Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005629.1 Hibiscus syriacus cultivar Beakdansim tig00013120_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: 107709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1626 original size:9 final size:9
Alignment explanation
Indices: 1588--1655 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
1578 TTTTCTTCAC
1588 TTTTTTCT-
1 TTTTTTCTA
1596 TTTTGTT-T-
1 TTTT-TTCTA
1604 TTTTCTTCTCA
1 TTTT-TTCT-A
1615 TTTTTTCTA
1 TTTTTTCTA
*
1624 TTTTTTC-C
1 TTTTTTCTA
1632 TTTTTTCTA
1 TTTTTTCTA
* *
1641 TTTTTCCTC
1 TTTTTTCTA
1650 TTTTTT
1 TTTTTT
1656 TTCTTTTTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 18 0.37
9 23 0.47
10 4 0.08
11 4 0.08
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTCTA
Found at i:1639 original size:27 final size:25
Alignment explanation
Indices: 1578--1663 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 25
1568 AAATAATTTA
*
1578 TTTTCTTCACTTTTTTCTTTTTGTTTTT
1 TTTTC-TCA-TTTTTTCTTTTT-TTCTT
1606 TTCTTCTCATTTTTTCTATTTTTTCCTT
1 TT-TTCTCATTTTTTCT-TTTTTT-CTT
1634 TTTTCT-ATTTTTCCTCTTTTTTTTCTT
1 TTTTCTCATTTTT--TC-TTTTTTTCTT
1661 TTT
1 TTT
1664 CCTTTTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
26 6 0.12
27 20 0.39
28 21 0.41
29 4 0.08
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTCTCATTTTTTCTTTTTTTCTT
Found at i:1645 original size:18 final size:17
Alignment explanation
Indices: 1615--1671 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1605 TTTCTTCTCA
1615 TTTTTTCTATTTTTTCC
1 TTTTTTCTATTTTTTCC
1632 TTTTTTCTA-TTTTTCC
1 TTTTTTCTATTTTTTCC
*
1648 TCTTTTT-TTTCTTTTTCC
1 T-TTTTTCTAT-TTTTTCC
1666 TTTTTT
1 TTTTTT
1672 TTTTCTTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 9 0.25
17 19 0.53
18 8 0.22
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTATTTTTTCC
Found at i:1678 original size:27 final size:26
Alignment explanation
Indices: 1588--1680 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 26
1578 TTTTCTTCAC
* *
1588 TTTTTTCTTTTTGTT-TTTTTCTTCTCA
1 TTTTTTCTTTTTTTTCTTTTTCTT-T-T
* *
1615 TTTTTTCTATTTTTTCCTTTTTTCTATT
1 TTTTTTCT-TTTTTTTC-TTTTTCTTTT
**
1643 TTTCCTCTTTTTTTTCTTTTTCCTTTT
1 TTTTTTCTTTTTTTTCTTTTT-CTTTT
1670 TTTTTTCTTTT
1 TTTTTTCTTTT
1681 CATCTTCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
26 5 0.10
27 28 0.54
28 11 0.21
29 1 0.02
30 7 0.13
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (26 bp):
TTTTTTCTTTTTTTTCTTTTTCTTTT
Found at i:1681 original size:17 final size:17
Alignment explanation
Indices: 1601--1681 Score: 76
Period size: 18 Copynumber: 4.8 Consensus size: 17
1591 TTTCTTTTTG
* *
1601 TTTTTTTCTTCTCATTT
1 TTTTTTTCTTTTCCTTT
*
1618 TTTCTATT-TTTTCCTTT
1 TTT-TTTTCTTTTCCTTT
* * *
1635 TTTCTAT-TTTTCCTCT
1 TTTTTTTCTTTTCCTTT
1651 TTTTTTTCTTTTTCCTTT
1 TTTTTTTC-TTTTCCTTT
1669 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
1682 ATCTTCAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
16 14 0.27
17 18 0.35
18 19 0.37
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTTCCTTT
Found at i:7535 original size:26 final size:25
Alignment explanation
Indices: 7490--7541 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
7480 TACTAATTTA
* *
7490 AAACCTAATTTTTATCTAAATTATT
1 AAACCTAATTTTTATATAAAATATT
*
7515 AAACCTAATTTTTTTTATAAAATATT
1 AAACCTAA-TTTTTATATAAAATATT
7541 A
1 A
7542 GATATTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
AAACCTAATTTTTATATAAAATATT
Found at i:11003 original size:7 final size:7
Alignment explanation
Indices: 10991--11020 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
10981 TGGATAATTC
10991 TAGTTCA
1 TAGTTCA
10998 TAGTTCA
1 TAGTTCA
11005 TAGTTCA
1 TAGTTCA
11012 TAGTTCA
1 TAGTTCA
11019 TA
1 TA
11021 TAACTAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (7 bp):
TAGTTCA
Found at i:11587 original size:6 final size:6
Alignment explanation
Indices: 11573--11624 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
11563 AAAAACAACA
* *
11573 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG AAAAAC AAAAAG -AAAAG
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
11622 AAA
1 AAA
11625 GAGACTCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
5 5 0.13
6 24 0.62
7 10 0.26
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:11596 original size:12 final size:12
Alignment explanation
Indices: 11560--11620 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
11550 CAAGTGCTGG
* *
11560 AACAAAAACAAC
1 AACAAAAAGAAA
*
11572 AA-AAAGAGAAA
1 AACAAAAAGAAA
*
11583 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
11596 AACAAAAAGAAA
1 AACAAAAAGAAA
11608 AACAAAAAGAAA
1 AACAAAAAGAAA
11620 A
1 A
11621 GAAAGAGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 8 0.19
12 24 0.57
13 10 0.24
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:17327 original size:13 final size:13
Alignment explanation
Indices: 17309--17334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17299 ATACTTAATG
17309 TTAATTTAAAATT
1 TTAATTTAAAATT
17322 TTAATTTAAAATT
1 TTAATTTAAAATT
17335 AATCACGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTTAAAATT
Found at i:19884 original size:24 final size:24
Alignment explanation
Indices: 19842--19939 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 24
19832 TTTTATAAAC
*
19842 TTAAGATAATAATAA-AATACATCT
1 TTAAGTTAATAA-AAGAATACATCT
*
19866 TTAAGTTAATAAAAGAATA-ATGTAT
1 TTAAGTTAATAAAAGAATACA--TCT
*
19891 ATTGAAGTTAAGATATAAAAAATACATCTT
1 -TT-AAGTT-A-ATA-AAAGAATACATC-T
19921 TTAAGTTAATAAAAGAATA
1 TTAAGTTAATAAAAGAATA
19940 ATATATATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
23 3 0.05
24 15 0.25
25 9 0.15
26 5 0.08
27 6 0.10
28 6 0.10
29 6 0.10
30 8 0.14
31 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (24 bp):
TTAAGTTAATAAAAGAATACATCT
Found at i:19932 original size:55 final size:56
Alignment explanation
Indices: 19842--19947 Score: 180
Period size: 55 Copynumber: 1.9 Consensus size: 56
19832 TTTTATAAAC
*
19842 TTAAGATAATAATAAAATACATCTTTAAGTTAATAAAAGAATAATGTATATTGAAG
1 TTAAGATAATAATAAAATACATCTTTAAGTTAATAAAAGAATAATATATATTGAAG
19898 TTAAGAT-ATAA-AAAATACATCTTTTAAGTTAATAAAAGAATAATATATAT
1 TTAAGATAATAATAAAATACATC-TTTAAGTTAATAAAAGAATAATATATAT
19948 ATATATATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
54 10 0.21
55 31 0.65
56 7 0.15
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (56 bp):
TTAAGATAATAATAAAATACATCTTTAAGTTAATAAAAGAATAATATATATTGAAG
Found at i:19947 original size:2 final size:2
Alignment explanation
Indices: 19940--19973 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19930 TAAAAGAATA
19940 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
19974 TTTGAAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20082 original size:31 final size:30
Alignment explanation
Indices: 19993--20165 Score: 127
Period size: 31 Copynumber: 5.6 Consensus size: 30
19983 AAGATATAAC
*
19993 AAAATATA-TTTTTAAGTTAATAAAAGAAT
1 AAAATATATTTTTTAAATTAATAAAAGAAT
* * **
20022 AAAATGTATTATTTAAA-T-ATAAATTAAT
1 AAAATATATTTTTTAAATTAATAAAAGAAT
20050 AAAATATATATTTTTAAATTAATAAAAGAAT
1 AAAATATAT-TTTTTAAATTAATAAAAGAAT
* * *
20081 AAAATACATTTTTTAAGTTAAAGTTAAAATTAAAAT
1 AAAATATATTTTTTAAATT-AA--T-AAA--AGAAT
** * *
20117 AAAATATATTTAATAAGTTGAATAAAAAAAT
1 AAAATATATTTTTTAAATT-AATAAAAGAAT
*
20148 AAATATATATATTTTAAA
1 AAA-ATATATTTTTTAAA
20166 CTTAGGACAT
Statistics
Matches: 113, Mismatches: 20, Indels: 19
0.74 0.13 0.12
Matches are distributed among these distances:
28 16 0.14
29 15 0.13
30 16 0.14
31 26 0.23
32 10 0.09
33 4 0.04
34 4 0.04
36 22 0.19
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAATATATTTTTTAAATTAATAAAAGAAT
Found at i:24795 original size:815 final size:811
Alignment explanation
Indices: 23227--24847 Score: 3037
Period size: 815 Copynumber: 2.0 Consensus size: 811
23217 AGTGGCTAAA
*
23227 TTGTAAAACTTCAGATTTTGGTGATTTAAATTGGATATTTGAATAGTTCAATGATTGGTTCAGAA
1 TTGTAAAACTTCAGATTTTGGTGATTTAAATTGGATATTTGAATAGTTCAATGATAGGTTCAGAA
23292 ATATTTCCTAAAAGTTTATAGTAATTATCCAAAGAATTAAAGGGCAAAATGGTCATTTAGCATGA
66 ATATTTCCTAAAAGTTTATAGTAATTATCCAAAGAATTAAAGGGCAAAATGGTCATTTAGCATGA
23357 AAGATATTTTTCCCCAATTATATGAATGAATCACGTGGGATGGGGAAAGAGTTATCTGAAAACTC
131 AAGATATTTTTCCCCAATTATATGAATGAATCACGTGGGATGGGGAAAGAGTTATCTGAAAACTC
* *
23422 TTTCTTCTTCTTTTCTTCTTCTCCCAACCGTGGAAGCTAGGCAAAGGTAAGGGTTTTCTGATTTG
196 TTTCTTCTTCTTTTCTTCTTCTCCCAACCCTGGAAGCTAGGCAAAGGTAAGGGTTTTCTGATTTA
*
23487 TTGGTTATTTTTTAAATTAAATGTTAGGTTTTGATCATTAGATGATAACTAAGCTTAAGGAAAGC
261 TTGGTTATTTGTTAAATTAAATGTTAGGTTTTGATCATTAGATGATAACTAAGCTTAAGGAAAGC
* *
23552 TTAAGTTTTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTTAAGAAAATGAGTTTTTATAT
326 TTAAGTTGTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTTAAGAAAACGAGTTTTTATAT
23617 GAAATCATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGATAATT
391 GAAATCATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGATAATT
*
23682 AAGGAATATGAAGTGTTAGAATTATATTTAGAACATATTGAAATTTGAGTATGATTCTTGTATTT
456 AAGGAATATGAAGTGTTAGAATTATATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATTT
23747 CATATGAAGGATAGGATTTTGAAGTTTAGATGATTTTCATGGATATAAGTTGGTTTAAGTAATGG
521 CATATGAAGGATAGGATTTTGAAGTTTAGATGATTTTCATGGATATAAGTTGGTTTAAGTAATGG
*
23812 TAGTTGAGATTAATGGCATGATAGGGGTTTAAAATAGAAGAATGAAGTGAAGAATTAATGATTTT
586 TAGTTGAGATTAATGACATGATAGGGGTTTAAAATAGAAGAATGAAGTGAAGAATTAATGATTTT
* *
23877 TGGGGTTAAAATACAATTTATGGGTAGAGGGAACTGATACCCTATGAATGGGAATCGATTCCCCC
651 CGGGGTTAAAATACAATTTATGGGTAGAGGGAACCGATACCCTATGAATGGGAATCGATTCCCCC
23942 TCTTGGACGAAAATTCCCAGAATGTCCAGGGGGTATCGATTCCCCCTGGGGGGGGGGTATCGATT
716 TCTTGGACGAAAATTCCCAGAATGTCCAGGGGGTATCGATTCCCCCT----GGGGGGTATCGATT
24007 CC-CCCTAAATGAAAAATGGAATTTGGTTCAGATT
777 CCTCCCTAAATGAAAAATGGAATTTGGTTCAGATT
24041 TTGTAAAACTTCAGATTTTGGTGATTTAAATTGGATATTTGAATAGTTCAATGATAGGTTCAGAA
1 TTGTAAAACTTCAGATTTTGGTGATTTAAATTGGATATTTGAATAGTTCAATGATAGGTTCAGAA
24106 ATATTTCCTAAAAGTTTATAGTAATTATCCAAAGAATTAAAGGGCAAAATGGTCATTTAGCATGA
66 ATATTTCCTAAAAGTTTATAGTAATTATCCAAAGAATTAAAGGGCAAAATGGTCATTTAGCATGA
24171 AAGATATTTTTCCCCAATTATATGAATGAATCACGTGGGATGGGGAAAGAGTTATCTGAAAACTC
131 AAGATATTTTTCCCCAATTATATGAATGAATCACGTGGGATGGGGAAAGAGTTATCTGAAAACTC
24236 TTTCTTCTTCTTTTCTTCTTCTCCCAACCCTGGAAGCTAGGCAAAGGTAAGGGTTTTCTGATTTA
196 TTTCTTCTTCTTTTCTTCTTCTCCCAACCCTGGAAGCTAGGCAAAGGTAAGGGTTTTCTGATTTA
24301 TTGGTTATTTGTTAAATTAAATGTTAGGTTTTGATCATTAGATGATAACTAAGCTTAAGGAAAGC
261 TTGGTTATTTGTTAAATTAAATGTTAGGTTTTGATCATTAGATGATAACTAAGCTTAAGGAAAGC
24366 TTAAGTTGTCTTATAATCAAAAAGATGAAGAAGTTATAAGAGATTTAAGAAAACGAGTTTTTATA
326 TTAAGTTGTCTTATAATC-AAAAGATGAAGAAGTTATAAGAGATTTAAGAAAACGAGTTTTTATA
24431 TGAAATCATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGATAAT
390 TGAAATCATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGATAAT
*
24496 TAAGGAATATGAAGTGTTAGAATTGTATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATT
455 TAAGGAATATGAAGTGTTAGAATTATATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATT
*
24561 TCATATGAAGGATATGATTTTGAAGTTTAGATGATTTTCATGGATATAAGTTGGTTTAAGTAATG
520 TCATATGAAGGATAGGATTTTGAAGTTTAGATGATTTTCATGGATATAAGTTGGTTTAAGTAATG
* * *
24626 GTAGTTGAGTTTAATGACATGATAGGGGTTTAAAATAGAAGAATTAAGTGAAGAATTGATGATTT
585 GTAGTTGAGATTAATGACATGATAGGGGTTTAAAATAGAAGAATGAAGTGAAGAATTAATGATTT
*
24691 TCGGGGTTAAAATACAATTTCTGGGTAGAGGGAACCGATACCCTATGAATGGGAATCGATTCCCC
650 TCGGGGTTAAAATACAATTTATGGGTAGAGGGAACCGATACCCTATGAATGGGAATCGATTCCCC
*
24756 CTCTTGGACGAAAATTTCCAGAATGTCCAGGGGGTATCGATTCCCCCTGGGGGGTATCGATTCCT
715 CTCTTGGACGAAAATTCCCAGAATGTCCAGGGGGTATCGATTCCCCCTGGGGGGTATCGATTCCT
24821 CCCTAAATGAAAAATGGAATTTGGTTC
780 CCCTAAATGAAAAATGGAATTTGGTTC
24848 TTTAATCTGG
Statistics
Matches: 788, Mismatches: 17, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
811 16 0.02
812 27 0.03
814 338 0.43
815 407 0.52
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (811 bp):
TTGTAAAACTTCAGATTTTGGTGATTTAAATTGGATATTTGAATAGTTCAATGATAGGTTCAGAA
ATATTTCCTAAAAGTTTATAGTAATTATCCAAAGAATTAAAGGGCAAAATGGTCATTTAGCATGA
AAGATATTTTTCCCCAATTATATGAATGAATCACGTGGGATGGGGAAAGAGTTATCTGAAAACTC
TTTCTTCTTCTTTTCTTCTTCTCCCAACCCTGGAAGCTAGGCAAAGGTAAGGGTTTTCTGATTTA
TTGGTTATTTGTTAAATTAAATGTTAGGTTTTGATCATTAGATGATAACTAAGCTTAAGGAAAGC
TTAAGTTGTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTTAAGAAAACGAGTTTTTATAT
GAAATCATGGAAAATAGTTGATAAGTTGAATTTGAAGTTAAATTTGACTTGTCATCATGATAATT
AAGGAATATGAAGTGTTAGAATTATATTTAGAACATATTGAAATTTGAGTATGATTCTTGAATTT
CATATGAAGGATAGGATTTTGAAGTTTAGATGATTTTCATGGATATAAGTTGGTTTAAGTAATGG
TAGTTGAGATTAATGACATGATAGGGGTTTAAAATAGAAGAATGAAGTGAAGAATTAATGATTTT
CGGGGTTAAAATACAATTTATGGGTAGAGGGAACCGATACCCTATGAATGGGAATCGATTCCCCC
TCTTGGACGAAAATTCCCAGAATGTCCAGGGGGTATCGATTCCCCCTGGGGGGTATCGATTCCTC
CCTAAATGAAAAATGGAATTTGGTTCAGATT
Found at i:24810 original size:20 final size:21
Alignment explanation
Indices: 24785--24824 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
24775 AGAATGTCCA
24785 GGGGGTATCGATTCC-CCCTG
1 GGGGGTATCGATTCCTCCCTG
24805 GGGGGTATCGATTCCTCCCT
1 GGGGGTATCGATTCCTCCCT
24825 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGATTCCTCCCTG
Found at i:25186 original size:14 final size:15
Alignment explanation
Indices: 25169--25197 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25159 TACATAATAT
25169 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
25183 GCATAAAACATAAGA
1 GCATAAAACATAAGA
25198 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:25525 original size:22 final size:19
Alignment explanation
Indices: 25475--25527 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
25465 AGGGTATTGT
*
25475 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
25494 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
25514 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
25528 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:31071 original size:19 final size:19
Alignment explanation
Indices: 31049--31092 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31039 CAGAGCAGAG
*
31049 ATCAAAGATCATAACAAAA
1 ATCAAAGATCAAAACAAAA
* * *
31068 ATCAGATATCAAAACAAAT
1 ATCAAAGATCAAAACAAAA
31087 ATCAAA
1 ATCAAA
31093 ATTCAGGATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (19 bp):
ATCAAAGATCAAAACAAAA
Found at i:35391 original size:15 final size:15
Alignment explanation
Indices: 35373--35408 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
35363 TTATGAAAAA
35373 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
35388 TGAATTACTGGAATT
1 TGAATTACTGAAATT
35403 TGAATT
1 TGAATT
35409 CTGTAAAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:35788 original size:23 final size:23
Alignment explanation
Indices: 35739--35789 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
35729 ATGTTATATT
**
35739 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
35762 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
35785 ATATT
1 ATATT
35790 GTTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:35911 original size:28 final size:30
Alignment explanation
Indices: 35874--35942 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
35864 TATATTATTA
*
35874 TAATATAATT-GATTATTTTATTATAAATAT
1 TAATA-AATTAGATTATATTATTATAAATAT
*
35904 TAA-AAATTTAATATTATATTATTATAAATAT
1 TAATAAA-TT-AGATTATATTATTATAAATAT
35935 TAATAAAT
1 TAATAAAT
35943 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 3 0.09
30 3 0.09
31 22 0.67
32 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
TAATAAATTAGATTATATTATTATAAATAT
Found at i:35918 original size:23 final size:23
Alignment explanation
Indices: 35892--35939 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
35882 TTGATTATTT
35892 TATTATAAATATTAAAAAT-TTAA
1 TATTAT-AATATTAAAAATATTAA
* *
35915 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
35938 TA
1 TA
35940 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:35935 original size:17 final size:17
Alignment explanation
Indices: 35885--35936 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
35875 AATATAATTG
*
35885 ATTATTTTATTATAAAT
1 ATTATATTATTATAAAT
**
35902 ATTA-AAAATT-T-AAT
1 ATTATATTATTATAAAT
35916 ATTATATTATTATAAAT
1 ATTATATTATTATAAAT
35933 ATTA
1 ATTA
35937 ATAAATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 4 0.15
17 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATATTATTATAAAT
Found at i:35944 original size:22 final size:22
Alignment explanation
Indices: 35895--35956 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
35885 ATTATTTTAT
*
35895 TATAA-ATATTAAAAAT-TTAA
1 TATAATATATTATAAATATTAA
*
35915 TATTATATTATTATAAATATTAA
1 TATAATA-TATTATAAATATTAA
*
35938 TA-AATATATTTTAAATATT
1 TATAATATATTATAAATATT
35957 TTAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 12 0.34
23 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAATATATTATAAATATTAA
Found at i:36226 original size:42 final size:42
Alignment explanation
Indices: 36170--36260 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
36160 TTCCTCCAAC
** *
36170 CAAACACTAGAAAACATTTTCCGGAAAAGGAATTACGTGAAA
1 CAAACACTAGAAAACATTTTCCGGAAAACAAATTACATGAAA
*
36212 CAAACAC-ATGAAAACATTTTCCGGAAAACAAATTATATGAAA
1 CAAACACTA-GAAAACATTTTCCGGAAAACAAATTACATGAAA
36254 CAAACAC
1 CAAACAC
36261 GGTATTTCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (42 bp):
CAAACACTAGAAAACATTTTCCGGAAAACAAATTACATGAAA
Found at i:36486 original size:21 final size:21
Alignment explanation
Indices: 36460--36502 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
36450 GACTATCGAA
36460 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
36481 TTGCGATTTTCCTAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
36502 T
1 T
36503 AAATCGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:37316 original size:24 final size:24
Alignment explanation
Indices: 37289--37338 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
37279 TCGAAATTTT
37289 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
37313 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
37337 AT
1 AT
37339 GATTTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:38725 original size:20 final size:20
Alignment explanation
Indices: 38700--38913 Score: 234
Period size: 20 Copynumber: 10.6 Consensus size: 20
38690 CTTTAAAAAT
38700 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38720 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
38740 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
38761 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
38781 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
38801 CGCGTTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
38821 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
38841 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
38861 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
38882 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
38903 CTCGTTGCGAT
1 CGCGTTGCGAT
38914 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 105 0.66
21 53 0.34
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38786 original size:40 final size:41
Alignment explanation
Indices: 38702--38913 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
38692 TTAAAAATCG
*
38702 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
38743 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
38783 CGTTGCGATTTACAGATACGCGTTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
38823 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
38864 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
38905 CGTTGCGAT
1 CGTTGCGAT
38914 AGTCAGAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 75 0.47
41 84 0.53
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:47607 original size:21 final size:21
Alignment explanation
Indices: 47590--47631 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
47580 AAATGGCCTC
47590 CAGATGAAGTTGAATGGCAAT
1 CAGATGAAGTTGAATGGCAAT
47611 CAGATGAAGTTGAATGGCAAT
1 CAGATGAAGTTGAATGGCAAT
47632 GGAATAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (21 bp):
CAGATGAAGTTGAATGGCAAT
Found at i:50762 original size:5 final size:5
Alignment explanation
Indices: 50754--50799 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
50744 GGTCAGTTTA
*
50754 GTCGG GTCGG GTCGG GTC-G GTCGG GTCGG GTCGG GTCAG GTCGG GT
1 GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG GT
50800 TAGACCGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.02, C:0.20, G:0.57, T:0.22
Consensus pattern (5 bp):
GTCGG
Found at i:50796 original size:24 final size:24
Alignment explanation
Indices: 50734--50797 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
50724 AACGGTCAAC
* **
50734 GGTCGGGTCAGGTCAGTTTAGTCG
1 GGTCGGGTCAGGTCGGTCGAGTCG
* *
50758 GGTCGGGTCGGGTCGGTCGGGTCG
1 GGTCGGGTCAGGTCGGTCGAGTCG
50782 GGTCGGGTCAGGTCGG
1 GGTCGGGTCAGGTCGG
50798 GTTAGACCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.06, C:0.19, G:0.52, T:0.23
Consensus pattern (24 bp):
GGTCGGGTCAGGTCGGTCGAGTCG
Found at i:50864 original size:10 final size:9
Alignment explanation
Indices: 50843--50885 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
50833 CAGTTCGAAT
50843 CGGTCAAAC
1 CGGTCAAAC
50852 CGGTCAGAAC
1 CGGTCA-AAC
*
50862 CGGGTGAAAAC
1 C-GGT-CAAAC
50873 CGGTCAAAC
1 CGGTCAAAC
50882 CGGT
1 CGGT
50886 TTCCAGCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 14 0.48
10 7 0.24
11 7 0.24
12 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.12
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:57956 original size:17 final size:17
Alignment explanation
Indices: 57934--57972 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
57924 AACGGTCAAC
*
57934 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
*
57951 GGTCAATGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
57968 GGTCA
1 GGTCA
57973 GACAGGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.18, G:0.46, T:0.23
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:57992 original size:19 final size:19
Alignment explanation
Indices: 57970--58037 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
57960 TCGGGTCGGG
*
57970 TCAGACAGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
57989 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
58008 TC-GAACCGGTCGAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
58027 TCAGAACCGGT
1 TCAG-ACCGGT
58038 TGAAAACCGG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.02
19 28 0.65
20 14 0.33
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:58024 original size:10 final size:9
Alignment explanation
Indices: 57977--58053 Score: 64
Period size: 10 Copynumber: 7.9 Consensus size: 9
57967 GGGTCAGACA
57977 GGTCAAACC
1 GGTCAAACC
*
57986 GGTTCAGACC
1 GG-TCAAACC
57996 GGTCAAACC
1 GGTCAAACC
* *
58005 GATTCGAACC
1 G-GTCAAACC
58015 GGTCGAAACC
1 GGTC-AAACC
58025 GGTCAGAACC
1 GGTCA-AACC
*
58035 GGTTGAAAACC
1 GG-T-CAAACC
58046 GGTCAAAC
1 GGTCAAAC
58054 AGGTTTCCAG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 16 0.30
10 30 0.56
11 7 0.13
12 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:58046 original size:21 final size:20
Alignment explanation
Indices: 57981--58050 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
57971 CAGACAGGTC
*
57981 AAACCGGTTCAG-ACCGG-TC
1 AAACCGG-TCAGAACCGGTTG
* *
58000 AAACCGATTC-GAACCGGTCG
1 AAACCG-GTCAGAACCGGTTG
58020 AAACCGGTCAGAACCGGTTG
1 AAACCGGTCAGAACCGGTTG
58040 AAAACCGGTCA
1 -AAACCGGTCA
58051 AACAGGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 15 0.37
20 15 0.37
21 10 0.24
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (20 bp):
AAACCGGTCAGAACCGGTTG
Found at i:64710 original size:28 final size:28
Alignment explanation
Indices: 64679--64735 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
64669 AGCCATACGC
64679 GACCCCATATTACCTTTAATGTTAATCG
1 GACCCCATATTACCTTTAATGTTAATCG
*
64707 GACCCCATATTATCTTTAATGTTAATCG
1 GACCCCATATTACCTTTAATGTTAATCG
64735 G
1 G
64736 GTTTCACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (28 bp):
GACCCCATATTACCTTTAATGTTAATCG
Found at i:65422 original size:6 final size:6
Alignment explanation
Indices: 65411--65446 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
65401 AGTGTGAGTT
65411 GTGTGA GTGTGA GTGTGA GTGTGA GTGTGA GCTGTG
1 GTGTGA GTGTGA GTGTGA GTGTGA GTGTGA G-TGTG
65447 TGAGCTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.14, C:0.03, G:0.50, T:0.33
Consensus pattern (6 bp):
GTGTGA
Found at i:70863 original size:11 final size:11
Alignment explanation
Indices: 70831--70864 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
70821 AGTTAAAACA
*
70831 TTATTATTAAT
1 TTATTATTATT
70842 TTATTATTATT
1 TTATTATTATT
*
70853 TTATTAGTATT
1 TTATTATTATT
70864 T
1 T
70865 AGAGTTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TTATTATTATT
Found at i:78115 original size:30 final size:30
Alignment explanation
Indices: 78067--78123 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
78057 TGTTAGGGGA
* * * *
78067 CGAATTTAAATTTTTAAAATTTTAAAAGAG
1 CGAACTTAAACTTATAAAATTTCAAAAGAG
78097 CGAACTTAAACTTATAAAATTTCAAAA
1 CGAACTTAAACTTATAAAATTTCAAAA
78124 TGCCAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (30 bp):
CGAACTTAAACTTATAAAATTTCAAAAGAG
Found at i:80442 original size:26 final size:26
Alignment explanation
Indices: 80413--80480 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
80403 ATAACAAAAA
80413 CAATAATA-ATAATATATATATATTTT
1 CAATAATATAT-ATATATATATATTTT
80439 CAATAATATATATATATATATA--TT
1 CAATAATATATATATATATATATTTT
80463 -AA-AATATATAT-TATATAT
1 CAATAATATATATATATATAT
80481 TTCAAAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.17
22 9 0.22
23 2 0.05
24 2 0.05
26 19 0.46
27 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
CAATAATATATATATATATATATTTT
Found at i:80445 original size:20 final size:20
Alignment explanation
Indices: 80423--80538 Score: 123
Period size: 20 Copynumber: 5.8 Consensus size: 20
80413 CAATAATAAT
80423 AATATATATATAT-TTTCAA
1 AATATATATATATATTTCAA
*
80442 TAATATATATATATATATATTAA
1 -AATATATATATATAT-T-TCAA
80465 AATATATATTATATATTTCAA
1 AATATATA-TATATATTTCAA
*
80486 AAT-TATATATGT-TTTCAA
1 AATATATATATATATTTCAA
*
80504 AATATATATATATATAT-ATA
1 AATATATATATATATTTCA-A
*
80524 TATATATATATATAT
1 AATATATATATATAT
80539 AAAACCATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
18 9 0.11
19 13 0.16
20 34 0.41
21 7 0.08
22 10 0.12
23 10 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (20 bp):
AATATATATATATATTTCAA
Found at i:80558 original size:2 final size:2
Alignment explanation
Indices: 80424--80539 Score: 72
Period size: 2 Copynumber: 61.5 Consensus size: 2
80414 AATAATAATA
*
80424 AT AT AT AT AT AT -T TT CA- AT A- AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
80463 A- AA AT AT AT AT -T AT AT AT TT CA- AA AT -T AT AT AT GT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
*
80501 CA- AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80540 AAACCATAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 26
0.73 0.06 0.20
Matches are distributed among these distances:
1 10 0.11
2 83 0.89
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80569 original size:18 final size:19
Alignment explanation
Indices: 80421--80568 Score: 77
Period size: 20 Copynumber: 7.3 Consensus size: 19
80411 AACAATAATA
80421 ATAATATATATATATTT-T
1 ATAATATATATATATTTAT
*
80439 CAATAATATATATATATATAT
1 --ATAATATATATATATTTAT
* *
80460 ATTAAAATATATATTATATAT
1 A-TAATATATATA-TATTTAT
* * *
80481 TTCAAAAT-TATATATGTTTT
1 AT-AATATATATATAT-TTAT
* *
80501 CAAAATATATATATATATAT
1 -ATAATATATATATATTTAT
*
80521 AT-ATATATATATATATAT
1 ATAATATATATATATTTAT
*
80539 AAAACCATAATAATATATATTTAT
1 -ATA--AT-AT-ATATATATTTAT
80563 ATAATA
1 ATAATA
80569 AAATTATATA
Statistics
Matches: 101, Mismatches: 14, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
18 16 0.16
19 6 0.06
20 40 0.40
21 22 0.22
22 2 0.02
23 4 0.04
24 11 0.11
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (19 bp):
ATAATATATATATATTTAT
Found at i:88571 original size:20 final size:22
Alignment explanation
Indices: 88530--88664 Score: 102
Period size: 23 Copynumber: 6.1 Consensus size: 22
88520 GAGAAAAGTA
*
88530 ATTTTAAAAATATATAATATAT
1 ATTTCAAAAATATATAATATAT
88552 ATTTCAAAAATATATAATATATAT
1 ATTTCAAAAATATAT-A-ATATAT
** *
88576 AATTTTTAAAA-A-CT-ATATAT
1 -ATTTCAAAAATATATAATATAT
88596 A-TTCAAAAATATATAATATAT
1 ATTTCAAAAATATATAATATAT
*
88617 ATTTTCAAAAACTATA-CATATA-
1 A-TTTCAAAAA-TATATAATATAT
**
88639 ATTTTTAAAATATAATATATATAT
1 ATTTCAAAAATAT-ATA-ATATAT
88663 AT
1 AT
88665 ATATATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
18 6 0.07
19 2 0.02
20 10 0.11
21 15 0.17
22 15 0.17
23 20 0.22
24 13 0.15
25 8 0.09
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTCAAAAATATATAATATAT
Found at i:88587 original size:27 final size:29
Alignment explanation
Indices: 88538--88594 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
88528 TAATTTTAAA
*
88538 AATATATAATATATATTTCAAAAATATAT
1 AATATATAATATATATTTAAAAAATATAT
* *
88567 AATATAT-ATA-ATTTTTAAAAACTATAT
1 AATATATAATATATATTTAAAAAATATAT
88594 A
1 A
88595 TATTCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.60
28 3 0.12
29 7 0.28
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
AATATATAATATATATTTAAAAAATATAT
Found at i:88594 original size:18 final size:17
Alignment explanation
Indices: 88570--88614 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
88560 AATATATAAT
* *
88570 ATATATAATTTTTAAAA
1 ATATATAATATTCAAAA
88587 ACTATAT-ATATTCAAAA
1 A-TATATAATATTCAAAA
88604 ATATATAATAT
1 ATATATAATAT
88615 ATATTTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAATATTCAAAA
Found at i:88598 original size:44 final size:44
Alignment explanation
Indices: 88546--88665 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 44
88536 AAAATATATA
*
88546 ATATATATTTCAAAAATATATAATATATATAATTTTTAAAAACT
1 ATATATATTTCAAAAATATATAATATATATAATTTTCAAAAACT
88590 ATATATA-TTCAAAAATATAT-A-ATATAT-ATTTTCAAAAACT
1 ATATATATTTCAAAAATATATAATATATATAATTTTCAAAAACT
**
88630 ATACATATAATTTTTAAAATATAATATATATATATA
1 AT--ATAT-ATTTCAAAAATAT-ATA-ATATATATA
88666 TATATATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
40 14 0.22
41 6 0.09
42 5 0.08
43 14 0.22
44 16 0.25
45 2 0.03
47 1 0.02
48 6 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (44 bp):
ATATATATTTCAAAAATATATAATATATATAATTTTCAAAAACT
Found at i:88621 original size:40 final size:43
Alignment explanation
Indices: 88546--88637 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 43
88536 AAAATATATA
*
88546 ATATATATTTCAAAAATATATAATATATATAATTTTTAAAAACT
1 ATATATA-TTCAAAAATATATAATATATATAATTTTCAAAAACT
88590 ATATATATTCAAAAATATAT-A-ATATAT-ATTTTCAAAAACT
1 ATATATATTCAAAAATATATAATATATATAATTTTCAAAAACT
*
88630 ATACATAT
1 ATATATAT
88638 AATTTTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 19 0.41
41 6 0.13
42 1 0.02
43 13 0.28
44 7 0.15
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (43 bp):
ATATATATTCAAAAATATATAATATATATAATTTTCAAAAACT
Found at i:88658 original size:65 final size:64
Alignment explanation
Indices: 88535--88662 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 64
88525 AAGTAATTTT
* *
88535 AAAAATATATAATATATATTTCAAAAATATATAATATATATAATTTTTAAAAACTATATATATTC
1 AAAAATATATAATATATATTTCAAAAATATATAATATATAT-ATTTTAAAAAAATATATATATTC
*
88600 AAAAATATATAATATATATTTTCAAAAACTATA-CATATA-AT-TTTTAAAATATAATATATATA
1 AAAAATATATAATATATA-TTTCAAAAA-TATATAATATATATATTTTAAAA-A-AATATATATA
88662 T
62 T
88663 ATATATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
63 7 0.12
64 1 0.02
65 30 0.54
66 14 0.25
67 4 0.07
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (64 bp):
AAAAATATATAATATATATTTCAAAAATATATAATATATATATTTTAAAAAAATATATATATTC
Found at i:88660 original size:2 final size:2
Alignment explanation
Indices: 88648--88678 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
88638 AATTTTTAAA
88648 AT AT A- 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
88679 TATTGTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94619 original size:21 final size:21
Alignment explanation
Indices: 94594--94718 Score: 83
Period size: 21 Copynumber: 5.8 Consensus size: 21
94584 GTAATTTGCA
*
94594 CCGAAGTGCCACATAATTGTC
1 CCGAAGTACCACATAATTGTC
*
94615 CCGAAAG-ACCACATAAATTTTC
1 CCG-AAGTACCACAT-AATTGTC
* *
94637 ACCGAATTACCACATAGGTT-TGC
1 -CCGAAGTACCACATA-ATTGT-C
* * *
94660 ACCGAAGTGCCACATATTTTTC
1 -CCGAAGTACCACATAATTGTC
* *
94682 CAGAAGGACCACATAATTGTC
1 CCGAAGTACCACATAATTGTC
* *
94703 CCAAAGAACCACATAA
1 CCGAAGTACCACATAA
94719 AACCCTCGAC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
21 38 0.46
22 16 0.20
23 28 0.34
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
CCGAAGTACCACATAATTGTC
Found at i:94648 original size:23 final size:23
Alignment explanation
Indices: 94586--94675 Score: 80
Period size: 23 Copynumber: 4.0 Consensus size: 23
94576 CACAGCTCGT
*
94586 AATTTGCACCGAAGTGCCACAT-
1 AATTTGCACCGAAGTACCACATA
94608 AA-TTGTC-CCGAAAG-ACCACATA
1 AATTTG-CACCG-AAGTACCACATA
* *
94630 AATTTTCACCGAATTACCACATA
1 AATTTGCACCGAAGTACCACATA
** *
94653 GGTTTGCACCGAAGTGCCACATA
1 AATTTGCACCGAAGTACCACATA
94676 TTTTTCCAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
21 12 0.22
22 11 0.20
23 31 0.57
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (23 bp):
AATTTGCACCGAAGTACCACATA
Found at i:96026 original size:23 final size:22
Alignment explanation
Indices: 95999--96089 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 22
95989 TCTGGAAAAA
*
95999 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAA-T
*
96022 TATGTGGCACTTCGGTGAAAATT
1 TATGTGGCACTTCGGTGCAAA-T
*
96045 TATGTGGTC-TTTCGG-G-ATAAT
1 TATGTGG-CACTTCGGTGCA-AAT
96066 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
96088 TA
1 TA
96090 CGAGCTGTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.24
22 9 0.16
23 33 0.57
24 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:96079 original size:21 final size:21
Alignment explanation
Indices: 95956--96089 Score: 92
Period size: 21 Copynumber: 6.1 Consensus size: 21
95946 GTCGAGGGTT
** * *
95956 TTATGTGGTTCTTTGGGACAA
1 TTATGTGGCACTTCGGGAAAA
*
95977 TTATGTGGTC-CTTCTGGAAAA
1 TTATGTGG-CACTTCGGGAAAA
* *
95998 ATATGTGGCACTTCGGTGCAAAC
1 TTATGTGGCACTTCGG-G-AAAA
*
96021 CTATGTGGCACTTCGGTGAAAA
1 TTATGTGGCACTTCGG-GAAAA
* *
96043 TTTATGTGGTC-TTTCGGGATAA
1 -TTATGTGG-CACTTCGGGAAAA
*
96065 TTATGTGGCACTTCGGTGCAAA
1 TTATGTGGCACTTCGG-GAAAA
96087 TTA
1 TTA
96090 CGAGCTGTGT
Statistics
Matches: 90, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.02
21 41 0.46
22 14 0.16
23 32 0.36
24 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
TTATGTGGCACTTCGGGAAAA
Found at i:100844 original size:22 final size:22
Alignment explanation
Indices: 100816--100859 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
100806 AGATGGTTAC
100816 ACAATAATCGGTGAATAACAAA
1 ACAATAATCGGTGAATAACAAA
100838 ACAATAATCGGTGAATAACAAA
1 ACAATAATCGGTGAATAACAAA
100860 CATTCTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (22 bp):
ACAATAATCGGTGAATAACAAA
Found at i:102399 original size:39 final size:39
Alignment explanation
Indices: 102315--102399 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
102305 ATATTTATAC
* *
102315 TAATATATGAATTATATCAATTTAAAATATAAAATATTA
1 TAATATATGAATTATATAAATTTAAAATATAAAAAATTA
* *
102354 TTATATATGAATTATATAAATTTAAACTATAATAAAATTA
1 TAATATATGAATTATATAAATTTAAAATATAA-AAAATTA
102394 -AATATA
1 TAATATA
102400 AATAATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 34 0.85
40 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (39 bp):
TAATATATGAATTATATAAATTTAAAATATAAAAAATTA
Found at i:106210 original size:23 final size:24
Alignment explanation
Indices: 106166--106210 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
106156 TGGTGTTGCG
* *
106166 AGAGAATGAGCTCTTTGTCAAATA
1 AGAGAATGAGCTCATTGCCAAATA
*
106190 AGAGAA-GTGCTCATTGCCAAA
1 AGAGAATGAGCTCATTGCCAAA
106211 ACGGAGGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (24 bp):
AGAGAATGAGCTCATTGCCAAATA
Done.