Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005010.1 Hibiscus syriacus cultivar Beakdansim tig00011247_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: 82825
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1298 original size:21 final size:21
Alignment explanation
Indices: 1251--1369 Score: 114
Period size: 21 Copynumber: 5.7 Consensus size: 21
1241 CCCGATGCTT
** *
1251 TCATCGTTCAAGAGGTGCTTC
1 TCATCGTTCAAGAGGCCCCTC
1272 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
*
1293 TCATCGTTCAAGATGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * * *
1314 CCACCGTTTAAGAGGCTCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
1335 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
1356 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
1370 CCCGATTCAC
Statistics
Matches: 78, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 76 0.97
22 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1298 original size:42 final size:42
Alignment explanation
Indices: 1251--1369 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
1241 CCCGATGCTT
* * * *
1251 TCATCGTTCAAGAGGTGCTTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTC
* * * * *
1293 TCATCGTTCAAGATGCCCCTCCCACCGTTTAAGAGGCTCCTG
1 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTC
1335 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1370 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.26
Consensus pattern (42 bp):
TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:4804 original size:14 final size:15
Alignment explanation
Indices: 4768--4805 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4758 GAAATCATTG
4768 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
4783 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
4798 AAAAATTA
1 AAAAATTA
4806 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:5027 original size:21 final size:20
Alignment explanation
Indices: 4961--5062 Score: 100
Period size: 20 Copynumber: 5.0 Consensus size: 20
4951 AACTAAAACC
*
4961 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
4980 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
5000 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
* *
5021 TGTTGCGAATTTG-ACTTCTT
1 TGTTGCGAATTTGAAATTC-G
*
5041 TGTTGCGAATTTAGAAAATCG
1 TGTTGCGAATTT-GAAATTCG
5062 T
1 T
5063 AATGTGATTC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 10 0.15
20 38 0.58
21 15 0.23
22 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:5546 original size:170 final size:170
Alignment explanation
Indices: 5217--5558 Score: 571
Period size: 170 Copynumber: 2.0 Consensus size: 170
5207 TTTTCTCTAT
*
5217 TTACATTTACGTTTTGGTCTCTGCTCGTTTAGATACTATTTTGATTAGTTACATAGGATGTTTGG
1 TTACATTTACGTTTTGGTATCTGCTCGTTTAGATACTATTTTGATTAGTTACATAGGATGTTTGG
*
5282 TTTATTTCCATGTTTGGTCACTATTCCTTTACTATGTTATCGATTTAGTCTCTATTTTGAATGGT
66 TTTATTTCCATGTTTGGTCACTATTCCTTTACTATGTTATCGATTTAGTCTCTATTTCGAATGGT
* *
5347 TTATATATTTTTTAGTCCCCATTTTTTTCTGACTATATTA
131 TAATATATATTTTAGTCCCCATTTTTTTCTGACTATATTA
* *
5387 TTACATTTATGTTTTGGTATTTGCTCGTTTAGATACTATTTTGATTAGTTACATAGGATGTTTGG
1 TTACATTTACGTTTTGGTATCTGCTCGTTTAGATACTATTTTGATTAGTTACATAGGATGTTTGG
* *
5452 TTTATTT-CAT-TCTTGGTCCCTATTCCTTTACTATGTTATTGATTTAGTCTCTATTTCGAATGG
66 TTTATTTCCATGT-TTGGTCACTATTCCTTTACTATGTTATCGATTTAGTCTCTATTTCGAATGG
*
5515 TTAATATATATTTTAGTCCCCATTATTTTTCTTACTATATTA
130 TTAATATATATTTTAGTCCCCATT-TTTTTCTGACTATATTA
5557 TT
1 TT
5559 TTAATCTCCG
Statistics
Matches: 161, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
168 1 0.01
169 73 0.45
170 87 0.54
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (170 bp):
TTACATTTACGTTTTGGTATCTGCTCGTTTAGATACTATTTTGATTAGTTACATAGGATGTTTGG
TTTATTTCCATGTTTGGTCACTATTCCTTTACTATGTTATCGATTTAGTCTCTATTTCGAATGGT
TAATATATATTTTAGTCCCCATTTTTTTCTGACTATATTA
Found at i:5912 original size:17 final size:18
Alignment explanation
Indices: 5890--5926 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5880 GCAATTGTAC
5890 TTTTAAT-AATAAAATTA
1 TTTTAATAAATAAAATTA
5907 TTTTAATAAAATAAAATTA
1 TTTTAAT-AAATAAAATTA
5926 T
1 T
5927 ATTCTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAATAAATAAAATTA
Found at i:7732 original size:51 final size:51
Alignment explanation
Indices: 7664--7799 Score: 141
Period size: 51 Copynumber: 2.7 Consensus size: 51
7654 TACCCGTAGC
* * ** **
7664 AGTAAAGCGCGCTCCCTGCCCCGCGCTATATGCTGATTTGGCGT-CACGTGG
1 AGTATAGCGCGCACCCTGAACCGCGCTATA-GCTGACATGGCGTACACGTGG
* * *
7715 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACATGGCTTACACGTGG
1 AGTATAGCGCGCACCCTGAACCGCGCTATA-GCTGACATGGCGTACACGTGG
* *
7767 -GTATAGCGCGGACCCTGATCCGCGCTATAGCTG
1 AGTATAGCGCGCACCCTGAACCGCGCTATAGCTG
7800 TCCGCGCTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
50 4 0.06
51 61 0.85
52 7 0.10
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.22
Consensus pattern (51 bp):
AGTATAGCGCGCACCCTGAACCGCGCTATAGCTGACATGGCGTACACGTGG
Found at i:7805 original size:15 final size:15
Alignment explanation
Indices: 7785--7815 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7775 CGGACCCTGA
7785 TCCGCGCTATAGCTG
1 TCCGCGCTATAGCTG
7800 TCCGCGCTATAGCTG
1 TCCGCGCTATAGCTG
7815 T
1 T
7816 TTATCTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (15 bp):
TCCGCGCTATAGCTG
Found at i:8030 original size:17 final size:18
Alignment explanation
Indices: 7994--8034 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
7984 ATATTATGTA
*
7994 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
8012 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
8029 TTTACT
1 TTTACT
8035 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:9706 original size:18 final size:18
Alignment explanation
Indices: 9683--9717 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9673 CAGCAGCCAC
*
9683 CGCAGCCATTTATGATGT
1 CGCAGCCATATATGATGT
9701 CGCAGCCATATATGATG
1 CGCAGCCATATATGATG
9718 CCGCCGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CGCAGCCATATATGATGT
Found at i:10286 original size:26 final size:24
Alignment explanation
Indices: 10215--10286 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
10205 TTATATTTGT
10215 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
10240 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
10262 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
10287 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:13697 original size:12 final size:12
Alignment explanation
Indices: 13677--13709 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
13667 AATAAGTATA
*
13677 ATAAAAAAATTT
1 ATAACAAAATTT
13689 ATAACAAAATTT
1 ATAACAAAATTT
13701 ATAACAAAA
1 ATAACAAAA
13710 AATCGCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAACAAAATTT
Found at i:21312 original size:72 final size:73
Alignment explanation
Indices: 21180--21320 Score: 239
Period size: 72 Copynumber: 1.9 Consensus size: 73
21170 AGAAAGGAAT
*
21180 TGAAGTTGCTAAGGATGACAATAACTAGTTTTTTCCTATAGATTCTAAAATGGTGTTTTCAGATT
1 TGAAGTTGCTAAGGATGACAATAACTAGTTTTTTCCCATAGATTCTAAAATGGTGTTTTCAGATT
21245 CTTCCAAG
66 CTTCCAAG
* * *
21253 TGAAGTTGCTAAGGATGGCAATATCTAG-TTTTTCCCATAGATTCTAAAATGGTGTTTTCATATT
1 TGAAGTTGCTAAGGATGACAATAACTAGTTTTTTCCCATAGATTCTAAAATGGTGTTTTCAGATT
21317 CTTC
66 CTTC
21321 TTACGGGACA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 38 0.59
73 26 0.41
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (73 bp):
TGAAGTTGCTAAGGATGACAATAACTAGTTTTTTCCCATAGATTCTAAAATGGTGTTTTCAGATT
CTTCCAAG
Found at i:23714 original size:2 final size:2
Alignment explanation
Indices: 23625--23704 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
23615 TCCCTACTTA
23625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23705 TAAGTATATA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23877 original size:16 final size:17
Alignment explanation
Indices: 23856--23895 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
23846 TGAACCAAAT
23856 ATTTATTATAAAT-ACG
1 ATTTATTATAAATAACG
*
23872 ATTTA-TATAAATAACT
1 ATTTATTATAAATAACG
23888 ATTTATTA
1 ATTTATTA
23896 AAAAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTATTATAAATAACG
Found at i:25118 original size:21 final size:20
Alignment explanation
Indices: 25093--25190 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
25083 AATCAGTTTC
25093 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
25114 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
25134 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
25154 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
25175 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
25191 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:25143 original size:41 final size:41
Alignment explanation
Indices: 25093--25190 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
25083 AATCAGTTTC
* *
25093 CAAAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGATT-TTCCAAAATCGCAACGCGAATA-T
* **
25134 CAAATTCGCATTGCGATTTTCCAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTTCCAAAATCGCAACGCGAATAT
*
25175 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
25191 ACACATAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 41 0.89
42 3 0.07
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGATTTTCCAAAATCGCAACGCGAATAT
Found at i:25200 original size:20 final size:20
Alignment explanation
Indices: 25177--25347 Score: 112
Period size: 20 Copynumber: 8.5 Consensus size: 20
25167 GCGAATATGA
25177 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
25197 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
25217 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
25237 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
25257 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
25277 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
25297 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
25317 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
25338 AAATCGCAAC
1 AAATCGCAAC
25348 ACGATATTTA
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 104 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:25221 original size:40 final size:40
Alignment explanation
Indices: 25157--25347 Score: 188
Period size: 40 Copynumber: 4.8 Consensus size: 40
25147 CGATTTTCCA
* ** *
25157 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CAT
* * * *
25197 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
** * * *
25237 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
* * * *
25277 ATATCGCAACGCGTATCGGTAAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCAT
25317 AAAATCGCAACGCGTATCCGTAAATCGCAAC
1 -AAATCGCAACGCGTATCCGTAAATCGCAAC
25348 ACGATATTTA
Statistics
Matches: 126, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 94 0.75
41 30 0.24
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCAT
Found at i:25242 original size:60 final size:60
Alignment explanation
Indices: 25157--25347 Score: 238
Period size: 60 Copynumber: 3.2 Consensus size: 60
25147 CGATTTTCCA
* ** * *
25157 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
25217 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
25277 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
25338 AAATCGCAAC
1 AAATCGCAAC
25348 ACGATATTTA
Statistics
Matches: 109, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.74
61 28 0.26
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:25772 original size:33 final size:33
Alignment explanation
Indices: 25733--25803 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
25723 TTCACTTAGA
25733 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
25766 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
25799 TTTCA
1 TTTCA
25804 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:25940 original size:19 final size:20
Alignment explanation
Indices: 25883--25957 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
25873 TGCAGAAGAG
* *
25883 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
25904 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
25924 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
25943 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
25958 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:25960 original size:14 final size:14
Alignment explanation
Indices: 25941--25997 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
25931 GCGAAATGAC
25941 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
25955 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
25974 AATCGCAACGAGAG
1 AATCGCAACGAGAG
25988 AATCGCAACG
1 AATCGCAACG
25998 GGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:25966 original size:33 final size:33
Alignment explanation
Indices: 25895--26002 Score: 144
Period size: 33 Copynumber: 3.1 Consensus size: 33
25885 GCAACGAGAT
25895 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
*
25934 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
25967 AAATGAAAATCGCAACGAGAGAATCGCAACGGG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
26000 AAA
1 AAA
26003 CCAAATCGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
33 44 0.67
36 1 0.02
38 1 0.02
39 20 0.30
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:25979 original size:19 final size:19
Alignment explanation
Indices: 25895--25983 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
25885 GCAACGAGAT
*
25895 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
***
25914 AGAATGACTGTCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
25934 AAATGACAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
25951 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
25967 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
25984 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 25 0.45
20 15 0.27
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:26049 original size:14 final size:14
Alignment explanation
Indices: 26030--26118 Score: 70
Period size: 14 Copynumber: 5.7 Consensus size: 14
26020 TTTTATTTCG
26030 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26044 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
*
26062 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
26076 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
26095 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26109 CGTTGCGATT
1 CGTTGCGATT
26119 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
14 29 0.48
15 4 0.07
16 2 0.03
17 5 0.08
18 10 0.17
19 10 0.17
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26096 original size:33 final size:33
Alignment explanation
Indices: 26013--26126 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
26003 CCAAATCGCA
*
26013 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
26046 TTGCGA-TTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
26078 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
26111 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
26127 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
32 30 0.40
33 45 0.60
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:26100 original size:19 final size:18
Alignment explanation
Indices: 26008--26104 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
25998 GGAAACCAAA
* *
26008 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGA-TTTCATT
26027 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
26041 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
26059 TCGCGTTACGA-TTC---
1 TCGCGTTGCGATTTCATT
*
26073 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
26092 TCGCGTTGCGATT
1 TCGCGTTGCGATT
26105 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 19 0.31
15 4 0.07
16 2 0.03
17 5 0.08
18 9 0.15
19 22 0.36
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:27986 original size:93 final size:93
Alignment explanation
Indices: 27824--28288 Score: 896
Period size: 93 Copynumber: 5.0 Consensus size: 93
27814 ATTGCTTAGT
*
27824 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
27889 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
*
27917 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTA
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
27982 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
28010 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
28075 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
28103 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
28168 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
*
28196 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
28261 TCTTTGTTTTGTCTTTTGGTTG-AAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
28288 A
1 A
28289 TGCAATCCAT
Statistics
Matches: 368, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 362 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:28361 original size:20 final size:19
Alignment explanation
Indices: 28336--28464 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
28326 TAGTTTACTT
* *
28336 TCGCAACACGAAAGTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
28356 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
28375 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
28394 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
28408 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
28427 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAATCAAAA
*
28441 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
28460 TCGCA
1 TCGCA
28465 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.52
20 12 0.13
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:28376 original size:19 final size:19
Alignment explanation
Indices: 28352--28464 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
28342 CACGAAAGTT
28352 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
28371 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
28390 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
28404 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
28423 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
28437 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
28456 AAAATCGCA
1 AAAATCGCA
28465 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:28415 original size:33 final size:32
Alignment explanation
Indices: 28372--28464 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
28362 CGCGAAACCA
**
28372 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
28404 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
28437 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
28465 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:28462 original size:52 final size:51
Alignment explanation
Indices: 28352--28464 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
28342 CACGAAAGTT
* *
28352 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
28404 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
28456 AAAATCGCA
1 AAAATCGCA
28465 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:28482 original size:19 final size:19
Alignment explanation
Indices: 28460--28594 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
28450 GAAACCAAAA
*
28460 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28479 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
28495 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
28512 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
28528 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
28545 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
28564 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
28584 TCGTGTTGCGA
1 TCGCGTTGCGA
28595 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28501 original size:14 final size:14
Alignment explanation
Indices: 28482--28538 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
28472 TTTCATTTCG
28482 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
28496 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
28513 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
28529 CGTTGCGATT
1 CGTTGCGATT
28539 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:28507 original size:33 final size:33
Alignment explanation
Indices: 28465--28557 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
28455 CAAAATCGCA
*
28465 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
28498 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
28531 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
28558 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:30509 original size:14 final size:14
Alignment explanation
Indices: 30490--30525 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
30480 ATTGTTTAAT
30490 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
30504 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
30518 TGATTTGT
1 TGATTTGT
30526 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30648 original size:19 final size:19
Alignment explanation
Indices: 30632--30733 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
30622 AAAAATGACT
30632 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30651 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30670 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30684 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30703 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
30723 ATCGCAATGCG
1 ATCGCAATGCG
30734 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30767 original size:14 final size:14
Alignment explanation
Indices: 30748--30802 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
30738 TAATTTCGCA
*
30748 TTGCGATTCTCTCG
1 TTGCGATTCTTTCG
30762 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
30779 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
30795 TTGCGATT
1 TTGCGATT
30803 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 8 0.23
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:30786 original size:19 final size:19
Alignment explanation
Indices: 30762--31068 Score: 385
Period size: 19 Copynumber: 17.4 Consensus size: 19
30752 GATTCTCTCG
30762 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30781 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
30795 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30814 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30852 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30871 TTGCGA--TT-ATGTCG--
1 TTGCGATTTTCATTTCGCA
30885 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30904 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30923 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30937 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30956 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30975 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30994 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31008 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31028 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
31042 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
31061 TTGCGATT
1 TTGCGATT
31069 GTAATTTCCG
Statistics
Matches: 254, Mismatches: 8, Indels: 52
0.81 0.03 0.17
Matches are distributed among these distances:
14 35 0.14
16 31 0.12
17 28 0.11
18 3 0.01
19 145 0.57
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30818 original size:52 final size:55
Alignment explanation
Indices: 30762--31040 Score: 356
Period size: 52 Copynumber: 5.2 Consensus size: 55
30752 GATTCTCTCG
30762 TTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
30814 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
30871 TTGCGA--TT-ATGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
30923 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
30975 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTT-CGCA
31028 TTGCGATTTTCAT
1 TTGCGATTTTCAT
31041 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 4, Indels: 23
0.89 0.02 0.10
Matches are distributed among these distances:
52 134 0.64
53 17 0.08
54 15 0.07
55 14 0.07
57 31 0.15
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (55 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
Found at i:30848 original size:71 final size:71
Alignment explanation
Indices: 30740--31068 Score: 445
Period size: 71 Copynumber: 4.8 Consensus size: 71
30730 TGCGTTTATA
* *
30740 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
30800 ATTTTC
66 ATTTTC
*
30806 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--
30871 TTGCGA--TT-
61 TTGCGATTTTC
*
30879 ATGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
30942 ATTTTC
66 ATTTTC
30948 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
31013 ATTTTC
66 ATTTTC
* *
31019 ATTTCCGCATTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
31069 GTAATTTCCG
Statistics
Matches: 241, Mismatches: 6, Indels: 31
0.87 0.02 0.11
Matches are distributed among these distances:
66 20 0.08
67 25 0.10
68 9 0.04
69 13 0.05
70 1 0.00
71 136 0.56
72 16 0.07
73 8 0.03
74 7 0.03
76 6 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
ATTTTC
Found at i:33365 original size:12 final size:12
Alignment explanation
Indices: 33348--33372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33338 TCTTCGGGGA
33348 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33360 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33372 C
1 C
33373 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:33581 original size:24 final size:24
Alignment explanation
Indices: 33547--33593 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33537 CTGAAACATC
33547 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
33571 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
33594 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:34302 original size:20 final size:20
Alignment explanation
Indices: 34274--34483 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
34264 AAATTTCAGT
* * *
34274 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34294 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
34314 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34334 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
34354 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
34374 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
34394 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
34414 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34434 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
34454 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
34474 GTTGCGATTT
1 GTTGCGATTT
34484 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:36296 original size:24 final size:24
Alignment explanation
Indices: 36269--36323 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
36259 AAAATCAGCA
*
36269 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
36293 AAGAAAAGTCAAGCACTCAAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
36317 AAGAAAA
1 AAGAAAA
36324 AGAAAAAAAA
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:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (24 bp):
AAGAAAAGTCAAGCACTCAAAAAG
Found at i:42462 original size:11 final size:13
Alignment explanation
Indices: 42431--42459 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42421 GGCCAAAGAT
42431 GAAAAGGTATGTA
1 GAAAAGGTATGTA
42444 GAAAAGGTATGT-
1 GAAAAGGTATGTA
42456 GAAA
1 GAAA
42460 GGTGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTA
Found at i:51567 original size:17 final size:18
Alignment explanation
Indices: 51545--51582 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
51535 ATCGTCGACC
51545 AAATTTTACTATTCATG-
1 AAATTTTACTATTCATGT
51562 AAA-TTTACTATTCATGT
1 AAATTTTACTATTCATGT
51579 AAAT
1 AAAT
51583 AGTAACCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (18 bp):
AAATTTTACTATTCATGT
Found at i:53858 original size:28 final size:28
Alignment explanation
Indices: 53818--53871 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
53808 ATTATAATAC
53818 GTGTTAGAATTTGTTATCAAAATTTTAT
1 GTGTTAGAATTTGTTATCAAAATTTTAT
*
53846 GTGTTAGAATTTGTTATCAAATTTTT
1 GTGTTAGAATTTGTTATCAAAATTTT
53872 TTTATATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.52
Consensus pattern (28 bp):
GTGTTAGAATTTGTTATCAAAATTTTAT
Found at i:56628 original size:135 final size:138
Alignment explanation
Indices: 56349--56628 Score: 417
Period size: 135 Copynumber: 2.1 Consensus size: 138
56339 ACAGAAGTGC
* * * *
56349 CGAAATGGAAATTCACAAACTTATTATGAATTCCATGGATGCACACATAGTGCCGAAAGTACACA
1 CGAAATGGAAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
* * *
56414 TAGTACTGATACGAAAATGCACCGTTATGCATTAAACAAAATCGATCGATAACTTTTATACATAA
66 TAGTAATGATACGAAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTTTATACATAA
56479 TTGTATAT
131 TTGTATAT
* * *
56487 CAAAATGGTAATTCAAAAACTCATTATGAATACCAT-GATTGTACATC-TAGTGCCAAAAGTACA
1 CGAAATGGAAATTCAAAAACTCATTATGAATACCATGGA-TGCACA-CATAGTGCCAAAAGTACA
56550 CA-A-TAATGATACGAAAATGCA-CATTATACATTAAACAAAATCGATCGATAACTTTTATACAT
64 CATAGTAATGATACGAAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTTTATACAT
56612 AATTGTATAT
129 AATTGTATAT
56622 CGAAATG
1 CGAAATG
56629 CACCTTTGAA
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
135 55 0.43
136 17 0.13
137 3 0.02
138 53 0.41
139 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (138 bp):
CGAAATGGAAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGCCAAAAGTACACA
TAGTAATGATACGAAAATGCACCATTATACATTAAACAAAATCGATCGATAACTTTTATACATAA
TTGTATAT
Found at i:64274 original size:10 final size:10
Alignment explanation
Indices: 64259--64283 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
64249 TGGGGATGGT
64259 AAATTTCTTC
1 AAATTTCTTC
64269 AAATTTCTTC
1 AAATTTCTTC
64279 AAATT
1 AAATT
64284 GGTTATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (10 bp):
AAATTTCTTC
Found at i:68790 original size:32 final size:32
Alignment explanation
Indices: 68739--68799 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
68729 CAAGTTAAAA
* ** * *
68739 TTTGGTTTGGGTTTCTTTCGGTTTGGATTGCT
1 TTTGGTTCGGGTTAATTTCGATTTCGATTGCT
68771 TTTGGTTCGGGTTAATTTCGATTTCGATT
1 TTTGGTTCGGGTTAATTTCGATTTCGATT
68800 TAAGTTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.08, C:0.10, G:0.28, T:0.54
Consensus pattern (32 bp):
TTTGGTTCGGGTTAATTTCGATTTCGATTGCT
Found at i:71659 original size:27 final size:28
Alignment explanation
Indices: 71608--71664 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
71598 GAGAACATTC
* * *
71608 ACATAGTATTTTTTTATCCTTAAACCGA
1 ACATAGTACTTTTTTATCCTCAAACAGA
71636 ACATAGT-CTTTTTTATCCTCAAACAGA
1 ACATAGTACTTTTTTATCCTCAAACAGA
71663 AC
1 AC
71665 TAAGAAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
ACATAGTACTTTTTTATCCTCAAACAGA
Found at i:75740 original size:18 final size:18
Alignment explanation
Indices: 75717--75764 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
75707 GTTGGCTACT
75717 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTGGAG
75735 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTGGAG
75753 TCATCTTCATCA
1 TCATCTTCATCA
75765 CTCTAAGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (18 bp):
TCATCTTCATCATTGGAG
Found at i:77144 original size:33 final size:33
Alignment explanation
Indices: 77099--77173 Score: 141
Period size: 33 Copynumber: 2.2 Consensus size: 33
77089 CAAAAAATTA
77099 AGCTCACAAGAAAACAATAAAAAGATTTGCAATG
1 AGCTCA-AAGAAAACAATAAAAAGATTTGCAATG
77133 AGCTCAAAGAAAACAATAAAAAGATTTGCAATG
1 AGCTCAAAGAAAACAATAAAAAGATTTGCAATG
77166 AGCTCAAA
1 AGCTCAAA
77174 CACAAGTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 35 0.85
34 6 0.15
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (33 bp):
AGCTCAAAGAAAACAATAAAAAGATTTGCAATG
Found at i:78712 original size:20 final size:18
Alignment explanation
Indices: 78687--78727 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
78677 ATTAGTTTGT
*
78687 AATAAAATATTTATAAAATA
1 AATAAAATAATTA-AAAA-A
78707 AATAAAATAATTAAAAAA
1 AATAAAATAATTAAAAAA
78725 AAT
1 AAT
78728 TCAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATAATTAAAAAA
Found at i:80030 original size:17 final size:17
Alignment explanation
Indices: 80010--80052 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
80000 ACCCCTCTTA
80010 TAAGTGTTCCCCTTTCG
1 TAAGTGTTCCCCTTTCG
80027 TAAGTGTTCCCCTTTCG
1 TAAGTGTTCCCCTTTCG
80044 TAAGTGTTC
1 TAAGTGTTC
80053 TACGGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (17 bp):
TAAGTGTTCCCCTTTCG
Found at i:81262 original size:27 final size:27
Alignment explanation
Indices: 81227--81312 Score: 133
Period size: 26 Copynumber: 3.3 Consensus size: 27
81217 GGTATACAAA
81227 ATAAA-AACGTTTGTATATATATATGG
1 ATAAATAACGTTTGTATATATATATGG
*
81253 ACAAATAACGTTTGTATATATATAT-G
1 ATAAATAACGTTTGTATATATATATGG
*
81279 ATAAATAA-GTTTGTATATACATATGG
1 ATAAATAACGTTTGTATATATATATGG
81305 ATAAATAA
1 ATAAATAA
81313 AAAATAATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
25 15 0.27
26 21 0.38
27 19 0.35
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (27 bp):
ATAAATAACGTTTGTATATATATATGG
Done.