Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013543.1 Kokia drynarioides strain JFW-HI SEQ_128569, 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: 319678
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 376 characters in sequence are not A, C, G, or T
Found at i:158 original size:4 final size:4
Alignment explanation
Indices: 151--193 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
141 TTCTTCCTTC
*
151 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
194 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:190 original size:11 final size:11
Alignment explanation
Indices: 148--204 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
138 TCCTTCTTCC
*
148 TTCTTCTTTCT
1 TTCTTTTTTCT
159 TTCTTTCTTTCTT
1 TTCTTT-TTTC-T
172 TCTCTTTTTTCT
1 T-TCTTTTTTCT
*
184 TTCTTTTTTCC
1 TTCTTTTTTCT
*
195 TTCATTTTTC
1 TTCTTTTTTC
205 GTTGGTCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:2521 original size:3 final size:3
Alignment explanation
Indices: 2482--2508 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2472 ATGGAGCCCG
2482 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
2509 GGGCTGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:9777 original size:25 final size:26
Alignment explanation
Indices: 9738--9788 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
9728 ACTTTAATTT
9738 TTTTTTTAAATTTTGAAT-ATTTTTA
1 TTTTTTTAAATTTTGAATAATTTTTA
*
9763 TTTTTTT-AATATTTGTATAATTTTTA
1 TTTTTTTAAAT-TTTGAATAATTTTTA
9789 AATTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 13 0.57
26 7 0.30
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTTAAATTTTGAATAATTTTTA
Found at i:10351 original size:30 final size:31
Alignment explanation
Indices: 10312--10379 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
10302 TAAAAAAAAT
* *
10312 AATTCAACTC-TTTTCAAAGATTGATGA-TCA
1 AATTTAACTCTTTTTAAAAGATTGA-GAGTCA
*
10342 AATTTAACTCTTTTTAAAAGGTTGAGAGTCA
1 AATTTAACTCTTTTTAAAAGATTGAGAGTCA
10373 AATTTAA
1 AATTTAA
10380 TTAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (31 bp):
AATTTAACTCTTTTTAAAAGATTGAGAGTCA
Found at i:20401 original size:11 final size:11
Alignment explanation
Indices: 20385--20410 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20375 ATTGAAGTAG
20385 GTTGGCGTACA
1 GTTGGCGTACA
20396 GTTGGCGTACA
1 GTTGGCGTACA
20407 GTTG
1 GTTG
20411 TGAACAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.38, T:0.31
Consensus pattern (11 bp):
GTTGGCGTACA
Found at i:24687 original size:3 final size:3
Alignment explanation
Indices: 24681--24723 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
24671 TTATTATCAC
* * *
24681 ATT ATT ATT ATT ATT ATT ATC ATT AAT ATT ATA ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
24724 TAAAACATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:30506 original size:28 final size:28
Alignment explanation
Indices: 30461--30523 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
30451 TTTAGCTTCT
* * *
30461 ATATATGGTCAGTCTTGCCGCTTGAATG
1 ATATATGGTCAGTCTTGCCGCCTAAATA
*
30489 ATATATGGTC-GATTTTGCCGCCTAAATA
1 ATATATGGTCAG-TCTTGCCGCCTAAATA
30517 ATATATG
1 ATATATG
30524 ATCGGTCCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (28 bp):
ATATATGGTCAGTCTTGCCGCCTAAATA
Found at i:30886 original size:457 final size:449
Alignment explanation
Indices: 30071--31424 Score: 1343
Period size: 457 Copynumber: 3.0 Consensus size: 449
30061 TACATTGTCA
* * * *
30071 ATCCTACCACCTGAGTATTATAGTGTACTAAAGTTAGAAAAT-AAAAGATTAACCGACTTCATAG
1 ATCCTACCGCCTGAGTATTATAGTGCACTAAAGTTAAAAAATAAAAAG-TTAACCGACTTTATAG
* * ** *
30135 AGTTGGTGTAACATTACTTGTAAGTCCTAAGTCTTTTGTAGTGGGTGCGTTAAACTCGTCGAGTT
65 AATTGGTGTAACATTACTTGTAAGTCCTAAATCTTTTGTAGT-GGT--GTT-GGCTCATCGAGTT
* * * *
30200 TCCAACATTTAACATTTCATTTCCATTTGTCTACTATTTTTTTCCTTTAGTAGTTTTCACGAGAG
126 TCCAACATCTAACATTTTATTTCCATCTGTCTACTA-TTTTTACCTTTAGTAGTTTTCACGAGAG
*
30265 AAGATTAAAATGAA-TTGAGAGAAACAAGTAAATTCAATTTCCCAACTTATACGTATAAAAAT-G
190 AAGATTAAAATGAATTTGA-AGAAACAAGTAAATTCAATTT-CCAACATATACGTATAAAAATGG
* * * *
30328 AGCATATTATAACAACTTCATG-AAGAGACAAATCGTT-AAAGTCCATAAATAAAAGGTGTTCTT
253 A-CATATTA-AA-AACTTCAAGCAA-AAACAAATCGTTCAAA-TCAATAAATAAAATGTGTTCTT
* * * * * * *
30391 TTCTCTTGTAATTGTAA-TTCTCGATTAAGCCTTAGGTTTTTAGGTACTTAATGCATTTGGTTTA
313 TTCTCTTGTAATTGTAAGTCCTCGAATAAACCTTAGGTTTTTAAGTACTTAATACACTTGGATTA
* * * * ** * * *
30455 GCTTCTATATATGGTCAGTCT-TGCCGCTTGAATGATATATGGTCGATTTTGCC-GCCTAAATAA
378 GATT-TATATATGAT-AGACTCTACCGCTTGAATGATATATAATCGACTCTACCAGCC-AAATAA
30518 TATATGATCG
440 TATATGATCG
* ** * *
30528 GTCCTGTCGCCTGAGCATTATAGTGCACTAAAGTTAAAAAAATAAAAAGTTAACCAACTTTATAG
1 ATCCTACCGCCTGAGTATTATAGTGCACTAAAGTT-AAAAAATAAAAAGTTAACCGACTTTATAG
* * ** *
30593 AATTGGTGTAACATTACTTGT-GGATCTTAAATCTTTTGTAGTCGGTGTATTGGGCTCATTAAAT
65 AATTGGTGTAACATTACTTGTAAG-TCCTAAATCTTTTGTAGT-GGTG--TT-GGCTCATCGAGT
* * *
30657 TTCCAATATCTAACATTTTATTTCCAACTGTCTACTATTTTTGCCTTTAGTAGTTTTCACGAGAG
125 TTCCAACATCTAACATTTTATTTCCATCTGTCTACTATTTTTACCTTTAGTAGTTTTCACGAGAG
* *
30722 AATATTAAAATGAATTTGAAGAAACAAGTAAATTCAATTTCCTAACATATGCGTATAAAAATGGA
190 AAGATTAAAATGAATTTGAAGAAACAAGTAAATTCAATTTCC-AACATATACGTATAAAAATGGA
* *
30787 CATATTAGAATAACTTCAAGCAAATACAAATCGTTCAAATCAATAAATAAAATGTATTCTTTTCT
254 CATATTA-AA-AACTTCAAGCAAAAACAAATCGTTCAAATCAATAAATAAAATGTGTTCTTTTCT
* *
30852 CTTGTAATTGTAAGTCCT-GAATAAATCTTAGGTTTTTAAGTACTTAGTACACTTGGATTAGATT
317 CTTGTAATTGTAAGTCCTCGAATAAACCTTAGGTTTTTAAGTACTTAATACACTTGGATTAGATT
* * * *
30916 TATTTATGATAGACTCTACTGCTTGAATGATATATAATCGACTCTACCATCCGAATAATATATGA
382 TATATATGATAGACTCTACCGCTTGAATGATATATAATCGACTCTACCAGCCAAATAATATATGA
30981 TCG
447 TCG
* * * * * * *
30984 ATCCTACCGTCTGAATATTTTAATGCCCTAAAGTT-AAAAATAAAAGGTTAACCGACTTTATAAA
1 ATCCTACCGCCTGAGTATTATAGTGCACTAAAGTTAAAAAATAAAAAGTTAACCGACTTTATAGA
* * *
31048 ATTGATGTAACATTACTTGTAAGTCCTAAATCCTCTGTAGTGG-G-TGGCTCATCGAGTTTCCAA
66 ATTGGTGTAACATTACTTGTAAGTCCTAAATCTTTTGTAGTGGTGTTGGCTCATCGAGTTTCCAA
* * * * *
31111 CATCTAACA---T-TTT-CATCTATCTA-TCATTTTTATCTTTAGTAATTTTTACGAGAAAAGAT
131 CATCTAACATTTTATTTCCATCTGTCTACT-ATTTTTACCTTTAGTAGTTTTCACGAGAGAAGAT
* * * * * * *
31170 TAAAATGAATTGGGAGAAATAAGTAAATTTAATTTCCCACATATACGCATAAAAATGAACATATT
195 TAAAATGAATTTGAAGAAACAAGTAAATTCAATTTCCAACATATACGTATAAAAATGGACATATT
* * * * * *
31235 -AAAACTTCAGGCAAAAACAAATTGTTCAAATCTATAAATAAAATATGTTCTTTACTCTTATAAT
260 AAAAACTTCAAGCAAAAACAAATCGTTCAAATCAATAAATAAAATGTGTTCTTTTCTCTTGTAAT
* * * * * * ** * *
31299 TGTTAGT-CTCGATTAAACTTTAAGTTTTTGACTTTTTAGTGCACTT-GAGTTA-ACTTTTATAT
325 TGTAAGTCCTCGAATAAACCTTAGGTTTTTAAGTACTTAATACACTTGGA-TTAGA--TTTATAT
* * * * * * * *
31361 ATGATCGATTCTATCGCCTGAATGATATATGATCGACTCTATC-GCCTGAATGATATATGATCG
387 ATGATAGACTCTACCGCTTGAATGATATATAATCGACTCTACCAGCC-AAATAATATATGATCG
31424 A
1 A
31425 CTCTATCGCT
Statistics
Matches: 753, Mismatches: 124, Indels: 57
0.81 0.13 0.06
Matches are distributed among these distances:
438 5 0.01
439 92 0.12
440 60 0.08
442 25 0.03
443 69 0.09
444 3 0.00
445 1 0.00
448 23 0.03
449 1 0.00
452 1 0.00
453 2 0.00
454 60 0.08
455 5 0.01
456 77 0.10
457 211 0.28
458 113 0.15
459 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (449 bp):
ATCCTACCGCCTGAGTATTATAGTGCACTAAAGTTAAAAAATAAAAAGTTAACCGACTTTATAGA
ATTGGTGTAACATTACTTGTAAGTCCTAAATCTTTTGTAGTGGTGTTGGCTCATCGAGTTTCCAA
CATCTAACATTTTATTTCCATCTGTCTACTATTTTTACCTTTAGTAGTTTTCACGAGAGAAGATT
AAAATGAATTTGAAGAAACAAGTAAATTCAATTTCCAACATATACGTATAAAAATGGACATATTA
AAAACTTCAAGCAAAAACAAATCGTTCAAATCAATAAATAAAATGTGTTCTTTTCTCTTGTAATT
GTAAGTCCTCGAATAAACCTTAGGTTTTTAAGTACTTAATACACTTGGATTAGATTTATATATGA
TAGACTCTACCGCTTGAATGATATATAATCGACTCTACCAGCCAAATAATATATGATCG
Found at i:30999 original size:28 final size:28
Alignment explanation
Indices: 30939--31000 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
30929 CTCTACTGCT
*
30939 TGAATGATATATAATCGACTCTACCATC
1 TGAATAATATATAATCGACTCTACCATC
* * *
30967 CGAATAATATATGATCGA-TCCTACCGTC
1 TGAATAATATATAATCGACT-CTACCATC
30995 TGAATA
1 TGAATA
31001 TTTTAATGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (28 bp):
TGAATAATATATAATCGACTCTACCATC
Found at i:31132 original size:17 final size:17
Alignment explanation
Indices: 31112--31145 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31102 AGTTTCCAAC
31112 ATCTAACATTTTCATCT
1 ATCTAACATTTTCATCT
* *
31129 ATCTATCATTTTTATCT
1 ATCTAACATTTTCATCT
31146 TTAGTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
ATCTAACATTTTCATCT
Found at i:31401 original size:28 final size:28
Alignment explanation
Indices: 31357--31467 Score: 159
Period size: 28 Copynumber: 4.0 Consensus size: 28
31347 GTTAACTTTT
*
31357 ATATATGATCGATTCTATCGCCTGAATG
1 ATATATGATCGACTCTATCGCCTGAATG
31385 ATATATGATCGACTCTATCGCCTGAATG
1 ATATATGATCGACTCTATCGCCTGAATG
* *
31413 ATATATGATCGACTCTATCGCTTGAATA
1 ATATATGATCGACTCTATCGCCTGAATG
* * * *
31441 ATATTTGGTCAACCCTATCGCCTGAAT
1 ATATATGATCGACTCTATCGCCTGAAT
31468 ATTATAATGC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (28 bp):
ATATATGATCGACTCTATCGCCTGAATG
Found at i:40073 original size:7 final size:6
Alignment explanation
Indices: 40041--40071 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
40031 ATAAATACAC
40041 TATAAA TATAAA TATAAA TATAAAA TATAAA
1 TATAAA TATAAA TATAAA TAT-AAA TATAAA
40072 ATTGAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TATAAA
Found at i:41233 original size:20 final size:22
Alignment explanation
Indices: 41208--41254 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41198 CATGTTAATA
41208 TATTTTT-ATCATG-TTTGTAT
1 TATTTTTAATCATGTTTTGTAT
* *
41228 TATTTTTAATTATGTTTTGTTT
1 TATTTTTAATCATGTTTTGTAT
41250 TATTT
1 TATTT
41255 GTTTTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 11 0.48
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (22 bp):
TATTTTTAATCATGTTTTGTAT
Found at i:48343 original size:225 final size:225
Alignment explanation
Indices: 47952--48395 Score: 816
Period size: 225 Copynumber: 2.0 Consensus size: 225
47942 CTAAAAGAAA
* * *
47952 ATCGAAAAATGACCTGAATCGAAGAGTTTAGATGGATTATAAAATTCAATTTTAAAACTTGCAGT
1 ATCGAAAAATGACCTGAATCAAAGAGTTTAGATGGATTATAAAATTCAAATTTAAAACTTGCAAT
48017 TATCAAAATTAAACAAAATTCTATTTTTTTATTTAATATATAACTAATTTAAATTTTTATCATGT
66 TATCAAAATTAAACAAAATTCTATTTTTTTATTTAATATATAACTAATTTAAATTTTTATCATGT
* *
48082 AATAAAATTAAATATTTTATATTTAAAACAGTGAAAATAATTTAAAGGTTTTTGAAAATTTGTTA
131 AATAAAATTAAATATTTTATATTTAAAACAGTGAAAATAACTTAAAGGTTTTTGAAAATTTATTA
48147 TTTTTTAAAAATATTTATAAAAAAAGTTGT
196 TTTTTTAAAAATATTTATAAAAAAAGTTGT
* *
48177 ATCGAAAAATGACCTGAATCAAAGAGTTTGGATGGATTATAAAATTCAAATTTAAAATTTGCAAT
1 ATCGAAAAATGACCTGAATCAAAGAGTTTAGATGGATTATAAAATTCAAATTTAAAACTTGCAAT
48242 TATCAAAATTAAACAAAATTCTATTTTTTTATTTAATATATAACTAATTTAAATTTTTATCATGT
66 TATCAAAATTAAACAAAATTCTATTTTTTTATTTAATATATAACTAATTTAAATTTTTATCATGT
*
48307 AATAAAATTAAATATTTTATATTTAAAACAGTGAAAATAACTTAAAGGTTTTTGAAAATTTATTG
131 AATAAAATTAAATATTTTATATTTAAAACAGTGAAAATAACTTAAAGGTTTTTGAAAATTTATTA
48372 TTTTTTAAAAATATTTATAAAAAA
196 TTTTTTAAAAATATTTATAAAAAA
48396 GTTTTAAAAT
Statistics
Matches: 211, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
225 211 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (225 bp):
ATCGAAAAATGACCTGAATCAAAGAGTTTAGATGGATTATAAAATTCAAATTTAAAACTTGCAAT
TATCAAAATTAAACAAAATTCTATTTTTTTATTTAATATATAACTAATTTAAATTTTTATCATGT
AATAAAATTAAATATTTTATATTTAAAACAGTGAAAATAACTTAAAGGTTTTTGAAAATTTATTA
TTTTTTAAAAATATTTATAAAAAAAGTTGT
Found at i:48807 original size:31 final size:30
Alignment explanation
Indices: 48751--48819 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
48741 TAAAAATATA
* *
48751 ATTTTTAAAAGATTAAATTTAAATTTTATT
1 ATTTTTAAAAAATTAAATATAAATTTTATT
48781 ATTTTTAAAAAAGTTAAA-ATACAATTTTATT
1 ATTTTTAAAAAA-TTAAATATA-AATTTTATT
48812 -TTTATTAA
1 ATTT-TTAA
48820 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTTAAAAAATTAAATATAAATTTTATT
Found at i:51734 original size:29 final size:30
Alignment explanation
Indices: 51702--51760 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
51692 TCACGTGTAT
*
51702 AATTGCAC-CAAATTAAAATTCATGTATAC
1 AATTACACACAAATTAAAATTCATGTATAC
* *
51731 AATTACACATTAAATTAAAGTTCATGTATA
1 AATTACACA-CAAATTAAAATTCATGTATA
51761 ATTTTGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
31 18 0.72
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (30 bp):
AATTACACACAAATTAAAATTCATGTATAC
Found at i:53446 original size:22 final size:21
Alignment explanation
Indices: 53421--53476 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
53411 TTTTCCTCGT
53421 AATTTTTGAAAATTTTATTTAA
1 AATTTTTG-AAATTTTATTTAA
* * *
53443 AATTTTTTGAATTTTTGTTTAT
1 AA-TTTTTGAAATTTTATTTAA
53465 AATTTTT-AAATT
1 AATTTTTGAAATT
53477 ATGTTTTGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 14 0.48
23 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
AATTTTTGAAATTTTATTTAA
Found at i:53455 original size:21 final size:22
Alignment explanation
Indices: 53423--53471 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53413 TTCCTCGTAA
*
53423 TTTTTGAAAATTTTATTTAAAAT
1 TTTTTG-AATTTTTATTTAAAAT
* *
53446 TTTTTGAATTTTTGTTTATAAT
1 TTTTTGAATTTTTATTTAAAAT
53468 TTTT
1 TTTT
53472 AAATTATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTTGAATTTTTATTTAAAAT
Found at i:56527 original size:22 final size:22
Alignment explanation
Indices: 56484--56527 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
56474 AATTTTTTAA
* * *
56484 TTTCATTGGTAAAATTTAAAAT
1 TTTCATCGATAAAATATAAAAT
*
56506 TTTCATCGATAAAATATCAAAT
1 TTTCATCGATAAAATATAAAAT
56528 AATTATTGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTCATCGATAAAATATAAAAT
Found at i:67393 original size:2 final size:2
Alignment explanation
Indices: 67388--67412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67378 ATCAATTTTT
67388 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
67413 TATGATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:68219 original size:29 final size:28
Alignment explanation
Indices: 68165--68335 Score: 69
Period size: 30 Copynumber: 5.8 Consensus size: 28
68155 AACTTGACAC
* *
68165 TTTTTCCTAATTTGGTACTTAAACTTTT
1 TTTTTACTAATTTGGTACCTAAACTTTT
* * **
68193 TTTTTACTCAATTTGGTTCCTAGACTTGACAC
1 TTTTTACT-AATTTGGTACCTAAACTT---TT
* * *
68225 TTTTTCCTAATTCGGTACCTAAAC-ATT
1 TTTTTACTAATTTGGTACCTAAACTTTT
** * * *
68252 TTTGGATCCAATTTGGTACTTGAACTTGGCATT
1 TTTTTA-CTAATTTGGTACCTAAACTT----TT
* *
68285 TTTTT--TATTTTGGTACCTAAGCTTTT
1 TTTTTACTAATTTGGTACCTAAACTTTT
*
68311 TTTTATATTCAATTTGGTACCTAAA
1 TTTT-TACT-AATTTGGTACCTAAA
68336 TTTATTAAAT
Statistics
Matches: 99, Mismatches: 30, Indels: 26
0.64 0.19 0.17
Matches are distributed among these distances:
26 6 0.06
27 4 0.04
28 21 0.21
29 16 0.16
30 27 0.27
31 13 0.13
32 7 0.07
33 5 0.05
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (28 bp):
TTTTTACTAATTTGGTACCTAAACTTTT
Found at i:68288 original size:59 final size:60
Alignment explanation
Indices: 68143--68332 Score: 172
Period size: 60 Copynumber: 3.2 Consensus size: 60
68133 TTAATATAAC
* * * ***
68143 ATTTAGTACCTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTTTACTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCGGTACCTAAACTTTTTGGATACTCA
*
68203 ATTTGGTTCCT-AGACTTGACACTTTTTCCTAATTCGGTACCTAAACATTTTTGGAT-C-CA
1 ATTTGGTACCTGA-ACTTGACACTTTTTCCTAATTCGGTACCTAAAC-TTTTTGGATACTCA
* * ** * * * ** *
68262 ATTTGGTACTTGAACTTGGCA-TTTTTTTTATTTTGGTACCTAAGCTTTTTTTTATATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCGGTACCTAAAC-TTTTTGGATACTCA
68322 ATTTGGTACCT
1 ATTTGGTACCT
68333 AAATTTATTA
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
58 26 0.25
59 19 0.18
60 54 0.51
61 6 0.06
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTCGGTACCTAAACTTTTTGGATACTCA
Found at i:69867 original size:10 final size:9
Alignment explanation
Indices: 69841--69866 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
69831 TCATAAACTC
69841 AAAAAAAAT
1 AAAAAAAAT
69850 AAAAAAAAT
1 AAAAAAAAT
69859 AAAAAAAA
1 AAAAAAAA
69867 AAATCTCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:71058 original size:87 final size:87
Alignment explanation
Indices: 70912--71084 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 87
70902 CCAAACCTTT
* * * * * *
70912 AATCGATGACCTACTTGTTGGCGTGAAGTTGACCACAACGTTCATCAATGATTCGTCAATCAATT
1 AATCGATGACCTACTTGCTAGCGTCAAGTTCACCACAACGTTCATCAATAATTCGTCAATCAACT
*
70977 CATCATTACAATCAATATCATG
66 CATCATCACAATCAATATCATG
* * ** *
70999 AATCGATGGCCTACTTGCTAGCGTCAAGTTCATCACGTCGTTCGTCAATAATTCGTCAATCAACT
1 AATCGATGACCTACTTGCTAGCGTCAAGTTCACCACAACGTTCATCAATAATTCGTCAATCAACT
*
71064 CATCATCATAATCAATATCAT
66 CATCATCACAATCAATATCAT
71085 CGTCCTGGAT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (87 bp):
AATCGATGACCTACTTGCTAGCGTCAAGTTCACCACAACGTTCATCAATAATTCGTCAATCAACT
CATCATCACAATCAATATCATG
Found at i:72088 original size:21 final size:21
Alignment explanation
Indices: 72062--72113 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
72052 ATTTTTATAC
72062 TTTTTATAATTTATATACATT
1 TTTTTATAATTTATATACATT
* * *
72083 TTTTTATATTTTTTATATATT
1 TTTTTATAATTTATATACATT
72104 TTTTTA-AATT
1 TTTTTATAATT
72114 CTTTTGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTATAATTTATATACATT
Found at i:72101 original size:23 final size:22
Alignment explanation
Indices: 72075--72118 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
72065 TTATAATTTA
* *
72075 TATACATTTTTTTATATT-TTT
1 TATATATTTTTTTAAATTCTTT
72096 TATATATTTTTTTAAATTCTTT
1 TATATATTTTTTTAAATTCTTT
72118 T
1 T
72119 GTATTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TATATATTTTTTTAAATTCTTT
Found at i:72118 original size:11 final size:10
Alignment explanation
Indices: 72053--72123 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
72043 TAATTTTTTA
*
72053 TTTTTATA-C
1 TTTTTATATT
72062 TTTTTATAATT
1 TTTTTAT-ATT
* * *
72073 TATATACATT
1 TTTTTATATT
72083 TTTTTATATT
1 TTTTTATATT
72093 TTTTATATATT
1 TTTT-TATATT
*
72104 TTTTTAAATT
1 TTTTTATATT
* *
72114 CTTTTGTATT
1 TTTTTATATT
72124 CTTTAATGCT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
9 7 0.15
10 27 0.56
11 14 0.29
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTTTATATT
Found at i:78683 original size:39 final size:40
Alignment explanation
Indices: 78612--78692 Score: 112
Period size: 39 Copynumber: 2.0 Consensus size: 40
78602 TAAAAAGTAT
78612 TTATATTAAAAACACTGACATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTGACATAAATATAATAAATATTTTA
* * *
78652 TTATATTAAAAA-ACAT-ATATAAATATGATAAATGTTTTA
1 TTATATTAAAAACAC-TGACATAAATATAATAAATATTTTA
78691 TT
1 TT
78693 GTTTTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 24 0.65
40 13 0.35
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (40 bp):
TTATATTAAAAACACTGACATAAATATAATAAATATTTTA
Found at i:78856 original size:16 final size:17
Alignment explanation
Indices: 78821--78858 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
78811 ATATAAATAT
*
78821 ATATATAATT-ATTTAC
1 ATATATAATTAATATAC
78837 ATATATAATTAATATA-
1 ATATATAATTAATATAC
78853 ATATAT
1 ATATAT
78859 TCGACCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATAATTAATATAC
Found at i:80078 original size:63 final size:63
Alignment explanation
Indices: 80005--80131 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
79995 GTTTTCTATT
80005 AATAGTGTTAATCAATTTTACTTATTTTCTTCAATATCAAGTGTATAAAGATTAAATCACTCG
1 AATAGTGTTAATCAATTTTACTTATTTTCTTCAATATCAAGTGTATAAAGATTAAATCACTCG
80068 AATAGTGTTAATCAATTTTACTTATTTTCTTCAATATCAAGTGTATAAAGATTAAATCACTCG
1 AATAGTGTTAATCAATTTTACTTATTTTCTTCAATATCAAGTGTATAAAGATTAAATCACTCG
80131 A
1 A
80132 TTCTATGTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (63 bp):
AATAGTGTTAATCAATTTTACTTATTTTCTTCAATATCAAGTGTATAAAGATTAAATCACTCG
Found at i:83681 original size:31 final size:31
Alignment explanation
Indices: 83614--83696 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
83604 AAATGATCAT
* **
83614 TGAAGTATTTGAAAG-TTTTCATTAAGTCAC
1 TGAACTATTTGAAAGTTTTTTTTTAAGTCAC
* *
83644 TAAACTATTTGAAAGTTTTTTTTTAATTCAC
1 TGAACTATTTGAAAGTTTTTTTTTAAGTCAC
**
83675 TGAACTATTCAAAAGTTTTTTT
1 TGAACTATTTGAAAGTTTTTTT
83697 GTCACTAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 13 0.30
31 31 0.70
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.47
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTTTTTTAAGTCAC
Found at i:115014 original size:18 final size:17
Alignment explanation
Indices: 114991--115030 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
114981 AAGAAATAAT
*
114991 TACATATAATTTAATTAA
1 TACATACAA-TTAATTAA
*
115009 TACATACAATTAATTTA
1 TACATACAATTAATTAA
115026 TACAT
1 TACAT
115031 CACACGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (17 bp):
TACATACAATTAATTAA
Found at i:118597 original size:15 final size:16
Alignment explanation
Indices: 118568--118616 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
118558 AGTGAAAAAT
* *
118568 ATTTTTAAATATTTTC
1 ATTTTAAAATATTTTA
118584 ATTTTAAAAT-TTTTA
1 ATTTTAAAATATTTTA
*
118599 ATTATTAAATTATTTTA
1 ATT-TTAAAATATTTTA
118616 A
1 A
118617 ATAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.25
16 15 0.54
17 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAAAATATTTTA
Found at i:133144 original size:43 final size:42
Alignment explanation
Indices: 133097--133192 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
133087 GATGTGAAAA
*
133097 ATTAAATAAA-AAATAAAAATAAATTTTTTTATAAATTTGAATG
1 ATTAAATAAATAAATAAAAAT-AA-TTTTTTATAAAATTGAATG
* * * *
133140 ATTAAATAAATTATTATAAATTATTTTTTATAAAATTGAATG
1 ATTAAATAAATAAATAAAAATAATTTTTTATAAAATTGAATG
*
133182 GTTAAATAAAT
1 ATTAAATAAAT
133193 TATTACACTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 28 0.61
43 11 0.24
44 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (42 bp):
ATTAAATAAATAAATAAAAATAATTTTTTATAAAATTGAATG
Found at i:133180 original size:42 final size:42
Alignment explanation
Indices: 133121--133215 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
133111 AAAAATAAAT
* *
133121 TTTTTTATAAATTTGAATGATTAAATAAATTATTATAAATTA
1 TTTTTTATAAAATTGAATGATTAAATAAATTATTACAAATTA
* **
133163 TTTTTTATAAAATTGAATGGTTAAATAAATTATTACACTTTA
1 TTTTTTATAAAATTGAATGATTAAATAAATTATTACAAATTA
133205 TTTTTTCATAA
1 TTTTTT-ATAA
133216 GAAATATAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (42 bp):
TTTTTTATAAAATTGAATGATTAAATAAATTATTACAAATTA
Found at i:139263 original size:31 final size:30
Alignment explanation
Indices: 139228--139293 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
139218 TAATAAAAAT
*
139228 AAAATTACATTTTGATTTTATT-AAAATTATA
1 AAAATTACA-TTTAATTTT-TTAAAAATTATA
**
139259 AAAATTTGATTTAATTTTTTAAAAATTATA
1 AAAATTACATTTAATTTTTTAAAAATTATA
139289 AAAAT
1 AAAAT
139294 ATAATAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 22 0.71
31 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
AAAATTACATTTAATTTTTTAAAAATTATA
Found at i:140247 original size:16 final size:16
Alignment explanation
Indices: 140214--140249 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
140204 GCCCTCAAAG
* *
140214 TTTAATTTTTTTTCAA
1 TTTAATTTTTTGTAAA
140230 TTTAATTTTTTGTAAA
1 TTTAATTTTTTGTAAA
140246 TTTA
1 TTTA
140250 CATTATGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTAATTTTTTGTAAA
Found at i:157637 original size:29 final size:30
Alignment explanation
Indices: 157579--157639 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
157569 TATTTAGAGG
157579 GTCCTTAGAGATATCTCCCATACCTATGTT
1 GTCCTTAGAGATATCTCCCATACCTATGTT
157609 GTCCTTAGAGATATC-CCCATACCTATGTT
1 GTCCTTAGAGATATCTCCCATACCTATGTT
157638 GT
1 GT
157640 TAACATGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (30 bp):
GTCCTTAGAGATATCTCCCATACCTATGTT
Found at i:164399 original size:19 final size:19
Alignment explanation
Indices: 164375--164413 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
164365 TAGTATCCGA
*
164375 TAAATATTAATTTTAAATT
1 TAAATATAAATTTTAAATT
*
164394 TAAATATAAATTTTATATT
1 TAAATATAAATTTTAAATT
164413 T
1 T
164414 GAGTGGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAATATAAATTTTAAATT
Found at i:165011 original size:18 final size:18
Alignment explanation
Indices: 164988--165030 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
164978 GAATAGATGT
164988 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
165006 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
165024 TTAATTA
1 TTAATTA
165031 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:184073 original size:47 final size:47
Alignment explanation
Indices: 184022--184111 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
184012 CCTAAGAATA
*
184022 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATTGAT
1 CTATCTATAATTAGTATTGGACAACGAAGAAAATCAGGGAGATTGAT
184069 CTATCTATAATTAGTATTGGACAACGAAGAAAATCAGGGAGAT
1 CTATCTATAATTAGTATTGGACAACGAAGAAAATCAGGGAGAT
184112 CGGTTTGCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (47 bp):
CTATCTATAATTAGTATTGGACAACGAAGAAAATCAGGGAGATTGAT
Found at i:190029 original size:2 final size:2
Alignment explanation
Indices: 190024--190070 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
190014 TCTCCCTTCA
* *
190024 CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT AT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
190066 CT CT C
1 CT CT C
190071 CATGTACACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:191580 original size:2 final size:2
Alignment explanation
Indices: 191573--191602 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
191563 ACAGAATTTG
191573 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
191603 TTGTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:195057 original size:18 final size:16
Alignment explanation
Indices: 195025--195068 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
195015 ATGGAATGAG
195025 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
195041 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
195055 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
195069 ATTCAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:195267 original size:14 final size:14
Alignment explanation
Indices: 195248--195278 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
195238 TAGATTTAAA
195248 AAATTTAATTAATT
1 AAATTTAATTAATT
*
195262 AAATTTATTTAATT
1 AAATTTAATTAATT
195276 AAA
1 AAA
195279 AATCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:199941 original size:21 final size:19
Alignment explanation
Indices: 199912--199954 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
199902 GCAATTTGGA
199912 GTAAAGACTTAAAAGTACTAT
1 GTAAAGACTTAAAA-T-CTAT
* *
199933 GTAATGACTTGAAATCTAT
1 GTAAAGACTTAAAATCTAT
199952 GTA
1 GTA
199955 TTTTGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (19 bp):
GTAAAGACTTAAAATCTAT
Found at i:202439 original size:16 final size:17
Alignment explanation
Indices: 202415--202463 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
202405 AATTTTTTTA
*
202415 TTATTAATT-TAAAATT
1 TTATAAATTATAAAATT
202431 TTATAAATTATAAAA-T
1 TTATAAATTATAAAATT
* *
202447 ATCTAAATTA-AAAATT
1 TTATAAATTATAAAATT
202463 T
1 T
202464 ATCAGAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAAATTATAAAATT
Found at i:202934 original size:17 final size:17
Alignment explanation
Indices: 202914--202990 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
202904 TTTAGATTTT
*
202914 AATTCATTTTAAGTTTA
1 AATTTATTTTAAGTTTA
* *
202931 AATTTATTATAAATTTA
1 AATTTATTTTAAGTTTA
* * **
202948 AGACTTGTTTGGAGTTTA
1 A-ATTTATTTTAAGTTTA
*
202966 AATTTATTTTAATTTTA
1 AATTTATTTTAAGTTTA
202983 AATTTATT
1 AATTTATT
202991 CTAAAATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
17 34 0.76
18 11 0.24
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAGTTTA
Found at i:203739 original size:21 final size:20
Alignment explanation
Indices: 203697--203741 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
203687 GCATTAATAG
* *
203697 TAAT-TAATAATTTTATTTA
1 TAATATAATAATATTATTAA
203716 TAATATAATAAATATTATTAA
1 TAATATAAT-AATATTATTAA
203737 TAATA
1 TAATA
203742 ATATTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATAATAATATTATTAA
Found at i:203746 original size:12 final size:12
Alignment explanation
Indices: 203691--203829 Score: 65
Period size: 12 Copynumber: 11.4 Consensus size: 12
203681 ATAAAGGCAT
*
203691 TAATAGTAATTAA
1 TAATATTAA-TAA
* * *
203704 TAATTTTATTTA
1 TAATATTAATAA
203716 TAATA-TAATAAA
1 TAATATTAAT-AA
*
203728 TATTATTAATAA
1 TAATATTAATAA
203740 TAATATTAATAA
1 TAATATTAATAA
* *
203752 TGACATTAATAA
1 TAATATTAATAA
203764 TAAATATCAGTAATAAA
1 T-AATAT---TAAT-AA
* *
203781 TGACATTAATAA
1 TAATATTAATAA
*
203793 -AA-ACTAAATAA
1 TAATA-TTAATAA
*
203804 -AATATTAATAT
1 TAATATTAATAA
203815 TAA-A-TAATAA
1 TAATATTAATAA
203825 TAATA
1 TAATA
203830 AAACTGAAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
10 9 0.09
11 19 0.20
12 40 0.42
13 17 0.18
16 7 0.07
17 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:203825 original size:13 final size:13
Alignment explanation
Indices: 203715--203831 Score: 50
Period size: 13 Copynumber: 9.1 Consensus size: 13
203705 AATTTTATTT
203715 ATAAT-ATAATAA
1 ATAATAATAATAA
* *
203727 ATATTATTAAT-A
1 ATAATAATAATAA
*
203739 ATAATATTAAT-A
1 ATAATAATAATAA
203751 ATGACATTAATAATAA
1 AT-A-A-TAATAATAA
*
203767 AT-ATCAGTAATAA
1 ATAAT-AATAATAA
* * *
203780 ATGACATTAATAA
1 ATAATAATAATAA
203793 A-AACT-A-AATAAA
1 ATAA-TAATAAT-AA
* *
203805 ATATTAATATTAA
1 ATAATAATAATAA
203818 ATAATAATAATAA
1 ATAATAATAATAA
203831 A
1 A
203832 ACTGAAAAGG
Statistics
Matches: 79, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
11 3 0.04
12 24 0.30
13 39 0.49
14 4 0.05
15 6 0.08
16 3 0.04
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:204063 original size:20 final size:20
Alignment explanation
Indices: 204038--204080 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
204028 AATCAACACC
204038 AATTTCTAAAGAACATTCGA
1 AATTTCTAAAGAACATTCGA
204058 AATTTCTAAAGAACATTCGA
1 AATTTCTAAAGAACATTCGA
204078 AAT
1 AAT
204081 ATGTCTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (20 bp):
AATTTCTAAAGAACATTCGA
Found at i:204960 original size:30 final size:30
Alignment explanation
Indices: 204915--205032 Score: 114
Period size: 30 Copynumber: 3.9 Consensus size: 30
204905 GGAGGTCTCT
* *
204915 AAACTGTCTAGAAATTATATTTTTAA-CCAT
1 AAACTTTCTA-AAATTATATTTTTAACCCAC
*
204945 AAACTTCTCTAAAATTATA-TTTTAACCCCC
1 AAACTT-TCTAAAATTATATTTTTAACCCAC
* *
204975 AAACTTTCTAAAAATTACATTTTTACCCCAC
1 AAACTTTCT-AAAATTATATTTTTAACCCAC
* * **
205006 GAACTTTCAAAAATTCCATTTTTAACC
1 AAACTTTCTAAAATTATATTTTTAACC
205033 TCGATTTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 9 0.12
30 45 0.61
31 20 0.27
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
AAACTTTCTAAAATTATATTTTTAACCCAC
Found at i:205011 original size:31 final size:30
Alignment explanation
Indices: 204915--205077 Score: 109
Period size: 30 Copynumber: 5.4 Consensus size: 30
204905 GGAGGTCTCT
* * * * **
204915 AAACTGTCTAGAAATTATATTTTTAACCAT
1 AAACTTTCTAAAAATTACATTTTTACCCCC
* *
204945 AAACTTCTCT-AAAATTATATTTTAACCCCC
1 AAACTT-TCTAAAAATTACATTTTTACCCCC
204975 AAACTTTCTAAAAATTACATTTTTACCCCAC
1 AAACTTTCTAAAAATTACATTTTTACCCC-C
* * * *
205006 GAACTTTC-AAAAATTCCATTTTTAACCTC
1 AAACTTTCTAAAAATTACATTTTTACCCCC
* * * *
205035 -GATTTATCCAAAAATTACCA-TTTTACCCTC
1 AAACTT-TCTAAAAATTA-CATTTTTACCCCC
*
205065 AAACTTTCCAAAA
1 AAACTTTCTAAAA
205078 TTCCAATTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.03
29 6 0.06
30 83 0.77
31 16 0.15
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTTCTAAAAATTACATTTTTACCCCC
Found at i:205157 original size:57 final size:57
Alignment explanation
Indices: 204979--205344 Score: 373
Period size: 57 Copynumber: 6.3 Consensus size: 57
204969 ACCCCCAAAC
* *
204979 TTTCTAAAAATTA-CATTTTTACCCCACGAACTTTCAAAAATTCCATTTTTAACCTCGATT
1 TTTCCAAAAATTACCA-TTTTA--CCTCGAACTTTCAAAAATTCCA-TTTTAACCTCGATT
* * * * *
205039 TATCCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCAATTTTGACCTTGATT
1 TTTCCAAAAATTACCATTTTA-CCTCGAACTTTCAAAAATTCC-ATTTTAACCTCGATT
* * *
205098 TTTCCAAAAAATACCATTTTACCTCGAACTTTCAAAAATTACATTTTAACCTTGATT
1 TTTCCAAAAATTACCATTTTACCTCGAACTTTCAAAAATTCCATTTTAACCTCGATT
* * * *
205155 TTTTC-AAAATTACTATTTTACCTTC-AACTTCCTAAAATTCCATTTTAACCTCGATT
1 TTTCCAAAAATTACCATTTTACC-TCGAACTTTCAAAAATTCCATTTTAACCTCGATT
*** * * * * *
205211 TTTTTTAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTAACCCCTA-T
1 TTTCCAAAAATTACCATTTTACCTC-GAACTTTCAAAAATTCCATTTTAACCTCGATT
* * * *
205268 TTTCCAAAAATTACCATTTTACCTCCGAACTTCCAAAAATTTCATTTTTGATCTCGATT
1 TTTCCAAAAATTACCATTTTACCT-CGAACTTTCAAAAATTCCA-TTTTAACCTCGATT
205327 TTTCC-AAAATTACCATTT
1 TTTCCAAAAATTACCATTT
205345 CCCCCAAGAT
Statistics
Matches: 259, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
56 47 0.18
57 71 0.27
58 66 0.25
59 56 0.22
60 17 0.07
61 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (57 bp):
TTTCCAAAAATTACCATTTTACCTCGAACTTTCAAAAATTCCATTTTAACCTCGATT
Found at i:205266 original size:29 final size:28
Alignment explanation
Indices: 204935--205263 Score: 121
Period size: 29 Copynumber: 11.3 Consensus size: 28
204925 GAAATTATAT
* **
204935 TTTTAACCATAAACTTCTCTAAAATTATA
1 TTTTAACCCTAAACTT-TCTAAAATTCCA
* *
204964 TTTTAACCCCCAAACTTTCTAAAAATTACA
1 TTTTAA-CCCTAAACTTTCT-AAAATTCCA
* * *
204994 TTTTTACCCCACGAACTTTCAAAAATTCCA
1 TTTTAACCCTA--AACTTTCTAAAATTCCA
** * *
205024 TTTTTAA-CCTCGATTTATCCAAAAATTACCA
1 -TTTTAACCCTAAACTT-T-CTAAAATT-CCA
*
205055 TTTT-ACCCTCAAACTTTCCAAAATTCCAA
1 TTTTAACCCT-AAACTTTCTAAAATTCC-A
* * * ** * *
205084 TTTTGACCTTGATTTTTCCAAAAAATACCA
1 TTTTAACCCTAAACTTT-C-TAAAATTCCA
* * *
205114 TTTT-A-CCTCGAACTTTCAAAAATTACA
1 TTTTAACCCT-AAACTTTCTAAAATTCCA
** * * *
205141 TTTTAA-CCTTGATTTTTTCAAAATTACTA
1 TTTTAACCCTAAACTTTCT-AAAATT-CCA
* * *
205170 TTTT-ACCTTCAACTTCCTAAAATTCCA
1 TTTTAACCCTAAACTTTCTAAAATTCCA
* *** *
205197 TTTTAACCTCGATTTTTTTTAAAATTACCA
1 TTTTAACC-CTAAACTTTCTAAAATT-CCA
*
205227 TTTTACCCCTAAACTTTCTAAAATTCCA
1 TTTTAACCCTAAACTTTCTAAAATTCCA
205255 TTTTAACCC
1 TTTTAACCC
205264 CTATTTTCCA
Statistics
Matches: 223, Mismatches: 55, Indels: 45
0.69 0.17 0.14
Matches are distributed among these distances:
27 22 0.10
28 39 0.17
29 70 0.31
30 67 0.30
31 25 0.11
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTTAACCCTAAACTTTCTAAAATTCCA
Found at i:205301 original size:29 final size:28
Alignment explanation
Indices: 205005--205308 Score: 156
Period size: 29 Copynumber: 10.6 Consensus size: 28
204995 TTTTACCCCA
*
205005 CGAACTTTCAAAAATT-CCATTTTTAACCT
1 CGAACTTCCAAAAATTACCA-TTTT-ACCT
**
205034 CGATTTATCCAAAAATTACCATTTTACCCT
1 CGAACT-TCCAAAAATTACCATTTTA-CCT
*
205064 CAAACTTTCC-AAAATT-CCAATTTTGACCT
1 CGAAC-TTCCAAAAATTACC-ATTTT-ACCT
* ** *
205093 TGATTTTTCCAAAAAATACCATTTTACCT
1 CGA-ACTTCCAAAAATTACCATTTTACCT
*
205122 CGAACTTTCAAAAATTA-CATTTTAACCT
1 CGAACTTCCAAAAATTACCATTTT-ACCT
* ** * *
205150 TGATTTTTTC-AAAATTACTATTTTACCTT
1 CGA-ACTTCCAAAAATTACCATTTTACC-T
*
205179 C-AACTTCCTAAAATT-CCATTTTAACCT
1 CGAACTTCCAAAAATTACCATTTT-ACCT
** *** *
205206 CGATTTTTTTTAAAATTACCATTTTACCC
1 CGA-ACTTCCAAAAATTACCATTTTACCT
* * * *
205235 CTAAACTTTCTAAAATT-CCATTTTAACCC
1 C-GAACTTCCAAAAATTACCATTTT-ACCT
* **
205264 CTATTTTCCAAAAATTACCATTTTACCT
1 CGAACTTCCAAAAATTACCATTTTACCT
205292 CCGAACTTCCAAAAATT
1 -CGAACTTCCAAAAATT
205309 TCATTTTTGA
Statistics
Matches: 210, Mismatches: 43, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
27 17 0.08
28 59 0.28
29 88 0.42
30 40 0.19
31 6 0.03
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (28 bp):
CGAACTTCCAAAAATTACCATTTTACCT
Found at i:205395 original size:172 final size:174
Alignment explanation
Indices: 205015--205407 Score: 462
Period size: 172 Copynumber: 2.3 Consensus size: 174
205005 CGAACTTTCA
205015 AAAATTCCATTTTTAACCTCG-ATTTATCCAAAAATTACCATTTTA-CCCTCAAACTTTCCAAAA
1 AAAATTCCATTTTTAACCTCGAATTT-TCCAAAAATTACCATTTTACCCCTCAAACTTTCCAAAA
* * *
205078 TTCCAATTTTGACCTTGATTTTTCCAAAAAATACCATTTTACCTCGAACTTTCAAAAATTACATT
65 TTCCAATTTTAACCCTGATTTTTCCAAAAAATACCATTTTACCTCGAACTTCCAAAAATTACATT
* * * ** * *
205143 TTAACCTTGATTTTTTCAAAATTACTATTTTACCTTCAACTTCCT
130 TTAACCTCGATTTTTCCAAAATTACCATTTTACCCCCAAATGCCT
* *** *
205188 AAAATTCCA-TTTTAACCTCGATTTTTTTTAAAATTACCATTTTACCCCT-AAACTTTCTAAAAT
1 AAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCCCTCAAACTTTCCAAAAT
* *
205251 TCC-ATTTTAACCCCT-A-TTTTCCAAAAATTACCATTTTACCTCCGAACTTCCAAAAATTTCAT
66 TCCAATTTTAA-CCCTGATTTTTCCAAAAAATACCATTTTACCT-CGAACTTCCAAAAATTACA-
* *
205313 TTTTGATCTCGATTTTTCCAAAATTACCA-TTT-CCCCCAAGATGCCT
128 TTTTAACCTCGATTTTTCCAAAATTACCATTTTACCCCCAA-ATGCCT
* * * * *
205359 AAAATTCCATTTTTAACCCCGAACTTTCCCAAAATTACAATTTTGCCCC
1 AAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCCC
205408 CGAGTGTCCA
Statistics
Matches: 186, Mismatches: 27, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
170 29 0.16
171 40 0.22
172 101 0.54
173 16 0.09
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.39
Consensus pattern (174 bp):
AAAATTCCATTTTTAACCTCGAATTTTCCAAAAATTACCATTTTACCCCTCAAACTTTCCAAAAT
TCCAATTTTAACCCTGATTTTTCCAAAAAATACCATTTTACCTCGAACTTCCAAAAATTACATTT
TAACCTCGATTTTTCCAAAATTACCATTTTACCCCCAAATGCCT
Found at i:205443 original size:27 final size:28
Alignment explanation
Indices: 205387--205447 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
205377 CCGAACTTTC
*
205387 CCAAAATTACAATTTTGCCCCCGAGTGT
1 CCAAAATTACAATTTTGACCCCGAGTGT
205415 CCAAAATTATC-ATTTT-ACCCCGAGTGT
1 CCAAAATTA-CAATTTTGACCCCGAGTGT
205442 CCAAAA
1 CCAAAA
205448 ATCGTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 16 0.52
28 14 0.45
29 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (28 bp):
CCAAAATTACAATTTTGACCCCGAGTGT
Found at i:207140 original size:21 final size:23
Alignment explanation
Indices: 207097--207140 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
207087 TTTAAATTTT
* *
207097 ATTATATTGATACTAATATTCAA
1 ATTATATTGATACTAAGACTCAA
207120 ATTA-ATTGA-ACTAAGACTCAA
1 ATTATATTGATACTAAGACTCAA
207141 CCAACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATTGATACTAAGACTCAA
Found at i:208771 original size:2 final size:2
Alignment explanation
Indices: 208764--208793 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
208754 GCATAAAAAC
208764 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
208794 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212053 original size:14 final size:14
Alignment explanation
Indices: 212030--212064 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
212020 TACAATATCC
*
212030 AAATAATAACAACA
1 AAATAGTAACAACA
212044 AAATAGTAACAACA
1 AAATAGTAACAACA
*
212058 TAATAGT
1 AAATAGT
212065 GAAATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:215933 original size:31 final size:29
Alignment explanation
Indices: 215866--215934 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
215856 ATGATAACGC
**
215866 AAGTGACTAAAATGTAACATTTCAAATAT
1 AAGTGACTAAAATGTAACATGACAAATAT
215895 AAGTGACTAAAATGTAACATGAGACAAACTA-
1 AAGTGACTAAAATGTAACAT--GACAAA-TAT
215926 AAGTGACTA
1 AAGTGACTA
215935 TTTTGGTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 20 0.57
31 13 0.37
32 2 0.06
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGACAAATAT
Found at i:218806 original size:21 final size:22
Alignment explanation
Indices: 218765--218818 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
218755 AAAAAAATAT
218765 ATATTTATATTATTTTAATTTA
1 ATATTTATATTATTTTAATTTA
218787 ATATTTAATATT-TTTT-ATTTA
1 ATATTT-ATATTATTTTAATTTA
*
218808 AAATTTTATAT
1 ATA-TTTATAT
218819 AATCATCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 13 0.45
23 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTATATTATTTTAATTTA
Found at i:230820 original size:2 final size:2
Alignment explanation
Indices: 230813--230848 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
230803 AACCGAAGTA
230813 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
230849 GCACTTAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231100 original size:11 final size:11
Alignment explanation
Indices: 231081--231136 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
231071 GGTTGGGCCC
*
231081 TTTTTAATTTA
1 TTTTAAATTTA
231092 TTTTAAATTTGA
1 TTTTAAATTT-A
231104 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
231115 ATTTAAATTAA
1 TTTTAAATTTA
*
231126 TCTTAAATTTA
1 TTTTAAATTTA
231137 AATTTAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:231121 original size:23 final size:23
Alignment explanation
Indices: 231105--231154 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
231095 TAAATTTGAT
231105 TTAAATTTAAATTTAAATTAATC
1 TTAAATTTAAATTTAAATTAATC
* *
231128 TTAAATTTAAATTTAAGTTAAAC
1 TTAAATTTAAATTTAAATTAATC
231151 TTAA
1 TTAA
231155 TTACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATC
Found at i:231125 original size:17 final size:16
Alignment explanation
Indices: 231083--231154 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 16
231073 TTGGGCCCTT
* *
231083 TTTAATTTATTTTAAA
1 TTTAAATTAATTTAAA
* *
231099 TTTGATTTAAATTTAAA
1 TTTAAATT-AATTTAAA
231116 TTTAAATTAATCTTAAA
1 TTTAAATTAAT-TTAAA
*
231133 TTTAAATTTAAGTTAAA
1 TTTAAA-TTAATTTAAA
*
231150 CTTAA
1 TTTAA
231155 TTACAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
16 10 0.21
17 33 0.70
18 4 0.09
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:231148 original size:11 final size:11
Alignment explanation
Indices: 231093--231154 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
231083 TTTAATTTAT
**
231093 TTTAAATTTGA
1 TTTAAATTAAA
231104 TTTAAATTTAAA
1 TTTAAA-TTAAA
231116 TTTAAATT-AA
1 TTTAAATTAAA
231126 TCTTAAATTTAAA
1 T-TTAAA-TTAAA
*
231139 TTTAAGTTAAA
1 TTTAAATTAAA
*
231150 CTTAA
1 TTTAA
231155 TTACAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 3 0.07
11 22 0.51
12 15 0.35
13 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:231154 original size:6 final size:6
Alignment explanation
Indices: 231093--231143 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
231083 TTTAATTTAT
*
231093 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
231139 TTTAA
1 TTTAA
231144 GTTAAACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 28 0.72
7 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:232990 original size:29 final size:29
Alignment explanation
Indices: 232950--233360 Score: 326
Period size: 29 Copynumber: 14.0 Consensus size: 29
232940 CCCCGGAGGT
232950 CCCT-AAACCTTCCAAAAATTACCATTTTA
1 CCCTCAAA-CTTCCAAAAATTACCATTTTA
*
232979 CCCTCAAACTTCCAAAAA-TCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A
* * *
233009 CCCTGAACCTTCTAAAAATTACCA-TTTA
1 CCCTCAAACTTCCAAAAATTACCATTTTA
* * *
233037 CCCCCAAACTTCCAAAAAAATCCCATTTTTGA
1 CCCTCAAACTTCC-AAAAATTACCA-TTTT-A
*
233069 CCC-CAAACCTTCCAAAAATTACCAATTTA
1 CCCTCAAA-CTTCCAAAAATTACCATTTTA
* *
233098 CCCTCGAACTTCCAAAAA-TCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A
* *
233128 CCC-CGAATCTTCCAAAAATTACCAATTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* *
233157 CCCTCGAACTTCCAAAAA-TCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A
*
233187 CCC-CGAATCTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
*
233216 CCCTCGAACTTCCAAAAA-T-CCTATTTTTGA
1 CCCTCAAACTTCCAAAAATTACC-A-TTTT-A
* *
233246 -CCTCGAACCTTCCAAAAATTATCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
233275 CCCCCGAACTTCCAAAAA-TCCCATTTTTA
1 CCCTCAAACTTCCAAAAATTACCA-TTTTA
* *
233304 ACCTCGAACCTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTCCAAAAATTACCATTTTA
* * *
233334 CCCCCGAACTTCCAAAAA-TCCCATTTT
1 CCCTCAAACTTCCAAAAATTACCATTTT
233361 CGACATCGAA
Statistics
Matches: 304, Mismatches: 48, Indels: 61
0.74 0.12 0.15
Matches are distributed among these distances:
27 2 0.01
28 35 0.12
29 121 0.40
30 102 0.34
31 34 0.11
32 10 0.03
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACCATTTTA
Found at i:233395 original size:59 final size:59
Alignment explanation
Indices: 232955--233360 Score: 634
Period size: 59 Copynumber: 6.9 Consensus size: 59
232945 GAGGTCCCTA
* *
232955 AACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCTG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
233014 AACCTTCTAAAAATTACCA-TTTACCCCCAAACTTCCAAAAAAATCCCATTTTTGACCCCA
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCC--AAAAATCCCATTTTTGACCCCG
*
233074 AACCTTCCAAAAATTACCAATTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
233133 AATCTTCCAAAAATTACCAATTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
233192 AATCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
233251 AACCTTCCAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
233310 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
1 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTT
233361 CGACATCGAA
Statistics
Matches: 326, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
58 16 0.05
59 257 0.79
60 38 0.12
61 15 0.05
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:234663 original size:20 final size:19
Alignment explanation
Indices: 234638--234688 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 19
234628 TTGAATGTAC
234638 AGTGATATTTTTTAAATATA
1 AGTGATATTTTTTAAA-ATA
*
234658 AGTGATATATTTTTTTAAATA
1 AGTG--ATATTTTTTAAAATA
234679 AGT-ATATTTT
1 AGTGATATTTT
234689 AAAATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.25
20 4 0.14
21 6 0.21
22 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
AGTGATATTTTTTAAAATA
Found at i:234670 original size:22 final size:20
Alignment explanation
Indices: 234642--234685 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
234632 ATGTACAGTG
234642 ATATTTTTTAAATATAAGTGAT
1 ATATTTTTTAAA-ATAAGT-AT
*
234664 ATATTTTTTTAAATAAGTAT
1 ATATTTTTTAAAATAAGTAT
234684 AT
1 AT
234686 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATATTTTTTAAAATAAGTAT
Found at i:234717 original size:23 final size:24
Alignment explanation
Indices: 234691--234739 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
234681 TATATTTTAA
234691 AATATTAAAATATAAT-AATTTTT
1 AATATTAAAATATAATGAATTTTT
* * *
234714 AATATTAATATTTAATGTATTTTT
1 AATATTAAAATATAATGAATTTTT
234738 AA
1 AA
234740 CATACTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AATATTAAAATATAATGAATTTTT
Found at i:235009 original size:18 final size:20
Alignment explanation
Indices: 234967--235010 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
234957 AACAGAAATA
*
234967 AAATTTTATTTATATCATGT
1 AAATTTTATTTATATCATAT
*
234987 AAATTTT-TTTATATTA-AT
1 AAATTTTATTTATATCATAT
235005 AAATTT
1 AAATTT
235011 AAATTTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 8 0.36
20 7 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
AAATTTTATTTATATCATAT
Found at i:243300 original size:20 final size:21
Alignment explanation
Indices: 243273--243323 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
243263 ATAAAATGAT
243273 TATTAATAAATATTTA-TAAAA
1 TATTAATAAAT-TTTATTAAAA
*
243294 T-TTAATATATTTTATTAAAA
1 TATTAATAAATTTTATTAAAA
243314 TATTAATAAA
1 TATTAATAAA
243324 AATATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTAATAAATTTTATTAAAA
Found at i:243468 original size:21 final size:23
Alignment explanation
Indices: 243434--243483 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
243424 GTATGTTTAA
243434 TAATAATTGAATATTATAATATT
1 TAATAATTGAATATTATAATATT
* *
243457 TAAT-ATT-AATATTTTAGTATT
1 TAATAATTGAATATTATAATATT
*
243478 TTATAA
1 TAATAA
243484 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 15 0.65
22 4 0.17
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATAATTGAATATTATAATATT
Found at i:247686 original size:9 final size:9
Alignment explanation
Indices: 247672--247750 Score: 56
Period size: 9 Copynumber: 8.7 Consensus size: 9
247662 ATAAATATCA
247672 ATAAAAATT
1 ATAAAAATT
*
247681 ATAAAAATC
1 ATAAAAATT
**
247690 ATTAAATTTT
1 A-TAAAAATT
247700 AATAAAAA-T
1 -ATAAAAATT
*
247709 ATAAAAAAT
1 ATAAAAATT
*
247718 -TAAAATTT
1 ATAAAAATT
247726 ATTAAAAA-T
1 A-TAAAAATT
247735 ATAAAAAATT
1 AT-AAAAATT
247745 ATAAAA
1 ATAAAA
247751 TACATCAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
8 14 0.26
9 22 0.41
10 17 0.31
11 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:247690 original size:19 final size:19
Alignment explanation
Indices: 247662--247741 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 19
247652 AAATTATAAA
*
247662 ATAAATATCAATAAAAATT
1 ATAAAAATCAATAAAAATT
* **
247681 ATAAAAATCATTAAATTTT
1 ATAAAAATCAATAAAAATT
*
247700 AATAAAAAT--ATAAAAAAT
1 -ATAAAAATCAATAAAAATT
* * *
247718 -TAAAATTTATTAAAAA-T
1 ATAAAAATCAATAAAAATT
247735 ATAAAAA
1 ATAAAAA
247742 ATTATAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
16 6 0.13
17 1 0.02
18 16 0.35
19 15 0.33
20 8 0.17
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAATCAATAAAAATT
Found at i:247726 original size:26 final size:26
Alignment explanation
Indices: 247671--247745 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
247661 AATAAATATC
*
247671 AATAAAAATTATAAAAATCATTAAATTTT
1 AATAAAAA-TATAAAAA--ATTAAAATTT
247700 AATAAAAATATAAAAAATTAAAATTT
1 AATAAAAATATAAAAAATTAAAATTT
*
247726 ATTAAAAATATAAAAAATTA
1 AATAAAAATATAAAAAATTA
247746 TAAAATACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 28 0.64
28 8 0.18
29 8 0.18
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAAAATATAAAAAATTAAAATTT
Found at i:247760 original size:28 final size:26
Alignment explanation
Indices: 247703--247762 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
247693 AAATTTTAAT
** *
247703 AAAAATATAAAAAATTAAAATTTATT
1 AAAAATATAAAAAATTAAAATACATC
247729 AAAAATATAAAAAATTATAAAATACATC
1 AAAAATATAAAAAA-T-TAAAATACATC
247757 AAAAAT
1 AAAAAT
247763 GCCTTTTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.48
27 1 0.03
28 14 0.48
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAATATAAAAAATTAAAATACATC
Found at i:247941 original size:20 final size:19
Alignment explanation
Indices: 247916--247980 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
247906 GTACGATAAT
247916 TTTTATAATTTTTTTACAAA
1 TTTTATAATTTTTTTAC-AA
* * *
247936 TTTTAT-ATTTCTTTATAT
1 TTTTATAATTTTTTTACAA
* *
247954 TTTTATAATTTTCTTACGA
1 TTTTATAATTTTTTTACAA
247973 TTTTATAA
1 TTTTATAA
247981 AATTTTATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 7 0.19
19 23 0.64
20 6 0.17
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTTACAA
Found at i:247994 original size:38 final size:39
Alignment explanation
Indices: 247911--247995 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
247901 TTTCAGTACG
* **
247911 ATAATTTTTATAATTTTTTTACAAATTTTATATTTCTTT
1 ATAATTTTTATAATTTTCTTACAAATTTTATAAATCTTT
*
247950 AT-ATTTTTATAATTTTCTTAC-GATTTTATAAAAT-TTT
1 ATAATTTTTATAATTTTCTTACAAATTTTAT-AAATCTTT
247987 ATAATTTTT
1 ATAATTTTT
247996 TTTCTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 12 0.30
38 26 0.65
39 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (39 bp):
ATAATTTTTATAATTTTCTTACAAATTTTATAAATCTTT
Found at i:248058 original size:29 final size:29
Alignment explanation
Indices: 248001--248067 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
247991 TTTTTTTTCT
**
248001 ATTTTTAAGAAAATTTAAACATTTCTATA
1 ATTTTTATTAAAATTTAAACATTTCTATA
*
248030 TTTTTTATTAAAATTTAATA-ATGTT-TATA
1 ATTTTTATTAAAATTTAA-ACAT-TTCTATA
248059 ATTTTTATT
1 ATTTTTATT
248068 GATTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTATTAAAATTTAAACATTTCTATA
Found at i:249444 original size:21 final size:20
Alignment explanation
Indices: 249420--249490 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
249410 ATTATATTGT
249420 TGTTTTGGTGTTATTTTTTAC
1 TGTTTTGGTGTT-TTTTTTAC
*
249441 TGTTTTGGT-TATTGTTTTTTC
1 TGTTTTGGTGT-TT-TTTTTAC
* *
249462 TGTTTTGGTGTTCTTTTTAT
1 TGTTTTGGTGTTTTTTTTAC
249482 TGTTTTGGT
1 TGTTTTGGT
249491 TGCTGTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 16 0.37
21 26 0.60
22 1 0.02
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:249511 original size:24 final size:24
Alignment explanation
Indices: 249470--249526 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
249460 TCTGTTTTGG
*
249470 TGTTCTTTTTATTGTTTTGGTTGC
1 TGTTATTTTTATTGTTTTGGTTGC
* * * *
249494 TGTTATTTTTTTTTTTTTTGTTGT
1 TGTTATTTTTATTGTTTTGGTTGC
*
249518 TGCTATTTT
1 TGTTATTTT
249527 AGCTGTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.05, C:0.05, G:0.16, T:0.74
Consensus pattern (24 bp):
TGTTATTTTTATTGTTTTGGTTGC
Found at i:249518 original size:21 final size:21
Alignment explanation
Indices: 249419--249518 Score: 71
Period size: 21 Copynumber: 4.6 Consensus size: 21
249409 AATTATATTG
*
249419 TTGTTTTGGTGTTATTTTTTA
1 TTGTTTTGGTGTTATTTTTTT
*
249440 CTGTTTT-G-GTTATTGTTTTT
1 TTGTTTTGGTGTTATT-TTTTT
*
249460 TCTGTTTTGGTGTTCTTTTTATT
1 T-TGTTTTGGTGTTATTTTT-TT
*
249483 GTT-TTGGTTGCTGTTATTTTTTT
1 -TTGTT--TTGGTGTTATTTTTTT
* *
249506 TTTTTTTGTTGTT
1 TTGTTTTGGTGTT
249519 GCTATTTTAG
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
19 6 0.10
20 5 0.08
21 19 0.30
22 8 0.13
23 12 0.19
24 13 0.21
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (21 bp):
TTGTTTTGGTGTTATTTTTTT
Found at i:249538 original size:12 final size:11
Alignment explanation
Indices: 249518--249562 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
249508 TTTTTGTTGT
249518 TGCTATTTTAGC
1 TGCTATTTT-GC
* *
249530 TGTTATTTTGT
1 TGCTATTTTGC
249541 TGCTATTTTTGC
1 TGCTA-TTTTGC
249553 TGCTATTTTG
1 TGCTATTTTG
249563 TTGTTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (11 bp):
TGCTATTTTGC
Found at i:249540 original size:23 final size:23
Alignment explanation
Indices: 249514--249565 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
249504 TTTTTTTTTG
*
249514 TTGTTGCTATTTTAGCTGTTATT
1 TTGTTGCTATTTTAGCTGCTATT
*
249537 TTGTTGCTATTTTTGCTGCTATT
1 TTGTTGCTATTTTAGCTGCTATT
249560 TTGTTG
1 TTGTTG
249566 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.62
Consensus pattern (23 bp):
TTGTTGCTATTTTAGCTGCTATT
Found at i:249566 original size:26 final size:24
Alignment explanation
Indices: 249508--249567 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
249498 ATTTTTTTTT
249508 TTTTTGTTGTTGCTATTTTAGCTG
1 TTTTTGTTGTTGCTATTTTAGCTG
* *
249532 TTATT-TTGTTGCTATTTTTGCTG
1 TTTTTGTTGTTGCTATTTTAGCTG
249555 CTATTTTGTTGTT
1 -T-TTTTGTTGTT
249568 TTTGTTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 17 0.57
24 5 0.17
25 3 0.10
26 5 0.17
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.65
Consensus pattern (24 bp):
TTTTTGTTGTTGCTATTTTAGCTG
Found at i:249602 original size:23 final size:21
Alignment explanation
Indices: 249561--249637 Score: 66
Period size: 23 Copynumber: 3.5 Consensus size: 21
249551 GCTGCTATTT
* *
249561 TGTTGTTTTTGTTATTGTTTTA
1 TGTTATTTTTGTT-GTGTTTTA
249583 CTGTTATTTTTGTTGCTGTTTTGA
1 -TGTTATTTTTGTTG-TGTTTT-A
* *
249607 TTGTTATTTTGGTTGT-TTATA
1 -TGTTATTTTTGTTGTGTTTTA
249628 TGTTATTTTT
1 TGTTATTTTT
249638 ATGCGTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.20
21 1 0.02
22 3 0.07
23 19 0.41
24 14 0.30
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (21 bp):
TGTTATTTTTGTTGTGTTTTA
Found at i:249615 original size:55 final size:58
Alignment explanation
Indices: 249523--249634 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 58
249513 GTTGTTGCTA
*
249523 TTTTAGCTGTTATTTTGTTGCTATTTTTGCTGCTATTTT-GTTGTTT-T-TGTTATTG
1 TTTTAGCTGTTATTTTGTTGCTAGTTTTGCTGCTATTTTGGTTGTTTATATGTTATTG
* *
249578 TTTTA-CTGTTATTTTTGTTGCT-GTTTTGATTGTTATTTTGGTTGTTTATATGTTATT
1 TTTTAGCTGTTA-TTTTGTTGCTAGTTTTG-CTGCTATTTTGGTTGTTTATATGTTATT
249635 TTTATGCGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
54 11 0.22
55 23 0.47
56 7 0.14
57 1 0.02
58 7 0.14
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.66
Consensus pattern (58 bp):
TTTTAGCTGTTATTTTGTTGCTAGTTTTGCTGCTATTTTGGTTGTTTATATGTTATTG
Found at i:249632 original size:44 final size:43
Alignment explanation
Indices: 249544--249637 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
249534 ATTTTGTTGC
*
249544 TATTTTTGCTGCTATTTTGTTGTTTTTGTTATTGTTTTACTGT
1 TATTTTTGCTGCTATTTTGTTGTTTTTGTGATTGTTTTACTGT
* * *
249587 TATTTTTGTTGCTGTTTTGATTGTTATTT-TGGTTGTTTATA-TGT
1 TATTTTTGCTGCTATTTTG-TTGTT-TTTGTGATTGTTT-TACTGT
249631 TATTTTT
1 TATTTTT
249638 ATGCGTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
43 17 0.39
44 22 0.50
45 5 0.11
ACGTcount: A:0.11, C:0.04, G:0.17, T:0.68
Consensus pattern (43 bp):
TATTTTTGCTGCTATTTTGTTGTTTTTGTGATTGTTTTACTGT
Found at i:255069 original size:2 final size:2
Alignment explanation
Indices: 255050--255083 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
255040 TAGCATCCAA
* *
255050 AT AT AT AC AT AT AC 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
255084 GAGTTGCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:263080 original size:29 final size:30
Alignment explanation
Indices: 263022--263080 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
263012 GAATTGAATC
* *
263022 AAATCAAAATATCATGTATAGCATTGCACA
1 AAATCAAAATATCATATATAGCATTACACA
263052 AAATCAAAAT-TCATATATA-CAATTACACA
1 AAATCAAAATATCATATATAGC-ATTACACA
263081 TTAAACCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.04
29 15 0.58
30 10 0.38
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATCAAAATATCATATATAGCATTACACA
Found at i:266307 original size:14 final size:15
Alignment explanation
Indices: 266288--266331 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 15
266278 AGAATAAGTT
266288 TTTAATTAA-TAAAA
1 TTTAATTAATTAAAA
266302 TTTAATTAATTAAAAAA
1 TTTAATTAATT--AAAA
266319 TTTAAATTAATTA
1 TTT-AATTAATTA
266332 CACTTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 1 0.04
17 7 0.27
18 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATTAATTAAAA
Found at i:266312 original size:18 final size:18
Alignment explanation
Indices: 266289--266331 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
266279 GAATAAGTTT
266289 TTAATTAATAAAATTT-AA
1 TTAATTAA-AAAATTTAAA
266307 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
266325 TTAATTA
1 TTAATTA
266332 CACTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:277114 original size:37 final size:35
Alignment explanation
Indices: 277058--277127 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
277048 ACAAATTTAA
277058 AATATAAATATTTATTTAAAAATAACTTATAATAAAT
1 AATATAAATATTTATTTAAAAATAA-TTA-AATAAAT
*
277095 AATA-AAATATATTATTTAAAATTAATTAAATAA
1 AATATAAATAT-TTATTTAAAAATAATTAAATAA
277128 TTGATAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 5 0.16
36 9 0.29
37 17 0.55
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATAAATATTTATTTAAAAATAATTAAATAAAT
Found at i:279876 original size:17 final size:17
Alignment explanation
Indices: 279844--279878 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
279834 TATTTTCCTA
* *
279844 AAAATTTTATATTTTAT
1 AAAATTTTAAAATTTAT
279861 AAAATTTTAAAATTTAT
1 AAAATTTTAAAATTTAT
279878 A
1 A
279879 TTTATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATTTTAAAATTTAT
Found at i:280079 original size:19 final size:19
Alignment explanation
Indices: 280055--280091 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
280045 GCACATTAAT
*
280055 AAATGACTTTGAAAATAGC
1 AAATGACTTTCAAAATAGC
280074 AAATGACTTTCAAAATAG
1 AAATGACTTTCAAAATAG
280092 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (19 bp):
AAATGACTTTCAAAATAGC
Found at i:285866 original size:28 final size:29
Alignment explanation
Indices: 285825--285901 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 29
285815 TATATGTAAG
*
285825 ATAAATTTAAAATATTTTTAATTAAA-ATT
1 ATAAA-TTAAAATATTATTAATTAAATATT
*
285854 ATAAATTAAAATAATAGTT--TTAAATATT
1 ATAAATTAAAATATTA-TTAATTAAATATT
*
285882 ATCAATTAAAATATTATTAA
1 ATAAATTAAAATATTATTAA
285902 ATATTCAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 7 0.17
28 26 0.65
29 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
ATAAATTAAAATATTATTAATTAAATATT
Found at i:288327 original size:31 final size:32
Alignment explanation
Indices: 288245--288327 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 32
288235 TTAAAAAAAA
* * *
288245 TTTTAATTTTAAATTCATTAAAAGCGTTATTAT
1 TTTTAATTTTAAAAT-ATCAAAAGAGTTATTAT
* * *
288278 TTTT-ATTATATAACTATCAAAAGAG-TATTTT
1 TTTTAATTTTA-AAATATCAAAAGAGTTATTAT
288309 TTTTAATTTTAAAATATCA
1 TTTTAATTTTAAAATATCA
288328 GCGTTTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
31 16 0.39
32 18 0.44
33 7 0.17
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTTAATTTTAAAATATCAAAAGAGTTATTAT
Found at i:292830 original size:31 final size:31
Alignment explanation
Indices: 292764--292831 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
292754 TTAACTGACC
* *
292764 AATGACTTAAACAATAATGTTCGAATAGTTG
1 AATGACTTAAACAATAATGTTAGAATAATTG
* * *
292795 AATGAGTTAAACAATCATGTCTAG-ATAATTT
1 AATGACTTAAACAATAATGT-TAGAATAATTG
292826 AATGAC
1 AATGAC
292832 CAATTTGTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (31 bp):
AATGACTTAAACAATAATGTTAGAATAATTG
Found at i:293857 original size:16 final size:16
Alignment explanation
Indices: 293837--293875 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
293827 TAACTCCTTC
*
293837 AAAATTTATA-AAAAT
1 AAAATTAATATAAAAT
293852 ATAAATTAATATAAAAT
1 A-AAATTAATATAAAAT
293869 AAAATTA
1 AAAATTA
293876 TGTTCTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTAATATAAAAT
Found at i:294442 original size:17 final size:17
Alignment explanation
Indices: 294422--294454 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
294412 ATTAAAGCAA
294422 ATAATAAAT-TAATATCG
1 ATAAT-AATCTAATATCG
294439 ATAATAATCTAATATC
1 ATAATAATCTAATATC
294455 CAAATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATAATAATCTAATATCG
Found at i:296001 original size:33 final size:33
Alignment explanation
Indices: 295939--296001 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
295929 AAATAAGGGT
*
295939 TAATTATAATATTAGCTAAGAATTCAAATTCAC
1 TAATTATAATATTAGCTAAGAATTAAAATTCAC
*
295972 TAATTATAAATATTTAGC-AAGTA-TAAAATT
1 TAATTAT-AATA-TTAGCTAAGAATTAAAATT
296002 TGATCTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 13 0.50
34 8 0.31
35 5 0.19
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (33 bp):
TAATTATAATATTAGCTAAGAATTAAAATTCAC
Found at i:297204 original size:15 final size:15
Alignment explanation
Indices: 297168--297210 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
297158 ATAATAAAAA
297168 TATAATTTTATCATTTT
1 TATAATTTT-T-ATTTT
*
297185 AATAATTTTTATTTT
1 TATAATTTTTATTTT
297200 TATAATTTTTA
1 TATAATTTTTA
297211 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 1 0.04
17 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TATAATTTTTATTTT
Found at i:304717 original size:23 final size:21
Alignment explanation
Indices: 304672--304717 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
304662 TTTTTTCACC
*
304672 ATTTTTAAATATAAAATATTT
1 ATTTTTAAATATAAAATAATT
*
304693 ATTTTTATATCATAAAAATAATT
1 ATTTTTAAAT-AT-AAAATAATT
304716 AT
1 AT
304718 AAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 10 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTTAAATATAAAATAATT
Found at i:305135 original size:18 final size:18
Alignment explanation
Indices: 305098--305131 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
305088 TATGCTGCCC
305098 TATGTATGTATACGTATG
1 TATGTATGTATACGTATG
305116 TATGTATGTATA-GTAT
1 TATGTATGTATACGTAT
305132 TGTAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (18 bp):
TATGTATGTATACGTATG
Found at i:305841 original size:6 final size:6
Alignment explanation
Indices: 305830--305862 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
305820 AATCAAATCA
305830 AATTCT AATTCT AATTCT AATTCT AATTC- AATT
1 AATTCT AATTCT AATTCT AATTCT AATTCT AATT
305863 GAAATCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTCT
Found at i:308838 original size:2 final size:2
Alignment explanation
Indices: 308831--308862 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
308821 TAACGGAGCA
308831 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
308863 TGATCTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:313335 original size:30 final size:30
Alignment explanation
Indices: 313301--313362 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
313291 ACTTATTTTA
* *
313301 TTGTTAATTTTGTTATTATTTTAGAAGTAT
1 TTGTTAATTATGTTACTATTTTAGAAGTAT
*
313331 TTGTTAATTATGTTACTATTTTAGAGGTAT
1 TTGTTAATTATGTTACTATTTTAGAAGTAT
313361 TT
1 TT
313363 ATTTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTATGTTACTATTTTAGAAGTAT
Found at i:313385 original size:33 final size:30
Alignment explanation
Indices: 313312--313397 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
313302 TGTTAATTTT
* * * *
313312 GTTATTATTTTAGAAGTATTTGTTAATTAT
1 GTTACTATTTTAGAGGTATTTATTAATTAA
*
313342 GTTACTATTTTAGAGGTATTTATTTATTAA
1 GTTACTATTTTAGAGGTATTTATTAATTAA
* *
313372 GTTGCATCTATTTTAGTGTTATTTAT
1 GTT--A-CTATTTTAGAGGTATTTAT
313398 GTATATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 28 0.61
32 1 0.02
33 17 0.37
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
GTTACTATTTTAGAGGTATTTATTAATTAA
Done.