Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009578.1 Hibiscus syriacus cultivar Beakdansim tig00116946_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: 651624
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:585370 original size:33 final size:33
Alignment explanation
Indices: 585328--585421 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
585318 AAAAATTACT
*
585328 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
585361 ATCGCAATGCGAAATGAAAATCGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
585394 ATCGCAATGCGAAATAAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
585422 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:585462 original size:19 final size:19
Alignment explanation
Indices: 585393--585455 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
585383 GCAACTAGAG
*
585393 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
585412 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
585431 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
585450 ATTCGC
1 AATCGC
585456 GTTGCGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:585473 original size:19 final size:19
Alignment explanation
Indices: 585451--585601 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
585441 CGAAACTAAA
585451 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
585470 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
585485 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
585503 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
585518 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
585536 TTCGTATTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
585551 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
585569 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
585588 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
585602 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 42 0.44
20 10 0.11
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:585497 original size:33 final size:33
Alignment explanation
Indices: 585455--585581 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
585445 ACTAAATTCG
*
585455 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
585488 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
585521 CGTTGCGATTTTCATTTCGTATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
585554 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
585582 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:585528 original size:14 final size:14
Alignment explanation
Indices: 585476--585563 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
585466 TCATTTCGCA
*
585476 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
585490 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
585507 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
585523 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
585540 TATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
585556 TTGCGATT
1 TTGCGATT
585564 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:585647 original size:20 final size:20
Alignment explanation
Indices: 585575--585647 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
585565 TCATTTCGCA
* *
585575 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
585595 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
585615 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
585636 TTGCGATAGTCA
1 TTGCGATAGTCA
585648 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:588534 original size:21 final size:20
Alignment explanation
Indices: 588491--588542 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
588481 TTTTCACAAT
*
588491 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
588511 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
588532 TCGCATTGCGA
1 TCGCAATGCGA
588543 TATTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:588598 original size:20 final size:20
Alignment explanation
Indices: 588573--588689 Score: 180
Period size: 20 Copynumber: 5.8 Consensus size: 20
588563 TAATACAAAA
* *
588573 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
588593 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
588613 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
588633 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
588653 TCACAACGAGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
588673 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
588690 AAATCGTAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:588988 original size:19 final size:19
Alignment explanation
Indices: 588966--589033 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
588956 GAAATGAAAA
588966 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
588985 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
589001 TCG--TTGCGATTGTCATT
1 TCGCATTGCGATTTTCATT
589018 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
589034 TCGTTGCGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
16 3 0.07
17 3 0.07
19 26 0.62
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:589007 original size:14 final size:14
Alignment explanation
Indices: 588990--589043 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
588980 TCATTTCGCA
588990 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
*
589004 TTGCGATTGTCATTTCG
1 TTGCGATT-T--TCTCG
589021 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
589037 TTGCGAT
1 TTGCGAT
589044 AGTCAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:589017 original size:33 final size:33
Alignment explanation
Indices: 588971--589063 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
588961 GAAAATCGCA
*
588971 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTGTCATTTCGCATTGCGATTTTCTCG
589004 TTGCGATTGTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTGTCATTTCGCATTGCGATTTTCTCG
* **
589037 TTGCGATAGTCAGTTTCGTGTTGCGAT
1 TTGCGATTGTCA-TTTCGCATTGCGAT
589064 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 43 0.78
34 12 0.22
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCATTGCGATTTTCTCG
Found at i:591062 original size:20 final size:20
Alignment explanation
Indices: 591037--591075 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
591027 GAAGAATAGT
591037 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
591057 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
591076 ATGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:591086 original size:20 final size:20
Alignment explanation
Indices: 591063--591169 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
591053 AAACTTACTT
*
591063 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
591083 TCGCAATGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
591103 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
591123 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
591143 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
591162 TCGCAACG
1 TCGCAACG
591170 ACAAAATCGC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 14 0.18
20 64 0.82
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:591087 original size:40 final size:40
Alignment explanation
Indices: 591043--591168 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 40
591033 TAGTTTACTT
* *
591043 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
** * *
591083 TCGCAATGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
* * * **
591123 TCGCAACGCGGAAATGGCTATCGCAATGCG-AAATGAAAA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
591162 TCGCAAC
1 TCGCAAC
591169 GACAAAATCG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 13 0.18
40 56 0.77
41 4 0.05
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:591177 original size:14 final size:14
Alignment explanation
Indices: 591158--591215 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
591148 ATGCGAAATG
591158 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
591172 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
591191 AAAATCACAACGAC
1 AAAATCGCAACGAC
591205 AAAATCGCAAC
1 AAAATCGCAAC
591216 ACGAAACACA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:591221 original size:33 final size:33
Alignment explanation
Indices: 591142--591214 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
591132 GGAAATGGCT
*
591142 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
591175 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
591208 ATCGCAA
1 ATCGCAA
591215 CACGAAACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:591229 original size:33 final size:33
Alignment explanation
Indices: 591142--591229 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 33
591132 GGAAATGGCT
** * *
591142 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACACGAAATCAAAATCACAACGACAAA
** *
591175 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACACGAAATCAAAATCACAACGACAAA
591208 ATCGCAACACGAAA-CACAAATC
1 ATCGCAACACGAAATCA-AAATC
591230 GCATTGCGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.02
33 49 0.98
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (33 bp):
ATCGCAACACGAAATCAAAATCACAACGACAAA
Found at i:591250 original size:19 final size:19
Alignment explanation
Indices: 591228--591324 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
591218 GAAACACAAA
591228 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
591247 TCGCGTTACGA-TTT--TG
1 TCGCATTGCGATTTTCATT
* *
591263 TAG--TTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
591280 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
591296 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
591313 TCGCATTGCGAT
1 TCGCATTGCGAT
591325 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 12 0.20
15 6 0.10
16 7 0.12
17 7 0.12
18 6 0.10
19 21 0.36
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:591278 original size:33 final size:33
Alignment explanation
Indices: 591236--591324 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
591226 AATCGCATTG
*
591236 CGATTTTCATTTCGCGTTACGATTTTGTAGTTA
1 CGATTTTCATTTCGCATTACGATTTTGTAGTTA
* * *
591269 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTACGATTTTGTAGTTA
*
591302 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTACGAT
591325 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTACGATTTTGTAGTTA
Found at i:591343 original size:20 final size:19
Alignment explanation
Indices: 591309--591363 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
591299 TTGCGATTTT
*
591309 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
591328 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
591348 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
591364 AAGTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:591928 original size:18 final size:18
Alignment explanation
Indices: 591905--591952 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
591895 CGGGTCGATC
591905 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
591923 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
591941 AGGTGATGGCTC
1 AGGTGATGGCTC
591953 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:593305 original size:20 final size:20
Alignment explanation
Indices: 593257--593315 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
593247 AATAGTTTCT
* *
593257 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
593277 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
593297 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
593316 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:593605 original size:22 final size:22
Alignment explanation
Indices: 593578--593621 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
593568 GATGGAGATA
593578 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
593600 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
593622 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:593907 original size:41 final size:41
Alignment explanation
Indices: 593788--593925 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
593778 CACTTTGAAA
* * *
593788 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
593829 ATTGCGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
593869 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
593910 ATCACGTTGCGATTTT
1 ATCGCGTTGCGATTTT
593926 CCAAATTCGC
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 33 0.42
41 46 0.58
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:593922 original size:20 final size:20
Alignment explanation
Indices: 593808--593921 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
593798 GATTATGTAT
*
593808 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
593828 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
593848 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
593868 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
593889 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
593909 TATCACGTTGCGA
1 TATCGCGTTGCGA
593922 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:593941 original size:41 final size:41
Alignment explanation
Indices: 593815--593943 Score: 111
Period size: 41 Copynumber: 3.2 Consensus size: 41
593805 TATTATCTCG
* ** ** *
593815 TTGCGAAAGTCAGTATTGCGTTGCGAAATT-AAGTATCG-A
1 TTGCGATAGTCAGTATCACGTTGCGATTTTCAAATATCGCA
* * ** * *
593854 GTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 -TTGCGATAGTCAGTATCACGTTGCGATTTTCAAATATCGCA
593896 TTGCGATAGTCAGTATCACGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCACGTTGCGATTTT-CAAATATCGCA
593937 TTGCGAT
1 TTGCGAT
593944 TTTTAAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 27 0.36
41 45 0.61
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCACGTTGCGATTTTCAAATATCGCA
Found at i:593942 original size:21 final size:21
Alignment explanation
Indices: 593916--593966 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
593906 CAGTATCACG
*
593916 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCAAAATTCGCA
*
593937 TTGCGATTTTTAAAATTCGCA
1 TTGCGATTTTCAAAATTCGCA
593958 TTGCGATTT
1 TTGCGATTT
593967 ACTTATTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTCAAAATTCGCA
Found at i:594025 original size:21 final size:22
Alignment explanation
Indices: 593977--594025 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
593967 ACTTATTCGT
593977 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
**
593998 AACGCGAAATT-GGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
594019 ATTGCGA
1 ATTGCGA
594026 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:596373 original size:34 final size:37
Alignment explanation
Indices: 596321--596390 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 37
596311 ATTTTTTAAC
* *
596321 CATTTGATTTCGGTTTCGGTTTAAATTTTGA-AAAAT
1 CATTTGATTTCGGATTCGGTTCAAATTTTGATAAAAT
*
596357 CATTT-ATTTC-GATTCGGTTCAATTTTTGATAAAA
1 CATTTGATTTCGGATTCGGTTCAAATTTTGATAAAA
596391 ACCGAACCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 16 0.53
35 9 0.30
36 5 0.17
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (37 bp):
CATTTGATTTCGGATTCGGTTCAAATTTTGATAAAAT
Found at i:602570 original size:28 final size:27
Alignment explanation
Indices: 602523--602582 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 27
602513 GGATTTGGGG
602523 TTTTTATAATTTAAGGAAAAATTAAAGTT
1 TTTTTATAATTTAA-GAAAAATT-AAGTT
602552 TTTTTATAAATTTAA-AAAAATTAAGTT
1 TTTTTAT-AATTTAAGAAAAATTAAGTT
602579 TTTT
1 TTTT
602583 AAATAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 9 0.30
28 7 0.23
29 7 0.23
30 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (27 bp):
TTTTTATAATTTAAGAAAAATTAAGTT
Found at i:602588 original size:28 final size:29
Alignment explanation
Indices: 602523--602589 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
602513 GGATTTGGGG
602523 TTTTT-AT-AATTTAAGGAAAAATTAAAGT
1 TTTTTAATAAATTTAA-GAAAAATTAAAGT
*
602551 TTTTTTATAAATTTAA-AAAAATT-AAGT
1 TTTTTAATAAATTTAAGAAAAATTAAAGT
602578 TTTTTAAATAAA
1 TTTTT-AATAAA
602590 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 9 0.26
28 17 0.49
29 2 0.06
30 7 0.20
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTTTAATAAATTTAAGAAAAATTAAAGT
Found at i:603198 original size:20 final size:20
Alignment explanation
Indices: 603173--603224 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
603163 CCCTTTGAAC
603173 AAAGGATCGATCCTCTTGAG
1 AAAGGATCGATCCTCTTGAG
603193 AAAGGATCGATCCTCTTGAG
1 AAAGGATCGATCCTCTTGAG
603213 AAAGGATCGATC
1 AAAGGATCGATC
603225 ACTTGGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (20 bp):
AAAGGATCGATCCTCTTGAG
Found at i:604305 original size:14 final size:15
Alignment explanation
Indices: 604279--604364 Score: 58
Period size: 14 Copynumber: 6.0 Consensus size: 15
604269 ATTTTTATAA
604279 ATTAATAATAATATT
1 ATTAATAATAATATT
604294 ATTAAT-ATAATATT
1 ATTAATAATAATATT
* *
604308 -TTTATAATTATA-T
1 ATTAATAATAATATT
604321 A-TACA-AATAATATT
1 ATTA-ATAATAATATT
* *
604335 -TTTATAATTATATAT
1 ATTAATAATAATAT-T
**
604350 ACAAATAATAATATT
1 ATTAATAATAATATT
604365 TAGAAAAGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
13 13 0.25
14 23 0.43
15 8 0.15
16 9 0.17
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAATAATAATATT
Found at i:604335 original size:27 final size:27
Alignment explanation
Indices: 604300--604359 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
604290 TATTATTAAT
604300 ATAATATTTTTATAATTATATATACAA
1 ATAATATTTTTATAATTATATATACAA
604327 ATAATATTTTTATAATTATATATACAA
1 ATAATATTTTTATAATTATATATACAA
604354 ATAATA
1 ATAATA
604360 ATATTTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAATATTTTTATAATTATATATACAA
Found at i:608114 original size:26 final size:26
Alignment explanation
Indices: 608076--608130 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
608066 TTCTACTGAT
*
608076 GCCCCTACTTGCTGCCCTGGGCCATC
1 GCCCCTACATGCTGCCCTGGGCCATC
*
608102 GCCCCTACATGCTGCCCTGGGCCGTC
1 GCCCCTACATGCTGCCCTGGGCCATC
608128 GCC
1 GCC
608131 TATCTGGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.07, C:0.47, G:0.25, T:0.20
Consensus pattern (26 bp):
GCCCCTACATGCTGCCCTGGGCCATC
Found at i:611491 original size:144 final size:142
Alignment explanation
Indices: 611261--611653 Score: 461
Period size: 144 Copynumber: 2.8 Consensus size: 142
611251 AACTAGAAAA
* * *
611261 GGAGGCTCTAATATTAATCCTAATCA-ATTTTAACCAATTATTAAGTCGAATAATCAACTTGGAC
1 GGAGGCTCTAATATTAATCCTAATCATTTTTTAACCAATTATTAAGTCAAATAATCAACGTGGAC
*** *
611325 CCTCAGGCATTTAAATGCGAAGGCCAAATCGAATTATTCCCTAAATTAAGAGACTAGGGTGAACT
66 CCTCAGGCATTTAAATGCGAAGGCCAAATCGAATTATTCCCTAAATTAAGAGACTAAAATGAAAT
611390 TTAGCCTAAAGT
131 TTAGCCTAAAGT
* * *
611402 GGAGGCTCTAATATTAACCCTAGTCATTTTTTATCCAAAATTATTGAA-TCAAATAATCAACGTG
1 GGAGGCTCTAATATTAATCCTAATCATTTTTTAACC--AATTATT-AAGTCAAATAATCAACGTG
* * * * *
611466 GTCCCTCAGGCATTTTAATGGGAAGGCCAAATCGAATTATTCCCTAAATTAAGGGATTAAAATGA
63 GACCCTCAGGCATTTAAATGCGAAGGCCAAATCGAATTATTCCCTAAATTAAGAGACTAAAATGA
611531 AATTTAGCCTAAAGT
128 AATTTAGCCTAAAGT
* * * ** ** *
611546 GGAGGCTCAAATATTAATCCTAATCGA--TTTTATCCAATTATTGAGTTGAGCAATCAACTTGGA
1 GGAGGCTCTAATATTAATCCTAATC-ATTTTTTAACCAATTATTAAGTCAAATAATCAACGTGGA
* * * * * *
611609 GCCTCGGGCATTTAAATGCAAAAGCCAAATTGAATTATTCACTAA
65 CCCTCAGGCATTTAAATGCGAAGGCCAAATCGAATTATTCCCTAA
611654 TTTCAAAAAG
Statistics
Matches: 213, Mismatches: 33, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
140 1 0.00
141 80 0.38
142 7 0.03
143 8 0.04
144 114 0.54
145 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (142 bp):
GGAGGCTCTAATATTAATCCTAATCATTTTTTAACCAATTATTAAGTCAAATAATCAACGTGGAC
CCTCAGGCATTTAAATGCGAAGGCCAAATCGAATTATTCCCTAAATTAAGAGACTAAAATGAAAT
TTAGCCTAAAGT
Found at i:612956 original size:144 final size:145
Alignment explanation
Indices: 612691--612958 Score: 355
Period size: 144 Copynumber: 1.9 Consensus size: 145
612681 ATCCTAATCG
* * * *
612691 AATTATTGAGTCGAATAATCAACTTGAACCCTCAGGCATTTAAATGCGAAAGGCCAAATCGAATT
1 AATTATTGAATCAAATAATCAACGTGAACCCTCAGACATTTAAATGCGAAAGGCCAAATCGAATT
* ** * *
612756 ATTCCCTAAATTAAGGTACTAAGGTGAAATTTAGCCTAAAGTGGAGGCTCTCATATTAACCATAG
66 ATTCCCTAAATGAAGGTACTAAAATGAAATTTAACCTAAAGTGGAGGCTCTAATATTAACCATAG
612821 TAATTTTTTATCCAA
131 TAATTTTTTATCCAA
** * *
612836 AATTATTGAATCAAATAATCAACGTGGTCCCTC-GAACATTTTAATGCG-AAGGTCAAATCGAAT
1 AATTATTGAATCAAATAATCAACGTGAACCCTCAG-ACATTTAAATGCGAAAGGCCAAATCGAAT
*
612899 TATTCCCTAAATGAAGAG-ACTAAAATGAAATTTAACCTAATA-TGGAGGTTCTAATATTAA
65 TATTCCCTAAATGAAG-GTACTAAAATGAAATTTAACCTAA-AGTGGAGGCTCTAATATTAA
612959 TCCTAATCGA
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
144 65 0.61
145 41 0.39
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (145 bp):
AATTATTGAATCAAATAATCAACGTGAACCCTCAGACATTTAAATGCGAAAGGCCAAATCGAATT
ATTCCCTAAATGAAGGTACTAAAATGAAATTTAACCTAAAGTGGAGGCTCTAATATTAACCATAG
TAATTTTTTATCCAA
Found at i:615263 original size:146 final size:147
Alignment explanation
Indices: 615096--615388 Score: 518
Period size: 146 Copynumber: 2.0 Consensus size: 147
615086 CGCCTCGTTG
615096 AGAGGGAAGAAAAAATAAAAAAAATTTAGTATA-AAATTGAGAAGAAGAAGATGAAGAAAGAAAA
1 AGAGGGAAGAAAAAAT-AAAAAAATTTAGTATAGAAATTGAGAAGAAGAAGATGAAGAAAGAAAA
*
615160 ATACGAATGTGTCTTAATCCAGCGTAGTGAACGAATTATAGAGAGATCTAAAAAAAGTAGAAAAT
65 ATACGAAGGTGTCTTAATCCAGCGTAGTGAACGAATTATAGAGAGATCTAAAAAAAGTAGAAAAT
615225 GAC-ATGCACAAATATTA
130 GACAATGCACAAATATTA
*
615242 AGAGGGAAGAAAAAATTAAAAAATTTAGTATAGAAATTGAGAAGAAGAAGATGAAGAAAGAAAAA
1 AGAGGGAAGAAAAAATAAAAAAATTTAGTATAGAAATTGAGAAGAAGAAGATGAAGAAAGAAAAA
* *
615307 TACGAAGGTGTCTTAATCCGGCGTAGTGAACGAATTGTAGAGAGATCTAAAAAAAGTAGAAAATG
66 TACGAAGGTGTCTTAATCCAGCGTAGTGAACGAATTATAGAGAGATCTAAAAAAAGTAGAAAATG
615372 ACATATGCACAAATATT
131 ACA-ATGCACAAATATT
615389 GATTTGTATG
Statistics
Matches: 140, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
145 15 0.11
146 112 0.80
148 13 0.09
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (147 bp):
AGAGGGAAGAAAAAATAAAAAAATTTAGTATAGAAATTGAGAAGAAGAAGATGAAGAAAGAAAAA
TACGAAGGTGTCTTAATCCAGCGTAGTGAACGAATTATAGAGAGATCTAAAAAAAGTAGAAAATG
ACAATGCACAAATATTA
Found at i:628045 original size:9 final size:8
Alignment explanation
Indices: 628031--628071 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
628021 GTCATAAGTC
628031 AAAGAAGAA
1 AAAGAA-AA
628040 AAAGAAAA
1 AAAGAAAA
628048 AAA-AAAA
1 AAAGAAAA
628055 AAAGAAAA
1 AAAGAAAA
*
628063 AGAGAAAA
1 AAAGAAAA
628071 A
1 A
628072 CGTTTGGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 7 0.23
8 17 0.57
9 6 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:629852 original size:24 final size:24
Alignment explanation
Indices: 629807--629853 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
629797 CGTCCTTGTT
* *
629807 TATAAATGTATTTATGCTATATAG
1 TATAAACGTATTTATGCAATATAG
629831 TATAAACGTATTATATG-AATATA
1 TATAAACGTATT-TATGCAATATA
629854 TATTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (24 bp):
TATAAACGTATTTATGCAATATAG
Found at i:631398 original size:19 final size:18
Alignment explanation
Indices: 631376--631423 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
631366 TTCATTTCTG
*
631376 TTTTTCTAATTATTAGTTA
1 TTTTTTTAATTATT-GTTA
* *
631395 TTTTTTTATTTATTTTTA
1 TTTTTTTAATTATTGTTA
631413 TTTTTTTAATT
1 TTTTTTTAATT
631424 TACCCATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTTTAATTATTGTTA
Found at i:631424 original size:19 final size:18
Alignment explanation
Indices: 631352--631425 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
631342 TTCTTTTTGA
*
631352 TTTTGTTTTTTTATTTCAT
1 TTTTATTTTTTTATTT-AT
* * * *
631371 TTCTGTTTTTCTAATTAT
1 TTTTATTTTTTTATTTAT
*
631389 TAGTTATTTTTTTATTTAT
1 T-TTTATTTTTTTATTTAT
631408 TTTTATTTTTTTAATTTA
1 TTTTATTTTTTT-ATTTA
631426 CCCATTTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 13 0.30
19 31 0.70
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTTTATTTAT
Found at i:632846 original size:23 final size:24
Alignment explanation
Indices: 632805--632857 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
632795 TTTTTATAAA
632805 TTTTTTAAAATTCCAAAAACATAT
1 TTTTTTAAAATTCCAAAAACATAT
*
632829 TTTTTTAAAGTTCCAAAAACATAT
1 TTTTTTAAAATTCCAAAAACATAT
632853 TTTTT
1 TTTTT
632858 ATCGGACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTTTAAAATTCCAAAAACATAT
Found at i:634545 original size:24 final size:26
Alignment explanation
Indices: 634518--634565 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
634508 CTTCCTTGTT
*
634518 TATAAATGTATT-TATG-CTATATCG
1 TATAAACGTATTATATGACTATATCG
634542 TATAAACGTATTATATGACTATAT
1 TATAAACGTATTATATGACTATAT
634566 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (26 bp):
TATAAACGTATTATATGACTATATCG
Found at i:634593 original size:17 final size:17
Alignment explanation
Indices: 634563--634616 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
634553 TATATGACTA
* * *
634563 TATATTTATTTATAATG
1 TATATATATATATATTG
634580 TATATATATATATATTG
1 TATATATATATATATTG
*
634597 TTTATAT-TATATATTG
1 TATATATATATATATTG
634613 TATA
1 TATA
634617 CACAATACGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
TATATATATATATATTG
Found at i:635924 original size:18 final size:19
Alignment explanation
Indices: 635889--635925 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
635879 TGTACGTTTT
*
635889 AATTTAATTGTTTTTTTAA
1 AATTTAATTGTCTTTTTAA
635908 AATTTAATTG-CTTTTTAA
1 AATTTAATTGTCTTTTTAA
635926 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTAATTGTCTTTTTAA
Found at i:638478 original size:31 final size:33
Alignment explanation
Indices: 638436--638514 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 33
638426 CGTTGTGTAC
* *
638436 TATA-ATTACATA-ATGTAT-ATATTATGTCGT
1 TATATATTACATACATATATAATATTATATCGT
638466 TATATATTACATAGCATATATACATATTATATCGT
1 TATATATTACATA-CATATATA-ATATTATATCGT
638501 TATATTATTACATA
1 TATA-TATTACATA
638515 TTATTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 8 0.20
33 5 0.12
35 15 0.37
36 9 0.22
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (33 bp):
TATATATTACATACATATATAATATTATATCGT
Found at i:639083 original size:16 final size:17
Alignment explanation
Indices: 639052--639086 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
639042 GTCCTGTACG
639052 TTTTAATTTAATTATTT
1 TTTTAATTTAATTATTT
639069 TTTTAATTTAA-TATTT
1 TTTTAATTTAATTATTT
639085 TT
1 TT
639087 AATTTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTAATTATTT
Found at i:639085 original size:14 final size:16
Alignment explanation
Indices: 639052--639091 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
639042 GTCCTGTACG
639052 TTTTAATTTAATTATTT
1 TTTTAATTTAATTA-TT
639069 TTTTAATTTAA-TA-T
1 TTTTAATTTAATTATT
639083 TTTTAATTT
1 TTTTAATTT
639092 TATGCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.43
16 2 0.09
17 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATTTAATTATT
Found at i:649883 original size:75 final size:74
Alignment explanation
Indices: 649759--649905 Score: 179
Period size: 75 Copynumber: 2.0 Consensus size: 74
649749 ATACTTCGCC
* * * * *
649759 TAGGATGAAAACCCAAAAGGGCGTCCTAAGTCGAAGAAGAAAAAGAAAAAAGAAAAGGAAAAAAA
1 TAGGATGAAAACCCAAAAGGGCGCCCTAAATCGAAGAA-AAAAAAAAAAAAAAAAAAGAAAAAAA
649824 AGAAAAAGTT
65 AGAAAAAGTT
* * * *
649834 TAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAA-AAAAAGAAAAAAAAAAAAAAAGAAAAAAT
1 TAGGATGAAAACCCAAAAGGGCGCCCTAAATCGAAGAAAAA-AAAAAAAAAAAAAAAGAAAAAAA
*
649898 TGAAAAAG
65 AGAAAAAG
649906 AAAAAGAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
73 3 0.05
74 28 0.46
75 30 0.49
ACGTcount: A:0.60, C:0.10, G:0.21, T:0.10
Consensus pattern (74 bp):
TAGGATGAAAACCCAAAAGGGCGCCCTAAATCGAAGAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
GAAAAAGTT
Found at i:649908 original size:6 final size:6
Alignment explanation
Indices: 649869--649926 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
649859 CTAAATTGAA
649869 AAAAAG AAAAA- AAAAA- AAAAAG AAAAAATTG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAA--G AAAAAG AAAAAG AAAAAG
649918 -AAAAG AAAA
1 AAAAAG AAAA
649927 TAAGGTGGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 15 0.32
6 21 0.45
7 5 0.11
8 5 0.11
9 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAAAG
Done.