Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001073.1 Hibiscus syriacus cultivar Beakdansim tig00002125_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: 143230
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:13093 original size:15 final size:15
Alignment explanation
Indices: 13070--13113 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
13060 GGGGTTTTTT
13070 AATTCTGAATTAATTA
1 AATT-TGAATTAATTA
13086 AATTTGAATTTAATTA
1 AATTTGAA-TTAATTA
**
13102 TTTTTGAATTAA
1 AATTTGAATTAA
13114 ATAACCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (15 bp):
AATTTGAATTAATTA
Found at i:15634 original size:64 final size:65
Alignment explanation
Indices: 15564--15791 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 65
15554 TGGAACACTT
* * * * *
15564 AGTGCATCGGTGCACT-AAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACAT
15627 A
65 A
* * *
15628 AGTGCATCGATGCATGGTGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACATG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACATA
* * * **
15693 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAACTGCATTCGATG--TTCAATTTATTCAT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAA-TAAAACAT
*
15756 T
65 A
* * *
15757 GGTGCATCGATGCATGGATTGGTGCATCGGTGCAT
1 AGTGCATCGATGCATGGAGT-GTGCATCGATGCAT
15792 CCATTTGAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
63 5 0.04
64 72 0.51
65 63 0.45
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACATA
Found at i:15735 original size:65 final size:64
Alignment explanation
Indices: 15584--15743 Score: 239
Period size: 65 Copynumber: 2.5 Consensus size: 64
15574 TGCACTAAGT
* * * * *
15584 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAATAAGCCTAAGTGCATCGATGCATGGTGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
* *
15648 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACATGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAT-AAACATAAGTGCATCGATGCATGGAGA
*
15713 GTGCATCGATGCATAAACTGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
15744 CAATTTATTC
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 35 0.40
65 52 0.60
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
Found at i:15779 original size:20 final size:20
Alignment explanation
Indices: 15754--15791 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15744 CAATTTATTC
15754 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
15774 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
15792 CCATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:15782 original size:65 final size:65
Alignment explanation
Indices: 15584--15791 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 65
15574 TGCACTAAGT
* * *
15584 GTGCATCGATGCATAAAATGCATTCGATGTTT--TGAATAAGCCTAAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCATTAA-AA-CATGAGTGCATCGATGCATGGAT
*
15646 GT
64 GA
15648 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACATGAGTGCATCGATGCATGGA-G
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCATTAAAACATGAGTGCATCGATGCATGGATG
15712 A
65 A
* * **
15713 GTGCATCGATGCATAAACTGCATTCGATG-TTCAATTTATTCATTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-ATTAAAACA-TGAGTGCATCGATGCATGGA-
15776 TG-
63 TGA
*
15778 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
15792 CCATTTGAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
63 3 0.02
64 52 0.41
65 66 0.52
66 3 0.02
67 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCATTAAAACATGAGTGCATCGATGCATGGATGA
Found at i:21352 original size:15 final size:15
Alignment explanation
Indices: 21328--21368 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
21318 ACTTTTTTTT
21328 CCTT-TTCATCAGAA
1 CCTTCTTCATCAGAA
*
21342 CCTTCTTCATCGGAA
1 CCTTCTTCATCAGAA
21357 CCTTCTTCATCA
1 CCTTCTTCATCA
21369 CTCCATGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (15 bp):
CCTTCTTCATCAGAA
Found at i:23209 original size:45 final size:46
Alignment explanation
Indices: 23149--23253 Score: 167
Period size: 45 Copynumber: 2.3 Consensus size: 46
23139 TGCACTAAGT
* *
23149 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAA
* *
23194 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAAACCTGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAA
23240 GTGCATCGATGCAT
1 GTGCATCGATGCAT
23254 GGAGAGTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 35 0.64
46 20 0.36
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAA
Found at i:29256 original size:20 final size:20
Alignment explanation
Indices: 29231--29281 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29221 AGTGAATTTG
29231 GTATCGATACCACAC-TACAA
1 GTATCGATACCACACTTAC-A
* **
29251 GTATCGATCCCTTACTTACA
1 GTATCGATACCACACTTACA
29271 GTATCGATACC
1 GTATCGATACC
29282 CAATGCATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27
Consensus pattern (20 bp):
GTATCGATACCACACTTACA
Found at i:31452 original size:21 final size:21
Alignment explanation
Indices: 31428--31480 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
31418 GCTTCCAGAT
31428 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
31449 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
31470 TCGCAATGCGA
1 TCGCAACGCGA
31481 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:31519 original size:21 final size:21
Alignment explanation
Indices: 31489--31777 Score: 179
Period size: 21 Copynumber: 14.0 Consensus size: 21
31479 GATTTACATA
*
31489 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
31510 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
**
31531 TTCGCGTTGCGATAGTAGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
31552 TTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
31575 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
31594 TTCGCTTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
31615 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** * *
31634 TTCGCGTTGCGATTTTCAAAA
1 TTCGCGTTGCGATAGTCCAAG
*
31655 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
31674 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
31697 TT--CGTTACGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
31718 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
31737 TTCGCGTTCCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
31760 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
31778 AATCGCAACG
Statistics
Matches: 210, Mismatches: 44, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
19 52 0.25
21 135 0.64
23 23 0.11
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:31581 original size:63 final size:61
Alignment explanation
Indices: 31514--31774 Score: 262
Period size: 63 Copynumber: 4.2 Consensus size: 61
31504 TCCAAGTTCG
* *
31514 CGTTGCGATAGTCAAAGTTCGCGTTGCGATAGTAGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCAAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* ** * * * * *
31577 CGTTGCGATAGTCGAAGTTCGCTTTGCGATTTTCCAAATT--CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATAGTCAAAGTTCG--TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
** *
31636 CGCGTTGCGATTTTCAAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATAGTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
31699 CGTTACGATTTATTCCAAA-TTCGTTGCGATAGTCGAAGTTCGCGTTCCGATTTATTCCAAATT
1 CGTTGCGA--TAGT-CAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
31762 CGTTGCGATAGTC
1 CGTTGCGATAGTC
31775 CAAAATCGCA
Statistics
Matches: 162, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
59 21 0.13
60 1 0.01
61 45 0.28
63 91 0.56
64 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (61 bp):
CGTTGCGATAGTCAAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:31623 original size:40 final size:40
Alignment explanation
Indices: 31495--31707 Score: 284
Period size: 40 Copynumber: 5.2 Consensus size: 40
31485 CATATTCGCA
* **
31495 TTGCGATAGTCCAAGTTCGCGTTGCGATAGT-CAAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAA-TT--CG
* *
31537 TTGCGATAGTAGAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
*
31579 TTGCGATAGTCGAAGTTCGCTTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
*
31619 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCAAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
31659 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
*
31701 TTACGAT
1 TTGCGAT
31708 TTATTCCAAA
Statistics
Matches: 154, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
40 76 0.49
41 4 0.03
42 66 0.43
43 1 0.01
44 3 0.02
45 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:32524 original size:21 final size:21
Alignment explanation
Indices: 32498--32704 Score: 178
Period size: 21 Copynumber: 9.9 Consensus size: 21
32488 ATTTTGGACT
*
32498 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
32519 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
32540 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAACTTGGAATAA
*
32561 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
32582 ATCGCAACGCGAACTTTGACT--
1 ATCGCAA--CGAACTTGGAATAA
32603 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
32624 ATCGCAACGCGAACTAGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
32645 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
32666 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
32687 ATCGCAACGAATTTGGAA
1 ATCGCAACGAACTTGGAA
32705 AATCGTAACG
Statistics
Matches: 150, Mismatches: 22, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
19 37 0.25
20 1 0.01
21 72 0.48
22 1 0.01
23 39 0.26
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:32565 original size:42 final size:42
Alignment explanation
Indices: 32519--32745 Score: 350
Period size: 42 Copynumber: 5.4 Consensus size: 42
32509 TTTGGAATAA
*
32519 ATCGCAACGAACTTGGAATAAATCGCAACACGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* *
32561 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTTGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
**
32603 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTAGGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
32645 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* *
32687 ATCGCAACGAATTTGG-A-AAATCGTAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
32727 ATCGCAACACGAACTTGGA
1 ATCGC-A-ACGAACTTGGA
32746 CTATCACAAT
Statistics
Matches: 171, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
40 27 0.16
41 2 0.01
42 142 0.83
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:32730 original size:21 final size:21
Alignment explanation
Indices: 32540--32760 Score: 143
Period size: 21 Copynumber: 10.6 Consensus size: 21
32530 CTTGGAATAA
*
32540 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
32561 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
32580 AAATCGCAACGCGAACTTTGACT
1 --ATCGCAACGCGAACTTCGACT
* *
32603 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
**
32622 AAATCGCAACGCGAACTAGGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
32645 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
32664 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
32687 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
32706 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
32727 ATCGCAACACGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
32748 ATCACAATGCGAA
1 ATCGCAACGCGAA
32761 TATGTAAATC
Statistics
Matches: 155, Mismatches: 31, Indels: 28
0.72 0.14 0.13
Matches are distributed among these distances:
19 42 0.27
21 85 0.55
23 28 0.18
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:33726 original size:2 final size:2
Alignment explanation
Indices: 33719--33748 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33709 AAGAGTTTCT
33719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33749 AAGAAACATT
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):
TA
Found at i:35256 original size:29 final size:25
Alignment explanation
Indices: 35204--35268 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 25
35194 TAAACACTCA
35204 AAATATTATTATTTTAAATATTTAAT
1 AAATA-TATTATTTTAAATATTTAAT
35230 ATAATATATTATTTTAATATCATTTTAAT
1 A-AATATATTATTTTAA-AT-A-TTTAAT
*
35259 AAAAATATTA
1 AAATATATTA
35269 ATCATTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 12 0.35
27 6 0.18
28 9 0.26
29 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATATATTATTTTAAATATTTAAT
Found at i:39043 original size:37 final size:35
Alignment explanation
Indices: 38965--39057 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 35
38955 TTAATATAGT
38965 TAATAATATATTATTCTTATTTTAATAAAAAATTAATA
1 TAAT-ATATATT-TT-TTATTTTAATAAAAAATTAATA
*
39003 TAATTTATATATTTTTTATTTTAATAAAATA-TAATAA
1 TAA--TATATATTTTTTATTTTAATAAAAAATTAAT-A
39040 TAATA-ATA-TTTTTATTTT
1 TAATATATATTTTTTATTTT
39058 TATTTACAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
33 10 0.20
34 3 0.06
35 2 0.04
36 4 0.08
37 19 0.37
38 5 0.10
39 7 0.14
40 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (35 bp):
TAATATATATTTTTTATTTTAATAAAAAATTAATA
Found at i:39118 original size:15 final size:14
Alignment explanation
Indices: 39073--39129 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
39063 ACAATTCTAT
*
39073 ATATATATATATATA
1 ATAT-TATATAAATA
* *
39088 ATATTTTATTAATA
1 ATATTATATAAATA
39102 ATATTGATATAAATA
1 ATATT-ATATAAATA
*
39117 ATATTAAATAAAT
1 ATATTATATAAAT
39130 TATTCTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
14 19 0.54
15 16 0.46
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATATTATATAAATA
Found at i:39140 original size:29 final size:29
Alignment explanation
Indices: 39108--39180 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
39098 AATAATATTG
39108 ATATAAATAATATTAAATA-AATTATTCTT
1 ATATAAATAATATTAAATATAATTATT-TT
* *
39137 ATATTAAA-AATAAT-AATATTATTATTTT
1 ATA-TAAATAATATTAAATATAATTATTTT
*
39165 TTAATAAATAATATTA
1 AT-ATAAATAATATTA
39181 TTTATTGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
28 11 0.31
29 20 0.57
30 4 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATAAATAATATTAAATATAATTATTTT
Found at i:39161 original size:23 final size:23
Alignment explanation
Indices: 39122--39186 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
39112 AAATAATATT
* *
39122 AAATAA-ATTATTCTTATATTAA
1 AAATAATAATATTATTATATTAA
**
39144 AAATAATAATATTATTAT-TTTT
1 AAATAATAATATTATTATATTAA
*
39166 TAATAAATAATATTATT-TATT
1 AAAT-AATAATATTATTATATT
39187 GTATTTTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATAATAATATTATTATATTAA
Found at i:39173 original size:26 final size:26
Alignment explanation
Indices: 39123--39182 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
39113 AATAATATTA
*
39123 AATAA-ATTATTCTTATATTAAAAAT
1 AATAATATTATTATTATATTAAAAAT
*
39148 AATAATATTATTATT-TTTTAATAAAT
1 AATAATATTATTATTATATTAA-AAAT
*
39174 AATATTATT
1 AATAATATT
39183 TATTGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATAATATTATTATTATATTAAAAAT
Found at i:39290 original size:14 final size:16
Alignment explanation
Indices: 39271--39311 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
39261 CAAACACCGT
39271 AAAATAATTT-C-TAA
1 AAAATAATTTACATAA
*
39285 AAAATATTTTACATAA
1 AAAATAATTTACATAA
*
39301 AATATAATTTA
1 AAAATAATTTA
39312 TTTTACGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 9 0.41
15 1 0.05
16 12 0.55
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATAATTTACATAA
Found at i:39323 original size:14 final size:14
Alignment explanation
Indices: 39306--39339 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39296 CATAAAATAT
*
39306 AATTTATTTTACGA
1 AATTTATTTTACAA
*
39320 AATTTATTTTTCAA
1 AATTTATTTTACAA
39334 AATTTA
1 AATTTA
39340 CTTTCCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
AATTTATTTTACAA
Found at i:43285 original size:16 final size:15
Alignment explanation
Indices: 43261--43294 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
43251 GTAAAATCTT
*
43261 TTTTTCCCGTTCTGGA
1 TTTTCCCCG-TCTGGA
43277 TTTTCCCCGTCTGGA
1 TTTTCCCCGTCTGGA
43292 TTT
1 TTT
43295 CGATCTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (15 bp):
TTTTCCCCGTCTGGA
Found at i:45228 original size:342 final size:343
Alignment explanation
Indices: 44332--45703 Score: 2611
Period size: 343 Copynumber: 4.0 Consensus size: 343
44322 AAAACACTCA
44332 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
1 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
* * *
44397 AATGAGCTAGGGTATTTATAGTTGAAACCTAGGGACTAATCTTTGAAAATACACTAAAGTGCAAT
66 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
44462 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
131 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
* *
44527 ATTCACTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGGTGGAAATCAATTTCCAACACGT
196 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
44592 TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
261 TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
44657 TTAGTTTTGATTCTTCCT
326 TTAGTTTTGATTCTTCCT
44675 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
1 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
44740 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
66 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
*
44805 GACTAAAGTATGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
131 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
44870 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
196 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
44935 TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
261 TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
45000 TTAGTTTTGATTCTTCCT
326 TTAGTTTTGATTCTTCCT
*
45018 CTACTCACAAGAAAGTTCTCTAGTATTGGGAGAAA-AAATGATTTTTGGGATGATTTTGAAGCTA
1 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
45082 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
66 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
45147 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
131 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
45212 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
196 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
* *
45277 TGTACCTAAATTAATTGGTTCTAAACACGTACCTCATTTTTAGAATTTTAAAGGTGAAACTGAAA
261 TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
45342 TTAGTTTTGATTCTTCCT
326 TTAGTTTTGATTCTTCCT
*
45360 CTACTCACAAGAAAGTTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
1 CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
*
45425 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATATCCTAAAGTGCAAT
66 AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
*
45490 GACTAAAGTGTGATTAACCCATTGTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
131 GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
*
45555 ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTTCCACTTTCGGTGGAAATCAATTTCCAACACG
196 ATTCAGTGCCTACCTTTTGAAATCTTGCAC-TTTCCACTTTCGATGGAAATCAATTTCCAACACG
45620 TTGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAA
260 TTGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAA
45685 ATTAGTTTTGATTCTTCCT
325 ATTAGTTTTGATTCTTCCT
45704 GCTCGATTTC
Statistics
Matches: 1012, Mismatches: 15, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
342 339 0.33
343 558 0.55
344 115 0.11
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (343 bp):
CTACTCACAAGAAAGCTCTCTAGTATTGGGAGAAAGAAATGATTTTTGGGATGATTTTGAAGCTA
AATGACCTAGGGTATTTATAGTTGAAACTTAGGGACTAATCTTTGAAAATACCCTAAAGTGCAAT
GACTAAAGTGTGATTAACCCATTTTAAAAAATCAACAAAATTTATTGCACCTTGACTTCTTGCAC
ATTCAGTGCCTACCTTTTGAAATCTTGCACTTTCCACTTTCGATGGAAATCAATTTCCAACACGT
TGTACCTAAATTAATTGGTTCTAAACGCGTACCTCATTTTTAGAATTTTAAAGGTGAAACCGAAA
TTAGTTTTGATTCTTCCT
Found at i:54968 original size:14 final size:14
Alignment explanation
Indices: 54949--54986 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
54939 AGCCTTTTAG
54949 TATCGATATTAACC
1 TATCGATATTAACC
54963 TATCGATATTAACC
1 TATCGATATTAACC
*
54977 TACCGATATT
1 TATCGATATT
54987 GATACACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (14 bp):
TATCGATATTAACC
Found at i:59441 original size:31 final size:31
Alignment explanation
Indices: 59327--59461 Score: 103
Period size: 31 Copynumber: 4.2 Consensus size: 31
59317 AAACCTTAAG
* *
59327 AAGAAGATATCGCAGAGGCAAGTTCACGGGAT
1 AAGAA-ATATCGCAGAGACAAGTTCACGGGAA
* * *
59359 AAGAAATCTTAC-CAGA-AGAAGATCACTGGGAA
1 AAGAAAT-AT-CGCAGAGACAAGTTCAC-GGGAA
* *
59391 AACGATGAATTTTCGCAGAGACAAGTTCACGGGAG
1 AA-GA--AA-TATCGCAGAGACAAGTTCACGGGAA
* *
59426 AAGAAATATCGCAGAGGCAAGCTCACGGGAA
1 AAGAAATATCGCAGAGACAAGTTCACGGGAA
59457 AAGAA
1 AAGAA
59462 GGGTATTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
31 35 0.43
32 18 0.22
33 3 0.04
34 3 0.04
35 14 0.17
36 9 0.11
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.15
Consensus pattern (31 bp):
AAGAAATATCGCAGAGACAAGTTCACGGGAA
Found at i:67750 original size:21 final size:23
Alignment explanation
Indices: 67724--67770 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
67714 TAAGTTTGGA
67724 CTTGTAA-C-CGGGCCTGTGTGC
1 CTTGTAATCTCGGGCCTGTGTGC
* *
67745 CTTGTAATCTTGGGCTTGTGTGC
1 CTTGTAATCTCGGGCCTGTGTGC
67768 CTT
1 CTT
67771 ATTTCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.09, C:0.23, G:0.30, T:0.38
Consensus pattern (23 bp):
CTTGTAATCTCGGGCCTGTGTGC
Found at i:67820 original size:14 final size:16
Alignment explanation
Indices: 67798--67838 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
67788 TCAGGGTTAA
67798 ATAATAATATTTATTAT
1 ATAATAATA-TTATTAT
67815 ATAATAATATTATTAT
1 ATAATAATATTATTAT
67831 AT-ATAATA
1 ATAATAATA
67839 ACGTATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.25
16 9 0.38
17 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATAATATTATTAT
Found at i:67822 original size:20 final size:18
Alignment explanation
Indices: 67797--67839 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
67787 TTCAGGGTTA
67797 AATAATAATATTTATTATAT
1 AATAATAATA-TTA-TATAT
*
67817 AATAATATTATTATATAT
1 AATAATAATATTATATAT
67835 AATAA
1 AATAA
67840 CGTATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 3 0.14
20 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATAATATTATATAT
Found at i:68936 original size:99 final size:99
Alignment explanation
Indices: 68790--69005 Score: 360
Period size: 99 Copynumber: 2.2 Consensus size: 99
68780 AGGTTTGATG
* *
68790 GATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATT
1 GATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATT
* *
68855 TTCATGCAAAAACATCCTACTATGAGGTTTTACA
66 TTCATGCAAAAACATCCTACCATGAGGCTTTACA
* *
68889 GATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATGGATTTCTTATT
1 GATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATT
*
68954 TTCATGCAAAAACATCCTACCCTGAGGCTTTACA
66 TTCATGCAAAAACATCCTACCATGAGGCTTTACA
*
68988 GATGACCCGAAGGATTTA
1 GATGACCCGGAGGATTTA
69006 CAAATTCATG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 109 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (99 bp):
GATGACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGATTTCTCATT
TTCATGCAAAAACATCCTACCATGAGGCTTTACA
Found at i:69619 original size:22 final size:22
Alignment explanation
Indices: 69591--69648 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
69581 GATAAAGCTT
*
69591 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
69613 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
*
69635 TCATCCTTGCAAAA
1 TCATCTTTG-AAAA
69649 TGTCGATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:77017 original size:21 final size:23
Alignment explanation
Indices: 76993--77034 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
76983 TAAGTTTGGG
*
76993 CTTGTAA-C-TGGGCCTGTGTGC
1 CTTGTAATCTTGGGCATGTGTGC
77014 CTTGTAATCTTGGGCATGTGT
1 CTTGTAATCTTGGGCATGTGT
77035 TGTAACAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (23 bp):
CTTGTAATCTTGGGCATGTGTGC
Found at i:77080 original size:14 final size:15
Alignment explanation
Indices: 77061--77093 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
77051 AGCTTAAATA
77061 ATAATATT-TATTAT
1 ATAATATTATATTAT
77075 ATAATATTACTATTAT
1 ATAATATTA-TATTAT
77091 ATA
1 ATA
77094 TAATAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATATTATATTAT
Found at i:77616 original size:3 final size:3
Alignment explanation
Indices: 77610--77662 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
77600 TTAAAAAAAA
*
77610 TAT TAT TAG TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
77655 TAT TAT TA
1 TAT TAT TA
77663 CATATTTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:77863 original size:29 final size:29
Alignment explanation
Indices: 77821--77877 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
77811 ACCGACCTAG
*
77821 GACGTAACCCGTTCAAAGTAGGGTTTCAA
1 GACGCAACCCGTTCAAAGTAGGGTTTCAA
*
77850 GACGCAACCTGTTCAAAGTAGGGTTTCA
1 GACGCAACCCGTTCAAAGTAGGGTTTCA
77878 GGACCCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (29 bp):
GACGCAACCCGTTCAAAGTAGGGTTTCAA
Found at i:79489 original size:59 final size:58
Alignment explanation
Indices: 79342--79557 Score: 168
Period size: 59 Copynumber: 3.7 Consensus size: 58
79332 TTTATGATTC
* * * * * * *
79342 AGTCCTTTAAATTTTTATTTTTTCCATTTTGGGTCC-TTAAACTTTCTATTTCTGCTATTT
1 AGTCCCTTAAATTTCTATTTGTACTATTTT-AGTCCTTTAAA-TGTCTATTT-TGCTATTT
* * **
79402 AGTCCCTTAATTTTCTATTTTTGTTATTTTAGTCCTTTAAATGTCTATATTTGCTATTT
1 AGTCCCTTAAATTTCTATTTGTACTATTTTAGTCCTTTAAATGTCTAT-TTTGCTATTT
* * * * *
79461 AGACCCTTAAGTTTCTATTTGTACTA-TTTAGTCCTTTCAGTTTCTATTTTTG-TCATTTT
1 AGTCCCTTAAATTTCTATTTGTACTATTTTAGTCCTTTAAATGTCTA-TTTTGCT-A-TTT
* * * *
79520 AGTCCTTTAAATTCCTGTTTGTACTATTTTGGTCCTTT
1 AGTCCCTTAAATTTCTATTTGTACTATTTTAGTCCTTT
79558 GAGTTTTTGT
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 1 0.01
58 22 0.17
59 64 0.50
60 41 0.32
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.56
Consensus pattern (58 bp):
AGTCCCTTAAATTTCTATTTGTACTATTTTAGTCCTTTAAATGTCTATTTTGCTATTT
Found at i:79518 original size:29 final size:30
Alignment explanation
Indices: 79342--79529 Score: 147
Period size: 29 Copynumber: 6.3 Consensus size: 30
79332 TTTATGATTC
* * *
79342 AGTCCTTTAAATTTTTATTTTT-TCCATTTT
1 AGTCCTTTAAGTTTCTATTTTTGTCTA-TTT
* * * *
79372 GGGTCCTTAAACTTTCTATTTCTG-CTATTT
1 -AGTCCTTTAAGTTTCTATTTTTGTCTATTT
* *
79402 AGTCCCTTAATTTTCTATTTTTGT-TATTTT
1 AGTCCTTTAAGTTTCTATTTTTGTCTA-TTT
* * *
79432 AGTCCTTTAAATGTCTATATTTG-CTATTT
1 AGTCCTTTAAGTTTCTATTTTTGTCTATTT
* *
79461 AGACCCTTAAGTTTCTA--TTTGTACTATTT
1 AGTCCTTTAAGTTTCTATTTTTGT-CTATTT
*
79490 AGTCCTTTCAGTTTCTATTTTTGTC-ATTTT
1 AGTCCTTTAAGTTTCTATTTTTGTCTA-TTT
79520 AGTCCTTTAA
1 AGTCCTTTAA
79530 ATTCCTGTTT
Statistics
Matches: 125, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.03
29 57 0.46
30 40 0.32
31 24 0.19
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (30 bp):
AGTCCTTTAAGTTTCTATTTTTGTCTATTT
Found at i:79549 original size:30 final size:30
Alignment explanation
Indices: 79342--79557 Score: 97
Period size: 30 Copynumber: 7.3 Consensus size: 30
79332 TTTATGATTC
** * * *
79342 AGTCCTTTAAATTTTTATTTTTTCCATTTT
1 AGTCCTTTAAATTCCTATTTGTACTATTTT
* * * *
79372 GGGTCC-TTAAACTTTCTATTTCTGCTA-TTT
1 -AGTCCTTTAAA-TTCCTATTTGTACTATTTT
* * * * **
79402 AGTCCCTTAATTTTCTATTTTTGTTATTTT
1 AGTCCTTTAAATTCCTATTTGTACTATTTT
*
79432 AGTCCTTTAAATGT-CTATATT-TGCTA-TTT
1 AGTCCTTTAAAT-TCCTAT-TTGTACTATTTT
* * * *
79461 AGACCCTTAAGTTTCTATTTGTACTA-TTT
1 AGTCCTTTAAATTCCTATTTGTACTATTTT
* * *
79490 AGTCCTTTCAGTTTCTATTTTTGT-C-ATTTT
1 AGTCCTTTAAATTCCTA--TTTGTACTATTTT
*
79520 AGTCCTTTAAATTCCTGTTTGTACTATTTT
1 AGTCCTTTAAATTCCTATTTGTACTATTTT
*
79550 GGTCCTTT
1 AGTCCTTT
79558 GAGTTTTTGT
Statistics
Matches: 149, Mismatches: 24, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
28 8 0.05
29 56 0.38
30 62 0.42
31 23 0.15
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.56
Consensus pattern (30 bp):
AGTCCTTTAAATTCCTATTTGTACTATTTT
Found at i:79569 original size:30 final size:30
Alignment explanation
Indices: 79458--79578 Score: 88
Period size: 30 Copynumber: 4.1 Consensus size: 30
79448 ATATTTGCTA
* * * *
79458 TTTAGACCCTTAAGTTTCTATTTGTACTA-
1 TTTAGTCCTTTAAGTTTTTGTTTGTACTAT
* *
79487 TTTAGTCCTTTCAGTTTCTATTTTTGT-C-AT
1 TTTAGTCCTTTAAGTTT-T-TGTTTGTACTAT
* **
79517 TTTAGTCCTTTAAATTCCTGTTTGTACTAT
1 TTTAGTCCTTTAAGTTTTTGTTTGTACTAT
* * *
79547 TTTGGTCCTTTGAGTTTTTGTTT-TGCTAT
1 TTTAGTCCTTTAAGTTTTTGTTTGTACTAT
79576 TTT
1 TTT
79579 GGTTCTTGCA
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
28 6 0.08
29 24 0.34
30 35 0.49
31 6 0.08
ACGTcount: A:0.16, C:0.15, G:0.12, T:0.57
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTTTGTTTGTACTAT
Found at i:79578 original size:59 final size:59
Alignment explanation
Indices: 79384--79578 Score: 157
Period size: 59 Copynumber: 3.3 Consensus size: 59
79374 GTCCTTAAAC
* * * * * ** * *
79384 TTTCTATTTCTGCTA-TTTAGTCCCTTAATTTTCTATTTTTGTTATTTTAGTCCTTTAAA
1 TTTCTATTTTTGCTATTTTAGACCCTTAAATTCCTATTTGTACTA-TTTAGTCCTTTCAG
* * * *
79443 TGTCTATATTTGCTA-TTTAGACCCTTAAGTTTCTATTTGTACTATTTAGTCCTTTCAG
1 TTTCTATTTTTGCTATTTTAGACCCTTAAATTCCTATTTGTACTATTTAGTCCTTTCAG
* * * * *
79501 TTTCTATTTTTG-TCATTTTAGTCCTTTAAATTCCTGTTTGTACTATTTTGGTCCTTTGAG
1 TTTCTATTTTTGCT-ATTTTAGACCCTTAAATTCCTATTTGTACTA-TTTAGTCCTTTCAG
79561 TTT-T-TGTTTTGCTATTTT
1 TTTCTAT-TTTTGCTATTTT
79579 GGTTCTTGCA
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
57 1 0.01
58 24 0.21
59 71 0.63
60 16 0.14
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (59 bp):
TTTCTATTTTTGCTATTTTAGACCCTTAAATTCCTATTTGTACTATTTAGTCCTTTCAG
Found at i:89838 original size:10 final size:11
Alignment explanation
Indices: 89818--89860 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
89808 GACGACTCCT
89818 ATCCAAAATCA
1 ATCCAAAATCA
89829 ATCC-AAATCA
1 ATCCAAAATCA
89839 ATCCAAAATCA
1 ATCCAAAATCA
89850 ATCCAAAATCA
1 ATCCAAAATCA
89861 CTCATTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (11 bp):
ATCCAAAATCA
Found at i:90148 original size:21 final size:21
Alignment explanation
Indices: 90122--90166 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
90112 TTTTTTAAAA
90122 TTTGACATCCA-AAATAATTTT
1 TTTGACA-CCACAAATAATTTT
**
90143 TTTGACACCACAAATTTTTTT
1 TTTGACACCACAAATAATTTT
90164 TTT
1 TTT
90167 AAAATTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTGACACCACAAATAATTTT
Found at i:91516 original size:126 final size:125
Alignment explanation
Indices: 91272--91527 Score: 397
Period size: 126 Copynumber: 2.0 Consensus size: 125
91262 AAAGAAAAAC
*
91272 TGAATTTTTAATTTCCAATGGATTACATGTTTTTAATCGAAAATTTAAATCTTAATTTAAAAAAC
1 TGAATTTTTAATTTCCAATGGATTACATGTTTTCAATCGAAAATTTAAATCTTAATTTAAAAAAC
**
91337 AAATGAGGGAAAATTTATCAGGATTATATCCTTAAAATTTTCATTCCCTCCAAAATATTA
66 AAATGAGGGAAAATTTATCAGGATTATATCCGAAAAATTTTCATTCCCTCCAAAATATTA
* * ***
91397 TGAATTTTTAATTTCCAATGGATTACATGTTTTCCATCGGAAATTTAAATCTTAATTTTTTTTAA
1 TGAATTTTTAATTTCCAATGGATTACATGTTTTCAATCGAAAATTTAAATCTTAA--TTTAAAAA
* *
91462 A-AAATGAGGGAAAATTTATCGGGATTATATCCGAAAAATTTTCATTCCCTCCAAAATATTC
64 ACAAATGAGGGAAAATTTATCAGGATTATATCCGAAAAATTTTCATTCCCTCCAAAATATTA
91523 TGAAT
1 TGAAT
91528 CTAAATTTTT
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 52 0.44
126 61 0.51
127 6 0.05
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (125 bp):
TGAATTTTTAATTTCCAATGGATTACATGTTTTCAATCGAAAATTTAAATCTTAATTTAAAAAAC
AAATGAGGGAAAATTTATCAGGATTATATCCGAAAAATTTTCATTCCCTCCAAAATATTA
Found at i:91570 original size:33 final size:33
Alignment explanation
Indices: 91497--91573 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
91487 TATATCCGAA
* * *
91497 AAATTTTCATTCCCTCCAAAATATTCTGAATCT
1 AAATTTTTATTCCCTCCAAAATATTCTAAATCC
* *
91530 AAATTTTTATTCCCTCCATAATGTTCTAAATCC
1 AAATTTTTATTCCCTCCAAAATATTCTAAATCC
91563 AAATTTTTATT
1 AAATTTTTATT
91574 TAATTAGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (33 bp):
AAATTTTTATTCCCTCCAAAATATTCTAAATCC
Found at i:92998 original size:92 final size:92
Alignment explanation
Indices: 92872--93151 Score: 474
Period size: 92 Copynumber: 3.1 Consensus size: 92
92862 GGAATGTTTG
* * * *
92872 AAATTTTACGTTTCAATAGAGGGAAATTGAAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
*
92937 TTGTGACGGAACATGTGAATCCATCAC
66 TTGTGACGGAACATGTGAATCCGTCAC
92964 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
93029 TTGTGACGGAACATGTGAATCCGTCAC
66 TTGTGACGGAACATGTGAATCCGTCAC
* *
93056 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCAGGTAATTAAAAAA-CTCTAAATT
1 AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
*
93120 TTGTGA-GGAACATGTGGATCCGTCAC
66 TTGTGACGGAACATGTGAATCCGTCAC
93146 AAATTT
1 AAATTT
93152 GTGACGGAAC
Statistics
Matches: 180, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
90 25 0.14
91 15 0.08
92 140 0.78
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (92 bp):
AAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAATGAGCGGGTAAGTAAAAAACCTCTAAATT
TTGTGACGGAACATGTGAATCCGTCAC
Found at i:93154 original size:30 final size:31
Alignment explanation
Indices: 93119--93182 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
93109 AACTCTAAAT
* * *
93119 TTTGTGA-GGAACATGTGGATCCGTCACAAA
1 TTTGTGACGGAACAAGTGGACCCATCACAAA
93149 TTTGTGACGGAACAAGTGGACCCATCACAAA
1 TTTGTGACGGAACAAGTGGACCCATCACAAA
93180 TTT
1 TTT
93183 TATGTTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (31 bp):
TTTGTGACGGAACAAGTGGACCCATCACAAA
Found at i:93242 original size:121 final size:122
Alignment explanation
Indices: 93028--93269 Score: 380
Period size: 121 Copynumber: 2.0 Consensus size: 122
93018 ACCTCTAAAT
* * *
93028 TTTGTGACGGAACATGTGAATCCGTCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
1 TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
* * *
93093 GAGCAGGTAATTAAAAAACTCTAAATTTTGTGA-GGAACATGTGGATCCGTCACAAA
66 GAGCAGGTAATTAAAAAACTCTAAATTTTGTGACGAAACATATGGACCCGTCACAAA
* *
93149 TTTGTGACGGAACAAGTGGACCCATCACAAATTTTATGTTTCAATGGAATG-AAATTGGAGGAAA
1 TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGG-AGGAAAATTGGAGGAAA
*
93213 TGAGCGGGTAATTAAAAAACTCTAAATTTTGTGACGAAACATATGGACCCGTCACAA
65 TGAGCAGGTAATTAAAAAACTCTAAATTTTGTGACGAAACATATGGACCCGTCACAA
93270 CTTTTATGTT
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
121 89 0.81
122 21 0.19
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (122 bp):
TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
GAGCAGGTAATTAAAAAACTCTAAATTTTGTGACGAAACATATGGACCCGTCACAAA
Found at i:93306 original size:91 final size:91
Alignment explanation
Indices: 93149--93364 Score: 317
Period size: 91 Copynumber: 2.4 Consensus size: 91
93139 CCGTCACAAA
* *
93149 TTTGTGACGGAACA-AGTGGACCCATCACAAATTTTATGTTTCAATGGAATGAAATTGGAGGAAA
1 TTTGTGACGGAACATA-TGGACCCGTCACAAATTTTATGTTTCAATGGAAGGAAATTGGAGGAAA
*
93213 TGAGCGGGTAATTAAAAAACTCTAAAT
65 TGAGCGGATAATTAAAAAACTCTAAAT
* * * *
93240 TTTGTGACGAAACATATGGACCCGTCACAACTTTTATGTTTCAATGGACGGAAATTGGAGGTAAT
1 TTTGTGACGGAACATATGGACCCGTCACAAATTTTATGTTTCAATGGAAGGAAATTGGAGGAAAT
*
93305 GAGCGGATAATTAAAAAACTCTGAAT
66 GAGCGGATAATTAAAAAACTCTAAAT
* * *
93331 TTTGTGACGGAACATGTGAACCTGTCACAAATTT
1 TTTGTGACGGAACATATGGACCCGTCACAAATTT
93365 GTGAGGGTCC
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 110 0.99
92 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (91 bp):
TTTGTGACGGAACATATGGACCCGTCACAAATTTTATGTTTCAATGGAAGGAAATTGGAGGAAAT
GAGCGGATAATTAAAAAACTCTAAAT
Found at i:93324 original size:212 final size:214
Alignment explanation
Indices: 92936--93368 Score: 671
Period size: 213 Copynumber: 2.0 Consensus size: 214
92926 ACCTCTAAAT
* *
92936 TTTGTGACGGAACATGTGAATCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
1 TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
* * *
93001 GAGCGGGTAAGTAAAAAACCTCTAAATTTTGTGACGGAACATGTGAATCCGTCACAAATTTTATG
66 GAGCGGGTAAGTAAAAAACCTCTAAATTTTGTGACGAAACATATGAACCCGTCACAAATTTTATG
93066 TTTCAATGGAGGAAAATTGGAGGAAATGAGCAGGTAATTAAAAAACTCTAAATTTTGTGA-GGAA
131 TTTCAATGGAGGAAAATTGGAGGAAATGAGCAGGTAATTAAAAAACTCTAAATTTTGTGACGGAA
*
93130 CATGTGGATCC-GTCACAAA
196 CATGT-GAACCTGTCACAAA
* *
93149 TTTGTGACGGAACAAGTGGACCCATCACAAATTTTATGTTTCAATGGAATG-AAATTGGAGGAAA
1 TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGG-AGGAAAATTGGAGGAAA
* * *
93213 TGAGCGGGTAATTAAAAAA-CTCTAAATTTTGTGACGAAACATATGGACCCGTCACAACTTTTAT
65 TGAGCGGGTAAGTAAAAAACCTCTAAATTTTGTGACGAAACATATGAACCCGTCACAAATTTTAT
* *
93277 GTTTCAATGGACGG-AAATTGGAGGTAATGAGC-GGATAATTAAAAAACTCTGAATTTTGTGACG
130 GTTTCAATGGA-GGAAAATTGGAGGAAATGAGCAGG-TAATTAAAAAACTCTAAATTTTGTGACG
93340 GAACATGTGAACCTGTCACAAA
193 GAACATGTGAACCTGTCACAAA
93362 TTTGTGA
1 TTTGTGA
93369 GGGTCCACAT
Statistics
Matches: 202, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
211 2 0.01
212 97 0.48
213 101 0.50
214 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (214 bp):
TTTGTGACGGAACAAGTGAACCCATCACAAATTTTATGTTTCAATGGAGGAAAATTGGAGGAAAT
GAGCGGGTAAGTAAAAAACCTCTAAATTTTGTGACGAAACATATGAACCCGTCACAAATTTTATG
TTTCAATGGAGGAAAATTGGAGGAAATGAGCAGGTAATTAAAAAACTCTAAATTTTGTGACGGAA
CATGTGAACCTGTCACAAA
Found at i:100568 original size:208 final size:207
Alignment explanation
Indices: 100206--100624 Score: 766
Period size: 208 Copynumber: 2.0 Consensus size: 207
100196 AACGAGGACG
* ** *
100206 ACGTTGACCTTCTTATTTGTGAACATTGCTAAGAGCTAGAAAGAAGAATAACACAGCTTGAGAAC
1 ACGTGGACCTTCTTATTTGTGAACATTGCTAAGAGAAAGAAAGAAGAATAACACAGCCTGAGAAC
*
100271 TACTTCGAACAACAACCAAAACTCAGCAAGAACCAATCCACATAGCTCCAGAATCGTCAGAGCGA
66 GACTTCGAACAACAACCAAAACTCAGCAAGAACCAATCCACATAGCTCCAGAATCGTCAGAGCGA
100336 ATGATACCATATCAAGTAACTCAAGAATGCACACTAATATTCAACACATAAAGGAATGAAGAAAG
131 ATGATACCATATCAAGTAACTCAAGAATGCACACTAATATTCAACACATAAAGGAATGAAGAAAG
100401 CTTCTTTTATTC
196 CTTCTTTTATTC
100413 ACGTGGACCTTCTTATTTGTGAACATTGCTAAAGAGAAAGAAAGAAGAATAACACAGCCTGAGAA
1 ACGTGGACCTTCTTATTTGTGAACATTGCT-AAGAGAAAGAAAGAAGAATAACACAGCCTGAGAA
*
100478 CGACTTCGAACAACAACCAAAACTCAGTAAGAACCAATCCACATAGCTCCAGAATCGTCAGAGCG
65 CGACTTCGAACAACAACCAAAACTCAGCAAGAACCAATCCACATAGCTCCAGAATCGTCAGAGCG
100543 AATGATACCATATCAAGTAACTCAAGAATGCACACTAATATTCAACACATAAAGGAATGAAGAAA
130 AATGATACCATATCAAGTAACTCAAGAATGCACACTAATATTCAACACATAAAGGAATGAAGAAA
*
100608 GCTTCTTTTGTTC
195 GCTTCTTTTATTC
100621 ACGT
1 ACGT
100625 AGAAAAGATG
Statistics
Matches: 204, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
207 29 0.14
208 175 0.86
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (207 bp):
ACGTGGACCTTCTTATTTGTGAACATTGCTAAGAGAAAGAAAGAAGAATAACACAGCCTGAGAAC
GACTTCGAACAACAACCAAAACTCAGCAAGAACCAATCCACATAGCTCCAGAATCGTCAGAGCGA
ATGATACCATATCAAGTAACTCAAGAATGCACACTAATATTCAACACATAAAGGAATGAAGAAAG
CTTCTTTTATTC
Found at i:104434 original size:15 final size:15
Alignment explanation
Indices: 104414--104444 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
104404 CTACAGATAG
104414 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
104429 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
104444 A
1 A
104445 TTTATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:113027 original size:23 final size:23
Alignment explanation
Indices: 112985--113041 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
112975 ATGTATTTAT
*
112985 AAAATTTATATTAAATTATTCT-A
1 AAAATTT-TATTAAATTATTATGA
113008 AAAATTTTATTCATAA-TATTATGA
1 AAAATTTTATT-A-AATTATTATGA
113032 AAATATTTTA
1 AAA-ATTTTA
113042 AAATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 13 0.45
24 6 0.21
25 6 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTTTATTAAATTATTATGA
Found at i:114657 original size:21 final size:21
Alignment explanation
Indices: 114631--114707 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
114621 ATGTCCCCCT
114631 GGTATCGATACTCTCTATATA
1 GGTATCGATACTCTCTATATA
*
114652 GGTATCGATACCTCTTCCATAT-
1 GGTATCGATA-CTC-TCTATATA
* * * *
114674 GGTATTGATATTGT-TCATACA
1 GGTATCGATACTCTCT-ATATA
114695 GGTATCGATACTC
1 GGTATCGATACTC
114708 CATGCATCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 4 0.09
21 21 0.49
22 12 0.28
23 6 0.14
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (21 bp):
GGTATCGATACTCTCTATATA
Found at i:117839 original size:11 final size:11
Alignment explanation
Indices: 117825--117850 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
117815 GAAATGGGCC
117825 TGAACGGGTTG
1 TGAACGGGTTG
117836 TGAACGGGTTG
1 TGAACGGGTTG
117847 TGAA
1 TGAA
117851 ATGGTCGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.42, T:0.27
Consensus pattern (11 bp):
TGAACGGGTTG
Found at i:127053 original size:16 final size:17
Alignment explanation
Indices: 127022--127055 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
127012 TGTATCGTCA
*
127022 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
127039 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
127055 A
1 A
127056 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:129461 original size:20 final size:20
Alignment explanation
Indices: 129432--129544 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
129422 CACAATTTAC
*
129432 GAATTTGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
129452 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
129472 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
* * *
129492 ACAATTTCGCAACACGAATTTC
1 -GAA-TTCGCAACTCGAATTTG
*** * *
129514 TTTTTCGCAACTCGATTTTT
1 GAATTCGCAACTCGAATTTG
*
129534 AAATTCGCAAC
1 GAATTCGCAAC
129545 ATGAGTTTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
20 61 0.78
21 2 0.03
22 15 0.19
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (20 bp):
GAATTCGCAACTCGAATTTG
Found at i:129476 original size:40 final size:42
Alignment explanation
Indices: 129411--129512 Score: 129
Period size: 40 Copynumber: 2.5 Consensus size: 42
129401 ACACGAAATC
* * *
129411 CAATTTCGTAACAC-AATTTACGAATTTGCAACTCGAATTTG-
1 CAATTTCGCAACACGAATTT-GGAATTCGCAACTCGAATTTGA
* *
129452 GAA-TTCGCAACTCGAATTTGGAATTCGCAACTCGAATTTGA
1 CAATTTCGCAACACGAATTTGGAATTCGCAACTCGAATTTGA
129493 CAATTTCGCAACACGAATTT
1 CAATTTCGCAACACGAATTT
129513 CTTTTTCGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 27 0.53
41 9 0.18
42 15 0.29
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (42 bp):
CAATTTCGCAACACGAATTTGGAATTCGCAACTCGAATTTGA
Found at i:129511 original size:62 final size:61
Alignment explanation
Indices: 129425--129544 Score: 143
Period size: 62 Copynumber: 2.0 Consensus size: 61
129415 TTCGTAACAC
* * *
129425 AATTTACGAATTTGCAACTCGAATTTGGAATTCGCAACTCGAATTTGGAATTCGCAACTCG
1 AATTTACGAATTTGCAACACGAATTTCGAATTCGCAACTCGAATTTGAAATTCGCAACTCG
*** * *
129486 AATTTGAC-AATTTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAATTCGCAAC
1 AATTT-ACGAATTT-GCAACACGAATTTCGAATTCGCAACTCGAATTTGAAATTCGCAAC
129545 ATGAGTTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
61 10 0.20
62 39 0.80
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (61 bp):
AATTTACGAATTTGCAACACGAATTTCGAATTCGCAACTCGAATTTGAAATTCGCAACTCG
Found at i:129559 original size:40 final size:40
Alignment explanation
Indices: 129475--129613 Score: 118
Period size: 40 Copynumber: 3.4 Consensus size: 40
129465 GAATTTGGAA
* * * *
129475 TTCGCAACTCGAATTTGACAATTTCGCAACACGAATTTCTTT
1 TTCGCAACACGAATTTTA-AA-TTCGCAACACGAGTTTCATT
* * * *
129517 TTCGCAACTCGATTTTTAAATTCGCAACATGAGTTTCCTT
1 TTCGCAACACGAATTTTAAATTCGCAACACGAGTTTCATT
* * * * * *
129557 TTCACAACAAG-ATTTTCTAATTCGTAACGCGAGTTTCAAT
1 TTCGCAACACGAATTTT-AAATTCGCAACACGAGTTTCATT
129597 TTCGCAACACGAATTTT
1 TTCGCAACACGAATTTT
129614 GTTTTCGCAA
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
39 4 0.05
40 51 0.65
41 7 0.09
42 16 0.21
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (40 bp):
TTCGCAACACGAATTTTAAATTCGCAACACGAGTTTCATT
Found at i:129601 original size:60 final size:60
Alignment explanation
Indices: 129517--129664 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 60
129507 GAATTTCTTT
* * * * **
129517 TTCGCAACTCGATTTTTAAA-TTCGCAACATGAGTTTCCTTTTCACAACAAGATTTTCTAA
1 TTCGCAACGCGA-ATTTAAATTTCGCAACACGAATTTCCTTTTCACAACAAGATTTTAGAA
* * * ** * **
129577 TTCGTAACGCGAGTTTCAATTTCGCAACACGAATTTTGTTTTCGCAACTCGATTTTAGAA
1 TTCGCAACGCGAATTTAAATTTCGCAACACGAATTTCCTTTTCACAACAAGATTTTAGAA
*
129637 TTCGCAATGCGAATTTAAATTTCGCAAC
1 TTCGCAACGCGAATTTAAATTTCGCAAC
129665 GCAAATGTTT
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
59 5 0.07
60 65 0.93
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (60 bp):
TTCGCAACGCGAATTTAAATTTCGCAACACGAATTTCCTTTTCACAACAAGATTTTAGAA
Found at i:129640 original size:20 final size:21
Alignment explanation
Indices: 129616--129664 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
129606 CGAATTTTGT
*
129616 TTTCGCAACT-CGATTTTAGAA
1 TTTCGCAACTGCGAATTTA-AA
129637 -TTCGCAA-TGCGAATTTAAA
1 TTTCGCAACTGCGAATTTAAA
129656 TTTCGCAAC
1 TTTCGCAAC
129665 GCAAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTCGCAACTGCGAATTTAAA
Found at i:133368 original size:20 final size:20
Alignment explanation
Indices: 133343--133438 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
133333 TGCCTAGTGA
133343 AAATTCGCAACTCGAAAATC
1 AAATTCGCAACTCGAAAATC
* *
133363 AAATTCGCAACTCAAAAATT
1 AAATTCGCAACTCGAAAATC
* *
133383 GAATTCGCAACTC-AATATTC
1 AAATTCGCAACTCGAA-AATC
*
133403 AAATTCGCAACTTGAAAATC
1 AAATTCGCAACTCGAAAATC
133423 AAATTCGCAACTCGAA
1 AAATTCGCAACTCGAA
133439 TTTCGAATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.03
20 61 0.94
21 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATC
Found at i:133405 original size:40 final size:41
Alignment explanation
Indices: 133343--133455 Score: 142
Period size: 40 Copynumber: 2.8 Consensus size: 41
133333 TGCCTAGTGA
* *
133343 AAATTCGCAACTCGAA-AATCAAATTCGCAACTCAAAAATT
1 AAATTCGCAACTCGAATATTCAAATTCGCAACTCAAAAATC
* **
133383 GAATTCGCAACTC-AATATTCAAATTCGCAACTTGAAAATC
1 AAATTCGCAACTCGAATATTCAAATTCGCAACTCAAAAATC
* *
133423 AAATTCGCAACTCGAAT-TTCGAATTCACAACTC
1 AAATTCGCAACTCGAATATTCAAATTCGCAACTC
133456 CATTTTGAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.03
40 57 0.92
41 3 0.05
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.26
Consensus pattern (41 bp):
AAATTCGCAACTCGAATATTCAAATTCGCAACTCAAAAATC
Found at i:133447 original size:20 final size:20
Alignment explanation
Indices: 133343--133455 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
133333 TGCCTAGTGA
*
133343 AAATTCGCAACTCGAAAATC
1 AAATTCGCAACTCGAAATTC
*
133363 AAATTCGCAACTCAAAAATT-
1 AAATTCGCAACTC-GAAATTC
*
133383 GAATTCGCAACTC-AATATTC
1 AAATTCGCAACTCGAA-ATTC
* *
133403 AAATTCGCAACTTGAAAATC
1 AAATTCGCAACTCGAAATTC
*
133423 AAATTCGCAACTCGAATTTC
1 AAATTCGCAACTCGAAATTC
* *
133443 GAATTCACAACTC
1 AAATTCGCAACTC
133456 CATTTTGAGT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
18 2 0.03
19 3 0.04
20 67 0.86
21 6 0.08
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.26
Consensus pattern (20 bp):
AAATTCGCAACTCGAAATTC
Found at i:133447 original size:60 final size:60
Alignment explanation
Indices: 133343--133455 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
133333 TGCCTAGTGA
*
133343 AAATTCGCAACTCGAAAATCAAATTCGCAACTCAAAAATTGAATTCGCAACTCAATATTC
1 AAATTCGCAACTCGAAAATCAAATTCGCAACTCAAAAATTGAATTCACAACTCAATATTC
* * *
133403 AAATTCGCAACTTGAAAATCAAATTCGCAACTC-GAATTTCGAATTCACAACTC
1 AAATTCGCAACTCGAAAATCAAATTCGCAACTCAAAAATT-GAATTCACAACTC
133456 CATTTTGAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 4 0.08
60 44 0.92
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.26
Consensus pattern (60 bp):
AAATTCGCAACTCGAAAATCAAATTCGCAACTCAAAAATTGAATTCACAACTCAATATTC
Found at i:133478 original size:19 final size:20
Alignment explanation
Indices: 133456--133495 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
133446 TTCACAACTC
133456 CATTTT-GAGTTGCGAATTT
1 CATTTTCGAGTTGCGAATTT
*
133475 CATTTTCGAGTTGCGATTTT
1 CATTTTCGAGTTGCGAATTT
133495 C
1 C
133496 GTGTTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.47
Consensus pattern (20 bp):
CATTTTCGAGTTGCGAATTT
Found at i:136949 original size:21 final size:21
Alignment explanation
Indices: 136904--137035 Score: 117
Period size: 21 Copynumber: 6.3 Consensus size: 21
136894 AGTATGGAAT
* *
136904 GTGGATCCTAAACGATGCG-G
1 GTGGATCCTGAACGATGGGAG
136924 GTGGATCCTGAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
* *
136945 GTGGATCTTGAACGATGAGAG
1 GTGGATCCTGAACGATGGGAG
*
136966 G-GG-TCTCTTGAACGATGAGAG
1 GTGGATC-C-TGAACGATGGGAG
* ** *
136987 GTGAATCCTGAATAATAGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
137008 GTGGAACCTGAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
137029 GTGGATC
1 GTGGATC
137036 AGGCTTCTTC
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.02
20 19 0.21
21 66 0.73
22 2 0.02
23 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:137385 original size:21 final size:21
Alignment explanation
Indices: 137361--137530 Score: 182
Period size: 21 Copynumber: 8.1 Consensus size: 21
137351 TGAAACAATC
*
137361 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
137382 TCACGTAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
137403 TCACGTAAAGCACTTACCTCA
1 TCACGTAAAGCACCTACCTCA
*
137424 CCACGTAAAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* **
137445 TCACGTAAAGCATC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
* *
137466 TCATGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
* * *
137487 TCACATAAAGCACATACCTTA
1 TCACGTAAAGCACCTACCTCA
*
137508 TCACGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
137529 TC
1 TC
137531 CCATGGAGGT
Statistics
Matches: 120, Mismatches: 25, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.02
21 116 0.97
22 2 0.02
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:137436 original size:63 final size:63
Alignment explanation
Indices: 137362--137521 Score: 239
Period size: 63 Copynumber: 2.5 Consensus size: 63
137352 GAAACAATCT
* **
137362 CACGTAGAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACTTACCTCAC
1 CACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCGACCTCAC
* * *
137425 CACGTAAAGCACCTACCTCATCACGTAAAGCATCATTGTCATCATGTAAAGCACCGACCTCAT
1 CACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCGACCTCAC
* * *
137488 CACATAAAGCACATACCTTATCACGTAAAGCACC
1 CACGTAAAGCACCTACCTCATCACGTAAAGCACC
137522 TAACTCATCC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (63 bp):
CACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCGACCTCAC
Found at i:137726 original size:42 final size:42
Alignment explanation
Indices: 137630--137870 Score: 258
Period size: 42 Copynumber: 6.0 Consensus size: 42
137620 GTGATGGAAT
*
137630 AGGTGATGGATCTCGGTGTCGAGG-TGTAGAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAGGTTG-AGAATCGGCTCGATG
* * * *
137669 AGGTGATGAATCTCGGTGTTGAGGTTTAGAATCGGCTCGATA
1 AGGTGATGGATCTCGGTGTCGAGGTTGAGAATCGGCTCGATG
*
137711 AGGTGATGGATCTCGGTGTCGA-ATTGGAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTT-GAGAATCGGCTCGATG
* *
137753 AGGTGATGGATCTCGGTGTCGAAGTAGAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTTGAGAATCGGCTCGATG
*
137795 AGGTGATGGATCTCGGTGTCGAGG-T--G--T-AG---GATG
1 AGGTGATGGATCTCGGTGTCGAGGTTGAGAATCGGCTCGATG
* * *
137828 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTTGAGAATCGGCTCGATG
137870 A
1 A
137871 AAAAGTGGGG
Statistics
Matches: 168, Mismatches: 19, Indels: 27
0.79 0.09 0.13
Matches are distributed among these distances:
33 27 0.16
36 2 0.01
37 1 0.01
38 1 0.01
39 32 0.19
40 1 0.01
41 3 0.02
42 100 0.60
43 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAGGTTGAGAATCGGCTCGATG
Found at i:137774 original size:24 final size:24
Alignment explanation
Indices: 137747--137816 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
137737 GAGAATCGGC
137747 TCGATGAGGTGATGGATCTCGGTG
1 TCGATGAGGTGATGGATCTCGGTG
* *
137771 TCGA--A-GT-A-GAGA-ATCGG-C
1 TCGATGAGGTGATG-GATCTCGGTG
137789 TCGATGAGGTGATGGATCTCGGTG
1 TCGATGAGGTGATGGATCTCGGTG
137813 TCGA
1 TCGA
137817 GGTGTAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
18 4 0.12
19 5 0.15
20 4 0.12
21 4 0.12
22 4 0.12
23 5 0.15
24 8 0.24
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.26
Consensus pattern (24 bp):
TCGATGAGGTGATGGATCTCGGTG
Found at i:137818 original size:21 final size:21
Alignment explanation
Indices: 137752--137820 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
137742 TCGGCTCGAT
137752 GAGGTGATGGATCTCGGTGTC
1 GAGGTGATGGATCTCGGTGTC
* *
137773 GAAGT-A-GAGA-ATCGGCTCGAT-
1 GAGGTGATG-GATCTCGG-T-G-TC
137794 GAGGTGATGGATCTCGGTGTC
1 GAGGTGATGGATCTCGGTGTC
137815 GAGGTG
1 GAGGTG
137821 TAGGATGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 16 0.44
22 5 0.14
23 5 0.14
ACGTcount: A:0.20, C:0.13, G:0.42, T:0.25
Consensus pattern (21 bp):
GAGGTGATGGATCTCGGTGTC
Found at i:140054 original size:20 final size:20
Alignment explanation
Indices: 140029--140281 Score: 126
Period size: 20 Copynumber: 12.6 Consensus size: 20
140019 AAATATTTGT
140029 GTTGCGAATTCGAAATTCGA
1 GTTGCGAATTCGAAATTCGA
* *
140049 GTTGCGAAAAT-GAAATTCGT
1 GTTGCG-AATTCGAAATTCGA
**
140069 GTTGCGAATTATAAATTCGA
1 GTTGCGAATTCGAAATTCGA
*** * *
140089 GTTGCGAAAGAGAAACTCGT
1 GTTGCGAATTCGAAATTCGA
** *
140109 GTTGCGAATTTAAAAATCGA
1 GTTGCGAATTCGAAATTCGA
***
140129 GTTGCGAAAAAGAAATTCGTA
1 GTTGCGAATTCGAAATTCG-A
140150 -TTGCGAAAATGTC-AAATTCGA
1 GTTGCG--AAT-TCGAAATTCGA
* * *
140171 GTTGCGAATTCG-ACTTATGT
1 GTTGCGAATTCGAAATT-CGA
**
140191 GTTGCGAATTATAAATTCGA
1 GTTGCGAATTCGAAATTCGA
*
140211 GTTGCAAATTCGGAAATT--A
1 GTTGCGAATTC-GAAATTCGA
* * *
140230 TGTTGCGAAATT-GGATTTCGT
1 -GTTGCG-AATTCGAAATTCGA
* *
140251 GTTGAGAATTTGAAATT-GA
1 GTTGCGAATTCGAAATTCGA
*
140270 GTTACGAATTCG
1 GTTGCGAATTCG
140282 TTGGTTATTT
Statistics
Matches: 171, Mismatches: 46, Indels: 33
0.68 0.18 0.13
Matches are distributed among these distances:
19 27 0.16
20 113 0.66
21 17 0.10
22 14 0.08
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTCGAAATTCGA
Found at i:140073 original size:40 final size:38
Alignment explanation
Indices: 140027--140178 Score: 178
Period size: 40 Copynumber: 3.8 Consensus size: 38
140017 CTAAATATTT
140027 GTGTTGCGAATTCGAAATTCGAGTTGCGAAAATGAAATTC
1 GTGTTGCGAATTC-AAATTCGAGTTGCGAAAA-GAAATTC
* *
140067 GTGTTGCGAATTATAAATTCGAGTTGCGAAAGAGAAACTC
1 GTGTTGCGAATT-CAAATTCGAGTTGCGAAA-AGAAATTC
* *
140107 GTGTTGCGAATTTAAAAATCGAGTTGCGAAAAAGAAATTC
1 GTGTTGCGAA-TTCAAATTCGAGTTGCG-AAAAGAAATTC
*
140147 GTATTGCGAAAATGTCAAATTCGAGTTGCGAA
1 GTGTTGCG--AAT-TCAAATTCGAGTTGCGAA
140179 TTCGACTTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
40 72 0.74
41 9 0.09
42 16 0.16
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (38 bp):
GTGTTGCGAATTCAAATTCGAGTTGCGAAAAGAAATTC
Found at i:140234 original size:40 final size:38
Alignment explanation
Indices: 140025--140238 Score: 171
Period size: 40 Copynumber: 5.3 Consensus size: 38
140015 CCCTAAATAT
**
140025 TTGTGTTGCGAATTCGAAATTCGAGTTGCGAAAATGAAA
1 TTGTGTTGCGAATTATAAATTCGAGTTGCG-AAATGAAA
*
140064 TTCGTGTTGCGAATTATAAATTCGAGTTGCGAAAGAGAAA
1 TT-GTGTTGCGAATTATAAATTCGAGTTGCGAAA-TGAAA
* * *
140104 CTCGTGTTGCGAATT-TAAAAATCGAGTTGCGAAAAAGAAA
1 -TTGTGTTGCGAATTAT-AAATTCGAGTTGCG-AAATGAAA
* * * * **
140144 TTCGTATTGCGAAAATGTCAAATTCGAGTTGCGAATTCGACT
1 TT-GTGTTGCG-AATTAT-AAATTCGAGTTGCGAAAT-GAAA
140186 TATGTGTTGCGAATTATAAATTCGAGTTGC-AAATTCGGAAA
1 T-TGTGTTGCGAATTATAAATTCGAGTTGCGAAA-T--GAAA
*
140227 TTATGTTGCGAA
1 TTGTGTTGCGAA
140239 ATTGGATTTC
Statistics
Matches: 141, Mismatches: 22, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
39 9 0.06
40 91 0.65
41 16 0.11
42 24 0.17
43 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (38 bp):
TTGTGTTGCGAATTATAAATTCGAGTTGCGAAATGAAA
Done.