Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008274.1 Hibiscus syriacus cultivar Beakdansim tig00110931_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: 1661830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:163 original size:41 final size:41
Alignment explanation
Indices: 118--213 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
108 CGATTTTCCC
*
118 AATTCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
159 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
200 AAATCGCAATGCGA
1 AATTCGCAATGCGA
214 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:173 original size:21 final size:20
Alignment explanation
Indices: 121--213 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
111 TTTTCCCAAT
*
121 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* * **
141 TCGTAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
161 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
182 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
203 TCGCAATGCGA
1 TCGCAATGCGA
214 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:227 original size:20 final size:20
Alignment explanation
Indices: 202--293 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
192 AATTGGGAAA
*
202 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
222 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
243 ATCGCAA-GAGTTACTTACT
1 ATCGCAACGCGATACTGACT
*
262 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
282 -TCGCAACGCGAT
1 ATCGCAACGCGAT
294 TTACATAGCG
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
19 19 0.34
20 29 0.52
21 8 0.14
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:274 original size:40 final size:41
Alignment explanation
Indices: 199--275 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 41
189 GCGAATTGGG
* *
199 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
* * *
240 AAAATCGCAA-GAGTTACTTACTTTCGCAACGCGATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGCGATA
276 CTGACTTCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 21 0.68
41 10 0.32
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAA
Found at i:859 original size:19 final size:19
Alignment explanation
Indices: 835--879 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
825 CGCACGAGAT
*
835 AATCGCAACACGAAATAAA
1 AATCGCAACACGAAACAAA
* *
854 AATCGCAACGCGAAACCAA
1 AATCGCAACACGAAACAAA
873 AATCGCA
1 AATCGCA
880 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.13, T:0.09
Consensus pattern (19 bp):
AATCGCAACACGAAACAAA
Found at i:897 original size:19 final size:19
Alignment explanation
Indices: 875--1058 Score: 149
Period size: 19 Copynumber: 10.1 Consensus size: 19
865 GAAACCAAAA
*
875 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
894 TCGCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
912 TCGCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
930 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
950 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
966 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
983 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
997 TCTCGTTGCGATAGTCCATT
1 TCGCGTTGCGAT-TTTCATT
*
1017 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1037 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1057 TC
1 TC
1059 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 15, Indels: 32
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 1 0.01
17 5 0.04
18 26 0.19
19 43 0.32
20 28 0.21
21 11 0.08
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1028 original size:35 final size:33
Alignment explanation
Indices: 945--1033 Score: 124
Period size: 33 Copynumber: 2.6 Consensus size: 33
935 GTTGCGATTT
* *
945 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
978 TCATTTTGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1011 TCCATTTCCGCGTTGCGATTCTC
1 T-CATTT-CGCGTTGCGATTCTC
1034 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 30 0.61
34 5 0.10
35 14 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:4498 original size:14 final size:14
Alignment explanation
Indices: 4479--4514 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4469 ATTGTTTAAT
4479 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
4493 TGATTTGTAAATGT
1 TGATTTGTAAAAGG
4507 TGATTTGT
1 TGATTTGT
4515 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4739 original size:33 final size:32
Alignment explanation
Indices: 4697--4823 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
4687 ATTAAATTCG
4697 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
4730 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
* *
4763 AGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
4796 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4824 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
31 3 0.04
33 75 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:4756 original size:19 final size:19
Alignment explanation
Indices: 4693--4823 Score: 69
Period size: 19 Copynumber: 7.7 Consensus size: 19
4683 CGAAATTAAA
*
4693 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
4712 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
4728 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
4745 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
4759 TTAG-AGTTGCGATTTTCAT
1 TTCGCA-TTGCGATTTTCAT
*
4778 TTTGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
4794 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
4811 TTCGCATTGCGAT
1 TTCGCATTGCGAT
4824 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 13, Indels: 34
0.64 0.10 0.26
Matches are distributed among these distances:
13 1 0.01
14 22 0.27
16 11 0.13
17 13 0.16
19 34 0.41
20 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:4786 original size:66 final size:66
Alignment explanation
Indices: 4698--4822 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
4688 TTAAATTCGC
4698 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
4763 A
66 A
* * *
4764 GTTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
4823 TAGTAATTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (66 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
A
Found at i:7345 original size:24 final size:24
Alignment explanation
Indices: 7311--7364 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7301 CTGAAACATC
* *
7311 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
7335 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
7359 ATCAAA
1 ATCAAA
7365 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:8486 original size:19 final size:20
Alignment explanation
Indices: 8456--8505 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
8446 GCGATTTTCG
8456 TTGCGA-TTTCATTT-CGCA
1 TTGCGATTTTCATTTCCGCA
8474 TTGCGATTTTCATTTCGCGCA
1 TTGCGATTTTCATTTC-CGCA
8495 TTGCGATTTTC
1 TTGCGATTTTC
8506 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.21
19 8 0.28
21 15 0.52
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:10551 original size:20 final size:19
Alignment explanation
Indices: 10497--10561 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
10487 TAGTTTACTT
* **
10497 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGACTA
*
10517 TCGCAACGCGAAATGACTA
1 TCGCAACACGAAATGACTA
* *
10536 TCGCAACACGGAAATGGCTG
1 TCGCAACAC-GAAATGACTA
10556 TCGCAA
1 TCGCAA
10562 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
19 11 0.30
20 26 0.70
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:10602 original size:33 final size:34
Alignment explanation
Indices: 10565--10652 Score: 137
Period size: 32 Copynumber: 2.7 Consensus size: 34
10555 GTCGCAATTG
*
10565 CGATTTTCATTTCACGTTGCGATTTTGTCGTT-A
1 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTGA
10598 CGA-TTTCATTTCGCGTTGCGATTTTGTCGTTGA
1 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTGA
*
10631 -GATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCGTTGCGAT
10653 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (34 bp):
CGATTTTCATTTCGCGTTGCGATTTTGTCGTTGA
Found at i:10671 original size:20 final size:19
Alignment explanation
Indices: 10637--10691 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
10627 TTGAGATTTT
*
10637 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
10656 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
10676 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
10692 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:11190 original size:18 final size:18
Alignment explanation
Indices: 11164--11208 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
11154 GTCGATCAGA
*
11164 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
11182 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
11200 TGATGGCTC
1 TGATGGCTC
11209 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:12550 original size:20 final size:20
Alignment explanation
Indices: 12525--12562 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12515 AATAGTTTCT
12525 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
12545 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
12563 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:13063 original size:20 final size:20
Alignment explanation
Indices: 13038--13131 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
13028 GATTATGTAT
13038 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
13058 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
13078 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
13099 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
13119 TATCGCATTGCGA
1 TATCGCGTTGCGA
13132 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:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:13132 original size:20 final size:20
Alignment explanation
Indices: 13018--13132 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
13008 CGCTTTGAAA
*
13018 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
13039 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
13059 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
13079 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
13100 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
13120 ATCGCATTGCGAT
1 ATCGCATTGCGAT
13133 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:13151 original size:41 final size:41
Alignment explanation
Indices: 13060--13194 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
13050 AAAGTCAGTA
* * * ** *
13060 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
13100 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
13142 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
13183 TCGCGTTGCGAT
1 TCGCGTTGCGAT
13195 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:13165 original size:20 final size:20
Alignment explanation
Indices: 13121--13213 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
13111 ATAGTCAGTA
* **
13121 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
13142 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
13162 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
13183 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
13203 TCGCATTGCGA
1 TCGCATTGCGA
13214 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:13195 original size:41 final size:41
Alignment explanation
Indices: 13121--13216 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
13111 ATAGTCAGTA
*
13121 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
13162 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
13203 TCGCATTGCGAATT
1 TCGCATTGCGAATT
13217 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:27656 original size:33 final size:33
Alignment explanation
Indices: 27605--27670 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
27595 CTCCAGGAGG
*** * *
27605 GGTCATAAAACTTTGTGAAGGTGGCGGCGACGA
1 GGTCATAAAACCAGGTGAAGGCGGCGACGACGA
27638 GGTCATAAAACCAGGTGAAGGCGGCGACGACGA
1 GGTCATAAAACCAGGTGAAGGCGGCGACGACGA
27671 CATCTGATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.36, T:0.15
Consensus pattern (33 bp):
GGTCATAAAACCAGGTGAAGGCGGCGACGACGA
Found at i:29398 original size:16 final size:16
Alignment explanation
Indices: 29374--29418 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
29364 TATATCTGCA
* *
29374 AAAAAATTAATTAAAT
1 AAAATATTAAATAAAT
29390 AAAATATTAAATAAAT
1 AAAATATTAAATAAAT
* *
29406 TAAATATAAAATA
1 AAAATATTAAATA
29419 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:29400 original size:12 final size:12
Alignment explanation
Indices: 29383--29423 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29373 AAAAAAATTA
29383 ATTAAATAAAAT
1 ATTAAATAAAAT
29395 ATTAAAT-AAAT
1 ATTAAATAAAAT
*
29406 -TAAATATAAAAT
1 ATTAA-ATAAAAT
29418 ATTAAA
1 ATTAAA
29424 AATATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.12
11 6 0.25
12 12 0.50
13 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:29406 original size:21 final size:21
Alignment explanation
Indices: 29377--29438 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
29367 ATCTGCAAAA
*
29377 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
29398 AAATAAATTAAATATAAAATATT
1 AAATAAATT-AA-ATAAAATATT
29421 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
29439 ACATTAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 10 0.27
20 2 0.05
21 11 0.30
22 4 0.11
23 10 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:46645 original size:30 final size:30
Alignment explanation
Indices: 46596--46664 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
46586 ATATACATAT
*
46596 AATTT-GGGATGAAACTGGAATGTT-AAAA
1 AATTTGGGGATAAAACTGGAATGTTCAAAA
* * *
46624 ATGTTTGGGGATAAAATTGGAATTTTCAAAA
1 A-ATTTGGGGATAAAACTGGAATGTTCAAAA
46655 AATTTGGGGA
1 AATTTGGGGA
46665 CCAATTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 3 0.09
30 24 0.73
31 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
AATTTGGGGATAAAACTGGAATGTTCAAAA
Found at i:46702 original size:61 final size:60
Alignment explanation
Indices: 46626--46779 Score: 157
Period size: 60 Copynumber: 2.5 Consensus size: 60
46616 TGTTAAAAAT
* * * * *
46626 GTTTGGGGATAAAATTGGAATTTTCAAAAAATTTGGGGACCAATTTAGAATGA-ATGTCATA
1 GTTTAGGGATAAAATTGAAATGTTC-AAAAATTTGAGGACAAATTTAGAATGATA-GTCATA
* * *
46687 GTTTAGGGATGAAATTGAAATGTTCAAAAGTTTGAGGATAAATTTAGAATGATAGTCATA
1 GTTTAGGGATAAAATTGAAATGTTCAAAAATTTGAGGACAAATTTAGAATGATAGTCATA
* * * * * *
46747 ATTTAGGGCTAAAGTTAAAATATTTAAAAATTT
1 GTTTAGGGATAAAATTGAAATGTTCAAAAATTT
46780 AGAGACTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
60 54 0.71
61 22 0.29
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (60 bp):
GTTTAGGGATAAAATTGAAATGTTCAAAAATTTGAGGACAAATTTAGAATGATAGTCATA
Found at i:46869 original size:35 final size:35
Alignment explanation
Indices: 46830--46920 Score: 164
Period size: 35 Copynumber: 2.6 Consensus size: 35
46820 TAATGTTATT
46830 AACTCTGATGTATATAACAAACATGTAATGCGATG
1 AACTCTGATGTATATAACAAACATGTAATGCGATG
*
46865 AACTCTGATGTATATAACAAACATGTAATGCGATT
1 AACTCTGATGTATATAACAAACATGTAATGCGATG
*
46900 AACTATGATGTATATAACAAA
1 AACTCTGATGTATATAACAAA
46921 AGGTATTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (35 bp):
AACTCTGATGTATATAACAAACATGTAATGCGATG
Found at i:56612 original size:14 final size:14
Alignment explanation
Indices: 56593--56619 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56583 TCTAAATCTA
56593 TAAATTCTTAAACT
1 TAAATTCTTAAACT
56607 TAAATTCTTAAAC
1 TAAATTCTTAAAC
56620 CTAATACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTCTTAAACT
Found at i:69128 original size:16 final size:16
Alignment explanation
Indices: 69109--69140 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
69099 AAAATTAATT
69109 AAATAAAATAGTTAAA
1 AAATAAAATAGTTAAA
*
69125 AAATTAAATAGTTAAA
1 AAATAAAATAGTTAAA
69141 TAAAATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAATAAAATAGTTAAA
Found at i:71076 original size:26 final size:26
Alignment explanation
Indices: 71040--71099 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
71030 TGTTTGCATA
71040 GAGGGTTTCTTATTTATAGGAGAGGG
1 GAGGGTTTCTTATTTATAGGAGAGGG
71066 GAGGGTTTCTTATTTATAGGAGAGGG
1 GAGGGTTTCTTATTTATAGGAGAGGG
71092 GAGGGTTT
1 GAGGGTTT
71100 AAAAGTTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.22, C:0.03, G:0.40, T:0.35
Consensus pattern (26 bp):
GAGGGTTTCTTATTTATAGGAGAGGG
Found at i:72857 original size:24 final size:24
Alignment explanation
Indices: 72785--72865 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 24
72775 GACATTTAAC
* * *
72785 TTTTAATGTAATTGTATACATATTT
1 TTTTAATGT-ACTATATACTTATTT
* * *
72810 TTTCTAGTGTACTTTGATATTTATTT
1 TTT-TAATGTACTAT-ATACTTATTT
*
72836 TTTTAATGTAGTATATACTTATTT
1 TTTTAATGTACTATATACTTATTT
72860 TTTTAA
1 TTTTAA
72866 ACTTATTTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
24 15 0.33
25 14 0.31
26 16 0.36
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTTAATGTACTATATACTTATTT
Found at i:84810 original size:18 final size:18
Alignment explanation
Indices: 84787--84832 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
84777 ACCGGTCACA
*
84787 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTT
84805 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
84823 ACCCGACCCG
1 ACCCGACCCG
84833 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:84814 original size:13 final size:13
Alignment explanation
Indices: 84809--84845 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
84799 CCGTTTACCC
84809 GACCCGACCCGTT
1 GACCCGACCCGTT
*
84822 TACCCGACCCGTT
1 GACCCGACCCGTT
84835 GACCCGACCCG
1 GACCCGACCCG
84846 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:84834 original size:31 final size:31
Alignment explanation
Indices: 84791--84871 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
84781 GTCACAACCC
* *
84791 GACCTGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
84822 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
84853 GACTCGACCTGTTGACCCG
1 GACCCGACCCGTTGACCCG
84872 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.16, C:0.44, G:0.21, T:0.19
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:84844 original size:18 final size:18
Alignment explanation
Indices: 84787--84861 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
84777 ACCGGTCACA
* *
84787 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTG
84805 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
84822 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
84836 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
84854 ACTCGACC
1 ACCCGACC
84862 TGTTGACCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 12 0.25
18 36 0.75
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:84892 original size:17 final size:16
Alignment explanation
Indices: 84858--84904 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
84848 CCGTTGACTC
84858 GACCTGTTGACCCGTT
1 GACCTGTTGACCCGTT
84874 GACC-GTTGACCGTCGTT
1 GACCTGTTGACC--CGTT
84891 GACCACTGTTGACC
1 GA-C-CTGTTGACC
84905 AAAACTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 6 0.23
18 1 0.04
19 1 0.04
20 7 0.27
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.28
Consensus pattern (16 bp):
GACCTGTTGACCCGTT
Found at i:87384 original size:12 final size:12
Alignment explanation
Indices: 87347--87385 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
87337 ATCTGATACT
87347 TGACATGGATTC
1 TGACATGGATTC
*
87359 TGATAT-GATATC
1 TGACATGGAT-TC
87371 TGACATGGATTC
1 TGACATGGATTC
87383 TGA
1 TGA
87386 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:87453 original size:24 final size:24
Alignment explanation
Indices: 87332--87449 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
87322 TCGATTTGAT
87332 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
87356 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
87380 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
87404 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
87427 TTTCTGATATGATACTTGACATG
1 -TTCTGATCTGATACTTGACATG
87450 ATTTATGTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:89634 original size:13 final size:13
Alignment explanation
Indices: 89629--89665 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
89619 CCGTTTACCC
89629 GACCCGACCCGTT
1 GACCCGACCCGTT
*
89642 TACCCGACCCGTT
1 GACCCGACCCGTT
89655 GACCCGACCCG
1 GACCCGACCCG
89666 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:89654 original size:31 final size:31
Alignment explanation
Indices: 89611--89691 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
89601 GTCACAACCC
* *
89611 GACCTGACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
89642 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
89673 GACTCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
89692 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:89664 original size:18 final size:18
Alignment explanation
Indices: 89607--89697 Score: 84
Period size: 18 Copynumber: 5.2 Consensus size: 18
89597 ACCGGTCACA
* *
89607 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTG
89625 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
89642 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
89656 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
89674 ACTCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
89695 ACC
1 ACC
89698 GTTGACCGTC
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
13 12 0.20
18 37 0.62
21 11 0.18
ACGTcount: A:0.16, C:0.46, G:0.20, T:0.18
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:89680 original size:13 final size:13
Alignment explanation
Indices: 89664--89688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89654 TGACCCGACC
89664 CGACCCGTTGACT
1 CGACCCGTTGACT
89677 CGACCCGTTGAC
1 CGACCCGTTGAC
89689 CCGTTGACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:89691 original size:8 final size:8
Alignment explanation
Indices: 89678--89724 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
89668 CCGTTGACTC
89678 GACCCGTT
1 GACCCGTT
89686 GACCCGTT
1 GACCCGTT
89694 GA-CCGTT
1 GACCCGTT
89701 GACCGTCGTT
1 GACC--CGTT
89711 GACCACTGTT
1 GACC-C-GTT
89721 GACC
1 GACC
89725 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:89701 original size:15 final size:16
Alignment explanation
Indices: 89681--89714 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
89671 TTGACTCGAC
89681 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
89696 CCGTTGACCGTCGTTGA
1 CCGTTGACCG-CGTTGA
89713 CC
1 CC
89715 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.26, T:0.26
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:92189 original size:48 final size:48
Alignment explanation
Indices: 92137--92268 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
92127 AATATTTTAC
*
92137 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
92185 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
92233 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
92269 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:92275 original size:24 final size:24
Alignment explanation
Indices: 92154--92268 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
92144 TCGATTTGAT
92154 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
92178 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
92202 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
92226 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
92249 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
92269 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:92291 original size:24 final size:24
Alignment explanation
Indices: 92205--92278 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
92195 ACATGGATTC
* * *
92205 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
92229 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
92253 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
92277 TG
1 TG
92279 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:104572 original size:62 final size:62
Alignment explanation
Indices: 104475--104610 Score: 245
Period size: 62 Copynumber: 2.2 Consensus size: 62
104465 AGTTGATGAG
104475 AACATGGGCTGTAGGTGAATTGGTCATGTTTAGTGCTTGAATGACCTTAGATGCCAAAGAGT
1 AACATGGGCTGTAGGTGAATTGGTCATGTTTAGTGCTTGAATGACCTTAGATGCCAAAGAGT
* *
104537 AACATGGGCTGTAGGTGAATTGGTCGTGTTTAGTGCTTGAATGACCTTTGATGCCAAAGAGT
1 AACATGGGCTGTAGGTGAATTGGTCATGTTTAGTGCTTGAATGACCTTAGATGCCAAAGAGT
*
104599 AACATGAGCTGT
1 AACATGGGCTGT
104611 GGGACAAAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.31
Consensus pattern (62 bp):
AACATGGGCTGTAGGTGAATTGGTCATGTTTAGTGCTTGAATGACCTTAGATGCCAAAGAGT
Found at i:108929 original size:23 final size:23
Alignment explanation
Indices: 108895--108954 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
108885 AGTTGAGCGC
108895 TACCTAAAATGTTACTTTTTTCT
1 TACCTAAAATGTTACTTTTTTCT
*
108918 TACTTAAAATGTTACTTTTTTCT
1 TACCTAAAATGTTACTTTTTTCT
*
108941 TACCGAAAATGTTA
1 TACCTAAAATGTTA
108955 ATTTCGCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (23 bp):
TACCTAAAATGTTACTTTTTTCT
Found at i:109578 original size:13 final size:13
Alignment explanation
Indices: 109560--109584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109550 ATGATACTCC
109560 AATTTTTTTTTTG
1 AATTTTTTTTTTG
109573 AATTTTTTTTTT
1 AATTTTTTTTTT
109585 ATAAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:109633 original size:21 final size:20
Alignment explanation
Indices: 109593--109659 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
109583 TTATAAATTT
*
109593 AATATAAAAACATTTAATAAAA
1 AATA-AAAAATATTT-ATAAAA
109615 AATAAAAATATATTTAT-AAA
1 AATAAAAA-ATATTTATAAAA
*
109635 ATTAAAAAATATTTATAAAA
1 AATAAAAAATATTTATAAAA
109655 TAATA
1 -AATA
109660 TCTCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.21
20 13 0.33
21 9 0.23
22 9 0.23
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAAAATATTTATAAAA
Found at i:109635 original size:19 final size:18
Alignment explanation
Indices: 109613--109657 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
109603 CATTTAATAA
109613 AAAATAAAAATATATTTAT
1 AAAATAAAAA-ATATTTAT
109632 AAAATTAAAAAATATTTAT
1 AAAA-TAAAAAATATTTAT
109651 AAAATAA
1 AAAATAA
109658 TATCTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
20 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAAAAAATATTTAT
Found at i:127270 original size:41 final size:39
Alignment explanation
Indices: 127204--127297 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 39
127194 AGTTTCCAAT
* * *
127204 TTCGCAACGCAAATATGTAAATCGC-ATTGCGACTTTCTAAA
1 TTCGCAACGCGAATATGTAAATCGCAACT--GAATTTC-AAA
127245 TTCGCAACGCGAA-A-GTCAAATTCGCAACTGAATTTCAAA
1 TTCGCAACGCGAATATGT-AAA-TCGCAACTGAATTTCAAA
127284 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
127298 TTAATTTCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 18 0.39
40 10 0.22
41 16 0.35
42 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (39 bp):
TTCGCAACGCGAATATGTAAATCGCAACTGAATTTCAAA
Found at i:127299 original size:20 final size:20
Alignment explanation
Indices: 127232--127310 Score: 90
Period size: 19 Copynumber: 4.0 Consensus size: 20
127222 AAATCGCATT
*
127232 GCGACTTTCTAAATTCGCAAC
1 GCGAATTTC-AAATTCGCAAC
**
127253 GCGAAAGTCAAATTCGCAAC
1 GCGAATTTCAAATTCGCAAC
*
127273 -TGAATTTCAAATTCGCAAC
1 GCGAATTTCAAATTCGCAAC
*
127292 GCGAATTT-AATTTCGCAAC
1 GCGAATTTCAAATTCGCAAC
127311 AGGTTTTAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 26 0.53
20 17 0.35
21 6 0.12
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (20 bp):
GCGAATTTCAAATTCGCAAC
Found at i:128077 original size:12 final size:12
Alignment explanation
Indices: 128056--128089 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
128046 ACCACATTTC
*
128056 CAATACCAAACA
1 CAATATCAAACA
128068 CAATATCAAACA
1 CAATATCAAACA
*
128080 CAATCTCAAA
1 CAATATCAAA
128090 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:128242 original size:24 final size:24
Alignment explanation
Indices: 128215--128268 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
128205 GTATTCGAAA
128215 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
128239 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
128263 TTTGAT
1 TTTGAT
128269 GATATGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:130554 original size:18 final size:18
Alignment explanation
Indices: 130531--130566 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
130521 AAGCAAAAGG
*
130531 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
130549 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
130567 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:130914 original size:20 final size:20
Alignment explanation
Indices: 130885--130938 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
130875 ACGCGAAATA
130885 AGCGTTGCGAATTTGACTAT
1 AGCGTTGCGAATTTGACTAT
* *
130905 AGCGTAGCGAATTTGACTTT
1 AGCGTTGCGAATTTGACTAT
*
130925 CGCGTTGCGAATTT
1 AGCGTTGCGAATTT
130939 ACCTTCAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (20 bp):
AGCGTTGCGAATTTGACTAT
Found at i:131041 original size:25 final size:25
Alignment explanation
Indices: 131003--131052 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
130993 CAATCAATTA
*
131003 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
131028 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
131053 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:131495 original size:20 final size:20
Alignment explanation
Indices: 131470--131554 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
131460 ACGTAAAAAC
131470 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
131490 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
* ** *
131509 ATTTCCAAATTCGCATTGCGA
1 ATTT-GACTTTCGCGTTGCGA
131530 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
131550 ATTTG
1 ATTTG
131555 GAAAATCGCA
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.10
20 41 0.80
21 5 0.10
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:131611 original size:20 final size:20
Alignment explanation
Indices: 131516--131611 Score: 52
Period size: 20 Copynumber: 4.8 Consensus size: 20
131506 GCGATTTCCA
* *
131516 AATTCGCATTGCG-AATTTG
1 AATTCGCGTTGCGAAATTGG
* *
131535 ACTTTCGCGTTGCGAATTTGG
1 A-ATTCGCGTTGCGAAATTGG
* ***
131556 AAAATCGCAACGCGAAATTGG
1 -AATTCGCGTTGCGAAATTGG
* * *
131577 AA-ACTGGGTTACGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
131597 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
131612 TTTGTTGGTC
Statistics
Matches: 53, Mismatches: 19, Indels: 9
0.65 0.23 0.11
Matches are distributed among these distances:
19 2 0.04
20 32 0.60
21 18 0.34
22 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:131992 original size:26 final size:26
Alignment explanation
Indices: 131953--132018 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
131943 TATTACTTTT
* * *
131953 TATTAATATCGTTACGATGTATTTCA
1 TATTAATATTGTTACAAAGTATTTCA
**
131979 TATTGGTATTGTTACAAAGTATTTCA
1 TATTAATATTGTTACAAAGTATTTCA
132005 TATTAATATTGTTA
1 TATTAATATTGTTA
132019 TTGCACATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (26 bp):
TATTAATATTGTTACAAAGTATTTCA
Found at i:132711 original size:60 final size:60
Alignment explanation
Indices: 132611--132723 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
132601 AATGGTCTCC
132611 TGACTATAGGGTGTTGTTTCGTTGAGTCCCTCACTAATTAAAAGTTACAAAATAATCATA
1 TGACTATAGGGTGTTGTTTCGTTGAGTCCCTCACTAATTAAAAGTTACAAAATAATCATA
* * * * *
132671 TGACTTTAGGGTGTTGCTTT-GTTGAGTTCCTTGA-TTATTAATAGTTACAAAAT
1 TGACTATAGGGTGTTG-TTTCGTTGAG-TCCCTCACTAATTAAAAGTTACAAAAT
132724 GATCTTCGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 38 0.83
61 8 0.17
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (60 bp):
TGACTATAGGGTGTTGTTTCGTTGAGTCCCTCACTAATTAAAAGTTACAAAATAATCATA
Found at i:133599 original size:21 final size:21
Alignment explanation
Indices: 133517--133615 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
133507 ATATTTATTT
133517 TTTATTTATTATTATTGT-TACTA
1 TTTA-TTATT-TTATT-TATACTA
*
133540 TTTAGTATTTTATATATATACATACA
1 TTTATTATTTTAT-T-TATAC-T--A
133566 TTT-TTA-TTT-TTTATA-TA
1 TTTATTATTTTATTTATACTA
133583 TTTTATTATTTTATTTATACTA
1 -TTTATTATTTTATTTATACTA
133605 TTTATTATTTT
1 TTTATTATTTT
133616 TTATTATGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
17 1 0.02
18 3 0.05
19 4 0.06
20 3 0.05
21 25 0.40
22 9 0.14
23 8 0.13
24 4 0.06
25 2 0.03
26 4 0.06
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTATTATTTTATTTATACTA
Found at i:134052 original size:33 final size:34
Alignment explanation
Indices: 133987--134054 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
133977 CGAATAGGCG
133987 GTTCAAGGGTGCTAATCCTTCCTTGACCGTAACC
1 GTTCAAGGGTGCTAATCCTTCCTTGACCGTAACC
134021 GTTCAAGGGTGCTAATCCTTCC-TGACCGTAACC
1 GTTCAAGGGTGCTAATCCTTCCTTGACCGTAACC
134054 G
1 G
134055 ACTCCCGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 12 0.35
34 22 0.65
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (34 bp):
GTTCAAGGGTGCTAATCCTTCCTTGACCGTAACC
Found at i:134733 original size:80 final size:82
Alignment explanation
Indices: 134607--134760 Score: 285
Period size: 80 Copynumber: 1.9 Consensus size: 82
134597 GTCTGGCAAG
134607 CCACGGGGGCATCGGCAAGGAGAACTCGGGTACCATTTTTAGAACCTAAACCATGAAGCTATGGA
1 CCACGGGGGCATCGGCAAGGAGAAC-CGGGTACCATTTTTAGAACCTAAACCATGAAGCTATGGA
134672 GAAATAGAGGCAAGCTAC
65 GAAATAGAGGCAAGCTAC
134690 CCACGGGGGCATC-GCAAGGAGAA-CGGGTACCATTTTTAGAACCTAAACCATGAAGCTATGGAG
1 CCACGGGGGCATCGGCAAGGAGAACCGGGTACCATTTTTAGAACCTAAACCATGAAGCTATGGAG
134753 AAATAGAG
66 AAATAGAG
134761 CCTACCCCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
80 48 0.68
82 10 0.14
83 13 0.18
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (82 bp):
CCACGGGGGCATCGGCAAGGAGAACCGGGTACCATTTTTAGAACCTAAACCATGAAGCTATGGAG
AAATAGAGGCAAGCTAC
Found at i:138312 original size:24 final size:24
Alignment explanation
Indices: 138274--138325 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
138264 ACAAAAGGGC
*
138274 AAAAAAAGAAGAAAAAC-AAAAGA
1 AAAAAAAGAACAAAAACAAAAAGA
*
138297 AAAATAAAGAACAAAATCAAAAAGA
1 AAAA-AAAGAACAAAAACAAAAAGA
138322 AAAA
1 AAAA
138326 GGACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.81, C:0.06, G:0.10, T:0.04
Consensus pattern (24 bp):
AAAAAAAGAACAAAAACAAAAAGA
Found at i:139176 original size:24 final size:24
Alignment explanation
Indices: 139149--139209 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
139139 GGGACAATAT
*
139149 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
*
139173 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
139197 TTTCAAAACTCTT
1 TTTCAAAACTCTT
139210 TTTTGATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTCTTAATTAAACATC
Found at i:139425 original size:17 final size:17
Alignment explanation
Indices: 139393--139426 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
139383 TCAACATCAA
* *
139393 ATATTGGGGATTTTTGG
1 ATATTGGGCATCTTTGG
139410 ATATTGGGCATCTTTGG
1 ATATTGGGCATCTTTGG
139427 GGATTCAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.32, T:0.44
Consensus pattern (17 bp):
ATATTGGGCATCTTTGG
Found at i:139907 original size:36 final size:36
Alignment explanation
Indices: 139859--139933 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
139849 GTGCCCACCA
*
139859 TTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAACT
1 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAA-AAACT
*
139895 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAACCT
1 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAAACT
139931 TTG
1 TTG
139934 AAATCGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (36 bp):
TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAAACT
Found at i:139950 original size:16 final size:16
Alignment explanation
Indices: 139929--139967 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
139919 TTAGAAAAAC
**
139929 CTTTGAAATCGTTTCT
1 CTTTGAAAAAGTTTCT
139945 CTTTGAAAAAGTTTCT
1 CTTTGAAAAAGTTTCT
139961 C-TTGAAA
1 CTTTGAAA
139968 CATACACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (16 bp):
CTTTGAAAAAGTTTCT
Found at i:140712 original size:106 final size:106
Alignment explanation
Indices: 140527--141094 Score: 740
Period size: 106 Copynumber: 5.4 Consensus size: 106
140517 TCAAATTTCA
* * *
140527 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
* **
140592 -AAGCGAAGGGGCGGCTGACTGTCAACAAACAACTTCCCAAT
66 CAA-CGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
* * * * *
140633 TTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
* * *
140698 CGACGAATGGG-CGGCTGATTGTCAAC-AA-AA-TT-TC-A-
66 CAACGAA-GGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
* * * * * *
140733 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCCCAAGTTTAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
140798 CAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
66 C-AACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
*
140840 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
* * * * *
140905 CAACGAAGGGATGGTTGGTTGACAACAAACAATTTCTCAAT
66 CAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
*
140946 TTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
* * *
141011 CAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCGAT
66 CAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
* * *
141052 TCCAGAGGCAATTTCAACTTCAC-GACGGAGGATATTGGACTCG
1 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTCG
141095 GAACAATGCT
Statistics
Matches: 404, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
100 60 0.15
101 20 0.05
102 3 0.01
103 4 0.01
104 4 0.01
105 4 0.01
106 246 0.61
107 63 0.16
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
CAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
Found at i:141896 original size:37 final size:37
Alignment explanation
Indices: 141843--141947 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
141833 CATTTTCGTC
141843 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
141880 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
141917 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
141948 TCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:142444 original size:31 final size:30
Alignment explanation
Indices: 142404--142461 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
142394 TACTTTGCGT
* *
142404 TATATTATATTATTTTCTTATTATTATATA
1 TATATTATATTATATTATTATTATTATATA
*
142434 TATATATATATTATATTATTATTTTTAT
1 TATAT-TATATTATATTATTATTATTAT
142462 CTATGTTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
TATATTATATTATATTATTATTATTATATA
Found at i:142445 original size:28 final size:26
Alignment explanation
Indices: 142404--142456 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
142394 TACTTTGCGT
* *
142404 TATATTATATTATTTTCTTATTATTA
1 TATATTATATTATTATATTATTATTA
142430 TATATATATATATATTATATTATTATT
1 TATAT-TATAT-TATTATATTATTATT
142457 TTTATCTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 5 0.22
28 13 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TATATTATATTATTATATTATTATTA
Found at i:142656 original size:7 final size:7
Alignment explanation
Indices: 142644--142683 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
142634 ATACATACAT
142644 TTTTATA
1 TTTTATA
142651 TTTTATA
1 TTTTATA
142658 TTTTATTA
1 TTTTA-TA
*
142666 TTTTATT
1 TTTTATA
142673 TATTTATA
1 T-TTTATA
142681 TTT
1 TTT
142684 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTATA
Found at i:142667 original size:15 final size:14
Alignment explanation
Indices: 142644--142683 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
142634 ATACATACAT
142644 TTTTATATTTTATA
1 TTTTATATTTTATA
*
142658 TTTTATTATTTTATT
1 TTTTA-TATTTTATA
142673 TATTTATATTT
1 T-TTTATATTT
142684 ATTTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 14 0.61
16 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATATTTTATA
Found at i:143549 original size:40 final size:40
Alignment explanation
Indices: 143505--143631 Score: 95
Period size: 40 Copynumber: 3.2 Consensus size: 40
143495 GGGGTTAACT
143505 CCACTTTATGAGTTATTTCCTTGTACTTCGTAGTAATTTA
1 CCACTTTATGAGTTATTTCCTTGTACTTCGTAGTAATTTA
* * * * *
143545 CCACTTTCTTG-G--ATGT-ATAGATA-TTACGT-GTATATTATTT
1 CCACTTT-ATGAGTTATTTCCTTG-TACTT-CGTAGTA-A-T-TTA
* *
143585 CCACGTTATGAGTTCTTTCCTTGTACTTCGTAGTAATTTA
1 CCACTTTATGAGTTATTTCCTTGTACTTCGTAGTAATTTA
143625 CCACTTT
1 CCACTTT
143632 CTTGGATGAT
Statistics
Matches: 62, Mismatches: 13, Indels: 24
0.63 0.13 0.24
Matches are distributed among these distances:
37 7 0.11
38 9 0.15
39 3 0.05
40 25 0.40
41 3 0.05
42 8 0.13
43 7 0.11
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.46
Consensus pattern (40 bp):
CCACTTTATGAGTTATTTCCTTGTACTTCGTAGTAATTTA
Found at i:149146 original size:60 final size:60
Alignment explanation
Indices: 149028--149152 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
149018 ATTGGGTGAT
* * *
149028 CATTTTGTAACTTTTAATAGTCGAGTAACTCAACAAAGCAACTTCCTATAACCGGGGGAC
1 CATTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAACTTCCTATAACCAGGGGAC
* * * * ***
149088 CATTTTATAACTTTTCATAGTCGGGGGACTCAACAAAG-AAGTATCCTATAGTTAGGGGAC
1 CATTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAACT-TCCTATAACCAGGGGAC
149148 CATTT
1 CATTT
149153 GTGTACTTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAACTTCCTATAACCAGGGGAC
Found at i:159437 original size:22 final size:22
Alignment explanation
Indices: 159377--159439 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
159367 CGCAACGCGA
*
159377 TTCTGACTATCGCATTACGATT
1 TTCTGACTATCGCATTGCGATT
* * *
159399 TT-TCA-AATTCGCGTTGCGATT
1 TTCTGACTA-TCGCATTGCGATT
159420 TTCTGACTATCGCATTGCGA
1 TTCTGACTATCGCATTGCGA
159440 ATATGTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.48
22 14 0.45
23 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (22 bp):
TTCTGACTATCGCATTGCGATT
Found at i:159474 original size:20 final size:20
Alignment explanation
Indices: 159451--159581 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
159441 TATGTAAATT
* *
159451 GCAATGCGAGTATGACTATC
1 GCAACGCGATTATGACTATC
* *
159471 GCAACGAGATTCTGACTATC
1 GCAACGCGATTATGACTATC
* *
159491 GCAACGAGATTCTGACTATC
1 GCAACGCGATTATGACTATC
* *
159511 GCAACGCGATTTTGACTGTC
1 GCAACGCGATTATGACTATC
* *
159531 GCAACGCGATTCTGACTGTC
1 GCAACGCGATTATGACTATC
** *
159551 GCAACGCGATGCTAACTATC
1 GCAACGCGATTATGACTATC
*
159571 GCAATGCGATT
1 GCAACGCGATT
159582 TTCAAAGCGT
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTATGACTATC
Found at i:159527 original size:60 final size:60
Alignment explanation
Indices: 159463--159583 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
159453 AATGCGAGTA
* *
159463 TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATTCTGACTATCGCAACGCGATTT
1 TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATGCTAACTATCGCAACGCGATTT
* * * * *
159523 TGACTGTCGCAACGCGATTCTGACTGTCGCAACGCGATGCTAACTATCGCAATGCGATTT
1 TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATGCTAACTATCGCAACGCGATTT
159583 T
1 T
159584 CAAAGCGTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (60 bp):
TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATGCTAACTATCGCAACGCGATTT
Found at i:159580 original size:40 final size:40
Alignment explanation
Indices: 159463--159581 Score: 166
Period size: 40 Copynumber: 3.0 Consensus size: 40
159453 AATGCGAGTA
* *
159463 TGACTATCGCAACGAGATTCTGACTATCGCAACGAGATTC
1 TGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTC
* *
159503 TGACTATCGCAACGCGATTTTGACTGTCGCAACGCGATTC
1 TGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTC
* * * *
159543 TGACTGTCGCAACGCGATGCTAACTATCGCAATGCGATT
1 TGACTATCGCAACGCGATTCTGACTATCGCAACGCGATT
159582 TTCAAAGCGT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
TGACTATCGCAACGCGATTCTGACTATCGCAACGCGATTC
Found at i:159789 original size:22 final size:22
Alignment explanation
Indices: 159764--159806 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
159754 GGCGACATCC
159764 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
159786 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
159807 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:160205 original size:19 final size:19
Alignment explanation
Indices: 160183--160270 Score: 79
Period size: 19 Copynumber: 4.5 Consensus size: 19
160173 AGAATCGCAA
160183 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
160202 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** *
160221 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTC-ATTTCGCGT
** *
160241 TGCGATAGTCATTTTTCGTGT
1 TGCGATTTTCA--TTTCGCGT
160262 TGCGATTTT
1 TGCGATTTT
160271 AAGTTTCAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 26 0.45
20 19 0.33
21 13 0.22
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:160263 original size:21 final size:20
Alignment explanation
Indices: 160194--160267 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
160184 GCGATTTTAG
**
160194 TTTCGCGTTGCGATTTTC-A
1 TTTCGCGTTGCGATAGTCAA
160213 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* *
160233 ATTCGCGTTGCGATAGTCATT
1 TTTCGCGTTGCGATAGTCA-A
*
160254 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
160268 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.34
20 19 0.40
21 12 0.26
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:162010 original size:18 final size:17
Alignment explanation
Indices: 161987--162036 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 17
161977 TTTACTCGTA
161987 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATT-ACC
162005 ATTTCACTTAGATGTACC
1 ATTTCACTTAGAT-TACC
162023 ATTTCACTTAGATT
1 ATTTCACTTAGATT
162037 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTTCACTTAGATTACC
Found at i:162308 original size:20 final size:20
Alignment explanation
Indices: 162257--162310 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
162247 ATTCTCTCAT
** *
162257 TGCGATAGTCAAATTCGCGT
1 TGCGATAGTCATTTTCGCGC
162277 TGCGATAGTCATTTTCGCGC
1 TGCGATAGTCATTTTCGCGC
162297 TGCGATAGTCATTT
1 TGCGATAGTCATTT
162311 GTGTTGCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
TGCGATAGTCATTTTCGCGC
Found at i:162914 original size:42 final size:41
Alignment explanation
Indices: 162807--162917 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 41
162797 GCCGACTCAC
* *
162807 CTGTCATCGTTCAAGAGT-CCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCCCT-CCC-ACCGTTCAAGAGGCCA
** * *
162849 CTGTCATCCCTCAAGAATCCCCTCCCACCGTTCAAGAGGTCA
1 CTGTCATCGTTCAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
*
162891 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCTCCCA
162918 ATATTCTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 49 0.88
43 4 0.07
44 3 0.05
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:164348 original size:14 final size:14
Alignment explanation
Indices: 164314--164375 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
164304 TTGCTTGTTT
*
164314 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
164328 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
164342 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
164357 TATTGATGTGTAAA
1 AATTGATTTGTAAA
164371 TAATT
1 -AATT
164376 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:164527 original size:20 final size:20
Alignment explanation
Indices: 164475--164527 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
164465 GGTACACTTT
* ** *
164475 CGCAACGCTAAACTCAAAAT
1 CGCAACGCGAAAGACAAAAG
*
164495 CGCAATGCGAAAGACAAAAG
1 CGCAACGCGAAAGACAAAAG
164515 CGCAACGCGAAAG
1 CGCAACGCGAAAG
164528 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.21, T:0.08
Consensus pattern (20 bp):
CGCAACGCGAAAGACAAAAG
Found at i:164563 original size:20 final size:20
Alignment explanation
Indices: 164521--164834 Score: 263
Period size: 20 Copynumber: 16.6 Consensus size: 20
164511 AAAGCGCAAC
*
164521 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
164540 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
164560 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
164574 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
164594 GAGATAATCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
*
164614 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
164634 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
164654 GCGATAGTCAAATAAC-CGTT
1 GCGATAGTCAAAT-TCGCGTT
*
164674 GCTATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
164694 GCGATAGTCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
164714 ACGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
164728 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
*
164748 GCGATAGTCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
* *
164768 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
164782 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
164802 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
164822 ACGATATTCAAAT
1 GCGATAGTCAAAT
164835 GAATGTGTAA
Statistics
Matches: 240, Mismatches: 34, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
14 33 0.14
16 3 0.01
18 3 0.01
19 9 0.04
20 191 0.80
21 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:164735 original size:54 final size:54
Alignment explanation
Indices: 164611--164826 Score: 261
Period size: 54 Copynumber: 3.9 Consensus size: 54
164601 TCAAATTCGT
* * ***
164611 GTTGCGATACTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATAACC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGAT--T----TTTGC
* *
164671 GTTGCTATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTACGATTTTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGATTTTTGC
* * * * *
164725 GTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGTGTTGCGATTTTTGA
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGATTTTTGC
*
164779 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGAT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGAT
164827 ATTCAAATGA
Statistics
Matches: 137, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
54 92 0.67
58 1 0.01
60 44 0.32
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGATTTTTGC
Found at i:164801 original size:74 final size:75
Alignment explanation
Indices: 164570--164834 Score: 232
Period size: 74 Copynumber: 3.5 Consensus size: 75
164560 GCGATTTTCT
* * * * * *
164570 CGTTGCGATAGTCAAATACCCGTTGAGATAATCAAATTCGTGTTGCGATACTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA-----GTTG
*
164635 CGATAGTCAAATTCG
61 CGATAATCAAATTCG
* * *
164650 CGTTGCGATAGTCAAATAAC-CGTTGCTATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCG-T
1 CGTTGCGATAGTCAAAT-TCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAGTTGCGAT
* ** *
164713 TA-CGATTTTTG
65 AATC-AAATTCG
* * * * ***
164724 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGTGTTGCGAT-TTTTGAGTTGCGATA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAGTTGCGATA
164788 ATCAAATTCG
66 ATCAAATTCG
* *
164798 CGTTGCGATAGTCAAATTCGCGTTACGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
164835 GAATGTGTAA
Statistics
Matches: 151, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
73 9 0.06
74 86 0.57
75 6 0.04
80 48 0.32
81 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (75 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAGTTGCGATA
ATCAAATTCG
Found at i:165057 original size:140 final size:140
Alignment explanation
Indices: 164805--165074 Score: 468
Period size: 140 Copynumber: 1.9 Consensus size: 140
164795 TCGCGTTGCG
* * *
164805 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAATATATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
*
164870 TAGCAATGTTCAAACTTAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
164935 ATTACACATA
131 ATTACACATA
* * *
164945 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
*
165010 TAGCAATGTTCAAACTCAAGTTACTTATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
165075 TACAACGTTT
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 122 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTACGATATTCAAATGAATATGTAACAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
ATTACACATA
Found at i:165157 original size:18 final size:18
Alignment explanation
Indices: 165134--165168 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
165124 AAGCCAGTTG
*
165134 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
165152 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
165169 GTCTTTTTCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:167459 original size:24 final size:24
Alignment explanation
Indices: 167432--167485 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
167422 CTGAAACATC
*
167432 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
167456 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
167480 ATCAAA
1 ATCAAA
167486 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:168361 original size:20 final size:20
Alignment explanation
Indices: 168315--168385 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
168305 AAATTCAGTG
* *
168315 TTGCGACAGTCAAAATCGCA
1 TTGCGATAGTCATAATCGCA
168335 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
168355 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
168375 TTGCGATAGTC
1 TTGCGATAGTC
168386 GGAAAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:175837 original size:21 final size:20
Alignment explanation
Indices: 175813--175863 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
175803 TAAAAATTAT
**
175813 AAAAATAAAATATAAAATGTC
1 AAAAAT-AAATATAAAAAATC
*
175834 -AAAATTAATATAAAAAATC
1 AAAAATAAATATAAAAAATC
175853 AAAAATTAAAT
1 AAAAA-TAAAT
175864 TTAACATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAATAAATATAAAAAATC
Found at i:175854 original size:19 final size:20
Alignment explanation
Indices: 175821--175861 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
175811 ATAAAAATAA
**
175821 AATATAAAATGTC-AAAATT
1 AATATAAAAAATCAAAAATT
175840 AATATAAAAAATCAAAAATT
1 AATATAAAAAATCAAAAATT
175860 AA
1 AA
175862 ATTTAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
AATATAAAAAATCAAAAATT
Found at i:176069 original size:16 final size:17
Alignment explanation
Indices: 176043--176074 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
176033 CGTCCTAAAA
176043 TTTATTTTTATTAATTT
1 TTTATTTTTATTAATTT
176060 TTTA-TTTTATTAATT
1 TTTATTTTTATTAATT
176075 ATGTTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTATTAATTT
Found at i:177303 original size:21 final size:21
Alignment explanation
Indices: 177257--177304 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
177247 ACATCTTATT
* *
177257 ATTTTT-ATGTATTTTAATTC
1 ATTTTTCATGTATTTCAATAC
* *
177277 AATTTTCATTTATTTCAATAC
1 ATTTTTCATGTATTTCAATAC
177298 ATTTTTC
1 ATTTTTC
177305 TTGTTTTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTTCATGTATTTCAATAC
Found at i:178358 original size:22 final size:22
Alignment explanation
Indices: 178330--178372 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
178320 ATTTTAGGGT
* *
178330 TTTTTTAAATTATCTTTTTAAG
1 TTTTTTAAATAATATTTTTAAG
178352 TTTTTTAAATAATATTTTTAA
1 TTTTTTAAATAATATTTTTAA
178373 AATTATTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTTAAATAATATTTTTAAG
Found at i:178851 original size:20 final size:21
Alignment explanation
Indices: 178826--178865 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
178816 CATCCAAAAA
*
178826 TATATTTT-ATAGTATATATC
1 TATATTTTAATAATATATATC
178846 TATATTTTAATAATATATAT
1 TATATTTTAATAATATATAT
178866 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
TATATTTTAATAATATATATC
Found at i:179363 original size:23 final size:23
Alignment explanation
Indices: 179320--179375 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
179310 TATTTGTGTT
*
179320 TGTTCATTTAACATTTGCGAACA
1 TGTTCGTTTAACATTTGCGAACA
*
179343 TGTTCGTTTAACATTCT-CGAATA
1 TGTTCGTTTAACATT-TGCGAACA
*
179366 TATTCGTTTA
1 TGTTCGTTTA
179376 GTGTTCGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (23 bp):
TGTTCGTTTAACATTTGCGAACA
Found at i:179391 original size:23 final size:23
Alignment explanation
Indices: 179365--179424 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
179355 ATTCTCGAAT
179365 ATATTCGTTTAGTGTTCGCAAAC
1 ATATTCGTTTAGTGTTCGCAAAC
* *
179388 ATATTCGTTTAGCGTTCGTAAAC
1 ATATTCGTTTAGTGTTCGCAAAC
*
179411 ATGTTCGTTTAGTG
1 ATATTCGTTTAGTG
179425 CTTGTATAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (23 bp):
ATATTCGTTTAGTGTTCGCAAAC
Found at i:180733 original size:16 final size:16
Alignment explanation
Indices: 180712--180744 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
180702 AAGTGACGTA
*
180712 AGAATAAAAGCTCATT
1 AGAATAAAAGCTAATT
180728 AGAATAAAAGCTAATT
1 AGAATAAAAGCTAATT
180744 A
1 A
180745 ATATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (16 bp):
AGAATAAAAGCTAATT
Found at i:186861 original size:37 final size:37
Alignment explanation
Indices: 186788--186862 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
186778 GTTAGAAAAT
*
186788 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
186825 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
186862 A
1 A
186863 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:188617 original size:2 final size:2
Alignment explanation
Indices: 188612--188642 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
188602 GTTCCCGTCT
188612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
188643 TTTTACTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:188838 original size:118 final size:117
Alignment explanation
Indices: 188631--188866 Score: 427
Period size: 118 Copynumber: 2.0 Consensus size: 117
188621 ATATATATAT
*
188631 ATATATATATATTTTTACTTGTTCCTCACTTTTGGTTCTACTTTTCTTAGGGGCGAAGAGTGAGT
1 ATATATATATATTTTTACTTGTTCCTCACTTTTGGTTCTACTTTTCTTAGGAGCGAAGAGTGAGT
188696 TAGTCGTCTTTTTTATATAATTAGTGACGCTTCGGTCACCGCTTATCTAAGC
66 TAGTCGTCTTTTTTATATAATTAGTGACGCTTCGGTCACCGCTTATCTAAGC
* * *
188748 ATATATATTTCTTTTTAACTTGTTCCTCACTTTTGGTTCTAGTTTTCTTAGGAGCGAAGAGTGAG
1 ATATATATATATTTTT-ACTTGTTCCTCACTTTTGGTTCTACTTTTCTTAGGAGCGAAGAGTGAG
188813 TTAGTCGTCTTTTTTATATAATTAGTGACGCTTCGGTCACCGCTTATCTAAGC
65 TTAGTCGTCTTTTTTATATAATTAGTGACGCTTCGGTCACCGCTTATCTAAGC
188866 A
1 A
188867 GTGACGATCA
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
117 14 0.12
118 100 0.88
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.44
Consensus pattern (117 bp):
ATATATATATATTTTTACTTGTTCCTCACTTTTGGTTCTACTTTTCTTAGGAGCGAAGAGTGAGT
TAGTCGTCTTTTTTATATAATTAGTGACGCTTCGGTCACCGCTTATCTAAGC
Found at i:196947 original size:21 final size:20
Alignment explanation
Indices: 196922--196963 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
196912 CCCAGAATGG
*
196922 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCC-TCAT
196943 AGGGAATCGATACCCCTCAT
1 AGGGAATCGATACCCCTCAT
196963 A
1 A
196964 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (20 bp):
AGGGAATCGATACCCCTCAT
Found at i:197136 original size:33 final size:35
Alignment explanation
Indices: 197091--197156 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
197081 ATATGTACCC
197091 GGGGAATAGATA-CCCCT-GGGGGAATCTGTTCTT
1 GGGGAATAGATACCCCCTGGGGGGAATCTGTTCTT
*
197124 GGGGAATCGATACCCCCTGGGGGGAATCTGTTC
1 GGGGAATAGATACCCCCTGGGGGGAATCTGTTC
197157 CCTCTGGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 11 0.37
34 5 0.17
35 14 0.47
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.24
Consensus pattern (35 bp):
GGGGAATAGATACCCCCTGGGGGGAATCTGTTCTT
Found at i:198572 original size:19 final size:20
Alignment explanation
Indices: 198529--198576 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
198519 TCAAAATCCT
*
198529 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
198549 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
198568 TTTTCAAAA
1 TTTTCAAAA
198577 GGAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:199705 original size:21 final size:21
Alignment explanation
Indices: 199679--199720 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
199669 CCAGAATGGG
*
199679 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
199700 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
199721 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:199872 original size:19 final size:19
Alignment explanation
Indices: 199848--199910 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 19
199838 ATCTGTACCC
199848 GGGGAATCGATACCCCTGG
1 GGGGAATCGATACCCCTGG
*
199867 GGGGAATCTG-T-TCCC---
1 GGGGAATC-GATACCCCTGG
199882 GGGGAATCGATACCCCCTGG
1 GGGGAATCGATA-CCCCTGG
199902 GGAGGAATC
1 GG-GGAATC
199911 TGTTCCCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
17 3 0.09
18 3 0.09
19 9 0.26
20 3 0.09
21 6 0.18
ACGTcount: A:0.21, C:0.25, G:0.37, T:0.17
Consensus pattern (19 bp):
GGGGAATCGATACCCCTGG
Found at i:199916 original size:36 final size:35
Alignment explanation
Indices: 199832--199917 Score: 140
Period size: 34 Copynumber: 2.5 Consensus size: 35
199822 AAACCATGCA
*
199832 GGGA-GAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGAGGAATCTGTTCCCGGGGAATCGATACCCCTG
199866 GGG-GGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGAGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
199901 GGGAGGAATCTGTTCCC
1 GGGAGGAATCTGTTCCC
199918 TCTGGGCAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
34 26 0.54
35 9 0.19
36 13 0.27
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (35 bp):
GGGAGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:201259 original size:19 final size:19
Alignment explanation
Indices: 201235--201271 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
201225 TATCATTAAC
201235 ATTTTAAACTTATAAAATA
1 ATTTTAAACTTATAAAATA
* *
201254 ATTTTAAATTTATCAAAT
1 ATTTTAAACTTATAAAAT
201272 TGTTACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTAAACTTATAAAATA
Done.