Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007888.1 Hibiscus syriacus cultivar Beakdansim tig00110270_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: 1558302
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:452937 original size:76 final size:76
Alignment explanation
Indices: 452822--452982 Score: 272
Period size: 76 Copynumber: 2.1 Consensus size: 76
452812 GGAAATGACT
* ** *
452822 ATCGCAA--CGCGGAAATGACTATCGCAATGCGAATTTGACTGTCGCAATGCGAATTTGACTATC
1 ATCGCAATGCGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATC
452885 GCAACGAGAGA
66 GCAACGAGAGA
452896 ATCGCAATGCGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATC
1 ATCGCAATGCGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATC
452961 GCAACGAGAGA
66 GCAACGAGAGA
452972 ATCGCAATGCG
1 ATCGCAATGCG
452983 ATTTTCATTT
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 7 0.09
76 74 0.91
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (76 bp):
ATCGCAATGCGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATC
GCAACGAGAGA
Found at i:453036 original size:20 final size:20
Alignment explanation
Indices: 453011--453120 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
453001 GATTCTCTCG
**
453011 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
453031 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
453051 TTGTGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
453071 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
453091 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
453111 TTGCGATAGT
1 TTGCGATAGT
453121 AAACTGTTCT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:453277 original size:22 final size:21
Alignment explanation
Indices: 453237--453277 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
453227 CAGTATTGGC
*
453237 AGCAATCGAATGAATTTACTA
1 AGCAATCGAATGAAATTACTA
*
453258 AGCAATCTAAGTGAAATTAC
1 AGCAATCGAA-TGAAATTAC
453278 GAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (21 bp):
AGCAATCGAATGAAATTACTA
Found at i:454908 original size:19 final size:19
Alignment explanation
Indices: 454866--454948 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
454856 TGAAACTTAA
*
454866 ATCGCAACACGAAATGA-A
1 ATCGCAACACGAAATGACT
**
454884 ATCGCAACAAAAAATGACT
1 ATCGCAACACGAAATGACT
* *
454903 ATCGCAACGCGAATTGACT
1 ATCGCAACACGAAATGACT
* **
454922 ATCGCAACGCGAAATGAAA
1 ATCGCAACACGAAATGACT
454941 ATCGCAAC
1 ATCGCAAC
454949 GACAGAATCG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 15 0.28
19 39 0.72
ACGTcount: A:0.45, C:0.24, G:0.17, T:0.14
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:455347 original size:22 final size:22
Alignment explanation
Indices: 455285--455350 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
455275 TGACCGTGAA
* *
455285 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
455307 TGATATCTTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
455329 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
455351 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:455618 original size:21 final size:21
Alignment explanation
Indices: 455566--455618 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
455556 ATTTACGTAT
*
455566 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
455587 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
455608 TCGTAATGCGA
1 TCGCAATGCGA
455619 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:455836 original size:31 final size:31
Alignment explanation
Indices: 455793--455868 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
455783 TCTTTAAAAA
* *
455793 ATTATATTTTAGTCACTTA-TATTATTGATTG
1 ATTAAATTTTAGTCACTTACT-CTATTGATTG
455824 ATTAAATTTTAGTCACTTACTCTATTGATTG
1 ATTAAATTTTAGTCACTTACTCTATTGATTG
* *
455855 -TTACATTTTGGTCA
1 ATTAAATTTTAGTCA
455869 TTGAATCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 12 0.30
31 27 0.68
32 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51
Consensus pattern (31 bp):
ATTAAATTTTAGTCACTTACTCTATTGATTG
Found at i:456146 original size:13 final size:13
Alignment explanation
Indices: 456128--456152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
456118 TGGACGTAAT
456128 ATTTTGATTATTG
1 ATTTTGATTATTG
456141 ATTTTGATTATT
1 ATTTTGATTATT
456153 ATCATTTACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTTTGATTATTG
Found at i:456213 original size:22 final size:22
Alignment explanation
Indices: 456171--456213 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
456161 CGTGTAATTT
*
456171 TATTATTAATATCTTTGAATAA
1 TATTATTAATATCTTTAAATAA
*
456193 TATTGTTAATTAT-TTTAAATA
1 TATTATTAA-TATCTTTAAATA
456214 TCCCTATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
TATTATTAATATCTTTAAATAA
Found at i:458952 original size:80 final size:81
Alignment explanation
Indices: 458859--459021 Score: 292
Period size: 80 Copynumber: 2.0 Consensus size: 81
458849 ATGACAATTT
*
458859 AATAATATTTGACTTCACCTATTTAATTAATTTCTAAATTTAATAAAGTATATAGG-TAAAAATC
1 AATAATATTTGACTTCACCTATTTAATTAATTTCTAAATTTAATAAAGTATATAGGCAAAAAATC
458923 AGATTTTAACCAAAAA
66 AGATTTTAACCAAAAA
* *
458939 AATAATATTTGACTTCTCCTATTTAATTAATTTCTAAATTTAATACAGTATATAGGCAAAAAATC
1 AATAATATTTGACTTCACCTATTTAATTAATTTCTAAATTTAATAAAGTATATAGGCAAAAAATC
459004 AGATTTTAACCAAAAA
66 AGATTTTAACCAAAAA
459020 AA
1 AA
459022 ATATTTTAAT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 54 0.68
81 25 0.32
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (81 bp):
AATAATATTTGACTTCACCTATTTAATTAATTTCTAAATTTAATAAAGTATATAGGCAAAAAATC
AGATTTTAACCAAAAA
Found at i:459087 original size:16 final size:16
Alignment explanation
Indices: 459066--459115 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
459056 ATTTGATCCT
459066 TTGTTTTTAGTTTTAA
1 TTGTTTTTAGTTTTAA
*
459082 TTGTTTTTAGGTCTATAA
1 TTGTTTTTA-GT-TTTAA
* *
459100 TTGTTATTAGCTTTAA
1 TTGTTTTTAGTTTTAA
459116 ATTCTCATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
18 12 0.43
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.60
Consensus pattern (16 bp):
TTGTTTTTAGTTTTAA
Found at i:459102 original size:18 final size:17
Alignment explanation
Indices: 459066--459109 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
459056 ATTTGATCCT
*
459066 TTGTTTTTA-GTTTTAA
1 TTGTTTTTAGGTTATAA
459082 TTGTTTTTAGGTCTATAA
1 TTGTTTTTAGGT-TATAA
*
459100 TTGTTATTAG
1 TTGTTTTTAG
459110 CTTTAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (17 bp):
TTGTTTTTAGGTTATAA
Found at i:462282 original size:34 final size:34
Alignment explanation
Indices: 462243--462316 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
462233 ATTTAATGTG
462243 CATGGAGGAATGAG-TGTATTTGAATTTAAATCAA
1 CATGGAGGAATG-GCTGTATTTGAATTTAAATCAA
462277 CATGGAGGAATGGCTGTATTTGAATTTAAATCAA
1 CATGGAGGAATGGCTGTATTTGAATTTAAATCAA
*
462311 CGTGGA
1 CATGGA
462317 AGATCAGATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (34 bp):
CATGGAGGAATGGCTGTATTTGAATTTAAATCAA
Found at i:463257 original size:68 final size:71
Alignment explanation
Indices: 463141--463325 Score: 241
Period size: 68 Copynumber: 2.6 Consensus size: 71
463131 TGCTTGTGTC
* * *
463141 ATGCACATTGATTATCTTATTTGGGGCCCATTGGGAGAGAATTAATGCCACCTGACATA-T-T-A
1 ATGCACATTGTTTATCTTATTTGGGGTCCATTGGGAGAGAAATAATGCCACCTGACATATTGTAA
463203 TGTGCT
66 TGTGCT
* * * * * *
463209 ATGCTCATTGTTTATCTTATTTGGGGTCAATTGGGAGAGAAATGATGCCGCTTGGCATATTGTAA
1 ATGCACATTGTTTATCTTATTTGGGGTCCATTGGGAGAGAAATAATGCCACCTGACATATTGTAA
*
463274 TGTTCT
66 TGTGCT
*
463280 ATGCACATTGTTTATCTTATTTTGGGGTCCATTGGGGGAGAAATAA
1 ATGCACATTGTTTATCTTA-TTTGGGGTCCATTGGGAGAGAAATAA
463326 GGCCCCCCTT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
68 50 0.51
69 1 0.01
70 1 0.01
71 24 0.24
72 23 0.23
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (71 bp):
ATGCACATTGTTTATCTTATTTGGGGTCCATTGGGAGAGAAATAATGCCACCTGACATATTGTAA
TGTGCT
Found at i:474014 original size:22 final size:22
Alignment explanation
Indices: 473977--474056 Score: 137
Period size: 21 Copynumber: 3.7 Consensus size: 22
473967 CGAACACATA
*
473977 TCTTTTA-AAAAAATAATGTTT
1 TCTTTTAGAGAAAATAATGTTT
473998 TCTTTTAGAGAAAATAATG-TT
1 TCTTTTAGAGAAAATAATGTTT
474019 TCTTTTAGAGAAAATAATGTTT
1 TCTTTTAGAGAAAATAATGTTT
474041 TCTTTTAGAGAAAATA
1 TCTTTTAGAGAAAATA
474057 CCCTCATTGA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
21 28 0.50
22 28 0.50
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (22 bp):
TCTTTTAGAGAAAATAATGTTT
Found at i:474195 original size:20 final size:19
Alignment explanation
Indices: 474172--474341 Score: 105
Period size: 20 Copynumber: 8.6 Consensus size: 19
474162 CCCAGTTTCC
*
474172 AAATTCGCAACGCGAATTGT
1 AAATTCGCAACACGAATT-T
* *
474192 AAA-TCGCAGCGCGAATTTGT
1 AAATTCGCAACACGAA-TT-T
* *
474212 AAA-TCGCAGCGCGAATTTGT
1 AAATTCGCAACACGAA-TT-T
*
474232 AAA-TCGCAACACAGAAGTT
1 AAATTCGCAACAC-GAATTT
*
474251 AAATTTGCAACACTGAATTT
1 AAATTCGCAACAC-GAATTT
*
474271 CAAATTCGCAAC-TGAATTT
1 -AAATTCGCAACACGAATTT
* * *
474290 CAAATTCACAACTCGATTTT
1 -AAATTCGCAACACGAATTT
*
474310 CGAATTCGCAACACGAATTT
1 -AAATTCGCAACACGAATTT
*
474330 AATTTCGCAACA
1 AAATTCGCAACA
474342 TGTTTTAGTT
Statistics
Matches: 127, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
19 42 0.33
20 72 0.57
21 13 0.10
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (19 bp):
AAATTCGCAACACGAATTT
Found at i:474204 original size:19 final size:20
Alignment explanation
Indices: 474176--474239 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
474166 GTTTCCAAAT
*
474176 TCGCAACGCGAA-TTGTAAA
1 TCGCAGCGCGAATTTGTAAA
474195 TCGCAGCGCGAATTTGTAAA
1 TCGCAGCGCGAATTTGTAAA
474215 TCGCAGCGCGAATTTGTAAA
1 TCGCAGCGCGAATTTGTAAA
474235 TCGCA
1 TCGCA
474240 ACACAGAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAGCGCGAATTTGTAAA
Found at i:474286 original size:19 final size:19
Alignment explanation
Indices: 474262--474340 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
474252 AATTTGCAAC
474262 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCGCA
*
474281 ACTGAATTTCAAATTCACA
1 ACTGAATTTCAAATTCGCA
* *
474300 ACTCGATTTTCGAATTCGCA
1 ACT-GAATTTCAAATTCGCA
* *
474320 ACACGAATTT-AATTTCGCA
1 AC-TGAATTTCAAATTCGCA
474339 AC
1 AC
474341 ATGTTTTAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 30 0.60
20 20 0.40
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (19 bp):
ACTGAATTTCAAATTCGCA
Found at i:474524 original size:16 final size:15
Alignment explanation
Indices: 474496--474534 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
474486 TCCACATCTC
474496 TAATTTTTTTTTACA
1 TAATTTTTTTTTACA
*
474511 TAATTTTATTTTTATA
1 TAATTTT-TTTTTACA
474527 TAATTTTT
1 TAATTTTT
474535 CAATGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTTTTTTTACA
Found at i:475321 original size:24 final size:23
Alignment explanation
Indices: 475286--475338 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
475276 AGTATTCAAA
475286 TTTGATTTGGTCAATACCCGGAC
1 TTTGATTTGGTCAATACCCGGAC
* *
475309 TTTGATCTTGGTCAATACTCGGAT
1 TTTGAT-TTGGTCAATACCCGGAC
475333 TTTGAT
1 TTTGAT
475339 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (23 bp):
TTTGATTTGGTCAATACCCGGAC
Found at i:477900 original size:29 final size:29
Alignment explanation
Indices: 477862--477919 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
477852 AAATTTGAAA
*
477862 TGCAAAAATCGCAATACGAATTTGACTTT
1 TGCAAAAATCGCAACACGAATTTGACTTT
* *
477891 TGCAACAATCGCAACGCGAATTTGACTTT
1 TGCAAAAATCGCAACACGAATTTGACTTT
477920 CGCGTTGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (29 bp):
TGCAAAAATCGCAACACGAATTTGACTTT
Found at i:477932 original size:20 final size:20
Alignment explanation
Indices: 477909--477947 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
477899 TCGCAACGCG
*
477909 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCGCATTGCA
477929 AATTTGACTTTCGCATTGC
1 AATTTGACTTTCGCATTGC
477948 GAAAGTGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
AATTTGACTTTCGCATTGCA
Found at i:479641 original size:20 final size:20
Alignment explanation
Indices: 479618--479655 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
479608 TCGCAACGCC
*
479618 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCACGTTGCG
479638 AATTTGACTTTCACGTTG
1 AATTTGACTTTCACGTTG
479656 TTTCGCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
AATTTGACTTTCACGTTGCG
Found at i:479705 original size:34 final size:34
Alignment explanation
Indices: 479658--479749 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
479648 TCACGTTGTT
* * *
479658 TCGCATTGTGAATTTGACTATCGTAACGCGAAAA
1 TCGCAATGCGAATTTGACTATCGTAACGAGAAAA
**
479692 TCGCAATGCGAATTTGACTATCACAACGAGAAAA
1 TCGCAATGCGAATTTGACTATCGTAACGAGAAAA
* * *
479726 TCACAACGCGAATTTGACTTTCGT
1 TCGCAATGCGAATTTGACTATCGT
479750 GTTGCGAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (34 bp):
TCGCAATGCGAATTTGACTATCGTAACGAGAAAA
Found at i:479893 original size:64 final size:64
Alignment explanation
Indices: 479814--479971 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
479804 GAAATTTAAC
479814 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
* * *
479878 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
479942 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
479972 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:481356 original size:21 final size:21
Alignment explanation
Indices: 481312--481451 Score: 140
Period size: 21 Copynumber: 6.7 Consensus size: 21
481302 GTGAATCGGG
* * * *
481312 CTCTTGAACGGTGGGAGAGAC
1 CTCTTGAACGATGAGAGGGGC
* *
481333 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
481354 CTCTTGAATGGTG-GAAGGGGC
1 CTCTTGAACGATGAG-AGGGGC
*
481375 CACTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
481396 CTCTTGAACGATTAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
**
481417 CTCTTGAACGAT-AGGAGACGC
1 CTCTTGAACGATGA-GAGGGGC
481438 CTCTTGAACGATGA
1 CTCTTGAACGATGA
481452 CAGGTGAATC
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.01
21 95 0.97
22 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:481444 original size:63 final size:63
Alignment explanation
Indices: 481312--481451 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 63
481302 GTGAATCGGG
* * * * * **
481312 CTCTTGAACGGTGGGAGAGACCTCTTGAACGATGACATGGGCCTCTTGAATGGTGGAAGGGGC
1 CTCTTGAACGATGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGACGC
* * * * *
481375 CACTTGAACGATGAGAGGGGCCTCTTGAACGATTAGAGGGGCCTCTTGAACGATAGG-AGACGC
1 CTCTTGAACGATGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GGAAGACGC
481438 CTCTTGAACGATGA
1 CTCTTGAACGATGA
481452 CAGGTGAATC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
63 61 0.97
64 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (63 bp):
CTCTTGAACGATGAGAGAGACCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGACGC
Found at i:481857 original size:63 final size:63
Alignment explanation
Indices: 481763--481884 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
481753 ACCACGTAGC
* * *
481763 GCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCGTACCTTATCACGCCAT
1 GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* ** **
481826 GCACCATTGTCTTCACGTAAAGTA-CCAACCTCATGACGCAAAGCACCGACCTCATCACG
1 GCACCATTGTCATCACGTAAAACATCC-ACCTCACCACGCAAAGCACCGACCTCATCACG
481885 TAACTCCCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.04
63 43 0.88
64 4 0.08
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:484139 original size:21 final size:21
Alignment explanation
Indices: 484096--484189 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
484086 TAAACGCGCT
* *
484096 TTGCGAATTTG-ACTTCTGTG
1 TTGCGAATTTGAAATTCAGTG
484116 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
484137 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
484158 TTGCGAATTTGGAAA-TC-GTG
1 TTGCGAATTT-GAAATTCAGTG
*
484178 TTGTGAATTTGA
1 TTGCGAATTTGA
484190 CTTCTGTGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
19 2 0.03
20 23 0.33
21 40 0.58
22 4 0.06
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCAGTG
Found at i:484278 original size:19 final size:19
Alignment explanation
Indices: 484237--484287 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
484227 TGGAAACTGG
* *
484237 GTTGCGAAATTGGAGTTCAC
1 GTTGCG-AATTTGAGATCAC
*
484257 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCAC
*
484276 GTTGCAAATTTG
1 GTTGCGAATTTG
484288 TTGGTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCAC
Found at i:490108 original size:21 final size:21
Alignment explanation
Indices: 490041--490118 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
490031 GTCCCTTTAC
490041 AAAAAGGATCGATCCATCGAGT
1 AAAAAGGATCGATCCATCGA-T
**
490063 -AAAAGGATCGAT-C-TCTTT
1 AAAAAGGATCGATCCATCGAT
490081 ACCAAAAGGATCGATCCATCGAT
1 A--AAAAGGATCGATCCATCGAT
**
490104 AAAAAATATCGATCC
1 AAAAAGGATCGATCC
490119 TTTCCTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 1 0.02
21 36 0.80
22 1 0.02
23 4 0.09
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAAAGGATCGATCCATCGAT
Found at i:490138 original size:42 final size:42
Alignment explanation
Indices: 490035--490121 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
490025 TGATCAGTCC
* *
490035 CTTTACAAAAAGGATCGATCCATCGAGTAAAAGGATCGATCT
1 CTTTACCAAAAGGATCGATCCATCGAGTAAAAAGATCGATCT
*
490077 CTTTACCAAAAGGATCGATCCATCGA-TAAAAAATATCGATC-
1 CTTTACCAAAAGGATCGATCCATCGAGT-AAAAAGATCGATCT
490118 CTTT
1 CTTT
490122 CCTTTAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (42 bp):
CTTTACCAAAAGGATCGATCCATCGAGTAAAAAGATCGATCT
Found at i:490556 original size:21 final size:21
Alignment explanation
Indices: 490489--490566 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
490479 GTCCCTTTAC
490489 AAAAAGGATCGATCCATCGAGT
1 AAAAAGGATCGATCCATCGA-T
**
490511 -AAAAGGATCGAT-C-TCTTT
1 AAAAAGGATCGATCCATCGAT
490529 ACCAAAAGGATCGATCCATCGAT
1 A--AAAAGGATCGATCCATCGAT
**
490552 AAAAAATATCGATCC
1 AAAAAGGATCGATCC
490567 TTTCCTTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 1 0.02
21 36 0.80
22 1 0.02
23 4 0.09
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAAAGGATCGATCCATCGAT
Found at i:490586 original size:42 final size:42
Alignment explanation
Indices: 490483--490569 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
490473 TGATCAGTCC
* *
490483 CTTTACAAAAAGGATCGATCCATCGAGTAAAAGGATCGATCT
1 CTTTACCAAAAGGATCGATCCATCGAGTAAAAAGATCGATCT
*
490525 CTTTACCAAAAGGATCGATCCATCGA-TAAAAAATATCGATC-
1 CTTTACCAAAAGGATCGATCCATCGAGT-AAAAAGATCGATCT
490566 CTTT
1 CTTT
490570 CCTTTAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (42 bp):
CTTTACCAAAAGGATCGATCCATCGAGTAAAAAGATCGATCT
Found at i:493572 original size:2 final size:2
Alignment explanation
Indices: 493565--493596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
493555 CTGCCCTACC
493565 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
493597 ACCTTGTAGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:494785 original size:14 final size:14
Alignment explanation
Indices: 494750--494785 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
494740 ATATATATAT
*
494750 ACACACACACATAC
1 ACACACATACATAC
494764 ACACACATACATAC
1 ACACACATACATAC
494778 ACACACAT
1 ACACACAT
494786 GACTTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (14 bp):
ACACACATACATAC
Found at i:495481 original size:29 final size:29
Alignment explanation
Indices: 495436--495493 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
495426 GTGTTGGTCA
*
495436 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
*
495465 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
495494 AAGAGATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.38, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:495555 original size:14 final size:14
Alignment explanation
Indices: 495536--495616 Score: 81
Period size: 14 Copynumber: 5.4 Consensus size: 14
495526 CGCTGGGCAT
495536 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
495550 CCGAGGCCATCCAA
1 CCGAGGCCATCCGA
495564 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
495583 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
*
495598 CCGAGGTCATCCGA
1 CCGAGGCCATCCGA
*
495612 ACGAG
1 CCGAG
495617 CTATGTGATG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
14 42 0.74
15 1 0.02
16 1 0.02
19 1 0.02
20 12 0.21
ACGTcount: A:0.25, C:0.38, G:0.28, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:495611 original size:10 final size:10
Alignment explanation
Indices: 495564--495597 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
495554 GGCCATCCAA
495564 CCGAGGCCAT
1 CCGAGGCCAT
495574 CCGAGAG-CAT
1 CCGAG-GCCAT
495584 CCGAGGCCAT
1 CCGAGGCCAT
495594 CCGA
1 CCGA
495598 CCGAGGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:495650 original size:33 final size:33
Alignment explanation
Indices: 495598--495682 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
495588 GGCCATCCGA
* * * * *
495598 CCGAGGTCATCCGAACGAGCTATGTGATGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
*
495631 CCGAGGGCAACTGAGCGAGCTATGTGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
495664 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
495683 GGTAGGTCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.36, T:0.14
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGTGAGGGAAT
Found at i:495763 original size:23 final size:23
Alignment explanation
Indices: 495729--495788 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
495719 CTCGGTTGCC
495729 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
495752 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
495775 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
495789 GTCGGATGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:495793 original size:14 final size:14
Alignment explanation
Indices: 495771--495803 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
495761 CCTCGCATAG
*
495771 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
495785 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
495799 CTCGG
1 CTCGG
495804 ATGCCCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:496987 original size:60 final size:59
Alignment explanation
Indices: 496885--497029 Score: 175
Period size: 60 Copynumber: 2.4 Consensus size: 59
496875 TGACAAAACG
* * * * *
496885 GGATCATGAAGCGTGCCTTCGCAGGGTTCTGTCCGAGTTGGCGCCACTGT-GGAAAGGTGC
1 GGATCATGAAGCGTACCTTCGCAGGGTTCTGTCAGAGCTGGCGCCAC-GTCAG-AAGGCGC
* * *
496945 GGATCATGAGGCGTACCTTCGTAGGGTTCTGTCAGAGCTGGCGTCACGTCAGAAGGCGC
1 GGATCATGAAGCGTACCTTCGCAGGGTTCTGTCAGAGCTGGCGCCACGTCAGAAGGCGC
**
497004 GGATCATGAAGCGCGCCTTCGCAGGG
1 GGATCATGAAGCGTACCTTCGCAGGG
497030 AAATCTAACA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 30 0.42
60 42 0.58
ACGTcount: A:0.18, C:0.24, G:0.37, T:0.21
Consensus pattern (59 bp):
GGATCATGAAGCGTACCTTCGCAGGGTTCTGTCAGAGCTGGCGCCACGTCAGAAGGCGC
Found at i:499950 original size:44 final size:44
Alignment explanation
Indices: 499900--500020 Score: 206
Period size: 44 Copynumber: 2.8 Consensus size: 44
499890 ACAATTAAAT
* *
499900 AATAAAAATATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
*
499944 AATAAAAACATTAAGAAACAAAATAAATAAAATGTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
*
499988 AATAAAAACATTAAGAAATAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
500021 CAAGTCTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
Found at i:499972 original size:25 final size:24
Alignment explanation
Indices: 499896--499975 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 24
499886 TCAAACAATT
499896 AAAT-AATAAAAATATTAAGAAACA
1 AAATAAATAAAAA-ATTAAGAAACA
*
499920 AAATAAATAAAAAGTT------CA
1 AAATAAATAAAAAATTAAGAAACA
*
499938 TAATTAAATAAAAACATTAAGAAACA
1 -AAATAAATAAAAA-ATTAAGAAACA
499964 AAATAAATAAAA
1 AAATAAATAAAA
499976 TGTCCATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 17
0.67 0.06 0.27
Matches are distributed among these distances:
18 2 0.05
19 12 0.28
20 2 0.05
24 6 0.14
25 19 0.44
26 2 0.05
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (24 bp):
AAATAAATAAAAAATTAAGAAACA
Found at i:502789 original size:2 final size:2
Alignment explanation
Indices: 502782--502827 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
502772 GGTATAAGTG
* *
502782 AT AT AT AT AT AT AT AT GT AT AT GT 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
502824 AT AT
1 AT AT
502828 GTTACATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:504690 original size:2 final size:2
Alignment explanation
Indices: 504683--504732 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
504673 AGTACGAATA
* * *
504683 AT AT AT AT AT AT AT AT AT A- AT AA AA AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504724 AT AT AT AT A
1 AT AT AT AT A
504733 ATTAATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:504880 original size:46 final size:48
Alignment explanation
Indices: 504776--504910 Score: 127
Period size: 46 Copynumber: 2.8 Consensus size: 48
504766 ACATATAATG
* * *
504776 GTAAAAAATAAATAAAGATAATTATAATATATATATAATATTAGACTTA
1 GTAAAAAAT-AATAAAGATAATTATAATATATATATAATAATAAAATTA
*
504825 -TAAGTAAAATATTAAAGA-AA-TAT-ATATATATATAATAATAAAATATA
1 GTAA--AAAATAATAAAGATAATTATAATATATATATAATAATAAAAT-TA
504872 GTAAAAAATAAATGAAA-ATAATTAATATATATATATATA
1 GTAAAAAAT-AAT-AAAGATAATT-ATA-ATATATATATA
504911 TACATATATA
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
46 23 0.33
47 8 0.11
48 13 0.19
49 8 0.11
50 7 0.10
52 11 0.16
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (48 bp):
GTAAAAAATAATAAAGATAATTATAATATATATATAATAATAAAATTA
Found at i:504951 original size:17 final size:18
Alignment explanation
Indices: 504918--504953 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
504908 ATATACATAT
*
504918 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
504936 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
504953 A
1 A
504954 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:505364 original size:37 final size:37
Alignment explanation
Indices: 505314--505418 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
505304 GTGCTTGTGG
* * * *
505314 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
505351 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
505388 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
505419 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:506264 original size:105 final size:105
Alignment explanation
Indices: 505960--506590 Score: 902
Period size: 105 Copynumber: 6.0 Consensus size: 105
505950 GCATTGTTCC
* ** *
505960 GAGTCCAATATCC-TCTGTCGTGAAGTTGAAATTGGCTCTG-GAACAGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGAC
* * * * *
506023 AACCAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
63 AAGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
506066 TAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
506126 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
506166 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
506231 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
506271 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
506336 CAGCGGTCCCTTGGACGTGAAGTTGAACTTGCTTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
506376 AAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
506441 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
506481 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
506546 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
506587 GAGT
1 GAGT
506591 GTCACGATAT
Statistics
Matches: 483, Mismatches: 32, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
99 1 0.00
100 81 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 303 0.63
106 82 0.17
107 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:506986 original size:107 final size:105
Alignment explanation
Indices: 506762--507082 Score: 456
Period size: 107 Copynumber: 3.1 Consensus size: 105
506752 TTCGTTAAAT
* * * * *
506762 TGTTTTCAAAGTTTATGTTTG-GAGAGAAAGTGTCTCAAGGGATACAAAA--TTC-GTTTCAAGG
1 TGTTTTCAATGTTTATG-TTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGG
* *
506823 GAAACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
65 GAAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
506863 TGTTTTCAATGTTTATGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
506928 AAACTATCTCAAGAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTC-AGAGAGAG-AAAAAATTCATTTCAAGGGAAA
* * **
506970 TGTTTTCAATGTTTATGTTTCAAGAAAAACTGTCTCAAATGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
507035 AAACTATCTCAG-GAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
507074 TGTTTTCAA
1 TGTTTTCAA
507083 GAGAAACTGT
Statistics
Matches: 199, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
100 3 0.02
101 41 0.21
103 3 0.02
104 48 0.24
105 6 0.03
106 7 0.04
107 91 0.46
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTGCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:507238 original size:36 final size:36
Alignment explanation
Indices: 507198--507311 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
507188 CTTTCGAGTG
* *
507198 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
507234 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
507270 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
507306 AAAACA
1 AAAACA
507312 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:507290 original size:72 final size:74
Alignment explanation
Indices: 507153--507327 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
507143 TAAAATCTTC
** * *
507153 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
507217 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
507228 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
507291 AAGTATGTT
66 AAGTATGTT
*
507300 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
507328 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
72 48 0.53
73 15 0.17
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:508782 original size:183 final size:183
Alignment explanation
Indices: 508468--509004 Score: 977
Period size: 183 Copynumber: 2.9 Consensus size: 183
508458 ATCAGGTTTA
*
508468 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
508533 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
508597 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
**
508651 ACTGAAGGGTTTGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
508716 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTTGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
508781 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGATGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
508834 ACTGAATGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
508899 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
508964 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
509005 CGGATTTAAT
Statistics
Matches: 341, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 340 1.00
184 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:513067 original size:9 final size:9
Alignment explanation
Indices: 513053--513128 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 9
513043 AAATAGTAAG
513053 TAAAAAAAA
1 TAAAAAAAA
513062 T--AAAAAA
1 TAAAAAAAA
* *
513069 TAAAATATA
1 TAAAAAAAA
*
513078 TATAAAAAA
1 TAAAAAAAA
513087 TAAAAAGAAA
1 TAAAAA-AAA
*
513097 AAGAAAATAAA
1 TA-AAAA-AAA
*
513108 TAAAACAAA
1 TAAAAAAAA
*
513117 TAAACAAAA
1 TAAAAAAAA
513126 TAA
1 TAA
513129 TAATAACAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
7 7 0.14
9 29 0.57
10 7 0.14
11 8 0.16
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:513071 original size:28 final size:25
Alignment explanation
Indices: 513053--513184 Score: 74
Period size: 25 Copynumber: 5.2 Consensus size: 25
513043 AAATAGTAAG
513053 TAAAAAAAATAAAAAATAAAATATA
1 TAAAAAAAATAAAAAATAAAATATA
* * *
513078 TATAAAAAATAAAAAGA-AAAAGAAAA
1 TAAAAAAAATAAAAA-ATAAAA-TATA
* * *
513104 TAAATAAAACAAATAAACAAAATA-A
1 TAAAAAAAATAAA-AAATAAAATATA
* * *
513129 TAATAACAAAGTACGAATAAT-ATATATA
1 TAA-AA-AAAATA--AAAAATAAAATATA
* *
513157 TAAAATAAATAAAAAGT-AAATATA
1 TAAAAAAAATAAAAAATAAAATATA
513181 TAAA
1 TAAA
513185 TTAATAAATT
Statistics
Matches: 80, Mismatches: 18, Indels: 19
0.68 0.15 0.16
Matches are distributed among these distances:
24 14 0.17
25 22 0.28
26 20 0.25
27 16 0.20
28 6 0.08
29 2 0.03
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAAAAAAATAAAAAATAAAATATA
Found at i:513104 original size:30 final size:30
Alignment explanation
Indices: 513064--513120 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
513054 AAAAAAAATA
* *
513064 AAAAATAAAATATATATAAA-AAATAAAAAG
1 AAAAAGAAAATAAATA-AAACAAATAAAAAG
513094 AAAAAGAAAATAAATAAAACAAATAAA
1 AAAAAGAAAATAAATAAAACAAATAAA
513121 CAAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (30 bp):
AAAAAGAAAATAAATAAAACAAATAAAAAG
Found at i:513128 original size:22 final size:21
Alignment explanation
Indices: 513084--513138 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
513074 TATATATAAA
*
513084 AAATAAAA-AGAAAAAGAAAAT
1 AAATAAAACA-AAAAACAAAAT
513105 AAATAAAACAAATAAACAAAAT
1 AAATAAAACAAA-AAACAAAAT
513127 -AATAATAACAAA
1 AAATAA-AACAAA
513139 GTACGAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.13
Consensus pattern (21 bp):
AAATAAAACAAAAAACAAAAT
Found at i:513396 original size:18 final size:17
Alignment explanation
Indices: 513375--513417 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
513365 ATATATACAT
513375 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
513393 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
513410 ATAA-AATA
1 ATAATAATA
513418 TCTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:513396 original size:56 final size:55
Alignment explanation
Indices: 513299--513429 Score: 126
Period size: 56 Copynumber: 2.3 Consensus size: 55
513289 TATTAAAGAT
*
513299 ATATATATATATATAATAATAATAAAATATAGTAAAAAATAAATGAAAATAATTTA
1 ATATATATATATATAATAATAATAAAATATAGTAAAAAAT-AATAAAAATAATTTA
* * *
513355 ATATATATATATAT-ATACAT-ATAATAATA-A-TAACATGAATAATAAAAATAAATGA
1 ATATATATATATATAATA-ATAATAA-AATATAGTAA-A-AAATAATAAAAATAATTTA
* *
513410 ATAAAATATCTATATAATAA
1 AT-ATATATATATATAATAA
513430 ATAAAGGGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
54 3 0.05
55 23 0.37
56 34 0.54
57 3 0.05
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (55 bp):
ATATATATATATATAATAATAATAAAATATAGTAAAAAATAATAAAAATAATTTA
Found at i:513424 original size:64 final size:62
Alignment explanation
Indices: 513284--513425 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 62
513274 GACTTATAAG
* * * *
513284 TAAAATATTAAAGATATATATATATATATAATAATAATAAAATATAGTAAAAAATAAATGAA
1 TAAAATATTATATATATATATATACATATAATAATAATAAAATATAATAAAAAATAAATGAA
* *
513346 -AATAATTTAATATATATATATATATACATATAATAATAATAACATGAATAAT-AAAAATAAATG
1 TAA-AA--TATTATATATATATATATACATATAATAATAATAAAAT--ATAATAAAAAATAAATG
513409 AA
61 AA
513411 TAAAATATCTATATA
1 TAAAATAT-TATATA
513426 ATAAATAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
61 2 0.03
62 2 0.03
63 2 0.03
64 39 0.59
65 15 0.23
66 6 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (62 bp):
TAAAATATTATATATATATATATACATATAATAATAATAAAATATAATAAAAAATAAATGAA
Found at i:513824 original size:37 final size:37
Alignment explanation
Indices: 513774--513878 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
513764 GTGCTTGTGG
* * *
513774 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAGAACTCT
* * * *
513811 ATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAGAACTCT
*
513848 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAG
513879 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCTTAGTAGAACTCT
Found at i:514874 original size:59 final size:60
Alignment explanation
Indices: 514777--514940 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 60
514767 GCACCTTTTG
* * * * * *
514777 CCAGCTCCGACGGAACCCCACAAAGGCACGCTTTATGATTCGCGTCTTCT-AACGTGACA
1 CCAGCTCGGACAGAACCCCGCGAAGGCACGCTTCATGATTCGCGCCTTCTCAACGTGACA
* * * * * * **
514836 CCAGCTCGGACAGAATCCCTCGAAGGCACGCCTCATGATAT-GTGCCTTTTCACCGTGGTA
1 CCAGCTCGGACAGAACCCCGCGAAGGCACGCTTCATGAT-TCGCGCCTTCTCAACGTGACA
*
514896 CCAGCTCGGACAGAACCCCGCGAAGGCACGCTTCATGATCCGCGC
1 CCAGCTCGGACAGAACCCCGCGAAGGCACGCTTCATGATTCGCGC
514941 TTTGTCAGAA
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
59 38 0.45
60 46 0.55
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (60 bp):
CCAGCTCGGACAGAACCCCGCGAAGGCACGCTTCATGATTCGCGCCTTCTCAACGTGACA
Found at i:523414 original size:16 final size:16
Alignment explanation
Indices: 523390--523431 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
523380 GAGCCCCAGG
*
523390 GGTGGCACTTTTGAGA
1 GGTGACACTTTTGAGA
*
523406 GGTGACACTTTTGATA
1 GGTGACACTTTTGAGA
523422 GGTGACACTT
1 GGTGACACTT
523432 GTATTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.33
Consensus pattern (16 bp):
GGTGACACTTTTGAGA
Found at i:530406 original size:30 final size:30
Alignment explanation
Indices: 530302--530408 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
530292 TGGATCATTT
*
530302 TTTTATTCGGATCAATATAAGATCGGTTGA
1 TTTTATTCGGATCAATATCAGATCGGTTGA
* *
530332 TTTT-TTGGGCGAGTCAATA-CGGATCGGTTAGA
1 TTTTATT-CG-GA-TCAATATCAGATCGGTT-GA
* * *
530364 TTTCAGTCGGATCAATATCAGATCGATTGA
1 TTTTATTCGGATCAATATCAGATCGGTTGA
*
530394 TTTTATTTGGATCAA
1 TTTTATTCGGATCAA
530409 CCTTTGGAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
29 2 0.03
30 25 0.42
31 20 0.33
32 12 0.20
33 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (30 bp):
TTTTATTCGGATCAATATCAGATCGGTTGA
Found at i:531196 original size:51 final size:54
Alignment explanation
Indices: 531119--531223 Score: 180
Period size: 51 Copynumber: 2.0 Consensus size: 54
531109 TTTAATAAAA
531119 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
1 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
*
531173 TATT-AAAA-ATTGGTGATT-AAATATAACACTTTAAAAGTTCAAGAATTACTT
1 TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
531224 GTGTAATTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
51 33 0.66
52 9 0.18
53 4 0.08
54 4 0.08
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (54 bp):
TATTAAAAATATTGATGATTAAAATATAACACTTTAAAAGTTCAAGAATTACTT
Found at i:534767 original size:117 final size:112
Alignment explanation
Indices: 534553--534845 Score: 393
Period size: 117 Copynumber: 2.6 Consensus size: 112
534543 AAGCGTTGGA
534553 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
534617 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAAT-AAA--AA-G
534670 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * * **
534735 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
* *
534783 --GAACAAGTTCTTCTCATTATGAAC-T-TTC-CC-CTTTAGGACGAGTTATTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTT-GGATGAGTTCTTCTCATTATGAAC
534842 TCTT
65 TCTT
534846 AATTAGAAAT
Statistics
Matches: 165, Mismatches: 8, Indels: 16
0.87 0.04 0.08
Matches are distributed among these distances:
106 4 0.02
107 28 0.17
109 3 0.02
110 1 0.01
111 24 0.15
113 1 0.01
114 2 0.01
116 1 0.01
117 96 0.58
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
Found at i:536210 original size:8 final size:8
Alignment explanation
Indices: 536199--536278 Score: 71
Period size: 8 Copynumber: 10.5 Consensus size: 8
536189 CCTTTTTCTC
536199 TTTTCATT
1 TTTTCATT
536207 TTTTCA--
1 TTTTCATT
*
536213 -TTTCTTT
1 TTTTCATT
536220 TTTTCA-T
1 TTTTCATT
536227 TTTTCATT
1 TTTTCATT
**
536235 TTTTTTTT
1 TTTTCATT
536243 TTTTCATT
1 TTTTCATT
536251 TTTTCATCT
1 TTTTCAT-T
536260 TTTT-ATT
1 TTTTCATT
* *
536267 TGTTCCTT
1 TTTTCATT
536275 TTTT
1 TTTT
536279 TTCTTCAAGC
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 4 0.07
7 11 0.19
8 37 0.65
9 5 0.09
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:536216 original size:13 final size:14
Alignment explanation
Indices: 536199--536257 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
536189 CCTTTTTCTC
536199 TTTTCATTTTTTCA
1 TTTTCATTTTTTCA
*
536213 -TTTCTTTTTTTCA
1 TTTTCATTTTTTCA
**
536226 TTTTTCATTTTTTTTTT
1 -TTTTCA--TTTTTTCA
536243 TTTTCATTTTTTCA
1 TTTTCATTTTTTCA
536257 T
1 T
536258 CTTTTTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
13 12 0.34
14 7 0.20
15 4 0.11
16 6 0.17
17 6 0.17
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCATTTTTTCA
Found at i:536222 original size:20 final size:19
Alignment explanation
Indices: 536193--536251 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
536183 AACCCTCCTT
*
536193 TTTCTCTTTTCATTTTTTCA
1 TTTCTTTTTTCA-TTTTTCA
536213 TTTCTTTTTTTCATTTTTCA
1 TTTC-TTTTTTCATTTTTCA
536233 TTT-TTTTTT--TTTTTCA
1 TTTCTTTTTTCATTTTTCA
536249 TTT
1 TTT
536252 TTTCATCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 10 0.27
18 6 0.16
20 14 0.38
21 7 0.19
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:536225 original size:21 final size:20
Alignment explanation
Indices: 536199--536242 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
536189 CCTTTTTCTC
536199 TTTTCATTTTTTCATTTCTTT
1 TTTTCA-TTTTTCATTTCTTT
536220 TTTTCATTTTTCATTT-TTT
1 TTTTCATTTTTCATTTCTTT
536239 TTTT
1 TTTT
536243 TTTTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCATTTTTCATTTCTTT
Found at i:536247 original size:23 final size:23
Alignment explanation
Indices: 536190--536277 Score: 81
Period size: 24 Copynumber: 3.9 Consensus size: 23
536180 TCAAACCCTC
* *
536190 CTTTTTCTCTTTTCATTTTT--T
1 CTTTTTTTTTTTTCATTTTTCAT
* *
536211 CATTTCTTTTTTTCATTTTTCAT
1 CTTTTTTTTTTTTCATTTTTCAT
*
536234 TTTTTTTTTTTTTCATTTTTTCAT
1 CTTTTTTTTTTTTCA-TTTTTCAT
* * *
536258 CTTTTTATTTGTTCCTTTTT
1 CTTTTTTTTTTTTCATTTTT
536278 TTTCTTCAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 16 0.30
23 18 0.34
24 19 0.36
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (23 bp):
CTTTTTTTTTTTTCATTTTTCAT
Found at i:549956 original size:117 final size:112
Alignment explanation
Indices: 549742--550034 Score: 384
Period size: 117 Copynumber: 2.6 Consensus size: 112
549732 AAGCGTTGGA
*
549742 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATAAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
*
549806 CTATTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAAT-AAA--AA-G
549859 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * * **
549924 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
*
549972 --GAACAAGTTCTTCTCATTATGAAC-T-TTC-CC-CTTTAGGACGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTT-GGATGAGTTCTTCTCATTATGAAC
550031 TCTT
65 TCTT
550035 AATTAGAAAT
Statistics
Matches: 164, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
106 4 0.02
107 29 0.18
109 3 0.02
110 1 0.01
111 24 0.15
113 1 0.01
114 2 0.01
116 1 0.01
117 94 0.57
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
Found at i:550482 original size:333 final size:334
Alignment explanation
Indices: 549858--550512 Score: 1028
Period size: 333 Copynumber: 2.0 Consensus size: 334
549848 TCAAACCAAG
* * * *
549858 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTCCTCGTTGGATGAATTCTTCTCATTATGAA
*
549923 CTCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
66 CTCTTCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
*
549988 TTATGAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTAATTAGAAATGTCAATCC
131 TTATGAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAATTAGAAATGTCAATCC
* *
550053 CTCAAGCGAGGTGTCACTGATTCAAAATGCCGTGAATCGAGTGATAGGTCGAACAAACTCTTCTC
196 CTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTCTC
*
550118 ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAACAC
261 ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAACAC
550183 TAATGCGAA
326 TAATGCGAA
* * *
550192 GTTGGACAAGTTTTTCT-ATTATGAAATTATTC-TCTCTCGTTGGATGAATTCTTCTTATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTC-CTCGTTGGATGAATTCTTCTCATTATGA
* * * * *
550255 ACTCTTCATTGGAAATTTTAATCCATCTCTTTCTTTGATGGATTTGAAAGGAACAAGTTCTTCTC
65 ACTCTTCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTC
* * * **
550320 ATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTATT-CTCTGGAAATGTTGAT
130 ATTATGAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAAT-TAGAAATGTCAAT
* * **
550384 CCCTCAAGCGAGGTGTCACTGATTCGAAACGCCATGAATCGAGTGATAGGTCGAATAGGCTCTTC
194 CCCTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTC
*
550449 TCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTTCATTGGAAA
259 TCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAA
550513 TGTTGATCAA
Statistics
Matches: 292, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
332 3 0.01
333 274 0.94
334 15 0.05
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (334 bp):
GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTCCTCGTTGGATGAATTCTTCTCATTATGAA
CTCTTCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
TTATGAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAATTAGAAATGTCAATCC
CTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTCTC
ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAACAC
TAATGCGAA
Found at i:551401 original size:14 final size:14
Alignment explanation
Indices: 551382--551487 Score: 63
Period size: 16 Copynumber: 7.1 Consensus size: 14
551372 TCTCAAACCC
551382 TCATTTTTCTCTTT
1 TCATTTTTCTCTTT
*
551396 TCATTTTT-TCATT
1 TCATTTTTCTCTTT
* *
551409 TCTTTTTTTTCATTTT
1 TCATTTTTCTC--TTT
*
551425 TCATTTTTTTTCTTTT
1 TCA-TTTTTCTC-TTT
*
551441 TCATTTTTTCTTTTTT
1 TCA-TTTTTC-TCTTT
551457 TCATTTTTTCATCTTT
1 TCA-TTTTTC-TCTTT
*
551473 TTATTTGTTC-CTTT
1 TCATTT-TTCTCTTT
551487 T
1 T
551488 TTTTCTTCAA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.14
14 15 0.19
15 3 0.04
16 39 0.51
17 9 0.12
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.75
Consensus pattern (14 bp):
TCATTTTTCTCTTT
Found at i:551448 original size:32 final size:33
Alignment explanation
Indices: 551385--551466 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 33
551375 CAAACCCTCA
*
551385 TTTTTCTCTTTTCATTTTTTC--A--TTTCTTT
1 TTTTTCTCTTTTCATTTTTTCTTATTTTTCATT
*
551414 TTTTTCAT-TTTTCATTTTTT-TTCTTTTTCA-T
1 TTTTTC-TCTTTTCATTTTTTCTTATTTTTCATT
*
551445 TTTTTCTTTTTTTCATTTTTTC
1 TTTTTC-TCTTTTCATTTTTTC
551467 ATCTTTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
29 18 0.42
30 1 0.02
31 8 0.19
32 16 0.37
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (33 bp):
TTTTTCTCTTTTCATTTTTTCTTATTTTTCATT
Found at i:551466 original size:16 final size:16
Alignment explanation
Indices: 551393--551490 Score: 89
Period size: 16 Copynumber: 6.2 Consensus size: 16
551383 CATTTTTCTC
*
551393 TTTTCATTTTTTCATT
1 TTTTCATTTTTTCTTT
* *
551409 TCTT--TTTTTTC-AT
1 TTTTCATTTTTTCTTT
551422 TTTTCATTTTTT-TTCT
1 TTTTCATTTTTTCTT-T
551438 TTTTCATTTTTTCTTT
1 TTTTCATTTTTTCTTT
*
551454 TTTTCATTTTTTCATCT
1 TTTTCATTTTTTC-TTT
*
551471 TTTT-ATTTGTTCCTTT
1 TTTTCATTT-TTTCTTT
551487 TTTT
1 TTTT
551491 TCTTCAAGCA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.06
14 7 0.10
15 6 0.09
16 40 0.59
17 11 0.16
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTCATTTTTTCTTT
Found at i:551488 original size:32 final size:31
Alignment explanation
Indices: 551384--551489 Score: 105
Period size: 32 Copynumber: 3.5 Consensus size: 31
551374 TCAAACCCTC
*
551384 ATTTTT-CTCTTTTCATTTTTTCAT-TTCTTT
1 ATTTTTCCTTTTTTCATTTTTTCATCTT-TTT
* *
551414 -TTTTT-CATTTTTCATTTTTT-TTCTTTTT
1 ATTTTTCCTTTTTTCATTTTTTCATCTTTTT
*
551442 CATTTTTTCTTTTTTTCATTTTTTCATCTTTTT
1 -A-TTTTTCCTTTTTTCATTTTTTCATCTTTTT
551475 ATTTGTTCCTTTTTT
1 ATTT-TTCCTTTTTT
551490 TTCTTCAAGC
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
28 4 0.06
29 20 0.32
31 8 0.13
32 23 0.37
33 7 0.11
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.76
Consensus pattern (31 bp):
ATTTTTCCTTTTTTCATTTTTTCATCTTTTT
Found at i:551488 original size:40 final size:40
Alignment explanation
Indices: 551407--551489 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
551397 CATTTTTTCA
* *
551407 TTTCTTTTTTTTCATTTTTCATTTTTTTTCTTTTTCATTT
1 TTTCTTTTTTTTCATTTTTCATTTTTTATCTTGTTCATTT
*
551447 TTTC-TTTTTTTCATTTTTTCATCTTTTTAT-TTGTTCCTTT
1 TTTCTTTTTTTTCA-TTTTTCAT-TTTTTATCTTGTTCATTT
551487 TTT
1 TTT
551490 TTCTTCAAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 9 0.24
40 23 0.61
41 6 0.16
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.78
Consensus pattern (40 bp):
TTTCTTTTTTTTCATTTTTCATTTTTTATCTTGTTCATTT
Found at i:571231 original size:84 final size:83
Alignment explanation
Indices: 571075--571244 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 83
571065 ATATTTGAAA
571075 GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCCGATAATTAAGGAACTTATTGATATT
1 GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCCGATAATTAAGGAACTTATTGATATT
571140 TCTTGAGGTTTTGGGTTT
66 TCTTGAGGTTTTGGGTTT
*
571158 GAGTTTGATCATAACTATTTAAGCACGAACCAAACAATCTCGATAATTAAGGAACTTATTGATAT
1 GAGTTTGATCATAACTATTTAAGCACGAACCAAA-AATCCCGATAATTAAGGAACTTATTGATAT
571223 TTCTTGAGGTTTTGGGTTT
65 TTCTTGAGGTTTTGGGTTT
571242 GAG
1 GAG
571245 CACCGTAAAT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 34 0.40
84 51 0.60
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (83 bp):
GAGTTTGATCATAACTATTTAAGCACGAACCAAAAATCCCGATAATTAAGGAACTTATTGATATT
TCTTGAGGTTTTGGGTTT
Found at i:575527 original size:24 final size:26
Alignment explanation
Indices: 575486--575533 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
575476 AAATTAAAGT
**
575486 AAAATGAAATT-ATGAAAAGATGATC
1 AAAATGAAATTAAAAAAAAGATGATC
575511 AAAAT-AAATTAAAAAAAAGATGA
1 AAAATGAAATTAAAAAAAAGATGA
575534 CTGTTGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (26 bp):
AAAATGAAATTAAAAAAAAGATGATC
Found at i:575691 original size:15 final size:15
Alignment explanation
Indices: 575671--575701 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
575661 TCAAAGTGCT
575671 AGCATATAAGTAAGA
1 AGCATATAAGTAAGA
575686 AGCATATAAGTAAGA
1 AGCATATAAGTAAGA
575701 A
1 A
575702 AAAGATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AGCATATAAGTAAGA
Found at i:576397 original size:24 final size:24
Alignment explanation
Indices: 576370--576452 Score: 157
Period size: 24 Copynumber: 3.5 Consensus size: 24
576360 CTATTCTTTC
*
576370 GCTTCAATCGATATTGAATTTCAA
1 GCTTCAATCGATCTTGAATTTCAA
576394 GCTTCAATCGATCTTGAATTTCAA
1 GCTTCAATCGATCTTGAATTTCAA
576418 GCTTCAATCGATCTTGAATTTCAA
1 GCTTCAATCGATCTTGAATTTCAA
576442 GCTTCAATCGA
1 GCTTCAATCGA
576453 GCTTCTAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (24 bp):
GCTTCAATCGATCTTGAATTTCAA
Found at i:576853 original size:13 final size:13
Alignment explanation
Indices: 576818--576857 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
576808 TCTTTTTCCC
576818 TCTTCTCTC-TTT
1 TCTTCTCTCTTTT
*
576830 TC-TCTCCCTTTT
1 TCTTCTCTCTTTT
576842 TCTTCTCTCTTTT
1 TCTTCTCTCTTTT
576855 TCT
1 TCT
576858 GTGTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 7 0.29
13 12 0.50
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TCTTCTCTCTTTT
Found at i:577136 original size:15 final size:15
Alignment explanation
Indices: 577116--577146 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
577106 CCATGATTAG
*
577116 TGTAAACGAATTCTC
1 TGTAAACGAACTCTC
577131 TGTAAACGAACTCTC
1 TGTAAACGAACTCTC
577146 T
1 T
577147 TGCATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (15 bp):
TGTAAACGAACTCTC
Found at i:588626 original size:16 final size:16
Alignment explanation
Indices: 588593--588631 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
588583 TCTAGTTAAC
588593 TTATAAATTGTTTATTA
1 TTAT-AATTGTTTATTA
* *
588610 TTATAATTTTTTGTTA
1 TTATAATTGTTTATTA
588626 TTATAA
1 TTATAA
588632 GATAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
TTATAATTGTTTATTA
Found at i:589187 original size:16 final size:16
Alignment explanation
Indices: 589158--589195 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
589148 GTATTATCCA
*
589158 ACCTGCTATCAACCTG
1 ACCTGTTATCAACCTG
*
589174 ACCTGTTATGAACCTG
1 ACCTGTTATCAACCTG
589190 ACCTGT
1 ACCTGT
589196 AAATGATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.29
Consensus pattern (16 bp):
ACCTGTTATCAACCTG
Found at i:599642 original size:30 final size:30
Alignment explanation
Indices: 599591--599662 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
599581 ATTTTTTATT
* * *
599591 TGCATGATATTAATTCTCCGTTCTGACATC
1 TGCATGAGATTAATTCACCGTTCTCACATC
* *
599621 TGCATGGGATTAGTTCACCGTTCTCACATC
1 TGCATGAGATTAATTCACCGTTCTCACATC
599651 TGCATGAGATTA
1 TGCATGAGATTA
599663 TATCTCTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (30 bp):
TGCATGAGATTAATTCACCGTTCTCACATC
Found at i:601659 original size:60 final size:60
Alignment explanation
Indices: 601588--601702 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
601578 TTGGGGACCA
* * * *
601588 ATTTAGAATGATAATCATAGTTTGAGGATGAAATTAGAATATTAAAAAATTTAAGGACTG
1 ATTTAAAATGATAATCATAATTTAAGGATGAAATTAAAATATTAAAAAATTTAAGGACTG
** * *
601648 ATTTAAAATGATGGTCATAATTTAAGGATGAAATTAAAATATTCAAAAGTTTAAG
1 ATTTAAAATGATAATCATAATTTAAGGATGAAATTAAAATATTAAAAAATTTAAG
601703 AACTAATTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (60 bp):
ATTTAAAATGATAATCATAATTTAAGGATGAAATTAAAATATTAAAAAATTTAAGGACTG
Found at i:602086 original size:35 final size:34
Alignment explanation
Indices: 602063--602139 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 34
602053 TTATTTTTAT
602063 TATTTT-TAAATAATAAATAATAATAATAATTTGA
1 TATTTTATAAATAATAAAT-ATAATAATAATTTGA
* * *
602097 TATTTTATAATTAATTAATATAATAGATTAATTCGA
1 TATTTTATAAATAATAAATATAATA-A-TAATTTGA
*
602133 TTTTTTA
1 TATTTTA
602140 ATTAAGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 12 0.33
35 11 0.31
36 13 0.36
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TATTTTATAAATAATAAATATAATAATAATTTGA
Found at i:602142 original size:34 final size:34
Alignment explanation
Indices: 602063--602144 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
602053 TTATTTTTAT
* *
602063 TATTTTTAAATAATAAATAATAATAATAATTTGA
1 TATTTTTAATTAATAAATAATAATAATAATTCGA
*
602097 TATTTTATAATTAATTAAT-ATAATAGATTAATTCGA
1 TATTTT-TAATTAATAAATAATAATA-A-TAATTCGA
602133 T-TTTTTAATTAA
1 TATTTTTAATTAA
602145 GCATAGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 19 0.45
35 15 0.36
36 8 0.19
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TATTTTTAATTAATAAATAATAATAATAATTCGA
Found at i:613591 original size:10 final size:10
Alignment explanation
Indices: 613576--613606 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
613566 ACTCAACCTA
613576 AAAAAAAAAG
1 AAAAAAAAAG
613586 AAAAAAAAAG
1 AAAAAAAAAG
613596 AAAAAAAAAG
1 AAAAAAAAAG
613606 A
1 A
613607 TTACAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:626788 original size:14 final size:14
Alignment explanation
Indices: 626760--626799 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
626750 TTTTTTTTGT
626760 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
626773 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
626787 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
626800 TATGAACGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:628444 original size:37 final size:34
Alignment explanation
Indices: 628291--628511 Score: 148
Period size: 35 Copynumber: 6.2 Consensus size: 34
628281 CTAAAAACTT
*
628291 ATATACAATATATAAGTTTTAAAAACATTTTGAAA
1 ATATATAATATAT-AGTTTTAAAAACATTTTGAAA
* * * *
628326 ATTATATAACATATATTTTTGAAATCATTTTG-AA
1 A-TATATAATATATAGTTTTAAAAACATTTTGAAA
*
628360 A-ATATAATGTATAGTTTAAAATAAAAACATTTTTGAAA
1 ATATATAATATATAGTTT----TAAAAACA-TTTTGAAA
*
628398 ATTTTATATAATATATAGTTTTAAAAATATTTTGGAAA
1 A---TATATAATATATAGTTTTAAAAACATTTT-GAAA
*
628436 ACTCATAT-A-ATAT--TTTTAAAATCATTTTTGAAA
1 A-T-ATATAATATATAGTTTTAAAAACA-TTTTGAAA
** * *
628469 ACTATATGGTATATAGTTTTGAAAACATTTTTAAA
1 A-TATATAATATATAGTTTTAAAAACATTTTGAAA
628504 TATATATA
1 -ATATATA
628512 GTTTAAAAAA
Statistics
Matches: 147, Mismatches: 20, Indels: 38
0.72 0.10 0.19
Matches are distributed among these distances:
32 17 0.12
33 16 0.11
34 11 0.07
35 32 0.22
36 28 0.19
37 13 0.09
38 15 0.10
42 15 0.10
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (34 bp):
ATATATAATATATAGTTTTAAAAACATTTTGAAA
Found at i:628463 original size:33 final size:31
Alignment explanation
Indices: 628408--628527 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 31
628398 ATTTTATATA
628408 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* *
628439 CATATAATA-TTTTTAAAATCATTTTTGAAAACTAT
1 -ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAAC--T
* * *
628474 ATGGTATATAGTTTTGAAAACATTTT--TAAA-T
1 A---TATATAGTTTTAAAAATATTTTGGAAAACT
*
628505 ATATATAGTTTAAAAAATATTTT
1 ATATATAGTTTTAAAAATATTTT
628528 TTGGGATATA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
28 19 0.26
31 2 0.03
32 13 0.18
33 14 0.19
34 4 0.06
35 1 0.01
36 8 0.11
37 11 0.15
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:628593 original size:18 final size:18
Alignment explanation
Indices: 628572--628610 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
628562 ATTATTTCTT
*
628572 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
628590 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
628608 TTC
1 TTC
628611 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:633998 original size:106 final size:106
Alignment explanation
Indices: 633808--635971 Score: 3988
Period size: 106 Copynumber: 20.4 Consensus size: 106
633798 AGAGTAAATT
*
633808 ACAAATTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
633873 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
633914 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
633979 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
634020 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634085 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
634126 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
* *
634191 AAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
634232 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
**
634296 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGTAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
634337 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634402 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
634443 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634508 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
634549 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634614 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
634655 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
634720 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
634761 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634826 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
634867 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
634932 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
634973 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
* *
635038 AAGTTCAACTTCACGACGAAGGTACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
635079 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
635144 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
635185 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
635250 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
635291 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
635356 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
635397 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
* *
635462 AAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
635503 ACAATTTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
* *
635568 AAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAGCAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * * *
635609 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
635674 ACGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
635715 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
635780 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
635821 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
635886 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
635927 ACAACTTCTCAATTTCAGAGCCAATCTCGACTTCACGACGAAGGA
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
635972 GCCATCTGCA
Statistics
Matches: 2001, Mismatches: 56, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
105 102 0.05
106 1899 0.95
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
Found at i:636394 original size:37 final size:36
Alignment explanation
Indices: 636178--636483 Score: 169
Period size: 36 Copynumber: 8.5 Consensus size: 36
636168 TTTGAAAGTG
*
636178 TTTTTGAAAA--ATATAACATATAG-TTTACAAAA-A
1 TTTTTGAAAATTATATAATATATAGTTTTA-AAAACA
* *
636211 TGGTTTCTGAAAATATATATAATATAGT-TTTTTAAAAAACG
1 T--TTT-TGAAAAT-TATATAATATA-TAGTTTT-AAAAACA
* *
636252 TTTCTAAAAACTTATATACA-ATATAAGTTTTAAAAACA
1 TTTTTGAAAA-TTATATA-ATATAT-AGTTTTAAAAACA
* * * *
636290 -TTTTGAAAATTATATAACATATATTTTTGAAATCA
1 TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
*
636325 -TTTTG-AAA--ATATAATGTATAGTTTAAAATAAAAACA
1 TTTTTGAAAATTATATAATATATAGTTT----TAAAAACA
*
636361 TTTTTGAAAATTTATATAATATATAGTTTTAAAAATA
1 TTTTTGAAAA-TTATATAATATATAGTTTTAAAAACA
* * *
636398 -TTTGGAAAACTCATAT-A-ATAT--TTTTAAAATCA
1 TTTTTGAAAA-TTATATAATATATAGTTTTAAAAACA
* ** *
636430 TTTTTGAAAACTATATGGTATATAGTTTTGAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
636466 TTTTT-AAATATATATATA
1 TTTTTGAAA-AT-TATATA
636484 GTTTAAAAAA
Statistics
Matches: 210, Mismatches: 32, Indels: 58
0.70 0.11 0.19
Matches are distributed among these distances:
32 26 0.12
33 9 0.04
34 11 0.05
35 23 0.11
36 51 0.24
37 25 0.12
38 23 0.11
39 17 0.08
40 8 0.04
41 17 0.08
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
Found at i:636483 original size:69 final size:69
Alignment explanation
Indices: 636279--636468 Score: 174
Period size: 73 Copynumber: 2.7 Consensus size: 69
636269 ACAATATAAG
* * * * *
636279 TTTTAAAAACA-TTTTGAAAAT-TATATAACATATATTTTTGAAATCATTTTGAAAA-T-ATAAT
1 TTTTAAAAACATTTTTGAAAATCTATATAATATATAGTTTTAAAAACATTTGGAAAACTCAT-AT
*
636340 GTATAGT
65 -AATA-T
* * *
636347 TTAAAATAAAAACATTTTTGAAAATTTATATAATATATAGTTTTAAAAATATTTGGAAAACTCAT
1 TT---TTAAAAACATTTTTGAAAATCTATATAATATATAGTTTTAAAAACATTTGGAAAACTCAT
636412 ATAATAT
63 ATAATAT
* ** *
636419 TTTTAAAATCATTTTTGAAAA-CTATATGGTATATAGTTTTGAAAACATTT
1 TTTTAAAAACATTTTTGAAAATCTATATAATATATAGTTTTAAAAACATTT
636469 TTAAATATAT
Statistics
Matches: 100, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
68 26 0.26
69 17 0.17
71 8 0.08
72 13 0.13
73 31 0.31
74 3 0.03
75 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (69 bp):
TTTTAAAAACATTTTTGAAAATCTATATAATATATAGTTTTAAAAACATTTGGAAAACTCATATA
ATAT
Found at i:639740 original size:18 final size:18
Alignment explanation
Indices: 639713--639749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
639703 AAATTAACCC
*
639713 ATTAAATGTTAGTTATAA
1 ATTAAATGTTAGGTATAA
*
639731 ATTAACTGTTAGGTATAA
1 ATTAAATGTTAGGTATAA
639749 A
1 A
639750 GTTGGGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (18 bp):
ATTAAATGTTAGGTATAA
Found at i:642823 original size:17 final size:17
Alignment explanation
Indices: 642778--642823 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
642768 GATAAAACAG
642778 TTTCTTTTAGAT-ATAA
1 TTTCTTTTAGATAATAA
*
642794 TTTCTTCTT-GATAATCA
1 TTTCTT-TTAGATAATAA
642811 TTTCTTTTAGATA
1 TTTCTTTTAGATA
642824 TTAGTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTCTTTTAGATAATAA
Found at i:642831 original size:17 final size:17
Alignment explanation
Indices: 642776--642831 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
642766 AGGATAAAAC
642776 AGTTTCTTTTAGATA-T
1 AGTTTCTTTTAGATATT
* *
642792 AATTTCTTCTT-GATAATC
1 AGTTTCTT-TTAGAT-ATT
642810 A-TTTCTTTTAGATATT
1 AGTTTCTTTTAGATATT
642826 AGTTTC
1 AGTTTC
642832 AAACACACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 15 0.47
17 16 0.50
18 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (17 bp):
AGTTTCTTTTAGATATT
Found at i:646031 original size:39 final size:39
Alignment explanation
Indices: 645977--646058 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
645967 AAATAGCACG
*
645977 CTAATTAATTAGGATGAATAGCAAATTTAAGTACAAAAA
1 CTAATTAATTAGGATGAATAACAAATTTAAGTACAAAAA
* *
646016 CTAATTAATTAGGATGAATAACAAATTTAATTATAAAAA
1 CTAATTAATTAGGATGAATAACAAATTTAAGTACAAAAA
646055 CTAA
1 CTAA
646059 GGAATTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (39 bp):
CTAATTAATTAGGATGAATAACAAATTTAAGTACAAAAA
Found at i:646045 original size:22 final size:22
Alignment explanation
Indices: 645981--646048 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
645971 AGCACGCTAA
*
645981 TTAATTAGGATGAATAGCAAAT
1 TTAATTAGGATGAATAACAAAT
* * *
646003 TTAAGTA-CA--AA-AACTAA-
1 TTAATTAGGATGAATAACAAAT
646020 TTAATTAGGATGAATAACAAAT
1 TTAATTAGGATGAATAACAAAT
646042 TTAATTA
1 TTAATTA
646049 TAAAAACTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 2 0.06
20 2 0.06
21 6 0.18
22 13 0.38
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (22 bp):
TTAATTAGGATGAATAACAAAT
Found at i:648375 original size:19 final size:19
Alignment explanation
Indices: 648351--648387 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
648341 AGTTATTCAA
*
648351 ATTCAACTATGAGTTTCGG
1 ATTCAACTACGAGTTTCGG
*
648370 ATTCAAGTACGAGTTTCG
1 ATTCAACTACGAGTTTCG
648388 AATATCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTCAACTACGAGTTTCGG
Found at i:650551 original size:31 final size:31
Alignment explanation
Indices: 650449--650565 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 31
650439 TTTCAGTACG
* * *
650449 TTACAAAATAATAATTAAACTTCTT-AAGTA
1 TTACAAAATAATCATTAAACTTATTAAACTA
* * * * *
650479 TTACAGAATAATCAATAAGCAGTATTAAATTA
1 TTACAAAATAATCATTAAAC-TTATTAAACTA
650511 TTACAAAATAGA-CATTAAACTTATTAAACTA
1 TTACAAAATA-ATCATTAAACTTATTAAACTA
** *
650542 TTATGAAATAATCCTTAAACTTAT
1 TTACAAAATAATCATTAAACTTAT
650566 CATAATATAT
Statistics
Matches: 68, Mismatches: 15, Indels: 7
0.76 0.17 0.08
Matches are distributed among these distances:
30 17 0.25
31 31 0.46
32 19 0.28
33 1 0.01
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (31 bp):
TTACAAAATAATCATTAAACTTATTAAACTA
Found at i:657349 original size:16 final size:16
Alignment explanation
Indices: 657321--657353 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
657311 GGGTTTACAT
657321 TAATTTTTGTACTTGA
1 TAATTTTTGTACTTGA
657337 TAATTCTTT-TACTTGA
1 TAATT-TTTGTACTTGA
657353 T
1 T
657354 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (16 bp):
TAATTTTTGTACTTGA
Found at i:661215 original size:24 final size:24
Alignment explanation
Indices: 661188--661296 Score: 173
Period size: 24 Copynumber: 4.5 Consensus size: 24
661178 ACATAGGTAG
*
661188 TGTATCGATACACATGTTGAGGAA
1 TGTATCGATACACATGTTAAGGAA
*
661212 TGTATCGATACACATGTTGAGGAA
1 TGTATCGATACACATGTTAAGGAA
* *
661236 TATATCGATACACATATTAAGGAA
1 TGTATCGATACACATGTTAAGGAA
*
661260 TGTATCAATACACATGTTAAGGAA
1 TGTATCGATACACATGTTAAGGAA
661284 TGTATCGATACAC
1 TGTATCGATACAC
661297 TATAGTGTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (24 bp):
TGTATCGATACACATGTTAAGGAA
Found at i:671246 original size:112 final size:113
Alignment explanation
Indices: 671023--671262 Score: 376
Period size: 112 Copynumber: 2.1 Consensus size: 113
671013 TTGTCGGTTT
*
671023 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATATAACATGTAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATATAACAGGTAAAAAATGACAAAAC
* * * * *
671088 CGATTTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 CGATCTAGAAATGACAAAACAGATAAAGCGCTACCAGATATATTGAAA
671136 GTGTCGATACTTTATAAAAATATATTGATCCATAAC-A-ATATAACAGGTAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATATAACAGGT-AAAAAATGACAAAA
* * *
671199 CCGATCTCGAAATGACAAAACCGATAAAGCGCTACCAGATATGTTGAAA
65 CCGATCTAGAAATGACAAAACAGATAAAGCGCTACCAGATATATTGAAA
671248 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
671263 TATAAGTATC
Statistics
Matches: 117, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
111 10 0.09
112 71 0.61
113 36 0.31
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (113 bp):
GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATATAACAGGTAAAAAATGACAAAAC
CGATCTAGAAATGACAAAACAGATAAAGCGCTACCAGATATATTGAAA
Found at i:671441 original size:182 final size:182
Alignment explanation
Indices: 671133--671588 Score: 786
Period size: 182 Copynumber: 2.5 Consensus size: 182
671123 GGATATATTG
* * *
671133 AAAGTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** *
671198 ACCGATCTCGAAATGACAAAACCGATAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGATCTCGAAATGACAAAACCGGTAAAAAGCTACCAGATATGTTAAAAGTGTCGATACTTTAT
671263 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
131 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
671315 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
671380 ACCGGTCTCGAAATGACAAAACCGGTAAAAAGCTACCATATATGTTAAAAGTGTTGATACTTTAT
66 ACCGATCTCGAAATGACAAAACCGGTAAAAAGCTACCAGATATGTTAAAAGTGTCGATACTTTAT
* *
671445 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAAT
131 TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
*
671497 AAAGTGTCGATAATTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
671562 ATCGATCTCGAAATGACAAAACCGGTA
66 ACCGATCTCGAAATGACAAAACCGGTA
671589 GTAAAAAAGT
Statistics
Matches: 259, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 259 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGATCTCGAAATGACAAAACCGGTAAAAAGCTACCAGATATGTTAAAAGTGTCGATACTTTAT
TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:677850 original size:17 final size:17
Alignment explanation
Indices: 677828--677889 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
677818 TATACCTTGT
677828 AATAAATATATTTATAA
1 AATAAATATATTTATAA
677845 AATAAA-ATGCATTTAT-A
1 AATAAATAT--ATTTATAA
* *
677862 AATAAATAAGATTTTTACA
1 AATAAAT-ATATTTATA-A
677881 AATAAATAT
1 AATAAATAT
677890 GTTTTCGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
16 2 0.06
17 18 0.50
18 7 0.19
19 9 0.25
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATAAATATATTTATAA
Found at i:678165 original size:22 final size:22
Alignment explanation
Indices: 678140--678184 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
678130 AAAGATTAAT
* *
678140 TGATCATTATATGATGTTTTTA
1 TGATCATTATATAATGATTTTA
**
678162 TGATGGTTATATAATGATTTTA
1 TGATCATTATATAATGATTTTA
678184 T
1 T
678185 TGAATAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (22 bp):
TGATCATTATATAATGATTTTA
Found at i:682269 original size:11 final size:11
Alignment explanation
Indices: 682253--682277 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
682243 TAAGGCCTCT
682253 AGAGAGGTCCC
1 AGAGAGGTCCC
682264 AGAGAGGTCCC
1 AGAGAGGTCCC
682275 AGA
1 AGA
682278 AAGTTCCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.24, G:0.36, T:0.08
Consensus pattern (11 bp):
AGAGAGGTCCC
Found at i:682513 original size:3 final size:3
Alignment explanation
Indices: 682499--682550 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
682489 TATCCCGGTT
* * *
682499 TTA TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
682545 TTA TTA
1 TTA TTA
682551 ATAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:682526 original size:12 final size:12
Alignment explanation
Indices: 682509--682560 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
682499 TTATTATTTT
682509 ATTATTATAATA
1 ATTATTATAATA
*
682521 ATTATTATTATA
1 ATTATTATAATA
* *
682533 ATTATT-TTATT
1 ATTATTATAATA
682544 ATTATTAATAAATA
1 ATTATT-AT-AATA
682558 ATT
1 ATT
682561 TTTACAGGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 10 0.30
12 17 0.52
13 1 0.03
14 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATAATA
Found at i:684821 original size:29 final size:28
Alignment explanation
Indices: 684800--684853 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
684790 TACTTTTTTC
*
684800 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATACTTATTA
*
684828 TTTTCATAATATTTATATATA-TTATT
1 TTTTCAAAATATTTATATATACTTATT
684854 TTATTAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTCAAAATATTTATATATACTTATTA
Found at i:684849 original size:30 final size:30
Alignment explanation
Indices: 684778--684859 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
684768 AAAAATTTAT
* * *
684778 ATATTTA-ATTTATACTTTTTTCTTTTCAA
1 ATATTTATATATATACTTTATTATTTTCAA
*
684807 A-ATTTTTATATATAC-TTATTATTTTCATA
1 ATATTTATATATATACTTTATTATTTTCA-A
*
684836 ATATTTATATATATTATTTTATTA
1 ATATTTATATATA-TACTTTATTA
684860 ATGCTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 14 0.33
29 10 0.24
30 10 0.24
31 2 0.05
32 6 0.14
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATTTATATATATACTTTATTATTTTCAA
Found at i:687792 original size:43 final size:43
Alignment explanation
Indices: 687725--687807 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
687715 TGGCGTTAGA
* *
687725 GAAGTTAGGAGGGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGCTATCCCCTATATGTAAAGTTTTGTT
* *
687768 GAAGTTAGGACTGAAAGCTGTCCCCTATATGTAAAGTTTT
1 GAAGTTAGGACGGAAAGCTATCCCCTATATGTAAAGTTTT
687808 TTTTGATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (43 bp):
GAAGTTAGGACGGAAAGCTATCCCCTATATGTAAAGTTTTGTT
Found at i:690784 original size:20 final size:20
Alignment explanation
Indices: 690752--690823 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 20
690742 GAAAAAAAGG
690752 AAAAAAG-AAAAAAAGAAAA
1 AAAAAAGAAAAAAAAGAAAA
*
690771 AAAAGA-AAAAAAAAG-AAA
1 AAAAAAGAAAAAAAAGAAAA
690789 AAAAAAGAAAAAAAAAGAAAA
1 AAAAAAG-AAAAAAAAGAAAA
690810 AAAAAAGGAAAAAA
1 AAAAAA-GAAAAAA
690824 TTGAACCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.17
19 13 0.28
20 9 0.20
21 15 0.33
22 1 0.02
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAAAGAAAA
Done.