Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold325
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: 667817
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 3 of 5
Found at i:355726 original size:19 final size:19
Alignment explanation
Indices: 355702--355764 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
355692 AGCGATACAT
355702 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
355721 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
355734 TGTATCGATACAGCACTTA
1 TGTATCGATACAACACTTA
355753 TGTATCGATACA
1 TGTATCGATACA
355765 TTTACTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.57
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:355735 original size:32 final size:32
Alignment explanation
Indices: 355627--355766 Score: 169
Period size: 32 Copynumber: 4.4 Consensus size: 32
355617 GTAATAGCTT
*
355627 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
* * * ** *
355659 TGTATCGATACATT-TCCTTGGTAGTA-GCTT-
1 TGTATCGATACATTGT-ATCGATACAACACTTA
*
355689 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
355721 TGTATCGATACATTGTATCGATACAGCACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
355753 TGTATCGATACATT
1 TGTATCGATACATT
355767 TACTGTTTGT
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
30 18 0.20
31 8 0.09
32 62 0.70
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:360725 original size:66 final size:66
Alignment explanation
Indices: 360621--360832 Score: 192
Period size: 66 Copynumber: 3.2 Consensus size: 66
360611 TTCATCTTGG
* * * * * *
360621 CCAAATGTCATTTTGGACTGAAATTCACCTTAATCAAGAATTGCTTTAACCAAAGGTTCACCTCA
1 CCAAATATCACTTTGGACTGAAATTCAACTCAGTCAAGAATTACTTTAACCAAAGGTTCACCTCA
360686 A
66 A
* * * ***
360687 CCAAATATCACTTTGGACTGAAATTTAACTCAGCCAAGAATTACTTTAACAACCCAAGGTTCTTT
1 CCAAATATCACTTTGGACTGAAATTCAACTCAGTCAAGAATTACTTT---AACCAAAGGTTCACC
*
360752 TCAG
63 TCAA
* * * * * * *
360756 CCAACTGTCACATTGGACTAAAATTCATC-CTAGTCAAGAATTACTTTAGCCTAAGGTTCACCTC
1 CCAAATATCACTTTGGACTGAAATTCAACTC-AGTCAAGAATTACTTTAACCAAAGGTTCACCTC
360820 AA
65 AA
*
360822 CCACATATCAC
1 CCAAATATCAC
360833 ATTAGACAAA
Statistics
Matches: 113, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
66 60 0.53
68 1 0.01
69 52 0.46
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (66 bp):
CCAAATATCACTTTGGACTGAAATTCAACTCAGTCAAGAATTACTTTAACCAAAGGTTCACCTCA
A
Found at i:360849 original size:33 final size:32
Alignment explanation
Indices: 360812--360890 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
360802 TAGCCTAAGG
*
360812 TTCACCTCAACCACATATCAC-ATTAGACAAAAA
1 TTCACCTCAACCAAATATCACTATT-GA-AAAAA
* *
360845 TTCACTTCAACCAAATGTCACTATTGAAAAAA
1 TTCACCTCAACCAAATATCACTATTGAAAAAA
* *
360877 TTAACCCCAACCAA
1 TTCACCTCAACCAA
360891 GATTCATCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 16 0.41
33 20 0.51
34 3 0.08
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.23
Consensus pattern (32 bp):
TTCACCTCAACCAAATATCACTATTGAAAAAA
Found at i:362611 original size:30 final size:31
Alignment explanation
Indices: 362568--362654 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
362558 TTTGTACAAT
* * *
362568 AATTAATTGAAATTAAAAATAT-AATAGTAA
1 AATTAAATAAAATTAAAAATAATAATAGTAA
* *
362598 AATTAAATAAAATTAAAATTAATAATGGTAA
1 AATTAAATAAAATTAAAAATAATAATAGTAA
* * *
362629 AATTCAACAAAATTAAAGCATAATAA
1 AATTAAATAAAATTAAA-AATAATAA
362655 AAAGAGTTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
30 18 0.39
31 22 0.48
32 6 0.13
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (31 bp):
AATTAAATAAAATTAAAAATAATAATAGTAA
Found at i:370234 original size:165 final size:164
Alignment explanation
Indices: 369910--370235 Score: 351
Period size: 165 Copynumber: 2.0 Consensus size: 164
369900 AATGAATTTT
* * *
369910 TATGAAATAAATAAGAATATTTGACGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCTCGAAA
1 TATGAAATAAATAAAAATATTTGACGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCCCAAAA
* * * *
369975 AAATTCTCGGAGTAGAAAACACTGTATTTCGAAAAAAGGAAAATTTGAAGAAAAAAATCAAAAAC
66 AAATTCTAGGAGTAGAAAACACCGTATTTCGAAAAAAGAAAAATTCGAAGAAAAAAATCAAAAAC
* * **
370040 TCATGAAAATGAATAAATTTTTGAAAACTGAATAA
131 TCA-GAAAATAAAAAAATTTTCAAAAACTGAATAA
* ** *
370075 TATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAATTAAGAAACA-TCCTCCCAAA
1 TATGAAATAAATAAAAATATTTGACGAATTTTAAAAATTAAAAACCAAGAAAAATTCC-CCCAAA
* * *
370139 AAAATT-TAAGGAG-AGGAAAATC-CCGTAATTT-GAAAATAGAAAGAATTCGAA-AAGAAAATT
65 AAAATTCT-AGGAGTA-GAAAA-CACCGT-ATTTCGAAAAAAGAAA-AATTCGAAGAAAAAAATC
*
370199 AATAACTCCA-AAAATAAAAAGAATTTTCAAAAACTGA
125 AAAAACT-CAGAAAATAAAAA-AATTTTCAAAAACTGA
370236 TTTAATGATA
Statistics
Matches: 134, Mismatches: 19, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
164 13 0.10
165 107 0.80
166 14 0.10
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.25
Consensus pattern (164 bp):
TATGAAATAAATAAAAATATTTGACGAATTTTAAAAATTAAAAACCAAGAAAAATTCCCCCAAAA
AAATTCTAGGAGTAGAAAACACCGTATTTCGAAAAAAGAAAAATTCGAAGAAAAAAATCAAAAAC
TCAGAAAATAAAAAAATTTTCAAAAACTGAATAA
Found at i:370713 original size:13 final size:13
Alignment explanation
Indices: 370695--370751 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
370685 TTCAACGATT
370695 TGTATCGATACAA
1 TGTATCGATACAA
370708 TGTATCGATACATAA
1 TGTATCGATAC--AA
370723 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
370740 TGTATCGATACA
1 TGTATCGATACA
370752 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:370732 original size:19 final size:18
Alignment explanation
Indices: 370708--370770 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
370698 ATCGATACAA
370708 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
370727 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
370740 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
370759 TGTATCGATACA
1 TGTATCGATACA
370771 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:370735 original size:32 final size:32
Alignment explanation
Indices: 370694--370778 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
370684 TTTCAACGAT
370694 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
370726 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
370758 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
370779 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:370841 original size:13 final size:13
Alignment explanation
Indices: 370823--370847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
370813 ATTACTCAAA
370823 TGTATCGATACAT
1 TGTATCGATACAT
370836 TGTATCGATACA
1 TGTATCGATACA
370848 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:370900 original size:52 final size:52
Alignment explanation
Indices: 370856--370984 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
370846 CACTGATCTT
370856 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
370908 TGTATCGATACATACAGGCAAATTTGCCCAGATATATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
370960 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATACAGGCAAATTT
370985 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:371852 original size:21 final size:21
Alignment explanation
Indices: 371828--371880 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
371818 CAGCCCATGA
371828 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
371849 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
371870 TTCATGCATTT
1 TTCATGCATTT
371881 ACAGCATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (21 bp):
TTCATGCATTTTGAGCTATGT
Found at i:374682 original size:128 final size:128
Alignment explanation
Indices: 374571--374886 Score: 309
Period size: 128 Copynumber: 2.5 Consensus size: 128
374561 AAATGAAGGG
* * ** *
374571 AAGTCTCCCGA-GTCTAAGCCAATGGGCAAAAGATTGAT-GA-GAAGTCTCTTGGGTCTAAGCCG
1 AAGTCT-CCGAGGTCTAAGCCAACGGGCAAAAGATTGATAAAGGAAGTCTCCCGAGTCTAAGCCG
* *
374633 ACAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTAAGCTGACAGGCAGACGAAAGATAGAA
65 ACAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTAAGCTGACAGGCAAACGAAAAATAGAA
* * * * * *
374697 AAGTCTCCTAGGTCTAAGCCGACGGGTAGATGATTGATAAAGGAAGTCTCCCGAGTCTAAGTCGA
1 AAGTCTCCGAGGTCTAAGCCAACGGGCAAAAGATTGATAAAGGAAGTCTCCCGAGTCTAAGCCGA
* * * *** * * * * * *
374762 CAGGCAGACAATTGATAAAGGAAGTATCTCAAGTCTAAGCCGA-TGAGCAGACGAAAGATGGAG
66 CAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTAAGCTGACAG-GCAAACGAAAAATAGAA
** * *
374825 AAGTCTCCTG-GGTCTAAGCTGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTAAGC
1 AAGTCTCC-GAGGTCTAAGCCAACGGGCAAAAGATTGATAAAGGAAGTCTCCCGAGTCTAAGC
374887 TAATGGGTAA
Statistics
Matches: 159, Mismatches: 26, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
125 3 0.02
126 28 0.18
127 2 0.01
128 126 0.79
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.20
Consensus pattern (128 bp):
AAGTCTCCGAGGTCTAAGCCAACGGGCAAAAGATTGATAAAGGAAGTCTCCCGAGTCTAAGCCGA
CAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTAAGCTGACAGGCAAACGAAAAATAGAA
Found at i:374701 original size:85 final size:85
Alignment explanation
Indices: 374612--374770 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 85
374602 GATTGATGAG
* * ** *
374612 AAGTCTCTTGGGTCTAAGCCGACAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTAAG-CTG
1 AAGTCTCCTAGGTCTAAGCCGACAGGCAAACAATTAATAAAGGAAGTCTCCCGAGTCTAAGTC-G
374676 ACAGGCAGACGAAAGATAGAA
65 ACAGGCAGACGAAAGATAGAA
* * * ** *
374697 AAGTCTCCTAGGTCTAAGCCGACGGGTAGATGATTGATAAAGGAAGTCTCCCGAGTCTAAGTCGA
1 AAGTCTCCTAGGTCTAAGCCGACAGGCAAACAATTAATAAAGGAAGTCTCCCGAGTCTAAGTCGA
374762 CAGGCAGAC
66 CAGGCAGAC
374771 AATTGATAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
85 61 0.98
86 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.20
Consensus pattern (85 bp):
AAGTCTCCTAGGTCTAAGCCGACAGGCAAACAATTAATAAAGGAAGTCTCCCGAGTCTAAGTCGA
CAGGCAGACGAAAGATAGAA
Found at i:374828 original size:85 final size:84
Alignment explanation
Indices: 374739--374952 Score: 270
Period size: 85 Copynumber: 2.5 Consensus size: 84
374729 ATTGATAAAG
* *
374739 GAAGTCTCCCGAGTCTAAGTCGACAGGCAGACAATTGATAAAGGAAGTATCTCAAGTCTAAGCCG
1 GAAGTCTCCCGAGTCTAAG-CGACAGGCAGACAATTGATAAAGGAAGTATCCCAAGTCTAAGCCA
*
374804 ATGAGCAGACGAAAGATGGA
65 ATGAGCAAACGAAAGATGGA
* * * * * * *
374824 GAAGTCTCCTGGGTCTAAGCTGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTAAGCTA
1 GAAGTCTCCCGAGTCTAAGC-GACAGGCAGACAATTGATAAAGGAAGTATCCCAAGTCTAAGCCA
* *
374889 ATGGGTAAACGAAAGATGGA
65 ATGAGCAAACGAAAGATGGA
*
374909 GAAGTCTCCCAAGTCTAAGCCGACAGGC--ACAATTGATAAAGGAA
1 GAAGTCTCCCGAGTCTAAG-CGACAGGCAGACAATTGATAAAGGAA
374953 ATCTCATGGG
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
83 15 0.14
84 1 0.01
85 93 0.85
86 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (84 bp):
GAAGTCTCCCGAGTCTAAGCGACAGGCAGACAATTGATAAAGGAAGTATCCCAAGTCTAAGCCAA
TGAGCAAACGAAAGATGGA
Found at i:374885 original size:43 final size:43
Alignment explanation
Indices: 374457--374957 Score: 257
Period size: 43 Copynumber: 11.8 Consensus size: 43
374447 ATCGAGCATG
* * * * * * *
374457 AGCCGACTGGCAAACGATTAATAACA-GAAGTCTCCTGGGACTG
1 AGCCGACGGGCAGACGATTGATAA-AGGAAGTCTCCCGAGTCTA
* * * * *
374500 AGCCGACGGGCAGATGATTGATAAAGAAAGTCTCCCAAGACTG
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* ** * * *** *
374543 AGCCTATAGGCAAATGAAAAATGAAGGGAAGTCTCCCGAGTCTA
1 AGCCGACGGGCAGACGATTGAT-AAAGGAAGTCTCCCGAGTCTA
* * * * * ** *
374587 AGCCAATGGGCAAAAGATTGAT-GA-GAAGTCTCTTGGGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* * * * ** *
374628 AGCCGACAGGCAAACAATTAATAAAGGAAGTCTCTTGGGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* * ** *
374671 AGCTGACAGGCAGACGAAAGATAGAA--AAGTCT-CCTAGGTCTA
1 AGCCGACGGGCAGACGATTGATA-AAGGAAGTCTCCCGA-GTCTA
* *
374713 AGCCGACGGGTAGATGATTGATAAAGGAAGTCTCCCGAGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* * * * * *
374756 AGTCGACAGGCAGACAATTGATAAAGGAAGTATCTCAAGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* * ** ** * *
374799 AGCCGATGAGCAGACGAAAGATGGA-GAAGTCTCCTGGGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
*
374841 AGCTGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
** * * * ** ** *
374884 AGCTAATGGGTAAACGAAAGATGGA-GAAGTCTCCCAAGTCTA
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
* * *
374926 AGCCGACAGGC--ACAATTGATAAAGGAAATCTC
1 AGCCGACGGGCAGACGATTGATAAAGGAAGTCTC
374958 ATGGGTCTAT
Statistics
Matches: 341, Mismatches: 106, Indels: 24
0.72 0.23 0.05
Matches are distributed among these distances:
40 7 0.02
41 39 0.11
42 82 0.24
43 176 0.52
44 37 0.11
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (43 bp):
AGCCGACGGGCAGACGATTGATAAAGGAAGTCTCCCGAGTCTA
Found at i:375858 original size:15 final size:15
Alignment explanation
Indices: 375840--375884 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
375830 GCATGATCGG
375840 ATGCCTATTGAAACC
1 ATGCCTATTGAAACC
375855 ATGCCTATTGAAACC
1 ATGCCTATTGAAACC
*
375870 ATACCTATTGAAACC
1 ATGCCTATTGAAACC
375885 TATGTCTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (15 bp):
ATGCCTATTGAAACC
Found at i:376726 original size:79 final size:77
Alignment explanation
Indices: 376606--377230 Score: 673
Period size: 79 Copynumber: 8.0 Consensus size: 77
376596 ATATTTCTCG
* * * *
376606 ATGAGAAATTTAATATTTTGGAGATAGTAAC-GGGGTTGGAGTATCCCCTTGAGAATAACGGGGT
1 ATGAGAAA-TCAATA-TTTGGAAATA-AAACTGGGGTTGGAGTATCCCCTCG-GAATAACGGGGT
376670 TGGAGTATCCCCGATT
62 TGGAGTATCCCCGATT
* * *
376686 ATGAAAAATCGATGATTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGGAGATAATGGGGTTG
1 ATGAGAAATCAAT-ATTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGGA-ATAACGGGGTTG
376751 GAGTATCCCCGATT
64 GAGTATCCCCGATT
* *
376765 ATGAGAAATTAATCTTT-----TAGAAA---GGGTTGGAGTATCCCCTCGGAAAATAACGGGGTT
1 ATGAGAAATCAATATTTGGAAATA-AAACTGGGGTTGGAGTATCCCCTCGG--AATAACGGGGTT
376822 GGAGTATCCCCGATT
63 GGAGTATCCCCGATT
* * * **
376837 GTGAAAAATCGATGATTTGGAAATAAAA-TCGGGACTGGAGTATCCCCTCGGAGATAACGGGGTT
1 ATGAGAAATCAAT-ATTTGGAAATAAAACT-GGGGTTGGAGTATCCCCTCGGA-ATAACGGGGTT
376901 GGAGTATCCCCGATT
63 GGAGTATCCCCGATT
* * * * * *
376916 ATGAGAAATTAATATTTTAGAAATAAAGCCGGGGTAGGAGTATCCCCTCGGAAATAATGGGGTTG
1 ATGAGAAATCAATA-TTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGG-AATAACGGGGTTG
376981 GAGTATCCCCGATT
64 GAGTATCCCCGATT
* * *
376995 GTGAAAAATCGATGATTTGGAAATAAAACCT-GGGTTGGAGTATCCCCTCGGAGATAACGGGGTT
1 ATGAGAAATCAAT-ATTTGGAAATAAAA-CTGGGGTTGGAGTATCCCCTCGGA-ATAACGGGGTT
377059 GGAGTATCCCCGATT
63 GGAGTATCCCCGATT
* ** * *
377074 ATGAGAAATTAATATTTTATAAAT-AAAGTCGGGGTAGGAGTATCCCCTCGGAAATAACGGGGTT
1 ATGAGAAATCAATA-TTTGGAAATAAAACT-GGGGTTGGAGTATCCCCTCGG-AATAACGGGGTT
377138 GGAGTATCCCCGATT
63 GGAGTATCCCCGATT
* * *
377153 ATGAGAAATCAATATTTTAGG-AATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
1 ATGAGAAATCAATA-TTT-GGAAATAAAACTGGGGTTGGAGTATCCCCTCG-GAATAACGGGGTT
377217 GGAGTATCCCCGAT
63 GGAGTATCCCCGAT
377231 GATTAACGGG
Statistics
Matches: 461, Mismatches: 55, Indels: 59
0.80 0.10 0.10
Matches are distributed among these distances:
71 20 0.04
72 34 0.07
73 6 0.01
74 3 0.01
77 4 0.01
78 17 0.04
79 345 0.75
80 32 0.07
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (77 bp):
ATGAGAAATCAATATTTGGAAATAAAACTGGGGTTGGAGTATCCCCTCGGAATAACGGGGTTGGA
GTATCCCCGATT
Found at i:377039 original size:158 final size:156
Alignment explanation
Indices: 376606--377230 Score: 885
Period size: 158 Copynumber: 4.0 Consensus size: 156
376596 ATATTTCTCG
* * * *
376606 ATGAGAAATTTAATATTTTGGAGATAGTAACGGGGTTGGAGTATCCCCT-TGAGAATAACGGGGT
1 ATGAGAAA-TTAATATTTTAGAAATA--AACGGGGTAGGAGTATCCCCTCGGA-AATAACGGGGT
376670 TGGAGTATCCCCGATTATGAAAAATCGATGATTTGGAAATAAAA-CTGGGGTTGGAGTATCCCCT
62 TGGAGTATCCCCGATTATGAAAAATCGATGATTTGGAAATAAAACCT-GGGTTGGAGTATCCCCT
*
376734 CGGAGATAATGGGGTTGGAGTATCCCCGATT
126 CGGAGATAACGGGGTTGGAGTATCCCCGATT
* *
376765 ATGAGAAATTAATCTTTTAG----AAA--GGGTTGGAGTATCCCCTCGGAAAATAACGGGGTTGG
1 ATGAGAAATTAATATTTTAGAAATAAACGGGGTAGGAGTATCCCCTCGG-AAATAACGGGGTTGG
* * *
376824 AGTATCCCCGATTGTGAAAAATCGATGATTTGGAAATAAAATC-GGGACTGGAGTATCCCCTCGG
65 AGTATCCCCGATTATGAAAAATCGATGATTTGGAAATAAAACCTGGG-TTGGAGTATCCCCTCGG
376888 AGATAACGGGGTTGGAGTATCCCCGATT
129 AGATAACGGGGTTGGAGTATCCCCGATT
*
376916 ATGAGAAATTAATATTTTAGAAATAAAGCCGGGGTAGGAGTATCCCCTCGGAAATAATGGGGTTG
1 ATGAGAAATTAATATTTTAGAAATAAA--CGGGGTAGGAGTATCCCCTCGGAAATAACGGGGTTG
*
376981 GAGTATCCCCGATTGTGAAAAATCGATGATTTGGAAATAAAACCTGGGTTGGAGTATCCCCTCGG
64 GAGTATCCCCGATTATGAAAAATCGATGATTTGGAAATAAAACCTGGGTTGGAGTATCCCCTCGG
377046 AGATAACGGGGTTGGAGTATCCCCGATT
129 AGATAACGGGGTTGGAGTATCCCCGATT
*
377074 ATGAGAAATTAATATTTTATAAATAAAGTCGGGGTAGGAGTATCCCCTCGGAAATAACGGGGTTG
1 ATGAGAAATTAATATTTTAGAAATAAA--CGGGGTAGGAGTATCCCCTCGGAAATAACGGGGTTG
* * * *
377139 GAGTATCCCCGATTATGAGAAATCAAT-ATTTTAGG-AATAAAGCCGGGGTTGGAGTATCCCCTC
64 GAGTATCCCCGATTATGAAAAATCGATGA-TTT-GGAAATAAAACCTGGGTTGGAGTATCCCCTC
* *
377202 GAAAATAACGGGGTTGGAGTATCCCCGAT
127 GGAGATAACGGGGTTGGAGTATCCCCGAT
377231 GATTAACGGG
Statistics
Matches: 430, Mismatches: 21, Indels: 31
0.89 0.04 0.06
Matches are distributed among these distances:
150 20 0.05
151 117 0.27
152 4 0.01
154 1 0.00
155 3 0.01
157 1 0.00
158 252 0.59
159 32 0.07
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (156 bp):
ATGAGAAATTAATATTTTAGAAATAAACGGGGTAGGAGTATCCCCTCGGAAATAACGGGGTTGGA
GTATCCCCGATTATGAAAAATCGATGATTTGGAAATAAAACCTGGGTTGGAGTATCCCCTCGGAG
ATAACGGGGTTGGAGTATCCCCGATT
Found at i:377245 original size:27 final size:27
Alignment explanation
Indices: 377182--377284 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
377172 GGAATAAAGC
*
377182 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTAT-CCC-CGATGAATAA
*
377210 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATGAATAA
*
377237 CGGGGTTGGAGTATCCCCGATGAAAAA
1 CGGGGTTGGAGTATCCCCGATGAATAA
* *
377264 TGGGGTAGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
377285 TGTGAAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.04
27 51 0.75
28 14 0.21
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATGAATAA
Found at i:377363 original size:52 final size:53
Alignment explanation
Indices: 377260--377398 Score: 198
Period size: 52 Copynumber: 2.7 Consensus size: 53
377250 TCCCCGATGA
* *
377260 AAAAT-GGGGTAGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAAT
1 AAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTTGGAAAT
377312 AAAATCGGGGTTGGAGTATCCCCGATTGTTG-AAAATTAGTG-TTTTTGGAAAT
1 AAAATCGGGGTTGGAGTATCCCCGATTG-TGAAAAATTAGTGTTTTTTGGAAAT
* *
377364 AAAACCGGGGTTGGAGTA--CCCGATTATGAAAAATT
1 AAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAATT
377399 GAGAAACTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
49 2 0.03
50 13 0.16
52 33 0.41
53 30 0.38
54 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (53 bp):
AAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTTGGAAAT
Found at i:379772 original size:13 final size:13
Alignment explanation
Indices: 379754--379779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379744 ACAAAGATCG
379754 ATGTATCGATACA
1 ATGTATCGATACA
379767 ATGTATCGATACA
1 ATGTATCGATACA
379780 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:379790 original size:21 final size:21
Alignment explanation
Indices: 379766--379807 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
379756 GTATCGATAC
379766 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
*
379787 AATGTATTGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
379808 GGCAGTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:379867 original size:13 final size:13
Alignment explanation
Indices: 379824--379905 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
379814 AGTTTCGTAG
*
379824 CGATATATTGTAT
1 CGATACATTGTAT
379837 CGATACAACTTATGTAT
1 CGATAC-A--T-TGTAT
379854 CGATACATTGTAT
1 CGATACATTGTAT
379867 CGATACAATACTTATGTAT
1 CGATAC---A--T-TGTAT
*
379886 CAATACATTGTAT
1 CGATACATTGTAT
379899 CGATACA
1 CGATACA
379906 ACACTTATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
13 27 0.48
14 3 0.05
16 4 0.07
17 11 0.20
18 1 0.02
19 10 0.18
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:379885 original size:32 final size:31
Alignment explanation
Indices: 379824--379924 Score: 159
Period size: 32 Copynumber: 3.2 Consensus size: 31
379814 AGTTTCGTAG
*
379824 CGATATATTGTATCGATAC-AACTTATGTAT
1 CGATACATTGTATCGATACAAACTTATGTAT
379854 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTGTATCGATACAA-ACTTATGTAT
*
379886 CAATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAA-ACTTATGTAT
379918 CGATACA
1 CGATACA
379925 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
30 18 0.28
31 1 0.02
32 46 0.71
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (31 bp):
CGATACATTGTATCGATACAAACTTATGTAT
Found at i:379886 original size:19 final size:18
Alignment explanation
Indices: 379832--379926 Score: 86
Period size: 19 Copynumber: 5.8 Consensus size: 18
379822 AGCGATATAT
379832 TGTATCGATAC-AACTTA
1 TGTATCGATACAAACTTA
379849 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
379862 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
*
379881 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
379894 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
379913 TGTATCGATACAAA
1 TGTATCGATACAAA
379927 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 23
0.72 0.02 0.26
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
17 11 0.17
18 3 0.05
19 23 0.36
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:380309 original size:78 final size:79
Alignment explanation
Indices: 380151--380329 Score: 256
Period size: 78 Copynumber: 2.3 Consensus size: 79
380141 ACATCGGGTA
* * *
380151 TTTGGGAAGGAAGGATATGATTGAGAATGTGTGTGAAGTGGCCCCATTTAGCCTTGTGATGCACC
1 TTTGGGAAAGAAGGATATGATTGAGAATATGTGGGAAGTGGCCCCATTTAGCCTTGTGATGCACC
380216 AATATCATTTGGTG
66 AATATCATTTGGTG
** *
380230 TTTGGGAAAGAAGGATATGATT-AGGAATATGTGGGAAGT-GCCCTTTTTGGCCTTGTGATGCAC
1 TTTGGGAAAGAAGGATATGATTGA-GAATATGTGGGAAGTGGCCCCATTTAGCCTTGTGATGCAC
*
380293 CAGTATCATCTT-GTG
65 CAATATCAT-TTGGTG
380308 TTTGGGAAAGAAGGATATGATT
1 TTTGGGAAAGAAGGATATGATT
380330 TGGAGTGAGA
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 55 0.60
79 36 0.40
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.32
Consensus pattern (79 bp):
TTTGGGAAAGAAGGATATGATTGAGAATATGTGGGAAGTGGCCCCATTTAGCCTTGTGATGCACC
AATATCATTTGGTG
Found at i:381054 original size:55 final size:55
Alignment explanation
Indices: 380988--381094 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
380978 TTCATTTGAT
* * *
380988 TTTTTTTTTACTTGAACACCTTTTCGAGTTTTCATCCAAGCATTGTCATTCAAAA
1 TTTTTTCTTACTTGAACACCCTTTCGAGTTTTCATCCAAGCATTGTAATTCAAAA
*
381043 TTTTTTCTTACTTGAACGCCCTTTCGAGTTTTCATCCAAGCATTGTAATTCA
1 TTTTTTCTTACTTGAACACCCTTTCGAGTTTTCATCCAAGCATTGTAATTCA
381095 TTTTTCATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.45
Consensus pattern (55 bp):
TTTTTTCTTACTTGAACACCCTTTCGAGTTTTCATCCAAGCATTGTAATTCAAAA
Found at i:381118 original size:19 final size:20
Alignment explanation
Indices: 381094--381132 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
381084 ATTGTAATTC
381094 ATTTTTCATTCATT-TTTTT
1 ATTTTTCATTCATTATTTTT
* *
381113 ATTTTTTATTTATTATTTTT
1 ATTTTTCATTCATTATTTTT
381133 TATGCATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTCATTCATTATTTTT
Found at i:382987 original size:20 final size:19
Alignment explanation
Indices: 382940--382990 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
382930 GTATTGATAC
** *
382940 ATTGTATCGATACATGTTC
1 ATTGTATCGATACACATTA
*
382959 ATAGTATCGATACACATTGA
1 ATTGTATCGATACACATT-A
382979 ATTGTATCGATA
1 ATTGTATCGATA
382991 TATAAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (19 bp):
ATTGTATCGATACACATTA
Found at i:389120 original size:13 final size:13
Alignment explanation
Indices: 389102--389126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389092 ACTGAAGTAA
389102 TGTATCGATACAT
1 TGTATCGATACAT
389115 TGTATCGATACA
1 TGTATCGATACA
389127 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:392754 original size:19 final size:20
Alignment explanation
Indices: 392714--392764 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
392704 TACAAGCCAA
*
392714 TGTATCGATACATATTTTTG
1 TGTATCGATACATATCTTTG
392734 TGTATCGATACATA-CTTTG
1 TGTATCGATACATATCTTTG
392753 TGTATCGATACA
1 TGTATCGATACA
392765 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATCTTTG
Found at i:395153 original size:4 final size:4
Alignment explanation
Indices: 395144--395184 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
395134 TTATAATAAT
*
395144 AATA AATA AATA AAT- ATTA AA-A AAT- AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
395185 TTTGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 8 0.25
4 24 0.75
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:395204 original size:25 final size:25
Alignment explanation
Indices: 395144--395204 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
395134 TTATAATAAT
* *
395144 AATAAATAAATAAATATTAAAAAAT
1 AATAAAAAAATAAATATTAAAAAAG
* *
395169 AATAAATAAATAAATATTTGAAAAAG
1 AATAAAAAAATAAATA-TTAAAAAAG
395195 AA-AAAAAAAT
1 AATAAAAAAAT
395205 CGAATTAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 23 0.72
26 9 0.28
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (25 bp):
AATAAAAAAATAAATATTAAAAAAG
Found at i:395277 original size:29 final size:29
Alignment explanation
Indices: 395243--395350 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
395233 TCATGCATTA
*
395243 CATTTCATGCATGCATCTCACGTAATTTT
1 CATTTCATGCATGCATTTCACGTAATTTT
* * *
395272 CATTTCATGCATGCATTTCTCATAATTGT
1 CATTTCATGCATGCATTTCACGTAATTTT
* *
395301 CATTTCATGCATGCATTTTACGTAATGTT
1 CATTTCATGCATGCATTTCACGTAATTTT
* *
395330 CATTGCATGCATTACATTTCA
1 CATTTCATGCA-TGCATTTCA
395351 TGCATGCATT
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 59 0.89
30 7 0.11
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (29 bp):
CATTTCATGCATGCATTTCACGTAATTTT
Found at i:395349 original size:43 final size:44
Alignment explanation
Indices: 395301--395398 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 44
395291 TCATAATTGT
* * *
395301 CATTTCATGCATGCATTTTACGTAATGTTCATTGCA-TGCATTA
1 CATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTA
* * *
395344 CATTTCATGCATGCATTTCACTTAATATTCATTTCATTACATTG
1 CATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTA
395388 C-TTTCATGCAT
1 CATTTCATGCAT
395399 TCATAATGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 42 0.88
44 6 0.12
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (44 bp):
CATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTA
Found at i:408863 original size:32 final size:32
Alignment explanation
Indices: 408807--408878 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
408797 ATTATGCATA
*
408807 AAAAAAAGAAAAATAAAATTAAAAAGAAAAAAG
1 AAAAAATGAAAAATAAAA-TAAAAAGAAAAAAG
* *
408840 GAAAAATGAAAAATGAAAA-AAAAAGAAAAACG
1 AAAAAATGAAAAAT-AAAATAAAAAGAAAAAAG
408872 AAAAAAT
1 AAAAAAT
408879 CAAATGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 18 0.53
33 12 0.35
34 4 0.12
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.08
Consensus pattern (32 bp):
AAAAAATGAAAAATAAAATAAAAAGAAAAAAG
Found at i:408874 original size:7 final size:6
Alignment explanation
Indices: 408809--408876 Score: 50
Period size: 7 Copynumber: 10.8 Consensus size: 6
408799 TATGCATAAA
* **
408809 AAAAAG AAAAAT AAAATT AAAAAG AAAAAAGG AAAAATG AAAAATG -AAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAA-G AAAAA-G AAAAA-G AAAAAG
408859 AAAAAG AAAAACG AAAAA
1 AAAAAG AAAAA-G AAAAA
408877 ATCAAATGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
5 4 0.08
6 23 0.44
7 24 0.46
8 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:410273 original size:42 final size:42
Alignment explanation
Indices: 410208--411028 Score: 286
Period size: 42 Copynumber: 19.6 Consensus size: 42
410198 TCCTACCCTC
* * * *
410208 AGTCTGCCTATCGACTTTAACCCTAGAAACTGCCTTATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * *** * **
410250 AGTCTGCTTGTTGGCTTTGACCCTGGAGAA-TTTTTTACCTTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGA-AACTGCCTTATCTAA
* * * * *
410292 AGTCTGTCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * *
410334 AGTTTGCCTGTCGACTTTGACCCTGGAGACTG-CTTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTT-ATCTAA
* * * *
410376 AGTCTGCCT-TCGGCTTTGACCCTGGAGACTTTCC-TACCCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAAC-TGCCTTA-TCTAA
* * * * *
410418 A-TCTACCCGTTGGCATTGACCTTGGAAACTGCCTTATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * * * * * **
410459 AGTCTACTTGTCAGCTTTGACTCTGAAAATTTTCC-TA-CTTTT
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAA-CTGCCTTATC-TAA
* * * * * * * *
410501 AGTTTGCCTGTCGGTTTTGACCATGTAGACTACCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * * * ** *
410543 AGTTTGCCTATCAGCTTTGACCTTGGAGACTTTCTTATCCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTAT-CTAA
*** * * * * * *
410586 A-TCTATTTGTCAGTTTTAACCCTGGATACTGCCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * ** * *
410627 AGTCTGCCTGTCGACTTTGACCTTGGAGACT-TTTCTACCCT-T
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCT-TA-TCTAA
* * * * *
410669 AGTCTGCCTTTCGACTTTGACCCTAGAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * * * **
410711 A-TCTGCCTTTCGGCTTTGACCCTAGAGACTTTCC-TACCTTTC
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAAC-TGCCTTATC-TAA
* * * * * *
410753 AGTCTGCCTGTTGGCTTTAACCCTTGAGACTGCCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * ** * * *
410795 AGTCTGTCTATCGGCTTTGACTTTGGAGATTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * ** * *
410837 AGTCTGTCTGTCGGCTTTGACCTTGGAGACT-TTTCTACCCT-C
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCT-TA-TCTAA
* * * * * *
410879 AGTCTGCTTATCGACTTTGACCCTGGAGACTGTCTTACCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* * * ** * *
410921 AGTCTGCCTGTTGGCTTTAACCCTGGAGACTTTCTTACTTTCA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTA-TCTAA
* * * * * * * *
410964 A-TTTGCCTATCGGCTTTGACCCTAGAGATTGCCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
* *
411005 AGTCTACCTATCGGCTTTGACCCT
1 AGTCTGCCTGTCGGCTTTGACCCT
411029 TTTTTACCTT
Statistics
Matches: 571, Mismatches: 179, Indels: 58
0.71 0.22 0.07
Matches are distributed among these distances:
41 81 0.14
42 444 0.78
43 46 0.08
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAAACTGCCTTATCTAA
Found at i:410380 original size:84 final size:83
Alignment explanation
Indices: 410243--410951 Score: 398
Period size: 84 Copynumber: 8.5 Consensus size: 83
410233 GAAACTGCCT
* * * *** * * ** *
410243 TATCTAAAGTCTGCTTGTTGGCTTTGACCCTGGAGAATTTTTTACCTTCAGTCTGTCTGTCAGCT
1 TATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCT
*
410308 TTGACCTTGGAGACTGCC
66 TTGACCTTGGAGACTTCC
* * * *
410326 TCATCTAAAGTTTGCCTGTCGACTTTGACCCTGGAGACTGCTTCATCTAAAGTCTGCCT-TCGGC
1 T-ATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGC
*
410390 TTTGACCCTGGAGACTTTCC
65 TTTGACCTTGGAGAC-TTCC
* * * * * * * * * * *
410410 TACCCTTAA-TCTACCCGTTGGCATTGACCTTGGAAACTGCCTTATCTAAAGTCTACTTGTCAGC
1 TA-TCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGC
* * *
410474 TTTGA-CTCTGAAAATTTTCC
65 TTTGACCT-TGGAGA-CTTCC
** * * * * * * * *
410494 TA-CTTTTAGTTTGCCTGTCGGTTTTGACCATGTAGACTACCTCATCTCAAGTTTGCCTATCAGC
1 TATC-TAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGC
*
410558 TTTGACCTTGGAGACTTTCT
65 TTTGACCTTGGAGAC-TTCC
* *** * * * * *
410578 TATCCTCAA-TCTATTTGTCAGTTTTAACCCTGGATACTGCCTCATTTAAAGTCTGCCTGTC-GA
1 TAT-CTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAG-
*
410641 CTTTGACCTTGGAGACTTTTC
64 CTTTGACCTTGGAGAC-TTCC
* * * * * * *
410662 TACCCT-TAGTCTGCCTTTCGACTTTGACCCTAGAGACTGCCTCATCTAAA-TCTGCCTTTCGGC
1 TA-TCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGC
* *
410725 TTTGACCCTAGAGACTTTCC
65 TTTGACCTTGGAGAC-TTCC
* ** * * * * * * *
410745 TACCTTTCAGTCTGCCTGTTGGCTTTAACCCTTGAGACTGCCTCATTTAAAGTCTGTCTATCGGC
1 TATC-TAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGC
*
410810 TTTGACTTTGGAGA-TTGCC
65 TTTGACCTTGGAGACTT-CC
* * ** * * * *
410829 TCATCTAAAGTCTGTCTGTCGGCTTTGACCTTGGAGACT-TTTCTACCCT-CAGTCTGCTTATC-
1 T-ATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTC-A-TCTAAAGTCTGCCTGTCA
* *
410891 GACTTTGACCCTGGAGACTGTCT
63 G-CTTTGACCTTGGAGACT-TCC
* * *
410914 TACCTAAAGTCTGCCTGTTGGCTTTAACCCTGGAGACT
1 TATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
410952 TTCTTACTTT
Statistics
Matches: 475, Mismatches: 125, Indels: 51
0.73 0.19 0.08
Matches are distributed among these distances:
82 3 0.01
83 98 0.21
84 340 0.72
85 32 0.07
86 2 0.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (83 bp):
TATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCT
TTGACCTTGGAGACTTCC
Found at i:410457 original size:125 final size:126
Alignment explanation
Indices: 410212--410461 Score: 299
Period size: 125 Copynumber: 2.0 Consensus size: 126
410202 ACCCTCAGTC
* *
410212 TGCCTATCGACTTTAACCCTAGAAACTGCCTTATCTAAAGTCTGCTTGTTGGCTTTGACCCTGGA
1 TGCCTATCGACTTTAACCCTAGAAACTGCCTTATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGA
** * ** * * *
410277 GAATTTTTTACCTTCAGTCTGTCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTT
66 GAATTTCCTACCTTCAATCTACCCGTCAGCATTGACCTTGGAAACTGCCTCATCTAAAGTT
* * * *
410338 TGCCTGTCGACTTTGACCCTGGAGACTG-CTTCATCTAAAGTCTGCCT-TCGGCTTTGACCCTGG
1 TGCCTATCGACTTTAACCCTAGAAACTGCCTT-ATCTAAAGTCTGCCTGTCGGCTTTGACCCTGG
* ** *
410401 AGACTTTCCTACCCTT-AATCTACCCGTTGGCATTGACCTTGGAAACTGCCTTATCTAAAGT
65 AGAATTTCCTA-CCTTCAATCTACCCGTCAGCATTGACCTTGGAAACTGCCTCATCTAAAGT
410462 CTACTTGTCA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
125 62 0.60
126 42 0.40
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (126 bp):
TGCCTATCGACTTTAACCCTAGAAACTGCCTTATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGA
GAATTTCCTACCTTCAATCTACCCGTCAGCATTGACCTTGGAAACTGCCTCATCTAAAGTT
Found at i:410757 original size:126 final size:124
Alignment explanation
Indices: 410627--411026 Score: 333
Period size: 126 Copynumber: 3.2 Consensus size: 124
410617 CCTCATTTAA
* * *
410627 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTTAGTCTGCCTTTCGACTTTGACCC
1 AGTCTGCCTATCGACTTTGACCTTGGAGAC-TGTCTACCCTTAGTCTGCCTTTCGGCTTTGACCC
* *
410692 TAGAGACTGCCTCATCTAAATCTGCCTTTCGGCTTTGACCCTAGAGACTTTCCTACCTTTC
65 TGGAGACTGCCTCATCTAAATCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTACC-TTC
* * * * * ** * *
410753 AGTCTGCCTGTTGGCTTTAACCCTT-GAGACTGCCT-CATTTAAAGTCTGTCTATCGGCTTTGAC
1 AGTCTGCCTATCGACTTTGA-CCTTGGAGACTGTCTACCCTT--AGTCTGCCTTTCGGCTTTGAC
** * * * * * * *
410816 TTTGGAGATTGCCTCATCTAAAGTCTGTCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTC
63 CCTGGAGACTGCCTCATCTAAA-TCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTACCTTC
* * * *
410879 AGTCTGCTTATCGACTTTGACCCTGGAGACTGTCTTA-CCTAAAGTCTGCCTGTT-GGCTTTAAC
1 AGTCTGCCTATCGACTTTGACCTTGGAGACTGTC-TACCCT-TAGTCTGCCT-TTCGGCTTTGAC
** * * * * * *
410942 CCTGGAGACTTTCTTACTTTCAATTTGCCTATCGGCTTTGACCCTAGAGA-TTGCCTCACCTTA
63 CCTGGAGACTGCCTCA-TCTAAATCTGCCTATCGGCTTTGACCCTAGAGACTTTCCT-ACCTTC
* *
411005 AGTCTACCTATCGGCTTTGACC
1 AGTCTGCCTATCGACTTTGACC
411027 CTTTTTTACC
Statistics
Matches: 210, Mismatches: 53, Indels: 22
0.74 0.19 0.08
Matches are distributed among these distances:
124 3 0.01
125 10 0.05
126 154 0.73
127 43 0.20
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (124 bp):
AGTCTGCCTATCGACTTTGACCTTGGAGACTGTCTACCCTTAGTCTGCCTTTCGGCTTTGACCCT
GGAGACTGCCTCATCTAAATCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTACCTTC
Found at i:410857 original size:168 final size:167
Alignment explanation
Indices: 410292--411028 Score: 569
Period size: 168 Copynumber: 4.4 Consensus size: 167
410282 TTTTACCTTC
* * * * * *
410292 AGTCTGTCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTGCCTGTCGACTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCC
*
410357 TGGAGACTGCTTCATCTAAAGTCTGCC-TTCGGCTTTGACCCTGGAGACTTTCCTACCCTT-AAT
66 TGGAGACTGCCTCATCTAAA-TCTGCCTTTCGGCTTTGACCCTGGAGACTTTCCTA-CCTTCAAT
* * * * * * *
410420 CTACCCGTTGGCATTGACCTTGGAAACTGCCTTATCTAA
129 CTACCTGTTGGCTTTAACCCTGGAGACTGCCTCATTTAA
* * * * * * * ** * *
410459 AGTCTACTTGTCAGCTTTGA-CTCTGAAAATTTTCCT-ACTTTTAGTTTGCCTGTCGGTTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCT-TGGAGA-TTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGAC
* * * * * * * * *
410522 CATGTAGACTACCTCATCTCAAGTTTGCCTATCAGCTTTGACCTTGGAGACTTTCTTATCC-TCA
64 CCTGGAGACTGCCTCATCT-AAATCTGCCTTTCGGCTTTGACCCTGGAGACTTTCCTA-CCTTCA
** ** * *
410586 ATCTATTTGTCAGTTTTAACCCTGGATACTGCCTCATTTAA
127 ATCTACCTGTTGGCTTTAACCCTGGAGACTGCCTCATTTAA
* ** * * *
410627 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTTTCT-ACCCT-TAGTCTGCCTTTCGACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-TTGCCTCA-CCTAAAGTCTGCCTGTCGGCTTTGAC
* * *
410690 CCTAGAGACTGCCTCATCTAAATCTGCCTTTCGGCTTTGACCCTAGAGACTTTCCTACCTTTCAG
64 CCTGGAGACTGCCTCATCTAAATCTGCCTTTCGGCTTTGACCCTGGAGACTTTCCTACC-TTCAA
* *
410755 TCTGCCTGTTGGCTTTAACCCTTGAGACTGCCTCATTTAA
128 TCTACCTGTTGGCTTTAACCCTGGAGACTGCCTCATTTAA
* * * * * *
410795 AGTCTGTCTATCGGCTTTGACTTTGGAGATTGCCTCATCTAAAGTCTGTCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCC
** * * * * * * *
410860 TGGAGACT-TTTCTACCCTCAGTCTG-CTTATCGACTTTGACCCTGGAGACTGTCTTACC-TAAA
66 TGGAGACTGCCTC-A-TCTAAATCTGCCTT-TCGGCTTTGACCCTGGAGACTTTCCTACCTTCAA
* ** * *
410922 GTCTGCCTGTTGGCTTTAACCCTGGAGACTTTCTTACTTTCA
128 -TCTACCTGTTGGCTTTAACCCTGGAGACTGCCTCA-TTTAA
* * * * * * *
410964 A-TTTGCCTATCGGCTTTGACCCTAGAGATTGCCTCACCTTAAGTCTACCTATCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGATTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCC
411028 T
66 T
411029 TTTTTACCTT
Statistics
Matches: 445, Mismatches: 109, Indels: 31
0.76 0.19 0.05
Matches are distributed among these distances:
166 4 0.01
167 104 0.23
168 296 0.67
169 41 0.09
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (167 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGATTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCC
TGGAGACTGCCTCATCTAAATCTGCCTTTCGGCTTTGACCCTGGAGACTTTCCTACCTTCAATCT
ACCTGTTGGCTTTAACCCTGGAGACTGCCTCATTTAA
Found at i:411572 original size:4 final size:4
Alignment explanation
Indices: 411563--411609 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
411553 TTATAATAAT
*
411563 AATA AATA AATA AA-A ATTA AA-A AAT- AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
411608 AA
1 AA
411610 AATTTGAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 8 0.21
4 30 0.79
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:411594 original size:25 final size:26
Alignment explanation
Indices: 411560--411611 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
411550 CATTTATAAT
*
411560 AATAATAAATAAATAAA-AATTAAAA
1 AATAATAAATAAATAAATAAATAAAA
411585 AATAATAAATAAATAAATAAATAAAA
1 AATAATAAATAAATAAATAAATAAAA
411611 A
1 A
411612 TTTGAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (26 bp):
AATAATAAATAAATAAATAAATAAAA
Found at i:411612 original size:25 final size:24
Alignment explanation
Indices: 411555--411612 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
411545 TTTAACATTT
*
411555 ATAATAATAATAAATAAATAAAAA
1 ATAAAAATAATAAATAAATAAAAA
*
411579 TTAAAAAATAATAAATAAATAAATAA
1 AT-AAAAATAATAAATAAATAAA-AA
411605 ATAAAAAT
1 ATAAAAAT
411613 TTGAGAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 25 0.86
26 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
ATAAAAATAATAAATAAATAAAAA
Found at i:411708 original size:29 final size:29
Alignment explanation
Indices: 411676--411776 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
411666 TTACATTTCG
*
411676 TGCATGCATCTCACGTAATTTTCATTCCA
1 TGCATGCATTTCACGTAATTTTCATTCCA
* * *
411705 TGCATGTATTTCACGTAATTTTTATTTCA
1 TGCATGCATTTCACGTAATTTTCATTCCA
* * *
411734 TGCATGCATTTTACGTAATGTTCATTGCA
1 TGCATGCATTTCACGTAATTTTCATTCCA
*
411763 TGCATTACATTTCA
1 TGCA-TGCATTTCA
411777 TGCATGCATT
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
29 53 0.88
30 7 0.12
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (29 bp):
TGCATGCATTTCACGTAATTTTCATTCCA
Found at i:411801 original size:43 final size:44
Alignment explanation
Indices: 411728--411824 Score: 126
Period size: 43 Copynumber: 2.2 Consensus size: 44
411718 CGTAATTTTT
* * *
411728 ATTTCATGCATGCATTTTACGTAATGTTCATTGCA-TGCATTAC
1 ATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTAC
* * *
411771 ATTTCATGCATGCATTTCACTTAATATTCATTTCATTACATTGC
1 ATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTAC
411815 -TTTCATGCAT
1 ATTTCATGCAT
411825 TCACAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 41 0.87
44 6 0.13
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (44 bp):
ATTTCATGCATGCATTTCACGTAATATTCATTGCATTACATTAC
Found at i:420524 original size:20 final size:19
Alignment explanation
Indices: 420469--420524 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
420459 AAAACCCTTA
*
420469 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
420489 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
420509 AATGTATCGATACATG
1 AAAGTATCGATACATG
420525 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:420601 original size:13 final size:13
Alignment explanation
Indices: 420583--420608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420573 TACAGCAAGT
420583 ATGTATCGATACA
1 ATGTATCGATACA
420596 ATGTATCGATACA
1 ATGTATCGATACA
420609 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:422858 original size:21 final size:21
Alignment explanation
Indices: 422825--422869 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
422815 TTGCAAGTTG
*
422825 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
422847 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
422867 AAA
1 AAA
422870 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:424693 original size:15 final size:15
Alignment explanation
Indices: 424673--424703 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
424663 TAAAAATGTC
*
424673 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
424688 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
424703 C
1 C
424704 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:426789 original size:20 final size:20
Alignment explanation
Indices: 426720--426799 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
426710 AATGTCCAAA
*
426720 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
426740 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
426765 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
* *
426785 TTGTATCAATACATT
1 ATGTATCGATACATT
426800 GTATCGATAC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 30 0.62
24 1 0.02
25 17 0.35
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:426803 original size:13 final size:13
Alignment explanation
Indices: 426785--426823 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
426775 ACATTTTTCT
426785 TTGTATCAATACA
1 TTGTATCAATACA
*
426798 TTGTATCGATACA
1 TTGTATCAATACA
*
426811 CTGTATCAATACA
1 TTGTATCAATACA
426824 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:426969 original size:21 final size:21
Alignment explanation
Indices: 426945--426991 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
426935 AAATCTTTTG
426945 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
426966 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
426986 CAAAAT
1 CAAAAT
426992 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:426988 original size:20 final size:19
Alignment explanation
Indices: 426947--426989 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
426937 ATCTTTTGCA
426947 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
426967 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
426987 AAA
1 AAA
426990 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:429384 original size:13 final size:13
Alignment explanation
Indices: 429366--429391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429356 TACAGCAAGT
429366 ATGTATCGATACA
1 ATGTATCGATACA
429379 ATGTATCGATACA
1 ATGTATCGATACA
429392 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:439482 original size:22 final size:22
Alignment explanation
Indices: 439452--439508 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
439442 AGCCTAGCTT
*
439452 TTCTATTTTTTTCTATATTTTC
1 TTCTTTTTTTTTCTATATTTTC
* * *
439474 TTCTTTTTTTCTCTCTCTTTTC
1 TTCTTTTTTTTTCTATATTTTC
*
439496 TCTCTTCTTTTTT
1 T-TCTTTTTTTTT
439509 GCTGAACTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTTTTTTTCTATATTTTC
Found at i:439499 original size:13 final size:12
Alignment explanation
Indices: 439469--439506 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
439459 TTTTTCTATA
*
439469 TTTTCT-TCTTT
1 TTTTCTCTCTTC
439480 TTTTCTCTC-TC
1 TTTTCTCTCTTC
439491 TTTTCTCTCTTC
1 TTTTCTCTCTTC
439503 TTTT
1 TTTT
439507 TTGCTGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTCTCTTC
Found at i:440266 original size:183 final size:180
Alignment explanation
Indices: 439951--440318 Score: 522
Period size: 183 Copynumber: 2.0 Consensus size: 180
439941 CTTTGTGTAA
* ** * *
439951 GAAAATCAATACATACAAAAATATCAAAATTAATGAAATAAATTAATTTTTTCAAAACTGAGTTA
1 GAAAATCAATACATACAAAAAAATCAAAATTAATGAAATAAATTAAAATTTTCAAAACTAAATTA
* * * *
440016 ATGGGACTTCAATAACAATATTAGATGCATTTTAAAAATTTTAGACCAAATAAGATCCCCTCGAA
66 ATGGGACATCAATAACAATATTAGATACATTTTAAAAATTTTAGACCAAAAAAAATCCCCTCGAA
* *
440081 AATATTCATGGAGTAGGAAACTCGGTTTGTCAGAGAAAGGGGATTTTAAG
131 AATATTCATGGAGTAGGAAACTCGGTTTGTCAGAGAAAGGAGATTTCAAG
*
440131 GAAAATCAATATATACAAAAAAAAATTCAAAATTAATGAAATAAATTAAAATTTTCAAAACTAAA
1 GAAAATCAATACATAC--AAAAAAA-TCAAAATTAATGAAATAAATTAAAATTTTCAAAACTAAA
* * *
440196 TTAATGGGAGATCAATGACATTATTAGATACATTTTAAAAATTTTAGACCAAAAAAAAT-CCCTC
63 TTAATGGGACATCAATAACAATATTAGATACATTTTAAAAATTTTAGACCAAAAAAAATCCCCT-
* * * *
440260 CGAAAATATTTATGGAGTAGGAAACTTGGTTTTTCGGAGAAAGGAGATTTCAAG
127 CGAAAATATTCATGGAGTAGGAAACTCGGTTTGTCAGAGAAAGGAGATTTCAAG
440314 GAAAA
1 GAAAA
440319 ATTCAAAATT
Statistics
Matches: 165, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
180 15 0.09
182 10 0.06
183 140 0.85
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (180 bp):
GAAAATCAATACATACAAAAAAATCAAAATTAATGAAATAAATTAAAATTTTCAAAACTAAATTA
ATGGGACATCAATAACAATATTAGATACATTTTAAAAATTTTAGACCAAAAAAAATCCCCTCGAA
AATATTCATGGAGTAGGAAACTCGGTTTGTCAGAGAAAGGAGATTTCAAG
Found at i:440524 original size:162 final size:163
Alignment explanation
Indices: 440303--440746 Score: 553
Period size: 166 Copynumber: 2.7 Consensus size: 163
440293 TCGGAGAAAG
* * * * * * *
440303 GAGATTTCAAGGAAAAATTCAAAATTCATGGAAATAAATGAATTTTTAAAAATTGAATTAATATG
1 GAGATTTCAAGAAAAAAATCAAAAATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATG
* * *
440368 AAATAAATAACAATATTTGGTGACTTTTAAAAATTAAAAATCAAGAAAAATCCCC-CTGAAAAAT
66 AAATAAATAA-AATATTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTC-AAAAAAT
* *
440432 ACA-G-AGT-GAAAA-ACTCCGTATTTCGAAAAAAAA
129 ACACGAAATAGAAAACA-T-CGTATTTCAAAAAAAAA
*
440465 GAGATTTC-AGAAAAAAATCAAAAATGAATGAAAATGAATGAATTTTTGAAAACTGAATTAATAT
1 GAGATTTCAAGAAAAAAATCAAAAAT-CATGAAAATGAATGAATTTTTGAAAACTGAATTAATAT
* *
440529 GAAATAACTTAAAATATTTGATGAATTTTAAAAATTAAAAA-CTAAGAAAAATTCCCTCAAAAAA
65 GAAATAA-ATAAAATATTTGATGAATTTTAAAAATTAAAAATC-AAGAAAAATCCCCTCAAAAAA
* *
440593 TTCACGAAATAGAAAACATTGTATTTCAAAAAAAAA
128 TACACGAAATAGAAAACATCGTATTTCAAAAAAAAA
*
440629 GAGAATTTCAAGAAAAAAATCAAAAACTCATGAAAATGAAT-ACATTTTTGAAAACGGAATTAAT
1 GAG-ATTTCAAGAAAAAAATCAAAAA-TCATGAAAATGAATGA-ATTTTTGAAAACTGAATTAAT
* *
440693 ATGAAATAAATAAAAATATTTGATGAATTTTAAAAATTAAAAATTAAAAAAAAT
63 ATGAAATAAAT-AAAATATTTGATGAATTTTAAAAATTAAAAATCAAGAAAAAT
440747 TCCTTCTGAA
Statistics
Matches: 246, Mismatches: 22, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
161 15 0.06
162 95 0.39
163 5 0.02
164 20 0.08
165 13 0.05
166 97 0.39
167 1 0.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (163 bp):
GAGATTTCAAGAAAAAAATCAAAAATCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATG
AAATAAATAAAATATTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCAAAAAATAC
ACGAAATAGAAAACATCGTATTTCAAAAAAAAA
Found at i:442933 original size:23 final size:24
Alignment explanation
Indices: 442886--442935 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
442876 TAAAAATTAT
*
442886 TAAAATTATATTTATATTAAATAA
1 TAAAATTATATTTATAGTAAATAA
442910 TAAAATTATATTTAT-GTAAATAA
1 TAAAATTATATTTATAGTAAATAA
442933 TAA
1 TAA
442936 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAATTATATTTATAGTAAATAA
Found at i:442957 original size:30 final size:31
Alignment explanation
Indices: 442865--442958 Score: 75
Period size: 33 Copynumber: 2.9 Consensus size: 31
442855 TGTGTTTATG
* *
442865 TAATAAATAATTAAAAATTATTAAAAT-TATAT
1 TAAT-AATAAATAAAAATTATT-AAATGTATAA
* * **
442897 TTATATTAAATAATAAAATTATATTTATGTA-AA
1 TAATAATAAAT-A-AAAATTAT-TAAATGTATAA
442930 TAATAATAAATAAAAATTATTAAATGTAT
1 TAATAATAAATAAAAATTATTAAATGTAT
442959 TTATATTAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
30 6 0.13
31 13 0.28
32 5 0.11
33 20 0.43
34 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
TAATAATAAATAAAAATTATTAAATGTATAA
Found at i:444739 original size:42 final size:42
Alignment explanation
Indices: 444683--444764 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
444673 AAGTATATAT
*
444683 ATAATAAATAAT-AAATA-ATTATTAAAATTTTATTTATATTAA
1 ATAATAAATAATAAAATATA-AATTAAAATTTTATTT-TATTAA
444725 ATAATAAA-ATATAAAATATAAATTAAAATTTTATTTTATT
1 ATAATAAATA-ATAAAATATAAATTAAAATTTTATTTTATT
444765 TTATTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 1 0.03
42 14 0.39
43 20 0.56
44 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
ATAATAAATAATAAAATATAAATTAAAATTTTATTTTATTAA
Found at i:444872 original size:33 final size:33
Alignment explanation
Indices: 444789--444873 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 33
444779 ATATATATTT
* *
444789 ATATTTATATGAAAAATAAAATATATATTAAAATT
1 ATATTTATATTAAAAAT--AATATATATTAAAATG
*
444824 ATACTTATATT--AAATAATA-ATGATTAAAATG
1 ATATTTATATTAAAAATAATATAT-ATTAAAATG
*
444855 CTATTTATATTAAAAATAA
1 ATATTTATATTAAAAATAA
444874 CTTAATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
30 2 0.05
31 21 0.50
33 10 0.24
35 9 0.21
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (33 bp):
ATATTTATATTAAAAATAATATATATTAAAATG
Found at i:444905 original size:26 final size:26
Alignment explanation
Indices: 444864--444928 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
444854 GCTATTTATA
**
444864 TTAAAAATAACTTAA-TAAAATAAATT
1 TTAAAAATAAAATAATTAAAA-AAATT
444890 TTAAAAATAAAATAATTTAAAAAAATT
1 TTAAAAATAAAATAA-TTAAAAAAATT
*
444917 TAAATAAATAAA
1 TTAA-AAATAAA
444929 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 13 0.39
27 8 0.24
28 12 0.36
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
TTAAAAATAAAATAATTAAAAAAATT
Found at i:444906 original size:17 final size:17
Alignment explanation
Indices: 444877--444912 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
444867 AAAATAACTT
444877 AATAAAATAAATTTTAAA
1 AATAAAATAAA-TTTAAA
444895 AATAAAAT-AATTTAAA
1 AATAAAATAAATTTAAA
444911 AA
1 AA
444913 AATTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAAATAAATTTAAA
Found at i:444915 original size:18 final size:18
Alignment explanation
Indices: 444877--444913 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
444867 AAAATAACTT
*
444877 AATAAAATAAATTTTAAA
1 AATAAAATAAATTTAAAA
444895 AATAAAAT-AATTTAAAA
1 AATAAAATAAATTTAAAA
444912 AA
1 AA
444914 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATAAATTTAAAA
Found at i:444934 original size:41 final size:41
Alignment explanation
Indices: 444864--444941 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
444854 GCTATTTATA
444864 TTAAAAATAACTTAATAAAATAAATTTTAAAAATAAAATAAT
1 TTAAAAATAACTTAATAAAATAAATTTTAAAAA-AAAATAAT
*
444906 TTAAAAA-AATTTAA-ATAAATAAATTTTAAAAAAAAA
1 TTAAAAATAACTTAATA-AAATAAATTTTAAAAAAAAA
444942 GTGATGGAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
40 5 0.15
41 22 0.65
42 7 0.21
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (41 bp):
TTAAAAATAACTTAATAAAATAAATTTTAAAAAAAAATAAT
Found at i:445096 original size:6 final size:6
Alignment explanation
Indices: 445085--445135 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
445075 TTATTAAAAA
* * * *
445085 ATTTAT ATTTAT ATTAAT ATTAAT A-TTA- ATATAT ATTTAT ATTTAA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
445131 ATTTA
1 ATTTA
445136 AATAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
4 1 0.03
5 4 0.11
6 33 0.87
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTTAT
Found at i:445421 original size:25 final size:25
Alignment explanation
Indices: 445376--445437 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
445366 AAAATATTAG
* *
445376 ATTAATATGTATATATAATTAAATA
1 ATTAAAATATATATATAATTAAATA
*
445401 ATTAAAAT-TATATTTATATTAAATA
1 ATTAAAATATATATATA-ATTAAATA
445426 A-TAAAATATATA
1 ATTAAAATATATA
445438 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAAAATATATATATAATTAAATA
Found at i:448611 original size:2 final size:2
Alignment explanation
Indices: 448604--448631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
448594 TATAAGCATT
448604 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
448632 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:448636 original size:2 final size:2
Alignment explanation
Indices: 448631--448661 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
448621 ACACACACAC
*
448631 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
448662 AGCACCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:450422 original size:33 final size:33
Alignment explanation
Indices: 450380--450461 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
450370 TACACAAAGT
450380 ATGTATCGATACATTGTATCAATACACCATAAA
1 ATGTATCGATACATTGTATCAATACACCATAAA
*
450413 ATGTATCGATACATTGTATCGATACACCATAAA
1 ATGTATCGATACATTGTATCAATACACCATAAA
450446 ATGTATCGATACATTG
1 ATGTATCGATACATTG
450462 GCTTGTAACG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACATTGTATCAATACACCATAAA
Found at i:450432 original size:13 final size:13
Alignment explanation
Indices: 450414--450438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450404 CACCATAAAA
450414 TGTATCGATACAT
1 TGTATCGATACAT
450427 TGTATCGATACA
1 TGTATCGATACA
450439 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:450452 original size:20 final size:20
Alignment explanation
Indices: 450394--450458 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
450384 ATCGATACAT
*
450394 TGTATCAATACACCATAAAA
1 TGTATCGATACACCATAAAA
450414 TGTATCGAT--A-CAT----
1 TGTATCGATACACCATAAAA
450427 TGTATCGATACACCATAAAA
1 TGTATCGATACACCATAAAA
450447 TGTATCGATACA
1 TGTATCGATACA
450459 TTGGCTTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 9 0.24
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
20 20 0.54
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACCATAAAA
Found at i:452651 original size:84 final size:84
Alignment explanation
Indices: 452490--452654 Score: 197
Period size: 84 Copynumber: 2.0 Consensus size: 84
452480 ACTCAAAGAA
* * * * *
452490 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
* *
452555 TATGAAAGAGTTGCAAAAT
66 TAAGAAAAAGTTGCAAAAT
* * * * * *
452574 GAAAGTAAATCAATGAGTTTAGAAAATAATTTTTTTAAAAAGAAAATAAATGAATTAGAGGAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
452639 -AAGAAATAAGTTGCAA
66 TAAGAAA-AAGTTGCAA
452655 GTGGAAAATG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 5 0.07
84 62 0.93
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAAAGTTGCAAAAT
Found at i:454247 original size:17 final size:17
Alignment explanation
Indices: 454225--454259 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
454215 TATCAAATCC
454225 AACAGTCCCATTCAAAA
1 AACAGTCCCATTCAAAA
*
454242 AACAGTCCCATTTAAAA
1 AACAGTCCCATTCAAAA
454259 A
1 A
454260 TTCAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.26, G:0.06, T:0.20
Consensus pattern (17 bp):
AACAGTCCCATTCAAAA
Found at i:455020 original size:14 final size:14
Alignment explanation
Indices: 455001--455028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
454991 CGTATTAAGG
455001 GGGAGAGTTTGTAT
1 GGGAGAGTTTGTAT
455015 GGGAGAGTTTGTAT
1 GGGAGAGTTTGTAT
455029 AAATTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (14 bp):
GGGAGAGTTTGTAT
Found at i:456208 original size:13 final size:13
Alignment explanation
Indices: 456190--456214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
456180 ACACAAAGTA
456190 TGTATCGATACAT
1 TGTATCGATACAT
456203 TGTATCGATACA
1 TGTATCGATACA
456215 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:456211 original size:32 final size:33
Alignment explanation
Indices: 456170--456237 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
456160 GTAGCCAAAC
*
456170 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
456202 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
456235 TTG
1 TTG
456238 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:461653 original size:21 final size:22
Alignment explanation
Indices: 461620--461662 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
461610 TAATTAATAT
*
461620 ATAAATATAAAAT-ATTTTTAA
1 ATAAAAATAAAATAATTTTTAA
*
461641 ATAAAAATTAAATAATTTTTAA
1 ATAAAAATAAAATAATTTTTAA
461663 TCAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAAAATAAAATAATTTTTAA
Found at i:462880 original size:21 final size:22
Alignment explanation
Indices: 462848--462900 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
462838 ACTAGCATTC
*
462848 ATAAAT-ATAAAAATT-TATTT
1 ATAAATCATAAAAATTATACTT
*
462868 ATTAATCATAAAAATTATACTT
1 ATAAATCATAAAAATTATACTT
462890 ATAAATCATAA
1 ATAAATCATAA
462901 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 14 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATCATAAAAATTATACTT
Found at i:462933 original size:13 final size:13
Alignment explanation
Indices: 462903--462933 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
462893 AATCATAATT
*
462903 AAAAATATATTAA
1 AAAAATATATAAA
462916 AAAAATATATAAA
1 AAAAATATATAAA
462929 AAAAA
1 AAAAA
462934 AAACTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATATATAAA
Found at i:463843 original size:16 final size:17
Alignment explanation
Indices: 463814--463845 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
463804 TGAGTTAAAT
463814 TAAATTATTTTAAATTG
1 TAAATTATTTTAAATTG
463831 TAAATTA-TTTAAATT
1 TAAATTATTTTAAATT
463846 ATTTTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAATTATTTTAAATTG
Found at i:463858 original size:17 final size:17
Alignment explanation
Indices: 463838--463902 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
463828 TTGTAAATTA
463838 TTTAAATTATTTTTTAG
1 TTTAAATTATTTTTTAG
* *
463855 TTTAAATAATTTTATA-
1 TTTAAATTATTTTTTAG
* *
463871 TTTAGATTA-TTTTAAG
1 TTTAAATTATTTTTTAG
*
463887 TTTAAATTAATTTTTA
1 TTTAAATTATTTTTTA
463903 AATTAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 4 0.11
16 15 0.39
17 19 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTAAATTATTTTTTAG
Found at i:463873 original size:33 final size:33
Alignment explanation
Indices: 463836--463900 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
463826 AATTGTAAAT
*
463836 TATTTAAATTATTTTTTAGTTTAAA-TAATTTTA
1 TATTTAAATTA-TTTTAAGTTTAAATTAATTTTA
*
463869 TATTTAGATTATTTTAAGTTTAAATTAATTTT
1 TATTTAAATTATTTTAAGTTTAAATTAATTTT
463901 TAAATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (33 bp):
TATTTAAATTATTTTAAGTTTAAATTAATTTTA
Found at i:463904 original size:12 final size:12
Alignment explanation
Indices: 463887--463913 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
463877 TTATTTTAAG
463887 TTTAAATTAATT
1 TTTAAATTAATT
463899 TTTAAATTAATT
1 TTTAAATTAATT
463911 TTT
1 TTT
463914 TTTAATTCAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATTAATT
Found at i:463917 original size:33 final size:32
Alignment explanation
Indices: 463842--463918 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 32
463832 AAATTATTTA
*
463842 AATTATTTTTT-AGTTTAAATAATTTTATATTT
1 AATT-TTTTTTAAGTTTAAATAATTTTATAATT
*
463874 AGA-TTATTTTAAGTTTAAATTAATTTT-TAAATT
1 A-ATTTTTTTTAAGTTTAAA-TAATTTTAT-AATT
463907 AATTTTTTTTAA
1 AATTTTTTTTAA
463919 TTCAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 5 0.14
32 12 0.32
33 20 0.54
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (32 bp):
AATTTTTTTTAAGTTTAAATAATTTTATAATT
Found at i:465211 original size:21 final size:20
Alignment explanation
Indices: 465176--465219 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
465166 TTATTTTATA
*
465176 AATAAAATTTATTTATAAATAT
1 AATAAAATATA-TT-TAAATAT
465198 AATAAAA-ATATTTAAATAT
1 AATAAAATATATTTAAATAT
465217 AAT
1 AAT
465220 TATCATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 2 0.10
21 2 0.10
22 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAAAATATATTTAAATAT
Found at i:465240 original size:17 final size:18
Alignment explanation
Indices: 465209--465242 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
465199 ATAAAAATAT
465209 TTAAATATAATTATCATG
1 TTAAATATAATTATCATG
465227 TTAAATAT-ATTATCAT
1 TTAAATATAATTATCAT
465243 TTTATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAAATATAATTATCATG
Found at i:465361 original size:16 final size:16
Alignment explanation
Indices: 465334--465375 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
465324 AAATAATAAA
*
465334 AAAATAAATTTAAATTT
1 AAAAT-AATTTAAATAT
465351 AAAATAATTTAAATAT
1 AAAATAATTTAAATAT
465367 AAAATAATT
1 AAAATAATT
465376 CGATCTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATAATTTAAATAT
Found at i:468210 original size:3 final size:3
Alignment explanation
Indices: 468202--468233 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
468192 TTTAGTAAGT
468202 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
468234 TACAAATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:468567 original size:10 final size:10
Alignment explanation
Indices: 468552--468581 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
468542 CATTTATGTG
468552 TGTTTTATAT
1 TGTTTTATAT
*
468562 TGTTTTATGT
1 TGTTTTATAT
468572 TGTTTTATAT
1 TGTTTTATAT
468582 ATGAAGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (10 bp):
TGTTTTATAT
Found at i:468629 original size:48 final size:48
Alignment explanation
Indices: 468535--468631 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 48
468525 AAAGTAGATT
* * *
468535 TGAAGTTCATTTATGTGTGTTTTATATTGTTTTATGTTGTTTTATATA
1 TGAAGTTCATTTATGTGTGTTTTATATTGTTTTATATTGATATATATA
468583 TGAAGTTCATTTATCG-GTGTTTTATATTGTTTTATATAT-ATATATATA
1 TGAAGTTCATTTAT-GTGTGTTTTATATTGTTTTATAT-TGATATATATA
468631 T
1 T
468632 ATATAATGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 42 0.95
49 2 0.05
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (48 bp):
TGAAGTTCATTTATGTGTGTTTTATATTGTTTTATATTGATATATATA
Found at i:468692 original size:18 final size:19
Alignment explanation
Indices: 468661--468712 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
468651 TTATATCAAT
*
468661 TATAT-AAATATTAAAATA
1 TATATAAAATTTTAAAATA
468679 -ATATAAAATTTT-AAATA
1 TATATAAAATTTTAAAATA
468696 TATATTAAAATTTTAAA
1 TATA-TAAAATTTTAAA
468713 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
18 9 0.31
19 9 0.31
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATAAAATTTTAAAATA
Found at i:468706 original size:19 final size:17
Alignment explanation
Indices: 468674--468715 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 17
468664 ATAAATATTA
468674 AAATAATATAAAATTTT
1 AAATAATATAAAATTTT
468691 AAATATATATTAAAATTTT
1 AAATA-ATA-TAAAATTTT
468710 AAATAA
1 AAATAA
468716 AAAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAATATAAAATTTT
Found at i:468737 original size:9 final size:9
Alignment explanation
Indices: 468720--468791 Score: 69
Period size: 9 Copynumber: 8.1 Consensus size: 9
468710 AAATAAAAAA
*
468720 ATATATATT
1 ATATTTATT
468729 ATATTTATT
1 ATATTTATT
*
468738 ATATTAATT
1 ATATTTATT
468747 ATATTTA--
1 ATATTTATT
*
468754 A-ATATATT
1 ATATTTATT
*
468762 ATATATATT
1 ATATTTATT
468771 ATATTATATTT
1 ATATT-TA-TT
468782 ATATTTATT
1 ATATTTATT
468791 A
1 A
468792 AAAATATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.08
7 1 0.02
8 1 0.02
9 36 0.68
10 4 0.08
11 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATATTTATT
Found at i:468762 original size:33 final size:35
Alignment explanation
Indices: 468722--468788 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 35
468712 ATAAAAAAAT
*
468722 ATATATTATATTTATTATATTA-A-TTATATTTAA
1 ATATATTATATATATTATATTATATTTATATTTAA
468755 ATATATTATATATATTATATTATATTTATATTTA
1 ATATATTATATATATTATATTATATTTATATTTA
468789 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 21 0.68
34 1 0.03
35 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
ATATATTATATATATTATATTATATTTATATTTAA
Found at i:468763 original size:24 final size:25
Alignment explanation
Indices: 468734--468802 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
468724 ATATTATATT
468734 TATTATATTAATTATATT-TAAATA
1 TATTATATTAATTATATTATAAATA
**
468758 TATTATA-TATATTATATTATATTTA
1 TATTATATTA-ATTATATTATAAATA
**
468783 TATT-TATTAAAAATATTATA
1 TATTATATTAATTATATTATA
468803 TTCATATTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 2 0.05
24 26 0.68
25 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATATTAATTATATTATAAATA
Found at i:468776 original size:38 final size:37
Alignment explanation
Indices: 468718--468803 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 37
468708 TTAAATAAAA
468718 AAATATA-TAT-TATATTTATTATA-TTA-ATTATATTT
1 AAATATATTATATATATTTATTATATTTATATT-TA-TT
468753 AAATATATTATATATATTATATTATATTTATATTTATT
1 AAATATATTATATATATT-TATTATATTTATATTTATT
*
468791 AAAAATATTATAT
1 AAATATATTATAT
468804 TCATATTAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
35 7 0.16
36 3 0.07
37 6 0.13
38 21 0.47
39 5 0.11
40 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (37 bp):
AAATATATTATATATATTTATTATATTTATATTTATT
Found at i:472148 original size:2 final size:2
Alignment explanation
Indices: 472137--472168 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
472127 AACAACATTG
472137 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
472169 TCTCTTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:472598 original size:14 final size:14
Alignment explanation
Indices: 472572--472608 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
472562 AATTTTTTTA
472572 TATATTA-AAAAAT
1 TATATTATAAAAAT
*
472585 TGTATTATAAAAAT
1 TATATTATAAAAAT
472599 TATATT-TAAA
1 TATATTATAAA
472609 TATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
TATATTATAAAAAT
Found at i:474231 original size:2 final size:2
Alignment explanation
Indices: 474224--474303 Score: 87
Period size: 2 Copynumber: 42.0 Consensus size: 2
474214 AAACACGATC
474224 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
* * * * *
474266 TT AT A- AA AT AT A- AA AT -T AT A- AT AT AA AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474304 TTTAAAATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:474285 original size:21 final size:21
Alignment explanation
Indices: 474267--474421 Score: 78
Period size: 19 Copynumber: 7.5 Consensus size: 21
474257 TATATATATT
474267 TATAAA-ATATAAAATTATAA
1 TATAAATATATAAAATTATAA
*
474287 TATAAATATATAAATATTTTAA
1 TATAAATATATAAA-ATTATAA
* ** *
474309 AATTTATATAATAAAA--ATTA
1 TATAAATAT-ATAAAATTATAA
474329 T-TAAAT-TATTAAAATT-T-A
1 TATAAATATA-TAAAATTATAA
*
474347 TATAAATATA-AAATATTTTAAA
1 TATAAATATATAAA-ATTAT-AA
** *
474369 TATATTTATAATATAAATAATATA
1 TATAAATAT-ATA-AAATTATA-A
474393 TATAAATATAT-AAA-TATAA
1 TATAAATATATAAAATTATAA
*
474412 TATAGATATA
1 TATAAATATA
474422 AATTGTATGC
Statistics
Matches: 102, Mismatches: 17, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 11 0.11
19 22 0.22
20 14 0.14
21 10 0.10
22 21 0.21
23 9 0.09
24 12 0.12
25 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
TATAAATATATAAAATTATAA
Found at i:474317 original size:60 final size:62
Alignment explanation
Indices: 474246--474423 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 62
474236 ATATATATAT
*
474246 ATATATATATATATATATATTTATAAAATATAAAATTATAATATAAATATATAAATATTTT-A
1 ATATATTTATATATATATATTTATAAAATATAAAATTATAATATAAATATA-AAATATTTTAA
* * *
474308 A-A-ATTTATATA-ATAAAAATTATTAAATTATTAAAATT-T-ATATAAATATAAAATATTTTAA
1 ATATATTTATATATAT-ATATTTA-TAAAATA-TAAAATTATAATATAAATATAAAATATTTTAA
* * *
474368 ATATATTTATAATATAAATAATATATATAAATATATAAA-TATAATATAGATATAAA
1 ATATATTTAT-ATATATAT-ATTTATA-AAATATA-AAATTATAATATAAATATAAA
474424 TTGTATGCAG
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
59 11 0.12
60 26 0.28
61 9 0.10
62 14 0.15
63 9 0.10
64 12 0.13
65 12 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.43
Consensus pattern (62 bp):
ATATATTTATATATATATATTTATAAAATATAAAATTATAATATAAATATAAAATATTTTAA
Found at i:474334 original size:33 final size:33
Alignment explanation
Indices: 474282--474390 Score: 105
Period size: 33 Copynumber: 3.2 Consensus size: 33
474272 AATATAAAAT
*
474282 TATAATATAAA-TATATAAATATTTTAAAATTTA
1 TATAATAAAAATTAT-TAAATATTTTAAAATTTA
*
474315 TATAATAAAAATTATTAAAT-TATTAAAATTTA
1 TATAATAAAAATTATTAAATATTTTAAAATTTA
* * *
474347 TATAAATATAAAATATTTTAAATATATTTATAATATA
1 TAT-AATA-AAAAT-TATTAAATAT-TTTAAAATTTA
*
474384 AATAATA
1 TATAATA
474391 TATATAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 14 0.22
33 19 0.30
34 8 0.13
35 7 0.11
36 5 0.08
37 10 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TATAATAAAAATTATTAAATATTTTAAAATTTA
Found at i:474347 original size:18 final size:18
Alignment explanation
Indices: 474320--474374 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
474310 ATTTATATAA
*
474320 TAAAAATTATTAAATTAT
1 TAAAATTTATTAAATTAT
474338 TAAAATTTATATAAA-TA-
1 TAAAATTTAT-TAAATTAT
474355 TAAAATATT-TTAAATATAT
1 TAAAAT-TTATTAAAT-TAT
474374 T
1 T
474375 TATAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 15 0.48
19 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTATTAAATTAT
Found at i:474362 original size:7 final size:8
Alignment explanation
Indices: 474345--474424 Score: 60
Period size: 8 Copynumber: 10.1 Consensus size: 8
474335 TATTAAAATT
474345 TATATAAA
1 TATATAAA
474353 TATA-AAA
1 TATATAAA
*
474360 TATTTTAAA
1 TA-TATAAA
**
474369 TATATTTA
1 TATATAAA
474377 TAATATAAA
1 T-ATATAAA
474386 TA-AT--A
1 TATATAAA
474391 TATATAAA
1 TATATAAA
474399 TATATAAA
1 TATATAAA
*
474407 TATAATATA
1 TAT-ATAAA
*
474416 GATATAAA
1 TATATAAA
474424 T
1 T
474425 TGTATGCAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
5 3 0.05
6 2 0.04
7 7 0.13
8 26 0.47
9 17 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:478164 original size:27 final size:28
Alignment explanation
Indices: 478110--478165 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
478100 ACATTCTTTT
* *
478110 TTGTTCTTTCATATATTTTTTTATTCAA
1 TTGTTCTTTCATATAATTTTTTACTCAA
* *
478138 TTGTT-TTTTATATAATTTTTTGCTCAA
1 TTGTTCTTTCATATAATTTTTTACTCAA
478165 T
1 T
478166 AAAAATTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.64
Consensus pattern (28 bp):
TTGTTCTTTCATATAATTTTTTACTCAA
Found at i:486727 original size:2 final size:2
Alignment explanation
Indices: 486720--486756 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
486710 ACTAATCATT
486720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
486757 GACCCATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:488352 original size:20 final size:23
Alignment explanation
Indices: 488318--488380 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 23
488308 AATATTTTTG
488318 ATATT-TTAATATAATAAATAAA-
1 ATATTATT-ATATAATAAATAAAT
488340 AT-TTATTAT-TAATATAATAAAT
1 ATATTATTATATAATA-AATAAAT
488362 ATAATTATTATATAATAAA
1 AT-ATTATTATATAATAAA
488381 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
22 6 0.17
24 9 0.26
25 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTATTATATAATAAATAAAT
Found at i:488355 original size:25 final size:25
Alignment explanation
Indices: 488319--488390 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
488309 ATATTTTTGA
488319 TATT-TTAATATAATAAATAAAATT
1 TATTATTAATATAATAAATAAAATT
*
488343 TATTATTAATATAATAAATATAA-T
1 TATTATTAATATAATAAATAAAATT
*
488367 TATTATATAATAAAAT-AATAAAAT
1 TATTAT-TAATATAATAAATAAAAT
488391 AAATTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 17 0.40
25 25 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTATTAATATAATAAATAAAATT
Found at i:488383 original size:21 final size:22
Alignment explanation
Indices: 488329--488383 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
488319 TATTTTAATA
*
488329 TAATA-AATAAAAT-TTATTAT
1 TAATATAATAAAATATAATTAT
488349 TAATATAAT-AAATATAATTAT
1 TAATATAATAAAATATAATTAT
488370 T-ATATAATAAAATA
1 TAATATAATAAAATA
488384 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATAATAAAATATAATTAT
Found at i:488395 original size:28 final size:25
Alignment explanation
Indices: 488328--488398 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 25
488318 ATATTTTAAT
* * *
488328 ATAATAAATAAAATTTATTATTAAT
1 ATAATAAATAAATTTTATTAATAAA
488353 ATAATAAATATAATTATTATATAATAAA
1 ATAATAAATA-AATT-TTAT-TAATAAA
488381 ATAATAAAATAAATTTTA
1 ATAAT-AAATAAATTTTA
488399 ATTATTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 10 0.26
26 3 0.08
27 7 0.18
28 14 0.36
29 5 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATAAATAAATTTTATTAATAAA
Found at i:489556 original size:32 final size:32
Alignment explanation
Indices: 489519--489581 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
489509 TTAATTGACA
*
489519 AAAAATTACTA-AATTGATTGACGAGTTCACGT
1 AAAAATTACTACAA-TGATTAACGAGTTCACGT
* *
489551 AAAAATTGCTACAATGATTAATGAGTTCACG
1 AAAAATTACTACAATGATTAACGAGTTCACG
489582 CATTTAGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (32 bp):
AAAAATTACTACAATGATTAACGAGTTCACGT
Found at i:489688 original size:8 final size:8
Alignment explanation
Indices: 489662--489724 Score: 56
Period size: 8 Copynumber: 8.0 Consensus size: 8
489652 CGTCACCTAT
489662 TATTATTA
1 TATTATTA
*
489670 TAATATTA
1 TATTATTA
489678 TATTATTA
1 TATTATTA
*
489686 TATTTTTA
1 TATTATTA
*
489694 T-TTTTTA
1 TATTATTA
* *
489701 AATTAATA
1 TATTATTA
**
489709 TAAGATTA
1 TATTATTA
489717 TATTATTA
1 TATTATTA
489725 ATAAAAGTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
7 6 0.14
8 36 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATTATTA
Found at i:489726 original size:19 final size:19
Alignment explanation
Indices: 489702--489742 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
489692 TATTTTTTAA
*
489702 ATTAATATAAGATTATATT
1 ATTAATAAAAGATTATATT
*
489721 ATTAATAAAAGTTTATATT
1 ATTAATAAAAGATTATATT
489740 ATT
1 ATT
489743 TTATATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTAATAAAAGATTATATT
Found at i:489769 original size:29 final size:29
Alignment explanation
Indices: 489714--489768 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
489704 TAATATAAGA
*
489714 TTATATTATTAATAAAAGTTTATATTATT
1 TTATATTAATAATAAAAGTTTATATTATT
489743 TTATATTAATAA-AAAA--TTATATTATT
1 TTATATTAATAATAAAAGTTTATATTATT
489769 AAGAGGCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 10 0.40
28 4 0.16
29 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTATATTAATAATAAAAGTTTATATTATT
Found at i:490021 original size:19 final size:19
Alignment explanation
Indices: 489997--490037 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
489987 ATTAATTTAA
*
489997 AATAATATAAACTTTTATT
1 AATAATATAAACTTATATT
*
490016 AATAATATAATCTTATATT
1 AATAATATAAACTTATATT
490035 AAT
1 AAT
490038 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATATAAACTTATATT
Done.