Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold199
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: 611138
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 5
Found at i:509124 original size:6 final size:6
Alignment explanation
Indices: 509102--509163 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
509092 TTAAGTTAAT
* * * * *
509102 TATATA CATACA TATATA TATATA TATATA TACATA CATATA CATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
509150 TATATA TATATA TA
1 TATATA TATATA TA
509164 ATGCAACACC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:509126 original size:10 final size:10
Alignment explanation
Indices: 509102--509163 Score: 79
Period size: 10 Copynumber: 6.2 Consensus size: 10
509092 TTAAGTTAAT
*
509102 TATATACATA
1 TATATATATA
*
509112 CATATATATA
1 TATATATATA
509122 TATATATATA
1 TATATATATA
* *
509132 TACATACATA
1 TATATATATA
*
509142 TACATATATA
1 TATATATATA
509152 TATATATATA
1 TATATATATA
509162 TA
1 TA
509164 ATGCAACACC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 45 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATATATA
Found at i:509136 original size:26 final size:26
Alignment explanation
Indices: 509102--509159 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
509092 TTAAGTTAAT
*
509102 TATATACATACATATATATATATATA
1 TATATACATACATATACATATATATA
509128 TATATACATACATATACATATATATA
1 TATATACATACATATACATATATATA
509154 TATATA
1 TATATA
509160 TATAATGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (26 bp):
TATATACATACATATACATATATATA
Found at i:509152 original size:4 final size:4
Alignment explanation
Indices: 509102--509163 Score: 79
Period size: 4 Copynumber: 15.5 Consensus size: 4
509092 TTAAGTTAAT
* * * * *
509102 TATA TACA TACA TATA TATA TATA TATA TATA CATA CATA TACA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
509150 TATA TATA TATA TA
1 TATA TATA TATA TA
509164 ATGCAACACC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:509519 original size:17 final size:19
Alignment explanation
Indices: 509482--509524 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
509472 ATCAAGTATA
509482 AATATTACATTCAATAAAT
1 AATATTACATTCAATAAAT
**
509501 AA-ATTA-ATTCAATTTAT
1 AATATTACATTCAATAAAT
509518 AATATTA
1 AATATTA
509525 TATAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 11 0.52
18 8 0.38
19 2 0.10
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTACATTCAATAAAT
Found at i:509858 original size:16 final size:18
Alignment explanation
Indices: 509834--509866 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
509824 TAAATATTAA
509834 ATTTATTATTAA-ATTTT
1 ATTTATTATTAATATTTT
509851 ATTT-TTATTAATATTT
1 ATTTATTATTAATATTT
509867 ACTATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTATTAATATTTT
Found at i:509944 original size:29 final size:29
Alignment explanation
Indices: 509832--509975 Score: 87
Period size: 29 Copynumber: 4.8 Consensus size: 29
509822 ATTAAATATT
* * *
509832 AAATTTATTATTAAATTTTATTTTTATTA
1 AAATTTACTATTAAATTTTAATTTAATTA
* * * **
509861 ATATTTACTATTATATTTTAAAATTAAAAA
1 AAATTTACTATTAAATTTT-AATTTAATTA
* * *
509891 TAAATTT-CTCACTCAATTTTTATTTAATTA
1 -AAATTTACT-ATTAAATTTTAATTTAATTA
*
509921 AAATTTACTATTAAACTTTAATTTTTAATTA
1 AAATTTACTATTAAATTTTAA--TTTAATTA
*
509952 AATATTT-CTGTTCAAA-TTTAATTT
1 AA-ATTTACTATT-AAATTTTAATTT
509976 TTAATGAAAT
Statistics
Matches: 86, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
29 33 0.38
30 15 0.17
31 31 0.36
32 7 0.08
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (29 bp):
AAATTTACTATTAAATTTTAATTTAATTA
Found at i:509951 original size:31 final size:31
Alignment explanation
Indices: 509913--510005 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 31
509903 TCAATTTTTA
509913 TTTAATTAAAATTTACTATT-AAACTTTAATT
1 TTTAATTAAAATTTACTATTCAAA-TTTAATT
*
509944 TTTAATTAAATATTT-CTGTTCAAATTTAATT
1 TTTAATTAAA-ATTTACTATTCAAATTTAATT
* * *
509975 TTTAA-TGAAATTTATTGTTCAACA-TTAATT
1 TTTAATTAAAATTTACTATTCAA-ATTTAATT
510005 T
1 T
510006 AAATTATCTA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
29 4 0.07
30 17 0.31
31 27 0.49
32 7 0.13
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATTAAAATTTACTATTCAAATTTAATT
Found at i:513664 original size:73 final size:73
Alignment explanation
Indices: 513545--513692 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
513535 ATAACCGAAT
513545 AAGATGACTCATACGACTTCATTTAAGATTTGTCTTGGGGATTACTTTTGGTTCACTAGTGGCCA
1 AAGATGACTCATACGACTTCATTTAAGATTTGTCTTGGGGATTACTTTTGGTTCACTAGTGGCCA
513610 CCTTGTAC
66 CCTTGTAC
513618 AAGATGACTCATACGACTTCATTTAAGATTTGTCTTGGGGATTACTTTTGGTTCACTAGTGGCCA
1 AAGATGACTCATACGACTTCATTTAAGATTTGTCTTGGGGATTACTTTTGGTTCACTAGTGGCCA
*
513683 TCTTGTAC
66 CCTTGTAC
513691 AA
1 AA
513693 AATGCTAAAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (73 bp):
AAGATGACTCATACGACTTCATTTAAGATTTGTCTTGGGGATTACTTTTGGTTCACTAGTGGCCA
CCTTGTAC
Found at i:513852 original size:24 final size:24
Alignment explanation
Indices: 513824--513870 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
513814 TAACCATGAC
* * *
513824 CTTAACATCCTAAACCGTAAACAA
1 CTTAAAATCATAAACCCTAAACAA
*
513848 CTTAAAATTATAAACCCTAAACA
1 CTTAAAATCATAAACCCTAAACA
513871 CTAAACTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (24 bp):
CTTAAAATCATAAACCCTAAACAA
Found at i:513983 original size:16 final size:16
Alignment explanation
Indices: 513929--513983 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
513919 CCTTGACCTT
* *
513929 AAAAAACCATAAAACC
1 AAAAAACCTTAAACCC
* *
513945 ATAAACCCTTAAAACCC
1 AAAAAACCTT-AAACCC
*
513962 TAAAAACCTTAAACCC
1 AAAAAACCTTAAACCC
513978 AAAAAA
1 AAAAAA
513984 ATTATCAGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAACCTTAAACCC
Found at i:513983 original size:25 final size:24
Alignment explanation
Indices: 513929--513983 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
513919 CCTTGACCTT
513929 AAAAAACCATAAAACCATAAACCC
1 AAAAAACCATAAAACCATAAACCC
** * *
513953 TTAAAACCCTAAAAACCTTAAACCC
1 AAAAAACCAT-AAAACCATAAACCC
513978 AAAAAA
1 AAAAAA
513984 ATTATCAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAACCATAAAACCATAAACCC
Found at i:517330 original size:20 final size:22
Alignment explanation
Indices: 517288--517329 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
517278 ATTCGTATAT
*
517288 TTTTATTATAATCGTATATTTTA
1 TTTTATCATAATCG-ATATTTTA
517311 TTTTATCATAATC-ATATTT
1 TTTTATCATAATCGATATTT
517330 AAATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATCATAATCGATATTTTA
Found at i:521665 original size:2 final size:2
Alignment explanation
Indices: 521660--521717 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
521650 ATAGATAGAT
521660 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
521702 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
521718 CAACACATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:523414 original size:2 final size:2
Alignment explanation
Indices: 523409--523440 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
523399 AGGAGTTTTT
523409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
523441 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:534523 original size:2 final size:2
Alignment explanation
Indices: 534506--534551 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
534496 GAATAGCCTC
* *
534506 AT AT AT GT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
534547 AT AT A
1 AT AT A
534552 ACTTTTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:538124 original size:2 final size:2
Alignment explanation
Indices: 538117--538143 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
538107 GTTTGTCAGG
538117 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
538144 CATTTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:541023 original size:45 final size:45
Alignment explanation
Indices: 540967--541060 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
540957 ACAAAGGCAA
*
540967 AGGACCAGAAACTATCCAATC-TGTTCAATATCCAGAAAAAGGTAG
1 AGGACCAGAAACTATCCAATCAT-TTCAAAATCCAGAAAAAGGTAG
*
541012 AGGACCAGAAACTATCCAATCATTTCAAAATCCAGAGAAAGGTAG
1 AGGACCAGAAACTATCCAATCATTTCAAAATCCAGAAAAAGGTAG
541057 AGGA
1 AGGA
541061 AAAGACATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (45 bp):
AGGACCAGAAACTATCCAATCATTTCAAAATCCAGAAAAAGGTAG
Found at i:541076 original size:45 final size:45
Alignment explanation
Indices: 540973--541076 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
540963 GCAAAGGACC
* * **
540973 AGAAACTATCCAATCTGTTCAATATCCAGAAAAAGGTAGAGGACC
1 AGAAACTAGCCAATCTGTTCAAAATCCAGAAAAAGGTAGAGGAAA
* *
541018 AGAAACTATCCAATCAT-TTCAAAATCCAGAGAAAGGTAGAGGAAA
1 AGAAACTAGCCAATC-TGTTCAAAATCCAGAAAAAGGTAGAGGAAA
* *
541063 AGACATTAGCCAAT
1 AGAAACTAGCCAAT
541077 AACCCTAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 50 0.98
46 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (45 bp):
AGAAACTAGCCAATCTGTTCAAAATCCAGAAAAAGGTAGAGGAAA
Found at i:543274 original size:15 final size:16
Alignment explanation
Indices: 543254--543299 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
543244 GAAAATAAAA
543254 ATATTAAAT-ATATTT
1 ATATTAAATAATATTT
543269 ATATTAAATACATATTT
1 ATATTAAATA-ATATTT
543286 ATATCTAAAATAAT
1 ATAT-T-AAATAAT
543300 GTATTAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.33
17 10 0.37
18 3 0.11
19 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAATAATATTT
Found at i:543284 original size:43 final size:42
Alignment explanation
Indices: 543203--543284 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
543193 ATATATATTT
* *
543203 AAATAAAAATATAATTATAATTTATTAACTACATATATTAAGA
1 AAATAAAAATATAAATATAATTTATTAAATACA-ATATTAAGA
*
543246 AAATAAAAATATTAAATATATTTATATTAAATAC-ATATT
1 AAATAAAAATA-TAAATATAATT-TATTAAATACAATATT
543285 TATATCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 16 0.47
44 9 0.26
45 9 0.26
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (42 bp):
AAATAAAAATATAAATATAATTTATTAAATACAATATTAAGA
Found at i:543297 original size:19 final size:17
Alignment explanation
Indices: 543254--543294 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
543244 GAAAATAAAA
543254 ATATTAAAT--ATATTT
1 ATATTAAATACATATTT
543269 ATATTAAATACATATTT
1 ATATTAAATACATATTT
543286 ATATCTAAA
1 ATAT-TAAA
543295 ATAATGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTAAATACATATTT
Found at i:543585 original size:14 final size:14
Alignment explanation
Indices: 543549--543586 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
543539 CCATTCAAGA
543549 TCTTTGTCTTTCTTT
1 TCTTT-TCTTTCTTT
543564 TCTTTTCTTT-TTT
1 TCTTTTCTTTCTTT
543577 TCTTCTTCTT
1 TCTT-TTCTT
543587 ATATAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TCTTTTCTTTCTTT
Found at i:544709 original size:3 final size:3
Alignment explanation
Indices: 544703--544752 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
544693 TTCCTCCCAA
544703 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
544751 AA
1 AA
544753 AGCCTATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:546400 original size:3 final size:3
Alignment explanation
Indices: 546394--546434 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
546384 TTTCACAAAG
546394 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
546435 GCATTTAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:546554 original size:11 final size:11
Alignment explanation
Indices: 546538--546576 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
546528 ATAATTATAA
546538 TATATTATATT
1 TATATTATATT
546549 TATATTAT-TT
1 TATATTATATT
* *
546559 TTTATTATAAT
1 TATATTATATT
546570 TATATTA
1 TATATTA
546577 AAAGATACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATATT
Found at i:546555 original size:21 final size:21
Alignment explanation
Indices: 546531--546576 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
546521 ATTTTTAATA
*
546531 ATTATAATATATTATATTTAT
1 ATTATAATATATTATAATTAT
** *
546552 ATTATTTTTTATTATAATTAT
1 ATTATAATATATTATAATTAT
546573 ATTA
1 ATTA
546577 AAAGATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATAATATATTATAATTAT
Found at i:546571 original size:16 final size:16
Alignment explanation
Indices: 546531--546576 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
546521 ATTTTTAATA
546531 ATTATAA-TATATTAT
1 ATTATAATTATATTAT
* *
546546 ATT-TATATTATTTTTT
1 ATTATA-ATTATATTAT
546562 ATTATAATTATATTA
1 ATTATAATTATATTA
546577 AAAGATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
14 2 0.08
15 4 0.17
16 16 0.67
17 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATAATTATATTAT
Found at i:546695 original size:20 final size:19
Alignment explanation
Indices: 546628--546696 Score: 62
Period size: 20 Copynumber: 3.9 Consensus size: 19
546618 ATTATATTTA
*
546628 AAATATTATATATTTATAT
1 AAATTTTATATATTTATAT
546647 AAAATTTTATATA-TTA-AT
1 -AAATTTTATATATTTATAT
546665 -AA--TT-TAT-TTTATAT
1 AAATTTTATATATTTATAT
546679 AAATTTTGATATATTTAT
1 AAATTTT-ATATATTTAT
546697 TTATATTATG
Statistics
Matches: 40, Mismatches: 1, Indels: 16
0.70 0.02 0.28
Matches are distributed among these distances:
13 6 0.15
14 4 0.10
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 6 0.15
20 16 0.40
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
AAATTTTATATATTTATAT
Found at i:546725 original size:24 final size:23
Alignment explanation
Indices: 546694--546770 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
546684 TTGATATATT
546694 TATT-TATATTATGTTTATTTTTA
1 TATTATATATTAT-TTTATTTTTA
546717 TATTATATA-TATTAATTATTTTTA
1 TATTATATATTATT--TTATTTTTA
* * **
546741 TA-TATATTTTATTATATAATTA
1 TATTATATATTATTTTATTTTTA
546763 TATTATAT
1 TATTATAT
546771 TTAAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 9 0.20
23 17 0.38
24 19 0.42
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (23 bp):
TATTATATATTATTTTATTTTTA
Found at i:546729 original size:17 final size:18
Alignment explanation
Indices: 546687--546771 Score: 83
Period size: 17 Copynumber: 5.0 Consensus size: 18
546677 ATAAATTTTG
546687 ATATAT-TTATTTATATT
1 ATATATATTATTTATATT
* *
546704 ATGTTTATT-TTTATATT
1 ATATATATTATTTATATT
*
546721 ATATATATTAATTAT-TT
1 ATATATATTATTTATATT
*
546738 TTATATA-TATTT-TATT
1 ATATATATTATTTATATT
546754 ATATA-ATTATATTATATT
1 ATATATATTAT-TTATATT
546772 TAAATTTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.04
16 13 0.24
17 29 0.54
18 10 0.19
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
ATATATATTATTTATATT
Found at i:546750 original size:65 final size:64
Alignment explanation
Indices: 546653--546773 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 64
546643 ATATAAAATT
* * *
546653 TTATATATTAATAATTTATTTTATATAAATTTTGATATATTTATTTATATTATGTTTATTTTTAT
1 TTATATATTAATAATTTATTTTATATAAATTTT-AT-TATATAATTATATTATATTTATTTTTAT
546718 A
64 A
* *
546719 TTATATA-TATTAA-TTATTTTTATATATATTTTATTATATAATTATATTATATTTA
1 TTATATATTAATAATTTA-TTTTATATAAATTTTATTATATAATTATATTATATTTA
546774 AATTTATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 18 0.37
64 5 0.10
65 19 0.39
66 7 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (64 bp):
TTATATATTAATAATTTATTTTATATAAATTTTATTATATAATTATATTATATTTATTTTTATA
Found at i:547365 original size:23 final size:24
Alignment explanation
Indices: 547339--547391 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
547329 TCTAACATAT
* *
547339 TTATATATTTATATTAT-TTTTAA
1 TTATATATTCATATTATATTTAAA
*
547362 TTATTTATTCATATTATATTTAAA
1 TTATATATTCATATTATATTTAAA
547386 TTATAT
1 TTATAT
547392 CTTAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATATATTCATATTATATTTAAA
Found at i:547718 original size:11 final size:11
Alignment explanation
Indices: 547704--547744 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
547694 TAAAATAATT
547704 TTATATTTATA
1 TTATATTTATA
547715 TTATATTTATA
1 TTATATTTATA
547726 TTAT-TTATATA
1 TTATATT-TATA
547737 TTATATTT
1 TTATATTT
547745 TTTATATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.07
11 24 0.86
12 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:547886 original size:15 final size:14
Alignment explanation
Indices: 547855--547903 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
547845 AATCGTATTT
547855 TTTTAATTATTAT-A
1 TTTTAATT-TTATAA
547869 TTTTAAGTTTTATAA
1 TTTTAA-TTTTATAA
*
547884 TTTTAATATTTAAAA
1 TTTTAAT-TTTATAA
547899 TTTTA
1 TTTTA
547904 TATCATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TTTTAATTTTATAA
Found at i:547923 original size:17 final size:15
Alignment explanation
Indices: 547882--547947 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
547872 TAAGTTTTAT
*
547882 AATTTTAATATTTAA
1 AATTTTAATATATAA
547897 AATTTT-ATATCATATA
1 AATTTTAATAT-ATA-A
*
547913 AATTTTAATATATTTA
1 AATTTTAATATA-TAA
* *
547929 TATTTTTATAT-TAA
1 AATTTTAATATATAA
547943 AATTT
1 AATTT
547948 AAAATATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.24
15 8 0.20
16 18 0.44
17 5 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTAATATATAA
Found at i:547933 original size:16 final size:16
Alignment explanation
Indices: 547855--547939 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 16
547845 AATCGTATTT
547855 TTTTAAT-TA-TTATA
1 TTTTAATATATTTATA
*
547869 TTTTAA-GT-TTTATAA
1 TTTTAATATATTTAT-A
* *
547884 TTTTAATAT-TTAAAA
1 TTTTAATATATTTATA
* *
547899 TTTT-ATATCATATAAA
1 TTTTAATAT-ATTTATA
547915 TTTTAATATATTTATA
1 TTTTAATATATTTATA
*
547931 TTTTTATAT
1 TTTTAATAT
547940 TAAAATTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 15 0.27
15 12 0.21
16 25 0.45
17 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (16 bp):
TTTTAATATATTTATA
Found at i:550245 original size:23 final size:22
Alignment explanation
Indices: 550214--550257 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
550204 AAAATATATT
*
550214 AAAAATATTTTATGATTTTAGTG
1 AAAAATATTTAATG-TTTTAGTG
*
550237 AAAATTATTTAATGTTTTAGT
1 AAAAATATTTAATGTTTTAGT
550258 ATTTAAATTT
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:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
AAAAATATTTAATGTTTTAGTG
Found at i:550477 original size:22 final size:22
Alignment explanation
Indices: 550427--550484 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
550417 AGCATTTTTT
550427 TATGAAATAA-AA-TTATAAAA
1 TATGAAATAATAATTTATAAAA
* * *
550447 GAGGTAAATAATAATTTTTAAAA
1 TATG-AAATAATAATTTATAAAA
*
550470 TATGAAATATTAATT
1 TATGAAATAATAATT
550485 GATTTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 6 0.21
22 12 0.41
23 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
TATGAAATAATAATTTATAAAA
Found at i:551421 original size:19 final size:19
Alignment explanation
Indices: 551385--551435 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
551375 CAATTTTACT
*
551385 TTTTATATTTTAAATATTTA
1 TTTTA-ATTTTAAATAATTA
551405 -TTT-A--TTAAATAATTA
1 TTTTAATTTTAAATAATTA
551420 TTTTAATTTTAAATAA
1 TTTTAATTTTAAATAA
551436 AATATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
15 10 0.38
16 3 0.12
17 2 0.08
19 11 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATTTTAAATAATTA
Found at i:551463 original size:20 final size:21
Alignment explanation
Indices: 551425--551483 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
551415 AATTATTTTA
* *
551425 ATTTTAAATAAAATATAAAATT
1 ATTTTATA-AAAATTTAAAATT
551447 ATTTT-TAAAAATTT-AAATT
1 ATTTTATAAAAATTTAAAATT
*
551466 TTTTTATAAAAATTTAAA
1 ATTTTATAAAAATTTAAA
551484 TTTTATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.28
20 15 0.47
21 3 0.09
22 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTATAAAAATTTAAAATT
Found at i:551484 original size:20 final size:19
Alignment explanation
Indices: 551442--551487 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
551432 ATAAAATATA
*
551442 AAATTATTTTTAAAAATTT
1 AAATTTTTTTTAAAAATTT
551461 AAATTTTTTTATAAAAATTT
1 AAATTTTTTT-TAAAAATTT
551481 AAATTTT
1 AAATTTT
551488 ATAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTTTTTTTAAAAATTT
Found at i:552840 original size:11 final size:11
Alignment explanation
Indices: 552824--552872 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
552814 CAACTTTATG
552824 ATATAAATAAT
1 ATATAAATAAT
*
552835 ATATAAAAAAT
1 ATATAAATAAT
552846 -TA-AAATAA-
1 ATATAAATAAT
552854 ATATAATATAAAT
1 ATATAA-AT-AAT
552867 ATATAA
1 ATATAA
552873 CTATATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 7 0.23
10 4 0.13
11 12 0.39
12 2 0.06
13 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATAAT
Found at i:552920 original size:11 final size:11
Alignment explanation
Indices: 552906--552947 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
552896 AAATATTTTA
*
552906 AATATAATTAT
1 AATATAAATAT
552917 AATATAAATAT
1 AATATAAATAT
552928 -ATATAAATAT
1 AATATAAATAT
552938 AATATAAATA
1 AATATAAATA
552948 CATAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:552932 original size:21 final size:21
Alignment explanation
Indices: 552907--552957 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
552897 AATATTTTAA
*
552907 ATATAATTATAATATAAATAT
1 ATATAATTATAATATAAATAC
*
552928 ATATAAATATAATATAAATAC
1 ATATAATTATAATATAAATAC
552949 ATA-AATTAT
1 ATATAATTAT
552958 TAAATTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAATTATAATATAAATAC
Found at i:552947 original size:6 final size:6
Alignment explanation
Indices: 552904--552947 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
552894 AAAAATATTT
*
552904 TAAATA TAATTA T-AATA TAAATA T--ATA TAAATA T-AATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
552948 CATAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
4 4 0.12
5 9 0.28
6 19 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATA
Found at i:552961 original size:27 final size:26
Alignment explanation
Indices: 552896--552962 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
552886 TATATTTTAA
*
552896 AAATATTTTAAATATAATTATAATAT
1 AAATATATTAAATATAATTATAATAT
552922 AAATATATATAAATATAA-TATAAATACAT
1 AAATATAT-TAAATATAATTAT-AAT--AT
552951 AAAT-TATTAAAT
1 AAATATATTAAAT
552963 TTACTTACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 10 0.28
27 17 0.47
28 3 0.08
29 6 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATATTAAATATAATTATAATAT
Found at i:552991 original size:17 final size:17
Alignment explanation
Indices: 552952--552993 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
552942 TAAATACATA
*
552952 AATTATTAAATTTACTT
1 AATTATTTAATTTACTT
*
552969 ACTTATTTAATCTTA-TT
1 AATTATTTAAT-TTACTT
552986 AATTATTT
1 AATTATTT
552994 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTATTTAATTTACTT
Found at i:553132 original size:10 final size:10
Alignment explanation
Indices: 553117--553150 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
553107 GATCCATTGT
*
553117 TATAAATAAA
1 TATAAATATA
553127 TATAAATATA
1 TATAAATATA
*
553137 TATATATATA
1 TATAAATATA
553147 TATA
1 TATA
553151 TATGAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATAAATATA
Found at i:554992 original size:323 final size:324
Alignment explanation
Indices: 554395--555043 Score: 1120
Period size: 323 Copynumber: 2.0 Consensus size: 324
554385 ACACACACAC
*
554395 ACACACACATACACATATAATTATAATTAAAACTGGTACATACCGCTGGCGTGGCCGATAGGGAC
1 ACACACACATACACATATAATTATAATTAAAACTGGTACATACCGCTGGCGTGGCCGATACGGAC
554460 TACATTGCCGAAGACTCCATAGTTGGCCTTATGCTTTCTACCTACTTACTATTTGGCGGAACTAA
66 TACATTGCCGAAGACTCCATAGTTGGCCTTATG-----T-CCTACTTACTATTTGGCGGAACTAA
*
554525 ATGGATTTTGTGCTTAGTATCAAGTCTGCAGAGTTTAAAAGCTGTTAAGATGAAGGCAACGACTT
125 ATGGATTTTGTGCTTACTATCAAGTCTGCAGAGTTTAAAAGCTGTTAAGATGAAGGCAACGACTT
554590 TTGAAAAGCCAATTCTTTCTCTATTATCAAGAAGAAAACAAAGAGTTAACTTACCTGATTTTCTT
190 TTGAAAAGCCAATTCTTTCTCTATTATCAAGAAGAAAACAAAGAGTTAACTTACCTGATTTTCTT
*
554655 TTGACTCAAGACAGTTGAAACCCTGCAGTTGTGTTGAAGATAGCAGTAGGAACTTACTATATATA
255 TTGACTCAAGACAGTTGAAACCCTGCAGTTGTGTTGAAGATAGCAGTAGAAACTTACTATATATA
554720 TATAT
320 TATAT
* *
554725 ACACACACATACACATATAATTATACTTAAAACTGGTACATACCGCTGGCGTGGCCGATACTGAC
1 ACACACACATACACATATAATTATAATTAAAACTGGTACATACCGCTGGCGTGGCCGATACGGAC
* *
554790 TACATTGCTGAAGAGTCCATAGTTGGCCTTATG-CCTACTTACTATTTGGCGGAACTAAATGGAT
66 TACATTGCCGAAGACTCCATAGTTGGCCTTATGTCCTACTTACTATTTGGCGGAACTAAATGGAT
*
554854 TTTGTGCTTACTATCAAGTCTGCAGAGTTTAGAAGCTGTTAAGATGAAGGCAACGACTTTTGAAA
131 TTTGTGCTTACTATCAAGTCTGCAGAGTTTAAAAGCTGTTAAGATGAAGGCAACGACTTTTGAAA
* *
554919 AGCCAATTCTTTCTCTATTATCAAGAGGAAAACAAAGAGTTAGCTTACCTGATTTTCTTTTGACT
196 AGCCAATTCTTTCTCTATTATCAAGAAGAAAACAAAGAGTTAACTTACCTGATTTTCTTTTGACT
* * *
554984 CGAGACAGTTGAAACCCTGCAGTTGTGTTGAAGATATCAGTAGAAACTTACTATTTATAT
261 CAAGACAGTTGAAACCCTGCAGTTGTGTTGAAGATAGCAGTAGAAACTTACTATATATAT
555044 GATAAATTGA
Statistics
Matches: 306, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
323 213 0.70
330 93 0.30
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (324 bp):
ACACACACATACACATATAATTATAATTAAAACTGGTACATACCGCTGGCGTGGCCGATACGGAC
TACATTGCCGAAGACTCCATAGTTGGCCTTATGTCCTACTTACTATTTGGCGGAACTAAATGGAT
TTTGTGCTTACTATCAAGTCTGCAGAGTTTAAAAGCTGTTAAGATGAAGGCAACGACTTTTGAAA
AGCCAATTCTTTCTCTATTATCAAGAAGAAAACAAAGAGTTAACTTACCTGATTTTCTTTTGACT
CAAGACAGTTGAAACCCTGCAGTTGTGTTGAAGATAGCAGTAGAAACTTACTATATATATATAT
Found at i:557288 original size:22 final size:22
Alignment explanation
Indices: 557263--557310 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
557253 ATGTAATAAT
*
557263 AAATAATATAATTTAAGAA-TTA
1 AAATAATAAAATTTAA-AATTTA
**
557285 AAATTTTAAAATTTAAAATTTA
1 AAATAATAAAATTTAAAATTTA
557307 AAAT
1 AAAT
557311 TTTTTACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATAATAAAATTTAAAATTTA
Found at i:557312 original size:7 final size:7
Alignment explanation
Indices: 557272--557312 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
557262 TAAATAATAT
557272 AATTTAA
1 AATTTAA
557279 GAA-TTAA
1 -AATTTAA
557286 AATTTTAA
1 AA-TTTAA
557294 AATTTAA
1 AATTTAA
557301 AATTTAA
1 AATTTAA
557308 AATTT
1 AATTT
557313 TTTACTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.06
7 21 0.68
8 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:557526 original size:22 final size:21
Alignment explanation
Indices: 557501--557542 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
557491 TTTTTAAATT
557501 ATATAA-AAATAATATTATAATG
1 ATATAATAAA-AATATT-TAATG
557523 ATATAATAAAAATATTTAAT
1 ATATAATAAAAATATTTAAT
557543 TTATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAATAAAAATATTTAATG
Found at i:558028 original size:13 final size:13
Alignment explanation
Indices: 557990--558048 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
557980 AATAAAATTA
*
557990 ATTTATAAATTTT
1 ATTTATTAATTTT
*
558003 -TTATCTTAA-TTT
1 ATT-TATTAATTTT
558015 ATTTATTAATTTT
1 ATTTATTAATTTT
**
558028 ATAAATTAATTTT
1 ATTTATTAATTTT
558041 A-TTATTAA
1 ATTTATTAA
558049 AAAAATTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
12 15 0.42
13 21 0.58
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTATTAATTTT
Found at i:558036 original size:25 final size:25
Alignment explanation
Indices: 557985--558048 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
557975 AATTAAATAA
* * * **
557985 AATTAATTTATAAATTTTTTATCTT
1 AATTTATTTATTAATTTTATAAATT
558010 AATTTATTTATTAATTTTATAAATT
1 AATTTATTTATTAATTTTATAAATT
558035 AATTT-TATTATTAA
1 AATTTAT-TTATTAA
558049 AAAAATTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTTATTTATTAATTTTATAAATT
Found at i:558650 original size:26 final size:26
Alignment explanation
Indices: 558604--558702 Score: 85
Period size: 26 Copynumber: 3.7 Consensus size: 26
558594 AATTCATGAT
* * *
558604 TTTTTTATTATAATTATATTTAAAATA
1 TTTTATATTAT-ATAATATTTATAATA
558631 TTTTATATTTATATAA-ATTT-TAATA
1 TTTTATA-TTATATAATATTTATAATA
* * *
558656 TATTAATAATTATATAATAATTATATTA
1 T-TTTAT-ATTATATAATATTTATAATA
*
558684 TTTTGTATTATATAATATT
1 TTTTATATTATATAATATT
558703 AATTAAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
25 5 0.09
26 28 0.48
27 16 0.28
28 9 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTTATATTATATAATATTTATAATA
Found at i:558736 original size:24 final size:24
Alignment explanation
Indices: 558709--558759 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
558699 TATTAATTAA
558709 ATATAA-AAATATATATTTAATATT
1 ATATAATAAAT-TATATTTAATATT
* *
558733 ATATAATACATTATATTTTATATT
1 ATATAATAAATTATATTTAATATT
558757 ATA
1 ATA
558760 AGTAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATAATAAATTATATTTAATATT
Found at i:559340 original size:29 final size:29
Alignment explanation
Indices: 559300--559379 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
559290 TTAAATTATT
*
559300 ATTTAATAATAAAATAATATTTTATATAA
1 ATTTAATTATAAAATAATATTTTATATAA
559329 ATTTAATTATAAAAT-ATATATTTAT-T-A
1 ATTTAATTATAAAATAATAT-TTTATATAA
559356 A--T-A-TA-AAAATAATATTTTATATAA
1 ATTTAATTATAAAATAATATTTTATATAA
559380 TATAAAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
22 10 0.22
23 7 0.15
24 2 0.04
25 1 0.02
27 2 0.04
28 5 0.11
29 19 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTTAATTATAAAATAATATTTTATATAA
Found at i:559360 original size:21 final size:22
Alignment explanation
Indices: 559331--559390 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
559321 TTATATAAAT
559331 TTAATTATAAAATATATA-TTTA
1 TTAA-TATAAAATATATATTTTA
559353 TTAATATAAAA-ATAATATTTTA
1 TTAATATAAAATAT-ATATTTTA
559375 TATAATATAAAATATA
1 T-TAATATAAAATATA
559391 CGTAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.06
21 10 0.29
22 9 0.26
23 11 0.32
24 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATATAAAATATATATTTTA
Found at i:559364 original size:22 final size:23
Alignment explanation
Indices: 559331--559390 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
559321 TTATATAAAT
559331 TTAAT-TATAAAATATATA-TTTA
1 TTAATATA-AAAATATATATTTTA
559353 TTAATATAAAAATA-ATATTTTA
1 TTAATATAAAAATATATATTTTA
559375 TATAATAT-AAAATATA
1 T-TAATATAAAAATATA
559391 CGTAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.09
22 22 0.65
23 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATATAAAAATATATATTTTA
Found at i:559527 original size:21 final size:21
Alignment explanation
Indices: 559484--559531 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
559474 TTGAACTAAG
* *
559484 ATATTATTTATTATTTTTAAT
1 ATATTTTTTATTATATTTAAT
559505 ATATTTTTTATTATCATTT-AT
1 ATATTTTTTATTAT-ATTTAAT
559526 ATATTT
1 ATATTT
559532 AAGATCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTTTTATTATATTTAAT
Found at i:560032 original size:49 final size:50
Alignment explanation
Indices: 559941--560035 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 50
559931 AATTATACAT
* *
559941 ATGTGATTTGGTTGGTAGATAAAAAGAATCAATGTTATTAAAAAATGCAG
1 ATGTGATTTGGCTAGTAGATAAAAAGAATCAATGTTATTAAAAAATGCAG
*
559991 ATGTGATTTGGCTAGTAGAT-AAAAGAATCAATGTTCTTAAAAAAT
1 ATGTGATTTGGCTAGTAGATAAAAAGAATCAATGTTATTAAAAAAT
560036 ATTGATGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 24 0.57
50 18 0.43
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (50 bp):
ATGTGATTTGGCTAGTAGATAAAAAGAATCAATGTTATTAAAAAATGCAG
Found at i:561346 original size:21 final size:21
Alignment explanation
Indices: 561313--561359 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
561303 CTCAAAATGA
* *
561313 ATTTTTT-TTTAAAATTTTTT
1 ATTTTTTATTAAAAATATTTT
561333 ATTTTGTTATTAAAAATATTTT
1 ATTTT-TTATTAAAAATATTTT
561355 ATTTT
1 ATTTT
561360 ATAACAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 2 0.09
22 16 0.70
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
ATTTTTTATTAAAAATATTTT
Found at i:564672 original size:17 final size:19
Alignment explanation
Indices: 564628--564672 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
564618 ATGATTTAAA
564628 AAATATTAATATATAATTT
1 AAATATTAATATATAATTT
**
564647 TTATATTAATATATAA-TT
1 AAATATTAATATATAATTT
564665 AAAT-TTAA
1 AAATATTAA
564673 ATAAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATTAATATATAATTT
Found at i:564838 original size:44 final size:44
Alignment explanation
Indices: 564775--564862 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
564765 TAAGTCGCTA
* * *
564775 GCGAGGTGCCATCCTTGATTAGGTCTCTGCATGGCGTTGGATCG
1 GCGAGCTGCCATCCTTGATTAGGTCCCTGCATGGCATTGGATCG
564819 GCGAGCTGCCATCCTTGATTAGGTCCCTGCATGGCATTGGATCG
1 GCGAGCTGCCATCCTTGATTAGGTCCCTGCATGGCATTGGATCG
564863 AGATTTCAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (44 bp):
GCGAGCTGCCATCCTTGATTAGGTCCCTGCATGGCATTGGATCG
Found at i:565062 original size:7 final size:7
Alignment explanation
Indices: 565050--565104 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
565040 TGAATATAAA
565050 AAATTAT
1 AAATTAT
565057 AAATTAT
1 AAATTAT
565064 AAATTAT
1 AAATTAT
*
565071 AAATAAT
1 AAATTAT
*
565078 AAATTTT
1 AAATTAT
*
565085 AAA-AAT
1 AAATTAT
565091 AAATATAT
1 AAAT-TAT
565099 AAATTA
1 AAATTA
565105 ATTAAATTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 4 0.10
7 30 0.75
8 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATTAT
Found at i:565069 original size:14 final size:14
Alignment explanation
Indices: 565045--565113 Score: 77
Period size: 14 Copynumber: 4.8 Consensus size: 14
565035 TAATTTGAAT
*
565045 ATAAAAAATTATAA
1 ATAATAAATTATAA
*
565059 ATTATAAATTATAA
1 ATAATAAATTATAA
*
565073 ATAATAAATTTTAA
1 ATAATAAATTATAA
565087 A-AATAAATATATAA
1 ATAATAAAT-TATAA
565101 ATTAATTAAATTA
1 A-TAA-TAAATTA
565114 GGATTTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
13 7 0.15
14 30 0.65
16 4 0.09
17 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAAATTATAA
Found at i:565074 original size:21 final size:21
Alignment explanation
Indices: 565050--565113 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
565040 TGAATATAAA
565050 AAATTATAAATTATAAATTAT
1 AAATTATAAATTATAAATTAT
* * *
565071 AAATAATAAATTTTAAA-AAT
1 AAATTATAAATTATAAATTAT
565091 AAATATATAAATTAATTAAATTA
1 AAAT-TATAAATT-A-TAAATTA
565114 GGATTTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.18
21 22 0.67
23 4 0.12
24 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTATAAATTATAAATTAT
Found at i:565404 original size:26 final size:27
Alignment explanation
Indices: 565349--565400 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
565339 GAATTAATTT
*
565349 TATTTGATTTATTATTTAATTAATAAA
1 TATTTGATTTATAATTTAATTAATAAA
565376 TATTTGATTTA-AATTTAATT-ATAAA
1 TATTTGATTTATAATTTAATTAATAAA
565401 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTTGATTTATAATTTAATTAATAAA
Found at i:565428 original size:17 final size:18
Alignment explanation
Indices: 565403--565436 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
565393 ATTATAAAAT
565403 ATAAAAATA-TTAATATA
1 ATAAAAATATTTAATATA
*
565420 ATAATAATATTTAATAT
1 ATAAAAATATTTAATAT
565437 TTATTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAAATATTTAATATA
Found at i:566024 original size:42 final size:39
Alignment explanation
Indices: 565978--566143 Score: 109
Period size: 47 Copynumber: 4.2 Consensus size: 39
565968 ATGATTTTTA
565978 TAATATAATTATATTTAAATTATTATATATTTATATAAATTT
1 TAATATAATTATA-TTAAATT-TTATATA-TTATATAAATTT
* *
566020 TAATAT-ATTA-A-T-AA-TTTA-A-AATATATAAAATT
1 TAATATAATTATATTAAATTTTATATATTATATAAATTT
* *
566052 TAATATAATTATATTAATTTTTATTATAAAATATTTATAATACAA-AT
1 TAATATAATTATATTAA--ATT-TTAT---ATA-TTAT-ATA-AATTT
566099 TAATATAATTATATTAAATTTTATATA--ATATAAATTAT
1 TAATATAATTATATTAAATTTTATATATTATATAAATT-T
566137 TAATATA
1 TAATATA
566144 TTAAAATTTA
Statistics
Matches: 99, Mismatches: 7, Indels: 40
0.68 0.05 0.27
Matches are distributed among these distances:
32 16 0.16
33 5 0.05
34 2 0.02
35 4 0.04
36 4 0.04
37 5 0.05
38 11 0.11
39 1 0.01
40 4 0.04
41 7 0.07
42 6 0.06
44 5 0.05
45 3 0.03
46 3 0.03
47 21 0.21
48 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TAATATAATTATATTAAATTTTATATATTATATAAATTT
Found at i:566043 original size:16 final size:16
Alignment explanation
Indices: 566009--566054 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
565999 ATTATATATT
* *
566009 TATATAAATTTTAATA
1 TATATAAAATTTAAAA
566025 TAT-TAATAATTTAAAA
1 TATATAA-AATTTAAAA
566041 TATATAAAATTTAA
1 TATATAAAATTTAA
566055 TATAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATAAAATTTAAAA
Found at i:566056 original size:14 final size:14
Alignment explanation
Indices: 566009--566058 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
565999 ATTATATATT
*
566009 TATATAAATTTTAA
1 TATATAAAATTTAA
566023 TATATTAATAATTTAAAA
1 TATA-TAA-AATTT--AA
566041 TATATAAAATTTAA
1 TATATAAAATTTAA
566055 TATA
1 TATA
566059 ATTATATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
14 10 0.32
15 3 0.10
16 9 0.29
17 3 0.10
18 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATAAAATTTAA
Found at i:566064 original size:20 final size:20
Alignment explanation
Indices: 565978--566065 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 20
565968 ATGATTTTTA
*
565978 TAATATAATTATATTTAAATT
1 TAATATAATTATA-TAAAATT
* * *
565999 ATTATATATTTATATAAATTT
1 -TAATATAATTATATAAAATT
566020 TAATAT-ATTA-AT--AATT
1 TAATATAATTATATAAAATT
566036 T-A-A-AA-TATATAAAATT
1 TAATATAATTATATAAAATT
566052 TAATATAATTATAT
1 TAATATAATTATAT
566066 TAATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 18
0.67 0.09 0.24
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 1 0.02
16 9 0.18
17 1 0.02
18 3 0.06
19 5 0.10
20 10 0.20
21 5 0.10
22 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATATAATTATATAAAATT
Found at i:566110 original size:32 final size:30
Alignment explanation
Indices: 566074--566158 Score: 82
Period size: 35 Copynumber: 2.7 Consensus size: 30
566064 ATTAATTTTT
566074 ATTATAAAATATTTATAATACAAATTAATATA
1 ATTATAAAATATTTATAATACAAATT-AT-TA
* *
566106 ATTATATTAAATTTTATATAATATAAATTATTA
1 ATTATA--AAATATT-TATAATACAAATTATTA
*
566139 ATATATTAAA-ATTTATAATA
1 AT-TATAAAATATTTATAATA
566159 TCTTGTCCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
30 7 0.16
31 2 0.04
32 9 0.20
33 4 0.09
34 11 0.24
35 12 0.27
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTATAAAATATTTATAATACAAATTATTA
Found at i:566126 original size:20 final size:20
Alignment explanation
Indices: 565980--566127 Score: 80
Period size: 20 Copynumber: 7.3 Consensus size: 20
565970 GATTTTTATA
565980 ATATAATTATATTTAAATTATT
1 ATATAATTATA-TTAAATT-TT
*
566002 ATATATTTATA-TAAATTTT
1 ATATAATTATATTAAATTTT
566021 A-ATATATTA-A-T-AA-TTT
1 ATATA-ATTATATTAAATTTT
* *
566037 A-A-AA-TATATAAAATTTA
1 ATATAATTATATTAAATTTT
*
566054 ATATAATTATATTAATTTTT
1 ATATAATTATATTAAATTTT
* * *
566074 ATTATAAAATATTTATAATACAAATTA
1 A-TAT---A-A-TTATATTA-AATTTT
566101 ATATAATTATATTAAATTTT
1 ATATAATTATATTAAATTTT
566121 ATATAAT
1 ATATAAT
566128 ATAAATTATT
Statistics
Matches: 97, Mismatches: 14, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
13 2 0.02
14 2 0.02
15 1 0.01
16 7 0.07
17 5 0.05
18 6 0.06
19 8 0.08
20 28 0.29
21 10 0.10
22 11 0.11
23 1 0.01
24 1 0.01
25 1 0.01
26 10 0.10
27 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAATTATATTAAATTTT
Found at i:566136 original size:58 final size:58
Alignment explanation
Indices: 565977--566147 Score: 148
Period size: 58 Copynumber: 2.8 Consensus size: 58
565967 TATGATTTTT
* **
565977 ATAATATAATTATATTTAAATTATTATATATTTATATAAATTTTAATATATTAATAATTTAAA
1 ATAATATAATTATA-TTAAATT-TTATATA---ATATAAATTATAATATATTAATAATACAAA
* * * * ** * *
566040 ATATATAAAATT-TAATATAATTATAT-TAATTTTTATTATAAAATATTTATAATACAAA
1 ATA-ATATAATTATATTA-AATTTTATATAATATAAATTATAATATATTAATAATACAAA
*
566098 TTAATATAATTATATTAAATTTTATATAATATAAATTATTAATATATTAA
1 ATAATATAATTATATTAAATTTTATATAATATAAATTA-TAATATATTAA
566148 AATTTATAAT
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
57 14 0.17
58 37 0.45
59 9 0.11
61 2 0.02
62 5 0.06
63 9 0.11
64 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (58 bp):
ATAATATAATTATATTAAATTTTATATAATATAAATTATAATATATTAATAATACAAA
Found at i:566157 original size:17 final size:17
Alignment explanation
Indices: 566102--566159 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
566092 TACAAATTAA
566102 TATAATTATATT-AAATT
1 TATAA-TATATTAAAATT
*
566119 T-T-ATATAATATAAA-T
1 TATAATATATTA-AAATT
566134 TATTAATATATTAAAATT
1 TA-TAATATATTAAAATT
566152 TATAATAT
1 TATAATAT
566160 CTTGTCCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 4 0.12
17 11 0.33
18 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATATTAAAATT
Found at i:568061 original size:23 final size:24
Alignment explanation
Indices: 568023--568068 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
568013 GCTCTTAGGT
568023 TGAGTTTGTTTTTAAGGAAAGATC
1 TGAGTTTGTTTTTAAGGAAAGATC
568047 TGAGTTT-TTTTTAAGGAAAGAT
1 TGAGTTTGTTTTTAAGGAAAGAT
568069 TTTGAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.43
Consensus pattern (24 bp):
TGAGTTTGTTTTTAAGGAAAGATC
Found at i:575557 original size:3 final size:3
Alignment explanation
Indices: 575549--575581 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
575539 AATAAACAAA
575549 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
575582 TGTTAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:575843 original size:15 final size:15
Alignment explanation
Indices: 575805--575846 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
575795 TTATTTTTTT
* *
575805 AATTTATTTTTTTAC
1 AATTTAATTTTTTAA
*
575820 AATAT-ATTTTTTAA
1 AATTTAATTTTTTAA
575834 AATTTAATTTTTT
1 AATTTAATTTTTT
575847 TTAATTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTTAATTTTTTAA
Found at i:575852 original size:15 final size:14
Alignment explanation
Indices: 575798--575852 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
575788 ACTTATATTA
575798 TTTTTTTAATTTAT
1 TTTTTTTAATTTAT
* *
575812 TTTTTTACAATATAT
1 TTTTTT-TAATTTAT
**
575827 TTTTTAAAATTTAAT
1 TTTTTTTAATTT-AT
575842 TTTTTTTAATT
1 TTTTTTTAATT
575853 AAGTTTCATA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTTAATTTAT
Found at i:575906 original size:20 final size:20
Alignment explanation
Indices: 575820--575914 Score: 54
Period size: 18 Copynumber: 5.3 Consensus size: 20
575810 ATTTTTTTAC
*
575820 AATATATTTTTTAA-AATTT
1 AATATATTTTTTAATAGTTT
575839 AAT-T-TTTTTTAATTAAGTTT
1 AATATATTTTTTAA-T-AGTTT
*
575859 CATA-A---TTTAAT-GTTT
1 AATATATTTTTTAATAGTTT
*
575874 -ATATA--TTTAAATAGTTT
1 AATATATTTTTTAATAGTTT
575891 AATATATTTTTTAATA-TTT
1 AATATATTTTTTAATAGTTT
575910 -ATATA
1 AATATA
575915 ATAAAAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 23
0.69 0.05 0.26
Matches are distributed among these distances:
14 3 0.05
15 5 0.08
16 5 0.08
17 13 0.21
18 16 0.26
19 6 0.10
20 13 0.21
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (20 bp):
AATATATTTTTTAATAGTTT
Found at i:584553 original size:3 final size:3
Alignment explanation
Indices: 584523--584565 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
584513 TTCAGCTGGC
* * * *
584523 GAT GAC GAT GAT GAA GAT AAT GAC GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
584566 TTGGGATCAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.37, C:0.05, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:585902 original size:30 final size:31
Alignment explanation
Indices: 585851--585987 Score: 122
Period size: 32 Copynumber: 4.4 Consensus size: 31
585841 AATAAAATTA
* *
585851 AATTTTTTTAATGA-TCGTTAAATTTATCAAT
1 AATTTATTTAAT-ATTCATTAAATTTATCAAT
*
585882 AA-TTATTTAATATTCATTAAATTTATGAAT
1 AATTTATTTAATATTCATTAAATTTATCAAT
* **
585912 AATTTTATTTAATATTCATAAAATTTAAAAAT
1 AA-TTTATTTAATATTCATTAAATTTATCAAT
585944 AATTATATTTAAT-TT-ATTAAAATTATGATCAAT
1 AATT-TATTTAATATTCATT-AAATT-T-ATCAAT
*
585977 -ATTAATTTAAT
1 AATTTATTTAAT
585988 TTTTAAAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
29 1 0.01
30 27 0.30
31 18 0.20
32 39 0.44
33 4 0.04
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (31 bp):
AATTTATTTAATATTCATTAAATTTATCAAT
Found at i:585925 original size:32 final size:32
Alignment explanation
Indices: 585851--585971 Score: 128
Period size: 32 Copynumber: 3.9 Consensus size: 32
585841 AATAAAATTA
* *
585851 AATTTT-TTTAATGA-TCGTTAAATTTATCAAT
1 AATTTTATTTAAT-ATTCATTAAATTTATGAAT
585882 AA--TTATTTAATATTCATTAAATTTATGAAT
1 AATTTTATTTAATATTCATTAAATTTATGAAT
* **
585912 AATTTTATTTAATATTCATAAAATTTAAAAAT
1 AATTTTATTTAATATTCATTAAATTTATGAAT
* *
585944 AATTATATTTAAT-TT-ATTAAAATTATGA
1 AATTTTATTTAATATTCATTAAATTTATGA
585972 TCAATATTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.04
30 32 0.42
31 4 0.05
32 37 0.49
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (32 bp):
AATTTTATTTAATATTCATTAAATTTATGAAT
Found at i:586512 original size:3 final size:3
Alignment explanation
Indices: 586504--586540 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
586494 TTTTATTTGG
586504 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
586541 TCTTATGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:592254 original size:17 final size:18
Alignment explanation
Indices: 592222--592255 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
592212 AAAATTAAAA
592222 TTTTATTATATATTTTAT
1 TTTTATTATATATTTTAT
*
592240 TTTTATT-TATTTTTTA
1 TTTTATTATATATTTTA
592256 AAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTATATATTTTAT
Found at i:593275 original size:16 final size:16
Alignment explanation
Indices: 593254--593286 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
593244 ACTTGATGGG
593254 TTTTTTTTTTTCTTTC
1 TTTTTTTTTTTCTTTC
*
593270 TTTTTTTTTTTTTTTC
1 TTTTTTTTTTTCTTTC
593286 T
1 T
593287 GGCTGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTCTTTC
Found at i:597999 original size:2 final size:2
Alignment explanation
Indices: 597992--598016 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
597982 ATTGTTCGTT
597992 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
598017 TAGATTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:604947 original size:42 final size:43
Alignment explanation
Indices: 604828--604972 Score: 102
Period size: 42 Copynumber: 3.4 Consensus size: 43
604818 TGTAGTCATG
* ** * * *
604828 GGACCTTGTTGAGACTGAT-TTGGGACT-TCGACTGAAGCAACA
1 GGACCTTGTTGAGACTGATCATGGGA-TGGAGACAGAAGTAATA
* * * * *
604870 GGACCTTGCTGAGA-TGGAT-TTTGGATGGAGGCAGAAGTAATT
1 GGACCTTGTTGAGACT-GATCATGGGATGGAGACAGAAGTAATA
* * *
604912 GGACCTTTTTGAGGCTGATCATGGGAT-GAGACAGAAGTCATA
1 GGACCTTGTTGAGACTGATCATGGGATGGAGACAGAAGTAATA
*
604954 GGGCCTTGTTGAGACTGAT
1 GGACCTTGTTGAGACTGAT
604973 TTTTTACTTC
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
41 2 0.03
42 71 0.90
43 6 0.08
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (43 bp):
GGACCTTGTTGAGACTGATCATGGGATGGAGACAGAAGTAATA
Found at i:609346 original size:34 final size:33
Alignment explanation
Indices: 609297--609394 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 33
609287 AAATATTAAA
* * *
609297 TATTAAAAATTTTAAAATATATATT-TACATATTT
1 TATTAAAAAATTTAAAA-ATATATTATAAATA-TC
* *
609331 TATTAAAAAACTTAAAAATATGTTATAAATATC
1 TATTAAAAAATTTAAAAATATATTATAAATATC
609364 TATATAAAAAATTTAAAAA-ATATTAATAAAT
1 TAT-TAAAAAATTTAAAAATATATT-ATAAAT
609395 CTAAAATGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
33 14 0.26
34 40 0.74
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
TATTAAAAAATTTAAAAATATATTATAAATATC
Found at i:609621 original size:23 final size:24
Alignment explanation
Indices: 609571--609628 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
609561 TTTTTTTTCT
* * *
609571 TAAATTTAATAAAAAATAATATAT
1 TAAATATAATAAAAAATAAAATAA
*
609595 TAAATATAA-AAAAATTAAAATAA
1 TAAATATAATAAAAAATAAAATAA
609618 TAAATA-AATAA
1 TAAATATAATAA
609629 TTTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 19 0.66
24 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATATAATAAAAAATAAAATAA
Found at i:610110 original size:29 final size:29
Alignment explanation
Indices: 610036--610119 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
610026 TATTTAAAAT
*
610036 TTTAAATATA-AATATAATATGTATATTAAA
1 TTTAAATATATTATATAATAT-TA-ATTAAA
*
610066 --TATATCATATTA-ATAATATTAATTAAA
1 TTTAAAT-ATATTATATAATATTAATTAAA
*
610093 TTTAAATATATTATATAATATTTATTA
1 TTTAAATATATTATATAATATTAATTA
610120 TAATATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
27 6 0.13
28 12 0.27
29 26 0.58
30 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TTTAAATATATTATATAATATTAATTAAA
Done.