Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 6 of 235
Found at i:1479647 original size:104 final size:104
Alignment explanation
Indices: 1479467--1479837 Score: 654
Period size: 104 Copynumber: 3.6 Consensus size: 104
1479457 TAACCGTTAT
* * * *
1479467 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1479532 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
1479571 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1479636 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
1479675 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1479740 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * **
1479779 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCT
1479838 TTNNNNNNNN
Statistics
Matches: 258, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
104 257 1.00
105 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:1493328 original size:14 final size:14
Alignment explanation
Indices: 1493287--1493328 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1493277 TTGTTATTAA
*
1493287 ATTTTAATAAAATT
1 ATTTTAATAAAAAT
*
1493301 ATTTT--TAAATAT
1 ATTTTAATAAAAAT
1493313 ATTTTAATAAAAAT
1 ATTTTAATAAAAAT
1493327 AT
1 AT
1493329 AAATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTAATAAAAAT
Found at i:1493335 original size:26 final size:26
Alignment explanation
Indices: 1493287--1493336 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1493277 TTGTTATTAA
* ***
1493287 ATTTTAATAAAATTATTTTTAAATAT
1 ATTTTAATAAAAATATAAATAAATAT
1493313 ATTTTAATAAAAATATAAATAAAT
1 ATTTTAATAAAAATATAAATAAAT
1493337 TTAATCATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTTAATAAAAATATAAATAAATAT
Found at i:1493409 original size:56 final size:58
Alignment explanation
Indices: 1493291--1493419 Score: 156
Period size: 56 Copynumber: 2.3 Consensus size: 58
1493281 TATTAAATTT
* * * * * * *
1493291 TAATAAAATTATTTTTAAATATATTTTAATAAAAATATAAATAAATTTAATCATATTT
1 TAATATAATTATTATTAAATACAATTTAATAAAAATATAAATAAATTTAATAACATTC
*
1493349 TAATATAATT-TTATTAAATACAATTTAAT-AAAATA-ATATATAATTTAATAACATTC
1 TAATATAATTATTATTAAATACAATTTAATAAAAATATAAATA-AATTTAATAACATTC
1493405 TAATATAATTATTAT
1 TAATATAATTATTAT
1493420 ATGAATTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
55 4 0.07
56 28 0.46
57 20 0.33
58 9 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (58 bp):
TAATATAATTATTATTAAATACAATTTAATAAAAATATAAATAAATTTAATAACATTC
Found at i:1493972 original size:26 final size:26
Alignment explanation
Indices: 1493936--1493988 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1493926 TAGAAAGAAG
1493936 ATAAATGAATGATTAACAACAATCTA
1 ATAAATGAATGATTAACAACAATCTA
1493962 ATAAATGAATGATTAACAACAATCTA
1 ATAAATGAATGATTAACAACAATCTA
1493988 A
1 A
1493989 CTTTAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (26 bp):
ATAAATGAATGATTAACAACAATCTA
Found at i:1496909 original size:2 final size:2
Alignment explanation
Indices: 1496902--1496926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1496892 AACAAAAGCA
1496902 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
1496927 GAAAAGAAAT
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:1498067 original size:21 final size:21
Alignment explanation
Indices: 1498043--1498082 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1498033 GGCAAAAATG
1498043 AAAAAAATAATCTTTTCAGAA
1 AAAAAAATAATCTTTTCAGAA
1498064 AAAAAAATAATCTTTTCAG
1 AAAAAAATAATCTTTTCAG
1498083 CATTCCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAAAATAATCTTTTCAGAA
Found at i:1501256 original size:44 final size:44
Alignment explanation
Indices: 1501159--1501270 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
1501149 ATACCAGCAA
** * *
1501159 CGAGTAAGACCATGACTGAAAA-ATGTTATGGTATCACGATTCTAT
1 CGAGTAAGACCAT-ACT-AAAAGACATTATGGAATCACGATTATAT
* * *
1501204 TGAATAAGACCATACTAAAAGACATTATGGAATCATGATTATAT
1 CGAGTAAGACCATACTAAAAGACATTATGGAATCACGATTATAT
*
1501248 CGAGTAAGACCATAGCTGAAAGA
1 CGAGTAAGACCATA-CTAAAAGA
1501271 TGCTATGGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
43 4 0.07
44 33 0.60
45 18 0.33
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (44 bp):
CGAGTAAGACCATACTAAAAGACATTATGGAATCACGATTATAT
Found at i:1501307 original size:45 final size:46
Alignment explanation
Indices: 1501116--1501374 Score: 138
Period size: 45 Copynumber: 5.7 Consensus size: 46
1501106 CCAGAGAATA
* *
1501116 AATAAGACCATAGTTGAAAGATACTATGGCA-C-C-ATACCAGCAACG
1 AATAAGACCATAGCTGAAAGATACTATGGCATCACGA-ATCA-CAACG
* * ** * * * **
1501161 AGTAAGACCAT-GACTGAAAAATGTTATGGTATCACGATTC-TATTG
1 AATAAGACCATAG-CTGAAAGATACTATGGCATCACGAATCACAACG
* * * * * * * *
1501206 AATAAGACCATA-CTAAAAGACATTATGGAATCATG-ATTATATCG
1 AATAAGACCATAGCTGAAAGATACTATGGCATCACGAATCACAACG
* *
1501250 AGTAAGACCATAGCTGAAAGATGCTATGGCATCACGAATCA-AACG
1 AATAAGACCATAGCTGAAAGATACTATGGCATCACGAATCACAACG
* * * *** * *
1501295 AATAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAATG
1 AATAAGACCATAGCTGAAAGATACTATGGCATCACGAATCACAACG
* * **
1501341 AATAAGACCATGGCTTAAAGGCACTATGGCATCA
1 AATAAGACCATAGCTGAAAGATACTATGGCATCA
1501375 AGACGAGAAT
Statistics
Matches: 161, Mismatches: 44, Indels: 17
0.73 0.20 0.08
Matches are distributed among these distances:
43 1 0.01
44 33 0.20
45 88 0.55
46 36 0.22
47 2 0.01
48 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (46 bp):
AATAAGACCATAGCTGAAAGATACTATGGCATCACGAATCACAACG
Found at i:1501366 original size:46 final size:45
Alignment explanation
Indices: 1501252--1501416 Score: 152
Period size: 45 Copynumber: 3.6 Consensus size: 45
1501242 TTATATCGAG
* ** * * *** *
1501252 TAAGACCATAGCTGAAAGATGCTATGGCATCACGAATCAAACGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACAAGACGAAAATGAA
*
1501297 TAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACAAGAC-GAAAATGAA
* * * * *
1501343 TAAGACCATGGCTT-AAAGGCACTATGGCATCAAGACGAGAATAAA
1 TAAGACCATAG-TTGAAAGACACTATGGCAACAAGACGAAAATGAA
* *
1501388 TAAGACCATTGTTGAAAGACACCATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
1501417 CACTCTGATC
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.02
45 61 0.61
46 35 0.35
47 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCAACAAGACGAAAATGAA
Found at i:1501415 original size:45 final size:46
Alignment explanation
Indices: 1501295--1501416 Score: 149
Period size: 46 Copynumber: 2.7 Consensus size: 46
1501285 GAATCAAACG
* *
1501295 AATAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAATG
1 AATAAGACCATAGTTGAAAGACACTATGGCAACAAGACGGAAAATA
* * * *
1501341 AATAAGACCATGGCTT-AAAGGCACTATGGCATCAAGAC-GAGAATA
1 AATAAGACCATAG-TTGAAAGACACTATGGCAACAAGACGGAAAATA
* *
1501386 AATAAGACCATTGTTGAAAGACACCATGGCA
1 AATAAGACCATAGTTGAAAGACACTATGGCA
1501417 CACTCTGATC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
44 2 0.03
45 30 0.46
46 31 0.48
47 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.17
Consensus pattern (46 bp):
AATAAGACCATAGTTGAAAGACACTATGGCAACAAGACGGAAAATA
Found at i:1503233 original size:15 final size:15
Alignment explanation
Indices: 1503213--1503242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1503203 CCTATAAATA
*
1503213 TCATCCCTCATCCCT
1 TCATCCATCATCCCT
1503228 TCATCCATCATCCCT
1 TCATCCATCATCCCT
1503243 CATAGCTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (15 bp):
TCATCCATCATCCCT
Found at i:1508149 original size:22 final size:21
Alignment explanation
Indices: 1508120--1508178 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
1508110 TGCACTAATG
1508120 AACAGAGAGCACTAAAGTGCT
1 AACAGAGAGCACTAAAGTGCT
*
1508141 ATACAGAGAGCAC-AGATGTGCT
1 A-ACAGAGAGCACTA-AAGTGCT
1508163 AATCAGAGAGCACTAA
1 AA-CAGAGAGCACTAA
1508179 CAGACTAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 3 0.09
22 29 0.88
23 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
AACAGAGAGCACTAAAGTGCT
Found at i:1509695 original size:3 final size:3
Alignment explanation
Indices: 1509687--1509758 Score: 80
Period size: 3 Copynumber: 24.3 Consensus size: 3
1509677 TCTTTAATTT
*
1509687 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATCA AT- ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
1509731 ATA AT- ATAA ATA ATA AT- ATA ATA TATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA -ATA A
1509759 ATATCTTTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
2 8 0.13
3 46 0.75
4 7 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1509891 original size:20 final size:18
Alignment explanation
Indices: 1509866--1509902 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1509856 ATAAATTTAT
1509866 TTATTTCATAATATAATATC
1 TTATTT-ATAAT-TAATATC
1509886 TTATTTATAATTAATAT
1 TTATTTATAATTAATAT
1509903 AAATTACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTATAATTAATATC
Found at i:1509917 original size:28 final size:26
Alignment explanation
Indices: 1509886--1509947 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
1509876 ATATAATATC
1509886 TTATTTATAATTAATATAAATTACAATA
1 TTATTTATAA-TAATATAAATTA-AATA
* *
1509914 TTATAATATAATAATATACATTAAATA
1 TTAT-TTATAATAATATAAATTAAATA
*
1509941 ATATTTA
1 TTATTTA
1509948 ATTACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 7 0.24
28 15 0.52
29 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATTTATAATAATATAAATTAAATA
Found at i:1511401 original size:4 final size:4
Alignment explanation
Indices: 1511392--1511418 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1511382 ATGTAACTCT
1511392 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1511419 TTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1512442 original size:6 final size:6
Alignment explanation
Indices: 1512433--1512491 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
1512423 AGAAAATAAA
*
1512433 AAAAAT -AAAAT AGAAAAT AAAAA- AAAAAT AACAAAAT ACAAAT AAAAAT
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT -A-AAAAT AAAAAT AAAAAT
1512482 AAAAAT AAAA
1 AAAAAT AAAA
1512492 CTGGGTTGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
5 10 0.22
6 23 0.50
7 8 0.17
8 5 0.11
ACGTcount: A:0.81, C:0.03, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1512487 original size:26 final size:27
Alignment explanation
Indices: 1512425--1512489 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
1512415 AACATGCAAG
* *
1512425 AAAATAAAAAAAATAAAATAGAAAATA
1 AAAATAAAAATAACAAAATAGAAAATA
*
1512452 AAAA-AAAAATAACAAAATA-CAAATA
1 AAAATAAAAATAACAAAATAGAAAATA
1512477 AAAATAAAAATAA
1 AAAATAAAAATAA
1512490 AACTGGGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.26
26 21 0.62
27 4 0.12
ACGTcount: A:0.82, C:0.03, G:0.02, T:0.14
Consensus pattern (27 bp):
AAAATAAAAATAACAAAATAGAAAATA
Found at i:1516669 original size:48 final size:48
Alignment explanation
Indices: 1516437--1516656 Score: 323
Period size: 48 Copynumber: 4.6 Consensus size: 48
1516427 ATGCCTCATA
* **
1516437 CCGATGCCATGTCCCAGACATGGTCTTACACTGACTCACATAATGATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACAATG
* * *
1516485 TCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCACATAAAAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACAATG
* * * *
1516533 CCGATGCCATGTCCCAAACATAGTCTTACAGTGGCTCACATAACGATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACAATG
* *
1516581 CCGATGCCATGTCCCAAACGTGGTCTTACACTGGCTCACATAACAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACAATG
*
1516629 CTGATGCCATGTCCCAGACATGGTCTTA
1 CCGATGCCATGTCCCAGACATGGTCTTA
1516657 TATGGGATCA
Statistics
Matches: 153, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 153 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAACAATG
Found at i:1518636 original size:21 final size:21
Alignment explanation
Indices: 1518612--1518651 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1518602 ATAGATGCCA
1518612 CTGTTCTCTGTTAAAAATCCT
1 CTGTTCTCTGTTAAAAATCCT
* * *
1518633 CTGTTTTCTTTTGAAAATC
1 CTGTTCTCTGTTAAAAATC
1518652 AACAGTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (21 bp):
CTGTTCTCTGTTAAAAATCCT
Found at i:1552548 original size:13 final size:14
Alignment explanation
Indices: 1552532--1552573 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1552522 TTTTAATTTT
1552532 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
1552545 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
1552560 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1552574 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1552558 original size:16 final size:16
Alignment explanation
Indices: 1552536--1552572 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1552526 AATTTTATTT
1552536 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
1552553 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
1552568 TAATA
1 TAATA
1552573 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:1554056 original size:13 final size:13
Alignment explanation
Indices: 1554037--1554075 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1554027 ATTATATTTT
1554037 TAAAAAAAT-ATA
1 TAAAAAAATAATA
1554049 TAAAAAAATAATA
1 TAAAAAAATAATA
*
1554062 TAAAAAATTAATA
1 TAAAAAAATAATA
1554075 T
1 T
1554076 GAACAGATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAAAATAATA
Found at i:1559631 original size:13 final size:14
Alignment explanation
Indices: 1559615--1559650 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1559605 CAATCTCATA
1559615 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
1559628 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
1559641 TCTC-ATTTCA
1 TCTCAATTTCA
1559651 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:1559640 original size:18 final size:19
Alignment explanation
Indices: 1559602--1559642 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
1559592 TGGTTCATGT
1559602 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
1559621 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
1559639 TTTC
1 TTTC
1559643 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:1559801 original size:25 final size:23
Alignment explanation
Indices: 1559747--1559804 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1559737 ATGGATTCCT
*
1559747 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAAAATATCCAA
1559770 CCCAAACACACCAAAATATCCAA
1 CCCAAACACACCAAAATATCCAA
*
1559793 CCCAAAAACACC
1 CCCAAACACACC
1559805 CGGAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.50, C:0.41, G:0.02, T:0.07
Consensus pattern (23 bp):
CCCAAACACACCAAAATATCCAA
Found at i:1560326 original size:15 final size:15
Alignment explanation
Indices: 1560306--1560352 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1560296 TAATATATAT
1560306 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
1560321 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
1560336 TTCAATCAATATAAA
1 TTCAATCAATATAAA
1560351 TT
1 TT
1560353 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:1561173 original size:13 final size:13
Alignment explanation
Indices: 1561155--1561186 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1561145 TTTTATTTCA
1561155 TTTATTTCTTTAT
1 TTTATTTCTTTAT
1561168 TTTATTTCTTTAT
1 TTTATTTCTTTAT
1561181 TTTATT
1 TTTATT
1561187 ATTAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:1561391 original size:13 final size:11
Alignment explanation
Indices: 1561361--1561388 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1561351 AAGTAAATAC
1561361 ACATGTATAAT
1 ACATGTATAAT
1561372 ACATGTATAAT
1 ACATGTATAAT
1561383 ACATGT
1 ACATGT
1561389 GTACCATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (11 bp):
ACATGTATAAT
Found at i:1578638 original size:43 final size:42
Alignment explanation
Indices: 1578526--1578659 Score: 135
Period size: 43 Copynumber: 3.1 Consensus size: 42
1578516 ACTGATGGAA
* *
1578526 TATACTGGCACACATAGTGCATTATC-GGATAAACCGAAGAAA
1 TATACTGGCACACATAGTGCATTATCAGG-TAAGCCGAAGAAT
* * * * *
1578568 TATATTGGCATACATAATGCATCATCAGGTAAGCCAAAGCAAT
1 TATACTGGCACACATAGTGCATTATCAGGTAAGCCGAAG-AAT
* * **
1578611 TATACTGGCACAGACAGTGCATTATCAGACAAGCCGAAGTAAT
1 TATACTGGCACACATAGTGCATTATCAGGTAAGCCGAAG-AAT
1578654 TATACT
1 TATACT
1578660 AACATACACA
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
42 30 0.41
43 43 0.59
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (42 bp):
TATACTGGCACACATAGTGCATTATCAGGTAAGCCGAAGAAT
Found at i:1581946 original size:15 final size:15
Alignment explanation
Indices: 1581896--1581946 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 15
1581886 ATTCAATATT
1581896 AATAT-TTAATAATA
1 AATATATTAATAATA
*
1581910 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
1581929 AATATATTAATAATA
1 AATATATTAATAATA
1581944 AAT
1 AAT
1581947 GTTTTGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 1 0.03
17 6 0.20
19 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:1596708 original size:30 final size:30
Alignment explanation
Indices: 1596674--1596772 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
1596664 AAAATTTACC
1596674 AAAAATTATGTAAGTTTAATTAAATTTCAA
1 AAAAATTATGTAAGTTTAATTAAATTTCAA
** * * * *
1596704 AAAAAGTTGCGTGA-TTT--TGAAAATTCACC
1 AAAAA-TTATGTAAGTTTAATTAAATTTCA-A
* * *
1596733 AAATATTGTGTAAGTTGAATTAAATTTCAA
1 AAAAATTATGTAAGTTTAATTAAATTTCAA
1596763 AAAAATTATG
1 AAAAATTATG
1596773 GAATTAAAGA
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 14 0.29
29 6 0.12
30 16 0.33
31 13 0.27
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (30 bp):
AAAAATTATGTAAGTTTAATTAAATTTCAA
Found at i:1597690 original size:31 final size:32
Alignment explanation
Indices: 1597649--1597712 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1597639 TCTCAGCTTA
1597649 AAATCTATTAATTTAACAC-CTAAAACTTTAAG
1 AAATCTATTAATTTAA-ACTCTAAAACTTTAAG
1597681 AAAT-TATTAATTTAAACTTTCTAAAACTTTAA
1 AAATCTATTAATTTAAAC--TCTAAAACTTTAA
1597713 CAGTTTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.07
31 11 0.38
32 4 0.14
33 12 0.41
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (32 bp):
AAATCTATTAATTTAAACTCTAAAACTTTAAG
Found at i:1598799 original size:32 final size:31
Alignment explanation
Indices: 1598757--1598835 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
1598747 CAAGTATACT
* * *
1598757 TTTTTTGACAATTTTAAGTACCAACTATGTA
1 TTTTTGGACAAGTTTAAGTACCAACTAGGTA
* *
1598788 CTTTTTGGACAAGTTCAAGTACCAGCTAGGTA
1 -TTTTTGGACAAGTTTAAGTACCAACTAGGTA
*
1598820 TTTTTGTACAAGTTTA
1 TTTTTGGACAAGTTTA
1598836 GGGGGCAAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTTTGGACAAGTTTAAGTACCAACTAGGTA
Found at i:1601458 original size:13 final size:13
Alignment explanation
Indices: 1601440--1601464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1601430 TTAGAGCAGC
1601440 TGGTGAATTTATT
1 TGGTGAATTTATT
1601453 TGGTGAATTTAT
1 TGGTGAATTTAT
1601465 CTGAGATGCC
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
TGGTGAATTTATT
Found at i:1601844 original size:7 final size:7
Alignment explanation
Indices: 1601832--1601857 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1601822 TAGTCGATTC
1601832 GTATTTA
1 GTATTTA
1601839 GTATTTA
1 GTATTTA
1601846 GTATTTA
1 GTATTTA
1601853 GTATT
1 GTATT
1601858 GTGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1602267 original size:24 final size:24
Alignment explanation
Indices: 1602235--1602287 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1602225 CGGAATACAT
1602235 GCCATGGTTTAGGATTCATGGCAA
1 GCCATGGTTTAGGATTCATGGCAA
1602259 GCCATGGTTTAGGATTCATGGCAA
1 GCCATGGTTTAGGATTCATGGCAA
1602283 GCCAT
1 GCCAT
1602288 ATTTACTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (24 bp):
GCCATGGTTTAGGATTCATGGCAA
Found at i:1603074 original size:54 final size:55
Alignment explanation
Indices: 1602992--1603117 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 55
1602982 TATTGTTTCA
* *
1602992 TTTAATAAAATAAAAATTGTTTTGAATAAAGT-A-ATTGT-AATTTACTTTTATATT
1 TTTAATAAAATAAAAATTCTTTTAAATAAAGTAATATTGTGAA--TACTTTTATATT
* * * * *
1603046 TTTAATAAAATAGAATTTCTTTTAAATAAGGTAATATTTTGAATATTTTTATATT
1 TTTAATAAAATAAAAATTCTTTTAAATAAAGTAATATTGTGAATACTTTTATATT
*
1603101 TTTAATAAAATATAAAT
1 TTTAATAAAATAAAAAT
1603118 AATGCAACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
54 27 0.45
55 27 0.45
56 4 0.07
57 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (55 bp):
TTTAATAAAATAAAAATTCTTTTAAATAAAGTAATATTGTGAATACTTTTATATT
Found at i:1605697 original size:126 final size:126
Alignment explanation
Indices: 1605356--1605857 Score: 767
Period size: 126 Copynumber: 4.0 Consensus size: 126
1605346 GCCAAATAGG
* * *
1605356 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTATTTTTGATGATAGTGCATCC
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCC
1605421 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTT-TCCAAAATTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCT-CAAAATTATTTTTTCAGA
* * * *
1605482 AACTACTGTAGAAAAAGAGCGTCCATGTGGGAG-ATTTTTCAGTACTTTTGCTGATAGTGCATTC
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCC
*
1605546 TGCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* * *
1605607 AACAACTGTAGAAAAAAAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATTC
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCC
* * *
1605672 TGCTTGAAGCGTTTTTGATACTATTTGTTCATAAACATCTTTTCAAAATTATTTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* ** *
1605733 AACTACTGTAGAAAAAAAACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGGCAATGCATCC
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCC
* * * * *
1605798 TACTTGAAGCGTTTTCGACACTATTTGTTTAAAAACATCTTCTTAAAATTA-TTTTTCAGA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
1605858 TACGTCTTCT
Statistics
Matches: 345, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
125 123 0.36
126 222 0.64
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
Found at i:1605855 original size:251 final size:251
Alignment explanation
Indices: 1605360--1605857 Score: 800
Period size: 251 Copynumber: 2.0 Consensus size: 251
1605350 AATAGGAACT
* * *
1605360 ACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTATTTTTGATGATAGTGCATCCTGCT
1 ACTGTAGAAAAAAAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGATGATAGTGCATCCTGCT
1605425 TGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTTCCAAAATTATTTTTTCAGAAACTACTG
66 TGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTTCCAAAATTATTTTTTCAGAAACTACTG
* * * * * * *
1605490 TAGAAAAAGAGCGTCCATGTGGGAGATTTTTCAGTACTTTTGCTGATAGTGCATTCTGCTTGAAG
131 TAGAAAAAAAACGTCCACGTGGGAGATTTTTCAGTACTTTTGCTGACAATGCATCCTACTTGAAG
* *
1605555 CGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCAGAAACA
196 CGTTTTCGACACTATTTGTTTAAAAACATCTTCTCAAAATTATTTTTTCAGAAACA
* *
1605611 ACTGTAGAAAAAAAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATTCTGCT
1 ACTGTAGAAAAAAAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGATGATAGTGCATCCTGCT
* * *
1605676 TGAAGCGTTTTTGATACTATTTGTTCATAAACATCTTTTCAAAATTATTTTTTCAGAAACTACTG
66 TGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTTCCAAAATTATTTTTTCAGAAACTACTG
* *
1605741 TAGAAAAAAAACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGGCAATGCATCCTACTTGAA
131 TAGAAAAAAAACGTCCACGTGGGAG-ATTTTTCAGTACTTTTGCTGACAATGCATCCTACTTGAA
*
1605806 GCGTTTTCGACACTATTTGTTTAAAAACATCTTCTTAAAATTA-TTTTTCAGA
195 GCGTTTTCGACACTATTTGTTTAAAAACATCTTCTCAAAATTATTTTTTCAGA
1605858 TACGTCTTCT
Statistics
Matches: 226, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
251 153 0.68
252 73 0.32
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (251 bp):
ACTGTAGAAAAAAAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGATGATAGTGCATCCTGCT
TGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTTCCAAAATTATTTTTTCAGAAACTACTG
TAGAAAAAAAACGTCCACGTGGGAGATTTTTCAGTACTTTTGCTGACAATGCATCCTACTTGAAG
CGTTTTCGACACTATTTGTTTAAAAACATCTTCTCAAAATTATTTTTTCAGAAACA
Found at i:1606281 original size:27 final size:28
Alignment explanation
Indices: 1606224--1606284 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
1606214 CCCTTTTTAG
1606224 TAAATAATAAAAAAATTAACTCATTTCTA
1 TAAATAATAAAAAAA-TAACTCATTTCTA
* *
1606253 TAAATATTAAAAAAA-AACT-TTTTCTTA
1 TAAATAATAAAAAAATAACTCATTTC-TA
1606280 TAAAT
1 TAAAT
1606285 TACACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 11 0.38
29 14 0.48
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAATAATAAAAAAATAACTCATTTCTA
Found at i:1608887 original size:18 final size:18
Alignment explanation
Indices: 1608864--1608906 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1608854 GTTCAAGGTG
1608864 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
1608882 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
1608900 TAATTAA
1 TAATTAA
1608907 AAATCTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:1611858 original size:19 final size:19
Alignment explanation
Indices: 1611793--1611860 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 19
1611783 AATTGATCGG
* *
1611793 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
1611811 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
1611830 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
1611848 TTATTCAGTAACA
1 TTATTCAGTAACA
1611861 GTTGATCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 28 0.68
19 13 0.32
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:1611987 original size:6 final size:6
Alignment explanation
Indices: 1611976--1612024 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
1611966 CCGAAGCTGG
1611976 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
1612024 A
1 A
1612025 CGGTACACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:1612302 original size:19 final size:20
Alignment explanation
Indices: 1612255--1612302 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1612245 CACTTTCCAA
*
1612255 TTTTCAATTAATTCATATTT
1 TTTTCAATTAACTCATATTT
*
1612275 TAATT-AATTAACT-ATATTT
1 T-TTTCAATTAACTCATATTT
1612294 TTTTCAATT
1 TTTTCAATT
1612303 CAATATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCAATTAACTCATATTT
Found at i:1613194 original size:20 final size:18
Alignment explanation
Indices: 1613158--1613202 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
1613148 AAACCTTCAA
1613158 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
1613176 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
1613196 -TTTCCCT
1 TTTTCCCT
1613203 GCTTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:1613399 original size:16 final size:15
Alignment explanation
Indices: 1613390--1613424 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1613380 TATTTATTAT
1613390 ATAATATATTATTTA
1 ATAATATATTATTTA
*
1613405 ATAATATACTTATATA
1 ATAATATA-TTATTTA
1613421 ATAA
1 ATAA
1613425 GTAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATATTATTTA
Found at i:1620916 original size:53 final size:53
Alignment explanation
Indices: 1620733--1620987 Score: 256
Period size: 55 Copynumber: 4.8 Consensus size: 53
1620723 ATTAGGGTTT
* *
1620733 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGGC
* * *
1620788 AAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
1620843 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
*
1620896 AAGGATACCATGTAAGACCATGTCC-AGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATG-CCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* * * * *
1620945 AAGAATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
1620988 GTACCCATGT
Statistics
Matches: 173, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
48 1 0.01
49 37 0.21
51 1 0.01
52 8 0.05
53 42 0.24
54 10 0.06
55 70 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:1620939 original size:108 final size:110
Alignment explanation
Indices: 1620740--1620940 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
1620730 TTTAAGGATA
*
1620740 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
*
1620805 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
1620850 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
1620912 ACCATGTCCAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
1620941 TCAAAAGAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:1621200 original size:16 final size:16
Alignment explanation
Indices: 1621179--1621209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1621169 ATAAATTTGA
1621179 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
1621195 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
1621210 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:1623088 original size:15 final size:15
Alignment explanation
Indices: 1623039--1623090 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1623029 CAATTCAAAT
*
1623039 AATCAATATATATTC
1 AATCAATATAAATTC
*
1623054 AATATATATATACCAATTC
1 AAT-CA-ATATA--AATTC
1623073 AATCAATATAAATTC
1 AATCAATATAAATTC
1623088 AAT
1 AAT
1623091 GAATTTATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 10 0.33
18 1 0.03
19 7 0.23
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:1623890 original size:15 final size:12
Alignment explanation
Indices: 1623859--1623888 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1623849 TTAATTGTTT
1623859 TATATTATATAA
1 TATATTATATAA
1623871 TATATTATGATAA
1 TATATTAT-ATAA
1623884 TATAT
1 TATAT
1623889 ATACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TATATTATATAA
Found at i:1630091 original size:49 final size:49
Alignment explanation
Indices: 1629889--1630154 Score: 230
Period size: 49 Copynumber: 5.6 Consensus size: 49
1629879 TATGTGTGCT
* ** * * *
1629889 AGTGTAAGACATGTCTGGGACAT-GCATCGTCCAC-AT-TATGGAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGACTCGATATATGAAAGCC
* * *
1629935 AGTGTAAGACATGTCTGGGACAT-GCATC-GACCTCGAGATATGCAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGA-CTCGATATATGAAAGCC
* * * * * * *
1629983 AGTATAAGGCTTGTCTGGGACATGGCATCGG-CTTG--ACATG--TGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGACTCGATATATGAAAGCC
* *
1630027 AGTGTAAGACCTGTCTGGGACATGGCATTGAGACT-GATATATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCG-GACTCGATATATGAAAGCC
* **
1630076 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAAGGT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGACTCGATATATGAAAGCC
* *
1630125 AGCGTAAGACCTGTCTGGGACATGACATCG
1 AGTGTAAGACCTGTCTGGGACATGGCATCG
1630155 ACTTAGATGT
Statistics
Matches: 181, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
44 28 0.15
45 2 0.01
46 36 0.20
47 5 0.03
48 34 0.19
49 75 0.41
50 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGGACTCGATATATGAAAGCC
Found at i:1630097 original size:93 final size:92
Alignment explanation
Indices: 1629935--1630107 Score: 242
Period size: 93 Copynumber: 1.9 Consensus size: 92
1629925 TATGGAAGCT
* * *
1629935 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATGCAAGCCAGTATAAGGCTTGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGAACTCGAGATATGCAAGCCAGTATAAGACCTGTCTG
1630000 GGACATGGCATCGGCTTGACATGTGTC
66 GGACATGGCATCGGCTTGACATGTGTC
* * * *
1630027 AGTGTAAGACCTGTCTGGGACATGGCATTGAGACT-GATATATG-AGAGCCAGTGTAAGACCTGT
1 AGTGTAAGACATGTCTGGGACAT-GCATCGA-ACTCGAGATATGCA-AGCCAGTATAAGACCTGT
1630090 CTGGGACATGGCATCGGC
63 CTGGGACATGGCATCGGC
1630108 CTCGATATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
92 23 0.32
93 46 0.65
94 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCGAACTCGAGATATGCAAGCCAGTATAAGACCTGTCTG
GGACATGGCATCGGCTTGACATGTGTC
Found at i:1630473 original size:201 final size:201
Alignment explanation
Indices: 1630121--1630523 Score: 770
Period size: 201 Copynumber: 2.0 Consensus size: 201
1630111 GATATATGAA
* *
1630121 AGGTAGCGTAAGACCTGTCTGGGACATGACATCGACTTAGATGTGTGCGCCAGTGTCAGACCACG
1 AGGTAGCGTAAGACCTGTCTGGGACATGACATCGACTTAGATGTGTGAGCCAGTGTAAGACCACG
1630186 TTTAGAACATGTCATCGGCATCGTACCCTATGTTTGAGGCTTAGTGATTATCCTGTGGTATTCCA
66 TTTAGAACATGTCATCGGCATCGTACCCTATGTTTGAGGCTTAGTGATTATCCTGTGGTATTCCA
1630251 AATGGTTCAATAGGAAATTTAAGGTTTAAGTTGAAATGATAGAGCTTATGGCTATGTTGTAAGTG
131 AATGGTTCAATAGGAAATTTAAGGTTTAAGTTGAAATGATAGAGCTTATGGCTATGTTGTAAGTG
1630316 ATATAG
196 ATATAG
* *
1630322 AGGTAGTGTAAGACCTGTCTGGGACATGACATCGACTTAGATGTGTGAGCCAGTGTAAGACCATG
1 AGGTAGCGTAAGACCTGTCTGGGACATGACATCGACTTAGATGTGTGAGCCAGTGTAAGACCACG
1630387 TTTAGAACATGTCATCGGCATCGTACCCTATGTTTGAGGCTTAGTGATTATCCTGTGGTATTCCA
66 TTTAGAACATGTCATCGGCATCGTACCCTATGTTTGAGGCTTAGTGATTATCCTGTGGTATTCCA
1630452 AATGGTTCAATAGGAAATTTAAGGTTTAAGTTGAAATGATAGAGCTTATGGCTATGTTGTAAGTG
131 AATGGTTCAATAGGAAATTTAAGGTTTAAGTTGAAATGATAGAGCTTATGGCTATGTTGTAAGTG
1630517 ATATAG
196 ATATAG
1630523 A
1 A
1630524 TACTTACATG
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 198 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (201 bp):
AGGTAGCGTAAGACCTGTCTGGGACATGACATCGACTTAGATGTGTGAGCCAGTGTAAGACCACG
TTTAGAACATGTCATCGGCATCGTACCCTATGTTTGAGGCTTAGTGATTATCCTGTGGTATTCCA
AATGGTTCAATAGGAAATTTAAGGTTTAAGTTGAAATGATAGAGCTTATGGCTATGTTGTAAGTG
ATATAG
Found at i:1634102 original size:11 final size:11
Alignment explanation
Indices: 1634086--1634110 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1634076 TTCAATTCAA
1634086 ATAATCAATAT
1 ATAATCAATAT
1634097 ATAATCAATAT
1 ATAATCAATAT
1634108 ATA
1 ATA
1634111 TATACACCAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:1652821 original size:18 final size:17
Alignment explanation
Indices: 1652790--1652847 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
1652780 CTTTTACCCC
*
1652790 TATTCTCTTCATTTATTT
1 TATT-TCTTTATTTATTT
1652808 TACTTTCTTTATTTTATTT
1 TA-TTTCTTTA-TTTATTT
*
1652827 TATTTCTTTATTCA-TT
1 TATTTCTTTATTTATTT
1652843 TATTT
1 TATTT
1652848 ATTTTTGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 7 0.19
17 3 0.08
18 15 0.42
19 11 0.31
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTCTTTATTTATTT
Found at i:1659195 original size:11 final size:11
Alignment explanation
Indices: 1659179--1659206 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1659169 ACTAAATAAT
1659179 TAATAATAAAA
1 TAATAATAAAA
1659190 TAATAATAAAA
1 TAATAATAAAA
1659201 TAATAA
1 TAATAA
1659207 AATATCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:1659233 original size:20 final size:21
Alignment explanation
Indices: 1659180--1659255 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
1659170 CTAAATAATT
*
1659180 AATAATAAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
1659199 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
1659220 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
1659241 TAATCATAAAATATC
1 -AATAATAAAATATC
1659256 ATCAACATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:1660460 original size:6 final size:6
Alignment explanation
Indices: 1660451--1660485 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1660441 ACATACACAG
*
1660451 TCAGAT TCAGAT TCAGAT TCAGAC TCAGAT TCAGA
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGA
1660486 CTTAAGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (6 bp):
TCAGAT
Found at i:1662930 original size:23 final size:23
Alignment explanation
Indices: 1662900--1662986 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 23
1662890 GCTATACTGA
*
1662900 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
* *
1662923 TCAGGCACCTTGTGTGTCGCA--
1 TCAGGCACCTTATGTGTCGTATT
* **
1662944 GCAGGCACCTCGTGTGTCG--TT
1 TCAGGCACCTTATGTGTCGTATT
1662965 TCAGGCA-CTTATGTGTCGTATT
1 TCAGGCACCTTATGTGTCGTATT
1662987 CTGATCAGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.17
21 23 0.44
22 2 0.04
23 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (23 bp):
TCAGGCACCTTATGTGTCGTATT
Found at i:1671398 original size:47 final size:49
Alignment explanation
Indices: 1671324--1671453 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 49
1671314 AACCCGCCCC
*
1671324 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATCCA
* *
1671372 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
*
1671417 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
1671454 TCAACCATCC
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 29 0.41
47 29 0.41
48 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA
Found at i:1671469 original size:46 final size:44
Alignment explanation
Indices: 1671326--1671469 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
1671316 CCCGCCCCTA
1671326 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
1671373 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
1671419 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
1671465 AGTGA
1 AGTGA
1671470 CATGTCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:1671907 original size:30 final size:30
Alignment explanation
Indices: 1671873--1671932 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1671863 ATTTAATACG
1671873 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
1671903 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
1671933 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:1675572 original size:24 final size:25
Alignment explanation
Indices: 1675545--1675591 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1675535 GTAAGGAGGG
1675545 GATAA-GGGAGAAGATTTAGGAGTT
1 GATAAGGGGAGAAGATTTAGGAGTT
1675569 GATAAGGGGAGAAGATTTAGGAG
1 GATAAGGGGAGAAGATTTAGGAG
1675592 CTTATCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.21
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGTT
Found at i:1677038 original size:27 final size:27
Alignment explanation
Indices: 1677008--1677114 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 27
1676998 AGCGTCCTGA
* *
1677008 TGGCTATGCCACATTTATCTGATCTGG
1 TGGCTCTGCCACATTTATCTGTTCTGG
*
1677035 TGGCTCTGCCACATATATCTGTTCTGG
1 TGGCTCTGCCACATTTATCTGTTCTGG
* *
1677062 CGGCTCTGCCACAATTATCTGTTCTGG
1 TGGCTCTGCCACATTTATCTGTTCTGG
* *
1677089 TGACTCTGTCACA-TTATCTGTTCTGG
1 TGGCTCTGCCACATTTATCTGTTCTGG
1677115 GAGCCATGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 13 0.18
27 58 0.82
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.37
Consensus pattern (27 bp):
TGGCTCTGCCACATTTATCTGTTCTGG
Found at i:1680484 original size:17 final size:15
Alignment explanation
Indices: 1680446--1680489 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
1680436 GAAAAGGTAA
*
1680446 AATTTTTAATTTTTT
1 AATTTTTATTTTTTT
1680461 AATTTTTATTTTTTT
1 AATTTTTATTTTTTT
1680476 ATATATTTTATTTT
1 A-AT-TTTTATTTT
1680490 AGTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.58
16 2 0.08
17 9 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
AATTTTTATTTTTTT
Found at i:1680753 original size:71 final size:72
Alignment explanation
Indices: 1680669--1680801 Score: 259
Period size: 71 Copynumber: 1.9 Consensus size: 72
1680659 CTCGATCTTC
1680669 TATGGTGTTGTTGAAAGATTGATACCTCATTTTTTGTATTCTGGAAATATCACT-TTTTTTTGAA
1 TATGGTGTTGTTGAAAGATTGATACCTCATTTTTTGTATTCTGGAAATATCACTGTTTTTTTGAA
1680733 AGAAAAT
66 AGAAAAT
1680740 TATGGTGTTGTTGAAAGATTGATACCTCATTTTTTGTATTCTGGAAATATCACTGTTTTTTT
1 TATGGTGTTGTTGAAAGATTGATACCTCATTTTTTGTATTCTGGAAATATCACTGTTTTTTT
1680802 ATTTGAAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
71 54 0.89
72 7 0.11
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.47
Consensus pattern (72 bp):
TATGGTGTTGTTGAAAGATTGATACCTCATTTTTTGTATTCTGGAAATATCACTGTTTTTTTGAA
AGAAAAT
Found at i:1682826 original size:25 final size:25
Alignment explanation
Indices: 1682798--1682851 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1682788 TATATTTACT
*
1682798 TATAAATATATTTATATGTATATAG
1 TATAAATATATTTATATGTATATAA
** *
1682823 TATAGGTATATTTGTATGTATATAA
1 TATAAATATATTTATATGTATATAA
1682848 TATA
1 TATA
1682852 TATGAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (25 bp):
TATAAATATATTTATATGTATATAA
Found at i:1682853 original size:27 final size:25
Alignment explanation
Indices: 1682804--1682851 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1682794 TACTTATAAA
*
1682804 TATATTTATATGTATATAGTATAGG
1 TATATTTATATGTATATAATATAGG
*
1682829 TATATTTGTATGTATATAATATA
1 TATATTTATATGTATATAATATA
1682852 TATGAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (25 bp):
TATATTTATATGTATATAATATAGG
Found at i:1684842 original size:19 final size:19
Alignment explanation
Indices: 1684818--1684857 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1684808 AGCTCCCATG
1684818 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
1684837 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
1684856 TA
1 TA
1684858 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:1686345 original size:12 final size:12
Alignment explanation
Indices: 1686314--1686345 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1686304 TATACAAGTT
1686314 AAAAAAAA-TTG
1 AAAAAAAATTTG
1686325 AAAAAAAATTTG
1 AAAAAAAATTTG
1686337 AAAAAAAAT
1 AAAAAAAAT
1686346 CAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:1691595 original size:19 final size:19
Alignment explanation
Indices: 1691571--1691610 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1691561 AGCTCCCATG
1691571 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
**
1691590 TAGCTCCGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
1691609 TA
1 TA
1691611 TTAGCTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:1698360 original size:24 final size:25
Alignment explanation
Indices: 1698325--1698375 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1698315 ATACATGTTC
1698325 ATAATATATAAAACATACACATAAT
1 ATAATATATAAAACATACACATAAT
**
1698350 ATAATAT-TAAAACATTTACATAAT
1 ATAATATATAAAACATACACATAAT
1698374 AT
1 AT
1698376 GTACACACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:1698472 original size:21 final size:21
Alignment explanation
Indices: 1698448--1698487 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1698438 AAGATATACT
*
1698448 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
1698469 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
1698488 ATACATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:1698570 original size:20 final size:21
Alignment explanation
Indices: 1698537--1698578 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1698527 TATAGTTAAA
*
1698537 ATAATAATATACATAATATAT
1 ATAATAATACACATAATATAT
*
1698558 ATAA-AATACACATACTATAT
1 ATAATAATACACATAATATAT
1698578 A
1 A
1698579 CGTATATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATACACATAATATAT
Found at i:1700950 original size:54 final size:54
Alignment explanation
Indices: 1700871--1701104 Score: 387
Period size: 54 Copynumber: 4.3 Consensus size: 54
1700861 GAAAAGTAGA
* *
1700871 TTTTGAAAAACAAAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
1700925 TTTTGAAAAACAGAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
1700979 TTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * *
1701033 TTTTGAAAAACAGAAGTTAAAATGCTCAACTCACCTCTCGCAATATGAGTCGAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
**
1701087 TTTTGGCAAACAGAAATT
1 TTTTGAAAAACAGAAATT
1701105 GAAATTACCT
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 170 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (54 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
Found at i:1701186 original size:14 final size:15
Alignment explanation
Indices: 1701167--1701198 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1701157 GAATTTTTTG
1701167 AAAAACAGAAATT-A
1 AAAAACAGAAATTGA
1701181 AAAAACAGAAATTGA
1 AAAAACAGAAATTGA
1701196 AAA
1 AAA
1701199 TACCTTAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAACAGAAATTGA
Found at i:1701245 original size:89 final size:89
Alignment explanation
Indices: 1701094--1701360 Score: 466
Period size: 89 Copynumber: 3.0 Consensus size: 89
1701084 GATTTTTGGC
* *
1701094 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1701159 ATTTTTTGAAAAACAGAAATTAAA
66 ATTTTTTGAAAAACAGAAATTAAA
*
1701183 AAACAGAAATTGAAAATACCTTAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1701248 ATTTTTTGAAAAACAGAAATTAAA
66 ATTTTTTGAAAAACAGAAATTAAA
* *
1701272 AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCACAATATGAGTTG-
1 AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1701336 A-TTTTTGAAAAAACAGAAATTAAA
66 ATTTTTTG-AAAAACAGAAATTAAA
1701360 A
1 A
1701361 GGCTCAACTC
Statistics
Matches: 171, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
87 6 0.04
88 18 0.11
89 147 0.86
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (89 bp):
AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
ATTTTTTGAAAAACAGAAATTAAA
Found at i:1701275 original size:14 final size:15
Alignment explanation
Indices: 1701256--1701287 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1701246 GAATTTTTTG
1701256 AAAAACAGAAATT-A
1 AAAAACAGAAATTGA
1701270 AAAAACAGAAATTGA
1 AAAAACAGAAATTGA
1701285 AAA
1 AAA
1701288 TACCTCAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAACAGAAATTGA
Found at i:1701410 original size:306 final size:305
Alignment explanation
Indices: 1701000--1701665 Score: 1109
Period size: 306 Copynumber: 2.2 Consensus size: 305
1700990 AGAAATTAAA
* * *
1701000 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAGTTAAAATGCTCAACTC
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
1701065 ACCTCTCGCAATATGAGTCGATTTTTGGCAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
66 ACCTCTCGCAATATGAGTCGATTTTTGGCAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
* *
1701130 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGAAAAACAGAAATTAAAAAACAGAAATTG
131 CTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAAACAGAAATTAAAAAACAAAAATTG
* * *
1701195 AAAATACCTTAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGAAAA
196 AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAA
* *
1701260 ACAGAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGCCTTG
261 ACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTG
1701305 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAAACAGAAATTAAAAGGCTCAACT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG-AAAAACAGAAATTAAAAGGCTCAACT
*
1701370 CACCTCTCGCAATATGAGTCGATTTTTGGCAAATAGAAATTGAAATTACCTCAGCGTGTCCTGAG
65 CACCTCTCGCAATATGAGTCGATTTTTGGCAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAG
* * *
1701435 GCTCAACTCACCTCTCACAATATGAGTTGACTTTTTTGAAAAGCAGAAATTGAAAAACAAAAATT
130 GCTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAAACAGAAATTAAAAAACAAAAATT
*
1701500 GAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTTTGAAA
195 GAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAA
* *
1701565 AGCAGAAATTGAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTG
260 AACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTG
* * * * *
1701611 AGCCTCAGCTCCCCTCTCCCAATATGAGTTGATTTTTTG-AAAACAGAAATAAAAA
1 AGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGAAAAACAGAAATTAAAA
1701666 CATCAAAATA
Statistics
Matches: 337, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
305 52 0.15
306 279 0.83
307 6 0.02
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (305 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTC
ACCTCTCGCAATATGAGTCGATTTTTGGCAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGG
CTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAAACAGAAATTAAAAAACAAAAATTG
AAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAA
ACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTG
Found at i:1701449 original size:217 final size:218
Alignment explanation
Indices: 1701187--1701579 Score: 657
Period size: 217 Copynumber: 1.8 Consensus size: 218
1701177 ATTAAAAAAC
* *
1701187 AGAAATTGAAAATACCTTAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTT
1 AGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTT
*
1701252 TTTGAAAAACAGAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTG-CCTTGAGGCTCAACTC
66 TTTGAAAAACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGACC-TGAGGCTCAACTC
1701316 ACCTCTCACAATATGAGTTGA-TTTTTGAAAAAACAGAAATT-AAAAGGCTCAACTCACCTCTCG
130 ACCTCTCACAATATGAGTTGACTTTTTG-AAAAACAGAAATTGAAAAGGCTCAACTCACCTCTCG
1701379 CAATATGAGTCGATTTTTGGCAAAT
194 CAATATGAGTCGATTTTTGGCAAAT
* * *
1701404 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTT
1 AGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTT
* *
1701469 TTTGAAAAGCAGAAATTGAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
66 TTTGAAAAACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
*
1701534 CCTCTCACAATATGAGTTGACTTTTTTGAAAAGCAGAAATTGAAAA
131 CCTCTCACAATATGAGTTGAC-TTTTTGAAAAACAGAAATTGAAAA
1701580 ACAAAAATTG
Statistics
Matches: 163, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
217 139 0.85
218 14 0.09
219 10 0.06
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (218 bp):
AGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGAATTT
TTTGAAAAACAGAAATTAAAAAACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCA
CCTCTCACAATATGAGTTGACTTTTTGAAAAACAGAAATTGAAAAGGCTCAACTCACCTCTCGCA
ATATGAGTCGATTTTTGGCAAAT
Found at i:1701489 original size:14 final size:14
Alignment explanation
Indices: 1701470--1701504 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1701460 GTTGACTTTT
* *
1701470 TTGAAAAGCAGAAA
1 TTGAAAAACAAAAA
1701484 TTGAAAAACAAAAA
1 TTGAAAAACAAAAA
1701498 TTGAAAA
1 TTGAAAA
1701505 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAAAAA
Found at i:1701557 original size:89 final size:89
Alignment explanation
Indices: 1701406--1701667 Score: 433
Period size: 89 Copynumber: 3.0 Consensus size: 89
1701396 TGGCAAATAG
* *
1701406 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1701471 TGAAAAGCAGAAATTGAAAAACAA
66 TGAAAAGCAGAAATTGAAAAACAA
1701495 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1701560 TGAAAAGCAGAAATTGAAAAACAA
66 TGAAAAGCAGAAATTGAAAAACAA
* * * * *
1701584 AAATTGAAAATACCTCAGCGTGCCCTGAGCCTCAGCTCCCCTCTCCCAATATGAGTTGA-TTTTT
1 AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
1701648 TGAAAA-CAGAAA-T-AAAAACA
66 TGAAAAGCAGAAATTGAAAAACA
1701668 TCAAAATACC
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
85 7 0.04
86 1 0.01
87 6 0.04
88 11 0.07
89 141 0.85
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (89 bp):
AAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTT
TGAAAAGCAGAAATTGAAAAACAA
Found at i:1701578 original size:14 final size:14
Alignment explanation
Indices: 1701559--1701593 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1701549 GTTGACTTTT
* *
1701559 TTGAAAAGCAGAAA
1 TTGAAAAACAAAAA
1701573 TTGAAAAACAAAAA
1 TTGAAAAACAAAAA
1701587 TTGAAAA
1 TTGAAAA
1701594 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAAAAA
Found at i:1702525 original size:8 final size:8
Alignment explanation
Indices: 1702512--1702549 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1702502 TTGATCCCCC
1702512 TTTTTCTT
1 TTTTTCTT
1702520 TTTTTC-T
1 TTTTTCTT
1702527 TTTTTCTT
1 TTTTTCTT
1702535 TTTCTCTCTT
1 TTT-T-TCTT
1702545 TTTTT
1 TTTTT
1702550 TAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.26
8 11 0.41
9 2 0.07
10 7 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1702532 original size:15 final size:17
Alignment explanation
Indices: 1702512--1702548 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
1702502 TTGATCCCCC
1702512 TTTTTCTTTTT-T-TCT
1 TTTTTCTTTTTCTCTCT
1702527 TTTTTCTTTTTCTCTCT
1 TTTTTCTTTTTCTCTCT
1702544 TTTTT
1 TTTTT
1702549 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTCTCTCT
Found at i:1714299 original size:24 final size:25
Alignment explanation
Indices: 1714264--1714314 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1714254 ATACATGTTC
1714264 ATAATATATAAAACATACACATAAT
1 ATAATATATAAAACATACACATAAT
* **
1714289 ATAATAT-TAAAATATTTACATAAT
1 ATAATATATAAAACATACACATAAT
1714313 AT
1 AT
1714315 GTACACACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:1714411 original size:21 final size:21
Alignment explanation
Indices: 1714387--1714426 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1714377 AAGATATACT
*
1714387 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
1714408 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
1714427 ATACATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:1716339 original size:24 final size:24
Alignment explanation
Indices: 1716306--1716366 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
1716296 TGCGGTTTGC
1716306 AATTGAAATTGATTG-ATTTAGTATGT
1 AATTG-AATTGATTGAATTTA-TAT-T
* *
1716332 GA-TGAATTTATTGAATTTATATT
1 AATTGAATTGATTGAATTTATATT
1716355 AATTGAATTGAT
1 AATTGAATTGAT
1716367 ATATATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
23 2 0.07
24 19 0.66
25 7 0.24
26 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (24 bp):
AATTGAATTGATTGAATTTATATT
Found at i:1716361 original size:15 final size:16
Alignment explanation
Indices: 1716340--1716386 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
1716330 GTGATGAATT
1716340 TATTGAATTTATATTA
1 TATTGAATTTATATTA
*
1716356 -ATTGAATTGATATATA
1 TATTGAATTTATAT-TA
*
1716372 TATTGAATATATATT
1 TATTGAATTTATATT
1716387 GATTATTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.46
16 3 0.12
17 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (16 bp):
TATTGAATTTATATTA
Found at i:1716376 original size:17 final size:16
Alignment explanation
Indices: 1716340--1716401 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 16
1716330 GTGATGAATT
*
1716340 TATTGAATTTATATTA
1 TATTGAATTGATATTA
1716356 -ATTGAATTGATATATA
1 TATTGAATTGATAT-TA
1716372 TATTGAATAT-ATATTGA
1 TATTGAAT-TGATATT-A
1716389 TTATTTGAATTGA
1 -TA-TTGAATTGA
1716402 ATTGAATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
15 12 0.32
16 3 0.08
17 12 0.32
18 4 0.11
19 7 0.18
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (16 bp):
TATTGAATTGATATTA
Found at i:1716383 original size:11 final size:11
Alignment explanation
Indices: 1716340--1716388 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1716330 GTGATGAATT
*
1716340 TATTGAATTTA
1 TATTGAATATA
1716351 TATT-AAT-TGA
1 TATTGAATAT-A
1716361 -ATTGATATATA
1 TATTGA-ATATA
1716372 TATTGAATATA
1 TATTGAATATA
1716383 TATTGA
1 TATTGA
1716389 TTATTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 18 0.55
12 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (11 bp):
TATTGAATATA
Found at i:1716383 original size:13 final size:12
Alignment explanation
Indices: 1716361--1716389 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1716351 TATTAATTGA
1716361 ATTGATATATAT
1 ATTGATATATAT
1716373 ATTGA-ATATAT
1 ATTGATATATAT
1716384 ATTGAT
1 ATTGAT
1716390 TATTTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (12 bp):
ATTGATATATAT
Found at i:1719255 original size:30 final size:30
Alignment explanation
Indices: 1719221--1719277 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1719211 CCAAAATTTT
* *
1719221 ACAATTTTCTTTGAAAATTTTAATTAACCC
1 ACAATTTTCTTTAAAAAGTTTAATTAACCC
* *
1719251 ACAATTTTTTTTAAAAAGTTTCATTAA
1 ACAATTTTCTTTAAAAAGTTTAATTAA
1719278 ACCTTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.46
Consensus pattern (30 bp):
ACAATTTTCTTTAAAAAGTTTAATTAACCC
Found at i:1720068 original size:27 final size:26
Alignment explanation
Indices: 1720010--1720069 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1720000 GCTATTAAAC
** **
1720010 TTAATATATATGAATATTTGTATGTA
1 TTAATATATATGAATATTTAAAAATA
1720036 TATAATATATATGAATATTTAAAAAATA
1 T-TAATATATATGAATATTT-AAAAATA
1720064 TTAATA
1 TTAATA
1720070 AATCTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.04
27 23 0.82
28 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (26 bp):
TTAATATATATGAATATTTAAAAATA
Found at i:1722789 original size:11 final size:11
Alignment explanation
Indices: 1722775--1722819 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
1722765 AGATAAATAT
1722775 TATTTTATTAA
1 TATTTTATTAA
*
1722786 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
1722799 TATTTTACTAA
1 TATTTTATTAA
1722810 TATTTTATTA
1 TATTTTATTA
1722820 TAAATAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 16 0.57
12 5 0.18
13 7 0.25
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:1737122 original size:3 final size:3
Alignment explanation
Indices: 1737114--1737163 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1737104 TAAACTAAAC
1737114 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1737162 AT
1 AT
1737164 AGGTAATAAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1737522 original size:15 final size:15
Alignment explanation
Indices: 1737504--1737553 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1737494 GAATATTTAA
1737504 TTTGATTTTATGAAT
1 TTTGATTTTATGAAT
1737519 TTTGATATATT-T-AA-
1 TTTGAT-T-TTATGAAT
1737533 TTTGATTTTATGAAT
1 TTTGATTTTATGAAT
1737548 TTTGAT
1 TTTGAT
1737554 ATGATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 8 0.27
15 14 0.47
16 2 0.07
17 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTGATTTTATGAAT
Found at i:1737531 original size:29 final size:29
Alignment explanation
Indices: 1737496--1737555 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1737486 GATTTTGTGA
1737496 ATATTTAATTTGATTTTATGAATTTTGAT
1 ATATTTAATTTGATTTTATGAATTTTGAT
1737525 ATATTTAATTTGATTTTATGAATTTTGAT
1 ATATTTAATTTGATTTTATGAATTTTGAT
1737554 AT
1 AT
1737556 GATAAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (29 bp):
ATATTTAATTTGATTTTATGAATTTTGAT
Found at i:1737548 original size:14 final size:14
Alignment explanation
Indices: 1737502--1737549 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1737492 GTGAATATTT
1737502 AATTTGATTTTATG
1 AATTTGATTTTATG
1737516 AATTTTGATATATT-T-
1 AA-TTTGAT-T-TTATG
1737531 AATTTGATTTTATG
1 AATTTGATTTTATG
1737545 AATTT
1 AATTT
1737550 TGATATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 13 0.45
15 8 0.28
16 2 0.07
17 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.58
Consensus pattern (14 bp):
AATTTGATTTTATG
Found at i:1739030 original size:19 final size:19
Alignment explanation
Indices: 1739006--1739043 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1738996 TATGCGGTAA
1739006 GATGCACTTCATGTGCCAG
1 GATGCACTTCATGTGCCAG
*
1739025 GATGCACTTCATGTTCCAG
1 GATGCACTTCATGTGCCAG
1739044 TATACGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (19 bp):
GATGCACTTCATGTGCCAG
Found at i:1739424 original size:18 final size:18
Alignment explanation
Indices: 1739401--1739438 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1739391 AAGGTAAGTG
1739401 AACTGAATTGATCATGCA
1 AACTGAATTGATCATGCA
*
1739419 AACTGAATTGGTCATGCA
1 AACTGAATTGATCATGCA
1739437 AA
1 AA
1739439 TTTGATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (18 bp):
AACTGAATTGATCATGCA
Found at i:1744512 original size:43 final size:42
Alignment explanation
Indices: 1744445--1744608 Score: 197
Period size: 42 Copynumber: 3.9 Consensus size: 42
1744435 TACCATACCA
* * * * *
1744445 ATGCCATATCCTAGATATAGTCTTACATG-GGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATCG
* * *
1744487 ATGCCAATAGCCCAGCTATGGTCTTACACAAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* *
1744530 ATGCCATATCCTAGATATGGTCTTACACGAAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
1744572 ATGCCATATCCCAGATATGGTCTTACAC-ATAGTCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGA-AGTCTCA
1744609 GTAACCCTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 71 0.68
43 32 0.30
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:1744575 original size:85 final size:84
Alignment explanation
Indices: 1744445--1744608 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 84
1744435 TACCATACCA
* * * *
1744445 ATGCCATATCCTAGATATAGTCTTACATGGGATCTCGTATCGATGCCAATAGCCCAGCTATGGTC
1 ATGCCATATCCTAGATATAGTCTTACACGAGATCTCATATCGATGCC-ATAGCCCAGATATGGTC
1744510 TTACACAAAGTCTCATATCG
65 TTACACAAAGTCTCATATCG
* * *
1744530 ATGCCATATCCTAGATATGGTCTTACACGA-AGTCTCATATTGATGCCATATCCCAGATATGGTC
1 ATGCCATATCCTAGATATAGTCTTACACGAGA-TCTCATATCGATGCCATAGCCCAGATATGGTC
*
1744594 TTACACATAGTCTCA
65 TTACACAAAGTCTCA
1744609 GTAACCCTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 30 0.43
85 40 0.57
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (84 bp):
ATGCCATATCCTAGATATAGTCTTACACGAGATCTCATATCGATGCCATAGCCCAGATATGGTCT
TACACAAAGTCTCATATCG
Found at i:1746663 original size:19 final size:20
Alignment explanation
Indices: 1746636--1746683 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1746626 GTTGGTAAAT
*
1746636 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
1746655 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
1746675 A-ATATGTAT
1 ACATATGTAT
1746684 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:1746684 original size:19 final size:20
Alignment explanation
Indices: 1746646--1746684 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1746636 ACATGTGTAA
1746646 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
1746666 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
1746685 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:1746828 original size:16 final size:15
Alignment explanation
Indices: 1746803--1746834 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1746793 AAAACAGGGG
1746803 AAAAAGAAAGAAAGA
1 AAAAAGAAAGAAAGA
1746818 AAAAGAGAAAGAAAGA
1 AAAA-AGAAAGAAAGA
1746834 A
1 A
1746835 GGAGAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:1747564 original size:11 final size:11
Alignment explanation
Indices: 1747548--1747572 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1747538 AATTGGTATA
1747548 TATATATTGAT
1 TATATATTGAT
1747559 TATATATTGAT
1 TATATATTGAT
1747570 TAT
1 TAT
1747573 TTGAATTGAA
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATATTGAT
Found at i:1747758 original size:41 final size:38
Alignment explanation
Indices: 1747701--1747836 Score: 123
Period size: 40 Copynumber: 3.5 Consensus size: 38
1747691 CCACTTCGAG
1747701 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGATT-A
* * *
1747741 TTCGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTA
1 -TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
* * * * *
1747778 GCCGATGCGACACTAGCTGTCAACTTATTACTTCGAATTA
1 -TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
*
1747818 TCTGATGAGGCACTGGGTG
1 TC-GATGAGACACTGGGTG
1747837 CCAAACTGGT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 17 0.23
38 11 0.15
39 3 0.04
40 23 0.31
41 20 0.27
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (38 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
Found at i:1750024 original size:35 final size:35
Alignment explanation
Indices: 1749978--1750045 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
1749968 GTACTAGAAG
*
1749978 ATATGTTGCGAGCCTGTATTGTTAATCTCGAAGCT
1 ATATGTTGCGAGCCTGTATAGTTAATCTCGAAGCT
1750013 ATATGTTGCGAGCCTGTATAGTTAATCTCGAAG
1 ATATGTTGCGAGCCTGTATAGTTAATCTCGAAG
1750046 TTAGCTGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (35 bp):
ATATGTTGCGAGCCTGTATAGTTAATCTCGAAGCT
Found at i:1750984 original size:47 final size:46
Alignment explanation
Indices: 1750897--1750987 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
1750887 TTTCAGCCCA
*
1750897 GCTATTTAGTTTGTAGGCCCATTTTATGTTTTATTTTGATTTTGGG
1 GCTATTTAGTTTGTAGGCCCATTTTACGTTTTATTTTGATTTTGGG
1750943 GCTATTTAGTTTGT-GGACCTACA-TTTACGTTTTATTTTGATTTTG
1 GCTATTTAGTTTGTAGG-CC--CATTTTACGTTTTATTTTGATTTTG
1750988 AGCAGATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
45 2 0.05
46 16 0.39
47 21 0.51
48 2 0.05
ACGTcount: A:0.16, C:0.10, G:0.20, T:0.54
Consensus pattern (46 bp):
GCTATTTAGTTTGTAGGCCCATTTTACGTTTTATTTTGATTTTGGG
Found at i:1755641 original size:18 final size:18
Alignment explanation
Indices: 1755606--1755643 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1755596 AACCGACCGA
*
1755606 TTAACCGAATTCGATCGG
1 TTAACCGAATTCAATCGG
1755624 TTAACCGAATT-AATTCGG
1 TTAACCGAATTCAA-TCGG
1755642 TT
1 TT
1755644 TTACCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (18 bp):
TTAACCGAATTCAATCGG
Found at i:1759083 original size:22 final size:20
Alignment explanation
Indices: 1759032--1759115 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 20
1759022 ATATATTTGG
1759032 TAATA-ATA-ATATAAAATAA
1 TAATATATACATA-AAAATAA
*
1759051 TAATATGTACATAAAAATACA
1 TAATATATACATAAAAATA-A
*
1759072 TATATATATACAT-ATAATAA
1 TA-ATATATACATAAAAATAA
* *
1759092 -AAGTATGTA-ATAATAATAA
1 TAA-TATATACATAAAAATAA
1759111 TAATA
1 TAATA
1759116 ATATCTACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
18 3 0.06
19 20 0.37
20 11 0.20
21 11 0.20
22 9 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATATATACATAAAAATAA
Found at i:1759642 original size:6 final size:7
Alignment explanation
Indices: 1759626--1759651 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1759616 GGGAGTTAGG
1759626 TTTTTCT
1 TTTTTCT
1759633 TTTTTCT
1 TTTTTCT
1759640 TTTTTCT
1 TTTTTCT
1759647 TTTTT
1 TTTTT
1759652 TTAGGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:1759680 original size:30 final size:29
Alignment explanation
Indices: 1759632--1759698 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 29
1759622 TAGGTTTTTC
1759632 TTTTTTCTTTTTTCTTTTTTTTAGGGTTAGG
1 TTTTTT-TTTTTTCTTTTTTTT-GGGTTAGG
1759663 TTTTTTTTCTTTT-TTTTTTTTGGGTTAGG
1 TTTTTTTT-TTTTCTTTTTTTTGGGTTAGG
1759692 TTTTTTT
1 TTTTTTT
1759699 GGGGGGCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 15 0.43
30 10 0.29
31 10 0.29
ACGTcount: A:0.04, C:0.04, G:0.15, T:0.76
Consensus pattern (29 bp):
TTTTTTTTTTTTCTTTTTTTTGGGTTAGG
Found at i:1760457 original size:91 final size:91
Alignment explanation
Indices: 1760354--1760887 Score: 385
Period size: 91 Copynumber: 6.0 Consensus size: 91
1760344 ATAGACAATA
* * *
1760354 AAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGA-CCTGAGGCTCAACTCACCTCTCGCAATACGAG
1760418 TCGATTTTTTTGAAAGGCAAAAATTGG
65 TCGATTTTTTTGAAAGGCAAAAATTGG
* * ** *
1760445 AAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGTCTTTCGCAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * ***** *
1760510 TGATTTTTTT--TA---TTTTTTTTG
66 CGATTTTTTTGAAAGGCAAAAATTGG
* * * *
1760531 ACAACAGAAATT-AAAATTACCTCA--GCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAATTGAAAA-TACCTCAGCGCGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAG
1760593 TCGATTTTTTTGAAAGGCAAAAATTGG
65 TCGATTTTTTTGAAAGGCAAAAATTGG
* * ** *
1760620 AAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGGCTTTCGCAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * ***** *
1760685 TGATTTTTTT--TA---TTTTTTTTG
66 CGATTTTTTTGAAAGGCAAAAATTGG
* * * *
1760706 ACAACAGAAATT-AAAATTACCTCA--GCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAATTGAAAA-TACCTCAGCGCGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAG
* *** *
1760768 TTGAATTTTTTTTGAAAAATATAAATT-G
65 TCG-A-TTTTTTTGAAAGGCAAAAATTGG
* * * ** *
1760796 AAAAGCAGAAATTGAAATTACCTAAAC-C-TG-CCTTGAGGCTCAACTCACCTCTTACAATATGA
1 AAAA-CAGAAATTGAAAATACCTCAGCGCGTGACC-TGAGGCTCAACTCACCTCTCGCAATACGA
* **
1760858 GTTGA-TTTTTTGAAAGATAAAAATT-G
64 GTCGATTTTTTTGAAAGGCAAAAATTGG
1760884 AAAA
1 AAAA
1760888 TACCTCAGCG
Statistics
Matches: 349, Mismatches: 71, Indels: 49
0.74 0.15 0.10
Matches are distributed among these distances:
84 75 0.21
85 9 0.03
86 48 0.14
88 24 0.07
89 22 0.06
90 13 0.04
91 154 0.44
92 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (91 bp):
AAAACAGAAATTGAAAATACCTCAGCGCGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
CGATTTTTTTGAAAGGCAAAAATTGG
Found at i:1760681 original size:175 final size:175
Alignment explanation
Indices: 1760390--1760818 Score: 761
Period size: 175 Copynumber: 2.4 Consensus size: 175
1760380 GCGTGAGCCA
1760390 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAAAAATTGGAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAAAAATTGGAAAACAGAAA
*
1760455 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGTCTTTCGCAATACGAGTTGATTTTTTT
66 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGGCTTTCGCAATACGAGTTGATTTTTTT
1760520 TATTTTTTTTGACAACAGAAATTAAAATTACCTCAGCATGTCCTG
131 TATTTTTTTTGACAACAGAAATTAAAATTACCTCAGCATGTCCTG
1760565 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAAAAATTGGAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAAAAATTGGAAAACAGAAA
1760630 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGGCTTTCGCAATACGAGTTGATTTTTTT
66 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGGCTTTCGCAATACGAGTTGATTTTTTT
1760695 TATTTTTTTTGACAACAGAAATTAAAATTACCTCAGCATGTCCTG
131 TATTTTTTTTGACAACAGAAATTAAAATTACCTCAGCATGTCCTG
* *** *
1760740 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTTGAAAAATATAAATT-GAAAAGCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTCG-A-TTTTTTTGAAAGGCAAAAATTGGAAAA-CAG
*
1760804 AAATTGAAATTACCT
63 AAATTGAAAATACCT
1760819 AAACCTGCCT
Statistics
Matches: 244, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
175 204 0.84
176 6 0.02
177 34 0.14
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (175 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAAAAATTGGAAAACAGAAA
TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGGCTTTCGCAATACGAGTTGATTTTTTT
TATTTTTTTTGACAACAGAAATTAAAATTACCTCAGCATGTCCTG
Found at i:1760914 original size:74 final size:73
Alignment explanation
Indices: 1760793--1761017 Score: 279
Period size: 74 Copynumber: 3.0 Consensus size: 73
1760783 AAAATATAAA
* * * * * **
1760793 TTGAAAAGCAGAAATTGAAATTACCTAAACCTGCCTTGAGGCTCAACTCACCTCTTACAATATGA
1 TTGAAAA-CAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1760858 GTTGATTTT
65 GTTGATTTT
* * **
1760867 TTGAAAGATAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
1 TTGAAA-ACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1760932 GTTGATTTTT
65 GTTGA-TTTT
* * * *
1760942 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCGCCTCTCGCAATATGAG
1 TTGAAAACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
1761007 TTGAATTTT
66 TTG-ATTTT
1761016 TT
1 TT
1761018 TTACGAACAG
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
74 118 0.91
75 11 0.09
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (73 bp):
TTGAAAACAAAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTT
Done.