Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001529.1 Hibiscus syriacus cultivar Beakdansim tig00002996_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: 61166
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:42 original size:20 final size:18
Alignment explanation
Indices: 19--64 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
9 TCAAATTCGC
19 GTTGCGATAGTCATTTTAGT
1 GTTGCGAT-GTC-TTTTAGT
* *
39 GTTGCGATTTCTTTTCGT
1 GTTGCGATGTCTTTTAGT
57 GTTGCGAT
1 GTTGCGAT
65 TTAAAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.58
19 2 0.08
20 8 0.33
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (18 bp):
GTTGCGATGTCTTTTAGT
Found at i:58 original size:18 final size:18
Alignment explanation
Indices: 32--66 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22 GCGATAGTCA
32 TTTTAGTGTTGCGATTTC
1 TTTTAGTGTTGCGATTTC
*
50 TTTTCGTGTTGCGATTT
1 TTTTAGTGTTGCGATTT
67 AAAGTTTCAG
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:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (18 bp):
TTTTAGTGTTGCGATTTC
Found at i:1929 original size:20 final size:20
Alignment explanation
Indices: 1904--2030 Score: 167
Period size: 20 Copynumber: 6.7 Consensus size: 20
1894 AGAATAGTTT
1904 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1924 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1944 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
1960 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1978 ATTACCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1998 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2018 ACTATCGCAATGC
1 ACTATCGCAATGC
2031 AAATTTAACT
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.06
16 4 0.04
17 4 0.04
18 4 0.04
20 75 0.81
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2041 original size:20 final size:20
Alignment explanation
Indices: 1904--2047 Score: 122
Period size: 20 Copynumber: 7.5 Consensus size: 20
1894 AGAATAGTTT
*
1904 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* *
1924 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* *
1944 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATA
* *
1960 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
* * *
1978 ATTACCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
*
1998 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
*
2018 ACTATCGCAATGC-AAATTTA
1 ACTATCGCAATGCGAAA-ATA
2038 ACTATCGCAA
1 ACTATCGCAA
2048 CGAAAGAATC
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
14 6 0.06
16 4 0.04
17 4 0.04
18 4 0.04
19 3 0.03
20 86 0.80
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATA
Found at i:2100 original size:20 final size:20
Alignment explanation
Indices: 2075--2206 Score: 228
Period size: 20 Copynumber: 6.6 Consensus size: 20
2065 GAAATGAAAA
**
2075 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTT
2095 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2115 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2135 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2155 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
2175 TCGCATTGCGATATTCATTT
1 TCGCATTGCGATAGTCATTT
*
2195 TCGCGTTGCGAT
1 TCGCATTGCGAT
2207 TTTAAGTTTC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:2728 original size:18 final size:19
Alignment explanation
Indices: 2689--2730 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2679 CTCACATGTC
2689 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2710 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2728 ATC
1 ATC
2731 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:4155 original size:14 final size:14
Alignment explanation
Indices: 4136--4171 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4126 ATTGTTTAAT
4136 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4150 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4164 TGATTTGT
1 TGATTTGT
4172 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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4335 original size:33 final size:33
Alignment explanation
Indices: 4277--4372 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
4267 CATAATTTCG
*
4277 CGTTGCGATTTTCATTTTCGAATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
4311 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
4344 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
4373 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 32 0.57
34 24 0.43
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:4369 original size:20 final size:20
Alignment explanation
Indices: 4344--4428 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
4334 GCGATTCTCT
4344 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
4364 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
4384 CATTTCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
4404 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
4424 CGTTG
1 CGTTG
4429 TGATTTCCGT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 53 0.96
21 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:6257 original size:24 final size:24
Alignment explanation
Indices: 6230--6276 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6220 CAAAATCCGA
6230 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
6254 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
6277 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:6285 original size:24 final size:24
Alignment explanation
Indices: 6234--6285 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6224 ATCCGAGTAT
** *
6234 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
6258 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
6282 TGAC
1 TGAC
6286 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:7156 original size:20 final size:20
Alignment explanation
Indices: 7133--7178 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
7123 TAGAATCTCG
7133 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
7153 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
7173 TTGCGA
1 TTGCGA
7179 ATTAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:7220 original size:21 final size:21
Alignment explanation
Indices: 7174--7220 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7164 GTATTCGCAT
*
7174 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGAAA
* * *
7195 CGCGAATTTGGGAAATCGAAA
1 TGCGAATTAGGAAAATCGAAA
7216 TGCGA
1 TGCGA
7221 TAGTTAGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGAAA
Found at i:9310 original size:16 final size:16
Alignment explanation
Indices: 9289--9327 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9279 TTGCGTGACT
9289 GGTTAAACAAATAACC
1 GGTTAAACAAATAACC
* * *
9305 GGTTAAATAAGTGACC
1 GGTTAAACAAATAACC
9321 GGTTAAA
1 GGTTAAA
9328 ATCTATACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (16 bp):
GGTTAAACAAATAACC
Found at i:11567 original size:24 final size:24
Alignment explanation
Indices: 11548--11603 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
11538 CGAAATTTAT
11548 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
11572 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
11595 ATATGAAAT
1 AT-TGAAAT
11604 GAACATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.32
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:11569 original size:18 final size:18
Alignment explanation
Indices: 11548--11584 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11538 CGAAATTTAT
11548 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
11566 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
11584 A
1 A
11585 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:14601 original size:21 final size:20
Alignment explanation
Indices: 14570--14622 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
14560 ATTCTAGTTC
*
14570 AAAAGTATCGACATGATTTA
1 AAAAGTATCGACATAATTTA
14590 AAAAGTTATCGACATAATTTA
1 AAAAG-TATCGACATAATTTA
14611 AAAAGGTATCGA
1 AAAA-GTATCGA
14623 TACATTATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 5 0.17
21 24 0.80
22 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAAGTATCGACATAATTTA
Found at i:14748 original size:221 final size:220
Alignment explanation
Indices: 14365--15022 Score: 836
Period size: 221 Copynumber: 3.1 Consensus size: 220
14355 CACGTGTAAT
*
14365 TTTAAAAACGTATCGAAACAATTTAAAAAGGTATTGATACATTATGTTGACCTATTTTCTAATTA
1 TTTAAAAA-GTATCGAAACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTA
14430 AACCGGTATATTTTTACCAGCTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGAT
65 AACCGGTATATTTTTACCAGCTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGAT
* * *
14495 GTTTTTGGAATCGATACTTACAATAAATGTATCGATACTTGATGCGTGCACCTCGTTGGGCATTC
130 GTTTTTGGAATCGATACTTACAATAAATGTATCGACACTTGATACGTACACCTCGTTGGGCATTC
** **
14560 ATTCTAGTTCAAAAGTATCGACATGA
195 ATTCTAGACCAAAAGTATCGACACAA
* * * *
14586 TTTAAAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTATCTATTTTCTAATTA
1 TTTAAAAAG-TATCGAAACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTA
* ** * *
14651 AATCGGTATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGAT
65 AACCGGTATATTTTTACCAGCTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGAT
* * * *
14716 GTTTTTGGGATCGATACTTACAATAAATGTATCGACACTTTATACGTATACCTTGTTGGGCATTC
130 GTTTTTGGAATCGATACTTACAATAAATGTATCGACACTTGATACGTACACCTCGTTGGGCATTC
*
14781 ATTCTGGACCAAAAGTATCGACACAA
195 ATTCTAGACCAAAAGTATCGACACAA
14807 TTTAAAAAG----G----AA-TT------G-AT--AT--ATTATGTTGACCTATTTTCTAATTAA
1 TTTAAAAAGTATCGAAACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAA
* * ** * *
14852 ACCGGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATATATATTAGTATCGATT
66 ACCGGTATATTTTTACCAGCTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATG
* * * *
14917 TTTTTGGGATCGATACTTACAATAAATGTATCGATACTTTAT-CTGTGCACCTCGTTGGGCATTC
131 TTTTTGGAATCGATACTTACAATAAATGTATCGACACTTGATAC-GTACACCTCGTTGGGCATTC
*
14981 ATTCTGGACCAAAAGTATCGACACAA
195 ATTCTAGACCAAAAGTATCGACACAA
15007 TTTAAAAAGGTATCGA
1 TTTAAAAA-GTATCGA
15023 TACATTATGT
Statistics
Matches: 394, Mismatches: 35, Indels: 31
0.86 0.08 0.07
Matches are distributed among these distances:
199 1 0.00
200 174 0.44
201 1 0.00
202 2 0.01
204 2 0.01
205 2 0.01
211 2 0.01
212 2 0.01
216 1 0.00
220 1 0.00
221 206 0.52
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (220 bp):
TTTAAAAAGTATCGAAACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAA
ACCGGTATATTTTTACCAGCTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATG
TTTTTGGAATCGATACTTACAATAAATGTATCGACACTTGATACGTACACCTCGTTGGGCATTCA
TTCTAGACCAAAAGTATCGACACAA
Found at i:14875 original size:200 final size:200
Alignment explanation
Indices: 14590--15744 Score: 1696
Period size: 200 Copynumber: 5.8 Consensus size: 200
14580 ACATGATTTA
* * * *
14590 AAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTATCTATTTTCTAATTAAATC
1 AAAAG-TATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
*
14655 GGTATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGATGTTT
65 GGTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTT
* ** *
14720 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATACGTATACCTTGTTGGGCATTCATTC
130 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
14785 TGGACC
195 TGGACC
* * *
14791 AAAAGTATCGACACAATTTAAAAAGGAATTGATATATTATGTTGACCTATTTTCTAATTAAACCG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* ** * *
14856 GTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATATATATTAGTATCGATTTTTT
66 GTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
*
14921 TGGGATCGATACTTACAATAAATGTATCGATACTTTAT-CTGTGCACCTCGTTGGGCATTCATTC
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGC-GTGCACCTCGTTGGGCATTCATTC
14985 TGGACC
195 TGGACC
*
14991 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACTG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* ** *
15056 ATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATAT-TGTTTCGATGTTTT
66 GTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
* *
15120 TGAGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
15185 GGACC
196 GGACC
* * *
15190 AAAAGTATTGACACAATTTAAAAAGCTATCGATACATTATGTTGACCTATTTTCTAATTAAATCG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* *
15255 GTATATTTTTACTTGTTACATTTTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
66 GTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
* * **
15320 TGGGATCAATACTTACAATAAATGTATCGACACTTTATGTGTGCACCTCGTTGAACATTCATTCT
131 TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
15385 GGACC
196 GGACC
* * * * **
15390 AAAAGTATCGTCACAATTTAAAAA-GTATCGAT-TATTATGTTGACCTATTCTCTCA-TAAAATG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* **
15452 GATATATTTTTACTGGTTACATTGTAAATTTACCTATTACTTTATA-ATTATCAATTTCGATGTT
66 G-TATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGGTTTCGATGTT
* ** *
15516 TTTGGGATAGATACTTATGATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATT
129 TTTGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATT
15581 CTGGACC
194 CTGGACC
* * * * *
15588 AAAAGTATCAACACAATTTAAAAA-GTATCGATACATTATGTTGACCTATTCTCTCATAAAACCA
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
* * *
15652 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACTTTATA-ATTATCGGTTTCGATATTT
66 GTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGGTTTCGATGTTT
* *
15716 TTGGGATCGATACTTATAATAAATATATC
130 TTGGGATCGATACTTACAATAAATGTATC
15745 AATACATCAA
Statistics
Matches: 868, Mismatches: 79, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
197 7 0.01
198 169 0.19
199 299 0.34
200 388 0.45
201 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (200 bp):
AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCG
GTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATGTTTT
TGGGATCGATACTTACAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
GGACC
Found at i:15264 original size:399 final size:399
Alignment explanation
Indices: 14590--15749 Score: 1738
Period size: 399 Copynumber: 2.9 Consensus size: 399
14580 ACATGATTTA
* * *
14590 AAAAGTTATCGACATAATTTAAAAAGGTATCGATACATTATGTTTATCTATTTTCTAATTAAATC
1 AAAAG-TATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATC
* * *
14655 GGTATATTTTTACTGGTTACATTGTAAATTTATCTATTACATTATATATATCGGTTTCGATGTTT
65 GATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCAGTTTCGATGTTT
* * ** *
14720 TTGGGATCGATACTTACAATAAATGTATCGACACTTTATACGTATACCTTGTTGGGCATTCATTC
130 TTGGGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
* * *
14785 TGGACCAAAAGTATCGACACAATTTAAAAAGGAATTGATATATTATGTTGACCTATTTTCTAATT
195 TGGACCAAAAGTATCGACACAATTTAAAAA-GTATCGATACATTATGTTGACCTATTTTCTAATT
* ** *
14850 AAACCGGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATATATATTAGTATCGA
259 AAACCGGTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGA
* **
14915 TTTTTTTGGGATCGATACTTACAATAAATGTATCGATACTTTATCTGTGCACCTCGTTGGGCATT
324 TATTTTTGGGATCGATACTTACAATAAATGTATCGATACTTTATCTGTGCACCTCGTTGAACATT
14980 CATTCTGGACC
389 CATTCTGGACC
14991 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAA-CT
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATC-
** *
15055 GATATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATATATAT-TGTTTCGATGTTT
65 GATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCAGTTTCGATGTTT
*
15119 TTGAGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
*
15184 TGGACCAAAAGTATTGACACAATTTAAAAAGCTATCGATACATTATGTTGACCTATTTTCTAATT
195 TGGACCAAAAGTATCGACACAATTTAAAAAG-TATCGATACATTATGTTGACCTATTTTCTAATT
* * *
15249 AAATCGGTATATTTTTACTTGTTACATTTTAAATTTACCTATTACATTATATATATCGGTTTCGA
259 AAACCGGTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGA
* * * *
15314 TGTTTTTGGGATCAATACTTACAATAAATGTATCGACACTTTATGTGTGCACCTCGTTGAACATT
324 TATTTTTGGGATCGATACTTACAATAAATGTATCGATACTTTATCTGTGCACCTCGTTGAACATT
15379 CATTCTGGACC
389 CATTCTGGACC
* * * * * *
15390 AAAAGTATCGTCACAATTTAAAAA-GTATCGAT-TATTATGTTGACCTATTCTCTCATAAAATGG
1 AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATCG
* *
15453 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACTTTATA-ATTATCAATTTCGATGTTT
66 ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCAGTTTCGATGTTT
* **
15517 TTGGGATAGATACTTATGATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
* * * *
15582 TGGACCAAAAGTATCAACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTCTCTCATAA
195 TGGACCAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTA
** *
15647 AACCAATATATTTTTACTGGTTACATTGTAAATTTACCTATTACTTTATA-ATTATCGGTTTCGA
260 AACCGGTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATA-TATCGGTTTCGA
* * *
15711 TATTTTTGGGATCGATACTTATAATAAATATATCAATAC
324 TATTTTTGGGATCGATACTTACAATAAATGTATCGATAC
15750 ATCAAGTTTG
Statistics
Matches: 690, Mismatches: 63, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
396 2 0.00
397 190 0.28
398 110 0.16
399 282 0.41
400 101 0.15
401 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (399 bp):
AAAAGTATCGACACAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTCTAATTAAATCG
ATATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCAGTTTCGATGTTTT
TGGGATCGATACTTACAATAAATGTATCAACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
GGACCAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAA
ACCGGTATATTTTTACTGGTTACATTGTAAATTTACCTATTACATTATATATATCGGTTTCGATA
TTTTTGGGATCGATACTTACAATAAATGTATCGATACTTTATCTGTGCACCTCGTTGAACATTCA
TTCTGGACC
Found at i:19435 original size:12 final size:12
Alignment explanation
Indices: 19420--19445 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19410 TGAATAGTAA
19420 TGAACAACACCG
1 TGAACAACACCG
19432 TGAACAACACCG
1 TGAACAACACCG
19444 TG
1 TG
19446 CTACAGTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.12
Consensus pattern (12 bp):
TGAACAACACCG
Found at i:20403 original size:32 final size:32
Alignment explanation
Indices: 20284--20408 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 32
20274 AACCTCGGCA
* * * *
20284 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* * *
20315 AATGTCCATATATTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
20346 ACTGTCCATATGTTCTG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTCCGTAGA-ACATAGGTAAT
* *
20378 TCTGTCCATATGTTCCGTAGAACATAAGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
20409 ACCCTCGACT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
30 3 0.04
31 43 0.58
32 26 0.35
33 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:25541 original size:183 final size:183
Alignment explanation
Indices: 25324--25972 Score: 868
Period size: 183 Copynumber: 3.6 Consensus size: 183
25314 TTATCAAAGT
* * * *
25324 ATCGAGACATTCAACATATCCGGTAGCACTTTACCGGTTTCGTCATAATGAAACCGGTTTTGTCA
1 ATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
*
25389 TATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTGATACTTTATAGGCG
66 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTGATACTTTATAGGCG
* *
25454 TTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTTGATACTTATTTGAATGAA
131 TTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAA
* ***
25507 ATCGATACTTTCAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAATTAGTTTTGTCA
1 ATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
*
25572 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTATAGGCG
66 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTGATACTTTATAGGCG
* *
25637 CTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGA
131 TTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAA
** * ** * *
25690 ATCGATACTTTCAACATATTTGGTATCGCTTTAAAGGTTTTGTCATTATGAAACCGGTTTTATC-
1 ATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
*
25754 -A--TTTACCTGTTATATTGTTATGTATCGATACATGTTTATAATAG-ATTGATACTTTAT---C
66 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAA-AGTATTGATACTTTATAGGC
* * *
25812 -TCTATTATTGTTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAAT-AGA
130 GT-TATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGA-A
** ** * * * *
25866 ATCGATACTTTCAACATATCCAATAGCGCTTTACCGAATTTGTCATATTGAACCCGATTTTCTCA
1 ATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
* * *
25931 TAGTTTTACCTGATATATTGTTATGTATCGGTACATGTTTTA
66 TATTTTTACCTGTTATATTGTTATGTATCGATACAT-TTTTA
25973 ATTGTATCGA
Statistics
Matches: 410, Mismatches: 48, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
176 98 0.24
178 1 0.00
179 51 0.12
180 32 0.08
181 5 0.01
183 223 0.54
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (183 bp):
ATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCA
TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTGATACTTTATAGGCG
TTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAA
Found at i:27571 original size:26 final size:26
Alignment explanation
Indices: 27536--27593 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
27526 AAGCCCGAAA
27536 GGGGTTTATAAGCCGAAAGAATATTG
1 GGGGTTTATAAGCCGAAAGAATATTG
27562 GGGGTTTATAAGCCGAAAGAATATTG
1 GGGGTTTATAAGCCGAAAGAATATTG
27588 GGGGTT
1 GGGGTT
27594 CCTAATTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (26 bp):
GGGGTTTATAAGCCGAAAGAATATTG
Found at i:46970 original size:21 final size:21
Alignment explanation
Indices: 46946--47003 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
46936 TTTTATAATG
*
46946 AACCTTAAACCCTAAAACATA
1 AACCTTAAACTCTAAAACATA
* * * *
46967 AACCATAAAGTCTAAATCTTA
1 AACCTTAAACTCTAAAACATA
*
46988 AACTTTAAACTCTAAA
1 AACCTTAAACTCTAAA
47004 CCCTAAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (21 bp):
AACCTTAAACTCTAAAACATA
Found at i:47010 original size:21 final size:20
Alignment explanation
Indices: 46972--47014 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
46962 ACATAAACCA
* * *
46972 TAAAGTCTAAATCTTAAACTT
1 TAAACTCTAAACCCTAAA-TT
46993 TAAACTCTAAACCCTAAATT
1 TAAACTCTAAACCCTAAATT
47013 TA
1 TA
47015 TACTTACCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAACTCTAAACCCTAAATT
Found at i:47095 original size:7 final size:7
Alignment explanation
Indices: 47085--47138 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
47075 CCCTATTTTA
47085 TAAACCC
1 TAAACCC
47092 TAAACCC
1 TAAACCC
*
47099 TAAATCC
1 TAAACCC
**
47106 TAAACTA
1 TAAACCC
*
47113 TAAACCT
1 TAAACCC
47120 TAAACCC
1 TAAACCC
47127 T-AACCTC
1 TAAACC-C
47134 TAAAC
1 TAAAC
47139 TCGATTATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
6 4 0.11
7 31 0.82
8 3 0.08
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:49754 original size:17 final size:17
Alignment explanation
Indices: 49732--49774 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
49722 ATTTGAGTTT
*
49732 GAGTTCGAGCTTGAATC
1 GAGTTCAAGCTTGAATC
*
49749 GAGTTCAAGCTTGAATT
1 GAGTTCAAGCTTGAATC
*
49766 GAGCTCAAG
1 GAGTTCAAG
49775 TCTCGAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (17 bp):
GAGTTCAAGCTTGAATC
Found at i:50600 original size:14 final size:14
Alignment explanation
Indices: 50575--50625 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
50565 TGAATCGGTC
50575 TGACTATTGACCAT
1 TGACTATTGACCAT
* * *
50589 TGATTTTTGACCGT
1 TGACTATTGACCAT
50603 TGACTATTGA-CAT
1 TGACTATTGACCAT
50616 TGACTATTGA
1 TGACTATTGA
50626 ATTTGATCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (14 bp):
TGACTATTGACCAT
Found at i:50620 original size:13 final size:13
Alignment explanation
Indices: 50575--50646 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 13
50565 TGAATCGGTC
50575 TGACTATTGACCAT
1 TGACTATTGA-CAT
* * *
50589 TGATTTTTGACCGT
1 TGACTATTGA-CAT
50603 TGACTATTGACAT
1 TGACTATTGACAT
50616 TGACTATTGA-ATT
1 TGACTATTGACA-T
50629 TGA-TCATTGACAAT
1 TGACT-ATTGAC-AT
50643 TGAC
1 TGAC
50647 AGTTAACTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
12 2 0.04
13 21 0.45
14 23 0.49
15 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (13 bp):
TGACTATTGACAT
Found at i:50625 original size:20 final size:20
Alignment explanation
Indices: 50602--50646 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
50592 TTTTTGACCG
*
50602 TTGACTATTGA-CATTGACTA
1 TTGACT-TTGATCATTGACAA
*
50622 TTGAATTTGATCATTGACAA
1 TTGACTTTGATCATTGACAA
50642 TTGAC
1 TTGAC
50647 AGTTAACTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGACTTTGATCATTGACAA
Found at i:51281 original size:52 final size:51
Alignment explanation
Indices: 51211--51429 Score: 217
Period size: 52 Copynumber: 4.2 Consensus size: 51
51201 GATAATATCT
*
51211 CCATCTTGTTT-TATGTTTTTTGTTTTGGGGTTCCTTTTGGAGGGTAAAGTCC
1 CCATCATGTTTCT-TGTTTTTTGTTTT-GGGTTCCTTTTGGAGGGTAAAGTCC
* * * * *
51263 CCATCATATTTCTTGTTTTTTGTTTTGGTTTCCTCTTCGAAGGGTAACA-TTC
1 CCATCATGTTTCTTGTTTTTTGTTTTGGGTTCCT-TTTGGAGGGTAA-AGTCC
* * *
51315 TCATCATGTTTCTTGTTTTTTGTTTTGGGTTCCTTTTCAGAGGGTAACGTCC
1 CCATCATGTTTCTTGTTTTTTGTTTTGGGTTCCTTTT-GGAGGGTAAAGTCC
* * * * * *
51367 CCACCATGTTTCCTGTTTTTTGTTTTGGATTCCTCTTCGGATGGTAACGTCC
1 CCATCATGTTTCTTGTTTTTTGTTTTGGGTTCCT-TTTGGAGGGTAAAGTCC
* *
51419 TCATCCTGTTT
1 CCATCATGTTT
51430 ATCTATGGCA
Statistics
Matches: 137, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
51 9 0.07
52 124 0.91
53 4 0.03
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (51 bp):
CCATCATGTTTCTTGTTTTTTGTTTTGGGTTCCTTTTGGAGGGTAAAGTCC
Found at i:51367 original size:104 final size:104
Alignment explanation
Indices: 51224--51429 Score: 297
Period size: 104 Copynumber: 2.0 Consensus size: 104
51214 TCTTGTTTTA
* * *
51224 TGTTTTTTGTTTTGGGGTTCCTTTTGGAGGGTAAAGTCCCCATCATATTTCTTGTTTTTTGTTTT
1 TGTTTTTTGTTTTGGGGTTCCTTTTAGAGGGTAAAGTCCCCACCATATTTCCTGTTTTTTGTTTT
* *
51289 GGTTTCCTCTTCGAAGGGTAACATTCTCATCATGTTTCT
66 GGATTCCTCTTCGAAGGGTAACATCCTCATCATGTTTCT
* *
51328 TGTTTTTTGTTTT-GGGTTCCTTTTCAGAGGGTAACGTCCCCACCATGTTTCCTGTTTTTTGTTT
1 TGTTTTTTGTTTTGGGGTTCCTTTT-AGAGGGTAAAGTCCCCACCATATTTCCTGTTTTTTGTTT
* * * *
51392 TGGATTCCTCTTCGGATGGTAACGTCCTCATCCTGTTT
65 TGGATTCCTCTTCGAAGGGTAACATCCTCATCATGTTT
51430 ATCTATGGCA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 11 0.12
104 79 0.88
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (104 bp):
TGTTTTTTGTTTTGGGGTTCCTTTTAGAGGGTAAAGTCCCCACCATATTTCCTGTTTTTTGTTTT
GGATTCCTCTTCGAAGGGTAACATCCTCATCATGTTTCT
Found at i:52218 original size:29 final size:29
Alignment explanation
Indices: 52185--52250 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
52175 TTAGATAGAT
52185 GAATCGATCGAAGTGTGAATGATATATCC
1 GAATCGATCGAAGTGTGAATGATATATCC
* * *
52214 GAATCGATCTAAGTGTGTATTATATATCC
1 GAATCGATCGAAGTGTGAATGATATATCC
52243 GAATCGAT
1 GAATCGAT
52251 GAGAGCCTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
GAATCGATCGAAGTGTGAATGATATATCC
Found at i:55597 original size:3 final size:3
Alignment explanation
Indices: 55589--55635 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
55579 GAAAAATGAA
55589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
55634 AA
1 AA
55636 ATAAAGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:55683 original size:21 final size:21
Alignment explanation
Indices: 55653--55718 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
55643 TAAATTGAGT
55653 AAGAAAAAAATAATAAAAATA
1 AAGAAAAAAATAATAAAAATA
*
55674 AAGGAAAAAATAATAAATAA-A
1 AAGAAAAAAATAATAAA-AATA
* *
55695 ATGAAAAAAATAAAATAAAATA
1 AAGAAAAAAATAATA-AAAATA
55717 AA
1 AA
55719 AAAGGATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 31 0.84
22 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (21 bp):
AAGAAAAAAATAATAAAAATA
Found at i:55688 original size:24 final size:25
Alignment explanation
Indices: 55656--55720 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
55646 ATTGAGTAAG
**
55656 AAAAA-AATAATAAAAAT-AAAGGA
1 AAAAATAATAATAAAAATGAAAAAA
55679 AAAAATAATAA-ATAAAATGAAAAAA
1 AAAAATAATAATA-AAAATGAAAAAA
55704 ATAAAATAA-AATAAAAA
1 A-AAAATAATAATAAAAA
55721 AGGATCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 6 0.17
24 10 0.29
25 11 0.31
26 8 0.23
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (25 bp):
AAAAATAATAATAAAAATGAAAAAA
Found at i:55701 original size:19 final size:19
Alignment explanation
Indices: 55658--55720 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
55648 TGAGTAAGAA
* *
55658 AAAAATAATAAAAATAAAGG
1 AAAAATAATAAATA-AAATG
55678 AAAAAATAATAAATAAAATG
1 -AAAAATAATAAATAAAATG
55698 AAAAA-AATAAAATAAAAT-
1 AAAAATAAT-AAATAAAATG
55716 AAAAA
1 AAAAA
55721 AGGATCAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.21
19 14 0.36
20 4 0.10
21 13 0.33
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAATAATAAATAAAATG
Found at i:56007 original size:16 final size:16
Alignment explanation
Indices: 55986--56020 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
55976 ACATTTCCCT
55986 TCATTCACCCATTTCC
1 TCATTCACCCATTTCC
56002 TCATTCACCCATTTCC
1 TCATTCACCCATTTCC
56018 TCA
1 TCA
56021 AGAAAACCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (16 bp):
TCATTCACCCATTTCC
Found at i:56757 original size:19 final size:20
Alignment explanation
Indices: 56724--56771 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
56714 AACCCCTTTG
56724 AAATACATGATTTTTAATGA
1 AAATACATGATTTTTAATGA
56744 AAATACATGA-TTTTAATGA
1 AAATACATGATTTTTAATGA
*
56763 AGATACATG
1 AAATACATG
56772 TTCTTGGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAATACATGATTTTTAATGA
Found at i:56960 original size:25 final size:25
Alignment explanation
Indices: 56929--56983 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 25
56919 AGTACACATG
*
56929 CTTGAATGATGCACATGGTAGCTTA
1 CTTGAATGATGCACATGGTAGCCTA
56954 CTTG-A--ATGCACATGGTAGCCTA
1 CTTGAATGATGCACATGGTAGCCTA
56976 CTTGAATG
1 CTTGAATG
56984 TACATGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 20 0.77
23 1 0.04
24 1 0.04
25 4 0.15
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (25 bp):
CTTGAATGATGCACATGGTAGCCTA
Found at i:56965 original size:22 final size:22
Alignment explanation
Indices: 56937--56990 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
56927 TGCTTGAATG
*
56937 ATGCACATGGTAGCTTACTTGA
1 ATGCACATGGTAGCCTACTTGA
56959 ATGCACATGGTAGCCTACTTGA
1 ATGCACATGGTAGCCTACTTGA
*
56981 ATGTACATGG
1 ATGCACATGG
56991 GTCTTCTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (22 bp):
ATGCACATGGTAGCCTACTTGA
Found at i:57673 original size:24 final size:24
Alignment explanation
Indices: 57646--57697 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
57636 GAATAACATG
57646 ACATGAGTTAATGAATGA-ATGAAA
1 ACATGAG-TAATGAATGATATGAAA
* * *
57670 ACATGTGTCATGAATGATATGCAA
1 ACATGAGTAATGAATGATATGAAA
57694 ACAT
1 ACAT
57698 AATAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (24 bp):
ACATGAGTAATGAATGATATGAAA
Found at i:58753 original size:9 final size:9
Alignment explanation
Indices: 58712--58757 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
58702 GACCTAGACC
58712 ATAAATAAA
1 ATAAATAAA
58721 A-AAATAAA
1 ATAAATAAA
*
58729 ATTAATAAA
1 ATAAATAAA
*
58738 ATGAAATAAG
1 AT-AAATAAA
58748 ATAAATAAA
1 ATAAATAAA
58757 A
1 A
58758 AATAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 8 0.26
9 16 0.52
10 7 0.23
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (9 bp):
ATAAATAAA
Found at i:58764 original size:19 final size:18
Alignment explanation
Indices: 58712--58766 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
58702 GACCTAGACC
58712 ATAAAT-AAAAAAATAAA
1 ATAAATAAAAAAAATAAA
* * *
58729 ATTAATAAAATGAAATAAG
1 ATAAATAAAA-AAAATAAA
58748 ATAAATAAAAAATAATAAA
1 ATAAATAAAAAA-AATAAA
58767 TATATATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 20 0.69
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
ATAAATAAAAAAAATAAA
Found at i:58771 original size:2 final size:2
Alignment explanation
Indices: 58766--58793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58756 AAAATAATAA
58766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58794 TTGAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58865 original size:34 final size:35
Alignment explanation
Indices: 58777--59156 Score: 353
Period size: 34 Copynumber: 11.0 Consensus size: 35
58767 TATATATATA
* *
58777 TATATATATATATA-TATTTGAAAATATTTT-AAAAC
1 TATATATATATA-AGT-TTTCAAAATGTTTTCAAAAC
**
58812 TATATATATAT-A--TTAAAAAATGTTTTCAAAAC
1 TATATATATATAAGTTTTCAAAATGTTTTCAAAAC
58844 TATATAT-TAT-AGTTTTCAAAAATGTTTT-AAAAC
1 TATATATATATAAGTTTTC-AAAATGTTTTCAAAAC
* *
58877 TAT-T-TATAT-ATTTTTCAAAAAATGTTTTTAAAAC
1 TATATATATATAAGTTTTC--AAAATGTTTTCAAAAC
* *
58911 TATATATATAT--GTTTTAAAAAATGTTTTCAAAAA
1 TATATATATATAAGTTTT-CAAAATGTTTTCAAAAC
*
58945 T-TATATTATATAAGTTTTCAAAATGATTTCAAAAC
1 TATATA-TATATAAGTTTTCAAAATGTTTTCAAAAC
* *
58980 TATATATTATATAACTTTTTCAAAATGATTTCAAAAAAC
1 TATATA-TATATAA-GTTTTCAAAATGTTTTC--AAAAC
* * *
59019 TATATTTATATAAGTTTTTCAAAATGATTTCAAAAA
1 TATATATATATAAG-TTTTCAAAATGTTTTCAAAAC
*
59055 TATAT-TATATAAGTTTTTAAAATGTTTTCAAAATC
1 TATATATATATAAGTTTTCAAAATGTTTTCAAAA-C
* * *
59090 TATATATATAT-ATTTTTCAAAATGATTTCAAAAG
1 TATATATATATAAGTTTTCAAAATGTTTTCAAAAC
*
59124 TATAT-TATATAAGTTTTTAAAATGTTTTCAAAA
1 TATATATATATAAGTTTTCAAAATGTTTTCAAAA
59157 AACGATATAA
Statistics
Matches: 297, Mismatches: 27, Indels: 43
0.81 0.07 0.12
Matches are distributed among these distances:
31 16 0.05
32 22 0.07
33 31 0.10
34 80 0.27
35 63 0.21
36 36 0.12
37 16 0.05
38 23 0.08
39 10 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
TATATATATATAAGTTTTCAAAATGTTTTCAAAAC
Found at i:59170 original size:69 final size:68
Alignment explanation
Indices: 58807--59157 Score: 374
Period size: 69 Copynumber: 5.1 Consensus size: 68
58797 AAAATATTTT
* ** * * *
58807 AAAACTATA-TATATATATTAAAAAATGTTTTCAAAACTATA-TAT-TATAGTTTTCAAAAATGT
1 AAAACTATATTATATATTTTTCAAAATGATTTCAAAAATATATTATATA-AGTTTT-TAAAATGT
58869 TTT--
64 TTTCA
* * * * *
58872 AAAACTAT-TTATATATTTTTCAAAAAATGTTTTTAAAACTATA-TATATATGTTTTAAAAAATG
1 AAAACTATATTATATATTTTTC--AAAATGATTTCAAAAATATATTATATAAGTTTT-TAAAATG
58935 TTTTCA
63 TTTTCA
* * *
58941 AAAATTATATTATATAAGTTTTCAAAATGATTTCAAAACTATATATTATATAACTTTTTCAAAAT
1 AAAACTATATTATAT-ATTTTTCAAAATGATTTCAAAA--ATATATTATATAAGTTTTT-AAAAT
*
59006 GATTTCAA
62 GTTTTC-A
59014 AAAACTATATTTATATAAGTTTTTCAAAATGATTTCAAAAATATATTATATAAGTTTTTAAAATG
1 AAAACTATA-TTATAT-A-TTTTTCAAAATGATTTCAAAAATATATTATATAAGTTTTTAAAATG
59079 TTTTCA
63 TTTTCA
* *
59085 AAATCTATATATATATATTTTTCAAAATGATTTCAAAAGTATATTATATAAGTTTTTAAAATGTT
1 AAAACTATAT-TATATATTTTTCAAAATGATTTCAAAAATATATTATATAAGTTTTTAAAATGTT
59150 TTCA
65 TTCA
59154 AAAA
1 AAAA
59158 ACGATATAAT
Statistics
Matches: 248, Mismatches: 22, Indels: 28
0.83 0.07 0.09
Matches are distributed among these distances:
65 17 0.07
67 38 0.15
68 2 0.01
69 74 0.30
70 8 0.03
71 24 0.10
72 30 0.12
73 27 0.11
74 8 0.03
75 20 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (68 bp):
AAAACTATATTATATATTTTTCAAAATGATTTCAAAAATATATTATATAAGTTTTTAAAATGTTT
TCA
Found at i:59224 original size:2 final size:2
Alignment explanation
Indices: 59217--59271 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
59207 ATTATACTAT
*
59217 TA TA TA TA TA TA TA TA -A TA TA TA TA TA GA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59257 TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA
59272 AAAAAACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:59248 original size:23 final size:22
Alignment explanation
Indices: 59209--59271 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
59199 AATCAAAAAT
*
59209 TATACTAT-TATAT-ATATATA
1 TATAATATATATATAATATATA
59229 TATAATATATATATAGATATATA
1 TATAATATATATATA-ATATATA
*
59252 TATTATATATATATAATATA
1 TATAATATATATATAATATA
59272 AAAAAACAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.18
21 5 0.13
22 5 0.13
23 21 0.55
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TATAATATATATATAATATATA
Found at i:60008 original size:85 final size:84
Alignment explanation
Indices: 59859--60523 Score: 832
Period size: 85 Copynumber: 7.9 Consensus size: 84
59849 ATACGTCATC
* * *** ** * *
59859 GAGCTGAATGAAATC-AGACTCGAAAGT-TTTGTTGACAGATAGATTTTCTCAACTTAAGTTATG
1 GAGCTGAATGTAATCGA-ACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
59922 CTGTAAATTTGACATGACCTT
65 CTGTAAATTTGATATG-CCTT
* * * * * * *
59943 GAGCTGAATGGAATCGAACTCGAAGGTATTTGTTGATAAATAACCCTTCCCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
60008 TGTAAATTTGATATGTCCTT
66 TGTAAATTTGATATG-CCTT
* * *
60028 GAGCTGAATATAATCGAAATCGAAGGTCTTTGTTGACAGATAGCCCTTATCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
60093 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCC-TT
** * * * *
60113 GATATGAATGTAATCCAACTCGAAGGTCTTTGTTGATAGATAGCCCTTATCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
60178 TGTAAATTTGATATGCATTT
66 TGTAAATTTGATATGC-CTT
* *
60198 GAGTTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTTTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
60263 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCC-TT
60283 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
60348 TGTAAATTTGATATACCTTT
66 TGTAAATTTGATATGCC-TT
* * * * *
60368 GAACTAAATGTAATTGAACTCGAAGGTCTTTTTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* *
60433 TGTAAATTTGATACGTCTTT
66 TGTAAATTTGATATG-CCTT
* * * * * * **
60453 GAGCTGAATGTAATCAAACTTGAAGGTGTTTGCTGACAGACA-ACCTTCTCGCCTTGATTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
60517 TGTAAAT
66 TGTAAAT
60524 AGTTCCTTTA
Statistics
Matches: 513, Mismatches: 62, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
84 51 0.10
85 461 0.90
86 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (84 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTT
Done.