Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 181 of 198
Found at i:56507822 original size:25 final size:25
Alignment explanation
Indices: 56507793--56507903 Score: 91
Period size: 25 Copynumber: 4.5 Consensus size: 25
56507783 AACCCTCTCT
56507793 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
* * * * *
56507818 TGAGCAATGTAACAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTCATG
* * * *
56507843 CGAGCTATATAACGGGAAGCCCATA
1 CGAGCCATATAACAGGAAGCTCATG
* * **
56507868 AGAGCCATA-ATCAATAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
56507892 CGAGCCA-ATAAC
1 CGAGCCATATAAC
56507904 GGGTAGCTTC
Statistics
Matches: 63, Mismatches: 22, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
23 1 0.02
24 17 0.27
25 45 0.71
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATG
Found at i:56507978 original size:23 final size:23
Alignment explanation
Indices: 56507948--56507995 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
56507938 GGATAGCCAT
*
56507948 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGTTCAAGAGAGCC
*
56507971 ATATCGGGAAGTTCTAGAGAGCC
1 ATATCGGGAAGTTCAAGAGAGCC
56507994 AT
1 AT
56507996 TAATTAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (23 bp):
ATATCGGGAAGTTCAAGAGAGCC
Found at i:56508055 original size:26 final size:26
Alignment explanation
Indices: 56507893--56508062 Score: 101
Period size: 26 Copynumber: 6.8 Consensus size: 26
56507883 AAGCTCATGC
* *
56507893 GAGCCA-ATAACGGGTAGCT-TCGAA
1 GAGCCATATAACGGGAAGCTCACGAA
* *
56507917 GAGCCAT-TAATGGGAAGCTC-CGGA
1 GAGCCATATAACGGGAAGCTCACGAA
* * * * *
56507941 TAGCCATATATCGGGAAGTTCAAG-C
1 GAGCCATATAACGGGAAGCTCACGAA
*
56507966 GAGCCATAT--CGGGAAGTTCTA-G-A
1 GAGCCATATAACGGGAAGCTC-ACGAA
** *
56507989 GAGCCAT-TAATTAGGAAGCTCACAAA
1 GAGCCATATAA-CGGGAAGCTCACGAA
*
56508015 GAGCC-TTTAATCGGGAAGCTCACGAA
1 GAGCCATATAA-CGGGAAGCTCACGAA
*
56508041 GAGCCATATAACGGGACGCTCA
1 GAGCCATATAACGGGAAGCTCA
56508063 TAAAAGCTGC
Statistics
Matches: 114, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
22 1 0.01
23 18 0.16
24 27 0.24
25 26 0.23
26 38 0.33
27 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACGAA
Found at i:56509890 original size:21 final size:21
Alignment explanation
Indices: 56509866--56509916 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
56509856 TCTTATACAT
56509866 TGTCATAGCAAACACTTTAGA
1 TGTCATAGCAAACACTTTAGA
*
56509887 TGTCATACCAAACACTTTAGA
1 TGTCATAGCAAACACTTTAGA
56509908 TGTCATAGC
1 TGTCATAGC
56509917 CGAGATACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (21 bp):
TGTCATAGCAAACACTTTAGA
Found at i:56510388 original size:148 final size:148
Alignment explanation
Indices: 56510087--56510422 Score: 410
Period size: 148 Copynumber: 2.3 Consensus size: 148
56510077 ATATCATTAC
* * ** * ** * * *
56510087 TTAACCTTGATGCTCGAACACCAAAGTATCCCC-CCGCAAGG-CCCGAAGCTTCACACATCCCGG
1 TTAACCTTGATGCTCCAACACCGAAGCGTCCCCTCCACAAGGTCTGGAA-CTTCACATATCTCAG
* *
56510150 TTT-ACACCCAGCAATATCGAATTGTGAAATCTAATGAAAATTACATTTCCCTATCTATCCATCC
65 TTTGA-ACCCAGCAATACCGAATTGAGAAATCTAATGAAAATTACATTTCCCTATCTATCCATCC
56510214 TTTCCTCTATTTTGCCACTT
129 TTTCCTCTATTTTGCCACTT
* * *
56510234 TTAACCTTGATGTTCCAACACCGAAGCGTCCCTTCCGCAAGGTCTGGAACTTCACATATCTCAGT
1 TTAACCTTGATGCTCCAACACCGAAGCGTCCCCTCCACAAGGTCTGGAACTTCACATATCTCAGT
* * ** *
56510299 TTGAACCCAGCAATACCGGATTGCAG-AATCTAATGAAAATTCCATTTCCCTATCTATCTGTCGT
66 TTGAACCCAGCAATACCGAATTG-AGAAATCTAATGAAAATTACATTTCCCTATCTATCCATCCT
56510363 TTCCTCTATTTTGCCACTT
130 TTCCTCTATTTTGCCACTT
* * *
56510382 TTAACCTTGATGCTCGAACACCGTAGTGTCCCCTCCACAAG
1 TTAACCTTGATGCTCCAACACCGAAGCGTCCCCTCCACAAG
56510423 TCCCAGGGAT
Statistics
Matches: 161, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
147 27 0.17
148 128 0.80
149 6 0.04
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30
Consensus pattern (148 bp):
TTAACCTTGATGCTCCAACACCGAAGCGTCCCCTCCACAAGGTCTGGAACTTCACATATCTCAGT
TTGAACCCAGCAATACCGAATTGAGAAATCTAATGAAAATTACATTTCCCTATCTATCCATCCTT
TCCTCTATTTTGCCACTT
Found at i:56512609 original size:24 final size:24
Alignment explanation
Indices: 56512555--56512609 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
56512545 TAGCTCTCCA
56512555 GAGCTTCGCAATGTTGGCTCGTTT
1 GAGCTTCGCAATGTTGGCTCGTTT
* *
56512579 GAACTTCTCAAT-TATGGCTC-TTAT
1 GAGCTTCGCAATGT-TGGCTCGTT-T
56512603 GAGCTTC
1 GAGCTTC
56512610 CCGTTATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (24 bp):
GAGCTTCGCAATGTTGGCTCGTTT
Found at i:56512648 original size:25 final size:25
Alignment explanation
Indices: 56512591--56512673 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
56512581 ACTTCTCAAT
**
56512591 TATGGCTCTTATGAGCTTCCCGTTA
1 TATGGCTCAAATGAGCTTCCCGTTA
**
56512616 TACAGCTCAAATGAGCTTCCCGTTA
1 TATGGCTCAAATGAGCTTCCCGTTA
* * **
56512641 CATGGCTCACATGAGCTTCTTGTTA
1 TATGGCTCAAATGAGCTTCCCGTTA
56512666 TATGGCTC
1 TATGGCTC
56512674 GAGAGAGAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (25 bp):
TATGGCTCAAATGAGCTTCCCGTTA
Found at i:56512691 original size:27 final size:25
Alignment explanation
Indices: 56512603--56512693 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
56512593 TGGCTCTTAT
* **
56512603 GAGCTTCCCGTTATACAGCTCA-AA
1 GAGCTTCCTGTTATATGGCTCACAA
* * *
56512627 TGAGCTTCCCGTTACATGGCTCACAT
1 -GAGCTTCCTGTTATATGGCTCACAA
* *
56512653 GAGCTTCTTGTTATATGGCTCGAGAGA
1 GAGCTTCCTGTTATATGGCTC-ACA-A
56512680 GAGCTTCCTGTTAT
1 GAGCTTCCTGTTAT
56512694 GTGCTTGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
25 37 0.70
26 3 0.06
27 13 0.25
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCACAA
Found at i:56525202 original size:9 final size:9
Alignment explanation
Indices: 56525188--56525213 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
56525178 TCAAACTTTG
56525188 TAGGTGCAA
1 TAGGTGCAA
56525197 TAGGTGCAA
1 TAGGTGCAA
56525206 TAGGTGCA
1 TAGGTGCA
56525214 TGTGTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.23
Consensus pattern (9 bp):
TAGGTGCAA
Found at i:56530516 original size:19 final size:19
Alignment explanation
Indices: 56530492--56530550 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
56530482 ATATATGTAT
56530492 AATAATAATATAATATAAC
1 AATAATAATATAATATAAC
* *
56530511 AATAATAATA-AATGCTAAT
1 AATAATAATATAAT-ATAAC
56530530 AATAAT-ATAGTAATA-AAC
1 AATAATAATA-TAATATAAC
56530548 AAT
1 AAT
56530551 TTAACAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 11 0.33
19 19 0.58
20 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AATAATAATATAATATAAC
Found at i:56531509 original size:2 final size:2
Alignment explanation
Indices: 56531502--56531526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56531492 GGCCTATTAC
56531502 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 A
56531527 AATAGAAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56532174 original size:4 final size:4
Alignment explanation
Indices: 56532167--56532209 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
56532157 ATATGTATGT
* *
56532167 ATAG ATAG ATAG ATGG ATAG ATAG ATAG ATAG ATAA ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
56532210 TTTGTACTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:56532560 original size:120 final size:120
Alignment explanation
Indices: 56532347--56532589 Score: 468
Period size: 120 Copynumber: 2.0 Consensus size: 120
56532337 ACAAAATTTA
*
56532347 GCACCCAATTGAGCCTTTAAAGATGAAAAATAATCAATCAAACTCCTCCATTGATGTTACCAAAT
1 GCACCCAATTGAGCCTTTAAAAATGAAAAATAATCAATCAAACTCCTCCATTGATGTTACCAAAT
56532412 TTGACCATTAAATTTTACTTATGTGAATGATAGACCAATTAGCCGACAACACATG
66 TTGACCATTAAATTTTACTTATGTGAATGATAGACCAATTAGCCGACAACACATG
*
56532467 GCACCCAATTGAGCCTTTAAAAATGAAAAATAATCAATCAAACTCCTCCATTGATGTTATCAAAT
1 GCACCCAATTGAGCCTTTAAAAATGAAAAATAATCAATCAAACTCCTCCATTGATGTTACCAAAT
56532532 TTGACCATTAAATTTTACTTATGTGAATGATAGACCAATTAGCCGACAACACATG
66 TTGACCATTAAATTTTACTTATGTGAATGATAGACCAATTAGCCGACAACACATG
56532587 GCA
1 GCA
56532590 ACCACTTGTA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (120 bp):
GCACCCAATTGAGCCTTTAAAAATGAAAAATAATCAATCAAACTCCTCCATTGATGTTACCAAAT
TTGACCATTAAATTTTACTTATGTGAATGATAGACCAATTAGCCGACAACACATG
Found at i:56532783 original size:10 final size:10
Alignment explanation
Indices: 56532768--56532792 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56532758 TTATTAAAAA
56532768 TAAAAATTAT
1 TAAAAATTAT
56532778 TAAAAATTAT
1 TAAAAATTAT
56532788 TAAAA
1 TAAAA
56532793 CCATGAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:56533521 original size:14 final size:14
Alignment explanation
Indices: 56533503--56533537 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
56533493 TCTTATATCT
56533503 TTTTTTTA-TATAA
1 TTTTTTTATTATAA
56533516 TTTTTTTATTATAA
1 TTTTTTTATTATAA
*
56533530 ATTTTTTA
1 TTTTTTTA
56533538 ACCGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTATTATAA
Found at i:56533527 original size:16 final size:14
Alignment explanation
Indices: 56533502--56533536 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
56533492 TTCTTATATC
56533502 TTTTTTTTATATAAT
1 TTTTTTTTATA-AAT
56533517 TTTTTTATTATAAAT
1 TTTTTT-TTATAAAT
56533532 TTTTT
1 TTTTT
56533537 AACCGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTTATAAAT
Found at i:56549437 original size:160 final size:160
Alignment explanation
Indices: 56549173--56549495 Score: 619
Period size: 160 Copynumber: 2.0 Consensus size: 160
56549163 TTCAATATCT
*
56549173 TGAATGGGAGTCTTCAAATGGTATGGGAGACTACTTTGGGGAAATATATGAAGATTTAAGACAAA
1 TGAATGGGAGTCTTCAAATGGTATGAGAGACTACTTTGGGGAAATATATGAAGATTTAAGACAAA
56549238 AATTCAATTGTGATGTCGTAGTTGATGCACGGCTTTCCTCTACATAACGGACTTTCAAAGTTAAA
66 AATTCAATTGTGATGTCGTAGTTGATGCACGGCTTTCCTCTACATAACGGACTTTCAAAGTTAAA
*
56549303 CTATTTTATCTAGTTTTTATTTGGAGACCA
131 CTATTTTATCTAGTTTTCATTTGGAGACCA
*
56549333 TGAATGGGAGTCTTCAAATGGTATGAGAGACTGCTTTGGGGAAATATATGAAGATTTAAGACAAA
1 TGAATGGGAGTCTTCAAATGGTATGAGAGACTACTTTGGGGAAATATATGAAGATTTAAGACAAA
56549398 AATTCAATTGTGATGTCGTAGTTGATGCACGGCTTTCCTCTACATAACGGACTTTCAAAGTTAAA
66 AATTCAATTGTGATGTCGTAGTTGATGCACGGCTTTCCTCTACATAACGGACTTTCAAAGTTAAA
56549463 CTATTTTATCTAGTTTTCATTTGGAGACCA
131 CTATTTTATCTAGTTTTCATTTGGAGACCA
56549493 TGA
1 TGA
56549496 TATCTTTTTA
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (160 bp):
TGAATGGGAGTCTTCAAATGGTATGAGAGACTACTTTGGGGAAATATATGAAGATTTAAGACAAA
AATTCAATTGTGATGTCGTAGTTGATGCACGGCTTTCCTCTACATAACGGACTTTCAAAGTTAAA
CTATTTTATCTAGTTTTCATTTGGAGACCA
Found at i:56550724 original size:18 final size:17
Alignment explanation
Indices: 56550701--56550753 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
56550691 ATATATTATG
*
56550701 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
56550719 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
56550736 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
56550754 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:56550758 original size:99 final size:97
Alignment explanation
Indices: 56550548--56550773 Score: 291
Period size: 99 Copynumber: 2.3 Consensus size: 97
56550538 AAGTAGATTA
*
56550548 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAAATTCATATAAGAATATTTAAT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAAATTCATATAAGAATATTTAAA
56550613 ACTAAGAATTTTATCAAATTATATATTTTTAT
66 ACTAAGAATTTTATCAAATTATATATTTTTAT
*
56550645 TAAATTATATTTAATAATAATTATTTTAAATTAT-TTTTA-TAGTATT-ATATATTATG-AT-TT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTA-AATTCATATA--A-GAATATT
* * * *
56550705 TAGTAAATTCATATATTTTATTAAATTATATATTTTTAT
62 TA--AAACTAAGA-ATTTTATCAAATTATATATTTTTAT
*
56550744 TAAATTATATTTAATAATAATTATGTTAAA
1 TAAATTATATTTAATAATAATTATTTTAAA
56550774 ATATGATTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
95 7 0.06
96 12 0.10
97 37 0.32
98 6 0.05
99 53 0.46
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (97 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAAATTCATATAAGAATATTTAAA
ACTAAGAATTTTATCAAATTATATATTTTTAT
Found at i:56550952 original size:39 final size:41
Alignment explanation
Indices: 56550901--56551006 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
56550891 TTTCCTTATG
* *
56550901 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
56550941 C-ATTATGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
56550986 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
56551007 ACAGCGAACC
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 8 0.15
40 1 0.02
41 8 0.15
42 1 0.02
43 1 0.02
44 23 0.42
45 4 0.07
46 9 0.16
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:56550963 original size:44 final size:46
Alignment explanation
Indices: 56550914--56551006 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
56550904 TTACACCTCT
* *
56550914 ATTCCATTCAACCAAACACAAGAA-TACC-ATTATGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
56550958 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
56551004 ATT
1 ATT
56551007 ACAGCGAACC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:56551017 original size:46 final size:42
Alignment explanation
Indices: 56550901--56551020 Score: 129
Period size: 46 Copynumber: 2.8 Consensus size: 42
56550891 TTTCCTTATG
* *
56550901 CTATTACACCTCTATTCCATT--CAACCAAACACAAGAATAC
1 CTATTACGCCTCTATTCCATTCACAACCAAACAAAAGAATAC
*
56550941 C-ATTATGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATT-CA--CAACCAAACAAAAGAA-TAC
56550986 CTATTACGCCTCTATTCCATTACAGCGAACCAAAC
1 CTATTACGCCTCTATTCCATT-CA-C-AACCAAAC
56551021 GAGCCCTTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
39 17 0.26
40 1 0.02
44 15 0.23
45 5 0.08
46 28 0.42
ACGTcount: A:0.37, C:0.32, G:0.05, T:0.27
Consensus pattern (42 bp):
CTATTACGCCTCTATTCCATTCACAACCAAACAAAAGAATAC
Found at i:56558329 original size:13 final size:13
Alignment explanation
Indices: 56558311--56558336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56558301 AAGGAAAATC
56558311 AGAGGTTTATCTT
1 AGAGGTTTATCTT
56558324 AGAGGTTTATCTT
1 AGAGGTTTATCTT
56558337 TTATGCTCAA
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
AGAGGTTTATCTT
Found at i:56558736 original size:97 final size:98
Alignment explanation
Indices: 56558565--56558755 Score: 226
Period size: 97 Copynumber: 2.0 Consensus size: 98
56558555 TCGAGGCTGC
* * * *
56558565 TTAAGCCATTTCCCACTAAAGCAAAGACGAGGCCTCATCATCATTGTATAATTATGCATAAACGT
1 TTAAGCCACTTCCCACTAAAACAAAGACCAGGCCTCATCATCATTGTACAATTATGCATAAACGT
* **
56558630 ATTATCTTGGCTTATGATAATCATCAAATTAAA
66 ATTAGCTTGGCTTAAAATAATCATCAAATTAAA
* * * *
56558663 TTAAGCCACTTCGCACTAAAACAAA-ACCTGGCTTCATCA-C-TTGTACAATTATGCATAGCCAC
1 TTAAGCCACTTCCCACTAAAACAAAGACCAGGCCTCATCATCATTGTACAATTATGCATA--AAC
* *
56558725 TTATTAGCTTGGCTTAAAATTATCATCAAAT
64 GTATTAGCTTGGCTTAAAATAATCATCAAAT
56558756 CAACTCAACT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
95 16 0.21
96 1 0.01
97 39 0.50
98 22 0.28
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (98 bp):
TTAAGCCACTTCCCACTAAAACAAAGACCAGGCCTCATCATCATTGTACAATTATGCATAAACGT
ATTAGCTTGGCTTAAAATAATCATCAAATTAAA
Found at i:56565087 original size:19 final size:17
Alignment explanation
Indices: 56565064--56565124 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
56565054 CAACAATAAT
56565064 TAAAAAATATAAAAATA
1 TAAAAAATATAAAAATA
56565081 TTCAAAAAA-ATATAAAATA
1 -T-AAAAAATATA-AAAATA
56565100 TAAAAAATTCATAAAAAT-
1 TAAAAAA-T-ATAAAAATA
56565118 TAAAAAA
1 TAAAAAA
56565125 ATTAGCATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.16
18 12 0.32
19 17 0.45
20 3 0.08
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAAATATAAAAATA
Found at i:56565090 original size:20 final size:18
Alignment explanation
Indices: 56565065--56565126 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
56565055 AACAATAATT
56565065 AAAAAATATAAAAATATTCA
1 AAAAAATATAAAAATA-T-A
56565085 AAAAAATAT-AAAATATA
1 AAAAAATATAAAAATATA
*
56565102 AAAAATTCATAAAAAT-TA
1 AAAAAAT-ATAAAAATATA
56565120 AAAAAAT
1 AAAAAAT
56565127 TAGCATGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 7 0.18
18 11 0.29
19 11 0.29
20 9 0.24
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAATATAAAAATATA
Found at i:56565124 original size:27 final size:27
Alignment explanation
Indices: 56565061--56565124 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
56565051 CATCAACAAT
56565061 AATTAAAAAATATAAAAATATTCAAAA
1 AATTAAAAAATATAAAAATATTCAAAA
* *
56565088 AAATATAAAATATAAAAA-ATTCATAAA
1 AATTAAAAAATATAAAAATATTCA-AAA
56565115 AATTAAAAAA
1 AATTAAAAAA
56565125 ATTAGCATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (27 bp):
AATTAAAAAATATAAAAATATTCAAAA
Found at i:56565770 original size:26 final size:26
Alignment explanation
Indices: 56565741--56565799 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
56565731 TAAAAAAAAT
*
56565741 ACAAAAT-ATTAAATTTCAATATAACA
1 ACAAAATAATTAAA-TTAAATATAACA
*
56565767 ACAAAATAATTAAATTAAATATAATA
1 ACAAAATAATTAAATTAAATATAACA
*
56565793 AAAAAAT
1 ACAAAAT
56565800 TCTTACCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (26 bp):
ACAAAATAATTAAATTAAATATAACA
Found at i:56565935 original size:26 final size:25
Alignment explanation
Indices: 56565886--56565942 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
56565876 AATAAATATG
*
56565886 AAAAAAATCGTAATATAAAATTAATT
1 AAAAAAATCGTAATACAAAATTAA-T
* **
56565912 AAAAAAATCTTAATACAATTTTAAT
1 AAAAAAATCGTAATACAAAATTAAT
56565937 AAAAAA
1 AAAAAA
56565943 TGAGAGTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAAAAATCGTAATACAAAATTAAT
Found at i:56565990 original size:22 final size:22
Alignment explanation
Indices: 56565965--56566014 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
56565955 GAGGATTGAA
*
56565965 AATTGAGTGAGAATTGAGAATG
1 AATTGAGAGAGAATTGAGAATG
* * *
56565987 AATTAAGAGAGAGTTGAGAGTG
1 AATTGAGAGAGAATTGAGAATG
56566009 AATTGA
1 AATTGA
56566015 AAAAGTAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (22 bp):
AATTGAGAGAGAATTGAGAATG
Found at i:56569211 original size:30 final size:30
Alignment explanation
Indices: 56569171--56569228 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56569161 TTGGGCATTT
* *
56569171 CCACATGGGCTGGCCACATGCCCGTGTGAG
1 CCACACGGGCTGGCCACATGCCCATGTGAG
*
56569201 CCACACGGGCTGGCCACGTGCCCATGTG
1 CCACACGGGCTGGCCACATGCCCATGTG
56569229 CCAGCCCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.33, T:0.16
Consensus pattern (30 bp):
CCACACGGGCTGGCCACATGCCCATGTGAG
Found at i:56570109 original size:10 final size:10
Alignment explanation
Indices: 56570094--56570118 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56570084 TTAAAAACAA
56570094 TAGTAATTAC
1 TAGTAATTAC
56570104 TAGTAATTAC
1 TAGTAATTAC
56570114 TAGTA
1 TAGTA
56570119 GAAAAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (10 bp):
TAGTAATTAC
Found at i:56571421 original size:22 final size:22
Alignment explanation
Indices: 56571393--56571457 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 22
56571383 CCGATGCTAT
56571393 TACCTTCAATAATATTCACTTA
1 TACCTTCAATAATATTCACTTA
*
56571415 TACCTTCAATGGAAATAATTCACTTT
1 TACCTTCAAT---AAT-ATTCACTTA
*
56571441 TACCTTCAATATTATTC
1 TACCTTCAATAATATTC
56571458 TCTTTAGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 14 0.38
23 2 0.05
25 3 0.08
26 18 0.49
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.42
Consensus pattern (22 bp):
TACCTTCAATAATATTCACTTA
Found at i:56571462 original size:22 final size:22
Alignment explanation
Indices: 56571392--56571462 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
56571382 GCCGATGCTA
*
56571392 TTACCTTCAATAATATTCACTT
1 TTACCTTCAATATTATTCACTT
* *
56571414 ATACCTTCAATGGAAATAATTCACTT
1 TTACCTTCAAT----ATTATTCACTT
*
56571440 TTACCTTCAATATTATTCTCTT
1 TTACCTTCAATATTATTCACTT
56571462 T
1 T
56571463 AGTAGTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 20 0.51
26 19 0.49
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.45
Consensus pattern (22 bp):
TTACCTTCAATATTATTCACTT
Found at i:56574626 original size:29 final size:29
Alignment explanation
Indices: 56574588--56574688 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 29
56574578 TGATACATAG
* *
56574588 TTATATATATGAATTTTTATTTGATGCAA
1 TTATACATATGAATTTTTATTTGATTCAA
* *
56574617 TTATACATATGAAATTTTGATTGTGGTTCAAA
1 TTATACATATG-AATTTTTATT-TGATTC-AA
* *
56574649 CATATACGTA-GAATTTTTATTTTGATTCAA
1 -TTATACATATGAATTTTTA-TTTGATTCAA
56574679 TTATACATAT
1 TTATACATAT
56574689 TTAAAGAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
29 17 0.30
30 11 0.20
31 16 0.29
32 5 0.09
33 7 0.12
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (29 bp):
TTATACATATGAATTTTTATTTGATTCAA
Found at i:56577977 original size:94 final size:93
Alignment explanation
Indices: 56577721--56577999 Score: 265
Period size: 94 Copynumber: 3.0 Consensus size: 93
56577711 TTAGTGTCAC
* * * * * * * * * * *
56577721 AGCTTCGTCTTGCTCCATTGCAACTTTAAGGAGCTAAGATTCGTTGTTGTAGTTTCAGTCTATTC
1 AGCTTCATCTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGTCTCAATCTA-AC
* *
56577786 CACTGCAACTTTAGGGATATAGGATTTGT
65 CACTGCAACTTTAGGGGTATAGGATTGGT
* * * * *
56577815 AGCTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAGATTTGC-GACTGTA-ACTTCATTCCAA
1 AGCTTCATCTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTG-TTGTAGTC-TCAAT-CTA
*
56577878 ACCACTGCAACTTTAGGGGTATATGATTGGT
63 ACCACTGCAACTTTAGGGGTATAGGATTGGT
* ** * *
56577909 AGCTTCATCTTGTTCTGTTGTAACTTCAGGGAGATAAGATTTGCTGTTGTAGTCTCAATCTGACC
1 AGCTTCATCTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGTCTCAATCT-AAC
* *
56577974 CACTGCAACTTCAGAGGTATAGGATT
65 CACTGCAACTTTAGGGGTATAGGATT
56578000 CATTATGATG
Statistics
Matches: 148, Mismatches: 31, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
93 2 0.01
94 142 0.96
95 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (93 bp):
AGCTTCATCTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCTGTTGTAGTCTCAATCTAACC
ACTGCAACTTTAGGGGTATAGGATTGGT
Found at i:56578055 original size:143 final size:143
Alignment explanation
Indices: 56577878--56578137 Score: 335
Period size: 143 Copynumber: 1.8 Consensus size: 143
56577868 TTCATTCCAA
* * * * *** ** *
56577878 ACCACTGCAACTTTAGGGGTATATGATTGGTAGCTTC-ATCTTGTTCTGTTGTAACTTCAGGGAG
1 ACCACTACAACTTCAGGGGTATAGGATTGGTAGCTTCAATC-TGCTCCACTACAACTTCAGGAAG
* * *
56577942 ATAAGATTTGCTGTTGTAG-TCTCAATCTGACCCACTGCAACTTCAGAGGTATAGGATTCATTAT
65 ATAAGATTCGCTATGGTAGAT-TCAATCTGACCCACTGCAACTTCAGAGGTATAGGATTCATTAT
56578006 GATGACTTCAATCTG
129 GATGACTTCAATCTG
*
56578021 ACCACTACAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGA
1 ACCACTACAACTTCAGGGGTATAGGATTGGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGA
* * *
56578086 TAAGATTCGCTATGGTAGATTCAATCTGACCCGCTGCAACTTTAGGGGTATA
66 TAAGATTCGCTATGGTAGATTCAATCTGACCCACTGCAACTTCAGAGGTATA
56578138 AGGTTTGTAA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
143 94 0.96
144 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (143 bp):
ACCACTACAACTTCAGGGGTATAGGATTGGTAGCTTCAATCTGCTCCACTACAACTTCAGGAAGA
TAAGATTCGCTATGGTAGATTCAATCTGACCCACTGCAACTTCAGAGGTATAGGATTCATTATGA
TGACTTCAATCTG
Found at i:56578070 original size:93 final size:94
Alignment explanation
Indices: 56577955--56578146 Score: 216
Period size: 93 Copynumber: 2.1 Consensus size: 94
56577945 AGATTTGCTG
* * * *
56577955 TTGTAGTCTCAATCTGACCCACTGCAACTTCA-GAGGTATAGGATTCATTATGAT-GACTTCAAT
1 TTGTAGTCTCAATCTGACCCACTACAACTTCAGGAAG-ATAAGATTCACTATGATAGA-TTCAAT
56578018 CTGA-CCACTACAACTTCAGGGGTAT-AGGAT
64 CTGACCCACTACAACTTCAGGGGTATAAGG-T
* *
56578048 TTGTAG-CTTCAATCTG-CTCCACTACAACTTCAGGAAGATAAGATTCGCTATGGTAGATTCAAT
1 TTGTAGTC-TCAATCTGAC-CCACTACAACTTCAGGAAGATAAGATTCACTATGATAGATTCAAT
* * *
56578111 CTGACCCGCTGCAACTTTAGGGGTATAAGGT
64 CTGACCCACTACAACTTCAGGGGTATAAGGT
56578142 TTGTA
1 TTGTA
56578147 ACTTGTAGCT
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
92 2 0.02
93 50 0.60
94 29 0.35
95 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (94 bp):
TTGTAGTCTCAATCTGACCCACTACAACTTCAGGAAGATAAGATTCACTATGATAGATTCAATCT
GACCCACTACAACTTCAGGGGTATAAGGT
Found at i:56578139 original size:50 final size:48
Alignment explanation
Indices: 56577963--56578139 Score: 145
Period size: 50 Copynumber: 3.7 Consensus size: 48
56577953 TGTTGTAGTC
* * * *
56577963 TCAATCTGACCCACTGCAACTTCAGAGGTATAGGATTCATTATGAT-GACT
1 TCAATCTGACCCACTACAACTTCAGGGGTATAAGATTC--TATGGTAGA-T
* *
56578013 TCAATCTGA-CCACTACAACTTCAGGGGTATAGGA-T-T-T-GTAGCT
1 TCAATCTGACCCACTACAACTTCAGGGGTATAAGATTCTATGGTAGAT
*
56578056 TCAATCTG-CTCCACTACAACTTCAGGAAG-ATAAGATTCGCTATGGTAGAT
1 TCAATCTGAC-CCACTACAACTTCAGG-GGTATAAGATT--CTATGGTAGAT
* * *
56578106 TCAATCTGACCCGCTGCAACTTTAGGGGTATAAG
1 TCAATCTGACCCACTACAACTTCAGGGGTATAAG
56578140 GTTTGTAACT
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
43 10 0.10
44 23 0.22
45 3 0.03
48 2 0.02
49 25 0.24
50 40 0.38
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (48 bp):
TCAATCTGACCCACTACAACTTCAGGGGTATAAGATTCTATGGTAGAT
Found at i:56584267 original size:16 final size:16
Alignment explanation
Indices: 56584246--56584278 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56584236 TTCTGGCCCT
56584246 CTTCTAAAGTGCCAAC
1 CTTCTAAAGTGCCAAC
56584262 CTTCTAAAGTGCCAAC
1 CTTCTAAAGTGCCAAC
56584278 C
1 C
56584279 GAGTTTTCCT
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:0.30, C:0.33, G:0.12, T:0.24
Consensus pattern (16 bp):
CTTCTAAAGTGCCAAC
Found at i:56587105 original size:2 final size:2
Alignment explanation
Indices: 56587098--56587129 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56587088 GAGCAAGTAA
56587098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56587130 GTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56587522 original size:14 final size:15
Alignment explanation
Indices: 56587505--56587537 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
56587495 AGTAAATATA
56587505 AATAAAGAC-ATAAC
1 AATAAAGACAATAAC
*
56587519 AATAATGACAATAAC
1 AATAAAGACAATAAC
56587534 AATA
1 AATA
56587538 CTAATAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (15 bp):
AATAAAGACAATAAC
Found at i:56587546 original size:15 final size:15
Alignment explanation
Indices: 56587514--56587577 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
56587504 AAATAAAGAC
* *
56587514 ATAACAATAATGACA
1 ATAACAATAATAATA
*
56587529 ATAACAATACTAATA
1 ATAACAATAATAATA
56587544 ATAGTA-AAT-ATAATA
1 ATA--ACAATAATAATA
56587559 ATAACAATAATAATA
1 ATAACAATAATAATA
56587574 ATAA
1 ATAA
56587578 AAGATGACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.02
14 3 0.07
15 33 0.80
16 3 0.07
17 1 0.02
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (15 bp):
ATAACAATAATAATA
Found at i:56587568 original size:12 final size:12
Alignment explanation
Indices: 56587519--56587574 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
56587509 AAGACATAAC
*
56587519 AATAATGACAAT
1 AATAATAACAAT
*
56587531 AACAAT-ACTAAT
1 AATAATAAC-AAT
*
56587543 AATAGTAA-ATAT
1 AATAATAACA-AT
56587555 AATAATAACAAT
1 AATAATAACAAT
56587567 AATAATAA
1 AATAATAA
56587575 TAAAAGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 3 0.08
12 31 0.86
13 2 0.06
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (12 bp):
AATAATAACAAT
Found at i:56592834 original size:41 final size:41
Alignment explanation
Indices: 56592789--56592950 Score: 159
Period size: 41 Copynumber: 4.0 Consensus size: 41
56592779 TTGTATAAAA
* * * *
56592789 CACCGACATAAAGCCTGCTAGGCACAAAGCCTGATACATTT
1 CACCGGCATAAAGCCTGCTAGACAAAAAGTCTGATACATTT
*
56592830 CACCGGCACAAAGCCTGCTAGACAAAAAGTCTGAAGTA-A-TT
1 CACCGGCATAAAGCCTGCTAGACAAAAAGTCTG-A-TACATTT
* * *
56592871 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAACATTT
1 CACCGGCATAAAGCCTGCTAGACAAAAAGTCTGATACATTT
* * ** *
56592912 CATCGGCATCAAGCCT-CTTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGC-TAGACAAAAAGTCTGATACAT
56592951 CTTATTTTCA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 97 0.92
42 2 0.02
43 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGACAAAAAGTCTGATACATTT
Found at i:56592926 original size:82 final size:82
Alignment explanation
Indices: 56592789--56592946 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 82
56592779 TTGTATAAAA
* *
56592789 CACCGACATAAAGCCTGCTAGGCACAAAGCCTGATACATTTCACCGGCACAAAGCCTGC-TAGAC
1 CACCGACATAAAGCCTGCTAGACACAAAGCCTGAAACATTTCACCGGCACAAAGCCT-CTTAGAC
56592853 AAAAAGTCTGAAGTAATT
65 AAAAAGTCTGAAGTAATT
* * * * *
56592871 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAACATTTCATCGGCATC-AAGCCTCTTAGAC
1 CACCGACATAAAGCCTGCTAGACACAAAGCCTGAAACATTTCACCGGCA-CAAAGCCTCTTAGAC
**
56592935 GTAAAGTCTGAA
65 AAAAAGTCTGAA
56592947 ACATCTTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.02
82 63 0.97
83 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (82 bp):
CACCGACATAAAGCCTGCTAGACACAAAGCCTGAAACATTTCACCGGCACAAAGCCTCTTAGACA
AAAAGTCTGAAGTAATT
Found at i:56605360 original size:92 final size:92
Alignment explanation
Indices: 56605256--56605440 Score: 302
Period size: 92 Copynumber: 2.0 Consensus size: 92
56605246 TCCTTGAAAG
* *
56605256 TTAAACTAATATCTATCCCAATCCTT-TTT-TATTTCAGATTTGGAACCTTAACACTCATTATTC
1 TTAAAATAATATCTATCCCAAT-CTTATTTGT-TTTCAGATTTGGAACCTAAACACTCATTATTC
56605319 TTGGTTTCTCCTTACTTTTTTGCTCATTT
64 TTGGTTTCTCCTTACTTTTTTGCTCATTT
*
56605348 TTAAAATAATATCTATCCCAATCTTATTTGTTTTCAGATTTGGAACCTAAATACTCATTATTCTT
1 TTAAAATAATATCTATCCCAATCTTATTTGTTTTCAGATTTGGAACCTAAACACTCATTATTCTT
*
56605413 GGTTTCTCCTTACTTTTTTGCTTATTT
66 GGTTTCTCCTTACTTTTTTGCTCATTT
56605440 T
1 T
56605441 CTTAGTTATG
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
91 3 0.03
92 83 0.95
93 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (92 bp):
TTAAAATAATATCTATCCCAATCTTATTTGTTTTCAGATTTGGAACCTAAACACTCATTATTCTT
GGTTTCTCCTTACTTTTTTGCTCATTT
Found at i:56606398 original size:253 final size:254
Alignment explanation
Indices: 56605950--56606461 Score: 929
Period size: 253 Copynumber: 2.0 Consensus size: 254
56605940 TAGGACTCTC
* *
56605950 AATTTGTAAATATGCACAAATCTCAACTATTGATATAACTTAATTTGTACCGTTGGATCTAGAGG
1 AATTTGTAAATATACACAAATCTCAACTATTGATATAACTCAATTTGTACCGTTGGATCTAGAGG
56606015 AGCTCAACTATGAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAATTGTAATCCTTCAAAGTA
66 AGCTCAACTATGAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAATTGTAATCCTTCAAAGTA
*
56606080 ATTGAGATACTTTGAGAGCATTTACTCAAACACATTGTGTGCGATATTTTTCTGTGACTTTTTGT
131 ATGGAGATACTTTGAGAGCATTTACTCAAACACATTGTGTGCGATATTTTTCTGTGACTTTTTGT
*
56606145 TCGTTTATGGCTTCTTTCTCTTTCGAGTTTGATTTT-AA-TTTATTTCGATGCCTTAGAG
196 TCGTTCATGGCTTCTTTCTCTTTCGAGTTTG-TTTTCAATTTTATTTCGATGCCTTAGAG
56606203 AATTTGTAAATATACACAAATCTCAACTATTGATATAACTCAATTTGTACCGTTGGATCTAGAGG
1 AATTTGTAAATATACACAAATCTCAACTATTGATATAACTCAATTTGTACCGTTGGATCTAGAGG
56606268 AGCTCAACTATGAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAATTGTAATCCTTCAAAGTA
66 AGCTCAACTATGAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAATTGTAATCCTTCAAAGTA
* *
56606333 ATGGAGATACTTTGAGAGCATTTACTCAAACACCTTGTGTGCGCTATTTTTCTGTGACTTTTTGT
131 ATGGAGATACTTTGAGAGCATTTACTCAAACACATTGTGTGCGATATTTTTCTGTGACTTTTTGT
* *
56606398 TTGTTCATGGCTTCTTTCTCTTTCGAGTTTGTTTTCAATTTTATTTTGATGCCTTAGAG
196 TCGTTCATGGCTTCTTTCTCTTTCGAGTTTGTTTTCAATTTTATTTCGATGCCTTAGAG
56606457 AATTT
1 AATTT
56606462 CTATTGAGAA
Statistics
Matches: 249, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
252 4 0.02
253 221 0.89
254 24 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (254 bp):
AATTTGTAAATATACACAAATCTCAACTATTGATATAACTCAATTTGTACCGTTGGATCTAGAGG
AGCTCAACTATGAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAATTGTAATCCTTCAAAGTA
ATGGAGATACTTTGAGAGCATTTACTCAAACACATTGTGTGCGATATTTTTCTGTGACTTTTTGT
TCGTTCATGGCTTCTTTCTCTTTCGAGTTTGTTTTCAATTTTATTTCGATGCCTTAGAG
Found at i:56616848 original size:57 final size:54
Alignment explanation
Indices: 56616746--56616862 Score: 171
Period size: 57 Copynumber: 2.1 Consensus size: 54
56616736 AAACCTAAAT
*
56616746 TATAAAAACAAAATATATTCTAATTTTTTCTTTTCTTATAATGGAAAAAGACTA
1 TATAAAAACAAAATATATTCTAATTTTTTCTTTTCTTATAATGGAAAAAAACTA
* *
56616800 TATAGAAACAAATTATATTCTAATTTTTTTTTCTTTTCTTATAATGGAAAAAAACTA
1 TATAAAAACAAAATATATTCTAA---TTTTTTCTTTTCTTATAATGGAAAAAAACTA
*
56616857 TGTAAA
1 TATAAA
56616863 GAAACAGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
54 21 0.38
57 34 0.62
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (54 bp):
TATAAAAACAAAATATATTCTAATTTTTTCTTTTCTTATAATGGAAAAAAACTA
Found at i:56618074 original size:32 final size:32
Alignment explanation
Indices: 56618038--56618100 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
56618028 TATAACATTA
56618038 TTGTTAGATAGCTTTCTCATTTT-GACCACTCG
1 TTGTTAGATAGCTTTCTCATTTTAG-CCACTCG
* *
56618070 TTGTTAGATAGTTTTTTCATTTTAGCCACTC
1 TTGTTAGATAGCTTTCTCATTTTAGCCACTC
56618101 CCCATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (32 bp):
TTGTTAGATAGCTTTCTCATTTTAGCCACTCG
Found at i:56618388 original size:141 final size:135
Alignment explanation
Indices: 56618152--56618406 Score: 293
Period size: 140 Copynumber: 1.8 Consensus size: 135
56618142 CATCTTTAAC
* * * *
56618152 TCATTTTATATTTTTAATTTCATTTTTTTATTTTTTTAGAATTAATTTTAACTTTTTCTAGTAAG
1 TCATTTTATATTTTAAATTTCATTTTTTTATTTTTTTAAAATCAATTTTAACTTTTTCTAGTAAA
* *
56618217 GGAAAAAAACATGAGTTTTTACAAAGAATTAATTGGGTTTTTGTAAGAAAATTTGGATTTTTACA
66 GGAAAAAAACATAAGTTTTTACAAAGAATTAATT-GGTTTTTAT-AGAAAATTTGGATTTTTACA
56618282 TGAAAAA
129 TGAAAAA
* * *
56618289 TCATTTTATCATTTTAAATTT-TTTTATATTTCTTCTTTTTAAAATCAATTTTAAGTTTTTCATA
1 TCATTTTAT-ATTTTAAATTTCATTT-T-TTTATT-TTTTTAAAATCAATTTTAACTTTTTC-TA
* *
56618353 GTAAAAGG-AAAAAAC-TCAAGTTTTTAC-ATGAAATTACTTGGTTTTTATAGAAAA
61 GT-AAAGGAAAAAAACAT-AAGTTTTTACAAAG-AATTAATTGGTTTTTATAGAAAA
56618407 AAAAACTTAG
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
137 12 0.12
138 11 0.11
139 11 0.11
140 34 0.34
141 27 0.27
142 4 0.04
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (135 bp):
TCATTTTATATTTTAAATTTCATTTTTTTATTTTTTTAAAATCAATTTTAACTTTTTCTAGTAAA
GGAAAAAAACATAAGTTTTTACAAAGAATTAATTGGTTTTTATAGAAAATTTGGATTTTTACATG
AAAAA
Found at i:56618423 original size:24 final size:23
Alignment explanation
Indices: 56618388--56618432 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56618378 ACATGAAATT
* *
56618388 ACTTGGTTTTTATAGAAAAAAAA
1 ACTTAGTTTTTACAGAAAAAAAA
56618411 ACTTAGTTATTTACAGAAAAAA
1 ACTTAGTT-TTTACAGAAAAAA
56618433 TTATTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (23 bp):
ACTTAGTTTTTACAGAAAAAAAA
Found at i:56618727 original size:36 final size:35
Alignment explanation
Indices: 56618656--56618727 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
56618646 CCCCCAAATG
* *
56618656 TTTTAATAATAATGTATTAATATTAATCATTATTA
1 TTTTAATAATAATGTATTAATATTAATAATAATTA
* *
56618691 TTTTGAATAATAATGTTTTAAT-TTAGTTAATAATTA
1 TTTT-AATAATAATGTATTAATATTA-ATAATAATTA
56618727 T
1 T
56618728 ATATATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (35 bp):
TTTTAATAATAATGTATTAATATTAATAATAATTA
Found at i:56618849 original size:10 final size:10
Alignment explanation
Indices: 56618834--56618870 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
56618824 AGACCTACAT
56618834 TTTTTATAGA
1 TTTTTATAGA
56618844 TTTTTATAGA
1 TTTTTATAGA
56618854 TTTGTTATA-A
1 TTT-TTATAGA
56618864 TTTTTAT
1 TTTTTAT
56618871 TTTGTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 4 0.15
10 17 0.65
11 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
TTTTTATAGA
Found at i:56618861 original size:21 final size:20
Alignment explanation
Indices: 56618832--56618870 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
56618822 CCAGACCTAC
*
56618832 ATTTTTTATAGATTTTTATAG
1 ATTTGTTATA-ATTTTTATAG
56618853 ATTTGTTATAATTTTTAT
1 ATTTGTTATAATTTTTAT
56618871 TTTGTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
ATTTGTTATAATTTTTATAG
Found at i:56619120 original size:19 final size:20
Alignment explanation
Indices: 56619096--56619133 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56619086 ACTTTTTAGA
56619096 CAAAAAA-TATATAATAAAG
1 CAAAAAATTATATAATAAAG
*
56619115 CAAAAAATTATATATTAAA
1 CAAAAAATTATATAATAAA
56619134 ATGAGACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
CAAAAAATTATATAATAAAG
Found at i:56619894 original size:25 final size:25
Alignment explanation
Indices: 56619861--56619910 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56619851 GCTGCAATCT
56619861 TCTCTCTAACAAAGAACAGATCTAA
1 TCTCTCTAACAAAGAACAGATCTAA
*
56619886 TCTCTCTAACAAAGAACATATCTAA
1 TCTCTCTAACAAAGAACAGATCTAA
56619911 CTCAACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (25 bp):
TCTCTCTAACAAAGAACAGATCTAA
Found at i:56624657 original size:27 final size:28
Alignment explanation
Indices: 56624605--56624657 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
56624595 AAAAAAATTA
* * *
56624605 TATTTATAATAATTTTATGTATTTTTAT
1 TATTTATAATAATTTCATATAATTTTAT
56624633 TATTT-TAATAATTTCATATAATTTT
1 TATTTATAATAATTTCATATAATTTT
56624658 CTAGATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TATTTATAATAATTTCATATAATTTTAT
Found at i:56640513 original size:90 final size:90
Alignment explanation
Indices: 56640360--56640550 Score: 373
Period size: 90 Copynumber: 2.1 Consensus size: 90
56640350 GGTCTAGTTG
56640360 TAGTGCCTGAGAAAATTTCTAAAGGGTTAACAACCTGCAAAGATGGACGCAAGGTTTGTGCATTG
1 TAGTGCCTGAGAAAATTTCTAAAGGGTTAACAACCTGCAAAGATGGACGCAAGGTTTGTGCATTG
56640425 ACTACAGGAGAAACAGTTCGCATGC
66 ACTACAGGAGAAACAGTTCGCATGC
56640450 TAGTGCCTGAGAAAATTTCTAAAGGGTTAACAACCTGCAAAGATGGACGCAAGGTTTGTGCATTG
1 TAGTGCCTGAGAAAATTTCTAAAGGGTTAACAACCTGCAAAGATGGACGCAAGGTTTGTGCATTG
56640515 ACTACAGGAGAAACAGTTCGCATGC
66 ACTACAGGAGAAACAGTTCGCATGC
*
56640540 TAGTACCTGAG
1 TAGTGCCTGAG
56640551 CTAGTTGAAG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 100 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (90 bp):
TAGTGCCTGAGAAAATTTCTAAAGGGTTAACAACCTGCAAAGATGGACGCAAGGTTTGTGCATTG
ACTACAGGAGAAACAGTTCGCATGC
Found at i:56640652 original size:102 final size:99
Alignment explanation
Indices: 56640487--56640685 Score: 281
Period size: 102 Copynumber: 2.0 Consensus size: 99
56640477 TAACAACCTG
*
56640487 CAAAGATGGACGCAAGGTTTGTGCATTGACTACAGGAGAAACAGTTCGCATGCTAGTACCTGAGC
1 CAAAGATGGACCCAAGGTTTGTGCATTGACTACAGGAGAAACAGTTCGCATGCTAGTACCTGAGC
*
56640552 TAGTTGAAGGGAGACCAGAAGCACCGGAAGGCCA
66 CAGTTGAAGGGAGACCAGAAGCACCGGAAGGCCA
* * * * **
56640586 CAAAGATGGACCCATGGTTTGTGTATTGACTACAGCTGGTGAAACAGTTTGCATGCTAGTGGCTG
1 CAAAGATGGACCCAAGGTTTGTGCATTGACTACA---GGAGAAACAGTTCGCATGCTAGTACCTG
**
56640651 AGCCAGTTGAAGGGAGACCAGAAGCAGTGGAAGGC
63 AGCCAGTTGAAGGGAGACCAGAAGCACCGGAAGGC
56640686 TGTTGAACCA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
99 31 0.36
102 56 0.64
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.20
Consensus pattern (99 bp):
CAAAGATGGACCCAAGGTTTGTGCATTGACTACAGGAGAAACAGTTCGCATGCTAGTACCTGAGC
CAGTTGAAGGGAGACCAGAAGCACCGGAAGGCCA
Found at i:56650989 original size:13 final size:13
Alignment explanation
Indices: 56650971--56650998 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56650961 TGTATGTAAG
56650971 TAGACCCATGATT
1 TAGACCCATGATT
56650984 TAGACCCATGATT
1 TAGACCCATGATT
56650997 TA
1 TA
56650999 ACTCAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (13 bp):
TAGACCCATGATT
Found at i:56657526 original size:6 final size:6
Alignment explanation
Indices: 56657515--56657553 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
56657505 GGAAAATTTT
* *
56657515 CCTTTC CCTTTC CCTTCC CCTTCC CCTTCC CCTTCC CCT
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CCT
56657554 ATCCTTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTTCC
Found at i:56660092 original size:14 final size:15
Alignment explanation
Indices: 56660070--56660146 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
56660060 CAATCAAACA
56660070 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
56660084 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
56660099 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
56660119 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
56660133 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
56660147 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:56660111 original size:20 final size:20
Alignment explanation
Indices: 56660086--56660125 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56660076 AATATTTTCC
*
56660086 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
56660106 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
56660126 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:56660131 original size:34 final size:35
Alignment explanation
Indices: 56660074--56660140 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
56660064 CAAACACCAG
*
56660074 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
56660109 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
56660141 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:56660147 original size:14 final size:14
Alignment explanation
Indices: 56660109--56660148 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
56660099 ACAGAAAAGT
*
56660109 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
56660123 AAATCATTTTACGG
1 AAAACATTTTACAG
56660137 AAAACATTTTAC
1 AAAACATTTTAC
56660149 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:56660609 original size:11 final size:11
Alignment explanation
Indices: 56660593--56660617 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56660583 AAGATGCTAA
56660593 TTGAGAAGAAT
1 TTGAGAAGAAT
56660604 TTGAGAAGAAT
1 TTGAGAAGAAT
56660615 TTG
1 TTG
56660618 TGAAATCGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (11 bp):
TTGAGAAGAAT
Found at i:56660997 original size:124 final size:125
Alignment explanation
Indices: 56660602--56661031 Score: 747
Period size: 125 Copynumber: 3.5 Consensus size: 125
56660592 ATTGAGAAGA
* *
56660602 ATTTGAGAAGAATTTGTG-AAATCGCGCCCTAGTGGACGCGCTTTTGCTACAGTAGGTCATGGAA
1 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGCTCATGGAA
56660666 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
66 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
* *
56660726 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGTGCTTTTGCTATAGTAGCTCATGGAA
1 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGCTCATGGAA
*
56660791 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGTATGCT
66 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
* * * *
56660851 ATTTGAGAAGAATTTGTGAAAATTGCGCCCTCGTGGATGCACTTTTACTACAGTAGCTCATGGAA
1 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGCTCATGGAA
* *
56660916 TAAATAA-TTTTTTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
66 GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
56660975 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGC
1 ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGC
56661032 ATGTTTGGGC
Statistics
Matches: 287, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
124 121 0.42
125 166 0.58
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (125 bp):
ATTTGAGAAGAATTTGTGAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGCTCATGGAA
GAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGGAGGATGCT
Found at i:56663228 original size:27 final size:27
Alignment explanation
Indices: 56663207--56663285 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
56663197 GGCCAATCAC
* *
56663207 ATTGGCGGCAGCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
56663234 ATTGGTGGCACCAATGGTGCCAAAGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
56663261 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
56663286 GACTAAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:56663467 original size:19 final size:19
Alignment explanation
Indices: 56663445--56663513 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
56663435 ACTTAATAGT
56663445 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
56663464 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
*
56663482 TTATTAAATTAAAATACAG
1 TTATTAAATTAAAATAGAG
56663501 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
56663514 AAACGAGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 19 0.45
19 23 0.55
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:56663487 original size:18 final size:18
Alignment explanation
Indices: 56663439--56663497 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
56663429 TTAATTACTT
*
56663439 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATGAA
* *
56663457 AATAGAGTTATTAAATGAG
1 AATAG-TTTATTAAATGAA
*
56663476 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATGAA
56663494 AATA
1 AATA
56663498 CAGTTATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
AATAGTTTATTAAATGAA
Found at i:56663489 original size:37 final size:37
Alignment explanation
Indices: 56663439--56663509 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
56663429 TTAATTACTT
*
56663439 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATACAGTTATTAAATGAG
56663476 AATAGTTTATTAAATTAAAATACAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATACAGTTATTAAAT
56663510 AAAAAAACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATACAGTTATTAAATGAG
Found at i:56663522 original size:20 final size:19
Alignment explanation
Indices: 56663482--56663522 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56663472 TGAGAATAGT
* *
56663482 TTATTAAATTAAAATACAG
1 TTATTAAATAAAAAAACAG
56663501 TTATTAAATAAAAAAACGAG
1 TTATTAAATAAAAAAAC-AG
56663521 TT
1 TT
56663523 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
TTATTAAATAAAAAAACAG
Found at i:56663759 original size:19 final size:19
Alignment explanation
Indices: 56663735--56663803 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
56663725 ACTTAATAGT
56663735 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
56663754 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
*
56663772 TTATTAAATTAAAATACAG
1 TTATTAAATTAAAATAGAG
56663791 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
56663804 AAATGAGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 19 0.45
19 23 0.55
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:56663771 original size:37 final size:37
Alignment explanation
Indices: 56663729--56663799 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
56663719 AGTATTACTT
*
56663729 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATACAGTTATTAAATGAG
56663766 AATAGTTTATTAAATTAAAATACAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATACAGTTATTAAAT
56663800 AAAAAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATACAGTTATTAAATGAG
Found at i:56663777 original size:18 final size:18
Alignment explanation
Indices: 56663729--56663787 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
56663719 AGTATTACTT
*
56663729 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATGAA
* *
56663747 AATAGAGTTATTAAATGAG
1 AATAG-TTTATTAAATGAA
*
56663766 AATAGTTTATTAAATTAA
1 AATAGTTTATTAAATGAA
56663784 AATA
1 AATA
56663788 CAGTTATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (18 bp):
AATAGTTTATTAAATGAA
Found at i:56664066 original size:37 final size:37
Alignment explanation
Indices: 56664024--56664094 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
56664014 AGTATTACTT
56664024 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
56664061 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
56664095 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:56664099 original size:19 final size:19
Alignment explanation
Indices: 56664030--56664098 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
56664020 ACTTAATAGT
56664030 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
56664049 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
56664067 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
56664086 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
56664099 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:56664357 original size:37 final size:37
Alignment explanation
Indices: 56664315--56664385 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
56664305 AGTATTACTT
56664315 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
56664352 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
56664386 AAAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:56664390 original size:19 final size:19
Alignment explanation
Indices: 56664321--56664389 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
56664311 ACTTAATAGT
56664321 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
56664340 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
56664358 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
56664377 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
56664390 AAATGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:56664407 original size:292 final size:291
Alignment explanation
Indices: 56663338--56664459 Score: 2084
Period size: 295 Copynumber: 3.8 Consensus size: 291
56663328 TTATTTTCTT
56663338 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
1 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
*
56663403 TATTTTAATTTAATAAACTATTAAGTTTAATTACTTAATAGTTTATTAAATTAAAATAGAGTTAT
66 TATTTTAATTTAA-AAA-AATTAAG--T-ATTACTTAATAGTTTATTAAATTAAAATAGAGTTAT
*
56663468 TAAATGAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAACGAGTTGAAGGGGAAT
126 TAAATGAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTGAAGGGGAAT
56663533 AAAAAGAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCA
191 AAAAAGAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCA
56663598 CAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAA
256 CAGCAGCAATTCACTTTCAAAATTCAAAATGGTAAA
56663634 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
1 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
56663699 TATTTTAATTT-AAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAAT
66 TATTTTAATTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAAT
56663763 GAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAA
131 GAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAA
56663828 GAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCA
196 GAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCG--CA-CA
56663893 GCAGCAATTCACTTTCAAAATTCAAAATGGTAAA
258 GCAGCAATTCACTTTCAAAATTCAAAATGGTAAA
*
56663927 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATTCTCTCATTTAATAACTC
1 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
56663992 TATTTTAATTTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
66 TATTTTAA-TTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAA
*
56664057 TGAGAATAGTTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAA
130 TGAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAA
*
56664122 AGAAAATAATAAATAAGGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGC
195 AGAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGC
56664187 AGCAATTCACTTTCAAAATTCAAAATGGTAAA
260 AGCAATTCACTTTCAAAATTCAAAATGGTAAA
56664219 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
1 TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
56664284 TATTTTAATTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAAT
66 TATTTTAATTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAAT
*
56664349 GAGAATAGTTTATTAAATTAAAATAGAGTTATTAAATAAAAAAATGAGTTGAAAGGGGAATAAAA
131 GAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTG-AAGGGGAATAAAA
*
56664414 AGAAAATAATAAATAAGGAGGGCTTAGAAGGCAATTAGCCACATTT
195 AGAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTT
56664460 TAGTCCTTTG
Statistics
Matches: 814, Mismatches: 6, Indels: 16
0.97 0.01 0.02
Matches are distributed among these distances:
290 163 0.20
291 109 0.13
292 169 0.21
293 116 0.14
294 6 0.01
295 175 0.21
296 76 0.09
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (291 bp):
TTTGCATGTCAGGTCCTTAAAACTGCAAATGGTCACTTAATTAGAATCCTCTCATTTAATAACTC
TATTTTAATTTAAAAAAATTAAGTATTACTTAATAGTTTATTAAATTAAAATAGAGTTATTAAAT
GAGAATAGTTTATTAAATTAAAATACAGTTATTAAATAAAAAAATGAGTTGAAGGGGAATAAAAA
GAAAATAATAAATAAAGAGGGCTTAGAAGGCAATTAGCCACATTTCAATTTTAGTGCGCACAGCA
GCAATTCACTTTCAAAATTCAAAATGGTAAA
Found at i:56664552 original size:27 final size:27
Alignment explanation
Indices: 56664465--56664543 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
56664455 CATTTTAGTC
*
56664465 CTTTGGCACCATTGGTGCCGCCAATCA
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
56664492 CTTTGGCACCATTGGTGCCACCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
56664519 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
56664544 GTGATTGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:56665743 original size:38 final size:37
Alignment explanation
Indices: 56665679--56665753 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
56665669 TTAAGTTTGT
*
56665679 AAAATTATTAATTAATAAACTGTATTAATGGTTAGTA
1 AAAATTATAAATTAATAAACTGTATTAATGGTTAGTA
* *
56665716 AAAATTATCAAATTATATAAA-TTTATTAATTGTTAGTA
1 AAAATTAT-AAATTA-ATAAACTGTATTAATGGTTAGTA
56665754 CCAGTCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 8 0.24
38 20 0.61
39 5 0.15
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
AAAATTATAAATTAATAAACTGTATTAATGGTTAGTA
Found at i:56665861 original size:17 final size:17
Alignment explanation
Indices: 56665794--56665861 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
56665784 TATGTGAATG
*
56665794 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
56665810 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
56665829 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
56665848 TAAAATTATTAATT
1 TAAAATTATTAATT
56665862 GTTAGTACCG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:56665884 original size:115 final size:115
Alignment explanation
Indices: 56665676--56666150 Score: 828
Period size: 115 Copynumber: 4.1 Consensus size: 115
56665666 AAATTAAGTT
* * * *
56665676 TGTAAAATTATTAATTAATAAACTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAATTTA
1 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTA
56665741 TTAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
65 TTAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
56665792 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
1 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
* *
56665857 TAATTGTTAGTACCGGTCAAAATATTTTTCCAAATCTAACATTATGTGAA
66 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
*
56665907 --TAAAATTATTAATTGATAAATTGTAGTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
1 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
*
56665970 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTTAA
66 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
* *
56666020 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAATTTGTCAAATTATATAAAATTAT
1 TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
56666085 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
66 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
*
56666135 AGTAAAATTATTAATT
1 TGTAAAATTATTAATT
56666151 TCATTTAGGG
Statistics
Matches: 342, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
113 109 0.32
115 197 0.58
116 36 0.11
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (115 bp):
TGTAAAATTATTAATTGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTAT
TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAA
Found at i:56666076 original size:228 final size:231
Alignment explanation
Indices: 56665677--56666150 Score: 837
Period size: 228 Copynumber: 2.1 Consensus size: 231
56665667 AATTAAGTTT
* * *
56665677 GTAAAATTATTAATTAATAAACTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAATTTAT
1 GTAAAATTATTAATTAATAAACTGTAGTAATGATTAGTAAAAATTATCAAATTATATAAAATTAT
56665742 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAT
66 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAT
*
56665807 TGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCG
131 TGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
*
56665872 GTCAAAATATTTTTCCAAATCTAACATTATGTG-AA
196 GTCAAAACATTTTTCCAAATCTAACATTATGTGAAA
* *
56665907 -TAAAATTATTAATTGATAAATTGTAGTAATGATTAGT-AAAATTATCAAATTATATAAAATTAT
1 GTAAAATTATTAATTAATAAACTGTAGTAATGATTAGTAAAAATTATCAAATTATATAAAATTAT
*
56665970 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTTAATGTAAAATTATTAAT
66 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAT
* *
56666035 TGATAAATTGTATTAATGATTAGTAAATTTGTCAAATTATATAAAATTATTAATTGTTAGTACCA
131 TGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
56666100 GTCAAAACATTTTTCCAAATCTAACATTATGTGAAA
196 GTCAAAACATTTTTCCAAATCTAACATTATGTGAAA
56666136 GTAAAATTATTAATT
1 GTAAAATTATTAATT
56666151 TCATTTAGGG
Statistics
Matches: 232, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 183 0.79
229 35 0.15
230 14 0.06
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (231 bp):
GTAAAATTATTAATTAATAAACTGTAGTAATGATTAGTAAAAATTATCAAATTATATAAAATTAT
TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAT
TGATAAATTGTATTAATGATTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
GTCAAAACATTTTTCCAAATCTAACATTATGTGAAA
Found at i:56666186 original size:23 final size:22
Alignment explanation
Indices: 56666155--56666305 Score: 164
Period size: 23 Copynumber: 6.8 Consensus size: 22
56666145 TTAATTTCAT
* *
56666155 TTAGGGTTTTTAATTTAATTAGA
1 TTAGGGTTTTTAAGTTAA-TAGG
* *
56666178 TTAGAGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATAGG
*
56666199 TTAGGGTTTTTAAGTTAA-GGG
1 TTAGGGTTTTTAAGTTAATAGG
* *
56666220 TTTAGTGTTTTTAAGTTAA-GGG
1 -TTAGGGTTTTTAAGTTAATAGG
*
56666242 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TAGG
*
56666265 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TAGG
56666288 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAAGTTAA
56666306 GGGTATTAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
21 37 0.32
22 20 0.17
23 58 0.50
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAATAGG
Found at i:56666238 original size:43 final size:44
Alignment explanation
Indices: 56666155--56666309 Score: 172
Period size: 43 Copynumber: 3.5 Consensus size: 44
56666145 TTAATTTCAT
* ** *
56666155 TTAGGGTTTTTAATTTAATTAGATTAGAGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAATGGGTTTAGAGTTTTTAAGTTAAGGG
*
56666199 TTAGGGTTTTTAAGTTAA-GGGTTTAGTGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAAGTTAATGGGTTTAGAGTTTTTAAGTTAAGGG
* * * * *
56666242 TTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAA-TGGGTTTAGAGTTTTTAAGTTAA--GGG
56666288 TTAGGGTTTTTAAGTTAA-GGGT
1 TTAGGGTTTTTAAGTTAATGGGT
56666310 ATTAATAGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
43 38 0.40
44 35 0.37
45 2 0.02
46 19 0.20
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTAATGGGTTTAGAGTTTTTAAGTTAAGGG
Found at i:56666401 original size:25 final size:25
Alignment explanation
Indices: 56666372--56666483 Score: 92
Period size: 25 Copynumber: 4.7 Consensus size: 25
56666362 AAATTTCTAC
56666372 TTTATTACATCAAATAAACTTATAT
1 TTTATTACATCAAATAAACTTATAT
56666397 TTTATTACATCAAAT-AA--TATCA-
1 TTTATTACATCAAATAAACTTAT-AT
** * * * * *
56666419 -AAATAAC-TAAAAAAAATTTCTAT
1 TTTATTACATCAAATAAACTTATAT
*
56666442 TTTATTACATCAAATAAACTTCTAT
1 TTTATTACATCAAATAAACTTATAT
*
56666467 TTTATTATATCAAATAA
1 TTTATTACATCAAATAA
56666484 TATCAAAATA
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
20 4 0.06
21 6 0.09
22 4 0.06
23 3 0.04
24 6 0.09
25 44 0.66
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATTACATCAAATAAACTTATAT
Found at i:56666448 original size:70 final size:70
Alignment explanation
Indices: 56666360--56666493 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
56666350 CAAAATATTC
56666360 AAAAATTTCTACTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTACTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAA
56666425 CTAAA
66 CTAAA
* * *
56666430 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATA
1 AAAAATTTCTACTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATA
56666494 TTCAAAATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (70 bp):
AAAAATTTCTACTTTATTACATCAAATAAACTTATATTTTATTACATCAAATAATATCAAAATAA
CTAAA
Found at i:56667612 original size:7 final size:7
Alignment explanation
Indices: 56667602--56667626 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56667592 TTATATACAT
56667602 AATACTA
1 AATACTA
56667609 AATACTA
1 AATACTA
56667616 AATACTA
1 AATACTA
56667623 AATA
1 AATA
56667627 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:56667833 original size:20 final size:20
Alignment explanation
Indices: 56667796--56667833 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56667786 CTTATTTTTA
*
56667796 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
56667816 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
56667834 TGCCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:56669085 original size:42 final size:42
Alignment explanation
Indices: 56669025--56669115 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
56669015 CCTAGAGGGT
* *
56669025 GCGATTTCCTGGCACGTCCCCTGACATCGCGCGGACGTGGCC
1 GCGATTTCCTGGCACGTCCCCTAACATCGCGCGGACGTGGAC
* * * * *
56669067 GCGATTTCCTGGCGCGTCCCTTAACTTCGCGCTGACGTGGAT
1 GCGATTTCCTGGCACGTCCCCTAACATCGCGCGGACGTGGAC
56669109 GCGATTT
1 GCGATTT
56669116 TTCGGAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (42 bp):
GCGATTTCCTGGCACGTCCCCTAACATCGCGCGGACGTGGAC
Found at i:56670873 original size:13 final size:13
Alignment explanation
Indices: 56670857--56670881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56670847 TTTAAACCAA
56670857 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
56670870 ACTTTTCAAAAG
1 ACTTTTCAAAAG
56670882 CAATGAAAAA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:56671237 original size:25 final size:22
Alignment explanation
Indices: 56671198--56671247 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
56671188 TTATGGATAT
*
56671198 TATTTTTTAGGAATATATTATA
1 TATTTTTTAGGAATATATTAAA
56671220 TATTTTTTAGGCAAAATATATTAAA
1 TATTTTTTAGG---AATATATTAAA
56671245 TAT
1 TAT
56671248 CTATCATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
25 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (22 bp):
TATTTTTTAGGAATATATTAAA
Found at i:56671453 original size:18 final size:18
Alignment explanation
Indices: 56671430--56671464 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56671420 ATTATTTTTC
56671430 AAATATAAATTTTTTAAA
1 AAATATAAATTTTTTAAA
* *
56671448 AAATATTATTTTTTTAA
1 AAATATAAATTTTTTAA
56671465 TTTTTAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATAAATTTTTTAAA
Found at i:56673938 original size:24 final size:25
Alignment explanation
Indices: 56673886--56673932 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56673876 TAGCCCTCTT
* *
56673886 GAGCTTCCCGTTATATGGTTCTTAC
1 GAGCTTCCCGTTATATAGCTCTTAC
56673911 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
56673933 CAGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTAC
Found at i:56674121 original size:25 final size:25
Alignment explanation
Indices: 56674093--56674144 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
56674083 CTCGCTTGAA
56674093 CTTCCCGA-TATATGGCTATCCGGAG
1 CTTCCCGATTA-ATGGCTATCCGGAG
*
56674118 CTTCCTGATTAATGGCTATCCGGAG
1 CTTCCCGATTAATGGCTATCCGGAG
56674143 CT
1 CT
56674145 ACCCCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (25 bp):
CTTCCCGATTAATGGCTATCCGGAG
Found at i:56676348 original size:12 final size:11
Alignment explanation
Indices: 56676329--56676362 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
56676319 AATGGGTGAG
56676329 AAAATGGCCTT
1 AAAATGGCCTT
56676340 AAAATTGGCCTT
1 AAAA-TGGCCTT
56676352 AAAAATGGCCT
1 -AAAATGGCCT
56676363 ATTTTCGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 13 0.62
13 4 0.19
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (11 bp):
AAAATGGCCTT
Found at i:56676819 original size:250 final size:250
Alignment explanation
Indices: 56676378--56677130 Score: 1488
Period size: 250 Copynumber: 3.0 Consensus size: 250
56676368 CGTCTACACA
56676378 GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
1 GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
56676443 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
66 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
56676508 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
131 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
56676573 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
196 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
**
56676628 GGCAGAGACATTTGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
1 GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
56676693 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
66 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
56676758 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
131 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
56676823 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
196 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
56676878 GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
1 GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
56676943 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
66 TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
56677008 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
131 GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
56677073 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
196 CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
56677128 GGC
1 GGC
56677131 CGTGTGTCCA
Statistics
Matches: 499, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 499 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (250 bp):
GGCAGAGACATGGGCGTGTGTCTCAGTTGTGTGTGACACATGGCCATGCGCACAGGCGTGTGGTT
TGGTAGTGTGTCCCCTGCACCTAATTTTTGAAAATTAAATTGTCCACATGGCCTAGCACACGGGT
GTGTAGATGGCCGCGTGACCCAACTCAAAGAGTTACACAGGTATGAATACGGGCTGGGACACAGT
CGTGTGCTGCCTCACATCGAATGCCCACACGGCCTGAAACACGAGTGTGCCACTT
Found at i:56681537 original size:30 final size:31
Alignment explanation
Indices: 56681497--56681556 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
56681487 CAAAGTCATT
56681497 GTTGAACTATTCAAAA-ATTTTATTTAAGTC
1 GTTGAACTATTCAAAAGATTTTATTTAAGTC
*
56681527 GTTGAGCTATTCAAAAGATTTTATTTAAGT
1 GTTGAACTATTCAAAAGATTTTATTTAAGT
56681557 TACTAGGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (31 bp):
GTTGAACTATTCAAAAGATTTTATTTAAGTC
Found at i:56683505 original size:6 final size:6
Alignment explanation
Indices: 56683494--56683519 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56683484 GGTTTTTGGT
56683494 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
56683520 TTGGTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:56684043 original size:25 final size:28
Alignment explanation
Indices: 56684014--56684065 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
56684004 TATATTAGTA
56684014 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
56684039 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
56684066 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:56688195 original size:13 final size:14
Alignment explanation
Indices: 56688163--56688196 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56688153 ACTGTTTTTT
*
56688163 TATTCAAAACAACG
1 TATTCAAAACAACA
56688177 TATTCAAAACAA-A
1 TATTCAAAACAACA
56688190 TATTCAA
1 TATTCAA
56688197 CATATTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (14 bp):
TATTCAAAACAACA
Found at i:56689427 original size:7 final size:7
Alignment explanation
Indices: 56689415--56689439 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56689405 TATTAGTTAT
56689415 ATACATA
1 ATACATA
56689422 ATACATA
1 ATACATA
56689429 ATACATA
1 ATACATA
56689436 ATAC
1 ATAC
56689440 TAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:56690642 original size:11 final size:11
Alignment explanation
Indices: 56690628--56690688 Score: 90
Period size: 11 Copynumber: 5.6 Consensus size: 11
56690618 AAATAGGGAT
56690628 TTGAGA-GAAA
1 TTGAGAGGAAA
56690638 TTTGAGAGGAAA
1 -TTGAGAGGAAA
*
56690650 TTGAGAGCAAA
1 TTGAGAGGAAA
56690661 TTGAGAGGAAA
1 TTGAGAGGAAA
56690672 TTGAGAGGAAA
1 TTGAGAGGAAA
56690683 TT-AGAG
1 TTGAGAG
56690689 AAAGGGTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
10 4 0.09
11 39 0.83
12 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.33, T:0.21
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:56697946 original size:25 final size:25
Alignment explanation
Indices: 56697921--56697967 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
56697911 AAGAAGGTTA
56697921 AAAGAACATAAAA-GAAAAAAATTT
1 AAAGAACATAAAATGAAAAAAATTT
**
56697945 AAATTACATAAAATGAAAAAAAT
1 AAAGAACATAAAATGAAAAAAAT
56697968 ATGAGGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.19
Consensus pattern (25 bp):
AAAGAACATAAAATGAAAAAAATTT
Found at i:56698136 original size:29 final size:31
Alignment explanation
Indices: 56698075--56698142 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 31
56698065 CGGCTCAGTG
* *
56698075 ACTAAAATGTTACAATTTGATAATATAAGTA
1 ACTAAAATGTAACAATTTGATAATATAAATA
*
56698106 ACTAAAATGTAAC-ATTTTA-AATATAAATA
1 ACTAAAATGTAACAATTTGATAATATAAATA
56698135 ACTAAAAT
1 ACTAAAAT
56698143 ACAAGTTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 17 0.50
30 5 0.15
31 12 0.35
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (31 bp):
ACTAAAATGTAACAATTTGATAATATAAATA
Found at i:56701191 original size:2 final size:2
Alignment explanation
Indices: 56701184--56701208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56701174 GTTGTTCTAC
56701184 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 A
56701209 AAGCTCTCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56706688 original size:2 final size:2
Alignment explanation
Indices: 56706681--56706705 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56706671 GTTTAATTAT
56706681 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
56706706 TTCCAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56710393 original size:3 final size:3
Alignment explanation
Indices: 56710380--56710420 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
56710370 TTTATAATGC
* * *
56710380 TAT TGT TAT TAT TAT TAT TAT TGT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56710421 ATATAAGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:56710406 original size:15 final size:15
Alignment explanation
Indices: 56710388--56710436 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
56710378 GCTATTGTTA
*
56710388 TTATTATTATTATTG
1 TTATTATTACTATTG
*
56710403 TTATTATTACTATTA
1 TTATTATTACTATTG
* * *
56710418 TTAATATAAGTATTG
1 TTATTATTACTATTG
56710433 TTAT
1 TTAT
56710437 CGTGTTGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATTATTACTATTG
Found at i:56715376 original size:11 final size:10
Alignment explanation
Indices: 56715323--56715369 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
56715313 AAAATAGAAA
56715323 AAAAAATATT
1 AAAAAATATT
*
56715333 ATAAAATATTT
1 AAAAAATA-TT
*
56715344 AAATAAATTTT
1 AAA-AAATATT
56715355 AAAAAATATT
1 AAAAAATATT
56715365 AAAAA
1 AAAAA
56715370 TTAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 18 0.58
11 9 0.29
12 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAAATATT
Found at i:56731316 original size:17 final size:17
Alignment explanation
Indices: 56731294--56731326 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
56731284 AATGAGAATG
56731294 TATAATAATCACATCTC
1 TATAATAATCACATCTC
56731311 TATAATAATCACATCT
1 TATAATAATCACATCT
56731327 TTCAATAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAATAATCACATCTC
Found at i:56731920 original size:16 final size:17
Alignment explanation
Indices: 56731899--56731931 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56731889 GAGTAATTAG
*
56731899 GTAT-AAGGATTAAATT
1 GTATAAAGGATGAAATT
56731915 GTATAAAGGATGAAATT
1 GTATAAAGGATGAAATT
56731932 TGAATTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (17 bp):
GTATAAAGGATGAAATT
Found at i:56733318 original size:30 final size:29
Alignment explanation
Indices: 56733255--56733319 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
56733245 ATAAAAATGC
56733255 ATGTATATATATAGATTATAAAATATATGT
1 ATGTATATATATAGATTATAAAATATA-GT
* *
56733285 ATGTATATATATATGTGTTTTAAAATATA-T
1 ATGTATATATATA-G-ATTATAAAATATAGT
56733315 ATGTA
1 ATGTA
56733320 AAAAAAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 19 0.61
31 1 0.03
32 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (29 bp):
ATGTATATATATAGATTATAAAATATAGT
Found at i:56735602 original size:37 final size:38
Alignment explanation
Indices: 56735534--56735610 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 38
56735524 GTCAATTTAC
* * **
56735534 TACTTCGGATTAATTCGATGAGGCACTAGGTGGCAATT
1 TACTTCGGATTAATCCGATGAGACAAAAGGTGGCAATT
* *
56735572 TACTTCGGTTTAA-CCGATGAGACAAAAGGTGTCAATT
1 TACTTCGGATTAATCCGATGAGACAAAAGGTGGCAATT
56735609 TA
1 TA
56735611 TTACTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (38 bp):
TACTTCGGATTAATCCGATGAGACAAAAGGTGGCAATT
Found at i:56736531 original size:20 final size:20
Alignment explanation
Indices: 56736506--56736543 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56736496 CAGACTGAGT
*
56736506 TTATTCTGTTTACTGTCTAA
1 TTATTCTGTATACTGTCTAA
56736526 TTATTCTGTATACTGTCT
1 TTATTCTGTATACTGTCT
56736544 GTTTGTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TTATTCTGTATACTGTCTAA
Found at i:56739235 original size:2 final size:2
Alignment explanation
Indices: 56739228--56739263 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
56739218 AAATCAATTC
*
56739228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56739264 TTCACATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:56742025 original size:25 final size:25
Alignment explanation
Indices: 56741997--56742044 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
56741987 TTATTTGTTT
56741997 TATTATAA-CATTATAATATAATATA
1 TATTATAACCATTATAA-ATAATATA
*
56742022 TATTATAACCTTTATAAATAATA
1 TATTATAACCATTATAAATAATA
56742045 AAAAAACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
TATTATAACCATTATAAATAATATA
Done.