Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009575.1 Hibiscus syriacus cultivar Beakdansim tig00116943_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: 458240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:329864 original size:2 final size:2
Alignment explanation
Indices: 329857--329886 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
329847 TTAATTAGTT
*
329857 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
329887 ATACATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:330996 original size:18 final size:20
Alignment explanation
Indices: 330955--330998 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
330945 TAAAACAATA
330955 ATAATATAACAAATCATAAC
1 ATAATATAACAAATCATAAC
*
330975 -TAATAT-ACAAAT-ATTAC
1 ATAATATAACAAATCATAAC
330992 ATAATAT
1 ATAATAT
330999 GAGTACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATATAACAAATCATAAC
Found at i:332850 original size:135 final size:134
Alignment explanation
Indices: 332511--332851 Score: 407
Period size: 135 Copynumber: 2.5 Consensus size: 134
332501 GTTCTAGTCG
* * * * **
332511 TCTAAGGGTGACACAGCTCCTACGTGATGAGGAGATTTGGTCAGG-GGATAACATTGTTCCTACG
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATATGGTC-GGTGGATGACACAGTT-CTACG
*
332575 TGATGAGGATGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACGAC
64 TGATGAGGACGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACGAC
*
332640 TGGTTA
129 TGGATA
* * * * * * *
332646 TCTAGGGCTGACCCGACTCCTACGTGATGAGGAGGTATGGTCAGTGGATGAGACAGTTCTTACAT
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACAGTTC-TACGT
** ** * *
332711 GATGAGGACGTTTTGGTTATCTTTAGGGATGGTGATAACACGGTTCCTATACGATGAGGAC-AGC
65 GATGAGGACGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACGA-C
332775 TGGATA
129 TGGATA
* * *
332781 TCTAGGGGTGATACGGCTCCTACGTGATGAGGAGATGTGGTCGGTGGATGACACAGTTACTACGC
1 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACAGTT-CTACGT
332846 GATGAG
65 GATGAG
332852 AATGACAGGC
Statistics
Matches: 171, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
134 3 0.02
135 167 0.98
136 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (134 bp):
TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACAGTTCTACGTG
ATGAGGACGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACGACTG
GATA
Found at i:333001 original size:36 final size:36
Alignment explanation
Indices: 332954--333075 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
332944 CATTTCAAAA
332954 GAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGG
1 GAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGG
**** * * *
332990 GAAA-TGCACTC-AAAGATTTTTAATTTTGTTTTAAGA
1 GAAACTG-ACTCAAAAGA-GACAAAATTTGTTTCAAGG
* *
333026 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGG
**
333062 GAAACAAACTCAAA
1 GAAACTGACTCAAA
333076 GATGATGTTT
Statistics
Matches: 62, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
35 7 0.11
36 49 0.79
37 6 0.10
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (36 bp):
GAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGG
Found at i:333106 original size:65 final size:65
Alignment explanation
Indices: 333016--333144 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
333006 TTTTTAATTT
* * * *
333016 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGA
1 TGTTTCAAGAAAAACTGTATCAAGAGAGACAAAATTCGTTTCAAGGGAAACAAACTCAAAGATGA
* *
333081 TGTTTCAAGAAAAACTGTATTAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATG
1 TGTTTCAAGAAAAACTGTATCAAGAGAGACAAAATTCGTTTCAAGGGAAACAAACTCAAAGATG
333145 GTTTTATTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.25
Consensus pattern (65 bp):
TGTTTCAAGAAAAACTGTATCAAGAGAGACAAAATTCGTTTCAAGGGAAACAAACTCAAAGATGA
Found at i:333139 original size:137 final size:137
Alignment explanation
Indices: 332883--333143 Score: 361
Period size: 137 Copynumber: 1.9 Consensus size: 137
332873 ATGATATTTC
*
332883 AAGAGAAACTATCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAGACTCAAAGATAGGCATT
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAAACTCAAAGATAGG-ATT
*
332948 TCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAATGCACTCAAAGATTTTTAA
65 TCAAAAGAAACTGACTCAAAAGAGACAAAATTCGTTTCAAGGGAAA-GCACTCAAAGATTTTTAA
333013 TTTTGTTTT
129 TTTTGTTTT
* * *
333022 AAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAAACTCAAAGATGATG-TT
1 AAGAGAAACTATCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAAACTCAAAGAT-AGGATT
* *
333085 TCAAGAA-AAACTGTA-TTAAGAGAGACAAAATTCGTTTCAAGGGAAA-CAATCTCAAAGAT
65 TCAA-AAGAAACTG-ACTCAAAAGAGACAAAATTCGTTTCAAGGGAAAGC-A-CTCAAAGAT
333144 GGTTTTATTT
Statistics
Matches: 110, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
135 1 0.01
136 1 0.01
137 49 0.45
138 30 0.27
139 29 0.26
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGAGAAACTATCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAAACTCAAAGATAGGATTT
CAAAAGAAACTGACTCAAAAGAGACAAAATTCGTTTCAAGGGAAAGCACTCAAAGATTTTTAATT
TTGTTTT
Found at i:335795 original size:10 final size:10
Alignment explanation
Indices: 335782--335829 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
335772 TGTCTTTTTC
335782 TTTCTTTGTT
1 TTTCTTTGTT
*
335792 TTTCTTTTTT
1 TTTCTTTGTT
*
335802 TTTCTTTTTT
1 TTTCTTTGTT
*
335812 TTTCCTTGTTT
1 TTTCTTTG-TT
335823 TTTCTTT
1 TTTCTTT
335830 TGCTTCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTCTTTGTT
Found at i:335799 original size:20 final size:19
Alignment explanation
Indices: 335774--335829 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 19
335764 GTGTTTCTTG
335774 TCTTTTTCTTTCTTTGTTTT
1 TCTTTTT-TTTCTTTGTTTT
*
335794 TCTTTTTTTTTCTTTTTTTT
1 TC-TTTTTTTTCTTTGTTTT
335814 TCCTTGTTTTTTCTTT
1 T-CTT-TTTTTTCTTT
335830 TGCTTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (19 bp):
TCTTTTTTTTCTTTGTTTT
Found at i:335809 original size:16 final size:16
Alignment explanation
Indices: 335782--335845 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
335772 TGTCTTTTTC
*
335782 TTTCTTTGTTTTTCTT
1 TTTCTTTTTTTTTCTT
335798 TTT-TTTTCTTTTT-TT
1 TTTCTTTT-TTTTTCTT
* *
335813 TTCCTTGTTTTTTCTT
1 TTTCTTTTTTTTTCTT
* * *
335829 TTGCTTCTTTTCTCTT
1 TTTCTTTTTTTTTCTT
335845 T
1 T
335846 GTTTTGATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.31
16 27 0.69
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTTTCTT
Found at i:335837 original size:30 final size:30
Alignment explanation
Indices: 335774--335845 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
335764 GTGTTTCTTG
* **
335774 TCTTTTTCTTTCTTTGTTTTTCTTTTTTTT
1 TCTTTTTCTTTCCTTGTTTTTCTTTTTGCT
*
335804 TCTTTTTTTTTCCTTGTTTTT-TCTTTTGCT
1 TCTTTTTCTTTCCTTGTTTTTCT-TTTTGCT
335834 TCTTTTCTCTTT
1 TCTTTT-TCTTT
335846 GTTTTGATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.03
30 30 0.86
31 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (30 bp):
TCTTTTTCTTTCCTTGTTTTTCTTTTTGCT
Found at i:335839 original size:27 final size:25
Alignment explanation
Indices: 335796--335850 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
335786 TTTGTTTTTC
* *
335796 TTTTTTTTTCTTTTTTTTTCCTTGT
1 TTTTTTTTTCTTCTTTTCTCCTTGT
*
335821 TTTTTCTTTTGCTTCTTTTCTCTTTGT
1 TTTTT-TTTT-CTTCTTTTCTCCTTGT
335848 TTT
1 TTT
335851 GATTGGATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 16 0.64
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTCTTCTTTTCTCCTTGT
Found at i:337685 original size:3 final size:3
Alignment explanation
Indices: 337677--337724 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
337667 AAAATGTGTA
* *
337677 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAC GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
337724 A
1 A
337725 TTTTTTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:338975 original size:2 final size:2
Alignment explanation
Indices: 338968--339014 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
338958 GCTAATTTTA
338968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339010 AT AT A
1 AT AT A
339015 GACTATCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:341269 original size:10 final size:11
Alignment explanation
Indices: 341243--341272 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
341233 ATATTTTACA
341243 ATTTAAATTTC
1 ATTTAAATTTC
341254 ATTTAAATTT-
1 ATTTAAATTTC
341264 ATTTAAATT
1 ATTTAAATT
341273 AAGTCGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTAAATTTC
Found at i:345112 original size:17 final size:18
Alignment explanation
Indices: 345081--345114 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
345071 AAATAATAAT
345081 AATAATTTATTTTTAAAA
1 AATAATTTATTTTTAAAA
345099 AATAATTT-TTTTTAAA
1 AATAATTTATTTTTAAA
345115 TATTTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAATTTATTTTTAAAA
Found at i:346924 original size:29 final size:29
Alignment explanation
Indices: 346889--346956 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
346879 CATTTTACAC
* * *
346889 AAATAGCACCCTTTTTAAAATATTTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
346918 AAATAGCACCCATTTCAAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
346947 GAATAGCACC
1 AAATAGCACC
346957 AAAACCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:347021 original size:13 final size:13
Alignment explanation
Indices: 347003--347027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
346993 GGTCAACGAT
347003 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
347016 CGGGTCGGGTCA
1 CGGGTCGGGTCA
347028 TGACCGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:354284 original size:29 final size:29
Alignment explanation
Indices: 354223--354296 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 29
354213 GTTGAACATT
* * * *
354223 TTACACAAATAGCACCCTTTTTAAAATAT
1 TTACAAAAATAGCACCCATTTCAAAATAA
* *
354252 TTACAAAAATAGCACCCATTTCGAATTAA
1 TTACAAAAATAGCACCCATTTCAAAATAA
* *
354281 TTACCAGAATAGCACC
1 TTACAAAAATAGCACC
354297 AAAACTGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (29 bp):
TTACAAAAATAGCACCCATTTCAAAATAA
Found at i:354306 original size:29 final size:29
Alignment explanation
Indices: 354274--354382 Score: 200
Period size: 29 Copynumber: 3.8 Consensus size: 29
354264 CACCCATTTC
*
354274 GAATTAATTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
354303 GAATTATTTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
354332 GAATTATTTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
354361 GAATTATTTATCAGAATAGCAC
1 GAATTATTTACCAGAATAGCAC
354383 TGGTCAACGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACT
Found at i:354420 original size:13 final size:13
Alignment explanation
Indices: 354402--354449 Score: 96
Period size: 13 Copynumber: 3.7 Consensus size: 13
354392 GTCAACGATC
354402 GGTCGGGTCAACG
1 GGTCGGGTCAACG
354415 GGTCGGGTCAACG
1 GGTCGGGTCAACG
354428 GGTCGGGTCAACG
1 GGTCGGGTCAACG
354441 GGTCGGGTC
1 GGTCGGGTC
354450 GGGTAAACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACG
Found at i:354423 original size:18 final size:18
Alignment explanation
Indices: 354413--354468 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
354403 GTCGGGTCAA
354413 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
354431 -----CGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* **
354444 CGGGTCGGGTAAACGATT
1 CGGGTCGGGTCAACGGGT
354462 CGGGTCG
1 CGGGTCG
354469 TGACCGGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 13 0.43
18 17 0.57
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:357293 original size:14 final size:14
Alignment explanation
Indices: 357271--357306 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
357261 GAAAAGAATA
357271 ATAAAAATATTAAT
1 ATAAAAATATTAAT
*
357285 ATAATAATATTAAT
1 ATAAAAATATTAAT
357299 A-AAAAATA
1 ATAAAAATA
357307 AATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:357794 original size:3 final size:3
Alignment explanation
Indices: 357788--357827 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
357778 ATAAAAAAAA
357788 AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
357828 AATGTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 30 0.88
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:358352 original size:83 final size:83
Alignment explanation
Indices: 358190--358434 Score: 346
Period size: 83 Copynumber: 2.9 Consensus size: 83
358180 TCGAAGGACT
* ** * * * * *
358190 TTGACAGATAGCCCTTCTTTCCTTGAGCTATGCTGTAAATTATGGTGCCTTTGAGCTGAGTGGAG
1 TTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-GTGCCTTGGAGCTGAGCGTAG
*
358255 TCGAACTCGGAGGTCCTTG
65 TCGAACTCGAAGGTCCTTG
*
358274 TTGACAGATAACCCTTCTAGCCCTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
358339 CGAACTCAAAGGTCTTTG
66 CGAACTCGAAGGTCCTTG
* * *
358357 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCTTGAAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
358422 CGAACTCGAAGGT
66 CGAACTCGAAGGT
358435 TTGATGTTTC
Statistics
Matches: 144, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 107 0.74
84 37 0.26
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (83 bp):
TTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCCTTG
Found at i:358500 original size:29 final size:28
Alignment explanation
Indices: 358441--358499 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
358431 AGGTTTGATG
*
358441 TTTCAAGAGAAACATTTTCAAAGGTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTT
* * *
358469 TTTCAAGAGAAATAATTTCGAGGGTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTT
358497 TTT
1 TTT
358500 TGTGTTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (28 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTT
Found at i:358526 original size:15 final size:15
Alignment explanation
Indices: 358506--358557 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
358496 TTTTTGTGTT
358506 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
*
358521 TCAAGAAAAACTTAGT-
1 TCAAGAGAAAC-T-GTC
*
358537 TCTAAAAGAAACTGTC
1 TC-AAGAGAAACTGTC
358553 TCAAG
1 TCAAG
358558 GGAGACGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 14 0.48
16 6 0.21
17 9 0.31
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:358619 original size:15 final size:15
Alignment explanation
Indices: 358599--358661 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 15
358589 TAAAAGATTT
358599 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
*
358614 TGTTTCAAGAGAGACAAAATT
1 TGTTTCAAG-G-G---AAA-C
358635 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
*
358650 TGTCTCAAGGGA
1 TGTTTCAAGGGA
358662 GACAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
15 20 0.51
16 4 0.10
17 1 0.03
19 1 0.03
20 4 0.10
21 9 0.23
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (15 bp):
TGTTTCAAGGGAAAC
Found at i:358640 original size:21 final size:21
Alignment explanation
Indices: 358614--358689 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
358604 CAAGGGAAAC
358614 TGTTTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAGACAAAATT
*
358635 TGTTTCAAG-G-G---AAA-C
1 TGTTTCAAGAGAGACAAAATT
* *
358650 TGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAGACAAAATT
358671 TGTTTCAAGAGAGACAAAA
1 TGTTTCAAGAGAGACAAAA
358690 CTTAGTTCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
15 8 0.18
16 4 0.09
17 1 0.02
19 1 0.02
20 4 0.09
21 26 0.59
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TGTTTCAAGAGAGACAAAATT
Found at i:358644 original size:36 final size:36
Alignment explanation
Indices: 358597--358679 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
358587 ATTAAAAGAT
*
358597 TTTGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
358633 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
358669 TTTGTTTCAAG
1 TTTGTTTCAAG
358680 AGAGACAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:358723 original size:58 final size:57
Alignment explanation
Indices: 358614--358737 Score: 178
Period size: 58 Copynumber: 2.2 Consensus size: 57
358604 CAAGGGAAAC
* * **
358614 TGTTTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
358671 TGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAC-GATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTG-TCTCAAGGGAGACAAAATT
*
358729 AGTTTCAAG
1 TGTTTCAAG
358738 GAAAACATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
57 20 0.33
58 40 0.67
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (57 bp):
TGTTTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:358850 original size:36 final size:35
Alignment explanation
Indices: 358768--358862 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
358758 TGCTTCAAGG
*
358768 GAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAA
* * *
358803 GAAACTATCTCAAGGGAGACAAAATTTGTTTCAGGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCA-AA
358839 GAAACTGTCTCAAGAGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
358863 ACTTAGTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 30 0.57
36 23 0.43
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAA
Found at i:358888 original size:38 final size:37
Alignment explanation
Indices: 358768--358889 Score: 133
Period size: 35 Copynumber: 3.4 Consensus size: 37
358758 TGCTTCAAGG
*
358768 GAAACTGTCTCAAGAGAGA-AAAAATTTGTTTC-AAA
1 GAAACTATCTCAAGAGAGACAAAAATTTGTTTCAAAA
* **
358803 GAAACTATCTCAAGGGAGAC-AAAATTTGTTTCAGGA
1 GAAACTATCTCAAGAGAGACAAAAATTTGTTTCAAAA
* * *
358839 GAAACTGTCTCAAGAGAGACAAAAACTTAGTTCCAAAA
1 GAAACTATCTCAAGAGAGACAAAAA-TTTGTTTCAAAA
* *
358877 GAAATTTTCTCAA
1 GAAACTATCTCAA
358890 AGGAGGCGAA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
35 29 0.41
36 19 0.27
37 4 0.06
38 19 0.27
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (37 bp):
GAAACTATCTCAAGAGAGACAAAAATTTGTTTCAAAA
Found at i:358908 original size:74 final size:72
Alignment explanation
Indices: 358761--358917 Score: 194
Period size: 74 Copynumber: 2.2 Consensus size: 72
358751 AATATTTTGC
* * *
358761 TTCAAGG-GAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAAGAAACTATCTCAAGGGAGACAA
1 TTCAAGGAGAAACTGTCTCAAGAGAGAAAAAATTAGTTCCAAAGAAACTATCTCAAAGGAGACAA
*
358825 AATTTGT
66 AATTAGT
* * *
358832 TTC-AGGAGAAACTGTCTCAAGAGAGACAAAAACTTAGTTCCAAAAGAAATTTTCTCAAAGGAGG
1 TTCAAGGAGAAACTGTCTCAAGAGAGA-AAAAA-TTAGTTCC-AAAGAAACTATCTCAAAGGAGA
*
358896 CGAAATTAGT
63 CAAAATTAGT
358906 TTCAAGGA-AAAC
1 TTCAAGGAGAAAC
358918 ATATTCAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
70 3 0.04
71 22 0.30
72 5 0.07
73 6 0.08
74 33 0.45
75 4 0.05
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.24
Consensus pattern (72 bp):
TTCAAGGAGAAACTGTCTCAAGAGAGAAAAAATTAGTTCCAAAGAAACTATCTCAAAGGAGACAA
AATTAGT
Found at i:359445 original size:106 final size:106
Alignment explanation
Indices: 359258--359596 Score: 471
Period size: 106 Copynumber: 3.2 Consensus size: 106
359248 TTTCGAGTCC
* * * * *
359258 AATTGGCTCTGGAACTGGGAAATTATTTGTTGACAGCCAGATCCCCCTTCGTTGTGAAGTTGAGC
1 AATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGATGCCCCTTCGTTGTGAAGTTGAGC
* *
359323 TTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGA
66 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
* * * * *
359364 AATTGACTATGAAACTGGGAAGTTGTTTGTTGACAATCAGTTGCCCCTTCATTGTGAAGTTGAGC
1 AATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGATGCCCCTTCGTTGTGAAGTTGAGC
* *
359429 TTGTGTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGA
66 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
* ** *
359470 AATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGCCCCTTTGTTGTGAAGTTGAGC
1 AATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGATGCCCCTTCGTTGTGAAGTTGAGC
* * * *
359535 TTGTGTTATCTTGAGTCCAATATCCTTCACTGTGAAATTGA
66 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
*
359576 AATTGGCTCTGAAATTGGGAA
1 AATTGGCTCTGAAACTGGGAA
359597 TCCCCTTCAT
Statistics
Matches: 206, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 206 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
AATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGATGCCCCTTCGTTGTGAAGTTGAGC
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
Found at i:360282 original size:32 final size:33
Alignment explanation
Indices: 360246--360308 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
360236 ATTCCCAAAG
*
360246 ATGCCCCAATATTCT-ATGTTGAATC-TCAAAAA
1 ATGCCCCAACATT-TGATGTTGAATCTTCAAAAA
360278 ATGCCCCAACATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATCTTCAAA
360309 GATGTCCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.04
32 22 0.79
33 5 0.18
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTTCAAAAA
Found at i:364317 original size:64 final size:64
Alignment explanation
Indices: 364247--364409 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 64
364237 CGGTGCACCA
* *
364247 AGTGTGCATCGATGCATGAAATGCATTTGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * * **
364311 CTTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
364376 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
364410 CAATTAATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 37 0.45
65 45 0.55
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:364381 original size:19 final size:19
Alignment explanation
Indices: 364357--364407 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
364347 GAAAATATTC
364357 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
364376 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
364395 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
364408 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:370366 original size:22 final size:21
Alignment explanation
Indices: 370340--370386 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
370330 AAGGTCAAAA
*
370340 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
370362 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
370382 ATCAA
1 ATCAA
370387 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:372589 original size:64 final size:66
Alignment explanation
Indices: 372484--372646 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 66
372474 CGGTGCACCA
* *
372484 AGTGTGCAACAATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCT-G-GTGCATCGATGCAT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATA-CCTAGAGTGCATCGATGCAT
372546 GG
65 GG
** * **
372548 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTTAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATACCTAGAGTGCATCGATGCATG
372612 G
66 G
* * * *
372613 AGAGTGCATCGGTGCATGGAATGCATTTGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
372647 CAATTAATTC
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 1 0.01
64 34 0.41
65 47 0.57
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATACCTAGAGTGCATCGATGCATG
G
Found at i:372618 original size:19 final size:19
Alignment explanation
Indices: 372594--372632 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
372584 GAAAATATTT
372594 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
372613 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
372632 A
1 A
372633 ATGCATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:374707 original size:24 final size:26
Alignment explanation
Indices: 374680--374728 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
374670 AGTCCTTGTT
374680 TATAAATGTATT-TATG-CTATATAA
1 TATAAATGTATTATATGACTATATAA
374704 TATAAATGTATTATATGACTATATA
1 TATAAATGTATTATATGACTATATA
374729 TTTATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (26 bp):
TATAAATGTATTATATGACTATATAA
Found at i:374763 original size:14 final size:15
Alignment explanation
Indices: 374746--374783 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
374736 ATAATGTATA
374746 GTATATATATA-AAT
1 GTATATATATATAAT
374760 GTATAT-TATATAAT
1 GTATATATATATAAT
*
374774 GTATACATAT
1 GTATATATAT
374784 CACACTGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 3 0.14
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (15 bp):
GTATATATATATAAT
Found at i:374769 original size:19 final size:18
Alignment explanation
Indices: 374725--374771 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
374715 TATATGACTA
*
374725 TATATT-TATTTATAATG
1 TATATTATATATATAATG
*
374742 TATAGTATATATATAAATG
1 TATATTATATATAT-AATG
374761 TATATTATATA
1 TATATTATATA
374772 ATGTATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 6 0.24
19 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TATATTATATATATAATG
Found at i:374769 original size:24 final size:24
Alignment explanation
Indices: 374680--374769 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 24
374670 AGTCCTTGTT
374680 TATAAATGTAT-TTAT-GCTATATAA
1 TATAAATGTATATTATAG-TATAT-A
374704 TATAAATG--TATTATA-TGACTATA
1 TATAAATGTATATTATAGT-A-TATA
** *
374727 TATTTATTTATAATGTATAGTATATA
1 TATAAATGTAT-AT-TATAGTATATA
374753 TATAAATGTATATTATA
1 TATAAATGTATATTATA
374770 TAATGTATAC
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
22 2 0.04
23 11 0.22
24 15 0.29
25 3 0.06
26 14 0.27
27 5 0.10
28 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TATAAATGTATATTATAGTATATA
Found at i:376293 original size:17 final size:17
Alignment explanation
Indices: 376259--376304 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
376249 CCTTTACATT
*
376259 TTTATTTA-TTTATCTA
1 TTTATTTATTTTATATA
376275 TTTATTTATTTTATATA
1 TTTATTTATTTTATATA
*
376292 TTTTTTTAATTTT
1 TTTATTT-ATTTT
376305 TTCTCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 8 0.31
17 13 0.50
18 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTATTTTATATA
Found at i:377801 original size:37 final size:38
Alignment explanation
Indices: 377719--377993 Score: 357
Period size: 37 Copynumber: 7.5 Consensus size: 38
377709 TATATATATA
377719 ATATATAATATA-A-TTTTTAAAACA-TTTTG-AAAAT
1 ATATATAATATATAGTTTTTAAAACATTTTTGAAAAAT
377753 ATATATAATATATA-TTTTTAAAACA-TTTTGAAAATAT
1 ATATATAATATATAGTTTTTAAAACATTTTTGAAAA-AT
377790 ATATATAATATATAGTTTTTTAAAACA-TTTTG-AAAAT
1 ATATATAATATATAG-TTTTTAAAACATTTTTGAAAAAT
*
377827 ATATATAATATATAGTTTTTTAAAACATTTTTGAAAACT
1 ATATATAATATATAG-TTTTTAAAACATTTTTGAAAAAT
* *
377866 -TATATAATATATAGTTCTTAAAATATTTTTGAAAAA-
1 ATATATAATATATAGTTTTTAAAACATTTTTGAAAAAT
*
377902 ATATATATTATATAGTTTTTAAAAACATTTTTG-AAAAT
1 ATATATAATATATAGTTTTT-AAAACATTTTTGAAAAAT
377940 ATATAT--TATATAGTTTTTAAAAACATTTTTG-AAAAT
1 ATATATAATATATAGTTTTT-AAAACATTTTTGAAAAAT
377976 ATATAT--TATATAGTTTTT
1 ATATATAATATATAGTTTTT
377994 GGAATATTTT
Statistics
Matches: 224, Mismatches: 7, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
34 12 0.05
35 17 0.08
36 51 0.23
37 85 0.38
38 39 0.17
39 20 0.09
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTAAAACATTTTTGAAAAAT
Found at i:379250 original size:13 final size:13
Alignment explanation
Indices: 379232--379256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379222 CCTTTTTTAT
379232 TTTTTTTATTTTG
1 TTTTTTTATTTTG
379245 TTTTTTTATTTT
1 TTTTTTTATTTT
379257 ATTATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTATTTTG
Found at i:389142 original size:59 final size:61
Alignment explanation
Indices: 389037--389162 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 61
389027 AAACATGTGA
* * * * *
389037 ATAATCAAGTGATCATTTTATAACATTTGATACTCATATGATTCAATAAAATAATG-ACAT
1 ATAATCAAATGATCATTTTATAACATTTAATAATCAAATGACTCAATAAAATAATGTACAT
* * *
389097 ATAATCAAATGAT-ATTTTATAA-ATTTTAATAATCAAATGGCTCAATAAGATTATGTACAT
1 ATAATCAAATGATCATTTTATAACA-TTTAATAATCAAATGACTCAATAAAATAATGTACAT
389157 A-AATCA
1 ATAATCA
389163 GTTGTGTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.02
59 38 0.68
60 17 0.30
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (61 bp):
ATAATCAAATGATCATTTTATAACATTTAATAATCAAATGACTCAATAAAATAATGTACAT
Found at i:393842 original size:24 final size:24
Alignment explanation
Indices: 393807--393856 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
393797 TTCTTTTAGT
393807 ACATGCACACTAAATATAACAAGG
1 ACATGCACACTAAATATAACAAGG
393831 ACATGC-CAACTAAATATAACAAGG
1 ACATGCAC-ACTAAATATAACAAGG
393855 AC
1 AC
393857 CCCATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (24 bp):
ACATGCACACTAAATATAACAAGG
Found at i:394478 original size:32 final size:31
Alignment explanation
Indices: 394437--394528 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 31
394427 CATACGTAAT
*
394437 TGTCCATATGTCCCGAAAGACATAGGTAATCA
1 TGTCCATATGTCCCGAAAGACATAGGTAA-AA
394469 TGTCCATATGTCCCGAAAGACATAGGTAAAA
1 TGTCCATATGTCCCGAAAGACATAGGTAAAA
* *
394500 TATCCATATGTCTCGAAAGACATAGGTAA
1 TGTCCATATGTCCCGAAAGACATAGGTAA
394529 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 28 0.49
32 29 0.51
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAAGACATAGGTAAAA
Found at i:394509 original size:31 final size:32
Alignment explanation
Indices: 394439--394528 Score: 146
Period size: 31 Copynumber: 2.8 Consensus size: 32
394429 TACGTAATTG
* *
394439 TCCATATGTCCCGAAAGACATAGGTAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATAATA
394471 TCCATATGTCCCGAAAGACATAGGTAA-AATA
1 TCCATATGTCCCGAAAGACATAGGTAATAATA
*
394502 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCCCGAAAGACATAGGTAA
394529 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 28 0.51
32 27 0.49
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATAATA
Found at i:402633 original size:2 final size:2
Alignment explanation
Indices: 402626--402657 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
402616 TTATCACTCA
402626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402658 TTCTTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:414241 original size:18 final size:18
Alignment explanation
Indices: 414218--414253 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
414208 TCTGCCCCTT
414218 CATTATCACCTATTTATG
1 CATTATCACCTATTTATG
414236 CATTATCACCTATTTATG
1 CATTATCACCTATTTATG
414254 AAGGTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
CATTATCACCTATTTATG
Found at i:419365 original size:28 final size:28
Alignment explanation
Indices: 419276--419374 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 28
419266 GAATTAATCT
419276 TTAATTTGACTA-TTAAATTTTAGAAATAA
1 TTAATTTGA-TATTTAAATTTTAGAAAT-A
419305 TACTAATTTGATATTT-AATTTTAGAGGAAATA
1 T--TAATTTGATATTTAAATTTT--A-GAAATA
*
419337 TTATTTTGAT-TTTAAATTTTAGACAATA
1 TTAATTTGATATTTAAATTTTAGA-AATA
419365 TTAATTTGAT
1 TTAATTTGAT
419375 CTCTAATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
27 2 0.03
28 14 0.23
29 4 0.07
30 22 0.37
31 10 0.17
32 3 0.05
33 5 0.08
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (28 bp):
TTAATTTGATATTTAAATTTTAGAAATA
Found at i:421046 original size:35 final size:36
Alignment explanation
Indices: 420970--421046 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
420960 TAAATAAAAA
* *
420970 AAAAAGGCAATTGCAAGAAGCAACCAATATCAAATTC
1 AAAAA-GCAATTGCAAGAAGCAACCAAGATCAAAGTC
* * *
421007 -AAAAGCAATTGCAAGATGCATCCAAGAT-GAAGTC
1 AAAAAGCAATTGCAAGAAGCAACCAAGATCAAAGTC
421041 AAAAAG
1 AAAAAG
421047 GCTTACTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.12
35 26 0.76
36 4 0.12
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.16
Consensus pattern (36 bp):
AAAAAGCAATTGCAAGAAGCAACCAAGATCAAAGTC
Found at i:425056 original size:230 final size:228
Alignment explanation
Indices: 424580--425215 Score: 948
Period size: 230 Copynumber: 2.8 Consensus size: 228
424570 GGCAAGTGGT
** *
424580 AAAAAA-ATGTATCACCCTAACACAGCCTAGCATGACCGACTAAAATATTGGCAACAGGGAAAAG
1 AAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGGAAAAG
* *
424644 AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCACAAAAATGTCTATTCTTCATCT
66 AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCTCAAAAATGTCTATTCTACATCT
* * *
424709 TACATGAGGG--CAACAACTTTAAGGTAGTTTGATAAAAACAATCAAAAGGTACTTTTAAAGAAC
131 TACACGAGGGAACACCAACTTTAAGGTAGTTTGATAAAAACAATCATAAGGTACTTTTAAAGAAC
* * *
424772 ATGTAGGTCCACTTATGCAATAGGTATAATCCA
196 ATGTAAGTCAACTTAGGCAATAGGTATAATCCA
*
424805 AAAAAAGATGTATCACCCTAATGCAGCCTAGCACGACCAACTAAAATATTGGCAACAGGGAAAAG
1 AAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGGAAAAG
* * * *
424870 AGGAGATTGCAAGAAAATAATCACCTCGGCAAAGTTGCCTCCTCGACAAATGTCTATTCTACATA
66 AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCTC-AAAAATGTCTATTCTACATC
*
424935 TTACACGAGGGAAACACCAACTTTAAGGTCA-TTTGATAAAAACAATCATAAGGTAGTTTTAAAG
130 TTACACGAGGG-AACACCAACTTTAAGGT-AGTTTGATAAAAACAATCATAAGGTACTTTTAAAG
424999 AACATGTAAGTCAACTTAGGCAATAGGTATAATCCA
193 AACATGTAAGTCAACTTAGGCAATAGGTATAATCCA
* *
425035 AAAAGAGATGTATCGCCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGG-AAA-
1 AAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGGAAAAG
* *
425098 A-GAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCGTAAAAAATGTCTATTCCACATC
66 AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCC-TCAAAAATGTCTATTCTACATC
* *
425162 TTACAC-AGGGCAACACCAACTTTAAGATAGTTTAATAAAAA-AATCATGAAGGTA
130 TTACACGAGGG-AACACCAACTTTAAGGTAGTTTGATAAAAACAATCAT-AAGGTA
425216 ATACCCACTT
Statistics
Matches: 373, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
225 13 0.03
226 131 0.35
227 88 0.24
228 2 0.01
229 3 0.01
230 135 0.36
231 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (228 bp):
AAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGGAAAAG
AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCTCAAAAATGTCTATTCTACATCT
TACACGAGGGAACACCAACTTTAAGGTAGTTTGATAAAAACAATCATAAGGTACTTTTAAAGAAC
ATGTAAGTCAACTTAGGCAATAGGTATAATCCA
Found at i:428293 original size:28 final size:27
Alignment explanation
Indices: 428233--428306 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
428223 GAGATGGGCT
*
428233 TAAAATTTTATGTTAGAAATGAATTTA
1 TAAAATTTTATATTAGAAATGAATTTA
428260 TAAAATTTTATATTAGAGAATGAATTTA
1 TAAAATTTTATATTAGA-AATGAATTTA
* *
428288 TGAAATTTTATCTTA-AAAT
1 TAAAATTTTATATTAGAAAT
428307 CTTACAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 17 0.40
28 23 0.53
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (27 bp):
TAAAATTTTATATTAGAAATGAATTTA
Found at i:428394 original size:2 final size:2
Alignment explanation
Indices: 428387--428475 Score: 103
Period size: 2 Copynumber: 45.5 Consensus size: 2
428377 ACCATTCTTT
* * * * *
428387 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TT TG T- TT TC T- TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
428428 -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
428469 TA TA TA T
1 TA TA TA T
428476 GTTTGTTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
1 3 0.04
2 76 0.96
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:455625 original size:5 final size:5
Alignment explanation
Indices: 455617--455844 Score: 269
Period size: 5 Copynumber: 45.8 Consensus size: 5
455607 ATATAATATA
*
455617 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG CAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* * * *
455667 TAATG CAATG TAATG CAATC TAATG CAATG TAATG TAATG TAATG TAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* * * * * * *
455717 TAATG CAATG CAATG CAATG CAATG CAATG CAATG CAATG TAATG TAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* * *
455767 TAATG CAATG T-ATG TAATG TAATG TAATG TAATG TAATG TAATA TAATA
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* * * * *
455816 TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATG TAATG TAATG TAATG TAATG TAAT
455845 ATAAAATCGA
Statistics
Matches: 207, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
4 4 0.02
5 203 0.98
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (5 bp):
TAATG
Done.