Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002254.1 Kokia drynarioides strain JFW-HI SEQ_114267, 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: 184989
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:667 original size:22 final size:23
Alignment explanation
Indices: 606--667 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
596 CTAGAGTAAG
*
606 TTATTTTGTTGTTGT-TTTCTTA
1 TTATTTTGTTGTTGTATTGCTTA
* * *
628 CTATTTTATTATTGTATTGC-TA
1 TTATTTTGTTGTTGTATTGCTTA
*
650 TTATTTTGTTGTTATATT
1 TTATTTTGTTGTTGTATT
668 TTTTATATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68
Consensus pattern (23 bp):
TTATTTTGTTGTTGTATTGCTTA
Found at i:6586 original size:9 final size:9
Alignment explanation
Indices: 6572--6611 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
6562 GTGAAATTTC
*
6572 ATAATTCGA
1 ATAATTTGA
6581 ATAATTTGA
1 ATAATTTGA
*
6590 ATCATTTGA
1 ATAATTTGA
*
6599 ATAATTTAA
1 ATAATTTGA
6608 ATAA
1 ATAA
6612 CAAATTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (9 bp):
ATAATTTGA
Found at i:6709 original size:18 final size:16
Alignment explanation
Indices: 6679--6723 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
6669 TCTCTCAACA
6679 AAAATTTTAAAAAATC
1 AAAATTTTAAAAAATC
*
6695 AAAATATTTATAAAAATTT
1 AAAAT-TTTA-AAAAA-TC
6714 AAAATTTTAA
1 AAAATTTTAA
6724 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 9 0.36
19 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAAAAATC
Found at i:8653 original size:11 final size:11
Alignment explanation
Indices: 8639--8670 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
8629 TTTTTATATA
8639 ATTATATTAAT
1 ATTATATTAAT
8650 ATTATATTAAT
1 ATTATATTAAT
8661 ATTTATATTA
1 A-TTATATTA
8671 GAGTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATATTAAT
Found at i:8692 original size:17 final size:18
Alignment explanation
Indices: 8642--8692 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
8632 TTATATAATT
*
8642 ATATTA-ATATTATATTA
1 ATATTATATATTATAGTA
*
8659 ATATT-TATATTAGAGTA
1 ATATTATATATTATAGTA
8676 ATATTATATATT-TAGTA
1 ATATTATATATTATAGTA
8693 TAAGTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
ATATTATATATTATAGTA
Found at i:17314 original size:186 final size:186
Alignment explanation
Indices: 16999--17368 Score: 535
Period size: 186 Copynumber: 2.0 Consensus size: 186
16989 AACCTAAAAG
* * * *
16999 GGATTTCACTCCTATTCCTTAGTAATCACTACTCAACCTATTGTTAATATCAAAGATTGCTCCGA
1 GGATTTCACTCCTATTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTCCGA
*
17064 CTCTTCGATTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAGGTATCTAAAACTTAGA
66 CTCTTCGATTTTCATAAAATACATTTGTCCTATACAAATTCAAACACAGGTATCTAAAACTTAGA
* * ***
17129 CCCAAATCCAAGCAATATAGATATCAAGCACAAGATTCATGGCAACTAGGCCAAAT
131 CCCAAATACAAGCAATATAGATATCAAACACAAGATTCAAAACAACTAGGCCAAAT
* * * *
17185 GGATTTCACTCCTTTTCCTTAGTAATCACAACTCACCCTATAGTTAGCATCATAGATAGCTCCGA
1 GGATTTCACTCCTATTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTCCGA
* * * * *
17250 CTCTTCGATTTTCATAAAATCCATTTGTCCTATACATATTCGAACA-TGAGTATCTAACACTTAG
66 CTCTTCGATTTTCATAAAATACATTTGTCCTATACAAATTCAAACACAG-GTATCTAAAACTTAG
* *
17314 ACCCAAATACAAGCAATATAGATATCAAACACTAGGTTCAAAACAACTAGGCCAA
130 ACCCAAATACAAGCAATATAGATATCAAACACAAGATTCAAAACAACTAGGCCAA
17369 GCAATCAACA
Statistics
Matches: 162, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
185 1 0.01
186 161 0.99
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (186 bp):
GGATTTCACTCCTATTCCTTAGTAATCACAACTCAACCTATAGTTAACATCAAAGATAGCTCCGA
CTCTTCGATTTTCATAAAATACATTTGTCCTATACAAATTCAAACACAGGTATCTAAAACTTAGA
CCCAAATACAAGCAATATAGATATCAAACACAAGATTCAAAACAACTAGGCCAAAT
Found at i:30381 original size:4 final size:4
Alignment explanation
Indices: 30372--30397 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30362 TTTATAAAAT
30372 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
30398 ATTAGACCTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:51680 original size:31 final size:31
Alignment explanation
Indices: 51638--51700 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
51628 ATCCAATAAT
*
51638 TTAAATAAAAACTTTCGAATACTTCACTGAC
1 TTAAATAAAAACTTTCAAATACTTCACTGAC
* * *
51669 TTAAATGAAAACTTTCAAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCAAATACTTCACTGAC
51700 T
1 T
51701 ATTTTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATACTTCACTGAC
Found at i:54916 original size:115 final size:115
Alignment explanation
Indices: 54714--54944 Score: 444
Period size: 115 Copynumber: 2.0 Consensus size: 115
54704 CTCAAATATA
*
54714 TAAATATAATAAATTTTAAATTATCACATCTACTTTTAACTCGGTGCATGCAAGCTTAGCTTTAT
1 TAAATATAATAAAATTTAAATTATCACATCTACTTTTAACTCGGTGCATGCAAGCTTAGCTTTAT
54779 TCCATTCCTTATATATTCTTTACCTTGAAAGCTAATTTTCAGCAAAAAGT
66 TCCATTCCTTATATATTCTTTACCTTGAAAGCTAATTTTCAGCAAAAAGT
*
54829 TAAATATAATAAAATTTAAATTATCACATCTACTTTTAACTCGGTGCATGCAAGCTTAGTTTTAT
1 TAAATATAATAAAATTTAAATTATCACATCTACTTTTAACTCGGTGCATGCAAGCTTAGCTTTAT
54894 TCCATTCCTTATATATTCTTTACCTTGAAAGCTAATTTTCAGCAAAAAGT
66 TCCATTCCTTATATATTCTTTACCTTGAAAGCTAATTTTCAGCAAAAAGT
54944 T
1 T
54945 GGGTTGGCAA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (115 bp):
TAAATATAATAAAATTTAAATTATCACATCTACTTTTAACTCGGTGCATGCAAGCTTAGCTTTAT
TCCATTCCTTATATATTCTTTACCTTGAAAGCTAATTTTCAGCAAAAAGT
Found at i:57689 original size:50 final size:50
Alignment explanation
Indices: 57614--57713 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
57604 AAAGTGGTTT
57614 TAAATTGTCTGAATTGTTTTCTGGTTGTAGTTTATGATATAACACAGAGA
1 TAAATTGTCTGAATTGTTTTCTGGTTGTAGTTTATGATATAACACAGAGA
57664 TAAATTGTCTGAATTGTTTTCTGGTTGTAGTTTATGATATAACACAGAGA
1 TAAATTGTCTGAATTGTTTTCTGGTTGTAGTTTATGATATAACACAGAGA
57714 GAAACATTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (50 bp):
TAAATTGTCTGAATTGTTTTCTGGTTGTAGTTTATGATATAACACAGAGA
Found at i:59946 original size:22 final size:22
Alignment explanation
Indices: 59921--59970 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
59911 TTGTTTTCAC
*
59921 ATTATTTTGCTA-TCATTTTGTT
1 ATTATTTTACTACT-ATTTTGTT
*
59943 ATTATATTACTACTATTTTGTT
1 ATTATTTTACTACTATTTTGTT
*
59965 GTTATT
1 ATTATT
59971 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (22 bp):
ATTATTTTACTACTATTTTGTT
Found at i:60780 original size:16 final size:17
Alignment explanation
Indices: 60759--60793 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
60749 GTTAGAGTGT
60759 AATTTTATTAATT-TAA
1 AATTTTATTAATTATAA
60775 AATTTTATTAATTATAA
1 AATTTTATTAATTATAA
60792 AA
1 AA
60794 AATTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTATTAATTATAA
Found at i:61654 original size:21 final size:22
Alignment explanation
Indices: 61613--61665 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
61603 AGTGAAATGA
61613 CAGCAAAACAGTGAAAAAATAG
1 CAGCAAAACAGTGAAAAAATAG
* * *
61635 TAGCAAAATAGTG-GAAAATAG
1 CAGCAAAACAGTGAAAAAATAG
61656 CAGCAAAACA
1 CAGCAAAACA
61666 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (22 bp):
CAGCAAAACAGTGAAAAAATAG
Found at i:65809 original size:20 final size:19
Alignment explanation
Indices: 65766--65810 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
65756 ATCATATTCG
*
65766 AATTAACATTTAAAGTCTA
1 AATTAACAATTAAAGTCTA
65785 AATTAACAATTATAAGT-TA
1 AATTAACAATTA-AAGTCTA
65804 ATATTAA
1 A-ATTAA
65811 AAAATTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTAACAATTAAAGTCTA
Found at i:67166 original size:2 final size:2
Alignment explanation
Indices: 67161--67194 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
67151 TTTTTATGAT
*
67161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67195 AGAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:70671 original size:166 final size:166
Alignment explanation
Indices: 70390--70806 Score: 622
Period size: 166 Copynumber: 2.5 Consensus size: 166
70380 TATGGACCAA
70390 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
1 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
* *
70455 TTTCTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCAAGACGTCTTCAATGGTTCTAACAGC
66 TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCAAGACGTCTTCAAGGGTTCTAACAGC
70520 AGCTATTGTGAACTTAC-AAATTTCTCCATAAACACT
131 AGCTATTGTGAACTTACAAAATTTCTCC-TAAACACT
** * *
70556 AGTTAATTAGAACGAGGAATAAGACCACAAAACAAAGCAAGCACAACATACAAACATGATACAAG
1 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
* * * ** *
70621 TTTGTTTTGCTAAAATCGAGTGCAACCGCCAATGTTTTTGAGATGTCTTCAAGGGTTCTAACAGC
66 TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCAAGACGTCTTCAAGGGTTCTAACAGC
*
70686 AGCTATTGTGAACTTACAAAATTTCTCCTAAGCACT
131 AGCTATTGTGAACTTACAAAATTTCTCCTAAACACT
* * *
70722 AGATAATTAGAATGAGGAA-AAGGACCATGAAACAAAGGTTGCAAACACAACATACAATCATGAC
1 AGTTAATTAGAACGAGGAATAA-GACCATGAAACAAA----GCAAACACAACATACAAACATGAC
70786 ACAAGTTTGTTTTGCTAAAAT
61 ACAAGTTTGTTTTGCTAAAAT
70807 TGCATATAAC
Statistics
Matches: 225, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
165 2 0.01
166 171 0.76
167 10 0.04
170 42 0.19
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (166 bp):
AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCAAGACGTCTTCAAGGGTTCTAACAGC
AGCTATTGTGAACTTACAAAATTTCTCCTAAACACT
Found at i:79717 original size:31 final size:29
Alignment explanation
Indices: 79644--79720 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
79634 TTTCTCTCAG
*
79644 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTACGTTTGAAAT
*
79673 GTTACGTTTTAGTCACTTACG-TT-AACAT
1 GTTACATTTTAGTCACTTACGTTTGAA-AT
79701 GTTGTAACATTTTAGTCACT
1 G-T-T-ACATTTTAGTCACT
79721 GAGCCATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 20 0.49
30 1 0.02
31 13 0.32
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTACGTTTGAAAT
Found at i:81150 original size:28 final size:28
Alignment explanation
Indices: 81102--81179 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
81092 AGACCCTTAT
* * *
81102 ATTTTTGGAAAATTCTCATTAAACATCTC-
1 ATTTTT-GAAAATTTTAATTAAA-ATCCCA
81131 ATTTTTGAAAATTTTAATT-AAATCCCAAA
1 ATTTTTGAAAATTTTAATTAAAATCCC--A
81160 ATTTTTGAAAATTTTAATTA
1 ATTTTTGAAAATTTTAATTA
81180 GCCTACCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.10
27 2 0.05
28 11 0.26
29 25 0.60
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (28 bp):
ATTTTTGAAAATTTTAATTAAAATCCCA
Found at i:99565 original size:192 final size:190
Alignment explanation
Indices: 99164--99856 Score: 779
Period size: 192 Copynumber: 3.7 Consensus size: 190
99154 AGCACATTGC
* * * * * *
99164 TATACTGACATAACACTCTCTAGAAAAGAATGTTCAGAACCTAGAAACTGATGTCTTTACGAGTA
1 TATACAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCTGGAAACCGATGTCTTTACGAGTA
* * * * *
99229 GCA-GTG---T-G-AACTC--ATGACTTGTATAATGAAATGTTTTTGATGTCTAGAGCATCCTTT
66 GGATGTGAATTCGTGACTCATATG-CTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCTTT
* * ** * * *
99286 TGATCGAAACCATATAAATG-TCCAGCTGCATATTATGAACTTGAATGAATGAAGCACGTTG
130 TGATTGAAGCCATATTCATGTTCTA-CTGCATATTATGAACTTGAATGAATGAAACATGTTG
* * *
99347 CTATACGGACGTAGCACCCTCTAGAAAAGAATGTTTA-AAACTGAGAAACCGATGTCTTTACGAG
1 -TATACAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCTG-GAAACCGATGTCTTTACGAG
* * * * * *
99411 CAGAGATGTGAA-TCTGCGACTTATATGCATTTATAATGAAATGTTTTCGATGTTTACAGCACCC
64 TAG-GATGTGAATTC-GTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCC
*
99475 GTTTTGGTTGAAGCCATATTCATGTTCTACTGCATATTATGAACTTGAATGAATGAAACATGTTG
127 -TTTTGATTGAAGCCATATTCATGTTCTACTGCATATTATGAACTTGAATGAATGAAACATGTTG
* *
99540 TATATCAG-CGTAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAAACGATGTCTTTACGAGT
1 TATA-CAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCTGGAAACCGATGTCTTTACGAGT
* * *
99604 AGGTATGGGAATTCGTGACGCATATGCTTTTATAATGAAATGTTTTC-AGTGTCTAAAGCACCCT
65 AGG-ATGTGAATTCGTGACTCATATGCTTTTATAATGAAATGTTTTCGA-TGTCTAGAGCACCCT
* * *
99668 TTTGATTGCAGCTATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGA-ATGTTG
128 TTTGATTGAAGCCATATTCATGTTCTACTGCATATTATGAACTTGAATGAATGAA-ACATGTTG
* * * * *
99731 --TGCCGACGCAACACCCTCTAGAAAAGAATGTTTAGAACCTGGAAACCAATGTCTTTATGAGTA
1 TATACAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCTGGAAACCGATGTCTTTACGAGTA
* *
99794 GCGAGGTGAATTCGTGACTCATATGCTTTTATACTGAAATGTTTTCGATGTCTAGAGCACCCT
66 G-GATGTGAATTCGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCT
99857 GCTTTATATT
Statistics
Matches: 433, Mismatches: 55, Indels: 37
0.82 0.10 0.07
Matches are distributed among these distances:
183 4 0.01
184 52 0.12
185 1 0.00
186 3 0.01
188 3 0.01
189 107 0.25
190 3 0.01
191 63 0.15
192 131 0.30
193 63 0.15
194 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (190 bp):
TATACAGACGTAACACCCTCTAGAAAAGAATGTTTAGAACCTGGAAACCGATGTCTTTACGAGTA
GGATGTGAATTCGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCTTTT
GATTGAAGCCATATTCATGTTCTACTGCATATTATGAACTTGAATGAATGAAACATGTTG
Found at i:99883 original size:163 final size:164
Alignment explanation
Indices: 99699--100019 Score: 445
Period size: 166 Copynumber: 2.0 Consensus size: 164
99689 GTTCTGCTGC
* *
99699 ATATTATGAACTTGAATGAATGAAG-A-AT-GTTGT-GCCGACGCAACACCCTCTAGAAAAGAAT
1 ATATTATGAACTTGAATGAATGAAGCACATCATT-TAACCGACGCAACACCCTCTAGAAAAGAAT
* * * **
99760 GTTTAGAACCTGGAAACCAATGTCTTTATGAGTAGC-GAGGTGAATTCGTGACTCATATGCTTTT
65 GTTTAGAACCCGGAAACCAATATCTTCACAAGTAGCTG-GGTGAATTCGTGACTCATATGCTTTT
99824 ATACTGAAATGTTTTCGATGTCTAGAGCACCCTGCTTT
129 A-A-TGAAATGTTTTCGATGTCTAGAGCACCCTGCTTT
* *
99862 ATATTATGAACTTGAATGAATGAAGCACATCATTTAACCGACGTAACACCCTCTAGAAAGGAATG
1 ATATTATGAACTTGAATGAATGAAGCACATCATTTAACCGACGCAACACCCTCTAGAAAAGAATG
* ** *
99927 TTTAGAACCCGGAAACCAATATCTTCACAAGTAGCTGTGTGAATTCGTGACTTGTATGGTTTTAA
66 TTTAGAACCCGGAAACCAATATCTTCACAAGTAGCTGGGTGAATTCGTGACTCATATGCTTTTAA
*
99992 TGAAATGTTTTTGATGTCTAGAGCACCC
131 TGAAATGTTTTCGATGTCTAGAGCACCC
100020 CTTTTGACTG
Statistics
Matches: 139, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
163 25 0.18
164 28 0.20
165 4 0.03
166 81 0.58
167 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (164 bp):
ATATTATGAACTTGAATGAATGAAGCACATCATTTAACCGACGCAACACCCTCTAGAAAAGAATG
TTTAGAACCCGGAAACCAATATCTTCACAAGTAGCTGGGTGAATTCGTGACTCATATGCTTTTAA
TGAAATGTTTTCGATGTCTAGAGCACCCTGCTTT
Found at i:100937 original size:55 final size:55
Alignment explanation
Indices: 100871--100981 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
100861 ACAAGGGGTG
100871 AGGATCAAATTTTTATAAATTAAAGTTGAAAGGATTAGTTTCTTGCGTTTTTGTA
1 AGGATCAAATTTTTATAAATTAAAGTTGAAAGGATTAGTTTCTTGCGTTTTTGTA
*
100926 AGGATCAAATTTTTATAAATTGAAGTTGAAAGGATTAGTTTCTTGCGTTTTTGTA
1 AGGATCAAATTTTTATAAATTAAAGTTGAAAGGATTAGTTTCTTGCGTTTTTGTA
100981 A
1 A
100982 AGTAGAAGGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (55 bp):
AGGATCAAATTTTTATAAATTAAAGTTGAAAGGATTAGTTTCTTGCGTTTTTGTA
Found at i:102198 original size:20 final size:21
Alignment explanation
Indices: 102154--102198 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
102144 AAAAATAAAA
*
102154 AAAATAAATTTTTATAATTTT
1 AAAATAAAGTTTTATAATTTT
*
102175 -AAATAAAGTTTTAT-TTTTT
1 AAAATAAAGTTTTATAATTTT
102194 AAAAT
1 AAAAT
102199 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAATAAAGTTTTATAATTTT
Found at i:104502 original size:55 final size:55
Alignment explanation
Indices: 104428--104539 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
104418 GTCCCTCCTA
* *
104428 AAAAAATTTAAGCAATTTAATTTCTGTCAATTTCAAAAGTGAGCAAACTAAGGAT
1 AAAAAATTTAAGCAATTTAATCTCTATCAATTTCAAAAGTGAGCAAACTAAGGAT
* * **
104483 AAAAATTTTGAGCAATTTAATCTCTATCAATTTTGAAAGTGAGCAAACTAAGGAT
1 AAAAAATTTAAGCAATTTAATCTCTATCAATTTCAAAAGTGAGCAAACTAAGGAT
104538 AA
1 AA
104540 TGAATCATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (55 bp):
AAAAAATTTAAGCAATTTAATCTCTATCAATTTCAAAAGTGAGCAAACTAAGGAT
Found at i:108422 original size:19 final size:18
Alignment explanation
Indices: 108383--108418 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
108373 ATTTTTAATT
* *
108383 TAAATTTTTTTATATTTA
1 TAAAATTTTTTAAATTTA
108401 TAAAATTTTTTAAATTTA
1 TAAAATTTTTTAAATTTA
108419 ATAATGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAAAATTTTTTAAATTTA
Found at i:109357 original size:31 final size:31
Alignment explanation
Indices: 109316--109384 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
109306 AAAAAAAAAC
* *
109316 TCAACGACTTAAATAAAAACATTCGAATAGT
1 TCAATGACTTAAATAAAAACATTCAAATAGT
* * *
109347 TCAATGACTTAGATAAAAACTTTTAAATAGT
1 TCAATGACTTAAATAAAAACATTCAAATAGT
*
109378 TTAATGA
1 TCAATGA
109385 TCATTTTGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (31 bp):
TCAATGACTTAAATAAAAACATTCAAATAGT
Found at i:110006 original size:30 final size:30
Alignment explanation
Indices: 109964--110045 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
109954 AGTTTATATC
109964 TTTATA-ATTTTTAAAAAATTAAA-TCAAAT
1 TTTATATATTTTT-AAAAATTAAAGTCAAAT
* *
109993 TTTATATATTTTTAAAAGTTAAAGTCTAAT
1 TTTATATATTTTTAAAAATTAAAGTCAAAT
*
110023 TTTATCAT-TTATTAAAAATTAAA
1 TTTAT-ATATTTTTAAAAATTAAA
110046 ATTATGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 15 0.33
30 29 0.63
31 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTATATATTTTTAAAAATTAAAGTCAAAT
Found at i:114516 original size:31 final size:33
Alignment explanation
Indices: 114480--114545 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 33
114470 TAAAATGGGG
* * *
114480 TTTTAGATTCTTTAAAAGTT-G-AAAAAACATT
1 TTTTAGATCCCTTAAAAGTTGGTAAAAAAAATT
*
114511 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAATT
1 TTTTAGATCCCTTAAAAGTTGGTAAAAAAAATT
114544 TT
1 TT
114546 GGGCCCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 17 0.59
32 1 0.03
33 11 0.38
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (33 bp):
TTTTAGATCCCTTAAAAGTTGGTAAAAAAAATT
Found at i:116557 original size:15 final size:14
Alignment explanation
Indices: 116537--116587 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 14
116527 TTTAAAATTA
116537 TTAAAATTATTTTGT
1 TTAAAATTATTTT-T
116552 TTAAAATATAATTTTT
1 TTAAAAT-T-ATTTTT
*
116568 TTTAAATTA-TTTT
1 TTAAAATTATTTTT
116581 TTAAAAT
1 TTAAAAT
116588 ATAAAATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 8 0.25
16 8 0.25
17 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:116571 original size:17 final size:15
Alignment explanation
Indices: 116537--116582 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
116527 TTTAAAATTA
*
116537 TTAAAATTATTTTGT
1 TTAAAATTATTTTTT
116552 TTAAAATATAATTTTTT
1 TTAAAAT-T-ATTTTTT
116569 TT-AAATTATTTTTT
1 TTAAAATTATTTTTT
116583 AAAATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 5 0.18
17 8 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTAAAATTATTTTTT
Found at i:116639 original size:29 final size:29
Alignment explanation
Indices: 116529--116639 Score: 100
Period size: 29 Copynumber: 3.7 Consensus size: 29
116519 CAAATAATTT
*
116529 TAAAATTATTAAAATTATTTTGTTTAAAATA
1 TAAAATTATT-AAATTAATTT-TTTAAAATA
** *
116560 TAATTTTTTTTAAATT-ATTTTTTAAAATA
1 TAA-AATTATTAAATTAATTTTTTAAAATA
** *
116589 TAAAATTACAAAAATTATTTTTTTAAAATAA
1 TAAAATTA-TTAAATTAATTTTTTAAAAT-A
116620 TAAAATTATTAAA-TAATTTT
1 TAAAATTATTAAATTAATTTT
116640 AATTTCCAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
28 2 0.03
29 23 0.37
30 17 0.27
31 17 0.27
32 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAATTATTAAATTAATTTTTTAAAATA
Found at i:128126 original size:31 final size:31
Alignment explanation
Indices: 128049--128251 Score: 148
Period size: 31 Copynumber: 6.6 Consensus size: 31
128039 TTGAAGTATC
*
128049 TAATTAGAATTTTTAAAAA-TTTAA-AGACT
1 TAATTAAAATTTTTAAAAATTTTAAGAGACT
* * *
128078 TATTTAGAATTTTTAAAAATTTTAAGAGACA
1 TAATTAAAATTTTTAAAAATTTTAAGAGACT
* * * *
128109 TAATTAAAACTTTTAAAAATTTTAAAAAGGCA
1 TAATTAAAATTTTTAAAAATTTT-AAGAGACT
* * * *
128141 TGA-TAAAAGATTTTCAAAATTTTGAGAGA-T
1 TAATTAAAA-TTTTTAAAAATTTTAAGAGACT
* * *
128171 CCAATTAAAATTTTTGAAACTTTTGAA-AGACT
1 -TAATTAAAATTTTTAAAAATTTT-AAGAGACT
* * * * *
128203 TAACTAATACTTTTAGAAATTTTAAGAGGCT
1 TAATTAAAATTTTTAAAAATTTTAAGAGACT
128234 TAATTAAAA-TTTTAAAAA
1 TAATTAAAATTTTTAAAAA
128252 GTTTCAAAGG
Statistics
Matches: 134, Mismatches: 31, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
29 18 0.13
30 15 0.11
31 74 0.55
32 27 0.20
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (31 bp):
TAATTAAAATTTTTAAAAATTTTAAGAGACT
Found at i:131826 original size:28 final size:28
Alignment explanation
Indices: 131769--131827 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
131759 TTTGATATTG
* *
131769 AGTAAATTAATTTTGTTTTTAATTTTAA
1 AGTAAATTAATTTTGTTGTTAATTTGAA
131797 AGTAAATTTAA-TTT-TTGTTAACTTTGAA
1 AGTAAA-TTAATTTTGTTGTTAA-TTTGAA
131825 AGT
1 AGT
131828 GAGTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.22
28 17 0.63
29 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (28 bp):
AGTAAATTAATTTTGTTGTTAATTTGAA
Found at i:132721 original size:61 final size:61
Alignment explanation
Indices: 132652--132775 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
132642 CTTTTATAGG
132652 TATATATATTAAAAATCAAGTTGTGGAAATTACTCATAATCCTCAGCTTTATATATATATA
1 TATATATATTAAAAATCAAGTTGTGGAAATTACTCATAATCCTCAGCTTTATATATATATA
* * *
132713 TATATATATTAAAAGTCAAGTTGTGGAAATTACTCGTAATCCTTAGCTTTATATATATATA
1 TATATATATTAAAAATCAAGTTGTGGAAATTACTCATAATCCTCAGCTTTATATATATATA
132774 TA
1 TA
132776 AAAGATATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (61 bp):
TATATATATTAAAAATCAAGTTGTGGAAATTACTCATAATCCTCAGCTTTATATATATATA
Found at i:134156 original size:43 final size:43
Alignment explanation
Indices: 134095--134195 Score: 184
Period size: 43 Copynumber: 2.3 Consensus size: 43
134085 AATGGGTCTG
134095 CTCACACGAGCTGTGAGTCGAGATGATAAACTACATGATGCAA
1 CTCACACGAGCTGTGAGTCGAGATGATAAACTACATGATGCAA
**
134138 CTCACACGAGCTGTGAGTCGAGATGATAAACTACATGATGCTG
1 CTCACACGAGCTGTGAGTCGAGATGATAAACTACATGATGCAA
134181 CTCACACGAGCTGTG
1 CTCACACGAGCTGTG
134196 GAAAATCCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (43 bp):
CTCACACGAGCTGTGAGTCGAGATGATAAACTACATGATGCAA
Found at i:146854 original size:18 final size:19
Alignment explanation
Indices: 146831--146877 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
146821 TAAATCTGTT
*
146831 AAAAAAAAC-AGATTGAAA
1 AAAAAAAACTAGATGGAAA
* *
146849 AAAAAAAACTTGATGGCAA
1 AAAAAAAACTAGATGGAAA
146868 AAAAAAAACT
1 AAAAAAAACT
146878 CAAAAATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAAAACTAGATGGAAA
Found at i:149287 original size:5 final size:5
Alignment explanation
Indices: 149274--149306 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
149264 GATTCAGCTC
*
149274 AATAA AATAC AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AATAA AAT
149307 TGAAAGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:150895 original size:18 final size:19
Alignment explanation
Indices: 150858--150895 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
150848 TTGTAAAATA
**
150858 TTTATTATATTATATTATT
1 TTTATTATATTATACAATT
150877 TTTA-TATATTATACAATT
1 TTTATTATATTATACAATT
150895 T
1 T
150896 ATAACACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATACAATT
Found at i:155353 original size:31 final size:32
Alignment explanation
Indices: 155317--155376 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
155307 TTAGACTAAA
155317 TTTGAGTATAAAAAATTTGA-TTTGAGATCGT
1 TTTGAGTATAAAAAATTTGAGTTTGAGATCGT
* **
155348 TTTGAGTTTAAATCATTTGAGTTTGAGAT
1 TTTGAGTATAAAAAATTTGAGTTTGAGAT
155377 TTGAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (32 bp):
TTTGAGTATAAAAAATTTGAGTTTGAGATCGT
Found at i:156601 original size:23 final size:24
Alignment explanation
Indices: 156575--156621 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
156565 AAAACTTTTG
*
156575 AAAATTCTCATTAAA-CCCTCAAA
1 AAAATTCTAATTAAATCCCTCAAA
* *
156598 AAAATTTTAATTAAATCTCTCAAA
1 AAAATTCTAATTAAATCCCTCAAA
156622 TTTTCTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAATTCTAATTAAATCCCTCAAA
Found at i:158007 original size:2 final size:2
Alignment explanation
Indices: 158000--158030 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
157990 AGCATAAGTG
158000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
158031 GGGTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:163436 original size:160 final size:157
Alignment explanation
Indices: 163171--163486 Score: 488
Period size: 160 Copynumber: 2.0 Consensus size: 157
163161 TATGCATTGA
* **
163171 GGTTCTGAGAGTCAAATGCTGCTTCCATCCATTGTTGATATGCCGGTTATTTTTGTGTGAATCTT
1 GGTTCTGAGAGTCAAATGCTGCTTCCATCCATTGTTAATATGCCGGTTATAGTTGTGTGAATCTT
** *
163236 GTGGTGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCACTCATCGTTAAACCGAACCTT
66 GTGGTGTCTGATATTAGTTCTTAACAAGATGTCATGTTTGCTCACTCAT-ATTAAACCGAACCTT
*
163301 CATCGTACTTATTGTGTATGGTTCTTTT
130 CATCGTACTTATTGTGTATGGTACTTTT
**
163329 GGTTCTGAGAGTCAAATGCTGCTTCCATCTGTTGTCTCAATATGCCGGTTATAGTTGTGTGAATC
1 GGTTCTGAGAGTCAAATGCTGCTTCCATCCATTGT-T-AATATGCCGGTTATAGTTGTGTGAATC
* * * *
163394 TTGTTGTGTCTGATGTTAGTTCTTAACAAGCTGTCATGTTTGCTCCCTCATATTAAACCGAACCT
64 TTGTGGTGTCTGATATTAGTTCTTAACAAGATGTCATGTTTGCTCACTCATATTAAACCGAACCT
163459 TCATCGTACTTATTGTGTATGGTACTTT
129 TCATCGTACTTATTGTGTATGGTACTTT
163487 CGTTTCTCTA
Statistics
Matches: 143, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
158 33 0.23
159 41 0.29
160 69 0.48
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (157 bp):
GGTTCTGAGAGTCAAATGCTGCTTCCATCCATTGTTAATATGCCGGTTATAGTTGTGTGAATCTT
GTGGTGTCTGATATTAGTTCTTAACAAGATGTCATGTTTGCTCACTCATATTAAACCGAACCTTC
ATCGTACTTATTGTGTATGGTACTTTT
Found at i:163761 original size:222 final size:221
Alignment explanation
Indices: 163329--164014 Score: 990
Period size: 222 Copynumber: 3.1 Consensus size: 221
163319 TGGTTCTTTT
* * **
163329 GGTTCTGAGAGTCAAATGCTGCTTCCAT-CTGTTGTCTCAATATGCCGGTTATAGTTGTGTGAAT
1 GGTTCTGAGAGTCAAATGCTGCTTCCATCCT-ATG--TCAGTATGCCGGTTATTTTTGTGTGAAT
* * * ** *
163393 CTTGTTGTGTCTGATGTTAGTTCTTAACAAGCTGTCATGTTTGCTCCCTCAT-ATTAAACCGAAC
63 CTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCGAAC
* *
163457 CTTCATCGTACTTATTGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAAGACTCGT
128 CTTCATCGTACTTATCGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAGGACTCGT
163522 TTAGTCCTTAGAATCGATTTTATGCATCGA
193 TTAGTCCTTA-AATCGATTTTATGCATCGA
* *
163552 GGTTCTGAGAGTCAAATGCTGCTTCAATCCTATGTCAGTATACCGGTTATTTTTGTGTGAATCTT
1 GGTTCTGAGAGTCAAATGCTGCTTCCATCCTATGTCAGTATGCCGGTTATTTTTGTGTGAATCTT
*
163617 GTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCAAACCTT
66 GTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCGAACCTT
* * * * * * *
163682 CATCGTACTTATCGTATATGATACTTTCATTTTTATAGCATCGTGTGAAAGCAAGGACTCATTTA
131 CATCGTACTTATCGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAGGACTCGTTTA
163747 GTCCTTACAATCGATTTTATGCATCGA
196 GTCCTTA-AATCGATTTTATGCATCGA
* * *
163774 GGTTCTGAGAGTCAAATGCTGCTTCCATCC-ATTGT-TGATATGCTGCTTATTTTTGTGTGAATC
1 GGTTCTGAGAGTCAAATGCTGCTTCCATCCTA-TGTCAG-TATGCCGGTTATTTTTGTGTGAATC
163837 TTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCGAACC
64 TTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCGAACC
*
163902 TTCATTGTACTTATCGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAGGACTCGTT
129 TTCATCGTACTTATCGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAGGACTCGTT
* *
163967 TAGTCCTT---TCGGTTTTATGCATTGA
194 TAGTCCTTAAATCGATTTTATGCATCGA
* *
163992 GGTTCTGAGGGTCAAATGTTGCT
1 GGTTCTGAGAGTCAAATGCTGCT
164015 CCTATCTGTT
Statistics
Matches: 418, Mismatches: 41, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
218 36 0.09
221 73 0.17
222 278 0.67
223 29 0.07
224 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (221 bp):
GGTTCTGAGAGTCAAATGCTGCTTCCATCCTATGTCAGTATGCCGGTTATTTTTGTGTGAATCTT
GTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTAAACCGAACCTT
CATCGTACTTATCGTGTATGGTACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAGGACTCGTTTA
GTCCTTAAATCGATTTTATGCATCGA
Found at i:165408 original size:17 final size:19
Alignment explanation
Indices: 165379--165414 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
165369 AATATTTTAT
165379 ATTATGTTATTTT-TATAA
1 ATTATGTTATTTTATATAA
165397 ATTATG-TATTTTATATAA
1 ATTATGTTATTTTATATAA
165415 CACATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTATGTTATTTTATATAA
Found at i:170992 original size:31 final size:30
Alignment explanation
Indices: 170951--171032 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
170941 TTTTGTGAGA
* * *
170951 TTAATGAAAATTTTGAAAATATTAGAAGAGT
1 TTAATGAAAATTTTAAAAAAATTAAAAGA-T
*
170982 TTAATTAAAATTTTCAAAAAAATTAAAAGAT
1 TTAATGAAAATTTT-AAAAAAATTAAAAGAT
* *
171013 ATAATGAAAATTTTCAAAAA
1 TTAATGAAAATTTTAAAAAA
171033 GGTAAGAGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 5 0.12
31 26 0.60
32 12 0.28
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (30 bp):
TTAATGAAAATTTTAAAAAAATTAAAAGAT
Found at i:171342 original size:23 final size:24
Alignment explanation
Indices: 171284--171345 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
171274 TGTCAGAATT
171284 AAATTATATATTTTTACGATAGTAA
1 AAATT-TATATTTTTACGATAGTAA
* **
171309 AAATGTA-ATTTTTAC-ATTTTAA
1 AAATTTATATTTTTACGATAGTAA
*
171331 TAATTTATATTTTTA
1 AAATTTATATTTTTA
171346 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 10 0.32
23 15 0.48
24 2 0.06
25 4 0.13
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (24 bp):
AAATTTATATTTTTACGATAGTAA
Found at i:184603 original size:233 final size:233
Alignment explanation
Indices: 184183--184625 Score: 717
Period size: 233 Copynumber: 1.9 Consensus size: 233
184173 GTTATTATGC
* * * *
184183 CAGTTTTTATTTTCGGGTTTCTCGAAGCATTTAGTACCTTTGTTGTAGTAGTTCTAGGAGGTGTC
1 CAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTAGTAGTTCTAGGAGGTATC
*
184248 TTGTTTGAGTAAGCGCTCGGACTATTGCTTCTCAGTCCAATTTTAGGCATAACAGGGAAAGAATC
66 TTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCAGTCCAATTTTAGGCATAACAGGGAAAGAATC
*
184313 CATACTCCGAGTTCGAGTGTGTCCAGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
131 CATACTCCGAGTTCCAGTGTGTCCAGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
184378 TGTATACTACTACTTGTATGAGATGTATACTGCTACTT
196 TGTATACTACTACTTGTATGAGATGTATACTGCTACTT
* * * *
184416 CAGTGTTTATTTTTGGCTTTCTCGATGCATTCAGTACCTTTGTTTTAGTAGTTCTAGTAGGTATC
1 CAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTAGTAGTTCTAGGAGGTATC
* * *
184481 TTGTTCGAGTAAGCGCTTGGACTATTGCTTCT-AGGTCCAATTTTAGGCATAAGAGGGTAAGAAT
66 TTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCA-GTCCAATTTTAGGCATAACAGGGAAAGAAT
* * * *
184545 CCATACTCTGAGTTCCAGTGTGTCCGGGTAATCTTTCCTGCATTTGTCGAATGATTTTGTAATAG
130 CCATACTCCGAGTTCCAGTGTGTCCAGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAG
184610 ATGTATACTACTACTT
195 ATGTATACTACTACTT
184626 CAGTGTTTAT
Statistics
Matches: 192, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
232 1 0.01
233 191 0.99
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (233 bp):
CAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTAGTAGTTCTAGGAGGTATC
TTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCAGTCCAATTTTAGGCATAACAGGGAAAGAATC
CATACTCCGAGTTCCAGTGTGTCCAGGTAATCTTTCCTGCATTTATCGAACGATTTTGTAATAGA
TGTATACTACTACTTGTATGAGATGTATACTGCTACTT
Found at i:184760 original size:210 final size:210
Alignment explanation
Indices: 184398--184832 Score: 717
Period size: 210 Copynumber: 2.1 Consensus size: 210
184388 TACTTGTATG
* * * *
184398 AGATGTATACTGCTACTTCAGTGTTTATTTTTGGCTTTCTCGATGCATTCAGTACCTTTGTTTTA
1 AGATGTATACTACTACTTCAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTA
*
184463 GTAGTTCTAGTAGGTATCTTGTTCGAGTAAGCGCTTGGACTATTGCTTCTAGGTCCAATTTTAGG
66 GTAGTTCTAGTAGGTATCTTGTTCGAGTAAGCGCTCGGACTATTGCTTCTAGGTCCAATTTTAGG
** * *
184528 CATAAGAGGGTAAGAATCCATACTCTGAGTTCCAGTGTGTCCGGGTAATCTTTCCTGCATTTGTC
131 CATAAGAGCATAAGAATCCATACTCTGAGTTCCAGTGTCTCCGGGTAATCTTTCCTGCATTTATC
*
184593 GAATGATTTTGTAAT
196 GAACGATTTTGTAAT
* *
184608 AGATGTATACTACTACTTCAGTGTTTATTTTCGGGTTTCTCGAAGCATTTAGTACCTTTGTTGTA
1 AGATGTATACTACTACTTCAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTA
* *
184673 GTAGTTCTAGTAGGTATCTTGTTCGAGTAAGCGCTCGGACTATTGCTTCTCGGTCCGATTTTAGG
66 GTAGTTCTAGTAGGTATCTTGTTCGAGTAAGCGCTCGGACTATTGCTTCTAGGTCCAATTTTAGG
* * *
184738 CATAATAGCATACGAATCCATACTCTGAGTTCGAGTGTCTCCGGGTAATCTTTCCTGCATTTATC
131 CATAAGAGCATAAGAATCCATACTCTGAGTTCCAGTGTCTCCGGGTAATCTTTCCTGCATTTATC
184803 GAACGATTTTGTAAT
196 GAACGATTTTGTAAT
184818 AGATGTATACTACTA
1 AGATGTATACTACTA
184833 ATTGTATGAG
Statistics
Matches: 208, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.39
Consensus pattern (210 bp):
AGATGTATACTACTACTTCAGTGTTTATTTTCGGCTTTCTCGAAGCATTCAGTACCTTTGTTGTA
GTAGTTCTAGTAGGTATCTTGTTCGAGTAAGCGCTCGGACTATTGCTTCTAGGTCCAATTTTAGG
CATAAGAGCATAAGAATCCATACTCTGAGTTCCAGTGTCTCCGGGTAATCTTTCCTGCATTTATC
GAACGATTTTGTAAT
Done.