Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006935.1 Hibiscus syriacus cultivar Beakdansim tig00017799_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: 70074
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:4697 original size:17 final size:17
Alignment explanation
Indices: 4663--4714 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
4653 ACCGGACAAA
* *
4663 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
4680 TTTATTAATTTACTGAG
1 TTTATTAATTTACAGAG
*
4697 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
4712 TTT
1 TTT
4715 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:6320 original size:21 final size:21
Alignment explanation
Indices: 6269--6321 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
6259 ATTATGACTA
6269 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
6290 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
6311 TCGCAATGCGA
1 TCGCAATGCGA
6322 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:6336 original size:20 final size:21
Alignment explanation
Indices: 6311--6362 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
6301 TTTTCCCAAT
*
6311 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
*
6331 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTAAGAAAA
6352 TCGCAATGCGA
1 TCGCAATGCGA
6363 TACTTACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:6341 original size:41 final size:41
Alignment explanation
Indices: 6296--6548 Score: 158
Period size: 41 Copynumber: 6.2 Consensus size: 41
6286 AATTTCGCGT
* *
6296 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * * *
6337 TGCGAATTTAGAAAATCGCAATGCG-ATACTTACTAGCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
* * * **
6378 TGCAATTTTCCTAATTCGCATTGC-AATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGAA--TACGTAAATCGCAA
*
6419 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * *
6460 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * * *
6501 TGCGA-ATACGTAAATCGCAATGCGAAT-CTTACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
6541 TGCGATTT
1 TGCGATTT
6549 ACATAGCGCC
Statistics
Matches: 160, Mismatches: 43, Indels: 18
0.72 0.19 0.08
Matches are distributed among these distances:
39 1 0.01
40 40 0.25
41 113 0.71
42 2 0.01
43 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:6402 original size:21 final size:21
Alignment explanation
Indices: 6373--6438 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
6363 TACTTACTAG
* *
6373 CGCAATGCAATTTTCCTAATT
1 CGCATTGCAATTTTCATAATT
* *
6394 CGCATTGCAATTTACGT-ATT
1 CGCATTGCAATTTTCATAATT
* *
6414 CGCGTTGCGATTTTCATAATT
1 CGCATTGCAATTTTCATAATT
6435 CGCA
1 CGCA
6439 ATGCGAATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
CGCATTGCAATTTTCATAATT
Found at i:6459 original size:20 final size:20
Alignment explanation
Indices: 6434--6545 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
6424 TTTTCATAAT
6434 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
6454 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
6474 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
6495 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
6515 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
6535 TCGCAATGCGA
1 TCGCAATGCGA
6546 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:7098 original size:33 final size:33
Alignment explanation
Indices: 7061--7139 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
7051 TAGTTTCGAG
7061 AATGAAAATCGCAACGAGAGAATCACAACGCGA
1 AATGAAAATCGCAACGAGAGAATCACAACGCGA
* *
7094 AATGAAAATCGCAACGAGATAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCACAACGCGA
**
7127 AACCAAAATCGCA
1 AATGAAAATCGCA
7140 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
AATGAAAATCGCAACGAGAGAATCACAACGCGA
Found at i:7176 original size:14 final size:14
Alignment explanation
Indices: 7157--7245 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
7147 TTTCATTTCG
7157 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7171 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
7190 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7204 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
7223 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
7237 CGTTGCGAT
1 CGTTGCGAT
7246 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 31 0.51
16 4 0.07
17 4 0.07
19 22 0.36
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7186 original size:33 final size:33
Alignment explanation
Indices: 7140--7266 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
7130 CAAAATCGCA
**
7140 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
7173 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
7206 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
7239 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATAGTCATTT-CGCGTTGCGATT
7267 TCATTATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 79 0.87
34 12 0.13
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:7286 original size:19 final size:18
Alignment explanation
Indices: 7140--7293 Score: 98
Period size: 19 Copynumber: 8.8 Consensus size: 18
7130 CAAAATCGCA
*
7140 TTGCGATTTTCATTTCGCG
1 TTGCGA-TTTCATTTCTCG
7159 TTGCGA-TTC---TCTCG
1 TTGCGATTTCATTTCTCG
* *
7173 TTGCGATAGTCATTTCGCG
1 TTGCGAT-TTCATTTCTCG
7192 TTGCGA-TTC---TCTCG
1 TTGCGATTTCATTTCTCG
* *
7206 TTGCGATAGTCATTTCGCG
1 TTGCGAT-TTCATTTCTCG
7225 TTGCGA-TTC---TCTCG
1 TTGCGATTTCATTTCTCG
* *
7239 TTGCGATAGTCATTTCCGCG
1 TTGCGAT-TTCATTT-CTCG
7259 TTGCGATTTCATTATCTCG
1 TTGCGATTTCATT-TCTCG
7278 TTGCGATTTTCATTTC
1 TTGCGA-TTTCATTTC
7294 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 13, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
14 30 0.29
16 6 0.06
17 7 0.07
19 43 0.41
20 18 0.17
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.43
Consensus pattern (18 bp):
TTGCGATTTCATTTCTCG
Found at i:9445 original size:21 final size:21
Alignment explanation
Indices: 9421--9487 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
9411 TCATTCCTCG
9421 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
9442 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
9463 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
9484 AGAG
1 AGAG
9488 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9445 original size:42 final size:42
Alignment explanation
Indices: 9369--9487 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
9359 GACTCGCCTG
* * * * * * *
9369 TCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
9411 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
9453 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
9488 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:10871 original size:14 final size:13
Alignment explanation
Indices: 10837--10873 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
10827 TTGATTGTTT
10837 AATTGATTTGTAA
1 AATTGATTTGTAA
10850 AATGTGATTTGTAA
1 AAT-TGATTTGTAA
10864 AAGTTGATTT
1 AA-TTGATTT
10874 TTTTAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 18 0.82
15 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:11033 original size:33 final size:32
Alignment explanation
Indices: 10986--11093 Score: 144
Period size: 33 Copynumber: 3.3 Consensus size: 32
10976 ATTACTATCA
*
10986 CAATACGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGA-AATCG
*
11019 CAATGCGAAATGAAAATCGCAACTAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGA-AATCG
* * *
11052 CAATGCGAAATAAAAACCGCAACGACAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAATCG
*
11084 CAACGCGAAA
1 CAATGCGAAA
11094 CTAAATTCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
32 14 0.21
33 53 0.79
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (32 bp):
CAATGCGAAATGAAAATCGCAACGAGAAATCG
Found at i:11038 original size:19 final size:18
Alignment explanation
Indices: 10986--11040 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
10976 ATTACTATCA
10986 CAATACGAAATGAAAATCG
1 CAAT-CGAAATGAAAATCG
*
11005 CAA-CG--A-GATAATCG
1 CAATCGAAATGAAAATCG
11019 CAATGCGAAATGAAAATCG
1 CAAT-CGAAATGAAAATCG
11038 CAA
1 CAA
11041 CTAGAGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (18 bp):
CAATCGAAATGAAAATCG
Found at i:11176 original size:14 final size:14
Alignment explanation
Indices: 11124--11210 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 14
11114 TCATTTCGCT
*
11124 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
11138 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
11155 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
11171 TTGCGATTTTCATTCG
1 TTGCGATTCTC--TCG
*
11187 TATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
11203 TTGCGATT
1 TTGCGATT
11211 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
14 24 0.41
16 13 0.22
17 6 0.10
18 10 0.17
19 6 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:11202 original size:32 final size:33
Alignment explanation
Indices: 11103--11228 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
11093 ACTAAATTCG
* *
11103 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
11136 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
11169 CGTTGCGATTTTCA-TTCGTATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
11201 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
11229 AGTAATTTCC
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 30 0.34
33 57 0.66
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:11208 original size:65 final size:66
Alignment explanation
Indices: 11103--11228 Score: 211
Period size: 65 Copynumber: 1.9 Consensus size: 66
11093 ACTAAATTCG
*
11103 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCTTTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
11168 T
66 T
*
11169 CGTTGCGATTTTCA-TTCG-TATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCT-TTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCGAT
11229 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 42 0.74
66 14 0.25
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
T
Found at i:13788 original size:24 final size:24
Alignment explanation
Indices: 13754--13807 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
13744 CTGAAACATC
*
13754 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* * *
13778 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
13802 ATCAAA
1 ATCAAA
13808 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:14706 original size:20 final size:20
Alignment explanation
Indices: 14673--14788 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
14663 TAATACAAAA
*
14673 TCGCAACG-GATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
14692 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
14712 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
14732 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
14752 TCGCAATGAGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
14772 TCGCAATGAGATTCTGA
1 TCGCAACGCGATTCTGA
14789 AAATCGTAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
19 8 0.09
20 85 0.91
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:14706 original size:60 final size:60
Alignment explanation
Indices: 14639--14783 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 60
14629 AAATCGTAAT
*
14639 GCGATACTGACTATCGCAATGAGATAAT-ACAAAATCGCAACG-GATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAATGAGATAATGAC--AATCGCAACGCGATACTGACTTTCGCAAC
* * ** ** * *
14699 GCGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACTTTCGCAAT
1 GCGATACTGACTTTCGCAATGAGATAATGACAATCGCAACGCGATACTGACTTTCGCAAC
* *
14759 GAGATTCTGACTTTCGCAATGAGAT
1 GCGATACTGACTTTCGCAATGAGAT
14784 TCTGAAAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 8 0.11
60 60 0.86
61 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (60 bp):
GCGATACTGACTTTCGCAATGAGATAATGACAATCGCAACGCGATACTGACTTTCGCAAC
Found at i:15036 original size:20 final size:20
Alignment explanation
Indices: 15011--15058 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
15001 CAACGGGGAA
*
15011 ATCGCAACGCGTAAATGGCT
1 ATCGCAACGCGAAAATGGCT
15031 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
15051 ATCGCAAC
1 ATCGCAAC
15059 TAGAAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:15064 original size:20 final size:20
Alignment explanation
Indices: 15011--15066 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
15001 CAACGGGGAA
* *
15011 ATCGCAACGCGTAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
15031 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
15051 ATCGCAACTAGAAAAT
1 ATCGCAACGAGAAAAT
15067 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGGCT
Found at i:16736 original size:41 final size:42
Alignment explanation
Indices: 16691--16769 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
16681 CGATGACAGT
*
16691 GGCCTCTTGAACG-GTGGGGGGGACTCTTGAGGGATGATATG
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATATG
*
16732 GGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGA
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGA
16770 CAGGTGAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.24
Consensus pattern (42 bp):
GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATATG
Found at i:17191 original size:20 final size:20
Alignment explanation
Indices: 17116--17222 Score: 126
Period size: 20 Copynumber: 5.4 Consensus size: 20
17106 TAGTTTACTT
* * * *
17116 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
17136 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
17156 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
17176 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
17196 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
17215 TCGCAACG
1 TCGCAACG
17223 ACAAAATCGC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 13 0.17
20 62 0.83
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:17230 original size:14 final size:14
Alignment explanation
Indices: 17211--17269 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
17201 ATGCGAAATG
17211 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
17225 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-C
17244 AAAATCGCAACGAC
1 AAAATCGCAACGAC
17258 AAAATCGCAACG
1 AAAATCGCAACG
17270 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:17237 original size:33 final size:33
Alignment explanation
Indices: 17195--17286 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
17185 GAAAATGGCT
*
17195 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
17228 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * *
17261 ATCGCAACGCGAAACACAAATCGCAA
1 ATCGCAATGCGAAATAAAAATCGCAA
17287 TGCGATTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:17283 original size:19 final size:18
Alignment explanation
Indices: 17195--17291 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
17185 GAAAATGGCT
*
17195 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAA-CAAA
17214 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAACAAA
*
17228 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAA-CAAA
17247 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAACAAA
*
17261 ATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAACA-AA
17280 ATCGCAATGCGA
1 ATCGCAATGCGA
17292 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 4 0.06
19 30 0.47
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (18 bp):
ATCGCAATGCGAAACAAA
Found at i:17303 original size:19 final size:19
Alignment explanation
Indices: 17281--17377 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
17271 GAAACACAAA
*
17281 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
17300 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
17316 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
17333 TCGCATTGCGATTTT--GT
1 TCGCATTGCGATTTTCATT
*
17350 T-G--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
17366 TCGCATTGCGAT
1 TCGCATTGCGAT
17378 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 7 0.12
17 7 0.12
18 3 0.05
19 25 0.42
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:17329 original size:33 final size:33
Alignment explanation
Indices: 17287--17377 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
17277 CAAATCGCAA
*
17287 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
*
17320 TGCGATTTTCATTTCGCATTGCGATTTTGTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
*
17353 TGTGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
17378 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCGT
Found at i:17396 original size:20 final size:19
Alignment explanation
Indices: 17362--17416 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
17352 TTGTGATTTT
*
17362 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
17381 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
17401 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
17417 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:17980 original size:18 final size:18
Alignment explanation
Indices: 17957--18004 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
17947 CGGGTCGATA
*
17957 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGAG
*
17975 AGGTGATAGCTCTGGGAG
1 AGGTGATGGCTCTGGGAG
17993 AGGTGATGGCTC
1 AGGTGATGGCTC
18005 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.46, T:0.25
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGAG
Found at i:19348 original size:20 final size:20
Alignment explanation
Indices: 19323--19365 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19313 AATAGTTTCT
19323 GAAAATGAAAATAGCAACAC
1 GAAAATGAAAATAGCAACAC
* * *
19343 GAAAATGACAATCGCAACGC
1 GAAAATGAAAATAGCAACAC
19363 GAA
1 GAA
19366 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATAGCAACAC
Found at i:19671 original size:22 final size:22
Alignment explanation
Indices: 19644--19687 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19634 GATGGAGATA
19644 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
19666 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
19688 TGAGAGAGTA
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:19907 original size:20 final size:20
Alignment explanation
Indices: 19874--19987 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
19864 GATTATGTAT
*
19874 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
19894 TATTGCGTTACGAAA-TTAGG
1 TATCGCGTTGCGAAAGTCA-G
*
19914 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
19934 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
19955 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
19975 TATCGCGTTGCGA
1 TATCGCGTTGCGA
19988 TTTTCCAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.07
20 52 0.69
21 16 0.21
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:19991 original size:41 final size:41
Alignment explanation
Indices: 19854--19989 Score: 168
Period size: 41 Copynumber: 3.3 Consensus size: 41
19844 CGCTTTGAAA
* *
19854 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * * *
19895 ATTGCGTTACGA-AAT-TAGGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTA-TTATCGCGTTGCGAAAGTCAGT
* *
19935 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
19976 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
19990 TTCCAAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.40
41 43 0.55
42 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:20006 original size:21 final size:21
Alignment explanation
Indices: 19977--20049 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
19967 ATAGTCAGTA
*
19977 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
19998 TCGCATTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
20019 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
20039 TCGCATTGCGA
1 TCGCATTGCGA
20050 ATTGGAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:20007 original size:41 final size:41
Alignment explanation
Indices: 19921--20009 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
19911 AGGTATCGAG
* ** * *
19921 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
19962 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCA
20003 TTGCGAT
1 TTGCGAT
20010 TTTCAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 40 0.95
42 2 0.05
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
Found at i:24318 original size:20 final size:20
Alignment explanation
Indices: 24293--24351 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
24283 ATATACTAAA
*
24293 CAGAATAAAAGTACTAACTG
1 CAGAATAACAGTACTAACTG
24313 CAGAATAACAGTACTAACTG
1 CAGAATAACAGTACTAACTG
24333 CAGAATAACAGTACTAACT
1 CAGAATAACAGTACTAACT
24352 AACTCAATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (20 bp):
CAGAATAACAGTACTAACTG
Found at i:24405 original size:15 final size:15
Alignment explanation
Indices: 24385--24424 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
24375 CAAAGAGAGG
24385 GAATACACGTGAGCT
1 GAATACACGTGAGCT
*
24400 GAATACACATGAGCT
1 GAATACACGTGAGCT
24415 GAATACACGT
1 GAATACACGT
24425 AAGCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (15 bp):
GAATACACGTGAGCT
Found at i:27494 original size:31 final size:31
Alignment explanation
Indices: 27456--27578 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
27446 CCCGAAGGAC
* * *
27456 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
27487 CAGTCCATATGTCCTGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
27518 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
27549 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
27579 CCCTCGACCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:28391 original size:21 final size:21
Alignment explanation
Indices: 28367--28411 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28357 TGTTGTTCGT
* *
28367 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28388 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28409 TTG
1 TTG
28412 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31724 original size:31 final size:31
Alignment explanation
Indices: 31686--31808 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
31676 CCCGAAGGAC
* * *
31686 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
31717 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
31748 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
31779 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
31809 CCCTCGACCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:32621 original size:21 final size:21
Alignment explanation
Indices: 32597--32641 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32587 TGTTGTTCGT
* *
32597 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32618 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32639 TTG
1 TTG
32642 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37145 original size:34 final size:34
Alignment explanation
Indices: 37102--37168 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
37092 GATAAGTTTC
37102 TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
1 TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
*
37136 TCAATTTTAAAATTAGGTGGTGTGATTCATATA
1 TCAATTTTAAAATTAGGAGGTGTGATTCATATA
37169 GGAACATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (34 bp):
TCAATTTTAAAATTAGGAGGTGTGATTCATATAT
Found at i:37553 original size:6 final size:6
Alignment explanation
Indices: 37542--37571 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
37532 GAAGACACGT
37542 ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
37572 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:38080 original size:6 final size:6
Alignment explanation
Indices: 38069--38116 Score: 96
Period size: 6 Copynumber: 8.0 Consensus size: 6
38059 TCTCGTCTCG
38069 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
38117 AGTAATATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:44261 original size:3 final size:3
Alignment explanation
Indices: 44255--44290 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
44245 AGGGAAGGGG
* *
44255 AGA AGA AGA CGA AGA AGA AGA AGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
44291 GTAGAGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:45920 original size:11 final size:12
Alignment explanation
Indices: 45891--45925 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
45881 GTTCGGAGCT
*
45891 TATTTTTTAAAA
1 TATTTTTGAAAA
45903 TATTTTTGAAAA
1 TATTTTTGAAAA
45915 TATTTTTGAAA
1 TATTTTTGAAA
45926 TATAATATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (12 bp):
TATTTTTGAAAA
Found at i:45926 original size:11 final size:11
Alignment explanation
Indices: 45894--45928 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
45884 CGGAGCTTAT
*
45894 TTTTTAAAATA
1 TTTTTGAAATA
45905 TTTTTGAAAATA
1 TTTTTG-AAATA
45917 TTTTTGAAATA
1 TTTTTGAAATA
45928 T
1 T
45929 AATATACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (11 bp):
TTTTTGAAATA
Found at i:46031 original size:36 final size:35
Alignment explanation
Indices: 45986--46098 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 35
45976 TAAAAATCGG
* *
45986 TTTTCCAAAATATATATTATATAGTTTTTGAAAACA
1 TTTTTCAAAATATATAATATATAG-TTTTGAAAACA
*
46022 TTTTTCAAAATATATAATATATAGTTTTGAAAACG
1 TTTTTCAAAATATATAATATATAGTTTTGAAAACA
*
46057 TTCTTTAAAAATATATACAATATATAG-TTTGAAAACA
1 TT-TTTCAAAATATAT--AATATATAGTTTTGAAAACA
46094 TTTTT
1 TTTTT
46099 ATATATATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 12 0.17
36 37 0.54
37 11 0.16
38 9 0.13
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTTTCAAAATATATAATATATAGTTTTGAAAACA
Found at i:46108 original size:36 final size:35
Alignment explanation
Indices: 46003--46107 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 35
45993 AAATATATAT
*
46003 TATATAGTTTTTGAAAACATTTTTCAAA-ATATATAA
1 TATATAG-TTTTGAAAACATTTTT-AAATATATACAA
*
46039 TATATAGTTTTGAAAACGTTCTTTAAAAATATATACAA
1 TATATAGTTTTGAAAACATT-TTT--AAATATATACAA
*
46077 TATATAG-TTTGAAAACATTTTTATATATATA
1 TATATAGTTTTGAAAACATTTTTAAATATATA
46108 TTTTCATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
34 8 0.13
35 12 0.20
36 13 0.21
37 14 0.23
38 14 0.23
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATAGTTTTGAAAACATTTTTAAATATATACAA
Found at i:46130 original size:13 final size:12
Alignment explanation
Indices: 46109--46162 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 12
46099 ATATATATAT
46109 TTTCA-TTTTCA
1 TTTCATTTTTCA
46120 TTTACATTTTT-A
1 TTT-CATTTTTCA
* *
46132 TTTCTTTTTTCT
1 TTTCATTTTTCA
46144 TATTCATTTTTC-
1 T-TTCATTTTTCA
46156 TTTCATT
1 TTTCATT
46163 CATTTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 15 0.42
12 8 0.22
13 13 0.36
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTCATTTTTCA
Found at i:46141 original size:24 final size:24
Alignment explanation
Indices: 46114--46159 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
46104 TATATTTTCA
46114 TTTTCATT-TACATTTTTATTTCTT
1 TTTTC-TTATACATTTTTATTTCTT
* *
46138 TTTTCTTATTCATTTTTCTTTC
1 TTTTCTTATACATTTTTATTTC
46160 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTCTTATACATTTTTATTTCTT
Found at i:46163 original size:15 final size:14
Alignment explanation
Indices: 46137--46181 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
46127 TTTTATTTCT
46137 TTTTTC-TTATTCA
1 TTTTTCTTTATTCA
46150 TTTTTCTTTCATTCA
1 TTTTTCTTT-ATTCA
46165 TTTTTCTTT-TTC-
1 TTTTTCTTTATTCA
46177 TTTTT
1 TTTTT
46182 TTTGGGGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.17
13 9 0.30
14 2 0.07
15 14 0.47
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCTTTATTCA
Found at i:47435 original size:4 final size:4
Alignment explanation
Indices: 47428--47496 Score: 58
Period size: 4 Copynumber: 18.0 Consensus size: 4
47418 TGTTAACCTG
* *
47428 ATTT ATTT A-TT ATTT ATTT ATTT A-AT ATTT -TTCT ATTT -TTCT TTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATT-T ATTT
*
47474 ATTT A-AT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT
47497 TTATTGTACA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
3 11 0.21
4 38 0.72
5 4 0.08
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:51724 original size:2 final size:2
Alignment explanation
Indices: 51713--51759 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
51703 TAAAGGCTAT
51713 TA TA -A 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
51754 TA TA TA
1 TA TA TA
51760 ATAAAGTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:56226 original size:36 final size:37
Alignment explanation
Indices: 56108--56276 Score: 139
Period size: 38 Copynumber: 4.5 Consensus size: 37
56098 TTATTTTCAA
* **
56108 AATATATAGTTTTTAGAAAACGGTTTTTGAAAGCATAT
1 AATATATAGTTTTT-GAAAACGATTTTTGAAAATATAT
* * * * *
56146 AATACATACTTTTTAAAAATCGATTTTTGAAATTTTAT
1 AATATATAGTTTTTGAAAA-CGATTTTTGAAAATATAT
* * *
56184 ATTATATTGTTTTTGAAAAC-ATTTTTCAAAATATAT
1 AATATATAGTTTTTGAAAACGATTTTTGAAAATATAT
* *
56220 AATATATAG-TTTTGAAAATG-TTCTTTAAAAAATATATAT
1 AATATATAGTTTTTGAAAACGATT-TTT--GAAA-ATATAT
56259 AATATATAG-TTTTGAAAA
1 AATATATAGTTTTTGAAAA
56277 TATTATAATA
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
35 11 0.10
36 23 0.22
37 5 0.05
38 43 0.41
39 24 0.23
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (37 bp):
AATATATAGTTTTTGAAAACGATTTTTGAAAATATAT
Found at i:58648 original size:17 final size:18
Alignment explanation
Indices: 58610--58649 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
58600 AACATTTTCA
* *
58610 GTAATCTTATTCCCGTCG
1 GTAATCCTATTCCCGACG
58628 GTAATCCTATTCCC-ACG
1 GTAATCCTATTCCCGACG
58645 GTAAT
1 GTAAT
58650 TATATTCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (18 bp):
GTAATCCTATTCCCGACG
Found at i:65719 original size:18 final size:18
Alignment explanation
Indices: 65698--65732 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65688 TTAACGTCTT
65698 AATGATTAAAAT-ATTAAA
1 AATGA-TAAAATAATTAAA
65716 AATGATAAAATAATTAA
1 AATGATAAAATAATTAA
65733 CCAACACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AATGATAAAATAATTAAA
Found at i:66463 original size:2 final size:2
Alignment explanation
Indices: 66456--66494 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
66446 TATATTTTCA
66456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66495 AGGAGTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68327 original size:29 final size:32
Alignment explanation
Indices: 68293--68369 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 32
68283 AAAGATAATT
68293 TCTATTTGACCCTTGAAA-CTTAGAT-AAATA
1 TCTATTTGACCCTTGAAAGCTTAGATGAAATA
* *
68323 T-TATTTGACGCTT-AAAGTTTAGATGAAATA
1 TCTATTTGACCCTTGAAAGCTTAGATGAAATA
* *
68353 TCAATTTAACCCTTGAA
1 TCTATTTGACCCTTGAA
68370 TTTCATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 17 0.45
30 7 0.18
31 9 0.24
32 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (32 bp):
TCTATTTGACCCTTGAAAGCTTAGATGAAATA
Done.