Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015212.1 Kokia drynarioides strain JFW-HI SEQ_130256, 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: 177470
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:584 original size:30 final size:29
Alignment explanation
Indices: 519--717 Score: 212
Period size: 30 Copynumber: 6.8 Consensus size: 29
509 GAAGGTCCGT
*
519 AAACTATCCAAAAATTCCATTCTTACCCCCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCCCG
*
550 -AACTTCAAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
579 AAACTTCCAAAAATTCCATTTTT-CCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
*
608 -AACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
637 AAACTTCCAAAAATGCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
667 AAACTTTCAAAAATTACCA-TTTTACCCTC-
1 AAACTTCCAAAAATT-CCATTTTTACCC-CG
*
696 AAA-TGTCCAAAAACTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
718 CAACCTCAAA
Statistics
Matches: 148, Mismatches: 10, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
28 29 0.20
29 42 0.28
30 74 0.50
31 3 0.02
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:627 original size:58 final size:56
Alignment explanation
Indices: 519--717 Score: 199
Period size: 58 Copynumber: 3.4 Consensus size: 56
509 GAAGGTCCGT
* *
519 AAACTATCCAAAAATTCCATTCTTACCCCCGAACTTCAAAAAATTCCATTTTTGACCCC
1 AAACTATCCAAAAATTCCATT-TT-TCCCCGAACTTCCAAAAATTCCATTTTT-ACCCC
578 GAAACT-TCCAAAAATTCCATTTTTCCCTCGAACTTCCAAAAATTCCATTTTTAACCCC
1 -AAACTATCCAAAAATTCCATTTTTCCC-CGAACTTCCAAAAATTCCATTTTT-ACCCC
* * *
636 AAAACT-TCCAAAAATGCCATTTTTGACCCCAAAACTTTCAAAAATTACCA-TTTTACCCTC
1 -AAACTATCCAAAAATTCCATTTTT--CCCC-GAACTTCCAAAAATT-CCATTTTTACCC-C
* *
696 AAA-TGTCCAAAAACTCCATTTT
1 AAACTATCCAAAAATTCCATTTT
718 CAACCTCAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
57 3 0.02
58 53 0.43
59 38 0.31
60 26 0.21
61 3 0.02
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.31
Consensus pattern (56 bp):
AAACTATCCAAAAATTCCATTTTTCCCCGAACTTCCAAAAATTCCATTTTTACCCC
Found at i:826 original size:28 final size:28
Alignment explanation
Indices: 791--862 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
781 CCAAATTTTC
791 CCAAAATTACCATTTTGCCCCCAAAAAT
1 CCAAAATTACCATTTTGCCCCCAAAAAT
819 CCAAAATTACCATTTTGCCCCCAAAAAT
1 CCAAAATTACCATTTTGCCCCCAAAAAT
847 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
863 ACCTCTCGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.39, C:0.31, G:0.03, T:0.28
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCAAAAAT
Found at i:6316 original size:24 final size:24
Alignment explanation
Indices: 6284--6330 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
6274 CAACTTCGTG
*
6284 AAATCAAATACAATGAAGAAAAAAT
1 AAATCAAATACAA-AAAGAAAAAAT
*
6309 AAAT-AAATAGAAAAAGAAAAAA
1 AAATCAAATACAAAAAGAAAAAA
6331 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (24 bp):
AAATCAAATACAAAAAGAAAAAAT
Found at i:6374 original size:18 final size:17
Alignment explanation
Indices: 6320--6392 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 17
6310 AATAAATAGA
*
6320 AAAAGAAAAAAGAAGAAG
1 AAAAGCAAAAA-AAGAAG
*
6338 AAGAG-AAAGAAAA-AAG
1 AAAAGCAAA-AAAAGAAG
6354 AAAAGCAAAAACAAGAAG
1 AAAAGCAAAAA-AAGAAG
* *
6372 AAAAACAAAAATAGAA-
1 AAAAGCAAAAAAAGAAG
6388 AAAAG
1 AAAAG
6393 GGAGAGGTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
16 13 0.28
17 14 0.30
18 19 0.41
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.01
Consensus pattern (17 bp):
AAAAGCAAAAAAAGAAG
Found at i:6382 original size:31 final size:29
Alignment explanation
Indices: 6319--6391 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
6309 AAATAAATAG
* * * *
6319 AAAAAGAAAAAAGAAGAAGAAGAGAAAGA
1 AAAAAGAAAAAAAAACAAGAAGAAAAACA
6348 AAAAAGAAAAGCAAAAACAAGAAGAAAAACA
1 AAAAAGAAAA--AAAAACAAGAAGAAAAACA
6379 AAAATAGAAAAAA
1 AAAA-AGAAAAAA
6392 GGGAGAGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 10 0.27
30 2 0.05
31 19 0.51
32 6 0.16
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (29 bp):
AAAAAGAAAAAAAAACAAGAAGAAAAACA
Found at i:6392 original size:34 final size:36
Alignment explanation
Indices: 6313--6392 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 36
6303 AAAAATAAAT
*
6313 AAATAG-AAAAAGAAAAAAGAAGAAGAAGAGAAAGA
1 AAATAGAAAAAAGAAAAAACAAGAAGAAGAGAAAGA
* *
6348 AAA-A-AGAAAAGCAAAAACAAGAAGAA-A-AACA-A
1 AAATAGAAAAAAGAAAAAACAAGAAGAAGAGAA-AGA
6380 AAATAGAAAAAAG
1 AAATAGAAAAAAG
6393 GGAGAGGTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
32 6 0.16
33 3 0.08
34 25 0.68
35 3 0.08
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (36 bp):
AAATAGAAAAAAGAAAAAACAAGAAGAAGAGAAAGA
Found at i:7661 original size:51 final size:49
Alignment explanation
Indices: 7593--7928 Score: 227
Period size: 50 Copynumber: 6.7 Consensus size: 49
7583 TCAGTACCAT
* * * *
7593 GAAGATATGAAGGGAAAGGTCTACGTCGCAACGGCAAGACCATGTACCTCA
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGC-AGACC-TGTACCTCA
* * * * *
7644 GAAGACATGAAGGGAAAGATTTAAGCCACAACGGCGGATCTAGTACCCCA
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGACCT-GTACCTCA
* *
7694 -AAGATACA-AAAGGGAAATG-TCTAAGTCGCAACGGCAAGACCGTGTACCTCA
1 GAAG--ACATGAAGGGAAA-GATCTAAGCCGCAACGGC-AGACC-TGTACCTCA
* * * * *
7745 GAAGACACGAAGGGAAAGATTTAAGCCGCAACAGCAAATCTAGTA-C-CA
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGACCT-GTACCTCA
* * * * *
7793 TGAAGACATGAAGGGAACGATCTAAGACCGCAACAGCGGATCCAGTACCACA
1 -GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCAGA-CCTGTACCTCA
* * * * *
7845 -AAGATACA-AAAGGGAAAGGTTTAAGTCGCAACGGCAGACTGTGTACCTCA
1 GAAG--ACATGAAGGGAAAGATCTAAGCCGCAACGGCAGAC-CTGTACCTCA
* * *
7895 GAAGACAAGAAGGGAAAGATTTAAGCTGCAACGG
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGG
7929 TGAATCCAAT
Statistics
Matches: 222, Mismatches: 43, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
48 2 0.01
49 32 0.14
50 97 0.44
51 82 0.37
52 9 0.04
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGACCTGTACCTCA
Found at i:7786 original size:101 final size:101
Alignment explanation
Indices: 7602--7791 Score: 308
Period size: 101 Copynumber: 1.9 Consensus size: 101
7592 TGAAGATATG
* *
7602 AAGGGAAAGGTCTACGTCGCAACGGCAAGACCATGTACCTCAGAAGACATGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACACGAAGGGAAAGATTTA
* **
7667 AGCCACAACGGCGGATCTAGTACCCCAAAGATACAA
66 AGCCACAACAGCAAATCTAGTACCCCAAAGATACAA
* *
7703 AAGGGAAATGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACACGAAGGGAAAGATTTA
*
7768 AGCCGCAACAGCAAATCTAGTACC
66 AGCCACAACAGCAAATCTAGTACC
7792 ATGAAGACAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (101 bp):
AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACACGAAGGGAAAGATTTA
AGCCACAACAGCAAATCTAGTACCCCAAAGATACAA
Found at i:7826 original size:101 final size:99
Alignment explanation
Indices: 7585--7818 Score: 299
Period size: 101 Copynumber: 2.3 Consensus size: 99
7575 TACAGGTCTC
* *
7585 AGTACCATGAAGATATGAAGGGAAAGGTCTACGTCGCAACGGCAAGACCATGTACCTCAGAAGAC
1 AGTACCATGAAGACATGAAGGGAAA-GTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGAC
* * **
7650 ATGAAGGGAAAGATTTAAGCCACAACGGCGGATCT
65 ACGAAGGGAAAGATTTAAGCCACAACAGCAAATCT
*** * *
7685 AGTACCCCAAAGATACA-AAAGGGAAATGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAG
1 AGTACCATGAAG--ACATGAAGGGAAA-GTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAG
*
7749 ACACGAAGGGAAAGATTTAAGCCGCAACAGCAAATCT
63 ACACGAAGGGAAAGATTTAAGCCACAACAGCAAATCT
*
7786 AGTACCATGAAGACATGAAGGGAACGATCTAAG
1 AGTACCATGAAGACATGAAGGGAAAG-TCTAAG
7819 ACCGCAACAG
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
99 4 0.04
100 22 0.20
101 84 0.75
102 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (99 bp):
AGTACCATGAAGACATGAAGGGAAAGTCTAAGTCGCAACGGCAAGACCATGTACCTCAGAAGACA
CGAAGGGAAAGATTTAAGCCACAACAGCAAATCT
Found at i:7926 original size:150 final size:150
Alignment explanation
Indices: 7644--7926 Score: 451
Period size: 150 Copynumber: 1.9 Consensus size: 150
7634 ATGTACCTCA
* * * *
7644 GAAGACATGAAGGGAAAGATTTAAGCCACAACGGCGGATCTAGTACCCCAAAGATACAAAAGGGA
1 GAAGACATGAAGGGAAAGATCTAAGCCACAACAGCGGATCCAGTACCACAAAGATACAAAAGGGA
* *
7709 AATGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTAAGCCGC
66 AAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGC
7774 AACAGCAAATCTAGTACCAT
131 AACAGCAAATCTAGTACCAT
* *
7794 GAAGACATGAAGGGAACGATCTAAGACCGCAACAGCGGATCCAGTACCACAAAGATACAAAAGGG
1 GAAGACATGAAGGGAAAGATCTAAG-CCACAACAGCGGATCCAGTACCACAAAGATACAAAAGGG
* * *
7859 AAAGGTTTAAGTCGCAACGGC-AGACTGTGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCTG
65 AAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCG
7923 CAAC
130 CAAC
7927 GGTGAATCCA
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
150 67 0.55
151 54 0.45
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.14
Consensus pattern (150 bp):
GAAGACATGAAGGGAAAGATCTAAGCCACAACAGCGGATCCAGTACCACAAAGATACAAAAGGGA
AAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGC
AACAGCAAATCTAGTACCAT
Found at i:9001 original size:205 final size:205
Alignment explanation
Indices: 8597--9290 Score: 991
Period size: 205 Copynumber: 3.4 Consensus size: 205
8587 TTAGCTTCTC
* * * *
8597 GATGAGATACAGAGAAGCGGATTGAAACAGACGATACGATCATCTTCCTGATGAGATACTAAGAA
1 GATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTAATGAGATACTGAGAA
* * *
8662 GAAGACCAAATCAAACTCACGCTCGATATGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATT
66 GAAGACCAAATCAAACTCACGCTCGATATGAGAAAATCTTCGAA-CCCAGCTTCCTGATGAGATA
* *
8727 CTGAGAAGCAAGTCGAAGTAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
130 CTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
8792 TTCGTCTTCCT
195 TTCGTCTTCCT
* * *
8803 GATGAGATATAGAGAAGCGGATTGAAACAAACGATGCGGTCATCTT-TTAAATGAGATACTGAGA
1 GATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCT-AATGAGATACTGAGA
*
8867 AGAAGACCAAATCAAACTCACGCTTGATATGAGAAAATCTTCGAACCCAGCTTCCTGATGAGATA
65 AGAAGACCAAATCAAACTCACGCTCGATATGAGAAAATCTTCGAACCCAGCTTCCTGATGAGATA
8932 CTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
130 CTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
8997 TTCGTCTTCCT
195 TTCGTCTTCCT
* * * *
9008 GATGAGATACAGAGAAGCGGATAGAAACAAATGACACGGTCATCTTCCTAATGAG--ACAGAGAA
1 GATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTAATGAGATACTGAGAA
*
9071 GAAGACCAAATCAAACCCACGCTCGATATGA-ACAAATCTTCGAACCCTAGCTTCCTGATGAGAT
66 GAAGACCAAATCAAACTCACGCTCGATATGAGA-AAATCTTCGAACCC-AGCTTCCTGATGAGAT
* * * * * *
9135 ACTGAGAAGCAGGTCGAAGCAATAAAGTGGTTAACTTCCTGATGAGATACGGAGAAGTGAACCTA
129 ACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAA
*
9200 ATCCGTCTTCCT
194 ATTCGTCTTCCT
* * * ** ** * * *
9212 GATGAAACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATAAGATACTGAGAA
1 GATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTAATGAGATACTGAGAA
* *
9277 GAAGGCCAAGTCAA
66 GAAGACCAAATCAA
9291 TGAAACCAGA
Statistics
Matches: 440, Mismatches: 42, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
202 1 0.00
203 50 0.11
204 131 0.30
205 141 0.32
206 117 0.27
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (205 bp):
GATGAGATACAGAGAAGCGGATTGAAACAAACGATACGGTCATCTTCCTAATGAGATACTGAGAA
GAAGACCAAATCAAACTCACGCTCGATATGAGAAAATCTTCGAACCCAGCTTCCTGATGAGATAC
TGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT
TCGTCTTCCT
Found at i:9702 original size:17 final size:17
Alignment explanation
Indices: 9626--9721 Score: 77
Period size: 17 Copynumber: 5.6 Consensus size: 17
9616 TCCAATTTTT
*
9626 AATTTTAATTTACTTTA
1 AATTTAAATTTACTTTA
* * *
9643 AGTTTGAATTT-GTTATA
1 AATTTAAATTTACTT-TA
* * *
9660 AATTTAAATTCATTTTTG
1 AATTTAAATTTA-CTTTA
*
9678 AGTTTAAATTTACTTTA
1 AATTTAAATTTACTTTA
*
9695 AATTTAAATTTACTGTA
1 AATTTAAATTTACTTTA
*
9712 AATTAAAATT
1 AATTTAAATT
9722 AATTGAAAAG
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
16 2 0.03
17 46 0.75
18 11 0.18
19 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTACTTTA
Found at i:11622 original size:29 final size:29
Alignment explanation
Indices: 11582--11802 Score: 192
Period size: 29 Copynumber: 7.8 Consensus size: 29
11572 TGGAGGTCCC
*
11582 TAAACTATCCAAAAATTCCATTCTTACCCT
1 TAAACT-TCCAAAAATTCCATTTTTACCCT
* *
11612 TTAACTTCCAAAAATTCCATTTTTGACCCC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCT
*
11642 AAAACTTCCAAAAAATT-CATTTTTACCCT
1 TAAACTTCC-AAAAATTCCATTTTTACCCT
**
11671 CGAACTTCCAAAAATTCCA--TTT----T
1 TAAACTTCCAAAAATTCCATTTTTACCCT
* *
11694 T-GAC-TCCAAAACTTCCATTTTTACCCT
1 TAAACTTCCAAAAATTCCATTTTTACCCT
* *
11721 -AAACTTCCAAAAATTCCATTTTGACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCT
* * *
11749 AAAACTTCTAAAAATTCCATTTTTAACCT
1 TAAACTTCCAAAAATTCCATTTTTACCCT
* *
11778 TGAAACTTTCTAAAATTACCATTTT
1 T-AAACTTCCAAAAATT-CCATTTT
11803 GCCCTTGGTG
Statistics
Matches: 154, Mismatches: 23, Indels: 27
0.75 0.11 0.13
Matches are distributed among these distances:
21 12 0.08
22 2 0.01
23 4 0.03
27 6 0.04
28 27 0.18
29 54 0.35
30 35 0.23
31 14 0.09
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCT
Found at i:11677 original size:59 final size:58
Alignment explanation
Indices: 11591--11802 Score: 230
Period size: 59 Copynumber: 3.8 Consensus size: 58
11581 CTAAACTATC
* *
11591 CAAAAATTCCATTCTTACCCTTTAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
1 CAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
* *
11649 CCAAAAAATT-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACTCCAAAA---
1 -C-AAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
*
11705 C-----TTCCATTTTTACCC-TAAACTTCCAAAAATTCCA-TTTTGACCCCAAAACTT
1 CAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
* * *
11756 CTAAAAATTCCATTTTTAACCTTGAAACTTTCTAAAATTACCATTTT
1 C-AAAAATTCCATTTTTACCCTTG-AACTTCCAAAAATT-CCATTTT
11803 GCCCTTGGTG
Statistics
Matches: 127, Mismatches: 11, Indels: 28
0.77 0.07 0.17
Matches are distributed among these distances:
48 13 0.10
49 19 0.15
50 11 0.09
51 1 0.01
55 1 0.01
57 13 0.10
58 1 0.01
59 55 0.43
60 10 0.08
61 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
Found at i:11726 original size:19 final size:21
Alignment explanation
Indices: 11677--11729 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
11667 CCCTCGAACT
*
11677 TCCAAAAATTCCATTTTTGAC
1 TCCAAAACTTCCATTTTTGAC
11698 TCCAAAACTTCCATTTTT-AC
1 TCCAAAACTTCCATTTTTGAC
*
11718 -CCTAAACTTCCA
1 TCCAAAACTTCCA
11730 AAAATTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (21 bp):
TCCAAAACTTCCATTTTTGAC
Found at i:11740 original size:49 final size:49
Alignment explanation
Indices: 11659--11756 Score: 162
Period size: 48 Copynumber: 2.0 Consensus size: 49
11649 CCAAAAAATT
* *
11659 CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACTCCAAAACTTC
1 CATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTGACCCCAAAACTTC
11709 CATTTTTACCCT-AAACTTCCAAAAATTCCATTTTGACCCCAAAACTTC
1 CATTTTTACCCTCAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTC
11757 TAAAAATTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 17 0.37
49 17 0.37
50 12 0.26
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.35
Consensus pattern (49 bp):
CATTTTTACCCTCAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTC
Found at i:11785 original size:78 final size:80
Alignment explanation
Indices: 11611--11775 Score: 221
Period size: 78 Copynumber: 2.1 Consensus size: 80
11601 ATTCTTACCC
* * *
11611 TTTAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATTCATTTTTACCCTCGAAC
1 TTTAAC-TCCAAAACTTCCATTTTTGACCCCAAAACTTCCAAAAAATTCATTTTGACCCTCAAAC
11676 TTCCAAAAATTCCATT
65 TTCCAAAAATTCCATT
* *
11692 TTTGACTCCAAAACTTCCATTTTT-A-CCCTAAACTTCC-AAAAATTCCATTTTGACCC-CAAAA
1 TTTAACTCCAAAACTTCCATTTTTGACCCCAAAACTTCCAAAAAATT-CATTTTGACCCTC-AAA
*
11753 CTTCTAAAAATTCCATT
64 CTTCCAAAAATTCCATT
11770 TTTAAC
1 TTTAAC
11776 CTTGAAACTT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
77 8 0.11
78 44 0.59
79 1 0.01
80 17 0.23
81 5 0.07
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (80 bp):
TTTAACTCCAAAACTTCCATTTTTGACCCCAAAACTTCCAAAAAATTCATTTTGACCCTCAAACT
TCCAAAAATTCCATT
Found at i:13928 original size:36 final size:36
Alignment explanation
Indices: 13867--14022 Score: 240
Period size: 36 Copynumber: 4.3 Consensus size: 36
13857 TTAGTACAAT
* * * * *
13867 ATATTTATTGTCACATGGAACGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAA
*
13903 ATATTTACTGTCTCGTGGCATGAATAACATACCCAA
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAA
13939 ATATTTACTGTCTCATGGCATGAATAACATACCCAA
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAA
* *
13975 ATATTTACTGTCTCATGGCATGAATAACATAGCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAA
14011 ATATTTACTGTC
1 ATATTTACTGTC
14023 ACAACAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 111 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (36 bp):
ATATTTACTGTCTCATGGCATGAATAACATACCCAA
Found at i:16585 original size:20 final size:20
Alignment explanation
Indices: 16547--16585 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16537 AAGTATATCA
*
16547 TTATCGATACTTCAAAAAAC
1 TTATCGATACTCCAAAAAAC
16567 TTATCGATAC-CCAACAAAA
1 TTATCGATACTCCAA-AAAA
16586 GGTATTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (20 bp):
TTATCGATACTCCAAAAAAC
Found at i:16745 original size:20 final size:20
Alignment explanation
Indices: 16693--16746 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
16683 TCAATACTCA
* *
16693 ACAACATATATTAATACTTG
1 ACAAAATATATTGATACTTG
*
16713 ACAAAAAATATTGATACTTG
1 ACAAAATATATTGATACTTG
16733 ACAAAATATATTGA
1 ACAAAATATATTGA
16747 AAAATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
ACAAAATATATTGATACTTG
Found at i:18519 original size:11 final size:11
Alignment explanation
Indices: 18503--18563 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
18493 CTTAATCACT
18503 TTAATATTAAA
1 TTAATATTAAA
18514 TTAATA-TAATA
1 TTAATATTAA-A
* *
18525 TTTATCATTAAT
1 TTAAT-ATTAAA
18537 TTAATATTAAA
1 TTAATATTAAA
* *
18548 -TATTATTATA
1 TTAATATTAAA
18558 TTAATA
1 TTAATA
18564 GAATATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
10 11 0.28
11 20 0.51
12 5 0.13
13 3 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:18540 original size:5 final size:6
Alignment explanation
Indices: 18503--18563 Score: 56
Period size: 5 Copynumber: 10.0 Consensus size: 6
18493 CTTAATCACT
*
18503 TTAATA TTAA-A TTAATA -TAATA TTTATCA TTAAT- TTAATA TTAAATA
1 TTAATA TTAATA TTAATA TTAATA TTAAT-A TTAATA TTAATA TT-AATA
18550 TTATTATA TTAATA
1 TTA--ATA TTAATA
18564 GAATATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
5 15 0.33
6 14 0.30
7 11 0.24
8 6 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:18552 original size:18 final size:17
Alignment explanation
Indices: 18502--18563 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 17
18492 ACTTAATCAC
18502 TTTAATATTAA-ATTAA
1 TTTAATATTAATATTAA
* *
18518 TATAATATTTATCATTAA
1 TTTAATATTAAT-ATTAA
18536 TTTAATATTAAATATT-A
1 TTTAATATT-AATATTAA
18553 -TT-ATATTAATA
1 TTTAATATTAATA
18564 GAATATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.10
15 5 0.13
16 11 0.28
17 1 0.03
18 16 0.41
19 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATTAATATTAA
Found at i:19200 original size:19 final size:20
Alignment explanation
Indices: 19158--19208 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
19148 AAAATAACAA
*
19158 AAATAAAAAAT-TTAAAAAT
1 AAATAATAAATATTAAAAAT
*
19177 AAATAATAAATATTCAAAAT
1 AAATAATAAATATTAAAAAT
19197 -AATAATTAAATA
1 AAATAA-TAAATA
19209 AAGAAAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAATAAATATTAAAAAT
Found at i:19851 original size:200 final size:198
Alignment explanation
Indices: 19492--19894 Score: 560
Period size: 200 Copynumber: 2.0 Consensus size: 198
19482 GTTATTGAAT
* * * * **
19492 AATAATGAATTGATTTATGTAAAATGAAGAGGTTTTTATATAGGCTAGTTAAGTACATCTAAATA
1 AATAATGAATTGATCTATGTAAAATAAAAAGGTCTTTATATAGGCTAGCGAAGTACATCTAAATA
* * * * *
19557 AAACTCTTAATTATACTAAAACTCTAATTACCTTAAATAAGTAGTTTTAAACTAAACTTTCTTGT
66 AAACACTT-AGTATACTAAAACTCTAATTACCTAAAAAAAGTAGTTTTAAACTAAACTTTATTGT
* *
19622 TAATATAAAACTCTTAAATAACTTAAAATACTT-AAAATTAATCCAAAATTC-AGAATAAATAAA
130 TAACATAAAACTCTTAAATAACCTAAAATACTTAAAAATT-ATCCAAAATTCGA-AATAAATAAA
19685 TAATAA
193 TAATAA
* * *
19691 AATAATTAATTGATCTGTGTACAATAAAAAGGTCTTTATATAGGCTAGCGAAGTACATCTAAATA
1 AATAATGAATTGATCTATGTAAAATAAAAAGGTCTTTATATAGGCTAGCGAAGTACATCTAAATA
*
19756 AAACACTT-GTATACTGAAACTCTAATTACCCTAAACAAAAAGTAGTTTTAAACTAAACTTTATT
66 AAACACTTAGTATACTAAAACTCTAATTA-CCT-AA-AAAAAGTAGTTTTAAACTAAACTTTATT
* *
19820 GTTGACATAACACTCTTAAATAACCTAAAATACTTAAAAATTATCCAAAATTCGAAATAAATAAA
128 GTTAACATAAAACTCTTAAATAACCTAAAATACTTAAAAATTATCCAAAATTCGAAATAAATAAA
19885 TAATAA
193 TAATAA
19891 AATA
1 AATA
19895 GTAAAACTTA
Statistics
Matches: 180, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
197 18 0.10
198 3 0.02
199 64 0.36
200 88 0.49
201 7 0.04
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (198 bp):
AATAATGAATTGATCTATGTAAAATAAAAAGGTCTTTATATAGGCTAGCGAAGTACATCTAAATA
AAACACTTAGTATACTAAAACTCTAATTACCTAAAAAAAGTAGTTTTAAACTAAACTTTATTGTT
AACATAAAACTCTTAAATAACCTAAAATACTTAAAAATTATCCAAAATTCGAAATAAATAAATAA
TAA
Found at i:22158 original size:25 final size:25
Alignment explanation
Indices: 22034--22158 Score: 99
Period size: 25 Copynumber: 4.9 Consensus size: 25
22024 CTCTCTTCCA
*
22034 AAAATTTA-GCTCTTATGAGCCCAGAC
1 AAAA-TTACGCTCTTACGAG-CCAGAC
* * * * *
22060 AGAGTTTCGCTCTTATGAGTCAGAC
1 AAAATTACGCTCTTACGAGCCAGAC
* *
22085 AAAATTACGCTCTTGCAAGCCAGAATC
1 AAAATTACGCTCTTACGAGCCAG-A-C
* * * *
22112 AGAATTATGCTATTACAAGCCAGAC
1 AAAATTACGCTCTTACGAGCCAGAC
22137 AAAATTACGCTCTTACGAGCCA
1 AAAATTACGCTCTTACGAGCCA
22159 AAAGCAGTTT
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
25 42 0.55
26 15 0.19
27 20 0.26
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (25 bp):
AAAATTACGCTCTTACGAGCCAGAC
Found at i:30172 original size:388 final size:388
Alignment explanation
Indices: 29454--31781 Score: 3329
Period size: 388 Copynumber: 6.0 Consensus size: 388
29444 TGTTGCACTA
* *
29454 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGACCAATAAAATCTTGATTGTAAGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* * * *
29519 CAGCAATCCTAACACCACCAAAATGGCCTCTATAAGGAGCATCATGGTAATGCTTCAAGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
* * * **
29584 AACATTTCCTCCTCAAGAGCATAGTGACGAATTATGTTGTCGGCACATACCTTGAACAGGTACAG
131 AACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* * *
29649 CTCATTCTAATGATACTTAGCAGCATCCCT-ACGAAATCTGACCTTTCTATGACCTGTTGCACTC
196 CTCATTCCAATGATACTTAGCAGCATCCCTGA-GAAATCTGACCTTCCTATGACCAGTTGCACTC
*
29713 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCATCCACAAA
260 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAA
* * * *
29778 GAATAATTTCTCTTCTGGAAATGCATTAACAATTTG-GTATTTATTTCCATCCTCGCTTCTAGCT
325 GAATAATTTCTCATCTGGAAATGCGTCAACAATTTGTG-ATTTATTTCCATCCTCGCTTCCAGCT
* * *
29842 TTGAGCAAAATTGTGTACATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* ** *
29907 CAGCAATCCTAACACCACCAAAATGGCCTCTATAGTTATCATCATGGCAATGCTTCAGGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
* * * * *
29972 AAAATTTCTTCCTCAAGAGCACAGTGACGAATGATGTCGTCGGCACATACCTTGAACAGATATGG
131 AACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* *
30037 CTCATTCTAATGATACTTAGGAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACTCA
196 CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACTCA
* * * *
30102 GTGGTAGCTTTTCATAGATTAGGTAATTGACTACATCTGCATACCATGGAGACGCGTCCACAATG
261 GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAG
** * * *
30167 AATAATTTCTCATCTAAAAATGCGTCAACAATTTGTAATTTATTTCCATCCTCACTGCCAGCT
326 AATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
* * * * *
30230 TTGACCAAAATTGTGTGCATCTCAAAACAATGTAGGCAAGTAAAATCTTGATTATAGGATCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
*
30295 CAGCAATCCTAACACCACCAAAATGGCCCCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
*
30360 AACATTTCCTCCTCAAGCACATC-GTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATG
131 AACATTTCCTCCTCAAGAACA-CAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATG
* * * *
30424 GCTCATTCCAATGATACTTAGCAACATTCTTGAGAAATCTGACCTTCCTATGACCTA-TTGTACT
195 GCTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACC-AGTTGCACT
* * * *
30488 CAGTGATAGCTTTCCATAGACTAGGTAATTGACTACATCTACATACCATGGAGACGAGTCCACAA
259 CAGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAA
* * * *
30553 AGAATAATTTCTTATCTGGAAATGCGTCAATAATTTGTAATTTATTTTCATCCTCGCTTCCAGCT
324 AGAATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
* * *
30618 TTGACCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTA
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
*
30683 CAGCAATCCTAACACCACCAAAATGGCC-CCTATAGAGAGCATCATGGCAATGCTTCAGGATAGA
66 CAGCAATCCTAACACCACCAAAATGGCCTCC-ATAGGGAGCATCATGGCAATGCTTCAGGATAGA
* * * * * *
30747 TAACATTTCCTTCTCAAGAACATAGCGAAGAATGATGTTGTCGGCATATAACTTGAACAGGTA-G
130 TAACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATG
* *
30811 GCTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACCCGTTGCACTC
195 GCTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACTC
* *
30876 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAAATGCATCCACAAA
260 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAA
* *
30941 GAATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTTCATCCTCGCTTCTAGCT
325 GAATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
* * *
31005 TTGAGCAAAATTATGTGCATCTCGAAACAATGTAGGCCAGTAAAATCCTGATTGTAAGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* * *
31070 CAGTAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCATGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
* * * **
31135 AACATTTCCTCCTCAAGAACATAGCGACGAATGATGTTGTCAGCGTATACCTTGAACAGGTATGG
131 AACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* * *
31200 CTCATTTCAATGATACTTAGCAGCATCCCTGAGAGATCTGACCTTCCTATGACCTGTTGCACTCA
196 CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACTCA
** * * *
31265 GTGGTAGCTTTCTGTAGACTAGGTAATTGACTACATCTGCATACTATGAAGATACGTCCACAAAG
261 GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAG
* * * * *
31330 AATAATTTCTCATATGGAAATACGTCGACAATGTGTGATTTATTTTCATCCTCGCTTCCAGCT
326 AATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
* ** * * *
31393 TTGAGCACAATTGTGTGCATCTTGAAACAATGTAGGCTAGTAAAATCCTAATTGTAAGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* * *
31458 CAGCAATCCTAACACCACCAAAATGGCCTCCATGGGGAGCATCATGACAATGCTTCAAGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
* * * * * * *
31523 AACATTTCCTCCTCAGGAACACAATGATGAATGATGTTATCGGCGCATACCTTGAACTGGTATGA
131 AACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* * * * *
31588 CTCATTCCAATGATACTTAACAACATCCATGAGAAATCTGACATTCTTATGACCTA-TTGCACTC
196 CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACC-AGTTGCACTC
* * * * * * * *
31652 AATGGTAGCTTTCAACAGACTAGGTAATTGACTACATCTACATACCATGTAGATACGTCGACTAA
260 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAA
* * * * * *
31717 GAATAATTTCTTATCTGAAAATACGTCGACAATTTGTGATTTATTTCCATCTTCGCTTCTAGCT
325 GAATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
31781 T
1 T
31782 CCACACGAGA
Statistics
Matches: 1756, Mismatches: 174, Indels: 20
0.90 0.09 0.01
Matches are distributed among these distances:
387 355 0.20
388 1398 0.80
389 3 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (388 bp):
TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
CAGCAATCCTAACACCACCAAAATGGCCTCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
AACATTTCCTCCTCAAGAACACAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACTCA
GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAG
AATAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCCAGCT
Found at i:31196 original size:775 final size:774
Alignment explanation
Indices: 29454--31781 Score: 3401
Period size: 775 Copynumber: 3.0 Consensus size: 774
29444 TGTTGCACTA
* *
29454 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGACCAATAAAATCTTGATTGTAAGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* * * *
29519 CAGCAATCCTAACACCACCAAAATGGCCTCTATAAGGAGCATCATGGTAATGCTTCAAGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCAAGATAGAT
* * **
29584 AACATTTCCTCCTCAAGAGCATAGTGACGAATTATGTTGTCGGCACATACCTTGAACAGGTACAG
131 AACATTTCCTCCTCAAGAACATAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* *
29649 CTCATTCTAATGATACTTAGCAGCATCCCT-ACGAAATCTGACCTTTCTATGACCTGTTGCACTC
196 CTCATTCCAATGATACTTAGCAGCATCCCTGA-GAAATCTGACCTTCCTATGACCTGTTGCACTC
29713 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCA-TCCACAA
260 AGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGA-G-AGTCCACAA
* * * *
29777 AGAATAATTTCTCT-TCTGGAAATGCATTAACAATTTGGTATTTATTTCCATCCTCGCTTCTAGC
323 AGAATAATTTCT-TATCTGGAAATGCGTCAACAATTT-GTATTTATTTTCATCCTCGCTTCCAGC
*
29841 TTTGAGCAAAATTGTGTACATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTT
386 TTTGAGCAAAATTGTGTGCATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTT
* ** *
29906 GCAGCAATCCTAACACCACCAAAATGGCCTCTATAGTTATCATCATGGCAATGCTTCAGGATAGA
451 GCAGCAATCCTAACACCACCAAAATGGCCCCTATAGAGAGCATCATGGCAATGCTTCAGGATAGA
* * * * *
29971 TAAAATTT-CTTCCTCAAGAGCACAGTGACGAATGATGTCGTCGGCACATACCTTGAACAGATAT
516 TAACATTTCCTT-CTCAAGAACACAGTGAAGAATGATGTTGTCGGCACATACCTTGAACAGGTAT
* * *
30035 GGCTCATTCTAATGATACTTAGGAGCATCCCTGAGAAATCTGACCTTCCTATGACCAGTTGCACT
580 GGCTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACCAGTTGCACT
* * *
30100 CAGTGGTAGCTTTTCATAGATTAGGTAATTGACTACATCTGCATACCATGGAGACGCGTCCACAA
645 CAGTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAA
* * * * * *
30165 TGAATAATTTCTCATCTAAAAATGCGTCAACAATTTGTAATTTATTTCCATCCTCACTGCCAGCT
710 AGAATAATTTCTCATCTGAAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCTAGCT
* * * * *
30230 TTGACCAAAATTGTGTGCATCTCAAAACAATGTAGGCAAGTAAAATCTTGATTATAGGATCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* *
30295 CAGCAATCCTAACACCACCAAAATGGCCCCCATAGGGAGCATCATGGCAATGCTTCAGGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCAAGATAGAT
* *
30360 AACATTTCCTCCTCAAGCACATCGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
131 AACATTTCCTCCTCAAGAACATAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* * * * *
30425 CTCATTCCAATGATACTTAGCAACATTCTTGAGAAATCTGACCTTCCTATGACCTATTGTACTCA
196 CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCTGTTGCACTCA
* *
30490 GTGATAGCTTTCCATAGACTAGGTAATTGACTACATCTACATACCATGGAGACGAGTCCACAAAG
261 GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGA-GAGTCCACAAAG
*
30555 AATAATTTCTTATCTGGAAATGCGTCAATAATTTGTAATTTATTTTCATCCTCGCTTCCAGCTTT
325 AATAATTTCTTATCTGGAAATGCGTCAACAATTTGT-ATTTATTTTCATCCTCGCTTCCAGCTTT
* * *
30620 GACCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTACA
389 GAGCAAAATTGTGTGCATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTGCA
30685 GCAATCCTAACACCACCAAAATGGCCCCTATAGAGAGCATCATGGCAATGCTTCAGGATAGATAA
454 GCAATCCTAACACCACCAAAATGGCCCCTATAGAGAGCATCATGGCAATGCTTCAGGATAGATAA
* * * *
30750 CATTTCCTTCTCAAGAACATAGCGAAGAATGATGTTGTCGGCATATAACTTGAACAGGTA-GGCT
519 CATTTCCTTCTCAAGAACACAGTGAAGAATGATGTTGTCGGCACATACCTTGAACAGGTATGGCT
*
30814 CATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACCCGTTGCACTCAGT
584 CATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACCAGTTGCACTCAGT
* *
30879 GGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAAATGCATCCACAAAGAA
649 GGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAGAA
* *
30944 TAATTTCTCATCTGGAAATGCGTCAACAATTTGTGATTTATTTTCATCCTCGCTTCTAGCT
714 TAATTTCTCATCTGAAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCTAGCT
* * *
31005 TTGAGCAAAATTATGTGCATCTCGAAACAATGTAGGCCAGTAAAATCCTGATTGTAAGACCTTTG
1 TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
* *
31070 CAGTAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCATGATAGAT
66 CAGCAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCAAGATAGAT
* * **
31135 AACATTTCCTCCTCAAGAACATAGCGACGAATGATGTTGTCAGCGTATACCTTGAACAGGTATGG
131 AACATTTCCTCCTCAAGAACATAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
* *
31200 CTCATTTCAATGATACTTAGCAGCATCCCTGAGAGATCTGACCTTCCTATGACCTGTTGCACTCA
196 CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCTGTTGCACTCA
** * * *
31265 GTGGTAGCTTTCTGTAGACTAGGTAATTGACTACATCTGCATACTATGAAGATACGTCCACAAAG
261 GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGAGA-GTCCACAAAG
* * * * *
31330 AATAATTTCTCATATGGAAATACGTCGACAATGTGTGATTTATTTTCATCCTCGCTTCCAGCTTT
325 AATAATTTCTTATCTGGAAATGCGTCAACAATTTGT-ATTTATTTTCATCCTCGCTTCCAGCTTT
* * * * * *
31395 GAGCACAATTGTGTGCATCTTGAAACAATGTAGGCTAGTAAAATCCTAATTGTAAGACCTTTGCA
389 GAGCAAAATTGTGTGCATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTGCA
* * * *
31460 GCAATCCTAACACCACCAAAATGGCCTCC-ATGGGGAGCATCATGACAATGCTTCAAGATAGATA
454 GCAATCCTAACACCACCAAAATGGCC-CCTATAGAGAGCATCATGGCAATGCTTCAGGATAGATA
* * * * * * * *
31524 ACATTTCCTCCTCAGGAACACAATGATGAATGATGTTATCGGCGCATACCTTGAACTGGTATGAC
518 ACATTTCCTTCTCAAGAACACAGTGAAGAATGATGTTGTCGGCACATACCTTGAACAGGTATGGC
* * * *
31589 TCATTCCAATGATACTTAACAACATCCATGAGAAATCTGACATTCTTATGACCTA-TTGCACTCA
583 TCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACC-AGTTGCACTCA
* * * * * * * *
31653 ATGGTAGCTTTCAACAGACTAGGTAATTGACTACATCTACATACCATGTAGATACGTCGACTAAG
647 GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAG
* * * *
31718 AATAATTTCTTATCTGAAAATACGTCGACAATTTGTGATTTATTTCCATCTTCGCTTCTAGCT
712 AATAATTTCTCATCTGAAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCTAGCT
31781 T
1 T
31782 CCACACGAGA
Statistics
Matches: 1392, Mismatches: 151, Indels: 18
0.89 0.10 0.01
Matches are distributed among these distances:
774 1 0.00
775 695 0.50
776 692 0.50
777 4 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (774 bp):
TTGAGCAAAATTGTGTGCATCTCAAAACAATGTAGGCCAGTAAAATCTTGATTGTAAGACCTTTG
CAGCAATCCTAACACCACCAAAATGGCCACCATAGGGAGCATCATGGCAATGCTTCAAGATAGAT
AACATTTCCTCCTCAAGAACATAGTGACGAATGATGTTGTCGGCACATACCTTGAACAGGTATGG
CTCATTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCCTATGACCTGTTGCACTCA
GTGGTAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGAGAGTCCACAAAGA
ATAATTTCTTATCTGGAAATGCGTCAACAATTTGTATTTATTTTCATCCTCGCTTCCAGCTTTGA
GCAAAATTGTGTGCATCTCGAAACAATGTAGGCCAGTAAAATCTTGATTGTAGGACCTTTGCAGC
AATCCTAACACCACCAAAATGGCCCCTATAGAGAGCATCATGGCAATGCTTCAGGATAGATAACA
TTTCCTTCTCAAGAACACAGTGAAGAATGATGTTGTCGGCACATACCTTGAACAGGTATGGCTCA
TTCCAATGATACTTAGCAGCATCCCTGAGAAATCTGACCTTCTTATGACCAGTTGCACTCAGTGG
TAGCTTTCCATAGACTAGGTAATTGACTACATCTGCATACCATGGAGATGCGTCCACAAAGAATA
ATTTCTCATCTGAAAATGCGTCAACAATTTGTGATTTATTTCCATCCTCGCTTCTAGCT
Found at i:37297 original size:31 final size:31
Alignment explanation
Indices: 37259--37353 Score: 190
Period size: 31 Copynumber: 3.1 Consensus size: 31
37249 ATACAAAAGG
37259 AATAAATTATACAATCATTTAAGGAGAAATT
1 AATAAATTATACAATCATTTAAGGAGAAATT
37290 AATAAATTATACAATCATTTAAGGAGAAATT
1 AATAAATTATACAATCATTTAAGGAGAAATT
37321 AATAAATTATACAATCATTTAAGGAGAAATT
1 AATAAATTATACAATCATTTAAGGAGAAATT
37352 AA
1 AA
37354 GTGTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (31 bp):
AATAAATTATACAATCATTTAAGGAGAAATT
Found at i:43309 original size:29 final size:29
Alignment explanation
Indices: 43267--43325 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
43257 ATTCATAAGT
*
43267 TAACATGTCATAACATTTCTATGCATATA
1 TAACATGTCATAACATTTCTACGCATATA
43296 TAACATGTCATAACATTTCTACGCATATA
1 TAACATGTCATAACATTTCTACGCATATA
43325 T
1 T
43326 GCCAACTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (29 bp):
TAACATGTCATAACATTTCTACGCATATA
Found at i:43337 original size:29 final size:29
Alignment explanation
Indices: 43274--43339 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
43264 AGTTAACATG
* **
43274 TCATAACATTTCTATGCATATATAACATG
1 TCATAACATTTCTACGCATATATAACAAC
**
43303 TCATAACATTTCTACGCATATATGCCAAC
1 TCATAACATTTCTACGCATATATAACAAC
*
43332 TTATAACA
1 TCATAACA
43340 CTAAGCAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (29 bp):
TCATAACATTTCTACGCATATATAACAAC
Found at i:52834 original size:27 final size:27
Alignment explanation
Indices: 52777--52835 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
52767 GGAGTGTTTT
****
52777 AGTTTAGCCATAAAAACTAAGGGTTCT
1 AGTTTAGCCATAAAAACTAAGGGAAAG
* *
52804 AGTTTAGCCATAAAAGCTAGGGGAAAG
1 AGTTTAGCCATAAAAACTAAGGGAAAG
52831 AGTTT
1 AGTTT
52836 TATCTAAGCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (27 bp):
AGTTTAGCCATAAAAACTAAGGGAAAG
Found at i:62884 original size:15 final size:16
Alignment explanation
Indices: 62852--62887 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
62842 TTAAAAATAA
*
62852 AATTTTATTTTCATTT
1 AATTTTATTTTAATTT
62868 AATTTTA-TTTAATTT
1 AATTTTATTTTAATTT
62883 AATTT
1 AATTT
62888 ATAATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTATTTTAATTT
Found at i:63050 original size:24 final size:22
Alignment explanation
Indices: 63015--63060 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
63005 ATATTTTAAT
* *
63015 TAAATATTATTTATATTTAAGA
1 TAAATATTATTTAAATTAAAGA
63037 TAAATATTAAATTTAAATTAAAGA
1 TAAATATT--ATTTAAATTAAAGA
63061 ATGCAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TAAATATTATTTAAATTAAAGA
Found at i:64587 original size:43 final size:43
Alignment explanation
Indices: 64489--64972 Score: 428
Period size: 43 Copynumber: 11.4 Consensus size: 43
64479 TTACGAGGAA
* * * *
64489 AAACGCCCCCAAAGAACATGGTCTTTAGCGATGCTT-TTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * *
64531 AAACACCGCTAAAGACCATGGTCTTTAGGGACACTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * **
64574 AAACGCCGCTAAAGACCATGGTCCTTAACGGTGCTTATCCCA-
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
** ** * * *
64616 AAACGGGGCTAAA-AACATTATCATTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * *
64658 AAACGCCGTTAAAAAACATGGTCATTAGCAACGCTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
** * * * * * *
64701 AAACGTTGCTAAAAAACATGATCTTTAGCGATGTTTTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * *
64744 AAACG-TGCTAAA-AACATGATCATTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * *
64785 AAATGCCGCTAAAGAACATGATCTTTAGTGGCGCTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
** *
64828 AAACATCGCTAAAGAACATGG-CTTTAGCGACGCTTATCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * *
64870 AAACGCCACTAAAGAACATGATCTTTAGCGTCGCTTATCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
* * * * * *
64913 AAACACC-CTAAA-AACATGGTCATTAAC-AGCACTTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGA-CGCTTATCCCAC
64954 AAACGCCGCTAAAGAACAT
1 AAACGCCGCTAAAGAACAT
64973 TGTCCCCACT
Statistics
Matches: 359, Mismatches: 74, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
41 77 0.21
42 108 0.30
43 174 0.48
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTATCCCAC
Found at i:64678 original size:84 final size:86
Alignment explanation
Indices: 64489--64972 Score: 448
Period size: 84 Copynumber: 5.7 Consensus size: 86
64479 TTACGAGGAA
* * * * * * * * *
64489 AAACGCCCCCAAAGAACATGGTCTTTAGCGATGCTT-TTCCACAAACACCGCTAAAGACCATGGT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
*
64553 CTTTAG-GGACACTTATCCCAC
66 CTTTAGCGG-CGCTTATCCCAC
* * * * ** ** *
64574 AAACGCCGCTAAAGACCATGGTCCTTAACGGTGCTTATCCCA-AAACGGGGCTAAA-AACATTAT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
* *
64637 CATTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTATCCCAC
* * ** *
64658 AAACGCCGTTAAAAAACATGGTCATTAGCAACGCTTATCCCACAAACGTTGCTAAAAAACATGAT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
** * * *
64723 CTTTAGCGATGTTTTTCCCAA
66 CTTTAGCGGCGCTTATCCCAC
* * * *
64744 AAACG-TGCT-AAAAACATGATCATTAGCGACGCTTTTCCCACAAATGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
*
64807 CTTTAGTGGCGCTTATCCCAC
66 CTTTAGCGGCGCTTATCCCAC
** * * * *
64828 AAACATCGCTAAAGAACATGG-CTTTAGCGACGCTTATCCCATAAACGCCACTAAAGAACATGAT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
*
64892 CTTTAGCGTCGCTTATCCCAC
66 CTTTAGCGGCGCTTATCCCAC
* * * * *
64913 AAACACC-CT-AAAAACATGGTCATTAAC-AGCACTTTTTCCACAAACGCCGCTAAAGAACAT
1 AAACGCCGCTAAAAAACATGGTCATTAGCGA-CGCTTATCCCACAAACGCCGCTAAAGAACAT
64973 TGTCCCCACT
Statistics
Matches: 324, Mismatches: 67, Indels: 17
0.79 0.16 0.04
Matches are distributed among these distances:
83 10 0.03
84 153 0.47
85 121 0.37
86 40 0.12
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAAAACATGGTCATTAGCGACGCTTATCCCACAAACGCCGCTAAAGAACATGAT
CTTTAGCGGCGCTTATCCCAC
Found at i:64695 original size:127 final size:127
Alignment explanation
Indices: 64503--64977 Score: 456
Period size: 127 Copynumber: 3.8 Consensus size: 127
64493 GCCCCCAAAG
* * * * * * **
64503 AACATGGTCTTTAGCGATGCTTTT-CCACAAACACCGCTAAAGACCATGGTCTTTAGGGACACTT
1 AACATGATCATTAGCGACGCTTTTCCCACAAACACCGCTAAAAAACATGGTCATTAGCAACACTT
* * * *
64567 ATCCCACAAACGCCGCTAAAGACCATGGTCCTTAACGGTGCTTATCCCAAAACGGGGCTAAA
66 ATCCCACAAACGCCGCTAAAGAACATGGTCCTTAGCGATGCTTATCCCAAAACGGCGCTAAA
* * * * *
64629 AACATTATCATTAGCGGCGCTTTTCCCACAAACGCCGTTAAAAAACATGGTCATTAGCAACGCTT
1 AACATGATCATTAGCGACGCTTTTCCCACAAACACCGCTAAAAAACATGGTCATTAGCAACACTT
** * * * * * *
64694 ATCCCACAAACGTTGCTAAAAAACATGATCTTTAGCGATGTTTTTCCCAAAAAC-GTGCTAAA
66 ATCCCACAAACGCCGCTAAAGAACATGGTCCTTAGCGATGCTTATCCC-AAAACGGCGCTAAA
** * * * *** *
64756 AACATGATCATTAGCGACGCTTTTCCCACAAATGCCGCTAAAGAACATGATCTTTAGTGGCGCTT
1 AACATGATCATTAGCGACGCTTTTCCCACAAACACCGCTAAAAAACATGGTCATTAGCAACACTT
** * * * *
64821 ATCCCACAAACATCGCTAAAGAACATGG-CTTTAGCGACGCTTATCCCATAAACGCCACTAAA
66 ATCCCACAAACGCCGCTAAAGAACATGGTCCTTAGCGATGCTTATCCCA-AAACGGCGCTAAA
* * * * *
64883 GAACATGATCTTTAGCGTCGCTTATCCCACAAACACC-CT-AAAAACATGGTCATTAACAGCACT
1 -AACATGATCATTAGCGACGCTTTTCCCACAAACACCGCTAAAAAACATGGTCATTAGCAACACT
* * *
64946 TTTTCCACAAACGCCGCTAAAGAACATTGTCC
65 TATCCCACAAACGCCGCTAAAGAACATGGTCC
64978 CCACTAATAT
Statistics
Matches: 281, Mismatches: 62, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
125 1 0.00
126 80 0.28
127 164 0.58
128 36 0.13
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (127 bp):
AACATGATCATTAGCGACGCTTTTCCCACAAACACCGCTAAAAAACATGGTCATTAGCAACACTT
ATCCCACAAACGCCGCTAAAGAACATGGTCCTTAGCGATGCTTATCCCAAAACGGCGCTAAA
Found at i:66573 original size:2 final size:2
Alignment explanation
Indices: 66566--66591 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66556 ATGGCAAGAA
66566 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
66592 TACCTAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72401 original size:21 final size:21
Alignment explanation
Indices: 72377--72416 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
72367 AGAACCCTGA
*
72377 TTTGTAATTCCAAACTAGTAT
1 TTTGTAATACCAAACTAGTAT
* *
72398 TTTGTGATACCAATCTAGT
1 TTTGTAATACCAAACTAGT
72417 TTCCGGTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTGTAATACCAAACTAGTAT
Found at i:90033 original size:17 final size:17
Alignment explanation
Indices: 90011--90050 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
90001 ATTTTTACTC
*
90011 ACAAAAAAAGTAAAAAT
1 ACAAAAAAAATAAAAAT
90028 ACAAAAAAAATAAAAAT
1 ACAAAAAAAATAAAAAT
90045 A-AAAAA
1 ACAAAAA
90051 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (17 bp):
ACAAAAAAAATAAAAAT
Found at i:92740 original size:7 final size:7
Alignment explanation
Indices: 92728--92753 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
92718 TTATATTATT
92728 TAATTAA
1 TAATTAA
92735 TAATTAA
1 TAATTAA
92742 TAATTAA
1 TAATTAA
92749 TAATT
1 TAATT
92754 CCAGGTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TAATTAA
Found at i:96410 original size:19 final size:19
Alignment explanation
Indices: 96386--96422 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
96376 AAAAAAAAAA
96386 ATTAAACATCAAA-TTAAAC
1 ATTAAA-ATCAAACTTAAAC
96405 ATTAAAATCAAACTTAAA
1 ATTAAAATCAAACTTAAA
96423 TACTTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (19 bp):
ATTAAAATCAAACTTAAAC
Found at i:101605 original size:15 final size:15
Alignment explanation
Indices: 101585--101617 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
101575 TGTTCTCTCC
101585 GTGATGGTGACGGTG
1 GTGATGGTGACGGTG
*
101600 GTGATGGTGGCGGTG
1 GTGATGGTGACGGTG
101615 GTG
1 GTG
101618 TTTATGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.06, G:0.58, T:0.27
Consensus pattern (15 bp):
GTGATGGTGACGGTG
Found at i:102495 original size:21 final size:22
Alignment explanation
Indices: 102452--102502 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
102442 TACAATATTC
*
102452 AAATAATATTAAAAAACAGT-A
1 AAATAATAATAAAAAACAGTAA
*
102473 AAATAATAATAAAAACGCA-TAA
1 AAATAATAATAAAAA-ACAGTAA
102495 AAATAATA
1 AAATAATA
102503 TCCAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (22 bp):
AAATAATAATAAAAAACAGTAA
Found at i:102524 original size:12 final size:12
Alignment explanation
Indices: 102507--102531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102497 ATAATATCCA
102507 AACAATCAAAAT
1 AACAATCAAAAT
102519 AACAATCAAAAT
1 AACAATCAAAAT
102531 A
1 A
102532 GTAGCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (12 bp):
AACAATCAAAAT
Found at i:102586 original size:23 final size:22
Alignment explanation
Indices: 102560--102702 Score: 101
Period size: 23 Copynumber: 6.4 Consensus size: 22
102550 AATAACAACA
*
102560 AAAATAATAATAAAAACAGCACC
1 AAAACAATAA-AAAAACAGCACC
* * * *
102583 AAAATAGTTAAAAAAATAGCATC
1 AAAACA-ATAAAAAAACAGCACC
* *
102606 AAAACAATAAACAAA-AGCATC
1 AAAACAATAAAAAAACAGCACC
* * *
102627 AAAACAGTAAAAACACAACACC
1 AAAACAATAAAAAAACAGCACC
* *
102649 AAAACAA-CAAAAAATAGCAACC
1 AAAACAATAAAAAAACAGC-ACC
* * *
102671 AAAATAACAAAAAAAACAGCACA
1 AAAACAA-TAAAAAAACAGCACC
102694 AAAACAATA
1 AAAACAATA
102703 TAATTTTTTA
Statistics
Matches: 93, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
21 25 0.27
22 27 0.29
23 29 0.31
24 12 0.13
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAACAATAAAAAAACAGCACC
Found at i:102616 original size:22 final size:22
Alignment explanation
Indices: 102526--102702 Score: 99
Period size: 23 Copynumber: 7.9 Consensus size: 22
102516 AATAACAATC
* *
102526 AAAATAGTAGCAAAA-AATAGAA
1 AAAATAGCACCAAAACAATA-AA
* * *
102548 AAAATAACAACAAAAATAATAATA
1 AAAATAGC-ACCAAAACAATAA-A
* * *
102572 AAAACAGCACCAAAATAGTTAAA
1 AAAATAGCACCAAAACA-ATAAA
*
102595 AAAATAGCATCAAAACAATAAA
1 AAAATAGCACCAAAACAATAAA
* * *
102617 CAAA-AGCATCAAAACAGTAAA
1 AAAATAGCACCAAAACAATAAA
* * * *
102638 AACACAACACCAAAACAA-CAA
1 AAAATAGCACCAAAACAATAAA
* *
102659 AAAATAGCAACCAAAATAACAAAA
1 AAAATAGC-ACCAAAACAA-TAAA
* *
102683 AAAACAGCACAAAAACAATA
1 AAAATAGCACCAAAACAATA
102703 TAATTTTTTA
Statistics
Matches: 118, Mismatches: 29, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
21 25 0.21
22 33 0.28
23 37 0.31
24 23 0.19
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAATAGCACCAAAACAATAAA
Found at i:102626 original size:21 final size:22
Alignment explanation
Indices: 102526--102702 Score: 83
Period size: 22 Copynumber: 7.9 Consensus size: 22
102516 AATAACAATC
* *
102526 AAAATAGTAGCAAAA-AATAGAA
1 AAAATAGCATCAAAACAATA-AA
* * *
102548 AAAATAACAACAAAAATAATAATA
1 AAAATAGCATC-AAAACAATAA-A
* * * *
102572 AAAACAGCACCAAAATAGTTAAA
1 AAAATAGCATCAAAACA-ATAAA
102595 AAAATAGCATCAAAACAATAAA
1 AAAATAGCATCAAAACAATAAA
* *
102617 CAAA-AGCATCAAAACAGTAAA
1 AAAATAGCATCAAAACAATAAA
* * * * *
102638 AACACAACACCAAAACAA-CAA
1 AAAATAGCATCAAAACAATAAA
* * *
102659 AAAATAGCAACCAAAATAACAAAA
1 AAAATAGC-ATCAAAACAA-TAAA
*
102683 AAAACAGCA-CAAAAACAATA
1 AAAATAGCATC-AAAACAATA
102703 TAATTTTTTA
Statistics
Matches: 119, Mismatches: 27, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
21 25 0.21
22 36 0.30
23 33 0.28
24 25 0.21
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAATAGCATCAAAACAATAAA
Found at i:105224 original size:22 final size:22
Alignment explanation
Indices: 105194--105249 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
105184 ACGCTAGCAC
*
105194 GCTTACTGTTTAGCACTGTGTGT
1 GCTT-CTGTTTAGCACTATGTGT
*
105217 GCTTCTGTTCAGCACTATGTGT
1 GCTTCTGTTTAGCACTATGTGT
*
105239 GCCTACTGTTT
1 G-CTTCTGTTT
105250 CTCAGCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.43
Consensus pattern (22 bp):
GCTTCTGTTTAGCACTATGTGT
Found at i:105284 original size:25 final size:25
Alignment explanation
Indices: 105244--105322 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
105234 TGTGTGCCTA
*
105244 CTGTTT-CTCAGCACTTATGAGCTT
1 CTGTTTCCCCAGCACTTATGAGCTT
*
105268 CTGTTTCCCCAGCACTTATGTGCTT
1 CTGTTTCCCCAGCACTTATGAGCTT
* * *
105293 TTGTTTCCCTAGCACTTATGCGCTT
1 CTGTTTCCCCAGCACTTATGAGCTT
105318 CTGTT
1 CTGTT
105323 AAGTACTTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 6 0.12
25 42 0.88
ACGTcount: A:0.13, C:0.28, G:0.16, T:0.43
Consensus pattern (25 bp):
CTGTTTCCCCAGCACTTATGAGCTT
Found at i:116012 original size:20 final size:18
Alignment explanation
Indices: 115983--116025 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
115973 GGTTAATTAT
*
115983 ATTAAGTAAACCATAGTTTA
1 ATTAAGTAAA-CA-AGGTTA
*
116003 ATTAATTAAACAAGGTTA
1 ATTAAGTAAACAAGGTTA
116021 ATTAA
1 ATTAA
116026 CATTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (18 bp):
ATTAAGTAAACAAGGTTA
Found at i:123900 original size:18 final size:18
Alignment explanation
Indices: 123877--123924 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
123867 TTGTGCTTAC
*
123877 TCTTCTCCTTCTCGGGCT
1 TCTTCTCCTTCTCAGGCT
*
123895 TCTTCTTGC-TCTCAGGCT
1 TCTTC-TCCTTCTCAGGCT
*
123913 TCTTTTCCTTCT
1 TCTTCTCCTTCT
123925 TTTCTTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.02, C:0.35, G:0.12, T:0.50
Consensus pattern (18 bp):
TCTTCTCCTTCTCAGGCT
Found at i:123925 original size:9 final size:9
Alignment explanation
Indices: 123911--123989 Score: 56
Period size: 9 Copynumber: 8.8 Consensus size: 9
123901 TGCTCTCAGG
123911 CTTCTTTTC
1 CTTCTTTTC
123920 CTTCTTTTC
1 CTTCTTTTC
*
123929 TTTCTTTTC
1 CTTCTTTTC
* *
123938 CTTCCTGTC
1 CTTCTTTTC
123947 CTTGTCTTTCTC
1 C-T-TCTTT-TC
*
123959 CTTCTTGT-
1 CTTCTTTTC
**
123967 CTT-TCAT-
1 CTTCTTTTC
123974 CTTCTTTTC
1 CTTCTTTTC
123983 CTTCTTT
1 CTTCTTT
123990 CCATGGCAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 32 0.59
10 5 0.09
11 4 0.07
12 3 0.06
ACGTcount: A:0.01, C:0.32, G:0.04, T:0.63
Consensus pattern (9 bp):
CTTCTTTTC
Found at i:126673 original size:12 final size:12
Alignment explanation
Indices: 126652--126684 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
126642 AAGGGATCCC
126652 TTTCTTTCTTGG
1 TTTCTTTCTTGG
*
126664 TTTTTTTCTTGG
1 TTTCTTTCTTGG
126676 TTTCTTTCT
1 TTTCTTTCT
126685 CAGCTTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTCTTTCTTGG
Found at i:156225 original size:57 final size:57
Alignment explanation
Indices: 156138--156250 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
156128 ATATATGTAA
*
156138 AAAAAAATATTGTTTTGTTCAGACTTTCTAAGTTTCTTTCACAAGGGATTCGTACTT
1 AAAAAAATATTGTTTTGTTCAGACTTTCTAAGTTTCTTTCACAAGGGATTCATACTT
156195 AAAAAAATATTGTTTTGTTCAGACTTTCTAAGTTTCTTTCACAAGGGATTCATACT
1 AAAAAAATATTGTTTTGTTCAGACTTTCTAAGTTTCTTTCACAAGGGATTCATACT
156251 CTGTTTAAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (57 bp):
AAAAAAATATTGTTTTGTTCAGACTTTCTAAGTTTCTTTCACAAGGGATTCATACTT
Found at i:176940 original size:45 final size:45
Alignment explanation
Indices: 176891--176980 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
176881 TGGACAGTAA
176891 CAGGGGACTAACTTCGAAAATTCACCAAAAATTGTATATAATGAG
1 CAGGGGACTAACTTCGAAAATTCACCAAAAATTGTATATAATGAG
*
176936 CAGGGGACTAACTTCGAAAATTCCCCAAAAATTGTATATAATGAG
1 CAGGGGACTAACTTCGAAAATTCACCAAAAATTGTATATAATGAG
176981 TTAAGCGTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (45 bp):
CAGGGGACTAACTTCGAAAATTCACCAAAAATTGTATATAATGAG
Done.