Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 202 of 216
Found at i:62764237 original size:12 final size:12
Alignment explanation
Indices: 62764222--62764310 Score: 51
Period size: 12 Copynumber: 7.3 Consensus size: 12
62764212 TTTAAAATAC
62764222 TTTTTTTTAAATTT
1 TTTTTTTTAAA--T
62764236 TTTTAATTTTAAA-
1 TTTT--TTTTAAAT
*
62764249 ATTTTTTTAAA-
1 TTTTTTTTAAAT
* *
62764260 ATTTTTTTAAAA
1 TTTTTTTTAAAT
*
62764272 TATTTTTTAAAT
1 TTTTTTTTAAAT
**
62764284 ACTTTTTT-AAT
1 TTTTTTTTAAAT
62764295 TTTTGTTTT-AAT
1 TTTT-TTTTAAAT
62764307 TTTT
1 TTTT
62764311 AAAACAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
11 23 0.37
12 26 0.41
13 3 0.05
14 4 0.06
16 7 0.11
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:62764243 original size:31 final size:28
Alignment explanation
Indices: 62764205--62764269 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
62764195 ATTTTTATTA
*
62764205 TTTTAATTTTAAAATACTTTTTTTTAAATTT
1 TTTTAATTTT-AAA-A-TTTTTTTAAAATTT
62764236 TTTTAATTTTAAAATTTTTTTAAAATTT
1 TTTTAATTTTAAAATTTTTTTAAAATTT
62764264 TTTTAA
1 TTTTAA
62764270 AATATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 19 0.58
29 1 0.03
30 3 0.09
31 10 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTAATTTTAAAATTTTTTTAAAATTT
Found at i:62764250 original size:17 final size:17
Alignment explanation
Indices: 62764205--62764258 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
62764195 ATTTTTATTA
**
62764205 TTTTAATTTTAAAATAC
1 TTTTAATTTTAAAATTT
62764222 TTTT--TTTT-AAATTT
1 TTTTAATTTTAAAATTT
62764236 TTTTAATTTTAAAATTT
1 TTTTAATTTTAAAATTT
62764253 TTTTAA
1 TTTTAA
62764259 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 8 0.25
15 4 0.12
16 4 0.12
17 16 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATTTTAAAATTT
Found at i:62766154 original size:98 final size:98
Alignment explanation
Indices: 62765985--62766179 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
62765975 ATACAATAAA
* *
62765985 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACTCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
62766050 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
62766083 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
62766148 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
62766180 CATGATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:62766883 original size:26 final size:27
Alignment explanation
Indices: 62766852--62766903 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
62766842 ATATAAATAT
62766852 GAAAATATTC-ATTAAAAAAAATATAG
1 GAAAATATTCGATTAAAAAAAATATAG
* *
62766878 GAAAATATTCGTTTTAAAAAAATATA
1 GAAAATATTCGATTAAAAAAAATATA
62766904 TACATGTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.31
Consensus pattern (27 bp):
GAAAATATTCGATTAAAAAAAATATAG
Found at i:62767683 original size:19 final size:19
Alignment explanation
Indices: 62767644--62767733 Score: 116
Period size: 19 Copynumber: 4.8 Consensus size: 19
62767634 AAATTAAATC
62767644 TCTAAGA-T-CATATC-T-
1 TCTAAGATTACATATCATA
62767659 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
62767678 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
62767699 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
62767718 TCTAAGATTACATATC
1 TCTAAGATTACATATC
62767734 CTCGAAGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
15 7 0.11
16 1 0.02
17 6 0.09
18 1 0.02
19 32 0.49
21 18 0.28
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:62767696 original size:21 final size:21
Alignment explanation
Indices: 62767670--62767732 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
62767660 CTAAGATTAC
62767670 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
62767691 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
62767710 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
62767731 AT
1 AT
62767733 CCTCGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:62768411 original size:132 final size:132
Alignment explanation
Indices: 62768243--62768698 Score: 795
Period size: 132 Copynumber: 3.5 Consensus size: 132
62768233 GAGATAGGAT
* * * *
62768243 TTGGTGGCTTAAATCTGCTTCCCACTATTTTAGAAAGATAAGATTTTCCGTTTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
* ** * *
62768308 ACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTTTCCGCTGCTGCTCAGGAAGACAAA
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
62768373 GC
131 GC
*
62768375 TTTGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
*
62768440 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGATGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
62768505 GC
131 GC
62768507 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
*
62768572 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
62768637 GC
131 GC
*
62768639 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCT
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCT
62768699 ACTTCGCTAT
Statistics
Matches: 309, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 309 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (132 bp):
TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTCC
ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAG
GC
Found at i:62768458 original size:44 final size:43
Alignment explanation
Indices: 62768410--62768594 Score: 131
Period size: 44 Copynumber: 4.2 Consensus size: 43
62768400 TATCTTGGAA
*
62768410 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTA-TGCTTAGGG
* * ** * * * * *
62768454 AGATAAGATCTACAATCTTCAACCTACTCCGCTGATGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACT-ATGCTTAGGG
* ** ** * * *
62768498 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTAT-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTATGCTTAGG-G
*
62768542 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTA-TGCTTAGGG
62768586 AGATAAGAT
1 AGATAAGAT
62768595 CTACAATCTT
Statistics
Matches: 100, Mismatches: 34, Indels: 14
0.68 0.23 0.09
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
44 80 0.80
45 6 0.06
46 4 0.04
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (43 bp):
AGATAAGATTTGCCGTCTTTAATCTGCTCCACTATGCTTAGGG
Found at i:62775874 original size:98 final size:98
Alignment explanation
Indices: 62775705--62775899 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
62775695 ATACAATAAA
*
62775705 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
62775770 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
* * *
62775803 ACTTTAAAAGAACATCCACTTATCCAAGATTTAATAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
62775868 CCTTTAGAATCTCAAACTCAGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTT
62775900 CATGATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
Found at i:62776600 original size:25 final size:26
Alignment explanation
Indices: 62776570--62776620 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
62776560 ATATAAATAT
62776570 GAAAATATTC-ATTAAAAAAATATAG
1 GAAAATATTCGATTAAAAAAATATAG
*
62776595 GAAAATATTCGTTTTAAAAAAATATA
1 GAAAATATTCG-ATTAAAAAAATATA
62776621 TACATGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
27 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAG
Found at i:62777398 original size:19 final size:19
Alignment explanation
Indices: 62777359--62777448 Score: 116
Period size: 19 Copynumber: 4.8 Consensus size: 19
62777349 AAATTAAATC
62777359 TCTAAGA-T-CATATC-T-
1 TCTAAGATTACATATCATA
62777374 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
62777393 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
62777414 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
62777433 TCTAAGATTACATATC
1 TCTAAGATTACATATC
62777449 CTCGAAGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
15 7 0.11
16 1 0.02
17 6 0.09
18 1 0.02
19 32 0.49
21 18 0.28
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:62777411 original size:21 final size:21
Alignment explanation
Indices: 62777385--62777447 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
62777375 CTAAGATTAC
62777385 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
62777406 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
62777425 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
62777446 AT
1 AT
62777448 CCTCGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 18 0.46
21 21 0.54
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:62779245 original size:35 final size:35
Alignment explanation
Indices: 62779206--62779338 Score: 95
Period size: 35 Copynumber: 3.7 Consensus size: 35
62779196 TTGAAAGTGA
* *
62779206 GCCCAGCTCTAGTTGGATAAACCAATAATGTTTGC
1 GCCCAGCGCTAGTCGGATAAACCAATAATGTTTGC
* *** *
62779241 GCCCAGCGCTAGTCGGATATATCGACAATAATAAAAGTGA
1 GCCCAGCGCTAGTCGGATA-AAC--CAATAAT--GTTTGC
* * * ***
62779281 GCCCAGCTCTAGTTGGATGAACCAACGGTGTTTGC
1 GCCCAGCGCTAGTCGGATAAACCAATAATGTTTGC
*
62779316 ACCCAGCGCTAGTCGGATAAACC
1 GCCCAGCGCTAGTCGGATAAACC
62779339 GACGATTGTG
Statistics
Matches: 71, Mismatches: 22, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
35 38 0.54
36 2 0.03
37 4 0.06
38 7 0.10
39 2 0.03
40 18 0.25
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (35 bp):
GCCCAGCGCTAGTCGGATAAACCAATAATGTTTGC
Found at i:62779255 original size:75 final size:76
Alignment explanation
Indices: 62779160--62779331 Score: 224
Period size: 75 Copynumber: 2.3 Consensus size: 76
62779150 CTGCAGAGAG
* * * * *
62779160 GTTTGCGCCCAACGCTAGTCGGGTTA-ATTGGA-AATATTGAAAGTGAGCCCAGCTCTAGTTGGA
1 GTTTGCGCCCAGCGCTAGTCGGGATATA-TCGACAATAATAAAAGTGAGCCCAGCTCTAGTTGGA
*
62779223 TAAACCAATAAT
65 TAAACCAACAAT
62779235 GTTTGCGCCCAGCGCTAGTC-GGATATATCGACAATAATAAAAGTGAGCCCAGCTCTAGTTGGAT
1 GTTTGCGCCCAGCGCTAGTCGGGATATATCGACAATAATAAAAGTGAGCCCAGCTCTAGTTGGAT
* **
62779299 GAACCAACGGT
66 AAACCAACAAT
*
62779310 GTTTGCACCCAGCGCTAGTCGG
1 GTTTGCGCCCAGCGCTAGTCGG
62779332 ATAAACCGAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
74 7 0.08
75 76 0.90
76 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (76 bp):
GTTTGCGCCCAGCGCTAGTCGGGATATATCGACAATAATAAAAGTGAGCCCAGCTCTAGTTGGAT
AAACCAACAAT
Found at i:62781356 original size:37 final size:37
Alignment explanation
Indices: 62781306--62781402 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
62781296 AGTACATCAT
*
62781306 CAACAAAAGCTCATAGAGCTGGTCCACCCGAACACAC
1 CAACAAAAGCTCATAGAGCTGATCCACCCGAACACAC
* **
62781343 CAACAGAAGCTCATAGAGCTGATCCACTTGAACACAC
1 CAACAAAAGCTCATAGAGCTGATCCACCCGAACACAC
* *
62781380 AAATGAAAA-CTCATAAGAGCTGA
1 CAA-CAAAAGCTCAT-AGAGCTGA
62781403 ATAGAACTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 40 0.78
38 11 0.22
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.14
Consensus pattern (37 bp):
CAACAAAAGCTCATAGAGCTGATCCACCCGAACACAC
Found at i:62781416 original size:20 final size:20
Alignment explanation
Indices: 62781387--62781443 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
62781377 CACAAATGAA
*
62781387 AACTCATAAGAGCTGAATAG
1 AACTCATAAGAGCTGAACAG
*
62781407 AACTCGTAAGAGCTGAACAG
1 AACTCATAAGAGCTGAACAG
*
62781427 AAGCTCAAAAGAGCTGA
1 AA-CTCATAAGAGCTGA
62781444 TCCACCCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (20 bp):
AACTCATAAGAGCTGAACAG
Found at i:62798488 original size:24 final size:24
Alignment explanation
Indices: 62798461--62798508 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
62798451 CACCAGGAAA
62798461 TTTGAAACCTTCAGGTTATTCAAC
1 TTTGAAACCTTCAGGTTATTCAAC
*
62798485 TTTGAAACCTTCAGGTTGTTCAAC
1 TTTGAAACCTTCAGGTTATTCAAC
62798509 ATAGATCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (24 bp):
TTTGAAACCTTCAGGTTATTCAAC
Found at i:62799569 original size:20 final size:21
Alignment explanation
Indices: 62799544--62799582 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62799534 AATTAAAAGT
*
62799544 TTAATTG-AATTGAAATTGCG
1 TTAATTGAAATTAAAATTGCG
62799564 TTAATTGAAATTAAAATTG
1 TTAATTGAAATTAAAATTG
62799583 TAAAGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (21 bp):
TTAATTGAAATTAAAATTGCG
Found at i:62801978 original size:14 final size:14
Alignment explanation
Indices: 62801952--62801989 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
62801942 GAAAATAAAG
62801952 AAAATAGAAAATATA
1 AAAATA-AAAATATA
*
62801967 AATATAAAAATATA
1 AAAATAAAAATATA
62801981 AAAATAAAA
1 AAAATAAAA
62801990 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATAAAAATATA
Found at i:62806105 original size:21 final size:21
Alignment explanation
Indices: 62806079--62806126 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
62806069 TTCTCTCAAA
62806079 CATCAAGCATCTAGCCATATC
1 CATCAAGCATCTAGCCATATC
*
62806100 CATCAAGCATCTGGCCATATC
1 CATCAAGCATCTAGCCATATC
62806121 CATCAA
1 CATCAA
62806127 ACTTCTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.23
Consensus pattern (21 bp):
CATCAAGCATCTAGCCATATC
Found at i:62808457 original size:20 final size:21
Alignment explanation
Indices: 62808432--62808476 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
62808422 CTTAGTTCAT
62808432 ATCTAACT-AAGTAACAAAAC
1 ATCTAACTGAAGTAACAAAAC
*
62808452 ATCTAATTGAAGTAACAAAAC
1 ATCTAACTGAAGTAACAAAAC
62808473 ATCT
1 ATCT
62808477 GCATGATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (21 bp):
ATCTAACTGAAGTAACAAAAC
Found at i:62810524 original size:19 final size:19
Alignment explanation
Indices: 62810497--62810543 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
62810487 CACATATGAA
*
62810497 AATTCTATTTATAAA-AAAT
1 AATTATATTTA-AAATAAAT
*
62810516 AATTATATTTAAAATAATT
1 AATTATATTTAAAATAAAT
62810535 AATTA-ATTT
1 AATTATATTT
62810544 TTTATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTATATTTAAAATAAAT
Found at i:62810652 original size:68 final size:70
Alignment explanation
Indices: 62810509--62810656 Score: 158
Period size: 68 Copynumber: 2.1 Consensus size: 70
62810499 TTCTATTTAT
* * * *
62810509 AAAAAATAATTATATTTAAAATAATTAATTAATTTTTTATATTATAATTTACCATACCCACAATG
1 AAAAAATAATTATATTTAAAATAATT-ATTAATTTATAATATTAGAATTTACCATACCCACAATA
* *
62810574 TGAGTG
65 TGAATA
*** **
62810580 AAAAAATAATTATATTTGTGATAATT-TT-ATTTATAATATTAGAATTTACCATACCGGCAATAT
1 AAAAAATAATTATATTTAAAATAATTATTAATTTATAATATTAGAATTTACCATACCCACAATAT
62810643 -ACATA
66 GA-ATA
62810648 AAAAAATAA
1 AAAAAATAA
62810657 ATATGTGACA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
67 1 0.02
68 39 0.60
69 2 0.03
71 23 0.35
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (70 bp):
AAAAAATAATTATATTTAAAATAATTATTAATTTATAATATTAGAATTTACCATACCCACAATAT
GAATA
Found at i:62810692 original size:16 final size:15
Alignment explanation
Indices: 62810666--62810706 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
62810656 AATATGTGAC
62810666 ATAAAAAAATTATAT
1 ATAAAAAAATTATAT
62810681 ATAAAGAAAATTATAT
1 ATAAA-AAAATTATAT
*
62810697 -CAAAAAAATT
1 ATAAAAAAATT
62810707 GGTTGATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 10 0.42
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAAAAATTATAT
Found at i:62810892 original size:15 final size:15
Alignment explanation
Indices: 62810871--62810910 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
62810861 AAAAATGTGA
62810871 AATTAAAAAACTTATT
1 AATTAAAAAACTT-TT
62810887 AA-TAAAAAA-TTTT
1 AATTAAAAAACTTTT
62810900 AATTAAAAAAC
1 AATTAAAAAAC
62810911 CTTAACAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 7 0.32
16 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTAAAAAACTTTT
Found at i:62813983 original size:19 final size:20
Alignment explanation
Indices: 62813959--62813999 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
62813949 GAATTTAGTA
*
62813959 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
62813978 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
62813998 AA
1 AA
62814000 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:62824603 original size:16 final size:16
Alignment explanation
Indices: 62824582--62824650 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
62824572 GATTAGCTAT
*
62824582 TACACCACTAATCCAA
1 TACACCTCTAATCCAA
62824598 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
62824615 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62824631 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
62824647 TACA
1 TACA
62824651 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:62824626 original size:33 final size:32
Alignment explanation
Indices: 62824582--62824650 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
62824572 GATTAGCTAT
62824582 TACACCACTAATCCAATACACCTCTAATCCCAA
1 TACACCACTAATCCAATACACCTCTAAT-CCAA
*
62824615 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCACTAATCCAATACACCTCTAATCCAA
62824647 TACA
1 TACA
62824651 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (32 bp):
TACACCACTAATCCAATACACCTCTAATCCAA
Found at i:62827633 original size:17 final size:18
Alignment explanation
Indices: 62827611--62827644 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
62827601 TCCAAAATGT
62827611 GTAGATAAAA-AACACAG
1 GTAGATAAAACAACACAG
62827628 GTAGATAAAACAACACA
1 GTAGATAAAACAACACA
62827645 CATATCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (18 bp):
GTAGATAAAACAACACAG
Found at i:62827658 original size:31 final size:31
Alignment explanation
Indices: 62827620--62827679 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
62827610 TGTAGATAAA
*
62827620 AAACACAGGTAGATAAAACAACACACATATC
1 AAACACAGGTAGATAAAAAAACACACATATC
*
62827651 AAACACAGGTAGATAAAAAAACACCCATA
1 AAACACAGGTAGATAAAAAAACACACATA
62827680 GGAAAGATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.12
Consensus pattern (31 bp):
AAACACAGGTAGATAAAAAAACACACATATC
Found at i:62832438 original size:4 final size:4
Alignment explanation
Indices: 62832429--62832460 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
62832419 ACAAACAGAA
62832429 GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG
62832461 TGTGTGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
GATG
Found at i:62832474 original size:12 final size:11
Alignment explanation
Indices: 62832457--62832498 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
62832447 TGGATGGATG
62832457 GATGTGTGTGT
1 GATGTGTGTGT
62832468 -ATGTGTGTGT
1 GATGTGTGTGT
*
62832478 G-TGTGTGTGC
1 GATGTGTGTGT
62832488 GCATGTGTGTG
1 G-ATGTGTGTG
62832499 GTACCTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 19 0.70
12 8 0.30
ACGTcount: A:0.07, C:0.05, G:0.45, T:0.43
Consensus pattern (11 bp):
GATGTGTGTGT
Found at i:62837001 original size:9 final size:9
Alignment explanation
Indices: 62836987--62837015 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
62836977 ACAAAACATT
62836987 AAAGAAAAG
1 AAAGAAAAG
62836996 AAAGAAAA-
1 AAAGAAAAG
62837004 AAAGAAAAG
1 AAAGAAAAG
62837013 AAA
1 AAA
62837016 AGTTAACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:62841527 original size:15 final size:15
Alignment explanation
Indices: 62841504--62841552 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
62841494 TTATTTTTCA
*
62841504 AAATATCATACCAAT
1 AAATTTCATACCAAT
*
62841519 AAATTTCATA--AAA
1 AAATTTCATACCAAT
62841532 AAATTTCATACCAAT
1 AAATTTCATACCAAT
62841547 AAATTT
1 AAATTT
62841553 AATAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 12 0.41
15 17 0.59
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTCATACCAAT
Found at i:62841537 original size:13 final size:13
Alignment explanation
Indices: 62841519--62841562 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
62841509 TCATACCAAT
62841519 AAATTTCATAAAA
1 AAATTTCATAAAA
*
62841532 AAATTTCATACCAAT
1 AAATTTCATA--AAA
*
62841547 AAATTTAATAAAA
1 AAATTTCATAAAA
62841560 AAA
1 AAA
62841563 ATTAACAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTTCATAAAA
Found at i:62841540 original size:28 final size:28
Alignment explanation
Indices: 62841503--62841562 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
62841493 GTTATTTTTC
*
62841503 AAAATATCATACCAATAAATTTCATAAA
1 AAAATATCATACCAATAAATTTAATAAA
*
62841531 AAAATTTCATACCAATAAATTTAATAAA
1 AAAATATCATACCAATAAATTTAATAAA
62841559 AAAA
1 AAAA
62841563 ATTAACAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAATATCATACCAATAAATTTAATAAA
Found at i:62842709 original size:22 final size:24
Alignment explanation
Indices: 62842667--62842711 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
62842657 ATAAATAATA
62842667 TTATTAATATTTTGTTGAAAATATT
1 TTATTAATA-TTTGTTGAAAATATT
62842692 TTATTAATA-TT-TTGAAAATA
1 TTATTAATATTTGTTGAAAATA
62842712 AATGTATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
25 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TTATTAATATTTGTTGAAAATATT
Found at i:62842745 original size:18 final size:17
Alignment explanation
Indices: 62842722--62842755 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62842712 AATGTATAGA
*
62842722 TTATAATTTATAAATATT
1 TTATAATATA-AAATATT
62842740 TTATAATATAAAATAT
1 TTATAATATAAAATAT
62842756 GAATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATAATATAAAATATT
Found at i:62845545 original size:51 final size:51
Alignment explanation
Indices: 62845467--62845692 Score: 224
Period size: 51 Copynumber: 4.4 Consensus size: 51
62845457 GTACCTATGA
*
62845467 ACATGTGTATAGTACTAAGTGCAGGCTACTACGTGTATC-AATAGACAATGGTC
1 ACATGTG--TAGTACTATGTGCAGGCTACTACGTGTATCGAAT-GACAATGGTC
* * * * * **
62845520 ACATGTGTAGTACTATGTACAGGCTACTATGTGTACCGGATTACCTTGGTC
1 ACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGACAATGGTC
* * * * * *
62845571 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTGGAAAG-C-TTGATC
1 ACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-TCGAATGACAATGGTC
* * *
62845621 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATGACAATGGTC
1 ACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGACAATGGTC
* *
62845672 ACATGGGTGGTACTATGTGCA
1 ACATGTGTAGTACTATGTGCA
62845693 AACCACCGAA
Statistics
Matches: 140, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 4 0.03
50 39 0.28
51 86 0.61
52 4 0.03
53 7 0.05
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (51 bp):
ACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGACAATGGTC
Found at i:62854658 original size:21 final size:20
Alignment explanation
Indices: 62854633--62854684 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
62854623 CCAAAAAATG
*
62854633 TTTTATAGACATCTAATCTAT
1 TTTTATAGAAATC-AATCTAT
* *
62854654 TTTTAGAAAAATCAATCTAT
1 TTTTATAGAAATCAATCTAT
62854674 TTTT-TAGAAAT
1 TTTTATAGAAAT
62854685 TATTTTCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 10 0.38
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
TTTTATAGAAATCAATCTAT
Found at i:62857862 original size:27 final size:25
Alignment explanation
Indices: 62857808--62857892 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 25
62857798 AATTCATATT
*
62857808 CGGGAATGCTCATATGAGCACATA-AA
1 CGGGAA-GCTCATCTGAGC-CATATAA
*
62857834 CGGGAAGCTCTCTCTCGAGCCATATAA
1 CGGGAAGCTC-ATCT-GAGCCATATAA
* *
62857861 CGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATCTGAGCCATATAA
62857886 CGGGAAG
1 CGGGAAG
62857893 ATTATCCGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 21 0.41
26 14 0.27
27 16 0.31
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATCTGAGCCATATAA
Found at i:62857942 original size:24 final size:25
Alignment explanation
Indices: 62857915--62857969 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
62857905 GTATAACAGA
*
62857915 AAGCTCATAAGAGCCA-TAATTAGG
1 AAGCTCATAAGAGCCATTAATCAGG
**
62857939 AAGCTCATGCGAGCCATTAATCAGG
1 AAGCTCATAAGAGCCATTAATCAGG
62857964 AAGCTC
1 AAGCTC
62857970 CAGATAGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (25 bp):
AAGCTCATAAGAGCCATTAATCAGG
Found at i:62857965 original size:25 final size:24
Alignment explanation
Indices: 62857907--62857969 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
62857897 TCCGGGTTGT
*
62857907 ATAA-CAGAAAGCTCATAAGAGCC
1 ATAATCAGGAAGCTCATAAGAGCC
* **
62857930 ATAATTAGGAAGCTCATGCGAGCC
1 ATAATCAGGAAGCTCATAAGAGCC
62857954 ATTAATCAGGAAGCTC
1 A-TAATCAGGAAGCTC
62857970 CAGATAGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 4 0.12
24 16 0.48
25 13 0.39
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (24 bp):
ATAATCAGGAAGCTCATAAGAGCC
Found at i:62857990 original size:25 final size:25
Alignment explanation
Indices: 62857962--62858037 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
62857952 CCATTAATCA
*
62857962 GGAAGCTCCAGATAGCCATATATCG
1 GGAAGCTCAAGATAGCCATATATCG
*
62857987 GGAAGTTCAAG-TGAGCC--ATATCG
1 GGAAGCTCAAGAT-AGCCATATATCG
*** *
62858010 GGAAGCTTTGGAGAGCCATATATCG
1 GGAAGCTCAAGATAGCCATATATCG
62858035 GGA
1 GGA
62858038 CGCTTATAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
23 17 0.43
24 1 0.03
25 22 0.55
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (25 bp):
GGAAGCTCAAGATAGCCATATATCG
Found at i:62859077 original size:43 final size:43
Alignment explanation
Indices: 62858971--62859083 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
62858961 GAAACAAACG
* * * *
62858971 CCGCTAAAGGTCACGACCTTTAGCGGCGTTTGTGACTTAAGCA
1 CCGCTAAAAGTCAAGATCTTTAGCGGCATTTGTGACTTAAGCA
* *
62859014 CCGCTAAAAGTCAAGCTCTTTAGCGGCATTTGTGACTTAAGCG
1 CCGCTAAAAGTCAAGATCTTTAGCGGCATTTGTGACTTAAGCA
* **
62859057 CCGCTAAAAGTTATTATCTTTAGCGGC
1 CCGCTAAAAGTCAAGATCTTTAGCGGC
62859084 TCTTTACCCA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (43 bp):
CCGCTAAAAGTCAAGATCTTTAGCGGCATTTGTGACTTAAGCA
Found at i:62859122 original size:43 final size:42
Alignment explanation
Indices: 62859075--62859260 Score: 171
Period size: 43 Copynumber: 4.3 Consensus size: 42
62859065 AGTTATTATC
* * *
62859075 TTTAGCGGCTCTTTACCCACAAACGCCGCTAAAGAGCTTGACT
1 TTTAGCGGCGCTTT-CCCACAAACGCCGCAAAAGACCTTGACT
* *
62859118 TTTAGCGGCGC-TTCCACTACAAACGCCGCAAAATACCTTGACC
1 TTTAGCGGCGCTTTCC-C-ACAAACGCCGCAAAAGACCTTGACT
** * * * *
62859161 TTTAGCGGCGCTTTGTGCA-AAGCACCGTTAAAA-ACCCTGACT
1 TTTAGCGGCGCTTT-CCCACAAACGCCG-CAAAAGACCTTGACT
*
62859203 TTTAGCGGCGCGTTTCTCACAAACGCCGCGAAAAGACCTTGACT
1 TTTAGCGGCGC-TTTCCCACAAACGCCGC-AAAAGACCTTGACT
*
62859247 TTTAGCGACGCTTT
1 TTTAGCGGCGCTTT
62859261 TCATAAAAAC
Statistics
Matches: 115, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.25
43 63 0.55
44 21 0.18
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (42 bp):
TTTAGCGGCGCTTTCCCACAAACGCCGCAAAAGACCTTGACT
Found at i:62859164 original size:86 final size:86
Alignment explanation
Indices: 62859074--62859260 Score: 207
Period size: 86 Copynumber: 2.2 Consensus size: 86
62859064 AAGTTATTAT
* * * * *
62859074 CTTTAGCGGCTCTTTACCCACAAACGCCGCTAAAGAGCTTGACTTTTAGCGGCGC-TTCCACTAC
1 CTTTAGCGGCGCTTTACCCA-AAACACCGCTAAAAACCCTGACTTTTAGCGGCGCGTTCCAC-AC
*
62859138 AAACGCCGC-AAAATACCTTGAC
64 AAACGCCGCGAAAAGACCTTGAC
*** * * * *
62859160 CTTTAGCGGCGCTTTGTGCAAAGCACCGTTAAAAACCCTGACTTTTAGCGGCGCGTTTCTCACAA
1 CTTTAGCGGCGCTTTACCCAAAACACCGCTAAAAACCCTGACTTTTAGCGGCGCGTTCCACACAA
62859225 ACGCCGCGAAAAGACCTTGAC
66 ACGCCGCGAAAAGACCTTGAC
* *
62859246 TTTTAGCGACGCTTT
1 CTTTAGCGGCGCTTT
62859261 TCATAAAAAC
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
85 39 0.46
86 45 0.54
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTACCCAAAACACCGCTAAAAACCCTGACTTTTAGCGGCGCGTTCCACACAA
ACGCCGCGAAAAGACCTTGAC
Found at i:62865128 original size:9 final size:9
Alignment explanation
Indices: 62865114--62865200 Score: 87
Period size: 9 Copynumber: 10.3 Consensus size: 9
62865104 AGTATATATG
62865114 AGTTATGTA
1 AGTTATGTA
62865123 AGTTATGT-
1 AGTTATGTA
*
62865131 A-TTACGTA
1 AGTTATGTA
62865139 AGTTATGT-
1 AGTTATGTA
62865147 A-TTATGTA
1 AGTTATGTA
62865155 AGTTATGTA
1 AGTTATGTA
*
62865164 CGTTATGTA
1 AGTTATGTA
*
62865173 AGTTAAGT-
1 AGTTATGTA
*
62865181 A-TTATATA
1 AGTTATGTA
*
62865189 AGTTATGCA
1 AGTTATGTA
62865198 AGT
1 AGT
62865201 CCGACAAGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
7 15 0.24
8 6 0.10
9 42 0.67
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (9 bp):
AGTTATGTA
Found at i:62865139 original size:16 final size:16
Alignment explanation
Indices: 62865116--62865446 Score: 122
Period size: 16 Copynumber: 18.7 Consensus size: 16
62865106 TATATATGAG
62865116 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
62865132 TTACGTAAGTTATGTA
1 TTATGTAAGTTATGTA
62865148 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
62865164 CGTTATGTAAGTTAAGTA
1 --TTATGTAAGTTATGTA
* *
62865182 TTATATAAGTTATGCAA
1 TTATGTAAGTTATG-TA
* ** *
62865199 GTCCGACAAGTTAATGTA
1 TTATG-TAAGTT-ATGTA
* * * *
62865217 TAATATAAATTAATTTA
1 TTATGTAAGTT-ATGTA
*
62865234 GTTATGTGAGTTATGTATAATA
1 -TTATGTAAGTTATG-----TA
*
62865256 TTATGTAACTTATTATGTTA
1 TTATGTAA---GTTATG-TA
62865276 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
62865293 GTTATGTAAGTTAAGTA
1 -TTATGTAAGTTATGTA
* *
62865310 TTATATAAGTTATGCAA
1 TTATGTAAGTTATG-TA
* ** *
62865327 GTCCGACAAGTTAATGTA
1 TTATG-TAAGTT-ATGTA
* * * *
62865345 TAATATAAATTAATTTA
1 TTATGTAAGTT-ATGTA
*
62865362 GTTATGTGAGTTATGTATAATA
1 -TTATGTAAGTTATG-----TA
*
62865384 TTATGTAACTTATTATGTTA
1 TTATGTAA---GTTATG-TA
62865404 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
62865420 TTATGTAAGTTAAGTA
1 TTATGTAAGTTATGTA
62865436 TTATGTAAGTT
1 TTATGTAAGTT
62865447 TTGCAAGTCC
Statistics
Matches: 230, Mismatches: 57, Indels: 56
0.67 0.17 0.16
Matches are distributed among these distances:
16 83 0.36
17 38 0.17
18 55 0.24
19 6 0.03
20 20 0.09
21 14 0.06
22 4 0.02
24 10 0.04
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:62865143 original size:25 final size:25
Alignment explanation
Indices: 62865114--62865200 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
62865104 AGTATATATG
*
62865114 AGTTATGTAAGTTATGTATTACGTA
1 AGTTATGTAAGTTATGTATTATGTA
62865139 AGTTATGT-A-TTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGT-A-TTATGTA
* * *
62865164 CGTTATGTAAGTTAAGTATTATATA
1 AGTTATGTAAGTTATGTATTATGTA
*
62865189 AGTTATGCAAGT
1 AGTTATGTAAGT
62865201 CCGACAAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.12
24 2 0.04
25 37 0.71
26 2 0.04
27 5 0.10
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (25 bp):
AGTTATGTAAGTTATGTATTATGTA
Found at i:62865290 original size:9 final size:9
Alignment explanation
Indices: 62865276--62865328 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
62865266 TATTATGTTA
62865276 TTATGTAAG
1 TTATGTAAG
62865285 TTATGTAAG
1 TTATGTAAG
62865294 TTATGTAAG
1 TTATGTAAG
*
62865303 TTAAGT-A-
1 TTATGTAAG
*
62865310 TTATATAAG
1 TTATGTAAG
*
62865319 TTATGCAAG
1 TTATGTAAG
62865328 T
1 T
62865329 CCGACAAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 4 0.11
8 2 0.05
9 31 0.84
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:62865421 original size:110 final size:113
Alignment explanation
Indices: 62865333--62865564 Score: 302
Period size: 126 Copynumber: 1.9 Consensus size: 113
62865323 GCAAGTCCGA
62865333 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTATT
1 CAAG-TAATG-ATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTATT
**
62865398 ATGTTATTATGTAAGTTATGTATTATGTAAGTTAAGTATTATGTAAGTTTTGCAAGTCC
64 ATGTTATTATGTAAGTTATGTATTA--T-A--TAAG--TTATGTAAG-TCCGCAAGT-C
62865457 GACAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
1 --CAAG-TAATG-ATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
*
62865522 TTATGTTATTATGTAAGTTATGTATTATGTAAGTTATGTAAGT
62 TTATGTTATTATGTAAGTTATGTATTATATAAGTTATGTAAGT
62865565 TAAGTATTAT
Statistics
Matches: 105, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
118 1 0.01
119 9 0.09
121 4 0.04
124 1 0.01
126 90 0.86
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (113 bp):
CAAGTAATGATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTATTAT
GTTATTATGTAAGTTATGTATTATATAAGTTATGTAAGTCCGCAAGTC
Found at i:62865519 original size:126 final size:128
Alignment explanation
Indices: 62865141--62865637 Score: 874
Period size: 128 Copynumber: 3.9 Consensus size: 128
62865131 ATTACGTAAG
*
62865141 TTATG-TATTATGTAAGTTATGTACGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
1 TTATGTTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
62865205 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
66 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
62865268 TTATGTTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
1 TTATGTTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
62865333 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
66 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
* *
62865396 TTATGTTATTATGTAAGTTATGT-A-TTATGTAAGTTAAGTATTATGTAAGTTTTGCAAGTCCGA
1 TTATGTTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
62865459 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
66 CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
62865522 TTATGTTATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCA
1 TTATGTTATTATGT-A---A-G--TTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCA
*
62865587 AGTCCGACAAGTTAATGTATAATATAAACTAATTTAGTTATGTGAGTTATG
59 AGTCCGACAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATG
62865638 CAAGTTGTTA
Statistics
Matches: 354, Mismatches: 6, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
126 114 0.32
127 7 0.02
128 144 0.41
130 1 0.00
131 1 0.00
133 6 0.02
134 1 0.00
135 80 0.23
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (128 bp):
TTATGTTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGA
CAAGTTAATGTATAATATAAATTAATTTAGTTATGTGAGTTATGTATAATATTATGTAACTTA
Found at i:62865544 original size:9 final size:9
Alignment explanation
Indices: 62865530--62865589 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
62865520 TATTATGTTA
62865530 TTATGTAAG
1 TTATGTAAG
62865539 TTATGT-A-
1 TTATGTAAG
62865546 TTATGTAAG
1 TTATGTAAG
62865555 TTATGTAAG
1 TTATGTAAG
*
62865564 TTAAGT-A-
1 TTATGTAAG
*
62865571 TTATATAAG
1 TTATGTAAG
*
62865580 TTATGCAAG
1 TTATGTAAG
62865589 T
1 T
62865590 CCGACAAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 10 0.24
8 4 0.10
9 28 0.67
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:62865549 original size:16 final size:16
Alignment explanation
Indices: 62865522--62865561 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
62865512 ATGTAACTTA
62865522 TTATGTTATTATGTAAG
1 TTATG-TATTATGTAAG
62865539 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
62865555 TTATGTA
1 TTATGTA
62865562 AGTTAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:62865579 original size:25 final size:25
Alignment explanation
Indices: 62865530--62865589 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
62865520 TATTATGTTA
* *
62865530 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTAAGTATTATATAAG
62865555 TTATGTAAGTTAAGTATTATATAAG
1 TTATGTAAGTTAAGTATTATATAAG
*
62865580 TTATGCAAGT
1 TTATGTAAGT
62865590 CCGACAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (25 bp):
TTATGTAAGTTAAGTATTATATAAG
Found at i:62865709 original size:16 final size:16
Alignment explanation
Indices: 62865688--62865737 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
62865678 TATTATGTAA
62865688 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
*
62865704 TAAG-T-T-TA-TATA
1 TAAGTTATGTATTATG
62865716 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
62865732 TAAGTT
1 TAAGTT
62865738 TATATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 2 0.07
15 3 0.11
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:62865721 original size:12 final size:12
Alignment explanation
Indices: 62865704--62865763 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
62865694 ATGTATTATG
62865704 TAAGTTTATATA
1 TAAGTTTATATA
*
62865716 TAAGTTATGTATTATG
1 TAAG-T-T-TA-TATA
62865732 TAAGTTTATATA
1 TAAGTTTATATA
62865744 TAAGTTGT-TATA
1 TAAGTT-TATATA
*
62865756 TAATTTTA
1 TAAGTTTA
62865764 ATTATGTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
11 1 0.03
12 22 0.56
13 4 0.10
14 2 0.05
15 3 0.08
16 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (12 bp):
TAAGTTTATATA
Found at i:62865721 original size:28 final size:28
Alignment explanation
Indices: 62865687--62865749 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
62865677 TTATTATGTA
62865687 ATAAGTTATGTATTATGTAAGTTTATAT
1 ATAAGTTATGTATTATGTAAGTTTATAT
62865715 ATAAGTTATGTATTATGTAAGTTTATAT
1 ATAAGTTATGTATTATGTAAGTTTATAT
62865743 ATAAGTT
1 ATAAGTT
62865750 GTTATATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (28 bp):
ATAAGTTATGTATTATGTAAGTTTATAT
Found at i:62865892 original size:21 final size:21
Alignment explanation
Indices: 62865862--62865960 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 21
62865852 AATTCTTTCT
62865862 AAAATTATAAAATTTATTATTG
1 AAAA-TATAAAATTTATTATTG
* *
62865884 AAAATAT-AAATGTTAATATTT
1 AAAATATAAAAT-TTATTATTG
* * *
62865905 AGAAA-ATAACATTTACAATTCTTTCT
1 A-AAATATAAAATTT---ATT-ATT-G
62865931 AAAATTATAAAATTTATTATTG
1 AAAA-TATAAAATTTATTATTG
62865953 AAAATATA
1 AAAATATA
62865961 GATGTTAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
20 4 0.07
21 19 0.32
22 14 0.24
23 2 0.03
24 5 0.08
25 5 0.08
26 2 0.03
27 8 0.14
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAATATAAAATTTATTATTG
Found at i:62865917 original size:69 final size:69
Alignment explanation
Indices: 62865842--62866097 Score: 419
Period size: 69 Copynumber: 3.7 Consensus size: 69
62865832 TTGAATTACG
*
62865842 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAAATGTTAATATTTAG
1 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
62865907 AAAA
66 AAAA
62865911 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
1 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
62865976 AAAA
66 AAAA
*
62865980 TAACATTTACAATTTTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
1 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
62866045 AAAAA
66 -AAAA
* * *
62866050 TAACATGTAC-ATTAGTTT-TAAAAATATAAAATTTATTATT-AACAATAT
1 TAACATTTACAATT-CTTTCTAAAATTATAAAATTTATTATTGAA-AATAT
62866098 TTAAATATAG
Statistics
Matches: 179, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
68 2 0.01
69 161 0.90
70 16 0.09
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (69 bp):
TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
AAAA
Found at i:62867476 original size:12 final size:12
Alignment explanation
Indices: 62867439--62867478 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
62867429 CAAATAGTTT
*
62867439 CAAACTTATGAA
1 CAAAATTATGAA
62867451 CAAAATTA-GTAA
1 CAAAATTATG-AA
62867463 CAAAATTATGAA
1 CAAAATTATGAA
62867475 CAAA
1 CAAA
62867479 CAGTATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:62867544 original size:12 final size:12
Alignment explanation
Indices: 62867527--62867552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
62867517 ACAGGATAGT
62867527 CAAAATTATGAA
1 CAAAATTATGAA
62867539 CAAAATTATGAA
1 CAAAATTATGAA
62867551 CA
1 CA
62867553 GTTTCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:62868337 original size:16 final size:17
Alignment explanation
Indices: 62868318--62868352 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
62868308 ATTTATTTCA
*
62868318 TAATTTTATC-TTTAAT
1 TAATTGTATCTTTTAAT
62868334 TAATTGTATCTTTTAAT
1 TAATTGTATCTTTTAAT
62868351 TA
1 TA
62868353 CTAAGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
TAATTGTATCTTTTAAT
Found at i:62868856 original size:7 final size:7
Alignment explanation
Indices: 62868831--62868971 Score: 74
Period size: 7 Copynumber: 20.1 Consensus size: 7
62868821 AACTTGAGTA
62868831 CCTAACC
1 CCTAACC
**
62868838 CCTAAATA
1 CCT-AACC
62868846 CCTAACC
1 CCTAACC
*
62868853 CCTAAGTC
1 CCTAA-CC
*
62868861 TCTAACC
1 CCTAACC
* *
62868868 CTTAAAC
1 CCTAACC
* *
62868875 CTTAATC
1 CCTAACC
*
62868882 CCAAACC
1 CCTAACC
*
62868889 CCAAACC
1 CCTAACC
*
62868896 CCAAACC
1 CCTAACC
62868903 ACC-AACC
1 -CCTAACC
* *
62868910 CCAAATC
1 CCTAACC
* *
62868917 CCAAATC
1 CCTAACC
62868924 CCTAACC
1 CCTAACC
62868931 CCTAACC
1 CCTAACC
*
62868938 CTTAACC
1 CCTAACC
62868945 CCTAA-C
1 CCTAACC
62868951 CCTAGA-C
1 CCTA-ACC
62868958 CCTAACC
1 CCTAACC
62868965 CC-AACC
1 CCTAACC
62868971 C
1 C
62868972 TTAAACCTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
6 13 0.12
7 84 0.77
8 12 0.11
ACGTcount: A:0.35, C:0.48, G:0.01, T:0.16
Consensus pattern (7 bp):
CCTAACC
Found at i:62868868 original size:15 final size:15
Alignment explanation
Indices: 62868829--62868857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62868819 CTAACTTGAG
62868829 TACCTAACCCCTAAA
1 TACCTAACCCCTAAA
62868844 TACCTAACCCCTAA
1 TACCTAACCCCTAA
62868858 GTCTCTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (15 bp):
TACCTAACCCCTAAA
Found at i:62868888 original size:21 final size:20
Alignment explanation
Indices: 62868864--62868995 Score: 63
Period size: 21 Copynumber: 6.4 Consensus size: 20
62868854 CTAAGTCTCT
*
62868864 AACCCTTAAACCTTAATCCCA
1 AACCC-TAAACCCTAATCCCA
* * * *
62868885 AACCCCAAACCCCAAACCACC
1 AACCCTAAACCCTAATCC-CA
* *
62868906 AACCCCAAATCCCAAATCCCTA
1 AACCCTAAA-CCCTAATCCC-A
* * *
62868928 ACCCCT-AACCCTTAACCCCT
1 AACCCTAAACCC-TAATCCCA
* *
62868948 AACCCTAGACCCTAA-CCCC
1 AACCCTAAACCCTAATCCCA
*
62868967 AACCCTTAAA-CCTAAATCCTA
1 AACCC-TAAACCCT-AATCCCA
62868988 AACCCTAA
1 AACCCTAA
62868996 TCAATACCCG
Statistics
Matches: 84, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 11 0.13
20 28 0.33
21 34 0.40
22 11 0.13
ACGTcount: A:0.38, C:0.46, G:0.01, T:0.15
Consensus pattern (20 bp):
AACCCTAAACCCTAATCCCA
Found at i:62868953 original size:14 final size:13
Alignment explanation
Indices: 62868923--62868995 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
62868913 AATCCCAAAT
62868923 CCCTAACCCCTAA
1 CCCTAACCCCTAA
62868936 CCCTTAACCCCTAA
1 CCC-TAACCCCTAA
62868950 CCCTAGA-CCCTAA
1 CCCTA-ACCCCTAA
* *
62868963 CCCCAACCCTTAA
1 CCCTAACCCCTAA
* **
62868976 ACCTAAATCCTAAA
1 CCCTAACCCCT-AA
62868990 CCCTAA
1 CCCTAA
62868996 TCAATACCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
12 1 0.02
13 26 0.54
14 21 0.44
ACGTcount: A:0.34, C:0.47, G:0.01, T:0.18
Consensus pattern (13 bp):
CCCTAACCCCTAA
Found at i:62868994 original size:7 final size:7
Alignment explanation
Indices: 62868864--62868995 Score: 55
Period size: 7 Copynumber: 19.1 Consensus size: 7
62868854 CTAAGTCTCT
62868864 AACCCTTA
1 AACCC-TA
*
62868872 AACCTTA
1 AACCCTA
*
62868879 ATCCC-A
1 AACCCTA
*
62868885 AACCCCA
1 AACCCTA
*
62868892 AACCCCA
1 AACCCTA
*
62868899 AACCAC-C
1 AACC-CTA
*
62868906 AACCCCA
1 AACCCTA
62868913 AATCCC-A
1 AA-CCCTA
62868920 AATCCCTA
1 AA-CCCTA
*
62868928 ACCCCT-
1 AACCCTA
62868934 AACCCTTA
1 AACCC-TA
*
62868942 ACCCCT-
1 AACCCTA
62868948 AACCCTA
1 AACCCTA
*
62868955 GACCCT-
1 AACCCTA
*
62868961 AACCC-C
1 AACCCTA
62868967 AACCCTTA
1 AACCC-TA
62868975 AA-CCTA
1 AACCCTA
*
62868981 AATCCTA
1 AACCCTA
62868988 AACCCTA
1 AACCCTA
62868995 A
1 A
62868996 TCAATACCCG
Statistics
Matches: 98, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
6 28 0.29
7 54 0.55
8 16 0.16
ACGTcount: A:0.38, C:0.46, G:0.01, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:62870462 original size:41 final size:40
Alignment explanation
Indices: 62870417--62870534 Score: 105
Period size: 41 Copynumber: 2.9 Consensus size: 40
62870407 CAAACGCCAC
62870417 TAAAAGACCCACCATTAGCGGCGTATACTTAAAAACACCGG
1 TAAAAGACCCACCATTAGCGGCGTATACTTAAAAACACC-G
* ** ** * *
62870458 TAAAAGTCATAAAATTTGTGGCGCTAT--TATAAAAACACCG
1 TAAAAGACCCACCATTAGCGGCG-TATACT-TAAAAACACCG
* *
62870498 TAAAAAACCCTACCATTAGCGGCGTATACTCAAAAAC
1 TAAAAGACCC-ACCATTAGCGGCGTATACTTAAAAAC
62870535 GCAGTTAAAT
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
40 11 0.20
41 41 0.73
42 4 0.07
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (40 bp):
TAAAAGACCCACCATTAGCGGCGTATACTTAAAAACACCG
Found at i:62874233 original size:11 final size:12
Alignment explanation
Indices: 62874214--62874245 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
62874204 ATAAATTGAG
62874214 AATTTAAGAGGA
1 AATTTAAGAGGA
62874226 AA-TTAAGA-GA
1 AATTTAAGAGGA
62874236 AATTTAAGAG
1 AATTTAAGAG
62874246 TGATTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (12 bp):
AATTTAAGAGGA
Found at i:62875125 original size:18 final size:18
Alignment explanation
Indices: 62875102--62875143 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
62875092 GCCCGAGTGG
* *
62875102 GAGGATTTCATGAACGCT
1 GAGGATTACATGAACGAT
*
62875120 GAGGATTACTTGAACGAT
1 GAGGATTACATGAACGAT
62875138 GAGGAT
1 GAGGAT
62875144 AAGTTCAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (18 bp):
GAGGATTACATGAACGAT
Found at i:62884326 original size:19 final size:19
Alignment explanation
Indices: 62884252--62884327 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
62884242 TAAGAAAATA
* *
62884252 TTTATTTCTTTATATATTT
1 TTTATTTATATATATATTT
* *
62884271 TTAAATTT-TATATATTATTA
1 TT-TATTTATATATA-TATTT
62884291 TTTATTGTCA-ATA-ATATTT
1 TTTATT-T-ATATATATATTT
62884310 TTTATTTATATATATATT
1 TTTATTTATATATATATT
62884328 AATTTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
17 1 0.02
18 4 0.09
19 25 0.56
20 12 0.27
21 3 0.07
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTATTTATATATATATTT
Found at i:62886539 original size:28 final size:28
Alignment explanation
Indices: 62886486--62886540 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
62886476 CAAGGTTGAT
* * *
62886486 AGTTATTTCTTTATCTTTGTTAATCTAC
1 AGTTATTTCATTATATTCGTTAATCTAC
62886514 AGTTATTTCATTATATGTCGTT-ATCTA
1 AGTTATTTCATTATAT-TCGTTAATCTA
62886541 TATGCTACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.55
Consensus pattern (28 bp):
AGTTATTTCATTATATTCGTTAATCTAC
Found at i:62904419 original size:84 final size:85
Alignment explanation
Indices: 62904322--62904557 Score: 236
Period size: 89 Copynumber: 2.7 Consensus size: 85
62904312 CCAATGATCC
* *
62904322 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAA-AACCACAGATCTTATCTCTCTGAAGTTGCA-G
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAGAACCA-AG-TCCTATCTCTCTGAAGTTGCAGG
62904385 A-G-A-AC-AGATCGCATCTAATCT
64 AGGTAGACAAGATCGCA---AATCT
* * *
62904406 TATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCCTATCTTTCTGAAGTTGCAGTG
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAG-AACCAAGTCCTATCTCTCTGAAGTTGCAG-G
*
62904471 AGGTAGACTGAAGATGGCAAATCT
64 AGGTAGAC--AAGATCGCAAATCT
* *
62904495 TATCTCCCTAAAGTTGCAGTGGAGCAGATT-AGAGCCGATTA-TCCTATCTCCCTGAAGTTGCAG
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAGAACC-A--AGTCCTATCTCTCTGAAGTTGCAG
62904558 TGGAGCGGAT
Statistics
Matches: 128, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
84 49 0.38
85 2 0.02
86 6 0.05
87 3 0.02
88 4 0.03
89 56 0.44
90 1 0.01
92 7 0.05
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (85 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAGAACCAAGTCCTATCTCTCTGAAGTTGCAGGAG
GTAGACAAGATCGCAAATCT
Found at i:62904464 original size:44 final size:43
Alignment explanation
Indices: 62904322--62905172 Score: 426
Period size: 44 Copynumber: 19.6 Consensus size: 43
62904312 CCAATGATCC
* * * *
62904322 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAA-AACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCT
* * * * * *
62904366 TATCTCTCTGAAGTTGCAG-AGAACAGA-T-CGCATCTAA-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAGTCT
* *
62904406 TATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
** * * *
62904450 TATCTTTCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * *
62904495 TATCTCCCTAAAGTTGCAGTGGAGCAGA-TTAG-AGCCGATTA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A--AGTCT
* * * **
62904539 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AAACTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
62904583 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCA-CATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* * *
62904623 TATCTCTCTGAAGTTGCAATGGAGCAGACTAAGCAAGCAAGTCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * *
62904667 TATCTTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCT
* * *
62904712 TATCTCCCTGAAGTTGTAGTGGAGCAGA-TTA-AAGCCGATAATAC-
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGT-CT
* * * * *
62904756 TATCTCCCTGAAGTTACAGTGGAGCGGATTAA-AACCTTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * ** * * * * * *
62904800 TATTTCTCTGAAATTTTAG-AGAGTAGA-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
62904840 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * **
62904884 TATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCT
* * * *
62904929 TATCTCCCTGAAGTTGCAGTGGAGCAG-GTTA-AAGCCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * * * * **
62904973 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAA-AATCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* ** * * * * *
62905017 TATCTCTCTGAAGTTGCAG-AAAGTAGA-T-CGTATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
62905057 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * **
62905101 TATC-CTCCTGAAGTTGCAGTGGGGCAAACTGAAGATGGCAAACCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCT
62905146 TATCTCCCTGAAGTTGCAGTGGAGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAG
62905173 GTTAAAGCCG
Statistics
Matches: 612, Mismatches: 140, Indels: 109
0.71 0.16 0.13
Matches are distributed among these distances:
40 79 0.13
41 34 0.06
42 25 0.04
43 39 0.06
44 289 0.47
45 142 0.23
46 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:62904698 original size:217 final size:217
Alignment explanation
Indices: 62904308--62905303 Score: 1526
Period size: 217 Copynumber: 4.6 Consensus size: 217
62904298 GAACAGATCA
* * ***
62904308 AAAGCCAATGATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
* * *
62904373 CTGAAGTTGCAGAGAACAGATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAA
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* * * * *
62904438 GTAAGCAAGTCCTATCTTTCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCC
*
62904503 TAAAGTTGCAGTGGAGCAGATT
196 TGAAGTTGCAGTGGAGCAGATT
* * * *
62904525 AGAGCCGATTATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAACTTGGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
* * *
62904590 CTGAAGTTGCAGAGAGCAGATCACATCTAGTCTTATCTCTCTGAAGTTGCAATGGAGCAGACTAA
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* * * * *
62904655 GCAAGCAAGTCATATCTTCCTGAAGTTGCAGTGAAGCAGACTGAAGATGGCAAATCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCC
*
62904720 TGAAGTTGTAGTGGAGCAGATT
196 TGAAGTTGCAGTGGAGCAGATT
* * * * *
62904742 AAAGCCGATAATACTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTAGATCTTATTTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
* ** *
62904807 CTGAAATTTTAGAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
*
62904872 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCC
*
62904937 TGAAGTTGCAGTGGAGCAGGTT
196 TGAAGTTGCAGTGGAGCAGATT
* *
62904959 AAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAATCTTGGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
* * *
62905024 CTGAAGTTGCAGAAAGTAGATCGTATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
* *
62905089 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAAACTGAAGATGGCAAACCTTATCTCCC
131 GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCC
*
62905154 TGAAGTTGCAGTGGAGCAGGTT
196 TGAAGTTGCAGTGGAGCAGATT
* *
62905176 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCTTGGATCTTATCTCT
1 AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
* *
62905241 CTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGACA-TTGCAGTGGAGTAGACT
66 CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACT
62905304 GCAGCACTAG
Statistics
Matches: 715, Mismatches: 63, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
217 714 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT
CTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
GTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCCC
TGAAGTTGCAGTGGAGCAGATT
Found at i:62905658 original size:5 final size:5
Alignment explanation
Indices: 62905650--62905676 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
62905640 AAAGGAAAGA
62905650 AAATC AAATC AAATC AAATC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AA
62905677 GCATATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:62906601 original size:20 final size:20
Alignment explanation
Indices: 62906570--62906620 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
62906560 TAGTAATTTC
62906570 TTATTA-TTTTTTAATGTAA
1 TTATTATTTTTTTAATGTAA
* * *
62906589 TTATTATTTTTTTCATTTAT
1 TTATTATTTTTTTAATGTAA
62906609 TTATTTATTTTT
1 TTA-TTATTTTT
62906621 CTCTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 8 0.30
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTATTTTTTTAATGTAA
Found at i:62908110 original size:33 final size:32
Alignment explanation
Indices: 62908073--62908171 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 32
62908063 AATGGTTGGC
* *
62908073 TGTCCATTGAGATGCCCGAACAGTCATGTGCTG
1 TGTCCATTGAG-TGCACGAACAGCCATGTGCTG
* *
62908106 TGTCCATTGGTGTGCACGAACAGCCTTGTGCTG
1 TGTCCATT-GAGTGCACGAACAGCCATGTGCTG
* *
62908139 TGTCCATTGATGTGCACGAACAGCTATGAGCTG
1 TGTCCATTGA-GTGCACGAACAGCCATGTGCTG
62908172 AGTAAGCTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 53 0.95
34 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (32 bp):
TGTCCATTGAGTGCACGAACAGCCATGTGCTG
Found at i:62910361 original size:27 final size:27
Alignment explanation
Indices: 62910330--62910385 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
62910320 TAAAAAACGG
** *
62910330 AATAAATGGGTAAATAATAATTATAAT
1 AATAAATGCATAAATAATAATAATAAT
*
62910357 AATAAATGCATTAATAATAATAATAAT
1 AATAAATGCATAAATAATAATAATAAT
62910384 AA
1 AA
62910386 AACTGATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (27 bp):
AATAAATGCATAAATAATAATAATAAT
Found at i:62913971 original size:23 final size:22
Alignment explanation
Indices: 62913931--62913980 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
62913921 AATTAAGGTT
*
62913931 AAAATAGTAATAAGTAAATA-AC
1 AAAATAGTAATAAATAAA-ACAC
*
62913953 AAAATATTAAATAAATAAAACAC
1 AAAATAGT-AATAAATAAAACAC
62913976 AAAAT
1 AAAAT
62913981 GACATGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATAGTAATAAATAAAACAC
Found at i:62914907 original size:44 final size:42
Alignment explanation
Indices: 62914859--62914974 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 42
62914849 ATGAGTATTT
62914859 GTGTAAGACCACGTCTGGGACATTGGCATCGA-TTTGAGGTTTAC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGACTTTGA---TTAC
*
62914903 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGACGTTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCGAC-TTTGATTAC
* *
62914946 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
62914975 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
43 29 0.45
44 30 0.47
46 5 0.08
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGACTTTGATTAC
Found at i:62914965 original size:43 final size:42
Alignment explanation
Indices: 62914860--62914974 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 42
62914850 TGAGTATTTG
* *
62914860 TGTAAGACCACGTCTGGGACATTGGCATCGATTTGAGGTTTACG
1 TGTAAGACCACGTCTGGGACAGTGGCATCGATTTGA-G-TTACA
62914904 TGTAAGACC-CTGTCTGGGACAGTGGCATCGACGTTTGA-TTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGA--TTTGAGTTACA
62914947 TGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TGTAAGACCACGTCTGGGACAG-TGGCAT
62914975 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
42 1 0.02
43 29 0.45
44 29 0.45
46 5 0.08
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATTTGAGTTACA
Found at i:62915815 original size:23 final size:23
Alignment explanation
Indices: 62915772--62915817 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
62915762 ATTAATTATA
* *
62915772 GACTTATAGATTGACGTATAATT
1 GACTTATAAATAGACGTATAATT
62915795 GACTTATAAATAGA-GTGATAATT
1 GACTTATAAATAGACGT-ATAATT
62915818 AGTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
GACTTATAAATAGACGTATAATT
Found at i:62920190 original size:24 final size:22
Alignment explanation
Indices: 62920161--62920223 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
62920151 AATTCTAAAC
62920161 CATTTAATAACTCATCTAATAACT
1 CATTTAATAACTCATCT-ATAA-T
62920185 CATTTAATGAAC-CAT-T-TAAT
1 CATTTAAT-AACTCATCTATAAT
62920205 CATTTAATAACTCCATCTA
1 CATTTAATAACT-CATCTA
62920224 CACAACAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
21 6 0.18
22 1 0.03
23 1 0.03
24 11 0.32
25 3 0.09
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (22 bp):
CATTTAATAACTCATCTATAAT
Found at i:62920200 original size:12 final size:12
Alignment explanation
Indices: 62920161--62920204 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
62920151 AATTCTAAAC
62920161 CATTTAATAACT
1 CATTTAATAACT
*
62920173 CATCTAATAACT
1 CATTTAATAACT
62920185 CATTTAATGAAC-
1 CATTTAAT-AACT
62920197 CATTTAAT
1 CATTTAAT
62920205 CATTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (12 bp):
CATTTAATAACT
Found at i:62931556 original size:15 final size:15
Alignment explanation
Indices: 62931536--62931570 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
62931526 ACAGATCGGG
*
62931536 TCAGTTTTTGGTTTC
1 TCAGTTTTTGGTTGC
*
62931551 TCAGTTTTTTGTTGC
1 TCAGTTTTTGGTTGC
62931566 TCAGT
1 TCAGT
62931571 CCTACTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.14, G:0.20, T:0.57
Consensus pattern (15 bp):
TCAGTTTTTGGTTGC
Found at i:62943442 original size:21 final size:22
Alignment explanation
Indices: 62943416--62943470 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 22
62943406 ATTCCCGTCT
62943416 CCTTCTCT-TTCTGTTTTCTTA
1 CCTTCTCTCTTCTGTTTTCTTA
62943437 CCTTCTCTATTTCTTCTGTTTTCTTA
1 CCTTCTC----TCTTCTGTTTTCTTA
62943463 CCTTCTCT
1 CCTTCTCT
62943471 ATTTCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
25 1 0.03
26 20 0.69
ACGTcount: A:0.05, C:0.31, G:0.04, T:0.60
Consensus pattern (22 bp):
CCTTCTCTCTTCTGTTTTCTTA
Found at i:62943457 original size:26 final size:26
Alignment explanation
Indices: 62943424--62943477 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
62943414 CTCCTTCTCT
62943424 TTCTGTTTTCTTACCTTCTCTATTTC
1 TTCTGTTTTCTTACCTTCTCTATTTC
62943450 TTCTGTTTTCTTACCTTCTCTATTTC
1 TTCTGTTTTCTTACCTTCTCTATTTC
62943476 TT
1 TT
62943478 TTAACGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.07, C:0.26, G:0.04, T:0.63
Consensus pattern (26 bp):
TTCTGTTTTCTTACCTTCTCTATTTC
Found at i:62948232 original size:52 final size:50
Alignment explanation
Indices: 62948127--62948328 Score: 247
Period size: 50 Copynumber: 4.1 Consensus size: 50
62948117 ATCACATTTA
62948127 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT---AC----CACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
*
62948171 TCACTTGTCACTGATCAGATAAGTGTAGCCTAAAGCTACCACTTATCAGTTG
1 TCACTTGTCACTGATCAGATAAGTGTAG-CT-AAGCTACCACTTATCACTTG
*
62948223 TCACCTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG
* * * * *
62948273 CCACTTGTCATTGATCAAATAAGTGTAGCTGAAGCTGCTACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
*
62948324 CCACT
1 TCACT
62948329 GATAAAAAGT
Statistics
Matches: 140, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
44 28 0.20
45 8 0.06
48 2 0.01
50 45 0.32
51 25 0.18
52 32 0.23
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (50 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG
Found at i:62953319 original size:13 final size:13
Alignment explanation
Indices: 62953301--62953325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62953291 TCCAGCAACT
62953301 ATGAATTTATTTC
1 ATGAATTTATTTC
62953314 ATGAATTTATTT
1 ATGAATTTATTT
62953326 GATGTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:62953538 original size:50 final size:50
Alignment explanation
Indices: 62953425--62953673 Score: 216
Period size: 50 Copynumber: 4.8 Consensus size: 50
62953415 ATTTGGGTAA
* * * * * *
62953425 AGAGATCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATTCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA--C-CGA-A--ATG
*
62953481 AGAGGTCCCATGTAAGACCATGT-TTGAGACATGGCGTTGGCACCGAAATG
1 AGAGGTCCCATGTAAGACCATGTCTAG-GACATGGCGTTGGCACCGAAATG
* *
62953531 AGAGGTCCCATGTAAGACTATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAAATG
* * * *
62953581 AGAGGTCCCCTATAAGATCATGTCTAGGACATGGC-TTGGGCACCGATA-G
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTT-GGCACCGAAATG
** * * * *
62953630 AAGAACATTCCATGTAAGACCATGCCTGGGACATGGCTTTGGCA
1 -AG-AGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA
62953674 TGTTTTTTAC
Statistics
Matches: 165, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
49 3 0.02
50 88 0.53
51 31 0.19
52 3 0.02
53 2 0.01
54 1 0.01
55 2 0.01
56 35 0.21
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAAATG
Found at i:62953623 original size:100 final size:103
Alignment explanation
Indices: 62953425--62953674 Score: 242
Period size: 100 Copynumber: 2.4 Consensus size: 103
62953415 ATTTGGGTAA
* *
62953425 AGAGATCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATTCTTGAGATCACGAGAGGTCCC
1 AGAGATCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA-TCTCGAGAT--CGAGAGGTCCC
* *
62953490 ATGTAAGACCATGTTTGAGACATGGCGTTGGCACCGAAATG
63 ATATAAGACCATGTTAGAGACATGGCGTTGGCACCGAAATG
* * * * *
62953531 AGAGGTCCCATGTAAGACTATGTCTAGGACATGGCGTTGGCA-C-CGAGAT-GAGAGGTCCCCTA
1 AGAGATCCCACGTAAGACCATGTCTAGGACATGGCATTGGCATCTCGAGATCGAGAGGTCCCATA
* *
62953593 TAAGATCATGTCTAG-GACATGGC-TTGGGCACCGATA-G
66 TAAGACCATGT-TAGAGACATGGCGTT-GGCACCGAAATG
* * * * * *
62953630 AAGAACATTCCATGTAAGACCATGCCTGGGACATGGCTTTGGCAT
1 -AG-AGATCCCACGTAAGACCATGTCTAGGACATGGCATTGGCAT
62953675 GTTTTTTACC
Statistics
Matches: 121, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
99 3 0.02
100 40 0.33
101 35 0.29
103 5 0.04
104 1 0.01
106 37 0.31
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (103 bp):
AGAGATCCCACGTAAGACCATGTCTAGGACATGGCATTGGCATCTCGAGATCGAGAGGTCCCATA
TAAGACCATGTTAGAGACATGGCGTTGGCACCGAAATG
Found at i:62956620 original size:23 final size:22
Alignment explanation
Indices: 62956594--62956637 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
62956584 AATTTTTTTA
*
62956594 TAAAATTATAAAATATATATTTC
1 TAAAATTATAAAA-AAATATTTC
*
62956617 TAAAATTCTAAAAAAATATTT
1 TAAAATTATAAAAAAATATTT
62956638 AAAGTTGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATTATAAAAAAATATTTC
Found at i:62956962 original size:25 final size:28
Alignment explanation
Indices: 62956911--62956964 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
62956901 AAGTCAAAAC
* *
62956911 TATTTATTAATATTTAATATTATATTTT
1 TATTTATTAATATTAAATATTAAATTTT
62956939 TATTT-TTAAT-TTAAAT-TTAAATTTT
1 TATTTATTAATATTAAATATTAAATTTT
62956964 T
1 T
62956965 TGTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 5 0.21
27 5 0.21
28 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTATTAATATTAAATATTAAATTTT
Found at i:62959586 original size:17 final size:18
Alignment explanation
Indices: 62959564--62959609 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
62959554 CGATGTAAAA
62959564 TAATATTATATAAATT-T
1 TAATATTATATAAATTGT
*
62959581 TAATA-TATAT-ATTTGT
1 TAATATTATATAAATTGT
*
62959597 TAGTATTATATAA
1 TAATATTATATAA
62959610 GTATATGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 10 0.42
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
TAATATTATATAAATTGT
Found at i:62975363 original size:17 final size:17
Alignment explanation
Indices: 62975333--62975366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62975323 AATAATTTCT
* *
62975333 AAAAATATGTATATGTA
1 AAAAAAATGCATATGTA
62975350 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
62975367 TTATAAAATG
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:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (17 bp):
AAAAAAATGCATATGTA
Found at i:62977523 original size:132 final size:131
Alignment explanation
Indices: 62977318--62978331 Score: 1438
Period size: 132 Copynumber: 7.7 Consensus size: 131
62977308 AGATCTGATT
* * ** * * * * *
62977318 TCTTCGATCGATTCCACTGCCGACTAGAGAGATAGAATTACTAGCTTCAATATATTCCACTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * ** * * *
62977383 CATTAGGGAGGTAAAATCTACCATCTTCGATCTATTCCACTACTGCCTAGGGAAATAAGATCTAT
66 CCTCAGGGAGGTAAAATCCACCATCTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62977448 AA
130 AA
* * *
62977450 TCTTCAATCTATTCCACTATTGCCTAGGGAGATAGAATTATTGGCTTCAATATACTCCACTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
** * * * *
62977515 CCTCAGGGAGGTAAAATCTGCCATCATTGATCTGTTCCACTACTACTTAGGGAGATAATATCTAT
66 CCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62977580 AA
130 AA
* * *
62977582 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTGCTCCACTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
62977647 CCTCAGGGAGGTAAAATCCGCCATCATTGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62977712 AA
130 AA
* * *
62977714 TATTCAATCTATTCAACTGTTGCCTAGGGAGATAGAATTACTAGCTTCAATAG-ACTCCACTGTA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAAT-GTACTCCACTGTA
* * *
62977778 ACCTCAGGGAGATAAAATCCGCCATCATTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTT
65 ACCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
62977843 TAA
129 TAA
* * *
62977846 TCTTCAATCTATTCCACTGCTGCCCAGAGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
62977911 CCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62977976 AA
130 AA
62977978 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * *
62978043 CTTTAGGGAGGTAAAATCCACCATCTCTGATCTGCTCCACTACTACTTAGGGAGATAAGATCCGT
66 CCTCAGGGAGGTAAAATCCACCATCT-TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62978108 AA
130 AA
* *
62978110 TCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCATTGTAA
1 TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* ** *
62978175 CCTCAGGAAGGTAAAATCTGCCATCCTTGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTGT
66 CCTCAGGGAGGTAAAATCCACCAT-CTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
62978240 AA
130 AA
* *
62978242 TCTTCAATCTATTCCACTGTTGCAC-ATGGAGATAAAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAATCTATTCCACTGTTGC-CTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
*
62978306 ACCTCAGGGAGGTAAAATTCACCATC
65 ACCTCAGGGAGGTAAAATCCACCATC
62978332 AACCTACTCC
Statistics
Matches: 801, Mismatches: 75, Indels: 13
0.90 0.08 0.01
Matches are distributed among these distances:
131 3 0.00
132 792 0.99
133 6 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (131 bp):
TCTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCCACCATCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
A
Found at i:62977597 original size:44 final size:44
Alignment explanation
Indices: 62977362--62978127 Score: 157
Period size: 44 Copynumber: 17.4 Consensus size: 44
62977352 GAATTACTAG
* * * **
62977362 CTTCAATATATTCCACT-GTAACATTAGGGAGGTAAAATCTACCAT
1 CTTCAATCTATTCCACTACT-AC-TTAGGGAGATAAAATCTATAAT
* * * * *
62977407 CTTCGATCTATTCCACTACTGCCTAGGGAAATAAGATCTATAAT
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
* * * * ***
62977451 CTTCAATCTATTCCACTATTGCCTAGGGAGATAGAAT-TATTGG
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
* * * * * ***
62977494 CTTCAATATACTCCACT-GTAACCTCAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTATTCCACTACT-A-CTTAGGGAGATAAAATCTATAAT
* * *
62977539 CATT-GATCTGTTCCACTACTACTTAGGGAGATAATATCTATAAT
1 C-TTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
* * ** * **
62977583 CTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAAT-TACT-GG
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTA-TAAT
* ** * * * ****
62977626 CTTCAATGTGCTCCACT-GTAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTATTCCACTACT-A-CTTAGGGAGATAAAATCTATAAT
* ** * * * *
62977671 CATT-GATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAAT
1 C-TTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
* * ** * * * *
62977715 ATTCAATCTATTCAACTGTTGCCTAGGGAGATAGAAT-TACT-AG
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTA-TAAT
** * * * ****
62977758 CTTCAATAGACTCCACT-GTAACCTCAGGGAGATAAAATCCGCCAT
1 CTTCAATCTATTCCACTACT-A-CTTAGGGAGATAAAATCTATAAT
* ** * * *
62977803 CATT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAAT
1 C-TTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
* * ** * * **
62977847 CTTCAATCTATTCCACTGCTGCCCAGAGAGATAGAAT-TACT-GG
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTA-TAAT
* * * * * * **
62977890 CTTCAATGTACTCCACT-GTAACCTCAGGGAGGTAAAATCCACCAT
1 CTTCAATCTATTCCACTACT-A-CTTAGGGAGATAAAATCTATAAT
** ** * * *
62977935 CTTTGATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAAT
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
** * * * **
62977979 CTTCAATCTATTCCACTGTTGCCTAGGGAGATAGAAT-TACT-GG
1 CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTA-TAAT
* * * * * **
62978022 CTTCAATGTACTCCACT-GTAACTTTAGGGAGGTAAAATCCACCAT
1 CTTCAATCTATTCCACTACT-AC-TTAGGGAGATAAAATCTATAAT
* ** * **
62978067 C-TCTGATCTGCTCCACTACTACTTAGGGAGATAAGATCCGTAAT
1 CTTC-AATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
62978111 CTTCAATCTATTCCACT
1 CTTCAATCTATTCCACT
62978128 GTTGCCCAGG
Statistics
Matches: 495, Mismatches: 189, Indels: 75
0.65 0.25 0.10
Matches are distributed among these distances:
42 5 0.01
43 87 0.18
44 309 0.62
45 82 0.17
46 12 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTCAATCTATTCCACTACTACTTAGGGAGATAAAATCTATAAT
Found at i:62979149 original size:13 final size:13
Alignment explanation
Indices: 62979131--62979155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62979121 AAATTGTCGA
62979131 GGATAACAAAGAT
1 GGATAACAAAGAT
62979144 GGATAACAAAGA
1 GGATAACAAAGA
62979156 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:62985453 original size:13 final size:13
Alignment explanation
Indices: 62985435--62985460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62985425 TGTTCAATTT
62985435 TTTACTAGAAAAC
1 TTTACTAGAAAAC
62985448 TTTACTAGAAAAC
1 TTTACTAGAAAAC
62985461 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:63002684 original size:16 final size:16
Alignment explanation
Indices: 63002663--63002695 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
63002653 TTTGGTTCGT
63002663 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
63002679 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
63002695 T
1 T
63002696 ATAATAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:63002955 original size:18 final size:17
Alignment explanation
Indices: 63002934--63002968 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
63002924 TTATTATTAA
*
63002934 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
63002952 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
63002969 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:63003022 original size:157 final size:157
Alignment explanation
Indices: 63002828--63003137 Score: 584
Period size: 157 Copynumber: 2.0 Consensus size: 157
63002818 CCCTTAGCAT
*
63002828 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
63002893 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
63002958 TTTAATAAAATTCTTAATAATTAGTAG
131 TTTAATAAAATTCTTAATAATTAGTAG
*
63002985 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
63003050 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
*
63003115 TTTAATATAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
63003138 ATATTCTTAT
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTAGTAG
Found at i:63003108 original size:16 final size:16
Alignment explanation
Indices: 63003071--63003112 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
63003061 TTAATCATAT
*
63003071 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
63003087 TT-AAATATATTATAA
1 TTAAAATATATTATAA
63003102 TTAAAATATAT
1 TTAAAATATAT
63003113 AATTTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:63003119 original size:14 final size:15
Alignment explanation
Indices: 63003080--63003123 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
63003070 TTTAAACATA
*
63003080 ATTATTATTAAATAT
1 ATTATAATTAAATAT
63003095 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
63003109 A-TATAATTTAATAT
1 ATTATAATTAAATAT
63003123 A
1 A
63003124 ATTCTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 9 0.35
14 6 0.23
15 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:63003201 original size:66 final size:63
Alignment explanation
Indices: 63003130--63003327 Score: 168
Period size: 66 Copynumber: 3.2 Consensus size: 63
63003120 TATAATTCTT
63003130 AATAATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAATTA
1 AATAATTAATATTCTTATATGAATTTACTCAAA-CATAATATATGATACT-TAAAATATAAATTA
* ** * * * **
63003195 ACATAATTATTATT-AAATAT--ATTATAATTAAA-AT-ATATA--AT--TTAAAAAAT-TCTT-
1 A-ATAATTAATATTCTTATATGAATT-TACTCAAACATAATATATGATACTTAAAATATAAATTA
63003249 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA-AAATTT
1 AATAATTAATATTCTTATATGAATTTACTCAAA-CATAATATATGATACT-TAAAATATAAA-TT
63003313 GA
63 -A
63003315 AATAATTAATATT
1 AATAATTAATATT
63003328 AAATATATTT
Statistics
Matches: 100, Mismatches: 16, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
53 11 0.11
54 5 0.05
55 8 0.08
56 10 0.10
57 3 0.03
58 5 0.05
59 2 0.02
60 2 0.02
61 5 0.05
62 3 0.03
63 9 0.09
64 8 0.08
65 5 0.05
66 24 0.24
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (63 bp):
AATAATTAATATTCTTATATGAATTTACTCAAACATAATATATGATACTTAAAATATAAATTA
Found at i:63003239 original size:14 final size:14
Alignment explanation
Indices: 63003181--63003241 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
63003171 TATGATACTG
63003181 TAAAATA-TA-AAT
1 TAAAATATTATAAT
* *
63003193 TAACATAATTATTAT
1 TAAAAT-ATTATAAT
63003208 TAAATATATTATAAT
1 TAAA-ATATTATAAT
63003223 TAAAATA-TATAATT
1 TAAAATATTATAA-T
63003237 TAAAA
1 TAAAA
63003242 AATTCTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 5 0.12
13 6 0.15
14 11 0.28
15 16 0.40
16 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:63003288 original size:119 final size:121
Alignment explanation
Indices: 63003069--63003364 Score: 494
Period size: 119 Copynumber: 2.5 Consensus size: 121
63003059 ATTTAATCAT
* *
63003069 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATATAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
63003134 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATA-AA
63003191 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAA-AAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
63003253 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATAAA
66 ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATAAA
* *
63003309 ATTTGAA-ATAATTAATATTAAATATATT-TAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
63003365 TAAAATAATT
Statistics
Matches: 166, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
118 23 0.14
119 92 0.55
120 48 0.29
121 2 0.01
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATAAA
Found at i:63003361 original size:17 final size:17
Alignment explanation
Indices: 63003330--63003363 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
63003320 TTAATATTAA
63003330 ATATATTTAATTAAAAT
1 ATATATTTAATTAAAAT
63003347 ATATGATTTAA-TAAAAT
1 ATAT-ATTTAATTAAAAT
63003364 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATTTAATTAAAAT
Found at i:63003377 original size:28 final size:27
Alignment explanation
Indices: 63003302--63003377 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
63003292 TGATACTATA
*
63003302 AAATAAAATTTGAAATAATTA-ATATT
1 AAATAAAATTTAAAATAATTATATATT
*
63003328 AAAT-ATATTTAATTAA-AA-TATATGATT
1 AAATAAAATTTAA--AATAATTATAT-ATT
*
63003355 TAATAAAATTTAAAATAATTATA
1 AAATAAAATTTAAAATAATTATA
63003378 ACTAATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
25 8 0.21
26 10 0.26
27 10 0.26
28 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
AAATAAAATTTAAAATAATTATATATT
Found at i:63003502 original size:91 final size:92
Alignment explanation
Indices: 63003394--63003586 Score: 264
Period size: 91 Copynumber: 2.1 Consensus size: 92
63003384 AATTATATTT
* * * *
63003394 TATGAATTTGTATAATTTAAAATGA-TAATTATTACATATAATTTAATAATAATATATAATTTCA
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCA
* *
63003458 TAAAATTCTTGATAAT-AAATTTTATAA
65 TAAAATTCTTAATAATAAAATGTTATAA
* * *
63003485 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTTAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCAT
* *
63003550 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTATAA
63003577 TATGAATTTA
1 TATGAATTTA
63003587 CTAAAATCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
91 68 0.76
92 21 0.24
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTATAA
Found at i:63003561 original size:47 final size:46
Alignment explanation
Indices: 63003429--63003567 Score: 126
Period size: 47 Copynumber: 3.0 Consensus size: 46
63003419 TAATTATTAC
* * *
63003429 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAAT-ATGATATATAATTTTATAAAATTCTTAATAATAA
* * ** *
63003476 AT-T--TTATAATATGAATTTATACA-ATT-TAAAATAATTAATATTAA
1 ATATAATT-TAATATG-ATATATA-ATTTTATAAAATTCTTAATAATAA
63003520 ATATAATTTAATAGTGATATATAATTTTATAAAATTCTTAATAATAA
1 ATATAATTTAATA-TGATATATAATTTTATAAAATTCTTAATAATAA
63003567 A
1 A
63003568 ATGTTCTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 15 0.21
47 22 0.31
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (46 bp):
ATATAATTTAATATGATATATAATTTTATAAAATTCTTAATAATAA
Found at i:63005013 original size:11 final size:11
Alignment explanation
Indices: 63004999--63005025 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
63004989 AAAAATCAAT
63004999 ACAAAAGTTTC
1 ACAAAAGTTTC
63005010 ACAAAAGTTTC
1 ACAAAAGTTTC
63005021 ACAAA
1 ACAAA
63005026 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:63007284 original size:15 final size:15
Alignment explanation
Indices: 63007264--63007293 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
63007254 TATTATGTAC
*
63007264 AATTGACGTAAAATT
1 AATTGACCTAAAATT
63007279 AATTGACCTAAAATT
1 AATTGACCTAAAATT
63007294 TGAAGGTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTGACCTAAAATT
Found at i:63013362 original size:16 final size:17
Alignment explanation
Indices: 63013343--63013384 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
63013333 TTTCTTTATT
*
63013343 TTCTATTCTCT-TTTGC
1 TTCTCTTCTCTGTTTGC
*
63013359 TTCTCTT-TCTGTTTTC
1 TTCTCTTCTCTGTTTGC
63013375 TTCTCTTCTC
1 TTCTCTTCTC
63013385 CATTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 17 0.77
17 2 0.09
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (17 bp):
TTCTCTTCTCTGTTTGC
Found at i:63015365 original size:19 final size:19
Alignment explanation
Indices: 63015309--63015367 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
63015299 ATATTAAGAA
*
63015309 TAAATTAAAATTAATTA-TA
1 TAAATTAAAA-TAATTATTT
* *
63015328 AAAATTATAAGTAATTATTT
1 TAAATTA-AAATAATTATTT
63015348 TAAATTAAAATAATTATTT
1 TAAATTAAAATAATTATTT
63015367 T
1 T
63015368 TATTTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAATTAAAATAATTATTT
Found at i:63016521 original size:23 final size:23
Alignment explanation
Indices: 63016495--63016541 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
63016485 TCGAATACAA
*
63016495 GTACTTAGAGGCTTATTTTGGAT
1 GTACTTAAAGGCTTATTTTGGAT
63016518 GTACTTAAAGGCTTATTTTGGAT
1 GTACTTAAAGGCTTATTTTGGAT
63016541 G
1 G
63016542 ATTTTATTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (23 bp):
GTACTTAAAGGCTTATTTTGGAT
Done.