Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004984.1 Hibiscus syriacus cultivar Beakdansim tig00011184_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: 139136
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:25 original size:19 final size:20
Alignment explanation
Indices: 1--49 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
*
1 TTCGCGTTGCGATTTT-GGT
1 TTCGCGTTGCGATTTTAAGT
20 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
40 TTCGTGTTGC
1 TTCGCGTTGC
50 AAAGTAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.08, C:0.16, G:0.29, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:268 original size:92 final size:93
Alignment explanation
Indices: 98--560 Score: 827
Period size: 93 Copynumber: 5.1 Consensus size: 93
88 ATGGATTGCA
98 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
162 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
190 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
254 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
282 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTT-AAGAATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
344 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
371 TTACTTTCAACCAAAAGACAAAACAAAGACAAAATACTATTTCACATTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAC-AAATACTATTTCACAGTGTTAAAGAATACACAG-
436 TTTAGCA-AATTGGCAGCAACCGAACAAAT
64 TTTAGCAGAATTGGCAGCAACCGAACAAAT
465 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAAT--ACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
528 TAGCAGAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
556 TTACT
1 TTACT
561 AAGCAATCTA
Statistics
Matches: 360, Mismatches: 3, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
89 33 0.09
90 32 0.09
91 79 0.22
92 88 0.24
93 89 0.25
94 39 0.11
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2263 original size:14 final size:14
Alignment explanation
Indices: 2244--2333 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2234 GTTGAAATGA
2244 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2258 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
2277 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2291 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2310 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2324 AATCGCAACG
1 AATCGCAACG
2334 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2282 original size:19 final size:19
Alignment explanation
Indices: 2258--2355 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
2248 GCAACGAGAG
*
2258 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
2277 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2291 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2310 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2324 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2343 AATCGCAATGCGA
1 AATCGCAACGCGA
2356 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2283 original size:33 final size:33
Alignment explanation
Indices: 2237--2350 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2227 TCTTTTGGTT
2237 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2269 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2302 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2335 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2351 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
32 6 0.08
33 73 0.92
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2386 original size:14 final size:14
Alignment explanation
Indices: 2367--2423 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2357 TTTGGTTTCG
2367 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2381 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
2400 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2414 CGTTGCGATT
1 CGTTGCGATT
2424 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2401 original size:33 final size:33
Alignment explanation
Indices: 2364--2428 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
2354 GATTTTGGTT
2364 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
2397 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
2429 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATA
Found at i:2434 original size:21 final size:21
Alignment explanation
Indices: 2408--2483 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2398 CGCGTTGCGA
2408 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2429 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
2449 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2470 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2484 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2464 original size:41 final size:41
Alignment explanation
Indices: 2407--2484 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
2397 TCGCGTTGCG
* *
2407 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
2448 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGAC
2485 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.14, C:0.26, G:0.15, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTACGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2605 original size:33 final size:33
Alignment explanation
Indices: 2563--2633 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2553 AATACTAACT
*
2563 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2596 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2629 TGAAA
1 TGAAA
2634 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3039 original size:20 final size:20
Alignment explanation
Indices: 3014--3204 Score: 201
Period size: 20 Copynumber: 9.7 Consensus size: 20
3004 CTTTAAATAT
3014 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3034 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3056 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3075 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3095 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3115 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3135 CACGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3154 CGAGTTGCGATTTA-TG-TT
1 CGCGTTGCGATTTACGGATA
* ** *
3172 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3192 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3205 TGGAAAATCG
Statistics
Matches: 142, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
18 13 0.09
19 20 0.14
20 93 0.65
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3221 original size:21 final size:21
Alignment explanation
Indices: 3191--3273 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3181 ATTTTCATAT
*
3191 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3212 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3233 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3254 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3274 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3264 original size:42 final size:43
Alignment explanation
Indices: 3171--3269 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3161 CGATTTATGT
* *
3171 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3212 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3254 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3270 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:6189 original size:37 final size:37
Alignment explanation
Indices: 6147--6222 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
6137 GTCCCGTACG
6147 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
* *
6184 TGACGGTATATGACGAGAGCCTTCTGCATTGCCTTTT
1 TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
6221 TG
1 TG
6223 TTTTGGTTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (37 bp):
TGACGGTATATAACGAGAGCCTTCTGCATCGCCTTTT
Found at i:6547 original size:22 final size:22
Alignment explanation
Indices: 6491--6547 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
6481 CGTTCGTGAA
**
6491 TTTTTTTCTAAAGTAGTTGATTT
1 TTTTTTTC-AAAAAAGTTGATTT
* * *
6514 TTTATATAAAAAAAGTTGATTT
1 TTTTTTTCAAAAAAGTTGATTT
6536 TTTTTTTCAAAA
1 TTTTTTTCAAAA
6548 TAAAATAGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTTTTTCAAAAAAGTTGATTT
Found at i:9607 original size:36 final size:36
Alignment explanation
Indices: 9560--9631 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
9550 CCAAGACGAC
9560 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
9596 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
1 ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
9632 TACTGCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (36 bp):
ATCTATTTCTGCAGTGCAGGGGATGATGAAGAAACT
Found at i:13182 original size:32 final size:32
Alignment explanation
Indices: 13141--13215 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
13131 TTATTGATCT
*
13141 ATTCGATTTTAGTCCCTCAGCCATTGACTCCC
1 ATTCGATTTTAGTCCCTCAACCATTGACTCCC
*
13173 ATTCGATTTTAGTCCCTCAACCGTTGACTCCC
1 ATTCGATTTTAGTCCCTCAACCATTGACTCCC
13205 ATTCGATTTTA
1 ATTCGATTTTA
13216 TTCCTTTAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (32 bp):
ATTCGATTTTAGTCCCTCAACCATTGACTCCC
Found at i:17378 original size:20 final size:20
Alignment explanation
Indices: 17355--17409 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
17345 TTCGCGTTGC
*
17355 ATTTCGCGTTGCGATTTTTA
1 ATTTCGCGTTGCGATTTTCA
* *
17375 ATTTTGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
17395 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
17410 AGTCTACAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCA
Found at i:17446 original size:19 final size:19
Alignment explanation
Indices: 17422--17469 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
17412 TCTACAGTTG
17422 TCGTTGCGATTTCCCAAAT
1 TCGTTGCGATTTCCCAAAT
**
17441 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTCCCAAAT
17460 TCGTTGCGAT
1 TCGTTGCGAT
17470 AGTCAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTCCCAAAT
Found at i:17592 original size:6 final size:6
Alignment explanation
Indices: 17581--17649 Score: 117
Period size: 6 Copynumber: 12.0 Consensus size: 6
17571 CACGTATTAT
17581 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
17629 CACGAC C-CGAC C-CGAC C-CGAC
1 CACGAC CACGAC CACGAC CACGAC
17650 TCGAGACGAG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.22
6 49 0.78
ACGTcount: A:0.30, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:18151 original size:6 final size:6
Alignment explanation
Indices: 18140--18175 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
18130 GTCCGTCTCG
18140 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
18176 ACGTGTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:18312 original size:22 final size:22
Alignment explanation
Indices: 18284--18336 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
18274 AATTTGGAAA
18284 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
18306 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
18328 ATCGCAACG
1 ATCGCAACG
18337 CGAAATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:18859 original size:29 final size:28
Alignment explanation
Indices: 18822--18881 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
18812 TGTGTTTTAT
* *
18822 AATGATTGATTTTAA-TCATAATTATATA
1 AATGATTGATTGTAACT-ACAATTATATA
18850 AATGTATTGATTGTAACTACAATTATATA
1 AATG-ATTGATTGTAACTACAATTATATA
18879 AAT
1 AAT
18882 TCGAATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 23 0.82
30 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (28 bp):
AATGATTGATTGTAACTACAATTATATA
Found at i:27375 original size:23 final size:23
Alignment explanation
Indices: 27334--27396 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
27324 TAGTGCAGGA
* *
27334 GGAATCGATACCCCC-TTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
27356 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
* *
27379 GTAACCAATTCCCCCTTT
1 GGAACCGATTCCCCCTTT
27397 AGGGAATAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAAGG
Found at i:30996 original size:23 final size:23
Alignment explanation
Indices: 30966--31024 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
30956 CTCGTATAAA
30966 TGCACCGAAGTGCCAAGTAGAAT
1 TGCACCGAAGTGCCAAGTAGAAT
* **
30989 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCAAGTAGAAT
* *
31012 TGAACCGTAGTGC
1 TGCACCGAAGTGC
31025 TATATAAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCAAGTAGAAT
Found at i:31657 original size:20 final size:20
Alignment explanation
Indices: 31634--31681 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
31624 GTATGTATCG
31634 ATGCACTCTACAGTGTATAA
1 ATGCACTCTACAGTGTATAA
**
31654 ATGCACTCTACAGTGTATCG
1 ATGCACTCTACAGTGTATAA
31674 ATGCACTC
1 ATGCACTC
31682 CTTAATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
ATGCACTCTACAGTGTATAA
Found at i:37906 original size:11 final size:11
Alignment explanation
Indices: 37890--37921 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
37880 TTCGACAGTT
37890 CTGGGGAAAAA
1 CTGGGGAAAAA
37901 CTGGGGAAAAA
1 CTGGGGAAAAA
37912 CTGGGGAAAA
1 CTGGGGAAAA
37922 CCCTTGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.38, T:0.09
Consensus pattern (11 bp):
CTGGGGAAAAA
Found at i:42947 original size:48 final size:48
Alignment explanation
Indices: 42876--42971 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
42866 AAGTTACATG
42876 TTTTAATAAAAGTTTAAATTTTCTGCTATTTTTACAATGGGTCGCTCT
1 TTTTAATAAAAGTTTAAATTTTCTGCTATTTTTACAATGGGTCGCTCT
42924 TTTTAATAAAAGTTTAAATTTTCTGCTATTTTTACAATGGGTCGCTCT
1 TTTTAATAAAAGTTTAAATTTTCTGCTATTTTTACAATGGGTCGCTCT
42972 GGTGGCCCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (48 bp):
TTTTAATAAAAGTTTAAATTTTCTGCTATTTTTACAATGGGTCGCTCT
Found at i:49464 original size:12 final size:12
Alignment explanation
Indices: 49447--49472 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49437 ATCAAACATC
49447 ATTTTAAATATA
1 ATTTTAAATATA
49459 ATTTTAAATATA
1 ATTTTAAATATA
49471 AT
1 AT
49473 ATTGAAGAGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAATATA
Found at i:49883 original size:19 final size:19
Alignment explanation
Indices: 49836--49883 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
49826 TAAAATATTC
49836 ATAAAGTTATAATTTTAAAA
1 ATAAA-TTATAATTTTAAAA
* **
49856 TTATTTTATAATTTTAAAA
1 ATAAATTATAATTTTAAAA
49875 ATAAATTAT
1 ATAAATTAT
49884 GAACATTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATAAATTATAATTTTAAAA
Found at i:51119 original size:19 final size:18
Alignment explanation
Indices: 51086--51123 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
51076 AATAAAAAAA
51086 AAATATTTAAATTATAAT
1 AAATATTTAAATTATAAT
*
51104 AAATGTTTATAATTATAAT
1 AAATATTTA-AATTATAAT
51123 A
1 A
51124 GTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAATATTTAAATTATAAT
Found at i:51571 original size:24 final size:24
Alignment explanation
Indices: 51533--51580 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
51523 ATAAAGACGG
* *
51533 AAAAAATTGTGTCATAAAAATAGA
1 AAAAAAATGTATCATAAAAATAGA
*
51557 AAAAAAATGTATCATAAAAGTAGA
1 AAAAAAATGTATCATAAAAATAGA
51581 GTTAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.23
Consensus pattern (24 bp):
AAAAAAATGTATCATAAAAATAGA
Found at i:54664 original size:34 final size:33
Alignment explanation
Indices: 54626--54690 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
54616 AAAATATTTA
*
54626 TATATTTTCTTTA-AAAATTTAAATTCATAAAATT
1 TATATTTT-TTTATAAAATTTAAAAT-ATAAAATT
54660 TATATTTTTTTATAAAATTTAAAATATAAAA
1 TATATTTTTTTATAAAATTTAAAATATAAAA
54691 AGGTTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TATATTTTTTTATAAAATTTAAAATATAAAATT
Found at i:64008 original size:17 final size:17
Alignment explanation
Indices: 63986--64026 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
63976 TAAGAATTCA
63986 AGTCGAGCTCAAGTTCG
1 AGTCGAGCTCAAGTTCG
*
64003 AGTCGAGCTCGAGTTCG
1 AGTCGAGCTCAAGTTCG
64020 AGTCGAG
1 AGTCGAG
64027 TCCATTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.22
Consensus pattern (17 bp):
AGTCGAGCTCAAGTTCG
Found at i:66362 original size:21 final size:21
Alignment explanation
Indices: 66336--66380 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66326 GATTTCTGGG
* *
66336 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
66357 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
66378 CAA
1 CAA
66381 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:68246 original size:23 final size:23
Alignment explanation
Indices: 68202--68246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
68192 ATCATTATAT
*
68202 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
68225 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
68247 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:71432 original size:21 final size:21
Alignment explanation
Indices: 71389--71433 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
71379 GATTTCTGGG
* * *
71389 CAAGGGGAATCGGTACTCATT
1 CAAGGGGAACCGATACCCATT
*
71410 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
71431 CAA
1 CAA
71434 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:84591 original size:37 final size:36
Alignment explanation
Indices: 84532--84651 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
84522 ATCTCATTAT
* *
84532 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
84568 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
84604 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
84639 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
84652 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:84607 original size:21 final size:21
Alignment explanation
Indices: 84583--84643 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
84573 TTCAAAGAAA
84583 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
84604 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
84618 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
84639 CATTT
1 CATTT
84644 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:84660 original size:35 final size:36
Alignment explanation
Indices: 84534--84678 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
84524 CTCATTATCA
*
84534 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
84569 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
84606 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
84642 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
84676 TTT
1 TTT
84679 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:88731 original size:15 final size:16
Alignment explanation
Indices: 88703--88733 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
88693 TATCGCCGAC
88703 CGAATTTCACTATTCA
1 CGAATTTCACTATTCA
88719 CGAATTT-ACTATTCA
1 CGAATTTCACTATTCA
88734 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (16 bp):
CGAATTTCACTATTCA
Found at i:89188 original size:22 final size:22
Alignment explanation
Indices: 89163--89225 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
89153 AAACATCTAC
89163 CAAACTTTGAAAAACTATTTTT
1 CAAACTTTGAAAAACTATTTTT
**
89185 CAAA---T---AAAC-ATTTAC
1 CAAACTTTGAAAAACTATTTTT
89200 CAAACTTTGAAAAACTATTTTT
1 CAAACTTTGAAAAACTATTTTT
89222 CAAA
1 CAAA
89226 GAAACATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
18 1 0.03
19 1 0.03
21 4 0.13
22 12 0.40
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (22 bp):
CAAACTTTGAAAAACTATTTTT
Found at i:89254 original size:21 final size:21
Alignment explanation
Indices: 89230--89290 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
89220 TTCAAAGAAA
89230 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
89251 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
89265 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
89286 CATTT
1 CATTT
89291 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:89264 original size:35 final size:37
Alignment explanation
Indices: 89142--89298 Score: 232
Period size: 37 Copynumber: 4.3 Consensus size: 37
89132 ATCCCATTAT
* *
89142 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
* *
89178 TATTTTTCAAATAAACATTTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
89215 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
89251 CA-TTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
89286 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
89299 TTGGTTATCA
Statistics
Matches: 113, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
35 35 0.31
36 13 0.12
37 65 0.58
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.32
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
Found at i:89275 original size:72 final size:73
Alignment explanation
Indices: 89142--89298 Score: 230
Period size: 72 Copynumber: 2.2 Consensus size: 73
89132 ATCCCATTAT
* * *
89142 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAATAAACATTTACCAAACT
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTTTCAAAGAAACATTTACCAAACT
89206 TTGAAAAAC
66 TTG-AAAAC
* *
89215 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA-TTTTCAAAGAAACATTTACCAAACT
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTTTCAAAGAAACATTTACCAAACT
89278 TTGAAAAC
66 TTGAAAAC
89286 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
89299 TTGGTTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
71 6 0.08
72 37 0.49
73 13 0.17
74 20 0.26
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.32
Consensus pattern (73 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATTTTTCAAAGAAACATTTACCAAACT
TTGAAAAC
Found at i:91716 original size:32 final size:31
Alignment explanation
Indices: 91692--91765 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
91682 ATATTGAGTG
*
91692 ATCAATTTGTTACAAATCGATAATATTAATA
1 ATCAATTTATTACAAATCGATAATATTAATA
* * ** *
91723 ATTAATTTATTATAAATCGATAACGTTAATT
1 ATCAATTTATTACAAATCGATAATATTAATA
*
91754 ACCAATTTATTA
1 ATCAATTTATTA
91766 TTTTAAAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (31 bp):
ATCAATTTATTACAAATCGATAATATTAATA
Found at i:92211 original size:23 final size:23
Alignment explanation
Indices: 92180--92226 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
92170 TAAATCTTGA
*
92180 TATCGTAAATAAAATAAATTAAG
1 TATCATAAATAAAATAAATTAAG
92203 TATCATAAATAAAATAAATTAAG
1 TATCATAAATAAAATAAATTAAG
92226 T
1 T
92227 CGAGTGTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (23 bp):
TATCATAAATAAAATAAATTAAG
Found at i:92613 original size:151 final size:151
Alignment explanation
Indices: 92340--92643 Score: 592
Period size: 151 Copynumber: 2.0 Consensus size: 151
92330 TCACCTTAGG
92340 CCCTAGAAACAACCCATACGGGACACCGTTGAATTTTTCTGAATGGTGGAGCTGAAAAACAAAGC
1 CCCTAGAAACAACCCATACGGGACACCGTTGAATTTTTCTGAATGGTGGAGCTGAAAAACAAAGC
92405 ATGGCCATTGGACACAGTTGGAAGAAGACAACCCCCAAATGTGCAAAAACCGTGTAGTATATTAT
66 ATGGCCATTGGACACAGTTGGAAGAAGACAACCCCCAAATGTGCAAAAACCGTGTAGTATATTAT
92470 T-ACCTGGTGAGCCGCAGCAA
131 TAACCTGGTGAGCCGCAGCAA
92490 CCCTAGAAACAACCCATACGGGACACCGTTGAATTTTTCTGAATGGTGGAGCTGAAAAAACAAAG
1 CCCTAGAAACAACCCATACGGGACACCGTTGAATTTTTCTGAATGGTGGAGCTG-AAAAACAAAG
92555 CATGGCCATTGGACACAGTTGGAAGAAGACAACCCCCAAATGTGCAAAAACCGTGTAGTATATTA
65 CATGGCCATTGGACACAGTTGGAAGAAGACAACCCCCAAATGTGCAAAAACCGTGTAGTATATTA
92620 TTAACCTGGTGAGCCGCAGCAA
130 TTAACCTGGTGAGCCGCAGCAA
92642 CC
1 CC
92644 TTCCTGAAGT
Statistics
Matches: 152, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
150 54 0.36
151 77 0.51
152 21 0.14
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (151 bp):
CCCTAGAAACAACCCATACGGGACACCGTTGAATTTTTCTGAATGGTGGAGCTGAAAAACAAAGC
ATGGCCATTGGACACAGTTGGAAGAAGACAACCCCCAAATGTGCAAAAACCGTGTAGTATATTAT
TAACCTGGTGAGCCGCAGCAA
Found at i:106016 original size:60 final size:60
Alignment explanation
Indices: 105872--106026 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 60
105862 AAAAATTAGG
* ** **
105872 GGACCAATTTAGAATGAA-GGTCATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTTTAA
1 GGACCAATTTAAAAT-AAGGGTCATAGTTTAAGGATGAAATTGAAACATTCAAAAGTTTAA
* *** * *
105932 GGACTAATTTAAAATAATAATCATAGTTTAAGGATGAAATTGAAACATTTAAAAGTTTAT
1 GGACCAATTTAAAATAAGGGTCATAGTTTAAGGATGAAATTGAAACATTCAAAAGTTTAA
* * *
105992 GTG-CCAATTTGAAATAAGGGTCATATTTTTAGGAT
1 G-GACCAATTTAAAATAAGGGTCATAGTTTAAGGAT
106027 ATGCGATACA
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
59 2 0.03
60 73 0.96
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (60 bp):
GGACCAATTTAAAATAAGGGTCATAGTTTAAGGATGAAATTGAAACATTCAAAAGTTTAA
Found at i:110975 original size:62 final size:65
Alignment explanation
Indices: 110909--111039 Score: 157
Period size: 62 Copynumber: 2.1 Consensus size: 65
110899 TTCGTATCAA
*
110909 GAATTTAC-ATTTCCCAA-TACGAATTTACCAAATGCGCAACTC-AGTTT-TCAAATTCGCAACT
1 GAATTTACAATTTCCCAACT-CGAATTTACCAAATGCGCAACTCGAATTTATCAAATTCGCAACT
110970 C
65 C
* * * * *
110971 GAA-TTCCAATTTCGCAACTCGAATTTACCAATTTCGCAACTCGAATTTATCAATTTCGCAACTC
1 GAATTTACAATTTCCCAACTCGAATTTACCAAATGCGCAACTCGAATTTATCAAATTCGCAACTC
111035 -AATTT
1 GAATTT
111040 TGCCGTATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
61 3 0.05
62 32 0.55
63 7 0.12
64 16 0.28
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (65 bp):
GAATTTACAATTTCCCAACTCGAATTTACCAAATGCGCAACTCGAATTTATCAAATTCGCAACTC
Found at i:111004 original size:22 final size:22
Alignment explanation
Indices: 110928--111039 Score: 135
Period size: 22 Copynumber: 5.3 Consensus size: 22
110918 TTTCCCAATA
* *
110928 CGAATTTACCAAATGCGCAACT
1 CGAATTTACCAATTTCGCAACT
* * *
110950 C-AGTTT-TCAAATTCGCAACT
1 CGAATTTACCAATTTCGCAACT
110970 CGAA-TT-CCAATTTCGCAACT
1 CGAATTTACCAATTTCGCAACT
110990 CGAATTTACCAATTTCGCAACT
1 CGAATTTACCAATTTCGCAACT
*
111012 CGAATTTATCAATTTCGCAACT
1 CGAATTTACCAATTTCGCAACT
111034 C-AATTT
1 CGAATTT
111040 TGCCGTATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
20 31 0.39
21 12 0.15
22 37 0.46
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (22 bp):
CGAATTTACCAATTTCGCAACT
Found at i:114169 original size:185 final size:184
Alignment explanation
Indices: 113848--114225 Score: 618
Period size: 185 Copynumber: 2.0 Consensus size: 184
113838 ATAAAATTTT
* *
113848 AAATTTTAAATATATTTTATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
1 AAATTTTAAATATATTATATATAACATATAGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
*
113913 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTTATATAAATTTA
* *
113978 TATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATTA-A
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTT-TGAATTATA
*
114032 AAATTATTAAATATATTATATATAACATATAGGCTCAGCCCAAACCATTTAAAA-CTCAATTAAT
1 AAATT-TTAAATATATTATATATAACATATAGGCTCAACCCAAACCATTTAAAATC-CAATTAAT
*
114096 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAA-TTTATATAAAAT
64 AATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTTATAT-AAAT
*
114160 TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTATA
128 TTATATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTATA
114217 AAATATTTA
1 AAAT-TTTA
114226 TTTTTTATAT
Statistics
Matches: 181, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
184 19 0.10
185 161 0.89
186 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATTTTAAATATATTATATATAACATATAGGCTCAACCCAAACCATTTAAAATCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTTATATAAATTTA
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTATA
Found at i:114373 original size:28 final size:30
Alignment explanation
Indices: 114319--114376 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
114309 TAATATTTTT
*
114319 GAAAAAAAATTCGGTTCGATTAACGATTAAA
1 GAAAAAAAATTCGGTTCAATT-ACGATTAAA
114350 GAAAAAAAATTCGGTT-AATT-CGATTAA
1 GAAAAAAAATTCGGTTCAATTACGATTAA
114377 TAGTAGTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
30 3 0.12
31 16 0.62
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.28
Consensus pattern (30 bp):
GAAAAAAAATTCGGTTCAATTACGATTAAA
Found at i:122575 original size:60 final size:60
Alignment explanation
Indices: 122501--122622 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
122491 GTCCTTAATA
* * * * * *
122501 TATGATCTTCATTCTAAATTATTTCTCAGAC-TTTTGAATATTTCAATTTCATCCCCAAAC
1 TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCAT-CCCAAAC
* * *
122561 TATGACCTTCATTCTACATTAGTCCCCAAACTTTTTGAACATTTTAATTTTATCCCAAAC
1 TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAAC
122621 TA
1 TA
122623 CATGTATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 34 0.65
61 18 0.35
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (60 bp):
TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAAC
Found at i:122728 original size:60 final size:60
Alignment explanation
Indices: 122651--122795 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 60
122641 ATCCATTGTT
*** * * *
122651 AATA-AATATTCAAAAAATTTGGGGACTAATTTAAAATGAGAGTCATAGTTTGGGGATGAA
1 AATAGAATATTC-AAAAATTTAAAGACTAATTTAAAATGAGAGTCATAGTTTAGAGATAAA
* * * *
122711 ATTAGAATGTTCAAAAATTTAAAGACTAATTTAGAATGAGAGTCATATTTTAGAGATAAA
1 AATAGAATATTCAAAAATTTAAAGACTAATTTAAAATGAGAGTCATAGTTTAGAGATAAA
122771 AATAGAATATTC-AAAATTTAAAGAC
1 AATAGAATATTCAAAAATTTAAAGAC
122796 CGGTTTGAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 13 0.18
60 53 0.74
61 6 0.08
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (60 bp):
AATAGAATATTCAAAAATTTAAAGACTAATTTAAAATGAGAGTCATAGTTTAGAGATAAA
Found at i:124867 original size:25 final size:26
Alignment explanation
Indices: 124814--124867 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
124804 CTTGTATGAA
124814 ATAATAACTTTAATTTAATAGTATATT
1 ATAATAAC-TTAATTTAATAGTATATT
*
124841 ATAATAA-TTAATTTTAATTGTAT-TT
1 ATAATAACTTAA-TTTAATAGTATATT
124866 AT
1 AT
124868 TTTTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 8 0.32
26 10 0.40
27 7 0.28
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (26 bp):
ATAATAACTTAATTTAATAGTATATT
Found at i:127000 original size:2 final size:2
Alignment explanation
Indices: 126993--127018 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
126983 GAAAGATCAC
126993 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
127019 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:127023 original size:2 final size:2
Alignment explanation
Indices: 127018--127065 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
127008 TCTCTCTCTC
* * *
127018 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
127060 CA TA TA
1 TA TA TA
127066 CAAGTTCATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:127027 original size:6 final size:6
Alignment explanation
Indices: 127019--127067 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
127009 CTCTCTCTCT
* * *
127019 ATATAT ATATAT ATATAT ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
127067 A
1 A
127068 AGTTCATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:133909 original size:24 final size:24
Alignment explanation
Indices: 133882--133958 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
133872 AGCTCATATA
133882 AATTTGTACCAAAGTGCCACATAG
1 AATTTGTACCAAAGTGCCACATAG
* * *
133906 AATTTGTCCCGAAG-GACCAAATAG
1 AATTTGTACCAAAGTG-CCACATAG
** * *
133930 AAATTTACACCAATGTGCCACGTAG
1 -AATTTGTACCAAAGTGCCACATAG
133955 AATT
1 AATT
133959 GCACCGTAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 1 0.03
24 23 0.57
25 15 0.38
26 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
AATTTGTACCAAAGTGCCACATAG
Found at i:134284 original size:14 final size:14
Alignment explanation
Indices: 134265--134307 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
134255 TTTACTGCAT
134265 ATTCATGTCATATA
1 ATTCATGTCATATA
* *
134279 ATTCATATAATATGA
1 ATTCATGTCATAT-A
*
134294 ATCCATGTCATATA
1 ATTCATGTCATATA
134308 TCATAATATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (14 bp):
ATTCATGTCATATA
Found at i:135210 original size:12 final size:12
Alignment explanation
Indices: 135183--135215 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
135173 CACATTTGGG
135183 AGAAGA-GAAGA
1 AGAAGATGAAGA
135194 AGAAGATGAAGA
1 AGAAGATGAAGA
*
135206 TGAAGATGAA
1 AGAAGATGAA
135216 TAAATTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.33, T:0.09
Consensus pattern (12 bp):
AGAAGATGAAGA
Found at i:137061 original size:22 final size:22
Alignment explanation
Indices: 137012--137090 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
137002 TTTTGGGCAA
*
137012 GGGGAATCAGTACCCATTCAA-
1 GGGGAATCGGTACCCATTCAAT
137033 -GGGAATCGGTACCCATTCAAT
1 GGGGAATCGGTACCCATTCAAT
137054 GGGGAATCGGTACCCATTCAAT
1 GGGGAATCGGTACCCATTCAAT
*
137076 GGGGAATCGATACCC
1 GGGGAATCGGTACCC
137091 CCCTCAAACG
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 19 0.35
22 35 0.65
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGGAATCGGTACCCATTCAAT
Found at i:138638 original size:99 final size:98
Alignment explanation
Indices: 138421--138622 Score: 313
Period size: 99 Copynumber: 2.1 Consensus size: 98
138411 GGGTCTACGC
* *
138421 GGTCCTTCGGGACATATGTATTCTTTGGAAACATGTATGAAGTCTGGTGAGACACATACTTGATC
1 GGTCCTTCGTGACATATATATTCTTTGGAAACATGTATGAAGTCTGGTGAGACACATACTTGATC
*
138486 CTTGCATATGTATATATTCTTAAGGAATGATATGT
66 CCT-CATATGTATATATTCTTAAGGAATGA-ATGT
*
138521 GGTCCTTCGTGACATATATATTCTTTGG-AACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GGTCCTTCGTGACATATATATTCTTTGGAAACATGTATGAAGTCTGGTGAGACACATACTTGATC
138585 CCT-ATATGTATATGATTCTTAAGG-ATG-ATGT
66 CCTCATATGTATAT-ATTCTTAAGGAATGAATGT
138616 GGTCCTT
1 GGTCCTT
138623 ATGGACATTA
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
95 11 0.11
97 13 0.13
98 10 0.10
99 37 0.38
100 26 0.27
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (98 bp):
GGTCCTTCGTGACATATATATTCTTTGGAAACATGTATGAAGTCTGGTGAGACACATACTTGATC
CCTCATATGTATATATTCTTAAGGAATGAATGT
Done.