Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001242.1 Hibiscus syriacus cultivar Beakdansim tig00002443_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: 235367
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
File 2 of 2
Found at i:220574 original size:46 final size:46
Alignment explanation
Indices: 220497--220718 Score: 345
Period size: 46 Copynumber: 4.8 Consensus size: 46
220487 TTTTACGTTT
* * * * * *
220497 ATCCATTCATTCCCTAATACATCCTTTCATGCATATTAATTATGGC
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGC
**
220543 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATTAC
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGC
* *
220589 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGTC
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGC
*
220635 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTCATTATGGC
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGC
220681 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTA
1 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTA
220719 CATACTTTAA
Statistics
Matches: 161, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 161 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (46 bp):
ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGC
Found at i:221205 original size:20 final size:20
Alignment explanation
Indices: 221180--221237 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
221170 TTCGATGTTT
*
221180 CATGGTATCGATACCCTTAC
1 CATGGTATCGATACCCATAC
221200 CATGGTATCGATACTACCATAC
1 CATGGTATCGATAC--CCATAC
* *
221222 TATGGTACCGATACCC
1 CATGGTATCGATACCC
221238 CCTTACGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
22 17 0.52
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (20 bp):
CATGGTATCGATACCCATAC
Found at i:221252 original size:95 final size:95
Alignment explanation
Indices: 221113--221288 Score: 244
Period size: 95 Copynumber: 1.9 Consensus size: 95
221103 AACCTTGTAC
* * * * * *
221113 CGATACTTCTATACTATAGTACTGATACCCCGTTCCGATATCGATACCAATGTTAGATTCGATGT
1 CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
* *
221178 TTCATGGTATCGATACCCTTACCATGGTAT
66 TGCATGGTATCCATACCCTTACCATGGTAT
* * *
221208 CGATACTACCATACTATGGTACCGATACCCCCTTACGACATCGATACCGATTTTAGATTCGATGT
1 CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
*
221273 TGCCTGGTATCCATAC
66 TGCATGGTATCCATAC
221289 TACCTCATCG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (95 bp):
CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
TGCATGGTATCCATACCCTTACCATGGTAT
Found at i:221302 original size:95 final size:94
Alignment explanation
Indices: 221113--221309 Score: 236
Period size: 95 Copynumber: 2.1 Consensus size: 94
221103 AACCTTGTAC
* * * * * *
221113 CGATACTTCTATACTATAGTACTGATACCCCGTTCCGATATCGATACCAATGTTAGATTCGATGT
1 CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
* *
221178 TTCATGGTATCGATACCCTTACCATGGTAT
66 TGCATGGTATCCATACCCTTA-CATGGTAT
* * *
221208 CGATACTACCATACTATGGTACCGATACCCCCTTACGACATCGATACCGATTTTAGATTCGATGT
1 CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
*
221273 TGCCTGGTATCCATACTACC-T-CATCGGTAT
66 TGCATGGTATCCATAC--CCTTACAT-GGTAT
221303 CGATACT
1 CGATACT
221310 GATTGAATCA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
94 3 0.03
95 81 0.93
96 1 0.01
97 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (94 bp):
CGATACTACCATACTATAGTACCGATACCCCCTTACGACATCGATACCAATGTTAGATTCGATGT
TGCATGGTATCCATACCCTTACATGGTAT
Found at i:225280 original size:20 final size:21
Alignment explanation
Indices: 225246--225300 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
225236 GATCCATCGA
**
225246 AGGATCAACTAAAACAAATAC
1 AGGATCATTTAAAACAAATAC
225267 AGGATCA-TTAAAACAAATAC
1 AGGATCATTTAAAACAAATAC
*
225287 AGGCTCATTTAAAA
1 AGGATCATTTAAAA
225301 GATGAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (21 bp):
AGGATCATTTAAAACAAATAC
Found at i:227361 original size:26 final size:26
Alignment explanation
Indices: 227325--227579 Score: 189
Period size: 26 Copynumber: 10.7 Consensus size: 26
227315 TGACCTAATT
* *
227325 CATCCTTTCATGCCTTTTAATTATAG
1 CATCCTTTCATGCATTTTAATTATGG
*
227351 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
* *
227371 CATCATTTCATGTATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
227397 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
227423 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
* *
227449 CATCCTTTTATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
* * * *
227469 CATCATTTCATGCATTTTTACTATGA
1 CATCCTTTCATGCATTTTAATTATGG
* * *
227495 CATCCTTTTATTC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
* *
227515 CATCCTTTCATGCATTTTCATTATGA
1 CATCCTTTCATGCATTTTAATTATGG
*
227541 CATCCTTTCATG--TCTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
227561 CATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTA
227580 CATACTCTAA
Statistics
Matches: 184, Mismatches: 24, Indels: 45
0.73 0.09 0.18
Matches are distributed among these distances:
20 47 0.26
21 8 0.04
22 9 0.05
23 7 0.04
24 9 0.05
25 6 0.03
26 98 0.53
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAATTATGG
Found at i:227361 original size:46 final size:46
Alignment explanation
Indices: 227291--227579 Score: 346
Period size: 46 Copynumber: 6.2 Consensus size: 46
227281 TCCATTTATA
* * *
227291 CATTTAAATTATGGCATCCATTCATGACC-TAATTCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATG-CCTTAATGCATCCTTTCATG
* * *
227337 CCTTTTAATTATAGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
227383 TATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATG
* *
227435 CATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * * * *
227481 CATTTTTACTATGACATCCTTTTATTCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
* * *
227527 CATTTTCATTATGACATCCTTTCATGTCTTAATGCATCCTTTCATG
1 CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
227573 CATTTTA
1 CATTTTA
227580 CATACTCTAA
Statistics
Matches: 210, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
45 2 0.01
46 161 0.77
47 2 0.01
48 2 0.01
49 2 0.01
50 2 0.01
51 2 0.01
52 37 0.18
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (46 bp):
CATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:227550 original size:72 final size:70
Alignment explanation
Indices: 227325--227552 Score: 214
Period size: 72 Copynumber: 3.2 Consensus size: 70
227315 TGACCTAATT
* * *
227325 CATCCTTTCATGCCTTTTAATTAT-AGCATCCTTTCATGCCTTAATGCATCATTTCATGTATTTT
1 CATCCTTTCATGCATTTTAATTATGA-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
227389 AATTATGG
65 -ATTAT-G
* * *
227397 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGC
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATGC
*
227462 --CTTA--ATG
60 ATTTTATTATG
* * * * *
227469 CATCATTTCATGCATTTTTACTATGACATCCTTTTATTCCTTAATGCATCCTTTCATGCATTTTC
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT-
227534 ATTATG
65 ATTATG
227540 ACATCCTTTCATG
1 -CATCCTTTCATG
227553 TCTTAATGCA
Statistics
Matches: 126, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
66 13 0.10
67 2 0.02
68 2 0.02
69 2 0.02
70 2 0.02
71 3 0.02
72 81 0.64
73 2 0.02
74 2 0.02
75 2 0.02
76 2 0.02
77 2 0.02
78 11 0.09
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (70 bp):
CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
TTATG
Found at i:227551 original size:144 final size:138
Alignment explanation
Indices: 227291--227579 Score: 357
Period size: 144 Copynumber: 2.1 Consensus size: 138
227281 TCCATTTATA
* * * * *
227291 CATTTAAATTATGGCATCCATTCATGACCTAATTCATCCTTTCATGCCTTTTAATTATAGCATCC
1 CATTTTAATTATGGCATCCATTCATGACCTAATGCATCATTTCATGCATTTTAACTATAGCATCC
* * *
227356 TTTCATGCCTTAATGCATCATTTCATGTATTTTAATTATGGCATCCTTTCATGCATTTTAATTAT
66 TTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCCTTTCATG--TCTT-A--AT
227421 GGCATCCTTTCATG
126 -GCATCCTTTCATG
* * *
227435 CATTTTAATTATGGCATCCTTTTATG-CCTTAATGCATCATTTCATGCATTTTTACTAT-GACAT
1 CATTTTAATTATGGCATCCATTCATGACC-TAATGCATCATTTCATGCATTTTAACTATAG-CAT
* * * *
227498 CCTTTTATTCCTTAATGCATCCTTTCATGCATTTTCATTATGACATCCTTTCATGTCTTAATGCA
64 CCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCCTTTCATGTCTTAATGCA
227563 TCCTTTCATG
129 TCCTTTCATG
227573 CATTTTA
1 CATTTTA
227580 CATACTCTAA
Statistics
Matches: 128, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
138 20 0.16
139 2 0.02
141 1 0.01
142 3 0.02
143 3 0.02
144 99 0.77
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (138 bp):
CATTTTAATTATGGCATCCATTCATGACCTAATGCATCATTTCATGCATTTTAACTATAGCATCC
TTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCCTTTCATGTCTTAATGCATC
CTTTCATG
Found at i:227566 original size:20 final size:20
Alignment explanation
Indices: 227448--227572 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
227438 TTTAATTATG
* *
227448 GCATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGTCTTAAT
* *
227468 GCATCATTTCATGCATTTTTACTAT
1 GCATCCTTTCATG---TCTTA--AT
*
227493 GACATCCTTTTAT-TCCTTAAT
1 G-CATCCTTTCATGT-CTTAAT
*
227514 GCATCCTTTCATGCATTTTCATTAT
1 GCATCCTTTCATG--TCTT-A--AT
227539 GACATCCTTTCATGTCTTAAT
1 G-CATCCTTTCATGTCTTAAT
227560 GCATCCTTTCATG
1 GCATCCTTTCATG
227573 CATTTTACAT
Statistics
Matches: 81, Mismatches: 10, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
20 33 0.41
21 6 0.07
22 3 0.04
23 9 0.11
24 3 0.04
25 6 0.07
26 21 0.26
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.46
Consensus pattern (20 bp):
GCATCCTTTCATGTCTTAAT
Found at i:228065 original size:95 final size:95
Alignment explanation
Indices: 227928--228116 Score: 245
Period size: 95 Copynumber: 2.0 Consensus size: 95
227918 GATACTTCTA
* * * *
227928 TACTATAGTACCGATACCCCCTTTCGGTATAGATACCAATTTTAGATTCAATGTTTCCTGGCAAT
1 TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTCG-AAT
* *
227993 -GATACCCTTACCATGGTATCGGTACTACCC
65 CGATACCCTTACAATGGTATCGATACTACCC
* * * * * *
228023 TACTATGGTACCAATACCCCCTTACGGTATCGATATCGATTTTAGATTCGATGTTGCCTCGTATC
1 TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTCGAATC
*
228088 GATACCCTTACAATGGTATTGATACTACC
66 GATACCCTTACAATGGTATCGATACTACC
228117 TCGTCATTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (95 bp):
TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTCGAATC
GATACCCTTACAATGGTATCGATACTACCC
Found at i:233917 original size:46 final size:46
Alignment explanation
Indices: 233852--233984 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 46
233842 ATACATCGTC
* * * ** *
233852 ATGTATTTTCTTTTGTGGCATCATTTCATGTTAATTATGC-TCTGTT
1 ATGTATTTTCATTTATGGCATCCTTTCATGCAAATTATGCATC-ATT
*
233898 AT-TCATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATCATT
1 ATGT-ATTTTCATTTATGGCATCCTTTCATGCAAATTATGCATCATT
233944 ATGTATTTTCATTTATGGCATCCTTTCATGCAAATTATGCA
1 ATGTATTTTCATTTATGGCATCCTTTCATGCAAATTATGCA
233985 CCGTTTTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
45 1 0.01
46 73 0.95
47 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (46 bp):
ATGTATTTTCATTTATGGCATCCTTTCATGCAAATTATGCATCATT
Found at i:233936 original size:22 final size:22
Alignment explanation
Indices: 233910--233982 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
233900 TCATTTTCAT
233910 TTATGGCATCCTTTCATGCCAA
1 TTATGGCATCCTTTCATGCCAA
* * ** *
233932 TTAT-GCATCATTATGTATTTTCAT
1 TTATGGCATCCTT-T-CA-TGCCAA
*
233956 TTATGGCATCCTTTCATGCAAA
1 TTATGGCATCCTTTCATGCCAA
233978 TTATG
1 TTATG
233983 CACCGTTTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 7 0.19
22 12 0.33
23 2 0.06
24 8 0.22
25 7 0.19
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATGGCATCCTTTCATGCCAA
Found at i:234126 original size:80 final size:81
Alignment explanation
Indices: 234026--234851 Score: 878
Period size: 81 Copynumber: 10.4 Consensus size: 81
234016 CATTGTACCA
* ** * * * * *
234026 AAATGCACAGTTACACATTTAGTCTTTTATCCCAAAGGGATTTAACCTTTCATCTAACTTGC-TT
1 AAATGCACAGCTAGGCATTTAATCTTTTA-CTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
* *
234090 ATTGGCACCTTTCTCT-
65 ATTGACACCTTTCTGTC
* *
234106 AAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTT-ACCTTTCATCTAACTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
234170 TTGACACCTTTC--TA
66 TTGACACCTTTCTGTC
* *
234184 AAATGCAC-GCTAGGCATTTAATC-TTTACTCAAAGGTATTT-ACCTTTCATCTAAATGGCATTA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
234246 TTGACACCTTTCTGTC
66 TTGACACCTTTCTGTC
* * * * * **
234262 AAAGGCACAACTAGGCATTT-AGCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACCGATATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* *
234326 TTGACAGCTTTATGTC
66 TTGACACCTTTCTGTC
* * * * * * * * **
234342 AAATGCACAACTAGGAATTTAGTCCTCTAGTCGAAGGTATTTAACGTTTCATCTAACTGTAAAT-
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTG-GCATG
*
234406 ATTGATACCTTTCTGTC
65 ATTGACACCTTTCTGTC
* * *
234423 AAACGCGCAGCTAGGCATTTAATCTTTTACACAAAGGTATTTAACCTTTCATCTAACTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
234488 TTGACACCTTTCAGTC
66 TTGACACCTTTCTGTC
* * * * * *
234504 AACTGCACAGTTAGTCATTTAATCTTTTACT-GAAGGTATTTAACCTTTCAACTAATTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* *
234568 -TGACACCTTTATGTT
66 TTGACACCTTTCTGTC
* * *
234583 AAATACACAACTAGG--TGTTAGT-TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
1 AAATGCACAGCTAGGCAT-TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
*
234645 A-TAACACCTTTCTGTC
65 ATTGACACCTTTCTGTC
* * ** * *
234661 AAATGCTCAGCTTGGCATTTAATCTTTTACTCAAAAATATTTAACTTTTCATCTAACTAGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* *
234726 TTGACACATTTTTGTC
66 TTGACACCTTTCTGTC
* * * *
234742 AAATGCACAACTTA-GCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAAGTAGCATG
1 AAATGCACAGC-TAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
*
234806 ATTGACACCTTTCTATC
65 ATTGACACCTTTCTGTC
* * *
234823 AAATGCATAACTAGG-AATTAATTCTTTTA
1 AAATGCACAGCTAGGCATTTAA-TCTTTTA
234852 TTTTAACACT
Statistics
Matches: 624, Mismatches: 103, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
76 49 0.08
77 22 0.04
78 92 0.15
79 77 0.12
80 151 0.24
81 229 0.37
82 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (81 bp):
AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
TTGACACCTTTCTGTC
Found at i:234762 original size:319 final size:315
Alignment explanation
Indices: 234065--234829 Score: 898
Period size: 319 Copynumber: 2.4 Consensus size: 315
234055 TCCCAAAGGG
* * * *
234065 ATTTAACCTTTCATCTAACTTGCTTATTGGCACCTTTCTCT-AAATGCAC-AGTTAGACATTTAA
1 ATTTAACCTTTCATCTAAC-TGCATATTGACACCTTTCTGTCAAATGCACAACTTAG-CATTTAA
234128 TCTTTTACTCAAAGGTATTT-ACCTTTCATCTAACTGGCATGATTGACACCTTTCTAAAATGCAC
64 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTAAAATGCAC
* *
234192 GCTAGGCATTTAATCTTTACTCAAAGGTATTTACCTTTCATCTAAATGGCATTATTGACACCTTT
129 GCTAGGCATTTAATCTTTACTCAAAGGTATTTACCTTTCAACTAAATGGCATGATTGACACCTTT
* * * *
234257 CTGTCAAAGGCACAACTAGGCATTTAGCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACCGAT
194 ATGTCAAAGACACAACTAGG-ATTTAGCTTTTACTCAAAGGTATTTAACCTTTCATCTAACCGAC
* * * * * **
234322 ATGATTGACAGCTTTATGTCAAATGCACAACTAGGAATTTAGTCCTCTAGTCGAAGGT
258 ATGATTAACACCTTTATGTCAAATGCACAACTAGGAATTTAATCCTCTACTCAAAAAT
* * * * * *
234380 ATTTAACGTTTCATCTAACTGTAAATATTGATACCTTTCTGTCAAACGCGCAGC-TAGGCATTTA
1 ATTTAACCTTTCATCTAACTG--CATATTGACACCTTTCTGTCAAATGCACAACTTA-GCATTTA
* * *
234444 ATCTTTTACACAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCAGTCAACTG
63 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC--TAAAATG
* * * *
234509 CACAGTTAGTCATTTAATCTTTTACT-GAAGGTATTTAACCTTTCAACTAATTGGCATGA-TGAC
126 CAC-GCTAGGCATTTAATC-TTTACTCAAAGGTATTT-ACCTTTCAACTAAATGGCATGATTGAC
* * *
234572 ACCTTTATGTTAAATACACAACTAGG-TGTTAGTTTTTACTCAAAGGTATTTAACCTTTCATCTA
188 ACCTTTATGTCAAAGACACAACTAGGAT-TTAGCTTTTACTCAAAGGTATTTAACCTTTCATCTA
* * * * * * * * *
234636 ACTGGCATGA-TAACACCTTTCTGTCAAATGCTCAGCTTGGCATTTAATCTTTTACTCAAAAAT
252 ACCGACATGATTAACACCTTTATGTCAAATGCACAACTAGGAATTTAATCCTCTACTCAAAAAT
* * * *
234699 ATTTAACTTTTCATCTAACTAGCATGATTGACACATTTTTGTCAAATGCACAACTTAGCATTTAG
1 ATTTAACCTTTCATCTAACT-GCAT-ATTGACACCTTTCTGTCAAATGCACAACTTAGCATTTAA
* *
234764 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAGTAGCATGATTGACACCTTTCTATCAAATGC
64 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTA--AAATGC
234829 A
127 A
234830 TAACTAGGAA
Statistics
Matches: 377, Mismatches: 56, Indels: 30
0.81 0.12 0.06
Matches are distributed among these distances:
314 2 0.01
315 18 0.05
316 14 0.04
317 35 0.09
318 37 0.10
319 146 0.39
320 52 0.14
321 48 0.13
322 25 0.07
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (315 bp):
ATTTAACCTTTCATCTAACTGCATATTGACACCTTTCTGTCAAATGCACAACTTAGCATTTAATC
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTAAAATGCACGC
TAGGCATTTAATCTTTACTCAAAGGTATTTACCTTTCAACTAAATGGCATGATTGACACCTTTAT
GTCAAAGACACAACTAGGATTTAGCTTTTACTCAAAGGTATTTAACCTTTCATCTAACCGACATG
ATTAACACCTTTATGTCAAATGCACAACTAGGAATTTAATCCTCTACTCAAAAAT
Found at i:234785 original size:400 final size:396
Alignment explanation
Indices: 234041--234797 Score: 983
Period size: 400 Copynumber: 1.9 Consensus size: 396
234031 CACAGTTACA
* * * * *
234041 CATTTAGTCTTTTATCCCAAAGGGATTTAACCTTTCATCTAACTTGCTTATTGGCACCTTTCTCT
1 CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGCTGATTGACACCTTTCTCT
*
234106 AAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTACCTTTCATCTAACTGGCATGAT
66 AAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTACCTTTCAACTAACTGGCATGAT
* *
234171 TGACACCTTTCTAAAATGCACGCTAGGCATTTAATCTTTACTCAAAGGTATTTACCTTTCATCTA
131 TGACACCTTTCTAAAATACACACTAGG-ATTTAATCTTTACTCAAAGGTATTTACCTTTCATCTA
* * **
234236 AATGGCATTATTGACACCTTTCTGTCAAAGGCACAACTAGGCATTTAGCTTTTACTCAAAGGTAT
195 AATGGCATGATTAACACCTTTCTGTCAAAGGCACAACTAGGCATTTAGCTTTTACTCAAAAATAT
* * *
234301 TTAGCCTTTCATCTAACCGATATGATTGACAGCTTTATGTCAAATGCACAACTAGGAATTTAGTC
260 TTAACCTTTCATCTAACAGACATGATTGACAGCTTTATGTCAAATGCACAACTAGGAATTTAGTC
* * *
234366 CTCTAGTCGAAGGTATTTAACGTTTCATCTAACTGTAAATATTGATACCTTTCTGTCAAACGCGC
325 CTCTACTCAAAGGTATTTAACCTTTCATCTAACTGTAAATATTGATACCTTTCTGTCAAACGCGC
234431 AGCTAGG
390 AGCTAGG
*
234438 CATTTAATCTTTTA-CACAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCAG
1 CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGC-TGATTGACACCTTTC--
* * * *
234502 TC-AACTGCACAGTTAGTCATTTAATCTTTTACT-GAAGGTATTTAACCTTTCAACTAATTGGCA
63 TCTAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTT-ACCTTTCAACTAACTGGCA
* * * *
234565 TGA-TGACACCTTTATGTTAAATACACAACTAGG-TGTTAGTTTTTACTCAAAGGTATTTAACCT
127 TGATTGACACC-TT-TCTAAAATACAC-ACTAGGAT-TTAATCTTTACTCAAAGGTATTT-ACCT
* * * * * *
234628 TTCATCTAACTGGCATGA-TAACACCTTTCTGTCAAATGCTCAGCTTGGCATTTAATCTTTTACT
187 TTCATCTAAATGGCATGATTAACACCTTTCTGTCAAAGGCACAACTAGGCATTT-AGCTTTTACT
* *
234692 CAAAAATATTTAACTTTTCATCTAACTAG-CATGATTGACA-CATTTTTGTCAAATGCACAACTT
251 CAAAAATATTTAACCTTTCATCTAAC-AGACATGATTGACAGC-TTTATGTCAAATGCACAAC-T
* * *
234755 A-GCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
313 AGGAATTTAGTCCTCTACTCAAAGGTATTTAACCTTTCATCTAA
234798 GTAGCATGAT
Statistics
Matches: 309, Mismatches: 38, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
396 29 0.09
397 42 0.14
398 52 0.17
399 63 0.20
400 120 0.39
401 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (396 bp):
CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGCTGATTGACACCTTTCTCT
AAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTACCTTTCAACTAACTGGCATGAT
TGACACCTTTCTAAAATACACACTAGGATTTAATCTTTACTCAAAGGTATTTACCTTTCATCTAA
ATGGCATGATTAACACCTTTCTGTCAAAGGCACAACTAGGCATTTAGCTTTTACTCAAAAATATT
TAACCTTTCATCTAACAGACATGATTGACAGCTTTATGTCAAATGCACAACTAGGAATTTAGTCC
TCTACTCAAAGGTATTTAACCTTTCATCTAACTGTAAATATTGATACCTTTCTGTCAAACGCGCA
GCTAGG
Done.