Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004617.1 Hibiscus syriacus cultivar Beakdansim tig00010329_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: 65478
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2840 original size:17 final size:18
Alignment explanation
Indices: 2818--2856 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2808 AGTATGAATG
2818 GTGTTGTCGTGGCAAA-T
1 GTGTTGTCGTGGCAAAGT
*
2835 GTGTTGTTGTGGCAAAGT
1 GTGTTGTCGTGGCAAAGT
2853 GTGT
1 GTGT
2857 AAGGATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (18 bp):
GTGTTGTCGTGGCAAAGT
Found at i:4612 original size:15 final size:15
Alignment explanation
Indices: 4594--4641 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4584 ATTTTTTTAA
4594 ATAGTATTATATTTT
1 ATAGTATTATATTTT
*
4609 ATAGTAATATATTTAT
1 ATAGTATTATATTT-T
* * *
4625 GTAATATTATTTTTT
1 ATAGTATTATATTTT
4640 AT
1 AT
4642 TAAAATATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATAGTATTATATTTT
Found at i:4635 original size:14 final size:14
Alignment explanation
Indices: 4594--4667 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
4584 ATTTTTTTAA
*
4594 ATAGTATTATATTTT
1 ATAGTAATATA-TTT
4609 ATAGTAATATATTT
1 ATAGTAATATATTT
4623 AT-GTAATATTATTTT
1 ATAGTAATA-TA-TTT
* * *
4638 TTATTAAAATATTT
1 ATAGTAATATATTT
* *
4652 ATAATTATATATTT
1 ATAGTAATATATTT
4666 AT
1 AT
4668 TTAGAATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
13 6 0.12
14 22 0.46
15 16 0.33
16 4 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
ATAGTAATATATTT
Found at i:4664 original size:29 final size:29
Alignment explanation
Indices: 4601--4671 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
4591 TAAATAGTAT
* *
4601 TATATTTTATAGTAATATATTTATGTAATA
1 TATATTTTTTAGTAAAATATTTA-GTAATA
*
4631 T-TATTTTTTATTAAAATATTTA-TAATTA
1 TATATTTTTTAGTAAAATATTTAGTAA-TA
4659 TATATTTATTTAG
1 TATATTT-TTTAG
4672 AATTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.09
28 3 0.09
29 23 0.68
30 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (29 bp):
TATATTTTTTAGTAAAATATTTAGTAATA
Found at i:9519 original size:37 final size:38
Alignment explanation
Indices: 9478--9637 Score: 258
Period size: 37 Copynumber: 4.3 Consensus size: 38
9468 AAAAAATCTT
*
9478 TTTTTGAAAATATATATAATATATAGTTTTGAAAA-TA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
9515 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
* *
9553 TTTTTG-AAATATATATATTATATAGTTTTGAAAACCA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
9590 TTTTTGAAAATATATAT--TATATAGTTTTGAAAACGA
1 TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
9626 TTTTT-AAAATAT
1 TTTTTGAAAATAT
9638 CTTATCCGAA
Statistics
Matches: 117, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 7 0.06
36 23 0.20
37 70 0.60
38 17 0.15
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTGAAAACGA
Found at i:10387 original size:20 final size:20
Alignment explanation
Indices: 10364--10538 Score: 181
Period size: 20 Copynumber: 8.7 Consensus size: 20
10354 GTTTCCAGAT
10364 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
10384 TCGCATTGCGATTTTTCGACTA
1 TCGCAACGCGA-TTCT-GACTA
* * * *
10406 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* *
10426 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTA
*
10446 TCGCAACGCGATTCTAACTA
1 TCGCAACGCGATTCTGACTA
* *
10466 TCACAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
10486 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
*
10506 TCGCAACGCGATGCTGACTA
1 TCGCAACGCGATTCTGACTA
*
10526 TCGCAATGCGATT
1 TCGCAACGCGATT
10539 TTCAAAACGC
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 107 0.83
21 6 0.05
22 15 0.12
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:10755 original size:22 final size:22
Alignment explanation
Indices: 10704--10756 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
10694 CACTCTCTAA
* * *
10704 GGCGACATCCGTCCCCATCTCT
1 GGCGAAATCAGTCCCCATCTCC
* *
10726 GACAAAATCAGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
10748 GGCGAAATC
1 GGCGAAATC
10757 CGTCTATCTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.40, G:0.17, T:0.19
Consensus pattern (22 bp):
GGCGAAATCAGTCCCCATCTCC
Found at i:11215 original size:20 final size:20
Alignment explanation
Indices: 11141--11208 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
11131 AGAATCGCAA
*
11141 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
11160 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
11180 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
11200 TGCGATTTT
1 TGCGATTTT
11209 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 9 0.21
20 34 0.79
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:12941 original size:18 final size:18
Alignment explanation
Indices: 12918--12967 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
12908 TTTACTCGTA
12918 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
12936 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
12954 ATTTCACTTAGATT
1 ATTTCACTTAGATT
12968 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:13135 original size:20 final size:20
Alignment explanation
Indices: 13110--13177 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
13100 TAGTTTACTT
13110 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
13130 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
13150 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
13170 TCGCAACG
1 TCGCAACG
13178 AAAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:13187 original size:34 final size:38
Alignment explanation
Indices: 13110--13196 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 38
13100 TAGTTTACTT
13110 TCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTATCGCAAC-CGAAAATGAC-A
**
13150 TCGCAACGCGAATTTGACTATCGCAA-CG-AAA-GA-A
1 TCGCAACGCGAAAATGACTATCGCAACCGAAAATGACA
*
13184 TCGCAATGCGAAA
1 TCGCAACGCGAAA
13197 TGAAAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
34 12 0.28
36 2 0.05
37 3 0.07
38 2 0.05
40 24 0.56
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (38 bp):
TCGCAACGCGAAAATGACTATCGCAACCGAAAATGACA
Found at i:13274 original size:20 final size:20
Alignment explanation
Indices: 13227--13275 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
13217 TCTCGTTACT
* *
13227 ATAGTCACTTTCGCGTTGCG
1 ATAGTCATTTTCGAGTTGCG
13247 ATAGTCATTTTCGAGTTGCG
1 ATAGTCATTTTCGAGTTGCG
13267 ATAGTCATT
1 ATAGTCATT
13276 CGTATTGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
ATAGTCATTTTCGAGTTGCG
Found at i:13825 original size:21 final size:21
Alignment explanation
Indices: 13773--13832 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
13763 CCCGACTCAC
* *
13773 CTGTCATCGTTCAAGAGTCCC
1 CTGTCATCGTTCAAGAGGCCA
** *
13794 CTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCA
*
13815 CTGTCATCGTTGAAGAGG
1 CTGTCATCGTTCAAGAGG
13833 TCCCTCCCAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCA
Found at i:15266 original size:14 final size:15
Alignment explanation
Indices: 15247--15283 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
15237 TTGCTTGTTT
15247 AATTGATTTA-TAAA
1 AATTGATTTAGTAAA
15261 AATTGA-TTAGTAAA
1 AATTGATTTAGTAAA
*
15275 AGTTGATTT
1 AATTGATTT
15284 GTTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 15 0.75
15 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (15 bp):
AATTGATTTAGTAAA
Found at i:15539 original size:20 final size:20
Alignment explanation
Indices: 15527--15821 Score: 137
Period size: 20 Copynumber: 15.8 Consensus size: 20
15517 CAAATACCCT
*
15527 TTGCGATAATCAAATTCGCA
1 TTGCGATACTCAAATTCGCA
*
15547 TTGCGATACTCAAATTCGCG
1 TTGCGATACTCAAATTCGCA
**
15567 TTGCGATACTCAAATTCGTG
1 TTGCGATACTCAAATTCGCA
* *
15587 TTGCGATAGTCAAATTCGCG
1 TTGCGATACTCAAATTCGCA
* *
15607 TTGCGAT--T----TTCTCG
1 TTGCGATACTCAAATTCGCA
* *
15621 TTGCGATAATCAAATTCGCG
1 TTGCGATACTCAAATTCGCA
* * **
15641 TTGCGATAGTCAAATTTGTG
1 TTGCGATACTCAAATTCGCA
** **
15661 TTGCGATAGACAAATTCGGG
1 TTGCGATACTCAAATTCGCA
* *
15681 TTGCGAT--T----TTTGCG
1 TTGCGATACTCAAATTCGCA
* * **
15695 TTGCGATAGTCATATTCGTG
1 TTGCGATACTCAAATTCGCA
* *
15715 TTGCGATAGTCAAATTCGCG
1 TTGCGATACTCAAATTCGCA
* *
15735 TTGCGATAGTCAAATTCGCG
1 TTGCGATACTCAAATTCGCA
*
15755 TTGCGAT--T----TTTG-A
1 TTGCGATACTCAAATTCGCA
* *
15768 GTTGCGATAATCAAATTCGCG
1 -TTGCGATACTCAAATTCGCA
*
15789 TTGCGATAGTCAAATTCG--
1 TTGCGATACTCAAATTCGCA
*
15807 TTGCGATATTCAAAT
1 TTGCGATACTCAAAT
15822 GAATGTGTAA
Statistics
Matches: 229, Mismatches: 26, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
14 33 0.14
16 3 0.01
18 16 0.07
20 177 0.77
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGCGATACTCAAATTCGCA
Found at i:15626 original size:94 final size:94
Alignment explanation
Indices: 15527--15761 Score: 278
Period size: 94 Copynumber: 2.5 Consensus size: 94
15517 CAAATACCCT
* * * *
15527 TTGCGATAATCAAATTCGCATTGCGATACTCAAATTCGCGTTGCGATACTCAAATTCGTGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATACACAAATTCGGGTTGCG
* *
15592 ATAGTCAAATTCGCG-TTG-CGATTTTC-TCG
66 ATAGTCAAATT-GCGATAGTC-ATATTCGT-G
* * *
15621 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTTGTGTTGCGATAGACAAATTCGGGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATACACAAATTCGGGTTGCG
** ****
15686 ATTTTTGCGTTGCGATAGTCATATTCGTG
66 ATAGTCAAATTGCGATAGTCATATTCGTG
*
15715 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
15762 TTTTGAGTTG
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 115 0.96
95 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (94 bp):
TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATACACAAATTCGGGTTGCG
ATAGTCAAATTGCGATAGTCATATTCGTG
Found at i:15627 original size:74 final size:74
Alignment explanation
Indices: 15547--15821 Score: 421
Period size: 74 Copynumber: 3.7 Consensus size: 74
15537 CAAATTCGCA
* *
15547 TTGCGATACTCAAATTCGCGTTGCGATACTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
15612 ATTTTCT-CG
66 ATTTT-TGCG
* * *
15621 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTTGTGTTGCGATAGACAAATTCGGGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
15686 ATTTTTGCG
66 ATTTTTGCG
* * * *
15695 TTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
*
15760 ATTTTTGAG
66 ATTTTTGCG
*
15769 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTC--GTTGCGATATTCAAAT
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAAT
15822 GAATGTGTAA
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
72 15 0.08
73 1 0.01
74 167 0.91
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (74 bp):
TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
ATTTTTGCG
Found at i:15664 original size:54 final size:54
Alignment explanation
Indices: 15465--15667 Score: 217
Period size: 54 Copynumber: 3.6 Consensus size: 54
15455 CGCGAAAGTC
* * * * *
15465 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGACAGTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAATCA
* * * * * * *
15519 AATACCCTTTGCGATAATCAAATTCGCATTGCGATACTCAAATTCGCGTTGCGATACTCA
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCTCGTTGCGATAATCA
*
15579 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAATCA
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAATCA
* *
15633 AATTCGCGTTGCGATAGTCAAATTTGTGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
15668 AGACAAATTC
Statistics
Matches: 122, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
54 76 0.62
56 1 0.01
58 1 0.01
60 44 0.36
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (54 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAATCA
Found at i:15696 original size:54 final size:54
Alignment explanation
Indices: 15638--15741 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
15628 AATCAAATTC
* *
15638 GCGTTGCGATAGTCAAATTTGTGTTGCGATAGACAAATTCGGGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGTGTTGCGATAGACAAATTCGCGTTGCGATTTTT
* *
15692 GCGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGTTGCGATAGTCAAATTCGTGTTGCGATAGACAAATTCGCGTTGCGAT
15742 AGTCAAATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGTGTTGCGATAGACAAATTCGCGTTGCGATTTTT
Found at i:16057 original size:140 final size:138
Alignment explanation
Indices: 15794--16061 Score: 491
Period size: 140 Copynumber: 1.9 Consensus size: 138
15784 TCGCGTTGCG
*
15794 ATAGTCAAATTCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATA
1 ATAGTCAAATTCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
*
15859 GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAA
66 GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAA
15924 TACACATA
131 TACACATA
*
15932 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAGCAACTGAACAGATCA
1 ATAGTCAAATT--CGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
15997 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
64 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
16062 TAGAACATTT
Statistics
Matches: 125, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
138 11 0.09
140 114 0.91
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (138 bp):
ATAGTCAAATTCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATA
GCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAA
TACACATA
Found at i:18453 original size:24 final size:24
Alignment explanation
Indices: 18426--18472 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
18416 CAAAATCCGA
18426 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
18450 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
18473 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:19314 original size:20 final size:20
Alignment explanation
Indices: 19289--19368 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
19279 GAAATTCAGT
19289 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
19309 GTTGCGACAGCCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
19329 GTTGCGATAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* * *
19349 ATTGCGATAGTCATAATCGC
1 GTTGCGACAGTCAGAATCGC
19369 ATTACGATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.23
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:19369 original size:20 final size:20
Alignment explanation
Indices: 19290--19478 Score: 114
Period size: 20 Copynumber: 9.3 Consensus size: 20
19280 AAATTCAGTG
* *
19290 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* * *
19310 TTGCGACAGCCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
19330 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
19350 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * * *
19370 TTACGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
19390 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
*
19410 TTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGTC--AGAATCGCA
** * * *
19432 ACGCGA-ATTTGGAAAATCGCA
1 TTGCGATA-GT-CAGAATCGCA
* *
19453 ATGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
19473 TTGCGA
1 TTGCGA
19479 ATCTGGAAAC
Statistics
Matches: 140, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.01
20 109 0.78
21 17 0.12
22 13 0.09
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:23668 original size:24 final size:24
Alignment explanation
Indices: 23636--23704 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
23626 TGTGACACGC
* * *
23636 TTTTCTCTGCTCTTGTGACATATG
1 TTTTCTCTGCTATTGTGACACATA
* *
23660 TTTTCTCTGTTATTGTGGCACATA
1 TTTTCTCTGCTATTGTGACACATA
* *
23684 TTTTCTCTACTATCGTGACAC
1 TTTTCTCTGCTATTGTGACAC
23705 GATCCTTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (24 bp):
TTTTCTCTGCTATTGTGACACATA
Found at i:26788 original size:2 final size:2
Alignment explanation
Indices: 26733--26770 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26723 TGTAAATCAA
26733 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
26771 TTCAAATTAA
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:27068 original size:12 final size:12
Alignment explanation
Indices: 27051--27101 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
27041 TTCAAAGAGG
27051 TTTTATATTTAA
1 TTTTATATTTAA
27063 TTTTATA-TTATA
1 TTTTATATTTA-A
*
27075 TTTGAT-TTTAA
1 TTTTATATTTAA
27086 TTTTA-ATATTAA
1 TTTTATAT-TTAA
27098 TTTT
1 TTTT
27102 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:27148 original size:52 final size:52
Alignment explanation
Indices: 27091--27258 Score: 291
Period size: 52 Copynumber: 3.2 Consensus size: 52
27081 TTTAATTTTA
27091 ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
** *
27143 ATATTAAAATTTTAAATAAATTAAATATTAATGTTTTAATATTATATTATAG
1 ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
*
27195 ATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
27247 ATATTTAATTTT
1 ATA-TTAATTTT
27259 ATATCATATA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 100 0.93
53 8 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (52 bp):
ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAG
Found at i:27155 original size:28 final size:28
Alignment explanation
Indices: 27091--27258 Score: 180
Period size: 24 Copynumber: 6.4 Consensus size: 28
27081 TTTAATTTTA
*
27091 ATATTAATTTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTTAATATTATATTATAG
27115 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
** *
27143 ATATTAAAATTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTTAATATTATATTATAG
*
27167 ATATTAATGTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
*
27195 ATATTAATTTTTTAA-A-TAAATTA-A-
1 ATATTAATTTTTTAATATTATATTATAG
*
27219 ATATTAGTTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
27247 ATATTTAATTTT
1 ATA-TTAATTTT
27259 ATATCATATA
Statistics
Matches: 119, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
24 42 0.35
25 5 0.04
26 30 0.25
27 5 0.04
28 30 0.25
29 7 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTATATTATAG
Found at i:27803 original size:31 final size:31
Alignment explanation
Indices: 27766--27824 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
27756 TAGTTGTATG
* *
27766 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
27797 AATTATTTAAATCTCAGTATTGCAAAAC
1 AATTATTTAAATCTCAGTATTGCAAAAC
27825 ACTTTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:30925 original size:45 final size:46
Alignment explanation
Indices: 30871--31232 Score: 292
Period size: 45 Copynumber: 8.0 Consensus size: 46
30861 AGTCAAATTG
* * * * *
30871 AGAATGACATCACTAAAAGGTTGACTTC-TCTTCACAAGAAAGTCA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * * * * ** * *
30916 AGAATGACATCAATAAAAGGTTGAC-TCCTAGTCGCAAGAAATTCA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * * *
30961 AGAAGGAAAACACTAAAAGAATGAC-TCTTCTTCACGAGAAAGTCA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * * * * * *
31006 AGAATGACATCACTAAAAGGTTCAC-TCCTCTTTGTGAGAAAGTCA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * * * *
31051 ATAAGGATAACATTAAAAGATTGAC-TCATCTTCGTGAGAAAGACA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* *
31096 AGAAGGACAACACTAAAAGATTGA-GTCAACTTCGCGAGAAAGTCA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * * * *
31141 AGAAGGATAACACTAAAAGATTAAC-TCCTCTTCGTGAGAAAGTTA
1 AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
* * *
31186 AGAATGACAACACTAAAA-AGTTGA-TTCATCTTTGTGAGAAAGTCA
1 AGAAGGACAACACTAAAAGA-TTGACTTCATCTTCGCGAGAAAGTCA
31231 AG
1 AG
31233 TTGAGGTTTC
Statistics
Matches: 257, Mismatches: 55, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
44 3 0.01
45 254 0.99
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (46 bp):
AGAAGGACAACACTAAAAGATTGACTTCATCTTCGCGAGAAAGTCA
Found at i:30986 original size:90 final size:88
Alignment explanation
Indices: 30881--31232 Score: 346
Period size: 90 Copynumber: 3.9 Consensus size: 88
30871 AGAATGACAT
* * * *
30881 CACTAAAAGGTTGACTTC-TCTTCACAAGAAAGTCAAGAATGACATCAATAAAAGGTTGACTCCT
1 CACTAAAAGATTGAC-TCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGGTTGACTCCT
* * *
30945 AGTCGCAAGAAATTCAAGAAGGAAAA
65 --TCGCGAGAAAGTCAAGAAGGATAA
* * * *
30971 CACTAAAAGAATGACTCTTCTTCACGAGAAAGTCAAGAATGACATCACTAAAAGGTTCACTCCTC
1 CACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGGTTGACT-C-C
* * *
31036 TTTGTGAGAAAGTCAATAAGGATAA
64 TTCGCGAGAAAGTCAAGAAGGATAA
* ** * * * *
31061 CATTAAAAGATTGACTCATCTTCGTGAGAAAGACAAGAAGGACAACACTAAAAGATTGAGTCAAC
1 CACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGGTTGACTC--C
31126 TTCGCGAGAAAGTCAAGAAGGATAA
64 TTCGCGAGAAAGTCAAGAAGGATAA
* * ** * * *
31151 CACTAAAAGATTAACTCCTCTTCGTGAGAAAGTTAAGAATGACAACACTAAAAAGTTGATTCATC
1 CACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGGTTGACTC--C
* *
31216 TTTGTGAGAAAGTCAAG
64 TTCGCGAGAAAGTCAAG
31233 TTGAGGTTTC
Statistics
Matches: 220, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
89 3 0.01
90 214 0.97
91 1 0.00
92 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (88 bp):
CACTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGGTTGACTCCTT
CGCGAGAAAGTCAAGAAGGATAA
Found at i:31113 original size:135 final size:135
Alignment explanation
Indices: 30871--31232 Score: 402
Period size: 135 Copynumber: 2.7 Consensus size: 135
30861 AGTCAAATTG
* * *** * *
30871 AGAATGACATCACTAAAAGGTTGACTTCTCTTCACAAGAAAGTCAAGAATGACATCAATAAAAGG
1 AGAATGACATCACTAAAAGGTTAACTCCTCTTCGTGAGAAAGTCAAGAATGACAACAATAAAAGA
* ** ** * **
30936 TTGACTCCTAGTCGCAAGAAATTCAAGAAGGAAAACACTAAAAGAATGACTCTTCTTCACGAGAA
66 TTGACTCATCTTCGTGAGAAAGTCAAGAAGGAAAACACTAAAAGAATGACTCAACTTCACGAGAA
31001 AGTCA
131 AGTCA
* * * * * *
31006 AGAATGACATCACTAAAAGGTTCACTCCTCTTTGTGAGAAAGTCAATAAGGATAACATTAAAAGA
1 AGAATGACATCACTAAAAGGTTAACTCCTCTTCGTGAGAAAGTCAAGAATGACAACAATAAAAGA
* * * * *
31071 TTGACTCATCTTCGTGAGAAAGACAAGAAGGACAACACTAAAAGATTGAGTCAACTTCGCGAGAA
66 TTGACTCATCTTCGTGAGAAAGTCAAGAAGGAAAACACTAAAAGAATGACTCAACTTCACGAGAA
31136 AGTCA
131 AGTCA
* * * * * *
31141 AGAAGGATAACACTAAAAGATTAACTCCTCTTCGTGAGAAAGTTAAGAATGACAACACTAAAA-A
1 AGAATGACATCACTAAAAGGTTAACTCCTCTTCGTGAGAAAGTCAAGAATGACAACAATAAAAGA
* *
31205 GTTGATTCATCTTTGTGAGAAAGTCAAG
66 -TTGACTCATCTTCGTGAGAAAGTCAAG
31233 TTGAGGTTTC
Statistics
Matches: 187, Mismatches: 39, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
134 1 0.01
135 186 0.99
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (135 bp):
AGAATGACATCACTAAAAGGTTAACTCCTCTTCGTGAGAAAGTCAAGAATGACAACAATAAAAGA
TTGACTCATCTTCGTGAGAAAGTCAAGAAGGAAAACACTAAAAGAATGACTCAACTTCACGAGAA
AGTCA
Found at i:31280 original size:37 final size:37
Alignment explanation
Indices: 31239--31427 Score: 132
Period size: 37 Copynumber: 5.1 Consensus size: 37
31229 CAAGTTGAGG
* * *
31239 TTTCTAGGGAAACAATCATGAGAATGACTAAAATGAA
1 TTTCTAGAGAAACAATCATAAGAAAGACTAAAATGAA
* * * ** *
31276 TTTCTAGAGAAACAGTCCTAAGAAGGACTCTAACGAA
1 TTTCTAGAGAAACAATCATAAGAAAGACTAAAATGAA
** * *
31313 TTTCTAGAGAAATGATCTTAAGAAAAACTAAAATGAA
1 TTTCTAGAGAAACAATCATAAGAAAGACTAAAATGAA
* * * * * * *
31350 TTTCTACAGAAATAATCCTAAGAAGGACTAGAGTGCAG
1 TTTCTAGAGAAACAATCATAAGAAAGACTAAAATG-AA
* * *
31388 TTTCTA-AGGAAAAAATCTTAAGAAAGA-AAAAATG-A
1 TTTCTAGA-GAAACAATCATAAGAAAGACTAAAATGAA
31423 TTTCT
1 TTTCT
31428 CAAAATAGAT
Statistics
Matches: 118, Mismatches: 32, Indels: 6
0.76 0.21 0.04
Matches are distributed among these distances:
35 5 0.04
37 90 0.76
38 23 0.19
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (37 bp):
TTTCTAGAGAAACAATCATAAGAAAGACTAAAATGAA
Found at i:31420 original size:74 final size:73
Alignment explanation
Indices: 31268--31434 Score: 173
Period size: 74 Copynumber: 2.3 Consensus size: 73
31258 GAGAATGACT
* * * ** **
31268 AAAATGAATTTCTAGAGAAACAGTCCTAAGAAGGACTCTAACGAATTTCTAGAGAAATGATCTTA
1 AAAATGAATTTCTACAGAAATAATCCTAAGAAGGACTAGAACGAATTTCTAGAGAAAAAATCTTA
31333 AGAAAAAC
66 AGAAAAAC
** *
31341 TAAAATGAATTTCTACAGAAATAATCCTAAGAAGGACTAGAGTGCAGTTTCTA-AGGAAAAAATC
1 -AAAATGAATTTCTACAGAAATAATCCTAAGAAGGACTAGAACG-AATTTCTAGA-GAAAAAATC
31405 TTAAGAAAGAA-
63 TTAAGAAA-AAC
31416 AAAATG-ATTTCT-CA-AAATA
1 AAAATGAATTTCTACAGAAATA
31435 GATTTTACAT
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
71 5 0.06
72 2 0.03
73 6 0.08
74 43 0.54
75 22 0.28
76 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (73 bp):
AAAATGAATTTCTACAGAAATAATCCTAAGAAGGACTAGAACGAATTTCTAGAGAAAAAATCTTA
AGAAAAAC
Found at i:31889 original size:18 final size:18
Alignment explanation
Indices: 31866--31901 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31856 CGCTTTATCA
*
31866 AAAGAATTTTGAATAATG
1 AAAGAATTTTGAAAAATG
31884 AAAGAATTTTGAAAAATG
1 AAAGAATTTTGAAAAATG
31902 TTTGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
AAAGAATTTTGAAAAATG
Found at i:34140 original size:34 final size:34
Alignment explanation
Indices: 34093--34188 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 34
34083 TTCGTGTACC
34093 TTAT-ATGATTGCACATGGAGTGCATATTTCTGT
1 TTATGATGATTGCACATGGAGTGCATATTTCTGT
* * * *
34126 TTCTGATGATTGCACTTGGAGCGCATATTTTTGT
1 TTATGATGATTGCACATGGAGTGCATATTTCTGT
* * * *
34160 TTATGATGATAGCACCTGTAGTGCTTATT
1 TTATGATGATTGCACATGGAGTGCATATT
34189 GCGCACACTC
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 3 0.06
34 49 0.94
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (34 bp):
TTATGATGATTGCACATGGAGTGCATATTTCTGT
Found at i:35621 original size:2 final size:2
Alignment explanation
Indices: 35614--35648 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35604 CAAATTTTTG
35614 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 A
35649 AAAGTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38262 original size:17 final size:17
Alignment explanation
Indices: 38237--38270 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38227 AATGAGATAA
*
38237 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
38254 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
38271 CGAGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:38962 original size:75 final size:74
Alignment explanation
Indices: 38805--38942 Score: 197
Period size: 75 Copynumber: 1.9 Consensus size: 74
38795 AAACATCTTA
* *
38805 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAATATTTAAAA
1 AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAA
*
38870 TAATATTCT
66 TAAAATTCT
* * *
38879 AAATCCTAATTAAAATAC-TAAAACCTATTTAAACTTAAATACCTAAAACAAAGATAAAATATAA
1 -AATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAA
38943 TGTTTAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 5 0.09
75 52 0.91
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.29
Consensus pattern (74 bp):
AATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAA
TAAAATTCT
Found at i:39351 original size:26 final size:25
Alignment explanation
Indices: 39298--39351 Score: 58
Period size: 25 Copynumber: 2.1 Consensus size: 25
39288 AGTTAATTAG
*
39298 TTTTGTCATAGCATTTTATCTTTAT
1 TTTTGTCATAGCATTTTATATTTAT
39323 TTTTGTGCATAG-ATTACTTATATTT-T
1 TTTTGT-CATAGCATT--TTATATTTAT
39349 TTT
1 TTT
39352 ACTATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 9 0.36
26 9 0.36
27 7 0.28
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (25 bp):
TTTTGTCATAGCATTTTATATTTAT
Found at i:43417 original size:2 final size:2
Alignment explanation
Indices: 43410--43439 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43400 ATAAAAACTG
43410 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
43440 GGTTCCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53462 original size:30 final size:30
Alignment explanation
Indices: 53411--53475 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
53401 TAGTCCCTTG
* *
53411 AATTTCTATTTTTTTTGTTTT-AGCCTTTTA
1 AATTTCTATTTTTTCTATTTTAAGCC-TTTA
* *
53441 AATTTTTATTTTTTCTATTTTAATCCTTTA
1 AATTTCTATTTTTTCTATTTTAAGCCTTTA
53471 AATTT
1 AATTT
53476 ATGTCTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.66
Consensus pattern (30 bp):
AATTTCTATTTTTTCTATTTTAAGCCTTTA
Found at i:53475 original size:60 final size:59
Alignment explanation
Indices: 53411--53543 Score: 135
Period size: 60 Copynumber: 2.3 Consensus size: 59
53401 TAGTCCCTTG
* * * * * *
53411 AATTTCTATTTTTTTTGTTTTAGCCTTTTAAATTTTTA-TTTTTTCTATTTTAATCCTTT
1 AATTTCTATCTTTTTTGTTATAGCCTTTT-AAGTTTTAGTTCTTACTATTTTAATACTTT
* * **
53470 AAATTTATGTCTTAATTGTTATAGCCTTTTAAGTTTTAGTTCTTACTATTTTAATACTTT
1 -AATTTCTATCTTTTTTGTTATAGCCTTTTAAGTTTTAGTTCTTACTATTTTAATACTTT
*
53530 AATTTC-ATGTTTTT
1 AATTTCTATCTTTTT
53544 GCTAGATCTA
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
58 4 0.07
59 12 0.21
60 41 0.72
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.62
Consensus pattern (59 bp):
AATTTCTATCTTTTTTGTTATAGCCTTTTAAGTTTTAGTTCTTACTATTTTAATACTTT
Found at i:55669 original size:23 final size:24
Alignment explanation
Indices: 55643--55688 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
55633 AATATAATTG
* *
55643 AATTTAAAATTCA-ATTAATGAGA
1 AATTAAAAAATCACATTAATGAGA
55666 AATTAAAAAATCACCATTAATGA
1 AATTAAAAAATCA-CATTAATGA
55689 ATCATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (24 bp):
AATTAAAAAATCACATTAATGAGA
Found at i:61698 original size:21 final size:22
Alignment explanation
Indices: 61658--61698 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61648 AACAAATAGC
*
61658 CTAATGTACACGAATGAGAATG
1 CTAATGTACACGAATCAGAATG
*
61680 CTAA-GTACACGAGTCAGAA
1 CTAATGTACACGAATCAGAA
61699 CGACTGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (22 bp):
CTAATGTACACGAATCAGAATG
Found at i:63827 original size:30 final size:29
Alignment explanation
Indices: 63775--63857 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
63765 CAAAATACAT
* * *
63775 AACTTTCAAAATTATGTTTTTAGTC-CCTA
1 AACTTTCAAAATT-TATATTTAGTCTACTA
*
63804 AACTTTTCCAAATTTATACTTTAG-CTACTA
1 AAC-TTTCAAAATTTATA-TTTAGTCTACTA
63834 AACTTTCAAAATTTATATTTAGTC
1 AACTTTCAAAATTTATATTTAGTC
63858 ATTAACCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
28 5 0.11
29 20 0.44
30 20 0.44
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.45
Consensus pattern (29 bp):
AACTTTCAAAATTTATATTTAGTCTACTA
Done.