Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007970.1 Hibiscus syriacus cultivar Beakdansim tig00110407_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: 487657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:366391 original size:17 final size:17
Alignment explanation
Indices: 366356--366393 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
366346 TATTTTTTCC
* *
366356 TTTTATTTTTTTTTTAT
1 TTTTATTTATTTTTAAT
366373 TTTTATTTATTTTTAAT
1 TTTTATTTATTTTTAAT
366390 TTTT
1 TTTT
366394 TTACTAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTATTTATTTTTAAT
Found at i:367961 original size:17 final size:17
Alignment explanation
Indices: 367939--367991 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
367929 AATTAAGAGT
367939 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
367956 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
367973 TAGTTTAATTAATTAAC
1 TAGTTTAATAAATGAAC
367990 TA
1 TA
367992 ACTTTATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:379783 original size:18 final size:19
Alignment explanation
Indices: 379737--379787 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 19
379727 CAGTTATAAG
379737 CATGTTAGAAAGTTAAGAT
1 CATGTTAGAAAGTTAAGAT
379756 CATG---GAAAGTTAAGAT
1 CATGTTAGAAAGTTAAGAT
*
379772 -GTGTTAGAAAGTTAAG
1 CATGTTAGAAAGTTAAG
379788 TTTAAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 12 0.43
18 10 0.36
19 4 0.14
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.29
Consensus pattern (19 bp):
CATGTTAGAAAGTTAAGAT
Found at i:382773 original size:21 final size:22
Alignment explanation
Indices: 382734--382784 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
382724 ATAATCAATG
*
382734 TTATTTT-AATTAAAATTATTA
1 TTATTTTAAATTAAAATTATCA
*
382755 TTATTTTAAATT-AATTTATCA
1 TTATTTTAAATTAAAATTATCA
382776 TT-TTTTAAA
1 TTATTTTAAA
382785 ATTTAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTTTAAATTAAAATTATCA
Found at i:383553 original size:2 final size:2
Alignment explanation
Indices: 383546--383604 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
383536 ACTAGTTTAA
383546 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
383588 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
383605 ATTATGAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:391573 original size:2 final size:2
Alignment explanation
Indices: 391566--391636 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
391556 CGTTAATGTA
391566 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
391608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
391637 CACACAATAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:391751 original size:107 final size:107
Alignment explanation
Indices: 391624--391819 Score: 257
Period size: 107 Copynumber: 1.8 Consensus size: 107
391614 ATATATATAT
* *
391624 ATATATATATATACACACAATAAATCTAAACTGTTCCTCTAAAGCAATTGGTTAAAAGCCCTAGC
1 ATATATATATATACACACAATAAAACTAAACTATTCCTCTAAAGCAATTGGTTAAAAGCCCTAGC
* **
391689 TTTATTGATAGATTTTTTCAGCTATCCACGTAAAAGCAAATA
66 TTTATAGATAGATTCCTTCAGCTATCCACGTAAAAGCAAATA
* * * * ** * * * *
391731 ATATATATGTATATATACAATAAAACTGAGTTATTCTTCTAAAGTAATTGGTTAAAAGTCTTAGC
1 ATATATATATATACACACAATAAAACTAAACTATTCCTCTAAAGCAATTGGTTAAAAGCCCTAGC
391796 TTTATAGATAGATTCCTTCAGCTA
66 TTTATAGATAGATTCCTTCAGCTA
391820 GCCAAACAAA
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
107 74 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (107 bp):
ATATATATATATACACACAATAAAACTAAACTATTCCTCTAAAGCAATTGGTTAAAAGCCCTAGC
TTTATAGATAGATTCCTTCAGCTATCCACGTAAAAGCAAATA
Found at i:392352 original size:22 final size:24
Alignment explanation
Indices: 392324--392427 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
392314 AGTAAGGGGT
392324 AACATTTTTCAAAA-C-TTCATCA
1 AACATTTTTCAAAATCTTTCATCA
*
392346 AACATTTTTCAAAATTCTTTCTTCA
1 AACATTTTTCAAAA-TCTTTCATCA
* *
392371 AAC-GTTTTCAAAATCTTTCATAA
1 AACATTTTTCAAAATCTTTCATCA
*
392394 AACA-TTTTCAAAA-CTTCTTCATTA
1 AACATTTTTCAAAATC-T-TTCATCA
392418 AAC-TTTTTCA
1 AACATTTTTCA
392428 CCTTTTGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
22 15 0.21
23 21 0.30
24 25 0.36
25 9 0.13
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.42
Consensus pattern (24 bp):
AACATTTTTCAAAATCTTTCATCA
Found at i:392396 original size:23 final size:23
Alignment explanation
Indices: 392324--392406 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
392314 AGTAAGGGGT
392324 AACATTTTTCAAAA-C-TTCATCA
1 AACA-TTTTCAAAATCTTTCATCA
*
392346 AACATTTTTCAAAATTCTTTCTTCA
1 AACA-TTTTCAAAA-TCTTTCATCA
* *
392371 AACGTTTTCAAAATCTTTCATAA
1 AACATTTTCAAAATCTTTCATCA
392394 AACATTTTCAAAA
1 AACATTTTCAAAA
392407 CTTCTTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.26
23 20 0.38
24 10 0.19
25 9 0.17
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.40
Consensus pattern (23 bp):
AACATTTTCAAAATCTTTCATCA
Found at i:392426 original size:47 final size:46
Alignment explanation
Indices: 392328--392427 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 46
392318 AGGGGTAACA
*
392328 TTTTTCAAAACTTCATCAAACATTTTTCAAAATTCTTTCTTCAAAC
1 TTTTTCAAAACTTCATAAAACATTTTTCAAAATTCTTTCTTCAAAC
*
392374 GTTTTCAAAATCTTTCATAAAACA-TTTTCAAAACTTC-TTCATT-AAAC
1 TTTTTCAAAA-C-TTCATAAAACATTTTTCAAAA-TTCTTTC-TTCAAAC
392421 TTTTTCA
1 TTTTTCA
392428 CCTTTTGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
46 9 0.19
47 23 0.49
48 15 0.32
ACGTcount: A:0.35, C:0.20, G:0.01, T:0.44
Consensus pattern (46 bp):
TTTTTCAAAACTTCATAAAACATTTTTCAAAATTCTTTCTTCAAAC
Found at i:394043 original size:6 final size:6
Alignment explanation
Indices: 394036--394114 Score: 131
Period size: 6 Copynumber: 13.0 Consensus size: 6
394026 TGGTATTTAA
*
394036 TATTAA TATTTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
1 TATTAT TAT-TAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
*
394085 TAATAT TATTAT TATTAT TATTAT TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT
394115 AGATTTCCTT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
6 64 0.93
7 5 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTAT
Found at i:394053 original size:3 final size:3
Alignment explanation
Indices: 394045--394114 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
394035 ATATTAATAT
*
394045 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
394093 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
394115 AGATTTCCTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:395166 original size:13 final size:13
Alignment explanation
Indices: 395148--395174 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
395138 ACAGGCAAAG
395148 TGTTTGCACTAAT
1 TGTTTGCACTAAT
395161 TGTTTGCACTAAT
1 TGTTTGCACTAAT
395174 T
1 T
395175 AAGCTCTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (13 bp):
TGTTTGCACTAAT
Found at i:399446 original size:17 final size:18
Alignment explanation
Indices: 399414--399451 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
399404 ATCATATCAA
399414 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
399432 ATTTT-AAATT-TT-TAT
1 ATTTTAAAATTATTATAT
399447 ATTTT
1 ATTTT
399452 CTATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 2 0.10
17 5 0.25
18 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:399955 original size:15 final size:16
Alignment explanation
Indices: 399935--399969 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
399925 AGTCATCGTG
399935 CCTTCCC-GCGTCTTC
1 CCTTCCCAGCGTCTTC
*
399950 CCTTCCCAGCGTTTTC
1 CCTTCCCAGCGTCTTC
399966 CCTT
1 CCTT
399970 TGTATCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.03, C:0.49, G:0.11, T:0.37
Consensus pattern (16 bp):
CCTTCCCAGCGTCTTC
Found at i:400375 original size:7 final size:7
Alignment explanation
Indices: 400353--400408 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
400343 CCGGGAGTGA
400353 AAGAAAG
1 AAGAAAG
**
400360 AAGGGAG
1 AAGAAAG
400367 AAGAAAG
1 AAGAAAG
400374 AAGACAA-
1 AAGA-AAG
*
400381 AAG-AGG
1 AAGAAAG
400387 AAGAAAG
1 AAGAAAG
400394 AAGAAGAG
1 AAGAA-AG
400402 AAGAAAG
1 AAGAAAG
400409 TTAAAGTCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 1 0.03
6 3 0.08
7 26 0.67
8 9 0.23
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:400383 original size:10 final size:10
Alignment explanation
Indices: 400365--400406 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
400355 GAAAGAAGGG
400365 AGAAGAAAGA
1 AGAAGAAAGA
400375 AGACA-AAAGA
1 AGA-AGAAAGA
*
400385 GGAAGAAAGA
1 AGAAGAAAGA
400395 AGAAGAGAAGA
1 AGAAGA-AAGA
400406 A
1 A
400407 AGTTAAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.04
10 20 0.74
11 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:401102 original size:20 final size:20
Alignment explanation
Indices: 401074--401119 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
401064 AGCGATGGTG
*
401074 TTATTATTATTTAATAAATA
1 TTATAATTATTTAATAAATA
*
401094 TTATAATTATTTATTAAATA
1 TTATAATTATTTAATAAATA
401114 TTATAA
1 TTATAA
401120 ATTTAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATAATTATTTAATAAATA
Found at i:402078 original size:5 final size:5
Alignment explanation
Indices: 402068--402349 Score: 426
Period size: 5 Copynumber: 57.8 Consensus size: 5
402058 ATGTATATTT
402068 TATAA TATAA TATAATA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A
1 TATAA TATAA TAT-A-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
402119 TATAA TAT-A TATAA TAT-A TATAA TATAA TATAA TATAA TATTAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA-TAA TATAA
*
402168 TATAA TAT-A -ATAA TATAA TATAA TATAA TA-AA TAT-A TAATAA TATTAC
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T-ATAA TA-TAA
402216 TATAA TA-AA TATAA TATAA TATAA TATAA TATAA TA-AA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
402264 TATAA T-T-A TATAA TA-AA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
402311 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
402350 CTAATACTAC
Statistics
Matches: 258, Mismatches: 2, Indels: 34
0.88 0.01 0.12
Matches are distributed among these distances:
3 4 0.02
4 34 0.13
5 203 0.79
6 13 0.05
7 4 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:402382 original size:14 final size:14
Alignment explanation
Indices: 402363--402408 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
402353 ATACTACTAC
402363 TATTTAATTTAATT
1 TATTTAATTTAATT
402377 TATTTAATTTAATT
1 TATTTAATTTAATT
*
402391 TATTT-ATTTATTT
1 TATTTAATTTAATT
402404 TATTT
1 TATTT
402409 CTTAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTAATTTAATT
Found at i:402383 original size:9 final size:9
Alignment explanation
Indices: 402364--402408 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
402354 TACTACTACT
402364 ATTTAATTTA
1 ATTT-ATTTA
402374 ATTTATTTA
1 ATTTATTTA
402383 ATTTAATTT-
1 ATTT-ATTTA
402392 ATTTATTTA
1 ATTTATTTA
*
402401 TTTTATTT
1 ATTTATTT
402409 CTTAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 4 0.12
9 20 0.62
10 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTATTTA
Found at i:402408 original size:5 final size:5
Alignment explanation
Indices: 402364--402405 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
402354 TACTACTACT
*
402364 ATTTA ATTTA ATTT- ATTTA ATTTA ATTT- ATTT- ATTTA TTTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
402406 TTTCTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
ATTTA
Found at i:409032 original size:120 final size:121
Alignment explanation
Indices: 408796--409033 Score: 347
Period size: 120 Copynumber: 1.9 Consensus size: 121
408786 AAAAAATATT
408796 ATACATAAATTAATTTTAAATTTTTAAAATTACGACTAAATTGATAGAATAAAGTATAAGAGAAC
1 ATACATAAATTAATTTTAAATTTTTAAAATTACGACTAAATTGATAG----AAGTATAAGAGAAC
* * *
408861 AAATATGTAATTATATGAATTTTATTAAATTTAAAAAGTTAATATGAGATAAAATGGTAG
62 AAATATGTAATTATATCAATTTTATTAAATTTAAAAAGTTAAGAAGAGATAAAATGGTAG
*
408921 ATACATAAATTAATTTT-AATTGTTTAAAATTACGACTAAATTGATAG-AGTATAAGTG-ACATA
1 ATACATAAATTAATTTTAAATT-TTTAAAATTACGACTAAATTGATAGAAGTATAAGAGAACA-A
* *
408983 ATGTGTAATTATATCAATTTTATTAAATTTTAAAAGTTAAGAAGAGATAAA
64 ATATGTAATTATATCAATTTTATTAAATTTAAAAAGTTAAGAAGAGATAAA
409034 TATATTTTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 9
0.88 0.05 0.08
Matches are distributed among these distances:
119 3 0.03
120 56 0.53
124 4 0.04
125 42 0.40
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (121 bp):
ATACATAAATTAATTTTAAATTTTTAAAATTACGACTAAATTGATAGAAGTATAAGAGAACAAAT
ATGTAATTATATCAATTTTATTAAATTTAAAAAGTTAAGAAGAGATAAAATGGTAG
Found at i:409071 original size:28 final size:28
Alignment explanation
Indices: 409031--409098 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
409021 AAGAAGAGAT
* *
409031 AAATATAT-TTTTTATGTTAAATAAGAAAA
1 AAATATATATTTTTA--ATAAATAACAAAA
*
409060 AAAT-TATATTTTTAATAAATAACAATA
1 AAATATATATTTTTAATAAATAACAAAA
409087 AAATATATATTT
1 AAATATATATTT
409099 ATTGTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 14 0.41
28 10 0.29
29 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATATATATTTTTAATAAATAACAAAA
Found at i:409246 original size:33 final size:34
Alignment explanation
Indices: 409197--409261 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
409187 ATTCCTAAAA
409197 ATACATAAATTATTATAAAATAAAGTTAATTATT
1 ATACATAAATTATTATAAAATAAAGTTAATTATT
409231 ATACAT-AATTATTATAAAATAAAGTTAATTA
1 ATACATAAATTATTATAAAATAAAGTTAATTA
409262 AGTTAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (34 bp):
ATACATAAATTATTATAAAATAAAGTTAATTATT
Found at i:409296 original size:27 final size:27
Alignment explanation
Indices: 409266--409342 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
409256 TAATTAAGTT
409266 AATTATTAAAAATCAAATATATACATA
1 AATTATTAAAAATCAAATATATACATA
409293 AATTATTATAAAATC-AAT-T-TA-AT-
1 AATTATTA-AAAATCAAATATATACATA
* * *
409316 TATTATAAAAAATCAAATATATCCATA
1 AATTATTAAAAATCAAATATATACATA
409343 CATACAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
22 6 0.15
23 9 0.22
24 3 0.07
25 3 0.07
26 3 0.07
27 11 0.27
28 6 0.15
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (27 bp):
AATTATTAAAAATCAAATATATACATA
Found at i:409327 original size:50 final size:54
Alignment explanation
Indices: 409230--409342 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 54
409220 AGTTAATTAT
*
409230 TATACAT-AATTATTATAAAATAAAGTTAATTAAGTTAATTATTAAAAATCAAATA
1 TATACATAAATTATTATAAAATAAAG-T-ATTAAGTTAATTATAAAAAATCAAATA
*
409285 TATACATAAATTATTATAAAATCAA-T-TTAA-TT-ATTATAAAAAATCAAATA
1 TATACATAAATTATTATAAAATAAAGTATTAAGTTAATTATAAAAAATCAAATA
*
409335 TATCCATA
1 TATACATA
409343 CATACAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
50 24 0.44
51 2 0.04
52 4 0.07
54 1 0.02
55 7 0.13
56 16 0.30
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (54 bp):
TATACATAAATTATTATAAAATAAAGTATTAAGTTAATTATAAAAAATCAAATA
Found at i:414002 original size:22 final size:23
Alignment explanation
Indices: 413977--414019 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
413967 AGGCAGAACC
*
413977 AGAAAGATCGGGGAA-GGGAGGA
1 AGAAAGATCGGAGAATGGGAGGA
*
413999 AGAAAGGTCGGAGAATGGGAG
1 AGAAAGATCGGAGAATGGGAG
414020 ATTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.05, G:0.49, T:0.07
Consensus pattern (23 bp):
AGAAAGATCGGAGAATGGGAGGA
Found at i:417144 original size:2 final size:2
Alignment explanation
Indices: 417128--417163 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
417118 TTATGTCAGT
*
417128 AG AG -G AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
417164 CTTGGCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:424332 original size:17 final size:17
Alignment explanation
Indices: 424310--424344 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
424300 ATTTTTATAA
424310 AAGTTATTAAAAATATG
1 AAGTTATTAAAAATATG
424327 AAGTTATTAAAAATATG
1 AAGTTATTAAAAATATG
424344 A
1 A
424345 TTATTGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (17 bp):
AAGTTATTAAAAATATG
Found at i:426804 original size:18 final size:18
Alignment explanation
Indices: 426778--426846 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
426768 GTAGAATTTT
*
426778 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
426796 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATG
* * *
426814 TCCTGAAAGATCACTATG
1 TCCCGAAGGACCACTATG
*
426832 TCCTGAAGGACCACT
1 TCCCGAAGGACCACT
426847 GATAATCCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:435757 original size:21 final size:21
Alignment explanation
Indices: 435731--435772 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
435721 TATATAGCTC
* *
435731 ACAACTCGAGCCTTACTGCTA
1 ACAACTCAAGCCTAACTGCTA
435752 ACAACTCAAGCCTAACTGCTA
1 ACAACTCAAGCCTAACTGCTA
435773 CTAATAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (21 bp):
ACAACTCAAGCCTAACTGCTA
Found at i:435844 original size:15 final size:15
Alignment explanation
Indices: 435824--435868 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
435814 CATAACGACA
*
435824 TGCACACATCATCTT
1 TGCACACATCAGCTT
*
435839 TGCACACATTAGCTT
1 TGCACACATCAGCTT
435854 TGCACACATCAGCTT
1 TGCACACATCAGCTT
435869 ACTTAACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (15 bp):
TGCACACATCAGCTT
Found at i:448653 original size:2 final size:2
Alignment explanation
Indices: 448648--448673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448638 TTTTTCACCA
448648 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
448674 GAAACCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449793 original size:17 final size:18
Alignment explanation
Indices: 449745--449793 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
449735 CAAGAACATA
*
449745 AAAAAGTGTTGTTAAAAT
1 AAAAAGTGATGTTAAAAT
*
449763 AAAAAAT-ATGTTAAAAT
1 AAAAAGTGATGTTAAAAT
*
449780 -AAAAGTGATCTTAA
1 AAAAAGTGATGTTAA
449794 TACTTGTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (18 bp):
AAAAAGTGATGTTAAAAT
Found at i:456551 original size:2 final size:2
Alignment explanation
Indices: 456544--456572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
456534 TTTTAAACTT
456544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
456573 TAACTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:459117 original size:162 final size:161
Alignment explanation
Indices: 458850--459365 Score: 638
Period size: 162 Copynumber: 3.1 Consensus size: 161
458840 ATCTTAAAAA
* *
458850 GACAAAACCGGTAAAGTGGTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
1 GACAAAACCGGTAAAG-GCTACCTGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* * *
458915 CTTTGTGAATTTAAAAGATAATCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATATA
65 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTA
458980 TCGATCCACAACGATATAACAAGTAAAAATAT
130 TCGATCCACAACGATATAACAAGTAAAAATAT
* *
459012 GACAAAACCGGTAAAGTGCTACCTGATATATTGAAAGTGTCGATACTTTAATATAAATATTGACA
1 GACAAAACCGGTAAAG-GCTACCTGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* * *
459077 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGTGTCTATAAAGTGTCGATACTTTATAACAATGTA
65 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTA
*
459142 TCGATCCACAGCGATATAACAAGTAAAAATAT
130 TCGATCCACAACGATATAACAAGTAAAAATAT
* * *
459174 GATAAAATCGGTCTCCAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATA
1 GACAAAACCGG--T--AAAGG-------C----T--A-C--CTG-ATATATTGAAAGTGTCGATA
*
459239 CTTTAATATAAGTATCGACACTTTGTGAATTAAAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTG
45 CTTTAATATAAGTATCGACACTTTGTGAATT-TAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTG
* * * *
459304 T-GATACTTTATAACAATGTATCGATCCACTACGATATAACATGAAAAAATAT
109 TCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAAGTAAAAATAT
459356 GACAAAACCG
1 GACAAAACCG
459366 ATATCTAAAG
Statistics
Matches: 307, Mismatches: 25, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
162 160 0.52
164 1 0.00
165 1 0.00
166 4 0.01
172 1 0.00
176 1 0.00
178 1 0.00
179 1 0.00
181 2 0.01
182 104 0.34
183 31 0.10
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (161 bp):
GACAAAACCGGTAAAGGCTACCTGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
TTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTAT
CGATCCACAACGATATAACAAGTAAAAATAT
Found at i:459319 original size:182 final size:181
Alignment explanation
Indices: 459012--459550 Score: 821
Period size: 182 Copynumber: 3.0 Consensus size: 181
459002 GTAAAAATAT
* * * * *
459012 GACAAAACCGGTAAAGTGCTACCTG-ATATATTGAAAGTGTCGATACTTTAATATAAATATTGAC
1 GACAAAACCGGTATAGAGCGACC-GAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
* *
459076 ACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGTGTCTATAAAGTGTCGATACTTTATAACAATGT
65 ACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGT
* * *
459141 ATCGATCCACAGCGATATAACAAGTAAAAATATGATAAAATCGGTCTCCAAAG
130 ATCGATCCACA-CGATATAACAAGTAAAAATATGACAAAACCGGTATCCAAAG
459194 GACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
1 GACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
459259 CTTTGTGAATTAAAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGT-GATACTTTATAACAATGT
66 CTTTGTGAATT-TAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGT
* * * *
459323 ATCGATCCACTACGATATAACATGAAAAAATATGACAAAACCGATATCTAAAG
130 ATCGATCCAC-ACGATATAACAAGTAAAAATATGACAAAACCGGTATCCAAAG
* * *
459376 GACAAAACCGATATAGAGAGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAA
1 GACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* *
459441 CTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
* *
459506 TCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCGGTA
131 TCGATCCA-CACGATATAACAAGTAAAAATATGACAAAACCGGTA
459551 AAGCGCTACC
Statistics
Matches: 327, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
181 33 0.10
182 262 0.80
183 32 0.10
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (181 bp):
GACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
TCGATCCACACGATATAACAAGTAAAAATATGACAAAACCGGTATCCAAAG
Found at i:463851 original size:19 final size:17
Alignment explanation
Indices: 463827--463869 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
463817 AATGTAGGGT
463827 TAATTTTGTATAAGATTTA
1 TAATTTTG--TAAGATTTA
*
463846 TAATTTTGTACGATTTA
1 TAATTTTGTAAGATTTA
463863 TAATTTT
1 TAATTTT
463870 CTATGTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (17 bp):
TAATTTTGTAAGATTTA
Found at i:464583 original size:198 final size:200
Alignment explanation
Indices: 464226--465379 Score: 1445
Period size: 200 Copynumber: 5.8 Consensus size: 200
464216 AACATATGTA
* *
464226 TCGATACATTTATAAAAAGTATCGACCCCAAAAACATCGAAA-CCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
** *
464290 AATTTTGTAATATAACCAATATAAATATACC-AGTTTTATGTGAGAATAAGTCTACATAATGTAT
66 AATTTTGTAATATAACCGGTATAAATATACCGA-TTTTATGTGAGAATAGGTCTACATAATGTAT
* *
464354 CGACACTTTTTAAATTGGTGTCGATACTTTTTGTCCATAATGAATTTCCAAAATGGTGAACGCAT
130 CGACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTGCCAAAATGGTGAACGCAT
464419 AAAGTG
195 AAAGTG
*
464425 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA-GT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
* * * *
464489 AATTTTGTAATATAA-TGGTATAAATATACTGATTTTATGTGAGAATAGGTTTACATAATGGATC
66 AATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATC
*
464553 GACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTTCCAAAATGGTGAACGCATA
131 GACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTGCCAAAATGGTGAACGCATA
464618 AAGTG
196 AAGTG
*
464623 TCGATACATTTATAAAAAGTATCGATCCTAGAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
* ** * * *
464688 AAATTTACAATATAACCGGTATAACTATA-CTAGTTTTATGAGAGAATAGGTCTACATAATGTAT
66 AATTTTGTAATATAACCGGTATAAATATACCGA-TTTTATGTGAGAATAGGTCTACATAATGTAT
* * ** * * * * * *
464752 CAACACTTATGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAA-TGCCTAAAATCGTGCACCCA
130 CGACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTGCC-AAAATGGTGAACGCA
*
464816 TAAAGTT
194 TAAAGTG
* * * * *
464823 TCAATACATTTTTTAAAAGTGTCGATCCCAGAGACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
* ** * * *
464888 AATTTTGTAATGTAACATGTATAAATATACCGGTTTTATGTTG-GAATAGATCTACATAATATAT
66 AATTTTGTAATATAACCGGTATAAATATACCGATTTTATG-TGAGAATAGGTCTACATAATGTAT
*
464952 CGACACATTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAA-TGCCCAAAATGGTGAACGCA
130 CGACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTG-CCAAAATGGTGAACGCA
465016 TAAAGTG
194 TAAAGTG
* * * * ** * *
465023 TCGATAAATTTTTAAAAAGTGTCAATCTTAGAGACATCG-AACCCATAATTATAATGTAATAGTT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
* * *
465087 AATTTTGTAATGTAACCGGTATAAATATACCGATTTTATTTGAGAATAGGTCTACATAATGTATA
66 AATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATC
* * * * *
465152 GACACTTTTT-AATTATGTGTCGATCCATTTTGTCCAGAATGAA-TGCCGAAAAAGTGGTGCATG
131 GACACTTTTTAAATT-GGTGTCGATACTTTTTGTCCAGAATGAATTGCC--AAAA-TGGTGAACG
465215 CATAAAGTG
192 CATAAAGTG
* * * * *
465224 TCAATACATTTATAAAAAATATCAATCTCAGAAACATCGAAACCCATTATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
* * * * * * *
465289 AATTTT-TCAATGTAATCGATATAAATATACCGGTTTTATGAGAAAATAGGTC-AGCATAAAGTA
66 AATTTTGT-AATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTA-CATAATGTA
* *
465352 TCGACAATTGTTAAATATGGT-TCGATAC
129 TCGACACTTTTTAAAT-TGGTGTCGATAC
465380 CATTTTAAAA
Statistics
Matches: 832, Mismatches: 104, Indels: 35
0.86 0.11 0.04
Matches are distributed among these distances:
198 177 0.21
199 192 0.23
200 313 0.38
201 54 0.06
202 90 0.11
203 5 0.01
204 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (200 bp):
TCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
AATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATC
GACACTTTTTAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTGCCAAAATGGTGAACGCATA
AAGTG
Found at i:466899 original size:6 final size:6
Alignment explanation
Indices: 466853--466898 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
466843 CAAGAGGTCA
* * *
466853 ATGAAG ATGAAG ATGAAG ATGACG ATGACG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
466899 TTATTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:468266 original size:24 final size:24
Alignment explanation
Indices: 468221--468267 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
468211 ATGTAATTGA
* *
468221 AGTTTGAATTTAAATTTCAATTTG
1 AGTTTGAATTTAAATATAAATTTG
* *
468245 AGTTTGAGTTTCAATATAAATTT
1 AGTTTGAATTTAAATATAAATTT
468268 CGCCTCCACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
AGTTTGAATTTAAATATAAATTTG
Found at i:470437 original size:400 final size:397
Alignment explanation
Indices: 469604--470969 Score: 1687
Period size: 400 Copynumber: 3.4 Consensus size: 397
469594 AGTTTCCCAT
* * * *
469604 AAAGTGTCGATTCATGTTTAAAAAGTATTGATCCCAAAAACATCGAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACAT-TTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* *
469669 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTGTTTTGAGAAAATA-GAT-ATAC
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACC-AGTT-TTATGAGAAAATATG-TCA-AC
* *
469732 ATAATGTATCGACACTTGTATAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGG
126 ATAATGTATCGACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAG-GG
* * * *
469797 -TGCACGCATACAATGTTGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAA
190 TTGTACGCATA-AATGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACCGATAA
* * ** * * ** * *
469861 TTATAATGTGATAGGTAATTTTGTAATATAACATGTATAAATATACTAGTTTTATGTGAGAATAG
254 TTATAATGTAATAGGTAAATTTACAATATAAC-CGTATAAATTTACCGGTTTTATGAGAAAATAG
* * *
469926 GT-ATACATAATGTGTCGACAC-TTTT-GAATTTTGTGTCGATACTTTTTGTCTAGAATGAATAC
318 GTGA-ACATAATGTATCGACACGTTTTAG-ATTTT-TGTCGATACATTTTGTCAAGAATGAAT-C
* * * *
469988 CCAAA-ATGGTGAACACAT
379 CCAAACGTGGTGCAGACAA
* * * *
470006 AAAGTGTCGATACATTTATAAAAAATATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTT-GAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * * * *
470071 ATAGGTAAATTTACAATGTAACCAATATAACTATACTAGTTTTATAAGAGAATATGTCTACATAA
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATATGTCAACATAA
* * *
470136 TGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATACCAAAAGGGTTGTA
130 TGTATCGACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTTGTA
* *
470201 CGCATAAAGTGTCGATACATTTTTAAAACGTATCGATCCCAAAAATATCGAAACTGATAATTATA
195 CGCATAAA-TGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACCGATAATTATA
* * *
470266 ATGTAATAAAGTAAATTTACAATGTAACCGATATAAATTTACCGGTTTTATAAGAAAATAGGTGA
259 ATGTAAT-AGGTAAATTTACAATATAACCG-TATAAATTTACCGGTTTTATGAGAAAATAGGTGA
* *
470331 ACATAATGTATCGACACGTTTTAGATTTTTGTCGATACATTTTGTCCAGAATGAATTCCAAACGT
322 ACATAATGTATCGACACGTTTTAGATTTTTGTCGATACATTTTGTCAAGAATGAATCCCAAACGT
* *
470396 TGTGCAGTCAA
387 GGTGCAGACAA
** * *
470407 AAAGTGTCGATACATTTGAAATTGTATCGATTCCAAAAACATCGAAACCAATAATTATAATGTAA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * * *
470472 TAGGTAAATTTACAATGTAACCGGTATAAATTTACCGGTTTTATGAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATATGTCAACATAAT
* * * *
470537 GTATCAACACATTTTAG-ATTTGTGTCGATA-TATTTTGTCCAGAATGAATGCC-AAA-CGTTGT
131 GTATCGACAC-TTGTAGAATTTGTGTCGATACT-TTTTGTCCAAAATGAATGCCAAAAGGGTTGT
* * * **
470598 GCAGACAAAAAATGTCGATACA-TTTGAAATTGTATCGATCCCAAAAATATCGAAACCGATAATT
194 AC-G-C-ATAAATGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACCGATAATT
*
470662 ATAATGTAATAGGTAAATTTACAATATAACCGGTATACATTTACCGGTTTTATGAGAAAATAGGT
256 ATAATGTAATAGGTAAATTTACAATATAACC-GTATAAATTTACCGGTTTTATGAGAAAATAGGT
* *
470727 GAACATAATGTATCGACACGTTTTAGATTTGTGTCGATACATTTTGTCAAGAATGAATGCCAAAC
320 GAACATAATGTATCGACACGTTTTAGATTTTTGTCGATACATTTTGTCAAGAATGAATCCCAAAC
*
470792 GGGGTGCAGACAA
385 GTGGTGCAGACAA
** * *
470805 AAAGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTATAACGTAA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * * * *
470870 TAGATAAATTTATAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAAT
66 TAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATATGTCAACATAAT
*
470935 GTATCGACACTTTTA-AATTTGTGTCGATACTTTTT
131 GTATCGACACTTGTAGAATTTGTGTCGATACTTTTT
470970 AAATAACGCG
Statistics
Matches: 844, Mismatches: 101, Indels: 43
0.85 0.10 0.04
Matches are distributed among these distances:
397 22 0.03
398 256 0.30
399 58 0.07
400 287 0.34
401 120 0.14
402 100 0.12
403 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (397 bp):
AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
TAGGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATATGTCAACATAAT
GTATCGACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTTGTAC
GCATAAATGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATATAACCGTATAAATTTACCGGTTTTATGAGAAAATAGGTGAACAT
AATGTATCGACACGTTTTAGATTTTTGTCGATACATTTTGTCAAGAATGAATCCCAAACGTGGTG
CAGACAA
Found at i:470533 original size:199 final size:198
Alignment explanation
Indices: 469604--470969 Score: 1618
Period size: 199 Copynumber: 6.8 Consensus size: 198
469594 AGTTTCCCAT
* * *
469604 AAAGTGTCGATTCATGTTTAAAAAGTATTGATCCCAAAAACATCGAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACAT-TTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * *
469669 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGATTTGTTTTGAGAAAATAGAT-ATACA
65 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCG-GTT-TTATGAGAAAATAGGTGA-ACA
*
469733 TAATGTATCGACACTTGTATA-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGG
127 TAATGTATCGACACTT-T-TAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGG
469797 TGCACG-CATA
190 TGCA-GACA-A
* * * *
469807 CAA-TGTTGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTG
1 AAAGTGTCGATACA-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* ** * ** ** * *
469871 ATAGGTAATTTTGTAATATAACATGTATAAATATACTAGTTTTATGTGAGAATAGGT-ATACATA
65 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGA-ACATA
* * * *
469935 ATGTGTCGACACTTTT-GAATTTTGTGTCGATACTTTTTGTCTAGAATGAATACCCAAA-ATGGT
129 ATGTATCGACACTTTTAG-A-TTTGTGTCGATACTTTTTGTCCAGAATGAAT-GCCAAACGTGGT
* * *
469998 GAACACAT
191 GCAGACAA
* * *
470006 AAAGTGTCGATACATTTATAAAAAATATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTT-TAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
** * ** * * * **
470071 ATAGGTAAATTTACAATGTAACCAATATAACTATACTAGTTTTATAAGAGAATATGTCTACATAA
65 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATAA
* * * * * * *
470136 TGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATACCAAAAG-GGTTGT
130 TGTATCGACACTTTTAG-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGG-TGC
*
470200 ACG-CAT
193 A-GACAA
* * *
470206 AAAGTGTCGATACATTTTTAAAACGTATCGATCCCAAAAATATCGAAACTGATAATTATAATGTA
1 AAAGTGTCGATACA-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * *
470271 ATAAAGTAAATTTACAATGTAACCGATATAAATTTACCGGTTTTATAAGAAAATAGGTGAACATA
65 AT-AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATA
* * * *
470336 ATGTATCGACACGTTTTAGATTTTTGTCGATACATTTTGTCCAGAATGAATTCCAAACGTTGTGC
129 ATGTATCGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTGC
*
470401 AGTCAA
193 AGACAA
* ** * *
470407 AAAGTGTCGATACATTTGAAATTGTATCGATTCCAAAAACATCGAAACCAATAATTATAATGTAA
1 AAAGTGTCGATACATTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
*
470472 TAGGTAAATTTACAATGTAACCGGTATAAATTTACCGGTTTTATGAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATAAT
* *
470537 GTATCAACACATTTTAGATTTGTGTCGATA-TATTTTGTCCAGAATGAATGCCAAACGTTGTGCA
131 GTATCGACAC-TTTTAGATTTGTGTCGATACT-TTTTGTCCAGAATGAATGCCAAACGTGGTGCA
470601 GACAA
194 GACAA
* * ** *
470606 AAAATGTCGATACATTTGAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAA
1 AAAGTGTCGATACATTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * *
470671 TAGGTAAATTTACAATATAACCGGTATACATTTACCGGTTTTATGAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATAAT
* * *
470736 GTATCGACACGTTTTAGATTTGTGTCGATACATTTTGTCAAGAATGAATGCCAAACGGGGTGCAG
131 GTATCGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTGCAG
470801 ACAA
195 ACAA
* ** * *
470805 AAAGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATTGAAACCGATAATTATAACGTAA
1 AAAGTGTCGATACATTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * * * *
470870 TAGATAAATTTATAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATATGTCAACATAAT
66 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATAAT
*
470935 GTATCGACACTTTTAAATTTGTGTCGATACTTTTT
131 GTATCGACACTTTTAGATTTGTGTCGATACTTTTT
470970 AAATAACGCG
Statistics
Matches: 1020, Mismatches: 123, Indels: 45
0.86 0.10 0.04
Matches are distributed among these distances:
198 24 0.02
199 450 0.44
200 326 0.32
201 130 0.13
202 87 0.09
203 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (198 bp):
AAAGTGTCGATACATTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGAACATAAT
GTATCGACACTTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTGCAGA
CAA
Found at i:474457 original size:200 final size:199
Alignment explanation
Indices: 474032--474728 Score: 759
Period size: 200 Copynumber: 3.5 Consensus size: 199
474022 ACCTAAATAT
* * * * * *
474032 GTGTCGATGCATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCACAAAAAACATCGAAACCGATAATTACAATATGA
* * * * * *
474095 TAGGTAAATTAACAATGTAACCGGTATAAATATATCGATTAATTAGAAAACATGTCAACATAATG
65 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATGAGAAAATATGTCAGCATAATG
474160 TATCGACACTTGTGT-AATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCA
130 TATCGACACTTGT-TAAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACG-GGTGCA
474224 CGCATAAA
192 CGCATAAA
* * *** ***
474232 GTGTCGATACATTTATTATAAGTATCGATCACAATAAAAC-T-GATACTTTTAAATTTGTATAT-
1 GTGTCGATACATTTATTAAAAGTATCGATCACAA-AAAACATCGAAACCGAT-AATTACAATATG
* *
474294 ATTATGTAAATTTACAATGTAACCGGTATAAATATACCGACTTTATGGGAAAATATGTCAGCATA
64 A-TAGGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTATGAGAAAATATGTCAGCATA
* *
474359 AAGTATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATGAATG-CCAAACGGGTGC
127 ATGTATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACGGGTGC
474423 ACGCATAAA
191 ACGCATAAA
* * * * *
474432 GTGTCAATACATTTATTAAAAGTATCGATCCCTAAAAACATCGAAACCGATCATTACAATGTGAT
1 GTGTCGATACATTTATTAAAAGTATCGATCACAAAAAACATCGAAACCGATAATTACAATATGAT
* * * * * * *
474497 AGGTAAATTTACAATGTATCCGATAGAAATATGCCGGTTTTATGAGAAAATATGTCTGAATAATG
66 AGGTAAATTTACAATGTAACCGGTATAAATATACC-GATTTATGAGAAAATATGTCAGCATAATG
* * * * * **
474562 TATTGACACTTTTTAAGTTTGTGTCGATACTTTTTTTCAGAATGAATGCCCAATGGGGTGCACGC
130 TATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGGGTGCACGC
474627 ATAAA
195 ATAAA
* * * *
474632 GTGTCGATACATTTCA--AATTA-TATCGATC-CAAAAAACATCGAAACCGATAATTATAATGTA
1 GTGTCGATACATTT-ATTAA-AAGTATCGATCACAAAAAACATCGAAACCGATAATTACAATATG
* * *
474693 ATAGGTAAATTTGCAATGTTACCGATATAAATATAC
64 ATAGGTAAATTTACAATGTAACCGGTATAAATATAC
474729 ATGTTTAGTT
Statistics
Matches: 419, Mismatches: 63, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
198 59 0.14
199 30 0.07
200 195 0.47
201 64 0.15
202 69 0.16
203 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATCGATCACAAAAAACATCGAAACCGATAATTACAATATGAT
AGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTATGAGAAAATATGTCAGCATAATGT
ATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGGGTGCACGCA
TAAA
Found at i:474886 original size:23 final size:23
Alignment explanation
Indices: 474836--474880 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
474826 TGCCTATTTT
* *
474836 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
474859 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
474881 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:483046 original size:21 final size:19
Alignment explanation
Indices: 483008--483047 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
482998 ACTTGATATA
483008 GATAAATTGTTCAGTGTCC
1 GATAAATTGTTCAGTGTCC
*
483027 GATAAGTTCGTTCATGTGTCC
1 GATAAATT-GTTCA-GTGTCC
483048 AAGGAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (19 bp):
GATAAATTGTTCAGTGTCC
Found at i:483624 original size:33 final size:33
Alignment explanation
Indices: 483585--483647 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
483575 TGTTCAAAGT
* *
483585 TTGGCCACTAACTAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
483618 TTGGCCACCAACCAAGATGAAATTTCCAAT
1 TTGGCCACCAACCAAGATGAAATTTCCAAT
483648 TTGTCAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTCCAATAAG
Done.