Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 138 of 172
Found at i:39679579 original size:12 final size:12
Alignment explanation
Indices: 39679552--39679596 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
39679542 TAATATACAC
*
39679552 AATAAACAAAAAA
1 AATAAA-AATAAA
39679565 AATAAAAATAAA
1 AATAAAAATAAA
39679577 AATAAAAATAAAA
1 AATAAAAAT-AAA
39679590 AATAAAA
1 AATAAAA
39679597 CATATAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 14 0.47
13 16 0.53
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.13
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:39682313 original size:2 final size:2
Alignment explanation
Indices: 39682308--39682346 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39682298 CCCTCCCCCC
39682308 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
39682347 CATATATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:39682406 original size:2 final size:2
Alignment explanation
Indices: 39682401--39682454 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
39682391 CTCAGCTGCA
*
39682401 TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39682443 TC TC TC TC TC TC
1 TC TC TC TC TC TC
39682455 CATATATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:39688967 original size:43 final size:42
Alignment explanation
Indices: 39688898--39689053 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 42
39688888 GGCTTGTACA
* *
39688898 ATGCCAACGTCCCAGACGTGGGCTTACATTTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACA-CTAATCACATATCG
* *
39688941 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACTAATCACATATCG
* * *
39688982 ATGCTAATGTCCCAGACATGGTCTTACACGT-ATACACA-ATTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACAC-TAAT-CACATA-TCG
39689025 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
39689054 GAAAATACAT
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
41 28 0.30
42 14 0.15
43 50 0.54
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACTAATCACATATCG
Found at i:39690732 original size:3 final size:3
Alignment explanation
Indices: 39690724--39690861 Score: 260
Period size: 3 Copynumber: 46.3 Consensus size: 3
39690714 GCATTAAACA
39690724 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39690772 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
39690819 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39690862 GCTGAGGTAG
Statistics
Matches: 132, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
2 2 0.02
3 130 0.98
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39691765 original size:117 final size:121
Alignment explanation
Indices: 39691631--39691869 Score: 324
Period size: 124 Copynumber: 2.0 Consensus size: 121
39691621 CTTCATCTAA
* *
39691631 TCTCTCTCTCTCTCTCTCCATATATATTAGCA-CT-TT-GATTTTTTATCAGAAAAATCT-AGCT
1 TCTCTCTCTCTCTCTCTCCATATATATTAACATCTCTTCGATTTTTTATCAGAAAAAACTCAGCT
*
39691692 ACAATAATGGTGCAAGGAGAAGTAAACAAGAAGGGAAAAGGGAAAGCCATTGTGAC
66 ACAACAATGGTGCAAGGAGAAGTAAACAAGAAGGGAAAAGGGAAAGCCATTGTGAC
* *
39691748 TCTCTCTCTCTCTCTCTCCATATATATTAACACTTTCTCTTCGCTTTTTTATTAGAAAAAACTCA
1 TCTCTCTCTCTCTCTCTCCATATATATTAACA---TCTCTTCGATTTTTTATCAGAAAAAACTCA
* * * * * *
39691813 GTTGCCACAATGGTGCAAGGAGAAGTAGACTAGAAGGGCAAAGGGAAAGCCATTGTG
63 GCTACAACAATGGTGCAAGGAGAAGTAAACAAGAAGGGAAAAGGGAAAGCCATTGTG
39691870 CCATGAAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
117 31 0.30
121 2 0.02
122 2 0.02
123 18 0.17
124 51 0.49
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (121 bp):
TCTCTCTCTCTCTCTCTCCATATATATTAACATCTCTTCGATTTTTTATCAGAAAAAACTCAGCT
ACAACAATGGTGCAAGGAGAAGTAAACAAGAAGGGAAAAGGGAAAGCCATTGTGAC
Found at i:39692040 original size:54 final size:54
Alignment explanation
Indices: 39691972--39692078 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
39691962 CAAAAGCTGA
39691972 AGGTAAAAGTTGGCAAGAACCCATATGCTAATAGTGCCAATCCTCATTTTCATT
1 AGGTAAAAGTTGGCAAGAACCCATATGCTAATAGTGCCAATCCTCATTTTCATT
*
39692026 AGGTAAAAGTTGGCAAGAACCCTTATGCTAATAGTGCCAATCCTCATTTTCAT
1 AGGTAAAAGTTGGCAAGAACCCATATGCTAATAGTGCCAATCCTCATTTTCAT
39692079 CCTTTCAGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
AGGTAAAAGTTGGCAAGAACCCATATGCTAATAGTGCCAATCCTCATTTTCATT
Found at i:39692581 original size:15 final size:17
Alignment explanation
Indices: 39692561--39692598 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
39692551 TCATCACTGC
39692561 CCATCCCT-T-GCTCCT
1 CCATCCCTATCGCTCCT
39692576 CCATCCCTATCGCTCCT
1 CCATCCCTATCGCTCCT
39692593 -CATCCC
1 CCATCCC
39692599 GCTGCCCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.11, C:0.55, G:0.05, T:0.29
Consensus pattern (17 bp):
CCATCCCTATCGCTCCT
Found at i:39701727 original size:14 final size:14
Alignment explanation
Indices: 39701704--39701734 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39701694 TGTCGCGTTC
*
39701704 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
39701718 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
39701732 TTA
1 TTA
39701735 AAATAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:39704805 original size:6 final size:6
Alignment explanation
Indices: 39704794--39704819 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39704784 CTATTAATTA
39704794 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
39704820 CATGTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:39705658 original size:21 final size:21
Alignment explanation
Indices: 39705632--39705671 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39705622 ATTTCTCCCA
39705632 TTTTTAGTTCTTTATTTTTGG
1 TTTTTAGTTCTTTATTTTTGG
* *
39705653 TTTTTATTTTTTTATTTTT
1 TTTTTAGTTCTTTATTTTT
39705672 TATTTAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTAGTTCTTTATTTTTGG
Found at i:39705664 original size:14 final size:14
Alignment explanation
Indices: 39705631--39705663 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39705621 TATTTCTCCC
39705631 ATTTTTAGTTCTTT
1 ATTTTTAGTTCTTT
*
39705645 ATTTTTGGTT-TTT
1 ATTTTTAGTTCTTT
39705658 ATTTTT
1 ATTTTT
39705664 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (14 bp):
ATTTTTAGTTCTTT
Found at i:39705704 original size:14 final size:13
Alignment explanation
Indices: 39705668--39705702 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
39705658 ATTTTTTTAT
39705668 TTTTTATTTAAGA
1 TTTTTATTTAAGA
39705681 TTTTTATTTAA-A
1 TTTTTATTTAAGA
39705693 TATTTTATTT
1 T-TTTTATTT
39705703 TATGTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTTATTTAAGA
Found at i:39707370 original size:28 final size:30
Alignment explanation
Indices: 39707315--39707376 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
39707305 ATGGATTTAA
39707315 ATTACTTATTATTTAAGCAAATAGATATTT
1 ATTACTTATTATTTAAGCAAATAGATATTT
* *
39707345 ATTATTTATT-TTTAAGTAAA-AGATATTT
1 ATTACTTATTATTTAAGCAAATAGATATTT
39707373 ATTA
1 ATTA
39707377 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.40
29 9 0.30
30 9 0.30
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50
Consensus pattern (30 bp):
ATTACTTATTATTTAAGCAAATAGATATTT
Found at i:39715199 original size:6 final size:6
Alignment explanation
Indices: 39715181--39715237 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
39715171 TCCCCTTACT
* * * *
39715181 CTCTCC CTTTCC CTCTCC CTCTCC CTCTCA TTCTCC TTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
*
39715229 CTCCCC CTC
1 CTCTCC CTC
39715238 CATATATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.02, C:0.61, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCTCC
Found at i:39717405 original size:37 final size:37
Alignment explanation
Indices: 39717355--39717433 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39717345 TTATTACGAA
* * *
39717355 GTCTTACCCGGACATAATCTCCACACGA-AGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATCGG
39717392 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
39717429 GTCTT
1 GTCTT
39717434 TAGAGCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
Found at i:39717929 original size:24 final size:23
Alignment explanation
Indices: 39717881--39717938 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
39717871 TAATCAAGCA
39717881 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
39717905 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
39717929 TTATT-TTATA
1 TTATTATTATA
39717939 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:39720818 original size:184 final size:176
Alignment explanation
Indices: 39720442--39720858 Score: 532
Period size: 184 Copynumber: 2.3 Consensus size: 176
39720432 ACGATAAATC
** * * * * *
39720442 AAAATTAGGTCAAGAATATAAAATAGAGCACGTGTAAGTCGATAAACTCATTGCCAAGTATGTGA
1 AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGAAAAACTCATTGCAAAGTATGAGA
* * * *
39720507 TAATTAATATGTACATCAATAAATACAAAAAAAATTATATAATAGAGCACGTGTAAGTCGATAAA
66 TAAGTAATATGCACATCAATAAATACAAAAAAAATTATATAATAGAACACGTATAAGTCGATAAA
* *
39720572 CCGGTCACAATTGAAACTATAAATCTTTGCATTGAAATAGAAGAAA
131 CCGGTCACAATTGAAACTATAAATCTTTGCATTAAAATAGAAAAAA
* *
39720618 AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGACAAACTCATTGTAAAGTATGAGA
1 AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGAAAAACTCATTGCAAAGTATGAGA
* *
39720683 TAAGTAATGTGCACATCAATAAATACGTAAAAAAAATTCAAAAGCATATAGTAGAACATC-TATA
66 TAAGTAATATGCACATCAATAAATAC--AAAAAAAATT-------ATATAATAGAACA-CGTATA
** * *
39720747 AGTCGATAAATTGGTTAC-ATTGAAACTATAAATCTTTGCATTAAAATATAAAAAA
121 AGTCGATAAACCGGTCACAATTGAAACTATAAATCTTTGCATTAAAATAGAAAAAA
*
39720802 AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGAAAAACTCGTTGCAAA
1 AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGAAAAACTCATTGCAAA
39720859 TTATACTATA
Statistics
Matches: 208, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
176 80 0.38
178 10 0.05
184 88 0.42
185 29 0.14
186 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (176 bp):
AAAATTAATTCAAGAATATAAAATAAAGCACGTGTAAGTTGAAAAACTCATTGCAAAGTATGAGA
TAAGTAATATGCACATCAATAAATACAAAAAAAATTATATAATAGAACACGTATAAGTCGATAAA
CCGGTCACAATTGAAACTATAAATCTTTGCATTAAAATAGAAAAAA
Found at i:39723686 original size:2 final size:2
Alignment explanation
Indices: 39723681--39723729 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
39723671 TCATTCCCCC
* *
39723681 CT CT CT CT CT CT CT CT CT CT CT AT CT CT AT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39723723 CT CT CT C
1 CT CT CT C
39723730 CTTCCCTCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:39733980 original size:5 final size:5
Alignment explanation
Indices: 39733970--39734028 Score: 72
Period size: 5 Copynumber: 12.2 Consensus size: 5
39733960 AATTATGTTT
39733970 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -T-TA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
39734017 TTATA TATATA T
1 TTATA T-TATA T
39734029 GACAAAGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.08
4 4 0.08
5 30 0.62
6 10 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:39733986 original size:13 final size:13
Alignment explanation
Indices: 39733970--39734022 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 13
39733960 AATTATGTTT
39733970 TTATATTATATTA
1 TTATATTATATTA
*
39733983 TTATTAATATATTATA
1 TTA-TATTATA-T-TA
39733999 TTATATTATATTA
1 TTATATTATATTA
39734012 TTATATTATAT
1 TTATATTATAT
39734023 ATATATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 16 0.46
14 7 0.20
15 7 0.20
16 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTATATTA
Found at i:39734002 original size:29 final size:29
Alignment explanation
Indices: 39733970--39734028 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
39733960 AATTATGTTT
39733970 TTATATTATATTATTATTAATATAT-TATA
1 TTATATTATATTATTA-TAATATATATATA
*
39733999 TTATATTATATTATTATATTATATATATA
1 TTATATTATATTATTATAATATATATATA
39734028 T
1 T
39734029 GACAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTATATTATATTATTATAATATATATATA
Found at i:39734094 original size:40 final size:41
Alignment explanation
Indices: 39734037--39734132 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 41
39734027 ATGACAAAGA
39734037 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
39734078 GAGAAAG-AAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
39734118 AAGAAAGAAAAGAAA
1 AAGAAAGAAAAGAAA
39734133 AGAAAAAGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 38 0.75
41 13 0.25
ACGTcount: A:0.66, C:0.08, G:0.26, T:0.00
Consensus pattern (41 bp):
AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:39734345 original size:13 final size:13
Alignment explanation
Indices: 39734327--39734358 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39734317 TTTCCAGCAA
39734327 TTATGAATTTATT
1 TTATGAATTTATT
39734340 TTATGAATTTATT
1 TTATGAATTTATT
*
39734353 TGATGA
1 TTATGA
39734359 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:39734566 original size:50 final size:50
Alignment explanation
Indices: 39734453--39734694 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
39734443 ATTTGGGTAA
* * *
39734453 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
39734509 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
39734559 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
39734609 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
39734659 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
39734695 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:39734642 original size:100 final size:103
Alignment explanation
Indices: 39734453--39734702 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
39734443 ATTTGGGTAA
39734453 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
39734518 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
39734559 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
39734621 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
39734659 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
39734703 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:39736367 original size:25 final size:24
Alignment explanation
Indices: 39736334--39736380 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
39736324 GCTTAGGGAT
39736334 TTTATTTTATTCAATATTAATATA
1 TTTATTTTATTCAATATTAATATA
*
39736358 TTTATATTTATTTAATATTAATA
1 TTTAT-TTTATTCAATATTAATA
39736381 CAAAATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTTATTCAATATTAATATA
Found at i:39738758 original size:2 final size:2
Alignment explanation
Indices: 39738751--39738798 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
39738741 GGAAAGCCGT
39738751 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39738792 TC TC TC T
1 TC TC TC T
39738799 GATAAAAAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39739182 original size:3 final size:3
Alignment explanation
Indices: 39739174--39739199 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39739164 TCAATCCCAG
39739174 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
39739200 TGAAGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39746775 original size:41 final size:41
Alignment explanation
Indices: 39746718--39746799 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
39746708 GTAGCAAAGT
39746718 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
39746759 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
39746800 TAAAGCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (41 bp):
CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
Found at i:39749053 original size:365 final size:365
Alignment explanation
Indices: 39748383--39749104 Score: 1354
Period size: 365 Copynumber: 2.0 Consensus size: 365
39748373 AGCATGAGTT
39748383 TCCATGAGGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATC
1 TCCATGAGGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATC
* *
39748448 TCAGCAAGCATATTTTGGAAGAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAA
66 TCAGCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAATCAA
*
39748513 CATCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTG
131 CAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTG
39748578 AGCAAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTATCCTG
196 AGCAAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTATCCTG
39748643 CTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAA
261 CTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAA
39748708 CTGTATACACAGACAATCAGAGGCAAATCTAGTGAGTTTA
326 CTGTATACACAGACAATCAGAGGCAAATCTAGTGAGTTTA
* *
39748748 TCCATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTTTTAACAATTTAAGAAACCAACATC
1 TCCATGAGGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATC
39748813 TCAGCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAATCAA
66 TCAGCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAATCAA
39748878 CAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTG
131 CAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTG
* *
39748943 AGCAGGAAAAAGATAACACGCATGACAGAAAATATTAAATAGGAAGTTTGTTTGATGTTATCCTG
196 AGCAAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTATCCTG
39749008 CTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAA
261 CTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAA
* * *
39749073 CTGTATTCACAGACAGTCAGAGGCGAATCTAG
326 CTGTATACACAGACAATCAGAGGCAAATCTAG
39749105 GGGGCAGGCA
Statistics
Matches: 347, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
365 347 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (365 bp):
TCCATGAGGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATC
TCAGCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAATCAA
CAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTG
AGCAAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTATCCTG
CTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAA
CTGTATACACAGACAATCAGAGGCAAATCTAGTGAGTTTA
Found at i:39755316 original size:7 final size:7
Alignment explanation
Indices: 39755304--39755329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39755294 ATTTTGATAA
39755304 AAATTTT
1 AAATTTT
39755311 AAATTTT
1 AAATTTT
39755318 AAATTTT
1 AAATTTT
39755325 AAATT
1 AAATT
39755330 AAATATTTTG
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:39757867 original size:50 final size:50
Alignment explanation
Indices: 39757739--39757987 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
39757729 GATAATAACA
* * ** * *
39757739 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
39757790 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
39757840 TGCCAACGCCATGTCCCAGACACGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
39757890 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
39757945 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
39757988 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39757916 original size:100 final size:104
Alignment explanation
Indices: 39757738--39757987 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
39757728 TGATAATAAC
**
39757738 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
39757803 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
39757840 -TGCCAACGCCATGTCCCAGACACGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
39757903 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
39757945 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39757988 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:39758103 original size:13 final size:13
Alignment explanation
Indices: 39758082--39758113 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39758072 GCTTGGACCA
*
39758082 TCATCAAATAAAT
1 TCATAAAATAAAT
39758095 TCATAAAATAAAT
1 TCATAAAATAAAT
39758108 TCATAA
1 TCATAA
39758114 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:39760161 original size:227 final size:230
Alignment explanation
Indices: 39759672--39760173 Score: 629
Period size: 227 Copynumber: 2.2 Consensus size: 230
39759662 CACTTAATTA
* * * *
39759672 TCTTTTGTTTCTTTCTTATAATA-CTCTTCTTTGATGCCATAAGTGATCTTTAAAAAATATTATC
1 TCTTTTGTTTCTTTCTTATAA-AGCTTTTCTTTGATGCCATAAGTGAGCATTAAAAAATATCATC
* *
39759736 AACCAACCAAATATTTCTCAAAATCAACAATTACCAAGTACACAACAATACTCGTTTCTCAAGAA
65 AACCAACCAAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCT-AAGAA
* * *
39759801 AAAGAAATGCAAGAATATTACCAATGGAGCAAATAGCCATAATATTCTTTCACCAACAAGGGTAA
129 AAAGAAATGCAAGAATATTACCAATGGAACAAATAGCCATAATATTCTTGCACCAACAAAGGTAA
** ***
39759866 TTCTGATCAAATGATAATCAAGTATTGCACTCAATTG
194 TTCTGATCAAATGATAATCAAGTATCACACTCAACCC
* * * * * * *
39759903 TCATTTGTTTCTTTTTTATAATGCCTTTCTTTGATGCCTTAAGTGAGCATTAATAAATCTCATCA
1 TCTTTTGTTTCTTTCTTATAAAGCTTTTCTTTGATGCCATAAGTGAGCATTAAAAAATATCATCA
* ** * **
39759968 ATCAAGTAAATATTTCCCAAAATCAACAATTA-CAAGTACACAACAATATTCATTTCT-TTAAAA
66 ACCAACCAAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAA
* *
39760031 A-AAATG-AAGAATCTTACCAATGGAAACAAATA-CTCATAATCTTCTTGCACCAACAAAGGTAA
131 AGAAATGCAAGAATATTACCAATGG-AACAAATAGC-CATAATATTCTTGCACCAACAAAGGTAA
* * * *
39760093 TTTTGATCAAATGGTAATTAAGTATCACACTCAGCCC
194 TTCTGATCAAATGATAATCAAGTATCACACTCAACCC
39760130 TCTTTTGTTTCTTTCTTATAAAGCTTTTCTTTGATGCCATAAGT
1 TCTTTTGTTTCTTTCTTATAAAGCTTTTCTTTGATGCCATAAGT
39760174 AATAATTAAT
Statistics
Matches: 230, Mismatches: 38, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
226 17 0.07
227 104 0.45
228 5 0.02
230 23 0.10
231 81 0.35
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (230 bp):
TCTTTTGTTTCTTTCTTATAAAGCTTTTCTTTGATGCCATAAGTGAGCATTAAAAAATATCATCA
ACCAACCAAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAA
AGAAATGCAAGAATATTACCAATGGAACAAATAGCCATAATATTCTTGCACCAACAAAGGTAATT
CTGATCAAATGATAATCAAGTATCACACTCAACCC
Found at i:39765457 original size:325 final size:327
Alignment explanation
Indices: 39764860--39765488 Score: 870
Period size: 325 Copynumber: 1.9 Consensus size: 327
39764850 TCTTTTGAGC
* * * **
39764860 TAAAAATATTTATTTTATTGTTGTTTATTTATATACACATTGCTAATGATCACTTCTCCATTTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * * *
39764925 AAATACTTTATCCTCCAAGAAAAATGGGATAAGCAAGAACAAAGGACGAAAACTTAGCTCGAGTG
66 AAATACCTCATCCTCCAAGAAAAATGGGATAAGCAAGAACAAAGGACAAAAACGTAGCTCGAGTA
* * * * * ** *
39764990 TAACCTTGACCTTCTAAAACCATCGAGTCTAGTAACTCTCCAAACCATCTATAGTGTGAATTGTT
131 TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
* ** *
39765055 CTCATTTTAGTGGCTATCCATACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
196 CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
* *
39765120 TGTGTTACTTAATTGTTAT-AT-TAAAAATAAGATGAATATTTGTTTTATTGTTATTTATCGTTA
261 TGTGTAACTTAATTGTTATCATATAAAAA-AAGATAAATATTTGTTTTATTGTTATTTATCGTTA
39765183 TAA
325 TAA
* **
39765186 TAAAAATATTTATTTTATTGATATTTATTTATATACACTTTGCTTGCGATCACTTCTCCACCTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * *
39765251 AAATACCTCATCCTCCAA-AAAAATGGGCTAAGCAATAAGAAAGTACAAAAACGTAGCTCGAGTA
66 AAATACCTCATCCTCCAAGAAAAATGGGATAAGCAAGAACAAAGGACAAAAACGTAGCTCGAGTA
* * *
39765315 TAACCTCGACCTTCTAAAACCACCAAATCTAGCGACTGTCCACACCATCTATAGTGTGAACCGCT
131 TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
* * *
39765380 CCCATTTTAGCAGCTCTCCACACCTCATATGATGTGAACTACTCC-CATTGTATTATTCGACATC
196 CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTAC-CCTCATTGTATTATTCGACATA
39765444 TTGTGTAACTTAATTGTTATCATAATAAAAAAAGATAAATATTTG
260 TTGTGTAACTTAATTGTTATCAT-ATAAAAAAAGATAAATATTTG
39765489 ATACATTGTC
Statistics
Matches: 262, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
325 166 0.63
326 77 0.29
327 13 0.05
328 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (327 bp):
TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
AAATACCTCATCCTCCAAGAAAAATGGGATAAGCAAGAACAAAGGACAAAAACGTAGCTCGAGTA
TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
TGTGTAACTTAATTGTTATCATATAAAAAAAGATAAATATTTGTTTTATTGTTATTTATCGTTAT
AA
Found at i:39765734 original size:14 final size:14
Alignment explanation
Indices: 39765715--39765744 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39765705 CTAAAATCTG
39765715 AACTCAAAACTTAA
1 AACTCAAAACTTAA
39765729 AACTCAAAACTTAA
1 AACTCAAAACTTAA
39765743 AA
1 AA
39765745 AAGAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (14 bp):
AACTCAAAACTTAA
Found at i:39768032 original size:26 final size:24
Alignment explanation
Indices: 39767988--39768040 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
39767978 AAGTTCAAGC
*
39767988 GAGCCATAACGGGTAGCTCATGAA
1 GAGCCATAACGGGTAGCTCATAAA
39768012 GAGCCATATATCGGG-ACGCTCATAAA
1 GAGCCATA-A-CGGGTA-GCTCATAAA
39768038 GAG
1 GAG
39768041 ATGTGGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 15 0.60
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (24 bp):
GAGCCATAACGGGTAGCTCATAAA
Found at i:39770600 original size:14 final size:15
Alignment explanation
Indices: 39770571--39770607 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
39770561 CTCACTTTCG
39770571 AAATTAATAGAAATT
1 AAATTAATAGAAATT
*
39770586 AAATTAGTA-AAATT
1 AAATTAATAGAAATT
39770600 AAA-TAATA
1 AAATTAATA
39770608 TAGGTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAATTAATAGAAATT
Found at i:39774420 original size:92 final size:92
Alignment explanation
Indices: 39774317--39774504 Score: 315
Period size: 92 Copynumber: 2.0 Consensus size: 92
39774307 CAAAACTCAA
39774317 AACAAGTTTCAAAATA-TCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTC
1 AACAAGTTTCAAAA-AGTCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTC
*
39774381 GACAAGATTTATTAAGTAGTGAAATCGC
65 GACAAGATTTATTAAGTAGTGAAATCAC
* * * *
39774409 AACAAGTTTCAAAAAGTTAAAATAACTTAAAATAGTGCAATGTTAAAAATAAGTGCCACTTCTCG
1 AACAAGTTTCAAAAAGTCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTCG
39774474 ACAAGATTTATTAAGTAGTGAAATCAC
66 ACAAGATTTATTAAGTAGTGAAATCAC
39774501 AACA
1 AACA
39774505 TAAATTATGC
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 1 0.01
92 89 0.99
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (92 bp):
AACAAGTTTCAAAAAGTCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTCG
ACAAGATTTATTAAGTAGTGAAATCAC
Found at i:39777798 original size:37 final size:36
Alignment explanation
Indices: 39777726--39777798 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 36
39777716 ATGACTAAAC
*
39777726 AATTCAATAATATAAATAATAAAAAAATGTGAAATTT
1 AATTCAATAATATAAATAATAAAAAAA-GTAAAATTT
* *
39777763 AATTTAATAATATAAATAGTAAATATAAA-TAAAATT
1 AATTCAATAATATAAATAATAAA-A-AAAGTAAAATT
39777799 ATTACTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 27 0.87
38 1 0.03
39 3 0.10
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (36 bp):
AATTCAATAATATAAATAATAAAAAAAGTAAAATTT
Found at i:39782478 original size:9 final size:9
Alignment explanation
Indices: 39782461--39782527 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
39782451 GTAGTGATTC
*
39782461 AATTTGGTT
1 AATTCGGTT
39782470 AATTCGGTT
1 AATTCGGTT
*
39782479 AATTCGGGT
1 AATTCGGTT
*
39782488 AATTTGGTT
1 AATTCGGTT
39782497 AATTCGGTT
1 AATTCGGTT
39782506 AATTCAGG-T
1 AATTC-GGTT
39782515 AATTCGGTT
1 AATTCGGTT
39782524 AATT
1 AATT
39782528 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
8 2 0.04
9 47 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39782493 original size:27 final size:27
Alignment explanation
Indices: 39782461--39782527 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
39782451 GTAGTGATTC
*
39782461 AATTTGGTTAATTCGGTTAATTCGGGT
1 AATTTGGTTAATTCGGTTAATTCAGGT
39782488 AATTTGGTTAATTCGGTTAATTCAGGT
1 AATTTGGTTAATTCGGTTAATTCAGGT
*
39782515 AATTCGGTTAATT
1 AATTTGGTTAATT
39782528 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (27 bp):
AATTTGGTTAATTCGGTTAATTCAGGT
Found at i:39784490 original size:42 final size:42
Alignment explanation
Indices: 39784443--39784531 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
39784433 TGTGACCATA
39784443 TGTATATGCAAGTATGCCAAAGGGTTAAATGGTTATCAACAT
1 TGTATATGCAAGTATGCCAAAGGGTTAAATGGTTATCAACAT
39784485 TGTATATGCAAGTATGCCAAAGGGTTAAATGGTTATCAACAT
1 TGTATATGCAAGTATGCCAAAGGGTTAAATGGTTATCAACAT
*
39784527 GGTAT
1 TGTAT
39784532 TTACTTGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (42 bp):
TGTATATGCAAGTATGCCAAAGGGTTAAATGGTTATCAACAT
Found at i:39794101 original size:9 final size:9
Alignment explanation
Indices: 39794070--39794112 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
39794060 GTTCAAGGTG
39794070 TAATTAATT
1 TAATTAATT
39794079 TAA-TAATT
1 TAATTAATT
39794087 TCAATTAATT
1 T-AATTAATT
* *
39794097 AAATTTATT
1 TAATTAATT
39794106 TAATTAA
1 TAATTAA
39794113 AAATCTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.21
9 17 0.61
10 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATTAATT
Found at i:39799842 original size:13 final size:13
Alignment explanation
Indices: 39799826--39799865 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
39799816 TTTAAACCAA
39799826 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
39799839 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
39799852 AATTTTCAAAAGC
1 ACTTTTCAAAAGC
39799865 A
1 A
39799866 TTGCCAAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39806479 original size:30 final size:34
Alignment explanation
Indices: 39806443--39806508 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 34
39806433 TAGTTAATAT
*
39806443 ATATTTTTAAAT-TT-AT-GGATTATTGA-ATTA
1 ATATTTTTAAATATTAATAGAATTATTGATATTA
39806473 ATATTTTTAAATATTAATAGAATTATTGATATTA
1 ATATTTTTAAATATTAATAGAATTATTGATATTA
39806507 AT
1 AT
39806509 TTATGAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.39
31 2 0.06
32 2 0.06
33 9 0.29
34 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (34 bp):
ATATTTTTAAATATTAATAGAATTATTGATATTA
Found at i:39815131 original size:18 final size:18
Alignment explanation
Indices: 39815108--39815149 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39815098 ATTCTCAAGT
39815108 TTTTAAGAA-AAATAATAA
1 TTTTAAGAAGAAATAA-AA
*
39815126 TTTTAA-AAGAAATCAAA
1 TTTTAAGAAGAAATAAAA
39815143 TTTTAAG
1 TTTTAAG
39815150 GAAACACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (18 bp):
TTTTAAGAAGAAATAAAA
Found at i:39817430 original size:5 final size:5
Alignment explanation
Indices: 39817420--39817448 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39817410 CCAGAAAACC
39817420 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
39817449 GCAGTGGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39821994 original size:37 final size:37
Alignment explanation
Indices: 39821938--39822045 Score: 117
Period size: 37 Copynumber: 2.8 Consensus size: 37
39821928 AATTCGAAGC
* *
39821938 AATAAGTTGACACCTAGTGCCTCATCGACTAAACCGA
1 AATAATTTGACACCCAGTGCCTCATCGACTAAACCGA
* * *
39821975 AATAATTTGGCACCCAGTGCCTCATCGAATTAATCCGA
1 AATAATTTGACACCCAGTGCCTCATCG-ACTAAACCGA
* *
39822013 AGTAAATAATTGACACCCAGTGTCTCATCGACT
1 AAT-AAT--TTGACACCCAGTGCCTCATCGACT
39822046 CGAAGTCGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 24 0.41
38 10 0.17
39 3 0.05
40 2 0.03
41 19 0.33
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (37 bp):
AATAATTTGACACCCAGTGCCTCATCGACTAAACCGA
Found at i:39822056 original size:42 final size:41
Alignment explanation
Indices: 39821918--39822060 Score: 111
Period size: 37 Copynumber: 3.6 Consensus size: 41
39821908 GTACCTAGTA
* * * * *
39821918 CTCATCGGAT-AATTCGAAGCAATAAGTTGACACCTAGTGC
1 CTCATCGAATGAATCCGAAGAAATAATTTGACACCCAGTGC
* * *
39821958 CTCATCGACT-AAACC---GAAATAATTTGGCACCCAGTGC
1 CTCATCGAATGAATCCGAAGAAATAATTTGACACCCAGTGC
* *
39821995 CTCATCGAATTAATCCGAAGTAAATAA-TTGACACCCAGTGT
1 CTCATCGAATGAATCCGAAG-AAATAATTTGACACCCAGTGC
*
39822036 CTCATCGACTCGAAGT-CGAAGAAAT
1 CTCATCGAAT-GAA-TCCGAAGAAAT
39822061 CCTTGAACTC
Statistics
Matches: 82, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
37 27 0.33
38 4 0.05
40 11 0.13
41 26 0.32
42 13 0.16
43 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
CTCATCGAATGAATCCGAAGAAATAATTTGACACCCAGTGC
Found at i:39822875 original size:11 final size:11
Alignment explanation
Indices: 39822859--39822897 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
39822849 ATCCTAACTT
39822859 TTTCTCTTTTC
1 TTTCTCTTTTC
39822870 TTTCTCTTTTCC
1 TTTCTCTTTT-C
39822882 TTT-TC-TTTC
1 TTTCTCTTTTC
39822891 TTTCTCT
1 TTTCTCT
39822898 GTTTTCGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 12 0.48
12 4 0.16
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTCTCTTTTC
Found at i:39822886 original size:17 final size:18
Alignment explanation
Indices: 39822858--39822891 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39822848 AATCCTAACT
39822858 TTTTCTCTTTTCTTTCTC
1 TTTTCTCTTTTCTTTCTC
39822876 TTTTC-CTTTTCTTTCT
1 TTTTCTCTTTTCTTTCT
39822892 TTCTCTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTCTTTTCTTTCTC
Found at i:39837759 original size:20 final size:20
Alignment explanation
Indices: 39837736--39837776 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39837726 TTATTTGGAA
*
39837736 TAATTAAAAAAATATTATTT
1 TAATTAAAAAAACATTATTT
*
39837756 TAATTAAAATAACATTATTT
1 TAATTAAAAAAACATTATTT
39837776 T
1 T
39837777 TTATTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATTAAAAAAACATTATTT
Found at i:39840494 original size:16 final size:16
Alignment explanation
Indices: 39840473--39840508 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39840463 TATATATGGA
39840473 TCAAGATAGAATGATC
1 TCAAGATAGAATGATC
*
39840489 TCAAGATAGGATGATC
1 TCAAGATAGAATGATC
39840505 TCAA
1 TCAA
39840509 AAAGAGTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (16 bp):
TCAAGATAGAATGATC
Found at i:39849551 original size:30 final size:30
Alignment explanation
Indices: 39849501--39849576 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
39849491 ATTTTTTAAG
* *
39849501 AAAATTTTAATTAAAATCTCTTG-AATTTTCTA
1 AAAATTTTAATT--AATCTCTCGAAATATT-TA
39849533 AAAATTCTT-ATTAATCTCTCGAAATATTTA
1 AAAATT-TTAATTAATCTCTCGAAATATTTA
39849563 AAAATTTTAATTAA
1 AAAATTTTAATTAA
39849577 ATTCTCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 2 0.05
30 21 0.54
31 5 0.13
32 9 0.23
33 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (30 bp):
AAAATTTTAATTAATCTCTCGAAATATTTA
Found at i:39850517 original size:20 final size:20
Alignment explanation
Indices: 39850494--39850546 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
39850484 AAGCCCTTTT
*
39850494 AAAATTTTAAAATTATTAAA-
1 AAAATTATAAAATTA-TAAAC
**
39850514 AAAACCATAAAATTATAAAC
1 AAAATTATAAAATTATAAAC
39850534 AAAATTCATAAAA
1 AAAATT-ATAAAA
39850547 AAAGCTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAATTATAAAC
Found at i:39854162 original size:2 final size:2
Alignment explanation
Indices: 39854110--39854148 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39854100 ACACACACAC
39854110 AT AT AT AT 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 AT AT AT AT A
39854149 AACAAACCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39854247 original size:23 final size:23
Alignment explanation
Indices: 39854220--39854271 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
39854210 AAAAAAAATT
*
39854220 ACCAATTTCTAAAACTAATGTAG
1 ACCAATTTATAAAACTAATGTAG
39854243 ACCAATTTATAAAACTAATGTAG
1 ACCAATTTATAAAACTAATGTAG
39854266 ACCAAT
1 ACCAAT
39854272 ATTTTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (23 bp):
ACCAATTTATAAAACTAATGTAG
Found at i:39854323 original size:29 final size:30
Alignment explanation
Indices: 39854291--39854348 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
39854281 AATTGATAAA
*
39854291 TTGAAAAATTAACTACTAAAAAA-TAAGTG
1 TTGAAAAAATAACTACTAAAAAATTAAGTG
*
39854320 TTGAAAAAATAAGTACTAAAAAATTAAGT
1 TTGAAAAAATAACTACTAAAAAATTAAGT
39854349 ATTTAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (30 bp):
TTGAAAAAATAACTACTAAAAAATTAAGTG
Found at i:39854340 original size:14 final size:14
Alignment explanation
Indices: 39854294--39854349 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
39854284 TGATAAATTG
* *
39854294 AAAAATTAACTACT
1 AAAAAATAAGTACT
**
39854308 AAAAAATAAGTGTT
1 AAAAAATAAGTACT
39854322 GAAAAAATAAGTACT
1 -AAAAAATAAGTACT
39854337 AAAAAATTAAGTA
1 AAAAAA-TAAGTA
39854350 TTTAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (14 bp):
AAAAAATAAGTACT
Found at i:39854953 original size:18 final size:18
Alignment explanation
Indices: 39854930--39854972 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39854920 ACCCAATCCA
*
39854930 AACCCAAGTATTC-AACCC
1 AACCCAAGTA-CCAAACCC
*
39854948 AACCCAATTACCAAACCC
1 AACCCAAGTACCAAACCC
39854966 AACCCAA
1 AACCCAA
39854973 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.44, C:0.42, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCAAACCC
Found at i:39855081 original size:9 final size:9
Alignment explanation
Indices: 39855067--39855097 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39855057 GTAGTGATTC
39855067 AATTCGGTT
1 AATTCGGTT
*
39855076 AATTCGGGT
1 AATTCGGTT
39855085 AATTCGGTT
1 AATTCGGTT
39855094 AATT
1 AATT
39855098 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39855545 original size:17 final size:18
Alignment explanation
Indices: 39855523--39855556 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39855513 ACAGGAAGAA
39855523 TTTTC-TTAATTCTTTAT
1 TTTTCTTTAATTCTTTAT
*
39855540 TTTTCTTTAGTTCTTTA
1 TTTTCTTTAATTCTTTA
39855557 CTGCTTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTCTTTAATTCTTTAT
Found at i:39860147 original size:17 final size:18
Alignment explanation
Indices: 39860125--39860158 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39860115 ACAGGAAGAA
39860125 TTTTC-TTAGTTCTTTAT
1 TTTTCTTTAGTTCTTTAT
39860142 TTTTCTTTAGTTCTTTA
1 TTTTCTTTAGTTCTTTA
39860159 CTGCTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTCTTTAGTTCTTTAT
Found at i:39866665 original size:22 final size:20
Alignment explanation
Indices: 39866640--39866692 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
39866630 TATTGAAAAT
**
39866640 AAAAATTAATATTTAATATCG
1 AAAAATTAATAACT-ATATCG
39866661 AAAAATTTAATAACTATATCG
1 AAAAA-TTAATAACTATATCG
39866682 AAAAATTAATA
1 AAAAATTAATA
39866693 GTTGGATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 16 0.55
22 7 0.24
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAAATTAATAACTATATCG
Found at i:39869340 original size:16 final size:16
Alignment explanation
Indices: 39869319--39869354 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39869309 TTTGGTTCGC
39869319 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39869335 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39869351 TGTA
1 TGTA
39869355 ATAGCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39869677 original size:157 final size:157
Alignment explanation
Indices: 39869477--39869793 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
39869467 TAGAATACCC
*
39869477 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * *
39869542 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAATA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA-A
39869607 ATATATAATTTAATAAAATTCTT-ATAA
130 ATATATAATTTAATAAAATTCTTAATAA
* *
39869634 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
39869699 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
39869764 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
39869791 TTA
1 TTA
39869794 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 24 0.16
157 128 0.84
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:39869764 original size:16 final size:16
Alignment explanation
Indices: 39869727--39869768 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39869717 TTAATCATAT
*
39869727 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39869743 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39869758 TTAAAATATAT
1 TTAAAATATAT
39869769 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39869775 original size:14 final size:15
Alignment explanation
Indices: 39869736--39869777 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39869726 TTTAAACATA
*
39869736 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39869751 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39869765 A-TATAATTTAATA
1 ATTATAATTAAATA
39869778 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39869827 original size:61 final size:61
Alignment explanation
Indices: 39869762--39869947 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
39869752 TTATAATTAA
39869762 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
39869823 AATATATGATACT-GTAAAA-TATAAAGTAA-CAA-ATT-TTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATTAATATTCTTATATGAATTTACTCA-AATCAT
39869880 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
39869941 AATATAT
1 AATATAT
39869948 GATACTATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
56 3 0.03
57 27 0.29
58 10 0.11
59 6 0.06
60 10 0.11
61 34 0.37
62 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:39869879 original size:118 final size:121
Alignment explanation
Indices: 39869730--39870020 Score: 484
Period size: 118 Copynumber: 2.4 Consensus size: 121
39869720 ATCATATTTA
39869730 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
39869795 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA-GT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AAATGTG
39869850 AACA-AATT-TTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39869913 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
* * *
39869969 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
39870021 TAAAATAATT
Statistics
Matches: 161, Mismatches: 6, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
117 3 0.02
118 104 0.65
119 10 0.06
120 44 0.27
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATGTG
Found at i:39869898 original size:57 final size:57
Alignment explanation
Indices: 39869730--39869899 Score: 139
Period size: 61 Copynumber: 2.9 Consensus size: 57
39869720 ATCATATTTA
* *
39869730 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACA-AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAA-TATAAAT
* * * * * * * * * *
39869789 AATTAATATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-GTAAAATATAAAGT
1 AA-CAA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATATAAA-T
39869850 AACAAATT-TTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
1 AACAAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
39869900 TCTTAATAAT
Statistics
Matches: 82, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
56 3 0.04
57 25 0.30
58 4 0.05
59 6 0.07
60 14 0.17
61 27 0.33
62 3 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (57 bp):
AACAAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATATAAAT
Found at i:39872442 original size:6 final size:6
Alignment explanation
Indices: 39872433--39872461 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39872423 TTGATGTTGG
39872433 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGG
39872462 TGGGGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:39873449 original size:16 final size:16
Alignment explanation
Indices: 39873428--39873479 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
39873418 TTTGGTTCGC
39873428 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39873444 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39873460 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39873476 TGTA
1 TGTA
39873480 ATAGCAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39873736 original size:18 final size:17
Alignment explanation
Indices: 39873715--39873749 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39873705 TTATTATTAA
*
39873715 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39873733 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39873750 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39873856 original size:18 final size:17
Alignment explanation
Indices: 39873835--39873869 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39873825 TTATTATTAA
*
39873835 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39873853 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39873870 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39873911 original size:120 final size:120
Alignment explanation
Indices: 39873698--39874080 Score: 730
Period size: 120 Copynumber: 3.2 Consensus size: 120
39873688 ATCATATTTA
39873698 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
39873763 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
39873818 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39873883 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
39873938 AACATAATTATTATTAAATATACTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39874003 TATTCTTATATTAATTTACTGAAATCATAATATGTGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
39874058 AACATAATAATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
39874081 AACTTGAAAA
Statistics
Matches: 257, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 257 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:39873989 original size:17 final size:18
Alignment explanation
Indices: 39873955--39873989 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39873945 TTATTATTAA
*
39873955 ATATACTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
39873973 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
39873990 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:39877186 original size:21 final size:21
Alignment explanation
Indices: 39877143--39877198 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
39877133 AAGCAGATGG
*
39877143 AGCCACTGCAAATAAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
39877165 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
39877186 AGCCACTGCAAAC
1 AGCCACTGCAAAC
39877199 GGGGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:39878309 original size:15 final size:15
Alignment explanation
Indices: 39878289--39878404 Score: 62
Period size: 15 Copynumber: 7.5 Consensus size: 15
39878279 AACATGGTAC
39878289 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
39878304 AGAAACA-AAAA-ACC
1 AGAAACAGAAAATA-G
**
39878318 A-CTACAGAAAATAG
1 AGAAACAGAAAATAG
* *
39878332 AGGAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
39878350 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
39878365 AGAAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
39878383 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
39878398 AGAAACA
1 AGAAACA
39878405 TAAAGCAGAC
Statistics
Matches: 76, Mismatches: 11, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
13 4 0.05
14 16 0.21
15 31 0.41
18 19 0.25
19 6 0.08
ACGTcount: A:0.62, C:0.13, G:0.17, T:0.08
Consensus pattern (15 bp):
AGAAACAGAAAATAG
Found at i:39878311 original size:33 final size:33
Alignment explanation
Indices: 39878269--39878404 Score: 185
Period size: 33 Copynumber: 4.3 Consensus size: 33
39878259 AAAAATGGCA
*
39878269 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
**
39878302 AGAGAAACAAAA-A----ACCA-CTACAGAAAAT
1 AGAGAAACAAAACATGGTA-CAGAAACAGAAAAT
*
39878330 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
39878363 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
39878396 AGAGAAACA
1 AGAGAAACA
39878405 TAAAGCAGAC
Statistics
Matches: 89, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
28 21 0.24
29 3 0.03
32 3 0.03
33 62 0.70
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.08
Consensus pattern (33 bp):
AGAGAAACAAAACATGGTACAGAAACAGAAAAT
Found at i:39878388 original size:18 final size:18
Alignment explanation
Indices: 39878335--39878389 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
39878325 AAAATAGAGG
39878335 AACAAAACATGGTACAGA
1 AACAAAACATGGTACAGA
*
39878353 AACAGAAA-A---TAGAGA
1 AACA-AAACATGGTACAGA
39878368 AACAAAACATGGTACAGA
1 AACAAAACATGGTACAGA
39878386 AACA
1 AACA
39878390 GAAAATAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.60, C:0.15, G:0.16, T:0.09
Consensus pattern (18 bp):
AACAAAACATGGTACAGA
Found at i:39884374 original size:15 final size:16
Alignment explanation
Indices: 39884342--39884374 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39884332 TGTATGTTTT
*
39884342 CTCCTTTCAGTCTTTG
1 CTCCTTTCAGTATTTG
39884358 CTCCTTTCAG-ATTTG
1 CTCCTTTCAGTATTTG
39884373 CT
1 CT
39884375 AGTTCTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.30, G:0.12, T:0.48
Consensus pattern (16 bp):
CTCCTTTCAGTATTTG
Found at i:39885811 original size:33 final size:34
Alignment explanation
Indices: 39885772--39885848 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
39885762 TAACTTGAAA
39885772 GTGTCTTCAACAGAGT-ACTC-TAATACTTCATTG
1 GTGTCTTCAACAGA-TAACTCTTAATACTTCATTG
* *
39885805 GTGTCTTCAACATATAACTCTTATTACTTCATTG
1 GTGTCTTCAACAGATAACTCTTAATACTTCATTG
39885839 GTGTCTTCAA
1 GTGTCTTCAA
39885849 AACTTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 1 0.03
33 17 0.43
34 22 0.55
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (34 bp):
GTGTCTTCAACAGATAACTCTTAATACTTCATTG
Found at i:39890961 original size:16 final size:17
Alignment explanation
Indices: 39890935--39890967 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39890925 GCACGCTGAT
*
39890935 TTTTCCATGTTTTTGCA
1 TTTTCCATGTTTCTGCA
39890952 TTTT-CATGTTTCTGCA
1 TTTTCCATGTTTCTGCA
39890968 ATTGCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTCCATGTTTCTGCA
Found at i:39908476 original size:2 final size:2
Alignment explanation
Indices: 39908469--39908523 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
39908459 TATAATTACA
39908469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39908511 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
39908524 CTGAATTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39910429 original size:11 final size:12
Alignment explanation
Indices: 39910393--39910430 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
39910383 TTTTTAAAAT
*
39910393 TTAAAAAGTATA
1 TTAAAAATTATA
39910405 -TAAAAATTATA
1 TTAAAAATTATA
39910416 TTAAAAATTA-A
1 TTAAAAATTATA
39910427 TTAA
1 TTAA
39910431 TTGTTGACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TTAAAAATTATA
Found at i:39912905 original size:13 final size:14
Alignment explanation
Indices: 39912883--39912920 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
39912873 ATTAATATAC
*
39912883 TTTAAAAATATT-A
1 TTTAATAATATTAA
*
39912896 TTTTATAATATTAA
1 TTTAATAATATTAA
39912910 TTTAATAATAT
1 TTTAATAATAT
39912921 AATGAACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAATAATATTAA
Found at i:39912923 original size:13 final size:13
Alignment explanation
Indices: 39912875--39912923 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
39912865 TGAAGTACAT
*
39912875 TAATATACTTTAA
1 TAATATAATTTAA
* * *
39912888 AAATATTATTTTA
1 TAATATAATTTAA
39912901 TAATATTAATTTAA
1 TAATA-TAATTTAA
39912915 TAATATAAT
1 TAATATAAT
39912924 GAACAATAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATATAATTTAA
Found at i:39916026 original size:128 final size:128
Alignment explanation
Indices: 39915653--39916036 Score: 594
Period size: 128 Copynumber: 3.0 Consensus size: 128
39915643 TTATATTGAT
39915653 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGA---TTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * *
39915715 GCTAGCATGATCTCATAAAACCTAAGGCACATTACAATATCATTGATAATGATGAACTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* * * * *
39915778 AATACTAAATAGAATGATGCTGATAATATCACCAAGGCTAATGATCTCTATTTGACTTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* *
39915843 GCTAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATCATGAGCTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* *
39915906 GATACTAAATAGAAAAATGTTGATAATATCACCAAGGCCAATGATCTTTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * * * *
39915971 GCTAGCCTGATCTCATAAAACCCAAGGCACATTATAGTATCACCGATAATGATGAGCTGAAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
39916034 GAT
1 GAT
39916037 TTACCTTCTT
Statistics
Matches: 232, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
125 41 0.18
128 191 0.82
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (128 bp):
GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
Found at i:39918461 original size:181 final size:181
Alignment explanation
Indices: 39918157--39918519 Score: 717
Period size: 181 Copynumber: 2.0 Consensus size: 181
39918147 AATAGGTAAA
39918157 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
39918222 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
*
39918287 CTCAGAAGGTGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
39918338 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
39918403 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
39918468 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
39918519 A
1 A
39918520 AAATTAACTA
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 181 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (181 bp):
AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
Found at i:39926795 original size:6 final size:6
Alignment explanation
Indices: 39926784--39926824 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
39926774 GAGTCTGCAA
39926784 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
39926825 TCTTAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:39937186 original size:3 final size:3
Alignment explanation
Indices: 39937180--39937229 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
39937170 TCCCCTAAAC
39937180 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39937228 TA
1 TA
39937230 ACACCAACCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39939361 original size:73 final size:73
Alignment explanation
Indices: 39939280--39939426 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
39939270 TTCTCATTGC
39939280 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
1 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
39939345 GGTAATGA
66 GGTAATGA
39939353 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
1 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
39939418 GGTAATGA
66 GGTAATGA
39939426 T
1 T
39939427 GTGTTGTAGG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (73 bp):
TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
GGTAATGA
Found at i:39946674 original size:12 final size:12
Alignment explanation
Indices: 39946657--39946689 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39946647 AGAGCCAGAT
39946657 TCATCTTCATCC
1 TCATCTTCATCC
*
39946669 TCATCTTCGTCC
1 TCATCTTCATCC
39946681 TCATCTTCA
1 TCATCTTCA
39946690 AACTTCTCCT
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:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:39950861 original size:40 final size:40
Alignment explanation
Indices: 39950811--39950901 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
39950801 CAACCTTTTT
** *
39950811 CAACCTTTTCATAGGATATCTGTTTCGGATATATCCTTTA
1 CAACCTTTTCATAGGATATCCATTTCGGATATACCCTTTA
* ** *
39950851 CAACCATTTCATTTGATATCCATTTCGGATATACCCTTTT
1 CAACCTTTTCATAGGATATCCATTTCGGATATACCCTTTA
39950891 CAACCTTTTCA
1 CAACCTTTTCA
39950902 AGAATTCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (40 bp):
CAACCTTTTCATAGGATATCCATTTCGGATATACCCTTTA
Found at i:39952291 original size:8 final size:8
Alignment explanation
Indices: 39952278--39952302 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39952268 CCACAATTAT
39952278 TCACATAA
1 TCACATAA
39952286 TCACATAA
1 TCACATAA
39952294 TCACATAA
1 TCACATAA
39952302 T
1 T
39952303 TTGCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TCACATAA
Found at i:39954040 original size:75 final size:75
Alignment explanation
Indices: 39953875--39954047 Score: 222
Period size: 75 Copynumber: 2.3 Consensus size: 75
39953865 AGATTACGCT
* * * *
39953875 CAGCGTTAGTCGGAT-TAACCGACAGTATTGAATGTGAGCCCAGCTTTAGTTGGATGAACCAACA
1 CAGCGTTAGTCGGATAT-ACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACA
*
39953939 ATGTTTGCGCC
65 ATGTTTGCACC
* * * * *
39953950 TAGCGCTAGTTGGATATACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAATAG
1 CAGCGTTAGTCGGATATACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
39954015 TGTTTGCACC
66 TGTTTGCACC
* *
39954025 CAGCATTAGTCGGATAGACCGAC
1 CAGCGTTAGTCGGATATACCGAC
39954048 GATTGTGTGC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
75 81 0.99
76 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (75 bp):
CAGCGTTAGTCGGATATACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
TGTTTGCACC
Found at i:39962582 original size:12 final size:12
Alignment explanation
Indices: 39962561--39962590 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39962551 GCCAGATTCA
39962561 TCTTCATCCTCG
1 TCTTCATCCTCG
*
39962573 TCTTCGTCCTCG
1 TCTTCATCCTCG
39962585 TCTTCA
1 TCTTCA
39962591 AACTTCTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.40, G:0.10, T:0.43
Consensus pattern (12 bp):
TCTTCATCCTCG
Found at i:39963888 original size:24 final size:24
Alignment explanation
Indices: 39963843--39963887 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39963833 CAATACTCTC
39963843 TTATTAATTAAATAGTTAAAAATA
1 TTATTAATTAAATAGTTAAAAATA
39963867 TTATTAAATT-AATA-TTAAAAA
1 TTATT-AATTAAATAGTTAAAAA
39963888 AATATGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTATTAATTAAATAGTTAAAAATA
Found at i:39974213 original size:13 final size:13
Alignment explanation
Indices: 39974195--39974222 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39974185 TATTGCATTA
39974195 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
39974208 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
39974221 TT
1 TT
39974223 GCCTTTGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGTTTCGGTTC
Found at i:39975999 original size:13 final size:13
Alignment explanation
Indices: 39975981--39976008 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39975971 TTTCTAAATC
39975981 AAAATTATTTTTG
1 AAAATTATTTTTG
39975994 AAAATTATTTTTG
1 AAAATTATTTTTG
39976007 AA
1 AA
39976009 CCCAAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
AAAATTATTTTTG
Found at i:39979255 original size:91 final size:91
Alignment explanation
Indices: 39979099--39979306 Score: 283
Period size: 91 Copynumber: 2.3 Consensus size: 91
39979089 TTGATTTTAG
* *
39979099 TAAATTCATATAAGAACATTTTATTATTAAAAATTTTACGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAAAATTTTACGAAATTATATATCACTATTAAATTAT
* *
39979164 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* * * *
39979191 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAAAATTTTACGAAATTATATATCACTATTAAATTATA
39979256 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
39979282 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
39979307 GTTATAATTA
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 84 0.82
92 19 0.18
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAAAATTTTACGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:39979481 original size:15 final size:15
Alignment explanation
Indices: 39979446--39979497 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
39979436 TTAAGAATTT
*
39979446 TATTAAATTAT-ATA
1 TATTTAATTATAATA
39979460 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
39979474 TATTTAATAATAAT-
1 TATTTAATTATAATA
39979488 TATGTTAATT
1 TAT-TTAATT
39979498 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:39979556 original size:120 final size:120
Alignment explanation
Indices: 39979322--39979618 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
39979312 AATTATTTTA
* * * *
39979322 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTATTTT
*
39979386 ATAGGATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGGATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
39979441 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATT-TATTT
*
39979505 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGGATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
39979561 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
39979619 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
119 51 0.31
120 113 0.68
121 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTATTTT
ACAGGATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:39979596 original size:16 final size:16
Alignment explanation
Indices: 39979575--39979616 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39979565 TTATTAAATT
*
39979575 ATATATTTTAATTATA
1 ATATATTTTAATAATA
39979591 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
39979606 AT-TATGTTTAA
1 ATATAT-TTTAA
39979617 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:39979601 original size:15 final size:15
Alignment explanation
Indices: 39979566--39979607 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39979556 TTAAGAATTT
*
39979566 TATTAAATTAT-ATA
1 TATTTAATTATAATA
39979580 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
39979594 TATTTAATAATAAT
1 TATTTAATTATAAT
39979608 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:39979851 original size:16 final size:16
Alignment explanation
Indices: 39979830--39979873 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
39979820 TTGATTTGCT
39979830 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
39979846 ATTACACCTCTATTCT
1 ATTACACCTCTATTCC
39979862 ATTACACCTCTA
1 ATTACACCTCTA
39979874 ATTTAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:39979884 original size:32 final size:32
Alignment explanation
Indices: 39979828--39979889 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
39979818 AGTTGATTTG
*
39979828 CTATTACACCTCTATTCCATTACACCTCTATT
1 CTATTACACCTCTATTCCAATACACCTCTATT
*
39979860 CTATTACACCTCTAATT-TAATACACCTCTA
1 CTATTACACCTCT-ATTCCAATACACCTCTA
39979890 ATCCAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (32 bp):
CTATTACACCTCTATTCCAATACACCTCTATT
Found at i:39979897 original size:16 final size:16
Alignment explanation
Indices: 39979832--39979899 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
39979822 GATTTGCTAT
* *
39979832 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
* * *
39979848 TACACCTCTATTCTAT
1 TACACCTCTAATCCAA
**
39979864 TACACCTCTAATTTAA
1 TACACCTCTAATCCAA
39979880 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39979896 TACA
1 TACA
39979900 GCGAACCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39989118 original size:17 final size:17
Alignment explanation
Indices: 39989096--39989131 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
39989086 AATGGATAGC
39989096 TTCCTAGCTGTCCAGCT
1 TTCCTAGCTGTCCAGCT
39989113 TTCCTAGCTGTCCAGCT
1 TTCCTAGCTGTCCAGCT
39989130 TT
1 TT
39989132 ACAATTTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.33, G:0.17, T:0.39
Consensus pattern (17 bp):
TTCCTAGCTGTCCAGCT
Found at i:39991121 original size:33 final size:32
Alignment explanation
Indices: 39991059--39991142 Score: 123
Period size: 33 Copynumber: 2.6 Consensus size: 32
39991049 TGGGCCCACA
*
39991059 TGCCCGTGTGGCCCACACGTCCAAATTGGCCT
1 TGCCCGTGTGGCCCACACGCCCAAATTGGCCT
* *
39991091 TGCCCGTGTGGGCCCATACGCCCAACTTGGCCT
1 TGCCCGTGT-GGCCCACACGCCCAAATTGGCCT
*
39991124 AGCCCGTGTGGCCCACACG
1 TGCCCGTGTGGCCCACACG
39991143 GCCACACTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 18 0.39
33 28 0.61
ACGTcount: A:0.14, C:0.39, G:0.27, T:0.19
Consensus pattern (32 bp):
TGCCCGTGTGGCCCACACGCCCAAATTGGCCT
Found at i:39994602 original size:16 final size:16
Alignment explanation
Indices: 39994581--39994616 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39994571 TTTGGTTCGC
39994581 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39994597 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39994613 TGTA
1 TGTA
39994617 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39994872 original size:16 final size:16
Alignment explanation
Indices: 39994835--39994876 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39994825 TTAATCATAT
*
39994835 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39994851 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39994866 TTAAAATATAT
1 TTAAAATATAT
39994877 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39994883 original size:14 final size:15
Alignment explanation
Indices: 39994844--39994885 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39994834 TTTAAACATA
*
39994844 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39994859 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39994873 A-TATAATTTAATA
1 ATTATAATTAAATA
39994886 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39995661 original size:13 final size:13
Alignment explanation
Indices: 39995643--39995672 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39995633 TTAAAAGCTA
39995643 AATTCAGAAAAAC
1 AATTCAGAAAAAC
39995656 AATTCAGAAAAAC
1 AATTCAGAAAAAC
39995669 AATT
1 AATT
39995673 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:39998427 original size:24 final size:25
Alignment explanation
Indices: 39998374--39998427 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
39998364 GTTCGAATTT
*
39998374 TATTATCTTAATTTATCAAATTATA
1 TATTATCTTAATTTATCAAATTAAA
* *
39998399 T-TTATTTTAATTTAT-AACTTAAA
1 TATTATCTTAATTTATCAAATTAAA
39998422 TATTAT
1 TATTAT
39998428 ATTGATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 17 0.68
25 1 0.04
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATCTTAATTTATCAAATTAAA
Found at i:40003605 original size:13 final size:13
Alignment explanation
Indices: 40003579--40003639 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
40003569 AGTTCTTCAT
* *
40003579 TGCTTTTAAAAAG
1 TGCTTTTGAGAAG
*
40003592 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
40003605 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
40003618 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
40003631 TGTTTTTGA
1 TGCTTTTGA
40003640 AAATTTTGAG
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Done.