTTCTTAGTGATGC
1 TTACTCCGATTATATCAAAACCAACGTGTGAAATTAATACACACTAAGTAATTTCTTAGTGATGC
*
344354 ATAAATAACCATAAACAAACTTATAAACATGAGTATAACATAACAAGTCTAATATCAAGTAACTC
66 ATAAATAACCATAAACAAACTTATAAACACGAGTATAACATAACAAGTCTAATATCAAGTAACTC
344419 TTTTAATTTATTATAAACGTTATAATTTTGTACCCGTAGTGCTAACATGGTAATT
131 TTTTAATTTATTATAAACGTTATAATTTTGTACCCGTAGTGCTAACATGGTAATT
344474 T
1 T
344475 ACCAACTTTA
Statistics
Matches: 183, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
183 154 0.84
184 3 0.02
185 26 0.14
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (185 bp):
TTACTCCGATTATATCAAAACCAACGTGTGAAATTAATACACACTAAGTAATTTCTTAGTGATGC
ATAAATAACCATAAACAAACTTATAAACACGAGTATAACATAACAAGTCTAATATCAAGTAACTC
TTTTAATTTATTATAAACGTTATAATTTTGTACCCGTAGTGCTAACATGGTAATT
Found at i:344599 original size:46 final size:49
Alignment explanation
Indices: 344532--344669 Score: 149
Period size: 46 Copynumber: 2.8 Consensus size: 49
344522 CTATATGGCC
* * *
344532 GTTCATCAACACAAGATGAATTTCGTGGGTTGCACACATAG-TGCT-T-
1 GTTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTTCCTCTA
344578 GTTCATCAACTCATGATGAA-TTCTGTGGGTTGCACACATAGTTCCTCTA
1 GTTCATCAACTCATGATGAATTTC-GTGGGTTGCACACATAGTTCCTCTA
* *
344627 CGGTTGCTCATCAACTCATGATGAATTCCGTGGGTTGTACACA
1 --G-T--TCATCAACTCATGATGAATTTCGTGGGTTGCACACA
344670 GTGCCTGTAC
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
45 3 0.04
46 35 0.45
47 3 0.04
48 1 0.01
51 1 0.01
52 1 0.01
54 31 0.40
55 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (49 bp):
GTTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTTCCTCTA
Found at i:348781 original size:65 final size:65
Alignment explanation
Indices: 348674--348813 Score: 199
Period size: 65 Copynumber: 2.2 Consensus size: 65
348664 TCTTCTCTGG
* * * *
348674 ACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCGAATGCATTTTGTGT
1 ACCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGT
* ** * *
348739 ACCGATGCACAAACCATGCATTGATGCACTCCTGGCTCTTTTGAAACATCGAATGTAATTAGTGT
1 ACCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGT
348804 ACCGATGCAC
1 ACCGATGCAC
348814 CCCTAGTGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (65 bp):
ACCGATGCACAAACCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGT
Found at i:351631 original size:21 final size:21
Alignment explanation
Indices: 351607--351663 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
351597 ACTTTTGGCT
351607 CAAAGGATCGATCCCTTTGAA
1 CAAAGGATCGATCCCTTTGAA
* * *
351628 CAAAAGATC-AACCCCTTGAA
1 CAAAGGATCGATCCCTTTGAA
351648 -AAAGGATCGATCCCTT
1 CAAAGGATCGATCCCTT
351664 GGATTCTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.24
20 14 0.48
21 8 0.28
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (21 bp):
CAAAGGATCGATCCCTTTGAA
Found at i:351662 original size:19 final size:20
Alignment explanation
Indices: 351607--351664 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
351597 ACTTTTGGCT
351607 CAAAGGATCGATCCCTTTGAA
1 CAAAGGATCGATCCC-TTGAA
* * *
351628 CAAAAGATCAACCCCTTGAA
1 CAAAGGATCGATCCCTTGAA
351648 -AAAGGATCGATCCCTTG
1 CAAAGGATCGATCCCTTG
351665 GATTCTAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 14 0.45
20 5 0.16
21 12 0.39
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAAGGATCGATCCCTTGAA
Found at i:355826 original size:3 final size:3
Alignment explanation
Indices: 355818--355859 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
355808 TTAAATTAAC
* *
355818 AAT AAT AAT AAT AAT AAT AAAT AAT AAT ACT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
355860 ATACAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:355846 original size:22 final size:22
Alignment explanation
Indices: 355818--355862 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
355808 TTAAATTAAC
355818 AATAATAATAATAATAATAAAT
1 AATAATAATAATAATAATAAAT
* *
355840 AATAATACTACTAATAATAAAT
1 AATAATAATAATAATAATAAAT
355862 A
1 A
355863 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAATAATAAAT
Found at i:355875 original size:12 final size:13
Alignment explanation
Indices: 355824--355875 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
355814 TAACAATAAT
355824 AATAATAATAATA-
1 AATAATAAT-ATAC
355837 AATAATAATACTAC
1 AATAATAATA-TAC
355851 TAATAATAA-ATAC
1 -AATAATAATATAC
355864 AAT-ATAATATAC
1 AATAATAATATAC
355876 CTAACTCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.11
12 8 0.23
13 14 0.40
14 1 0.03
15 8 0.23
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAATATAC
Found at i:356028 original size:17 final size:16
Alignment explanation
Indices: 355987--356031 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
355977 ATATTTTTTT
*
355987 AAAA-ATATATTTTTC
1 AAAATATATATATTTC
*
356002 AATATATATATATTTC
1 AAAATATATATATTTC
356018 AAAACTATATATAT
1 AAAA-TATATATAT
356032 GTATTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 3 0.12
16 13 0.52
17 9 0.36
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATATATATATTTC
Found at i:356029 original size:21 final size:20
Alignment explanation
Indices: 356003--356093 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 20
355993 ATATTTTTCA
356003 ATATATATATATTTCAAAACT
1 ATATATATATATTTC-AAACT
* *
356024 ATATATATGTA-TT-ATA-T
1 ATATATATATATTTCAAACT
**
356041 ATATATATATATTAAAAACT
1 ATATATATATATTTCAAACT
* *
356061 CTATATATGT-TTTCAAACAT
1 ATATATATATATTTCAAAC-T
356081 AATATATATATAT
1 -ATATATATATAT
356094 ATTATAATGA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
17 11 0.21
18 3 0.06
19 8 0.15
20 12 0.23
21 18 0.34
22 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATATATATATTTCAAACT
Found at i:356086 original size:37 final size:37
Alignment explanation
Indices: 355991--356089 Score: 107
Period size: 37 Copynumber: 2.7 Consensus size: 37
355981 TTTTTTAAAA
*
355991 ATATAT-TTTTC-AATAT-ATATATATTTCAAAACTAT
1 ATATATGTTTTCAAATATAATATATA-TTAAAAACTAT
* * *
356026 ATATATGTATT-ATATATATATATATATTAAAAACTCT
1 ATATATGTTTTCAAATATA-ATATATATTAAAAACTAT
*
356063 ATATATGTTTTCAAACATAATATATAT
1 ATATATGTTTTCAAATATAATATATAT
356090 ATATATTATA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
35 6 0.12
36 7 0.13
37 27 0.52
38 12 0.23
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATATGTTTTCAAATATAATATATATTAAAAACTAT
Found at i:356219 original size:53 final size:50
Alignment explanation
Indices: 356103--356219 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 50
356093 TATTATAATG
356103 AATATAATATACATATATATTTTAAAAAAATCATACATACATTTTCAAAT
1 AATATAATATACATATATATTTTAAAAAAATCATACATACATTTTCAAAT
* * * *
356153 AATAAACATATATATATATATATATATTAAAAAA-CTATATATACATTTTCAAGCAT
1 AATATA-ATATACATATATAT-T-T-TAAAAAAATC-ATACATACATTTTCAA--AT
356209 AATATAATATA
1 AATATAATATA
356220 AGATAAGATT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
50 5 0.09
51 13 0.24
52 1 0.02
53 2 0.04
54 22 0.40
55 5 0.09
56 7 0.13
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.38
Consensus pattern (50 bp):
AATATAATATACATATATATTTTAAAAAAATCATACATACATTTTCAAAT
Found at i:357250 original size:14 final size:15
Alignment explanation
Indices: 357220--357250 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
357210 TGGTTTACAA
357220 TATTTATATGATTTT
1 TATTTATATGATTTT
357235 TATTTATATG-TTTT
1 TATTTATATGATTTT
357249 TA
1 TA
357251 ATACAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTATATGATTTT
Found at i:363619 original size:134 final size:133
Alignment explanation
Indices: 363378--363645 Score: 504
Period size: 135 Copynumber: 2.0 Consensus size: 133
363368 TATATTGGGC
363378 TATTGTCTACGGTTTATTGACTATGGATTATGTTTTATTGGTTAATAATGGTAACCATGCAAATA
1 TATTGTCTACGGTTTATTGACTATGGATTATGTTTTATTGGTTAATAATGGTAACCATGCAAATA
363443 AGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAATAATAATAAGCTTATGAGCTTATG
66 AGCTTATGAGCTTACGGAATAATGGCAAGTATATTG-AAAA-AATAATAAGCTTATGAGCTTATG
363508 GAATT
129 GAATT
363513 TATTGTCTACGGTTTATTGACTATGGATTATGTTTTATTGG-TAATAATGGTAACCATGCAAATA
1 TATTGTCTACGGTTTATTGACTATGGATTATGTTTTATTGGTTAATAATGGTAACCATGCAAATA
363577 AGCTTATGAGCTTACGG-ATAATGGCAAGTATATTGAAAAAATAATAAGCTTATGAGCTTATGGA
66 AGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAATAATAAGCTTATGAGCTTATGGA
363641 ATT
131 ATT
363644 TA
1 TA
363646 AATGGTAAGT
Statistics
Matches: 133, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
131 30 0.23
132 4 0.03
133 18 0.14
134 40 0.30
135 41 0.31
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (133 bp):
TATTGTCTACGGTTTATTGACTATGGATTATGTTTTATTGGTTAATAATGGTAACCATGCAAATA
AGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAATAATAAGCTTATGAGCTTATGGA
ATT
Found at i:364671 original size:29 final size:29
Alignment explanation
Indices: 364629--364694 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
364619 ATAACAAGTA
364629 AGCATCATTGTGTAGCTCGGGGGTTATAT
1 AGCATCATTGTGTAGCTCGGGGGTTATAT
364658 AGCATCATTGTGTAGCTCGGGGGTTATAT
1 AGCATCATTGTGTAGCTCGGGGGTTATAT
364687 AGCATCAT
1 AGCATCAT
364695 GAGACTCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (29 bp):
AGCATCATTGTGTAGCTCGGGGGTTATAT
Found at i:365928 original size:45 final size:44
Alignment explanation
Indices: 365862--366094 Score: 306
Period size: 45 Copynumber: 5.2 Consensus size: 44
365852 TATCCTTTAT
* * * *
365862 TTTCATTTATAGCATCCTTTCATACTTATAATGCACCGTTATTCA
1 TTTCATTTATGGCATCCTTTCATCCGT-TAATGCACCGTTATGCA
* * *
365907 TTTCATTTATGGGATCATTTCATGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCAT-CCGTTAATGCACCGTTATGCA
*
365952 TTTCATTTATGGCATCCTTTCATGCCGTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCAT-CCGTTAATGCACCGTTATGCA
*
365997 TTTCATTTATGGCATCC-TTCTATGCTGTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTC-AT-CCGTTAATGCACCGTTATGCA
* *
366042 TTTCATTCATGGCATCCTTTCATGCCGTTAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCAT-CCGTTAATGCACCGTTATGCA
366087 TTTCATTT
1 TTTCATTT
366095 TGTCATTCAT
Statistics
Matches: 168, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
44 3 0.02
45 161 0.96
46 4 0.02
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (44 bp):
TTTCATTTATGGCATCCTTTCATCCGTTAATGCACCGTTATGCA
Found at i:366137 original size:90 final size:90
Alignment explanation
Indices: 365862--366121 Score: 220
Period size: 90 Copynumber: 2.9 Consensus size: 90
365852 TATCCTTTAT
* * * * * * *
365862 TTTCATTTATAGCATCCTTTCAT-ACTTATAATGCACCGTTATTCATTTCATTTATGGGATCATT
1 TTTCATTCATGGCATCCTTTCATGCCGT-TAATGCACCATTATGCATTTCATTTATGGCATCATT
* * * * ***
365926 -TCATGCCGATAATGCACCGTTATGCA
65 CT-AAGCAGTTAATACACCAAAATGCA
* *
365952 TTTCATTTATGGCATCCTTTCATGCCGTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
1 TTTCATTCATGGCATCCTTTCATGCCGTTAATGCACCATTATGCATTTCATTTATGGCATCATTC
* * * ***
366017 TATGCTGTTAATGCACCGTTATGCA
66 TAAGCAGTTAATACACCAAAATGCA
* * *
366042 TTTCATTCATGGCATCCTTTCATGCCGTTAATGCACCGTTATGTATTTCATTT-TGTCATTCATT
1 TTTCATTCATGGCATCCTTTCATGCCGTTAATGCACCATTATGCATTTCATTTATGGCA-TCATT
* *
366106 TTAGAGCAGTTCATAC
65 CTA-AGCAGTTAATAC
366122 TCTAAAATTC
Statistics
Matches: 147, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
89 4 0.03
90 132 0.90
91 11 0.07
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (90 bp):
TTTCATTCATGGCATCCTTTCATGCCGTTAATGCACCATTATGCATTTCATTTATGGCATCATTC
TAAGCAGTTAATACACCAAAATGCA
Found at i:366137 original size:135 final size:135
Alignment explanation
Indices: 365862--366121 Score: 310
Period size: 135 Copynumber: 1.9 Consensus size: 135
365852 TATCCTTTAT
* * *
365862 TTTCATTTATAGCATCCTTTCATACTTATAATGCACCGTTATTCATTTCATTTATGGGATCATTT
1 TTTCATTTATAGCATCCTTTCATACTTATAATGCACCGTTATGCATTTCATTCATGGCATCATTT
* * * * **
365927 CATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGTTAATGCACCATT
66 CATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCAAGCAGTTAATACACCAAA
365992 ATGCA
131 ATGCA
* * *
365997 TTTCATTTATGGCATCC-TTCTATGCTGT-TAATGCACCGTTATGCATTTCATTCATGGCATCCT
1 TTTCATTTATAGCATCCTTTC-ATACT-TATAATGCACCGTTATGCATTTCATTCATGGCATCAT
* * * * *
366060 TTCATGCCGTTAATGCACCGTTATGTATTTCATTT-TGTCATTCATTTTAGAGCAGTTCATAC
64 TTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCA-TCATTTCA-AGCAGTTAATAC
366122 TCTAAAATTC
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
134 7 0.07
135 90 0.85
136 9 0.08
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (135 bp):
TTTCATTTATAGCATCCTTTCATACTTATAATGCACCGTTATGCATTTCATTCATGGCATCATTT
CATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCAAGCAGTTAATACACCAAA
ATGCA
Found at i:366567 original size:95 final size:95
Alignment explanation
Indices: 366424--366719 Score: 430
Period size: 95 Copynumber: 3.1 Consensus size: 95
366414 CCCTGCCATG
* * *
366424 GTATCGATATTTCTATATTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTACATTAT
1 GTATCGATACTTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTACATTCT
* * *
366489 GTAATTCATGGTATCGATACCATTCTATTA
66 GAAATTCATGGTATCGATACCTTTCTCTTA
* * *
366519 GTATTGATACTTCTATACTATGGTACCGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTACATTCT
* *
366584 GGAATTCATGGTATCAATACCTTTCTCTTA
66 GAAATTCATGGTATCGATACCTTTCTCTTA
* * *
366614 GTATCCATACTTCCATACTATGGTACTGATACTCCCTTGCAGTATCGATACCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTACATTCT
* * *
366679 GGAAATCCCTGGTATCGATACCTTTCTCTTG
66 -GAAATTCATGGTATCGATACCTTTCTCTTA
366710 GTATCGATAC
1 GTATCGATAC
366720 CCACAGCAGT
Statistics
Matches: 178, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
95 144 0.81
96 34 0.19
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (95 bp):
GTATCGATACTTCTATACTATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTACATTCT
GAAATTCATGGTATCGATACCTTTCTCTTA
Found at i:374646 original size:15 final size:15
Alignment explanation
Indices: 374611--374639 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
374601 GTGCTTCAAC
374611 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
374625 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
374640 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:398947 original size:17 final size:17
Alignment explanation
Indices: 398925--398958 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
398915 CTAAGCGAAC
398925 CTCATTCTTTTTAATAA
1 CTCATTCTTTTTAATAA
398942 CTCATTCTTTTTAATAA
1 CTCATTCTTTTTAATAA
398959 TTAAGTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (17 bp):
CTCATTCTTTTTAATAA
Found at i:401584 original size:45 final size:45
Alignment explanation
Indices: 401533--401620 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
401523 ACTGAGAGAC
*
401533 TTAGGAAATAAGTTGGGTAATACTAGTAATAACTCTAACATAGAA
1 TTAGGAAATAAGTTGGGTAATACTAGTAATAACTCCAACATAGAA
* * *
401578 TTAGGAAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAG
1 TTAGGAAATAAGTTGGGTAATACTAGTAATAACTCCAACATAG
401621 TGAGACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (45 bp):
TTAGGAAATAAGTTGGGTAATACTAGTAATAACTCCAACATAGAA
Found at i:403293 original size:20 final size:20
Alignment explanation
Indices: 403268--403360 Score: 186
Period size: 20 Copynumber: 4.7 Consensus size: 20
403258 ATCCAAGTGA
403268 GTAGTATCGATACACAACTT
1 GTAGTATCGATACACAACTT
403288 GTAGTATCGATACACAACTT
1 GTAGTATCGATACACAACTT
403308 GTAGTATCGATACACAACTT
1 GTAGTATCGATACACAACTT
403328 GTAGTATCGATACACAACTT
1 GTAGTATCGATACACAACTT
403348 GTAGTATCGATAC
1 GTAGTATCGATAC
403361 CCTATGGTAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
GTAGTATCGATACACAACTT
Found at i:403563 original size:70 final size:70
Alignment explanation
Indices: 403450--403581 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 70
403440 ATACTACTAC
* * * *
403450 AAACCTTAATTTTAGCCTCGATTCAACCAGTATCGATAATGTTCATCCCAATATCGATACTCCTT
1 AAACCCTAATTTTAGCCCCAATTCAACCAGTATCGATAATGTTCATCCCAATATCAATACTCCTT
403515 TCTAG
66 TCTAG
* * * *
403520 AAACCCTAATTTTAGCCCCAATTTAACTAGTAAT-GATATTGTTCATCCCATTATCAATACTC
1 AAACCCTAATTTTAGCCCCAATTCAACCAGT-ATCGATAATGTTCATCCCAATATCAATACTC
403582 AAACCCTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
70 51 0.96
71 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (70 bp):
AAACCCTAATTTTAGCCCCAATTCAACCAGTATCGATAATGTTCATCCCAATATCAATACTCCTT
TCTAG
Found at i:405684 original size:60 final size:60
Alignment explanation
Indices: 405608--405724 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
405598 AACTTGCATG
*
405608 ATTGACACATTCCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATATA
1 ATTGACACATTCCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAAAGGTATATA
* * *
405668 ATTGACACATTTCTGCCAAATACATAGGTAGGCCATTAATCTTTTACTCAAAGGTAT
1 ATTGACACATTCCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAAAGGTAT
405725 TTAACCTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (60 bp):
ATTGACACATTCCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAAAGGTATATA
Found at i:405800 original size:81 final size:81
Alignment explanation
Indices: 405665--407165 Score: 1983
Period size: 81 Copynumber: 18.6 Consensus size: 81
405655 TCAAAGGTAT
* * * *
405665 ATAATTGACACATTTCTGCCAAATACATAGGTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
405730 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* * * * *
405746 ATAATTGACACCTTTCTGCCAAATGCATAACTAGACTATTAATCTTTTACTCAAAGGTATTTAGC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
* *
405811 ATTTCATCTAATTGGC
66 CTTTCATCTAACTGGC
* * * *
405827 ATAATTGATACCTTTATGCCAAATGCACAGCTAAGACATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
405892 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *** * * * *
405908 AAAACCAACACCTTTCT-CACAAAT--ACA--TA-ACCATTATTATTTTACTTAAAGGTATTTAA
1 ATAATTGACACCTTTCTGC-CAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAA
* *
405967 CCTTTCATCTAACTTGA
65 CCTTTCATCTAACTGGC
* * * * * *
405984 AAAATTGACACATTTATACTAAATACACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406049 CTTTCATCTAACTAGC
66 CTTTCATCTAACTGGC
* * *
406065 ATAATTGACACCTTTATGCCAAATGCATAGCTAGGCCATTAATATTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
**
406130 CTTTCATCTAACTACC
66 CTTTCATCTAACTGGC
*
406146 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTTAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
* *
406211 CTTTCATCTTACTAGC
66 CTTTCATCTAACTGGC
* * **
406227 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTAATCATTTACTCAAATATATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406292 CTTTCATCTAACTAGC
66 CTTTCATCTAACTGGC
* * * * * *
406308 GTAATTGACACATTTCTGCGAAATACACAGCTAGGCCTTTAATCATTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406373 CTTTCATCTAATTGGC
66 CTTTCATCTAACTGGC
* * * *
406389 ATAATTGACACATTTATGCCAAATGCACAACTAGGACATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
**
406454 CTTTCGCCTAACTGGC
66 CTTTCATCTAACTGGC
* * * * *
406470 ATAAATGACACCTTTCTGCCAAATGCACAACTAGACCATTAATCTTTTACTTAAAGATATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
406535 CTTTCATCTAACTGG-
66 CTTTCATCTAACTGGC
* * * * * *
406550 AAAACTTGACACC-CTCTACTAAATGCACAGGTAGGCCATTAATATTTTACTCAAAGGTATTTAA
1 ATAA-TTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAA
*
406614 CCTTTCATCTAACTGGT
65 CCTTTCATCTAACTGGC
* * * * * *
406631 ATAATTCACACCTTTCTGACAAATGCATAGCTAGGCCATTAATATTTTACTCAAAGGTATATAAT
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
* *
406696 ATTTCATTTAACTGGC
66 CTTTCATCTAACTGGC
* *
406712 ATAATTGACACCTTTCTGCCAAATGCATAGCTAGGCCATTAATATTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406777 CTTTCATCTAACTGCC
66 CTTTCATCTAACTGGC
* * * *
406793 ATAATTGACATCTTTTTGCCGAATGCACAGCTAGGTCATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406858 CTTTCATCTAACTAGC
66 CTTTCATCTAACTGGC
* * * *
406874 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAAACATTTACTCAAAGATAGTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
*
406939 CTTTCATCTAACTAGC
66 CTTTCATCTAACTGGC
* * * * * *
406955 GTAATTGACACATTTTTGCCATATACACAGCTAGGCCTTTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
* *
407020 CTTTCATCTAATTAGC
66 CTTTCATCTAACTGGC
* * * *
407036 ATAATTGACACATTTATGCCCAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
407101 CTTTCATCTAACTGGC
66 CTTTCATCTAACTGGC
* *
407117 ATAATTGACACCTTTCTTCCAAATGCACTGCTAGGCCATTAATCTTTTA
1 ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
407166 TTTTAGAATA
Statistics
Matches: 1242, Mismatches: 168, Indels: 20
0.87 0.12 0.01
Matches are distributed among these distances:
76 56 0.05
77 3 0.00
78 3 0.00
79 3 0.00
80 71 0.06
81 1106 0.89
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
ATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAAC
CTTTCATCTAACTGGC
Found at i:407334 original size:54 final size:53
Alignment explanation
Indices: 407276--407396 Score: 134
Period size: 54 Copynumber: 2.2 Consensus size: 53
407266 ATTCACAGTG
* * *
407276 TTATTATAATTTACGTCGGTTGTACACACACTACCAATACAGAAATTCATAAAC
1 TTATTATAATTTA-GTAGGTTGCACACAAACTACCAATACAGAAATTCATAAAC
* ** * * *
407330 TTATTATTAATTTATTATTTTGCACACAAAGTGCCCATACAGAAATTCATAAAC
1 TTATTA-TAATTTAGTAGGTTGCACACAAACTACCAATACAGAAATTCATAAAC
407384 TTATTATGAATTT
1 TTATTAT-AATTT
407397 CTTAGTTTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 1 0.02
54 48 0.86
55 7 0.12
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (53 bp):
TTATTATAATTTAGTAGGTTGCACACAAACTACCAATACAGAAATTCATAAAC
Found at i:407766 original size:20 final size:21
Alignment explanation
Indices: 407738--407790 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
407728 AGGCTCAATA
* *
407738 GTATTGATACCCT-TATTATG
1 GTATCGATACCCTATACTATG
*
407758 GTATCGATACTTCTATACTATG
1 GTATCGATAC-CCTATACTATG
*
407780 GTACCGATACC
1 GTATCGATACC
407791 TTTCTCTCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 9 0.35
21 2 0.08
22 15 0.58
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (21 bp):
GTATCGATACCCTATACTATG
Found at i:412545 original size:81 final size:81
Alignment explanation
Indices: 412404--413299 Score: 1213
Period size: 81 Copynumber: 11.1 Consensus size: 81
412394 GCATTTTGTA
* * * * *
412404 TTTTACCCAAAGGTATTTTATCCTTTCATCTAACTTGCATGATTGACACATTCCTGCCAAATGCA
1 TTTTACTCAAAGGTA-TTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCA
412469 CAGCTAGGCCATTAATC
65 CAGCTAGGCCATTAATC
* * * * *
412486 TTTTACACAAAGGTATTTAACCTGTCATCTAACTGGTATAATTGACACATTTCTACCAAATGCAT
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
*
412551 AGCTAGGCCAATAATC
66 AGCTAGGCCATTAATC
* * * * *
412567 TTTTACTCAAAAGAATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATTCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
*
412632 AGCTAGGTCATTAATC
66 AGCTAGGCCATTAATC
* * * * * * * *
412648 TATTACTCAAAGGTATTTAATCTTTCATCTAATTGCCATATTTGACACCTTTCTTCCAAATGCAT
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
**
412713 TTCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* * * *
412729 ATTTACACAAAGGTATTTAATCTTTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
* *
412794 AACTAGACCATTAATC
66 AGCTAGGCCATTAATC
* * *
412810 TTTTACTCAAAGGTATTTAACCTTTCATCGAACTGGCATAATTGACACCTTTCTGCCAAATACAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
412875 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
*
412891 TTTTACTCAAAGGTATTTAACCTTT-ACTCTAACTGGCATAATTGACATC-TTTCTTCCAAATGC
1 TTTTACTCAAAGGTATTTAACCTTTCA-TCTAACTGGCATAATTGACA-CATTTCTGCCAAATGC
* * *
412954 ACATCTAGTCCATTAATA
64 ACAGCTAGGCCATTAATC
* * * ** *
412972 TTTTACTCAAAGGTATTTAATCGTTCATCAAACTACCATAATTGACATATTTCTGCCAAATGCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
* *
413037 AACTAGGCCAATAATC
66 AGCTAGGCCATTAATC
*
413053 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAT
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
413118 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
** * *
413134 TTTTACTCAAAGGTATTTAACCTTTCATCTAACAAGCATAATTGACACATTTCTACCAAATGCAT
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
* *
413199 AGCTAGGTCATTAATA
66 AGCTAGGCCATTAATC
* * *
413215 TTTTACTCAAAGGTATTTAACGTTTCATCTAACTGGCATAATTGACACATTTCTACCAAATTCAC
1 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
*
413280 AACTAGGCCA-TAATC
66 AGCTAGGCCATTAATC
413295 TTTTA
1 TTTTA
413300 TTTTATAACA
Statistics
Matches: 714, Mismatches: 96, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
80 10 0.01
81 688 0.96
82 16 0.02
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (81 bp):
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCAC
AGCTAGGCCATTAATC
Found at i:413510 original size:55 final size:55
Alignment explanation
Indices: 413446--413552 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
413436 CACACTACCA
*
413446 ATACAGAAATTCATAAACTTATTATGAATTTATTATTTTTGCACACAAAGTTCCC
1 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTTCCC
* * * * *
413501 ATACGGAAATTCATTAACTTATTATGAATTTCTTAGTTTTGTACACATAGTT
1 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTT
413553 TCATTTGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (55 bp):
ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTTCCC
Found at i:417904 original size:2 final size:2
Alignment explanation
Indices: 417897--417944 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
417887 ACTTACTTGG
417897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
417939 TA TA TA
1 TA TA TA
417945 GGCCTTAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:424561 original size:20 final size:20
Alignment explanation
Indices: 424538--424576 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
424528 TACTACACTT
*
424538 ATAAGGAAAAAAAGAAAAAA
1 ATAAAGAAAAAAAGAAAAAA
*
424558 ATAAAGAAAAAGAGAAAAA
1 ATAAAGAAAAAAAGAAAAA
424577 TGAAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
ATAAAGAAAAAAAGAAAAAA
Found at i:426571 original size:11 final size:12
Alignment explanation
Indices: 426544--426572 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
426534 TTATCTCTGT
426544 TTTTTCTTTTAG
1 TTTTTCTTTTAG
426556 TTTTT-TTTTAG
1 TTTTTCTTTTAG
426567 TTTTTC
1 TTTTTC
426573 GAAACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTCTTTTAG
Found at i:427410 original size:25 final size:26
Alignment explanation
Indices: 427361--427410 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
427351 ATAATCTTTT
*
427361 TTTTTTATTTTGTTGTAATTGATTAG
1 TTTTTTATTTTGTTGTAAGTGATTAG
427387 TTTTTTATTTCTGTT-TAAGT-ATTA
1 TTTTTTATTT-TGTTGTAAGTGATTA
427411 ATTATCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (26 bp):
TTTTTTATTTTGTTGTAAGTGATTAG
Found at i:439260 original size:23 final size:23
Alignment explanation
Indices: 439212--439260 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
439202 TCTAAGTGTG
* *
439212 TAAAATATAAAAAATCAACAGGA
1 TAAAATAGAAAAAATCAACAGAA
* *
439235 TAAAATAGAAAAGATCAACATAA
1 TAAAATAGAAAAAATCAACAGAA
439258 TAA
1 TAA
439261 CAAACAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.18
Consensus pattern (23 bp):
TAAAATAGAAAAAATCAACAGAA
Found at i:442465 original size:172 final size:173
Alignment explanation
Indices: 442261--442593 Score: 632
Period size: 172 Copynumber: 1.9 Consensus size: 173
442251 TATGATTTCA
442261 ACATCCAATAGGACACTTACTGTTCCCATATTTTCACATCAATTTGAGAAGAGAACGTTTTGTTT
1 ACATCCAATAGGACACTTACTGTTCCCATATTTTCACATCAATTTGAGAAGAGAACGTTTTGTTT
442326 CAAGTACTATCTCATAGTAGTACTAAAAATAGTTATATCAAACTCATACAAGTATAACTTTTCAA
66 CAAGTACTATCTCATAGTAGTACTAAAAATAGTTATATCAAACTCATACAAGTATAACTTTTCAA
442391 CC-AACCTATATTGTAATATTATGTTCAACATAACCAATGAAG
131 CCAAACCTATATTGTAATATTATGTTCAACATAACCAATGAAG
442433 ACATCCAATAGGACACTTACTGTTCCCATATTTTCACATCAATTTGAGAAGAGAACGTTTTGTTT
1 ACATCCAATAGGACACTTACTGTTCCCATATTTTCACATCAATTTGAGAAGAGAACGTTTTGTTT
442498 CAAGTACTATCTCATAGTAGTACTAAAAATAGTTATATCAAACTCATACAAGTATAACTTTTCAA
66 CAAGTACTATCTCATAGTAGTACTAAAAATAGTTATATCAAACTCATACAAGTATAACTTTTCAA
442563 CCAAGAAACCTATATTGTAATATTATGTTCA
131 CC---AAACCTATATTGTAATATTATGTTCA
442594 CCCTCACTAA
Statistics
Matches: 157, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
172 132 0.84
176 25 0.16
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (173 bp):
ACATCCAATAGGACACTTACTGTTCCCATATTTTCACATCAATTTGAGAAGAGAACGTTTTGTTT
CAAGTACTATCTCATAGTAGTACTAAAAATAGTTATATCAAACTCATACAAGTATAACTTTTCAA
CCAAACCTATATTGTAATATTATGTTCAACATAACCAATGAAG
Found at i:446377 original size:21 final size:21
Alignment explanation
Indices: 446353--446421 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 21
446343 TTATTGATAG
446353 TTTTAATAATATAATATAATA
1 TTTTAATAATATAATATAATA
*
446374 TTTTAATTTATTTATATAATTATATTA
1 TTTTAA--TA---ATATAA-TATAATA
*
446401 TTATAAT-ATATAATATAATA
1 TTTTAATAATATAATATAATA
446421 T
1 T
446422 ATTATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 7 0.18
21 12 0.31
23 2 0.05
25 1 0.03
26 6 0.15
27 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAATAATATAATATAATA
Found at i:446451 original size:52 final size:53
Alignment explanation
Indices: 446358--446457 Score: 134
Period size: 52 Copynumber: 1.9 Consensus size: 53
446348 GATAGTTTTA
* *
446358 ATAATATAATATAATATTTTAATTTATTTATATAATTATATT-ATTATAATAT
1 ATAATATAATATAATATTTTAATTCATTTATATAATAATATTAATTATAATAT
*
446410 ATAATATAATATATTATTTTAATATCATTT-TAATAA-AATATTAATTAT
1 ATAATATAATATAATATTTTAAT-TCATTTAT-ATAATAATATTAATTAT
446458 TAAATTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
52 28 0.67
53 14 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (53 bp):
ATAATATAATATAATATTTTAATTCATTTATATAATAATATTAATTATAATAT
Found at i:446511 original size:125 final size:125
Alignment explanation
Indices: 446284--446511 Score: 397
Period size: 125 Copynumber: 1.8 Consensus size: 125
446274 TTTTATATCC
446284 ATAATATTAATATATTATTTTAATATCATTTTAATAAAATATTAATTATTAAATTTTATTTATTG
1 ATAATATTAATATATTATTTTAATATCATTTTAATAAAATATTAATTATTAAATTTTATTTATTG
**
446349 ATAGTTTTAATAATATAATATAATATTTTAATTTATTTATATAATTATATTATTATAATAT
66 ATAGTTTTAATAATATAATATAATATCATAA-TTATTTATATAATTATATTATTATAATAT
446410 ATAATA-TAATATATTATTTTAATATCATTTTAATAAAATATTAATTATTAAATTTTATTTATTG
1 ATAATATTAATATATTATTTTAATATCATTTTAATAAAATATTAATTATTAAATTTTATTTATTG
446474 ATAGTTTTAATAATATAATATAACTAATCATAA-TATTT
66 ATAGTTTTAATAATATAATATAA-T-ATCATAATTATTT
446512 TTTTAATGAA
Statistics
Matches: 98, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
125 86 0.88
126 7 0.07
127 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (125 bp):
ATAATATTAATATATTATTTTAATATCATTTTAATAAAATATTAATTATTAAATTTTATTTATTG
ATAGTTTTAATAATATAATATAATATCATAATTATTTATATAATTATATTATTATAATAT
Found at i:449454 original size:33 final size:34
Alignment explanation
Indices: 449409--449483 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
449399 AGCAACTCTC
449409 GGCCAT-ACAACTTGGTAGAGGCATCAAGAAAGG
1 GGCCATGACAACTTGGTAGAGGCATCAAGAAAGG
449442 GGCCATGA-AACTTGGTAGAGGCATCAAGAAAGG
1 GGCCATGACAACTTGGTAGAGGCATCAAGAAAGG
449475 GGCCATGAC
1 GGCCATGAC
449484 TTATTTGACC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.32, T:0.15
Consensus pattern (34 bp):
GGCCATGACAACTTGGTAGAGGCATCAAGAAAGG
Found at i:466181 original size:117 final size:117
Alignment explanation
Indices: 465964--466193 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 117
465954 GCAAGGTACA
* * * * * *
465964 CAATAAGCACATAAGTGCCACAATGATGTATAGGTAGTGTGGTACACAACGACACTATACTAACA
1 CAATAAGAACATAAGTGCCACAATGATGTATAGGTACTATAGTACAAAACAACACTATACTAACA
* * *
466029 ATTCCGGAGTAGTAATTCGTTATTAATATCTTCCTTGCACACAAAGTGTGCC
66 ATTCCGGAGTAGTAATTCATTATGAATATCATCCTTGCACACAAAGTGTGCC
* * * * *
466081 CAATAAGAACCTAAGTTCCACAATGATGTATATGTACTATAGTATAAAACAACACTATACTAATA
1 CAATAAGAACATAAGTGCCACAATGATGTATAGGTACTATAGTACAAAACAACACTATACTAACA
* * *
466146 ATTCTGGAGTGGTAATTCATTATGACTATCATCCTTGCACACAAAGTG
66 ATTCCGGAGTAGTAATTCATTATGAATATCATCCTTGCACACAAAGTG
466194 CCATATTACA
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
117 96 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (117 bp):
CAATAAGAACATAAGTGCCACAATGATGTATAGGTACTATAGTACAAAACAACACTATACTAACA
ATTCCGGAGTAGTAATTCATTATGAATATCATCCTTGCACACAAAGTGTGCC
Found at i:466285 original size:24 final size:26
Alignment explanation
Indices: 466225--466322 Score: 121
Period size: 26 Copynumber: 3.9 Consensus size: 26
466215 ATTACCATCT
* * *
466225 TTGCACTC-ATAGTGCCCTTTATCTC
1 TTGCACTCGAAAGTGCCATTTATCAC
466250 TTGCACTCGAAAGTGCCATTT-T-AC
1 TTGCACTCGAAAGTGCCATTTATCAC
* * *
466274 TTGCTCTAGAAAGTGCCATTTATCAA
1 TTGCACTCGAAAGTGCCATTTATCAC
466300 TTGCACTCGAAAGTGCCATTTAT
1 TTGCACTCGAAAGTGCCATTTAT
466323 ACCAAAGACT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
24 20 0.32
25 10 0.16
26 32 0.52
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (26 bp):
TTGCACTCGAAAGTGCCATTTATCAC
Found at i:468156 original size:17 final size:17
Alignment explanation
Indices: 468105--468159 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
468095 TTGCATTTAA
* *
468105 TAAAGCATGTCGTTCAT
1 TAAAGCATCTAGTTCAT
*
468122 TTAAGCATGC-A-TTGCAT
1 TAAAGCAT-CTAGTT-CAT
468139 TAAAGCATCTAGTTCAT
1 TAAAGCATCTAGTTCAT
468156 TAAA
1 TAAA
468160 TAAACTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 3 0.10
17 25 0.83
18 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (17 bp):
TAAAGCATCTAGTTCAT
Found at i:472770 original size:34 final size:34
Alignment explanation
Indices: 472691--472771 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
472681 TCATTTAGGG
* *
472691 AAAGTAGTTCATTTATGCATCTAGTTCATTAAAT
1 AAAGTAGTTCATTCATACATCTAGTTCATTAAAT
* * *
472725 AAACTAATTCATTCATACATTTAGTTCATT-AAT
1 AAAGTAGTTCATTCATACATCTAGTTCATTAAAT
472758 AAAGTTAGTTCATT
1 AAAG-TAGTTCATT
472772 AATTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAGTAGTTCATTCATACATCTAGTTCATTAAAT
Found at i:472783 original size:17 final size:17
Alignment explanation
Indices: 472711--472815 Score: 88
Period size: 17 Copynumber: 6.2 Consensus size: 17
472701 ATTTATGCAT
*
472711 CTAGTTCATTAAATAAA
1 CTAGTTCATTAATTAAA
* * *
472728 CTAATTCATTCA-TACAT
1 CTAGTTCATTAATTA-AA
*
472745 TTAGTTCATTAA-TAAA
1 CTAGTTCATTAATTAAA
*
472761 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
472779 CTAGTTCAATCATTAAA
1 CTAGTTCATTAATTAAA
* *
472796 CTAGTGCATTAATCAAA
1 CTAGTTCATTAATTAAA
472813 CTA
1 CTA
472816 ACTCATATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.04
17 64 0.90
18 4 0.06
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:472806 original size:51 final size:51
Alignment explanation
Indices: 472712--472808 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
472702 TTTATGCATC
* ** *
472712 TAGTTCATTAAATAAACTAATTCATTCATACATTTAGTTCATTAATAAAGT
1 TAGTTCATTAAATAAACTAATTCAATCATACAACTAGTGCATTAATAAAGT
* *
472763 TAGTTCATTAATTAAACTAGTTCAATCATTA-AACTAGTGCATTAAT
1 TAGTTCATTAAATAAACTAATTCAATCA-TACAACTAGTGCATTAAT
472809 CAAACTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 37 0.95
52 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (51 bp):
TAGTTCATTAAATAAACTAATTCAATCATACAACTAGTGCATTAATAAAGT
Found at i:473345 original size:22 final size:22
Alignment explanation
Indices: 473317--473366 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
473307 TCATTCATAT
473317 GAACCAAGCTATTGAATATGAA
1 GAACCAAGCTATTGAATATGAA
473339 GAACCAAGCTATTGAATATGAA
1 GAACCAAGCTATTGAATATGAA
473361 GAACCA
1 GAACCA
473367 CCTTTCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
GAACCAAGCTATTGAATATGAA
Found at i:483822 original size:2 final size:2
Alignment explanation
Indices: 483815--483873 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
483805 ATACATAAAT
483815 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
483857 AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC A
483874 TATATATATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:483878 original size:2 final size:2
Alignment explanation
Indices: 483873--483904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
483863 ACACACACAC
483873 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
483905 CTTTATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:484210 original size:2 final size:2
Alignment explanation
Indices: 484203--484281 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
484193 TTGATGTTAG
484203 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
484245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
484282 TAGAGGTTCG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:486958 original size:16 final size:16
Alignment explanation
Indices: 486937--486970 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
486927 AAAAATCACT
*
486937 TTGAAAAAATTTACTC
1 TTGAAAAAATTAACTC
486953 TTGAAAAAATTAACTC
1 TTGAAAAAATTAACTC
486969 TT
1 TT
486971 ACTGCCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
TTGAAAAAATTAACTC
Found at i:488224 original size:16 final size:16
Alignment explanation
Indices: 488181--488224 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
488171 TTTGATTGAT
488181 TTTTGTGTTTTGGATA
1 TTTTGTGTTTTGGATA
*
488197 TTTGGT-TGTTTGGATA
1 TTTTGTGT-TTTGGATA
488213 TTTTGTGTTTTG
1 TTTTGTGTTTTG
488225 AATGTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.09, C:0.00, G:0.27, T:0.64
Consensus pattern (16 bp):
TTTTGTGTTTTGGATA
Found at i:488524 original size:15 final size:16
Alignment explanation
Indices: 488481--488514 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
488471 AAGGGGCAGT
*
488481 AAGAGTTAATTTTTTC
1 AAGAGTAAATTTTTTC
488497 AAGAGTAAATTTTTTC
1 AAGAGTAAATTTTTTC
488513 AA
1 AA
488515 AGTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
AAGAGTAAATTTTTTC
Found at i:494655 original size:17 final size:17
Alignment explanation
Indices: 494615--494660 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
494605 TGCATTATAT
*
494615 ATCTAGTTCATTTAGGG
1 ATCTAGTTCATTTAGGC
** *
494632 AAGTAGTTCATTTATGC
1 ATCTAGTTCATTTAGGC
494649 ATCTAGTTCATT
1 ATCTAGTTCATT
494661 AAATAAACTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (17 bp):
ATCTAGTTCATTTAGGC
Found at i:494706 original size:30 final size:31
Alignment explanation
Indices: 494636--494706 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
494626 TTAGGGAAGT
*
494636 AGTTCATTT-ATGCATCTAGTTCATTAAATAA
1 AGTT-ATTTCATGCATCTAATTCATTAAATAA
* * *
494667 A-CTACTTCATGCATTTAATTCATT-AATAA
1 AGTTATTTCATGCATCTAATTCATTAAATAA
494696 AGTTATTTCAT
1 AGTTATTTCAT
494707 TAATTAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
29 9 0.28
30 22 0.69
31 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTATTTCATGCATCTAATTCATTAAATAA
Found at i:502286 original size:33 final size:33
Alignment explanation
Indices: 502239--502379 Score: 212
Period size: 33 Copynumber: 4.2 Consensus size: 33
502229 ACTCGAACCG
*
502239 GACCTGAATATCACACTTAAAAAAACCTGACCC
1 GACCCGAATATCACACTTAAAAAAACCTGACCC
* *
502272 GACCCGAATATCACACTTAAAAAAACCCGATCC
1 GACCCGAATATCACACTTAAAAAAACCTGACCC
502305 GACCCGAATATCACACTTAAAAAAA-CTCGACCC
1 GACCCGAATATCACACTTAAAAAAACCT-GACCC
* *
502338 GACCCGAATATCAAACTTTAAAAAAACCTGACTC
1 GACCCGAATATCACAC-TTAAAAAAACCTGACCC
502372 GACCCGAA
1 GACCCGAA
502380 CCCGAATTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
32 1 0.01
33 74 0.76
34 21 0.21
35 2 0.02
ACGTcount: A:0.43, C:0.31, G:0.10, T:0.16
Consensus pattern (33 bp):
GACCCGAATATCACACTTAAAAAAACCTGACCC
Found at i:502462 original size:32 final size:32
Alignment explanation
Indices: 502426--502513 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 32
502416 AAATTTAAAA
*
502426 AAAAAACCCAACCCGACCCAAATATCACACTT
1 AAAAAACCCAACCCGACCCAAATATCAAACTT
*
502458 AAAAAACCTGACCAGACCCGACCCGAATATCAAACTT
1 AAAAAA-C---CCA-ACCCGACCCAAATATCAAACTT
*
502495 AAAAAACCCGACCCGACCC
1 AAAAAACCCAACCCGACCC
502514 GCTCCCGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
32 15 0.31
33 3 0.06
36 4 0.08
37 26 0.54
ACGTcount: A:0.44, C:0.38, G:0.08, T:0.10
Consensus pattern (32 bp):
AAAAAACCCAACCCGACCCAAATATCAAACTT
Found at i:502477 original size:37 final size:37
Alignment explanation
Indices: 502436--502514 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
502426 AAAAAACCCA
* *
502436 ACCCGACCCAAATATCACACTTAAAAAACCTGACCAG
1 ACCCGACCCAAATATCAAACTTAAAAAACCCGACCAG
* *
502473 ACCCGACCCGAATATCAAACTTAAAAAACCCGACCCG
1 ACCCGACCCAAATATCAAACTTAAAAAACCCGACCAG
502510 ACCCG
1 ACCCG
502515 CTCCCGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.41, C:0.38, G:0.10, T:0.11
Consensus pattern (37 bp):
ACCCGACCCAAATATCAAACTTAAAAAACCCGACCAG
Found at i:504008 original size:2 final size:2
Alignment explanation
Indices: 503997--504039 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
503987 TTATATTGTT
503997 TA TA TA -A TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
504037 TA T
1 TA T
504040 TCAACATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:504021 original size:19 final size:19
Alignment explanation
Indices: 503997--504039 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
503987 TTATATTGTT
503997 TATATAATATATATATATA
1 TATATAATATATATATATA
504016 TATATAATATATATATATA
1 TATATAATATATATATATA
504035 TATAT
1 TATAT
504040 TCAACATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATAATATATATATATA
Found at i:505109 original size:238 final size:235
Alignment explanation
Indices: 504668--505546 Score: 790
Period size: 255 Copynumber: 3.7 Consensus size: 235
504658 TGGAAATAGT
**
504668 TTACTAA-TAAGCAAA-TTTGGAAATCACTTTCGTACTTTTCAAAAATTTCATTTTCTGAAAATA
1 TTACTAAGTAAG-AAACTTTGGAAATCACTTTC-TACTTTTCAAAAATTTCATTTTCAAAAAAT-
* * * * * * * * *
504731 CTGAACGAGAAACTTTGAAAATCGC--TCTCATTTTTTAAAAATCACGTGAGAACATCCTGCCCC
63 TTAAATGAGAAACTTTGGAAATCGCTTTCTCA-TTTTTCAAAATCATGTGAAAACATCCTACCCG
* * * *
504794 AAGGTCTTATGGATGGCCCGAAAGACTTGTAATCTT-GTTCAAA-A--ACAGATGACCCGAAGGA
127 AAGGTCTTATGGATGGCCCGAAGGACTTATAATCTTCCTTGAAAGACTACAGATGACCCGAAGGA
* *
504855 TTTAATCATCATGCTCGAAAGACTTAGTGATAGAC-CTAAGGAC
192 TTTAATCATCATGCTCGAAAGACTTACTGATAGACTCGAAGGAC
* * *
504898 TTATTAATTAAGAAACTTTGGAAATCATTTTCATACTTTTCAAAAATTTCATTTTCAAAAAGGAT
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTC-TACTTTTCAAAAATTTCATTTTCAAAAA--AT
* * *
504963 TTAAATAAGAAACTTTGGAAACCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTATCCGA
63 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTACCCGA
*
505028 AGATCTTATGGATGGCCCGAAGGACTTA-ATATCTTCCTTGAAAGACTTACAGATGACCCGAAGG
128 AGGTCTTATGGATGGCCCGAAGGACTTATA-ATCTTCCTTGAAAGAC-TACAGATGACCCGAAGG
* * *
505092 ATTTAATCATCATGCTCGAAATG-CTTATTGAT-GGCTCGAATGAC
191 ATTTAATCATCATGCTCGAAA-GACTTACTGATAGACTCGAAGGAC
* * *
505136 TTACTAAGTAAGAAACTTTGGAAATCGCTTTCTAACTTTTCAAAGATTTCATTTTCTGAAAACA-
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTCT-ACTTTTCAAAAATTTCATTTTC--AAAAAAT
** *
505200 TTAAATGAGAAACTTT-GAAATTACTTTCTCATTTTTC-AATTCATGTGAAAACAT-CTAGCCCG
63 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTA-CCCG
* * * * * * *
505262 AAGGTCTTATAGATGGCTCTAAGGACTTATCATCTTCCTCGAAAGGCTCACAGATGACCCAAAGG
127 AAGGTCTTATGGATGGCCCGAAGGACTTATAATCTTCCTTGAAAGACT-ACAGATGACCCGAAGG
* * * *
505327 AATTAATCATCATGCTCGAAAGATTTACTGATA-CCCCGAAGGTCTTATCATC
191 ATTTAATCATCATGCTCGAAAGACTTACTGATAGACTCGAAGG-------A-C
* *
505379 TTCAGAAATAGTCTATTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTGAAAGATTTCATT
1 -T------TA--C---TAAGTAAGAAACTTTGGAAATCACTTTC-TACTTTTCAAAAATTTCATT
* * * * *
505444 TTCTGAAAACA-TTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTTC-AAGTCATG-AAAAA
53 TTC--AAAAAATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAA
* * *
505506 CATCCTACCCAAAGATCTTATAGATGGCCCGAAGGACTTAT
116 CATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
505547 CATCCTGCTC
Statistics
Matches: 542, Mismatches: 62, Indels: 65
0.81 0.09 0.10
Matches are distributed among these distances:
230 9 0.02
231 45 0.08
232 20 0.04
233 59 0.11
234 15 0.03
235 107 0.20
236 18 0.03
237 18 0.03
238 101 0.19
239 1 0.00
240 4 0.01
242 1 0.00
243 1 0.00
244 1 0.00
250 2 0.00
252 1 0.00
255 109 0.20
256 30 0.06
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (235 bp):
TTACTAAGTAAGAAACTTTGGAAATCACTTTCTACTTTTCAAAAATTTCATTTTCAAAAAATTTA
AATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTGAAAACATCCTACCCGAAGG
TCTTATGGATGGCCCGAAGGACTTATAATCTTCCTTGAAAGACTACAGATGACCCGAAGGATTTA
ATCATCATGCTCGAAAGACTTACTGATAGACTCGAAGGAC
Found at i:506195 original size:41 final size:40
Alignment explanation
Indices: 506129--506252 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 40
506119 CATATGAAAA
* * * *
506129 CATCTTGCCGAAAGGTCTTATAGATGGCCCGAAGGAGTTAT
1 CATCTTGTCGAAAGG-CTTACAGATGGCCCAAAGGACTTAT
* * *
506170 CATCTTGTTCGAAAGGCTTACAGATGACCCAAAGAATTTAAT
1 CATCTTG-TCGAAAGGCTTACAGATGGCCCAAAGGACTT-AT
* * *
506212 CATCATGCTCAAAAGGCTTACTGATGGCCCAAAGGACTTAT
1 CATCTTG-TCGAAAGGCTTACAGATGGCCCAAAGGACTTAT
506253 TAAGTAAGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 27 0.40
42 41 0.60
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (40 bp):
CATCTTGTCGAAAGGCTTACAGATGGCCCAAAGGACTTAT
Found at i:506437 original size:239 final size:239
Alignment explanation
Indices: 506019--506594 Score: 704
Period size: 239 Copynumber: 2.4 Consensus size: 239
506009 GTCTACTAAA
* * * * *
506019 TAAGAAACTTTGGAAAT-TACTTTCTTTCTTTTCAAAGATTTCATTTTCTGAAAA-CA-TTAAAT
1 TAAGAAACTTTGAAAATGT--TTTCTTACTTTTCAAAAATTTCATTTTC-AAAAAGGATTTAAAT
* * * * * * *
506081 GAAAAACTTCGAAAAATCACTTTCTCATTTTTC-AAATTCATATGAAAACATCTTGCCGAAAGGT
63 GAGAAACTTTG-GAAATCTCTTTCTCATTTTTCAAAAATCATATGAAAACATCCTACCGAAAGGT
* * * *
506145 CTTATAGATGGCCCGAAGGAGTTATCATCTTGTTCGAAAGGCTTACAGATGACCCAAAGAATTTA
127 CTTATAGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTTA
* * * **
506210 ATCATCATGCTCAAAAGGCTTACTGA-TGGCCCAAAGGACTTATTAAG
192 ACCATCATGCTCAAAAGACTTACTGATTGCCCCAAAGGACTTACCAAG
506257 TAAGAAACTTTGCAAAATGTTTTCTTACTTTTCAAAAATTTCATTTTCAAAAAGGATTTAAATGA
1 TAAGAAACTTTG-AAAATGTTTTCTTACTTTTCAAAAATTTCATTTTCAAAAAGGATTTAAATGA
506322 GAAACTTTGGAAATCTCTTTCTCATTTTTCAAAAATCA-AGTGAAAACATCCTACCTG-AAGGTC
65 GAAACTTTGGAAATCTCTTTCTCATTTTTCAAAAATCATA-TGAAAACATCCTACC-GAAAGGTC
* * * *
506385 TTATAGATGACCGGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAA
128 TTATAGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTTAA
* * *
506450 CCATCATGCTCGAAAGACTTACTGATTGCCCCGAATGACTTACCAAG
193 CCATCATGCTCAAAAGACTTACTGATTGCCCCAAAGGACTTACCAAG
* *
506497 TAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCATAAAGGATTTAAATGA
1 TAAGAAACTTTGAAAAT-GTTTTCTTACTTTTCAAAAATTTCATTTTCAAAAAGGATTTAAATGA
* *
506562 GAAA-TCTGGACAT-TGCTTT-TGCATTTTTCAAAA
65 GAAACTTTGGAAATCT-CTTTCT-CATTTTTCAAAA
506595 TAACTTAATG
Statistics
Matches: 295, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
237 4 0.01
238 61 0.21
239 150 0.51
240 80 0.27
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (239 bp):
TAAGAAACTTTGAAAATGTTTTCTTACTTTTCAAAAATTTCATTTTCAAAAAGGATTTAAATGAG
AAACTTTGGAAATCTCTTTCTCATTTTTCAAAAATCATATGAAAACATCCTACCGAAAGGTCTTA
TAGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGAATTTAACCA
TCATGCTCAAAAGACTTACTGATTGCCCCAAAGGACTTACCAAG
Found at i:506443 original size:41 final size:42
Alignment explanation
Indices: 506384--506470 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
506374 ACCTGAAGGT
* * *
506384 CTTATAGATGACCGGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
*
506425 CTTATAGATGACCCGAAGGATTTAACCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
506467 CTTA
1 CTTA
506471 CTGATTGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 21 0.51
42 20 0.49
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAACCATCATGCTCGAAAGA
Found at i:508465 original size:99 final size:99
Alignment explanation
Indices: 508294--508483 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
508284 TTGTAATTTT
* * * * *
508294 CCTTTATCAGGCTAGTTGAATCTTATCCATAAAACTGGCGCGTTTAACCAATTGCTCTAGAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAACCGGAGCATTTAACCAATTACTCTAGAGGGA
*
508359 CAACTCAAGCTTTATTATATATATATTATAATCA
66 CAACTCAAGCTTTATTATATACATATTATAATCA
* *
508393 CCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACCAATTACTCTAGAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAACCGGAGCATTTAACCAATTACTCTAGAGGGA
* * *
508458 CATCTCAAGTTTTATTGTATACATAT
66 CAACTCAAGCTTTATTATATACATAT
508484 AATATTATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (99 bp):
CCTTTATCAGGCTAGCTGAATCTTATCCATAAAACCGGAGCATTTAACCAATTACTCTAGAGGGA
CAACTCAAGCTTTATTATATACATATTATAATCA
Found at i:510182 original size:20 final size:22
Alignment explanation
Indices: 510156--510208 Score: 83
Period size: 20 Copynumber: 2.5 Consensus size: 22
510146 ACCATTCAGG
*
510156 GGGGAATCGGTA-CCCCTTGGT
1 GGGGAATCGGTACCCCCTTGAT
510177 -GGGAATCGGTACCCCCTTGAT
1 GGGGAATCGGTACCCCCTTGAT
510198 GGGGAATCGGT
1 GGGGAATCGGT
510209 TCCCTATGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.38
21 8 0.28
22 10 0.34
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (22 bp):
GGGGAATCGGTACCCCCTTGAT
Found at i:512152 original size:21 final size:21
Alignment explanation
Indices: 512114--512153 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
512104 CAATGGGATT
* *
512114 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTAGATTTTG
*
512135 AGGATTTGGAAGTAGATTT
1 AGGATTAGGAAGTAGATTT
512154 GGTTGACGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTAGATTTTG
Found at i:512910 original size:20 final size:21
Alignment explanation
Indices: 512856--512918 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
512846 GATTCCCCTG
512856 TGGGGGGAATCGGTTCCTCTTCAA
1 TGGGGGG-ATCGGTTCC-C-TCAA
* *
512880 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
512900 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
512919 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:518223 original size:19 final size:20
Alignment explanation
Indices: 518199--518246 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
518189 TGGAGCGTGG
518199 GGGGAATCGGTA-CCCCTAT
1 GGGGAATCGGTACCCCCTAT
518218 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
518238 GGGGAATCG
1 GGGGAATCG
518247 ATTCCTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:520640 original size:47 final size:46
Alignment explanation
Indices: 520549--520642 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 46
520539 TTAAACATTA
* * *
520549 AAACTTAACCTCATGATATCTACTTCGCATGCTTATTCGAGAAAAGT
1 AAACCTAACCGCATGATATCTACTTCGCATACTTATTC-AGAAAAGT
* *
520596 AAACCTAACCGCATGATTTCTAGTTCGCATACATTTATTC-GAAAAGT
1 AAACCTAACCGCATGATATCTACTTCGCATAC--TTATTCAGAAAAGT
520643 GAAAATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 34 0.85
49 6 0.15
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (46 bp):
AAACCTAACCGCATGATATCTACTTCGCATACTTATTCAGAAAAGT
Found at i:530410 original size:24 final size:24
Alignment explanation
Indices: 530379--530450 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
530369 AATACATGAC
530379 CTGAATTCTGTTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * * * *
530403 CTGGATTCTGTTCTGATATATGTT
1 CTGAATTCTGTTATGATTTCTGAT
*
530427 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
530451 ATCTCCATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:530438 original size:12 final size:12
Alignment explanation
Indices: 530356--530448 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
530346 ATTTCCGACT
530356 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
530368 T-AATACATGACC
1 TGAATTC-TGTTC
*
530380 TGAATTCTGTTA
1 TGAATTCTGTTC
* *
530392 TGATTTCTGATC
1 TGAATTCTGTTC
*
530404 TGGATTCTGTTC
1 TGAATTCTGTTC
*
530416 TG-ATATATGTTC
1 TGAAT-TCTGTTC
*
530428 TGAATTCTGTTT
1 TGAATTCTGTTC
*
530440 TGATTTCTG
1 TGAATTCTG
530449 ATATCTCCAT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 6 0.10
12 48 0.80
13 6 0.10
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:530447 original size:48 final size:48
Alignment explanation
Indices: 530342--530450 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
530332 AAATATTTTA
* *
530342 TATGATTTCCGA-CTTGAATTCTGTTCTAATACATGACCTGAATTCTGT
1 TATGATTTCTGATC-TGGATTCTGTTCTAATACATGACCTGAATTCTGT
* * **
530390 TATGATTTCTGATCTGGATTCTGTTCTGATATATGTTCTGAATTCTGT
1 TATGATTTCTGATCTGGATTCTGTTCTAATACATGACCTGAATTCTGT
*
530438 TTTGATTTCTGAT
1 TATGATTTCTGAT
530451 ATCTCCATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (48 bp):
TATGATTTCTGATCTGGATTCTGTTCTAATACATGACCTGAATTCTGT
Found at i:533317 original size:45 final size:45
Alignment explanation
Indices: 533244--533413 Score: 279
Period size: 45 Copynumber: 3.8 Consensus size: 45
533234 TATAAAATTT
* *
533244 CTTATCATTTA-TCCTATAAGCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
533289 CATACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
533334 CTTGCCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
533379 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
533414 GCATGCTTAC
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
45 114 0.97
46 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:533567 original size:40 final size:40
Alignment explanation
Indices: 533493--533568 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
533483 AGTCACATAT
* *
533493 TGCACCGAAGTGCTGAGGTCGAGCATTTCTCACCTAATAA
1 TGCACCGAAGTGCAGAGGTCGAGCATTTCCCACCTAATAA
* *
533533 TGCACCGTAGTGCAGAGGTCGGGC-TTTACCCACCTA
1 TGCACCGAAGTGCAGAGGTCGAGCATTT-CCCACCTA
533569 GTACACCGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.10
40 28 0.90
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24
Consensus pattern (40 bp):
TGCACCGAAGTGCAGAGGTCGAGCATTTCCCACCTAATAA
Found at i:537112 original size:6 final size:6
Alignment explanation
Indices: 537101--537788 Score: 1112
Period size: 6 Copynumber: 115.7 Consensus size: 6
537091 AGACATTTAC
537101 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
537149 TATACA TATACA TATACA TACACA TACATACA TATACA TATAC- -ATACA
1 TATACA TATACA TATACA TATACA T--ATACA TATACA TATACA TATACA
* * * * * *
537197 TATACA TATACA TACATA CATACA TACACA TACACA TACATACA TACACA
1 TATACA TATACA TATACA TATACA TATACA TATACA T--ATACA TATACA
* *
537247 TACATACA TATACA TATACA TATACA TACACA TACACA TATAC- -ATACA
1 T--ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
* * * *
537295 CATACA CATACA CATACA TATAC- -ATACA CATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
537341 TATACA CATACA TATACA TATAC- -ATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537387 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537434 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537481 TATACA TATAC- -ATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537527 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537575 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537623 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537671 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537719 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
537767 TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATA
537789 TGATTAGTTT
Statistics
Matches: 646, Mismatches: 18, Indels: 36
0.92 0.03 0.05
Matches are distributed among these distances:
4 24 0.04
6 607 0.94
8 15 0.02
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
TATACA
Found at i:538101 original size:2 final size:2
Alignment explanation
Indices: 538094--538125 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
538084 GCATACATAC
538094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
538126 GGTTTGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:539556 original size:67 final size:67
Alignment explanation
Indices: 539432--539595 Score: 208
Period size: 66 Copynumber: 2.5 Consensus size: 67
539422 TTTTTTGGGG
* * *
539432 TTTAGA-TATTTGGATATTTGTATGAATTTAT-CATCTTGAATGATTTTTCATACTTTGGTTGTG
1 TTTAGATTATTTGGATATTTGGATGATTTTATGCATCTTGAATGATTTTTCATACTTTGGTTGCG
539495 GA
66 GA
* ** * *
539497 TTTGGATTATTTGGATATTTGGATGATTTTATGTTTTTTGGATGATTTTTCATACTTTGGTTGCG
1 TTTAGATTATTTGGATATTTGGATGATTTTATGCATCTTGAATGATTTTTCATACTTTGGTTGCG
539562 GA
66 GA
* * *
539564 TTTAGATGA-TTGAATATTTTGATGATTTTATG
1 TTTAGATTATTTGGATATTTGGATGATTTTATG
539596 GATATTTATA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 5 0.06
66 44 0.52
67 36 0.42
ACGTcount: A:0.23, C:0.04, G:0.21, T:0.52
Consensus pattern (67 bp):
TTTAGATTATTTGGATATTTGGATGATTTTATGCATCTTGAATGATTTTTCATACTTTGGTTGCG
GA
Found at i:543140 original size:20 final size:21
Alignment explanation
Indices: 543115--543157 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
543105 CCCCCAAATC
*
543115 TCTAAAC-CTAAATCCTTAAA
1 TCTAAACTCAAAATCCTTAAA
*
543135 TCTAAACTCAAAATCTTTAAA
1 TCTAAACTCAAAATCCTTAAA
543156 TC
1 TC
543158 CCAACACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
TCTAAACTCAAAATCCTTAAA
Found at i:544681 original size:21 final size:21
Alignment explanation
Indices: 544655--544695 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
544645 GATCATGATC
544655 ATGATCGAACAATTCAACTTA
1 ATGATCGAACAATTCAACTTA
544676 ATGATCGAACAATTCAACTT
1 ATGATCGAACAATTCAACTT
544696 TCACTTTTAC
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:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (21 bp):
ATGATCGAACAATTCAACTTA
Found at i:549486 original size:157 final size:156
Alignment explanation
Indices: 549143--549487 Score: 523
Period size: 156 Copynumber: 2.2 Consensus size: 156
549133 GATAGAAACG
* *
549143 TTTCAGTGATATATCAGACCATTGAATGATGTTTTTGACTTATTTCCCTTTAATGAAAAACATCA
1 TTTCAGTGATATATCAGACAATTGAATGATGTCTTTGACTTATTTCCCTTTAATGAAAAACATCA
* *
549208 TTTTCTCATAGACCATTTAATACACAATGAAAAAATCTTTTCAGTTCCCAATCATTTTATTTCAG
66 TTTTCTCATAGACCATTTAATACACAATGAAAAAATCTTTTCAATTCCCAATCACTTTATTTCAG
*
549273 AAACTTTTCAGTGATATATCACTTCA
131 AAACTTTTCAATGATATATCACTTCA
* * * *
549299 TTTCAGTGAAATATCAAACAATTGAATGATGTCTTTGACTTGTTTCCCTTTAATGAAAAACTTCA
1 TTTCAGTGATATATCAGACAATTGAATGATGTCTTTGACTTATTTCCCTTTAATGAAAAACATCA
*
549364 TTTTCTCATAGACCATTTAGTACACAATGACAAACAA-CTTTTCAATGT-CCAATCACTTTATTT
66 TTTTCTCATAGACCATTTAATACACAATGA-AAA-AATCTTTTCAAT-TCCCAATCACTTTATTT
* * *
549427 TAGAAACTTTTCAATGATGTATTACTTCA
128 CAGAAACTTTTCAATGATATATCACTTCA
*
549456 TTTCATTGATATATCAGACAATTGAATGATGT
1 TTTCAGTGATATATCAGACAATTGAATGATGT
549488 TTTTAACCAT
Statistics
Matches: 170, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
156 88 0.52
157 79 0.46
158 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (156 bp):
TTTCAGTGATATATCAGACAATTGAATGATGTCTTTGACTTATTTCCCTTTAATGAAAAACATCA
TTTTCTCATAGACCATTTAATACACAATGAAAAAATCTTTTCAATTCCCAATCACTTTATTTCAG
AAACTTTTCAATGATATATCACTTCA
Found at i:550093 original size:24 final size:26
Alignment explanation
Indices: 550046--550101 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 26
550036 TATTGAATTG
550046 TAATGTAATGTAAGAGTTAATGTTTC
1 TAATGTAATGTAAGAGTTAATGTTTC
550072 TAAT-TAATGT-AG-GTGTAATGTTTC
1 TAATGTAATGTAAGAGT-TAATGTTTC
550096 TAATGT
1 TAATGT
550102 GTGGGTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.07
24 15 0.54
25 7 0.25
26 4 0.14
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (26 bp):
TAATGTAATGTAAGAGTTAATGTTTC
Found at i:557280 original size:2 final size:2
Alignment explanation
Indices: 557275--557323 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
557265 ATATATATAT
* * *
557275 AG AG AG AG AG AG AG AG AG -G GG GG AG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
557316 AG AG AG AG
1 AG AG AG AG
557324 TCGGGGCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
AG
Found at i:557904 original size:16 final size:16
Alignment explanation
Indices: 557883--557922 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
557873 CAATCGAATG
557883 ATGCCACGTATCACTA
1 ATGCCACGTATCACTA
557899 ATGCCACGTATCACTA
1 ATGCCACGTATCACTA
557915 ATGCCACG
1 ATGCCACG
557923 ACCAATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.23
Consensus pattern (16 bp):
ATGCCACGTATCACTA
Found at i:558045 original size:27 final size:25
Alignment explanation
Indices: 558004--558080 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
557994 TATTTTTATA
*
558004 TATATTAAC-TATAAAAAAATATTTT
1 TATATTAACTTAT-TAAAAATATTTT
*
558029 TATATTAACTTATTAAATATA-TTT
1 TATATTAACTTATTAAAAATATTTT
558053 TATGATTAACTTAATTTAAAAATATTTT
1 TAT-ATTAACTT-A-TTAAAAATATTTT
558081 CTCCATTGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.14
25 23 0.52
26 4 0.09
27 8 0.18
28 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (25 bp):
TATATTAACTTATTAAAAATATTTT
Found at i:564203 original size:15 final size:15
Alignment explanation
Indices: 564183--564231 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
564173 ATTTAGTTGG
564183 GCGGGCGGATGCGGT
1 GCGGGCGGATGCGGT
* *
564198 GCGGGCGGATACGGG
1 GCGGGCGGATGCGGT
**
564213 GCGGGTAGATGCGGT
1 GCGGGCGGATGCGGT
564228 GCGG
1 GCGG
564232 ATGCGGGGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.10, C:0.18, G:0.59, T:0.12
Consensus pattern (15 bp):
GCGGGCGGATGCGGT
Found at i:564231 original size:26 final size:25
Alignment explanation
Indices: 564197--564245 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
564187 GCGGATGCGG
564197 TGCGGGCGGATACGGGGCGGGTAGA
1 TGCGGGCGGATACGGGGCGGGTAGA
*
564222 TGCGGTGCGGATGCGGGGCGGGTA
1 TGCGG-GCGGATACGGGGCGGGTA
564246 AGGTCTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.12, C:0.16, G:0.57, T:0.14
Consensus pattern (25 bp):
TGCGGGCGGATACGGGGCGGGTAGA
Found at i:564970 original size:22 final size:23
Alignment explanation
Indices: 564922--564970 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
564912 TATTTTATTC
*
564922 ATTTCAATATTTTATTCAATATT
1 ATTTCAATATTTTATTCAATATA
*
564945 ATTTCAA-ATTTTAATTC-GTATA
1 ATTTCAATATTTT-ATTCAATATA
564967 ATTT
1 ATTT
564971 TTATGAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTCAATATTTTATTCAATATA
Found at i:568161 original size:95 final size:95
Alignment explanation
Indices: 567960--568162 Score: 257
Period size: 95 Copynumber: 2.1 Consensus size: 95
567950 TCGATTCCAC
*
567960 AGTAAGGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATCGATACCGAAGGGGGGTATC
1 AGTAAGGGTATCGATACCAGGAAACATCGAACCTAAATTTGGTATCGATACCGAAGGGGGGTATC
* * *
568025 GGTACCATAGCATAGTAGTATCGATATCAT
66 GATACCATAGCAGAGTAGTACCGATATCAT
* * ** * *
568055 GGTAAGAGTATCGATACCAGGCTACATCGAAGCTAAATTTGGTATCGATACTGGAA-GGGGGTAT
1 AGTAAGGGTATCGATACCAGGAAACATCGAACCTAAATTTGGTATCGATAC-CGAAGGGGGGTAT
* *
568119 CGATACCATAGTAGGGTAGTACCGATA-CTAT
65 CGATACCATAGCAGAGTAGTACCGATATC-AT
*
568150 AGTAGGGGTATCG
1 AGTAAGGGTATCG
568163 GTACTGAGGA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 87 0.96
96 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (95 bp):
AGTAAGGGTATCGATACCAGGAAACATCGAACCTAAATTTGGTATCGATACCGAAGGGGGGTATC
GATACCATAGCAGAGTAGTACCGATATCAT
Found at i:568968 original size:45 final size:45
Alignment explanation
Indices: 568558--568974 Score: 448
Period size: 45 Copynumber: 9.3 Consensus size: 45
568548 TGAAAATACT
*** * *
568558 AATGCATATGGGTACATTATTGGCATG-AAA-TAATGCCATTGTTGA
1 AATGCATATGGGTACATTATCAACA-GAAAAGT-ATGCTATAGTTGA
* * ** *
568603 AATGCATATGGGTAGATTATGAACAGAAAAGTATAATATGGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
568648 AATGTATATGGGTACATTATCAACAGAAAA-TATGTTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * *
568692 AATGCATATGGGTGCATTATCAACAGAAATGTATGCTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * *
568737 AATGCATATGGGTTCATTATCAACA-AAAGAGCATGCTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAA-AGTATGCTATAGTTGA
* * * *
568782 AATGTATATCGGTACATTATCAACAGAAAAGTATACTATGGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * * *
568827 AATGTATATGGGTACATTACCAACAGAAAAGTATACTATGGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* **
568872 AATGTATATGGGTACATTATCAACAGAAAAGTATATTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* * * * *
568917 AATGCATATGGGTGCATTATCAACACAAAAG-ATGTTATAATTTA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
568961 AAGTGCATAATGGG
1 AA-TGCAT-ATGGG
568975 GTATTATAAA
Statistics
Matches: 325, Mismatches: 40, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
44 54 0.17
45 262 0.81
46 9 0.03
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
Found at i:574566 original size:11 final size:11
Alignment explanation
Indices: 574538--574575 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
574528 TTAAGATAGG
574538 ATAAATTT-TA
1 ATAAATTTATA
574548 ATAGAAATTTATA
1 AT--AAATTTATA
574561 ATAAATTTATA
1 ATAAATTTATA
574572 ATAA
1 ATAA
574576 TAGTACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 6 0.24
13 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
ATAAATTTATA
Found at i:575262 original size:111 final size:111
Alignment explanation
Indices: 575068--575296 Score: 318
Period size: 111 Copynumber: 2.1 Consensus size: 111
575058 GCCATAGGTG
** * * *
575068 CATTTCGAAATACTTTGTGTATGATAGTATCGATCGATTTTGTTTAATGCATAACGGTGCATTTT
1 CATTTCGAAATACTTCATGTATGAAAGTATCGATCGATTTTGCTTAATGCATAACGGGGCATTTT
*
575133 TGGCATAAAAGGTGCCACCCATTGTATTCATAATAA-GTTGAATTAC
66 TGGCATAAAAGGTGCCACCCATGGTATTCATAATAATG-TGAATTAC
* * *
575179 CATTTCGACATACTTCATTTATGAAAGTTATCGATCGATTTTGCTTAATGCGTAACGGGGCA-TT
1 CATTTCGAAATACTTCATGTATGAAAG-TATCGATCGATTTTGCTTAATGCATAACGGGGCATTT
* * *
575243 TTGGTATAAAATGTGCCACCCATGGTATTCATAATGATGTGAATTAC
65 TTGGCATAAAAGGTGCCACCCATGGTATTCATAATAATGTGAATTAC
575290 CATTTCG
1 CATTTCG
575297 GCACTTCAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
111 72 0.69
112 32 0.31
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (111 bp):
CATTTCGAAATACTTCATGTATGAAAGTATCGATCGATTTTGCTTAATGCATAACGGGGCATTTT
TGGCATAAAAGGTGCCACCCATGGTATTCATAATAATGTGAATTAC
Found at i:576975 original size:22 final size:22
Alignment explanation
Indices: 576950--576995 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
576940 TTTTATGGAT
576950 TTTTCATAAAAAGGATCGAT-TC
1 TTTTC-TAAAAAGGATCGATCTC
* *
576972 TTTTCTCAAATGGATCGATCTC
1 TTTTCTAAAAAGGATCGATCTC
576994 TT
1 TT
576996 AAGGCAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (22 bp):
TTTTCTAAAAAGGATCGATCTC
Found at i:583473 original size:24 final size:23
Alignment explanation
Indices: 583446--583505 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
583436 GATTAAAATA
583446 TATATTATATTTATTATTATATAC
1 TATATTATATTTATTATTAT-TAC
* *
583470 TATAGTATGA-TTATTATTATTAT
1 TATATTAT-ATTTATTATTATTAC
583493 TAATATTAT-TTTA
1 T-ATATTATATTTA
583506 CAATATTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 6 0.20
24 23 0.77
25 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
TATATTATATTTATTATTATTAC
Found at i:586709 original size:45 final size:47
Alignment explanation
Indices: 586615--586713 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 47
586605 ATATTTTTCC
* * *
586615 TTTCAAATAAATGCATGCGAATTAGAGATCATGTGGTTAGGTTTGTT
1 TTTCAAATAAATGCATGCGAATTAAAGATCATGCGGTTAGATTTGTT
* *
586662 TTTCAAA-AAA-GTATGCGAATTAAATATCATGCGGTTAGAATTT-TT
1 TTTCAAATAAATGCATGCGAATTAAAGATCATGCGGTTAG-ATTTGTT
586707 TTT-AAAT
1 TTTCAAAT
586714 GACAAAGCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
44 3 0.07
45 29 0.64
46 6 0.13
47 7 0.16
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (47 bp):
TTTCAAATAAATGCATGCGAATTAAAGATCATGCGGTTAGATTTGTT
Found at i:587382 original size:20 final size:20
Alignment explanation
Indices: 587357--587396 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
587347 TAATACCTCG
*
587357 TGCATTTGCATTA-TTATTTT
1 TGCATTGGC-TTATTTATTTT
587377 TGCATTGGCTTATTTATTTT
1 TGCATTGGCTTATTTATTTT
587397 GATATTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (20 bp):
TGCATTGGCTTATTTATTTT
Found at i:590419 original size:14 final size:15
Alignment explanation
Indices: 590398--590435 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
590388 TAGGGATAAT
*
590398 AAAG-AAAAAAGAGC
1 AAAGAAAAAAAAAGC
590412 AAA-AAAAAAAAAGC
1 AAAGAAAAAAAAAGC
590426 AAAGAAAAAA
1 AAAGAAAAAA
590436 TGTAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAGC
Found at i:590447 original size:14 final size:13
Alignment explanation
Indices: 590398--590447 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
590388 TAGGGATAAT
590398 AAAGAAAAAAGAGC
1 AAAGAAAAAA-AGC
*
590412 AAAAAAAAAAAAGC
1 -AAAGAAAAAAAGC
* *
590426 AAAGAAAAAATGT
1 AAAGAAAAAAAGC
590439 AAAGAAAAA
1 AAAGAAAAA
590448 GGGATGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 19 0.61
14 3 0.10
15 9 0.29
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAAAGC
Found at i:591123 original size:32 final size:32
Alignment explanation
Indices: 591077--591170 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 32
591067 ATAAGAAGGC
*
591077 CAAACCATTAACCAAAAATAACCTGAGACATT
1 CAAACCATTGACCAAAAATAACCTGAGACATT
*
591109 CAAACCATTGACCAAAAACAACCTGAGACATT
1 CAAACCATTGACCAAAAATAACCTGAGACATT
591141 CAAACCATTGACCAAACACAATAACCTGAG
1 CAAACCATTGACC-AA-A-AATAACCTGAG
591171 TTTCATTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 43 0.77
33 2 0.04
34 1 0.02
35 10 0.18
ACGTcount: A:0.48, C:0.28, G:0.09, T:0.16
Consensus pattern (32 bp):
CAAACCATTGACCAAAAATAACCTGAGACATT
Found at i:591577 original size:32 final size:32
Alignment explanation
Indices: 591524--591755 Score: 338
Period size: 32 Copynumber: 7.2 Consensus size: 32
591514 AAGCAATAGA
*
591524 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
* *
591556 GGCCATTTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
591588 AGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * *
591621 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
591653 GGGCATCTTTGGAGATTCAACATTAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
591685 GGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * *
591718 GGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
591750 TGGCAT
1 GGGCAT
591756 TAAATATCCT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
32 118 0.66
33 61 0.34
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:591658 original size:65 final size:64
Alignment explanation
Indices: 591524--591755 Score: 338
Period size: 65 Copynumber: 3.6 Consensus size: 64
591514 AAGCAATAGA
* * *
591524 GGGCATCTTTGAAGATTCAACATCAAATGTTGGGCCATTTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATGTTG
* * * *
591588 AGGCATCTTTGGAGATTCAACATCAAAATGTTGGGGCATCTTTGGAGATTCAATATCGAATATTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTGGGGCATCTTTGGAGATTCAACATCAAATGTTG
*
591653 GGGCATCTTTGGAGATTCAACATTAAATGTTGGGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * * *
591718 GGGCATCTTTGGAGATTCAATATCGAATATTGTGGCAT
1 GGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCAT
591756 TAAATATCCT
Statistics
Matches: 149, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
64 53 0.36
65 96 0.64
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (64 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTGGGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:591690 original size:97 final size:97
Alignment explanation
Indices: 591524--591755 Score: 383
Period size: 97 Copynumber: 2.4 Consensus size: 97
591514 AAGCAATAGA
* * * * * *
591524 GGGCATCTTTGAAGATTCAACATCAAATGTTGGGCCATTTTTGGAGATTCAACATCAAATGTTGA
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTGA
591589 GGCATCTTTGGAGATTCAACATCAAAATGTTG
66 GGCATCTTTGGAGATTCAACATCAAAATGTTG
* *
591621 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATTAAATGTTGG
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTGA
591686 GGCATCTTTGGAGATTCAACATCAAAATGTTG
66 GGCATCTTTGGAGATTCAACATCAAAATGTTG
*
591718 GGGCATCTTTGGAGATTCAATATCGAATATTGTGGCAT
1 GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCAT
591756 TAAATATCCT
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 126 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (97 bp):
GGGCATCTTTGGAGATTCAATATCGAATATTGGGGCATCTTTGGAGATTCAACATCAAATGTTGA
GGCATCTTTGGAGATTCAACATCAAAATGTTG
Found at i:591898 original size:34 final size:34
Alignment explanation
Indices: 591863--592017 Score: 222
Period size: 34 Copynumber: 4.6 Consensus size: 34
591853 ATTTTTTTTT
* * * *
591863 GTCTCACTCGAGACAATTTCTCAAAATAAATTTT
1 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTG
* *
591897 GTCTTAG-TTGAGACAATTTCTCATAACAAATTTG
1 GTC-TCGCTTGAGACAATTTCTCAAAACAAATTTG
*
591931 GTCTCGCTTGAGACCATTTCTCAAAACAAATTTG
1 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTG
*
591965 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTCTCAAAACAAATTTG
591999 GTCTCGCTTGAGACAATTT
1 GTCTCGCTTGAGACAATTT
592018 TTCTCTAAGA
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
33 2 0.02
34 105 0.97
35 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (34 bp):
GTCTCGCTTGAGACAATTTCTCAAAACAAATTTG
Found at i:592440 original size:36 final size:36
Alignment explanation
Indices: 592321--592431 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 36
592311 CACTCAAGAT
*
592321 AGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGAC
1 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
* * *
592357 AGTTTCTCTCGAAACAAATTTTGTCTCTCTTGAGAC
1 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
592393 -GATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
1 AG-TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
592429 AGT
1 AGT
592432 CTAGCTTGAG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.02
36 64 0.97
37 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (36 bp):
AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
Found at i:592949 original size:89 final size:90
Alignment explanation
Indices: 592579--592997 Score: 664
Period size: 90 Copynumber: 4.7 Consensus size: 90
592569 ATTTTCAAGA
* *
592579 GTTTCTTGATTTTTAAGTCCTTCGGGCCAACCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
592644 GATCTAAGAAACTGAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
*
592669 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGGGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
592734 GATCTAAGAAACTGAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
*
592759 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
** *
592824 GATCTAAGAAACTGAGATTTCGAGG
66 GATCTAAGAAACTGAGCCTTCGGGG
*
592849 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCTGTAAGACCTTCA-TGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
592913 GATTTAAGAAACTAAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
* * * * **
592938 GTTTCTTGATTTTTTAAGTCCTTCAGG-CAACCATAAGACCTTC-GGGCAAAATGTTTTCAA
1 GTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAA
592998 CATTTCCATT
Statistics
Matches: 307, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
89 75 0.24
90 232 0.76
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (90 bp):
GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGA
GATCTAAGAAACTGAGCCTTCGGGG
Found at i:596536 original size:24 final size:24
Alignment explanation
Indices: 596492--596538 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
596482 ATTCATACCC
*
596492 AAAATCATTCATAAACCATTTCAG
1 AAAATCATTCATAAAACATTTCAG
*
596516 AAAATCATT-ATGAAAATATTTCA
1 AAAATCATTCAT-AAAACATTTCA
596539 TAATAGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAATCATTCATAAAACATTTCAG
Found at i:597727 original size:12 final size:13
Alignment explanation
Indices: 597701--597729 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
597691 AACATGTTCT
597701 TCATGAATCTTAA
1 TCATGAATCTTAA
597714 TCATGAAT-TTAA
1 TCATGAATCTTAA
597726 TCAT
1 TCAT
597730 CCAAGCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (13 bp):
TCATGAATCTTAA
Found at i:599222 original size:18 final size:17
Alignment explanation
Indices: 599199--599233 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
599189 ATTAAACAAC
599199 AATAAAACAACATAAAAA
1 AATAAAACAA-ATAAAAA
*
599217 AATAAAAGAAATAAAAA
1 AATAAAACAAATAAAAA
599234 TAAAGGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (17 bp):
AATAAAACAAATAAAAA
Found at i:600571 original size:2 final size:2
Alignment explanation
Indices: 600566--600701 Score: 168
Period size: 2 Copynumber: 69.0 Consensus size: 2
600556 TGTATTAATA
* *
600566 AT AT AT AT AT AT AT AT AT A- AT AT AT AT GT AT AT GT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
600606 AT AT AT AT AT AT AT AC AT AT AT AT AC AT AT AT AC AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
600648 AT AT AT AC AT AT AT AC AT AT AT AC 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
*
600690 AT AT AT GT AT AT
1 AT AT AT AT AT AT
600702 CGTGAAATGT
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
1 2 0.02
2 110 0.98
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:601639 original size:57 final size:57
Alignment explanation
Indices: 601552--601710 Score: 237
Period size: 57 Copynumber: 2.8 Consensus size: 57
601542 ACCAAATTAT
* *
601552 CTTTGAGTTAGATATCCTTCGTTGTCAAGTTGAAATCCAATCTTGAATATTGTTCGG
1 CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTGTTCGG
* *
601609 CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCACTCTTGTATATTGTTCGG
1 CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTGTTCGG
* * * * *
601666 TTTTGAGTTGGATATCATTTGTTGCGAAGTTCAAATCCAATCTTG
1 CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTG
601711 TATGAATTTC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (57 bp):
CTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAATATTGTTCGG
Found at i:602614 original size:5 final size:6
Alignment explanation
Indices: 602596--602626 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
602586 TGAACCCACC
602596 TTATTT TTATTT TTATTT TTA-TT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
602627 CTCTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:602620 original size:11 final size:12
Alignment explanation
Indices: 602596--602626 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
602586 TGAACCCACC
602596 TTATTTTTATTT
1 TTATTTTTATTT
602608 TTATTTTTA-TT
1 TTATTTTTATTT
602619 TTATTTTT
1 TTATTTTT
602627 CTCTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:602698 original size:11 final size:11
Alignment explanation
Indices: 602674--602714 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
602664 CCCTAAACAT
602674 TTTTC-TTTTA
1 TTTTCTTTTTA
602684 -TTTCTTTTCT-
1 TTTTCTTTT-TA
602694 TTTTCTTTTTA
1 TTTTCTTTTTA
602705 TTTTCTTTTT
1 TTTTCTTTTT
602715 CCTCTTCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.15
10 4 0.15
11 19 0.70
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTA
Found at i:609753 original size:18 final size:20
Alignment explanation
Indices: 609717--609755 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
609707 ATATGAATGT
609717 AAAAACATGGAAAATATAAA
1 AAAAACATGGAAAATATAAA
609737 AAAAACAT-GAAAA-ATAAA
1 AAAAACATGGAAAATATAAA
609755 A
1 A
609756 TGCAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
20 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAACATGGAAAATATAAA
Found at i:613224 original size:21 final size:21
Alignment explanation
Indices: 613164--613227 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
613154 ACTCCAAGTG
613164 AAATAAA-AATAAAAAAT-AAA
1 AAATAAATAA-AAAAAATAAAA
** *
613184 AAACCAATAAAACAACATAAAA
1 AAATAAATAAAA-AAAATAAAA
*
613206 AAATAAATAAAAGAAATAAAA
1 AAATAAATAAAAAAAATAAAA
613227 A
1 A
613228 TAAAGGGGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 7 0.21
21 14 0.41
22 13 0.38
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (21 bp):
AAATAAATAAAAAAAATAAAA
Found at i:620772 original size:23 final size:24
Alignment explanation
Indices: 620746--620796 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
620736 TCAAAATTCT
620746 TTGTAAATGG-ATTAAATAGCCAA
1 TTGTAAATGGTATTAAATAGCCAA
*
620769 TTGTAAATGGTCTATTAAGTAGCCAA
1 TTGTAAATGG--TATTAAATAGCCAA
620795 TT
1 TT
620797 TATAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
26 14 0.58
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (24 bp):
TTGTAAATGGTATTAAATAGCCAA
Found at i:626893 original size:14 final size:14
Alignment explanation
Indices: 626874--626924 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
626864 AAAACCGAAA
626874 TCGGTTTTTTCGGT
1 TCGGTTTTTTCGGT
626888 TCGGTTCTTTTAACGGT
1 TCGGTT-TTTT--CGGT
626905 TCGAG-TTTTTCGGT
1 TCG-GTTTTTTCGGT
626919 TCGGTT
1 TCGGTT
626925 CGGTTCGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 14 0.44
15 4 0.12
16 4 0.12
17 8 0.25
18 1 0.03
ACGTcount: A:0.06, C:0.16, G:0.27, T:0.51
Consensus pattern (14 bp):
TCGGTTTTTTCGGT
Found at i:627738 original size:21 final size:22
Alignment explanation
Indices: 627696--627740 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
627686 GTTTACCCTA
* *
627696 AATTATAGATTACTTTAAATTT
1 AATTATAGAATACTTGAAATTT
627718 AATTATAGAATA-TTGAAATTT
1 AATTATAGAATACTTGAAATTT
627739 AA
1 AA
627741 GATTACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTATAGAATACTTGAAATTT
Found at i:629461 original size:28 final size:28
Alignment explanation
Indices: 629424--629488 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
629414 TCAGGTTGTA
* * *
629424 TATTTCCTTGCTAATATATATGTTTTAT
1 TATTTACTTGATAATACATATGTTTTAT
* *
629452 TATTTACTTGATATTACATTTGTTTTAT
1 TATTTACTTGATAATACATATGTTTTAT
629480 TGA-TTACTT
1 T-ATTTACTT
629489 TTAAATATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTACTTGATAATACATATGTTTTAT
Found at i:636254 original size:25 final size:25
Alignment explanation
Indices: 636221--636269 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
636211 TTAAGATATG
636221 ATAAAACATTGTTTTATCAAAACAT
1 ATAAAACATTGTTTTATCAAAACAT
*
636246 ATAATACATTGTTTTATCAAAACA
1 ATAAAACATTGTTTTATCAAAACA
636270 GGCGAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (25 bp):
ATAAAACATTGTTTTATCAAAACAT
Done.