Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_pilon, 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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:631817 original size:24 final size:26
Alignment explanation
Indices: 631779--631826 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
631769 TATATATATA
631779 TATTATTTCTATTTTATTTA-ATCTTT
1 TATTATTTCTATTTT-TTTATATCTTT
631805 TATT-TTT-TATTTTTTTATATCT
1 TATTATTTCTATTTTTTTATATCT
631827 ATCATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 3 0.14
26 4 0.19
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (26 bp):
TATTATTTCTATTTTTTTATATCTTT
Found at i:631834 original size:56 final size:55
Alignment explanation
Indices: 631764--631875 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 55
631754 TTATACGTTA
*
631764 TTATATATATATATATATTAT-TTCTATTTTATTTAATCTTTTATT-TTTTATTTTT
1 TTATATATATATATATATTATATT-TATTTTATTT-ATCTTTTATTACTTTATTTTT
* * * * *
631819 TTATATCTATCATATATTTTATATTTATTTTGTTTTTTTTTTATTACTTTATTTTT
1 TTATATATAT-ATATATATTATATTTATTTTATTTATCTTTTATTACTTTATTTTT
631875 T
1 T
631876 ATTATTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
55 17 0.35
56 29 0.60
57 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (55 bp):
TTATATATATATATATATTATATTTATTTTATTTATCTTTTATTACTTTATTTTT
Found at i:631846 original size:51 final size:48
Alignment explanation
Indices: 631769--631863 Score: 113
Period size: 51 Copynumber: 1.9 Consensus size: 48
631759 CGTTATTATA
631769 TATATATATATATTATTTCTATTTTATTTAATCTTTTATTTTTTATTTTTT
1 TATATATATATATTATTTCTATTTTATTT--TCTTTT-TTTTTTATTTTTT
* *
631820 TATATCTATCATA-TATTT-TATATTTATTTTGTTTTTTTTTTATT
1 TATATATAT-ATATTATTTCTAT-TTTATTTTCTTTTTTTTTTATT
631864 ACTTTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
48 9 0.22
49 5 0.12
50 3 0.08
51 20 0.50
52 3 0.08
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (48 bp):
TATATATATATATTATTTCTATTTTATTTTCTTTTTTTTTTATTTTTT
Found at i:631987 original size:3 final size:3
Alignment explanation
Indices: 631976--632010 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
631966 GATTTTTTTT
631976 TTA TATA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
632011 GGTATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:632231 original size:23 final size:23
Alignment explanation
Indices: 632196--632254 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
632186 ATTACTTTCC
632196 TTTTTTA-TT-TTTTTATCTATT
1 TTTTTTATTTATTTTTATCTATT
**
632217 TTTTTTATTTATTTTCCTCTATT
1 TTTTTTATTTATTTTTATCTATT
*
632240 TTTATT-TTTATTTTT
1 TTTTTTATTTATTTTT
632255 TTACATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.22
22 10 0.31
23 15 0.47
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTATTTATTTTTATCTATT
Found at i:632262 original size:22 final size:23
Alignment explanation
Indices: 632197--632264 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
632187 TTACTTTCCT
*
632197 TTTTTATTTTTTTATCTATTTTTT
1 TTTTTATTTTTTTA-CTATTTTTA
**
632221 TTATTTATTTTCCT-CTATTTTTA
1 TT-TTTATTTTTTTACTATTTTTA
632244 TTTTTATTTTTTTAC-ATTTTT
1 TTTTTATTTTTTTACTATTTTT
632265 CCGTTAATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 15 0.41
23 11 0.30
24 2 0.05
25 9 0.24
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTATTTTTTTACTATTTTTA
Found at i:634899 original size:17 final size:17
Alignment explanation
Indices: 634849--634904 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
634839 TAACCATTAA
* *
634849 ATTAATTTTATTAAATG
1 ATTAATTTTATTAGATT
* *
634866 ATTCA-TTTAGT-GATT
1 ATTAATTTTATTAGATT
634881 ATTAATTTTATTAGATT
1 ATTAATTTTATTAGATT
*
634898 ATAAATT
1 ATTAATT
634905 ATATATAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 6 0.20
16 10 0.33
17 14 0.47
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (17 bp):
ATTAATTTTATTAGATT
Found at i:635360 original size:14 final size:14
Alignment explanation
Indices: 635341--635371 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
635331 TTAAATTATT
*
635341 AATTATTTTTTTTA
1 AATTATTTTTGTTA
635355 AATTATTTTTGTTA
1 AATTATTTTTGTTA
635369 AAT
1 AAT
635372 AATTCATTTG
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:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
AATTATTTTTGTTA
Found at i:637792 original size:16 final size:17
Alignment explanation
Indices: 637764--637812 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
637754 ATAATCATTA
637764 AATTAATTTTATTAGAT
1 AATTAATTTTATTAGAT
*
637781 AATTCA-TTTATTA-AT
1 AATTAATTTTATTAGAT
*
637796 TATTAATTTTATTAGAT
1 AATTAATTTTATTAGAT
637813 TAAAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
AATTAATTTTATTAGAT
Found at i:638656 original size:14 final size:15
Alignment explanation
Indices: 638632--638669 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
638622 GATGATGAAG
638632 GAAGAAGAAGAAAAT
1 GAAGAAGAAGAAAAT
*
638647 GAAG-AGAAGAAAAA
1 GAAGAAGAAGAAAAT
*
638661 CAAGAAGAA
1 GAAGAAGAA
638670 TAACGAGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.26, T:0.03
Consensus pattern (15 bp):
GAAGAAGAAGAAAAT
Found at i:640042 original size:21 final size:18
Alignment explanation
Indices: 639985--640042 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
639975 CAACAATTGA
639985 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
*
640003 TAACAATTGGCATCCTTTT
1 TAACAATTGGTAT-CTTTT
*
640022 GTAAACAATTGGTATATTTT
1 -T-AACAATTGGTATCTTTT
640042 T
1 T
640043 CATTGAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 12 0.35
19 6 0.18
20 5 0.15
21 11 0.32
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:640268 original size:22 final size:22
Alignment explanation
Indices: 640240--640322 Score: 139
Period size: 22 Copynumber: 3.8 Consensus size: 22
640230 AAAAAATGCT
*
640240 AATGGGTATCGATACCCCTATG
1 AATGGGTACCGATACCCCTATG
640262 AATGGGTACCGATACCCCTATG
1 AATGGGTACCGATACCCCTATG
640284 AATGGGTACCGATACCCCTATG
1 AATGGGTACCGATACCCCTATG
* *
640306 AATGGGTATCAATACCC
1 AATGGGTACCGATACCC
640323 TGGGTACCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (22 bp):
AATGGGTACCGATACCCCTATG
Found at i:640358 original size:36 final size:37
Alignment explanation
Indices: 640286--640358 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
640276 CCCCTATGAA
640286 TGGGTACCGATACCCCTATGAATGGGTATCAATACCC
1 TGGGTACCGATACCCCTATGAATGGGTATCAATACCC
* *
640323 TGGGTACCGATACCCCTA-GACTGGGTATCATTACCC
1 TGGGTACCGATACCCCTATGAATGGGTATCAATACCC
640359 CTATGACTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (37 bp):
TGGGTACCGATACCCCTATGAATGGGTATCAATACCC
Found at i:640623 original size:124 final size:124
Alignment explanation
Indices: 640475--640726 Score: 504
Period size: 124 Copynumber: 2.0 Consensus size: 124
640465 CGACTAGCAA
640475 CAACTAGTTAAATTTGAATTTAACAAAGGTAGTACCGATACCCCTTGAAGGGGTACCGATACCCC
1 CAACTAGTTAAATTTGAATTTAACAAAGGTAGTACCGATACCCCTTGAAGGGGTACCGATACCCC
640540 CTGTTATGGATAACCTTGTTTTGCAGAAAAATCATCCCCAAACGGCTCCAATTCATCCC
66 CTGTTATGGATAACCTTGTTTTGCAGAAAAATCATCCCCAAACGGCTCCAATTCATCCC
640599 CAACTAGTTAAATTTGAATTTAACAAAGGTAGTACCGATACCCCTTGAAGGGGTACCGATACCCC
1 CAACTAGTTAAATTTGAATTTAACAAAGGTAGTACCGATACCCCTTGAAGGGGTACCGATACCCC
640664 CTGTTATGGATAACCTTGTTTTGCAGAAAAATCATCCCCAAACGGCTCCAATTCATCCC
66 CTGTTATGGATAACCTTGTTTTGCAGAAAAATCATCCCCAAACGGCTCCAATTCATCCC
640723 CAAC
1 CAAC
640727 GGCTATATAC
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 128 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (124 bp):
CAACTAGTTAAATTTGAATTTAACAAAGGTAGTACCGATACCCCTTGAAGGGGTACCGATACCCC
CTGTTATGGATAACCTTGTTTTGCAGAAAAATCATCCCCAAACGGCTCCAATTCATCCC
Found at i:644100 original size:4 final size:4
Alignment explanation
Indices: 644091--644186 Score: 60
Period size: 4 Copynumber: 25.5 Consensus size: 4
644081 ATAATTATTT
* * * *
644091 TATA TATA TATA TATA TATA TA-A TAT- TA-A TAAA TTTA -ATT TAAA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * *
644135 TATA AATA AATA TATA TATA TA-A TATT TATA TATT TA-A TTTA AATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
644181 TATA TA
1 TATA TA
644187 CCCAGCTCGA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
3 12 0.17
4 57 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:644102 original size:6 final size:6
Alignment explanation
Indices: 644091--644186 Score: 60
Period size: 6 Copynumber: 17.0 Consensus size: 6
644081 ATAATTATTT
* * * *
644091 TATATA TATATA TATATA TATA-A TAT-TA -ATAAA TTTA-A TTTAAA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * *
644135 TATAAA TAAATA TATATA TATA-A TATTTA TATATT TA-ATT TAAATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
644181 TATATA
1 TATATA
644187 CCCAGCTCGA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
4 2 0.03
5 20 0.27
6 51 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:644148 original size:44 final size:44
Alignment explanation
Indices: 644091--644182 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
644081 ATAATTATTT
* *
644091 TATATATATATATATATATATAATATTAATAAATTTAATTTAAA
1 TATAAATAAATATATATATATAATATTAATAAATTTAATTTAAA
* *
644135 TATAAATAAATATATATATATAATATTTATATATTTAATTTAAA
1 TATAAATAAATATATATATATAATATTAATAAATTTAATTTAAA
644179 TATA
1 TATA
644183 TATACCCAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (44 bp):
TATAAATAAATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:644633 original size:141 final size:143
Alignment explanation
Indices: 644379--644667 Score: 564
Period size: 141 Copynumber: 2.0 Consensus size: 143
644369 TCCCTAGTTC
644379 TCTTAGAAACCCATACTTGTCTTATTTTATAAAATTTTATTTTCTTTATAGGAAAAATATTAGAA
1 TCTTAGAAACCCATACTTGTCTTATTTTATAAAATTTTATTTTCTTTATAGGAAAAATATTAGAA
644444 TTATGACCATGATAATGACAATGTGAACATTTTGTTATTATTGACTTTGATGAATTATTAGAAAC
66 TTATGACCATGATAATGACAATGTGAACATTTTGTTATTATTGACTTTGATGAATTATTAGAAAC
644509 AA-TTT-TTTTTT
131 AATTTTATTTTTT
644520 TCTTAGAAACCCATACTTGTCTTATTTTATAAAATTTTATTTTCTTTATAGGAAAAATATTAGAA
1 TCTTAGAAACCCATACTTGTCTTATTTTATAAAATTTTATTTTCTTTATAGGAAAAATATTAGAA
644585 TTATGACCATGATAATGACAATGTGAACATTTTGTTATTATTGACTTTGATGAATTATTAGAAAC
66 TTATGACCATGATAATGACAATGTGAACATTTTGTTATTATTGACTTTGATGAATTATTAGAAAC
644650 AATTTTATTTTTT
131 AATTTTATTTTTT
644663 TCTTA
1 TCTTA
644668 AGCTATCAAG
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
141 132 0.90
142 3 0.02
143 11 0.08
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (143 bp):
TCTTAGAAACCCATACTTGTCTTATTTTATAAAATTTTATTTTCTTTATAGGAAAAATATTAGAA
TTATGACCATGATAATGACAATGTGAACATTTTGTTATTATTGACTTTGATGAATTATTAGAAAC
AATTTTATTTTTT
Found at i:644738 original size:17 final size:17
Alignment explanation
Indices: 644718--644760 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
644708 AAAATTTTCA
644718 TTTTTAAAAGCTCTATTT
1 TTTTTAAAAGCTC-ATTT
**
644736 TTTTTAAAATTTCA-TT
1 TTTTTAAAAGCTCATTT
644752 TTTTTAAAA
1 TTTTTAAAA
644761 TCCAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTTTAAAAGCTCATTT
Found at i:646730 original size:21 final size:21
Alignment explanation
Indices: 646706--646751 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
646696 TGAGGAAACT
* *
646706 ATCCTTTTGGTGAAGAGATCG
1 ATCCTTTTGGTCAAGAGATCA
*
646727 ATCCTTTTGTTCAAGAGATCA
1 ATCCTTTTGGTCAAGAGATCA
646748 ATCC
1 ATCC
646752 AAAAGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
ATCCTTTTGGTCAAGAGATCA
Found at i:646810 original size:21 final size:20
Alignment explanation
Indices: 646771--646810 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
646761 TAGAATCCAA
**
646771 GGGATCGATCTTTTTTCAAG
1 GGGATCGATCTTTGGTCAAG
646791 GGGATCGATCCTTTGGTCAA
1 GGGATCGAT-CTTTGGTCAA
646811 AGAGATCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
GGGATCGATCTTTGGTCAAG
Found at i:648782 original size:35 final size:36
Alignment explanation
Indices: 648711--648783 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
648701 GTTATAAAAT
* *
648711 ATTTATATATTTCCTTTAGAAAATTTAAATTCATAAA
1 ATTTATATATTT-CTTTAGAAAATTAAAAATCATAAA
*
648748 ATTTATATAATTT-TTTATAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTCTTTAGAAAATTAAAAATCATAAA
648783 A
1 A
648784 AGATTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.19
36 14 0.44
37 8 0.25
38 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTCTTTAGAAAATTAAAAATCATAAA
Found at i:650965 original size:18 final size:20
Alignment explanation
Indices: 650928--650965 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
650918 TTATAATAAA
650928 ATTTGTAAAATAAATTATAT
1 ATTTGTAAAATAAATTATAT
*
650948 ATTT-TAAAA-AATTTATAT
1 ATTTGTAAAATAAATTATAT
650966 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTGTAAAATAAATTATAT
Found at i:650971 original size:14 final size:16
Alignment explanation
Indices: 650939--650971 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
650929 TTTGTAAAAT
650939 AAATTATATATTTTAAA
1 AAATT-TATATTTTAAA
650956 AAATTTATA-TTTAAA
1 AAATTTATATTTTAAA
650971 A
1 A
650972 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTATATTTTAAA
Found at i:651180 original size:15 final size:14
Alignment explanation
Indices: 651152--651198 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
651142 ATGGTATAAA
651152 ATTA-TAATATTTT
1 ATTATTAATATTTT
*
651165 ATTATTGATAATTTT
1 ATTATTAAT-ATTTT
*
651180 AATAATTAATATTTT
1 -ATTATTAATATTTT
651195 ATTA
1 ATTA
651199 GAATAATACC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 4 0.15
14 6 0.22
15 10 0.37
16 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTATTAATATTTT
Found at i:651334 original size:11 final size:12
Alignment explanation
Indices: 651292--651344 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
651282 ATATTAATTA
651292 TATTAATAAT-T
1 TATTAATAATAT
651303 TATT-AT-ATAT
1 TATTAATAATAT
651313 TATTAAAATAATAT
1 TATT--AATAATAT
651327 TATT-ATAATAT
1 TATTAATAATAT
651338 T-TTAATA
1 TATTAATA
651345 TAATTGTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
9 2 0.06
10 9 0.25
11 15 0.42
13 2 0.06
14 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTAATAATAT
Found at i:651342 original size:24 final size:23
Alignment explanation
Indices: 651296--651349 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
651286 TAATTATATT
651296 AATAATTTATTATATATTATTAA
1 AATAATTTATTATATATTATTAA
651319 AATAATATTATTATAATATT-TTAA
1 AATAAT-TTATTAT-ATATTATTAA
*
651343 TATAATT
1 AATAATT
651350 GTGTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.25
24 16 0.57
25 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATTTATTATATATTATTAA
Found at i:651394 original size:17 final size:17
Alignment explanation
Indices: 651374--651406 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
651364 ATATTTAAAA
651374 TTATAGAATAT-TTTTAT
1 TTATA-AATATATTTTAT
651391 TTATAAATATATTTTA
1 TTATAAATATATTTTA
651407 AATATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATAAATATATTTTAT
Found at i:651519 original size:15 final size:14
Alignment explanation
Indices: 651497--651533 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
651487 TAATAGTTAT
651497 TATTTTAATAAATA
1 TATTTTAATAAATA
*
651511 TATTATTAATTAATA
1 TATT-TTAATAAATA
651526 TATTTTAA
1 TATTTTAA
651534 ATATAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTTAATAAATA
Found at i:652626 original size:19 final size:20
Alignment explanation
Indices: 652602--652652 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
652592 AGTAGAGACT
652602 AAAAATAAAAATAAAATA-A
1 AAAAATAAAAATAAAATATA
*
652621 ATAAAT--AAATAAAATATA
1 AAAAATAAAAATAAAATATA
652639 AAAAAGTAAAAATA
1 AAAAA-TAAAAATA
652653 TATGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 10 0.38
18 5 0.19
19 6 0.23
21 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAATAAAAATAAAATATA
Found at i:652693 original size:21 final size:21
Alignment explanation
Indices: 652669--652716 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
652659 AAAAAGAGTA
652669 AAATA-TAATAATAATA-ATAAT
1 AAATAGTAAT-ATAATATA-AAT
652690 AAATAGTAATATAATATAAAT
1 AAATAGTAATATAATATAAAT
652711 AAATAG
1 AAATAG
652717 AGAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATAGTAATATAATATAAAT
Found at i:653548 original size:12 final size:12
Alignment explanation
Indices: 653531--653555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
653521 TAAAACTCTA
653531 ACTTGGTTGTTG
1 ACTTGGTTGTTG
653543 ACTTGGTTGTTG
1 ACTTGGTTGTTG
653555 A
1 A
653556 TGGGCGCTGA
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:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (12 bp):
ACTTGGTTGTTG
Found at i:654006 original size:20 final size:20
Alignment explanation
Indices: 653981--654021 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
653971 TTTTAACTAT
*
653981 TAAAGTA-AGGAGTATTAATA
1 TAAAGTAGAGGA-TATCAATA
654001 TAAAGTAGAGGATATCAATA
1 TAAAGTAGAGGATATCAATA
654021 T
1 T
654022 CTAATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (20 bp):
TAAAGTAGAGGATATCAATA
Found at i:657483 original size:251 final size:249
Alignment explanation
Indices: 656856--657698 Score: 1076
Period size: 251 Copynumber: 3.4 Consensus size: 249
656846 ATGTTGGGGT
* ** * * *
656856 ACGATATCCTTCATTGTGAAGTTGAAATCGTAAAGTGGCTCATTCG-CTATGAAGTTCAACATTG
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGA-TGGCCCATTCGTC-ATGAAGTTGAACCTTG
* * *
656920 AATTGGATATCATTCGTCGTGAAATTGAAATCCAATC-T-TGT--G-CG--TTGTTTCGAGTCCA
64 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCGAGTCCA
* *
656978 ATATCCTTCGCC-TGGAAGTTGAAATTGGCTCTGAGTAAAATTGGGAAGCCCCTTCGCTGTGAAG
129 ATATCCTTCGCCGT-GAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGCCCCTTCGCTGTGAAG
* *
657042 TTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTAGC
193 TTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTTAGC
* * * * * ** *
657099 ACGATATCCTTCGTCATGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAA
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCGTCATGAAGTTGAACCTTGAA
* * * * * *
657164 TTGGATATCCTTCCTCATGAAGTTTAAATCCAATCTTGAGTAAATTGTATTATTTCGAGTCCAAT
66 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCGAGTCCAAT
* *
657229 ATCCTTTGCCGTGAAGTTGAAATTGGCTTTGAATAAAACTGGGAAGCCCCTTCGCTGTGAAGTTG
131 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGCCCCTTCGCTGTGAAGTTG
* * *
657294 AGCTTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAATTTTGTGTATAAAC
196 AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGT-T-AGC
* * *
657350 ACGATATCTTTTATCGTGAAGTTGAAATCGTGGATGACCCATTCGTCATGAAGTTGAACCTTGAA
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCGTCATGAAGTTGAACCTTGAA
* *
657415 TTGGATATCCTTCTTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCAAGTCCAAT
66 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCGAGTCCAAT
* *
657480 ATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGAAGTTG
131 ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGCCCCTTCGCTGTGAAGTTG
* * * * **
657545 AGCTTCGAATTGGATATTCTTCGTTGTGATGTTGAAATCCAATGC-TGCTTGTGGGC
196 AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT-CTTG--TGTTAGC
* * * ** * *
657601 ACAATATCCTTCATTGTGAAGTTGAAATTGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAT
1 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCGTCATGAAGTTGAACCTTGAA
657666 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
66 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
657699 GTATTATTTG
Statistics
Matches: 512, Mismatches: 74, Indels: 20
0.84 0.12 0.03
Matches are distributed among these distances:
242 52 0.10
243 29 0.06
244 2 0.00
247 1 0.00
249 120 0.23
250 2 0.00
251 303 0.59
253 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (249 bp):
ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCATTCGTCATGAAGTTGAACCTTGAA
TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTTGTATTGTTTCGAGTCCAAT
ATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATAAAACTGGGAAGCCCCTTCGCTGTGAAGTTG
AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTTAGC
Found at i:658455 original size:9 final size:8
Alignment explanation
Indices: 658441--658483 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
658431 CCGGGATGCA
658441 TTTTTTCT
1 TTTTTTCT
*
658449 CTTTTTTGT
1 -TTTTTTCT
*
658458 TCTTTTCT
1 TTTTTTCT
658466 TTTTTTCT
1 TTTTTTCT
658474 TTTTCTTCT
1 TTTT-TTCT
658483 T
1 T
658484 CGACTTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 17 0.59
9 12 0.41
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:667197 original size:21 final size:21
Alignment explanation
Indices: 667157--667197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
667147 TTTTTTTTAA
* *
667157 AAACAATCCCACATGGCTAAG
1 AAACAATCCCAAAAGGCTAAG
*
667178 AAACAATCCCAAAAGTCTAA
1 AAACAATCCCAAAAGGCTAA
667198 AGAGTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.27, G:0.10, T:0.15
Consensus pattern (21 bp):
AAACAATCCCAAAAGGCTAAG
Found at i:669030 original size:38 final size:38
Alignment explanation
Indices: 668976--669061 Score: 118
Period size: 38 Copynumber: 2.3 Consensus size: 38
668966 AAATAATTAT
*
668976 TATATATATATATATAATATTAATAAATTTAATTTAAA
1 TATAAATATATATATAATATTAATAAATTTAATTTAAA
* * * *
669014 TTTAAATATATGTATAATATTTATATATTTAATTTAAA
1 TATAAATATATATATAATATTAATAAATTTAATTTAAA
*
669052 TATATATATA
1 TATAAATATA
669062 CCCAGCCCGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (38 bp):
TATAAATATATATATAATATTAATAAATTTAATTTAAA
Found at i:669032 original size:32 final size:32
Alignment explanation
Indices: 668991--669061 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
668981 ATATATATAT
668991 AATAT-TA-ATAA-ATTTA-AT-TTAAATTTA
1 AATATATATATAATATTTATATATTAAATTTA
* *
669018 AATATATGTATAATATTTATATATTTAATTTA
1 AATATATATATAATATTTATATATTAAATTTA
669050 AATATATATATA
1 AATATATATATA
669062 CCCAGCCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 4 0.11
30 5 0.14
31 2 0.06
32 19 0.53
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
AATATATATATAATATTTATATATTAAATTTA
Found at i:670465 original size:15 final size:15
Alignment explanation
Indices: 670445--670489 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
670435 TAGAGAATAA
670445 AAATAAAAATAAAAT
1 AAATAAAAATAAAAT
670460 AAATAACAAAT-AAAT
1 AAATAA-AAATAAAAT
670475 AAATAAAATATAAAA
1 AAATAAAA-ATAAAA
670490 ATATAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:670495 original size:15 final size:15
Alignment explanation
Indices: 670445--670555 Score: 58
Period size: 15 Copynumber: 7.3 Consensus size: 15
670435 TAGAGAATAA
670445 AAATAAAA-ATAAAAT
1 AAATAAAATAT-AAAT
670460 AAATAACAA-ATAAAT
1 AAATAA-AATATAAAT
670475 AAATAAAATATAAA-
1 AAATAAAATATAAAT
670489 AATATAAGAA-A-AAA-
1 AA-ATAA-AATATAAAT
* *
670503 AGAGTAAAATA-GAAT
1 A-AATAAAATATAAAT
670518 -AATAATAATAATAAAT
1 AAATAA-AAT-ATAAAT
*
670534 AGTAATATAATATAAAT
1 A--AATAAAATATAAAT
670551 AAATA
1 AAATA
670556 GAGAACAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
13 6 0.08
14 17 0.22
15 32 0.41
16 9 0.12
17 7 0.09
18 3 0.04
19 4 0.05
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (15 bp):
AAATAAAATATAAAT
Found at i:670533 original size:21 final size:20
Alignment explanation
Indices: 670509--670557 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
670499 AAAAAGAGTA
670509 AAATAGAATAATAATA-ATAAT
1 AAATAGAAT-ATAATATA-AAT
670530 AAATAGTAATATAATATAAAT
1 AAATAG-AATATAATATAAAT
670551 AAATAGA
1 AAATAGA
670558 GAACAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
AAATAGAATATAATATAAAT
Found at i:671719 original size:2 final size:2
Alignment explanation
Indices: 671714--671759 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
671704 TAAAAACATA
671714 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
671756 AT AT
1 AT AT
671760 CTGTTATGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:673052 original size:21 final size:21
Alignment explanation
Indices: 673026--673099 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
673016 GATGCATGGG
* *
673026 GTATCGATACCTGTATGAACA
1 GTATCGATACCTATATGAAGA
673047 GTATCGATACC-ATATGAAAGA
1 GTATCGATACCTATATG-AAGA
* *
673068 GGTATCGATACCTATATGGAGG
1 -GTATCGATACCTATATGAAGA
673090 GTATCGATAC
1 GTATCGATAC
673100 TTGGGGAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.09
21 24 0.52
22 13 0.28
23 5 0.11
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (21 bp):
GTATCGATACCTATATGAAGA
Found at i:673196 original size:36 final size:36
Alignment explanation
Indices: 673149--673225 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
673139 GTAGGGTATC
* *
673149 GGTACCCTAGCATAGAGGTATCGGTACCTTGAGGGT
1 GGTACCATAGCATAGAGGTATCGGTACCTTGAGGAT
673185 GGTACCATAGCATAGAGGTATCGGTACCTTGAGGAT
1 GGTACCATAGCATAGAGGTATCGGTACCTTGAGGAT
673221 GGTAC
1 GGTAC
673226 TGATACCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (36 bp):
GGTACCATAGCATAGAGGTATCGGTACCTTGAGGAT
Found at i:681934 original size:70 final size:70
Alignment explanation
Indices: 681834--681976 Score: 232
Period size: 70 Copynumber: 2.0 Consensus size: 70
681824 ATTATTAACT
*
681834 GAACCAAATTAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTAACCGTTAATC
1 GAACCAAATCAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTAACCGTTAATC
681899 GAACC
66 GAACC
* * * *
681904 GAACCAAATCAATCGATTTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATC
1 GAACCAAATCAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTAACCGTTAATC
*
681969 GAATC
66 GAACC
681974 GAA
1 GAA
681977 ATTTATTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (70 bp):
GAACCAAATCAACCGAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTAACCGTTAATC
GAACC
Found at i:682101 original size:81 final size:81
Alignment explanation
Indices: 682004--682180 Score: 302
Period size: 81 Copynumber: 2.2 Consensus size: 81
681994 TAACCGAATA
*
682004 AAATAAATTTGGGTTCGATTAATGGTTAAAGAAAAAAATTC-AGTTAATAATTTTCAAATAAATT
1 AAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGA-TTAATAATTTTCAAATAAATT
*
682068 TCAGTTCGATTAACGGTC
64 TCAATTCGATTAACGGTC
682086 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGATTAATAATTTTCAAATAAATTTC
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGATTAATAATTTTCAAATAAATTTC
682151 AATTCGATTAACGGTC
66 AATTCGATTAACGGTC
*
682167 AATTAATTTCGGTT
1 AAATAATTTCGGTT
682181 AATTTGGTTC
Statistics
Matches: 91, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
81 86 0.95
82 5 0.05
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (81 bp):
AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCGATTAATAATTTTCAAATAAATTTC
AATTCGATTAACGGTC
Found at i:684197 original size:185 final size:188
Alignment explanation
Indices: 683900--684245 Score: 527
Period size: 185 Copynumber: 1.9 Consensus size: 188
683890 TTTTAATTTA
*
683900 AATATTAGTAGGATAACTACTCTTTTAATAAGTCAATGTAAAAAAGATATTTGTTATATTTTTAA
1 AATATTAGTAGGATAACTACTCTTTGAATAAGTCAATGTAAAAAAGATATTTGTTATATTTTTAA
* * * *
683965 TTTTAAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATATGTTTAAG
66 CTTTAAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATACATATTTAAA
684030 TTTGAATAGTAAAAGGAG-TTTACCTTTTGACCATTGTAAATTAAATATATTATTTTG
131 TTTGAATAGTAAAAGGAGTTTTACCTTTTGACCATTGTAAATTAAATATATTATTTTG
* * * * *
684087 AATATTAGTGGGATAATTACTCTTTGAATATGTCAATTTAAAAAA-ATATTTGTTATCTTTTTAA
1 AATATTAGTAGGATAACTACTCTTTGAATAAGTCAATGTAAAAAAGATATTTGTTATATTTTTAA
* * *
684151 CTTTGAATATT-AAATATAATTATATACTTTTGTATATTTTAAATTAAAATAATACATATTTAAA
66 CTTTAAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATACATATTTAAA
* * *
684215 TTTGAATGGTAAAATGAGTTTTATCTTTTGA
131 TTTGAATAGTAAAAGGAGTTTTACCTTTTGA
684246 ATATTTCAAA
Statistics
Matches: 142, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
185 64 0.45
186 38 0.27
187 40 0.28
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (188 bp):
AATATTAGTAGGATAACTACTCTTTGAATAAGTCAATGTAAAAAAGATATTTGTTATATTTTTAA
CTTTAAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATACATATTTAAA
TTTGAATAGTAAAAGGAGTTTTACCTTTTGACCATTGTAAATTAAATATATTATTTTG
Found at i:686008 original size:34 final size:32
Alignment explanation
Indices: 685948--686017 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
685938 CCTTACAAAC
*
685948 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
685980 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
686014 TCCC
1 TCCC
686018 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:686507 original size:20 final size:19
Alignment explanation
Indices: 686482--686541 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
686472 ATCTGTTCTC
686482 GGGGAATCGATACCCCCTGG
1 GGGGAATCG-TACCCCCTGG
* *
686502 GGGGAATATGTTCCCCCTGG
1 GGGGAAT-CGTACCCCCTGG
686522 GGGGAATCTGTACCCCCTGG
1 GGGGAATC-GTACCCCCTGG
686542 ACAATCTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (19 bp):
GGGGAATCGTACCCCCTGG
Found at i:686514 original size:35 final size:34
Alignment explanation
Indices: 686432--686516 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
686422 AAACCATGCA
*
686432 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
* *
686466 GGGAGAATCTGTTCTCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
*
686501 GGGGGAATATGTTCCC
1 GGGGGAATCTGTTCCC
686517 CCTGGGGGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 25 0.57
35 19 0.43
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:688499 original size:3 final size:3
Alignment explanation
Indices: 688491--688531 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
688481 TACGTCCTCA
* *
688491 TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
688532 CCTTTCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:689582 original size:34 final size:32
Alignment explanation
Indices: 689522--689591 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
689512 CCTTACAAAC
*
689522 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
689554 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
689588 TCCC
1 TCCC
689592 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:689902 original size:21 final size:21
Alignment explanation
Indices: 689876--689915 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
689866 AGAATGGGGC
*
689876 GAATCGGTACCCCTTCATAGG
1 GAATCGATACCCCTTCATAGG
689897 GAATCGATACCCCTTCATA
1 GAATCGATACCCCTTCATA
689916 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGG
Found at i:690049 original size:15 final size:15
Alignment explanation
Indices: 690029--690085 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
690019 AACCATGCAG
690029 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
690044 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
690060 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
690078 GGGGAATC
1 GGGGAATC
690086 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:690102 original size:35 final size:34
Alignment explanation
Indices: 690028--690112 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
690018 AAACCATGCA
*
690028 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
690062 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
*
690097 GGGGGAATTTGTTCCC
1 GGGGGAATCTGTTCCC
690113 CCTGAGGGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 27 0.56
35 21 0.44
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:690124 original size:22 final size:22
Alignment explanation
Indices: 690078--690138 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
690068 ATCTGTTCCC
690078 GGGGAATC-GATACCCCCT--GG
1 GGGGAATCTG-TACCCCCTGAGG
* *
690098 GGGGAATTTGTTCCCCCTGAGG
1 GGGGAATCTGTACCCCCTGAGG
690120 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
690139 GACAATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 19 0.56
ACGTcount: A:0.16, C:0.28, G:0.34, T:0.21
Consensus pattern (22 bp):
GGGGAATCTGTACCCCCTGAGG
Found at i:690964 original size:30 final size:30
Alignment explanation
Indices: 690917--690975 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
690907 TTCTTGCTTA
690917 TTTTATTTTTCACTTTTTATTTCAT-TTTTG
1 TTTTATTTTTCACTTTTT-TTTCATCTTTTG
*
690947 TTTTATTTTTTTA-TTTTTTTTCATCTTTT
1 TTTTA-TTTTTCACTTTTTTTTCATCTTTT
690976 AATGTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 14 0.54
31 6 0.23
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (30 bp):
TTTTATTTTTCACTTTTTTTTCATCTTTTG
Found at i:691017 original size:12 final size:11
Alignment explanation
Indices: 690981--691018 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
690971 CTTTTAATGT
690981 TTTTATTATTA
1 TTTTATTATTA
690992 -TTTATTATGTA
1 TTTTATTAT-TA
691003 TTTTATTATTAA
1 TTTTATTATT-A
691015 TTTT
1 TTTT
691019 CTCTCTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 3 0.12
12 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:691966 original size:37 final size:37
Alignment explanation
Indices: 691925--692029 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
691915 GTACTTGTGG
* * * *
691925 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
691962 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
691999 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
692030 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:692882 original size:105 final size:105
Alignment explanation
Indices: 692572--693127 Score: 746
Period size: 105 Copynumber: 5.3 Consensus size: 105
692562 GCATTGTTCC
* * ** *
692572 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAAGCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
692636 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
692678 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
692738 CAGCAGTCCCTTCATCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
692778 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
692843 CAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
692883 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
692948 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
692988 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * * *
693053 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
693093 GAGTAGCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAAT
693128 CGTGGATGTT
Statistics
Matches: 404, Mismatches: 37, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
100 83 0.21
101 1 0.00
102 7 0.02
104 5 0.01
105 249 0.62
106 35 0.09
107 2 0.00
108 22 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:704372 original size:37 final size:37
Alignment explanation
Indices: 704322--704426 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
704312 GTGCTTGTGG
* * * *
704322 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCC
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCC
* * * **
704359 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCC
704396 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
704427 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCC
Found at i:705368 original size:25 final size:24
Alignment explanation
Indices: 705323--705373 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
705313 CACTTGGTAT
*
705323 TATTTTAGGTTTAAATCTTAATAA
1 TATTTTAGGTTTAAATCTTAAAAA
* * *
705347 TATTTATATGTTTATATTTTAAAAA
1 TATTT-TAGGTTTAAATCTTAAAAA
705372 TA
1 TA
705374 ACCTAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
TATTTTAGGTTTAAATCTTAAAAA
Found at i:707125 original size:21 final size:20
Alignment explanation
Indices: 707095--707142 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
707085 AATGAATTTT
707095 ATTT-ATTTTAA-TATATATA
1 ATTTAATTTTAATTAT-TATA
707114 ATTTTAATTTTAATTATTATA
1 A-TTTAATTTTAATTATTATA
707135 ATTTAATT
1 ATTTAATT
707143 AGATTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.38
21 12 0.46
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATTTTAATTATTATA
Found at i:707233 original size:2 final size:2
Alignment explanation
Indices: 707226--707263 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
707216 AAATATAAAC
707226 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
707264 TAAGATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:708532 original size:81 final size:81
Alignment explanation
Indices: 708439--708688 Score: 403
Period size: 81 Copynumber: 3.1 Consensus size: 81
708429 AAGCATTTAG
* * * *
708439 TCTTTTACTCAAAGGAATTTAGCCTTTCATCTAACTTGCATGAA-TGACACATTTCTGCTAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCAT-AATTGACACATTTCTGCCAAATG
*
708503 CACAGATAGGCCATTAT
65 CACAGCTAGGCCATTAT
*
708520 TCTTTTACTCAAAGGTATTTAACCTATCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
*
708585 ATAGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
* *
708601 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTAACACATTTCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
708666 ACAGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
708682 TCTTTTA
1 TCTTTTA
708689 TTTAGAACAA
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
80 2 0.01
81 155 0.99
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
ACAGCTAGGCCATTAT
Found at i:715324 original size:81 final size:81
Alignment explanation
Indices: 715239--715407 Score: 248
Period size: 81 Copynumber: 2.1 Consensus size: 81
715229 AAGCATTTAG
* * * *
715239 TCTTTTACTCAACGACATTTAGCCTTTCATCTAACTTGCATGATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGC
*
715304 ACAGCTATGCCATTAT
66 ACAGCTAGGCCATTAT
** * * *
715320 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTTCCAAATGC
1 TCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGC
715385 ACAGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
715401 TCTTTTA
1 TCTTTTA
715408 TTTAGAACAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAAAGACATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGC
ACAGCTAGGCCATTAT
Found at i:724193 original size:19 final size:20
Alignment explanation
Indices: 724171--724213 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
724161 TAAAATTATT
*
724171 AAAAAACAAAT-TATCGAAA
1 AAAAAACAAATAAATCGAAA
**
724190 AAAAATTAAATAAATCGAAA
1 AAAAAACAAATAAATCGAAA
724210 AAAA
1 AAAA
724214 GGACCTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAAACAAATAAATCGAAA
Found at i:736683 original size:85 final size:85
Alignment explanation
Indices: 736582--736747 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
736572 ATACAATCAC
* * * * *
736582 GACACACGAATGTGTGTCATCTT-TTTTATTGGCGTGTGCTTCAATGACACACAATGTAA-GTCA
1 GACACACAAATGTGTGTCATCTTAATTTA-TGACGGGGGCTTCAATGACACACAATG-AACGTCA
* **
736645 TACATGCGTGTCATAAATTTAT
64 TAAATGCGCATCATAAATTTAT
* *
736667 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACGCTCAATGAACGTCATA
1 GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACACAATGAACGTCATA
736732 AATGCGCATCATAAAT
66 AATGCGCATCATAAAT
736748 GTGTGTCATA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 63 0.91
86 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACACAATGAACGTCATA
AATGCGCATCATAAATTTAT
Found at i:736743 original size:13 final size:13
Alignment explanation
Indices: 736725--736773 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
736715 GCTCAATGAA
736725 CGTCATAAATGCG
1 CGTCATAAATGCG
* *
736738 CATCATAAATGTG
1 CGTCATAAATGCG
*
736751 TGTCATAAATGCG
1 CGTCATAAATGCG
736764 CGTCATAAAT
1 CGTCATAAAT
736774 TTATGACGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:736748 original size:26 final size:26
Alignment explanation
Indices: 736719--736773 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
736709 AATGACGCTC
736719 AATGAACGTCATAAATGCGCATCATA
1 AATGAACGTCATAAATGCGCATCATA
*** *
736745 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATGCGCATCATA
736771 AAT
1 AAT
736774 TTATGACGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (26 bp):
AATGAACGTCATAAATGCGCATCATA
Found at i:738914 original size:20 final size:20
Alignment explanation
Indices: 738885--738962 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
738875 CAATACTAAG
* *
738885 CCCTTTAGTATC-AGTACTGA
1 CCCTTGAGTATCGA-TACTTA
738905 CCCTTGAGTATCGATACTTA
1 CCCTTGAGTATCGATACTTA
*
738925 CCCTTGGGTATCGATACTTA
1 CCCTTGAGTATCGATACTTA
*
738945 CCCTTGGGTATCGATACT
1 CCCTTGAGTATCGATACT
738963 AACATGGCCA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 53 0.98
21 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (20 bp):
CCCTTGAGTATCGATACTTA
Found at i:741093 original size:17 final size:18
Alignment explanation
Indices: 741071--741110 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
741061 ATAATTTTTT
741071 TAAATAAT-A-AAAATGTG
1 TAAATAATGATAAAATG-G
741088 TAAAT-ATGATAAAATGG
1 TAAATAATGATAAAATGG
741105 TAAATA
1 TAAATA
741111 TATATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.10
17 12 0.60
18 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (18 bp):
TAAATAATGATAAAATGG
Found at i:741452 original size:16 final size:17
Alignment explanation
Indices: 741429--741467 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
741419 AATGTTACAC
*
741429 TATTATTATTGATTATATT
1 TATTA-TATAGATTAT-TT
741448 TATTATATAGATTATTT
1 TATTATATAGATTATTT
741465 TAT
1 TAT
741468 GCTAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTATATAGATTATTT
Found at i:742075 original size:20 final size:20
Alignment explanation
Indices: 742050--742101 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
742040 AATACTGTAG
742050 GGGTATCGATACCTTAAGTA
1 GGGTATCGATACCTTAAGTA
*
742070 GGGTATTGATACCTTAAGTA
1 GGGTATCGATACCTTAAGTA
742090 GGGTATCGATAC
1 GGGTATCGATAC
742102 TGTAGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (20 bp):
GGGTATCGATACCTTAAGTA
Found at i:742491 original size:46 final size:46
Alignment explanation
Indices: 742426--742521 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
742416 ATGAGTTCCT
* *
742426 TTAGAAAGATAGTAGGGCTGAAAGTATAGATTCAGTCTGAATATCC
1 TTAGAAAGATAGTAAGGCTGAAAGTATAGATTCAGTCTAAATATCC
742472 TTAGAAAGATAGTAAGGCTGAAAGTATAGATTCAGTCTAAATATCC
1 TTAGAAAGATAGTAAGGCTGAAAGTATAGATTCAGTCTAAATATCC
742518 TTAG
1 TTAG
742522 GGAGTGCGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (46 bp):
TTAGAAAGATAGTAAGGCTGAAAGTATAGATTCAGTCTAAATATCC
Found at i:748234 original size:3 final size:3
Alignment explanation
Indices: 748222--748272 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
748212 CGTCTTTTAA
748222 TAT T-T 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
748269 TAT T
1 TAT T
748273 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:750220 original size:2 final size:2
Alignment explanation
Indices: 750213--750268 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
750203 TGCATAGTGC
750213 AT 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 AT AT
750254 AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
750269 GTTTATACCG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:755103 original size:27 final size:27
Alignment explanation
Indices: 755073--755126 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
755063 CCCCGTTCTT
755073 TGGACATCTCATTGGAAATTTGTCCAA
1 TGGACATCTCATTGGAAATTTGTCCAA
755100 TGGACATCTCATTGGAAATTTGTCCAA
1 TGGACATCTCATTGGAAATTTGTCCAA
755127 GAATTTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
TGGACATCTCATTGGAAATTTGTCCAA
Found at i:762588 original size:113 final size:113
Alignment explanation
Indices: 762390--762594 Score: 383
Period size: 113 Copynumber: 1.8 Consensus size: 113
762380 GGTTCGATCT
* *
762390 TGATTCAATGGATCAAATCCCCCAGATCTGATATTTCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 TGATTCAATGGATCAAATCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
762455 TATCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTTTATCC
66 TATCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTTTATCC
762503 TGATTCAATGGATCAAATCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
1 TGATTCAATGGATCAAATCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
*
762568 TATCCAAGATTTGTTATTCCCTTCAGA
66 TATCCAAGATTTGATATTCCCTTCAGA
762595 ATAAACGGAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 89 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (113 bp):
TGATTCAATGGATCAAATCCCCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
TATCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTTTATCC
Found at i:762612 original size:48 final size:48
Alignment explanation
Indices: 762534--762628 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
762524 CCAGATCTGA
* *
762534 TATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTATCCAAGATTTGT
1 TATTCCCTTCAGAATAAACGGAACAGGTCTCTCTTATCCAAGATTTGT
* *
762582 TATTCCCTTCAGAATAAACGGAATATGTCTCTCTTATCCAAGATTTG
1 TATTCCCTTCAGAATAAACGGAACAGGTCTCTCTTATCCAAGATTTG
762629 AGTGACAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (48 bp):
TATTCCCTTCAGAATAAACGGAACAGGTCTCTCTTATCCAAGATTTGT
Found at i:762821 original size:111 final size:111
Alignment explanation
Indices: 762627--762913 Score: 459
Period size: 111 Copynumber: 2.6 Consensus size: 111
762617 ATCCAAGATT
* *
762627 TGAGTGACAATGGAACAATTCTACCCTGATTCAATGGATCAACTCTCCCAGATCTGATATTCCCT
1 TGAGTGACAGTGGAACAAATCTACCCTGATTCAATGGATCAACTCTCCCAGATCTGATATTCCCT
*
762692 CAGAGGAAGCGGAACATATCTCTTTCTTTCAAGATTTGATATTCCC
66 CAGAGGAAGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCC
* * *
762738 TGAGTGACAGTGGAACAAATCTGCCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCT
1 TGAGTGACAGTGGAACAAATCTACCCTGATTCAATGGATCAACTCTCCCAGATCTGATATTCCCT
762803 CAGAGGAAGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCC
66 CAGAGGAAGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCC
* * * * *
762849 TGAGTAACAGCGGAACAAGTCTACTCTGATTCAATGAATCAACATCT-CCAGATCTGATATTCCC
1 TGAGTGACAGTGGAACAAATCTACCCTGATTCAATGGATCAAC-TCTCCCAGATCTGATATTCCC
762913 T
65 T
762914 GAATGACAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
111 158 0.98
112 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (111 bp):
TGAGTGACAGTGGAACAAATCTACCCTGATTCAATGGATCAACTCTCCCAGATCTGATATTCCCT
CAGAGGAAGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCC
Found at i:767418 original size:42 final size:42
Alignment explanation
Indices: 767301--767420 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
767291 TTTCCCCGAA
* *
767301 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
767343 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
767385 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
767421 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:767657 original size:22 final size:23
Alignment explanation
Indices: 767610--767670 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
767600 TAATTATTAA
* *
767610 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
767631 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
767654 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
767671 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:767723 original size:29 final size:28
Alignment explanation
Indices: 767709--767784 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
767699 TAAGATATTA
767709 TATTTTTATTTTAATAATATATAATAAA
1 TATTTTTATTTTAATAATATATAATAAA
* *
767737 TTTTTTTATATTTAATAATGA-ATAAT-AT
1 TATTTTTAT-TTTAATAAT-ATATAATAAA
* *
767765 TATTTATATTTCAATAATAT
1 TATTTTTATTTTAATAATAT
767785 TTTAGTAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.03
27 8 0.20
28 16 0.40
29 14 0.35
30 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTTTATTTTAATAATATATAATAAA
Found at i:767733 original size:54 final size:52
Alignment explanation
Indices: 767636--767738 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
767626 TTATTAATAT
*
767636 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
767688 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
767739 TTTTTATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:768028 original size:20 final size:20
Alignment explanation
Indices: 767950--768019 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
767940 TTTCCAGATG
767950 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
767970 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
767990 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
768010 TTTTCCAGAA
1 TTTTCCAGAA
768020 TTCAAATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:768028 original size:40 final size:40
Alignment explanation
Indices: 767950--768028 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
767940 TTTCCAGATG
* **
767950 TTTTCCAGAAATGTAATTCATTTTCCAAAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTCA
* *
767990 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTC
768029 TAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTCA
Found at i:768038 original size:15 final size:15
Alignment explanation
Indices: 768002--768083 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
767992 TTACAGAAAT
**
768002 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
768017 G-AATTCAAATTCTA
1 GTAATTCAAATTCCA
**
768031 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
768046 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
768061 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
768076 GTAATTCA
1 GTAATTCA
768084 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.19
15 47 0.81
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:768054 original size:30 final size:30
Alignment explanation
Indices: 768002--768083 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
767992 TTACAGAAAT
*
768002 GTAATTCATTTTCCAG-AATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
768031 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
768061 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
768084 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:768079 original size:45 final size:44
Alignment explanation
Indices: 768002--768088 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
767992 TTACAGAAAT
** *
768002 GTAATTCATTTTCCAGAATTCAAATTCTAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
768046 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
768089 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:769203 original size:23 final size:23
Alignment explanation
Indices: 769177--769223 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
769167 TGATAAAAAA
769177 TTAATTCATATAATT-A-ATTAATT
1 TTAATTC-TAT-ATTAAGATTAATT
769200 TTAATTCTATATTAAGATTAATT
1 TTAATTCTATATTAAGATTAATT
769223 T
1 T
769224 GAAACTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.14
22 4 0.18
23 15 0.68
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTCTATATTAAGATTAATT
Found at i:771891 original size:7 final size:7
Alignment explanation
Indices: 771849--771875 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
771839 GACATACGAT
771849 TTTTTTA
1 TTTTTTA
771856 TTTTTTA
1 TTTTTTA
771863 TTTTTTA
1 TTTTTTA
771870 TTTTTT
1 TTTTTT
771876 TAATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:772911 original size:17 final size:18
Alignment explanation
Indices: 772885--772919 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
772875 TAAATTCATT
772885 ATTTTCTTTT-AATTTTA
1 ATTTTCTTTTAAATTTTA
*
772902 ATTTTTTTTTAAATTTTA
1 ATTTTCTTTTAAATTTTA
772920 TCAAGCCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTCTTTTAAATTTTA
Found at i:773803 original size:19 final size:19
Alignment explanation
Indices: 773779--773818 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
773769 CGCCTGACCC
*
773779 TGTAGATCCTGGTTGTCCT
1 TGTAGATCCTGGCTGTCCT
*
773798 TGTAGATCTTGGCTGTCCT
1 TGTAGATCCTGGCTGTCCT
773817 TG
1 TG
773819 GGCGTCTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.28, T:0.42
Consensus pattern (19 bp):
TGTAGATCCTGGCTGTCCT
Found at i:789652 original size:23 final size:23
Alignment explanation
Indices: 789626--789704 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
789616 ATGGCAATAC
*
789626 GGTGCAATTCTATGTGGCACTTT
1 GGTGCAATTCTACGTGGCACTTT
* *
789649 GGTGCATTTCTACGCGGTC-CTTT
1 GGTGCAATTCTACGTGG-CACTTT
*
789672 GG-GACAATTTCTACGTGGCACTTC
1 GGTG-CAA-TTCTACGTGGCACTTT
789696 GGTGCAATT
1 GGTGCAATT
789705 TATACAAGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 1 0.02
23 25 0.56
24 18 0.40
25 1 0.02
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (23 bp):
GGTGCAATTCTACGTGGCACTTT
Found at i:789703 original size:24 final size:24
Alignment explanation
Indices: 789625--789705 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
789615 TATGGCAATA
*
789625 CGGTGCAA-TTCTATGTGGCACTT
1 CGGTGCAATTTCTACGTGGCACTT
* *
789648 TGGTGC-ATTTCTACGCGGTC-CTT
1 CGGTGCAATTTCTACGTGG-CACTT
*
789671 TGG-GACAATTTCTACGTGGCACTT
1 CGGTG-CAATTTCTACGTGGCACTT
789695 CGGTGCAATTT
1 CGGTGCAATTT
789706 ATACAAGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 2 0.04
23 21 0.45
24 23 0.49
25 1 0.02
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (24 bp):
CGGTGCAATTTCTACGTGGCACTT
Found at i:796651 original size:59 final size:60
Alignment explanation
Indices: 796526--796686 Score: 168
Period size: 59 Copynumber: 2.7 Consensus size: 60
796516 TACCCTTATT
* * * * ***
796526 TAAATT-GATCCCTAAACTTTTAAATATTTCAATTTCATTCCTAAATTATGGTTTTAATTC
1 TAAATTAG-TCCCAAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACATTAATTC
* *
796586 TAAATTAGTCCTC-AAACTTTTCAATATTTC-ATTTCATCCCCAAACTATGACATTCATTC
1 TAAATTAGTCC-CAAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACATTAATTC
*
796645 TAAATTAGTCCCAAAACTTTTTGAAA-ATTCCAATTTCATCCC
1 TAAATTAGTCCCAAAAC-TTTT-AAATATTTCAATTTCATCCC
796687 AAATTATATG
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
58 1 0.01
59 37 0.44
60 33 0.39
61 14 0.16
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
TAAATTAGTCCCAAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACATTAATTC
Found at i:798305 original size:25 final size:25
Alignment explanation
Indices: 798277--798324 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
798267 AATATTTTTA
798277 TTCT-TTTAAAATTTTATAAATTTGT
1 TTCTCTTT-AAATTTTATAAATTTGT
*
798302 TTCTCTTTCAATTTTATAAATTT
1 TTCTCTTTAAATTTTATAAATTT
798325 ATTTTCCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TTCTCTTTAAATTTTATAAATTTGT
Found at i:798815 original size:26 final size:24
Alignment explanation
Indices: 798753--798815 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
798743 CATTTTAATC
798753 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
798777 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
798800 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
798816 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:798817 original size:22 final size:23
Alignment explanation
Indices: 798787--798833 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
798777 AAAATATATT
798787 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
798810 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
798832 TA
1 TA
798834 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:798847 original size:32 final size:32
Alignment explanation
Indices: 798781--798860 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
798771 ATATTTAAAA
* *
798781 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
798813 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
798845 TATATTATAATAATAT
1 TATATT-TATTAATAT
798861 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:798974 original size:19 final size:18
Alignment explanation
Indices: 798950--799018 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
798940 ATATTATTAA
798950 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
798969 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
798987 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
799009 ATT-TTAATAA
1 ATTATTAATAA
799019 AGATATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:799039 original size:23 final size:23
Alignment explanation
Indices: 799013--799057 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
799003 AATAATATTT
799013 TAATAAAGATATATAAAATATAC
1 TAATAAAGATATATAAAATATAC
* * * *
799036 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATATAAAATATA
799058 ATATAACACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATAAAGATATATAAAATATAC
Found at i:799218 original size:29 final size:29
Alignment explanation
Indices: 799160--799219 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
799150 ATTATAAAAA
*
799160 TAATATTTTAATAATAAATAAATTTATTT
1 TAATATTTTAATAATAAATAAATTAATTT
799189 TAATATTTTAA-AAT-AATAATATTAAGTTT
1 TAATATTTTAATAATAAATAA-ATTAA-TTT
799218 TA
1 TA
799220 TGATAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.18
28 7 0.25
29 16 0.57
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TAATATTTTAATAATAAATAAATTAATTT
Found at i:803310 original size:4 final size:4
Alignment explanation
Indices: 803301--803327 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
803291 TTCAACTATG
803301 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
803328 GTATACATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:805172 original size:6 final size:6
Alignment explanation
Indices: 805161--805187 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
805151 GTTTTCATGC
805161 TTGGTT TTGGTT TTGGTT TTGGTT TTG
1 TTGGTT TTGGTT TTGGTT TTGGTT TTG
805188 TATGGAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (6 bp):
TTGGTT
Found at i:805687 original size:3 final size:3
Alignment explanation
Indices: 805681--805729 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
805671 GTGTTGAAGT
805681 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
805729 A
1 A
805730 AGTATGCCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:812244 original size:21 final size:21
Alignment explanation
Indices: 812220--812262 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
812210 TGCTGATGAT
*
812220 GAGGATAGTGAAAATGCCTCG
1 GAGGATAGTGAAAATGCATCG
* * *
812241 GAGGCTGGTGACAATGCATCG
1 GAGGATAGTGAAAATGCATCG
812262 G
1 G
812263 GCAGTGAGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.37, T:0.19
Consensus pattern (21 bp):
GAGGATAGTGAAAATGCATCG
Found at i:816967 original size:141 final size:139
Alignment explanation
Indices: 816681--816955 Score: 489
Period size: 141 Copynumber: 2.0 Consensus size: 139
816671 AGGTGAGAAC
*
816681 TTTAATATTCTCATTCCAAGCTTTCATTCAAGCTCTCAATGACAAGTTTTGGTTATGCTAACCAA
1 TTTAATATTCTCATTCCAAGCTTTCATTCAAGCTCTCAATGACAAGTTTTGGTCATGCTAACCAA
*
816746 ATATGGGTTTTAGTGGGGGTTTAGGAACCCAAGTGTAACTAGCTCATTTTTTTTTAGAGATTTAA
66 ATATGGGTTTTAGTGGGGGTTTAGGAACCCAAGTGTAACTAGCTCA--TTTTTTGAGAGATTTAA
816811 ACCTATAAAAA
129 ACCTATAAAAA
*
816822 TTTAATCTTCTCATTCCAAGCTTTCATTCAAGCTCTCAATGACAAGTTTTGGTCATGCTAACCAA
1 TTTAATATTCTCATTCCAAGCTTTCATTCAAGCTCTCAATGACAAGTTTTGGTCATGCTAACCAA
*
816887 ATATGGGTTTTAGTGGGGGTTTAGGAACCTAAGTGTAACTAGCTCA-TTTTTGAGAGATTTAAAC
66 ATATGGGTTTTAGTGGGGGTTTAGGAACCCAAGTGTAACTAGCTCATTTTTTGAGAGATTTAAAC
816951 CTATA
131 CTATA
816956 TAAACGTTTT
Statistics
Matches: 130, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
138 22 0.17
141 108 0.83
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (139 bp):
TTTAATATTCTCATTCCAAGCTTTCATTCAAGCTCTCAATGACAAGTTTTGGTCATGCTAACCAA
ATATGGGTTTTAGTGGGGGTTTAGGAACCCAAGTGTAACTAGCTCATTTTTTGAGAGATTTAAAC
CTATAAAAA
Found at i:818395 original size:28 final size:28
Alignment explanation
Indices: 818355--818409 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
818345 TCAAATCCAC
818355 TAGATTTGATTACCTTTAAGGACAAGGG
1 TAGATTTGATTACCTTTAAGGACAAGGG
818383 TAGATTTGATTACCTTTAAGGACAAGG
1 TAGATTTGATTACCTTTAAGGACAAGG
818410 TGTAACCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (28 bp):
TAGATTTGATTACCTTTAAGGACAAGGG
Found at i:818976 original size:21 final size:21
Alignment explanation
Indices: 818858--818970 Score: 145
Period size: 21 Copynumber: 5.4 Consensus size: 21
818848 TCATTCAAGG
**
818858 GAAGGGATCGATCCTTTTCAT
1 GAAGGGATCGATCCTTTTGGT
*
818879 CAAGGGATCGATCCTTTTGGT
1 GAAGGGATCGATCCTTTTGGT
818900 GAAGGGATCGATCCTTTTGGT
1 GAAGGGATCGATCCTTTTGGT
* **
818921 GAAGGGATCGATCATTTTCCT
1 GAAGGGATCGATCCTTTTGGT
* *
818942 CAAGGGATCGATCCTTTTTGT
1 GAAGGGATCGATCCTTTTGGT
*
818963 AAAGGGAT
1 GAAGGGAT
818971 TAATCCCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (21 bp):
GAAGGGATCGATCCTTTTGGT
Found at i:822360 original size:9 final size:9
Alignment explanation
Indices: 822346--822371 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
822336 GGAGGAGCTC
822346 CCAAAATAT
1 CCAAAATAT
822355 CCAAAATAT
1 CCAAAATAT
822364 CCAAAATA
1 CCAAAATA
822372 AGACAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (9 bp):
CCAAAATAT
Found at i:826706 original size:18 final size:18
Alignment explanation
Indices: 826683--826718 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
826673 AGGAACTTGT
826683 AATAACCTTATCTTATTC
1 AATAACCTTATCTTATTC
826701 AATAACCTTATCTTATTC
1 AATAACCTTATCTTATTC
826719 TGAAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAACCTTATCTTATTC
Found at i:836606 original size:64 final size:64
Alignment explanation
Indices: 836489--836631 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
836479 TGCACTAAGA
* * *
836489 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTAT-
1 GTGCATCGATGCATAAAATGCATTCGA-GTTTTCAAAAAGCCTGAGTGAATCGATGCATGGAATG
* *
836553 GTGCATCGATGCATAAAATGCATTCGA-TTTTCAATTTAATCCATG-GTGAATCGATGCATGGAA
1 GTGCATCGATGCATAAAATGCATTCGAGTTTTCAA--AAAGCC-TGAGTGAATCGATGCATGGAA
836616 TG
63 TG
*
836618 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
836632 CACTTTGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
62 6 0.09
64 48 0.70
65 15 0.22
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGAGTTTTCAAAAAGCCTGAGTGAATCGATGCATGGAATG
Found at i:837337 original size:24 final size:23
Alignment explanation
Indices: 837304--837352 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
837294 AACAACAAAT
837304 AAGTTAAAACATCCAAAAACTATC
1 AAGTTAAAACATCCAAAAAC-ATC
* * *
837328 AAGTTTAAACATGCAGAAACATC
1 AAGTTAAAACATCCAAAAACATC
837351 AA
1 AA
837353 AATCAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.20
Consensus pattern (23 bp):
AAGTTAAAACATCCAAAAACATC
Found at i:849314 original size:21 final size:21
Alignment explanation
Indices: 849288--849328 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
849278 GGGAAGAGAT
849288 CGATCCTTTTCATCAAGGGAC
1 CGATCCTTTTCATCAAGGGAC
* *
849309 CGATCCTTTTCGTGAAGGGA
1 CGATCCTTTTCATCAAGGGA
849329 TCAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
CGATCCTTTTCATCAAGGGAC
Found at i:852608 original size:20 final size:20
Alignment explanation
Indices: 852583--852656 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
852573 TAGGTTTGAG
*
852583 TATCGATATTGGATAAATAA
1 TATCGATATTGGATAAACAA
*
852603 TATCGATATTGGATGAACAA
1 TATCGATATTGGATAAACAA
*
852623 TATCGATATTGGATTAACAA
1 TATCGATATTGGATAAACAA
852643 TATCGATATTGGAT
1 TATCGATATTGGAT
852657 GAAATGGGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATATTGGATAAACAA
Found at i:852645 original size:40 final size:40
Alignment explanation
Indices: 852583--852659 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
852573 TAGGTTTGAG
*
852583 TATCGATATTGGATAAATAATATCGATATTGGATGAACAA
1 TATCGATATTGGATAAACAATATCGATATTGGATGAACAA
*
852623 TATCGATATTGGATTAACAATATCGATATTGGATGAA
1 TATCGATATTGGATAAACAATATCGATATTGGATGAA
852660 ATGGGATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (40 bp):
TATCGATATTGGATAAACAATATCGATATTGGATGAACAA
Found at i:852796 original size:25 final size:25
Alignment explanation
Indices: 852761--852814 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
852751 TCTGATACCG
*
852761 ATACCAACACTAGAAATAGGTTCTA
1 ATACCAACACTAGAAATAAGTTCTA
* *
852786 ATACCAGCACTGGAAATAAGTTCTA
1 ATACCAACACTAGAAATAAGTTCTA
852811 ATAC
1 ATAC
852815 TAGTGCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (25 bp):
ATACCAACACTAGAAATAAGTTCTA
Found at i:854878 original size:13 final size:13
Alignment explanation
Indices: 854860--854937 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
854850 GTCATAAATC
*
854860 TATGACGCGCATT
1 TATGACACGCATT
*
854873 TATGACACGTATT
1 TATGACACGCATT
854886 TATGACACGCATT
1 TATGACACGCATT
*
854899 TATGACACACATT
1 TATGACACGCATT
* *
854912 TATGACGCTCATT
1 TATGACACGCATT
* *
854925 TACGACGCGCATT
1 TATGACACGCATT
854938 GAGAGTCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (13 bp):
TATGACACGCATT
Done.