Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014963.1 Kokia drynarioides strain JFW-HI SEQ_130007, 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: 411358
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 371 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:304647 original size:20 final size:19
Alignment explanation
Indices: 304625--304706 Score: 69
Period size: 18 Copynumber: 4.3 Consensus size: 19
304615 ATATTAGATT
*
304625 TTTTTTATAATTTTTATAA
1 TTTTTTAAAATTTTTATAA
304644 -TTTTTAAAATTTTTATAAA
1 TTTTTTAAAATTTTTAT-AA
* * *
304663 TATTTTAAAA-TTTAAAAA
1 TTTTTTAAAATTTTTATAA
* *
304681 TTATTTTGAATTATTTTATAA
1 TT-TTTTAAAAT-TTTTATAA
304702 TTTTT
1 TTTTT
304707 GTTTATTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
18 18 0.37
19 12 0.24
20 11 0.22
21 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTTTTAAAATTTTTATAA
Found at i:304656 original size:29 final size:29
Alignment explanation
Indices: 304624--304706 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
304614 TATATTAGAT
304624 TTTTTTTATAAT-TTTTATAATTTTTAAAA
1 TTTTTTTA-AATATTTTATAATTTTTAAAA
* * *
304653 TTTTTATAAATATTTTA-AAATTTAAAAA
1 TTTTTTTAAATATTTTATAATTTTTAAAA
* *
304681 TTATTTTGAATTATTTTATAATTTTT
1 TT-TTTTTAAATATTTTATAATTTTT
304707 GTTTATTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 14 0.33
29 24 0.56
30 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTTTTTAAATATTTTATAATTTTTAAAA
Found at i:304850 original size:24 final size:24
Alignment explanation
Indices: 304813--304868 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
304803 TAATCGAGTT
* *
304813 ATTCGAATTAACTCGAATAATTTA
1 ATTCGATTTGACTCGAATAATTTA
*
304837 ATTTGATTTGACTCGAATAATTTA
1 ATTCGATTTGACTCGAATAATTTA
304861 ATTCGATT
1 ATTCGATT
304869 ATTTTCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (24 bp):
ATTCGATTTGACTCGAATAATTTA
Found at i:304885 original size:27 final size:26
Alignment explanation
Indices: 304855--304910 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
304845 TGACTCGAAT
304855 AATTTA-ATTCGATTATTTTCAAATTCA
1 AATTTATATTCGATT-TTTTCAAA-TCA
* *
304882 AATTTATTTTTGATTTTTTCAAATCA
1 AATTTATATTCGATTTTTTCAAATCA
304908 AAT
1 AAT
304911 CGAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 14 0.54
28 6 0.23
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.52
Consensus pattern (26 bp):
AATTTATATTCGATTTTTTCAAATCA
Found at i:304917 original size:27 final size:28
Alignment explanation
Indices: 304865--304919 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
304855 AATTTAATTC
**
304865 GATTATTTTCAAATTCAAATTTATTTTT
1 GATTATTTTCAAATTCAAATGAATTTTT
304893 GATT-TTTTCAAA-TCAAATCGAATTTTT
1 GATTATTTTCAAATTCAAAT-GAATTTTT
304920 ACTTAACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 14 0.58
28 4 0.17
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (28 bp):
GATTATTTTCAAATTCAAATGAATTTTT
Found at i:304918 original size:26 final size:28
Alignment explanation
Indices: 304865--304918 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
304855 AATTTAATTC
** *
304865 GATTATTTTCAAATTCAAATTTATTTTT
1 GATTATTTTCAAATTCAAATCGAATTTT
304893 GATT-TTTTCAAA-TCAAATCGAATTTT
1 GATTATTTTCAAATTCAAATCGAATTTT
304919 TACTTAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.48
27 8 0.35
28 4 0.17
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (28 bp):
GATTATTTTCAAATTCAAATCGAATTTT
Found at i:309225 original size:40 final size:40
Alignment explanation
Indices: 309167--309247 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
309157 ACTTATTAAT
* *
309167 TGAAGTTTTGTCATATTGTGAGACACTGAGACTATCATGA
1 TGAAGTTTTGTCAAATTGTGAGACACTCAGACTATCATGA
* * *
309207 TGAAGTTTTGTCAAATTGTGAGAGACTCTGACTATTATGA
1 TGAAGTTTTGTCAAATTGTGAGACACTCAGACTATCATGA
309247 T
1 T
309248 CCACGCATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (40 bp):
TGAAGTTTTGTCAAATTGTGAGACACTCAGACTATCATGA
Found at i:313274 original size:66 final size:68
Alignment explanation
Indices: 313168--313306 Score: 212
Period size: 66 Copynumber: 2.1 Consensus size: 68
313158 GGGAAAATAA
* *
313168 GGAGAGTGTTAGCTTTATGCTTCACTTTTGGCACATGTTCGACTCTATGAGTC-T-TTTGGTGTG
1 GGAGAGTGTTAGCTTTATGCTTCACTTATGGCACATGTTCGACTCTACGAGTCATATTTGGTGTG
313231 TTT
66 TTT
*
313234 GGAGAGTGTTAG-TTATATGCTTCACTTATGGGACATGTTCGACTCTACGAGTCATATTTGGTGT
1 GGAGAGTGTTAGCTT-TATGCTTCACTTATGGCACATGTTCGACTCTACGAGTCATATTTGGTGT
313298 GTTT
65 GTTT
*
313302 TGAGA
1 GGAGA
313307 TCCACGTATC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
65 2 0.03
66 47 0.71
67 1 0.02
68 16 0.24
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.41
Consensus pattern (68 bp):
GGAGAGTGTTAGCTTTATGCTTCACTTATGGCACATGTTCGACTCTACGAGTCATATTTGGTGTG
TTT
Found at i:313561 original size:23 final size:23
Alignment explanation
Indices: 313493--313567 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
313483 TGAAAGATAA
*
313493 TTAAATATTAATGTGATTTGTGA
1 TTAAATATTAATGTGATTTGTGT
313516 TTAAATATTAATGTGATTTGTGT
1 TTAAATATTAATGTGATTTGTGT
*
313539 TTAAAAATTAATGTGATTTGTGT
1 TTAAATATTAATGTGATTTGTGT
*
313562 GTAAAT
1 TTAAAT
313568 GAACCCATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTGTGT
Found at i:314691 original size:21 final size:21
Alignment explanation
Indices: 314667--314709 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
314657 ATTAAAAATG
* *
314667 ATAAAATTTTAATTAAGATTA
1 ATAAAATCTTAATAAAGATTA
**
314688 ATAATGTCTTAATAAAGATTA
1 ATAAAATCTTAATAAAGATTA
314709 A
1 A
314710 ATGAATTAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
ATAAAATCTTAATAAAGATTA
Found at i:316379 original size:17 final size:17
Alignment explanation
Indices: 316347--316457 Score: 91
Period size: 17 Copynumber: 6.5 Consensus size: 17
316337 GGATCAAACT
* * *
316347 TTTAAATTTATATTAAG
1 TTTAAATTGATTTTAAA
316364 TTTAAATTGATTTTAAA
1 TTTAAATTGATTTTAAA
** *
316381 TTTATTTCTGAATTTAAA
1 TTTAAAT-TGATTTTAAA
316399 TTTAAAATTG-TTTTAAA
1 TTT-AAATTGATTTTAAA
* *
316416 TTTAAATTTA-GTTAAA
1 TTTAAATTGATTTTAAA
* *
316432 TTTAAAAATGGTTTTAAA
1 TTT-AAATTGATTTTAAA
316450 TTTAAATT
1 TTTAAATT
316458 TAAAATTGAA
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
16 13 0.18
17 36 0.49
18 22 0.30
19 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTAAATTGATTTTAAA
Found at i:316446 original size:34 final size:33
Alignment explanation
Indices: 316394--316459 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
316384 ATTTCTGAAT
*
316394 TTAAATTTAAAATTGTTTTAAATTTAAATTTAG
1 TTAAATTTAAAATGGTTTTAAATTTAAATTTAG
316427 TTAAATTTAAAAATGGTTTTAAATTTAAATTTA
1 TTAAATTT-AAAATGGTTTTAAATTTAAATTTA
316460 AAATTGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 8 0.26
34 23 0.74
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (33 bp):
TTAAATTTAAAATGGTTTTAAATTTAAATTTAG
Found at i:317169 original size:3 final size:3
Alignment explanation
Indices: 317163--317223 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
317153 AACATTAATC
*
317163 TAA TAA TAA TAA TGA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
317209 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
317224 ATAAATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:318834 original size:59 final size:59
Alignment explanation
Indices: 318397--318861 Score: 434
Period size: 59 Copynumber: 7.9 Consensus size: 59
318387 CATAAATCTT
* * *
318397 ATTTTGACCCCTGAACTTT-TCCAAAATTCCATTTTTAACCTCGAA-CTTCACAAAAATCAC
1 ATTTTTACCCC-GAACTTTCT-CAAAATTCCATTTTTAACCTCGAATTTTC-CAAAAATTAC
* ** *
318457 A-TTTTATCCCCGAACTTTC-C-AAATTCCATTTTTAACCTCAAATTTTTTAAAAATTAT
1 ATTTTTA-CCCCGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTAC
* * * *
318514 ATTTTTACCCTCAAACTTTC-CAAAATTCCATTTTTGACCCCAAATTTTCCAAAAATTAC
1 ATTTTTACCC-CGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTAC
*** *
318573 ATTTTTACCTATAAACTTTCT-AAAATTCAATTTTTAACCTCGAATTTTCCAAAAATTAC
1 ATTTTTACC-CCGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTAC
** * * * *
318632 ATTTTTACTCTTGAATTTTC-CAAAATTCCATTTTTGACC-CTAAATTTTCCAAAAATTAT
1 ATTTTTAC-CCCGAACTTTCTCAAAATTCCATTTTTAACCTC-GAATTTTCCAAAAATTAC
* * * *
318691 ATTTTTACCCTTGAAATTTC-CAAAATTCCCA-TTTTGACCCCGAATTTTCCAAAAATTAC
1 ATTTTTACCC-CGAACTTTCTCAAAATT-CCATTTTTAACCTCGAATTTTCCAAAAATTAC
* * *
318750 ATTTTTTCCCTCGAACTTTC-CAAAATTCCATTTTTAACCTCGAAGTTTCCAAAAAATAC
1 ATTTTTACCC-CGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTAC
* * * **
318809 ATTTTTATCCCCGAA-TGTCTAAAAATTTCATTTTTAACCTCGAGGTTTCCAAA
1 ATTTTTA-CCCCGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAA
318862 GTTACCTTTT
Statistics
Matches: 346, Mismatches: 42, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
57 32 0.09
58 25 0.07
59 276 0.80
60 13 0.04
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (59 bp):
ATTTTTACCCCGAACTTTCTCAAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTAC
Found at i:318881 original size:29 final size:29
Alignment explanation
Indices: 318840--318918 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 29
318830 AAAATTTCAT
* * * * *
318840 TTTTAACCTCGAGGTTTCCAAAGTTACCT
1 TTTTACCCCCGAGGTATCCAAAATTACCC
* * *
318869 TTTTGCGCCCGA-GTGTCCAAAATTACCC
1 TTTTACCCCCGAGGTATCCAAAATTACCC
318897 TTTTACCCCCG-GGTATCCAAAA
1 TTTTACCCCCGAGGTATCCAAAA
318919 ATCTCATTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
28 31 0.79
29 8 0.21
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCGAGGTATCCAAAATTACCC
Found at i:330730 original size:23 final size:23
Alignment explanation
Indices: 330699--330757 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
330689 GACCTCGAAT
* *
330699 CTTTTTTTTTTTTTTACTTTAAA
1 CTTTATTTTTTTTTTAATTTAAA
* ** *
330722 CTTTGTTTTAATTTTAATTTAAC
1 CTTTATTTTTTTTTTAATTTAAA
*
330745 CCTTATTTTTTTT
1 CTTTATTTTTTTT
330758 ATCTTTTTTA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (23 bp):
CTTTATTTTTTTTTTAATTTAAA
Found at i:330884 original size:29 final size:29
Alignment explanation
Indices: 330834--330918 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
330824 AGTGTTATTT
* * *
330834 CCATTTTAATTTTTTTTCTTTTTAAATTTAA
1 CCATTTT-ATTATATTT-TTTTTAAATTAAA
*
330865 CCCTTTTATTATATTTTTTTCT-AATTAAA
1 CCATTTTATTATATTTTTTT-TAAATTAAA
* * *
330894 TCATTTTATTCTCTTTTTTTTAAAT
1 CCATTTTATTATATTTTTTTTAAAT
330919 AATCCTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.66
30 8 0.18
31 6 0.14
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.64
Consensus pattern (29 bp):
CCATTTTATTATATTTTTTTTAAATTAAA
Found at i:330892 original size:28 final size:27
Alignment explanation
Indices: 330852--330928 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
330842 ATTTTTTTTC
* *
330852 TTTTTAAATTTAACCCTTTTATTATATT
1 TTTTTTAA-TTAATCCTTTTATTATATT
* * *
330880 TTTTTCTAATTAAATCATTTTATTCTCTT
1 TTTTT-TAATT-AATCCTTTTATTATATT
*
330909 TTTTTTAAATAATCCTTTTA
1 TTTTTTAATTAATCCTTTTA
330929 ATCTATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
27 9 0.22
28 11 0.28
29 20 0.50
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTTTAATTAATCCTTTTATTATATT
Found at i:333648 original size:25 final size:26
Alignment explanation
Indices: 333615--333664 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
333605 AAGTCTTCCA
*
333615 AAAATTTAGCTCATACGAGCCTAGAC
1 AAAATTTAGCTCATACAAGCCTAGAC
333641 AAAA-TTAGCTCATACAAGCCTAGA
1 AAAATTTAGCTCATACAAGCCTAGA
333665 TAGCTTAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (26 bp):
AAAATTTAGCTCATACAAGCCTAGAC
Found at i:333684 original size:24 final size:23
Alignment explanation
Indices: 333620--333701 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
333610 TTCCAAAAAT
* *
333620 TTAGCTCATACGAGCCTAGACAAAA
1 TTAGCTCATACGAGCCTAG--ATAG
*
333645 TTAGCTCATACAAGCCTAGATAG
1 TTAGCTCATACGAGCCTAGATAG
* *
333668 CTTAGCTCTTACGAGCCCAGATAAG
1 -TTAGCTCATACGAGCCTAGAT-AG
333693 TTAGCTCAT
1 TTAGCTCAT
333702 TTGAGCCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.04
24 26 0.54
25 20 0.42
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (23 bp):
TTAGCTCATACGAGCCTAGATAG
Found at i:335186 original size:59 final size:59
Alignment explanation
Indices: 334997--335413 Score: 409
Period size: 59 Copynumber: 7.0 Consensus size: 59
334987 TTTGGGAAAA
* * * *
334997 TTTGGGGTTTAAAAATGAAATTTATAGACA-TTCGAGGGT-AAAAGGGTAA-TTTT-GAGAGT
1 TTTGGGG-TTAAAAATGAGATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGGA-AGT
* * ** *
335056 TTCGAGGTCGAAAATGGAGA-TTTTGGAAATTCGAGGG-AAAAATGGAATTTTTGGAAGT
1 TTTGGGGTTAAAAAT-GAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
* * * **
335114 TTCGAGGTCAAAAATGACTTTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
1 TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
** *
335173 TTTAAGGTTAAAAATGAGATTTTTTTGGAAGTT-TAGGGATAAAAATGGAATTTTTGGAAGT
1 TTTGGGGTTAAAAATGAGA--TTTTTGGAAGTTCGAGGG-TAAAAATGGAATTTTTGGAAGT
* * * * *
335234 TTTGGGGTCAATAATGAGATTTTTGGAAGTT-TAGGGGTAAAAATGGGATTTTTAGAAGT
1 TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTGGAAGT
* * * * *
335293 TTGGGGGTTAAAAATGGGATTTTTGGATGTTCGAGGGTAAAAATAGAATTTTTGGAATT
1 TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
* * **
335352 TTTGGGGTTAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAAATAAAATTTTTGGAAAGT
1 TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGG-AAGT
335412 TT
1 TT
335414 AGGGACCTCT
Statistics
Matches: 306, Mismatches: 39, Indels: 25
0.83 0.11 0.07
Matches are distributed among these distances:
57 5 0.02
58 62 0.20
59 177 0.58
60 13 0.04
61 49 0.16
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
TTTGGGGTTAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
Found at i:335359 original size:29 final size:29
Alignment explanation
Indices: 335066--335413 Score: 289
Period size: 29 Copynumber: 11.8 Consensus size: 29
335056 TTCGAGGTCG
*
335066 AAAATGGAGA-TTTTGGAA-ATTCGAGGG-A
1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
*
335094 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
*
335124 AAAAT-GACTTTTTTGGAAG-TTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
** *
335153 AAAATGGAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAG-TTTCGGGGTA
* * *
335183 AAAATGAGATTTTTTTGGAAGTTTAGGGATA
1 AAAATG-GA-ATTTTTGGAAGTTTCGGGGTA
*
335214 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
335244 ATAAT-GAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTCGGGGTA
* * *
335273 AAAATGGGATTTTTAGAAGTTTGGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* *
335303 AAAATGGGATTTTTGGATG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* * *
335332 AAAATAGAATTTTTGGAATTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* *
335362 AAAATGGGATTTTTAGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
**
335391 AAAATAAAATTTTTGGAAAGTTT
1 AAAATGGAATTTTTGG-AAGTTT
335414 AGGGACCTCT
Statistics
Matches: 262, Mismatches: 37, Indels: 39
0.78 0.11 0.12
Matches are distributed among these distances:
27 1 0.00
28 18 0.07
29 107 0.41
30 106 0.40
31 20 0.08
32 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:335417 original size:29 final size:28
Alignment explanation
Indices: 335066--335417 Score: 271
Period size: 30 Copynumber: 11.9 Consensus size: 28
335056 TTCGAGGTCG
* *
335066 AAAATGGAGA-TTTTGGAAATTCGAGGG-A
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
*
335094 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAG-GGT-A
* *
335124 AAAAT-GACTTTTTTGGAAGTTCGAGGGTA
1 AAAATGGA-ATTTTTGGAAGTT-TAGGGTA
*
335153 AAAATGGAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAG-TTT-AGGGTA
*
335183 AAAATGAGATTTTTTTGGAAGTTTAGGGATA
1 AAAATG-GA-ATTTTTGGAAGTTTAGGG-TA
*
335214 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGT-A
*
335244 ATAAT-GAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTA-GGGTA
* * *
335273 AAAATGGGATTTTTAGAAGTTTGGGGGTTA
1 AAAATGGAATTTTTGGAAGTTT-AGGG-TA
* * *
335303 AAAATGGGATTTTTGGATGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTT-TAGGGTA
* * *
335332 AAAATAGAATTTTTGGAATTTTTGGGGTTA
1 AAAATGGAATTTTTGGAA-GTTTAGGG-TA
* * *
335362 AAAATGGGATTTTTAGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTT-TAGGGTA
**
335391 AAAATAAAATTTTTGGAAAGTTTAGGG
1 AAAATGGAATTTTTGG-AAGTTTAGGG
335418 ACCTCTAGGG
Statistics
Matches: 260, Mismatches: 40, Indels: 47
0.75 0.12 0.14
Matches are distributed among these distances:
27 2 0.01
28 20 0.08
29 95 0.37
30 119 0.46
31 14 0.05
32 10 0.04
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:336382 original size:19 final size:19
Alignment explanation
Indices: 336358--336401 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
336348 AATTTCCATT
336358 TATTTATTTA-ATATTATAA
1 TATTTATTTATATATTAT-A
*
336377 TATTTA-TTATTTATTATA
1 TATTTATTTATATATTATA
336395 TATTTAT
1 TATTTAT
336402 GGTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATTTATATATTATA
Found at i:346889 original size:11 final size:11
Alignment explanation
Indices: 346846--346891 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
346836 TAAAACCCAA
346846 AAAAAGAAAAG
1 AAAAAGAAAAG
*
346857 AAAAATAAAA-
1 AAAAAGAAAAG
346867 AAATAAGAAAAG
1 AAA-AAGAAAAG
*
346879 AAAAAGGAAAG
1 AAAAAGAAAAG
346890 AA
1 AA
346892 GAAAAAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 24 0.80
12 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:347815 original size:17 final size:16
Alignment explanation
Indices: 347793--347880 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 16
347783 ATTTCACCCA
347793 AAAAAAAAGAAGAAAAG
1 AAAAAAAAGAA-AAAAG
*
347810 AAAAAAAAAGGAAAAAG
1 -AAAAAAAAGAAAAAAG
*
347827 -GAAAAAAGAAAAAATG
1 AAAAAAAAGAAAAAA-G
* *
347843 AAAAAGAAGAAAGAAG
1 AAAAAAAAGAAAAAAG
347859 AAAGAAGAAAG-AAAAAG
1 AAA-AA-AAAGAAAAAAG
347876 AAAAA
1 AAAAA
347881 GGAGAGGTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.21
16 7 0.12
17 26 0.45
18 13 0.22
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:347824 original size:7 final size:6
Alignment explanation
Indices: 347792--347881 Score: 76
Period size: 7 Copynumber: 13.8 Consensus size: 6
347782 TATTTCACCC
*
347792 AAAA-A AAAAGAA GAAAAGA AAAA-A AAAGGA AAAAGGAA AAAAGAA AAAATGA
1 AAAAGA AAAAG-A -AAAAGA AAAAGA AAAAGA AAAA-G-A AAAAG-A AAAA-GA
347844 AAAAGA AGAAAGA AGAAAGA AGAAAGA AAAAGA AAAAG
1 AAAAGA A-AAAGA A-AAAGA A-AAAGA AAAAGA AAAAG
347882 GAGAGGTCGA
Statistics
Matches: 75, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
5 8 0.11
6 21 0.28
7 35 0.47
8 11 0.15
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:348283 original size:37 final size:37
Alignment explanation
Indices: 348228--348304 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
348218 AGTTTGCACT
348228 CAAAGTTATCGCAACATTATTACTTCCAGATTACACC
1 CAAAGTTATCGCAACATTATTACTTCCAGATTACACC
* ** * * *
348265 CAAAGTTGTCGCCGCATTATTATTTCTAGATTGCACC
1 CAAAGTTATCGCAACATTATTACTTCCAGATTACACC
348302 CAA
1 CAA
348305 GACTGTCGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (37 bp):
CAAAGTTATCGCAACATTATTACTTCCAGATTACACC
Found at i:348312 original size:37 final size:37
Alignment explanation
Indices: 348242--348313 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
348232 GTTATCGCAA
*
348242 CATTATTACTTCCAGATTACACCCAAAGTTGTCGCCG
1 CATTATTACTTCCAGATTACACCCAAAGCTGTCGCCG
* * *
348279 CATTATTATTTCTAGATTGCACCC-AAGACTGTCGC
1 CATTATTACTTCCAGATTACACCCAAAG-CTGTCGC
348314 TGTATAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.10
37 27 0.90
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (37 bp):
CATTATTACTTCCAGATTACACCCAAAGCTGTCGCCG
Found at i:352637 original size:37 final size:37
Alignment explanation
Indices: 352557--352639 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
352547 TTGTTTAGAT
* * *
352557 TGCACCCAAAGTTGTCGCCGCATTATTACTTCCATAT
1 TGCACCCAAAGTTGTCACCGCATTATTACTTCCAGAA
* * **
352594 TACACCCAAAGTTGTCACCGCATTATTATTTCTGGAA
1 TGCACCCAAAGTTGTCACCGCATTATTACTTCCAGAA
352631 TGCACCCAA
1 TGCACCCAA
352640 GACTTTCGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (37 bp):
TGCACCCAAAGTTGTCACCGCATTATTACTTCCAGAA
Found at i:355118 original size:42 final size:42
Alignment explanation
Indices: 355053--355493 Score: 450
Period size: 42 Copynumber: 10.9 Consensus size: 42
355043 TTACATCATC
* * *
355053 CCATTCAATCTCTTACCCCGACCATAGGGCAAATTGAAGACA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* * * *
355095 CCATCCAATCTCTAACCCTGACCATGAGGCAGATTGAATACA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
*
355137 CCATTCAATCTCTTACCCC-AGCCATGGGGCAGATTG-A-A-A
1 CCATCCAATCTCTTACCCCGA-CCATGGGGCAGATTGAAGACA
* * *
355176 TCATCCAATCTCTTACCCCGACCATGAGGCAAATTGAAGA-A
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
*** * *
355217 TTGT-CAATCTCTTACCCCGACCATGAGGCAAATTGAAGACA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
*
355258 CCATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAGA-A
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* * *
355299 TC-GCCAATCTCTTACGCCGACCATGGGGCAGATTGAAGACA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* * *
355340 CTATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAG---
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* *
355379 CGATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAG---
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* * * *
355418 TCATCC-ATCTCTTACCCCGACCATAGGACAGATTAAAGA-A
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
* ***
355458 --ATTCAATCTCTTACCTTAACCATGGGGCAGATTGAA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAA
355494 TTAAAGAAGT
Statistics
Matches: 338, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
38 32 0.09
39 94 0.28
40 72 0.21
41 11 0.03
42 129 0.38
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (42 bp):
CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACA
Found at i:355274 original size:121 final size:122
Alignment explanation
Indices: 355058--355444 Score: 513
Period size: 121 Copynumber: 3.2 Consensus size: 122
355048 TCATCCCATT
* * *
355058 CAATCTCTTACCCCGACCATAGGGCAAATTGAAGACACCATCCAATCTCTAACCCTGACCATGAG
1 CAATCTCTTACCCCGACCATA-GGCAAATTGAAGACACTATCCAATCTCTTACCCCGACCATGAG
* *
355123 GCAGATTGAATACACCATTC-AATCTCTTACCCC-AGCCATGGGGCAGATTGAAATCATC
65 GCAAATTGAAGACACCA-TCAAATCTCTTACCCCGA-CCATGGGGCAGATTGAAATCATC
* *
355181 CAATCTCTTACCCCGACCATGAGGCAAATTGAAGA-ATTGT-CAATCTCTTACCCCGACCATGAG
1 CAATCTCTTACCCCGACCAT-AGGCAAATTGAAGACACTATCCAATCTCTTACCCCGACCATGAG
*
355244 GCAAATTGAAGACACCATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAGAATC-GC
65 GCAAATTGAAGACACCATCAAATCTCTTACCCCGACCATGGGGCAGATTG-A-AATCATC
* * * * *
355303 CAATCTCTTACGCCGACCATGGGGCAGATTGAAGACACTATCCAATCTCTTACCCCGATCATGGG
1 CAATCTCTTACCCCGACCAT-AGGCAAATTGAAGACACTATCCAATCTCTTACCCCGACCATGAG
* *
355368 GCAAATTGAAG---CGATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAGTCATC
65 GCAAATTGAAGACACCATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAATCATC
355423 C-ATCTCTTACCCCGACCATAGG
1 CAATCTCTTACCCCGACCATAGG
355445 ACAGATTAAA
Statistics
Matches: 236, Mismatches: 20, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
118 2 0.01
119 20 0.08
120 5 0.02
121 99 0.42
122 37 0.16
123 40 0.17
124 33 0.14
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (122 bp):
CAATCTCTTACCCCGACCATAGGCAAATTGAAGACACTATCCAATCTCTTACCCCGACCATGAGG
CAAATTGAAGACACCATCAAATCTCTTACCCCGACCATGGGGCAGATTGAAATCATC
Found at i:355295 original size:82 final size:82
Alignment explanation
Indices: 355057--355493 Score: 486
Period size: 82 Copynumber: 5.4 Consensus size: 82
355047 ATCATCCCAT
* * * * *
355057 TCAATCTCTTACCCCGACCATAGGGCAAATTGAAGACACCATCCAATCTCTAACCCTGACCATGA
1 TCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATGG
*
355122 GGCAGATTGAATACACCAT-
66 GGCAGATTGAAGA-A--ATG
*
355141 TCAATCTCTTACCCC-AGCCATGGGGCAGATTG-A-A-ATCATCCAATCTCTTACCCCGACCATG
1 TCAATCTCTTACCCCGA-CCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATG
* * *
355202 AGGCAAATTGAAGAATTG
65 GGGCAGATTGAAGAAATG
* * *
355220 TCAATCTCTTACCCCGACCATGAGGCAAATTGAAGACACCATCAAATCTCTTACCCCGACCATGG
1 TCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATGG
355285 GGCAGATTGAAG-AATCG
66 GGCAGATTGAAGAAAT-G
* * * *
355302 CCAATCTCTTACGCCGACCATGGGGCAGATTGAAGACACTATCCAATCTCTTACCCCGATCATGG
1 TCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATGG
* **
355367 GGCAAATTGAAGCGA--
66 GGCAGATTGAAGAAATG
* *
355382 TCAAATCTCTTACCCCGACCATGGGGCAGATTGAAG---TCATCC-ATCTCTTACCCCGACCATA
1 TC-AATCTCTTACCCCGACCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATG
* *
355443 GGACAGATTAAAGAAAT-
65 GGGCAGATTGAAGAAATG
***
355460 TCAATCTCTTACCTTAACCATGGGGCAGATTGAA
1 TCAATCTCTTACCCCGACCATGGGGCAGATTGAA
355494 TTAAAGAAGT
Statistics
Matches: 305, Mismatches: 38, Indels: 27
0.82 0.10 0.07
Matches are distributed among these distances:
77 57 0.19
78 7 0.02
79 28 0.09
80 4 0.01
81 71 0.23
82 107 0.35
83 3 0.01
84 28 0.09
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (82 bp):
TCAATCTCTTACCCCGACCATGGGGCAGATTGAAGACACCATCCAATCTCTTACCCCGACCATGG
GGCAGATTGAAGAAATG
Found at i:355521 original size:163 final size:156
Alignment explanation
Indices: 355055--355493 Score: 469
Period size: 163 Copynumber: 2.7 Consensus size: 156
355045 ACATCATCCC
* * *
355055 ATTCAATCTCTTACCCCGACCATAGGGCAAATTGAAGACACCATCCAATCTCTAACCCTGACCAT
1 ATTCAATCTCTTACCCCGACCATGGGGCAAATTGAAG--ACCATCC-ATCTCTTACCCCGACCAT
* * *
355120 GAGGCAGATTGAATACACCATTCAATCTCTTACCCCAGCCATGGGGCAGATTG-A-AATCATCCA
63 -AGGCAGATT-AA-AGA-AATTCAATCTCTTA-CCCAACCATGGGGCAGATTGAAGAATCATCCA
* *
355183 ATCTCTTACCCCGACCATGAGGCAAATTGAAG-A
123 ATCTCTTACCCCGATCATGGGGCAAATTGAAGCA
* *
355216 ATTGTCAATCTCTTACCCCGACCATGAGGCAAATTGAAGACACCATCAAATCTCTTACCCCGACC
1 A-T-TCAATCTCTTACCCCGACCATGGGGCAAATTGAAG--ACCATC-CATCTCTTACCCCGACC
* * * *
355281 ATGGGGCAGATTGAAG-AATCGCCAATCTCTTACGCCGACCATGGGGCAGATTGAAGACA-CTAT
61 AT-AGGCAGATTAAAGAAAT--TCAATCTCTTAC-CCAACCATGGGGCAGATTGAAGA-ATC-AT
*
355344 CCAATCTCTTACCCCGATCATGGGGCAAATTGAAGCG
120 CCAATCTCTTACCCCGATCATGGGGCAAATTGAAGCA
* *
355381 A-TCAAATCTCTTACCCCGACCATGGGGCAGATTGAAG-TCATCCATCTCTTACCCCGACCATAG
1 ATTC-AATCTCTTACCCCGACCATGGGGCAAATTGAAGACCATCCATCTCTTACCCCGACCATAG
*
355444 GACAGATTAAAGAAATTCAATCTCTTACCTTAACCATGGGGCAGATTGAA
65 G-CAGATTAAAGAAATTCAATCTCTTACC-CAACCATGGGGCAGATTGAA
355494 TTAAAGAAGT
Statistics
Matches: 239, Mismatches: 24, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
157 1 0.00
158 31 0.13
159 29 0.12
160 8 0.03
161 29 0.12
162 5 0.02
163 99 0.41
164 36 0.15
165 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (156 bp):
ATTCAATCTCTTACCCCGACCATGGGGCAAATTGAAGACCATCCATCTCTTACCCCGACCATAGG
CAGATTAAAGAAATTCAATCTCTTACCCAACCATGGGGCAGATTGAAGAATCATCCAATCTCTTA
CCCCGATCATGGGGCAAATTGAAGCA
Found at i:355590 original size:47 final size:46
Alignment explanation
Indices: 355508--355690 Score: 262
Period size: 47 Copynumber: 4.0 Consensus size: 46
355498 AGAAGTCATT
355508 CAATCTTTTACCCCTAA-TCAAGAGGGGCAAATTGAAGCCACCATC
1 CAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGCCACCATC
* *
355553 CAGTCTTTTACCCCTAAGTCAAGAAGGGGCAAATTGAAGCTACCATC
1 CAATCTTTTACCCCTAAGTCAAG-AGGGGCAAATTGAAGCCACCATC
** ** *
355600 CAATCTTTTACCCCTAAGTCAAGAGGGATAAATTGAAATCACTATC
1 CAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGCCACCATC
* *
355646 CAATCTTTTACCCCTAAGT-AAGAGGGGCATATTGAAGCTACCATC
1 CAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGCCACCATC
355691 TCACAGAAGC
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
45 35 0.29
46 41 0.34
47 44 0.37
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (46 bp):
CAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTGAAGCCACCATC
Found at i:355647 original size:93 final size:90
Alignment explanation
Indices: 355508--355690 Score: 276
Period size: 93 Copynumber: 2.0 Consensus size: 90
355498 AGAAGTCATT
* * *
355508 CAATCTTTTACCCCTAATCAAGAGGGGCAAATTGAAGCCACCATCCAGTCTTTTACCCCTAAGTC
1 CAATCTTTTACCCCTAATCAAGAGGGACAAATTGAAACCACCATCCAATCTTTTACCCCTAAGT-
355573 AAGAAGGGGCAAATTGAAGCTACCATC
65 AAG-AGGGGCAAATTGAAGCTACCATC
* * *
355600 CAATCTTTTACCCCTAAGTCAAGAGGGATAAATTGAAATCACTATCCAATCTTTTACCCCTAAGT
1 CAATCTTTTACCCCTAA-TCAAGAGGGACAAATTGAAACCACCATCCAATCTTTTACCCCTAAGT
*
355665 AAGAGGGGCATATTGAAGCTACCATC
65 AAGAGGGGCAAATTGAAGCTACCATC
355691 TCACAGAAGC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 22 0.27
92 20 0.24
93 41 0.49
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (90 bp):
CAATCTTTTACCCCTAATCAAGAGGGACAAATTGAAACCACCATCCAATCTTTTACCCCTAAGTA
AGAGGGGCAAATTGAAGCTACCATC
Found at i:356614 original size:4 final size:4
Alignment explanation
Indices: 356605--356630 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
356595 GTTTGCATTG
356605 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
356631 CGAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:358223 original size:108 final size:109
Alignment explanation
Indices: 358020--358223 Score: 324
Period size: 108 Copynumber: 1.9 Consensus size: 109
358010 TTCTTTTATT
*
358020 TTAGGGAATTCGAGAAATTGTGCCCTAAAGTGTTGGGTATATTTTTTTCTTTGAACCTAAATAAT
1 TTAGGGAACTCGAGAAATTGTGCCCTAAAGTGTTGGGTATATTTTTTTCTTTGAACCTAAATAAT
* *
358085 TGAGTATTATATTTAAAATTGATAAATGTTTAATGTTTTGTTAC
66 TGAATATCATATTTAAAATTGATAAATGTTTAATGTTTTGTTAC
*
358129 TTAGGGAACTCGAGAAATTGTGTCCTAACA-TGTTGGGTAT-TATTTTTTC-TTGAACCTAAATA
1 TTAGGGAACTCGAGAAATTGTGCCCTAA-AGTGTTGGGTATAT-TTTTTTCTTTGAACCTAAATA
*
358191 ATTGAATATCCTATTTAAAATTGATAAATGTTT
64 ATTGAATATCATATTTAAAATTGATAAATGTTT
358224 TTATTTTCGA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
108 44 0.50
109 43 0.49
110 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (109 bp):
TTAGGGAACTCGAGAAATTGTGCCCTAAAGTGTTGGGTATATTTTTTTCTTTGAACCTAAATAAT
TGAATATCATATTTAAAATTGATAAATGTTTAATGTTTTGTTAC
Found at i:360081 original size:28 final size:28
Alignment explanation
Indices: 359996--360082 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
359986 TTTTTATTTG
*
359996 AATTTGACACTTAAGTTCAATCATTTTA
1 AATTTGACACTTAAGTTCAATTATTTTA
* * * * *
360024 AATTT---ATTTTAG-T-ATTTTTATTTG
1 AATTTGACACTTAAGTTCAATTAT-TTTA
360048 AATTTGACACTTAAGTTCAATTATTTTA
1 AATTTGACACTTAAGTTCAATTATTTTA
360076 AATTTGA
1 AATTTGA
360083 TGTCGTTTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
23 3 0.07
24 9 0.21
25 5 0.12
27 5 0.12
28 16 0.38
29 4 0.10
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (28 bp):
AATTTGACACTTAAGTTCAATTATTTTA
Found at i:360093 original size:58 final size:52
Alignment explanation
Indices: 359977--360080 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
359967 AAGTTAGGTC
359977 ATTTTAGGATTTTTATTTGAATTTGACACTTAAGTTCAATCATTTTAAATTT
1 ATTTTAGGATTTTTATTTGAATTTGACACTTAAGTTCAATCATTTTAAATTT
* *
360029 ATTTTAGTATTTTTATTTGAATTTGACACTTAAGTTCAATTATTTTAAATTT
1 ATTTTAGGATTTTTATTTGAATTTGACACTTAAGTTCAATCATTTTAAATTT
360081 GATGTCGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.54
Consensus pattern (52 bp):
ATTTTAGGATTTTTATTTGAATTTGACACTTAAGTTCAATCATTTTAAATTT
Found at i:360698 original size:20 final size:20
Alignment explanation
Indices: 360673--360711 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
360663 AGGACGTGGC
360673 AGGGTGATTACCAACATGAT
1 AGGGTGATTACCAACATGAT
*
360693 AGGGTGATTACCATCATGA
1 AGGGTGATTACCAACATGA
360712 AGCACTTGAG
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:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
AGGGTGATTACCAACATGAT
Found at i:363209 original size:22 final size:22
Alignment explanation
Indices: 363184--363248 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
363174 TAAATATGAT
* **
363184 AAAATTTTAATTTAATTTTTTA
1 AAAATTATAATTTAATTTCGTA
* *
363206 AAAATTATATTTTTAATATCGTA
1 AAAATTATA-ATTTAATTTCGTA
363229 AAAATTATAATTTAATTTCG
1 AAAATTATAATTTAATTTCG
363249 ACCATCCTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
AAAATTATAATTTAATTTCGTA
Found at i:364014 original size:24 final size:26
Alignment explanation
Indices: 363964--364010 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
363954 AGTGTTCATC
*
363964 TCTTTTTTACTTATTATGTATTGTGT
1 TCTTTTTTACTTATTATGCATTGTGT
363990 TCTTTTTT-C-TATTAT-CATTGT
1 TCTTTTTTACTTATTATGCATTGT
364011 TGTTAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 1 0.05
26 8 0.40
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.66
Consensus pattern (26 bp):
TCTTTTTTACTTATTATGCATTGTGT
Found at i:367967 original size:15 final size:15
Alignment explanation
Indices: 367947--367980 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
367937 TCCACACTTC
367947 GTGTGATTTTGATCT
1 GTGTGATTTTGATCT
367962 GTGTGATTTTGATCT
1 GTGTGATTTTGATCT
367977 GTGT
1 GTGT
367981 TGAGTGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (15 bp):
GTGTGATTTTGATCT
Found at i:382776 original size:21 final size:22
Alignment explanation
Indices: 382752--382793 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
382742 AGAAGTGAAA
382752 TCCTACTTCACGCAAC-CAAAT
1 TCCTACTTCACGCAACTCAAAT
*
382773 TCCTACTTCATGCAACTCAAA
1 TCCTACTTCACGCAACTCAAA
382794 ACTTGTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (22 bp):
TCCTACTTCACGCAACTCAAAT
Found at i:383910 original size:8 final size:8
Alignment explanation
Indices: 383897--383921 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
383887 TGAATCATAT
383897 TTTTAATA
1 TTTTAATA
383905 TTTTAATA
1 TTTTAATA
383913 TTTTAATA
1 TTTTAATA
383921 T
1 T
383922 CTTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAATA
Found at i:386666 original size:23 final size:22
Alignment explanation
Indices: 386614--386666 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
386604 AGGAGCAAAT
386614 ACAAGC-CCCATGCCCAAACAC
1 ACAAGCACCCATGCCCAAACAC
* *
386635 ACATGCACCCTTGCCCTATAACA-
1 ACAAGCACCCATGCCC-A-AACAC
386658 ACAAGCACC
1 ACAAGCACC
386667 AAGCTCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 8 0.31
23 9 0.35
24 4 0.15
ACGTcount: A:0.36, C:0.43, G:0.09, T:0.11
Consensus pattern (22 bp):
ACAAGCACCCATGCCCAAACAC
Found at i:388876 original size:16 final size:16
Alignment explanation
Indices: 388855--388923 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
388845 TAGTTTCGAG
388855 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
* *
388871 TTTAAATAAATTTTATA
1 TTTAAAT-TATTTTAAA
* *
388888 TTTAAATTATTTTGAG
1 TTTAAATTATTTTAAA
*
388904 TTTAAAATA-TTTAAA
1 TTTAAATTATTTTAAA
388919 TTTAA
1 TTTAA
388924 TATTCAAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
15 9 0.21
16 20 0.47
17 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:397626 original size:27 final size:27
Alignment explanation
Indices: 397574--397626 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
397564 AGGAAGAGTG
* * *
397574 CGTATCCATCACCTGACCGCCTTGGAA
1 CGTATCCATCACCTGAACACCCTGGAA
397601 CGTATCCATCACCTGAACACCCTGGA
1 CGTATCCATCACCTGAACACCCTGGA
397627 TGATACGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
CGTATCCATCACCTGAACACCCTGGAA
Found at i:399574 original size:10 final size:11
Alignment explanation
Indices: 399535--399599 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 11
399525 AATACTTATT
399535 TATTACTTTTAA
1 TATTA-TTTTAA
399547 TATTA--TTAA
1 TATTATTTTAA
399556 TATAATATTTTATA
1 TAT--TATTTTA-A
399570 TTATTACTTTTAA
1 -TATTA-TTTTAA
399583 TATTATTTT-A
1 TATTATTTTAA
399593 TATTATT
1 TATTATT
399600 CGAGACATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
9 7 0.15
10 8 0.17
11 6 0.13
12 10 0.22
13 6 0.13
14 6 0.13
15 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:400443 original size:18 final size:18
Alignment explanation
Indices: 400420--400461 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
400410 ATACCCCTTT
400420 TTTTAAATAAATTTAATA
1 TTTTAAATAAATTTAATA
**
400438 TTTTAAATATTTTTAATA
1 TTTTAAATAAATTTAATA
400456 TTTTAA
1 TTTTAA
400462 TATTAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAATAAATTTAATA
Found at i:400459 original size:8 final size:8
Alignment explanation
Indices: 400431--400465 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
400421 TTTAAATAAA
400431 TTTAATAT
1 TTTAATAT
400439 TTTAAATATT
1 TTT-AATA-T
400449 TTTAATAT
1 TTTAATAT
400457 TTTAATAT
1 TTTAATAT
400465 T
1 T
400466 AGAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 13 0.52
9 8 0.32
10 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAATAT
Found at i:401335 original size:277 final size:277
Alignment explanation
Indices: 400836--402088 Score: 1289
Period size: 277 Copynumber: 4.4 Consensus size: 277
400826 AGAGAGATAA
* * * * * *
400836 TGTGTTCAATTATTAAATAGATAAATT-AAA-AGTGTAATGAAAATTTTGGTTTTTT-GATCATT
1 TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAG-CCATT
* * * * * * * *
400898 TATGTTGAACAAAGAATGTA-ACAAACGAGGTGTACTCAATTATCAAATAAGTAAATCAAAAGAA
65 TATGTTAAACAAAGAGTGTAGA-GAA-GGGGTTTGCTCAATTATCAAATAGGTAAATTAAAAG-A
* * * * * *
400962 TGTGAT-GAAAAATTTGG---TT-ACCATTTATGTTAAATAAAGAGTGTATGGGAAGGGGTTTGC
127 TGTAATCGAAAATTTTGGTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAGGG-AGGGG-GTGC
* * * *
401022 TCAATTATTAAATAGGTAAACTAAAAGAGTGTGATGAAAAATTCAATTTTTTGGCCATTTATGTT
190 TCAATTATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTT
*
401087 GAACAAAGAGTGTAAGAGGAGGGG
255 AAACAAAGAGTGTAAG-GGAGGGG
* * * *
401111 TGTGCTCAATTATCAAATAGGTAAATTAAAATAGTGTGATGAAAATTTTGATTTTTTGGCCATTT
1 TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTT
* *
401176 ATGTTAAACAAAGAGTGTATGGGAAGGGTTTTGCTCAATTATCAAATAGGTAAATTAAAAGA-GT
66 ATGTTAAACAAAGAGTGTA-GAGAAGGGGTTTGCTCAATTATCAAATAGGTAAATTAAAAGATGT
* * *
401240 CAT-GAAAATTTTGGTTTTTGGTCATTTATGTTAAACAAAGAGTGCAAGGGAGGGGGTGCTCAAT
130 AATCGAAAATTTTGGTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGGGGTGCTCAAT
** * * * * *
401304 TATCAAATAGAAAAATTAAAAGAGAGTGATGAAAATTTTGAGTTTTTAGCCATTTATGTTAAATA
195 TATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACA
* *
401369 AATAGTGTAAGAGAGGGAG
260 AAGAGTGTAAGGGAGGG-G
* *
401388 TTTGCTCAATTATCAAATAGAAAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTT
1 TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTT
*
401453 ATGTTAAACAAAGAGTGTA-AGAGAGGAGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGT
66 ATGTTAAACAAAGAGTGTAGAGA-AGG-GGTTTGCTCAATTATCAAATAGGTAAATTAAAAGA-T
*
401517 GTAATCGAAAATTTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAG
128 GTAATCGAAAA-TT-------T-TG-----------G--TTTTTGGCCATTTATGTTAAACAAAG
** *
401582 AGTGTAAGGGAGGGGGTTTGCTCAATTATCAAATATTTAAATTAAAAGAGTGTAATGAAAAATTC
171 AGTGTAAGGGAGGGGG--TGCTCAATTATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTC
* * * **
401647 GATTTTTTGGCCATTCATGTTAAACAAAGAGTGTAAGGTA-AAG
234 GATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGGG
* *
401690 -GTGCTCAATTATCAATTAGATAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTT
1 TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTT
* * * *
401754 ATGTTAAACAAAGAGCGTAAGGGAGGGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTG
66 ATGTTAAACAAAGAGTGT-AGAGAAGGGGTTTGCTCAATTATCAAATAGGTAAATTAAAAGA-TG
* * * * *
401819 TAATGGAAAA-TTCGATTTTTGGCAATTTATGTTAAACAAAGAGTGTAAGGTA-GGGGTGCTCAA
129 TAATCGAAAATTTTGGTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGGGGTGCTCAA
*
401882 TTATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTCGGTTTTTTAGCCATTTATGTTAAAC
194 TTATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAAC
* **
401947 AAAAAGCATAAGGGAGGGGG
259 AAAGAGTGTAAGGGA-GGGG
* * * * * *
401967 TTTACTCAATTATCAAATAGGTAAATTTAAAGAGTGTAATGAAAAATTCGATTTTTTTA-CCATT
1 TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGA-TTTTTTAGCCATT
* * * * *
402031 TATGTTAAATAAAGAGTGTAAAGAAGGGGGTGTGCGCAATTATCAAAAAGGTAAATTA
65 TATGTTAAACAAAGAGTGTAGAGAA-GGGGTTTGCTCAATTATCAAATAGGTAAATTA
402089 GAAAAGAGTA
Statistics
Matches: 825, Mismatches: 107, Indels: 89
0.81 0.10 0.09
Matches are distributed among these distances:
275 117 0.14
276 12 0.01
277 266 0.32
278 138 0.17
279 36 0.04
280 5 0.01
281 2 0.00
288 1 0.00
289 2 0.00
291 1 0.00
292 1 0.00
299 1 0.00
300 1 0.00
301 124 0.15
302 43 0.05
303 2 0.00
304 73 0.09
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (277 bp):
TGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTT
ATGTTAAACAAAGAGTGTAGAGAAGGGGTTTGCTCAATTATCAAATAGGTAAATTAAAAGATGTA
ATCGAAAATTTTGGTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGGGGTGCTCAATT
ATCAAATAGGTAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAA
AGAGTGTAAGGGAGGGG
Found at i:401394 original size:183 final size:183
Alignment explanation
Indices: 400841--402097 Score: 984
Period size: 183 Copynumber: 6.7 Consensus size: 183
400831 GATAATGTGT
* * * * * ** *
400841 TCAATTATTAAATAGATAAATTAAAAG-TGTAATGAAAATTTTGGTTTTTTGATCATTTATGTTG
1 TCAATTATCAAATAGGTAAATTAAAAGAGGTAATGAAAA-ATTCGTTTTTTGGCCATTTATGTTA
* *** * * * *
400905 AACAAAGAATGTAACAAACGAGGTGTACTCAATTATCAAATA-AGTAAATCAAAAGAATGTGATG
65 AACAAAGAGTGTAAGGGA-G-GGGGTGCTCAATTATCAAATAGA-TAAATTAAAAGAGTGTGATG
* *
400969 AAAAATTTG-G---TTA-CCATTTATGTTAAATAAAGAGTGTATGGGAAGGGGTTTGC
127 AAAAATTTGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGG-AGGGGTTTGC
* * * *
401022 TCAATTATTAAATAGGTAAACTAAAAGAGTGTGATGAAAAATTCAATTTTTTGGCCATTTATGTT
1 TCAATTATCAAATAGGTAAATTAAAAGAG-GTAATGAAAAATTC-GTTTTTTGGCCATTTATGTT
* * *
401087 GAACAAAGAGTGTAAGAGGAGGGGTGTGCTCAATTATCAAATAGGTAAATTAAAATAGTGTGATG
64 AAACAAAGAGTGTAAG-GGAGGGG-GTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATG
* * * * *
401152 AAAATTTTGATTTTTTGGCCATTTATGTTAAACAAAGAGTGTATGGGAAGGGTTTTGC
127 AAAAATTTGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGG-AGGGGTTTGC
* * * * *
401210 TCAATTATCAAATAGGTAAATTAAAAGA-GTCATGAAAATTTTGGTTTTTGGTCATTTATGTTAA
1 TCAATTATCAAATAGGTAAATTAAAAGAGGTAATGAAAAATTCGTTTTTTGGCCATTTATGTTAA
* * *
401274 ACAAAGAGTGCAAGGGAGGGGGTGCTCAATTATCAAATAGAAAAATTAAAAGAGAGTGATGAAAA
66 ACAAAGAGTGTAAGGGAGGGGGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAA
* * * *
401339 TTTTGAGTTTTTAGCCATTTATGTTAAATAAATAGTGTAAGAGAGGGAGTTTGC
131 ATTTGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGG-GTTTGC
** * * *
401393 TCAATTATCAAATAGAAAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTTATGTT
1 TCAATTATCAAATAGGTAAATTAAAAGAG-GTAATGAAAAATTCG-TTTTTTGGCCATTTATGTT
* * *
401458 AAACAAAGAGTGTAAGAGAGGAGGTTTGCTCAATTATCAAATATG-TAAATTAAAAGAGTGTAAT
64 AAACAAAGAGTGTAAGGGAGG-GG-GTGCTCAATTATCAAATA-GATAAATTAAAAGAGTGTGAT
*** *** * * ** ***
401522 CG-AAAATTTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTA-TGTTAAACAAAGAGT
126 -GAAAAATTT----GAGT-T-TTTAGCCATT---TATGTTAAACAAAGAGTG-T-----AAG-G-
** *
401585 GTAAGGGAG-GGGG
173 G--AGGG-GTTTGC
* * ***
401598 T---TTGCTCAATTATCAAATATTTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCCA
1 TCAATT-ATCAAATAGGTAA-A-TT-AA----AAGAG-GTAATGAAAAATTCG-TTTTTTGGCCA
* * ** *
401660 TTCATGTTAAACAAAGAGTGTAAGGTA-AAGGTGCTCAATTATCAATTAGATAAATTAAAAGAGT
56 TTTATGTTAAACAAAGAGTGTAAGGGAGGGGGTGCTCAATTATCAAATAGATAAATTAAAAGAGT
* * *
401724 GTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAGGGGGTTTGC
121 GTGATGAAAAATTTGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGA-GGGGTTTGC
* * * *
401788 TCAATTATCAAATATGTAAATTAAAAGAGTGTAATGGAAAATTCGATTTTTGGCAATTTATGTTA
1 TCAATTATCAAATAGGTAAATTAAAAGAG-GTAATGAAAAATTCGTTTTTTGGCCATTTATGTTA
* *
401853 AACAAAGAGTGTAAGGTA-GGGGTGCTCAATTATCAAATAGGTAAATTAAAAGAGTGTGATGAAA
65 AACAAAGAGTGTAAGGGAGGGGGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAA
* * ** *
401917 AATTCG-GTTTTTTAGCCATTTATGTTAAACAAAAAGCATAAGGGAGGGGGTTTAC
130 AATTTGAG-TTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGA-GGGGTTTGC
* **
401972 TCAATTATCAAATAGGTAAATTTAAAGAGTGTAATGAAAAATTCGATTTTTTTACCATTTATGTT
1 TCAATTATCAAATAGGTAAATTAAAAGAG-GTAATGAAAAATTCG-TTTTTTGGCCATTTATGTT
* * * * * *
402037 AAATAAAGAGTGTAAAGAAGGGGGTGTGCGCAATTATCAAAAAGGTAAATTAGAAAAGAGT
64 AAACAAAGAGTGTAAGGGA-GGGG-GTGCTCAATTATCAAATAGATAAATT--AAAAGAGT
402098 AACAAAGAGT
Statistics
Matches: 877, Mismatches: 138, Indels: 113
0.78 0.12 0.10
Matches are distributed among these distances:
181 25 0.03
182 8 0.01
183 191 0.22
184 177 0.20
185 95 0.11
186 46 0.05
187 7 0.01
188 127 0.14
189 6 0.01
190 15 0.02
191 2 0.00
192 14 0.02
193 6 0.01
194 4 0.00
196 2 0.00
197 9 0.01
198 9 0.01
199 1 0.00
201 4 0.00
202 6 0.01
203 12 0.01
204 2 0.00
205 4 0.00
206 10 0.01
207 40 0.05
208 1 0.00
210 54 0.06
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (183 bp):
TCAATTATCAAATAGGTAAATTAAAAGAGGTAATGAAAAATTCGTTTTTTGGCCATTTATGTTAA
ACAAAGAGTGTAAGGGAGGGGGTGCTCAATTATCAAATAGATAAATTAAAAGAGTGTGATGAAAA
ATTTGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAGGGGTTTGC
Found at i:401528 original size:94 final size:92
Alignment explanation
Indices: 400841--401530 Score: 738
Period size: 94 Copynumber: 7.5 Consensus size: 92
400831 GATAATGTGT
* * * *
400841 TCAATTATTAAATAGATAAATT-AAA-AGTGTAATGAAAATTTTGGTTTTTT-GATCATTTATGT
1 TCAATTATCAAATAG-TAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAG-CCATTTATGT
* * * * * * *
400903 TGAACAAAGAATGTAACAAACGAGGTGTAC
64 TAAACAAAGAGTGTAAGAGA-GGGGTTTGC
* * * *
400933 TCAATTATCAAATAAGTAAATCAAAAGAATGTGATGAAAAATTTG----GTTA-CCATTTATGTT
1 TCAATTATCAAAT-AGTAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
* * *
400993 AAATAAAGAGTGTATGGGAAGGGGTTTGC
65 AAACAAAGAGTGTAAGAG-AGGGGTTTGC
* * * ** *
401022 TCAATTATTAAATAGGTAAACTAAAAGAGTGTGATGAAAAATTCAATTTTTTGGCCATTTATGTT
1 TCAATTATCAAATA-GTAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
* *
401087 GAACAAAGAGTGTAAGAGGAGGGGTGTGC
65 AAACAAAGAGTGTAAGA-GAGGGGTTTGC
* *
401116 TCAATTATCAAATAGGTAAATTAAAATAGTGTGATGAAAATTTTGATTTTTTGGCCATTTATGTT
1 TCAATTATCAAATA-GTAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
* * *
401181 AAACAAAGAGTGTATGGGAAGGGTTTTGC
65 AAACAAAGAGTGTAAGAG-AGGGGTTTGC
* * * *
401210 TCAATTATCAAATAGGTAAATTAAAAGA--GTCATGAAAATTTTG-GTTTTTGGTCATTTATGTT
1 TCAATTATCAAATA-GTAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
* * *
401272 AAACAAAGAGTGCAAGGGAGGGG-GTGC
65 AAACAAAGAGTGTAAGAGAGGGGTTTGC
* * *
401299 TCAATTATCAAATAGAAAAATTAAAAGAGAGTGATGAAAATTTTGAGTTTTTAGCCATTTATGTT
1 TCAATTATCAAATAG-TAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
* *
401364 AAATAAATAGTGTAAGAGAGGGAGTTTGC
65 AAACAAAGAGTGTAAGAGAGGG-GTTTGC
* *
401393 TCAATTATCAAATAGAAAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTTATGTT
1 TCAATTATCAAATAG-TAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTT
401458 AAACAAAGAGTGTAAGAGAGGAGGTTTGC
65 AAACAAAGAGTGTAAGAGAGG-GGTTTGC
*
401487 TCAATTATCAAATATGTAAATTAAAAGAGTGTAATCGAAAATTT
1 TCAATTATCAAATA-GTAAATTAAAAGAGTGTGAT-GAAAATTT
401531 AAAAGAGTGT
Statistics
Matches: 510, Mismatches: 66, Indels: 41
0.83 0.11 0.07
Matches are distributed among these distances:
88 2 0.00
89 92 0.18
90 7 0.01
91 47 0.09
92 66 0.13
93 9 0.02
94 277 0.54
95 10 0.02
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (92 bp):
TCAATTATCAAATAGTAAATTAAAAGAGTGTGATGAAAATTTTGATTTTTTAGCCATTTATGTTA
AACAAAGAGTGTAAGAGAGGGGTTTGC
Found at i:401549 original size:116 final size:115
Alignment explanation
Indices: 401407--401645 Score: 406
Period size: 116 Copynumber: 2.1 Consensus size: 115
401397 TTATCAAATA
** *
401407 GAAAAATTAAAAGAGTGTGATGAAAAATTTGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTA
1 GAAAAATTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTA
401472 AGAGAGGAGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAAT
66 AGAGAGGAGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAAT
*
401522 CGAAAATTTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGT
1 -GAAAAATTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGT
* * *
401587 AAGGGAGGGGGTTTGCTCAATTATCAAATATTTAAATTAAAAGAGTGTAAT
65 AAGAGAGGAGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAAT
401638 GAAAAATT
1 GAAAAATT
401646 CGATTTTTTG
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
115 7 0.06
116 108 0.94
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (115 bp):
GAAAAATTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTA
AGAGAGGAGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAAT
Found at i:401551 original size:22 final size:22
Alignment explanation
Indices: 401507--401548 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
401497 AATATGTAAA
*
401507 TTAAAAGAGTGTAATCGAAAAT
1 TTAAAAGAGTGTAATCAAAAAT
*
401529 TTAAAAGAGTGTGA-CAAAAA
1 TTAAAAGAGTGTAATCAAAAA
401549 ATTCGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (22 bp):
TTAAAAGAGTGTAATCAAAAAT
Found at i:401681 original size:210 final size:206
Alignment explanation
Indices: 401313--401736 Score: 591
Period size: 210 Copynumber: 2.0 Consensus size: 206
401303 TTATCAAATA
** * * * *
401313 GAAAAATTAAAAGAGAGTGATGAAAATTTTGAGTTTTTAGCCATTTATGTTAAATAAATAGTGTA
1 GAAAAATTAAAAGAGAGTGACAAAAAATTCGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTA
* *
401378 AGAGAGGGAGTTTGCTCAATTATCAAATAGAAAAATTAAAAGAGTGTGATGAAAAATTTGATTTT
66 AGAGAGGGAGTTTGCTCAATTATCAAATAGAAAAATTAAAAGAGTGTAATGAAAAATTCGATTTT
* *
401443 TTAGCCATTTATGTTAAACAAAGAGTGTAAGAG-AGGAGGTTTGCTCAATTATCAAATATG-TAA
131 TTAGCCATTCATGTTAAACAAAGAGTGTAAG-GTA-AAGG--TGCTCAATTATCAAATA-GATAA
401506 ATTAAAAGAGTGTAAT
191 ATTAAAAGAGTGTAAT
* * *
401522 CGAAAATTTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGT
1 -GAAAAATTAAAAGAGAGTGACAAAAAATTCGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGT
* * ***
401587 AAGGGAGGGGGTTTGCTCAATTATCAAATATTTAAATTAAAAGAGTGTAATGAAAAATTCGATTT
65 AAGAGAGGGAGTTTGCTCAATTATCAAATAGAAAAATTAAAAGAGTGTAATGAAAAATTCGATTT
* *
401652 TTTGGCCATTCATGTTAAACAAAGAGTGTAAGGTAAAGGTGCTCAATTATCAATTAGATAAATTA
130 TTTAGCCATTCATGTTAAACAAAGAGTGTAAGGTAAAGGTGCTCAATTATCAAATAGATAAATTA
*
401717 AAAGAGTGTGAT
195 AAAGAGTGTAAT
401729 GAAAAATT
1 GAAAAATT
401737 CGATTTTTTA
Statistics
Matches: 190, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
206 8 0.04
207 34 0.18
209 4 0.02
210 144 0.76
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.32
Consensus pattern (206 bp):
GAAAAATTAAAAGAGAGTGACAAAAAATTCGAGTTTTTAGCCATTTATGTTAAACAAAGAGTGTA
AGAGAGGGAGTTTGCTCAATTATCAAATAGAAAAATTAAAAGAGTGTAATGAAAAATTCGATTTT
TTAGCCATTCATGTTAAACAAAGAGTGTAAGGTAAAGGTGCTCAATTATCAAATAGATAAATTAA
AAGAGTGTAAT
Found at i:401836 original size:94 final size:94
Alignment explanation
Indices: 401529--402097 Score: 767
Period size: 94 Copynumber: 6.1 Consensus size: 94
401519 AATCGAAAAT
* **
401529 TTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
1 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
**
401594 GGGGTTTGCTCAATTATCAAATATTTAAA
66 GGGGTTTGCTCAATTATCAAATAGGTAAA
* * *
401623 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCCATTCATGTTAAACAAAGAGTGTAAGGTA-
1 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
** * *
401687 AAGG--TGCTCAATTATCAATTAGATAAA
66 GGGGTTTGCTCAATTATCAAATAGGTAAA
* *
401714 TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
1 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
*
401779 GGGGTTTGCTCAATTATCAAATATGTAAA
66 GGGGTTTGCTCAATTATCAAATAGGTAAA
* * * *
401808 TTAAAAGAGTGTAATGGAAAATTCGA-TTTTTGGCAATTTATGTTAAACAAAGAGTGTAAGGTA-
1 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
401871 GGGG--TGCTCAATTATCAAATAGGTAAA
66 GGGGTTTGCTCAATTATCAAATAGGTAAA
* * * **
401898 TTAAAAGAGTGTGATGAAAAATTCGGTTTTTTAGCCATTTATGTTAAACAAAAAGCATAAGGGAG
1 TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
*
401963 GGGGTTTACTCAATTATCAAATAGGTAAA
66 GGGGTTTGCTCAATTATCAAATAGGTAAA
* * * *
401992 TTTAAAGAGTGTAATGAAAAATTCGATTTTTTTA-CCATTTATGTTAAATAAAGAGTGTAAAGAA
1 TTAAAAGAGTGTAATGAAAAATTCGA-TTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGA
* * *
402056 GGGGGTGTGCGCAATTATCAAAAAGGTAAA
65 GGGGGTTTGCTCAATTATCAAATAGGTAAA
402086 TTAGAAAAGAGT
1 TT--AAAAGAGT
402098 AACAAAGAGT
Statistics
Matches: 413, Mismatches: 52, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
90 45 0.11
91 110 0.27
92 10 0.02
93 35 0.08
94 199 0.48
95 7 0.02
96 7 0.02
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (94 bp):
TTAAAAGAGTGTAATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
GGGGTTTGCTCAATTATCAAATAGGTAAA
Found at i:401961 original size:184 final size:185
Alignment explanation
Indices: 401529--402097 Score: 870
Period size: 184 Copynumber: 3.1 Consensus size: 185
401519 AATCGAAAAT
** *
401529 TTAAAAGAGTGTGACAAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGTGTAAGGGAG
1 TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
*
401594 GGGGTTTGCTCAATTATCAAATATTTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCC
66 GGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCC
* ** * *
401659 ATTCATGTTAAACAAAGAGTGTAAGGTAAAGGTGCTCAATTATCAATTAGATAAA
131 ATTTATGTTAAACAAAGAGTGTAAGGTAGGGGTGCTCAATTATCAAATAGGTAAA
401714 TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
1 TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
* *
401779 GGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAATGGAAAATTCGA-TTTTTGGCA
66 GGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCC
401843 ATTTATGTTAAACAAAGAGTGTAAGGTAGGGGTGCTCAATTATCAAATAGGTAAA
131 ATTTATGTTAAACAAAGAGTGTAAGGTAGGGGTGCTCAATTATCAAATAGGTAAA
* * *
401898 TTAAAAGAGTGTGATGAAAAATTCGGTTTTTTAGCCATTTATGTTAAACAAAAAGCATAAGGGAG
1 TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
* * * **
401963 GGGGTTTACTCAATTATCAAATAGGTAAATTTAAAGAGTGTAATGAAAAATTCGATTTTTTTACC
66 GGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCC
* * * * *
402028 ATTTATGTTAAATAAAGAGTGTAAAGAAGGGGGTGTGCGCAATTATCAAAAAGGTAAA
131 ATTTATGTTAAACAAAGAGTGTAAGGTA--GGG-GTGCTCAATTATCAAATAGGTAAA
402086 TTAGAAAAGAGT
1 TT--AAAAGAGT
402098 AACAAAGAGT
Statistics
Matches: 352, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
184 171 0.49
185 146 0.41
187 3 0.01
188 24 0.07
190 8 0.02
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (185 bp):
TTAAAAGAGTGTGATGAAAAATTCGATTTTTTAGCCATTTATGTTAAACAAAGAGCGTAAGGGAG
GGGGTTTGCTCAATTATCAAATATGTAAATTAAAAGAGTGTAATGAAAAATTCGATTTTTTGGCC
ATTTATGTTAAACAAAGAGTGTAAGGTAGGGGTGCTCAATTATCAAATAGGTAAA
Found at i:402134 original size:60 final size:58
Alignment explanation
Indices: 402041--402155 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 58
402031 TATGTTAAAT
* *
402041 AAAGAGTGTAAAGAAGGGGGTGTGCGCAATTATCAAAAAGGTAAATTAGAAAAGAGTAAC
1 AAAGAGTGTAAAGAAGGGGATGCGCGCAATTATCAAAAAGGTAAATT--AAAAGAGTAAC
* * * *
402101 AAAGAGTGTAAGGGAGGGGATGCGCTCAATTATCAAATAGGTAAATTAAAAGAGT
1 AAAGAGTGTAAAGAAGGGGATGCGCGCAATTATCAAAAAGGTAAATTAAAAGAGT
402156 GCGATGAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 8 0.16
60 41 0.84
ACGTcount: A:0.44, C:0.07, G:0.29, T:0.20
Consensus pattern (58 bp):
AAAGAGTGTAAAGAAGGGGATGCGCGCAATTATCAAAAAGGTAAATTAAAAGAGTAAC
Found at i:402264 original size:70 final size:70
Alignment explanation
Indices: 402146--402277 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 70
402136 AATAGGTAAA
402146 TTAAAAGAGTGCGATGAAAAAAATTAGTTTTTTAACCATTTATATTAAACAAAGAGTGTAAGGGA
1 TTAAAAGAGTGCGATG-AAAAAATTAGTTTTTTAACCATTTATATTAAACAAAGAGTGTAAGGGA
402211 GATAAG
65 GATAAG
* * ** *
402217 TTAAAAGAGTGTGATG-AAAAATTCGGTTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAG
1 TTAAAAGAGTGCGATGAAAAAATT-AGTTTTTTAACCATTTATATTAAACAAAGAGTGTAAG
402278 AGAAGGGGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
69 7 0.13
70 33 0.60
71 15 0.27
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (70 bp):
TTAAAAGAGTGCGATGAAAAAATTAGTTTTTTAACCATTTATATTAAACAAAGAGTGTAAGGGAG
ATAAG
Found at i:402356 original size:60 final size:60
Alignment explanation
Indices: 402263--402376 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
402253 ATTTATGTTA
*
402263 AACAAAGAGTGTAAGAGAAGGGGTGTGCTCAATTATCAAATAGGTAAACTAAAAAAGAGT
1 AACAAAGAGTGCAAGAGAAGGGGTGTGCTCAATTATCAAATAGGTAAACTAAAAAAGAGT
* *
402323 AACAAAGAGTGCAAG-GAAGGAGGTTTGCTCAATTATCAAATAGGTAAATTAAAA
1 AACAAAGAGTGCAAGAGAAGG-GGTGTGCTCAATTATCAAATAGGTAAACTAAAA
402377 GAGTGCAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 5 0.10
60 45 0.90
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.21
Consensus pattern (60 bp):
AACAAAGAGTGCAAGAGAAGGGGTGTGCTCAATTATCAAATAGGTAAACTAAAAAAGAGT
Found at i:402390 original size:225 final size:223
Alignment explanation
Indices: 401995--402435 Score: 663
Period size: 225 Copynumber: 2.0 Consensus size: 223
401985 AGGTAAATTT
* *
401995 AAAGAGTGTAATGAAAAATTCGATTTTTTTACCATTTATGTTAAATAAAGAGTGTAAAGAAGGGG
1 AAAGAGTGTAATGAAAAATTCGATTTTTTGACCATTTATGTTAAACAAAGAGTGTAAAGAAGGGG
* * * *
402060 GTGTGCGCAATTATCAAAAAGGTAAATTAGAAAAGAGTAACAAAGAGTGTAAGGGAGGGGATGCG
66 GTGTGCGCAATTATCAAAAAGGTAAACTAAAAAAGAGTAACAAAGAGTGCAAGGAAGGGGATGCG
*
402125 CTCAATTATCAAATAGGTAAATTAAAAGAGTGCGATGAAAAAAATTAG-TTTTTTAACCATTTAT
131 CTCAATTATCAAATAGGTAAATTAAAAGAGTGCAATG--AAAAATTAGATTTTTT-ACCATTTAT
*
402189 ATTAAACAAAGAGTGTAAGGGAGATAAGTTA
193 ATTAAACAAAGAGTGTAAAGGAGATAAGTTA
* * *
402220 AAAGAGTGTGATGAAAAATTCGGTTTTTTGGCCATTTATGTTAAACAAAGAGTGTAAGAGAA-GG
1 AAAGAGTGTAATGAAAAATTCGATTTTTTGACCATTTATGTTAAACAAAGAGTGTAA-AGAAGGG
* * *
402284 GGTGTGCTCAATTATCAAATAGGTAAACTAAAAAAGAGTAACAAAGAGTGCAAGGAAGGAGG-TT
65 GGTGTGCGCAATTATCAAAAAGGTAAACTAAAAAAGAGTAACAAAGAGTGCAAGGAAGG-GGATG
* * *
402348 TGCTCAATTATCAAATAGGTAAATTAAAAGAGTGCAATGAAAAATTTGATTTTTTACCATTTATG
129 CGCTCAATTATCAAATAGGTAAATTAAAAGAGTGCAATGAAAAATTAGATTTTTTACCATTTATA
402413 TTAAACAAAGAGTGTAAAGGAGA
194 TTAAACAAAGAGTGTAAAGGAGA
402436 ACTCCGTGTA
Statistics
Matches: 196, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
223 39 0.20
224 6 0.03
225 145 0.74
226 6 0.03
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (223 bp):
AAAGAGTGTAATGAAAAATTCGATTTTTTGACCATTTATGTTAAACAAAGAGTGTAAAGAAGGGG
GTGTGCGCAATTATCAAAAAGGTAAACTAAAAAAGAGTAACAAAGAGTGCAAGGAAGGGGATGCG
CTCAATTATCAAATAGGTAAATTAAAAGAGTGCAATGAAAAATTAGATTTTTTACCATTTATATT
AAACAAAGAGTGTAAAGGAGATAAGTTA
Found at i:402690 original size:34 final size:34
Alignment explanation
Indices: 402652--402720 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
402642 ATCAAATAGG
402652 TAAATTAAAATAGTCTAATGAAAAATTCGAGTTT
1 TAAATTAAAATAGTCTAATGAAAAATTCGAGTTT
*
402686 TAAATTAAAATAGTGTAATGAAAAATTCGAGTTT
1 TAAATTAAAATAGTCTAATGAAAAATTCGAGTTT
402720 T
1 T
402721 TGGCCATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.36
Consensus pattern (34 bp):
TAAATTAAAATAGTCTAATGAAAAATTCGAGTTT
Found at i:403008 original size:93 final size:95
Alignment explanation
Indices: 402686--403044 Score: 471
Period size: 94 Copynumber: 3.8 Consensus size: 95
402676 ATTCGAGTTT
* * * * * *
402686 TAAATTAAAATAGTGTAATGAAAAATTCGA-GTTTTTGGCCATTTAGGTTAAATAAAGAGTGTAA
1 TAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTTTGCCATTTATGTTAAACAAAGAGTGTAA
* *
402750 GAGAGGGGGTGTGCTCAATTATCAAATAGG
66 GGGAAGGGGTGTGCTCAATTATCAAATAGG
* * * *
402780 TAAATTAAAAGAGTGTGATGAAAAATTCGA--TTTTTTGACTATTTATGTTAAAAAAAGGAGCGC
1 TAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTTTG-CCATTTATGTTAAACAAA-GAGTGT
*
402843 AAGGGAAGGGGTGTGCTCAATTATCAAATAAG
64 AAGGGAAGGGGTGTGCTCAATTATCAAATAGG
*
402875 T-AATTAAAAGAGTGTGATGAAAAATTCGATTTTGTTTGCCATTTATGTTAAACAAA-ATGTGTA
1 TAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTTTGCCATTTATGTTAAACAAAGA-GTGTA
* * *
402938 AGGGAGGGGGTGTGCTCGATTATTAAATAGG
65 AGGGAAGGGGTGTGCTCAATTATCAAATAGG
* *
402969 TAAATTAAAAGA-T-TGATGAAAATTTTGATTTTTTTTGCCATTTATGTTAAACAAAGAGTGTAA
1 TAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTTTGCCATTTATGTTAAACAAAGAGTGTAA
403032 GGGAAGGGGTGTG
66 GGGAAGGGGTGTG
403045 ATGAAAAATT
Statistics
Matches: 234, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
93 64 0.27
94 104 0.44
95 60 0.26
96 6 0.03
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (95 bp):
TAAATTAAAAGAGTGTGATGAAAAATTCGATTTTTTTTGCCATTTATGTTAAACAAAGAGTGTAA
GGGAAGGGGTGTGCTCAATTATCAAATAGG
Found at i:406298 original size:17 final size:18
Alignment explanation
Indices: 406276--406318 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
406266 ATAGTTTGCA
406276 TGCATTTTTA-TTGTCAT
1 TGCATTTTTATTTGTCAT
406293 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA-TTTGTCAT
406312 TGCATTT
1 TGCATTT
406319 CTTAAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (18 bp):
TGCATTTTTATTTGTCAT
Found at i:406951 original size:19 final size:18
Alignment explanation
Indices: 406909--406964 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
406899 AGTCACTTGA
406909 AAAAGGAAAATGAGAAAAAG
1 AAAA-GAAAA-GAGAAAAAG
406929 -AAAGAAAAGAGAAAAGAG
1 AAAAGAAAAGAGAAAA-AG
406947 AAAAGAAAAGAAGAAAAA
1 AAAAGAAAAG-AGAAAAA
406965 ATGTTTGCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 13 0.39
20 6 0.18
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAGAGAAAAAG
Found at i:406958 original size:24 final size:24
Alignment explanation
Indices: 406909--406954 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
406899 AGTCACTTGA
406909 AAAAGGAAAATGAGAAAAAGAAAG
1 AAAAGGAAAATGAGAAAAAGAAAG
406933 AAAAGAGAAAA-GAG-AAAAGAAA
1 AAAAG-GAAAATGAGAAAAAGAAA
406955 AGAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (24 bp):
AAAAGGAAAATGAGAAAAAGAAAG
Done.