Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008660.1 Hibiscus syriacus cultivar Beakdansim tig00111657_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: 1057077
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 5
Found at i:887 original size:21 final size:21
Alignment explanation
Indices: 826--888 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
816 TTCCTCGAGA
826 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
** * *
847 G-CCACTGTCATCGTTGAAGAG
1 GTCC-CTCCCACCGTTCAAGAG
*
868 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCGTTCAAGAG
889 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.37, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCGTTCAAGAG
Found at i:2243 original size:14 final size:14
Alignment explanation
Indices: 2224--2259 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2214 ATTGTTTAAT
2224 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2238 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2252 TGATTTGT
1 TGATTTGT
2260 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2492 original size:33 final size:33
Alignment explanation
Indices: 2442--2534 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
2432 ATTAATTTCG
2442 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2474 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
2507 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2535 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 8 0.14
33 50 0.86
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:4839 original size:12 final size:12
Alignment explanation
Indices: 4822--4846 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4812 TCTTCGGGGA
4822 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4834 CTTTTTCTTCTT
1 CTTTTTCTTCTT
4846 C
1 C
4847 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6715 original size:20 final size:20
Alignment explanation
Indices: 6690--6740 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
6680 ATTCATTTGA
*
6690 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
6710 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
6730 TTATCGCAACG
1 CTATCGCAACG
6741 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:6790 original size:14 final size:15
Alignment explanation
Indices: 6770--6842 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
6760 TGAAAATCGC
6770 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
6785 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
6802 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
6820 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
6836 -TTGCGAT
1 ATTGCGAT
6843 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:6807 original size:19 final size:19
Alignment explanation
Indices: 6766--6832 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
6756 GAAATGAAAA
6766 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
6782 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6799 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
6817 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
6833 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6965 original size:14 final size:14
Alignment explanation
Indices: 6948--6984 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6938 ACATCATTAA
6948 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
6962 ACAAATCATCTTTT
1 ACAAATCAACATTT
6976 ACAAATCAA
1 ACAAATCAA
6985 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:8900 original size:14 final size:14
Alignment explanation
Indices: 8881--8938 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
8871 ATGCGAAATG
8881 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
8895 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
8911 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
8927 AAAATCGCAACG
1 AAAATCGCAACG
8939 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:8923 original size:32 final size:33
Alignment explanation
Indices: 8865--8943 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
8855 GGAAATGGCT
*
8865 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
8898 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
8930 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
8944 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:8972 original size:19 final size:18
Alignment explanation
Indices: 8950--9014 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
8940 GAAACACAAA
*
8950 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
8969 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
8985 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
9001 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
9015 TGTCGTTGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.28
16 4 0.10
18 14 0.36
19 10 0.26
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:8991 original size:14 final size:14
Alignment explanation
Indices: 8972--9026 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
8962 TTTCATTTCG
8972 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
8986 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
9002 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
9018 CGTTGCGAT
1 CGTTGCGAT
9027 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 20 0.57
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9002 original size:32 final size:32
Alignment explanation
Indices: 8955--9045 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
8945 ACAAATCGCA
8955 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
8988 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
* *
9020 TTGCGATAGTCATTTTCGTGTTGCGA
1 TTGCGAT-TTCA-TTTCGCGTTGCGA
9046 AAGTAAACTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.61
33 9 0.17
34 12 0.22
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:9543 original size:18 final size:18
Alignment explanation
Indices: 9517--9561 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
9507 GTCGATCAGA
*
9517 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
9535 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
9553 TGATGGCTC
1 TGATGGCTC
9562 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:10906 original size:20 final size:20
Alignment explanation
Indices: 10881--10918 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10871 AATAGTTTTT
10881 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
10901 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
10919 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11207 original size:22 final size:22
Alignment explanation
Indices: 11182--11225 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11172 GATTTAGATA
11182 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
11204 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
11226 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:11438 original size:20 final size:20
Alignment explanation
Indices: 11413--11506 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
11403 GATTATGTAT
11413 TATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTTAG
*
11433 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTTAG
* *** *
11453 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTTAG
* * *
11474 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTTAG
*
11494 TATCGCATTGCGA
1 TATCGCGTTGCGA
11507 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTTAG
Found at i:11478 original size:41 final size:41
Alignment explanation
Indices: 11433--11510 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
11423 CGAAAGTTAG
* * *
11433 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
11474 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
11511 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:11507 original size:20 final size:20
Alignment explanation
Indices: 11393--11507 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
11383 CGCTTTGAAA
*
11393 ATCGCATTGCGATTA-TGTATT
1 ATCGCATTGCGA-TAGT-TAGT
* *
11414 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAGTTAGT
* * *
11434 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTTAGT
* * ** *
11454 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTTAGT
*
11475 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTTAGT
11495 ATCGCATTGCGAT
1 ATCGCATTGCGAT
11508 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
20 51 0.67
21 25 0.33
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTTAGT
Found at i:11526 original size:41 final size:41
Alignment explanation
Indices: 11433--11528 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
11423 CGAAAGTTAG
* * * ** *
11433 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
11474 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
11516 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
11529 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:12123 original size:6 final size:6
Alignment explanation
Indices: 12108--12140 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12098 TCTCGTCTCG
*
12108 GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
12141 AATACGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:13677 original size:5 final size:5
Alignment explanation
Indices: 13659--13958 Score: 125
Period size: 5 Copynumber: 60.0 Consensus size: 5
13649 TGAAAATTTC
* * * *
13659 ATATT ATATAT ATATT ATATT ATTATT GT-TG AGATTT AGTATT ACATAT
1 ATATT ATAT-T ATATT ATATT A-TATT ATATT ATA-TT A-TATT ATAT-T
* * * *
13708 ATACT ATATA ATGTTT ATATT ATA-T ATTATT -T-TT A-ATAT ATAGT
1 ATATT ATATT AT-ATT ATATT ATATT A-TATT ATATT ATAT-T ATATT
* *
13752 ATATT AT-GT ATTATT ATATT ATATA ATACTT ATATT -T-TT ATA-T ACTA-T
1 ATATT ATATT A-TATT ATATT ATATT ATA-TT ATATT ATATT ATATT A-TATT
* *
13800 ATATAT ATATT ACATT ATATT AATATTT ATATT ATATT ATAGT ATATT
1 ATAT-T ATATT ATATT ATATT -ATA-TT ATATT ATATT ATATT ATATT
* * *
13848 AT-TAT ATAGT AT-TT ATATT GTA-T AGTGTT ATATT ATATT ATA-T ATA-T
1 ATAT-T ATATT ATATT ATATT ATATT A-TATT ATATT ATATT ATATT ATATT
* *
13895 ATATT ATAGT ATA-- ATATT A-ATAT ATATT GCATAAT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT --ATATT ATATT ATATT
* *
13940 AT-TT TTATT ATATT TTATT
1 ATATT ATATT ATATT ATATT
13959 CTTATTATTA
Statistics
Matches: 223, Mismatches: 36, Indels: 72
0.67 0.11 0.22
Matches are distributed among these distances:
3 7 0.03
4 31 0.14
5 135 0.61
6 43 0.19
7 7 0.03
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:13896 original size:31 final size:29
Alignment explanation
Indices: 13723--13921 Score: 129
Period size: 31 Copynumber: 7.0 Consensus size: 29
13713 ATATAATGTT
*
13723 TATATTATA-TATTAT-TTTTA-ATATATA
1 TATATTATAGT-TTATATTATATATATATA
*
13750 GTATATTAT-GTAT-TATTATAT-TATATA
1 -TATATTATAGTTTATATTATATATATATA
*
13777 -ATACTTATA-TTTTTA-TATACTATATATA
1 TATA-TTATAGTTTATATTATA-TATATATA
* *
13805 TATATTACA--TTATATTA-ATATTTATA
1 TATATTATAGTTTATATTATATATATATA
* *
13831 TTATATTATAGTATATTATTATATAGTATTTA
1 -TATATTATAGTTTA-TATTATATA-TATATA
13863 TAT-TGTATAGTGTTATATTATATTATATATA
1 TATAT-TATAGT-TTATATTATA-TATATATA
*
13894 TATATTATAGTATAATATTA-ATATATAT
1 TATATTATAGT-TTATATTATATATATAT
13922 TGCATAATAT
Statistics
Matches: 137, Mismatches: 14, Indels: 39
0.72 0.07 0.21
Matches are distributed among these distances:
25 3 0.02
26 18 0.13
27 27 0.20
28 21 0.15
29 12 0.09
30 7 0.05
31 40 0.29
32 9 0.07
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (29 bp):
TATATTATAGTTTATATTATATATATATA
Found at i:13933 original size:2 final size:2
Alignment explanation
Indices: 13704--13921 Score: 74
Period size: 2 Copynumber: 118.0 Consensus size: 2
13694 TTAGTATTAC
* * * *
13704 AT AT AT ACT AT AT A- AT GT TT AT AT -T AT AT AT -T AT TT TT A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13743 AT AT AT AGT AT AT -T AT GT AT -T AT -T AT AT -T AT AT A- AT ACT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
13782 -T AT AT TT TT AT AT ACT AT AT AT AT AT AT -T AC AT -T AT AT -T
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13821 A- AT AT TT AT AT -T AT AT -T AT AGT AT AT -T AT -T AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* * *
13860 TT AT AT -T GT AT AGT GT -T AT AT -T AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13899 -T AT AGT AT A- AT AT -T A- AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT
13922 TGCATAATAT
Statistics
Matches: 165, Mismatches: 17, Indels: 68
0.66 0.07 0.27
Matches are distributed among these distances:
1 26 0.16
2 125 0.76
3 14 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (2 bp):
AT
Found at i:16795 original size:21 final size:21
Alignment explanation
Indices: 16764--16815 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
16754 GGTCCCATCT
*
16764 GAATTGAAAGTAGCA-AAGAAA
1 GAATTGGAAGTAG-AGAAGAAA
* *
16785 GAATTTGAAGTAGAGAAGAAG
1 GAATTGGAAGTAGAGAAGAAA
16806 GAATTGGAAG
1 GAATTGGAAG
16816 AAAAACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.50, C:0.02, G:0.31, T:0.17
Consensus pattern (21 bp):
GAATTGGAAGTAGAGAAGAAA
Found at i:22714 original size:19 final size:19
Alignment explanation
Indices: 22690--22737 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
22680 CTCTCAGTTC
22690 ATTTAATCATAATTTATTT
1 ATTTAATCATAATTTATTT
22709 ATTTAATCATAATTTATTT
1 ATTTAATCATAATTTATTT
*
22728 ATTTCATCAT
1 ATTTAATCAT
22738 CTTTCACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAATCATAATTTATTT
Found at i:31834 original size:28 final size:29
Alignment explanation
Indices: 31798--31856 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
31788 ACTGGATCTA
* *
31798 TGTTAAAAAAGAGAGAAAATTTTCCGATC
1 TGTTAAAAAAAAGAGAAAATTTTCCAATC
31827 TGTT-AAAAAAAGAGAAAATTTTCCAATC
1 TGTTAAAAAAAAGAGAAAATTTTCCAATC
31855 TG
1 TG
31857 GTAGAGGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (29 bp):
TGTTAAAAAAAAGAGAAAATTTTCCAATC
Found at i:34064 original size:12 final size:12
Alignment explanation
Indices: 34047--34077 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34037 AACATAATAC
34047 ACATAATGCAAA
1 ACATAATGCAAA
34059 ACATAATGCAAA
1 ACATAATGCAAA
34071 ACA-AATG
1 ACATAATG
34078 ACATGCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (12 bp):
ACATAATGCAAA
Found at i:38259 original size:59 final size:59
Alignment explanation
Indices: 38175--38568 Score: 565
Period size: 59 Copynumber: 6.7 Consensus size: 59
38165 ATGGCACTAA
** * * * * *
38175 GTGTGCTAAGCTGATAAGGAAATCATCCTAAGAGAATGAATTTCCATATAGGGCACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
* * *
38234 GTGTGATAAAATGATAAGGAAATCATGCTAAGTGTACGAATTTCCAGATAGGACACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
*
38293 GTGTGCTAAAATAATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
* * *
38352 GTGTGCTAAAATGATAATGAAATCATATTAAGTGTATGAATTTCCAGATAGGGCACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
*
38411 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
* * * * * * *
38470 GTGTGCT-AAATGATAAGAAAATAATATTAAGTGTTTGGATTTCCAGATATGACACTTC
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
* *
38528 GTGTGCTAAAATAATGAGGAAATCATACTAAGTGTATGAAT
1 GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAAT
38569 ATTTGTAGGG
Statistics
Matches: 300, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
58 50 0.17
59 250 0.83
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGACACTTT
Found at i:39100 original size:45 final size:45
Alignment explanation
Indices: 39051--39171 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 45
39041 TAAACATAAC
*
39051 ATAAAAGGCATGAAAAAATGCCATAAATGAAA-GGTATAATAGTGT
1 ATAAAAGGCATGAAAGAATGCCAT-AATGAAATGGTATAATAGTGT
* * *
39096 ATAAAAGGCATGAAAGGATACCATAATGGAAATGGTATAATTGTGT
1 ATAAAAGGCATGAAAGAATGCCATAAT-GAAATGGTATAATAGTGT
* * *
39142 -TATAA-GCATGAAGGAATGCTATCAATGAAA
1 ATAAAAGGCATGAAAGAATGCCAT-AATGAAA
39172 ATAAAGGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
44 20 0.31
45 32 0.50
46 12 0.19
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (45 bp):
ATAAAAGGCATGAAAGAATGCCATAATGAAATGGTATAATAGTGT
Found at i:43100 original size:20 final size:20
Alignment explanation
Indices: 43052--43104 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
43042 GCCAAAAAGG
43052 GGTATCGATACCAGAGTATA
1 GGTATCGATACCAGAGTATA
*
43072 GAAGTATCGATACCAGGGTAGT-
1 G--GTATCGATACCAGAGTA-TA
43094 GGTATCGATAC
1 GGTATCGATAC
43105 TATTGGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 11 0.38
22 17 0.59
23 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAGAGTATA
Found at i:43574 original size:59 final size:59
Alignment explanation
Indices: 43436--43824 Score: 611
Period size: 59 Copynumber: 6.6 Consensus size: 59
43426 TACTAAGTGA
* *
43436 GCTAAATTGATAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCAC--TGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
*
43493 GCTAAAATGATAAGGAAATCATAGTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
* * *
43552 GCTAAAATGATAAGGAAATCATACTAAGTGTATAAATTTCTAGATAGGGAACTTTGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
* **
43611 GCGAAAATGATAAATAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
* *
43670 GCTAAAATGATAAGGCAATCATACTAAGTGTATGAATTTCCAGATAGGTCACTTTGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
** *
43729 GCTAAAATGATAATTAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCGTGT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
* * *
43788 GCTAAAATAATAAGGAAAACATACTACGTGTATGAAT
1 GCTAAAATGATAAGGAAATCATACTAAGTGTATGAAT
43825 ATTTGTGGGG
Statistics
Matches: 302, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
57 49 0.16
59 253 0.84
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (59 bp):
GCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
Found at i:44354 original size:45 final size:46
Alignment explanation
Indices: 44305--44397 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 46
44295 TAAGCAGAAC
*
44305 ATAAAAGGCATGAAAGAACGCCATAAAT-GAAA-GGTATAATAGTGT
1 ATAAAAGGAATGAAAGAACGCCAT-AATGGAAATGGTATAATAGTGT
* * *
44350 ATAAAAGGAATGAAAGGATGCCATAATGGAAATGGTATAATGGTGT
1 ATAAAAGGAATGAAAGAACGCCATAATGGAAATGGTATAATAGTGT
44396 AT
1 AT
44398 TATAAGCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 3 0.07
45 25 0.60
46 14 0.33
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (46 bp):
ATAAAAGGAATGAAAGAACGCCATAATGGAAATGGTATAATAGTGT
Found at i:50501 original size:34 final size:34
Alignment explanation
Indices: 50457--50606 Score: 122
Period size: 34 Copynumber: 4.1 Consensus size: 34
50447 GCATCTGTTC
*
50457 ATGCCAATAATGCACCCATATGCATTATTCTTTT
1 ATGCTAATAATGCACCCATATGCATTATTCTTTT
*
50491 ATGCTGATAATGCACCCATATGCATTTCAGTTATGGCATCATTT
1 ATGCTAATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT
* * * *
50535 CATGCCAGTAATGCACCTATATGCATTACTCTTTT
1 -ATGCTAATAATGCACCCATATGCATTATTCTTTT
* *
50570 CTGCTAATAATGCACCCATATTCATTATTC-TTT
1 ATGCTAATAATGCACCCATATGCATTATTCTTTT
50603 ATGC
1 ATGC
50607 AATCATTTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
33 6 0.07
34 46 0.51
35 5 0.05
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 5 0.05
45 20 0.22
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (34 bp):
ATGCTAATAATGCACCCATATGCATTATTCTTTT
Found at i:50503 original size:79 final size:79
Alignment explanation
Indices: 50407--50595 Score: 281
Period size: 79 Copynumber: 2.4 Consensus size: 79
50397 TTGTGGTATA
* *
50407 CTTTTATGCCGATAATGCACCCATATGCATTTCGGCTATGGCATC-TGTTCATGCCAATAATGCA
1 CTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGGCATCAT-TTCATGCCAATAATGCA
*
50471 CCCATATGCATTATT
65 CCCATATGCATTACT
* *
50486 CTTTTATGCTGATAATGCACCCATATGCATTTCAGTTATGGCATCATTTCATGCCAGTAATGCAC
1 CTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
*
50551 CTATATGCATTACT
66 CCATATGCATTACT
* * *
50565 CTTTTCTGCTAATAATGCACCCATATTCATT
1 CTTTTATGCTGATAATGCACCCATATGCATT
50596 ATTCTTTATG
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 99 0.99
80 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (79 bp):
CTTTTATGCTGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
CCATATGCATTACT
Found at i:52297 original size:57 final size:59
Alignment explanation
Indices: 52140--52306 Score: 196
Period size: 57 Copynumber: 2.9 Consensus size: 59
52130 TATACGCACC
* *
52140 ATAGTGCTAA-CCCGAGTAGGACACATAAGGTCGTGCCCACCATCTGCACTAGTTATACT
1 ATAGTGC-AATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
* * * * * * * *
52199 TTAGTGCAGTCACGAATATGACACATAAGGGCGTTCCCACCATATGCACTTG-TA-CCT
1 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
**
52256 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGGTCACCATATGCACTA
1 ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTA
52307 ATATTTTAGT
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
57 44 0.50
58 3 0.03
59 41 0.47
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (59 bp):
ATAGTGCAATCCCGAGTATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACT
Found at i:56250 original size:23 final size:24
Alignment explanation
Indices: 56191--56254 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
56181 GGACTGCGAA
* *
56191 AATTTTTTCCTGAAGGACCACGTAG
1 AATTTGTTCC-GAAGGACCACATAG
* *
56216 AATATGTTCCGAATGACCACATAG
1 AATTTGTTCCGAAGGACCACATAG
56240 -ATTTGTTCCGAAGGA
1 AATTTGTTCCGAAGGA
56255 TCGCGTAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 13 0.39
24 12 0.36
25 8 0.24
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (24 bp):
AATTTGTTCCGAAGGACCACATAG
Found at i:56263 original size:23 final size:23
Alignment explanation
Indices: 56192--56263 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
56182 GACTGCGAAA
*
56192 ATTTTTTCCTGAAGGACCACGTAG
1 ATTTGTTCC-GAAGGACCACGTAG
* * *
56216 AATATGTTCCGAATGACCACATAG
1 -ATTTGTTCCGAAGGACCACGTAG
* *
56240 ATTTGTTCCGAAGGATCGCGTAG
1 ATTTGTTCCGAAGGACCACGTAG
56263 A
1 A
56264 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 19 0.50
24 12 0.32
25 7 0.18
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (23 bp):
ATTTGTTCCGAAGGACCACGTAG
Found at i:63300 original size:3 final size:3
Alignment explanation
Indices: 63294--63335 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
63284 TCCATTTTGT
*
63294 TTA TTA TTA TTA TTA -TA TTA TTA TATA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
63336 ATAAATGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63346 original size:22 final size:21
Alignment explanation
Indices: 63298--63348 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
63288 TTTTGTTTAT
* * *
63298 TATTATTATTATATTATTATA
1 TATTTTTATTATATTAATAAA
63319 TATTTTTATTATTATTAATAAA
1 TATTTTTATTA-TATTAATAAA
*
63341 TGTTTTTA
1 TATTTTTA
63349 AATAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTTTTATTATATTAATAAA
Found at i:63409 original size:14 final size:14
Alignment explanation
Indices: 63390--63418 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63380 GGAAGCCTAT
63390 CATACTGGCCCAAA
1 CATACTGGCCCAAA
63404 CATACTGGCCCAAA
1 CATACTGGCCCAAA
63418 C
1 C
63419 CCAATAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.14, T:0.14
Consensus pattern (14 bp):
CATACTGGCCCAAA
Found at i:76231 original size:19 final size:17
Alignment explanation
Indices: 76207--76253 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
76197 ATTATGGTTG
76207 AAGAAAGAAAAAAATGAAA
1 AAGAAA-AAAAAAATG-AA
*
76226 AAGAAAAAATGAAATGAA
1 AAGAAAAAA-AAAATGAA
76244 AAGAAAAAAA
1 AAGAAAAAAA
76254 TGATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGAAAAAAAAAATGAA
Found at i:76234 original size:14 final size:15
Alignment explanation
Indices: 76205--76239 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
76195 ATATTATGGT
76205 TGAAGAAAGAAAAAAA
1 TGAA-AAAGAAAAAAA
76221 TGAAAAAG-AAAAAA
1 TGAAAAAGAAAAAAA
76235 TGAAA
1 TGAAA
76240 TGAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 4 0.21
16 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
TGAAAAAGAAAAAAA
Found at i:76599 original size:18 final size:18
Alignment explanation
Indices: 76572--76609 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
76562 CAAGATTATC
*
76572 TTTTTGAAATTCAATTTA
1 TTTTTAAAATTCAATTTA
76590 TTTTTAAAATTCAATTTA
1 TTTTTAAAATTCAATTTA
76608 TT
1 TT
76610 CTTTTACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTTAAAATTCAATTTA
Found at i:77966 original size:112 final size:112
Alignment explanation
Indices: 77761--78319 Score: 506
Period size: 112 Copynumber: 4.9 Consensus size: 112
77751 GCAAAGATTC
* * * * * *
77761 GAATCCATCA-TTCGATGGATCAAC-TGTTCTAGAAGAAGTTCATGATGAGAATAACTCATTTAA
1 GAATTCATCACTT-GATGGATCAACAT-TTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGA
* * *
77824 AGAAGGAAGAAGAAGTTTATAATGATAAGAACTTGTTTAACCTTTTGCTT
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTT
* * * * *
77874 GAGTTCATCA-TTCGATGGATCAACATTTCCAGAAGGGCTCATAATGAGATGAACTCATCTGATG
1 GAATTCATCACTT-GATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
77938 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTT-ACCTTTTACTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTT
* * * * * *
77985 GAATTCATCACTTGATGGATTAGCATTACCAGGTAGGGTTCATAATGAGAAGAACTCATCTCAAG
1 GAATTCATCACTTGATGGATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
78050 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTAATT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT-TAACCTTTTACTT
* * * * *
78099 GAATTCATCACATGATGGATCAACTTTTCCAGAGAAAAGTTCATAATGAGAAGACCTTATCTGAA
1 GAATTCATCACTTGATGGATCAACATTTCC--AGAAGAGTTCATAATGAGAAGAACTCATCTGAA
* *
78164 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTCTTCAACCTTTGT--TT
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTT-TACTT
* * * *
78211 G-ATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAAGTGTTCATAATAAGAAGAA
1 GAATTC-ATCAC---------TTGAT--GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAA
* **
78275 CTCATCTGAATAAGGAA-ACTAAGTTCATAATGAGAAGAACTTGTT
54 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
78320 CAATCTTGAC
Statistics
Matches: 366, Mismatches: 59, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
111 37 0.10
112 124 0.34
113 37 0.10
114 67 0.18
115 27 0.07
116 1 0.00
121 56 0.15
122 5 0.01
123 12 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
GAATTCATCACTTGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTACTT
Found at i:78684 original size:17 final size:17
Alignment explanation
Indices: 78662--78694 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
78652 TTCATTTTGT
78662 TTATTATTATTATTATA
1 TTATTATTATTATTATA
*
78679 TTATTATTTTTATTAT
1 TTATTATTATTATTAT
78695 TAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATTATTATTATA
Found at i:78712 original size:3 final size:3
Alignment explanation
Indices: 78662--78696 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
78652 TTCATTTTGT
*
78662 TTA TTA TTA TTA TTA -TA TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
78697 ATAATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:80079 original size:3 final size:3
Alignment explanation
Indices: 80071--80097 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
80061 AATATATTTA
80071 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
80098 TAATCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:86871 original size:11 final size:11
Alignment explanation
Indices: 86855--86880 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
86845 TGAATAACAG
86855 AAATAAAAATA
1 AAATAAAAATA
86866 AAATAAAAATA
1 AAATAAAAATA
86877 AAAT
1 AAAT
86881 TATCATAAAT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:87024 original size:30 final size:30
Alignment explanation
Indices: 86989--87067 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
86979 ATAAATAAAT
*
86989 AAAAAGTTAGCGGTTAGT-GATTAGTAGTTA
1 AAAAAGTTAGCGATTAGTAG-TTAGTAGTTA
* **
87019 AAAAAGGTATTGATTAGTAGTTAGTAGTTA
1 AAAAAGTTAGCGATTAGTAGTTAGTAGTTA
* *
87049 GAAAAGTTAG-TATTAGTAG
1 AAAAAGTTAGCGATTAGTAG
87068 AGTTCAAACC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 8 0.20
30 31 0.77
31 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAAAGTTAGCGATTAGTAGTTAGTAGTTA
Found at i:87193 original size:29 final size:28
Alignment explanation
Indices: 87172--87257 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 28
87162 GTGGTCAGAG
87172 TGCAATAAAATAAACGTTAGTGGTTAATA
1 TGCAATAAAATAAA-GTTAGTGGTTAATA
*
87201 TGTAATAAAATAAATGTTAGTGGTTAATA
1 TGCAATAAAATAAA-GTTAGTGGTTAATA
*
87230 TGCAATAAAATGAAAGTTAGTAGTTAAT
1 TGCAATAAAAT-AAAGTTAGTGGTTAAT
87258 TCAAAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 49 0.94
30 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.34
Consensus pattern (28 bp):
TGCAATAAAATAAAGTTAGTGGTTAATA
Found at i:88903 original size:128 final size:128
Alignment explanation
Indices: 88724--88977 Score: 328
Period size: 128 Copynumber: 2.0 Consensus size: 128
88714 ATGTTTTTTG
* ** * * * * * *
88724 TTGAGGAAGTCTGATTGTCTGTGTATGACACTGTTCCTTCGTGTTAAGGAGATATGGTAGGTGGA
1 TTGAGGAAGTCTGATTATCTAAGTACGACACTGCTCCTTCATATTAAGGAGATATAGTAGGTAGA
* * * *
88789 CGACATTGTTCCTTCATGTTGAGGACGTCTAGCCGTATTTGGAGATAACATTGTTCCTTCGCA
66 CAAAATTGTTCCTTCATGTTGAGGACGTCTAGCCCTATTTAGAGATAACATTGTTCCTTCGCA
* * * * *
88852 TTGAGGAATTCTGATTATCTAAGTACGACACTGCTCCTTCATATTGAGGAGATCTAGTTGGTATA
1 TTGAGGAAGTCTGATTATCTAAGTACGACACTGCTCCTTCATATTAAGGAGATATAGTAGGTAGA
* *
88917 CAAAATTGTTCCTTCGTGTTGAGGATGTCTAGCCCTATTTAGAGATAACATTGTTCCTTCG
66 CAAAATTGTTCCTTCATGTTGAGGACGTCTAGCCCTATTTAGAGATAACATTGTTCCTTCG
88978 TGTTTAGTAT
Statistics
Matches: 106, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
128 106 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (128 bp):
TTGAGGAAGTCTGATTATCTAAGTACGACACTGCTCCTTCATATTAAGGAGATATAGTAGGTAGA
CAAAATTGTTCCTTCATGTTGAGGACGTCTAGCCCTATTTAGAGATAACATTGTTCCTTCGCA
Found at i:96376 original size:29 final size:29
Alignment explanation
Indices: 96321--96377 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
96311 GTTGTTAAAG
* **
96321 TGCAATAAAATAAAAGTTAGTGGTTAATA
1 TGCAATAAAACAAAAGTTAGTACTTAATA
*
96350 TGCAATAAAACGAAAGTTAGTACTTAAT
1 TGCAATAAAACAAAAGTTAGTACTTAAT
96378 TTGAAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (29 bp):
TGCAATAAAACAAAAGTTAGTACTTAATA
Found at i:96385 original size:29 final size:29
Alignment explanation
Indices: 96324--96385 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
96314 GTTAAAGTGC
* ** *
96324 AATAAAATAAAAGTTAGTGGTTAATATGC
1 AATAAAACAAAAGTTAGTACTTAATATGA
* *
96353 AATAAAACGAAAGTTAGTACTTAATTTGA
1 AATAAAACAAAAGTTAGTACTTAATATGA
96382 AATA
1 AATA
96386 TAAAATGTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.31
Consensus pattern (29 bp):
AATAAAACAAAAGTTAGTACTTAATATGA
Found at i:99464 original size:5 final size:5
Alignment explanation
Indices: 99454--99495 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
99444 AACGGTCAAC
* *
99454 GGTCG GGTCG GGTCG GGTCG GG-CC GGTC- GATCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
99496 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 6 0.19
5 26 0.81
ACGTcount: A:0.02, C:0.24, G:0.55, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:99489 original size:23 final size:24
Alignment explanation
Indices: 99461--99511 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
99451 AACGGTCGGG
*
99461 TCGGGTCGGGTCGGGCCGGTC-GA
1 TCGGGTCGGGTCGGACCGGTCAGA
*
99484 TCGGGTCGGGTCTGACCGGTCAGA
1 TCGGGTCGGGTCGGACCGGTCAGA
99508 TCGG
1 TCGG
99512 CTCAAAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.08, C:0.25, G:0.47, T:0.20
Consensus pattern (24 bp):
TCGGGTCGGGTCGGACCGGTCAGA
Found at i:108106 original size:19 final size:21
Alignment explanation
Indices: 108066--108110 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
108056 ACTTGGCAAA
*
108066 TTTTTGTTTTCTTTCTCTTTC
1 TTTTTCTTTTCTTTCTCTTTC
108087 TTTTTCTTTT-TTTC-CTTTC
1 TTTTTCTTTTCTTTCTCTTTC
108106 TTTTT
1 TTTTT
108111 TTAACCTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTTCTTTCTCTTTC
Found at i:129389 original size:20 final size:20
Alignment explanation
Indices: 129328--129398 Score: 117
Period size: 21 Copynumber: 3.5 Consensus size: 20
129318 GACCAAGAGT
*
129328 ATGTATTTTCACT-AAAATC
1 ATGTATTTTCATTAAAAATC
129347 ATGTATTTTCATTAAATAATC
1 ATGTATTTTCATTAAA-AATC
129368 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATC
129388 ATGTATTTTCA
1 ATGTATTTTCA
129399 AAGGGATTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 12 0.24
20 17 0.35
21 20 0.41
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATC
Found at i:133003 original size:714 final size:716
Alignment explanation
Indices: 131602--133025 Score: 1880
Period size: 714 Copynumber: 2.0 Consensus size: 716
131592 CTTTAAACCT
* *
131602 TTACATCTACCACCCTTAACCATTCTTTTGTGACCTTCACTTGCTGCTGATGCTTCCTTCCTTCC
1 TTACATCTACCACCCTTAACAATTCTTTTGTGACCTTCACTTGCTGCTGATGCTTCATTCCTTCC
* * * * * * * *
131667 TAGGTCTTACAATCAAGTTGTCGTTATTCTTTAAGTTCATAGAGGCATTCCCCAATATGTATCAA
66 TAGGTCTTACAATAAAGTTGTCATCATACTCTAAGTTCATAGAGGCATGCCCCAACATATATCAA
* *
131732 CTGTATTAAAGATAAACGTACTCAAGGATTTTGAGAGCAAAAAGATGCCAATCAAAGAGAAAAAA
131 CTGTATTAAAGATAAACGTACTAAAGGATTATGAGAGCAAAAAGATGCCAATCAAAGAGAAAAAA
* * *
131797 AGTGGAAAGGCTGGAAGATGATCGTGCATCTCAACAAAGAATGGGAAATCGAGGTATAAGGCCTA
196 AGTGGAAAGGCTGGAAGATGATCATGCATCTCAACAAAGAATGAGAAATCGAGGTATAAGGCCCA
* * * *
131862 AAGGTTTCGTCCACCAATGGATGATAACCTTGATAATAACAAAATTTCCATTCCACTATTCCAAG
261 AAGATTTCATCCACCAATGGATGATAACCTTGATAACAACAAAATTTCCATGCCACTATTCCAAG
* * * * * * * * *
131927 ACAAGATGGATCGCAAGGCTTACCACGTGTGGGGAAAGAAGGTTGAGCATATCTTCAGGTTCCAC
326 ACAAGACGAATCACAAGACTTACCACGAGTGCGAAAAGAAGGTTGAGCACATCTTCAGGTGCCAC
* * * * *
131992 AATTATTCTGATCTTAAGATGGTAAAACTCGTTACCATTGAGTTAACTGATTATGCACTAATATG
391 AATTATTCTGATCATAAGAAGGTAAAACTCGGTACCATTGAGTTAACAGATTATGAACTAATATG
* ** *
132057 GTAGGATCAATATACACCAAGTACGAGCTACAATGGAGAATATCCTATCACTACATGGGATGAAA
456 GTAGGATCAATATACACCAAGTACGAGCTACAATAGAGAATATAATATCACTACATAGGATGAAA
* * * * *
132122 TGAAAACGGTAATGTGAAGGCGATTTATTCCATCCCACTCCCATCGGGAGTTATTCAACTATCTT
521 TGAAAACGATAATGCGAAGGCAATTTATTCCAACCCACTACCATCGGGAGTTATTCAACTATCTT
* * * *
132187 TAAAACCTTTTACAACGTAACCAAAATGTTGAATACTACCACAAAGAGAGTGAGATGACCATGTT
586 CAAAACCTTTTACAACGTAACCAAAATGTTGAAGACTACCAAAAAAAGAGTGAGATGACCATGTT
* * *
132252 TTAGGCCAACATTGAAGAGGATCGAGAAACCACAATGGCAAGATTCCTAGCGAGACTTTTATGAT
651 CTAGGCCAACATTGAAGAGGATCAAGAAACCACAATGGCAAGATTCCTAACGAGACTTTTATGAT
132317 C
716 C
* * * * *
132318 TTACATCTCCCACCCTTAACAATT-TTTT-TGGCCTTCACTTGTTG-TCGGTGCTTCATTTCTTC
1 TTACATCTACCACCCTTAACAATTCTTTTGTGACCTTCACTTGCTGCT-GATGCTTCATTCCTTC
* * * *
132380 CTAGGTCTTACAATAAAG-TGATCATCGTACTCTGAGTTCATAGAGGCGTGCCCCAACCTATATC
65 CTAGGTCTTACAATAAAGTTG-TCATCATACTCTAAGTTCATAGAGGCATGCCCCAACATATATC
* * **
132444 AACTGTATTGAAGATGAACGTACTAAAGGATTATGAGAGCAAAAAGATGCCAATCAGGGAGAAAA
129 AACTGTATTAAAGATAAACGTACTAAAGGATTATGAGAGCAAAAAGATGCCAATCAAAGAGAAAA
* *
132509 AAAGTGGAAAGGCTGGAAGATGATCATGCATCTCAATAAAGAATGAGAAATCGAGGTGTAAGGCC
194 AAAGTGGAAAGGCTGGAAGATGATCATGCATCTCAACAAAGAATGAGAAATCGAGGTATAAGGCC
** *
132574 CAAAGATTTCATCCACCAATGGATGATAACCTTGATAACATTAAGATTTCCATGCCACTATTCCA
259 CAAAGATTTCATCCACCAATGGATGATAACCTTGATAACAACAAAATTTCCATGCCACTATTCCA
* ** * *
132639 AGACAAGACGAATTATGAGACTTACCTA-GAGTGCGAAAAGAATGTTGAGCACATCTTTAGGTGC
324 AGACAAGACGAATCACAAGACTTACC-ACGAGTGCGAAAAGAAGGTTGAGCACATCTTCAGGTGC
* ** *
132703 CACAATTATTCTTATCATAAGAAGGTAATGCTCGGTGCCATTGAGTTAACAGATTATGAACTAAT
388 CACAATTATTCTGATCATAAGAAGGTAAAACTCGGTACCATTGAGTTAACAGATTATGAACTAAT
* * * * **
132768 ATGGTATGATCAAT-TGACATCAAGTACGAGAC-ATAATAGAGAATATAATGTCACTATGTAGGA
453 ATGGTAGGATCAATAT-ACACCAAGTACGAG-CTACAATAGAGAATATAATATCACTACATAGGA
* *
132831 TGAAAT-AAAATCGATAATGCGAAGGCAATTTATTCCAACCCACTACTATCGGGAGTTATTTAAC
516 TGAAATGAAAA-CGATAATGCGAAGGCAATTTATTCCAACCCACTACCATCGGGAGTTATTCAAC
* *
132895 TATCTTCAAAACCTTTTAGAAGGTAACCAAAATGTTGAAGACTACCAAAAAAAGA-TG-GATGTG
580 TATCTTCAAAACCTTTTACAACGTAACCAAAATGTTGAAGACTACCAAAAAAAGAGTGAGA--TG
* * * *
132958 GCCATGATTCTA-GCCAACATTGACGAGGATTAAGAAGCCACAATGGCAAGATTCCTAACGAGAC
643 ACCATG-TTCTAGGCCAACATTGAAGAGGATCAAGAAACCACAATGGCAAGATTCCTAACGAGAC
133022 TTTT
707 TTTT
133026 GGTGGACTAA
Statistics
Matches: 609, Mismatches: 90, Indels: 20
0.85 0.13 0.03
Matches are distributed among these distances:
712 2 0.00
713 10 0.02
714 565 0.93
715 10 0.02
716 22 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (716 bp):
TTACATCTACCACCCTTAACAATTCTTTTGTGACCTTCACTTGCTGCTGATGCTTCATTCCTTCC
TAGGTCTTACAATAAAGTTGTCATCATACTCTAAGTTCATAGAGGCATGCCCCAACATATATCAA
CTGTATTAAAGATAAACGTACTAAAGGATTATGAGAGCAAAAAGATGCCAATCAAAGAGAAAAAA
AGTGGAAAGGCTGGAAGATGATCATGCATCTCAACAAAGAATGAGAAATCGAGGTATAAGGCCCA
AAGATTTCATCCACCAATGGATGATAACCTTGATAACAACAAAATTTCCATGCCACTATTCCAAG
ACAAGACGAATCACAAGACTTACCACGAGTGCGAAAAGAAGGTTGAGCACATCTTCAGGTGCCAC
AATTATTCTGATCATAAGAAGGTAAAACTCGGTACCATTGAGTTAACAGATTATGAACTAATATG
GTAGGATCAATATACACCAAGTACGAGCTACAATAGAGAATATAATATCACTACATAGGATGAAA
TGAAAACGATAATGCGAAGGCAATTTATTCCAACCCACTACCATCGGGAGTTATTCAACTATCTT
CAAAACCTTTTACAACGTAACCAAAATGTTGAAGACTACCAAAAAAAGAGTGAGATGACCATGTT
CTAGGCCAACATTGAAGAGGATCAAGAAACCACAATGGCAAGATTCCTAACGAGACTTTTATGAT
C
Found at i:136836 original size:17 final size:17
Alignment explanation
Indices: 136816--136860 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
136806 CTAAGTAGTC
136816 CATTTATTAAAAAAGTT
1 CATTTATTAAAAAAGTT
* * **
136833 CATTCATCAAACTAGTT
1 CATTTATTAAAAAAGTT
136850 CATTTATTAAA
1 CATTTATTAAA
136861 TTAACTCTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (17 bp):
CATTTATTAAAAAAGTT
Found at i:139959 original size:20 final size:22
Alignment explanation
Indices: 139932--139983 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
139922 CATGTTGGCT
139932 TAATGAGCTAATGA-ACA-CATG
1 TAATGAGCTAATGATA-ATCATG
139953 T-ATGAGCT-ATGATAATCATG
1 TAATGAGCTAATGATAATCATG
139973 TAATGAGCTAA
1 TAATGAGCTAA
139984 ATAAAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 8 0.30
22 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (22 bp):
TAATGAGCTAATGATAATCATG
Found at i:139987 original size:20 final size:20
Alignment explanation
Indices: 139949--139987 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
139939 CTAATGAACA
*
139949 CATGTATGAGCTATGATAAT
1 CATGTATGAGCTATAATAAT
139969 CATGTAATGAGCTA-AATAA
1 CATGT-ATGAGCTATAATAA
139988 AATAGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATGAGCTATAATAAT
Found at i:142318 original size:234 final size:233
Alignment explanation
Indices: 141909--142375 Score: 925
Period size: 234 Copynumber: 2.0 Consensus size: 233
141899 GATGTCATCT
141909 TTATTCAACCACTACAAAGCATATGGGCTGGAATGTTTGATAGTTGTAAGCCCCTTATTTTCTAC
1 TTATTCAACCACTACAAAGCATATGGGCTGGAATGTTTGATAGTTGTAAGCCCCTTATTTTCTAC
141974 CATATATGTGCTAGCAAGTTTTGCACAACTCTCCTAATCTAACATATGATGCGTCATCCATTGAT
66 CATATATGTGCTAGCAAGTTTTGCACAACTCTCCTAATCTAACATATGATGCGTCATCCATTGAT
142039 GTATCTATATGAATAAATAAACTAAAGAAATATAAGTGACGCAAGCTTTGATCAAGTAAAATCAT
131 GTATCTATATGAATAAATAAACTAAAGAAATATAAGTGACGCAAGCTTTGATCAAGTAAAA-CAT
142104 GATGTCGTGAATATACACTCACTTATAAACTAGATATGA
195 GATGTCGTGAATATACACTCACTTATAAACTAGATATGA
142143 TTATTCAACCACTACAAAGCATATGGGCTGGAATGTTTGATAGTTGTAAGCCCCTTATTTTCTAC
1 TTATTCAACCACTACAAAGCATATGGGCTGGAATGTTTGATAGTTGTAAGCCCCTTATTTTCTAC
142208 CATATATGTGCTAGCAAGTTTTGCACAACTCTCCTAATCTAACATATGATGCGTCATCCATTGAT
66 CATATATGTGCTAGCAAGTTTTGCACAACTCTCCTAATCTAACATATGATGCGTCATCCATTGAT
142273 GTATCTATATGAATAAATAAACTAAAGAAATATAAGTGACGCAAGCTTTGATCAAGTAAAACATG
131 GTATCTATATGAATAAATAAACTAAAGAAATATAAGTGACGCAAGCTTTGATCAAGTAAAACATG
142338 ATGTCGTGAATATACACTCACTTATAAACTAGATATGA
196 ATGTCGTGAATATACACTCACTTATAAACTAGATATGA
142376 ATGATGTGAG
Statistics
Matches: 233, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
233 42 0.18
234 191 0.82
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (233 bp):
TTATTCAACCACTACAAAGCATATGGGCTGGAATGTTTGATAGTTGTAAGCCCCTTATTTTCTAC
CATATATGTGCTAGCAAGTTTTGCACAACTCTCCTAATCTAACATATGATGCGTCATCCATTGAT
GTATCTATATGAATAAATAAACTAAAGAAATATAAGTGACGCAAGCTTTGATCAAGTAAAACATG
ATGTCGTGAATATACACTCACTTATAAACTAGATATGA
Found at i:143233 original size:21 final size:21
Alignment explanation
Indices: 143207--143265 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
143197 AATGTCTTTA
143207 ATCC-AAGGTTTGTGTTATGTC
1 ATCCAAAGG-TTGTGTTATGTC
143228 ATCCAAAGGTTGTGTTATGTTC
1 ATCCAAAGGTTGTGTTATG-TC
* *
143250 -TCTAAAGATTGTGTTA
1 ATCCAAAGGTTGTGTTA
143266 CTTTGAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (21 bp):
ATCCAAAGGTTGTGTTATGTC
Found at i:143879 original size:130 final size:131
Alignment explanation
Indices: 143645--143906 Score: 517
Period size: 130 Copynumber: 2.0 Consensus size: 131
143635 TTAAGTCACT
143645 GAAACTTGTACGAACTTGGATGCTCTATGGTCTTCAATTCCAACTTGTCTACCATTATTGTGCTT
1 GAAACTTGTACGAACTTGGATGCTCTATGGTCTTCAATTCCAACTTGTCTACCATTATTGTGCTT
143710 GCTACATTGGTATAGCTTCCACCATCAATAATCATTAAGCAAAGTTTGTCATGAAGCTTGCATCA
66 GCTACATTGGTATAGCTTCCACCATCAATAATCATTAAGCAAAGTTTGTCATGAAGCTTGCATCA
143775 A
131 A
143776 GAAACTTGTACGAACTT-GATGCTCTATGGTCTTCAATTCCAACTTGTCTACCATTATTGTGCTT
1 GAAACTTGTACGAACTTGGATGCTCTATGGTCTTCAATTCCAACTTGTCTACCATTATTGTGCTT
143840 GCTACATTGGTATAGCTTCCACCATCAATAATCATTAAGCAAAGTTTGTCATGAAGCTTGCATCA
66 GCTACATTGGTATAGCTTCCACCATCAATAATCATTAAGCAAAGTTTGTCATGAAGCTTGCATCA
143905 A
131 A
143906 G
1 G
143907 TATAGGATAT
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
130 114 0.87
131 17 0.13
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (131 bp):
GAAACTTGTACGAACTTGGATGCTCTATGGTCTTCAATTCCAACTTGTCTACCATTATTGTGCTT
GCTACATTGGTATAGCTTCCACCATCAATAATCATTAAGCAAAGTTTGTCATGAAGCTTGCATCA
A
Found at i:144934 original size:24 final size:24
Alignment explanation
Indices: 144902--144956 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
144892 ACACTTGATC
144902 TTCATCAACATCATGGTATTATTT
1 TTCATCAACATCATGGTATTATTT
*
144926 TTCATCAACATCATGGTATTGTTT
1 TTCATCAACATCATGGTATTATTT
144950 TTCATCA
1 TTCATCA
144957 CGCCTTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (24 bp):
TTCATCAACATCATGGTATTATTT
Found at i:147543 original size:93 final size:92
Alignment explanation
Indices: 147379--148042 Score: 579
Period size: 93 Copynumber: 7.1 Consensus size: 92
147369 GCGTGTATCA
* *
147379 TTGGATAAGTTAACCTCTTTAGTTCGTCAACATCAAAGTGTTTAGTTAAAACATTTCAATGATAT
1 TTGGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACATTT-AATGATAT
* *
147444 TCAAACTTTCATCTATTGATGTAACAAC
65 TCAAACTTTCATCCATTAATGTAACAAC
* * * * * * *
147472 TTGGATAAGTTAACTTCTTTAGTTCATAAGCATCAAAGTGGTTGGTTAAGATATTTGAATGATTT
1 TTGGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACATTT-AATGATAT
* *
147537 TTAAACTTTCATCCATTAATGTAACATC
65 TCAAACTTTCATCCATTAATGTAACAAC
* * * * *
147565 TAT-GTTAAGTTAACCTCTTTAGTCCATAAACATCAAAGTATTTAGTTAAGACATATTAA-CAGT
1 T-TGGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACAT-TTAATGA-T
* * *
147628 ATTAAAACATTCATCCATTAATGGAACAAC
63 ATTCAAACTTTCATCCATTAATGTAACAAC
* * * *
147658 TTGGATAAG-TAGACCACTTTAGTTCGTAAATATCAAAGTGTTTTA-TTAAGACATTTTAACGCT
1 TTGGATAAGTTA-ACCTCTTTAGTTCGTAAACATCAAAGTG-TTTAGTTAAGACA-TTTAATGAT
* *
147721 ATTCAAACTTTCATCCATTATTATAACAAC
63 ATTCAAACTTTCATCCATTAATGTAACAAC
* * * * * **
147751 ATGGATAAGTTAATCTATTCT-GTTTGTAAACATCAAAGTGTTTAGTTAAGACGTTTAAACACT-
1 TTGGATAAGTTAACCTCTT-TAGTTCGTAAACATCAAAGTGTTTAGTTAAGACATTTAATGA-TA
*
147814 TTCAAGCTTTCATCCATTAATGTAACAAC
64 TTCAAACTTTCATCCATTAATGTAACAAC
** * * * * * * *
147843 TTGGATAAGTTAAAATCTTTAGTCTTGTAAGCATCAAAGTGTTCAATTAAAACTTTTCAA-CATT
1 TTGGATAAGTTAACCTCTTTAGT-TCGTAAACATCAAAGTGTTTAGTTAAGACATTT-AATGA-T
** ***
147907 ATTCATTCTTTTCATCTGCTAATGTAACAAC
63 ATTCAAAC-TTTCATCCATTAATGTAACAAC
* * * * * ***
147938 TTGGATAAGATAACCACTTTAGTGCGTAAACATCAAAGTGTTTAGTTAAAATATTTCAACCTTAT
1 TTGGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACATTT-AATGATAT
* * *
148003 TCAAACTTACAT-CATCAAAGTAACAAC
65 TCAAACTTTCATCCATTAATGTAACAAC
**
148030 TCAGATAAGTTAA
1 TTGGATAAGTTAA
148043 AAGTGTTGAA
Statistics
Matches: 461, Mismatches: 92, Indels: 37
0.78 0.16 0.06
Matches are distributed among these distances:
91 1 0.00
92 76 0.16
93 291 0.63
94 54 0.12
95 39 0.08
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (92 bp):
TTGGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACATTTAATGATATT
CAAACTTTCATCCATTAATGTAACAAC
Found at i:147880 original size:279 final size:279
Alignment explanation
Indices: 147379--148015 Score: 689
Period size: 279 Copynumber: 2.3 Consensus size: 279
147369 GCGTGTATCA
* * * * *
147379 TTGGATAAGTTAACCTCTTTAGTTCGTCAACATCAAAGTGTTTAGTTAAAACATTTCAATGATAT
1 TTGGATAAGATAACCACTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAAACATTTCAACGCTAT
* * * *
147444 TCAAACTTTCATCTATTGATGTAACAACTTGGATAAGTTAACTTCTTTAGTTCATAAGCATCAAA
66 TCAAACTTTCATCCATTGATATAACAACATGGATAAGTTAAC-TCTTTAGTTCATAAACATCAAA
* * ** * * * *
147509 GTGGTTGGTTAAGATATTTGAATGATTTTTAAACTTTCATCCATTAATGTAACATCTATGTTAAG
130 GTGGTTAGTTAAGACATTTGAAACACTTTCAAACTTTCATCCATTAATGTAACAACTATGATAAG
** * * *
147574 TTAACCTCTTTAGTCCATAAACATCAAAGTATTTAGTTAAGACATATT-AACAGTATTAAAAC-A
195 TTAAAATCTTTAGTCCATAAACATCAAAGTATTCAATTAAAAC-TATTCAACAGTATTAAAACTA
*
147637 TTCATCCATTAATGGAACAAC
259 TTCATCCACTAATGGAACAAC
* * *
147658 TTGGATAAG-TAGACCACTTTAGTTCGTAAATATCAAAGTGTTTTA-TTAAGACATTTTAACGCT
1 TTGGATAAGATA-ACCACTTTAGTTCGTAAACATCAAAGTG-TTTAGTTAAAACATTTCAACGCT
* **
147721 ATTCAAACTTTCATCCATT-ATTATAACAACATGGATAAGTTAA-TCTATTCTGTTTGTAAACAT
64 ATTCAAACTTTCATCCATTGA-TATAACAACATGGATAAGTTAACTCT-TT-AGTTCATAAACAT
* * *
147784 CAAAGTGTTTAGTTAAGACGTTT-AAACACTTTCAAGCTTTCATCCATTAATGTAACAACT-TGG
126 CAAAGTGGTTAGTTAAGACATTTGAAACACTTTCAAACTTTCATCCATTAATGTAACAACTAT-G
** * * * * *
147847 ATAAGTTAAAATCTTTAGTCTTGTAAGCATCAAAGTGTTCAATTAAAACTTTTCAACATTATTCA
190 ATAAGTTAAAATCTTTAGTC-CATAAACATCAAAGTATTCAATTAAAACTATTCAACAGTATTAA
** * ** *
147912 TTCTTTTCATCTGCTAATGTAACAAC
254 AACTATTCATCCACTAATGGAACAAC
* *
147938 TTGGATAAGATAACCACTTTAGTGCGTAAACATCAAAGTGTTTAGTTAAAATATTTCAAC-CTTA
1 TTGGATAAGATAACCACTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAAACATTTCAACGC-TA
*
148002 TTCAAACTTACATC
65 TTCAAACTTTCATC
148016 ATCAAAGTAA
Statistics
Matches: 296, Mismatches: 50, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
277 4 0.01
278 57 0.19
279 150 0.51
280 83 0.28
281 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (279 bp):
TTGGATAAGATAACCACTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAAACATTTCAACGCTAT
TCAAACTTTCATCCATTGATATAACAACATGGATAAGTTAACTCTTTAGTTCATAAACATCAAAG
TGGTTAGTTAAGACATTTGAAACACTTTCAAACTTTCATCCATTAATGTAACAACTATGATAAGT
TAAAATCTTTAGTCCATAAACATCAAAGTATTCAATTAAAACTATTCAACAGTATTAAAACTATT
CATCCACTAATGGAACAAC
Found at i:147936 original size:95 final size:94
Alignment explanation
Indices: 147831--148005 Score: 239
Period size: 94 Copynumber: 1.9 Consensus size: 94
147821 TTTCATCCAT
* *
147831 TAATGTAACAACTTGGATAAGTTAA-AATCTTTAGT-CTTGTAAGCATCAAAGTGTTCAATTAAA
1 TAATGTAACAACTTGGATAAGATAACAA-CTTTAGTGC--GTAAACATCAAAGTGTTCAATTAAA
147894 ACT-TTTCAACATTATTCATTCTTTTCATCTGC
63 A-TATTTCAACATTATTCATTCTTTTCATCTGC
* * *
147926 TAATGTAACAACTTGGATAAGATAACCACTTTAGTGCGTAAACATCAAAGTGTTTAGTTAAAATA
1 TAATGTAACAACTTGGATAAGATAACAACTTTAGTGCGTAAACATCAAAGTGTTCAATTAAAATA
*
147991 TTTCAACCTTATTCA
66 TTTCAACATTATTCA
148006 AACTTACATC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
93 1 0.01
94 37 0.52
95 31 0.44
96 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (94 bp):
TAATGTAACAACTTGGATAAGATAACAACTTTAGTGCGTAAACATCAAAGTGTTCAATTAAAATA
TTTCAACATTATTCATTCTTTTCATCTGC
Found at i:148206 original size:94 final size:92
Alignment explanation
Indices: 148084--148335 Score: 285
Period size: 93 Copynumber: 2.7 Consensus size: 92
148074 ATATTTTCGA
* * * * * *
148084 ACTAAGGATGTAAACTTATCCAAGTTGTTACAGTAATTGATGGGAGTTTGATTAGCATTCAAAAT
1 ACTAAGGAGGTTAACTTAT-CAAGTTGTTACATTAATGGATGGAAGTTTGAATAGCATT-AAAAT
* *
148149 ATCTTAA-CTAAACATTTTGAT-TCTTATGG
64 ATCTTAATC-AAACACTTTGATGT-TTATAG
* * * *
148178 GCTAAGGAGGTTAACTCATGCAAGTTGTTACATTAGTGGATGGAAGTTTGAATAGCATTAAAATG
1 ACTAAGGAGGTTAACTTAT-CAAGTTGTTACATTAATGGATGGAAGTTTGAATAGCATTAAAATA
148243 TCTTAATCAAACACTTTGATGTTTATAG
65 TCTTAATCAAACACTTTGATGTTTATAG
* * *
148271 ACTACA-GAGGTTAAATTATCTAAGTGGTTACATTAATGGATGGAAGTTTGAATAGCATTGAAAT
1 ACTA-AGGAGGTTAACTTATC-AAGTTGTTACATTAATGGATGGAAGTTTGAATAGCATTAAAAT
148335 A
64 A
148336 CCTTTAACCA
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
92 1 0.01
93 81 0.60
94 52 0.39
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (92 bp):
ACTAAGGAGGTTAACTTATCAAGTTGTTACATTAATGGATGGAAGTTTGAATAGCATTAAAATAT
CTTAATCAAACACTTTGATGTTTATAG
Found at i:167093 original size:19 final size:20
Alignment explanation
Indices: 167069--167121 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
167059 TTTGGTCAAG
167069 ATCATGTATTTTCATT-AAA
1 ATCATGTATTTTCATTAAAA
167088 ATCATGTATTTTCATTAAAA
1 ATCATGTATTTTCATTAAAA
*
167108 ATCTTGTATTTTCA
1 ATCATGTATTTTCA
167122 ATGGGATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (20 bp):
ATCATGTATTTTCATTAAAA
Found at i:170246 original size:13 final size:13
Alignment explanation
Indices: 170228--170274 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
170218 GGTTTGGGGG
170228 TGTGTTGTTCATT
1 TGTGTTGTTCATT
170241 TGTGTTG-TCTATT
1 TGTGTTGTTC-ATT
170254 TGT-TT-TTCATT
1 TGTGTTGTTCATT
170265 TGTGATTGTT
1 TGTG-TTGTT
170275 TGAATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 6 0.21
12 6 0.21
13 15 0.52
14 2 0.07
ACGTcount: A:0.09, C:0.06, G:0.21, T:0.64
Consensus pattern (13 bp):
TGTGTTGTTCATT
Found at i:178979 original size:44 final size:44
Alignment explanation
Indices: 178929--179017 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
178919 ACAGAAAGTG
* *
178929 CCATAGTGCATAAAGTACTACTCCAAGTACACAAAGTACTCTTA
1 CCATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTA
*
178973 CCATAGTACACAAAGTACTACTCCAAGTACACAGAGTACTCTTA
1 CCATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTA
179017 C
1 C
179018 GAAAATGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (44 bp):
CCATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTA
Found at i:178984 original size:23 final size:21
Alignment explanation
Indices: 178940--179012 Score: 103
Period size: 21 Copynumber: 3.4 Consensus size: 21
178930 CATAGTGCAT
178940 AAAGTACTACTCCAAGTACAC
1 AAAGTACTACTCCAAGTACAC
178961 AAAGTACT-CTTACCATAGTACAC
1 AAAGTACTAC-T-CCA-AGTACAC
178984 AAAGTACTACTCCAAGTACAC
1 AAAGTACTACTCCAAGTACAC
*
179005 AGAGTACT
1 AAAGTACT
179013 CTTACGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.49
22 6 0.13
23 16 0.34
24 1 0.02
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (21 bp):
AAAGTACTACTCCAAGTACAC
Found at i:182590 original size:46 final size:46
Alignment explanation
Indices: 182531--182674 Score: 150
Period size: 45 Copynumber: 3.1 Consensus size: 46
182521 ATAATGCACC
* * *
182531 ATTATGCATTTTTACTTATAGCAACCATTCATGCCTTTTTATATACT
1 ATTATACA-TTTTATTTATAGCAACCTTTCATGCCTTTTTATATACT
* *
182578 ATTATACATTTTATTTATTGCATCCTTTCATG--TTTTT-TATACT
1 ATTATACATTTTATTTATAGCAACCTTTCATGCCTTTTTATATACT
* * * * *
182621 CCATTATACATTTCATTTATGGAAACCTTTCATGCCTTTTTATACACC
1 --ATTATACATTTTATTTATAGCAACCTTTCATGCCTTTTTATATACT
182669 ATTATA
1 ATTATA
182675 TTCTATACAT
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
43 6 0.07
44 5 0.06
45 28 0.35
46 26 0.32
47 12 0.15
48 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (46 bp):
ATTATACATTTTATTTATAGCAACCTTTCATGCCTTTTTATATACT
Found at i:182627 original size:45 final size:46
Alignment explanation
Indices: 182529--182674 Score: 154
Period size: 46 Copynumber: 3.2 Consensus size: 46
182519 TTATAATGCA
* * *
182529 CCATTATGCATTTTTACTTATAGCAACCATTCATGCCTTTTTATATACT
1 CCATTATACA-TTTTATTTATAGCAACCTTTCATG-CTTTTT-TATACT
* *
182578 --ATTATACATTTTATTTATTGCATCCTTTCATG-TTTTTTATACT
1 CCATTATACATTTTATTTATAGCAACCTTTCATGCTTTTTTATACT
* * * * *
182621 CCATTATACATTTCATTTATGGAAACCTTTCATGCCTTTTTATACA
1 CCATTATACATTTTATTTATAGCAACCTTTCATGCTTTTTTATACT
182667 CCATTATA
1 CCATTATA
182675 TTCTATACAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
43 6 0.07
44 5 0.06
45 28 0.34
46 37 0.45
47 7 0.08
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (46 bp):
CCATTATACATTTTATTTATAGCAACCTTTCATGCTTTTTTATACT
Found at i:182781 original size:68 final size:67
Alignment explanation
Indices: 182696--183373 Score: 876
Period size: 68 Copynumber: 10.0 Consensus size: 67
182686 TATTATTTCA
* * * * * *
182696 CTCAAAGGAATTTAGCCTTTCATCTAACTAGCATGATTGACACCATCCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTA
182761 GGC
65 GGC
* *
182764 CTCAAAGGCACTTAGCCTTTCATCTAAATGGCATAATTGACACCTTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTA
182829 GGC
65 GGC
* * *
182832 CTCAAAGGCACTTATCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAGTTA
182897 GGC
65 GGC
* * * *
182900 CTGAAAGGCACTTCGCCTTTCATCTAACTGATATAATTGACACCTTTCTGTCAAATGCACAGGTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAGTTA
182965 GGC
65 GGC
* * *** * *
182968 CTTAAAGGCATTTATAGTTTCATATAACTGGCATAATTGACACCTTTATGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTA
183033 GGC
65 GGC
* *
183036 GTCAAAGGCACTTAGCCTTTCATCTAAATGCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
183101 GC
66 GC
* * * *
183103 CTCAAAGGCACTTAGCCTTTCA--TATCTGGCATAATTGGCA-CTTTCCTATCAAATGCACAATT
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTT-CTGTCAAATGCACAGTT
183165 AGGC
64 AGGC
* * * *
183169 ATAAAAGGCATTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAGTTA
183234 GGC
65 GGC
* * * * *
183237 TTCAAAGGCACGTAGCCTTTCATTTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTA
183302 GGC
65 GGC
* * * *
183305 CTCAAAGGCACTTAGCCTTTCATCGAACTGGCAAAATTGACACATTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTA
183370 GGC
65 GGC
183373 C
1 C
183374 ATTAATCTTT
Statistics
Matches: 531, Mismatches: 70, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
65 7 0.01
66 49 0.09
67 60 0.11
68 409 0.77
69 6 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (67 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
GC
Found at i:183359 original size:337 final size:339
Alignment explanation
Indices: 182697--183372 Score: 982
Period size: 337 Copynumber: 2.0 Consensus size: 339
182687 ATTATTTCAC
* * *
182697 TCAAAGGAATTTAGCCTTTCATCTAACTAGCATGATTGACACCATCCTGTCAAATGCACAGCTAG
1 TCAAAGGAACTTAGCCTTTCATCTAAATAGCATAATTGACACCATCCTGTCAAATGCACAGCTAG
*
182762 GCCTCAAAGGCACTTAGCCTTTCATCTAAATGGCATAATTGACACCTTTCTGTCAAATGCACAAT
66 GCCTCAAAGGCACTTAGCCTTTCA-CTAAATGGCATAATTGACACCTTTCTATCAAATGCACAAT
* * *
182827 TAGGCCTCAAAGGCACTTATCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCAC
130 TAGGCATAAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCAC
* * * * *
182892 AGTTAGGCCTGAAAGGCACTTCGCCTTTCATCTAACTGATATAATTGACACCTTTCTGTCAAATG
195 AGTTAGGCCTCAAAGGCACGTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGCCAAATG
* * * * * * * *
182957 CACAGGTAGGCCTTAAAGGCATTTATAGTTTCATATAACTGGCATAATTGACACCTTTATGTCAA
260 CACAGCTAGGCCTCAAAGGCACTTAGACTTTCATAGAACTGGCAAAATTGACACATTTATGTCAA
*
183022 ATGCACAGTTAGGCG
325 ATGCACAATTAGGCG
* * * *
183037 TCAAAGGCACTTAGCCTTTCATCTAAAT-GCATAATTGACACCTTTCTGTCAAATGCACAGTTAG
1 TCAAAGGAACTTAGCCTTTCATCTAAATAGCATAATTGACACCATCCTGTCAAATGCACAGCTAG
** *
183101 GCCTCAAAGGCACTTAGCCTTTCA-TATCTGGCATAATTGGCA-CTTTCCTATCAAATGCACAAT
66 GCCTCAAAGGCACTTAGCCTTTCACTAAATGGCATAATTGACACCTTT-CTATCAAATGCACAAT
* *
183164 TAGGCATAAAAGGCATTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGCAC
130 TAGGCATAAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCAC
* *
183229 AGTTAGGCTTCAAAGGCACGTAGCCTTTCATTTAACT-AGCATAATTGACACCTTTCTGCCAAAT
195 AGTTAGGCCTCAAAGGCACGTAGCCTTTCATCTAACTGA-CATAATTGACACCTTTCTGCCAAAT
* * *
183293 GCACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCGAACTGGCAAAATTGACACATTTCTGTCA
259 GCACAGCTAGGCCTCAAAGGCACTTAGACTTTCATAGAACTGGCAAAATTGACACATTTATGTCA
183358 AATGCACAATTAGGC
324 AATGCACAATTAGGC
183373 CATTAATCTT
Statistics
Matches: 299, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
336 5 0.02
337 213 0.71
339 56 0.19
340 25 0.08
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (339 bp):
TCAAAGGAACTTAGCCTTTCATCTAAATAGCATAATTGACACCATCCTGTCAAATGCACAGCTAG
GCCTCAAAGGCACTTAGCCTTTCACTAAATGGCATAATTGACACCTTTCTATCAAATGCACAATT
AGGCATAAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGCACA
GTTAGGCCTCAAAGGCACGTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCTCAAAGGCACTTAGACTTTCATAGAACTGGCAAAATTGACACATTTATGTCAAA
TGCACAATTAGGCG
Found at i:183848 original size:59 final size:59
Alignment explanation
Indices: 183725--184223 Score: 772
Period size: 59 Copynumber: 8.5 Consensus size: 59
183715 TTCCCATATA
* *
183725 GAAATTCAGAAACTTAGTATGAATTTCTTATCA-TTTAGCACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
* * * *
183783 GAAATTCATACACTTACTATGAATTTCATATCATTTTAGCACACAAAGTACCCTATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
* *
183842 GAAATTCATACATTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCAAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
* *
183901 AAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAA-TGTCCCAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTG-CCCAATACG
* * * *
183960 GAAATTCATACACTTAGTATGATTTTCTTATCATATTAGCACACAAAGTGCTCTATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
*
184019 GAAATTCATACACTTGGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
* *
184078 GAAATTCATACAC--AGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCTATACA
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
* * *
184135 GAAATTCATACACTTTGTATGAATTTCTTATCAATTTAACACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
*
184194 AAAATTCATACACTTAGTATGAATTTCTTA
1 GAAATTCATACACTTAGTATGAATTTCTTA
184224 ACTTTGCATA
Statistics
Matches: 399, Mismatches: 37, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
57 54 0.14
58 31 0.08
59 312 0.78
60 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (59 bp):
GAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCAATACG
Found at i:188447 original size:45 final size:46
Alignment explanation
Indices: 188374--188490 Score: 193
Period size: 45 Copynumber: 2.6 Consensus size: 46
188364 ATGGAAACCG
* *
188374 TTCATTCCTTTTTATATC-CTATTATACATTTCATTTATGGCATCCT
1 TTCATGCCTTTTTATA-CACCATTATACATTTCATTTATGGCATCCT
188420 TTCATGCC-TTTTATACACCATTATACATTTCATTTATGGCATCCT
1 TTCATGCCTTTTTATACACCATTATACATTTCATTTATGGCATCCT
188465 TTCATGCCTTTTTATACACCATTATA
1 TTCATGCCTTTTTATACACCATTATA
188491 TTTTATACAT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
44 1 0.01
45 42 0.63
46 24 0.36
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.48
Consensus pattern (46 bp):
TTCATGCCTTTTTATACACCATTATACATTTCATTTATGGCATCCT
Found at i:188624 original size:68 final size:68
Alignment explanation
Indices: 188515--188942 Score: 401
Period size: 68 Copynumber: 6.3 Consensus size: 68
188505 TATTTTTCTT
* * * * * * * **
188515 AAAGGCATTTAACCATTCATCTAACTGGCATGAGTGACACCTTCCTATCAAATGCACACCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
188580 CTC
66 CTC
*
188583 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCATAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
188648 CTC
66 CTC
* * * * * * * * *
188651 AAAGGCATTTAGCCTTTTATCTAAGT-AACATAATTGACACCTTTATGTCAAATGCATAGTTTGA
1 AAAGGCACTTAGCCTTTCATCTAACTGGA-ATAATTGACACCTTTCTATCAAATGCACAGTTAGG
*
188715 CGTC
65 CCTC
* * * * * * * * * * * *
188719 AAAGGCACTCAACTTTTCATCTAACT-CATGTAATTCACACATTTATGTCAAATGCAAAGCTAGA
1 AAAGGCACTTAGCCTTTCATCTAACTGGA-ATAATTGACACCTTTCTATCAAATGCACAGTTAGG
*
188783 CCTT
65 CCTC
* * * * **
188787 AAAGGCACTTAGCCTTTCATCTAATTGGCATACTTGACACATTTCTGGCAAATGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
*
188852 CTG
66 CTC
* * * * *
188855 AAAGGCACCTAGCATTTCATCTAACTGGCATAATTGACACGTTTCTATCAAAGGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
188920 CTC
66 CTC
* *
188923 AAAGTCACTTTGCCTTTCAT
1 AAAGGCACTTAGCCTTTCAT
188943 TTGACACATT
Statistics
Matches: 295, Mismatches: 63, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
67 1 0.00
68 294 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (68 bp):
AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCACAGTTAGGC
CTC
Found at i:188705 original size:136 final size:135
Alignment explanation
Indices: 188515--189247 Score: 711
Period size: 136 Copynumber: 5.5 Consensus size: 135
188505 TATTTTTCTT
* * * * * * * **
188515 AAAGGCATTTAACCATTCATCTAACTGGCATGAGTGACACCTTCCTATCAAATGCACACCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAA-TGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
* * * *
188580 CTCAAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTATCAAATGCATAGTTA
65 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
188645 GGCCTC
130 GGCCTC
* * ** * * * *
188651 AAAGGCATTTAGCCTTTTATCTAAGTAACATAATTGACACCTTTATGTCAAATGCATAGTTTGAC
1 AAAGGCACTTAGCCTTTCATCTAA-TGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
* * * * * * * *
188716 GTCAAAGGCACTCAACTTTTCATCTAACT--CATGTAATTCACACATTTATGTCAAATGCAAAGC
65 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCA--TAATTGACACATTTCTGTCAAATGCACAGT
* *
188779 TAGACCTT
128 TAGGCCTC
* * *
188787 AAAGGCACTTAGCCTTTCATCTAATTGGCATACTTGACACATTTCTGGCAAATGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAA-TGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
* * * * * *
188852 CTGAAAGGCACCTAGCATTTCATCTAACTGGCATAATTGACACGTTTCTATCAAAGGCACAGTTA
65 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
188917 GGCCTC
130 GGCCTC
* * * ***
188923 AAAGTCACTTTG-C---C-T-T--T--CAT--TTGACACATTTCTGTCAAATGCACAGTTAGTTT
1 AAAGGCACTTAGCCTTTCATCTAATGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
* * * * *
188976 TCAAAGGCACTTTGCGTTTCATCTAACTGGCATAGTTGATACATTTCTGTCAAATGCACAATTAG
66 TCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAG
189041 GCCTC
131 GCCTC
* * * * * * *
189046 TAAGGCAGTTAGCCTTTTATCTAAATGGCATAGTTGACACCTTTTTGTCAAATGCATAGCTAGGC
1 AAAGGCACTTAGCCTTTCATCT-AATGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
* * * * *
189111 CTCAAAGGCACTTAGCCTTTAATCTAACTGGCATAATTGACACCTCTCTGTCAAATGCATAGCTA
65 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTA
189176 GGCCTC
130 GGCCTC
** *
189182 AAAGGCACTTAGCCTTTCATCTAACTGTTATAATTGACACCTCTCTGTCAAATGCACAGTTAGGC
1 AAAGGCACTTAGCCTTTCATCTAA-TGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
189247 C
65 C
189248 ATTAATCTTT
Statistics
Matches: 475, Mismatches: 104, Indels: 36
0.77 0.17 0.06
Matches are distributed among these distances:
123 97 0.20
124 1 0.00
125 3 0.01
127 1 0.00
128 1 0.00
129 1 0.00
130 1 0.00
131 1 0.00
132 2 0.00
134 4 0.01
135 3 0.01
136 358 0.75
138 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (135 bp):
AAAGGCACTTAGCCTTTCATCTAATGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
TCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAG
GCCTC
Found at i:188972 original size:55 final size:55
Alignment explanation
Indices: 188888--188997 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
188878 ACTGGCATAA
* *
188888 TTGACACGTTTCTATCAAAGGCACAGTTAGGCCTCAAAGTCACTTTGCCTTTCAT
1 TTGACACATTTCTATCAAAGGCACAGTTAGGCCTCAAAGGCACTTTGCCTTTCAT
* * *** *
188943 TTGACACATTTCTGTCAAATGCACAGTTAGTTTTCAAAGGCACTTTGCGTTTCAT
1 TTGACACATTTCTATCAAAGGCACAGTTAGGCCTCAAAGGCACTTTGCCTTTCAT
188998 CTAACTGGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (55 bp):
TTGACACATTTCTATCAAAGGCACAGTTAGGCCTCAAAGGCACTTTGCCTTTCAT
Found at i:189041 original size:123 final size:123
Alignment explanation
Indices: 188820--189201 Score: 332
Period size: 123 Copynumber: 3.0 Consensus size: 123
188810 ATTGGCATAC
*
188820 TTGACACATTTCTGGCAAATGCACAGTTAGGCCTGAAAGGCACCTAGCATTTCATCTAACTGGCA
1 TTGACACATTTCTGGCAAATGCACAGTTAGGCCTCAAAGGCACCTAGCATTTCATCTAACTGGCA
* *
188885 TAATTGACACGTTTCTATCAAAGGCACAGTTAGGCCTCAAAGTCACTTTGCCTTTCAT
66 TAATTGACACATTTCTATCAAAGGCACAATTAGGCCTCAAAGTCACTTTGCCTTTCAT
* *** * * *
188943 TTGACACATTTCTGTCAAATGCACAGTTAGTTTTCAAAGGCACTTTGCGTTTCATCTAACTGGCA
1 TTGACACATTTCTGGCAAATGCACAGTTAGGCCTCAAAGGCACCTAGCATTTCATCTAACTGGCA
* * * * * **
189008 TAGTTGATACATTTCTGTCAAATGCACAATTAGGCCTCTAAGGCAGTTAGCCTTTTATCTAAATG
66 TAATTGACACATTTCTATCAAAGGCACAATTAGGCCTC-AA---AGTCA--C-TTTGCCT---T-
*
189073 GCAT
120 TCAT
* * * * * * * *
189077 AGTTGACACCTTTTTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTAATCTAACTGG
1 --TTGACACATTTCTGGCAAATGCACAGTTAGGCCTCAAAGGCACCTAGCATTTCATCTAACTGG
* * * * * ** * *
189142 CATAATTGACACCTCTCTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTCAT
64 CATAATTGACACATTTCTATCAAAGGCACAATTAGGCCTCAAAGTCACTTTGCCTTTCAT
189202 CTAACTGTTA
Statistics
Matches: 205, Mismatches: 41, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
123 89 0.43
124 2 0.01
125 3 0.01
126 1 0.00
127 4 0.02
129 5 0.02
130 6 0.03
132 3 0.01
133 1 0.00
134 3 0.01
135 2 0.01
136 86 0.42
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (123 bp):
TTGACACATTTCTGGCAAATGCACAGTTAGGCCTCAAAGGCACCTAGCATTTCATCTAACTGGCA
TAATTGACACATTTCTATCAAAGGCACAATTAGGCCTCAAAGTCACTTTGCCTTTCAT
Found at i:189068 original size:68 final size:68
Alignment explanation
Indices: 188943--189247 Score: 385
Period size: 68 Copynumber: 4.5 Consensus size: 68
188933 TGCCTTTCAT
* *** * *
188943 TTGACACATTTCTGTCAAATGCACAGTTAGTTTTCAAAGGCACTTTGCGTTTCATCTAACTGGCA
1 TTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCA
*
189008 TAG
66 TAA
* * * * * * *
189011 TTGATACATTTCTGTCAAATGCACAATTAGGCCTCTAAGGCAGTTAGCCTTTTATCTAAATGGCA
1 TTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCA
*
189076 TAG
66 TAA
* * * *
189079 TTGACACCTTTTTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTAATCTAACTGGCA
1 TTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCA
189144 TAA
66 TAA
* * * **
189147 TTGACACCTCTCTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGTTA
1 TTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCA
189212 TAA
66 TAA
*
189215 TTGACACCTCTCTGTCAAATGCACAGTTAGGCC
1 TTGACACCTTTCTGTCAAATGCACAGTTAGGCC
189248 ATTAATCTTT
Statistics
Matches: 208, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 208 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (68 bp):
TTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCA
TAA
Found at i:189085 original size:191 final size:191
Alignment explanation
Indices: 188755--189247 Score: 484
Period size: 191 Copynumber: 2.5 Consensus size: 191
188745 CATGTAATTC
*
188755 ACACATTTATGTCAAATGCAAAGCTAGACCTTAAAGGCACTTAGCCTTTCATCTAATTGGCATAC
1 ACACATTTATGTCAAATGCAAAGCTAGACCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAC
* * *
188820 TTGACACATTTCTGGCAAATGCACAGTTAGGCCTGAAAGGCACCTAGCATTTCATCTAACTGGCA
66 TTGACACATTTCTGGCAAATGCACAATTAGGCCTCAAAGGCACCTAGCATTTCATCTAAATGGCA
* * * *
188885 TAATTGACACGTTTCTATCAAAGGCACAGTTAGGCCTCAAAGTCACTTTGCCTTTCATTTG
131 TAATTGACACCTTTCTATCAAAGGCACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATTTG
* * * ** * *
188946 ACACATTTCTGTCAAATGCACAGTTAG-TTTTCAAAGGCACTTTGCGTTTCATCTAACTGGCATA
1 ACACATTTATGTCAAATGCAAAGCTAGACCTT-AAAGGCACTTAGCCTTTCATCTAACTGGCATA
* * * * ** * *
189010 GTTGATACATTTCTGTCAAATGCACAATTAGGCCTCTAAGGCAGTTAGCCTTTTATCTAAATGGC
65 CTTGACACATTTCTGGCAAATGCACAATTAGGCCTCAAAGGCACCTAGCATTTCATCTAAATGGC
* * * * *
189075 ATAGTTGACACCTTTTTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTAATCTAACT
130 ATAATTGACACCTTTCTATCAAAGGCACAGCTAGGCCTCAAAGGCACTTAGCC-----T-T---T
189140 GGCATAATTG
186 --CAT--TTG
* * * * * * ** *
189150 ACACCTCTCTGTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGTTATAA
1 ACACATTTATGTCAAATGCAAAGCTAGACCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAC
* * * *
189215 TTGACACCTCTCTGTCAAATGCACAGTTAGGCC
66 TTGACACATTTCTGGCAAATGCACAATTAGGCC
189248 ATTAATCTTT
Statistics
Matches: 243, Mismatches: 44, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
190 2 0.01
191 151 0.62
196 1 0.00
197 1 0.00
200 1 0.00
202 3 0.01
204 83 0.34
205 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (191 bp):
ACACATTTATGTCAAATGCAAAGCTAGACCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAC
TTGACACATTTCTGGCAAATGCACAATTAGGCCTCAAAGGCACCTAGCATTTCATCTAAATGGCA
TAATTGACACCTTTCTATCAAAGGCACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATTTG
Found at i:189726 original size:59 final size:59
Alignment explanation
Indices: 189592--189978 Score: 559
Period size: 59 Copynumber: 6.6 Consensus size: 59
189582 CATATTTCCC
* *
189592 ATACGAAAATTCATACACATAGTATGAATTTC-TATCA-TCTAGCACACAAAGT-CCCGA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCC-A
* * * *
189649 ATATGGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
* * * *
189708 ATACGAAAATTCACACACTTAATATAAATTTCTTATTATTTTAGCACACAAAGTGCCCA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
** *
189767 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACATGAAGTGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
189826 ATAC-AGAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
1 ATACGA-AAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
* *
189885 ATACGAAAATTCATACACTTGGTATGAATTTCTTATCATTTTAGCACACGAAA-TGCCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC-AAAGTGCCCA
* *
189944 ATACGGAAATTCGTACACTTAGTATGAATTTCTTA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTA
189979 ACTTTGCACA
Statistics
Matches: 295, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
57 29 0.10
58 6 0.02
59 253 0.86
60 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (59 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACACAAAGTGCCCA
Found at i:201551 original size:20 final size:20
Alignment explanation
Indices: 201526--201565 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
201516 CATTCACAAC
201526 TGTTCCATTGTCAGATTATG
1 TGTTCCATTGTCAGATTATG
201546 TGTTCCATTGTCAGATTATG
1 TGTTCCATTGTCAGATTATG
201566 ATCTGACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
TGTTCCATTGTCAGATTATG
Found at i:212878 original size:24 final size:23
Alignment explanation
Indices: 212846--212896 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
212836 GGAATCGATA
*
212846 CCCCCTTGAAGGGGAACTGATTC
1 CCCCCTTGAAGGGGAACCGATTC
212869 CCCCCTTTGAAGGGGAACCGATTC
1 CCCCC-TTGAAGGGGAACCGATTC
212893 CCCC
1 CCCC
212897 TAGGGAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:212895 original size:23 final size:23
Alignment explanation
Indices: 212835--212897 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
212825 ATAGGGCAGA
* *
212835 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
212857 GGGAACTGATTCCCCCCTTTGAAG
1 GGGAACCGATT-CCCCCTTTGAAG
212881 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
212898 AGGGAATCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 8 0.23
23 11 0.31
24 16 0.46
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:212908 original size:18 final size:18
Alignment explanation
Indices: 212881--212915 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
212871 CCCTTTGAAG
*
212881 GGGAACCGATTCCCCCTA
1 GGGAACCGATACCCCCTA
*
212899 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
212916 GGGGTTCTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (18 bp):
GGGAACCGATACCCCCTA
Found at i:216133 original size:28 final size:28
Alignment explanation
Indices: 216093--216148 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
216083 AAGAATTGGG
216093 GTATATTCTTGAGGGAGTTGTAAGGTTA
1 GTATATTCTTGAGGGAGTTGTAAGGTTA
216121 GTATATTCTTGAGGGAGTTGTAAGGTTA
1 GTATATTCTTGAGGGAGTTGTAAGGTTA
216149 TCTCTTTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.39
Consensus pattern (28 bp):
GTATATTCTTGAGGGAGTTGTAAGGTTA
Found at i:220007 original size:2 final size:2
Alignment explanation
Indices: 219995--220058 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
219985 TAATAAAAGG
* *
219995 AT AT GAT AT AT AT -T AT AT TT AG AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220037 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
220059 CTAAATGGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:220381 original size:29 final size:29
Alignment explanation
Indices: 220307--220387 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
220297 AAATAATGGC
* *
220307 ATTGAAATGTAAAT-AATCAGAAATAAAGT
1 ATTGGAATGTAAATAAAT-AAAAATAAAGT
* *
220336 GTTGGAATATAAATAAATAAAAATAAAGT
1 ATTGGAATGTAAATAAATAAAAATAAAGT
220365 ATTGGAATGTAAATAAAGTAAAA
1 ATTGGAATGTAAATAAA-TAAAA
220388 CAAAATGCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 36 0.82
30 8 0.18
ACGTcount: A:0.57, C:0.01, G:0.15, T:0.27
Consensus pattern (29 bp):
ATTGGAATGTAAATAAATAAAAATAAAGT
Found at i:235292 original size:36 final size:36
Alignment explanation
Indices: 235251--235392 Score: 221
Period size: 36 Copynumber: 3.9 Consensus size: 36
235241 ATTTAGAAGT
* * * *
235251 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
235287 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
235323 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
235359 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
235393 AGATTGTATC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:241014 original size:36 final size:36
Alignment explanation
Indices: 240974--241099 Score: 189
Period size: 36 Copynumber: 3.5 Consensus size: 36
240964 TAATATGGGC
* * *
240974 GTGATAATGGTGGTGGAATATGGTGACGATATAGGT
1 GTGATAATGGTGATGGACTATGGTGATGATATAGGT
* * *
241010 GTGATAGTGGAGATGGACTATGGTGATGATAAAGGT
1 GTGATAATGGTGATGGACTATGGTGATGATATAGGT
*
241046 GTGATAATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATGGTGATGGACTATGGTGATGATATAGGT
241082 GTGATAATGGTGATGGAC
1 GTGATAATGGTGATGGAC
241100 AGATTGTATC
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (36 bp):
GTGATAATGGTGATGGACTATGGTGATGATATAGGT
Found at i:241726 original size:240 final size:240
Alignment explanation
Indices: 241321--241800 Score: 960
Period size: 240 Copynumber: 2.0 Consensus size: 240
241311 TAATCTCACA
241321 AAGGATTTTTAATATCAAAAGGGTTGGTTTACAAATGAATGCCAAAGCCCATTTATAGATTTGTA
1 AAGGATTTTTAATATCAAAAGGGTTGGTTTACAAATGAATGCCAAAGCCCATTTATAGATTTGTA
241386 AAGGCTTGGCCGAATAAATACATGTCTTTTCGGCAAAATACATGTCTTAAAACGAAAATAAATGA
66 AAGGCTTGGCCGAATAAATACATGTCTTTTCGGCAAAATACATGTCTTAAAACGAAAATAAATGA
241451 TGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCATAACTCTTCATCTTGGCGCCAACT
131 TGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCATAACTCTTCATCTTGGCGCCAACT
241516 TGAAGCATGATGATGTTTAGGCCGAATAGAGAGAAACCTTTTCAT
196 TGAAGCATGATGATGTTTAGGCCGAATAGAGAGAAACCTTTTCAT
241561 AAGGATTTTTAATATCAAAAGGGTTGGTTTACAAATGAATGCCAAAGCCCATTTATAGATTTGTA
1 AAGGATTTTTAATATCAAAAGGGTTGGTTTACAAATGAATGCCAAAGCCCATTTATAGATTTGTA
241626 AAGGCTTGGCCGAATAAATACATGTCTTTTCGGCAAAATACATGTCTTAAAACGAAAATAAATGA
66 AAGGCTTGGCCGAATAAATACATGTCTTTTCGGCAAAATACATGTCTTAAAACGAAAATAAATGA
241691 TGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCATAACTCTTCATCTTGGCGCCAACT
131 TGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCATAACTCTTCATCTTGGCGCCAACT
241756 TGAAGCATGATGATGTTTAGGCCGAATAGAGAGAAACCTTTTCAT
196 TGAAGCATGATGATGTTTAGGCCGAATAGAGAGAAACCTTTTCAT
241801 TTTGGCGCCT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
240 240 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (240 bp):
AAGGATTTTTAATATCAAAAGGGTTGGTTTACAAATGAATGCCAAAGCCCATTTATAGATTTGTA
AAGGCTTGGCCGAATAAATACATGTCTTTTCGGCAAAATACATGTCTTAAAACGAAAATAAATGA
TGCTTGGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCATAACTCTTCATCTTGGCGCCAACT
TGAAGCATGATGATGTTTAGGCCGAATAGAGAGAAACCTTTTCAT
Found at i:244620 original size:41 final size:42
Alignment explanation
Indices: 244561--244643 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
244551 CTATTCTTGC
244561 AAAAATATTGATTCACCTCATTCTATGATGAAATC-AATAAA
1 AAAAATATTGATTCACCTCATTCTATGATGAAATCAAATAAA
* * *
244602 AAAAATGTTGATAT-ACCTCATTCTGTGATGGAATCAAATAAA
1 AAAAATATTGAT-TCACCTCATTCTATGATGAAATCAAATAAA
244644 GTTTTGATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (42 bp):
AAAAATATTGATTCACCTCATTCTATGATGAAATCAAATAAA
Found at i:244835 original size:44 final size:44
Alignment explanation
Indices: 244755--244845 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
244745 GGTCCAGCTC
* *
244755 CTTCTATGATGGAATCGAACGAAATGACAACATTGAT-TCACCTT
1 CTTCTATGATGGAATCAAACAAAATGACAACATTGATCT-ACCTT
* *** *
244799 CTTCTGTGATGGAATCAAACAAAATGTTGACGTTGATCTACCTT
1 CTTCTATGATGGAATCAAACAAAATGACAACATTGATCTACCTT
244843 CTT
1 CTT
244846 TTGTTATAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (44 bp):
CTTCTATGATGGAATCAAACAAAATGACAACATTGATCTACCTT
Found at i:246856 original size:19 final size:17
Alignment explanation
Indices: 246832--246875 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
246822 TTTATTTCTT
246832 CTTTTTCTCTATTATTTCC
1 CTTTTTCTCTATT-TTT-C
* *
246851 CTTTTTCCCTCTTTTTC
1 CTTTTTCTCTATTTTTC
246868 CTTTTTCT
1 CTTTTTCT
246876 ATTTCTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 11 0.50
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTTTCTCTATTTTTC
Found at i:246885 original size:22 final size:21
Alignment explanation
Indices: 246863--246916 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
246853 TTTTCCCTCT
246863 TTTTCCTTTTTCTATTTCT-TC
1 TTTTCCTTTTTCT-TTTCTATC
*
246884 TTTTCTCTTTATTCTTTTCTATA
1 TTTTC-CTTT-TTCTTTTCTATC
246907 TTTTCCTTTT
1 TTTTCCTTTT
246917 CTTCAAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 6 0.21
22 13 0.45
23 10 0.34
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCCTTTTTCTTTTCTATC
Found at i:246889 original size:14 final size:13
Alignment explanation
Indices: 246870--246918 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
246860 TCTTTTTCCT
246870 TTTTCTATTTCTTC
1 TTTTCTATTT-TTC
*
246884 TTTTCTCTTTATTC
1 TTTTCTATTT-TTC
246898 TTTTCTATATTTTCC
1 TTTTCTAT-TTTT-C
246913 TTTTCT
1 TTTTCT
246919 TCAAGTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCTATTTTTC
Found at i:251150 original size:215 final size:215
Alignment explanation
Indices: 250564--251377 Score: 957
Period size: 215 Copynumber: 3.8 Consensus size: 215
250554 TTACCCAATA
* * * *
250564 GGCACTAAATGTACATTTC-CTGAAATTCATCTTATGTGGATGAATAACCGTTTCAGCACTAAGT
1 GGCACTAAGTGTACATTTCAC-GAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGT
* * * *
250628 GTGTATTTTACAGAATTTATCATATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTT-AC
65 GTGCATTTTACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCAC
** * *
250692 -GAAATTCATCCTAGGTGGATGAATAACTGTTTCGGCACTAATTGTACATTTTACGGAATTCATC
130 TG-AATTCATCCTAGGTGGATGAATAACCATTTCGGCACTAAGTGT-CATTTTACAGAATTCATC
*
250756 TTATGTGGATGAATAATCGTTTC
193 ATATGTGGATGAATAATCGTTTC
* * * * * *
250779 GACACTAAATATACATTTCACTG-AATTCATCCTAGGTGGATGAATAACCATTTCGACACTAAGC
1 GGCACTAAGTGTACATTTCAC-GAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGT
* * * *
250843 ATGCATTTCACATAATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAAGTGTGCATTTCAC
65 GTGCATTTTACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCAC
** * *
250908 AT-AATTCATTATATGTGGATGAATAACCATTTCGGCACTAAGTGTGCATTTTACAGAATTTATC
130 -TGAATTCATCCTAGGTGGATGAATAACCATTTCGGCACTAAGTGT-CATTTTACAGAATTCATC
* *
250972 ATATGTGGATGAATAACCGTTTT
193 ATATGTGGATGAATAATCGTTTC
* * * * *
250995 GGCACTAAGTGTTCATTT-AGCGAAATTCATCCTAGGT-GATAAATAACTGTTTTGGCACTAATT
1 GGCACTAAGTGTACATTTCA-CGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGT
* * * * *
251058 GTGCATTTTAC-GAAATTCATCCTATGTGGATGAATAACCGTTTCAACACTAAATATACACTTCA
65 GTGCATTTTACAG-AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCA
* * ** * *
251122 CTGAATTCCTCCTAGGTGGATGAATAACCGTTTCGGCACTAAGCATCATTTCACAGAATTCATCC
129 CTGAATTCATCCTAGGTGGATGAATAACCATTTCGGCACTAAGTGTCATTTTACAGAATTCATCA
251187 TATGTGGATGAATAATCGTTTC
194 TATGTGGATGAATAATCGTTTC
* *
251209 GGCACTAAGTGTACATTTCAC-AGAATTCATTCT-GTGTGGATGAATAACCGTTTTGGCACTAAG
1 GGCACTAAGTGTACATTTCACGA-AATTCATCCTAG-GTGGATGAATAACCGTTTCGGCACTAAG
* * *
251272 TGTGCATTTTATAGAATTTATCCTATGTGGATGAATAATCGTTT-AGGCACTAAGTGTGCATTTC
64 TGTGCATTTTACAGAATTCATCCTATGTGGATGAATAACCGTTTCA-GCACTAAGTGTGCATTTC
* * * * *
251336 ACAGAATTTATCCCAGGTGGATGAATAACAATTTCGACACTA
128 ACTGAATTCATCCTAGGTGGATGAATAACCATTTCGGCACTA
251378 GGCGTGCAAA
Statistics
Matches: 505, Mismatches: 80, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
213 2 0.00
214 67 0.13
215 328 0.65
216 108 0.21
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (215 bp):
GGCACTAAGTGTACATTTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTG
TGCATTTTACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACT
GAATTCATCCTAGGTGGATGAATAACCATTTCGGCACTAAGTGTCATTTTACAGAATTCATCATA
TGTGGATGAATAATCGTTTC
Found at i:251385 original size:54 final size:54
Alignment explanation
Indices: 250564--251364 Score: 880
Period size: 54 Copynumber: 14.9 Consensus size: 54
250554 TTACCCAATA
* * * *
250564 GGCACTAAATGTACATTTC-CTGAAATTCATCTTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
250618 AGCACTAAGTGTGTATTTTACAGAATTTATCATATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
250672 GGCACTAAGTGTGCATTT-AC-GAAATTCATCCTAGGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
250725 GGCACTAATTGTACATTTTACGGAATTCATCTTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * * *
250779 GACACTAAATATACATTTCACTGAATTCATCCTAGGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* ** * *
250833 GACACTAAGCATGCATTTCACATAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** *
250887 AGCACTAAGTGTGCATTTCACATAATTCATTATATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
250941 GGCACTAAGTGTGCATTTTACAGAATTTATCATATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
250995 GGCACTAAGTGTTCATTT-AGC-GAAATTCATCCTAGGT-GATAAATAACTGTTTT
1 GGCACTAAGTGTGCATTTCA-CAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* *
251048 GGCACTAATTGTGCATTTTAC-GAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
** * * * * * * *
251102 AACACTAAATATACACTTCACTGAATTCCTCCTAGGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
** *
251156 GGCACTAAGCAT-CATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
251209 GGCACTAAGTGTACATTTCACAGAATTCATTCTGTGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
251263 GGCACTAAGTGTGCATTTTATAGAATTTATCCTATGTGGATGAATAATCGTTTA
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
251317 GGCACTAAGTGTGCATTTCACAGAATTTATCCCAGGTGGATGAATAAC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAAC
251365 AATTTCGACA
Statistics
Matches: 636, Mismatches: 101, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.00
53 139 0.22
54 492 0.77
55 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:251470 original size:430 final size:429
Alignment explanation
Indices: 250619--251470 Score: 1005
Period size: 430 Copynumber: 2.0 Consensus size: 429
250609 AACCGTTTCA
* * ** * *
250619 GCACTAAGTGTGTATTTTACAGAATTTATCATATGTGGATGAATAACCGTTTCGGCACTAAGTGT
1 GCACTAAGTGTGCATTTTACAGAATTCATCATATGTGGATGAATAACCGTTTCAACACTAAATAT
* * * * * *
250684 GCATTTACGAAATTCATCCTAGGTGGATGAATAACTGTTTCGGCACTAATTGTACATTTTACGGA
66 ACATTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAA-TGCACATTTCACAGA
* *
250749 ATTCATCTTATGTGGATGAATAATCGTTTCGACACTAAATATACATTTCACTGAATTCATCCTAG
130 ATTCATCCTATGTGGATGAATAATCGTTTCGACACTAAATATACATTTCACAGAATTCATCCTAG
*
250814 GTGGATGAATAACCATTTCGACACTAAGCATGCATTTCACATAATTCATCCTATGTGGATGAATA
195 GTGGATGAATAACCATTTCGACACTAAGCATGCATTTCACAGAATTCATCCTATGTGGATGAATA
* * * * * *
250879 ATCGTTTCAGCACTAAGTGTGCATTTCACATAATTCATTATATGTGGATGAATAACCATTTCGGC
260 ATCGTTTCAGCACTAAGTGTGCATTTCACAGAATTCATCACAGGTGGATGAATAACAATTTCGAC
* **** * * *** * *
250944 ACTAAGTGTGCATTTTACAGAATTTATCATATGTGGATGAATAACCGTTTTGGCACTAAGTGTTC
325 ACTAAGCGTGCAAACCACAGAATTTATAATATGTGGATGAAAAACCGAAATGGCACTAAGAGTGC
** ** *
251009 ATTTAGCGAAATTCATCCTAGGTGATAAATAACTGTTTTG
390 ATTTAAAGAAATTCATAATAGCTGATAAATAACTGTTTTG
* *
251049 GCACTAATTGTGCATTTTAC-GAAATTCATCCTATGTGGATGAATAACCGTTTCAACACTAAATA
1 GCACTAAGTGTGCATTTTACAG-AATTCATCATATGTGGATGAATAACCGTTTCAACACTAAATA
*
251113 TACACTTCACTG-AATTCCTCCTAGGTGGATGAATAACCGTTTCGGCACTAA-GCATCATTTCAC
65 TACA-TTCAC-GAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAATGCA-CATTTCAC
* * * *
251176 AGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTACATTTCACAGAATTCATTC
127 AGAATTCATCCTATGTGGATGAATAATCGTTTCGACACTAAATATACATTTCACAGAATTCATCC
* * * ** * * *
251241 T-GTGTGGATGAATAACCGTTTTGGCACTAAGTGTGCATTTTATAGAATTTATCCTATGTGGATG
192 TAG-GTGGATGAATAACCATTTCGACACTAAGCATGCATTTCACAGAATTCATCCTATGTGGATG
* *
251305 AATAATCGTTT-AGGCACTAAGTGTGCATTTCACAGAATTTATCCCAGGTGGATGAATAACAATT
256 AATAATCGTTTCA-GCACTAAGTGTGCATTTCACAGAATTCATCACAGGTGGATGAATAACAATT
* * * ** * *
251369 TCGACACTAGGCGTGCAAACCATAGAATTTGTAATATGTTTATGAAAAATCGAAATGGCACTACG
320 TCGACACTAAGCGTGCAAACCACAGAATTTATAATATGTGGATGAAAAACCGAAATGGCACTAAG
* * *
251434 AGTGCATTGTAAAGAAA-TGATAATATCTGGTAAATAA
385 AGTGCATT-TAAAGAAATTCATAATAGCTGATAAATAA
251471 TGAATTGGTA
Statistics
Matches: 350, Mismatches: 65, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
429 5 0.01
430 297 0.85
431 47 0.13
432 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (429 bp):
GCACTAAGTGTGCATTTTACAGAATTCATCATATGTGGATGAATAACCGTTTCAACACTAAATAT
ACATTCACGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAATGCACATTTCACAGAA
TTCATCCTATGTGGATGAATAATCGTTTCGACACTAAATATACATTTCACAGAATTCATCCTAGG
TGGATGAATAACCATTTCGACACTAAGCATGCATTTCACAGAATTCATCCTATGTGGATGAATAA
TCGTTTCAGCACTAAGTGTGCATTTCACAGAATTCATCACAGGTGGATGAATAACAATTTCGACA
CTAAGCGTGCAAACCACAGAATTTATAATATGTGGATGAAAAACCGAAATGGCACTAAGAGTGCA
TTTAAAGAAATTCATAATAGCTGATAAATAACTGTTTTG
Found at i:256415 original size:4 final size:4
Alignment explanation
Indices: 256406--256432 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
256396 ATAAAATAAC
256406 ACAA ACAA ACAA ACAA ACAA ACAA ACA
1 ACAA ACAA ACAA ACAA ACAA ACAA ACA
256433 TGATTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:256506 original size:2 final size:2
Alignment explanation
Indices: 256501--256542 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
256491 ATATTCTGTT
256501 TA TA TA TA TA TA 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 TA TA TA TA TA TA
256543 AAGAAAACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:256961 original size:29 final size:28
Alignment explanation
Indices: 256901--256973 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
256891 AAATAATCGG
* *
256901 AAATAAAGTG-TTAAAGTTAATAAAGAA
1 AAATAAAGTGCTAAAAGTAAATAAAGAA
*
256928 AAATAAAGTGCTAAAACGTAAATAAAGTA
1 AAATAAAGTGCTAAAA-GTAAATAAAGAA
*
256957 AAATAAAATGCTGAAAA
1 AAATAAAGTGCT-AAAA
256974 ATGAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 10 0.26
28 4 0.10
29 21 0.54
30 4 0.10
ACGTcount: A:0.60, C:0.04, G:0.14, T:0.22
Consensus pattern (28 bp):
AAATAAAGTGCTAAAAGTAAATAAAGAA
Found at i:260366 original size:79 final size:78
Alignment explanation
Indices: 260237--260468 Score: 306
Period size: 79 Copynumber: 3.0 Consensus size: 78
260227 TTATGTTGAT
* * ** * *
260237 AATGTACCCATATGCATTTCAACTTTGGCATCCTTT-TTGCCAATAATGCACCCACATGCATTAT
1 AATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
*
260301 TCTTTTATTCTGAT
66 TCTTTTATTC-GAC
* * * * *
260315 AATTCACCCCTATGTATTTTAGCTAAGGCA-CACTTTCATGCCAATAATGCACCCATATACATTA
1 AATGCACCCATATGCATTTCAGCTAAGGCATC-CTTTCATGCCAATAATGCACCCATATGCATTA
260379 TTCTTTTATGTCGAC
65 TTCTTTTAT-TCGAC
*
260394 AATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATACACCCATATGCATTAT
1 AATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
260459 TCTTTTATTC
66 TCTTTTATTC
260469 ATTTGTTCTA
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 28 0.21
79 100 0.76
80 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (78 bp):
AATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
TCTTTTATTCGAC
Found at i:267137 original size:46 final size:46
Alignment explanation
Indices: 267055--267150 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
267045 ATTATTCCTT
* * *
267055 ATTTTCATTTATAACATCCATTCACGTTTATCATGCA-CCATTATGC
1 ATTTTCAATTATAACATCCATTCACGTTGATAATGCACCCA-TATGC
* * * *
267101 ATTTTCAATTATAACATGCTTTTATGTTGATAATGCACCCATATGC
1 ATTTTCAATTATAACATCCATTCACGTTGATAATGCACCCATATGC
267147 ATTT
1 ATTT
267151 CAACTTTGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 39 0.93
47 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (46 bp):
ATTTTCAATTATAACATCCATTCACGTTGATAATGCACCCATATGC
Found at i:267287 original size:34 final size:34
Alignment explanation
Indices: 267244--267472 Score: 172
Period size: 34 Copynumber: 6.1 Consensus size: 34
267234 TAAGGCATCA
267244 TTTCATGCCAATAATGCACCCATATGCATTATTC
1 TTTCATGCCAATAATGCACCCATATGCATTATTC
* *
267278 TTTCATGCCAATAATGCTCCCACATGCATTATTC
1 TTTCATGCCAATAATGCACCCATATGCATTATTC
* *
267312 TTTTATACCAATAAAT-CACCCATATGCATTTTAGCTAAGGCATCC
1 TTTCATGCCAAT-AATGCACCCATATGCA--TTA--T------T-C
267357 TTTCATGCCAATAATGCACCCATATGCATTATTC
1 TTTCATGCCAATAATGCACCCATATGCATTATTC
* * * *
267391 TTTTATGTCGATAAAGCACCCATATGCATTTCAGCTAAGGCATC
1 TTTCATGCCAATAATGCACCCATATGCA-TT-A--T------TC
267435 ATTTCATGCCAATAATGCACCCATATGCATTATTC
1 -TTTCATGCCAATAATGCACCCATATGCATTATTC
267470 TTT
1 TTT
267473 TATTCATGCG
Statistics
Matches: 155, Mismatches: 16, Indels: 48
0.71 0.07 0.22
Matches are distributed among these distances:
34 80 0.52
35 8 0.05
36 4 0.03
38 2 0.01
41 2 0.01
43 4 0.03
44 8 0.05
45 47 0.30
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (34 bp):
TTTCATGCCAATAATGCACCCATATGCATTATTC
Found at i:267293 original size:79 final size:79
Alignment explanation
Indices: 267130--267299 Score: 232
Period size: 79 Copynumber: 2.2 Consensus size: 79
267120 TTTTATGTTG
* ** * * *
267130 ATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGTAGCCATATGCATT
1 ATAATGCACCCATATGAATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATT
* * *
267195 TTTCTTTTATGCCG
66 ATTCTTTCATGCCA
* *
267209 GTAATGCACCCGTATGAATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGCACCCATATGAATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATT
267274 ATTCTTTCATGCCA
66 ATTCTTTCATGCCA
*
267288 ATAATGCTCCCA
1 ATAATGCACCCA
267300 CATGCATTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
ATAATGCACCCATATGAATTTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATT
ATTCTTTCATGCCA
Found at i:267362 original size:113 final size:113
Alignment explanation
Indices: 267164--267420 Score: 338
Period size: 113 Copynumber: 2.3 Consensus size: 113
267154 CTTTGGCATC
* * * ** *
267164 CTTTCATGCCAATAATG-TAGCCATATGCATTTTTCTTTTATGCCGGTAATGCACCCGTATGAAT
1 CTTTCATGCCAATAATGCT-CCCATATGCATTATTCTTTTATACCAATAATGCACCCATATGAAT
267228 TTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATT
65 TTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATT
* *
267277 CTTTCATGCCAATAATGCTCCCACATGCATTATTCTTTTATACCAATAAAT-CACCCATATGCAT
1 CTTTCATGCCAATAATGCTCCCATATGCATTATTCTTTTATACCAAT-AATGCACCCATATGAAT
* * *
267341 TTTAGCTAAGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
65 TTCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATT
* * * * *
267390 CTTTTATGTCGATAAAGCACCCATATGCATT
1 CTTTCATGCCAATAATGCTCCCATATGCATT
267421 TCAGCTAAGG
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
113 121 0.97
114 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (113 bp):
CTTTCATGCCAATAATGCTCCCATATGCATTATTCTTTTATACCAATAATGCACCCATATGAATT
TCAACTAAGGCATCATTTCATGCCAATAATGCACCCATATGCATTATT
Found at i:267372 original size:79 final size:79
Alignment explanation
Indices: 267277--267475 Score: 326
Period size: 79 Copynumber: 2.5 Consensus size: 79
267267 ATGCATTATT
* * *
267277 CTTTCATGCCAATAATGCTCCCACATGCATTATTCTTTTATACCAATAAATCACCCATATGCATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATACCAATAAAGCACCCATATGCATT
*
267342 TTAGCTAAGGCATC
66 TCAGCTAAGGCATC
** *
267356 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGTCGATAAAGCACCCATATGCATT
1 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATACCAATAAAGCACCCATATGCATT
267421 TCAGCTAAGGCATC
66 TCAGCTAAGGCATC
*
267435 ATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
1 CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
267476 TCATGCGTTC
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 112 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
CTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATACCAATAAAGCACCCATATGCATT
TCAGCTAAGGCATC
Found at i:269457 original size:13 final size:14
Alignment explanation
Indices: 269426--269460 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
269416 TTTCATTCAG
269426 AAATAATATGAAGT
1 AAATAATATGAAGT
*
269440 AAATAATAT-AATT
1 AAATAATATGAAGT
269453 AAATAATA
1 AAATAATA
269461 CTTTATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (14 bp):
AAATAATATGAAGT
Found at i:273134 original size:25 final size:25
Alignment explanation
Indices: 273106--273160 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
273096 CTGTATCTTG
*
273106 TGCAACCCAAGTCACAAAGGGCTTA
1 TGCAACCCAAGTCACAAAAGGCTTA
*
273131 TGCAACCCAAGTCACAAAAGGCTTG
1 TGCAACCCAAGTCACAAAAGGCTTA
273156 TGCAA
1 TGCAA
273161 ATATATGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.16
Consensus pattern (25 bp):
TGCAACCCAAGTCACAAAAGGCTTA
Found at i:276044 original size:24 final size:21
Alignment explanation
Indices: 276006--276051 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
275996 ATTGGCACAT
*
276006 TCTTTTGAATTTCAAGAGGTACA
1 TCTTTTGAATGTCAA-AGG-ACA
276029 TCTTTTGAAATGTCAAAGGACA
1 TCTTTTG-AATGTCAAAGGACA
276051 T
1 T
276052 GTCTTGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (21 bp):
TCTTTTGAATGTCAAAGGACA
Found at i:277375 original size:15 final size:15
Alignment explanation
Indices: 277340--277368 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
277330 GTGCTTCAAC
277340 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
277354 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
277369 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:284020 original size:9 final size:9
Alignment explanation
Indices: 284006--284032 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
283996 TTCTTTTTCT
284006 TTTTGTTGC
1 TTTTGTTGC
284015 TTTTGTTGC
1 TTTTGTTGC
284024 TTTTGTTGC
1 TTTTGTTGC
284033 AGAACTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (9 bp):
TTTTGTTGC
Found at i:284501 original size:36 final size:35
Alignment explanation
Indices: 284407--284517 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 35
284397 TTGGTGGTTA
* * * * * *
284407 TATAGGCGTGAAATAGTGATAGAAGATGGTAATGA
1 TATAGGCGTAAAATGGTAATGGAAGATGGTGATGT
**
284442 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTAAAATGGTAATGGAAGATGGTGATGT
**
284477 TATAGGCGTTAAAATGGTGGTGGAAGATGGTGATGT
1 TATAGGCG-TAAAATGGTAATGGAAGATGGTGATGT
284513 T-TAGG
1 TATAGG
284518 TAGTATCTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 41 0.63
36 24 0.37
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TATAGGCGTAAAATGGTAATGGAAGATGGTGATGT
Done.