Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold229
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: 751352
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 14889 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:379455 original size:54 final size:54
Alignment explanation
Indices: 379349--379455 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
379339 CTAACAATGT
* * * * * *
379349 TTTACATTTGTTGGCTTTTAAAATTCCCGAATCGTGTAATAGAAGCTCTGTTGA
1 TTTACATTTGTTCGCTTATAAAAATCCCGAATCGAGTAATAAAACCTCTGTTGA
* *
379403 TTTAGATTTGTTCGCTTATAAAAATCCCGAATCGAGTTATAAACACCT-TGTTG
1 TTTACATTTGTTCGCTTATAAAAATCCCGAATCGAGTAATAAA-ACCTCTGTTG
379456 GTTTTGATCT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 41 0.93
55 3 0.07
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (54 bp):
TTTACATTTGTTCGCTTATAAAAATCCCGAATCGAGTAATAAAACCTCTGTTGA
Found at i:380587 original size:21 final size:22
Alignment explanation
Indices: 380563--380605 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
380553 TATTGGAGGA
*
380563 TGGTATCA-TTATATTTTTATT
1 TGGTATCACTTATATATTTATT
*
380584 TGGTATCACTTTTATATTTATT
1 TGGTATCACTTATATATTTATT
380606 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (22 bp):
TGGTATCACTTATATATTTATT
Found at i:394239 original size:11 final size:11
Alignment explanation
Indices: 394216--394248 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
394206 GAATGAAAAT
*
394216 TTTTA-AATAA
1 TTTTATAATTA
394226 TTTTATAATTA
1 TTTTATAATTA
394237 TTTTATAATTA
1 TTTTATAATTA
394248 T
1 T
394249 GTGATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:415304 original size:44 final size:44
Alignment explanation
Indices: 415250--415695 Score: 190
Period size: 44 Copynumber: 9.7 Consensus size: 44
415240 GATTGAAGTT
*
415250 ACAAAACTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * **
415294 ACAAATCTTATCTTCC-TGAAGTTGCAGTGGAATAGATTGAAGAT
1 ACAAATCTTATC-TCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * * * * * *
415338 AGCAAATCTTATCT-CTCTGAAATTGTAGTAGAGCAAATTAAAACT
1 A-CAAATCTTATCTCCT-TGAAGTTGCAGTGGAGTAGATTAAAGCC
* * ** *
415383 ACAAATCTTATTTTCC-TAAAGTTGCAGTGGAACATATTAAAGCTAC
1 ACAAATCTTA-TCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGC--C
415429 AAATTACAAATCTTATCT-CTCTGAAGTTGCAGTGGAGTAGATTGAAA--C
1 -----ACAAATCTTATCTCCT-TGAAGTTGCAGTGGAGTAGATT-AAAGCC
* * * * * * * *
415477 ATAAGTCCTAT-ACCTCTGAATTTGTAGTTG-GTCAGATTAAATCC
1 ACAAATCTTATCTCCT-TGAAGTTGCAGTGGAGT-AGATTAAAGCC
* * *
415521 ACCATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAATAGACTAAAGCTACAAGCT
1 A-C--A--AA-TCTTATCTCCTTGAAGTTGCAGTGGAGTAGA-T-----TA-AAGCC
* * * * * *
415578 ACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAAATTAAAGCT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * * * *
415622 ACAAGTCTAATCTCCTTGAAGTTGTAGTGGAGTAGATTGAAGCA
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * *
415666 ACAAATCATATAC-CTTTAAAGTTGCAGTGG
1 ACAAATCTTAT-CTCCTTGAAGTTGCAGTGG
415696 GTTAGAATGA
Statistics
Matches: 299, Mismatches: 67, Indels: 72
0.68 0.15 0.16
Matches are distributed among these distances:
42 5 0.02
43 28 0.09
44 129 0.43
45 39 0.13
46 1 0.00
47 1 0.00
48 1 0.00
49 2 0.01
50 22 0.07
51 58 0.19
52 5 0.02
54 1 0.00
56 3 0.01
57 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
Found at i:415378 original size:89 final size:88
Alignment explanation
Indices: 415221--415414 Score: 228
Period size: 89 Copynumber: 2.2 Consensus size: 88
415211 TCTCTACCCT
* * * * * * *
415221 TGAAGTTGCAATGAAAAAAGATTGAAGTTACAAAACTTATCTCCTTGAAGTTGCAGTGGAGTAGA
1 TGAAGTTGCAGTG-GAAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGCAAA
*
415286 TTAAAGCCACAAATCTTATCTTCC
65 TTAAAACCACAAATCTTATCTTCC
* * *
415310 TGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTATCT-CTCTGAAATTGTAGTAGAGCAA
1 TGAAGTTGCAGTGGAAAAGATTGAAGATA-CAAAACTTATCTCCT-TGAAATTGCAGTAGAGCAA
* *
415374 ATTAAAACTACAAATCTTATTTTCC
64 ATTAAAACCACAAATCTTATCTTCC
*
415399 TAAAGTTGCAGTGGAA
1 TGAAGTTGCAGTGGAA
415415 CATATTAAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 15 0.17
89 74 0.83
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (88 bp):
TGAAGTTGCAGTGGAAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGCAAAT
TAAAACCACAAATCTTATCTTCC
Found at i:415470 original size:140 final size:142
Alignment explanation
Indices: 415294--415603 Score: 346
Period size: 144 Copynumber: 2.2 Consensus size: 142
415284 GATTAAAGCC
* *
415294 ACAAATCTTATCT-TCCTGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTAT-CTCTCTG
1 ACAAATCTTATCTCT-CTGAAGTTGCAGTGGAATAGATTGAA-ACA-CAAATCCTATAC-CTCTG
* *
415357 AAATTGTAGTAGAG-CAAATTAAA-A-C-TA-CAAATCTTATTTTCCTAAAGTTGCAGTGGAACA
62 AAATTGTAGTAG-GTCAAATTAAACACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACA
* * *
415417 TATTAAAGCTACAAATT
126 GACTAAAGCTACAAACT
* * * *
415434 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAACATAAGTCCTATACCTCTGAATT
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAATAGATTGAAACACAAATCCTATACCTCTGAAAT
* * * * *
415499 TGTAGTTGGTCAGATTAAATCCACCATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAATAGAC
66 TGTAGTAGGTCAAATTAAA--CACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAGAC
*
415564 TAAAGCTACAAGCT
129 TAAAGCTACAAACT
*
415578 ACAAATCTTATCTCCCTGAAGTTGCA
1 ACAAATCTTATCTCTCTGAAGTTGCA
415604 ATAGAGCAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
137 1 0.01
138 30 0.21
139 3 0.02
140 38 0.27
141 2 0.01
142 1 0.01
143 2 0.01
144 66 0.46
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (142 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTGGAATAGATTGAAACACAAATCCTATACCTCTGAAAT
TGTAGTAGGTCAAATTAAACACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTA
AAGCTACAAACT
Found at i:415927 original size:7 final size:7
Alignment explanation
Indices: 415915--415941 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
415905 TATCATTCCT
415915 TTATTTA
1 TTATTTA
415922 TTATTTA
1 TTATTTA
415929 TTATTTA
1 TTATTTA
415936 TTATTT
1 TTATTT
415942 TAGTATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:420469 original size:2 final size:2
Alignment explanation
Indices: 420410--420451 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
420400 CATGCAGGGA
420410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
420452 TGAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:426734 original size:105 final size:108
Alignment explanation
Indices: 426602--426808 Score: 323
Period size: 110 Copynumber: 1.9 Consensus size: 108
426592 GGTTGTAACT
426602 AATTCCAATTAATGGAAGAATTGGTTT-G-G-TTTGATTTGATAATATATTATTGGTTTT-TATG
1 AATTCCAATTAATGGAAGAATTGGTTTGGTGATTTGATTTGATAATATATTATTGGTTTTAT-TG
*
426663 TTATTAGGTAATGTTTTTAGAACCGGATCAATAGTCATGCCATC
65 TTATTAGGTAATGTCTTTAGAACCGGATCAATAGTCATGCCATC
* *
426707 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATTTGATAATATTTTATTGGTTTTATT
1 AATTCCAATTAATGGAAGAATTGGTTTGG--TGATTTGATTTGATAATATATTATTGGTTTTATT
*
426772 GTTATTAGGTAATGTCTTTAGAACCGGATTAATAGTC
64 GTTATTAGGTAATGTCTTTAGAACCGGATCAATAGTC
426809 GAACCAATCA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
105 26 0.28
106 1 0.01
109 1 0.01
110 63 0.68
111 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (108 bp):
AATTCCAATTAATGGAAGAATTGGTTTGGTGATTTGATTTGATAATATATTATTGGTTTTATTGT
TATTAGGTAATGTCTTTAGAACCGGATCAATAGTCATGCCATC
Found at i:432730 original size:36 final size:36
Alignment explanation
Indices: 432689--432803 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
432679 CTTTATAATT
432689 TTAAAGTATTGTATCAAAATTTTATATTTTGAGAGA
1 TTAAAGTATTGTATCAAAATTTTATATTTTGAGAGA
* * ** ** * * **
432725 TTAAAGTGCAATTTTA-CCAGCTTAAATCTTAT-A-ATT
1 TTAAAGT---ATTGTATCAAAATTTTATATTTTGAGAGA
432761 TTAAAGTATTGTATCAAAATTTTATATTTTGAGAGA
1 TTAAAGTATTGTATCAAAATTTTATATTTTGAGAGA
432797 TTAAAGT
1 TTAAAGT
432804 GCAATTTTAC
Statistics
Matches: 53, Mismatches: 20, Indels: 12
0.62 0.24 0.14
Matches are distributed among these distances:
33 5 0.09
34 9 0.17
35 1 0.02
36 23 0.43
37 1 0.02
38 9 0.17
39 5 0.09
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.43
Consensus pattern (36 bp):
TTAAAGTATTGTATCAAAATTTTATATTTTGAGAGA
Found at i:432769 original size:72 final size:73
Alignment explanation
Indices: 432670--432815 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 73
432660 CCATTTTAAT
*
432670 AGCTTATATCTTTATAATTTTAAAGTATTGTATCAAAATTTTATATTTTGAGAGATTAAAGTGCA
1 AGCTTAAATCTTTATAATTTTAAAGTATTGTATCAAAATTTTATATTTTGAGAGATTAAAGTGCA
432735 ATTTTACC
66 ATTTTACC
432743 AGCTTAAATC-TTATAATTTTAAAGTATTGTATCAAAATTTTATATTTTGAGAGATTAAAGTGCA
1 AGCTTAAATCTTTATAATTTTAAAGTATTGTATCAAAATTTTATATTTTGAGAGATTAAAGTGCA
432807 ATTTTACC
66 ATTTTACC
432815 A
1 A
432816 CTAATTTAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 63 0.88
73 9 0.12
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (73 bp):
AGCTTAAATCTTTATAATTTTAAAGTATTGTATCAAAATTTTATATTTTGAGAGATTAAAGTGCA
ATTTTACC
Found at i:433361 original size:4 final size:4
Alignment explanation
Indices: 433352--433384 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
433342 ACAAATTATG
433352 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
433385 CTAAGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:433532 original size:1 final size:1
Alignment explanation
Indices: 433526--433560 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
433516 TTTTCACTCG
**
433526 TTTTTTTTTTTTTTTTTTTTTTAATTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
433561 AAATCTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:433561 original size:13 final size:13
Alignment explanation
Indices: 433526--433562 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
433516 TTTTCACTCG
433526 TTTTTTTTTTT--
1 TTTTTTTTTTTAA
433537 TTTTTTTTTTTAA
1 TTTTTTTTTTTAA
433550 TTTTTTTTTTTAA
1 TTTTTTTTTTTAA
433563 ATCTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
13 13 0.54
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTAA
Found at i:434489 original size:43 final size:44
Alignment explanation
Indices: 434437--434520 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
434427 CTCTAATTCA
434437 TGTAGGTTTAACCCAAA-AGGGTAACCAAACACTATA-TTTCTCG
1 TGTAGGTTTAACCCAAATA-GGTAACCAAACACTATACTTTCTCG
* * *
434480 TGTAGGTTTATCTCAAATAGGTAACCAGACACTATACTTTC
1 TGTAGGTTTAACCCAAATAGGTAACCAAACACTATACTTTC
434521 ACCTATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (44 bp):
TGTAGGTTTAACCCAAATAGGTAACCAAACACTATACTTTCTCG
Found at i:435633 original size:13 final size:13
Alignment explanation
Indices: 435615--435649 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
435605 CTCAGTCTGT
435615 CACACGGCTTGGC
1 CACACGGCTTGGC
435628 CACACGGCTTGGC
1 CACACGGCTTGGC
435641 CACACGGCT
1 CACACGGCT
435650 ATATGATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (13 bp):
CACACGGCTTGGC
Found at i:436441 original size:12 final size:12
Alignment explanation
Indices: 436424--436450 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
436414 AATAATTTTA
436424 ATATATACATAT
1 ATATATACATAT
436436 ATATATACATAT
1 ATATATACATAT
436448 ATA
1 ATA
436451 AAAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACATAT
Found at i:436600 original size:27 final size:27
Alignment explanation
Indices: 436570--436653 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
436560 ATTGGTTCTT
436570 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
* * * * * *
436597 TGAAACAAGCGCCA--CAAGCT-TG-GC
1 TGAAAC-TGCACAAGTCCATCTATGACC
436621 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
436648 TGAAAC
1 TGAAAC
436654 AAGCACCACA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
23 4 0.10
24 7 0.17
25 6 0.15
26 6 0.15
27 13 0.32
28 4 0.10
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.19
Consensus pattern (27 bp):
TGAAACTGCACAAGTCCATCTATGACC
Found at i:436646 original size:51 final size:51
Alignment explanation
Indices: 436570--436672 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
436560 ATTGGTTCTT
*
436570 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCGCCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
436621 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
436672 T
1 T
436673 AGAGCTATGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (51 bp):
TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
Found at i:442273 original size:26 final size:26
Alignment explanation
Indices: 442232--442282 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
442222 CAGTTTGCAT
*
442232 ATTGAGCTTGTATATCGAGCTCGCAC
1 ATTGAGCTCGTATATCGAGCTCGCAC
* *
442258 ATTGAGCTCGTGTATCGGGCTCGCA
1 ATTGAGCTCGTATATCGAGCTCGCA
442283 TGATACTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (26 bp):
ATTGAGCTCGTATATCGAGCTCGCAC
Found at i:450301 original size:189 final size:190
Alignment explanation
Indices: 449979--450337 Score: 551
Period size: 189 Copynumber: 1.9 Consensus size: 190
449969 GACCGATAAT
** *** *
449979 GAGGATGAATTTTGATGTTTCCGGTATGATCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
* *
450044 TATGATCGTATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGACAATTAGCTGAATGAACAGA
66 TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGAAAATTAGCTGAATGAACAGA
450109 GTTTAAACAAGCTAGAACTAGTGAACT-AGACTGATTTCCGGTCATGCCTTATGTGACCG
131 GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCGGTCATGCCTTATGTGACCG
* ** *
450168 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTTCGCGAGGGCTTAATTTAAGCGTTCTTGAA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
* * *
450233 TATGATCATATCAGTTTCATGCTTAGAAAACTAGAGGAATCATGAAAAATT-GTTGAATGAATAG
66 TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATG-AAAATTAGCTGAATGAACAG
*
450297 AGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGATTTCC
130 AGTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCC
450338 CATTCTGCCT
Statistics
Matches: 152, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
189 135 0.89
190 17 0.11
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (190 bp):
GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGAAAATTAGCTGAATGAACAGA
GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCGGTCATGCCTTATGTGACCG
Found at i:465103 original size:25 final size:24
Alignment explanation
Indices: 465072--465133 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
465062 TTTTTAAAAA
465072 ATATTTGAAATGGTTTTTGTTGGT
1 ATATTTGAAATGGTTTTTGTTGGT
* *
465096 ATGATTTGAAAT--TATTTGTTTGT
1 AT-ATTTGAAATGGTTTTTGTTGGT
*
465119 ATATTTCAAATGGTT
1 ATATTTGAAATGGTT
465134 CTAAATGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 8 0.26
23 11 0.35
24 3 0.10
25 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (24 bp):
ATATTTGAAATGGTTTTTGTTGGT
Found at i:468936 original size:24 final size:21
Alignment explanation
Indices: 468892--468937 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
468882 CCGCCCATAT
468892 TATTTTTAATTTTTTTAAAAA
1 TATTTTTAATTTTTTTAAAAA
*
468913 TATTTGTTATATTTTATTTTAAAA
1 TATTT-TTA-ATTTT-TTTAAAAA
468937 T
1 T
468938 TTCATACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 5 0.24
24 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTTTTAATTTTTTTAAAAA
Found at i:478813 original size:391 final size:392
Alignment explanation
Indices: 477965--478822 Score: 1603
Period size: 392 Copynumber: 2.2 Consensus size: 392
477955 ATTAGTTTTA
*
477965 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACAACTCTTTTTTTGTCGTTATGGATATAATAGC
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
478030 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
66 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
478095 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
131 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
*
478160 TTTAATTATTCAATTAAGTATTAATGTATAGTGTGTTTTAAATCGATAAGATACATATATGTATT
196 TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
* *
478225 AGATTGTTTCAAAAATTTATATATATGATAAGTATAATTATATCAATAAATTTAATACAGATAAA
261 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
478290 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
326 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
478355 AT
391 AT
*
478357 AAAGTCAATGCAAAATAAGGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
*
478422 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTTAATCGTCATATTTTACATTTCATTCA
66 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
* * *
478487 TATAGATATTGCATGTCAAAATTATTATAAATTTTTAATTTTTAATTTTTTATTTATATAAAAAA
131 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
478552 TTTAATTATTCAA-TAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
196 TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
478616 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
261 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
*
478681 TCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAG-
326 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
478745 AT
391 AT
478747 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAAATAG
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATAT-AATAG
478812 CAATTGACAAC
65 CAATTGACAAC
478823 AAAACATTTA
Statistics
Matches: 454, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
390 60 0.13
391 192 0.42
392 202 0.44
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (392 bp):
AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
AT
Found at i:483795 original size:96 final size:97
Alignment explanation
Indices: 483679--483871 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 97
483669 TTAAAAAATC
483679 ATATAAAAACTATTGATTATTCTTTATTTACTTTAAAAAAAAATTAGAAATCTAACAAGCACAAA
1 ATATAAAAACTATTGATTATTCTTTATTTACTTTAAAAAAAAATTAGAAATCTAACAAGCACAAA
483744 ATAAAATTCATTTTGTCAAAACAAACCTAAAG
66 ATAAAATTCATTTTGTCAAAACAAACCTAAAG
483776 ATATAAAAAC-ATTGATTATTCTTTATTTACTTTAAAAAAAAATTAGAAATCTAACAAGCACAAA
1 ATATAAAAACTATTGATTATTCTTTATTTACTTTAAAAAAAAATTAGAAATCTAACAAGCACAAA
483840 ATAAAATTCATTTTGTCAAAACAAACCTAAAG
66 ATAAAATTCATTTTGTCAAAACAAACCTAAAG
483872 TTTCAAAATC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 86 0.90
97 10 0.10
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (97 bp):
ATATAAAAACTATTGATTATTCTTTATTTACTTTAAAAAAAAATTAGAAATCTAACAAGCACAAA
ATAAAATTCATTTTGTCAAAACAAACCTAAAG
Found at i:492215 original size:4 final size:4
Alignment explanation
Indices: 492201--492267 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
492191 AGAAAATTGA
*
492201 TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
492249 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
492268 AATATTTATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:498735 original size:23 final size:23
Alignment explanation
Indices: 498708--498759 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
498698 CCAAACAATT
498708 ATATGCAATATTCGCTTCAGGGA
1 ATATGCAATATTCGCTTCAGGGA
*
498731 ATATGCCATATTCGCTTCAGGGA
1 ATATGCAATATTCGCTTCAGGGA
498754 ATATGC
1 ATATGC
498760 TAAAATCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (23 bp):
ATATGCAATATTCGCTTCAGGGA
Found at i:509961 original size:1 final size:1
Alignment explanation
Indices: 509955--509988 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
509945 CCCAACTCTC
509955 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
509989 GTCAATTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:510100 original size:168 final size:168
Alignment explanation
Indices: 509822--510142 Score: 633
Period size: 168 Copynumber: 1.9 Consensus size: 168
509812 CTTCGGAGGC
509822 TCAATTGGTTTGTTGCGAACCTGCAATTATAAATAATACAATACTGGAGTCAATCCTCACGGAAA
1 TCAATTGGTTTGTTGCGAACCTGCAATTATAAATAATACAATACTGGAGTCAATCCTCACGGAAA
509887 CCCTCTACCTAAACGGAGTGCGAAAAAGAAACCAGAATTAACATATTTAATTCCAATACCCAACT
66 CCCTCTACCTAAACGGAGTGCGAAAAAGAAACCAGAATTAACATATTTAATTCCAATACCCAACT
*
509952 CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
131 CCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
509990 TCAATTGGTTTGTTGCGAACCTGCAATTATAAATAATACAATACTGGAGTCAATCCTCACGGAAA
1 TCAATTGGTTTGTTGCGAACCTGCAATTATAAATAATACAATACTGGAGTCAATCCTCACGGAAA
510055 CCCTCTACCTAAACGGAGTGCGAAAAAGAAACCAGAATTAACATATTTAATTCCAATACCCAACT
66 CCCTCTACCTAAACGGAGTGCGAAAAAGAAACCAGAATTAACATATTTAATTCCAATACCCAACT
510120 CCCAAAAAAAAAAAAAAAAAAAA
131 CCCAAAAAAAAAAAAAAAAAAAA
510143 CAAGAAGATA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 152 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.21
Consensus pattern (168 bp):
TCAATTGGTTTGTTGCGAACCTGCAATTATAAATAATACAATACTGGAGTCAATCCTCACGGAAA
CCCTCTACCTAAACGGAGTGCGAAAAAGAAACCAGAATTAACATATTTAATTCCAATACCCAACT
CCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
Found at i:518666 original size:87 final size:88
Alignment explanation
Indices: 518519--518691 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 88
518509 ATATATTTTT
518519 ACGATAGTAAAAATATAATTTCATCGTTTTAAATTTTTATTATCTAAATCTTTATAAATTTTAAA
1 ACGATAGTAAAAATATAATTTCATCGTTTTAAATTTTTATTATCTAAATCTTTATAAATTTTAAA
518584 GAATTAAATAAAAAATTTATTTA
66 GAATTAAATAAAAAATTTATTTA
518607 ACGATAGT-AAAATATAATTTCATCGTTTTAAATTTTTATTATCTAAATCTTTATAAATTTTAAA
1 ACGATAGTAAAAATATAATTTCATCGTTTTAAATTTTTATTATCTAAATCTTTATAAATTTTAAA
518671 GAATTAAATAAAAAATTTATT
66 GAATTAAATAAAAAATTTATT
518692 ATTTTTAGGG
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 77 0.91
88 8 0.09
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (88 bp):
ACGATAGTAAAAATATAATTTCATCGTTTTAAATTTTTATTATCTAAATCTTTATAAATTTTAAA
GAATTAAATAAAAAATTTATTTA
Found at i:521321 original size:17 final size:17
Alignment explanation
Indices: 521299--521334 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
521289 TAAAAACACT
521299 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
521316 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
521333 AA
1 AA
521335 TTTGACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAATCCAAC
Found at i:522343 original size:72 final size:73
Alignment explanation
Indices: 522225--522369 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 73
522215 GTGTTACAAG
522225 TCAACATATAATTTCGTGTTTAAAAATATTATATAATATTTATACATATCATATAAAATGAAATA
1 TCAACATATAATTTCGTGTTTAAAAATATTATATAATATTTATACATATCATATAAAATGAAATA
522290 AATACATT
66 AATACATT
522298 TCAACATAT-ATTTCGTGTTTAAAAATATTATATAATATTTATACATATCATATAAAATGAAATA
1 TCAACATATAATTTCGTGTTTAAAAATATTATATAATATTTATACATATCATATAAAATGAAATA
522362 AATACATT
66 AATACATT
522370 CTTTTCTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 63 0.88
73 9 0.12
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (73 bp):
TCAACATATAATTTCGTGTTTAAAAATATTATATAATATTTATACATATCATATAAAATGAAATA
AATACATT
Found at i:523903 original size:3 final size:3
Alignment explanation
Indices: 523895--523922 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
523885 TAGATTCATG
523895 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
523923 TTTTTTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:526454 original size:19 final size:19
Alignment explanation
Indices: 526408--526455 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
526398 GTATATATTT
526408 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
526426 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
526445 TAAATTTTATT
1 TAAATTTTATT
526456 CATATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:526504 original size:42 final size:42
Alignment explanation
Indices: 526458--526547 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
526448 ATTTTATTCA
* *
526458 TATTTTATT-TTATCTTTTAGTAGTTTATTAGAATAAGGGAAT
1 TATTTT-TTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
* *
526500 TATTTTTTCTTATGTTTTAGTAGTTGATTAGAATAAATGAAT
1 TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
526542 TATTTT
1 TATTTT
526548 CCCAATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (42 bp):
TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
Found at i:531138 original size:19 final size:19
Alignment explanation
Indices: 531092--531139 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
531082 AGGGAGGGTT
531092 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
531110 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
531129 TAAGTTTTATT
1 TAAATTTTATT
531140 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:535673 original size:9 final size:9
Alignment explanation
Indices: 535659--535695 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
535649 TATAGTTTGA
535659 TATTCGAAT
1 TATTCGAAT
535668 TATTCGAAT
1 TATTCGAAT
*
535677 TATTCGAGT
1 TATTCGAAT
535686 TATTCGAAT
1 TATTCGAAT
535695 T
1 T
535696 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:535767 original size:9 final size:9
Alignment explanation
Indices: 535750--535780 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
535740 TCGAGTTGAT
535750 TCGAATAAC
1 TCGAATAAC
*
535759 TCGATTAAC
1 TCGAATAAC
535768 TCGAATAAC
1 TCGAATAAC
535777 TCGA
1 TCGA
535781 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:536220 original size:29 final size:29
Alignment explanation
Indices: 536171--536227 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
536161 CAATGGTACC
* *
536171 TTTGAACCAATAACTCAGATATCACTTGG
1 TTTGAACCAACAACTCAGATACCACTTGG
* *
536200 TTTGAACCAACAGCTCGGATACCACTTG
1 TTTGAACCAACAACTCAGATACCACTTG
536228 TCATGGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (29 bp):
TTTGAACCAACAACTCAGATACCACTTGG
Found at i:542524 original size:48 final size:48
Alignment explanation
Indices: 542431--542927 Score: 338
Period size: 48 Copynumber: 10.4 Consensus size: 48
542421 AATTGGAGCA
* * * **
542431 CCAATAGGTGCACCACCCCCCAGTGCATCAGCTGCAGTACCAGGCACT-
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCA-TG
* * * **
542479 CCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
** * ** * * * * * * **
542527 CCGGTAGGAGCAGCACCTCCTGGGGAAGCAGTTGCAAAACAAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * ***
542575 CCAATAGGAGCGCCATCT-CCAGGTGCAACAGCTGCAACATTGGGCATG
1 CCAATAGGAGCACCACCTCCCA-GTGCACCAGCTGCAACACCAGGCATG
* **
542623 CCAATAGGAGCACCACCT-CCTG-GCACAGCAGCTGCAACACCAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCAC--CAGCTGCAACACCAGGCATG
* ** *
542671 CCAGTAGGAGCACCACCTCCC-GACACACCAACTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAG-TGCACCAGCTGCAACACCAGGCATG
* ** **
542719 GCAATAGGAGCACCACCTCCTGGCACACCAGCTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * *** * * *
542767 GCAATAGGCGCACCATCTCTTGGTACATCAGCTGGAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * * *
542815 CCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCTGACATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * * * **
542863 CCAATTGGAGCAACTCCTCCCAGTGCAGCAGCTGCAGCACCAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* *
542911 CCTATAGAAGCACCACC
1 CCAATAGGAGCACCACC
542928 ACCTGGCACT
Statistics
Matches: 354, Mismatches: 87, Indels: 16
0.77 0.19 0.04
Matches are distributed among these distances:
46 3 0.01
47 2 0.01
48 343 0.97
49 3 0.01
50 3 0.01
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.12
Consensus pattern (48 bp):
CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
Found at i:542640 original size:96 final size:96
Alignment explanation
Indices: 542459--542936 Score: 395
Period size: 96 Copynumber: 5.0 Consensus size: 96
542449 CCCAGTGCAT
** * * * * *
542459 CAGCTGCAGTACCAGGCACTCCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
** ** * *
542524 ACACCGGTAGGAGCAGCACCTCCTGGGGA-AG
66 ATGCCAATAGGAGCACCACCTCCT-GGCACAG
* * * * * * ***
542555 CAGTTGCAAAACAAGGCACACCAATAGGAGCGCCATCTCCAGGTGCAACAGCTGCAACATTGGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
542620 ATGCCAATAGGAGCACCACCTCCTGGCACAG
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
* * * ** *
542651 CAGCTGCAACACCAGGCACACCAGTAGGAGCACCACCTCCCGACACACCAACTGCAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
* *
542716 ATGGCAATAGGAGCACCACCTCCTGGCACAC
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
*** * ** * *
542747 CAGCTGCAACACCAGGCATGGCAATAGGCGCACCATCTCTTGGTACATCAGCTGGAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
** * *
542812 ATGCCAATAGGAGCACCACCTCCCAGTACAT
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
* * * ** * * * * *
542843 CAGTTGCAACACCTGACATGCCAATTGGAGCAAC-TCCTCCCA-GTGCAGCAGCTGCAGCACCAG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCAT-CT-CCAGGTACACCAGCTGCAACACCAG
** * * *
542906 GCACACCTATAGAAGCACCACCACCTGGCAC
64 GCATGCCAATAGGAGCACCACCTCCTGGCAC
542937 TCAAGCTGAA
Statistics
Matches: 305, Mismatches: 74, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
95 4 0.01
96 300 0.98
97 1 0.00
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.12
Consensus pattern (96 bp):
CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
ATGCCAATAGGAGCACCACCTCCTGGCACAG
Found at i:543169 original size:48 final size:48
Alignment explanation
Indices: 543092--543246 Score: 157
Period size: 48 Copynumber: 3.2 Consensus size: 48
543082 ATGACAACAA
* * *
543092 GAGCACCAACTCCTGATGCACCAGATGCAACACCTGGCAAGCCAATAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
* * * * *
543140 AAGCACCACCTCCTGGTGCACCAGCTGCAAGACCAGGTACGCCAATAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
** * * * * * * *
543188 GTTCACCATCTCTTGCTGCGCCAGCTGCAACAACAGGCATGCCAGTAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
543236 GAGCACCACCT
1 GAGCACCACCT
543247 ACCAGTGCAC
Statistics
Matches: 84, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 84 1.00
ACGTcount: A:0.28, C:0.35, G:0.22, T:0.15
Consensus pattern (48 bp):
GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
Found at i:543395 original size:33 final size:33
Alignment explanation
Indices: 543326--543396 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
543316 CAAGGCTCAC
* **
543326 CAATAGGAGCACCAGCAGCAACACCAGGAATGT
1 CAATAGGAGCACCAGCAGCAACACCAAGAACAT
* * *
543359 CAATTGGAGCACCAGCTGCAACACCAAGCACAT
1 CAATAGGAGCACCAGCAGCAACACCAAGAACAT
543392 CAATA
1 CAATA
543397 AGAACGCCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (33 bp):
CAATAGGAGCACCAGCAGCAACACCAAGAACAT
Found at i:543444 original size:48 final size:48
Alignment explanation
Indices: 543367--543603 Score: 136
Period size: 48 Copynumber: 4.9 Consensus size: 48
543357 GTCAATTGGA
* * *
543367 GCACCAGCTGCAACACCAAGCACATCAATAAGAACGCCACCTCCTGGT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* * * * ***
543415 GCACCGGCCGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAAT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* * * * ** *
543463 GCACCAGCTGCAACA-CTAGGAAAGCCAATTGGAGCACCACCTCCTGGT
1 GCACCAGCCGCAACACCAAGCACA-CCAATAAGAACACCACCTCCTGGT
* * * * * * * * * *
543511 GCACCTGCTGTAGCATCAGGGACACCAATAGGATCACCACCTCATGGT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* ** * * * *
543559 GCACAAGATGCAACACCACA-CACATCTATAGGAGCACCACCTCCT
1 GCACCAGCCGCAACACCA-AGCACACCAATAAGAACACCACCTCCT
543604 CTTGCACCCG
Statistics
Matches: 145, Mismatches: 41, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
47 4 0.03
48 136 0.94
49 5 0.03
ACGTcount: A:0.31, C:0.37, G:0.19, T:0.13
Consensus pattern (48 bp):
GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
Found at i:557621 original size:28 final size:28
Alignment explanation
Indices: 557590--557691 Score: 89
Period size: 28 Copynumber: 3.7 Consensus size: 28
557580 AAGTCATTTT
* * * *
557590 GCAGTTCGCCACTTCGTGGTGTCATCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* *
557618 GCAGCTCTCCACTTCGCAGAGACATCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* * *
557646 GTAGTTCTCCACTT-GTGGAGACAGCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* * *
557673 GCACTTCACTACTTCGCGG
1 GCAGTTCTCCACTTCGCGG
557692 TGTCAACTCG
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
27 20 0.35
28 37 0.65
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (28 bp):
GCAGTTCTCCACTTCGCGGAGACATCTC
Found at i:557872 original size:5 final size:5
Alignment explanation
Indices: 557862--557902 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
557852 TTACTCATTT
557862 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
557903 GTTTTAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:560362 original size:72 final size:72
Alignment explanation
Indices: 560272--560492 Score: 408
Period size: 72 Copynumber: 3.1 Consensus size: 72
560262 ACTTGATCAC
560272 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACGAAGGTTCACAAGATCAAAAATGGAATACG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACGAAGGTTCACAAGATCAAAAATGGAATACG
560337 GTATGGG
66 GTATGGG
560344 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACGAAGGTTCACAAGATCAAAAATGGAATACG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACGAAGGTTCACAAGATCAAAAATGGAATACG
560409 GTATGGG
66 GTATGGG
*
560416 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCA-GTAAGGTTCACAAGATAAAAAATGGAATAC
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACG-AAGGTTCACAAGATCAAAAATGGAATAC
*
560480 GGTATTGG
65 GGTATGGG
560488 ACCAC
1 ACCAC
560493 CAATGTCATT
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
71 1 0.01
72 145 0.99
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACGAAGGTTCACAAGATCAAAAATGGAATACG
GTATGGG
Found at i:562722 original size:54 final size:54
Alignment explanation
Indices: 562636--562740 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
562626 TCTCAGTTTA
* *
562636 CAAATTAATAAAATCTCAATTATATCACATAAAAGTCTATCCCATTTTATACGG
1 CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATACGG
* * * *
562690 CAAATTAATAAAATCTTAGTTGTACCATATAAAAGTCTATCCCACTTTATA
1 CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATA
562741 TATGAATCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (54 bp):
CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATACGG
Found at i:574643 original size:21 final size:20
Alignment explanation
Indices: 574612--574653 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
574602 ACTTTAGTTA
574612 AAAATAATTTAT-CATATTTT
1 AAAATAATTTATACAT-TTTT
574632 AAAATAATTTTATACATTTTT
1 AAAATAA-TTTATACATTTTT
574653 A
1 A
574654 TTTATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 10 0.50
22 3 0.15
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTTATACATTTTT
Found at i:574650 original size:20 final size:20
Alignment explanation
Indices: 574612--574651 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
574602 ACTTTAGTTA
*
574612 AAAATAATTTATCATATTTT
1 AAAATAATTTATCACATTTT
574632 AAAATAATTTTAT-ACATTTT
1 AAAATAA-TTTATCACATTTT
574652 TATTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTTATCACATTTT
Found at i:577500 original size:3 final size:3
Alignment explanation
Indices: 577492--577538 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
577482 ATTTTATTGT
577492 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
577539 TTGATTTCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:578821 original size:145 final size:145
Alignment explanation
Indices: 578569--578840 Score: 485
Period size: 145 Copynumber: 1.9 Consensus size: 145
578559 TGTCAAAAAT
578569 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
1 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
*
578634 CTTTATTGAGGTGTGATCGGCTCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
66 CTTTATTGAGGTGTGATCGGCCCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
578699 GAAGTTGTCGAAACC
131 GAAGTTGTCGAAACC
578714 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCA-CGATC
1 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
* *
578778 CTTTATTGAGGTGTGATCGGCCCACCTTAAAAAAAA-TATTCTGGTCTACGAAATTTGAGAAAA
66 CTTTATTGAGGTGTGATCGGCCCA-C-AAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAA
578841 TGAGTTCGGG
Statistics
Matches: 122, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
144 28 0.23
145 86 0.70
146 8 0.07
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (145 bp):
ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
CTTTATTGAGGTGTGATCGGCCCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
GAAGTTGTCGAAACC
Found at i:579683 original size:19 final size:18
Alignment explanation
Indices: 579646--579690 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
579636 ATAAAACATG
579646 AAAATATAAATATTATAA
1 AAAATATAAATATTATAA
* *
579664 AAAATATGAATGTATATAA
1 AAAATATAAATAT-TATAA
*
579683 AATATATA
1 AAAATATA
579691 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATATAAATATTATAA
Found at i:579722 original size:30 final size:30
Alignment explanation
Indices: 579649--579724 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
579639 AAACATGAAA
*
579649 ATAT-AAATAT-TATAAAAAATATGAATGT
1 ATATAAAATATATATAAAAAATATAAATGT
579677 ATATAAAATATATATAAAAAATA-AAATGAT
1 ATATAAAATATATATAAAAAATATAAATG-T
*
579707 ATGATAATAAAATATATA
1 AT-ATAA-AATATATATA
579725 CGTACTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 4 0.10
29 10 0.24
30 14 0.34
31 4 0.10
32 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
ATATAAAATATATATAAAAAATATAAATGT
Found at i:579820 original size:14 final size:15
Alignment explanation
Indices: 579803--579836 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
579793 ATTTACGTGC
579803 AATAATAATTATA-T
1 AATAATAATTATACT
579817 AATAATAATTATACT
1 AATAATAATTATACT
579832 AATAA
1 AATAA
579837 ACAATATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATTATACT
Found at i:581385 original size:106 final size:106
Alignment explanation
Indices: 581215--581412 Score: 290
Period size: 106 Copynumber: 1.9 Consensus size: 106
581205 ATTTTCGGGA
* * * * **
581215 ATTCGAGACTTCGTGCCCTAACTTACGGGGCATGTTTTTCTTCACAATTAACTTGAAATACGAAG
1 ATTCGAGACTTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAAG
581280 ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
66 ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
* *
581321 ATTCGAGACATT-GTACCCTAACTTACGAGACATGATTTTCTTCCCTATTAACTCAAAATACGAA
1 ATTCGAGAC-TTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAA
* *
581385 GATATTTTTCATAAAATTTGATTTAATT
65 GACATTCTTCATAAAATTTGATTTAATT
581413 AGCGATATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 79 0.98
107 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (106 bp):
ATTCGAGACTTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAAG
ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
Found at i:584894 original size:21 final size:22
Alignment explanation
Indices: 584872--584911 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
584862 AATTTTATTA
584872 AAATA-ATTTAT-CATATTTTT
1 AAATACATTTATGCATATTTTT
*
584892 AAATACTTTTATGCATATTT
1 AAATACATTTATGCATATTT
584912 ATTTATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (22 bp):
AAATACATTTATGCATATTTTT
Found at i:590177 original size:72 final size:72
Alignment explanation
Indices: 590058--590198 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 72
590048 TTGATCACAC
* * ** * **
590058 CACTCAAGTTGTTTGATGACAAATCAAGATAACTAATGTTCGTAAGATCAAAAAGGGAATCGGGT
1 CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATAAGGT
590123 ATTGGAT
66 ATTGGAT
* * *
590130 CACTCAAGTTGTTTGAAGACAAGTCAAG-TAAAGTAAGGTTCACAAGATAAAAAATGGAATAAGG
1 CACTCAAGTTGTTTGAAGACAAATCAAGAT-AACTAAGGTTCACAAGATAAAAAAGGGAATAAGG
590194 TATTG
65 TATTG
590199 AACCACCGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 57 0.98
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.26
Consensus pattern (72 bp):
CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATAAGGT
ATTGGAT
Found at i:596413 original size:44 final size:42
Alignment explanation
Indices: 596341--596438 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 42
596331 ATATAAGTTA
* ** *
596341 TCGTGTAAGACCATGTATGGGACGTCGGCATC-AATTTGAGATT
1 TCGTGTAAGACCATATATGAAACATCGGCATCGAATTT--GATT
* *
596384 TACGTGTAAGACCATATCTGAAACATCGGCATCGTATTTGATT
1 T-CGTGTAAGACCATATATGAAACATCGGCATCGAATTTGATT
596427 TCGTGTAAGACC
1 TCGTGTAAGACC
596439 CTATTTGGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
42 11 0.23
43 6 0.13
44 26 0.55
45 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCATATATGAAACATCGGCATCGAATTTGATT
Found at i:610720 original size:72 final size:72
Alignment explanation
Indices: 610580--610738 Score: 214
Period size: 72 Copynumber: 2.2 Consensus size: 72
610570 ACTTGATCAC
* *
610580 ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAATATG
1 ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAACACG
610645 GTATTGG
66 GTATTGG
* * * *
610652 ACCACTCAAGTTGTTTGATGACAAATCAAG-TGAAGTAAGGTTCACAAGATCAAAAATGGAACAC
1 ACCACTCAAGTTATTTGATGACAAATCAAGAT-AACTAAGGTACACAAGATCAAAAATGAAACAC
* *
610716 GGTATCGA
65 GGTATTGG
610724 ACCAC-CAATGTTATT
1 ACCACTCAA-GTTATT
610739 ATAACTCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
71 4 0.05
72 72 0.95
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAACACG
GTATTGG
Found at i:612116 original size:12 final size:13
Alignment explanation
Indices: 612089--612118 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
612079 AGCAAATCAG
612089 CAACTTCATGCTC
1 CAACTTCATGCTC
612102 CAACTTCAT-CTC
1 CAACTTCATGCTC
612114 CAACT
1 CAACT
612119 GCTGCATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.27, C:0.40, G:0.03, T:0.30
Consensus pattern (13 bp):
CAACTTCATGCTC
Found at i:613101 original size:28 final size:29
Alignment explanation
Indices: 613061--613115 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
613051 ATAATTTTAA
613061 AAAATAAAGATAAAAAATTC-TAAATTCT
1 AAAATAAAGATAAAAAATTCATAAATTCT
** *
613089 AAAATAATTATAAAAAGTTCATAAATT
1 AAAATAAAGATAAAAAATTCATAAATT
613116 TTCAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAATAAAGATAAAAAATTCATAAATTCT
Found at i:613298 original size:43 final size:43
Alignment explanation
Indices: 613237--613409 Score: 346
Period size: 43 Copynumber: 4.0 Consensus size: 43
613227 CAAAAGATTG
613237 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
613280 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
613323 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
613366 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
613409 A
1 A
613410 CTCAAAAAAT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 130 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (43 bp):
AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
Found at i:613441 original size:86 final size:84
Alignment explanation
Indices: 613258--613441 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 84
613248 AACTCCTATT
*
613258 AAAATGCCAAAAGATAAATTTAAGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AAAATGACAAAAGATAAATTTAAGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
* * * ** *
613323 AGGTTCAATTTAACTCCTATT
66 A-GCTCAA-TAAAATAATATA
*
613344 AAAATGCCAAAAGATAAATTTAAGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AAAATGACAAAAGATAAATTTAAGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
613409 A-CTCAA-AAAATAATAATA
66 AGCTCAATAAAATAAT-ATA
613427 ACCAAATTGACAAAA
1 A--AAA-TGACAAAA
613442 AATATGAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
82 4 0.05
83 3 0.03
84 4 0.05
85 3 0.03
86 73 0.84
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (84 bp):
AAAATGACAAAAGATAAATTTAAGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
AGCTCAATAAAATAATATA
Found at i:620709 original size:42 final size:42
Alignment explanation
Indices: 620645--620739 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
620635 TAGTTGGATT
* * *
620645 TTAATCATGGATTATGAGTGTTAAATAAAATTTGATGGTATC
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
620687 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATT
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
620729 TTAATAATGAA
1 TTAATCATGAA
620740 AATACTGATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (42 bp):
TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
Found at i:624564 original size:21 final size:21
Alignment explanation
Indices: 624540--624592 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
624530 CATTGTTTCT
**
624540 AATCTCACCGCTACAGTGTCC
1 AATCTCACCGCTACAGTAACC
*
624561 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
624582 AATCTCACCGC
1 AATCTCACCGC
624593 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.38, G:0.11, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:626378 original size:12 final size:12
Alignment explanation
Indices: 626363--626388 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
626353 TTTTGTTTCG
626363 TTTTTTATTTAT
1 TTTTTTATTTAT
626375 TTTTTTATTTAT
1 TTTTTTATTTAT
626387 TT
1 TT
626389 CGAAATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:627203 original size:22 final size:23
Alignment explanation
Indices: 627120--627203 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
627110 TAATTGCTCT
* *
627120 TATATATATGTATATTTTTTGTA
1 TATATATATATATACTTTTTGTA
* *
627143 TATATATACATATA-TTTTTTTA
1 TATATATATATATACTTTTTGTA
* *
627165 TATACTTACATACATACTTTTTGTA
1 TATA--TATATATATACTTTTTGTA
*
627190 -ATATATATGTATAC
1 TATATATATATATAC
627204 ATATACACTT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 19 0.40
23 12 0.25
24 10 0.21
25 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (23 bp):
TATATATATATATACTTTTTGTA
Found at i:629188 original size:25 final size:25
Alignment explanation
Indices: 629121--629188 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
629111 TAGGACATGA
* *
629121 TATGATAT-AATAAGATATGCTATGC
1 TATGAT-TCAATATGATATGATATGC
* * *
629146 TATGATTGAATGTAATATGATATGC
1 TATGATTCAATATGATATGATATGC
*
629171 TATGATTCAGTATGATAT
1 TATGATTCAATATGATAT
629189 TGTACGTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.40
Consensus pattern (25 bp):
TATGATTCAATATGATATGATATGC
Found at i:632893 original size:72 final size:71
Alignment explanation
Indices: 632760--632896 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
632750 AAAGTGAACA
* * *
632760 AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTGTTTGATGACAAATCAA
1 AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAAT-ACAAATCAA
632825 GCCTAGT
65 GCCTAGT
* **
632832 AAGGTTCAAAAGATTAAAAATGGAATTTGGTATTGGACCAC-CAATGTTATTATAACT-CAAATC
1 AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAA-GTTATT-TAA-TACAAATC
632895 AA
63 AA
632897 CCTCTTGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
71 3 0.05
72 50 0.89
73 2 0.04
74 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (71 bp):
AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAATACAAATCAAG
CCTAGT
Found at i:643739 original size:39 final size:39
Alignment explanation
Indices: 643690--643769 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
643680 AGCACCGGCA
* *
643690 GTCATTGAATTTATACCAAAGGCCTATCCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
* *
643729 GTCATAGAATTTATACCATAGGCCCATGCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
643768 GT
1 GT
643770 TTGCATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (39 bp):
GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
Found at i:647805 original size:54 final size:54
Alignment explanation
Indices: 647723--647830 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
647713 AAAACAACAA
647723 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
647777 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
647831 TTACAGTCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (54 bp):
ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
Found at i:650354 original size:14 final size:14
Alignment explanation
Indices: 650316--650354 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
650306 AAGGTTCGAG
* *
650316 GTTTATGATTCGAA
1 GTTTAGGATTTGAA
*
650330 GTTTAGGATTTGAT
1 GTTTAGGATTTGAA
650344 GTTTAGGATTT
1 GTTTAGGATTT
650355 AAGGTTCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTTAGGATTTGAA
Found at i:650367 original size:14 final size:14
Alignment explanation
Indices: 650350--650394 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
650340 TGATGTTTAG
*
650350 GATTTAAGGTTCAT
1 GATTTAAGGTTCAA
*
650364 GATTTGA-GTTCAA
1 GATTTAAGGTTCAA
*
650377 GATTTAAGGTTCGA
1 GATTTAAGGTTCAA
650391 GATT
1 GATT
650395 CAAGATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (14 bp):
GATTTAAGGTTCAA
Found at i:650394 original size:27 final size:28
Alignment explanation
Indices: 650336--650388 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
650326 CGAAGTTTAG
* *
650336 GATTTGATGTTTAGGATTTAAGGTTCAT
1 GATTTGATGTTCAAGATTTAAGGTTCAT
650364 GATTTGA-GTTCAAGATTTAAGGTTC
1 GATTTGATGTTCAAGATTTAAGGTTC
650389 GAGATTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (28 bp):
GATTTGATGTTCAAGATTTAAGGTTCAT
Found at i:651018 original size:2 final size:2
Alignment explanation
Indices: 651011--651039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
651001 ATAACATAGA
651011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
651040 AATTGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:662830 original size:1 final size:1
Alignment explanation
Indices: 662795--662823 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
662785 TCTGATTTCG
662795 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
662824 CCTTTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:672129 original size:105 final size:105
Alignment explanation
Indices: 672015--672225 Score: 413
Period size: 105 Copynumber: 2.0 Consensus size: 105
672005 GTGAAAATAT
672015 AAAAAAGAAAGAAAAATTCCCTAGAAACTTAACAGGTTCAATTCCAATATTACCAGATGCTCTTA
1 AAAAAAGAAAGAAAAATTCCCTAGAAACTTAACAGGTTCAATTCCAATATTACCAGATGCTCTTA
672080 AATATAAAAAAAAAAAAAAAAAATAACCTCCATCTGGCTC
66 AATATAAAAAAAAAAAAAAAAAATAACCTCCATCTGGCTC
672120 AAAAAAGAAAGAAAAATTCCCTAGAAACTTAACAGGTTCAATTCCAATATTACCAGATGCTCTTA
1 AAAAAAGAAAGAAAAATTCCCTAGAAACTTAACAGGTTCAATTCCAATATTACCAGATGCTCTTA
*
672185 AATATAAAAAAAAAAAAAAAAAATCACCTCCATCTGGCTC
66 AATATAAAAAAAAAAAAAAAAAATAACCTCCATCTGGCTC
672225 A
1 A
672226 CCAGCTACCT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (105 bp):
AAAAAAGAAAGAAAAATTCCCTAGAAACTTAACAGGTTCAATTCCAATATTACCAGATGCTCTTA
AATATAAAAAAAAAAAAAAAAAATAACCTCCATCTGGCTC
Found at i:673216 original size:13 final size:13
Alignment explanation
Indices: 673198--673225 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
673188 AGAGAGAGAA
673198 GAGGAGGGGAGGG
1 GAGGAGGGGAGGG
673211 GAGGAGGGGAGGG
1 GAGGAGGGGAGGG
673224 GA
1 GA
673226 AGGGAAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (13 bp):
GAGGAGGGGAGGG
Found at i:686121 original size:36 final size:37
Alignment explanation
Indices: 686055--686134 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
686045 TCTCCACCTT
*
686055 CCCCT-CCCACAACCCAATCCTCCGCCCCTTCACCC-G
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTC-CCCTG
** *
686091 -CCCTCCCCACAACCCCTTCCCCCGCTCCTTCCCCTG
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
686127 CCCCTCCC
1 CCCCTCCC
686135 AAAACACCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 7 0.19
36 23 0.62
37 7 0.19
ACGTcount: A:0.11, C:0.68, G:0.05, T:0.16
Consensus pattern (37 bp):
CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
Found at i:688603 original size:24 final size:22
Alignment explanation
Indices: 688576--688621 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
688566 ATCAAATACA
*
688576 CTAAAAATATTGAAAGAAATGTTT
1 CTAAAAACATT-AAA-AAATGTTT
*
688600 CTAAATACATTAAAAAATGTTT
1 CTAAAAACATTAAAAAATGTTT
688622 AATACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (22 bp):
CTAAAAACATTAAAAAATGTTT
Found at i:690006 original size:36 final size:36
Alignment explanation
Indices: 689959--690031 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
689949 ATACTCCCTT
*
689959 CCTAGCATTGATACCAATATTTACACAGTCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
* *
689995 CCTAGCATTGATACCAATGTTTACATAATCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
690031 C
1 C
690032 TTGGCGGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (36 bp):
CCTAGCATTGATACCAATATTTACACAATCACACAG
Found at i:691804 original size:3 final size:3
Alignment explanation
Indices: 691796--691823 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
691786 AGTAAAATCT
691796 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
691824 AAGATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:701193 original size:19 final size:21
Alignment explanation
Indices: 701169--701217 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
701159 AAAAAACTAC
*
701169 AAATTATAAG-ATT-TTTTTG
1 AAATTATAAGAATTAATTTTG
*
701188 AAATTACAAGAATTAATTTTG
1 AAATTATAAGAATTAATTTTG
*
701209 AAATCATAA
1 AAATTATAA
701218 TTTGTGAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (21 bp):
AAATTATAAGAATTAATTTTG
Found at i:715112 original size:10 final size:11
Alignment explanation
Indices: 715086--715111 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
715076 TTAAAAATAA
715086 AAAAATATTTT
1 AAAAATATTTT
715097 AAAAATATTTT
1 AAAAATATTTT
715108 AAAA
1 AAAA
715112 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:727315 original size:105 final size:105
Alignment explanation
Indices: 727133--727384 Score: 504
Period size: 105 Copynumber: 2.4 Consensus size: 105
727123 CCGTACAGAT
727133 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATTTTTTACTTTCTAGTTGACCGTAC
1 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATTTTTTACTTTCTAGTTGACCGTAC
727198 ATATATTTAAAAAAAACACAGATTTTATTAATAAGTTGAA
66 ATATATTTAAAAAAAACACAGATTTTATTAATAAGTTGAA
727238 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATTTTTTACTTTCTAGTTGACCGTAC
1 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATTTTTTACTTTCTAGTTGACCGTAC
727303 ATATATTTAAAAAAAACACAGATTTTATTAATAAGTTGAA
66 ATATATTTAAAAAAAACACAGATTTTATTAATAAGTTGAA
727343 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATT
1 ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATT
727385 AAAATACAGA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 147 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (105 bp):
ATGTAACCATAGAGAAATTAAAACCCAAAGTTTTGTCAAATTTTTTACTTTCTAGTTGACCGTAC
ATATATTTAAAAAAAACACAGATTTTATTAATAAGTTGAA
Found at i:733612 original size:16 final size:15
Alignment explanation
Indices: 733586--733617 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
733576 CGTGCGTTTA
733586 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
733601 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
733617 C
1 C
733618 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:733862 original size:16 final size:15
Alignment explanation
Indices: 733836--733867 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
733826 CGTGCGTTTA
733836 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
733851 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
733867 C
1 C
733868 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:733949 original size:250 final size:250
Alignment explanation
Indices: 733508--734236 Score: 1293
Period size: 250 Copynumber: 3.0 Consensus size: 250
733498 AAAAGGGGGA
733508 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
1 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
733573 AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
66 AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
733638 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
131 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
733703 GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
196 GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
733758 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
1 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
733823 AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
66 AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
733888 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
131 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
733953 GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
196 GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
734008 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
1 ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
734073 AAGCGTGCGTTTACTGAAAAGAACAATGC----------C---G-AA-GAAGACAACTGTGGTTA
66 AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
734123 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCC------ATTTGGATTTGGTTAAGG
131 ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
* *
734182 GAGGTTGCATCGGATCTTTTTGTTTCCTTTACTATTGGAAAAAACACATCTCCAG
196 GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
734237 TCCCTCTTAA
Statistics
Matches: 477, Mismatches: 2, Indels: 21
0.95 0.00 0.04
Matches are distributed among these distances:
229 71 0.15
235 58 0.12
236 2 0.00
237 1 0.00
240 1 0.00
250 344 0.72
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (250 bp):
ACTAAAGAGTGAATGTGAGATGTGGTGAGCGAAAAAGATTCCTGGTAAACGGAAATGGAGGGCTC
AAGCGTGCGTTTACTGAAAAGAACAATGCTGAAGAAGAACAATGCAATGAAGACAACTGTGGTTA
ATGCAAAACGGGTTTTTCGCGAAATGGAAGGAGAATCGTCCATTTGGATTTGGATTTGGTTAAGG
GAGATTGCATCGGATCTTTTTGTTTCCTTTACTATTGGCAAAAACACATCTCCAG
Found at i:737234 original size:11 final size:11
Alignment explanation
Indices: 737218--737246 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
737208 AAAAAACTTG
737218 TATATAAATTT
1 TATATAAATTT
737229 TATATAAATTT
1 TATATAAATTT
737240 TAT-TAAA
1 TATATAAA
737247 CATGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATAAATTT
Found at i:749198 original size:122 final size:123
Alignment explanation
Indices: 748980--749223 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 123
748970 GGCAAACTTG
748980 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
749045 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
66 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
*
749103 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAA-GGCAAAAGTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
*
749167 AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTG
66 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTG
749224 ATGTGGTTAA
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 75 0.63
123 44 0.37
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (123 bp):
AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
Done.