Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008804.1 Hibiscus syriacus cultivar Beakdansim tig00111957_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: 529415
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:409186 original size:25 final size:28
Alignment explanation
Indices: 409138--409195 Score: 95
Period size: 25 Copynumber: 2.2 Consensus size: 28
409128 CCTAAGAAGA
409138 AAAATAAATAAAGAAAAACAAGAAAAAG
1 AAAATAAATAAAGAAAAACAAGAAAAAG
409166 AAAA-AAA-AAAGAAAAA-AAGAAAAAG
1 AAAATAAATAAAGAAAAACAAGAAAAAG
409191 AAAAT
1 AAAAT
409196 GAGAGGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 13 0.45
26 9 0.31
27 3 0.10
28 4 0.14
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (28 bp):
AAAATAAATAAAGAAAAACAAGAAAAAG
Found at i:409188 original size:17 final size:17
Alignment explanation
Indices: 409131--409189 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
409121 TATTACACCT
* * *
409131 AAGAAGAAAAATAAATA
1 AAGAAAAAAAAGAAAAA
*
409148 AAGAAAAACAAGAAAAA
1 AAGAAAAAAAAGAAAAA
409165 GAA-AAAAAAAAGAAAAA
1 -AAGAAAAAAAAGAAAAA
409182 AAGAAAAA
1 AAGAAAAA
409190 GAAAATGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAAAGAAAAA
Found at i:409268 original size:24 final size:24
Alignment explanation
Indices: 409236--409316 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
409226 AGCCTTGAAA
409236 CCAAGGAAGGATTTGAGTTGAAAAC
1 CCAA-GAAGGATTTGAGTTGAAAAC
*
409261 CCATGAAGGATTTGAGTTGAAAAC
1 CCAAGAAGGATTTGAGTTGAAAAC
409285 CCAAGAAGGATTTGAGTTGAAAAC
1 CCAAGAAGGATTTGAGTTGAAAAC
409309 CCAA-AAGG
1 CCAAGAAGG
409317 GCGGCTCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.07
24 47 0.87
25 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (24 bp):
CCAAGAAGGATTTGAGTTGAAAAC
Found at i:410619 original size:136 final size:135
Alignment explanation
Indices: 410180--410754 Score: 690
Period size: 136 Copynumber: 4.2 Consensus size: 135
410170 GAACCGATCA
* * * * *
410180 ATTTCAAATGGAGAGTTTATATTGAGAAGAACTTATCCGACAAAGGGAGAAGAAGTTCATAATGA
1 ATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * * ** * * *
410245 GAAGAGCTTGTTCGACCTATCGCTTGATTCACGGTATTTCGAATTAGTGACGCCTCGCTTGAGAG
65 GAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGG
*
410310 ATTGATG
130 ATTGA-C
* * * *
410317 TTTTCAATGAAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 ATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAG
* * ** * *
410382 AAGAGCTTGTTCAATCTATCACTCGATTTA--ACATTTTAAATCAGTGACGCCAT-ACTTGAGGG
66 AAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACC-TCGCTTGAGGG
*
410444 ATTGAA
130 ATTGAC
* * * *
410450 ATTTTCAATGAAGAGTTCATAATGAGAAGAACTCGTCTGACAGAGGGAGAAAAAGTTCATTATGA
1 A-TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGA
* * * * * *
410515 GAAGAGCTTGTTCAACCTTTCACTCAATCCACGACATTTTGAATCAGTAACACCTCGCTTTAGGG
65 GAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGG
410580 ATTGAC
130 ATTGAC
* *
410586 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAA-TTCATAATG
1 ATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAA-AAAGTTCATAATG
* *
410650 AGAAGATCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGATACCTCGCTTGAGG
64 AGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGG
410715 GATTGAC
129 GATTGAC
* *
410722 ATTTTCGATGGAGAGTTCATATTGAGAAGAACT
1 A-TTTCAATGGAGAGTTCATAATGAGAAGAACT
410755 TGTTCGACCT
Statistics
Matches: 381, Mismatches: 49, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
134 112 0.29
135 6 0.02
136 252 0.66
137 11 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (135 bp):
ATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAAAAGTTCATAATGAG
AAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGA
TTGAC
Found at i:410820 original size:96 final size:96
Alignment explanation
Indices: 410641--410821 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 96
410631 GGAGAAGAAA
* * **
410641 TTCATAATGAGAAGATCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGATACCT
1 TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACATTTCGAATCAGCCATACCT
* **
410706 CGCTTGAGGGATTGACATTTTCGATGGAGAG
66 CACTTGAGGGATCAACATTTTCGATGGAGAG
* * ** *
410737 TTCATATTGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTT-GAATTAGCCATACC
1 TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACA-TTTCGAATCAGCCATACC
410801 TCACTAT-AGGGATCAACATTT
65 TCACT-TGAGGGATCAACATTT
410822 CCAAAAGAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
96 67 0.94
97 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (96 bp):
TTCATAATGAGAAGAACTTGTTCAACCTATCACTCGATTCACAACATTTCGAATCAGCCATACCT
CACTTGAGGGATCAACATTTTCGATGGAGAG
Found at i:411039 original size:24 final size:22
Alignment explanation
Indices: 411012--411064 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
411002 AAGCCCAACC
411012 AAACCCAGA-CCCATAACCAAGCTA
1 AAACCCA-ACCCCA-AACCAA-CTA
*
411036 AAACCTCAACCCCAAACCAATTA
1 AAACC-CAACCCCAAACCAACTA
411059 AAACCC
1 AAACCC
411065 CTAAACTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.04
23 7 0.27
24 12 0.46
25 6 0.23
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (22 bp):
AAACCCAACCCCAAACCAACTA
Found at i:412539 original size:10 final size:10
Alignment explanation
Indices: 412524--412555 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
412514 TATGTTTATG
412524 TTTATTTTTT
1 TTTATTTTTT
412534 TTTATTTTTT
1 TTTATTTTTT
*
412544 GTTATTTTTT
1 TTTATTTTTT
412554 TT
1 TT
412556 GTTTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:412562 original size:10 final size:11
Alignment explanation
Indices: 412510--412559 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
412500 CTCATATTTA
*
412510 TGTTTATGTTTA
1 TGTTTAT-TTTT
412522 TGTTTATTTTT
1 TGTTTATTTTT
412533 T-TTTATTTTT
1 TGTTTATTTTT
*
412543 TGTTATTTTTTT
1 TGTT-TATTTTT
412555 TGTTT
1 TGTTT
412560 TTTAATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 10 0.29
11 7 0.21
12 17 0.50
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (11 bp):
TGTTTATTTTT
Found at i:421208 original size:17 final size:17
Alignment explanation
Indices: 421186--421221 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
421176 CTAACATTCC
421186 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
421203 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
421220 GA
1 GA
421222 TCGGTGATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:421277 original size:29 final size:30
Alignment explanation
Indices: 421235--421304 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
421225 GTGATCGGTG
* *
421235 CTATTTTAGTAATTAA-TTCAAAATAGGTA
1 CTATTTTAGTAATTAATTTAAAAAGAGGTA
*
421264 CTATTTTAGTAATTAATTTAAAAAGAGGTG
1 CTATTTTAGTAATTAATTTAAAAAGAGGTA
421294 CTA-TTTAGTAA
1 CTATTTTAGTAA
421305 AATGGTTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (30 bp):
CTATTTTAGTAATTAATTTAAAAAGAGGTA
Found at i:422235 original size:42 final size:41
Alignment explanation
Indices: 422173--422339 Score: 271
Period size: 42 Copynumber: 4.0 Consensus size: 41
422163 GGAAGTATTA
*
422173 CCAGGTCCCTTTGCTATGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
422215 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
422257 CCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
*
422299 CCAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
422340 TCCTAGGCTC
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
41 4 0.03
42 115 0.97
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:428586 original size:30 final size:29
Alignment explanation
Indices: 428518--428586 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
428508 ACCGTTGATC
* ** *
428518 GGTGTTATTTTAGTAATTAATTCGAAATA
1 GGTGATATTTTAGTAATTAATTAAAAAGA
428547 GGTGATATTTTAGTAATTAATTTAAAAAGA
1 GGTGATATTTTAGTAATTAA-TTAAAAAGA
*
428577 GGTGCTATTT
1 GGTGATATTT
428587 CTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTAATTAAAAAGA
Found at i:429531 original size:42 final size:41
Alignment explanation
Indices: 429469--429635 Score: 253
Period size: 42 Copynumber: 4.0 Consensus size: 41
429459 GGAAGTATTA
429469 CCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
* * *
429511 CCAGGTCCCTTTGTTATGTGCGAAGGTAAGCCTTACAGTTTA
1 CCAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
429553 CCAGGTCCCTTTGCTGTTTGCAAGGGTAAGCCTTACAGTTTC
1 CCAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTC
*
429595 CCAGGTCCCTTTGCTGTGTGCAAGGATAACCCTTACAGTTT
1 CCAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
429636 TCCTAGGCTC
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 4 0.04
42 110 0.96
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
CCAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:433331 original size:122 final size:121
Alignment explanation
Indices: 433196--433478 Score: 381
Period size: 122 Copynumber: 2.3 Consensus size: 121
433186 CTTTGTAATG
* * ** **
433196 AGGAAATTGGGTCAATCCGGAGAT-ATTACGGTGTTGAAGACGACTCTGGTCATCTGTGTTAAAG
1 AGGAAATTGGGTCAATCTGGAGATAATT-TGGTGTTGAAGACGACTCTACTCATCCATGTTAAAG
* * * *
433260 AGTTCTAGCTGCTTTCAGGTAAATTGTTTGTTGAAGATGACATTGTTCCTTCT-TGTT
65 AGATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCT-TT
* *
433317 AAGGAAGTTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTGAAG
1 -AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTAAAG
* * *
433382 AGATCTAGTTGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTTTTCATTATCTTT
65 AGATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCTTT
*
433439 AGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
1 AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
433479 AGTTCTAGAA
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
121 38 0.27
122 100 0.70
123 4 0.03
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (121 bp):
AGGAAATTGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGACTCTACTCATCCATGTTAAAGA
GATCTAGCTGCTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCATTATCTTT
Found at i:434655 original size:7 final size:6
Alignment explanation
Indices: 434634--434697 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 6
434624 TCTGTCCTTA
* *
434634 TTTTCT TTTTCT TTTTCAT TTTTCTT CTTTTTT TTTTTT TTTTCT TTTT-T
1 TTTTCT TTTTCT TTTTC-T TTTTC-T -TTTTCT TTTTCT TTTTCT TTTTCT
*
434684 TGTTTCA TTTTCT T
1 T-TTTCT TTTTCT T
434698 CTATTCAGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 2 0.04
6 34 0.69
7 9 0.18
8 4 0.08
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:434671 original size:16 final size:16
Alignment explanation
Indices: 434642--434684 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
434632 TATTTTCTTT
**
434642 TTCTTTTTCATTTTTC
1 TTCTTTTTTTTTTTTC
*
434658 TTCTTTTTTTTTTTTTT
1 TTC-TTTTTTTTTTTTC
434675 TTCTTTTTTT
1 TTCTTTTTTT
434685 GTTTCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTC
Found at i:441216 original size:77 final size:79
Alignment explanation
Indices: 441084--441236 Score: 215
Period size: 77 Copynumber: 2.0 Consensus size: 79
441074 ATATAGTAGG
*
441084 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATTGATATTTAATTTGGAA-TAATT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTT-GAATTAATT
441148 AAATAAGATTTTAAA
65 AAATAAGATTTTAAA
** * *
441163 TAAACATT-AAAGGGTGTAATTTAGATTATAAGTC-TTTAA-TGTATATTTAATTTGAATTAATT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTG-ATATTTAATTTGAATTAATT
441225 AAATAAGATTTT
65 AAATAAGATTTT
441237 TATTAATTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
76 5 0.07
77 33 0.49
78 21 0.31
79 8 0.12
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.43
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTTGAATTAATTA
AATAAGATTTTAAA
Found at i:445111 original size:17 final size:18
Alignment explanation
Indices: 445076--445116 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
445066 TGTTTGTTTA
*
445076 TCGAAAG-GAAGTTTTTC
1 TCGAAAGAGAAGTTTCTC
445093 TCGAAAGAGAA-TTTCTC
1 TCGAAAGAGAAGTTTCTC
445110 TC-AAAGA
1 TCGAAAGA
445117 AAGGGAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (18 bp):
TCGAAAGAGAAGTTTCTC
Found at i:449276 original size:10 final size:10
Alignment explanation
Indices: 449242--449294 Score: 56
Period size: 11 Copynumber: 5.3 Consensus size: 10
449232 TATTTTTTTC
449242 AAAAAAA-CA
1 AAAAAAACCA
**
449251 AAAAAAGGC-
1 AAAAAAACCA
449260 AAAAAAACCAA
1 AAAAAAACC-A
449271 AAAAAAACCAA
1 AAAAAAACC-A
449282 AAAAAAACCA
1 AAAAAAACCA
449292 AAA
1 AAA
449295 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 13 0.34
10 5 0.13
11 20 0.53
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:456972 original size:32 final size:32
Alignment explanation
Indices: 456936--457043 Score: 135
Period size: 32 Copynumber: 3.4 Consensus size: 32
456926 GATTCTGTTG
*
456936 AGACCATGCCCAGCTGCAAGCTGATCCTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
***
456968 AGACCATATCCAGCTGCAAGCTGATCCTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
* * * *
457000 GGACCACGTCCAGCTGTAAGCTGATCTTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
*
457032 AGTCCACGCCCA
1 AGACCACGCCCA
457044 ACTACCCAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.23
Consensus pattern (32 bp):
AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
Found at i:462880 original size:32 final size:32
Alignment explanation
Indices: 462844--462904 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
462834 CCTGGGTCAT
*
462844 CTGATTCTATCGGGACCACGTCCAGCTACAAG
1 CTGATCCTATCGGGACCACGTCCAGCTACAAG
* * *
462876 CTGATCCTATCTGGTCCACGTCTAGCTAC
1 CTGATCCTATCGGGACCACGTCCAGCTAC
462905 CCAGGAGGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (32 bp):
CTGATCCTATCGGGACCACGTCCAGCTACAAG
Found at i:466548 original size:5 final size:5
Alignment explanation
Indices: 466534--466563 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
466524 ATCAAAGATA
*
466534 AAAAT AAAAT TAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
466564 TTGAATGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:466576 original size:21 final size:20
Alignment explanation
Indices: 466528--466578 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
466518 CCTTATATCA
466528 AAGATAAAAATAAAATTAAAT
1 AAGAT-AAAATAAAATTAAAT
* *
466549 AAAATAAAATAAAATTTGAAT
1 AAGATAAAATAAAA-TTAAAT
*
466570 GAGATAAAA
1 AAGATAAAA
466579 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AAGATAAAATAAAATTAAAT
Found at i:467356 original size:35 final size:32
Alignment explanation
Indices: 467286--467413 Score: 127
Period size: 32 Copynumber: 3.9 Consensus size: 32
467276 TTAGTTTGTG
*
467286 CAATAAATTAAAATGTTAGTAA-GTTAGTAAT-AA
1 CAATAAAATAAAA-GTTAG-AATGTTAGT-ATGAA
467319 CAATAAAAATCAAAAGTTAGTAATGTTAGTATGAA
1 CAAT-AAAAT-AAAAGTTAG-AATGTTAGTATGAA
* *
467354 CAATAAAATAAAAGTTAGAATATTAAT-TCGAA
1 CAATAAAATAAAAGTTAGAATGTTAGTAT-GAA
* *
467386 CGATAAAATAAATGTTAGAATGTTAGTA
1 CAATAAAATAAAAGTTAGAATGTTAGTA
467414 GATTAGTGAC
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.01
32 33 0.40
33 13 0.16
34 19 0.23
35 16 0.20
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTATGAA
Found at i:471758 original size:5 final size:5
Alignment explanation
Indices: 471748--471783 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
471738 AATAGTTATC
471748 TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA T
1 TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA T
471784 CGGAGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (5 bp):
TTAGA
Found at i:472213 original size:2 final size:2
Alignment explanation
Indices: 472206--472252 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
472196 ATAACTTTGT
472206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
472247 TA TA TA
1 TA TA TA
472253 GCTTGACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:473488 original size:15 final size:16
Alignment explanation
Indices: 473462--473492 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
473452 TGGGTATGCA
473462 GAGGAGGAAGAAGGAG
1 GAGGAGGAAGAAGGAG
473478 GAGGA-GAAGAAGGAG
1 GAGGAGGAAGAAGGAG
473493 AAGAAGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (16 bp):
GAGGAGGAAGAAGGAG
Found at i:473493 original size:9 final size:9
Alignment explanation
Indices: 473463--473502 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
473453 GGGTATGCAG
473463 AGGAGGAAGA
1 AGGA-GAAGA
473473 AGGAG--G-
1 AGGAGAAGA
473479 AGGAGAAGA
1 AGGAGAAGA
473488 AGGAGAAGA
1 AGGAGAAGA
473497 AGGAGA
1 AGGAGA
473503 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.19
7 1 0.04
8 1 0.04
9 16 0.59
10 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (9 bp):
AGGAGAAGA
Found at i:474652 original size:31 final size:29
Alignment explanation
Indices: 474559--474831 Score: 122
Period size: 29 Copynumber: 9.4 Consensus size: 29
474549 AACACTTATT
*
474559 AAATATATTTTACTT-TTATTTTAAATTAA
1 AAATATATTTTA-TTCTTATTTTAATTTAA
* *
474588 AAATATTTTTTAATCTTATTTTAATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* *
474617 AAATATATTTTATTCTTATCTTAATTTTTAC
1 AAATATATTTTATTCTTATTTTAA--TTTAA
* ** * *
474648 AAATATATTTAATTAAATCCACATATTAAAATTAA
1 AAATATA-TT--TT--ATTCTTAT-TTTAATTTAA
** * *
474683 AAA-A-A--ACATTC-TATCTTAAAATT--
1 AAATATATTTTATTCTTAT-TTTAATTTAA
474706 AAATAT-TTTTATT-TTAATTTTAATTTAA
1 AAATATATTTTATTCTT-ATTTTAATTTAA
* **
474734 AAATATATTTTAATCTTATTTTAGCTT-A
1 AAATATATTTTATTCTTATTTTAATTTAA
* * * *
474762 AAATGTATTTTTATTTTTATGTTAATTTATG
1 AAATATA-TTTTATTCTTATTTTAATTTA-A
*
474793 AAATATATTTGACTT-TTATTTTAATTT-A
1 AAATATATTTTA-TTCTTATTTTAATTTAA
*
474821 AGATATATTTT
1 AAATATATTTT
474832 TAAAAGTTAA
Statistics
Matches: 182, Mismatches: 39, Indels: 47
0.68 0.15 0.18
Matches are distributed among these distances:
23 3 0.02
24 1 0.01
25 10 0.05
26 13 0.07
27 2 0.01
28 23 0.13
29 74 0.41
30 17 0.09
31 19 0.10
32 2 0.01
33 1 0.01
34 3 0.02
35 6 0.03
36 5 0.03
37 3 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAATTTAA
Found at i:474743 original size:30 final size:28
Alignment explanation
Indices: 474708--474833 Score: 119
Period size: 30 Copynumber: 4.3 Consensus size: 28
474698 TTAAAATTAA
474708 ATATTTTTATTTTAATTTTAATTTAAAAAT
1 ATATTTTTATTTT-ATTTTAATTT-AAAAT
* * **
474738 ATATTTTAATCTTATTTTAGCTTAAAAT
1 ATATTTTTATTTTATTTTAATTTAAAAT
* *
474766 GTATTTTTATTTTTATGTTAATTTATGAAAT
1 ATATTTTTA-TTTTATTTTAATTTA--AAAT
* *
474797 ATA-TTTGACTTTTATTTTAATTTAAGAT
1 ATATTTTTA-TTTTATTTTAATTTAAAAT
474825 ATATTTTTA
1 ATATTTTTA
474834 AAAGTTAATA
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
28 18 0.24
29 23 0.30
30 29 0.38
31 6 0.08
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (28 bp):
ATATTTTTATTTTATTTTAATTTAAAAT
Found at i:474812 original size:59 final size:58
Alignment explanation
Indices: 474708--474833 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 58
474698 TTAAAATTAA
* * *
474708 ATATTTTTATTTTAATTTTAATTTAAAAATATATTTTAATCTTATTTTAGCTTAAAAT
1 ATATTTTTATTTTAATGTTAATTTAAAAATATATTTGAATCTTATTTTAACTTAAAAT
* * * * * * *
474766 GTATTTTTATTTTTATGTTAATTTATGAAATATATTTGACTTTTATTTTAATTTAAGAT
1 ATATTTTTATTTTAATGTTAATTTA-AAAATATATTTGAATCTTATTTTAACTTAAAAT
474825 ATATTTTTA
1 ATATTTTTA
474834 AAAGTTAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
58 22 0.39
59 34 0.61
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (58 bp):
ATATTTTTATTTTAATGTTAATTTAAAAATATATTTGAATCTTATTTTAACTTAAAAT
Found at i:474914 original size:10 final size:10
Alignment explanation
Indices: 474868--474916 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
474858 ATATATATAT
474868 ATAAAGTTAAA
1 ATAAA-TTAAA
474879 ATAAGATTAAA
1 ATAA-ATTAAA
* *
474890 ATATATTTTAA
1 ATA-AATTAAA
474901 ATAAATTAAA
1 ATAAATTAAA
474911 ATAAAT
1 ATAAAT
474917 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 11 0.34
11 19 0.59
12 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:474943 original size:20 final size:18
Alignment explanation
Indices: 474917--474954 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
474907 TAAAATAAAT
474917 ATATTTTTTAATGTTAAG
1 ATATTTTTTAATGTTAAG
474935 ATATTTTTTAATGTTAAG
1 ATATTTTTTAATGTTAAG
474953 AT
1 AT
474955 GTGAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
ATATTTTTTAATGTTAAG
Found at i:474965 original size:19 final size:19
Alignment explanation
Indices: 474923--474979 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
474913 AAATATATTT
* **
474923 TTTAATGTTAAGATAT-TT
1 TTTAATGTTAAGATGTGAA
474941 TTTAATGTTAAGATGTGAA
1 TTTAATGTTAAGATGTGAA
*
474960 TTTAATTTTATA-ATGTGAA
1 TTTAATGTTA-AGATGTGAA
474979 T
1 T
474980 CTAAACTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.45
19 17 0.52
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
TTTAATGTTAAGATGTGAA
Found at i:478016 original size:3 final size:3
Alignment explanation
Indices: 478008--478036 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
477998 GGCTCAAACT
478008 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
478037 CCTATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:482306 original size:26 final size:26
Alignment explanation
Indices: 482277--482328 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
482267 CAAAATAAAA
*
482277 TAGTATAGTA-AAATTATTTCAGTTTT
1 TAGTATAGTAGAAA-TATTTCACTTTT
*
482303 TAGTTTAGTAGAAATATTTCACTTTT
1 TAGTATAGTAGAAATATTTCACTTTT
482329 GAAGAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.50
Consensus pattern (26 bp):
TAGTATAGTAGAAATATTTCACTTTT
Found at i:484814 original size:16 final size:16
Alignment explanation
Indices: 484788--484843 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
484778 TTTATATATA
484788 TATATTTTAATTATTAT
1 TATA-TTTAATTATTAT
* *
484805 TATATTTAATAATTAA
1 TATATTTAATTATTAT
*
484821 TAT-TATTAGTTATTAT
1 TATAT-TTAATTATTAT
*
484837 TAAATTT
1 TATATTT
484844 TTGATTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 25 0.81
17 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATATTTAATTATTAT
Found at i:494523 original size:27 final size:27
Alignment explanation
Indices: 494493--494548 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
494483 ATCTGAATGT
494493 TAGAATAAAGCTAGGGATTTGTGATTA
1 TAGAATAAAGCTAGGGATTTGTGATTA
494520 TAGAATAAAGCTAGGGATTTGTGATTA
1 TAGAATAAAGCTAGGGATTTGTGATTA
494547 TA
1 TA
494549 ATAAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (27 bp):
TAGAATAAAGCTAGGGATTTGTGATTA
Found at i:494871 original size:37 final size:37
Alignment explanation
Indices: 494830--494909 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
494820 CGTACCGTGC
* * *
494830 CATCCCGTAACCTGTAATTTTAGGAATTGTCGTTTTT
1 CATCCCGTAACCCGTAATTTCAAGAATTGTCGTTTTT
**
494867 CATCCCGTCCCCCGTAATTTCAAGAATTGTCGTTTTT
1 CATCCCGTAACCCGTAATTTCAAGAATTGTCGTTTTT
*
494904 CGTCCC
1 CATCCC
494910 CGTCCTCGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.39
Consensus pattern (37 bp):
CATCCCGTAACCCGTAATTTCAAGAATTGTCGTTTTT
Found at i:496673 original size:107 final size:108
Alignment explanation
Indices: 496486--496706 Score: 417
Period size: 107 Copynumber: 2.1 Consensus size: 108
496476 GTTCCTCTTC
496486 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
1 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
* *
496551 ATACAAGCTCAATCGGCTTTGATTCTTGATAGCGGGATGACAT
66 AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
496594 ACTTACCATTGA-TTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
1 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
496658 AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
66 AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
496701 ACTTAC
1 ACTTAC
496707 AGAACCTCTA
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 99 0.89
108 12 0.11
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (108 bp):
ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
Found at i:498594 original size:554 final size:548
Alignment explanation
Indices: 497551--498655 Score: 2156
Period size: 554 Copynumber: 2.0 Consensus size: 548
497541 TCCATGTGGC
497551 CTTTTTTTCAACCTTAAATTCTGTCGTTTTCCCCTCCGAATCACTAGAATTAGATATTTTTTACT
1 CTTTTTTTCAACCTTAAATTCTGTCGTTTTCCCCTCCGAATCACTAGAATTAGATATTTTTTACT
497616 ATTTATGGTAATATTTCGATTGTCAATTAGGAAGTCAATTTAAATCCGATTTAAGTCGGATTTTT
66 ATTTATGGTAATATTTCGATTGTCAATTAGGAAGTCAATTTAAATCCGATTTAAGTCGGATTTTT
497681 TGGAGATTGCTTATTTATTTCGAATTTCAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGAC
131 TGGAGATTGCTTATTTATTTCGAATTTCAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGAC
497746 AAATTCGAATAAAACGATTTTTGGCTATAAGAGTCCGGCTTGTGGACTGATTTTGGTATTGTTTG
196 AAATTCGAATAAAACGATTTTTGGCTATAAGAGTCCGGCTTGTGGACTGATTTTGGTATTGTTTG
497811 ATTTGATAATATTTATTAAACCCTAGAGACTTTTTTCTCTGGATTTTTTTGGGCGAATTTTCTCT
261 ATTTGATAATATTTATTAAACCCTAGAGACTTTTTTCTCTGGATTTTTTTGGGCGAATTTTCTCT
497876 TGTGAATCATCTGTTGGAGCGCTTGCAGGATAATCATTATTCTGTCTGACGTCAAACGGGAACGA
326 TGTGAATCATCTGTTGGAGCGCTTGCAGGATAATCATTATTCTGTCTGACGTCAAACGGGAACGA
497941 CCACATTAACATGGTGTACATTTCTGGATAGCATTCATTCATGGAAATTTACGATAGATGATTTA
391 CCACATTAACATGGTGTACATTTCTGGATAGCATTCATTCATGGAAATTTACGATAGATGATTTA
498006 GTGTCGTGAATGAGGCCAATTTTGTTTACTGTGGCATTTTGATCGGCTTGGATTTGCTTGTGTCT
456 GTGTCGTGAATGAGGCCAATTTTGTTTACTGTGGCATTTTGATCGGCTTGGATTTGCTTGTGTCT
498071 GAAAACTGCACACCCTTGATTTTTCGTA
521 GAAAACTGCACACCCTTGATTTTTCGTA
498099 CTTTTTTTCAACCTTAAATTCTGTCGTTTTCCCCTCCGAATCACTAGAATTAGATATTTTTTACT
1 CTTTTTTTCAACCTTAAATTCTGTCGTTTTCCCCTCCGAATCACTAGAATTAGATATTTTTTACT
498164 ATTTATGGTAATATTTCGATTGTCAATTAGGAAGTCAATTTAAATCCGATTTAAGTCGGATTTTT
66 ATTTATGGTAATATTTCGATTGTCAATTAGGAAGTCAATTTAAATCCGATTTAAGTCGGATTTTT
498229 TGGAGATTGCTTATTTTATTTCGAATTTCAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGA
131 TGGAGATTGCTTA-TTTATTTCGAATTTCAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGA
498294 CAAAATTCGAATAAAAACGATTTTTGGCTATAAGAGTCCGGCTTGTGGACTGATTTTGGTATTGT
195 C-AAATTCGAAT-AAAACGATTTTTGGCTATAAGAGTCCGGCTTGTGGACTGATTTTGGTATTGT
498359 TTGATTTGATAATATTTTATTAAACCCTAGAGACTTTTTTTTCTCTGGATTTTTTTGGGCGAATT
258 TTGATTTGATAATA-TTTATTAAACCCTAGAGAC--TTTTTTCTCTGGATTTTTTTGGGCGAATT
498424 TTCTCTTGTGAATCATCTGTTGGAGCGCTTGCAGGATAATCATTATTCTGTCTGACGTCAAACGG
320 TTCTCTTGTGAATCATCTGTTGGAGCGCTTGCAGGATAATCATTATTCTGTCTGACGTCAAACGG
498489 GAACGACCACATTAACATGGTGTACATTTCTGGATAGCATTCATTCATGGAAATTTACGATAGAT
385 GAACGACCACATTAACATGGTGTACATTTCTGGATAGCATTCATTCATGGAAATTTACGATAGAT
498554 GATTTAGTGTCGTGAATGAGGCCAATTTTGTTTACTGTGGCATTTTGATCGGCTTGGATTTGCTT
450 GATTTAGTGTCGTGAATGAGGCCAATTTTGTTTACTGTGGCATTTTGATCGGCTTGGATTTGCTT
498619 GTGTCTGAAAACTGCACACCCTTGATTTTTCGTA
515 GTGTCTGAAAACTGCACACCCTTGATTTTTCGTA
498653 CTT
1 CTT
498656 ATTTGAATGT
Statistics
Matches: 551, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
548 143 0.26
549 52 0.09
550 10 0.02
551 66 0.12
552 19 0.03
554 261 0.47
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (548 bp):
CTTTTTTTCAACCTTAAATTCTGTCGTTTTCCCCTCCGAATCACTAGAATTAGATATTTTTTACT
ATTTATGGTAATATTTCGATTGTCAATTAGGAAGTCAATTTAAATCCGATTTAAGTCGGATTTTT
TGGAGATTGCTTATTTATTTCGAATTTCAATTTAGAGTGATTTTCGGGATTTTGCTATTTTTGAC
AAATTCGAATAAAACGATTTTTGGCTATAAGAGTCCGGCTTGTGGACTGATTTTGGTATTGTTTG
ATTTGATAATATTTATTAAACCCTAGAGACTTTTTTCTCTGGATTTTTTTGGGCGAATTTTCTCT
TGTGAATCATCTGTTGGAGCGCTTGCAGGATAATCATTATTCTGTCTGACGTCAAACGGGAACGA
CCACATTAACATGGTGTACATTTCTGGATAGCATTCATTCATGGAAATTTACGATAGATGATTTA
GTGTCGTGAATGAGGCCAATTTTGTTTACTGTGGCATTTTGATCGGCTTGGATTTGCTTGTGTCT
GAAAACTGCACACCCTTGATTTTTCGTA
Found at i:507669 original size:82 final size:81
Alignment explanation
Indices: 507500--507792 Score: 293
Period size: 82 Copynumber: 3.6 Consensus size: 81
507490 AGTTGTGCCA
* * * * * * * *
507500 TTTATTACAAAAACATCGGTAAGGTGCATGACTATAGCGACGTTTATTACAAAAGCGCTGCTAAA
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTA-T-CAAAAACACCGCT-AA
507565 GTGCATGATTATTGCGGTG
63 GTGCATGATTATTGCGGTG
* * *
507584 TTTATTACAAAAATACCGCTAAAGTGCATGATTATTGCAGCGTTTATCAAAAACACCGCTAAGGT
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCAAAAACACCGCTAA-GT
* * *
507649 GCATGACTATTGTGGCG
65 GCATGATTATTGCGGTG
* * * * * * * *
507666 TTTACTGCAAAAACATCACTAAAGTGCATGACTATTGCGGTGTTTATTACAAAACACCACTAAAT
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCA-AAAACACCGCTAAGT
*
507731 GCATGATTATTGCGGTA
65 GCATGATTATTGCGGTG
* * *
507748 TTTA-TA-AAAAATACCGCTAAAGTGCATAACTATTGCGGCATTTAT
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTAT
507793 TACAAAAATA
Statistics
Matches: 171, Mismatches: 36, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
80 33 0.19
81 3 0.02
82 84 0.49
83 13 0.08
84 38 0.22
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (81 bp):
TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCAAAAACACCGCTAAGTG
CATGATTATTGCGGTG
Found at i:507803 original size:42 final size:42
Alignment explanation
Indices: 507500--507800 Score: 317
Period size: 42 Copynumber: 7.3 Consensus size: 42
507490 AGTTGTGCCA
* * * * *
507500 TTTATTACAAAAACATCGGTAAGGTGCATGACTATAGCGACG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * * * *
507542 TTTATTACAAAAGCGCTGCTAAAGTGCATGATTATTGCGGTG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * *
507584 TTTATTACAAAAATACCGCTAAAGTGCATGATTATTGCAGCG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* *
507626 TTTA-T-CAAAAACACCGCTAAGGTGCATGACTATTGTGGCG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * * * *
507666 TTTACTGCAAAAACATCACTAAAGTGCATGACTATTGCGGTG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * **
507708 TTTATTAC-AAAACACCACTAAA-TGCATGATTATTGCGGTA
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * *
507748 TTTA-TA-AAAAATACCGCTAAAGTGCATAACTATTGCGGCA
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
507788 TTTATTACAAAAA
1 TTTATTACAAAAA
507801 TACTGCCTTA
Statistics
Matches: 217, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
39 14 0.06
40 73 0.34
41 17 0.08
42 113 0.52
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
Found at i:508767 original size:39 final size:38
Alignment explanation
Indices: 508724--508991 Score: 269
Period size: 37 Copynumber: 6.9 Consensus size: 38
508714 AAAGTTTTTG
* * *
508724 AATATATATATATAATATAG-TTTTGAAAAAAATTGGAAA
1 AATATATATA-AT-ATATAGTTTTTGAAAACATTTTGAAA
*
508763 AATATATATAATATATAGCTTTTGAAAACATTTTGAAAACCTA
1 AATATATATAATATATAGTTTTTGAAAACATTTTG--AA---A
**
508806 TATATAATATATAATATATAGTTTTTG-AAATTTTTTG-AA
1 -A-AT-ATATATAATATATAGTTTTTGAAAACATTTTGAAA
508845 AATATATATAATATATAGTTTTTGAAAACATTTTGAAAAA
1 AATATATATAATATATAGTTTTTGAAAACATTTTG--AAA
*
508885 AATATATATAATATATAATTTTTGAAAACATTTTG-AA
1 AATATATATAATATATAGTTTTTGAAAACATTTTGAAA
* *
508922 AACATATATAATATATAGTTTTCGAAAACATTTTGAAA
1 AATATATATAATATATAGTTTTTGAAAACATTTTGAAA
* * *
508960 ACGTATATAT--TATATAGATTTTGAAAAGATTT
1 A-ATATATATAATATATAGTTTTTGAAAACATTT
508992 AAATGTATTT
Statistics
Matches: 197, Mismatches: 17, Indels: 32
0.80 0.07 0.13
Matches are distributed among these distances:
36 21 0.11
37 69 0.35
38 19 0.10
39 17 0.09
40 38 0.19
42 1 0.01
43 1 0.01
44 1 0.01
45 10 0.05
46 20 0.10
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (38 bp):
AATATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:508908 original size:122 final size:117
Alignment explanation
Indices: 508718--508938 Score: 327
Period size: 122 Copynumber: 1.8 Consensus size: 117
508708 TAATATAAAG
* * *
508718 TTTTTGAATATATATATATAATATAGTTTTGAAAAAAATTGGAAAAATATATATAATATATAGCT
1 TTTTTGAAAATATATATATAATATAGTTTTGAAAAAAATTGAAAAAATATATATAATATATAACT
508783 TTTGAAAACATTTTGAAAACCTATATATAATATATAATATATAGTTTTTGAAAT
66 TTTGAAAACATTTTGAAAA-C-ATATATAATATATAATATATAGTTTTTGAAAT
**
508837 TTTTTGAAAATATATATA-ATATATAGTTTTTGAAAACATTTTGAAAAAAATATATATAATATAT
1 TTTTTGAAAATATATATATA-ATATAG-TTTTGAAAA-AAATTG-AAAAAATATATATAATATAT
*
508901 AATTTTTGAAAACATTTTGAAAACATATATAATATATA
62 AACTTTTGAAAACATTTTGAAAACATATATAATATATA
508939 GTTTTCGAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
118 1 0.01
119 23 0.25
120 23 0.25
121 5 0.05
122 40 0.43
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (117 bp):
TTTTTGAAAATATATATATAATATAGTTTTGAAAAAAATTGAAAAAATATATATAATATATAACT
TTTGAAAACATTTTGAAAACATATATAATATATAATATATAGTTTTTGAAAT
Found at i:509014 original size:5 final size:5
Alignment explanation
Indices: 509004--509063 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
508994 ATGTATTTTA
* *
509004 TATAT TATAT TGTACA TATAT TATAT TATAGT ATAGTAT TATAT TATA-
1 TATAT TATAT TATA-T TATAT TATAT TATA-T -TA-TAT TATAT TATAT
509052 TATAT TAT-T TAT
1 TATAT TATAT TAT
509064 TATGGTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
4 8 0.17
5 27 0.59
6 6 0.13
7 3 0.07
8 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:509029 original size:21 final size:19
Alignment explanation
Indices: 509004--509052 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 19
508994 ATGTATTTTA
509004 TATATTATATTGTACATA-TAT
1 TATATTATA-TGT--ATAGTAT
509025 TATATTATA-GTATAGTAT
1 TATATTATATGTATAGTAT
509043 TATATTATAT
1 TATATTATAT
509053 ATATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 12 0.46
19 2 0.08
21 9 0.35
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TATATTATATGTATAGTAT
Found at i:518153 original size:17 final size:17
Alignment explanation
Indices: 518117--518160 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
518107 TCAAACATTC
*
518117 AACACACAAAATATCCA
1 AACACATAAAATATCCA
518134 AACA-ATAAAATATCCAA
1 AACACATAAAATATCC-A
518151 AACACATAAA
1 AACACATAAA
518161 TCCATCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.64, C:0.23, G:0.00, T:0.14
Consensus pattern (17 bp):
AACACATAAAATATCCA
Found at i:518161 original size:17 final size:16
Alignment explanation
Indices: 518120--518161 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
518110 AACATTCAAC
518120 ACACA-AAATATCCAA
1 ACACATAAATATCCAA
518135 ACA-ATAAAATATCCAAA
1 ACACAT-AAATATCC-AA
518152 ACACATAAAT
1 ACACATAAAT
518162 CCATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.13
16 8 0.35
17 9 0.39
18 2 0.09
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (16 bp):
ACACATAAATATCCAA
Found at i:519556 original size:12 final size:13
Alignment explanation
Indices: 519539--519571 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
519529 AATGGGCAAA
*
519539 TTTGAAAACT-AT
1 TTTGAAAACTAAG
519551 TTTGAAAACTAAG
1 TTTGAAAACTAAG
519564 TTTGAAAA
1 TTTGAAAA
519572 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTAAG
Done.