Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1710028 original size:33 final size:33
Alignment explanation
Indices: 1709986--1710076 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1709976 AAAATTGCAA
1709986 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1710019 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1710052 TGCGA-TTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1710077 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 18 0.33
33 35 0.64
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1710314 original size:92 final size:93
Alignment explanation
Indices: 1710157--1710626 Score: 885
Period size: 92 Copynumber: 5.1 Consensus size: 93
1710147 TTGAATGGAT
1710157 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1710221 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1710249 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1710313 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1710341 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1710406 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1710434 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1710498 AGTTTAGCGGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1710526 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1710590 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1710618 AAATTTACT
1 AAATTTACT
1710627 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 5, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
91 10 0.03
92 264 0.71
93 96 0.26
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1710468 original size:185 final size:185
Alignment explanation
Indices: 1710157--1710626 Score: 899
Period size: 185 Copynumber: 2.6 Consensus size: 185
1710147 TTGAATGGAT
1710157 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1710221 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1710286 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1710341 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1710406 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
* *
1710471 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCGGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1710526 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1710590 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1710627 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 106 0.38
185 176 0.62
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1712345 original size:14 final size:14
Alignment explanation
Indices: 1712323--1712412 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1712313 GTTGAATGAA
1712323 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1712337 AATCACAACGCGAGATG
1 AATCGCAA--CGAGA-G
1712354 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1712370 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1712389 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1712403 AATCGCAACG
1 AATCGCAACG
1712413 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1712360 original size:33 final size:33
Alignment explanation
Indices: 1712317--1712429 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
1712307 CTTTTGGTTG
*
1712317 AATGAAAATCGCAACGAGAGAATCACAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
* *
1712350 GATGACAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
1712383 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
1712416 AATGAAAATCGCAA
1 AATGAAAATCGCAA
1712430 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:1712364 original size:19 final size:18
Alignment explanation
Indices: 1712322--1712434 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
1712312 GGTTGAATGA
1712322 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
1712337 -AATCACAACGCGAGATG
1 AAATCGCAACGCGAGATG
1712354 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1712370 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1712387 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1712403 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1712420 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1712435 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
16 15 0.19
17 12 0.16
19 27 0.35
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1712465 original size:14 final size:14
Alignment explanation
Indices: 1712446--1712500 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1712436 TTTGGTTTCG
1712446 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1712460 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1712479 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1712493 CGTTGCGA
1 CGTTGCGA
1712501 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1712478 original size:33 final size:33
Alignment explanation
Indices: 1712430--1712500 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1712420 AAAATCGCAA
**
1712430 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1712463 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1712496 TGCGA
1 TGCGA
1712501 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1712508 original size:33 final size:33
Alignment explanation
Indices: 1712441--1712522 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1712431 GCGATTTTGG
***
1712441 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1712474 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1712507 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1712523 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1712527 original size:20 final size:20
Alignment explanation
Indices: 1712453--1712541 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1712443 TCGCGTTGCG
1712453 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1712473 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1712486 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1712506 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1712526 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1712542 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1712663 original size:33 final size:33
Alignment explanation
Indices: 1712621--1712690 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1712611 AATACTAACT
*
1712621 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1712654 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1712687 TGAA
1 TGAA
1712691 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1712924 original size:22 final size:22
Alignment explanation
Indices: 1712872--1712926 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1712862 TGGTTGTGAG
**
1712872 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1712894 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1712916 GGATTTCTTCG
1 GGATTTCTTCG
1712927 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1713235 original size:60 final size:60
Alignment explanation
Indices: 1713072--1713240 Score: 239
Period size: 60 Copynumber: 2.8 Consensus size: 60
1713062 TTTAATATCG
** *
1713072 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
1713133 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
1713193 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA
1713241 ATTTGTACTA
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 66 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:1713240 original size:20 final size:20
Alignment explanation
Indices: 1713070--1713224 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
1713060 GCTTTAATAT
1713070 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1713090 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1713112 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1713131 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1713151 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1713171 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1713191 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1713211 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
1713225 TGTGTTCGCG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 98 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1713302 original size:20 final size:20
Alignment explanation
Indices: 1713277--1713328 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1713267 AAGAATCGCG
*
1713277 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1713297 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1713317 TTGCGATTCTGG
1 TTGCGATTCTGG
1713329 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1719980 original size:27 final size:27
Alignment explanation
Indices: 1719950--1720039 Score: 72
Period size: 27 Copynumber: 3.6 Consensus size: 27
1719940 ATTTAAAAAA
1719950 AAATTTATTATTTTTATATTTTAAATT
1 AAATTTATTATTTTTATATTTTAAATT
* *
1719977 AAA--T-TCA-----ATATTTTATATT
1 AAATTTATTATTTTTATATTTTAAATT
* *
1719996 AAATTTACTATTTTTATAATTTAAATT
1 AAATTTATTATTTTTATATTTTAAATT
1720023 AAATTTGA-TATTTTTAT
1 AAATTT-ATTATTTTTAT
1720040 TAAATTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
19 14 0.29
21 1 0.02
22 1 0.02
24 2 0.04
25 1 0.02
27 28 0.58
28 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (27 bp):
AAATTTATTATTTTTATATTTTAAATT
Found at i:1720007 original size:19 final size:18
Alignment explanation
Indices: 1719962--1720009 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1719952 ATTTATTATT
1719962 TTTATATTTTAAATTAAA
1 TTTATATTTTAAATTAAA
* *
1719980 TTCAATATTTTATATTAAA
1 TT-TATATTTTAAATTAAA
1719999 TTTACTATTTT
1 TTTA-TATTTT
1720010 TATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATATTTTAAATTAAA
Found at i:1720008 original size:46 final size:45
Alignment explanation
Indices: 1719950--1720046 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 45
1719940 ATTTAAAAAA
* *
1719950 AAATTTATTATTTTTATATTTTAAATTAAATTCAATATTTTATATT
1 AAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTT-TATT
**
1719996 AAATTTACTATTTTTATAATTTAAATTAAATTTGATATTTTTATT
1 AAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTTTATT
1720041 AAATTT
1 AAATTT
1720047 TTATAATTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 10 0.21
46 37 0.79
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (45 bp):
AAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTTTATT
Found at i:1720128 original size:28 final size:29
Alignment explanation
Indices: 1720096--1720158 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1720086 ATTTCTAAAA
*
1720096 ATAAATAT-GAAAATATTAAATTTAATTT
1 ATAAATATAGAAAATAATAAATTTAATTT
*
1720124 ATAAATATAGAAAATAATAATTTTAATTT
1 ATAAATATAGAAAATAATAAATTTAATTT
1720153 -TAAATA
1 ATAAATA
1720159 GCTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATAAATATAGAAAATAATAAATTTAATTT
Found at i:1720337 original size:32 final size:33
Alignment explanation
Indices: 1720276--1720337 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
1720266 ATTATTTATT
* *
1720276 TTTATTTTTCTATAATTGACAATAGTATAAAAC
1 TTTATTTTTCTATAATTAACAATAATATAAAAC
* *
1720309 TTTA-TTTTCTATCATTAATAATAATATAA
1 TTTATTTTTCTATAATTAACAATAATATAA
1720338 GATAAATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTATTTTTCTATAATTAACAATAATATAAAAC
Found at i:1720496 original size:19 final size:20
Alignment explanation
Indices: 1720468--1720507 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1720458 TCTTAATTTT
1720468 TTAAATTTTAAT-TTATTTAA
1 TTAAATTTT-ATGTTATTTAA
1720488 TTAAA-TTTATGTTATTTAA
1 TTAAATTTTATGTTATTTAA
1720507 T
1 T
1720508 CAAACGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.63
20 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTAAATTTTATGTTATTTAA
Found at i:1720574 original size:6 final size:6
Alignment explanation
Indices: 1720565--1720597 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1720555 ATTAAAATAA
1720565 AATTAG AATTAG AATTAG AATTAG AATTA- AATT
1 AATTAG AATTAG AATTAG AATTAG AATTAG AATT
1720598 GATTGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (6 bp):
AATTAG
Found at i:1721528 original size:31 final size:31
Alignment explanation
Indices: 1721490--1721564 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
1721480 AAACTTTCTA
* *
1721490 AAAAAATCAATTACACTATCAAACTTAGCCC
1 AAAAAATCAATTACACCATCAAACTTAACCC
1721521 AAAAAATCAATTACACCATCAAACTTAACCC
1 AAAAAATCAATTACACCATCAAACTTAACCC
1721552 AAAAAATCAATTA
1 AAAAAATCAATTA
1721565 AGTTCATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.21
Consensus pattern (31 bp):
AAAAAATCAATTACACCATCAAACTTAACCC
Found at i:1722158 original size:24 final size:23
Alignment explanation
Indices: 1722125--1722175 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1722115 CCTATTTTAG
*
1722125 TTTTCAAAAATTAAAAATTAAAACTA
1 TTTT-AAAAA-TAAAAA-TAAAAATA
1722151 TTTTAAAAATAAAAATAAAAATA
1 TTTTAAAAATAAAAATAAAAATA
1722174 TT
1 TT
1722176 CATAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 6 0.25
25 5 0.21
26 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
TTTTAAAAATAAAAATAAAAATA
Found at i:1722181 original size:24 final size:24
Alignment explanation
Indices: 1722130--1722187 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1722120 TTTAGTTTTC
* *
1722130 AAAAATTAAAAATTAAAACTATTTT
1 AAAAA-TAAAAATTAAAAATATTAT
1722155 AAAAATAAAAA-TAAAAATATTCAT
1 AAAAATAAAAATTAAAAATATT-AT
*
1722179 AAATATAAA
1 AAAAATAAA
1722188 TTAACATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.31
24 15 0.52
25 5 0.17
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAATAAAAATTAAAAATATTAT
Done.